Home » Intelligent Design » Michael Behe, Eric Anderson, David Chiu, Kirk Durston mentioned favorably in ID-sympathetic Peer-Reviewed Article

Michael Behe, Eric Anderson, David Chiu, Kirk Durston mentioned favorably in ID-sympathetic Peer-Reviewed Article

Congratulations to Michael Behe, Eric Anderson, David Chiu, Kirk Durston (members of ISCID). They were mentioned in the peer reviewed journal International Journal of Molecular Sciences. References were made to Darwin’s Black Box by Michael Behe, “Irreducible Comlexity Reduced” in ISCID’s PCID by Eric Anderson, and peer-reviewed works by David Chiu and Kirk Durston.

Here is the paper: The Capabilities of Chaos and Complexity

Great paper!

The cause and evolution of complexity are frequently addressed in the literature [10, 134-141]. How complexity relates to life has attracted innumerable papers [6, 142-148]. Systems Biology emphasizes the growing genomic and epigenetic complexity [149-151]. Attempts to deal with Behe’s “irreducible complexity” [152] are appearing more often in scientific literature [153-157].

The much vaunted Avida community is indirectly criticized:

Despite the appealing similarities of terms like “chromosomes,” GA’s have no relevance whatsoever to molecular evolution or gene emergence. Inanimate nature cannot define a fitness function over measures of the quality of representations of solutions. GAs are no model at all of natural process. GA’s are nothing more than multiple layers of abstract conceptual engineering. Like language, we may start with a random phase space of alphabetical symbols. But no meaning or function results without deliberate and purposeful selection of letters out of that random phase space. No abiotic primordial physicodynamic environment could have exercised such programming prowess.

Neither physics nor chemistry can dictate formal optimization, any more than physicality itself generates the formal study of physicality. Human epistemological pursuits are formal enterprises of agent minds. Natural process GAs have not been observed to exist. The GAs of living organisms are just metaphysically presupposed to have originated through natural process. We can liberally employ GAs and so-called evolutionary algorithms for all sorts of productive tasks. But GAs cannot be used to model spontaneous life origin through natural process because GAs are formal.

The OOL community is indirectly criticized. “Choice with intent” might be a stealth phrase for intelligence. “Choice with intent” is required of any agency that creates organization:

Organization ≠ order. Disorganization ≠ disorder. Self-ordering of many kinds occurs spontaneously every day in nature in the absence of any organization. Spontaneous bona fide self-organization, on the other hand, has never been observed.

“Self-organization” is logically a nonsense term. Inanimate objects cannot organize themselves into integrated, cooperative, holistic schemes. Schemes are formal, not physical. To organize requires choice contingency, not just chance contingency and law-like necessity. Sloppy definitions lead to fallacious inferences, especially to category errors. Organization requires 1) decision nodes, 2) steering toward a goal of formal function, 3) algorithmic optimization, 4) selective switch-setting to achieve integration of a circuit, 5) choice with intent.

The only entity that logically could possibly The only entity that logically could possibly be considered to organize itself is an agent. But not even an agent self-organizes. Agents organize things and events in their lives. They do not organize their own molecular biology, cellular structure, organs and organ systems. Agents do not organize their own being. Agents do not create themselves.

We will point to hundreds of peer-reviewed papers with “self-organization” in their titles. But when all of these papers are carefully critiqued with a proper scientific skepticism, our embarrassment only grows with each exposure of the blatant artificial selection that was incorporated into each paper’s experimental design. Such investigator involvement is usually readily apparent right within Materials and Methods of the paper.

passing mention of macro evolution is made:

Linear digital prescription in physical nucleic acid has thus far invariably been associated with life. A fully post modern anthropocentrism cannot argue a logically consistent macroevolutionary paradigm.

the conclusion:

To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it:

“Physicodynamics cannot spontaneously traverse The Cybernetic Cut [9]: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.”

HT: chunkdz at Telic Thoughts

Notes:

1. “choice is the defining feature of intelligence” — William Dembski

2. The relationship of “choice” versus “chance and necessity” as well as the relationship of “choice” and “intelligence” was discussed peripherally at UD here: Cosmological ID in 1744?

3. The only mention of Darwin in this paper was in the title of with Behe’s book and in sentences with words like “confused”.

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382 Responses to Michael Behe, Eric Anderson, David Chiu, Kirk Durston mentioned favorably in ID-sympathetic Peer-Reviewed Article

  1. 1
    AmerikanInKananaskis

    I’m not seeing how this is sympathetic to ID. I started reading it on your recommendation, and even in page 3 I found this line:

    To stem the growing swell of Intelligent Design intrusions, it is imperative that we provide stand-alone natural process evidence of non trivial self-organization at the edge of chaos.

    Sounds to me like these authors are quite unhappy with ID.

  2. AmericaninKansas,

    Thank you for your comment.

    Fuller quote:

    Attempts to relate complexity to self-organization are too numerous to cite [4, 21, 169-171]. Under
    careful scrutiny, however, these papers seem to universally incorporate investigator agency into their
    experimental designs.
    To stem the growing swell of Intelligent Design intrusions, it is imperative that
    we provide stand-alone natural process evidence of non trivial self-organization at the edge of chaos.

    The “Intelligent Design” intrustions are the intrusions by researchers who misrepresent their experiments as models of natural processes when in fact they are the results of their own “Intelligent Design.”

  3. Excellent paper!!!

    Let’s briefly analyze the author’s use of “choice with intent.”

    1. Intent implies the desire to perform something in the future. This would require foresight.

    2. The choice that the author describes in the paper can be summed up as:

    Choice occurs when there are a number of possibilities, yet out of all possible states, only one possibility will provide for a future function or goal. Since that future function does not yet exist, it can not necessitate what happens (the choosing of that one possibility) in the present. Therefore, the choice to utilize that one state is neither best defined by necessity (since it is the future, not-yet-existent goal which defines the state that must be utilized) nor by chance unless it can be shown that chance, described as randomness, will produce the functions described in the paper.

    3. I have been attempting to show that the basic definition of intelligence can be summed up as “foresight”: the ability to envision a future goal which does not yet exist and then engineer matter and energy to accomplish that future goal. This “foresight” would provide for “choice” as the author has used the term. Therefore, “foresight” as the basic definition/requirement of intelligence encompasses the authors use of the term “choice with intent.”

    4. Hence, the paper seems to make the claim that foresight and the application of foresight, thus intelligence (foresight and choice), are required to produce those points mentioned in the conclusion unless the null hypothesis is falsified.

    5. It doesn’t matter whether the author wishes for the null hypothesis to be falsified or not, it seems that he has just provided a pro-ID hypothesis with potential falsifiability.

    6. In reply to AmerikanInKananaskis, point number 1 – 5 stand regardless of the authors emotional state towards ID Theory. He is merely stating a fact that must be contended with in order to “stem the growing swell of Intelligent Design intrusions.” IOW, he is merely telling the Darwin side (which may well include himself) to put their money where their mouth is.

  4. I agree with AmerikaninKananaskis that saying this is supportive of ID is a stretch. The mention of Behe et all seems at best neutral if anything. For one thing the article says “Attempts to deal with Behe’s “irreducible complexity” [152] are appearing more often in scientific literature [153-157]. But at least a couple of authors of papers cited are quite critical of Behe (e.g, Aird Pennock)

    Also, there is an implicit acknowledgement of the importance of peer-review articles (hence the congratulations I assume). And one of the people who is congratulated is a member of ISCID and has published in that organization’s PCID journal. Yet that journal has not published anything since November 2005. If peer-reviewed articles are so important to ID, why not?

  5. JTaylor wrote:

    I agree with AmerikaninKananaskis that saying this is supportive of ID is a stretch.

    Thank you for your comment. Do you think then since this isn’t supportive of ID that such papers (written in more accessible english) would be appropriate to discuss in biology classes in Kansas since this isn’t formally ID. :-)

  6. Dawkins is criticized:

    the description of all of the above models often seems
    more poetic or cartoon-like than real. Kauffman’s and Dawkin’s publications, for example, are often
    devoid of any consideration of the biochemical catastrophic realities that plague life-origin bench
    scientists [20-22, 58-63].
    …..

    61. Dawkins, R. The Selfish Gene, 2nd Ed.; Oxford Univerisy Press: Oxford, UK, 1989
    62. Dawkins, R. The Blind Watchmaker. W. W. Norton and Co.: New York, 1986.
    63. Dawkins, R. Climbing Mount Impossible. W. W. Norton and Co.: New York, 1996

  7. From the paper:

    Many thanks
    to Kirk Durston and David Chiu at the University of Guelph for their willingness to share their
    impressive experimental data.

    Kirk is mentioned by Barry Arrington at UD here:Durston Continued.

    Perhaps this paper is ID symapthetic on the grounds of “guilt by association.” :-)

  8. Scordova said: “Thank you for your comment. Do you think then since this isn’t supportive of ID that such papers (written in more accessible english) would be appropriate to discuss in biology classes in Kansas since this isn’t formally ID”

    OK, perhaps saying the paper is supportive of ID is not the right thing to say. Your post says that it is favorable to Behe et al…from which I suppose one could imply that it is therefore supportive of ID. But the paper seems neutral on Behe – if anything the citations listed refer to authors who are deeply critical of Behe’s work. I don’t see where the congratulations are due. I think you stretching here.

    But as to whether the paper should be taught in high school is probably beyond the realm of expertise (I’m not a scientist). My impression though is that this paper is probably too advanced for high school.

  9. The paper takes a subtle swipe at materialistic science. I believe the verbage is deliberately subtle, but it is there.

    [Note: Abel's null hypothesis (default hypothesis) is that naturalistic processes (physicodhynamic processes)cannot create life]

    Let the reader provide the supposedly easy falsification of the null hypothesis [that there is no physico dynamic origin of life]. Inability to do so should
    cause pangs of conscience in any scientist who equates metaphysical materialism with science. On the
    other hand, providing the requested falsification of this null hypothesis would once-and-for-all end a lot of unwanted intrusions into science from philosophies competing with metaphysical materialism.

    “philosophies competing with metaphysical materialism” ? such as philosophies that allow ID? :-)

    The phrase “methaphysical materialism” reminds me of something once said in ID circles:

    If we view the predominant materialistic science as a giant tree, our strategy is intended to function as a “wedge”

    We are building on this momentum, broadening the wedge with a positive scientific alternative to materialistic scientific theories, which has come to be called the theory of intelligent design (ID). Design theory promises to reverse the stifling dominance of the materialist worldview

  10. 10

    Sal,

    I see you are now an “author” here, so I really have to apply a test to see if you are now a full fledged member of the Intelligent Design oligarchy here. I will soon find out.

    Only a “born that way,” “dyed-in-the-wool,” “prescribed” atheist could be blind to the ordered, planned, purposeful, goal-directed and now fully realized universe that is perfectly obvious to any mentally unimpaired student of the real world. There is nothing to discuss and certainly nothing to debate.

    I wonder how long this carefully considered opinion will take to surface here at the “new” Uncommon Descent where its enemies are unmoderated while this particular Intelligent Design pioneer has his every word delayed without any explanation whatsoever.

    It is hard to believe isn’t it?

    Not at all. It is the policy of the “new” Uncommon Descent. It is downright Biblical in its implications. It is called “love thy enemy.” The “new” policy more accurately reflects the attitude – “who needs friends?” Certainly not Uncommon Descent.

    “A past evolution is undeniable, a present evolution undemonstrable.”

  11. 11

    Thank you for the rapid response.

  12. Uh, this is not such a “subtle” swipe.

  13. John,

    I didn’t put you in any moderation queue. I can only release your comments when and if I find them in the queue.

    A little forebearance is requested of you from me.

    Thank you.

    Salvador

  14. scordova @13

    I didn’t put you in any moderation queue. I can only release your comments when and if I find them in the queue.

    Alternatively, you could support the new and open moderation policy by removing Dr. Davison (and myself, for that matter) from the list that subjects us to moderation delays.

    JJ

  15. really have to apply a test to see if you are now a full fledged member of the Intelligent Design oligarchy here

    John,

    I don’t think it is polite to insult the people who have been kind enough to host your comments.

    Perhaps a little more gracious communication would be in order.

    You don’t have to like us, but could you refrain from insulting those who are hosting your comments? You’re insulting my friends and collegues here at UD by such comments.

    You’ve asked favors of me in the past, and I am asking favors of you.

    I’m afraid you’ll have to wait to get your comments released, but I am under the same constraints on other threads of UD. Ergo, you don’t have much grounds to complain given I have to wait (sometimes an entire day) to see my comments posted on other threads at UD by other authors.

    Sal

  16. Gentleman,

    I have to wait through the delays here at UD too.

    I commend the volunteer work going on around at UD.

    Perhaps patience with those who are kind enough to give there time to moderate UD is in order.

    I thank everyone who is willing to wait in line.

    On my threads, I don’t recall every deleting a comment unless it was outright spam.

    Save your posts if you value them, just in case I accidentally delete them.

    Thanks in advance.

    Sal

  17. JayM wrote:

    you could support the new and open moderation policy by removing Dr. Davison (and myself, for that matter) from the list that subjects us to moderation delays.

    I don’t have that authority nor do I seek it. I’m sorry.

    I prefer not to have all the headaches of being a moderator.

    Anyone here is welcome to open another weblog where they can moderate the discussion themselves as they see fit. I will be happy to allow posting of links to such discussions.

    Sal

  18. But most people’s posts – such as this one – always go through immediately. There must be something that causes some people’s posts to be caught in moderation and others to not.

  19. There must be something that causes some people’s posts to be caught in moderation and others to not

    Some people have been put on a moderation list. That decision is at a level higher than me at UD, and I will respect those decisions.

    However even after some people are removed from the list sometimes the restriction persists for technical reasons. Such is the case with me. In 2008, I was banned, restricted, and moderated by about 4 layers of software in 2008. But my pennance has been recognized, my sins forgiven, and I have received an indulgence to return after 8 months of exile.

    My comments on threads I author go through immediately, on other threads I can wait more than a day.

  20. 20

    Sal, I appreciate your forthrightness. Is there a way we can contact this “higher level”? I can’t seem to get in direct contact with that “higher level.” The utter silence of UD’s “higher level” makes me doubt its existence.

  21. scordova @20

    However even after some people are removed from the list sometimes the restriction persists for technical reasons. Such is the case with me In 2008, I was banned, restricted, and moderated by about 4 layers in 2008. But my pennance has been recognized, my sins forgiven, and I have received an indulgence to return after 8 months of exile.

    So much for respect for free and open discussion.

    Doesn’t it bother you that some of the people moderating this site give the impression that they really don’t want to hear any dissent? It certainly gives the impression of lack of confidence in the ID position.

    As one of the more recognizable names in the ID movement, you could use your bully pulpit to encourage more respect for open discussion. Are you interested in doing so?

    JJ

  22. Sal,

    Gentleman,

    I have to wait through the delays here at UD too.

    First, props to you for your quick responses, and my apologies for hijacking your thread. I have to admit I’m baffled by the moderation policy here at UD, though. I have never been moderated in the several weeks I’ve been here, in spite of some fairly sharp questioning on my part. My posts have all appeared instantly. I’m surprised to hear that you of all people have your posts delayed. Does each contributor to UD have his or her own moderation policy?

    And while I’m here, I just have to ask what is up with Allen_MacNeill’s posts being held for 12 hours or more? In a recent thread, I just happened to notice some of his posts suddenly appear, but of course they did not show up in the Recent Posts area. I think it’s likely many of us completely missed his contribution to the thread.

  23. In the introduction to the paper, Abel writes:

    Life-origin science is not especially interested in:

    1. [snip]

    2. [snip]

    3. Information defined in terms of the reduced uncertainty of subjective “observers” and “knowers”, who did not exist for 99.9% of life’s history.

    In other words, Shannon information. This is an amazing statement, because in an earlier paper (“Chance and necessity do not explain the origin of life“) Abel and his co-author Jack Trevors relied on a faulty application of Shannon information to make thier argument:

    Natural mechanisms are all highly self-ordering. Reams of data can be reduced to very simple compression algorithms called the laws of physics and chemistry. No natural mechanism of nature reducible to law can explain the high information content of genomes. This is a mathematical truism, not a matter subject to overturning by future empirical data. The cause-and-effect necessity described by natural law manifests a probability
    approaching 1.0. Shannon uncertainty is a probability function (-log2 p). When the probability of natural law events approaches 1.0, the Shannon uncertainty content becomes miniscule ( -log2 p = -log2 1.0 = 0 uncertainty). There is simply not enough Shannon uncertainty in cause-and-effect determinism and its reductionistic laws to retain instructions for life. Prescriptive information (instruction) can only be explained by algorithmic programming. Such DNA programming requires extraordinary bit measurements often extending into megabytes and even gigabytes. That kind of uncertainty reflects freedom from law-like constraints. This is exactly what we find at each decision-node selection of an additional untemplated nucleotide.

    Does Abel now admit that the earlier paper was bogus?

  24. My comments, too, are languishing in the moderation queue for 20 hours or more (that is, when they are not deleted outright).

    What is the real moderation policy at UD?

  25. Sal, I appreciate your forthrightness. Is there a way we can contact this “higher level”? I can’t seem to get in direct contact with that “higher level.” The utter silence of UD’s “higher level” makes me doubt its existence.

    I think posting here is the most likely channel. I try to be sparing in direct correspondence with UD admins.

    For example, the last e-mail I sent directly to Bill Dembski or Denyse O’Leary or Barry Arrington or DaveScot was almost a year ago.

    I sent a few e-mails to Clyve Hayden and that was it. Given they are unpaid volunteers, I want to minimize the requests I make of them.

    So, in as much as I’d like to help, in deference to Clyve’s time, I’m regret to say I’m reluctant to forward your request to through my direct channel as I use that channel maybe a few times a year if at all.

    I hope you receive a response from management.

  26. Why not just create new profiles and write from them uncensored instead?

    About teaching this in high school… I dont see the point. There is enough evolution/ID neutral things to teach that to introduce things of this nature is over-kill.

  27. First, props to you for your quick responses, and my apologies for hijacking your thread. I have to admit I’m baffled by the moderation policy here at UD, though.

    There are at least 4 (maybe more)layers of moderation.

    The first layer is “banned”, names of people who will not even be able to login.

    The second layer is a spam layer. If a certain word (something that sound vulgar) is caught it goes to a spam moderation queue. Even UD authors will be subject to this one.

    The third layer is a list of people that have to go through an approval process before their posts appear, this is the “pending approval” moderation queue.

    The fourth layer is author release of comments. If it is a thread I am author of, I can release comments from both the “spam” and “pending approval” queue, providing I find it and don’t delete it accidentally. The spam queue sometimes holds as many as 100,000 posts! I cannot release comments in threads by other authors. That is their jurisdiction.

    If I’m not around, a moderator or admin can release the comment. It may be that I may releae a comment and then a moderator can over-ride the decision. That is the fifth layer of moderation.

    There are some other software layers that prevent posting that I don’t think we’ve collectively figured out.

    What is the moderation policy?

    If you’re not on a list you can get through most of the time. What constitutes people being put on a list? The discretion of the moderator. The moderator acts like the editor of a news paper. He can release whatever opinions he likes or has time to review for the readers.

  28. There are at least two alternative reasons why many critics’ comments are held for many hours, while most favorable comments appear virtually immediately. They are:

    • that such delays are accidental

    or

    • that such delays are deliberate.

    For once, I must admit I’m strongly inclined toward the “ID” hypothesis, as it would explain what would otherwise be inexplicable. That is, the fact that ID critics are moderated to the point that most or all of our comments finally appear after most threads have either wound down or run out, while ID supporters are almost never moderated (not even when they display a streak of incivility that borders on megalomaniacy).

    I also find it very interesting that under the previous “administration” at UD my comments appeared almost immediately (i.e. I never received a not that my comments were awaiting moderation), but now under the newer, “gentler” administration my comments take at least a day to show up (and sometimes never do).

  29. Skeech plus wrote:

    Does Abel now admit that the earlier paper was bogus?

    No he does not. I think you’re misreading what was written in both papers.

  30. Allen and David,

    You are university professors in relevant fields. You have my vote to be removed from the list and given full privileges.

    That is all I can offer. The final decision is in the hands of others. Barring that, you can suggest another place to manage the dialogue and you can moderate it yourselves.

    regards,
    Salvador

  31. Sal,

    You are going to screw these poor people up. You have to say “This paper is anti-ID!!! How dare they!!!” Then they will probably win a Nobel.

    My comments on threads I author go through immediately, on other threads I can wait more than a day.

    That’s pretty weird.

  32. Thank you, Sal; I appreciate your efforts and recognize that you are doing the best you can.

    As for people being moderated for making ad hominem comments, I personally believe that it is incumbent on each person to conform to the following basic rules of academic debate:

    1) to present one’s arguments as clearly and thoughtfully as possible, with sufficient evidence (and/or citations to evidence) that everyone engaged in the debate can see for themselves if such evidence supports one’s arguments (or not);

    2) to be as skeptical as possible about any argument (and the evidence presented in support of any argument), regardless of whether the argument agrees with one’s own understanding of the subject being debated (or not);

    3) to point out as completely and as forcefully as possible what one perceives as invalid arguments and/or non-supporting evidence (and especially the lack of supporting evidence), even if such invalid arguments and/or evidence agrees with one’s own understanding of the subject being debated (or not); and

    4) to do the foregoing without attacking the character or motives of the persons making such arguments.

    I believe that every person reading and commenting on the posts here (and elsewhere) can do all of these things, and can recognize when valid arguments and evidence are being presented.

    I also believe that we can all recognize when someone is relying primarily on ad hominem attacks, character assassination, and guilt by association (along with other logically fallacious forms of argument).

    Personally, I will always try as hard as I can to adhere to the four principles outlined above. I also refuse to engage with any person who consistently resorts to ad hominem attacks, character assassination, and guilt by association (along with other logically fallacious forms of argument), and strongly recommend that the rest of those in this community who value clarity and intellectual integrity to so as well. If we do so, those individuals who cannot seem to bring themselves to make valid arguments and present valid evidence in support of those arguments will eventually tire of their lack of effect here and go somewhere else to rant at their reflections in the dark.

    Regards as well,
    –Allen

  33. scordova @28

    The moderator acts like the editor of a news paper. He can release whatever opinions he likes or has time to review for the readers.

    That is not how Barry Arrington explains the moderation policy:

    UD’s moderation policy is fairly simple: As a general rule, so long as your comment is not defamatory profane, or a vicious personal attack, you can say pretty much what you want. We have no interest in censoring viewpoints, because we believe ID is true and consequently in any full and fair debate we will win — and if we don’t win we either need to learn to debate better or change our position.

    Either UD is a forum to discuss ID openly and honestly or it is a forum to present opinions the moderators find acceptable. Claiming to be one while actually being the other is dishonest and hypocritical.

    As a leading light in the ID movement, Mr. Cordova, you have the ability to influence how this, probably the best known ID site, portrays that movement. Will you make any effort to eliminate the perception that ID proponents lack the confidence to debate on a level playing field?

    JJ

  34. John,

    You’re verbally abusing my friends here. Please leave.

    Sal

  35. Will you make any effort to eliminate the perception that ID proponents lack the confidence to debate on a level playing field?

    Sure. I’m building a new website that will invite discussion by qualified members.

    I’m intending to invite Allen MacNeill and David Kellog as participants and co-moderators.

    If you want to participate state your full name and instititutional affiliation and your qualifications.

    The website skeleton is here:

    http://www.IDCSNetwork.com

    It is not built out yet, maybe in a few weeks.

    Sal

  36. 37

    Just beautiful.

    On a thread devoted to yet another Abel paper that rips through the inability of material elements to coordinate the function necessary for metabolising/recording life systems…and the comments are whining about moderation – each of them APPEARING on the thread.

    Pathetic.

  37. scordova @38
    But you won’t use your influence here? Very disappointing.

    I’m building a new website that will invite discussion by qualified members.

    Ideas are qualified, not people. Why restrict discussion to those you deem qualified? Graduate students have skewered the arguments of full professors often in the past.

    I find it very peculiar that so many ID proponents complain bitterly about being excluded from science curricula, but turn their backs on the principle of free speech when they have the opportunity to be in control.

    Open the discussion and let the best arguments win.

    JJ

  38. Upright BiPed @39

    and the comments are whining about moderation – each of them APPEARING on the thread.

    That is primarily due to the fact that Mr. Cordova is courteous enough to rapidly approve comments in the moderation queue. This discussion could not take place if the usual moderators were controlling it.

    JJ

  39. 40

    Upright BiPed, I think the reason for that — and I agree that it’s pathetic — is that this is the one place where our comments show up in a reasonable time. We not only are in perpetual detention, we are unable even to inquire about why we are being treated like children or indeed to contact the adminstrators directly. This is the most direct path.

    I disagree about the Abel paper, though. I’m still reading it, but it doesn’t offer much besides awful writing and a great sense of self-importance.

  40. But you won’t use your influence here? Very disappointing.

    I don’t tell the people kind enough to invite me to their house how to run their household. It’s bad manners.

    Ideas are qualified, not people. Why restrict discussion to those you deem qualified? Graduate students have skewered the arguments of full professors often in the past.

    Fine, post a link to a weblog where people can have access to your fine ideas. You’ll get all the attention your fine ideas demand. :-)

  41. By the way JayM, if you don’t offer some meaningful comments regarding the paper, provide links to your website, and kindly invite yourself off the thread.

    If you can stay on topic, you’re welcome to participate.

    Good manners imply you’ll honor the request of your host. :-)

  42. 43
    AmerikanInKananaskis

    Okay, so I got curious about where this article was coming from and I googled the author’s affiliation.

    http://www.us.net/life/

    The Origin-of-Life Science Foundation should not be confused with “creation science”or “intelligent design” groups. It has no religious affiliations of any kind, nor are we connected in any way with any New Age, Gaia, or “Science and Spirit” groups.

    In other words–if they needed to spell it out–they are affiliated with at least one, if not all of these things, so maybe this is a pro-ID article after all.

    Then I looked up the importance of the journal (which I was curious about, because you don’t often see articles written entirely in MS Word). The Eigenfactor score is 0.0016356. Compare that to Nature (1.9917), Science (1.905), Evolution (0.072355), Molecular Ecology (0.072076), etc. Let’s not rest on our laurels. This is a good start for ID, but in my opinion, it’s only very, very weakly supportive and it’s in a no-name journal.

    The most important thing we can do as ID supporters is to make sure the science is right. Until then, we have to keep the public aware of how dangerous unbridled Darwinism really is.

  43. David Kellogg,

    Would you be willing to co-moderate a discussion elsewhere sometime?

    You’ll have much freer reign.

    You’ll be freer to dictate the flow of the discussion.

    I will help host the discussion. Would you at least be willing to consider it and dialogue about the format somewhere.

    Sal

  44. Sal, I checked out the website, I dont see a place to post any details there. But in response to your request in [38], I am an interested masters (of virology) student.

  45. 46

    Sal [46], hmmm, probably not. That would inevitably be a major time suck. I spend too much of my time on such boards as it is. :-) Thanks for the offer though.

  46. 47

    I asked:

    Does Abel now admit that the earlier paper was bogus?

    scordova replied:

    No he does not. I think you’re misreading what was written in both papers.

    He can’t have it both ways. Either Shannon information is relevant to OOL or it isn’t.

    Abel has reversed his position.

  47. Dear Skeech Plus,

    Are you saying Abel said Shannon information is not relevant to OOL in his first paper?

    If you are arguing that, you are mistaken. Abel stated there is not the capacity for Shannon information where there is no uncertainty. He did not state there no uncertainty as a universal principle, only in certain circumstances.

    So tell me, what does this mean to you:

    The cause-and-effect necessity described by natural law manifests a probability
    approaching 1.0. Shannon uncertainty is a probability function (-log2 p). When the probability of natural law events approaches 1.0, the Shannon uncertainty content becomes miniscule ( -log2 p = -log2 1.0 = 0 uncertainty). There is simply not enough Shannon uncertainty in cause-and-effect determinism and its reductionistic laws to retain instructions for life.

    Shannon is relevant. It demonstrates that there is low uncertainty hence low information capacity in deterministic physical laws.

    Are you going to argue there is uncertainty in a deterministic law (necessity)?

    Shannon information can exist in an environment where there is uncertainty (chance).

    Note the title: “Chance and Necessity do not explain the origin of life”.

    You are trying to represent their objections to determistic laws as the whole of the argument. That is not correct.

    Sal

  48. 49

    Sal,

    Thank you for promptly approving my comments.

    Are you saying Abel said Shannon information is not relevant to OOL in his first paper?

    No, it’s the other way around. In the first paper, he and Trevors attempt to use Shannon information to show that genetic instructions could not have arisen via “necessity” in an OOL scenario.

    In the second paper he says that Shannon information is uninteresting for OOL, and the reason he gives — that observers “did not exist for 99.9% of life’s history” — undermines the very argument that he and Trevors made in the first paper.

  49. 50

    I have no intention of leaving Sal. Anonymous nothings are immune to abuse. You should be ashamed of yourself for having anyhing to do with the “new” Uncommon Descent which cultivates and encourages its sworn enemies as it treats an ally with contempt. I guess you will just have to banish me DaveScot style. I have little more of substance to offer here in any event.

    It is hard to believe isn’t it?

    Not it all. Insecure, protectionist oligarchies are like that wherever one finds them.

  50. It’s quite revealing when someone comments that they don’t think that the paper is supportive of ID because the author states that evidence is still required to stop ID Theory, even though the whole paper provides a falsifiable hypothesis for ID Theory and shows that ID Theory may be correct unless the null hypothesis is falsified. I have already discussed how the paper is supportive of ID at comment #3.

    Instead of quote mining to “prove” what they wish to think about a paper, the concepts of the paper as a whole need to be discussed.

    Then that same person comments that they “dug a little deeper” and discover that through guilt by association the author of the paper may actually be sympathetic to ID. Thus, the paper may actually be supportive of ID.

    Tell me, how can someone state that a paper is not sympathetic to ID when the concept of the whole paper is indeed sympathetic and the one quote that they reference actually indicates that ID Theory has a point; yet that same person can turn around and claim that the paper actually may be sympathetic to ID merely because they are able to find a possibility of “guilt by association.”

    Don’t essays speak for themselves anymore? What does a person’s affiliations have to do with the quality and content of their argument?

    Obviously I’m a little frustrated by some people’s lack of *consistent* critical thinking or their selective skepticism; and I thought I’d just vent for a second.

  51. 52

    Could post 51 actually address post 50 please?

    Your argument reduces to the information being held in the events of physical need. You can’t get there – no matter how hard you try.

  52. 53

    Upright,

    I can explain what’s wrong with T & A’s first paper, if you like, but do you really want me to bother if Abel’s new paper — the topic of this thread — says that Shannon information is inapplicable to OOL?

  53. Sal,

    Thank you for promptly approving my comments.

    You’re welcome, however, I caution, once I’m logged off, it will be slow. Thank you for your forbearance.

    skeech wrote:

    In the second paper he says that Shannon information is uninteresting for OOL, and the reason he gives — that observers “did not exist for 99.9% of life’s history” — undermines the very argument that he and Trevors made in the first paper.

    Thank you for clarifying your position. I apologize if I did not represent you accurately.

    However, rather than rejecting their claims, they repeat their claims in this new paper:

    As the probability of an event approaches 1.0, its Shannon
    uncertainty approaches 0 bits [186]. 0 bits of uncertainty is maximum order.

    It is the same claim as in the first paper.

    The cause-and-effect necessity described by natural law manifests a probability
    approaching 1.0. Shannon uncertainty is a probability function (-log2 p). When the probability of natural law events approaches 1.0, the Shannon uncertainty content becomes miniscule ( -log2 p = -log2 1.0 = 0 uncertainty).

    Shannon information is a necessary but not sufficient condition for the existence of Prescriptive Information.

    For example, in a computer for there to be meainingful text stored in the computer, there has to be a mechanism of storing bits in a space of uncertain outcomes (we call this memory). We measure this the amount of memory in bits along the lines that Shannon defined.

    But the capacity for storing informmation as defined by Shannon does not imply the information will be meaningful or prescriptive. The existence of Shannon uncertainty is necessary, but not sufficient for meaningful information to exist.

    An MP3 might have 3 megs of Bits as defined by Shannon. It does not guarantee the 3 megs will be meaningful, intuitive information.

    What they pointed out was that deterministic laws don’t even get one to first base (shannon information), much less to home plate (prescriptive information).

    But even providing there is a capacity for Shannon information, there is insufficient to achieve prescriptive information.

    Dissipative structures are usually destructive, not cybernetically constructive (e.g., tornadoes,
    hurricanes). Trying to use “chaos” and “complexity” to provide mechanism for “self-organization” is
    like trying to use the Shannon transmission engineering to explain intuitive information, meaning and
    function.

    The problem is why do these structures look intuitive. They inspire the notions of “function” and meaning and purpose, i.e. The DNA appears to be intended to be translated into protein.

    Is the perception that there is something special about life a subjective accident of our perception, or we can accept that there is objective reality in saying life is special and set apart from the non living world?

    I would argue that whether the perception is subjective or not, stochastic chance processes are not an adequate explanation for our perception of designed structures.

  54. skeech plus:
    “In the second paper he says that Shannon information is uninteresting for OOL, and the reason he gives — that observers “did not exist for 99.9% of life’s history” — undermines the very argument that he and Trevors made in the first paper.”

    I can see how that can be quite confusing, however having read through the whole paper, it seems clear to me that the quote from the intro which you cite deals specifically with any measure of uncertainty which relies on *subjective* observers. In those first three points, the author shows that in order for OOL to be explained in purely material terms, there can be no room whatsoever for subjective manipulations. So, he merely clears the air and shows three points which can have nothing to do with any materialistic OOL scenario.

    IOW, the materialist must argue from the bottom up — from objective, mathematically described, “stand alone” complexity.

    Continuing on to page 5, it seems that the author does indeed think that “Shannon’s Information Theory” is or at least can be used as an objective, mathematical measure of complexity. He states that it is “An unequivocal, pristine, mathematical definition of linear “complexity”.”

    He then continues to describe Shannon Complexity and treat it as an objectively useful measure of complexity and randomness.

    Thus, it seems that the author sees a difference between “Information defined in terms of the reduced uncertainty of subjective “observers”” and the “unequivocal, pristine, mathematical definition … Shannon’s basic measurement of uncertainty in linear sequence complexity.”

    IOW, in order to explain OOL materialistically, we can not use:

    1. Human applications of a theory.

    2. Investigator involvement (artificial selection).

    3. Information defined in terms of relation to subjective agents.

    However, Shannon Information can describe complexity of a system without reference to subjective notions of uncertainty. This is how the author was able to use Shannon Information as an argument in his previous article.

    If you combine the two articles, you will see that, first, the author explains how there is not enough Shannon Information/Uncertainty in Law to explain the complexity of life; then in this new paper, the author explains how merely having a system of high Shannon Information/Uncertainty will also not necessarily generate life since high Shannon Information on its own only equates with randomness.

    Thus, there is something other than law (low shannon uncertainty) or randomness (high shannon uncertainty) within life and also necessary to generate life.

  55. eintown wrote:

    Sal, I checked out the website, I dont see a place to post any details there. But in response to your request in [38], I am an interested masters (of virology) student

    I sent you an e-mail based on the address you provided through UD. It has more info there.

    regards,
    Sal

  56. 57

    Sal writes:

    However, rather than rejecting their claims, they repeat their claims in this new paper:

    As the probability of an event approaches 1.0, its Shannon uncertainty approaches 0 bits [186]. 0 bits of uncertainty is maximum order.

    Sal,

    That is an uncontroversial claim that follows directly from the definition of Shannon information (in bits) as equal to -log2 p. As p approaches 1, -log2 p approaches 0. Who could possibly disagree?

    I’ve been speaking of a different claim that they make in the first paper:

    There is simply not enough Shannon uncertainty in cause and-effect determinism and its reductionistic laws to retain instructions for life. Prescriptive information (instruction) can only be explained by algorithmic programming.

    That’s a direct application of Shannon information to the question of the origin of genetic information. Yet in the second paper, Abel writes:

    Those trained in information theory will be quick to point out at this point that “information is always defined in terms of an observer or knower.” They argue that information is not in the law’s parsimonious statement or equation, but in the difference R between all of the uncertainty of the raw data, and the lesser amount of uncertainty generated by knowing the law. The problem with this concept of information is that for most of life’s history, linear digital genetic instructions have been prescribing exquisite metabolic organization long before any observers or knowers existed. Observers and knowers themselves would not exist except for the extraordinary amount of cellular programming and organization that produced humans.

    The contradiction couldn’t be more evident. In the first paper, Trevors and Abel rely on Shannon information to make their argument. In the second paper, Abel argues that Shannon information is inapplicable because there were no “observers or knowers” at the time of life’s origin.

    CJYman,

    Some comments:

    1. Abel writes that “Complexity in linear digital strings is fully measurable by the degree to which each string can be algorithmically compressed.” True enough, but what he is referring to is Kolmogorov complexity, not Shannon information. Therefore, when he proceeds to present the formula for Shannon entropy, it is a total nonsequitur. It’s like discussing Newton’s third law and then presenting the formula “E = mc2″.

    2. To compute the Shannon entropy, you need to know the probability of each successive symbol from the receiver’s point of view. If Abel is advocating the use of Shannon entropy to make his case, he has not only confused it with Kolmogorov complexity, he has also reintroduced the subjectivity he was just warning against.

    3. Determining the Kolmogorov complexity of a string does not require knowing any probabilities. The fact that the Shannon formula requires probabilities should have alerted Abel that he was making a big mistake.

    4. Abel is wrong to claim that Shannon information can only be measured with respect to human receivers. Shannon theory is perfectly applicable to machine-machine communication, even when no human ever becomes aware of the information being transmitted.

    5. Abel writes that

    Those trained in information theory will be quick to point out at this point that “information is always defined in terms of an observer or knower.”

    Not true. Those trained in information theory know that Kolmogorov information is not defined in terms of an observer, while Shannon information is.

    Abel is clearly in over his head when it comes to information theory. Evidently, so were the paper’s reviewers.

  57. Hi, Sal:
    I’m not sure if this constitutes hijacking the thread, but here’s a very interesting article:

    http://www.sciencedaily.com/re.....143457.htm

    Cornell is a big place, and so I don’t know these people personally, but if their algorithm does what they say it does, it would be very interesting to try it out on some of the issues being discussed here.

  58. Sal, Re #38:
    Like David, I have a lot on my plate, and I’m already moderating my own four websites, so I probably won’t have time to moderate at IDCSNetwork.com. However, I would be happy to participate (when I have the time, OC). Please keep me posted as to progress on getting the site up and running. You can email me at the address listed in my profile, or you can post messages as comments at http://evolutionlist.blogspot.com and they’ll be forwarded to me as the list moderator.

    And may I say that I appreciate your civility and attitude very much, and hope that we can prove worthy adversaries for each other – en garde, mon ami!

  59. “As the probability of an event approaches 1.0, its Shannon uncertainty approaches 0 bits. 0 bits of uncertainty is maximum order.

    Forgive my ignorance (I’m not formally trained in information theory), but to me this sounds very much like the classical definition of entropy, which is perhaps why Shannon took von Neumann’s advice and decided to call his measure of information “entropy”. That is, as a system approaches maximum order, it’s entropy approaches zero.

    However, there seems to be a paradox here, as classical thermodynamics predicts that the probability of the entropy of a closed system increasing is always higher than the probability of it decreasing, which seems to imply that a system in maximum entropy would also have the highest probability. What am I missing?

  60. The contradiction couldn’t be more evident. In the first paper, Trevors and Abel rely on Shannon information to make their argument. In the second paper, Abel argues that Shannon information is inapplicable because there were no “observers or knowers” at the time of life’s origin.

    I did a search on the entire paper, and the word “inapplicble” is not there.

    Furthermore, your interpretation seems hard to defend in light of the fact they use Shannon to help define functional information:

    Durston and Chiu at the University of Guelph developed a method of measuring what they call
    functional uncertainty (Hf) [195]. They extended Shannon uncertainty to measure a joint variable (X,F), where X represents the variability of data, and F its functionality.

    It would appear hard to say they find it inapplcable and then they not only apply it but extend it.

    Those trained in information theory know that Kolmogorov information is not defined in terms of an observer, while Shannon information is.

    I googled the phrase “kolmogorov information”. Your usage is a bit obscure. If one refers to Algorithmic Information, then one is still dealing with an observer, since in algorithmic information theory there is the notion of “symbol”. Symbol is rather meaningless with out an observer, traditionally. You’re welcome of course to believe the notion of “symbol” has meaning without an observer.

    The argument you offer is also hard to defend in that Abel also mentions Kolmogorov as well as give a diagram that describes algorithmic compressible information on page 252.

    Finally you wrote:

    I’ve been speaking of a different claim that they make in the first paper

    There is simply not enough Shannon uncertainty in cause and-effect determinism and its reductionistic laws to retain instructions for life. Prescriptive information (instruction) can only be explained by algorithmic programming.

    And they were referring to this fact in the 2nd which you said no one would disagree with:

    As the probability of an event approaches 1.0, its Shannon uncertainty approaches 0 bits [186]. 0 bits of uncertainty is maximum order….
    A law of physics also contains very little information because the data it compresses is so highly ordered. The best way to view a parsimonious physical law is as a compression algorithm for reams of data.

    But that is not a different claim as you assert. They write in the first paper essentially the same claim they repeat in the 2nd paper:

    Natural mechanisms are all highly self-ordering. Reams of data can be reduced to very simple compression algorithms called the laws of physics and chemistry. No natural mechanism of nature reducible to law can explain the high information content of genomes. This is a mathematical truism, not a matter subject to overturning by future empirical data. The cause-and-effect necessity described by natural law manifests a probability
    approaching 1.0. Shannon uncertainty is a probability
    function (-log2 p). When the probability of natural law events approaches 1.0, the Shannon uncertainty content becomes miniscule (-log2p =-log2 1.0 = 0
    uncertainty). There is simply not enough Shannon uncertainty in cause-and-effect determinism and its
    reductionistic laws to retain instructions for life.

    I don’t think you can argue they’ve retracted their position in light of comparing the two passages as I have just done.

  61. 62

    Preliminary note to jerry: Thanks for following up. I’ve responded in the other thread, but it’ll probably be in pointless moderation for a while.

    Now, to Sal: Andrey Kolmogorov was one of the most interesting mathematicians of the twentieth century. His was a wide-ranging, restless mind. A very well-known mathematician once told me that perhaps nobody in the last century made real contributions to so many different fields of mathematics.

    It does seem to be the case that Shannon and Kolmogorov have radically different ways of understanding information. Sometimes their vocabulary is kind of similar, though, which makes talking about both of them very slippery.

    The thing to Google is not “Kolmogorov information,” I think, but “Kolmogorov complexity.”

  62. but to me this sounds very much like the classical definition of entropy, which is perhaps why Shannon took von Neumann’s advice and decided to call his measure of information “entropy”. That is, as a system approaches maximum order, it’s entropy approaches zero.

    There is similarity. But instead of “order” Shannon substitutes “certainty”. Instead of high disorder, Shannon uses high uncertainty.

    From Wiki as Shannon defined the measure of information (entropy):

    The entropy, H, of a discrete random variable X is a measure of the amount of uncertainty associated with the value of X.

    Here is an account from Fortune’s Forumula by Poundstone page 57

    This is Shannon’s point: the essence of a message is its improbability….

    As he developed these ideas, Shannon needed a name for the incompressible stuff of messages. Nyuist had used intelligence, and Hartley used information. In his earliest writings, Shannon favored Nyquist’s term….

    John von Neumann of Princeton’s Institute for Advanced Study advised Shannon to use the word entropy. Entropy is a physics term loosely described as a measure of randomness, disorder, or uncertainty. The concept of entropy grew out of the study of steam engines….

    Use of the word “entropy” and you can never lose a debate, von Neumann told Shannon — because no one realy knows what “entropy” means. Von Neumann’s suggestion was not entirely flippant. The equation for entropy in physics takes the same form as the equation for information in Shannon’s theory….
    Shannon accepted von Neumann’s suggestion. He used both the word “entropy” and its usual algebraic symbol, H. Shannon later christened his Massachusetts home “Entropy House”….

    “I didn’t like the term ‘information theory’.” Robert Fano said. “Claude [Shannon] didn’t like it either.” But the familiar word “information” proved too appealing. it was this term that has stuck, both for Shannon’s theory and for its measure of message content.

    And back to Allen’s question:

    However, there seems to be a paradox here, as classical thermodynamics predicts that the probability of the entropy of a closed system increasing is always higher than the probability of it decreasing, which seems to imply that a system in maximum entropy would also have the highest probability. What am I missing?

    The confusion lies in the fact that the equations are similar but represent perhaps different ideas.

    As a loose analogy, we say a computer has 2000 Megs of RAM. That is 2000 Megs in the Shannon sense. That number 2000 Megs (a measure of Shannon entropy) is independent of the information in the memory. You don’t have any more or less RAM unless you change the hardware. We don’t increase a computer’s memory capacity by somehow making it more disorderly (in the colloquial sense). Yes, in the shannon sense when we add more memory cards we have increased the Shannon “entropy”, but colloquially this seems a little bit of a forced use of language.

    With shannon we are dealing with the improbability(uncertainty) of seeing a symbol. We often use this measure when we say a computer file has a certain number of bits.

    With statistical mechanics the improbability of being in a particular state increases with disorder. But the notion of increasing disorder is feels clumsy when we see way shannon defined probability.

    To understand what Abel was referring to. Consider a coin with heads and tails. The probability of heads is (1/2).

    -log2(1/2) = 1 bit.

    If the coin has two heads (and no tails) the probability is 1.0.

    -log2(1.0) = 0 bits

    Hence there is no uncertainty.

    The notion of “order” in the thermodynamic sense does not easily fit. It feels a little clumsy to be saying a regular coin has more disorder than a coin with two heads.

    We could say that 8 coins have the capacity for 256 configurations.

    -log2(1/256) = 8 bits

    But if we configure all the 8 coins to show heads, is this more ordered? Well in a colloquial sense yes, but we would still say the measure of information is:

    -1og2(1/256) = 8 bits

    Rearanging the coins into an orderly fashion (all heads) does not necessarily mean we have somehow less entropy in the coins in the Shannon sense. The entropy is a measure of the a priori (before the event or observation) improbability of each configuration, not necessarily what we may perceive as orderly after the fact (a posteriori, after the observation or event).

    But let’s say we have a 1000 coins.

    -log2( 1/ 2^1000) = 1000 bits

    If we make all the coins heads in our mind we have made them “orderly”. But from the standpoint of a priori probabilities, the entropy of the system of 1000 coins is independent of how we configure them from time to time.

    Again, the notion of adding more computer memory cards does not normally fit our colloquial notions of increasing system entropy, but that is what is happening in the shannon sense!

    The parallels only go so far, but they are compelling parallels nonetheless as Shannon himself stated.

    Notes:

    In Shannon’s famous paper Mathematical Theory of Communication (referenced by Abel), he writes:

    The fundamental problem of communication is that of reproducing at one point either exactly or approximately
    a message selected at another point. Frequently the messages have meaning; that is they refer
    to or are correlated according to some system with certain physical or conceptual entities. These semantic aspects of communication are irrelevant to the engineering problem.

    ….

    The form of H will be recognized as that of entropy as defined in certain formulations of statistical mechanics where p_i is the probability of a system being in cell i of its phase space. H is then, for example, the H in Boltzmann’s famous H theorem.

  63. 64

    A number of terms are used by both Shannon and Kolmogorov that have different (and sometimes incompatible) meanings: these include information, complexity, and entropy.

  64. 65

    Sal

    Allen MacNeill is the quintessential neo-Darwinian. It is revealing that he is allowed to post without moderation and he certainly is not being told to go away. So you can have Allen MacNeill who has no sympathy for Intelligent Design whatsoever. I am amazed that you are so out of touch with reality that you believe you can reason with any Darwinian let alone a devout one like Allen MacNeill. I can assure you that it is quite impossible that 150 years of an ideological and congenital atheist fixation can ever be resolved through debate or discussion. The scientific studies on separated monozygotic twins have made that conclusion inescapable.

    Your idealism blinds you to the truth. There is absolutely NOTHING in the Darwinian fairy tale that ever had anything to do with the appearance of any life form, any new organ system or any other of the thousands of characteristics that characterize the enormous diversity of the organic world. Darwinism is mythology now as it was at its inception, a fantasy conjured up out of thin air by a pair of Victorian naturalists, one of whom, Alfred Russel Wallace, rejected it in its entirety later in life. Consider the title of his last book -

    “The World of Life: A Manifestation of Creative Power, Directive Mind and Ultimate Purpose.” (1911).

    Wallace was a much better naturalist and was ten times the scientist as Charles Darwin.

    I recommend Wallace’s “Mans Place in the Universe” in which he predicted the dangers of an increasing level of atmospheric carbon dioxide. His was a great mind.

    Darwinism, like ultra-liberalism with which it is invariably closely associated, is a congenital, deficiency disease for which there is now and probably never will be a cure.

    So now with a great sigh of relief, I turn the balance of this thread over to Allen MacNeill who I am certain will grasp this opportunuity to further the Darwinian fairy tale to the best of his abilities. He really can’t help it. He was “born that way.”

  65. Allen wrote:

    system in maximum entropy would also have the highest probability.

    I think this is a mistake but I could be wrong, so I’m reluctant to comment.

    The probability does not refer to the likelihood of disorder happening or increasing, but rather the probability of individual components (like molecules) existing in a particular kinetic energy state.

    I actually think maximum entropy implies highest improbability of system components being in particular energy states. In other words, highest disorder means actually the lowest probability of individual components of a system existing in certain states.

    But I could be mistaken. I haven’t studied statistical mechanics in school yet. Next summer!

    Any physicists are welcome to comment in plain English. I would appreciate a correction here if I misstated.

    I believe Dr. Granville Sewell might be able to enlighten us.

    Thanks in advance.

  66. John wrote:

    he certainly is not being told to go away.

    Allen has been far kinder to me and ID proponents in the university than you have.

    Allen stuck his neck out for my fellow pro-ID students at Cornell.

    Sorry, John, it’s not a matter of ID or Darwin at this point, but a matter of your rude manners. If shouting insults is what you want to do, what’s the point of dialogue?

    You’ve been a professor of biology some 40 years. Tossing you seems a little heartless, so I haven’t deleted a single one of your comments.

    With respect to entertaining opposing viewpoints, I learned this from Darwinist John Angus Campbell of the Discovery Institute quoting John Stewart Mill:

    But the peculiar evil of silencing the expression of an opinion is, that it is robbing the human race; posterity as well as the existing generation; those who dissent from the opinion, still more than those who hold it. If the opinion is right, they are deprived of the opportunity of exchanging error for truth: if wrong, they lose, what is almost as great a benefit, the clearer perception and livelier impression of truth, produced by its collision with error. …

    We have now recognized the necessity to the mental well-being of mankind (on which all their other well-being depends) of freedom of opinion, and freedom of the expression of opinion, on four distinct grounds; which we will now briefly recapitulate.

    First, if any opinion is compelled to silence, that opinion may, for aught we can certainly know, be true. To deny this is to assume our own infallibility.

    Secondly, though the silenced opinion be an error, it may, and very commonly does, contain a portion of truth; and since the general or prevailing opinion on any subject is rarely or never the whole truth, it is only by the collision of adverse opinions that the remainder of the truth has any chance of being supplied.

    Thirdly, even if the received opinion be not only true, but the whole truth; unless it is suffered to be, and actually is, vigorously and earnestly contested, it will, by most of those who receive it, be held in the manner of a prejudice, with little comprehension or feeling of its rational grounds.

    And not only this, but fourthly, the meaning of the doctrine itself will be in danger of being lost, or enfeebled, and deprived of its vital effect on the character and conduct: the dogma becoming a mere formal profession, inefficacious for good, but encumbering the ground, and preventing the growth of any real and heartfelt conviction, from reason or personal experience.

    Such a dialogue is not possible without some modicum of civility even toward our debate opponents.

    Even enemies will gather together under a flag of truce. That is what these sort of discussions are for. Opposing viewpoints have gathered under a flag of truce.

  67. Gentleman,

    I’m loggin off. This means I won’t be around to release comments from any of the queues. Those who don’t have any restrictions are free to post. Otherwise one can expect the usual delays.

    Thanks to all for their participation.

    Sal

  68. 69

    Sal, Campbell’s a Darwinist? He’s a Darwin scholar, that’s for sure. But I’d call him an ID advocate within his area (that is, “teach the controversy”). He’s had pro-ID views for a long time. Consider his report from the Mere Creation conference of 1997:

    also enjoyed the meeting’s oppositional character. The conference had the feel of dissent. Not that we all were of one mind–but that all of us believe the current philosophic/scientific establishment has been deluded by a mistaken philosophy and we intend to do our parts to expose it and open the academy and the culture to reasoned debate. I was reminded in private conversations of the courage of our members in the biological sciences who risk careers and the possibility of future grants by being associated with our movement. I am particularly grateful to Behe, Wells, Bradley, and many others in the sciences for their courage and integrity.

    That doesn’t sound like a Darwinist to me.

  69. Sal:

    Thank you so much for the quotation from John Stuart Mill. It expresses much more eloquently than I can the reason why I invite my intellectual opponents to make presentations in my classes. It also expresses why I believe that it would be a mistake to ban certain individuals from commenting here. Nothing could be more damaging to their own position than the megalomania and paranoia (indeed, the obvious malignant terror) expressed in their own words. This is a virtual world here, and the only “actions” why which we can know them are their words, posted here for all to read. And so, to paraphrase,

    “By their words shall we know them”

    You are a gentleman and a scholar, sir, and I look forward to many more enlightening encounters. Until next time…

  70. 71

    JTaylor: “My impression though is that this paper is probably too advanced for high school.”

    eintown: “About teaching this in high school… I dont see the point.”

    And we wonder why the United States public education system sucks. We don’t expect excellence from high schools and high school students. Public education is merely living up to its low expectations.

  71. David Kellogg,

    Is it possible for someone to believe in the Darwinian view of evolution and also be open to, even demand that there should be open dialogue on the topic? I watched the video of Campbell on the rhetoric in Darwin’s OOS and he took it apart showing it to be nothing but non sequiturs and not have any definitive proof of anything. He also expressed his dismay at the attitudes of fellow faculty members who were suppressing debate on the topic.

    Such a person could believe in Darwinian evolution and still hold such opinions. Such a person could also believe in an intelligent input for the creation of the universe and the creation of life and hold such a position about evolution. I have no idea on what Campbell’s actual beliefs are because he did not express them.

    Now the quote you provided mentions a mistaken philosophy and that could be a reference to philosophical naturalism which you have to admit is prevalent in the academy, especially in evolutionary biology. He could be against that and still believe in Darwinian evolution.

  72. Let the reader provide the supposedly easy falsification of the null hypothesis [that there is no physico dynamic origin of life]. Inability to do so should
    cause pangs of conscience in any scientist who equates metaphysical materialism with science. On the
    other hand, providing the requested falsification of this null hypothesis would once-and-for-all end a lot of unwanted intrusions into science from philosophies competing with metaphysical materialism.

    I notice Abel doesn’t cite anyone who thinks creating life is easy! He just throws out there the idea that falsifying his null hypothesis (creating life) is “supposedly easy”. Who thinks that is true?

  73. For complex adaptive systems to progress in the direction of achieving formal utility, selection for
    potential function must take place at individual decision nodes, logic gates, and configurable switch
    settings prior to the realization of that function. An inanimate environment cannot do this.

    This directly contradicted by John Holland’s Schema Theorem. Selection at the entity level is an implicit and parallel selection process across all nodes at once.

  74. In addition,
    the syntax of such choices for utility must be integrated into programmable circuits to achieve
    computational halting.

    Can anyone even tell me what this means? Is Abel saying that it is impossible that the STOP codon evolved? How does a syntax for choice acheive computational halting?

    I am troubled by the use of ‘must’ in these sentences. This kind of assertion should be supported by citation, or by proof. Otherwise this is just an op-ed piece, not a scientific paper.

  75. Ok,

    I have to clarify something I wrote pertaining to statistical mechanics.

    The “easiest” read on the subject is here.

    Entropy is sometimes described as a measure of “disorder,” and if you ponder the definition given above, you can see that in a narrow sense that is true. However, the word “disorder” has all sorts of esthetic, moral, and political meanings that have nothing to do with k log N. The identification of entropy with disorder in the broader sense (combined, sometimes, with neglect of the Second Law’s proviso about isolated systems) has been used to justify many specious arguments, such as the claims that the Second Law disproves evolution or that it proves that technology is evil. It’s better just to keep the Boltzmann definition, which is wonderfully simple, firmly in mind. Entropy has to do with the number of ways that the microstate can rearrange itself without affecting the macrostate.

    and

    This makes sense; if there are many different ways to have a certain set of macroscopic parameters, that ought to increase the likelihood of the system being in that macrostate. It’s like rolling a pair of dice. Suppose that the “macrostate” is the total of the dice. There are six ways to get a total of 7 from the “microstates” of the two dice, but only one way to get a total of 2 (snake-eyes) or 12 (boxcars), so 7 is more likely.
    Each die can have any of six “microstates”, and for each microstate of one die, the other die can be in any microstate, so the number of microstates of the whole system is 6*6 = 36. In general, if you combine two systems into a bigger system, the number of possible microstates multiplies.
    If you have hundreds of fair dice and put them all together, the total for which the number of possible microstates is at a maximum is (if you work it out) at a value of 3.5 times the number of dice. If you just shake these dice up in a bag it will be extremely improbable for you to get a total which is much different from that; if you do the experiment many times, the average deviation from this number is nearly certain to be much smaller than the total. If you carefully put the dice into the bag so that they show some vastly different total, then shake up the bag, the total of the uppermost faces of all the dice will converge rapidly on the value (the “macrostate”) for which the number of ways to make it from individual dice (“microstates”) is at a maximum. It’s just the same for the macrostates of an isolated system (except for the additional restriction that some quantities, like the total energy, may be subject to conservation laws); thermal fluctuations do the “shaking,” and the macroscopically measurable quantities converge on the values with the largest number of microstates. This is what the Second Law says.

    Ok, so if I have 1000 dice and each showed the number “1″, the total of all of the dice would be 1000.

    If I put them in a bag and shook them, the total of all of the dice would most likely be around 3,500. [isn't physics wonderful].

    There is only one way to achieve the number 1000 with 1000 dice, however there are many ways to achieve 3500. In fact for the number 3500, we have the maximum number of ways to achieve that number than any other number.

    So revisiting Allen’s question, when there is maxium entropy there is the maximum number of microstates.

    But with more microstates the probability of each individual microstate state gets lower as more states are made possible.

    By way of loose analogy, adding coins expands the possible number of configurations. But as there are more configurations the probability for each configuration to appearing gets lower. i.e.

    for 1 coins the probability of each configuration is 1/2

    for 2 coins, 1/4

    for 3 coins, 1/8

    for 4 coins, 1/16

    etc.

  76. Is Abel saying that it is impossible that the STOP codon evolved?

    No!

    A “stop” codon is not what is meant by computational halting. Neither is taking dynamite and blasting your computer a means of creating computational halting. Even though in that sense the compter is physically “halted”, using dynamite is not the way a computer is computationally “halted”.

    Computational halting implies the existence of a system that is capable of computing and the system has computable problems presented to it.

    Computational halting is rather meaningless if the system can’t compute in the first place.

    To understand the real meaning of halting see: Halting Problem.

    Computers that computationally halt don’t spontaneously emerge from random chemical soups.

  77. Not only are symbol systems used, but a bijection must occur between two independent symbol
    systems. Bijection (translation; a symbol system to symbol system correspondence) is rule-based, not
    physical law-based.

    A ‘must’ again… Assuming the first symbol system is tRNA triplets, is the other system the set of amino acids used in protein synthesis? I think so. But this is not a bijection, because there is no amino acid corresponding to the STOP codons. Why introduce mathematical jargon if it cannot be used correctly?

    No cause-and-effect necessity exists in the linking of anticodons, amino acids,
    tRNAs, and amino acyl tRNA synthetases with codons. The anticodon is located on the opposite end
    of tRNA from the amino acid. The correspondence between the two languages is arbitrary and
    abstract. By arbitrary, we do not mean random. Arbitrary means free from physicodynamic determinism. Bijection rules are freely selected. Translation of this linear digital prescription into
    functionally specific polyamino acid chains cannot be explained by physicodynamics.

    There is a rich literature (uncited by Abel) on the optimality of the codon table, and the way it reflects selection for function and/or historical contingency. The idea that the codon table is arbitrary would be disputed by ID supporters and MET supporters, though for different reasons.

    Was this published April 1? I am tempted to call Sokol on this paper…

  78. Wow! What a wonderful paper.

    And somebody here even doubts that it is pro ID? But this paper contains the best of ID. Maybe not all ID (the positive design inference is not touched), but there is a very good and complete treatment of many of ID’s arguments. Perhaps one of the best treatments I have read.

    I think there are a lot of things about this paper which we could discuss. I will definitely use it a lot in the future, quoting from it, and using its arguments. And who cares if the score of the journal is law? There is a much more inportant score at stake here, the score of meaning and credibility and value. And, kuckily, that score is not based on sheer authority…

    For the moment, just a couple of comments to Nakashima:

    1) “Assuming the first symbol system is tRNA triplets, is the other system the set of amino acids used in protein synthesis? I think so. But this is not a bijection, because there is no amino acid corresponding to the STOP codons. Why introduce mathematical jargon if it cannot be used correctly?”

    OK, then is we assume the first set of tRNA triplets “except” the stop codon, that should be a bijection anyway. What changes? Are you out for purely formal criticism, ignoring the substance of the paper?

    “There is a rich literature (uncited by Abel) on the optimality of the codon table, and the way it reflects selection for function and/or historical contingency. The idea that the codon table is arbitrary would be disputed by ID supporters and MET supporters, though for different reasons.”

    That has nothing to do with what Abel is saying. He says:

    “No cause-and-effect necessity exists in the linking of anticodons, amino acids,
    tRNAs, and amino acyl tRNA synthetases with codons.”

    He is obviously speaking of cause and effect mechanisms based on physical and biochemical laws, not of the supposed effect of NS or of other unproved theories, which are the subject of the discussion.

  79. 80

    The absolute certainty with which you address OOL has been duly noted.

    Now, if you’d like to prove up that the patterns observed in nucleic sequencing (the convention in the codon table, indeed language) are a product of mechanical need, then by all means – you have the floor.

  80. 81

    Oops, my comment was address to Nakashima.

  81. 82

    Sal

    “Debate” is for lawyers, referees, politicians and high school teams. There is no place for debate in science and it has never played a significant role in advancing the truth. It was the IDists who demanded a debate from the Darwinians and that is exactly what they got. There is absolutely nothing to debate concerning either ontogeny or phylogeny. Neither could ever have happened by chance and to assume, even to insist, otherwise is inexcusable and intellectually dishonest. Thanks for allowing me to express myself on your thread. You now have my blessings to return to the hopeless task of trying to convince “prescribed” “born that way” ideologues through that useless rhetoric called “debate.”

    “Truth is incontrovertible, malice may attack it, ignorance may deride it, but in the end, there it is.”
    Winston Churchill

  82. Off topic-

    If people want an open discussion pertaining to ID and evolution then they should have the courtesy to come to the discussion prepared.

    I say that because it has become painfully obvious that people like JayM, David Kellogg and Allen MacNeill do not appear to understand what is being debated.

    Carry on…

  83. Mr. gpuccio,

    In a bijection, the two sets have the same number of elements. This is chapter one set theory. It will take more than arbitrarily dropping 3 of 64 codon triplets to repair Abel’s argument.

    Since Abel doesn’t spell out what the two symbol sets are, we are left to speculate and assume they take the most common values. From the quotes in Abel about computational halting, I think Abel actually thinks the STOP codon is pretty important part of the system.

    The point remains that calling it a bijection adds nothing to the strength of his argument. It seems to me that Abel is trying to throw in some maths jargon to bolster the case that the codon table has some ‘formal’ properties. This would be more successful argument if he knew what these terms meant.
    I suppose there are 64! possible codon tables. Maybe someone better with combinatorics can correct me. The one we actually use is very good at a grouping similar amino acids together. That is a non-arbitrary property. I don’t think it is a result of chance or necessity. It is the operation of selection and contingency very early in the history of life.

  84. Mr. Upright,

    I am not the one saying “must” all the time. The person evincing certainty is Abel. There “must” be a psychological theorem somewhere that the more certain we are, the less evidence we need to support our certainty. From all the “must”s in Abel’s text, I think he is absolutely certain, and therefore his need to cite evidence has fallen to zero.

  85. John Davison,

    I agree with you on a couple things you say.

    The truth about Darwinism is so obvious in the sense that it never did anything creative. But apparently the intelligentsia of evolutionary biology has thrown Darwin under the bus while keeping a few of his ideas.

    They keep common descent which I understand is also part of your theory. They keep natural selection but only as a housekeeping function of cleaning up the riff raff of evolution and not as any creative function. So Darwin’s vaunted force or process is left for the maids to dust up.

    The pro Darwin or anti ID people who come here are mostly immune to logic and as you say “prescribed” “born that way” ideologues. Few of us here who support ID would disagree with that assessment. Now you lump Allen MacNeill into that group and that is wrong.

    Allen is an advocate of the Gould wing of naturalistic evolution and is anti Darwin. He has more than once pronounced Darwin dead and only keeps Darwin barely breathing and available for minor duties but really is in the Gouldian camp. The Gouldian camp and its offshoots takes aim at adaptation, the heart of Darwin, and says change comes from somewhere else. Namely, the slow mutation of non coding regions caused by various events such as duplication and retroposition by reverse transcriptase. While we recognize this is as a new fantasy, it is the one that has to be dealt with currently. Adaptation as a major force is dead but exaptation is now overseeing the realm for a large number of the faithful.

    While we recognize the intransigence of the anti ID people, they are remarkably predictable but they are not the target for the discussions here. There are plenty of reasonable people who read this site and look to it for information and that is who the target is. I haven’t seen one anti ID person move an inch since I have been here. They are intractable. Probably as you say they are prescribed.

    Thus, when you make your assertions which are true, they are not helpful for those who read the discussions here and are not aware of your experiences on the topic. So anything you can contribute on the substance of the discussions would help these people and us in the future. I could go into your writings linked above but would rather have you present your ideas than for others to act as interpreters.

  86. Joseph @85

    If people want an open discussion pertaining to ID and evolution then they should have the courtesy to come to the discussion prepared.

    I say that because it has become painfully obvious that people like JayM, David Kellogg and Allen MacNeill do not appear to understand what is being debated.

    Barry Arrington:

    As a general rule, so long as your comment is not defamatory profane, or a vicious personal attack, you can say pretty much what you want. . . . Don’t get me wrong. I’m not opening this site up to nasty juvenile name-calling fests like one see so often at Panda’s Thumb.

    We learn more about the moderation policy with every post from people like Joseph.

    And by the way, Joseph, a good indication that someone is unprepared for this discussion is if they claim that evolutionary theory makes no predictions.

    JJ

  87. Nakashima:
    “From all the “must”s in Abel’s text, I think he is absolutely certain, and therefore his need to cite evidence has fallen to zero.”

    … because a lot of the “must”s describe quite basic ideas, and it seems that he goes on to explain each “must.” Why does it matter for the sake of his argument if he is actually convinced by it? Of course, you’ll never hear scientists [especially Darwinists] speak in terms of “must”s, and “facts”, and “proof”, and “overwhelming evidence”, and “everyone agrees with me”. Riiiiiiiight!?!?!?

    In fact, it is the author of this paper himself who states that:
    “Science celebrates positive and parsimonious descriptions of presumed objectivity. But we must never forget that our knowledge is only “best thus far.” Even the most fundamental laws of physics technically must be viewed as “tentative.” We rightly eschew diatribes of metaphysical pontifications. Science proceeds through open-mindedness and the falsification of null hypotheses, not through the rhetorical pronouncement of dogmas. Popper and many since have exposed the problems associated with trying to prove any positive hypothesis [176, 177]. Neither induction nor deduction is foolproof. Theses that cannot be proven ought not to be proclaimed as positive statements of fact. At the same time, we have spent much of the last century arguing to the lay community that we have proved the current biological paradigm. Unfortunately, very few in the scientific community seem critical of this indiscretion. One would think that if all this evidence is so abundant, it would be quick and easy to falsify the null hypothesis put forward above.”

    Now let’s review some of his “must”s. Most of them seem to be in relation to theoretical constructs for which he seems to provide adequate explanation. Other “must”s just seem to be self evident statements akin to stating ‘if you wish to disprove someone’s theory, you *must* provide evidence.’ Do you disagree with that “must” statement? Let’s continue on to review some of the author’s “must”s (asterisk added):

    “To address these questions, chaos, complexity, self-ordered states, and organization *must* all be carefully defined and distinguished. In addition their cause-and-effect relationships and mechanisms of action *must* be delineated.”

    “If Pasteur and Virchow’s First Law of Biology (“All life *must* come from previously existing life”) is to be empirically falsified, direct observation of spontaneous generation is needed.”

    “To stem the growing swell of Intelligent Design intrusions, it is imperative that we provide stand-alone natural process evidence of non trivial self-organization at the edge of chaos. We *must* demonstrate on sound scientific grounds the formal capabilities of naturally-occurring physicodynamic complexity. Evolutionary algorithms, for example, *must* be stripped of all artificial selection and the purposeful steering of iterations toward desired products. The latter intrusions into natural process clearly violate sound evolution theory [172, 173]. Evolution has no goal [174, 175]. Evolution provides no steering toward potential computational and cybernetic function [4, 6-11].”

    Can you provide some of the “must”s for which think the author does not provides an explanation or which you disagree with?

  88. Nakashima:

    Is Abel saying that it is impossible that the STOP codon evolved?

    I did a search on the document, the phrase “STOP codon” is not even mentioned in the article.

    So no, he is not arguing that.

    He is arguing:

    Neither fixed/forced laws nor chance can logically make non trivial computationally halting programming decisions.

    Do you agree or disagree with that claim?

  89. 90

    Nakashima,

    The idea that a materialist would come on to the UD board and complain about certainties is a rich irony indeed.

    The certainty we are most familiar with is the one were there must be a material cause for inanimate material coordinating itself into energy-metabolising entities driven by highly-organized information processing systems and spontaneously recording its existence into a conventional code of digital information that is not contingent on material need.

    We are quite aware of the seizing power that the word must plays in materialism, and that everything must follow it and there must not be any exceptions. The fact that all inferences point in another direction is simply a hapless bystander who is institutionally ignored.

    - – - – - – - -

    Now if you’ve become satisfied that your complaint about Abel’s use of the word “must” has been registered, then you can proceed to show how the language observed in nucleic sequencing is a product of mechanical need – after all, it must be, right?

  90. Nakashima:
    “In a bijection, the two sets have the same number of elements. This is chapter one set theory. It will take more than arbitrarily dropping 3 of 64 codon triplets to repair Abel’s argument.”

    A bijection is a one-to-one mapping that satisfies the function f(x)=y.
    The mapping from codon to amino acid is a one to one mapping which satisfies f(codon)=amino acid. First, it must be understood that the amino acid is a function of the codon. The codon determines the amino acid and not vice versa (the Central “dogma” of biology as per Francis Crick). The amino acid is dependent on the codon. As far as I understand, it makes no difference that different codons will code for the same amino acid, since that still produces a one codon to one amino acid mapping of a function where multiple x values can equal similar y values and we can still have a mathematical function. Furthermore, the stop codons still satisfy f(x)=y, and in this case, y (amino acid)=0. The whole system still provides a one codon-to-one amino acid mapping.

    If on the other hand, one codon could be mapped onto multiple amino acids, there would be no mathematical function since multiple y values would then produce similar x values; no f(x)=y. However, that is not the reality of the situation. Thus, it seems that the mapping of codon to amino acid is indeed a bijection.

    Nakashima:
    “Since Abel doesn’t spell out what the two symbol sets are, we are left to speculate and assume they take the most common values.”

    Not sure what you mean here.

    Nakashima:
    “From the quotes in Abel about computational halting, I think Abel actually thinks the STOP codon is pretty important part of the system.”

    1. Which quote makes you thinks this?

    2. Would the system halt and produce an output (amino acid) if there were no stop codon?

    Nakashima:
    “The point remains that calling it a bijection adds nothing to the strength of his argument.”

    No that point does not remain. The point which does remain is the point made by the author of the paper:
    “Not only are symbol systems used, but a bijection must occur between two independent symbol systems. Bijection (translation; a symbol system to symbol system correspondence) is rule-based, not physical law-based. No cause- and-effect necessity exists in the linking of anticodons, amino acids, tRNAs, and amino acyl tRNA synthetases with codons. The anticodon is located on the opposite end of tRNA from the amino acid. The correspondence between the two languages is arbitrary and abstract. By arbitrary, we do not mean random. Arbitrary means free from physicodynamic determinism. Bijection rules are freely selected. Translation of this linear digital prescription into functionally specific polyamino acid chains cannot be explained by physicodynamics. It is not lawbased, and it certainly is not random.”

    Basically he is stating that there is no physical/chemical property which necessitates that nucleotides must produce amino acids, a symbol system, and a bijection.

    That forms a part of his null hypothesis re: what complexity and chaos can not on their own produce, which he invites everyone to examine, test, and attempt to falisify.

    Nakashima:
    “It seems to me that Abel is trying to throw in some maths jargon to bolster the case that the codon table has some ‘formal’ properties. This would be more successful argument if he knew what these terms meant.”

    Can you provide evidence that he is incorrect?

    He uses the word “formal” and “physicodynamic” to distinguish between arbitrarily mapped sign systems which produce one output per input in which the organization is not defined by the physical properties of the units utilized and organizations which are defined by physical properties of the material units utilized, respectively.

    This takes us back to Michael Polonyi:

    ““A shaping of boundaries may be said to go beyond a mere fixing of boundaries and establishes a ‘controlling principle.’ It achieves control of the boundaries by imprinting a significant pattern on the boundaries of the system. Or, to use information language, we may say that it puts the system under the control of a non-physical-chemical principle by a profoundly informative intervention.”

    –Michael Polanyi, “Life Transcending Physics and Chemistry,” Chemical & Engineering News (21 August 1967): 64

    Nakashima:
    “I suppose there are 64! possible codon tables. Maybe someone better with combinatorics can correct me. The one we actually use is very good at a grouping similar amino acids together. That is a non-arbitrary property. I don’t think it is a result of chance or necessity. It is the operation of selection and contingency very early in the history of life.”

    I’m not really sure what you are saying here, and it seems that you are using a different definition of “arbitrary” than the author uses, but can complexity and chaos with chance and necessity provide the laws of nature and the structure necessary for the required selection to begin?

    Please provide evidence.

  91. Mr. CJYman,

    The ‘must’s I found most troubling are the ones in my posts above at 76, 77 and 80. Let’s discuss those.

    Mr. Cordova,

    Thanks for a topic that generates such a lot of discussions. I agree that the text of the paper does not contain the string “STOP codon”. This was my attempt to understand what Abel is talking about. What does he mean by a syntax for computational halting? The only thing I could think of was the STOP codon.

    Mr. BiPed,
    I don’t think the codon table we use is the product of mechanical need. I’ve said twice that I think it is the product of selection and historical contingency. Work in the synthetic biology field where codons are reassigned to other amino acids is a falsification of that idea of necessity.

  92. Nakashima:

    1) “Assuming the first symbol system is tRNA triplets, is the other system the set of amino acids used in protein synthesis? I think so.

    The problem appears to be that your reading is uncharitable, not that Abel is wrong.

    The fact that Abel referred to Hamming block codes indicates he was treating synonymous codons as a single conceptual abstract entity, not merely as mutiple discrete individual entities!

    Because Abel referred in his comments to the topic of Hamming Block Codes, the grouping of synonymous codons as representing a single conceptual enetity is a more faithful interpretation of what was said than the inerpretation you put forward.

    It is true because of Code degeneracy that several codons can symbolize either the same amino acid or stop codon. But this is consistent with the idea of Hamming Block Codes.

    I will illustrate.

    Take codons for phenylalinine:

    UUU
    UUC

    there is a surjective mapping from the codons to the concept of a valid phenylalinine symbol

    f(UUU) = f(UUC) = valid_phe_symbol

    this is arguably part of “symbol system” for DNA

    Take leucine codons:

    UUU
    UUG
    CUU
    CUC
    CUA
    CUG

    f(UUU) = f(UUG) = f(CUU) = f(CUC) = f(CUA) = C(CUG) = valid_leu_symbol

    this also part of a “symbol system”

    and then isoleucine

    AUU
    AUC
    AUA

    f(AUU) = f(AUC) = f(AUA) = valid_lle_symbol

    etc.

    but then there is a bijective mapping from these conceptually valid symbols in DNA to a symbols sytem composed of amino acids.

    f(valid_phe_symbol) = phenylalinine
    f(valid_leu_symbol) = leucine
    f(valid_lle_symbol) = isoleucine
    …..

    If one treats the stop codons as a metasymbol, then there is a bijection. Even if one does not treat the stop codons as a metasymbol, you can still argue for a bijection if one allows “no amino acid” as a conceptual entity. Either way a bijection results.

    So there is a bijection somewhere at some level if one allows views the mapping in terms of conceptual entities such as suggested by Hamming Block Codes.

    There is a correspondence between the conceptual DNA symbol system and the conceptual amino acid system just as Abel said:

    Not only are symbol systems used, but a bijection must occur between two independent symbol
    systems. Bijection (translation; a symbol system to symbol system correspondence)

    The noise-reducing Hamming “block coding” of triplets of nucleotides to prescribe each specific
    amino acid is all the more abstract and formally conceptual.

  93. Mr CJYman,

    Let’s look at Wikipedia on Bijection.
    If X and Y are finite sets, then there exists a bijection between the two sets X and Y if and only if X and Y have the same number of elements.
    The set of amino acids is finite, x=20. The set of codons is finite, y=64. 20 =/= 64. Therefore the map from codons to amino acids and vice versa is not a bijection.
    The function from codons to amino acids is surjective (many to one). Except for the three STOP codons, of course!

    About the two symbol systems, you were not sure what I was referring to. Let’s look at the sentence you quote from the text a little later in your post.
    Not only are symbol systems used, but a bijection must occur between two independent symbol systems.
    What are these “two independent symbol systems”? Throughout these discussions, you and I and everyone else has assumed that one symbol system is the set of 64 codon triplets, and the other symbol system is the set of 20 amino acids. But Abel never says that explicitly in the paper. Since there are alternatives, such as expanding the list of amino acids to 21 or 22, I was trying to make my own assumptions clear.

  94. 95

    jerry in #88

    Gould was an atheist Darwinian through and through. He slandered Otto Schindewolf and ignored Leo Berg, Robert Broom and for all practical purposes, Henry Fairfield Osborn, Richard B. Goldschmidt, William Bateson and Pierre Grasse as well, not one of whom was either a religious fanatic or a Darwinian mystic. Not one of MacNeill’s sources ever made a significant contribution to the great twin mysteries of ontogeny and phylogeny. Allen MacNeill is a “true believer” and there is nothing that can be done for him.

    I am not at all convinced of a single common descent. Neither was Leo Berg as I have made very clear right here at Uncommon Descent. Obviously you have not read my comments or you wouldn’t be making your assuptions about what I believe and do not believe.

    To paraphrase an old saw -

    “You can lead a man to the literature but you can’t make him comprehend it.”

  95. Nakashima:
    “The ‘must’s I found most troubling are the ones in my posts above at 76, 77 and 80. Let’s discuss those.”

    Nakashima:
    “This directly contradicted by John Holland’s Schema Theorem. Selection at the entity level is an implicit and parallel selection process across all nodes at once.”

    Unfortunately I am unable to discuss this specific aspect. Maybe scordova will be more able to do so?

    Nakashima:
    “Can anyone even tell me what this means? Is Abel saying that it is impossible that the STOP codon evolved? How does a syntax for choice acheive computational halting?”

    It seems that scordova has answered that above in #91 and I have also begun to address your question in #93.

    The author of the paper:
    “No cause-and-effect necessity exists in the linking of anticodons, amino acids, tRNAs, and amino acyl tRNA synthetases with codons. The anticodon is located on the opposite end of tRNA from the amino acid. The correspondence between the two languages is arbitrary and abstract. By arbitrary, we do not mean random. Arbitrary means free from physicodynamic determinism. Bijection rules are freely selected. Translation of this linear digital prescription into functionally specific polyamino acid chains cannot be explained by physicodynamics.”

    Nakashima:
    “There is a rich literature (uncited by Abel) on the optimality of the codon table, and the way it reflects selection for function and/or historical contingency. The idea that the codon table is arbitrary would be disputed by ID supporters and MET supporters, though for different reasons.”

    Again, you are using a different definition for “arbitrary” than the author is using and thus you are missing the point and are not able to respond to it.

    So I reiterate from my comment #93:

    “Basically he is stating that there is no physical/chemical property which necessitates that nucleotides must produce amino acids, a symbol system, and a bijection.

    That forms a part of his null hypothesis re: what complexity and chaos can not on their own produce, which he invites everyone to examine, test, and attempt to falisify.

    Can you provide evidence that he is incorrect?

    He uses the word “formal” and “physicodynamic” to distinguish between arbitrarily mapped sign systems which produce one output per input in which the organization is not defined by the physical properties of the units utilized and organizations which are defined by physical properties of the material units utilized, respectively.

    This takes us back to Michael Polonyi:

    ““A shaping of boundaries may be said to go beyond a mere fixing of boundaries and establishes a ‘controlling principle.’ It achieves control of the boundaries by imprinting a significant pattern on the boundaries of the system. Or, to use information language, we may say that it puts the system under the control of a non-physical-chemical principle by a profoundly informative intervention.”

    –Michael Polanyi, “Life Transcending Physics and Chemistry,” Chemical & Engineering News (21 August 1967): 64

    … can complexity and chaos with chance and necessity provide the laws of nature and the structure necessary for the required selection to begin?

    Please provide evidence.

  96. Nakashima:
    “The set of amino acids is finite, x=20. The set of codons is finite, y=64. 20 =/= 64. Therefore the map from codons to amino acids and vice versa is not a bijection.
    The function from codons to amino acids is surjective (many to one). Except for the three STOP codons, of course!”

    Scordova’s assessment in #95 in conjunction with what I’ve stated at the beginning of #93 should suffice to provide an adequate explanation of what the author has stated.

  97. Mr. Cordova,

    Thanks for a topic that generates such a lot of discussions.

    You are welcome, and thank you for participating. Controversy over a topic always helps generate web traffic.

    Welcome to Uncommon Descent.

    Sal

  98. 99

    Nakashima,

    I’ve said twice that I think it is the product of selection and historical contingency.

    To say “selection” has some necessary assumptions, particularly as you’ve used it in this thread (#76 “at the entity level”).

    Selection is generally understood to mean that there are two like entities with a difference between them. This difference is written into the information that instructs the entity, and further, that the entity with the instruction set which is most fit to their continued existence will out-produce the one of lesser fitness.

    Are you assuming that a metabolizing entity existed prior to the instructions that organize the elements of the cell and its constituents? Or, are you assuming that the difference (to be selected) existed prior to the onset of the instructions that would contain the difference to be selected? How would that selection take place?

    In other words, selection does not seem to precede metabolism, reproduction, instructions, the information contained in those instructions, or the language they are written in.

    There is one saving grace for selection as a mechanism though – it could have existed at the original nucleic (information) level – but that would infer volitional agency. Neither chance nor physical need is inferred based on their quantifiable abilities to “make” the selections called for. They are not seen as a source for written language or the coordination of independent results; nor do they infer the foresight that is logically inherent the existence of instructions. Instructions are typically seen as having meaning.

  99. 100

    Regarding Sal@63:

    I wrote:

    The contradiction couldn’t be more evident. In the first paper, Trevors and Abel rely on Shannon information to make their argument. In the second paper, Abel argues that Shannon information is inapplicable because there were no “observers or knowers” at the time of life’s origin.

    Sal replied:

    I did a search on the entire paper, and the word “inapplicble” is not there.

    I didn’t claim that Abel used the word “inapplicable”; I said that he argued that Shannon information is inapplicable to questions of life’s origin. Come on, Sal — you know better than to make that kind of argument. The word “emancipation” doesn’t appear in the Emancipation Proclamation; would you argue that Lincoln wasn’t writing about emancipation?

    Abel wrote:

    Those trained in information theory will be quick to point out at this point that “information is always defined in terms of an observer or knower”… The problem with this concept of information is that for most of life’s history, linear digital genetic instructions have been prescribing exquisite metabolic organization long before any observers or knowers existed.

    Shannon information is defined with respect to a particular observer. Abel’s statement therefore rules out the use of Shannon information in OOL scenarios (though he’s wrong to do so, as I explained in an earlier comment).

    Sal continues:

    Furthermore, your interpretation seems hard to defend in light of the fact they use Shannon to help define functional information:

    Durston and Chiu at the University of Guelph developed a method of measuring what they call
    functional uncertainty (Hf) [195]. They extended Shannon uncertainty to measure a joint variable (X,F), where X represents the variability of data, and F its functionality.

    Durston and Chiu’s “extension” of Shannon uncertainty still requires that an observer be specified. This should be obvious, because the term “uncertainty” itself invites the obvious question “uncertain to whom?”. If Abel advocates the application of Durston and Chiu’s concept, he is ignoring his own (incorrect) warning about the lack of observers at the time of life’s origin.

    I wrote:

    Those trained in information theory know that Kolmogorov information is not defined in terms of an observer, while Shannon information is.

    Sal replied:

    I googled the phrase “kolmogorov information”. Your usage is a bit obscure. If one refers to Algorithmic Information, then one is still dealing with an observer, since in algorithmic information theory there is the notion of “symbol”.

    As David pointed out, the more common term is “Kolmogorov complexity”. I used “Kolmogorov information” to stress to readers that we were talking about two different measures of information: Shannon’s and Kolmogorov’s.

    And no, an observer is not required in order to define Kolmogorov information. The Kolmogorov complexity of a string of symbols is defined as the length of the shortest program that will produce that string of symbols using some universal programming language. It remains the same whether or not there is an observer present to interpret the symbols.

    Sal:

    The argument you offer is also hard to defend in that Abel also mentions Kolmogorov as well as give a diagram that describes algorithmic compressible information on page 252.

    Sorry, but I can’t see any way in which Abel’s diagram or his mention of Kolmogorov contradicts or mitigates what I’ve been saying.

    Sal:

    And they were referring to this fact in the 2nd which you said no one would disagree with:


    As the probability of an event approaches 1.0, its Shannon uncertainty approaches 0 bits [186]. 0 bits of uncertainty is maximum order….
    A law of physics also contains very little information because the data it compresses is so highly ordered. The best way to view a parsimonious physical law is as a compression algorithm for reams of data.

    Good grief, Sal. I said that no one would disagree with this:

    As the probability of an event approaches 1.0, its Shannon uncertainty approaches 0 bits [186]. 0 bits of uncertainty is maximum order.

    You added the following text which I did not quote and which does not occur until the bottom of the next page in Abel’s paper:

    A law of physics also contains very little information because the data it compresses is so highly ordered. The best way to view a parsimonious physical law is as a compression algorithm for reams of data.

    This is obviously wrong. Consider someone who knows the masses and current positions of the sun and planets, but knows nothing about gravity. Such a person can’t predict where the planets will be tomorrow, much less in 500 years. Send them a message containing the law of gravity, and their uncertainty about future planetary positions drops dramatically. To such a person, the law of gravity contains a huge amount of information, even though the law is deterministic.

    I don’t think you can argue they’ve retracted their position in light of comparing the two passages as I have just done.

    I haven’t argued that they’ve “retracted their position.” I’ve argued that Abel has reversed his.

    The funny thing is that Abel comes off badly either way. If he thinks that Shannon uncertainty doesn’t apply to OOL, then he has reversed himself, as I claim. If he thinks that Shannon uncertainty still applies, as you claim, then he has contradicted himself by ignoring his own warning about the lack of observers at the time of OOL — a warning that is itself bogus.

    And to top it off, he confuses Shannon information with Kolmogorov complexity and claims that physical laws contain very little information. What a muddle that paper is.

  100. Mr BiPed,

    Yes, it seems Abel does accept selection as an important aspect, equal in power with chance and necessity.

    We are talking about how we arrive at the current state of the world, where almost all life uses the same codon table. But if we go back, there could have been a time when diferent codon tables were used by different sets of life. Selection for function, such as resistance to point mutation, or set of amino acids coded for, would create differential success. This is selection without volition. This is what I meant by selection and historical contingency.

  101. Mr Cordova,

    Yes, I see how your understanding leads to a bijection. How unfortunate that the text is not clearer. Following your interpretation, the phrase “a bijection must occur” is completely tautological. It tells us nothing new.

  102. Mr Cordova,

    As a followup comment, I think your interpretation is not helpful to Abel’s argument. He really wants to make the point that the physical system has certain formal properties, and by pointing out how unusual a state of affairs that is, lead us on to some conclusion. If the thing that has the formal property “bijection” is no longer the actual physical system of the codon table, but an abstraction and particular understanding of the codon table, then this program is seriously undercut.

  103. Hello Nakashima,

    You state:
    “Selection for function, such as resistance to point mutation, or set of amino acids coded for, would create differential success. This is selection without volition. This is what I meant by selection and historical contingency.”

    To which I ask, do you have any evidence or even any reason to suppose that your idea of selection and historical contingency alone will overcome his null hypothesis?

    The author argues that outside of “choice with intent” all that we are left with is any grouping of high and low complexity [which includes selection and historical contingency]; and that no matter how much or little complexity (randomness or law) you have, one will not be able to arrive at the systems described within his null hypothesis since these systems are neither defined merely by law nor by randomness nor by any combination of the two.

    Nakashima:
    “Yes, I see how your understanding leads to a bijection. How unfortunate that the text is not clearer.”

    It does seem that the reader needs to put some pieces of the puzzle together for himself, however since the author does discuss the error correcting or “noise reducing” Hamming block codes in relation to bijections, it seems that the author does indeed explain himself.

    Nakashima:
    “Following your interpretation, the phrase “a bijection must occur” is completely tautological. It tells us nothing new.”

    I don’t see how that could be correct. Reading the paragraph prior to and the one containing that quote, the author tells us that in order for life to transfer information from the code storage space to a functional space, “a bijection must occur between two independent symbol
    systems.”

    The significance is provided in the very next sentences:

    “Not only are symbol systems used, but a bijection must occur between two independent symbol systems. Bijection (translation; a symbol system to symbol system correspondence) is rule-based, *not physical law-based*.” (asterisk added).

    The author then continues:

    “No cause-and-effect necessity exists in the linking of anticodons, amino acids, tRNAs, and amino acyl tRNA synthetases with codons. The anticodon is located on the opposite end of tRNA from the amino acid. The correspondence between the two languages is arbitrary and abstract. By arbitrary, we do not mean random. Arbitrary means free from physicodynamic determinism. Bijection rules are freely selected. Translation of this linear digital prescription into functionally specific polyamino acid chains cannot be explained by physicodynamics. It is not lawbased, and it certainly is not random.”

    That provides evidence for the authors stance that the system under description is neither defined nor caused by merely a collection of law and chance (degrees of complexity, chaos, and the selection arising from them) and that “choice with intent” is a valid consideration for the generation of the type of system seen at the foundation of life — unless of course, the null hypothesis is falsified.

  104. Mr CJYman,

    I’m rying to understand this from your perspective. Are you saying that when Abel says “a bijection must occur”, he is making a statement that it is a requirement that there be two different symbol systems, and that they be related via a bijection, otherwise life cannot develop? Is that your understanding?

    I think that the way Abel stated his null hypothesis at the end of the text, he will not be satisfied with anything less than the creation of a lifelike process “in the test tube”, not with any simulation or argumentation such as we are capable of here. Even a system such as Hiroki Sayama’s evoloops would not satisfy him. Even though self reproducing systems arise spontaneously, and optimize over time, in this system, it is not our real-world physics and chemistry.
    In the mean time, I am still trying to understand what is the relevance of “computational halting” to his hypothesis.

  105. Mr Cordova,

    Yes, I see how your understanding leads to a bijection. How unfortunate that the text is not clearer. Following your interpretation, the phrase “a bijection must occur” is completely tautological. It tells us nothing new.

    That is not correct, because of the fact Hamming Block codes are pereceived. If there weas not the perception of Hamming block codes the objection you put forward might have some merit.

  106. Mr Cordova,

    As a followup comment, I think your interpretation is not helpful to Abel’s argument. He really wants to make the point that the physical system has certain formal properties, and by pointing out how unusual a state of affairs that is, lead us on to some conclusion. If the thing that has the formal property “bijection” is no longer the actual physical system of the codon table, but an abstraction and particular understanding of the codon table, then this program is seriously undercut.

    Thank you for your comment, but the perception of Hamming block codes suggests the abstraction is valid and it is an abstraction that is valid in engineering practice. Thus it is not merely a matter of convenience that the mapping is perceived that way. It would appear to be the correct characterization of the system.

  107. 108

    Nakashima,

    “Abel does accept selection as an important aspect, equal in power with chance and necessity”.

    As mechanistic realities operating in nature? Perhaps.

    As causal mechanisms for selection at the nucleic level? Hardly.

    The entirety of his last three research papers dispute this repeatedly.

    “…there could have been a time when diferent codon tables were used by different sets of life. ”

    We can speculate anything.

    “Selection for function, such as resistance to point mutation, or set of amino acids coded for, would create differential success.”

    This position does not address the logical issues I raised in my previous post, but if you’d like to skip over that we can.

    We can simply say that if you have these mechanisms in mind, then describe them in some further detail and lets see how far we get.

  108. Hello Nakashima,

    Abel’s statement that “a bijection must occur between two independent symbol systems” is in reference to the way that life actually is — a description of life as we know it.

    He makes no statement re: a definition of life or life requiring a bijection. He seems to be merely showing how life works and showing that it is an example of a bijection by defintion … thus the “must” language. Of course, this is my interpretation of what he wrote and it seems consistent with everything else he states, especially since he does not give a definition of life or assess requirements of life; he only describes life as we know it (in which case, one could say that he provides requirements of life as we know it — since any difference (ie: no bijection) that may still be classified as life may no longer be “life as we know it.” I hope I am making sense to you here.

    Nakashima:
    “I think that the way Abel stated his null hypothesis at the end of the text, he will not be satisfied with anything less than the creation of a lifelike process “in the test tube”, not with any simulation or argumentation such as we are capable of here.”

    I don’t see that as correct. Although science does require verification, simulations and logical arguments do play an important role. Can someone show how his understanding of complexity and physicodynamics and how it relates to bijections and such systems to be incorrect? I see no reason why he wouldn’t be open to such dialogue and arguments.

    As to simulations, we are able to simulate complexity and chaos to a certain extent and to that extent we can test his statements regarding the output of such systems. I see no problem here; and I see no reason to suppose that the author would have any problem with testing via simulations with such systems.

    Nakashima:
    “Even a system such as Hiroki Sayama’s evoloops would not satisfy him. Even though self reproducing systems arise spontaneously, and optimize over time, in this system, it is not our real-world physics and chemistry.”

    As long as they can be defined in terms of complexity, chaos, and other terms provided and explained within the paper I see no reason why we can’t analyze these systems’ inputs and outputs and see if they overcome the author’s null hypothesis. Nor do I see any objections on the part of the author stated within the paper.

    Nakashima:
    “In the mean time, I am still trying to understand what is the relevance of “computational halting” to his hypothesis.”

    Will a system which is a result of mere measures of complexity (absent selection for *potential* function e.g., artificial selection for formal function — choice with intent.), generate turing machines which halt and provide a formally functioning output based on specific input.

    “Formally” (or non-lawfully and *potentially* goal oriented) organized function as opposed to “Physicodynamic” order (as a result of regularities and physical properties of the material and laws utilized).

  109. Skeech wrote:

    I didn’t claim that Abel used the word “inapplicable”; I said that he argued that Shannon information is inapplicable to questions of life’s origin.

    What you say about about what Abel said is not correct. You are giving an uncharitable reading and not representing what he said accurately.

    And no, an observer is not required in order to define Kolmogorov information.

    Algorithmic information deals with symbols. Does a symbol exist without an observer? You just made an assertion “an observer is not required in order to define Kolmogorov information” instead of dealing with the objection that I put forward to your argument.

    In fact the compression technique is dependent on the interpretive capacities of compressor, which implies observational sensitivity. But more to the point, are you arguing the notion of symbols exist without MIND? :-) Whichever way you answer, you know it will lead to problems. So I look forward to your response.

    Abel wrote:

    A law of physics also contains very little information because the data it compresses is so highly ordered. The best way to view a parsimonious physical law is as a compression algorithm for reams of data.

    you responded:

    This is obviously wrong. Consider someone who knows the masses and current positions of the sun and planets, but knows nothing about gravity. Such a person can’t predict where the planets will be tomorrow, much less in 500 years.

    Your objection is mistaken. It can be argued Newton (or at least his predecessors) didn’t have knowledge of universal gravitation, but they were able to synthesize if for the very reason the laws of physics have low information content (in the sense of algorthimic compression). The great IBM physicist Rolf Landauer said the laws of physics are algorithms.

    The faith that the laws of physics are compressible is why we can write the fundamental laws on a single piece of paper! This is proof positive the laws are not information rich in the algorithmic sense. That is what Chaitin points out here in Irreducible Complexity in Pure Mathematics .

    To put it bluntly, from the point of view of AIT [algorithmic information theory], mathematics and physics are not that different. In both cases, theories are compressions of facts, in one case facts we discover in a physics lab, in the other case, numerical facts discovered using a computer.

    But to put a nail in your objection, consider this paper by Physcist Paul Davies: How Bio Friendly is Our Universe

    The laws of physics have very low
    information content:
    they describe how input information at time t1 is converted to output
    information at time t2, but they cannot add any information on the way. So the laws of physics cannot alone generate the informational content of life. Schrödinger clearly recognized this in his pioneering study of the structure of the genome (Schrödinger, 1944), which he termed ‘an aperiodic crystal.’ Normal, periodic, crystals are very low in information content. And crystals are written into the basic laws of physics: the structure of a crystal follows automatically from the geometrical symmetries encoded in those laws. But an information-rich molecule like a genome does not reflect the information content of the laws of physics, and so will not be generated inexorably from the operation of those laws.

    I respect your valiant attempt to discredit a paper unfavorable to your position, but your attempt is not consistent with the mainstream literature.

  110. Skeech wrote:

    And to top it off, he confuses Shannon information with Kolmogorov complexity and claims that physical laws contain very little information. What a muddle that paper is.

    Given my previous post, it appears your assessment is pre-mature at best.

    The quotations by Chaitin and Davies show that you are not giving sufficient credit to Abel’s knowledge of the current literature, in fact the citations I provided above in contrast to what you said suggest you may not have been acquainted with the mainstream view, or at the very least were unwilling to acknowledge the mainstream view.

    And to top it off, he confuses Shannon information with Kolmogorov complexity

    No he does not, that is just a bald assertion.

    Given that you argued that Abel’s claim :

    “A law of physics also contains very little information”

    was (in your words) “obviously wrong” when in fact it was obviously right, suggests that perhaps the charge that Abel is confusing matters is merely the result of your own misperception rather than Abel’s confusion.

  111. CJ said,

    “Bijection (translation; a symbol system to symbol system correspondence) is rule-based, not physical law-based.”

    I thought I’d expand since there was objection to the use of bijection as a term…

    bijection from wiki…
    f(x)=y
    “Alternatively, f is bijective if it is a one-to-one correspondence between those sets; i.e., both one-to-one (injective) and onto (surjective). (One-to-one function means one-to-one correspondence (i.e., bijection) to some authors, but injection to others.)

    Bijective function f is not limited to a one-to-one correspondance, but includes surjection

    From wiki…
    Surjection:
    In mathematics, a function f is said to be surjective or onto, if its values span its whole codomain; that is…,

    for every y in the codomain, there is at least one x in the domain such that f(x) = y .

    bingo.

    Bijection – Surjection Funcion Ex. mapping

    Bijection is not limited to equal sets of one to one mapping, but allows for many to one as well. Thus bijection as a mathematical term by Abel is fine. And provides for the relational database aspect of life. Codons and Amino Acid are a good example of Bijection(Surjection) mappings.

    Otherwise, I guess one could argue for Injective Function. But that would be Junk DNA.

    Bijection is valid as CJYMan stated it and as utilized by Abel in the paper.

  112. DATCG,

    Bijective function f is not limited to a one-to-one correspondance, but includes surjection

    Eh? Any bijective function must be one-to-one and it must also be a surjection. Both conditions must be satisified.

  113. 114

    Madsen,

    …and they have been. Perhaps, it’s time to move on to your next significant objection.

  114. Salvador wrote:

    Is the perception that there is something special about life a subjective accident of our perception, or we can accept that there is objective reality in saying life is special and set apart from the non living world?

    I would argue that whether the perception is subjective or not, stochastic chance processes are not an adequate explanation for our perception of designed structures.

    The New Jersey Lottery: Give Your Dreams a Chance (c) organization repeats a poorly controlled operation until the outcome matches, in a prespecified sense, at least one of an enormous number of purchased lottery tickets.

    When John Doe, who has told friends of his promise to God that he will split his take with the Orphanage of the Holy Mother if he should he win the lottery, in fact wins $95 million, it is a miracle. Right? In any case, the story makes the news, and the children who suffer the consequences of a de facto poor tax do not.

    Saying that something unseen used the genome to send messages to the proteome is on par with saying that something unseen used the lottery to send money to the orphanage.

  115. Hi, Sal:
    I’m not sure if this constitutes hijacking the thread, but here’s a very interesting article:

    http://www.sciencedaily.com/re…..143457.htm

    Cornell is a big place, and so I don’t know these people personally, but if their algorithm does what they say it does, it would be very interesting to try it out on some of the issues being discussed here.

    Hi again Allen,

    Apologies for my delay in responding, but in light of my citations of Chaitin and Davies, your comments has much more significance now.

    The article you referenced said:

    The researchers have taught a computer to find regularities in the natural world that become established laws – yet without any prior scientific knowledge on the part of the computer. They have tested their method, or algorithm, on simple mechanical systems and believe it could be applied to more complex systems ranging from biology to cosmology and be useful in analyzing the mountains of data generated by modern experiments that use electronic data collection.

    Chaitin said:

    from the point of view of AIT [algorithmic information theory], mathematics and physics are not that different. In both cases, theories are compressions of facts

    As you are probably aware, computers and people can be (not always) good at compressing facts into a more succinct form. They can take a large amount of data and completely represent that data in a more succinct form.

    When we run a compression algorithm on a file, we have compressed an idea into a more succinct form. When we take diverse phenomenon with many many data points like planetary positions over time, we can compress these ideas quite well in terms of Kepler’s celestial mechanics.

    Such compressions are possible especially when there is repetition or redundany. Sometimes the redundancies and repetitions are not so obvious. A physicist or a computer can sometimes find these redundancies or regularities. Genius is finding the parallels, the redundancies, the metaphors, which are not obvious to most people.

    Biology, at its core, however seems to be incompressible beyond a certain point. It cannot be reduced to simpler, more succinct descriptions like the accepted laws of physics. This fact was acknowledge by Chaitin in Can Darwinian evolution be made into a mathematical theory? Is there a fundamental mathematical theory for biology?

    Chaitin concludes:

    Pure mathematics has infinite complexity and is therefore like biology

    But what did chaitin say about pure mathametics? He said there is Irreducible Complexity in Pure Mathematics

    His phrase “irreducible complexity” does not mean “irreducible complexity” in the sense used by Behe, but in the sense of the inability to characterize biology the same kind of “simple” laws that we characterize physics. Therefore, biology is irreducibly complex at least according to Chatiin’s definition of “irreducible complex”. It is a matter of active debate whether biology is also “irreducibly complex” in the way behe defines “irreducibly complex”.

    Some success has been achieved in finding simple, succint descriptions of apparently complex data in the DNA. Dr. Pellionitz (who has posted here) has found fractal patterns in DNA. So he has found a succinct descriptions of some aspects of DNA, but I think most feel that DNA is not fundamentally simple (like the laws of physics), but is complex in the sense that it resists simple mathematical description. It is, as Chaitin suggests, irreducibly complex.

    A falsifiable prediction therefore, is that the computer algorithm described in the article will not be able to describe biology with very simple mathematical laws because such laws do not exist even in principle.

  116. Mr CJYman,

    You answer to me
    Will a system which is a result of mere measures of complexity (absent selection for *potential* function e.g., artificial selection for formal function — choice with intent.), generate turing machines which halt and provide a formally functioning output based on specific input.

    OK, things halt all the time, why is it a big deal to be repeated over and over in the text? You’d think a guy talking about OOL would be more interested in how things started than in how they stop. :)

    But seriously, now you bring up Turing machines. I don’t think Abel claims that the cellular machinery is a Turing machine. That’s a good thing, because I’m petty sure it isn’t.

  117. Mr DATCG,

    Keep reading that Bijection wiki page, down to the section on Cardinality.

  118. 119

    “…because such laws do not exist even in principle”

    ta-dah!

    Materialists, running from the implications of their necessities.

    Their followers, trying to make sense of what’s most common among us.

  119. Sal Gal:

    When John Doe, who has told friends of his promise to God that he will split his take with the Orphanage of the Holy Mother if he should he win the lottery, in fact wins $95 million, it is a miracle. Right?

    Thank you for your comment as this raises a good point.

    In response to your question, “it is a miracle. Right? ”

    Perhaps, but not in the same way that we would classify something as a miracle coming from a stochastic process.

    A lottery guarantees a “miracle” will eventually be granted to someone, a stochastic process does not. That is the difference.

    It is possible you can go to the casino and roll the dice and play the snake eyes hop bet ( a chance of 1 in 36) and win the snake eyes hop bet 50 times in a row ( a probabiliy of 1 in 36^50). That would be a stochastic miracle (not to mention you’d be phenomenally rich!).

    But such a stochastic “miracle” is not the same kind of “miracle” that happens in the lottery, because the lottery pretty much guarantees an eventual winner (or at least it is supposed to).

    Now back to the lottery, I suppose however, from the perspective of the observer, John Doe, it is a miracle.

    One might argue that our perception of the miracle of life is an artifact of our perception. Perhaps.

    But one cannot argue that the miracle of life is probable on stochastic grounds. Stochastic processes do not guarantee the emergence of life in the way a lottery guarantees the eventual emergence of a winner.

    One might argue then that life is not a miracle because life is the winner of lottery. But how does one justify using the lottery model over the stochastic model?

    One might say that life is a unique unrepeatble event that just happens to coverge on specified patterns we normally regard as designed. Fine.

    But at some point such unique, unrepeatable events become indistinguishable from miracles. If one wishes to label all miracles perfectly natarual occurances, fine. But I don’t think such “natural miracles” are probable under the assumption of stochastic processes — certainly not in the sense that lotteries make “miracles” eventually probable to someone somewhere.

  120. Nakashima wrote:

    I don’t think Abel claims that the cellular machinery is a Turing machine. That’s a good thing, because I’m petty sure it isn’t.

    [By the way Nakashima, youf facility with English would put many Americans to shame. You are very fluent.]

    But with respect to your comment, Abel wrote in Chance and Necessity

    How did inanimate nature write

    (1) the conceptual instructions needed to organize
    metabolism?

    (2) a language/operating system needed to symbolically
    represent, record and replicate those instructions?

    (3) a bijective coding scheme (a one-to-one correspondence
    of symbol meaning) with planned redundancy
    so as to reduce noise pollution between triplet codon
    ‘‘block code’’ symbols (‘‘bytes’’) and amino acid
    symbols?
    We could even add a fourth question. How did
    inanimate nature design and engineer

    (4) a cell [Turing machine? (Turing, 1936)] capable of
    implementing those coded instructions?

    So he does regard cells as a Turing machine. Many biologists regard the cell as a Turing machine if they view the cell as a computer.

  121. Nakashima:

    I think you are right that, if we consider the set of individual codons, Abel should have used the term “surjection” rather than “bijection”. But Sal’s point that the set can be defined so that a bijection takes place is true too. I don’t know if Abel used the wrong mathemathical term, or if he was thinking the way Sal suggests. What I know is that in both cases his argument has the same validity: I can’t see why a surjection would be less good an example of a strict mathematical relationship between two sets which is obviously used to build up all the proteome from the genome.

    Regarding Turing machines, I dfo believe that Abel is saying that the cell, or some parts of it, behave like a Turing machine, and that the concept of halting is obviously the concept of computational halting. I understand that you may have objections to that concept, and I am interested in them. as I am not a mathematician, however, all I can say is that for me the relevant concept is that the cell, and many parts of it, do accomplish computational tasks, and very functional ones. The whole translation system accomplishes the task of compution the output of the final protein from the input of a protein coding gene. That implies a lot of different processes, all of them strictly controlled: The gene must be made available for transcription, transcription has to be correctly started and ended, at the right moment and in the right conditions and in the right cell (in multicellular organisms), the mRNA has to be processed (introns spliced), which implies qualitative and quantitattive control), then the mRNA is transferred to the cytoplasm, where translation proper happens through our much discussed surjection, and then there is still a complex set of post translational modifications which bring to the final, functional protein. I don’t know of all that satisfies the mathemathical requirements for a Turing machine (again, I am not a mathemathician), but I do know that it satisfies my requirements for a very organized and efficient systems which efficiently processes and transforms information.

    Again, regarding your discussion about the DNA code being otpimized because of selection: I have to remind you that the optimization of the code is one of many examples of functional information which are exactly the object of Abel’s paper and of our discussions in ID. We in ID don’t believe that those things were generated by NS, and think that they are the product of design. Abel is just arguing that there is at present no satisfying theory of how they emerged (which is a very correct statement IMO, if you don’t want to explicitly bring about a design theory, which is apparently Abel’s position). You probably believe that all those things were generated by darwinian mechanisms.

    Well, everybody is entitled to his own convictions, but the point you seem to miss is that you cannot use your final (and controversial) conclusion to support your reasoning in favor of those conclusions: that would be circular reasoning.

    IOW, Abel is simply stating that there is no “mechanical” (I think his term is “phisicodynamic”) reason why the DNA code is what it is. The laws of physics and biochemistry cannot explain that. You cannot object to that that darwinian selection could have done that. The power of darwinian selection (or other models) to explain that kind of things is exactly what we are discussing here, and Abel is discussing in his paper.

  122. #117:

    On any given night of Texas hold’em – so I am told – the first time one of the other players at the table gets a royal flush you should go home. Failing that, the second time one of the other players at the table gets a royal flush you should draw your gun.

  123. With respect to bijection, here is perhaps a better way to understand what Abel is saying, and it runs deeper than arguments about codon tables.

    As I showed above, the bijection exists between the codons symbols and amino acids if one accepts Hamming block code representations.

    However, there is the larger bijection that is at play.

    For a cell to reproduce a copy of itself, it must completely be able to represent itself. That is to say, there is a bijective mapping from the parent to the child for certain critical functions. But not only that, there is a bijective mapping from conceptual symbols in the parent to the physical description of the child.

    The cell must be able to store a complete description of itself symbolically. This is a bit harder than it seems at first glance.

    To illustrate to the computer literate the nature of the problem, try writing in a program which will print out an exact copies of the source code. Not so easy, eh? :-)

    To write such a program, one is creating a bijection from the parent source code to the child source code. No so easy!

    That in sum, is the real bijection problem!

    We call such self-referential bijections, Quines. See: The Quine Page.

    The bijection problem is articulated in this pro-ID peer-reviewed article by Albert Voie (a biologist and a specialist in artificial intelligence): Biological function and the genetic code are interdependent

    The problem of biological Quines is far more difficult than the source code Quines described above. The biological Quine must also have not only the source code Quine, but a copy of the computer that the Quine runs on, the manufacturing instructions for the computer parts, the operating system, etc.

    To get even a sense of the difficulty of creating a cell, consider the difficulty facing a programmer who writes Quine that also implements a Turing complete language. Now that would be impressive!!!! But that is the problem that OOL must solve from mindless processes.

    And that is the real problem of bijection from parent to child.

  124. so I am told – the first time one of the other players at the table gets a royal flush you should go home. Failing that, the second time one of the other players at the table gets a royal flush you should draw your gun.

    In such case the dealer might be somone like this:
    Steve Forte and the 4 Kings

    :-)

  125. 126

    Sal writes:

    What you say about about what Abel said is not correct. You are giving an uncharitable reading and not representing what he said accurately.

    So you say, but where is your evidence? You claim that I’m wrong, yet here are the facts:

    1. Abel (with Trevors) used Shannon information to argue that genetic instructions could not have arisen via “necessity.”

    2. Shannon information is measured with respect to a specified observer.

    3. Abel now says that concepts of information that are specified with respect to an observer can’t be applied to OOL, because “for most of life’s history, linear digital genetic instructions have been prescribing exquisite metabolic organization long before any observers or knowers existed.”

    4. By simple logic, therefore, Abel’s statement rules out the application of Shannon information to OOL (he’s wrong about that, but that’s a separate issue).

    5. In other words, he has contradicted what he and Trevors wrote in the earlier paper.

    If you disagree, then show us specifically where my analysis fails.

    Regarding Kolmogorov complexity, you claim that since it involves symbols, it cannot be defined without reference to an observer. You go on to say that “the compression technique is dependent on the interpretive capacities of compressor, which implies observational sensitivity”.

    Apparently you don’t realize that this actually undercuts Abel’s argument, because he has already told us that any concept of information that is defined with respect to an observer is ineligible for application to OOL problems. If you’re correct, then Abel must rule out algorithmic complexity as a tool. Oops.

    Regarding your quotes from Chaitin and Davies, you are making the same mistake as Abel: confusing Kolmogorov complexity with Shannon information. The Chaitin and Davies quotes refer to Kolmogorov complexity. You even acknowledge this when you write “This is proof positive the laws are not information rich in the algorithmic sense. That is what Chaitin points out here…”. In the algorithmic (i.e. Kolmogorov) sense, not the Shannon sense.

    Abel’s and Trevors’ claim is that Shannon information, not Kolmogorov complexity, rules out the origin of genetic instructions by “necessity”.

    Again:

    There is simply not enough Shannon uncertainty in cause-and-effect determinism and its reductionistic laws to retain instructions for life.

    Not only does this contradict what Abel says in the new paper, but it is also wrong. Why? Because if it were true, then Shannon information could not be transmitted within a deterministic universe. Yet this is obviously false. An omniscient being might not be able to derive any Shannon information from a deterministic universe, but a finite observer within the universe certainly could.

    I wrote:

    And to top it off, he [Abel] confuses Shannon information with Kolmogorov complexity…

    Sal:

    No he does not, that is just a bald assertion.

    Okay, then what is your explanation for why Abel places the equation for Shannon entropy in a section dealing with algorithmic complexity — a total nonsequitur?

    I realize that as a YEC you don’t get a lot of good news, Sal. But the fact is, Abel’s paper is not the good news you were hoping for.

  126. anonym (#125):

    In a sense, that’s exatly what we are doing here: drawing our guns against darwinists! :-)

    Although I do believe they would have been happier if we had gone home…

  127. To further clarify the involvement of Hamming block codes, from Abel’s earlier paper: Chance and Necessity:

    Code bijection is a one-to-one correspondence of ‘‘meaning’’ between alphanumeric symbols in different languages or operating systems. The phrase ‘‘genetic
    code’’ should be reserved for describing this one-to-one
    correspondence between each triplet codon and its corresponding amino acid (Yockey, 1992, 2000,
    2002a,b,c). Proper use of the term genetic code applies only to the redundant (usually erroneously called degenerative in the literature), noise-reducing table of
    codon assignments. These assignments are widely regarded as an amazingly optimal coding system
    (Bradley, 2002; Freeland and Hurst, 1998; Gilis et al., 2001; Labouygues and Figureau, 1984). Such optimization makes it all the more difficult to explain the
    molecular evolution of such exquisite non-human genetic algorithms. Random walks (Markov Processes) (Holland, 2003) will never provide an adequate explanation for the generation of such a highly refined translative coding system. Nor will it provide an explanation for the codonic operating system and specific programs generated through selection of each nucleotide in a strand.

    There is “one-to-one” correspondence only if synonymous codons are regarded to convey the same “meaning”.

  128. 129

    Sal

    Thanks for letting me speak here. That is more than Allen MacNeill will do at his blog where I have been summarily manished just as I was at EvC, ARN, richarddawkins.net, Pharyngula (where I may be found in P.Z.’s celebrated DUNGEON), Panda’s Thumb and of course Wesley Elsberry’s “inner sanctum,” After the Bar Closes. There were others who have banished me, so I am grateful, that as obnoxious as I may seem to be, Uncommon Descent has matured enough to at least allow me to hold forth about a subject of great importance to me both as a citizen and a scientist. As you and I both know Uncommon Descent was not always so tolerant.

  129. 130

    Sal writes:

    To illustrate to the computer literate the nature of the problem, try writing in a program which will print out an exact copies of the source code. Not so easy, eh?

    It’s extremely easy. Here’s how you would do it in C on a Linux machine. Put the following code in a file called printself.c . Compile it and run the executable in the same directory:

    #include [stdio.h]
    int main ()
    {
    FILE *fp;
    int c;

    fp = fopen (“printself.c”,”r”);
    if (fp != NULL)
    {
    while ((c = fgetc(fp)) != EOF)
    putchar(c);

    fclose (fp);
    }
    return 0;
    }

    That’s all there is to it. Apologies for the formatting; WordPress eats indentations and disallows angle brackets.

  130. So you say, but where is your evidence? You claim that I’m wrong,

    Actully the burden is on you to demonstrate you are capable of interpreting Abel correctly. In light the fact my citations of Davies and Chaitin cast doubt on your previous interpretations, I’d say there is a credebility gap emerging with the interpretations you are putting forward.

    Regarding your quotes from Chaitin and Davies, you are making the same mistake as Abel: confusing Kolmogorov complexity with Shannon information.

    Really, it appears you are the one making the mistakes.

    Recall Abel said:

    A law of physics also contains very little information

    to which you said:

    this is obviously wrong

    But as I have shown, in light of what Davies said, you are the one that said something obviously wrong, not Abel:

    The laws of physics have very low
    information content

    –Paul Davies

    Are you willing now to admit you were the one that was obviously wrong? :-)

    What I sense here is that you are now beginning to resort to argumentum ad nauseam. But since you have made a mistake, argumentum ad nauseam might not be the best line of discourse to strengthen the credebility of your interpretations. Why is that? Because as long as you persist doing so, I can keep reminding the readers of your mistake.

    Are you going to keep insisting that I can’t distinguish between Shannon’s notions of information and Kolmogorov’s? You’ll have to explain then how it is you weren’t obviously wrong.

    So if you keep asserting your interpretations of Abel are accurate, I’ll keep reasserting your mistake.

    So, do you still maintain that Abel’s claim:

    A law of physics also contains very little information

    is obviously wrong? :-)

  131. Abel’s and Trevors’ claim is that Shannon information, not Kolmogorov complexity, rules out the origin of genetic instructions by “necessity”.

    But there is not the possibility of Kolmogorov complexity if there is no possibility of Shannon information. Do I have to give you a mathematical proof? I’m willing to if you will answer some questions. :-)

    If there is no Shannon entropy, then there is no possibilty of meaningful symbols as there are no alternatives. Essentially 0 bits.

    What is the Kolmogorov complexity of a 0 bits?

    You’re invited to give an answer for our readers. :-)

  132. To help skeech along in his answer, here is a paper by Grunwald and Vitanyi:

    Shannon Information and Kolmogorov Complexity

    Shannon information theory, usually called just `information’ theory was introduced in 1948, [22], by C.E. Shannon (1916{2001). Kolmogorov complexity theory, also known as `algorithmic information’ theory, was introduced with di®erent motivations (among which Shannon’s probabilistic notion of information), independently by R.J. Solomono® (born 1926), A.N. Kolmogorov (1903{1987) and G. Chaitin (born 1943) in 1960/1964, [24], 1965, [10], and 1969 [3], respectively. Both theories aim at providing a means for measuring `information’. They use the same unit to do this: the bit. In both cases, the amount of information in an object may be interpreted as the length of a description of the object. In the Shannon approach, however,
    the method of encoding objects is based on the presupposition that the objects to be encoded are outcomes of a known random source|it is only the characteristics of that random source that determine the encoding, not the characteristics of the objects that are its outcomes. In the Kolmogorov complexity approach we consider the individual objects themselves, in isolation so-to-speak, and the encoding of an object is a short computer program (compressed version of the object) that generates it and then halts. In the Shannon approach we are interested in the minimum expected number of bits to transmit a message from a random source of known characteristics through an error-free channel
    ….

    In Kolmogorov complexity we are interested in the minimum number of bits from which a particular message or file can be effectively be reconstructed: the minimum number of bits that suffice to store the file in reproducible format.

    In light of these facts, if a concept is represented by zero bits (in terms of Shannon entropy), how much Kolmogorov complexity should we expect? :-)

    One can see that as the Shannon entropy goes to zero, the Kolmogorov complexity must necessarily approach zero as well. Hence, it is a moot point which measure of information we are trying to apply when we are dealing with such small quantities.

    QED.

  133. It’s extremely easy. Here’s how you would do it in C on a Linux machine.

    Skeech,

    Your program is not consistent with the spirit of what a Quine is. That is what was at issue.

    I appreciate your work however, but that is not what was intended by my reference to Quines.

    Your program basically goes to a file that contains a copy of itself. That is not the spirit of a Quine. It must be able to create a copy of itself through a self-contained copy, not an external copy (such as stored on a file system, as your program does).

    I appreciate your work however. In anycase, I provided a link to short programming examples.

    Sal

    PS

    I can read C code, so I spotted the problem right away. I do appreciate the effort because readers need to understand the subtleties between your program and that of a real Quine. Thank you.

  134. 135

    Sal,

    I laid out my arguments in detail in comment #128. Of all the points I raised in that comment, you’ve responded to only one (see below). Why is that?

    And the single response you provided is incorrect.

    You wrote:

    One can see that as the Shannon entropy goes to zero, the Kolmogorov complexity must necessarily approach zero as well. Hence, it is a moot point which measure of information we are trying to apply when we are dealing with such small quantities.

    QED.

    Despite your triumphant “QED”, this is wrong. Kolmogorov complexity does not approach zero as the Shannon entropy goes to zero. This should be obvious. It takes a finite-length program, not a zero-length program, to produce an arbitrary string of symbols. So even if the Shannon information of the string is zero (meaning that the receiver knows in advance what the string will be), the Kolmogorov complexity is nonzero.

    QED.

  135. I see that the Origin of Life Science Foundation mentioned at the top of the paper has a website.

  136. (Sorry AmerikanInKananaskis – I missed your earlier post. Moderators, feel free to zap this comment and my previous one.)

  137. 138

    Sal wrote:

    To illustrate to the computer literate the nature of the problem, try writing in a program which will print out an exact copies of the source code. Not so easy, eh?

    I supplied a short C program that satisfied those requirements. Now Sal has changed the problem statement:

    Your program basically goes to a file that contains a copy of itself. That is not the spirit of a Quine. It must be able to create a copy of itself through a self-contained copy, not an external copy (such as stored on a file system, as your program does).

    Okay, but it’s still very easy. You simply declare a character array inside the program. Every character of C code you enter into the program gets duplicated in the character array, except that you don’t duplicate the contents of the character array as that would lead to an infinite regress. Instead, you leave the duplicated definition empty, like this:
    char prog = {};

    The program amounts to

    1. Printing out the contents of the character array, stopping when it finds a right curly brace immediately following a left curly brace it just printed;

    2. Remembering the position where this happened;

    3. Printing the entire array from the beginning to the end; and

    4. Printing the array from the saved position to the end.

    The output will match the source code, character by character.

  138. Madsen, Nakashima, Scrodova, CJ,

    Madsen first,

    poor choice of words on my part. Its been awhile since I cracked a math book.

    Et al,
    Unless I’m missing something I can see why Nakashima/Madsen hesitates about “bijective function.” Except Abel did not state “bijective function”. So, he gets away with a little ambiguity?

    I was thinking of bijective compositions and notice Scordova is careful to say “correspondence” and “meaning.”

    Bijective Composition may satify the relation between function g of f? If still not satisfying critics. Narrowing the definition of a symbol mapping to surjective seems OK, it is still relational.

    Bijection makes Abel’s point stronger for flexible “rules-based” system for injective and surjective qualities.

    “a one-to-one function is injective, but may fail to be surjective, while a one-to-one correspondence is both injective and surjective.”

    Injective and Surjective(Bijective)

    Bottomline, what do you call mapped relationships between nucleiotides, codons and amino acids? They’re not lego pieces. Lego pieces need minds to construct bijectively compositional forms as lego cars or windmills for example.

    The lego parts are members of both injective and surjective functions.

    So, are Codon/Amino mappnigs merely “the appearance” of a symbolic functional relationship?

    We observe the mappings to functional components. It is not a metaphor or analogy. And error detection is real. Error detection is foresight.

    A rock does not repair itself, nor does it signal for mulitple type repairs systems dependent upon damage type and bijective correspondence.

    I’d like to see what more Scordova has to say about Hamming block codes or what Abel is thinking in relation to codons, parity bits, chains, checkpoints, etc.

    I imagine Hamming type block codes as a possible coordinating mechanism between sender and receiver. Without some similar mechanism, life would break down irreversibly quick.

    ————-

    Nice thread.

  139. On laws of physics:

    Abel observes:

    A law of physics also contains very little information because the data it compresses is so highly ordered. The best way to view a parsimonious physical law is as a compression algorithm for reams of data. This is an aspect of valuing Occam’s razor so highly in science. Phenomena should be explained with as few assumptions as possible. The more parsimonious a statement that reduces all of the data, the better [188, 189]. A sequence can contain much order with frequently recurring patterns, yet manifest no utility. Neither order nor recurring pattern is synonymous with meaning or function.

    In short, laws of physics state conditions of mechanical necessity tracing to regularly observable forces of ORDER.

    So, they are of low contingency and so that which is mere outworking of mechanical necessity has little information in it, as information is highly dependent on contingency.

    From a different perspective — one that is tied into cosmological finetuning — the presence of a given highly fine tuned set of physical laws that fosters a C-chemistry, cell-based life facilkitating cosmos will have a lot of information in it indeed.

    So, the issue seems to be: [a] that which is driven by mechanical laws of order has in it little contingency (apart form in its initial conditions and external constraints, which are NOT the acting laws), but [b] the apparent fintetuning and contingencies on those laws and associated parameters, may indeed have in it high contingency and probable directed choice.

    So, much depends on what specifically you are looking at!

    GEM of TKI

  140. Executing a program that prints itself is a bit tricky. I have done quite a bit c programming myself, so yes, Sal is correct with his observation, this program by Skeech:


    #include [stdio.h]
    int main ()
    {
    FILE *fp;
    int c;

    fp = fopen (”printself.c”,”r”);
    if (fp != NULL)
    {
    while ((c = fgetc(fp)) != EOF)
    putchar(c);

    fclose (fp);
    }
    return 0;
    }

    …will not suffice.

    Maybe this is more inline with Quine:


    #include[stdio.h]
    char *duplicate="#include%cchar *duplicate=%c%s%c;%c%cint main(void)%c{%c%cprintf(duplicate,%cHello World%c);%c%creturn 0;%c%c}%c";
    int main(void)
    {
    printf(duplicate,"Hello World");
    return 0;

    }

    Notice self-containment using string specifier %s, and special character mapping using %c specifier. Notice the char pointer to an array of chars to print itself maps its own line (ie: c = ” of the beginning quotation. %s = whats inside the quotes and %c = ” ending quotation)

  141. AB,

    Thank you! You’re a genius!

    From one of the links above, here is a classic C Quine.

    char*f=”char*f=%c%s%c;main()
    {printf(f,34,f,34,10);}%c”;
    main(){printf(f,34,f,34,10);}

    One can only imagine building a quine that is capable of:

    1. error correction from quantum noise and other physical damage

    2. self-healing

    3. implementing a turing complete language

    4. manufacturing of hardware

    Add to that the capabilities of any sort of sexual reproduction, and one quickly sees the staggerring difficulties.

    Mathematician Hofstadter wrote in detail about the problem of Quines and Life in Godel Escher Bach an Eternal Golden Braid

    The Origin of Life

    A natural and fundamental question to ask, on learning of these incredibly intricately interlocking pieces of software and hardware is: “How did they ever get started in the first place?” It is truly a baffling thing. One has to imagine some sort of a bootstrap process occurring, somewhat like that which is used in the development of new computer languages –but a bootstrap from simple molecules to entire cells is almost beyond one’s power to imagine…..For the moment, we will have to content ourselves with a sense of wonder and awe, rather than with an answer. And perhaps experiencing that sense of wonder and awe is more satisfying than having an answer–at least for a while.

    Douglas Hofstadter
    page 548
    Godel, Escher, Bach: An Eternal Golden Braid

    PS
    Hoftstadter’s book is widely viewed as the ultimate Geek Classic. :-)

  142. Mr Cordova,

    With respect to Abel’s opinion on Turing machines, please note that ‘?’ he sticks in there! Having done language design in the computer field, I think the leap from codon table to Turing machine is too great. But on this point I am happy to be convinced by demonstrations to the contrary. A cell that computes the digits of pi would be a very convincing to me! :)

    Since you mention Abel’s Chance and Necessity, may I recommend to you another paper named Chance and Necessity? (You will have to print it out to read it. I got a headache trying to read it online.) Dr. Benner’s lab is always doing cool stuffs in OOL research.

  143. Skeech wrote:

    So even if the Shannon information of the string is zero (meaning that the receiver knows in advance what the string will be), the Kolmogorov complexity is nonzero.

    So are you arguing that the Kolmogorov Complexity of a 0 length string is non-zero?

    Consider the definition of K-complexity:

    If a description of s, d(s), is of minimal length—i.e. it uses the fewest number of characters—it is called a minimal description of s. Then the length of d(s)—i.e. the number of characters in the description—is the Kolmogorov complexity of s, written K(s).

    The most compact description of nothing is nothing. The length of nothing is zero. :-)

    QED

    Sorry to be a little ungracious Skeech, but I have to stick up for my side. I hope you understand it is nothing personal and I salute your valiant attempt to discredit Abel’s writings, but I’d appreciate a response to the following:

    Recall Abel said:

    A law of physics also contains very little information

    to which you said:

    this is obviously wrong

    But as I have shown, in light of what Davies said, you are the one that said something obviously wrong, not Abel:

    The laws of physics have very low
    information content

    –Paul Davies

    Are you willing now to admit your assessment of Abel was was obviously wrong or will I have to keep reminding the readers until you concede the mistake?

    Sorry to be ungracious here Skeech. Nothing personal, but I have some obligation to the brotherhood of the wedge to defend their ideas.

    regards,
    Salvador

  144. Mr Cordova,

    With respect to Abel’s opinion on Turing machines, please note that ‘?’ he sticks in there! Having done language design in the computer field, I think the leap from codon table to Turing machine is too great. But on this point I am happy to be convinced by demonstrations to the contrary. A cell that computes the digits of pi would be a very convincing to me!

    First of all I wish to be properly polite, should I address you as Mr. Nakashima or Dr. Nakashima? I didn’t want to presumptuous, but since you have been kind in enough to refer to me as Mr. Cordova, I would like to extend the same courtesies to you.

    The references to cells as computers are growing more frequent. The father of BioInformatics, Hubert Yockey has this view. It is articulated in the book: Information Theory, Evolution and the Origin of Life. Yockey does not think the OOL problem is solvable by science. Yockey was a student of Oppenheimer.

    And then Bentolila in the IEEE:

    Two operative concepts for the post-genomic era : the “mémoire vive” of the cell and a molecular algebra

    The first successes in cloning experiments and stem cell “reprogramming” have already demonstrated the primordial role of cellular working-space memory and regulatory mechanisms, which use the knowledge stored in the DNA database in read mode. We present an analogy between living systems and informatics systems by considering : 1) the cell cytoplasm as a memory device accessible as read/write; 2/ the mechanisms of regulation as a programming language defined by a grammar, a molecular algebra; 3) biological processes as volatile programs which are executed without being written; 4) DNA as a database in read only mode. We also present applications to two biological algorithms : the immune response and
    glycogen metabolism.

    I – Introduction

    1/ Biology and Informatics, two main streams It is noteworthy that Turing (Turing 36) and Von Neumann (Von Neumann 45) were interested in
    human brain function in order to construct the principles of computer architecture by analogy, at a moment in history in which there was great progress in both the electronic and the cognitive
    sciences. Considerable theoretical progress took place due to development of informatics, in terms of logic, theory of languages and calculability theory. It seems only fair that these theories can, in turn, serve to model the behavior of the cell in terms of the information flow it receives
    and generates.

    It is also noteworthy that the Avida developers advertise that one of the features of their work is that they represent living organisms as Turing Complete machines!

    And from Mike Gene’s book, Design Matrix he quotes a computer scientist:

    Ion Petre, a scientist from the Turku Center for Computer Science in Finland, echoes this same theme and further provides an example of an interesting convergence between cells and computers:

    Viewed as information processing systems, biological organisms posses amazing capabilities to perform information-handling tasks such as: control, pattern recognition, adaptability, information-storage, etc. Thus, the functioning of biological organisms as information-processing systems is of great interest to computer scientists, and we are witnessing now a fast growing research in the field. This research is genuinely interdisciplinary in nature, involving both computer scientists and molecular scientists (biologists, biochemists, biophysicists, crystallographers…). One of the leading paradigms of this research is “cell as computer.

  145. Woah, a lot has gone on since I was here last night. I’ll try to catch up and then join the discussion again if anything more can be/need be said.

    Overall a very interesting and thought stimulating post. We need more posts like this that deal with theoretical constraints and mathematical descriptions of systems which we can model and may provide more of an insight into what law and chance (absent “choice with intent”) can and can not do.

  146. Recall Abel said:

    “A law of physics also contains very little information”

    Skeech:
    “this is obviously wrong.”

    scordova has already pointed out above that Paul Davies agrees with Abel’s assessment and I would like to add to that.

    A law by definition contains very little shannon information. A law refers to either a mathematical description of regularity or the appearance of that regularity.

    Regularities have very little information content in the shannon sense and are the opposite of random in the K-Complexity sense; again showing a low complexity and thus low information.

    Of course a set of laws and the interactions that result may be very complex (high shannon information content) however Abel also deals with that as well. It is obvious that when he states that laws of physics contain very little information, he is referring to the fact that laws describe regularities and regularities are the opposite of complexities — high information.

    Thus laws of physics don’t have information available to input into a system … the “selection” of *sets of laws* is where the information must come from.

    Abel then continues on to deal with different types of selection and which types of patterns each type of selection can and has been observed to account for.

  147. Nakashima,

    The wikipedia article on Turing Machines has an informal description which includes a “more precise” description of a turing machine. It describes the foundation of life almost perfectly.

    Furthermore, scordova has already pointed out that the father of bioinformatics, Hubert Yockey, has shown that the living cell is indeed a coded information processor following the same engineering principles as utilized in any communication transfer system including computation — which results from turing machines. For more info please refer to:

    “Origin of life on earth and Shannon’s theory of communication,” Hubert P. Yockey, Computers and Chemistry 24 (2000) 105–123.

    It is a very informative paper and is complementary to the article we are discussing in this thread.

  148. 149

    Sal wrote:

    Sorry to be ungracious here Skeech. Nothing personal, but I have some obligation to the brotherhood of the wedge to defend their ideas.

    Um, Sal… shouldn’t your decision to defend an idea depend on whether the idea is true, not whether it comes from the “brotherhood of the wedge”?

    I’m glad you admitted that, though. It explains a lot that has gone on in this thread.

    Regarding your Kolmogorov evasions:

    You wrote:

    One can see that as the Shannon entropy goes to zero, the Kolmogorov complexity must necessarily approach zero as well.

    1. As I already explained, this is wrong (see my earlier comment).

    2. Even for a zero-length string, it is wrong, because a zero-length program is not a program at all. Even a bare-bones Turing machine needs to be told to halt. A zero-length string has a finite Kolmogorov complexity.

    3. Even if you were right, it wouldn’t help your case. Trevors and Abel were talking about genetic instructions, which are not zero-length.

    Sal:

    Are you willing now to admit your assessment of Abel was was obviously wrong or will I have to keep reminding the readers until you concede the mistake?

    I already explained why my assessment of Abel was correct:

    Trevors and Abel wrote:

    There is simply not enough Shannon uncertainty in cause-and-effect determinism and its reductionistic laws to retain instructions for life.

    I explained their error:

    Not only does this contradict what Abel says in the new paper, but it is also wrong. Why? Because if it were true, then Shannon information could not be transmitted within a deterministic universe. Yet this is obviously false. An omniscient being might not be able to derive any Shannon information from a deterministic universe, but a finite observer within the universe certainly could.

    Now how about answering the arguments I laid out in comment #128? Or does this business of “reminding the readers until you concede the mistake” apply only to your opponents?

  149. Woah, a lot has gone on since I was here last night.

    CJYman,

    Yeah, I was up late last night worrying about the financial markets. I was up watching the S&P Futures trading on the other side of the world. So I was killing time watching them….

    Thank you for the Yockey reference!! And for you comments on this thread.

    Nakashima,

    Thank you also for the paper you provided.

    Sal

  150. Hello again Nakashima,

    You wrote above:
    “OK, things halt all the time, why is it a big deal to be repeated over and over in the text? You’d think a guy talking about OOL would be more interested in how things started than in how they stop.”

    You will notice that the author precedes “halting” with “computational.” This is an interesting phenomenon which needs to be explained since computational halting, according to wikipedia, is indeed related to turing machines:

    (from wikipedia)”The halting problem is a decision problem about properties of computer programs on a fixed Turing-complete model of computation. The problem is to determine, given a program and an input to the program, whether the program will eventually halt when run with that input.”

    …and…

    “In his original proof Turing formalized the concept of algorithm by introducing Turing machines. However, the result is in no way specific to them; it applies equally to any other model of computation that is equivalent in its computational power to Turing machines, such as Markov algorithms, Lambda calculus, Post systems, register machines, or tag systems.”

    So, at the very minimum, computational halting requires a model of computation “equivalent in computational power to Turing machines.”

    Does computational halting indeed happen “all the time” when *not* preceded by “choice with intent” as the selection mechanism to program the [equivalent of a] turing machine for “potential function” or “solving a potential problem” or “whatever else would cause the system to halt *computationally*?”

  151. Sal:
    I don’t have an email address for you, so I must resort to posting here – please feel free to delete it after reading it.

    This thread is exactly the kind of thing I look for when searching for an open and honest debate among intellectuals. Not many minds get changed, but a whole lot of ideas get clarified, on both sides. Bravo!

  152. Hello scordova, are you a trader as well or an “interested bystander?”

    Again, thank you for providing this thread. I find this type of discussion the most fascinating and containing the most potential for a purely natural mathematical model for ID Theory.

  153. 154

    ab wrote:

    Sal is correct with his observation, this program by Skeech…will not suffice.

    Suffice for what? It meets Sal’s stated requirements precisely:

    To illustrate to the computer literate the nature of the problem, try writing in a program which will print out an exact copies of the source code. Not so easy, eh?

    And even Salvador’s revised requirement that the program be “self-contained” (i.e a “Quine”) is easy to satisfy, as I showed in comment #140.

  154. Sal (again, I am using this channel in lieu of emailing, so edit or delete as you see fit):

    There is an interesting debate going on at Telic Thoughts that relates in some ways to what is being discussed here:

    http://telicthoughts.com/against-darwinism/

    I hope for many more threads like this one. It helps me immensely in clarifying what I think about these issues. Sometimes I even find (usually in retrospect) that I’ve changed my mind in some respects. What more could one ask?

    As a possible follow-up, might I suggest a similar discussion based on the following:

    For the sake of argument, let us grant for the moment that the question of the origin of life, the genetic code, and fully functional cells is currently an unresolved issue (I believe this to be the case, but that’s not what I’m interested in right now). How many of the issues raised in this thread apply to the evolution of life following its origin, and why? If it would help move the discussion along, you might perhaps focus on a specific issue, such as the origin of eukaryotic cells or divergence of the hominid line from other Primates (your call, of course).

  155. Kairosfocus,

    Something that I just realized is that the definition of a bijection in conjunction with a turing machine may provide a purely mathematical description for “functionally specified” in FSCI.

    Since, the definition of “specified” in ID THeory = an event which can be formulated as an independent pattern, it seems that a bijection as a mapping of one set onto another that satisifies f(x)=y will give us an event in one set which can then be formulated as a pattern in the other set — f(pattern)=event.

    Kairosfocus, if you are around, what do you think?

  156. CJYman,

    I’m a trader. My professional evolution is as follows:

    Music Student
    Software Developer
    Electrical Engineer
    Systems Engineer
    Financial Engineer and Physics Student

    I’m studying physics partly because it is very applicable to modern finance.

    The book that unifies Finance, Gambling, Physics, Mathematics, Engineering and Information Theory is Fortune’s Forumula The Untold Story of the Scientific Betting System That Beat the Casinos and Wall Street. I quoted from the book earlier in this thread.

    Live long and prosper!

  157. In #154 CJYman wrote:

    “I find this type of discussion the most fascinating and containing the most potential for a purely natural mathematical model for ID Theory.”

    Personally, as an evolutionary biologist I am not sanguine about the possibility of a purely natural mathematical model for evolutionary theory. Indeed, I think that the search for one has been generally misguided. However, the fact that at least some people think this is a realistic (and even positive) goal for ID theory is itself an interesting commentary on ID. For more, see:

    http://evolutionlist.blogspot......views.html

  158. Here’s something I wrote on this issue earlier:

    There are many processes in biology, and especially in organismal (i.e. “skin out” biology) that are so resistant to quantification or mathematical formalization that I have a nagging suspicion that they cannot in principle be so quantified or formalized. It is, of course, logically impossible to “prove” a negative assertion like this – after all, our inability to produce a Seldonian “psychohistory” that perfectly formalizes and therefore predicts animal (and human) behavior could simply be the result of a deficiency in our mathematics or our ability to measure and separately analyze all causative factors.

    However, my own experience as a field and laboratory biologist (I used to study field voles – Microtus pennsylvanicus – and now I study people) has instilled in me what could be called “Haldane’s Suspicion:” that biology “is not only queerer than we suppose, it is queerer than we can suppose.” That is, given the complexity and interlocking nature of biological causation, it may be literally impossible to convert biology into a mathematically formal science like astronomy, chemistry, or physics.

    But that’s one of the main reasons I love biology so much. Mathematical formalisms, to me, may be elegant, but they are also sterile. The more perfect the formalism, the more boring and unproductive it seems to me. The physicists’ quest for a single unifying “law of everything” is apparently very exciting to people who are enamored of mathematical formalism for its own sake. But to me, it is the very multifariousness – one could even say “cussedness” – of biological organisms and processes that makes them interesting to me. That biology may not have a single, mathematical “grand unifying theory” (yes, evolution isn’t it, AFAIK) means to me that there will always be a place for people like me, who marvel at (and even revel in) the individuality, peculiarity, and outright weirdness of life and living things.

  159. Hello Allen,

    Interesting commentary. I guess I’m just a little too “scientific minded” in that I want to quantify everything. I do understand that this does break down at some point (at subjective experience), although I would really like to push that as far as possible.

    As far as ID Theory can be a theory of information I definitely believe that it should be pursued. And yes, those slight nuances which indicate that we may not be able to *completely* formalize it mathematically does not make it any less scientific — possibly similar to your thoughts on biology and evolution. In fact, I see evolution and ID to be perfectly compatible. Evolution is both a mechanism of intelligence and evidence of intelligence.

    Allan, you state that:
    “There are many processes in biology, and especially in organismal (i.e. “skin out” biology) that are so resistant to quantification or mathematical formalization that I have a nagging suspicion that they cannot in principle be so quantified or formalized.”

    The same can be said with regard to certain aspects of how intelligence, especially foresight (choice with intent as the author of the paper discussed in this thread puts it) operates. However, the ability to quantify *some* of the patterns produced by intelligence and show that these patterns are also not described by either law or chance provides evidence that ID Theory definitely has it’s place at the seat of mathematics and scientific investigation (around the same area of the table as evolution, properly understood).

    …and yes it is always a positive goal to at least attempt to quantify something. We obviously learn many amazing things through the quantification of those things and then the application of those quantities.

  160. Mr CJYman,

    Yes, this question of ‘is it possible to prove whether any and every program of Turing machine will halt’ was important in 20th century, but it is already proven result that the answer is no.

    Any program, it either halts or not. So what is a “syntax for computational halting”? If the whole cell is taken as the “Turing machine” then the STOP codon is not a halt condition, the cell is still very busy doing other metabolic stuffs. All these little machines are independent, as long as they keep bumping into ATP molecule to get some power up, they won’t stop.
    This is why I think “cell=Turing machine” is an overdone analogy.

  161. A purely mathematical description of ID would be difficult if not impossible (I lean toward the impossible side).

    The reason I say this has been the horrifying discoveries in Artificial Intelligence (AI). Computer scientists had hoped to be able to characterize intelligence in purely mathematical, axiomatic, algorithmic terms. The quest to do this was the grand goal of Strong AI. The quest is failing.

    The outcome appears to be that Intelligence is Irreducibly Complex (in the manner that Chaitin defines IC, not Behe). That means there is no mathematical description of intelligence even in principle.

    Ergo, ID theories must be indirect. They must be relegated toward recognizing specified complexity and making negative arguments using No Free Lunch theorems.

    I’m symathetic to the idea that ID is science, but I don’t invest a lot of time trying to argue for classifying ID as science or not. It matters more to me that ID is true, its classification as science is a peripheral concern. I mean, if ID is true, doesn’t every other question somewhat pale in comparison (even the politics of public schools)?

    The Life as a Quine is a powerful metaphor for design. The fact that we have in life a specification that can specify itself solves the problem of findind “detachable specifications” as required by Dembski’s Explanatory Filter. Computer scientists know that as a matter of principle, Quines are very special patterns! We know Quine patterns exist even before we elucidate them .

    PS

    AB just elucidated a new Quine pattern in his C program which he presented today in this thread.

  162. scordova,

    Wow, a book that includes and relates all my interests! I’ll have to check it out.

    Re: your professional evolution …

    Do all engineers also have an interest in music? I also was a student of music for a while.

    Finance and markets are a relatively new interest for myself and I believe there is potential for application of ID Theory to the markets and/or at the least something we can learn from the markets to apply to ID Theory. I say this as a technical trader identifying non-random patterns resulting from the foresight (whether correct or not) of a group of intelligent traders. The closer the majority of traders are correct as to their foresight, the stronger the pattern indicating a correct move. This is actually somewhat applicable to Abel’s paper since the paper includes a discussion of chaos theory. Anywho … ya, markets are a relatively new interest.

  163. Do all engineers also have an interest in music? I also was a student of music for a while.

    Engineers, musicians, and some evolutionary biologists have experimentally verifiable similarities in brain physiology.

    I did not think evoltuionary biologists were musical, but the fact John Davison and Allen MacNeill and his colleagues are excellent musicians caused me to revise my views.

    See the post on this at UD where I did an informal poll and explored the results of medical brain scans and the relationship of brain physiology to the ID debate.

    Wistar Convention, Salem Hypothesis and Music

  164. Mr Cordova,

    In Japanese, it is typical to add -san to somebody’s name if you are talking to them or about them. Dr. Sayama would be Sayama-sensei, because sensei means teacher.

    I apologize to anyone on this site if I write Mr X, but you are really Ms X! Wow, that would be embarassing…

    But if I could give some career advice, trading with transaction costs is like gambling in a casino. The house has an edge, and the longer you play, the more certain you are to lose. That is the law of large numbers at work. To avoid the same problem in the financial market, you have to minimize the number of trades and essentially give up trading on price movements in favor of investing in values. There is no trader that ever got as rich as Warren Buffet.
    Many years ago, I knew a man who was a trader on the NY Commodities Exchange. (It was in one of the smaller WTC buildings before 9/11.) He told me he could make a comfortable living trading in the inefficient markets for petroleum contracts 6 to 9 months out. But once a contract got closer to delivery, the market became crowded and efficiently priced, and even he – a floor trader with a seat on the exchange – could not make money.
    Of course today algorithmic trading makes all markets far more efficient than it was back then.
    To bring this back to the topic, the analogies of physics and math to the messy reality of finance and biology are at best imprecise.

  165. Hello Nakashima,

    Unfortunately, I can’t agree with your assessment that the living cell = turing machine is an overdone analogy since:

    1. A description of a turing machine also describes the operations which occur inside a living cell, as I’ve shown above.

    2. Your problem of the living cell constantly running many different programs even when one of them computationally halts makes no difference to its equivalence with a turing machine as it relates to computational halting. As the wikipedia article on halting begins:

    “In computability theory, the halting problem is a decision problem which can be stated as follows: given a description of a program and a finite input, decide whether the program finishes running or will run forever, given that input.”

    There are many input-output “decisions” happening at a time and constantly (as far as I understand you are saying), yet each one of those “decisions” can be described as finite input (DNA) being “run” by transcription and translation machinery to finish running and produce an output. There are also many other programs running at the same time where logic gates are involved.

    Thus, a more accurate description of the cell would be that it includes many different turing machines, halting and then starting again, and operating at the same time. That is more accurate than stating that no part of the living cell can be equated with a turing machine.

    3. The authority figures, as referenced by scordova and myself above, seem to have no problem treating the operations within the living cell as turing machines. If there was a legitimate concern with such an equivalence (or even a mere analogy), they would have probably brought it up.

    4. So yes, it seems that a better description of the living cell would be that it is the “housing” for an array of interconnected turing machines where computational halting is constantly occuring.

    5. Back to the authors question. Will any combination of mere complexity (law and randomness) create computational halting, [especially when the turing machine responsible for the halting has a formal organization not defined by physicodynamics]? There is no reason to suppose that any combination of mere complexity (absent choice with intent) will produce such an organized system since mere complexity only defines physicodynamic systems. That seems to be one part of the author’s argument in a nutshell.

  166. Personally, as an evolutionary biologist I am not sanguine about the possibility of a purely natural mathematical model for evolutionary theory. Indeed, I think that the search for one has been generally misguided. However, the fact that at least some people think this is a realistic (and even positive) goal for ID theory is itself an interesting commentary on ID. For more, see:

    http://evolutionlist.blogspot……views.html

    Allen,

    Your essay is wonderful and your writing style is the envy of us all.

    5) PLATONIC VS. DARWINIAN WORLDVIEWS: It seems to me that many ID theorists come at science from what could be called a “platonic” approach. That is, a philosophical approach that assumes a priori that platonic “ideal forms” exist and are the basis for all natural forms and processes. To a person with this worldview, mathematics are the most “perfect” of the sciences, as they literally deal only with platonic ideal forms. Astronomy, chemistry, and physics are only slightly less “prefect,” as the objects and processes they describe can be reduced to purely mathematical formalisms (without stochastic elements, at least at the macroscopic level), and when they are so reduced, the predictive precision of such formalisms increases, rather than decreases.

    By contrast, I come at science from what could be called a “darwinian” approach. Darwin’s most revolutionary (and subversive) idea was not natural selection. Indeed, the idea had already been suggested by Edward Blythe. Rather, Darwin’s most “dangerous” idea was that the variations between individual organisms (and, by extension, between different biological events) were irreducibly “real.” As Ernst Mayr has pointed out, this kind of “population thinking” fundamentally violates platonic idealism, and therefore represents a revolutionary break with mainstream western philosophical traditions.

    With respect to you suggestion:

    For the sake of argument, let us grant for the moment that the question of the origin of life, the genetic code, and fully functional cells is currently an unresolved issue (I believe this to be the case, but that’s not what I’m interested in right now). How many of the issues raised in this thread apply to the evolution of life following its origin, and why? If it would help move the discussion along, you might perhaps focus on a specific issue, such as the origin of eukaryotic cells or divergence of the hominid line from other Primates (your call, of course).

    Only a handful of IDers (JohnDavison, Paul Nelson, Stephen Meyers) have the depth of knowledge to deal with organic evolution. Origin of life requires a much smaller and highly specialized knowledge base (in engineering, information science, computers, chemistry).

    So unfortunately I would only be able to offer uninformed commentary on the issues that are close to your heart!

    With respect to Platonic Forms, David Chiu (one of those mentioned by Abel) has suggested that the search for certain platonic forms might help us elucidate biology. I posted on the idea here How IDers can win the war. If the plantonic view is as strong as we speculate then it might seriously advance medical science. This can also translate into monetary rewards for companies formed along the lines of Rosetta Genomics (Nasdaq ticker ROSG). Given how Rosetta Genomics is suffering financially, they really could use ID’s help.

    I personally think this would be a fruitful area of investigation of ID. The bashing of Natural Selection and OOL research becomes utterly boring at some point…..maybe a more positive vision would be elevating to the movement, and if healing and medical science are advanced as a result, then who can complain?

  167. 168

    There is not a word in Darwin’s Origin of Species that ever had anything to do with that title. The central problem of phylogeny has always been the same. What is the mechanism by which evolution took (past tense) place?

    At present everything being discovered in the laboratory pleads for a determined, goal directed, preplanned, “prescribed” sequence in which chance played no role whatsoever. Evolution is proving to be exactly as William Bateson proposed in 1914 –

    “an unpacking of an original complex which contained within itself the whole range of diversity which living things present.”
    Inaugural address. The Australian meeting of the Britsh Association. Nature 93: 635-642.

    The next year, 1915, Reginald C. Punnett supported Bateson’s position –

    “Natural selection is a real factor in connection with mimicry, but its function is to conserve and render preponderant an ALREADY EXISTING LIKENESS, not to build up that likeness through the accumulation of small variations, as is so generally assumed.
    Mimicry in Butterflies, page 152, (my emphasis in caps).

    Seven years later, in 1922, Leo Berg further endorsed Bateson with –
    “Evolution is in a great measure an unfolding of pre-existing rudiments.”
    Nomogenesis, page 406.

    Both my Prescribed Evolutionary Hypothesis (PEH)and the closely related Universal Genome Hypothesis (UGH)lend further support to this alternative to the Darwinian myth which has never received a scintilla of verificaton from either the experimental laboratory or the final arbiter of undeniable reality, the fossil record.

    The Darwinian fairy tale has been sustained by six generations (150 years) of mass hysteria passed from professors to their students in some of our most prestigious institutions such as Harvard, Oxford and Cornell. It is the most failed hypothesis in the history of science which I believe has persisted only because of a congenital inability of its proponents to recognize what is transparent to some of us: phylogeny was planned. The atheist mentality simply cannot cope with the real world, a world, both animate and inanimate, in which there never was a significant role for chance.

    …the plan has gone on; and we may feel sure that it cannot fail to meet its goal.”
    Robert Broom, Finding the Missing Link, page 100. 1950.

    Everything is determined…by forces over which we have no control.”
    Albert Einstein

  168. Allen,

    I read your essay from a couple years ago and think it is interesting and thought provoking and was initially writing a much longer reaction to it than what I am now presenting here. The point here which I disagree on with you is that ID is somehow different.

    Trying to separate out ID or an ID researcher from regular biology I think it not valid. ID agrees with most of modern biology and evolutionary biology so where is ID different in kind. You wrote two essays recently on the Modern Synthesis and Natural Selection and there is nothing there which ID has any problems with. ID has no problems with your 50+ engines of variation. The only difference is in the conclusions as to what all these processes can lead to. An ID researcher would likely design the same experiment as any other biologist, could work side by side with any evolutionary biologist you name in the world and you wouldn’t know the difference. They could execute the identical experiment and write down the same results. Where you would notice a difference is that the ID researcher would look to a wider range of possibilities in the conclusions section of the study but at the same time would also consider every possibility that the non ID scientist would consider.

    So you can try to make a distinction but in end the ID scientist would look the same as the current crop of evolutionary biologists up to the conclusions section.

  169. Allen, quoted by Scordova,

    “Rather, Darwin’s most “dangerous”
    idea was that the variations between individual organisms (and, by extension, between different biological events) were irreducibly “real.””

    I do not understand how this idea is dangerous or new. Variations were recognized long before Darwin as “real.” Just not as materialist, unguided events of gradualistic miniature changes over time. Behe has so far defended well his point in Edge of Evolution against all comers.

    Turns out NS is a weak force explanation, gradualism is oversold and insufficient as well. And MET has run aground giving way to HGT.

    But the intro of HGT creates more problems than it solves. It tears apart the TOL(see Koonin, Doolittle, Baptiste) and leaves a messy web and LUCA in a mire of hazy guesses.

    Essentially, it appears the dangerous idea was not that great of an explanatory power and in fact was DOA.

    I think at best he attempted to formalize obervations at the time, but his theory has been falsified. There are no gradualistic fossil records. This is why Gould introduced Punquated Equilibrium.

    And now, Koonin, Doolittle and others are cojecturing about a big bang of information explosion for life as well.

    This is far different than what Darwin thought possible and points to rapid events.

  170. re above comment – typo – conjectur… not coj.

    With regards to ideal forms or platonic view. That appeals maybe to arguments with traditional Creationist. Perfect forms with degeneration to modern day. That would be John Sanford’s argument for Genetic Entropy.

    But I’m not sure any IDist is pushing ideal forms or non-evolutionary forms. Just guided pathways.

    I do see Allen’s point about the two different approaches. Dawinian approach is necessarily messy. It is a must mixed bag of results. It is a kludge of solutions. This explains the consensus of vestigial organs and Junk DNA.

    Whereas IDers are not tied to either/or if I understand correctly. So there is a finer distinction to be made between them and traditional Creationist.

    It is somewhat interesting thought since both sides are in awe of the beauty of life darwinian or idist.

    FLE does not require an idealized form, merely frontloaded Information – I assume like Mr. Davison’s PEH. Information is prescribed, but does not force perfect forms or perfect mathematical solutions, but a combinatory factor of coordinated solutions which brings us to a language based system. Which brings it back to Abel’s paper.

    So I think part of the problem traditional Darwinian evolutionist have with the loose crowd of IDers is in projecting old Creationist traditions onto ID. Its not entirely Dawinist fault as ID is still defining itself, growing, searching out territory.

    The point about mathematics is valid, but to simplistic. Allen did not mention the field of Information or Computational Sciences(link not working, maybe he did) leaking into, taking over biology. It can incorporate all areas of physics, math, etc., including random variation. Engineering nomenclature runs abundantly across research works today for practical purposes in reverse engineering life.

    Information sciences and language allows pure mathematics, genetic algorithms, etc., in combinations of meta systems with hierarchical data structures to be coordinated across shared space.

    What we observe are math, physics and code, with degenerational mutations that can break down or damage the system(s) in place.

    I don’t pretend to understand OOL.

    However, researchers have to utilize engineering language, indeed machine language to elucidate cellular mechanisms.

    I think Biology is the last of the sciences to go hard science because we knew so little for so long. Whereas math, later physics were utilized long before cells were found to be so complex. ‘

    And I think as the field continues to grow the hard sciences will increasingly take over as specialization creeps in because life forms can be analysed as functional relations.

    It is the functional relations that matter coordinated by code. Math and physics are part of the explanation and underpinnings, but can never give the full overview. Only coded language can suffice. We are not going to find elegant equations of reduction for the overall explanation. Neither do we find random structures, but conserved information.

    Are the current observations strong enough to change the open mind to a design paradigm? I think so. I was once an evolutionist. What convinced me was not that I approached biology with ideal forms or from pure mathematics, but that in the last few years, what I see unfolding demands answers only engineers can solve.

    Highly specialized Information Engineers to wade through Meta-Information in the Code of Life. Information stored that unfolds nano-machine technology that is self-replicating and self-sufficient to gain and story energy and repair itself.

    Abel’s null hypothesis sharpens the lines and is needed for clarification…

    “Physicodynamics cannot spontaneously traverse The Cybernetic Cut [9]: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization,
    computational halting, and circuit integration.”

    As he states…
    “A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.”

    I think he is giving an honest evaluation of what has yet to occur on the Darwinian side. Everything so far has been conjecture, guided lab work or simulations that do not past muster.

  171. Mr. Scordova,

    “The bashing of Natural Selection and OOL research becomes utterly boring at some point…”

    Well, yes and no. It gets boring maybe personally. But, I think there needs to be a high profile on such issues for society at large. To bring into account the failures of explanation so far by Darwinist after 200yrs. To many people don’t know the weakness of unguided, evolutionary arguments.

    “..maybe a more positive vision would be elevating to the movement, and if healing and medical science are advanced as a result, then who can complain?”

    Of course, but can it not be argued it is already happening? When researchers determine specific solutions for targeted applications of functional proteins and mechanisms, they are doing ID work. How else can you target populations if structures are not conserved information? How can you heal an undesigned cellular mechanism? How do they inhibit or block a gene experssion if not for a specified code?

    I think ID work is being done every single day in research and health services.

  172. I am not yet convinced that we may dismiss self-organization as a relevant subject without taking a closer look first:

    http://plus.maths.org/issue37/.....index.html

    Would Sal care to comment?

  173. 174

    Below is a summary of my experience here at Uncommon Descent along with my invitation to paticipate on my weblog.

    http://jadavison.wordpress.com.....mment-1775

    My present terminal message.

  174. Platonic forms have been discovered in molecular biology. I believe we’ve only touched the tip of the iceberg.

    Michael Denton wrote an ID-sympathetic article: The protein folds as Platonic forms: New support for the pre-Darwinian conception of evolution by natural law

    NOTE: Pre-Darwinian = NON-Darwinian

    Before the Darwinian revolution many biologists considered organic forms to be determined by natural law like atoms or crystals and therefore necessary, intrinsic and immutable features of the world order, which will occur throughout the cosmos wherever there is life. The search for the natural determinants of organic form the celebrated “Laws of Form” – -was seen as one of the major tasks of biology. After Darwin, this Platonic conception of form was abandoned and natural selection, not natural law, was increasingly seen to be the main, if not the exclusive, determinant of organic form. However, in the case of one class of very important organic forms-the basic protein folds- advances in protein chemistry since the early 1970s have revealed that they represent a finite set of natural forms, determined by a number of generative constructional rules, like those which govern the formation of atoms or crystals, in which functional adaptations are clearly secondary modifications of primary “givens of physics.” The folds are evidently determined by natural law, not natural selection, and are “lawful forms” in the Platonic and pre-Darwinian sense of the word, which are bound to occur everywhere in the universe where the same 20 amino acids are used for their construction. We argue that this is a major discovery which has many important implications regarding the origin of proteins, the origin of life and the fundamental nature of organic form. We speculate that it is unlikely that the folds will prove to be the only case in nature where a set of complex organic forms is determined by natural law, and suggest that natural law may have played a far greater role in the origin and evolution of life than is currently assumed.

    I disagree that physical law is capale of creating biological platonic forms. These forms arise by design, not by physics. However, Denton is correct that such platonic forms exist in biology.

  175. Scordova,

    That is interesting quote from Denton. Is this what Allen was thinking as platonic forms?

    Maybe I’ve misunderstood and oversimplied the issue.

    But how does this not lead to Emergence Theory?

  176. That is interesting quote from Denton. Is this what Allen was thinking as platonic forms?

    I believe so, but Allen would be the best to answer what his idea of platonic forms is. In Darwin’s time, the platonic forms were morphological not molecular, but the same idea of the non-Darwinian era was extended by Denton down to the platonic forms of proteins.

    To understand the platonic forms, the idea is that every creature fits into an archetype, much like all cars are cars, but there are variations in the architecture of cars.

    In like manner fish are fish, mammals are mammals, each has it’s archetype. This also fits well into the creationist view of immutable kinds. i.e, a fish will never evolve into a bird, but that is exactly what Darwinism argues.

    The forms are not an artifact of our perception, but rather imperfect representation of ideals in the mind of God.

    We recognized them as forms, not because of our tendency to project classifications onto objects, but because the objects actually abide by a pre-determined architecture in the mind of an Intelligent Designer. We are merely reverse engineering what the forms are.

    Denton does not argue the theistic bent of platonic forms, but historically the idea of platonic forms in biology had some relation to theology.

    I belive if we can reverse engineer and discover platonic forms, it will advance medical science. Biological reality has a message for us, we must understand that message if we are to have great advance in medicine. One can sense that Denton’s search for platonic forms in proteins might help advance our knowledge of biology. I believe we haven’t even touched the surface of what may be done.

    The first biotech firms to jump on this might become rich beyond their wildest dreams!

  177. Mr Cordova,

    Is it a discovery? Maybe it was in 2002.
    I don’t see how this article is so positive for ID. Denton is saying that protein folds are seriously constrained by the laws of physics. Fewer degrees of freedom in proteins means fewer degrees of freedom in the DNA that codes for them. That undercuts all the tornado in a junkyard improbability calculations. This is saying proteins are closer to snowflakes than computer programs.

  178. Is M. Denton still arguing pro ID? According to Wikipedia

    Denton’s views have changed over the years. His second book Nature’s Destiny argues for a law-like evolutionary unfolding of life and therefore assumes evolution as a given

  179. Nakashima-san,

    You are correct that Denton’s interpretation, if true, would undercut ID, but I don’t think his interpretation is completely correct.

    He is correct to assert the existence of platonic forms. Beyond that, I disagree…

    Even if there are lawful forms, functional proteins are still improbable. Denton merely points out, and I think correctly, that there are certain lawful achitectures for function.

    With respect to morphology, platonic forms would strongly suggest that transitionals don’t exist. And if there are only lawful morphological forms, transitionals forms, even in principle, couldn’t exist.

    Transitional forms and Platonic Forms don’t fit well together in any theory. It appears the two are mutually exculsive.

    In engineering we have many platonic forms. As engineers we are taught to recognize and implement certain canned architectures.

    A lot of systems biology is mapping biological forms to the forms engineers recognize.

    I think DNA sequence comparisons across taxa will help us discover platoic forms more effectively.

    For example, proteins seem to practically have street signs pointing to the active sites when we look for “conserved” sequences. I think we can continue to find even more intereting patterns through comparative sequencing without any reference to common descent. These patterns will act as road maps to help us understand function in biology. We know there a lots of parts in biology, but many times we don’t know what these parts do.

    I suspect there are lots of broken parts in the human genome. Clues to how to fix these broken designs might be reposited in other creatures. Finding these clues might lead to interesting advances in medical science. Comparative sequencing might help us recover the documentation the intelligent designer intended for us to discover. Far fetched? Yes, but if it ever makes money, who will complain then?

    This quest for “correct designs” to repair our “broken designs” makes sense in a world of ideal forms, platonic forms.

    We instinctively have platonic forms in our mind. We have a sense that a defect is a defect, that an error is an error.

    In the Darwinian world, it’s all about selective advantage. A blind cave fish is “selectively advantaged”. Defect is only a relative term.

    However in the eyes of plato, a blind cave fish is less than the ideal, it is a broken form. In such case, natural seleciton helped to infuse the defect in the population and thus introduce a defect that is not consistent with the ideal pattern.

    The notion of platonic forms does not seem to be compatible with Darwinian evolution.

  180. “Fewer degrees of freedom in proteins means fewer degrees of freedom in the DNA that codes for them. That undercuts all the tornado in a junkyard improbability calculations. This is saying proteins are closer to snowflakes than computer programs.”

    No, just the opposite. If the proteins that are functional are extremely limited, then the odds of one showing by some random process goes down exponentially if not impossibly. It is like finding a single spec of gold dust on a prairie by a random walk. This means that it will be almost impossible to have a DNA sequence mutate into a sequence that can be transcripted and translated into a usable protein or other useful polymer.

    Thank you Nakashima for helping to make the ID case.

    If I may extend the point it’s like going from lego blocks that can always extend upon a system incrementally to pieces that can only fit together in limited fashions. — Admin

  181. Hello Nakashima,

    Denton’s article understood in conjunction with other articles which explain how biological forms won’t occur if the relations between laws of physics are slightly different show a “knife’s edge” balancing act between the laws of physics constraining and allowing biological forms. However, these biological forms are still formal system and are not defined by physicodynamic laws as Abel discussed. Denton’s paper merely shows that these forms are constrained by our set of laws of physics. This can provide an idea of “platonic form” in the sense of a pre-existing template (finite set) of potential form. IOW, the universe can only pick from a finite set of form and function determined/constrained by pre-natural-selection laws.

    Improbability calculations still come into play since the laws don’t cause the forms. You still need to get *to* the formal patterns from pure physicodynamics. Thus information measures still apply.

    This is still different from snowflakes since there is no formal system created — the snowflakes are described by regular patterns (laws) as a result of physicodynamics. Also no further mapping to produce function occur with snowflakes.

    Its like saying that our universe’s laws are fine tuned to allow a very specific set of computer programs. Yet law and chance are powerless on their own to produce those computer programs. The only way to get around this is to say that the universe is programmed to produce those future potential formal programs — but this brings in choice with [future] intent — unless Abel’s null hypothesis is falsified.

    This brings in the two type of selection that Abel discussed: artificial (choice with intent) selection and natural selection, yet the laws which constrain protein formation are a pre-natural-selection concept (pre-Darwinian as stated by Denton).

  182. Denton makes the case there are no real transitionals in proteins. We do have protein families where the members are sisters, but one protein family doesn’t seem to have transitionals to another protein family. The isolation seems to be very much intact. The heirarchies actually argue more strongly for platonic forms than they do common descent according to denton. Actually, the heirarchy is more concpetual than one that is implementable via common descent. (see an example below with a paper by Paul Nelson).

    Denton used platonic argument at the morphological level in his book, Evoution a Theory in Crisis. He pointed out there doesn’t seem to be any living transitionals. For example, amphibians don’t really seem like living transitionals between fish and birds. The architectures of fish, amphibians, and birds seem distinct and separated. One might argue they are in the same grouping of “tetrapod”, but there does not appear to be any living transitionals.

    Actually, I think for a long time, it was believed that living transitionals existed. That view has been abandoned. The transitionals even in theory seem a little forced. For example, see this problem of platonic forms presented by Paul Nelson:

    PROBLEMS WITH CHARACTERIZING THE PROTOSTOME-DEUTEROSTOME ANCESTOR

    Protostomes and Deuterostomes are arguably platonic forms. The existence of the forms is more suggestive of immutability of form rather than common descent. Nelson argues his point exceptionally well, imho.

  183. scordova:
    “You are correct that Denton’s interpretation, if true, would undercut ID, but I don’t think his interpretation is completely correct.”

    FINALLY … I found something you state which I disagree with.

    Denton’s interpretation is the same as mine, yet I accept the fundamentals of ID as correct. Just because the universe is programmed to produce life does not mean that law and chance absent foresight/intelligence (choice with intent) will produce these types of patterns. Thus intelligence is detectable and ID is correct.

    In fact, I take abiogenesis to also be correct. At one point there is no universe, then BANG there’s a universe without life then BANG or g-r-a-d-u-a-l-l-y (whichever the process) life appears. Unless the designer formed life outside the universe and then placed it in the universe or intervened in the universe to manipulate matter into life — which I don’t see why the designer would do if he/she/it could just program the universe to do it — then some process [albeit guided in the sense of a programmer purposefully guiding his program] must have occured which can be described as matter and energy converging to form life.

    Anywho … what think you?

  184. With respect to natural seleciton in OOL, the problem is that physcodynamics would appear to prevent natural selection. Abel alluded to it, and I quoted it earlier:

    the description of all of the above models often seems
    more poetic or cartoon-like than real. Kauffman’s and Dawkin’s publications, for example, are often
    devoid of any consideration of the biochemical catastrophic realities that plague life-origin bench
    scientists [20-22, 58-63].
    …..

    61. Dawkins, R. The Selfish Gene, 2nd Ed.; Oxford Univerisy Press: Oxford, UK, 1989
    62. Dawkins, R. The Blind Watchmaker. W. W. Norton and Co.: New York, 1986.
    63. Dawkins, R. Climbing Mount Impossible. W. W. Norton and Co.: New York, 1996

    The quantum noise at the molecular level is severe. Nano-engineers are discovering this to their dismay!!

    That means, without error correction, self-replicating molecular architectures with any degree of complexity will start to come apart (except maybe for rather regular autocatalytic reactions).

    But how can error correction evolve?

    Error correction is a minimual requirement for the first life, otherwise a population with any degree of “genomic” complexity will cease to exist, but if the population ceases to exist, how can it evolve error correction?

    The problem of the evolution of error correction is the classic question of “which came first, the chicken or the egg?”

    PS
    The answer is: “the chicken”

  185. 186

    Does anyone have a currently valid email address for Michael Denton? I want to invite him to participate on my weblog. I am sure he would use his real name.

  186. 187

    I would like to believe that the origin and evolution of life followed from natural laws myself. But what kinds of laws might they be? Surely not the laws from thermodynamics or contemporary biochemistry. Every living organism violates all known physical laws from the time of its conception until its death. That is why I insist on a role for the supernatural, perhaps not at present but most certainly at least in the distant past.

    Pierre Grasse had an interesting comment on this question and I believe it was his only reference to God. None of my other sources ever made any reference to God that I am aware of.

    “Let us not invoke God in realities in which He NO LONGER HAS TO INTERVENE. The single absolute act of creation was enough for Him.”
    Pierre Grasse, Evolution of Living Organisms, page 166. The words in cap in italics in the original.

    He also added this on page 245, the whole statement in italics –

    “Any system that purports to account for evolution must invoke a mechanism not mutational and aleatory.”

    That is exactly what the Prescribed Evolutionary Hypotheis offers as an alternative to Darwinian mythology.

  187. CJY:

    Sorry, I have been busy elsewhere.

    Interesting.

    Elaborate?

    (I have mostly thought of functionality as an observation [i.e. objective], and in contexts where information is material, as a rule, it is fairly specific. So in a configuration space — and yes that is a cut down phase space — we have the islands of function in a sea of non-function effect. E.g. The c code above would break down rapidly if members of the ordered sequences of glyphs were modified at random. Similarly, we would be challenged to come up with a viable C program through random search — and the forces odf nature are just not in the C-code writing business. Intelligent targetted design routinely does so in brief compass.)

    GEM of TKI

  188. Nakashima (#178):

    Maybe I am missing something in Denton’s argument and in your comment about it. Let’s try to clarify. You say:

    Denton is saying that protein folds are seriously constrained by the laws of physics.

    That is certainly true, and well known. In other words, only a very minuscule subset of all possible primary sequences of aminoacids has the capacity to comply with the very strict requirements which allow a protein to correctly fold. I think we all agree with that. That is one of the most important points in ID.

    Fewer degrees of freedom in proteins means fewer degrees of freedom in the DNA that codes for them.

    I am not sure what you mean here. The DNA sequence codes the protein’s primary structure. So, the only logical consequence is that, if only a very minuscule subset of all possible primary sequences of aminoacids has the capacity to fold (whicyh is perfectly true), then only a very minuscule subset of all possible sequences of nucleotides in DNA will code for a folding protein.

    That undercuts all the tornado in a junkyard improbability calculations.

    Here I don’t follow your logic. That is a complete non sequitur. The above considerations are exactly a full example of the tornado in a junkyard example.

    Let’s clarify that. The final airplane we have to build is the folding (and functional) protein. We say that a flying airplane is “seriously constrained by the laws of physics”. I think you will agree about that. It has not so many “degrees of freedom”. On the other hand, there are a lot of random assemblages which can come out of the action of the tornado which, not being functional, will not fly like an airplane. So, the degrees of freedom of what can come out of the tornado remain very high.

    Now, let’s suppose that the tornado does not generate the airplane but rather, by acting on an appropriate junkyard where paper and pencils abound, generates the detail plans of the airplane itself. Is that more likely? I don’t think so. It is, maybe, even less likely.

    Well, the degrees of freedom of the correct plans is certainly very low, but the degrees of freedom of anything which can come out of the tornado (torn paper, random signs on the paper, etc.) is not low at all.

    This is saying proteins are closer to snowflakes than computer programs.

    Absolutely not! I really can’t follow you. Snowflakes get their form because of specific laws, which we know (even if they act on random seeds). There is no known (or even conceivable) law that prescribes that a nucleotide sequence in DNA has to preferentially assume, for biochemical magics, exactly that sequence which, if translated by an appropriate and complex symbolic translation system, will provide a protein which can fold.

    IOW, an useless, non functional DNA sequence, and therefore an useless, non functional protein, has by biochemical laws exactly the same probability to come out as a functional sequence. Only, non functional sequences are a little bit more numerous…

    So, where is the similarity with snowflakes? Please, explain.

  189. jerry:

    I realize only now that you had essentially already answered Nakashima at 181. I had not read that, otherwise I would have quoted you in my previous post. :-)

  190. 191

    As I pointed out in the link I provided in #174, I do not really exist here at Uncommon Descent. My questions go unanswered, my challenges to the Darwinian fairy tale are ignored, while others carry on their mutual dialogues in perfect bliss.

    I have never before seen a forum quite like this one. Even in ghettos like After the Bar Closes, skeptics are at least insulted, denigrated and treated with contempt. Consider the way they treat my friend Daniel Smith at Ellsberry’s “inner sanctum.” Here we don’t even exist, at least this one doesn’t.

    I will continue to demand answers until either they appear or I am banished, whichever comes first. Trust me.

    It is hard to believe isn’t it?

    Not at all. This is the “new” Uncommon Descent with all “new” rules of engagement that apparently preclude recognition of certain selected opinions and the person who has presented them. I have never before seen anything like it. Has anyone?

  191. To understand platonic forms a litte more and the issues surrounding them consider Computer languages (and to a lesser extent human languages).

    There are constructs that are gramatically correct and then those that aren’t. Especially in computer languages, grammatically incorrect constructs are rejected out right.

    In a sense grammatically correct constructs are to computer languages what platonic forms are to biology. There are lawful forms. The “intermediates” between the forms are usually non-functional.

    However, the problem of forms goes further than this. Not all grammatically correct forms are implemented. Only a very narrow subset are.

    We see this in biology. Lewontin notes very strange enigmas. For example, why are there no birds capable of eating leaves?? Biological forms seem to be constrained to specific morphological forms, even though in principle, it would appear selection should have created different ones than the ones that appear.

    Lewontin notes in Santa Fe Winter 2003

    The real problem for the evolutionist is not to explain the kinds of organisms that have actually ever existed. The real problem for the evolutionist is how it is that most kinds of potential and seemingly reasonable organisms have never existed. The problem is to explain the location of the empty spaces in the clustered assemblage of occupied points. It is easy to describe organisms that have never existed. There are snakes that live in the grass, but there are no grasseating snakes. Birds perch in trees, yet , aside from a few exceptions, they do not eat all that greenery around them, but rather spend a great deal of energy searching for food. So why are there virtually no leafeating birds? The fact that the measure of the unoccupied space is so big compared to the measure of the
    occupied space, means that explanations of that lack of occupancy are not so easy to come by.

    and

    IN ORDER TO DISCUSS complications that arise in the understanding of evolutionary processes, it is first necessary to make clear what the evolutionary explanation is to accomplish. For this purpose the concept of “taxonomic space” is a useful one. We owe this notion to G. Evelyn Hutchinson, but Walter Fontana and others have since used it in one form or another. This
    taxonomic space of organisms has a huge number of dimensions, each corresponding to some character that might be used in the characterization of an individual.
    If one looks at the occupancy of such a space one is struck by the fact that it has a structure to it. Individual organisms are clustered in the space and those clusters are themselves clustered. And there are
    clusters of clusters of clusters, rather like the stars in the cosmos. The most important thing for the evolutionist is that nearly the entire space is empty, not only when extant organisms are considered, but when all organisms known to have ever existed are considered. The measure of the emptiness of that space is nearly one, and the measure of the occupancy is nearly zero.
    …..
    HIERARCHICAL CLUMPING
    THE STRUCTURE OF THE OCCUPANCY is another matter.

    Organisms are underdispersed in taxonomic space and we need to understand the causes of the hierarchical clumping. One reason for hierarchical clumping in taxonomic space is simply that organisms arise one from another. If an organism is someplace in taxonomic space it is likely that its immediate descendants will be someplace close by in the space rather than someplace far away. It may not be that a particular region in the space is impossible to fill or that you can’t get there from here, but that there has not been enough time for evolution to fill that space. On the other hand, the structure of accessibility may make it impossible to get there from here without retracing the steps to a remote branch point that led
    from a distant ancestral state. One remarkable evolutionary example of not being able to get there from here is that no vertebrate has ever succeeded in evolving wings without giving up something. There are no hexapod vertebrates. Bats and birds have had to give up their forelimbs to produce wings. We will never evolve into a race of angels because we do not have the genotype that will allow for the possession of arms, legs, and wings. There is no general structural problem of evolving multiple limbs and multiple wings. Insects have succeeded in evolving six legs and four wings. So the problem for vertebrates is that of not being able to get there from here without retracing the evolution of vertebrates from invertebrates.

    The problem of this heirachal clumping is not easily explained by common descent. It was supposed at first that common descent explains heirchical clustering, but Denton demonstrated the difficulty of this.

    Nelson’s paper is a good example of the problem which heirarchical clumping poses for common descent. What at first seemed a good argument in favor of common descent now seems a good argument against common descent.

    On nagging problem for me personally, what would the common ancester of plants and animals look like even in principle. These are the sort of heirachical problems that seem to favor the platonic view of biology versus the Darwinian view.

    Biological systems seem to be better unified under a paradigm of common design rather than common descent.

    I suppose it is hypothetically possible to preserve both common descent and common design, but then one one would need very interesting mechanisms of front loading, i.e. reptiles would have to be giving birth to birds in one generation.

    As Dr. Davison noted,some accept this idea:

    “the first bird hatched from a reptile’s egg”,

    – Otto Schindewolf

    PS

    If Shindewolf is correct, then the answer to the Chicken-Egg paradox would be, “the egg” or better yet, the reptile.

    But I still think the correct answer to the chicken-egg paradox is “the chicken” :-)

  192. JohnADavison:

    Personally, I hve no reason to ignore you, and I would be pleased to discuss with you about anything interesting for both. Usually, I don’t select who I am doscussing with according to the personality of the poster, or his identity (with a few exceptions, and you are certainly not one of them). Recently, I have read your many posts about anonimous posting, but frankly I was not interested in that subject (I respect your opinion, but very simply I am more interested in the than in identities).

    I suppose we could agree on many things, being, if I understand well, both on the side of ID. But I am equally certain that we could disagree on various aspects, which is always a good start for discussion.

    So, please accept my sincere interest in your opinions, and, I am certain that many others here share the same attitude. So, if you want to discuss with me any spèecific point, I will be happy to do that “in perfect bliss”.

  193. John Davison,

    I have tried several times to get you to participate in something since you agree there is no debate going on here. The pro Darwinist generally snipe at anything ID says and their purpose is to disrupt any discussion and rarely contribute anything. They are amazingly consistent. When pressed for any details they usually run or present irrelevant trivia. Except one resorted yesterday to Taoism when pressed for why there is/was no God or the universe was not designed.

    You have a lot of knowledge but mostly resort to conclusions based on this knowledge. I am reluctant to quote you or interpret your ideas since you pounced on me when I tried once. You could help us by laying out the basis for your various conclusions from time to time. Just saying that Darwinian processes never work is not helping us. We generally agree on this but it would be good to know your reasons.

    For example a question I have is, what is the origin of all the bird species? I have my own thoughts that they are just variations that arose genetically through breeding over the 10′s of millions of years (through a culling of an original gene pool) but represent essentially no new information. Each species represents a very restricted gene pool of the original. The question then becomes if this is true, is where did the original gene pool come from. If you have a different take, then I and I am sure a lot of others would be interested in your thoughts.

  194. jerry,

    For example a question I have is, what is the origin of all the bird species

    It is well established that birds arose from theropod dinosaurs. are these dinosaurs the original gene pool you envision?

  195. 196

    gpuccio, an alias I must presume.

    We already disagree on pseudonymity. (that may not be a word) Do you disagree with me that there is not a word in “On the Origin of Species” that ever had anything to do with the title of that work or that there is not a shred of verifiable evidence that creative evolution is still in progress? Those are just some of the questions I have posed here only to see them ignored.

    Even Salvador pretends I do not exist here. He even went so far as to beg me to go away. What kind of an “author” would say such a thing to someone who was establishing Intelligent Design with hard facts when he, Salvador, was still in diapers?

    And where are the “true believers” who should be defending the Darwinian hoax?: and a hoax it is and always was! What kind of a forum has Uncommon Descent become?

    Is it nothing more than a debating society where each contestant chooses his opponent and ignores everyone else? So it seems to this evolutionist. I cannot respond where I do not exist. Who can?

    This is the “new” Uncommon Descent. Frankly, I prefer the old one, complete with its nasty comments, intolerance, ad hominem exchanges and summary banishment. At least you could tell what people really believed and were willing to risk expulsion for. I speak as one who was eliminated three times all of which were over fundamental difference on how to interpret the real world, a world which, in my opinion, never had any role for chance.

    Uncommon Descent hss become a nightmare as a venue for intellectual dialogue. It boggles my ancient mind to see this happen to a cause with which I have great sympathy. It smacks of an isolationist protectionism comparable with what one finds at Pharyngula, richarddawkins.net, EvC, ARN, After the Bar Closes and Panda’s Thumb.

    I think maybe I will go away. I am still trying to make up my mind.

  196. Sal:
    The idea of Platonic forms in biology is an old one. The now mostly defunct tradition of orthogenesis is essentially a version of Platonic ideal forms applied to biology (and an argument can also be made that Lamarck’s theory of evolution is as well).

    Applying the concepts of orthogenesis to ID is problematic, because in its early 20th century form, orthogenesis was considered to be progressive, but not goal oriented (i.e. teleological).

    The newly emerging science of evolutionary developmental biology (“evo-devo”) has some similarities to orthogenesis, especially insofar as both are attempts to explain why the evolution of overall form (i.e. phenotype) appears to be constrained to certain types of forms, rather than all possible forms. The orthogenesists asserted that there are certain forms that are much more likely than others. These forms are very similar in some ways to Platonic forms, in that there is no necessarily materialistic explanation for the predominance of certain forms.

    In addition to the early orthogenesists, two other names stand out in this tradition: D’Arcy Thompson and Stephen Jay Gould. Both were primarily concerned with the origin and evolution of form, and both developed theories of evolution based on this. Even J.B.S. Haldane (one of the founders of the “modern evolutionary synthesis”) wrote in this tradition in his short book On Being the Right Size, which you can read here:

    http://irl.cs.ucla.edu/papers/right-size.html

    Haldane’s musings on the relationship between size and constraints on form have become known as “Haldane’s Principle”, and have recently been applied to urban planning.

    Evo-devo, by contrast, explains the similarities within “formal types” with reference to shared developmental programming, especially among eukaryotes. This shared developmental programming is based on the hierarchical gene regulation systems based on homeotic gene regulatory mechanisms. Similar developmental constrains appear to exist among plants and fungi, but not so much among prokaryotes and multicellular protists.

    So, looking for Platonic ideal forms in biology will probably involve identifying and categorizing the various developmental “channels” which are produced by the homeotic gene regulatory systems.

    None of this, of course, says how the various hierarchical gene regulation systems originally evolved. This is another of those “deep time” problems, such as the origin of life and the genetic code. As I have commented repeatedly in the past, I believe that questions about such origins are almost certainly unanswerable using current empirical methods.

    For more on the question of Platonic forms in biology, see:

    http://evolutionlist.blogspot......esign.html

    and

    http://evolutionlist.blogspot......final.html

    Also, I personally believe that the question of the origin of Platonic ideal forms (if such things exist and are empirically distinguishable from the various “channels” produced by the action of homeotic gene regulatory mechanisms) is both an open question and one that is almost certainly not answerable using empirical methods.

  197. Personally, I find the “new” UD to be not much different from the “old”, with the exception that on the “old” UD my comments appeared without moderation. If this means that the moderators are attempting to enforce some modicum of civility, then I suppose I can live with the time lag between posting a comment and its appearance here.

    I also find that the relatively lower frequency of ad hominem attacks recently has been an encouraging development. Some people (who shall remain nameless) find their greatest fulfillment in calling other people names and attacking their character, rather than attacking their positions using reasoned arguments supported by evidence. If such individuals find the “new” UD less than congenial, then I certainly hope that they will, like the little playground bully with the overblown ego, go elsewhere to pick pointless and counterproductive fights.

    Good riddance! Those of us on both sides of the EB/ID divide who value civility and courtesy will not miss you…

  198. I’ve written a blog post on the subject of Platonic ideal forms in biology. See

    http://evolutionlist.blogspot......ersus.html

  199. Allen—your post is quite interesting, but I wonder what you’re driving at.

    “Platonic forms” are self-existent ideas. They do not come into being through any process and in fact are conceived as a force of pure resistance to the forces of change.

    Plato’s notion of forms reflects his belief that intellect is the good and the source of all goodness seen in nature. He came up with the notion of the “form” or idea in order to explain how the supreme intellect could have conveyed its qualities to embodied beings without polluting itself with matter or disturbing its supernal reverie.

    The potential deal-breaker in Darwinism for philosophers (if you can find any) should be the overwhelming beauty of nature. According to Plato, “nothing comes from nothing.” It is not possible for something of great aesthetic value to have come into being from something that has no sense of aesthetic value in itself—i.e., from purely undirected natural processes.

    Think of it—how can nothingness produce beauty? Why would nature, working on its own as a blind watchmaker, produce a stunningly beautiful watch? Darwinism provides a fairly plausible explanation for how nature might produce a functional watch—but it has no explanatory power at all when it comes to beauty.

    The evolutionists you cite were trying to wrestle with this prickly problem. Darwin himself claimed that the beauty of the species is the result of sexual selection. Just one problem: no such impetus to formal excellence is evident in nature itself, as is suggested by his own doleful example of pure-bred dogs left to their own devices.

    So are you hinting that something like Platonic forms might actually exist and can account for the formal excellence of nature (in which case evolution is not undirected)? Or are you simply reminding us of the various attempts at explaining away the form-gap that have already been offered by Darwinists?

  200. Mr Cordova,

    Since you brought up an interesting article, here is another you might like. 10 out of 20 amino acids are common

    A simpler metabolism of 10 amino acids could be coded in two base codons instead of three base codons. A smaller genetic code would be a “transitional form”, now extinct.

  201. —-John Davison: “Allen MacNeill and Salvador, the “author” of this thread both continue to pretend that John A. Davison does not exist here at Uncommon Descent.”

    John, why not just take a chunk of Allen’s work and critique it right here on this blog. If you do that, you will not be ignored for very long.

  202. I respond to people who make reasoned arguments, supported by evidence and citations to published work. I do not respond to people who revel in character assassination and calling people names. In my opinion, people whose regular stock in trade consists mostly of ad hominem arguments, character assassination, and “argument by assertion” do not deserve the attention of people who value civility and rational argument.

  203. My recommendation is that anyone who cannot conduct a rational argument using civility, courtesy, and respect for her/his opponents be banned from Uncommon Descent on the grounds that s/he is both incompetent and unwilling to conduct a fair and honest discussion of any subject whatsoever.

  204. 205

    Stephen B

    There is absolutely NOTHING in the Darwnian model to which MacNeill adheres that ever had anything to do with creative evolution beyond the generation of intraspecific varieties which are all evolutionary “blind alleys” in any event. Is that a sufficient critique for you?

    I recommend you read my papers and the writings of my sources. You obviously have not. I am waiting for a ruling on my recent proposal and have neither time nor patience for any more of this semantic nonsense.

  205. But John, your alternative hypothesis explains a lot less than the current ToE.

    The ToE explains how organisms occupy the niches they do. Your semimeiosis idea doesn’t tackle how organisms appear at the right time ,in the right environment.

  206. JohnADavison:

    gpuccio is not an alias.

    You say:

    “Do you disagree with me that there is not a word in “On the Origin of Species” that ever had anything to do with the title of that work or that there is not a shred of verifiable evidence that creative evolution is still in progress?”

    I completely disagree with Darwin and his followers, so in a sense I think I agree with you. I don’t know if creative evolution is still in progress ot not. That’s a point on which I try to keep an open mind.

    Salvador begged you to go away because you were very aggressive on the point of anonimty (and I can agree with him on that). I respect your point of view on that issue, but don’t agree with it.

    I respect you for establishing ID when Salvador was in diapers, and I respect him for defending it now that he has grown up. Anyone who sinerely and with competence defends ID deserves my respect, whatever his age or history.

    You say:

    “And where are the “true believers” who should be defending the Darwinian hoax?: and a hoax it is and always was! What kind of a forum has Uncommon Descent become?”

    I am not sure I understand your point. Some of those true believers are here around (see, for instamce, my recent long exchange with Adel DiBagno on another thread). That a hoax it is, and always was, I have no doubt.

    You say:

    “I cannot respond where I do not exist. Who can?”

    You can certainly respond to me. For me, you do exist.

    You say:

    “This is the “new” Uncommon Descent. Frankly, I prefer the old one,”

    You are entitled to your personal preferences. I do prefer the new one.

    “Uncommon Descent hss become a nightmare as a venue for intellectual dialogue. It boggles my ancient mind to see this happen to a cause with which I have great sympathy. It smacks of an isolationist protectionism comparable with what one finds at Pharyngula, richarddawkins.net, EvC, ARN, After the Bar Closes and Panda’s Thumb.”

    Again, I can’t see your point. IMO, the old UD was much more isolationist. But again, I am more interested in debating ID than in debating UD.

    “I think maybe I will go away. I am still trying to make up my mind.”

    I hope you stay.

  207. Nakashima:

    What about jerry’s post #181 and my post #189? Are you going to answer them?

  208. I don’t want John Davison or Alan Fox to leave.

    Or Faded Glory for that matter.

  209. Re my comment #206:

    Compare the civility and tone in comment #208 with that in comment #210. Which of these people would you want to have a private conversation with, much less a public argument? I don’t recognize Alan Fox, and hence cannot tell which side of the argument he supports. However, it is clear to me that, whichever side of the argument he supports, he is at least attempting to make reasoned arguments in a civil tone.

    Ergo, if I disagree with Alan Fox, I will write about my disagreement and attempt to show why using rational argument and evidence. If I agree with him, I will do the same.

    I will not ever, under any circumstances, in any venue anywhere address anyone who does not respect even the most basic principles of civility, courtesy, and rational argument. It appears that this has recently become a generally shared opinion on this list, and for that reason I have come to have a much higher opinion of some of the people who post and comment here than was formerly the case. This is also why I comment regularly at Telic Thoughts (one of my favorite venues for discussions and debates of this type), but very rarely at Panda’s Thumb and virtually never at After the Bar Closes, AntiEvolution, and similar sites, where invective and name-calling seem to be the primary avocation.

    As I suspect was probably the case for many on this list, I was bullied in public school for being a nerd and a weirdo who liked books and science more than sports. Now that I no longer am forced to interact with bullies on a daily basis, I am thankful that most of the people here can recognize an intellectual bully when they read one, and like me will have nothing to do with one, regardless of which side of the issue the bully “supports”.

  210. In #200 allanius wrote:

    “The potential deal-breaker in Darwinism for philosophers (if you can find any) should be the overwhelming beauty of nature.”

    IMO, the problem with this argument is that “beauty” is not a primary attribute that can even be discussed in rational terms. Indeed, it appears to me that beauty (including the beauty many perceive in nature) is quite literally “in the eye of the beholder”. Yes, Plato made arguments about beauty, as did Aristotle, but as far as I know their arguments for any rational basis for the assessment of beauty have no objective basis whatsoever.

    As just one example, I find descriptions and photographs of supernova SN 2005gl (see http://www.sciencedaily.com/re.....092717.htm ) both beautiful and fascinating. However, I would definitely not like to be anywhere near such an event, nor would I expect that most of the people I went to public school with would find anything like it “beautiful” or “fascinating”.

    In the same comment, allanius wrote:

    “Darwinism provides a fairly plausible explanation for how nature might produce a functional watch—but it has no explanatory power at all when it comes to beauty.”

    I completely agree, and would go further to say that science has absolutely no business attempting to analyze, quantify, or somehow “explain” beauty, nor truth either, for that matter. Science is about “reasonable confidence based on statistical analysis of empirical data”, not beauty and not truth.

    Nor ethics, neither:

    “And what is good, Phædrus,
    And what is not good…
    Need we ask anyone to tell us these things?”

    Quod erat disputandem?

  211. P.S. I’ve lived with both mongrel and purebred dogs, and generally found the former much more “beautiful” than the latter, especially when it came to personality.

    But then, de gustibus non est disputandem, eh?

    And that, in a nutshell, was my point in the preceding comment as well.

  212. In comment #200 allanius also asked:

    “[A]re you hinting that something like Platonic forms might actually exist and can account for the formal excellence of nature (in which case evolution is not undirected)?

    I wasn’t “hinting” at this, I was stating it fairly plainly. What Plato refers to as “ideal forms” (actually, he uses the Greek word eidos) come into existence in our minds when we begin to perceive a regularity in the objects and processes we observe around (and within) us. However, this begs the question: I believe that what you are asking is, “are the regularities we perceive real or imaginary”?

    Personally, I think the answer is “yes”. That is, the regularities are “real”, but only insofar as we perceive them, and therefore they are also “imaginary”. We must infer the existence of regularities, because regularities are not primary qualities of individual objects and processes.

    So, what causes the regularities? I have written about this elsewhere:

    Similar causes have similar effects

    and vice-versa. When we perceive a regularity in the objects and processes around and within us, we assume that this perception is “real” – that it represents a causal regularity in the world around and within us. But, as the preceding sentence clearly states, this is a “representation”, not a ding an sich (which cannot have any regularities at all, being individual objects and/or processes).

    Where I differ with Plato and platonists (and I suspect that this is the case with most scientists) is that I believe that the regularities in nature “come first” and our perception of them follows. Said another way, natural regularities do not depend upon anyone perceiving them, including Plato’s demiurge (as far as we can tell using empirical methods).

    And yes, I recognize that I used the word “believe” in the previous paragraph. This usage was not accidental; inference is always a “belief”, and couldn’t be anything else.

    What does one get from believing that the “ideal forms” do not depend on the actual entities in which they are expressed, and (even more ridiculous) can exist even in the absence of such actual entities?

  213. BTW, here’s a link to a comment at Telic Thoughts (where many of the same issues are currently being debated):

    http://telicthoughts.com/again.....ent-226099

    I agree with the position expressed by the commentator; he expresses my position on this matter quite well.

  214. Mr Cordova,

    Since you brought up an interesting article, here is another you might like. 10 out of 20 amino acids are common

    A simpler metabolism of 10 amino acids could be coded in two base codons instead of three base codons. A smaller genetic code would be a “transitional form”, now extinct.

    Nakashima-san,

    Thank you for the reference.

    The article presumes the Urey-Miller experiment is a valid representation of early pre-biotic Earth.

    However, this would be problematic under the presumption of an RNA world (the current rage). Further,
    there are chemical barriers to an amino acid soup. Miller’s experiments yielded racemic soups and energetic fusions of amino monomers into amino acid polymers yield racemic polymers which can’t yield functional proteins.

    The fact the paper ignores these rather obvious facts from known chemsitry makes the reasoning not only wrong but circular.

    To quote Bradly, Thaxton, Olsen:

    But what if polypeptides and other biopolymers had formed in the prebiotic soup? What would their fate have been? In general the half-lives of these polymers in contact with water are on the order of days and months—time spans which are surely geologically insigificant.

    Besides breaking up polypetides, hydrolysis would have destroyed many amino acids. In acid solution hydroloysis would consume most of the tryptophan, and some of the serine and threonine. Further, acid hydrolysis would convert cysteine to cystine, and hydrolysis would destroy serine, threonine, cystine, cysteine, and arginine in the alkaline solution generally regarded to have characterized the early ocean. An alkaline solution would also have caused several deamidations.

    If there ever was a primitive soup, then we would expect to find at least somewhere on this planet either massive sediments containing enormous amounts of the various nitrogenous organic compounds, amino acids, purines, pyrimidines, and the like, or alternatively in much-metamorphosed sediments we should find vast amounts of nitrogenous cokes. In fact no such materials have been found anywhere on earth.

    Also, changing the number of amino acids might not be so easy. Consider the problem of adding a new codon to the table and a re-mapping resulted. What half of all an organism’s isoleucine molecules suddenly were replaced by cysteine (or some other acid) molecules because of codon table change. All the proteins would likely fail to catalyze, and the results would likely be death.

    In such case there will be no transitionals.

  215. Allen wrote:

    So, looking for Platonic ideal forms in biology will probably involve identifying and categorizing the various developmental “channels” which are produced by the homeotic gene regulatory systems.

    None of this, of course, says how the various hierarchical gene regulation systems originally evolved. This is another of those “deep time” problems, such as the origin of life and the genetic code. As I have commented repeatedly in the past, I believe that questions about such origins are almost certainly unanswerable using current empirical methods.

    Thank you for your comment. Actually, I think Paul Nelson and Jonathan Wells would argue that the identification of forms would be independent of develomental mechanism. In fact, the form would be all the more astonishing if the same form were arrived at via different developmental pathways.

    Homology a Concept in Crisis

    Since homologies cannot be explained by equating developmental information with DNA sequences, some biologists have attempted to explain it by attributing it to similar developmental pathways. Although DNA determines the amino acid sequence of proteins essential for development, such pathways also involve other factors, such as the localization of cytoplasmic constituents in the egg cell, physical constraints resulting from the size of the embryo, and so on. (Wells, 1992)

    Efforts to correlate homology with developmental pathways, however, have been uniformly unsuccessful. First, similar developmental pathways may produce very dissimilar features. At the molecular level, it is well known that virtually identical inducers may participate in the development of non-homologous structures in different animals. (Gilbert, 1994) At the multicellular level, the pattern of embryonic cell movements which generates body form in birds also generates body form in a few species of frogs. (Elinson, 1987) And even at the organismal level, morphologically indistinguishable larvae may develop into completely different species. (de Beer, 1958) Clearly, similar developmental pathways may produce dissimilar results.

    Second, and more dramatically, similar features are often produced by very different developmental pathways. No one doubts that the gut is homologous throughout the vertebrates, yet the gut forms from different embryonic cells in different vertebrates. The neural tube, embryonic precursor of the spinal cord, is regarded as homologous throughout the chordates, yet in some its formation depends on induction by the underlying notochord while in others it does not. (Gilbert, 1994) Evidently, “structures can owe their origin to different methods of induction without forfeiting their homology.” (de Beer, 1958, p. 151) Indeed, as developmental biologist Pere Alberch noted in 1985, it is “the rule rather than the exception” that “homologous structures form from distinctly dissimilar initial states” (see Figure 2). (Alberch, 1985, p. 51)

    Production of similar forms from dissimilar pathways is also common at later stages of development. Many types of animals pass through a larval stage on their way to adulthood, a phenomenon known as indirect development. For example, most frogs begin life as swimming tadpoles, and only later metamorphose into four-legged animals. There are many species of frogs, however, which bypass the larval stage and develop directly. Remarkably, the adults of some of these direct developers are almost indistinguishable from the adults of sister species which develop indirectly. In other words, very similar frogs can be produced by direct and indirect development, even though the pathways are obviously radically different. The same phenomenon is common among sea urchins and ascidians (see Figure 3). (Raff, 1996)

    Even the classic example of vertebrate limbs shows that homology cannot be explained by similarities in developmental pathways. Skeletal patterns in vertebrate limbs are initially laid down in the form of cartilage condensations, which later ossify into bone. The sequence of cartilage condensation is the developmental pathway which determines the future pattern of bones in the limb. Yet similar bone patterns in different species (i.e., homologies) arise from different sequences of cartilage condensation. (Shubin, 1991) In the words of biologist Richard Hinchliffe: “Embryology does not contribute to comparative morphology by providing evidence of limb homology in the form of an unchanging pattern of condensation common to all tetrapod limbs.” (Hinchliffe, 1990, p. 121)

    The constancy of final patterns despite varying pathways has prompted developmental biologist Günter Wagner to suggest that homology might be due to conserved developmental “constraints”. (Wagner, 1989) Wagner’s critics, however, object that this notion is too vague to be useful. Although developmental constraints emphasize the fact that embryos are capable of producing similar end-points by a variety of routes, they do not constitute a naturalistic mechanism accessible to empirical investigation.
    So embryology has not solved the problem of homology. In 1958, Gavin de Beer observed that “correspondence between homologous structures cannot be pressed back to similarity of position of the cells in the embryo, or of the parts of the egg out of which the structures are ultimately composed, or of developmental mechanisms by which they are formed.” (de Beer, 1958, p. 152) Subsequent research has overwhelmingly confirmed the correctness of de Beer’s observation. Homology, whether defined morphologically or phylogenetically, cannot be attributed to similar developmental pathways any more than it can be attributed to similar genes. So far, the naturalistic mechanisms proposed to explain homology do not fit the evidence.

    It would appear this only underscores Abel’s thesis of the independence of life from physicodynamic processes.

    Perhaps one way to conceptualize the problem is understanding the independence of software from hardware. In principle, software can be run on various computer architectures. Even the chemistry of the physical computers can be radically different, but software will have an independence from the underlying physical implementation.

    We see that there are layers of forms which are independent of physical implementation. This is especially prononounced in morphological features with completely different means of development.

    Also astonishing is the independent mechanisms involved in creating males and females. Cleary a theme of gender exists, but the different mechanisms which implement gender suggest that sex evolved (or was created) independently numerous times.

  216. Allen MacNeill:

    Ergo, if I disagree with Alan Fox, I will write about my disagreement and attempt to show why using rational argument and evidence.

    I have tried that and found it doesn’t work.

    Oh well…

  217. Allen,

    You said you do not follow a thread after it reaches a 100 comments. That you are doing that here (following a thread after a 100 comments) is a change in behavior. Can we expect more of that from you here in the future?

  218. That depends: most threads degenerate pretty quickly, and in most cases a thread that passes the 100 mark has long since degenerated into name calling and argument by (repeated) assertion. This thread didn’t do that, and continued to present interesting and thought provoking ideas worth working on. Any thread that does that in the future (and in which the participants can remain courteous and civil) will probably hold my attention for as long as this one has (assuming that my other duties to my family and my students are taken care of).

  219. And yes, the change in my behavior vis-a-vis long threads is almost certainly at least partly due to the change in moderation policy and tone here, along with Sal’s very interesting questions and comments (it appears that both of us may have indeed changed, in ways that I find encouraging). I guess it just goes to show that old dogs can learn new tricks, if they’re willing to do so.

  220. Allen,

    I’m very grateful for the example you have set.

    Your Cornell biology class in 2006 was one of the few University classes to actively study the works of Bill Dembski, Michael Behe, and Phil Johnson. For that I am profoundly grateful.

    I’m something of a pragmatist. I think there will be strong disgreements over origins, however, perhaps the one area where there can be constructive cooperation would be in the are of medical advances.

    Hence, even if we might disagree on the origin of platonic forms, resolving the question of whether they really exist and whether medical sciece can be advanced by exploration of those forms would be valuable.

    Denton is not an ID proponent, but neither is he a Darwinian. He is a medical doctor. He explored the topic of platonic forms with far less metaphysical baggage than others. This might be a fruitful topic of debate. Fruitful, in as much as it might help the human condition.

    How does this relates to Abel’s findings? I do not believe Denton is correct that the source of the platonic forms in proteins is due to physics. Physics allows these forms to exist, physics tells us which forms will be optimal for protein function, but physics does not make these forms inevitable.

    There is parallel in engineering. Physics dictates what the optimal designs would be for airplanes and buildings. In that sense physics dictates to some degree what the forms would ideally be. They are platonic in that sense. But physics doesn’t actually make these designs inevitable. Physics doesn’t mandate that man will create airplanes and skyscrapers.

    Denton’s belief that physics may somehow make platonic forms is where Denton is mistaken, imho.

    The possibility of a platonically defined biology may offer opportunity for medical advancements. Perhaps this might be one investigation worth revisiting.

    Sal

  221. 222

    All hail the Salvador Cordova/Allen MacNeill dynamic union, the only instance in all of cyberdumb in which a Darwinian atheist and a Christian Theist have joined forces in the utterly inconceivable attempt to convince the world that there really is no conflict in evolutionary science, that both sides are of a single mind with respect to the twin mysteries of ontogeny and phylogeny, that all that is required is patiently to let everyone present his views knowing that sooner or later a consensus will surely be found.

    Thank you Salvador. You have proven to be the magic elixir that Uncommon Descent has lacked all these years.

    I have just deleted “Young Cosmos” from the blogs for which I have respect.

    You now have my permission to continue deleting every new message I present without a word of explanation. Good luck to you and your joint “author,” Allen MacNeill.

    It isn’t so hard to believe any more is it.

  222. Mr Gpuccio,

    Sorry for not responding earlier. I’ve been off reading stuffs recommended by Mr Vjtorley on another thread.

    Well, we should be clear that all DNA codes for protein, and all protein has some final shape. That shape may have low function in the cell, but it is a shape!

    Also, I should make clear that I have not seen the full test of Denton’s article, only the abstract. So my comments can only relate to what is said in that abstract.

    There are forms that appear very commonly in proteins, such as the alpha helix and the beta sheet. It is not clear to me from the abstract if this is what Denton means by a common form, or if he is referring to some class of 3D protein shapes that appear repeatedly in proteins of different DNA sequence. Have you read the complete article?

    If he is saying that basic electrochemistry is driving protein folding into alpha helix and beta sheet forms, I don’t think he is making an argument like ‘the idea of the alpha helix exists independent of the physical universe’.

    Water, when it freezes in air, makes snowflakes for thermodynamic and electrochemical reasons, beautiful examples of law, chance, and necessity. It seems to me that Denton is pointing out that protein folding is dominated by the same forces.

    As an example, I was just reading about the serotonin receptor 5-HT2a, which is coded on chromosome 13 by the HTR2A gene. There are 255 known variants of this gene. (For context, the gene is over 62,000 base pairs long)

    All 255 variants fold into almost the same shape, and function almost the same in our bodies. The relevance to improbability calculations is that instead of counting 62663^4 and throwing up our hands, Denton is saying no, a lot of those are going to fold into functional shapes. Maybe not the best shapes, maybe not shapes that work in all cell types where the gene is expressed, but useful shapes nonetheless.

    In physics there is an idea called perturbation analysis. I don’t know if a lot of perturbation analysis is done on genes. I expect we need more computer power to it well. But the idea would be to test individual subtitutions for changes in shape.

    Here is a simple idea to help think about the issue. We all know that there is such a thing as the cube square law. As the volume grows by the cube of the radius, the surface only grows by the square of the radius. For proteins, that means that the bigger they are, the less of them (on average) is on the surface, contributing to the charge surface. Changes deep inside due to amino acid substitutions don’t have as big a chance to affect the surface charge as they would in smaller proteins. HTR2A might code for over 20,000 amino acids, but most of them are inside the 3D shape.

    Don’t take the preceding too seriously, because a lot of protiens are not spheres! It is just to motivate the idea that geometry and chemistry can dominate the eventual shape, not function.

  223. Nakashima:

    Thank you for your answer. I have not read Denton’s paper, so I can only comment on your comments. A few clarifications:

    1)The alpha helix and the beta sheet are very common aspects of secondary structure. Even if many sequences will not even assume one of these two fundamental aspects, in reality many primary sequences may have parts assuming one of those two configurations. But secondary structure is only the basic element contributing to final form. In reality, it is tertiary structure which especially allows proteins to get their final form, and is connected to the final function. Moreover, tertiary structure is extremely more varied and complex than secondary structure, and the constraints are much more strict. Therefore, we should look to tertiary structure as the true “functional target”.

    2) You say:

    Water, when it freezes in air, makes snowflakes for thermodynamic and electrochemical reasons, beautiful examples of law, chance, and necessity. It seems to me that Denton is pointing out that protein folding is dominated by the same forces.

    There is no doubt that protein folding is dominated by physical/biochemical forces (by what else should it be dominated?), even if the working of those forces in protein folding is so complex that we still scarcely understand the rules. But that is not the point. The point is that no known (or imaginable) force of physics or biochemistry can be held responsible of the primary structure, and it is the primary structure which determines the folding (or non folding) of a protein according to laws of necessity. So, the point is not to understand the details of necessity which rule protein folding (which is difficult, but in principle trivial), but rather to understand why we have the correct genes coding for the correct primary structures. That is the point in the discussion about darwinism or ID, and not the rules of protein folding.

    3)You say:

    As an example, I was just reading about the serotonin receptor 5-HT2a, which is coded on chromosome 13 by the HTR2A gene. There are 255 known variants of this gene. (For context, the gene is over 62,000 base pairs long)

    Well, I have checked and the human gene is given at about 20000 base pairs where I looked, but that is not important. The protein should however be 471 AAs long (there are two very long introns).

    All 255 variants fold into almost the same shape, and function almost the same in our bodies. The relevance to improbability calculations is that instead of counting 62663^4 and throwing up our hands, Denton is saying no, a lot of those are going to fold into functional shapes. Maybe not the best shapes, maybe not shapes that work in all cell types where the gene is expressed, but useful shapes nonetheless

    I think there is some confusion here. Again, I cannot refer to Denton, so I will comment on what you say.

    The fact that 255 functional variants of a 471 AAs protein are known is no surprise. All proteins can exist in different functional variants. That problem is well known in ID, and is usually called “the problem of target space calculation”. We are perfectly aware, when we try our probability calculations, that the functional target is not represented by one sequence. But we are absolutely convinced that our improbability calculations remain completely valid.

    Let’s make an example. First of all, let’s clarify the trivial calculation, because you make an error in your post (probably just a trivial typo): the correct calculation for a 62663 nucleotides sequence is not 62663^4, but 4^62663, which is all another number!

    So, for our protein of 471 AAs, the search space is 20^471. My excel refuses to give me the equivalent in base 10, but that is certainly a very, very big number.

    Now, we know that different sequences of that space can have the desired function. We know 255 of them, but certainly there could be many more. In reality, nobody knows exactly how many. That is the problem of calculating the target space, which is still unsolved.

    So, darwinists hope that the target space is as big as possible. The problem is that their hopes are not realistic. And the bigger problem (for them) is that protein engineering and other branches of science are going to give us more definite answers in a very short time, and I am sure that they will not like them.

    Because, you see, the target space can never be so big that darwinian mechanisms become credible. Let’s take our example. We have a search space of 20^471. Let’s imagine it corresponds to 10^600. Dembski’s UPB (which is, IMO, by far an excessive threshold in favour of darwinism) is 10^150. So, just to approach the limit of credibility of a random search in the whole universe, the target space should be as big as 10^450! We are a little bit distant from our known 255 functional variants…

    4)You say:

    Changes deep inside due to amino acid substitutions don’t have as big a chance to affect the surface charge as they would in smaller proteins.

    But the forces determining protein folding are related more to AAs which fall inside the protein than to those at the surface! So, it’s exactly the opposite. I quote form Wikipedia:

    “Most folded proteins have a hydrophobic core in which side chain packing stabilizes the folded state, and charged or polar side chains on the solvent-exposed surface where they interact with surrounding water molecules. It is generally accepted that minimizing the number of hydrophobic side-chains exposed to water is the principal driving force behind the folding process”

    So, folding is determined by the whole sequence, and is not only a problem of surface residues. Folding is very complex issue.Functional foldings are not so numerous, in nature there is only a certain number of them known, that’s why proteins can easily be grouped in superfamilies and so on. There are many 3D forms that a sequence can assume, but only a very tiny subset of them can be considered functional folding. Functional folding is so difficult that bigger proteins need the assistance of chaperones to fold correctly. The only “Synthetic, computationally designed sequence” in SCOP classification, 1qys, can fold, but its creator admits that its folding process is very unsatisfying compared with the folding of natural proteins. That’s how difficult folding is to achieve, even with the most recent engineering understanding.

    So, to sum up: we have all the reasons to believe that most possible protein sequences are completely non functional. Most of them will not fold in any useful way, and the very restricted subset which can in some way fold is not certainly functional by default. Function requires much more than simple folding. And a specific function, which can be used in a specific context, is extremely more restricted. The search space, instead, is always the same, and easily computable: and believe me, it is huge beyond imagination.

  224. A correction:

    I forgot to close the blockquote in the previous post. The whole part form “But the forces…” to the end is my discourse, not Nakashima’s. I apologize.

  225. GP:

    Re: 20^471

    Calculator/Spreadsheet trick.

    Let’s work in logs, in light of the laws of indices and def’n of logarithms.

    Rounding . . .

    471 * log[10] 20
    = 612.785
    = 612 + 0.785

    So:

    20^471 = 10^0.785 * 10^612

    Antilog 0.785 = 6.097

    So 20^471 = 6.097 *10^612

    Hope that helps.

    Such a config space is something like the square of the square of the number of quantum states of the atoms of our observed cosmos across its lifetime. Utterly beyond reasonably likely to succeed search by non-foresighted, intelligently directed, active information based processes.

    And that is the point of the Hoylean tornado in a junkyard challenge: to get TO the shores of complex function. (And this is for just one protein. For that protein to be functional, it has to be a part of a complex environment of other similar entities, and the system has to be self-replicating which entails storing a blueprint and having pre-existing assembly machinery, which are of course again highly complex, algorithmic, data structure based and irreducibly complex.)

    GEM of TKI

    PS: Hint: never dismiss Sir Fred! (He may be wrong, but never simplistically so. Indeed, his highly instructive errors — e.g. on the Steady State Theory — have been the occasion of major advances in science across the 2nd half of C20.)

  226. gpuccio writes:

    So, to sum up: we have all the reasons to believe that most possible protein sequences are completely non functional

    This reminds me of a point I was going to make about oxytocin. There are 512 billion possible choices for a nine-amino-acid sequence. One is oxytocin. Of the remaining 500 or so billion, how many have some biological function or activity? Without checking all such combinations in all known biological systems, how can we know whether it has biological funtion?

    So what are “all the reasons to believe” that unknown sequences are not functional?

  227. 228

    Allen MacNeill is the fox in Uncommon Descent’s hen house, especially here on scordova’s thread. MacNeill is one of the last few “true believers” in the Darwinian hoax. With P.Z. Myers, Wesley Ellsberry and Richard Dawkins, he is still clinging to the absurd notion that natural selection has produced new structures that were not present in an organism’s ancestor.

    What distinguyishes MacNeill from the other three is only he still remains a real Darwinian. The Myers/Dawkins/Ellsberry triumvirate long ago abandoned any pretense of defending natural selection. They don’t even use the words any more, because they recognize that the sine qua non of the Darwinian hypothesis is without foundation. That is why they have completely abandoned any pretense of science to expend all their energies attacking the only conceivable alternative to Darwinism which is a planned evolution.

    MacNeill still “clings” to the absurd position that everything in the world, living and dead, is the result of a series of happy accidents. His is the mentality of Stephen Gould when he claimed that “intelligence was an evolutionary accident” and evolution was like a drunk reeling back and forth betwen the gutter and the barroom door. MacNeill’s heroes are all armchair Darwinian theoreticians like J.B.S. Haldane, Ernst Mayr, Sir Ronald Fisher and Sewell Wright. Sewell Wright, at least in his youth, was a real geneticist who decided suddenly to abandon that field to devote the rest of his life to cranking out cute little equations which had lttle or nothing to do with the real world. Not one of MacNeill’s heroes ever scratched the surface of the great mystery of phylogeny, yet he goes blithely right on treating them as the pillars of an evolutionary mechanism which is not even a bona fide hypothesis. Hypotheses are testable. Darwinism is the ONLY proposal of which I am aware, that is so designed that it cannot be tested. Accordingly it is not science. It is mysticism pure and simple.

    It is hard to believe isn’t it?

    Now be sure to delete this Sal before anyone gets a chance to read it. They can find it on my weblog if they miss it here.

  228. Alan Fox:

    Your example of oxytocin, while interesting, is not completely appropriate. Oxytocin is a small peptide which works as a hormone, IOW it is a rather simple molecule which is recognized by much more complex molecules, and conveys a signal. It is not a good model to discuss of proteins, whose functional activity is bound to a very complex 3D folding and to specific biochemical functions, like accelerating biochemical reactions which could never take place without the specific enzyme.

    But even in the case of oxytocin, I don’t know if someone will ever take time to inquire how many of the 5 x 10^11 combinations are functional (maybe something is already known, I have not searched the literature), but do you really believe that many nine aminoacids combinations could perform the task of oxytocin? If you read the Wikipedia pages about oxytocin and vasopressine, you will see that even small differences change the function of the hormone, or the species specificity. That is not probably due to intrinsic properties of the molecule, but rather to the fact that, as already said, these peptides are signals, and the specificity is linked to the ability of the receptor to recognized the signal. And what use is a signal which is not specific enough?

    The problem is much more complex for proteins, where the function is linked to the tertiary structure, and is sometimes very sophisticated. You ask why I say that there are all the reasons to believe that unknown sequences are not functional. I say that because of what is known from protein engineering, and form the pioneering work about protein folding and random sequences. And from another approach, which is found in Durston’s paper:

    “Measuring the functional sequence complexity of proteins”

    repeatedly, and deservedly, quoted on this site.

    And many other considerations, but the argument is very vast and important, and for the moment I would stop here. If you are interested, we could discuss that more in detail, but probably not on this “old” thread.

  229. Off topic or inflammatory material is at risk of deletion.

    Discussion of what physicodynamic process can create and can not create is welcome.

    Discussion of individuals, their character, their motivation, their heredity is rude. Participants are free to do so outside of this discussion (more likely outside of this website), but not under the terms of this dialogue.

    From comment policy:

    we don’t have the time or inclination to get into debates over our editing decisions. Nagging us about a comment that didn’t get approved is only going to make us even less likely to approve your future comments.

    Stay On Topic – If you take off on a tangent unrelated to or only tenuously related to the topic it makes topical dialog in the commentary difficult for others. Off topic comments may be deleted if they appear to interrupt the flow of topical comments.


    Try to be polite.

  230. John Davison,

    Allen MacNeill is on record here as saying Darwin is dead. He is more a believer in Gould’s exaptation theory as the reason for biological change. So we all agree that Darwin is dead here. Most of the anti ID people who come here have not gotten the message yet but they eventually will. It is just the year of Darwin so it is hard for them to sh__ can him this year.

    Four years ago Eldredge edited a book on macro evolution and in it is the basis for the new synthesis. Still as atheistic as the old but not saddled with negatives of Darwin such as natural selection or gradual adaptive changes. It maintains common descent and focuses on the origin of new variation.

    If you still have access to a library electronically then you can probably download the relevant articles. They were in paleobiology in 2005.

    However, Gould’s theory is just as atheistic based as Darwin’s so on that front there is not much movement. So now the fight is over protein functionality and what percentage of proteins are functional. Quite small from what I understand.

  231. 232

    Salvador Corddova, the “author” of this revealing thread, reminds me of Neville Chamberlain, the British Prime Minister who went to Germany to “reason” with Adolf Hitler. He returned to reassure the Britsh that there would be “peace in our time.” Days later Germany invaded Poland and Britain declared war on Germany. This prompted Winston Churchill to describe Nevile Chamberlain as -

    “A sheep in sheep’s clothing.”

    Salvador does not yet understand that one cannot reason with ideologues like P.Z. Myers, Richard Dawkins and Allen MacNeill. They are immune to reason and always will be. There is about as much chance of converting Allen MacNeill as there is of Pope Benedict XVI converting Christopher Hitchens to Roman Catholicism. MacNeill is a “true believer” exactly like Ernst Mayr who described himself as -

    “a dyed-in-the-wool Darwinian like myself.”
    The Growth of Biological Thought, page 132

    All true conversions come from within like that by Anthony Flew and never as a result of discussion or debate. I can’t think of single example of the success of such a venture and I dare say neither can anyone else. Quite the contrary, prolonged exchange only hardens ones position as this thread clearly demonstrates.

    One cannot reason with “prescribed” ideologues like P.Z. Myers, Richard Dawkins and Allen MacNeill. They were undoubtedly “born that way,” the perfect synonym for “dyed-in-the-wool.”

    Now don’t forget to delete this one. You haven’t been keeping up lately!

  232. Below is an example of a rude, inflammatory tone. Lots of editorializing, sparse on educational value, heavy on polemics and rhetoric, and indirect personal swipes at other commenters.

    It is inconsistent with the terms of dialogue here, especially in light of the fact a non-political, non theological, non-philosophical issue is being discussed..

    Such postings are free to be expressed in other venues, but not under the terms of this discussion and given the topic at hand (Abel’s paper, and surrounding issues), it seems inappropriate.

    Allen MacNeill is the fox in Uncommon Descent’s hen house, especially here on scordova’s thread.
    ….
    His is the mentality of Stephen Gould when he claimed that “intelligence was an evolutionary accident” and evolution was like a drunk reeling back and forth betwen the gutter and the barroom door. MacNeill’s heroes are all armchair Darwinian theoreticians like J.B.S. Haldane, Ernst Mayr, Sir Ronald Fisher and Sewell Wright. Sewell Wright, at least in his youth, was a real geneticist who decided suddenly to abandon that field to devote the rest of his life to cranking out cute little equations which had lttle or nothing to do with the real world. Not one of MacNeill’s heroes ever scratched the surface of the great mystery of phylogeny, yet he goes blithely right on treating them as the pillars of an evolutionary mechanism which is not even a bona fide hypothesis. Hypotheses are testable.
    ….
    Now be sure to delete this Sal before anyone gets a chance to read it. They can find it on my weblog if they miss it here.

    Such assertions are of little use to learning, great fodder for polemics and only incite.

    R.A Fisher was metioned in the above passage by JohnDavison. A proper critique of RA Fisher rather than an assertion better serve the education of readers. An example of my disucssion of RA Fisher:

    my comment on Fisher here.

    Below also is an example of rational and constructive dialogue:

    1)The alpha helix and the beta sheet are very common aspects of secondary structure. Even if many sequences will not even assume one of these two fundamental aspects, in reality many primary sequences may have parts assuming one of those two configurations. But secondary structure is only the basic element contributing to final form. In reality, it is tertiary structure which especially allows proteins to get their final form, and is connected to the final function. Moreover, tertiary structure is extremely more varied and complex than secondary structure, and the constraints are much more strict. Therefore, we should look to tertiary structure as the true “functional target”.

  233. Mr Gpuccio,

    Thank you for correcting my post! Do you have a reference for the size of HTR2A? I was looking at the NCBI, but it was the first time I ever tried to do such a search, I confess.

    I think we are agreeing on the need for perturbation analysis to tell us more about how large and scattered are the islands of function in protein space. Whatever the surprises, I hope can learn these things quickly. It’s a good use of all that spare computing power given to us by Moore’s Law! :)

    I’m not sure I follow your response to my point about the interior of the final state of the protein. Sure, during the process of folding the hydrophobic parts are being pushed into the interior. But once the final shape is achieved, they don’t play a part in determining the charge surface of the protein.

    If we continue to use the example of HTR2A, and continue to pretend that the protein and each amino acid is a sphere (and a few other simplifying assumptions) then I estimate that of the 471 AAs, about 35 are on the exterior and contributing to the charge surface. I admit this is complete handwaving and back of the napkin.

    I think a larger criticism of Hoyle’s argument in the context of OOL is that it assumes a DNA first world, in which first DNA is strung together, somehow it is mapped to a protein, and then the protein is tested for function in some context. I don’t think this model is so popular anymore, because of the many real problems it has.

  234. Immediately below is a good example of indirect personal swipes and off topic discussion. Hardly educational to people on either side of the aisle:

    Salvador Corddova, the “author” of this revealing thread, reminds me of Neville Chamberlain, the British Prime Minister who went to Germany to “reason” with Adolf Hitler. He returned to reassure the Britsh that there would be “peace in our time.” Days later Germany invaded Poland and Britain declared war on Germany. This prompted Winston Churchill to describe Nevile Chamberlain as -

    “A sheep in sheep’s clothing.”

    Salvador does not yet understand that one cannot reason with ideologues like P.Z. Myers, Richard Dawkins and Allen MacNeill. They are immune to reason and always will be. There is about as much chance of converting Allen MacNeill as there is of Pope Benedict XVI converting Christopher Hitchens to Roman Catholicism. MacNeill is a “true believer” exactly like Ernst Mayr who described himself as -

    “a dyed-in-the-wool Darwinian like myself.”
    The Growth of Biological Thought, page 132

    All true conversions come from within like that by Anthony Flew and never as a result of discussion or debate. I can’t think of single example of the success of such a venture and I dare say neither can anyone else. Quite the contrary, prolonged exchange only hardens ones position as this thread clearly demonstrates.

    One cannot reason with “prescribed” ideologues like P.Z. Myers, Richard Dawkins and Allen MacNeill. They were undoubtedly “born that way,” the perfect synonym for “dyed-in-the-wool.”

    Now don’t forget to delete this one. You haven’t been keeping up lately!

    and

    Salvador does not yet understand that one cannot reason with ideologues like P.Z. Myers, Richard Dawkins and Allen MacNeill.

    The discussion goes forward for the benefit of onlookers and those on the fence, not necessarily an attempt to change their minds.

    Now, John, I’ve let a few of your offtopic comments go through. It is one thing to argue ID is true, it is another thing to demonstrate through presentation of evidence and logical deduction to the best conclusions.

    Your above posting is lacking:

    1. citatiation of physical evidence (in the scientific sense) relevant to the topic of Abel’s paper

    2. logical dedcuction from evidence relevant to Abel’s paper

    Your posting has:

    3. personal swipes at me and other commenters on this thread

    4. a generally rude and condescending tone, commentary on my character and actions (which has little to do with the topic at hand)

    Here is an example of productive discussion for the benefit or readers:

    Mr Cordova,

    Since you brought up an interesting article, here is another you might like. 10 out of 20 amino acids are common

    A simpler metabolism of 10 amino acids could be coded in two base codons instead of three base codons. A smaller genetic code would be a “transitional form”, now extinct.

  235. For the reader’s benefit, here is an example of a productive exchange and one that is relevant to the topic at hand.

    This was between Nakashima-san and Gpuccio:

    Mr Gpuccio,

    Thank you for correcting my post! Do you have a reference for the size of HTR2A? I was looking at the NCBI, but it was the first time I ever tried to do such a search, I confess.

    I think we are agreeing on the need for perturbation analysis to tell us more about how large and scattered are the islands of function in protein space. Whatever the surprises, I hope can learn these things quickly. It’s a good use of all that spare computing power given to us by Moore’s Law!

  236. Nakashima:

    I think you are right about the length of the genomic region of HTR2A. I read the 20000 value somewhere yesterday, but I could not find it again today. So, I looked further and finally I found the value on GeneCards and GeneLoc: the region is 62,663 bases, and the gene should be formed by 3 exons, for a total of 3006 bases. That is still too much for 471 AAs, but probably there are still non coding parts to be considered. Indeed, I rarely consult the gene databases, and I am more familiar with working with proteins, so I apologize for my imprecision.

    Regarding proteins, my idea is as follows: the complete primary sequence determines if and how a protein will fold, and not only the AAs which in the end will be at the surface. I have discussed that also with my son, who is studying biophysics, and he seems to agre on that. We could argue that, once a correct folding has been achieved, the AAs on the surface of the molecule may be more important for specific functions (recognition sequences and similar). But you certainly know that the 3D form of the molecule is equally important, providing the correct position for the recognition sequences, for instance. And, as you say, most proteins are not spherical, and have complex 3D forms which are essential for function (see the transmembrane proteins, for instance).

    My point is that all the primary sequence can be important, even is obviously there are aminoacids which are essential, and can never change, and others which can be easily substituted by other similar residues. So, I am not saying that in a 471 AAs protein all the AAs have to be exactly those we observe. The Durston method to calculate Shannon’s uncertainty in protein families is a very good way to approach the problem, and shows that there are proteins with a higher functional information content, and others with a lower one.

    I am very interested to your concept of perturbation analysis, but I am not sure how much that can be done by computing, given that as far as I know the rules of protein folding are still not completely understood. I think that mcuh information will come form two different sources: a better understanding of those theoretical rules, and further experiments in the practical field of protein engineering, especially of protein engineering through partial random search. I believe that all those who discuss that there is no way to test ID, or to test darwinian evolution, or to falsify one or the other, will have great surprises from the advancements in those fields.

    And I can absolutely share you point: Whatever the surprises, I hope we can learn these things quickly.

  237. Yockey’s book, information theory, evolution, and the origin of life explore the probablities based on mutations in the codon table.

    My friend Dr. Royal Truman (a chemist) explored the probability of evolving cytochrome-c here: Protein Families Chance or Design.

    There have been critiques of Truman’s calculations, and the arguments go back and forth.

    Dr. Sauer used some sort of cassette mutagenesis to estimate the the separation of functional islands in protein space. His numbers were not as improbable as Truman’s.

    One of the issues however is that even if we have a catalyzing protein, some of the amino acid elements are essential for essential non-catalyzing activities. For example some theorize glutamine and asparagine amino acids serve as molecular clocks to signal when it is time for a protein to be dispensed with:

    see: Distribution of asparagine and glutamine

    Without this garbage collection feature, it would be interesting to see how viable life would be.

    I would argue, at the very least, homo-chirality is a necessary condition for protein folding. Thus, a racemic (non-homochiral) soup as Stanley Miller speculated, would not allow protein formation.

    I should mention, Durston and Chiu (mentioned in the title), are specialists in bio-physics, the appropriate discipline for these sorts of questions.

    So, in sum the question of protein improbability is an open question.

  238. Mr Cordova,

    Thank you for acknowledging my small words as helpful.

    Homo-chiral or not, a string of AAs will assume some final shape. It isn’t helpful to say it doesn’t fold. Whether that shape does anything useful at any rate in a specific chemical context is another story.

    Did Miller speculate or did he achieve something? Have others, making different assumptions, also achieved things? Let us give them credit for trying.

  239. Mr Gpuccio,

    It is great to hear that you have a son, and he is studying such an exciting science, and you have a good relationship to discuss deep things with him. It’s fun to drink sake and shout at sumo wrestlers on TV together, but a quiet conversation is true satisfaction, ne?

    Are there “rules” for protein folding beyond thermodynamics and elctrochemistry? I think the search has been disappointing, but we are always looking for patterns. It is a very human trait! :)

    So we are left with brute force computational simulation of folding. If you run Folding@Home you can see it yourself. Fascinating stuffs.

    If we continue to focus on OOL issues, the question of protein function in context becomes quite fuzzy. The context is being negotiated by the set of proteins available. We are really asking if any metabolic cycle can emerge, not if a specific cycle with specific protein functions can emerge.

  240. Did Miller speculate or did he achieve something? Have others, making different assumptions, also achieved things? Let us give them credit for trying

    Agreed, he deserves credit for trying. As matter of principle I encourage continued work, experimentation and observation.

  241. Nakashima:

    Thank you for the kind notes on happy family life! :-)

    Regarding OOL, it seems that you raise the point of “any possible function”. I can happily admit that, in OOL context, we can imagine that “any possible life system” could have emerged, even if it is equally true that we are not aware of any different life system from the one (or ones) we can observe. That is not a problem for me, because I do believe (and I am not alone) that no theory about OOL at present is even vaguely credible (except design, obviously). I think that all serious thinkers should agree on that, even if they are not on the side of ID. Beyond the recent Abel paper, I would like to remind the rather recent paper from Shapiro which more or less gave the same scenario: we have no reasonable theory for OOL.

    Instead, I must say that for all that comes after (let’s say origin of species), the point of “any possible function” is no more valid. I am absolutely convinced that, once you have a complex scenario already working (and prokaryotes, as you certainly know, are a more than complex scenario in themselves) than the restraints for what can represent a new useful function become very severe. IOW, the darwinists’ illusion that nature, or NS, or whatever, being blind, can go any possible direction, is in reality exactly that: an illusion. Once you have a very complex and articulate set of mechanisms, there are extreme restraints to where you can go and how. And if you are blind, your options are easily computable…

  242. 243

    JohnADavison.

    I’m tempted to put you back in the moderation list. scardova is right, you have been demeaning, and if you keep it up, you’ll be put back in moderation prison :) I agree with you on evolution being one of the central falsehoods in our modern web of falsehoods. I really do. I think you add a lot to the discussion and I don’t want to have to moderate you, but I will–and that would be a shame, because you add a nice counterbalance to the Darwinians here like Allen and the lot at Panda’s Thumb who only want to posit Darwin. Please don’t argue with me about this, just be respectful, and you’ll be fine.

  243. So we are left with brute force computational simulation of folding

    If I may offer a daring hypothesis, the search for specified complexity and platonic forms may aid in understanding.

    For example, search for “conserved” regions in DNA sequence comparisons across tax help us identify active sites. This spares us having to do a lot of computation and experimental trial-and-error.

    I suspect comparative sequencing will help us in other aspects such as understanding folding.

    Someone merely needs to step forward and try to identify if there is a linguistic patterns across taxa that can be exploitable by biotechnologists.

    The monetary rewards could be immense. :-)

    “Mike Gene” provided some more exceprts from Denton’s paper here:

    http://tinyurl.com/dmcjcb

  244. Denton argues that the characteristics of amino acid sequence comparisons across taxa are suggestive of platonic forms in proteins.

    His chapter “A Biochemical Echo of Typology” from his famous book, Evolution a Theory in Crisis is available for free (by permission) here:

    A Bio-Chemical Echo of Typology

  245. Sal:

    I’m always interesting in why people believe what they believe. In particular, I’m very interested in why people become so committed to a particular belief that they…well, not to put too fine a point on it, they become “crackpots”. And I freely admit that people like Einstein and Margulis were considered to be crackpots until their theories were borne out by empirical research.

    So, for what it’s worth, here’s a link to Pascal Boyer’s [1] “functional analysis” of crackpottery:

    http://www.cognitionandculture.....;Itemid=34

    I realize that many people on both sides of the EB/ID divide consider people on the other side of the divide to be crackpots. Ergo, it might be interesting to see if the patterns that Boyer has identified fit one’s preconceptions of what constitutes crackpottery, or not.

    Feel free to start a new thread for this, as this one seems to be winding down (and I don’t want to be accused of hijacking, especially on the subject of crackpottery ;-)

    [1] Pascal Boyer is an anthropologist, perhaps most famous for his book, Religion Explained; The Evolutionary Origins of Religious Thought ( http://books.google.com/books?.....8;resnum=4 )

  246. Mr Gpuccio,

    With respect to OOL, I fear we have eaten all of our siblings! Other systems that may have existed have all been out competed by our ancestors. I personally do not hold out much hope for finding “alien life” here on Earth in some hard to find niche.

    If we move on to the molecular events of evolution, then we have to abandon this pretty analogy of tornadoes and junkyards. Now mutation is tinkering at the edge of an island of functionality, not building an island of functionality as in OOL. I think this was the point of another commenter.

  247. Hi Allen,

    I probably won’t start another thread for a while. This last one was very time consuming.

    Being a pragmatist, as far as scientific theories go, if one can make a technological innovation with a theory, then the issues of crackpottery are quickly forgotten.

    It is for that reason I encourage exploration of “for-profit” applications of ideas within the ID community (and I don’t mean just the money from books and speaking tours).

    Let’s say for the sake of argument someone has questionable or suspect motives for believing something. If that person’s ideas result in fruitful and productive technology and science, then all the personal issues are pretty much irrelevant.

    The best example to my mind is Kepler’s attempt to unify music and planetary orbits. You as a musician can attempt to “hear” Kepler’s ideas. He actually wrote the musical notes down!

    See: Birth of a New Physics

    5. the clefts of the muscisal scale, or pitches of the system, and the kinds of harmonies, the major and the minor, are expressed by certain movements.

    6. each musical Tone or Mode is in a certain way expressed by one of the planets.
    …..
    8. four kinds of voice are expressed in the planets, soprano, alto, tenor, and bass.

    9. in order to secure this harmonic arrangement, those very planetary eccentricities which any planet has as its own, and no others, had to be set up

    You see that the hypothesis was outrageous. This was the ultimate quest to unify platonic forms in music and planetary motion. Yet this outrageous hypothesis led to one of the legendary disciplines in physics, namely, celestial mechanics.

    To quote Seneca, “there is no great genius without a tinge of insanity.”

    The means of judging the worthiness of a scientific hypothesis is via experiment and empiricism. I leave the psychoanalysis to others.

    As far as my own views, I had once accepted the mainstream hypothesis of Darwinian evolution. I accepted the mainstream hypothesis in physics. I studied under recognized names in the mainstream. So it was not by cultural means that I have my current views.

    Let us even suppose that there are physiological or professional reasons some people might accept ID more than others. This was the “Salem Hypothesis”. Some attempt at looking for physiological causes for accepting ID were made under the assumption that human physiology inclines us toward wrong inferences.

    But let us grant that humans are prone to make bad inferences, that is no surprise. To be human is to make mistakes! Pilots are deeply aware how human physiology inclines us to make wrong inferences, hence they have to have their innate tendencies trained out of the lest they crash during insturment landings!

    So how do we judge good theories? Do we judge them based on the cognitive and cultural background or brain physiology. I think the final decision comes from brute empiricism.

    As long as good operational science comes out of ID, then there will be less to complain about as far as motives or any other personal issue. I’m hoping that good operational, medically useful science will come out of these explorations. I will leave the theology and politics and psychoanalysis to others.

    How does this relates to Abel’s paper? The question of what defines function and detectable reality was touched upon in Abel’s paper. Is the percepion of design, the perception of function, the preception of “choice with intent” an artifact of our post-dictive projections or is that perception real?

    Rather than trying to resolve this philosophical question, the question should be whether fruitful science and technology emerge by assuming the appearance of design and function is real and has a place in science. That question is answerable by empiricism, the other questions are a matter more of philosophy.

    For example, the question arises whether it is appropriate to assume the cell is a computer. Whether the cell really is or is not a computer might never be decided formally. However, from a practical standpoint, perhaps it is the right assumption to make. I would expect the scientists who make that assumption will be more empirically effective than those who don’t.

    The argument from “cell as computer” is at the heart of Abel’s thesis. Having myself been trained in the science of computers, it is very difficult to accept cells with all their computational capabilities could emerge without intelligent design. So that is my belief. Is the perception that the cell is a computer an artifact of my psychology or is that perception “real”. I argue it is a moot point provided real science proceeds from that assumption. As Dembski himself stated in No Free Lunch:

    Thus, a scientist may view design and its appeal to a designer as simply a fruitful device for understanding the world, not attaching any significance to questions such as whether a theory of design is in some ultimate sense true or whether the designer actually exists.

    That expresses my pragmatism, although personally I believe an Inteligent Designer exists.

    Now, the question is whether one belief or assumption will be more effective in the application of empirical science. I have suggested that the exploration of platonic forms and genetic entropy would influence medical science. At this time, these ideas are in their infancy, but for ID to advance beyond negative criticisms of OOL and Darwinian evolution, these are the fields where the ID community might find fruitful and profitable opportunities.

  248. Nakashima:

    Other systems that may have existed have all been out competed by our ancestors.

    That’s a possibility, but you will admit, I think, that there is not a single trace of evidence that such other systems ever existed. It remains a gratuitous exertion of imagination, and nothing more. And, obviously, completely untestable and unfalsifiable (not that I want to appear a strict Popperian, which I am not!).

    If we move on to the molecular events of evolution, then we have to abandon this pretty analogy of tornadoes and junkyards. Now mutation is tinkering at the edge of an island of functionality, not building an island of functionality as in OOL. I think this was the point of another commenter.

    That’s a point often made by darwinists, and IMO a completely wrong one. When mutation is tinkering at the edge of an island of functionality, all it can do is generate small variants (the so called “microevolution”). Strange to say, microevolution isonly part of darwinian theory for which some evidence exists (and which we in ID very serenely accept).

    But the fact is: islands of functionality do exist. Many of them. Completely separate one from the other. Just think of different protein superfamilies, just to stay on solid ground. And what about different body plans in different phyla? Just to expand a little the concept.

    So, one of the two: either you accept that all islands of functionality were generated at OOL (a bizarre concept IMO, and against which there is a lot of evidence in natural history), or you have to explain how “tinkering at the edge of an island of functionality” so easily and so often becomes “building an island of functionality”. Or am I missing something?

  249. Ergo, it might be interesting to see if the patterns that Boyer has identified fit one’s preconceptions of what constitutes crackpottery, or not.

    Mathematician George Cantor was in and out of asylums. Kurt Godel was only in marginally better shape than Cantor. John Nash won the Nobel Prize for his application of math to economics, but he was also admitted to mental hospitals for schizophrenia. There are probably many others.

    If we judge their strength of their theories by their mental constitution the world would be poorer for having done so.

    So for me, the best judge is the idea itself, and a better judge is an empirical application.

    I run into all sorts of who argue for a new physics. I ask them how we can make money by creating new devices with their new physics. How soon will the device be brought to market. That usually puts an end to the conversation. :-)

  250. That’s a possibility, but you will admit, I think, that there is not a single trace of evidence that such other systems ever existed.

    There are alternative biological coding tables still in existence. From Harvard:

    Variant Codes

    The question is not whether other implementations of life are possible. Consider that there are practically an infinite number of ways of physically assembling a computer. One can use vacuum tubes, magnetic switches, transistors made of silicon,transistors made of germanium, or even DNA!

    The way to estimate probablilties is suppose that given any material you desire, how likely is it for a computer to emerge for ANY given material. Given the most favorable possible chemistry, how likely is it for computers to arise without intelligent design?

    If we accept “the cell as computer” we know the number is remote. Von Neumann estimated components for a self-replicating computer on the order of 150,000 integrated parts.

    Hoyle estimates for a fully function biological computer, the improbability is something on the order of 10^40,000.

    I would suppose most computer scientists would think at the bare minimum a computer is not easily the result of chance.

  251. Mr Gpuccio,

    The how often would appear to be every time any of us reproduces, given error rates in copying vs size of genome, and that must be part of how easily, also. But there are the rest of Dr. MacNeil’s list of meschanism’s to choose from as well.

  252. Mr Cordova,

    Dr. von Neumann’s estimate for a self replicating computer was in his original 29 state cellular automata. This has been reduced over the years, and the Wikipedia page for “Langton’s loops” lists the Perrier loop as being self reproducing and a universal Turing machine in a CA of 64 states and 158 cells.

    I think these evoloops variants do say something about how easy life is to generate. I don’t think they say anything about whether our cells are Turing machines. I have yet to hear someone argue that being a Turing machine was of differential survival value to some organism.

  253. Nakashima:

    The how often would appear to be every time any of us reproduces, given error rates in copying vs size of genome, and that must be part of how easily, also.

    I am not sure I understand what you mean here. My point was:

    “or you have to explain how “tinkering at the edge of an island of functionality” so easily and so often becomes “building an island of functionality”.”

    The point should be clear: how easily and how often refers ro the many instances of new and different protein superfamilies and families, completely dofferent one form another, the many different body plans, egineering solutions, biological machines, and so on, which continuosly emerge in the natural history of life. Those are the “islands of fucntionality” which have to be explained, and which were certainly not all present at OOL (unless one is a fan of extreme front-loading, which I am not).

    The error rates and numbers of reproduction are probabilistic resources, which can be easily accounted for, and which in no way explain those islands of functionality.

    But there are the rest of Dr. MacNeil’s list of meschanism’s to choose from as well.

    Dr. McNeill’s “mechanisms” are a complete enigma for me. I can’t see how any of them is a mechanism, in the sense of an explanatory model. Dr. McNeill just says: that can happen, but never explains why that should happen or how likely it is that it happen. Moreover, there is a strange mix of supposed randomness and supposed necessity in that list, which makes anyhing vague and, IMO, completely useless.

    Just to give an example, point 4) in the list says:

    “changes in promoter or terminator sequences (increasing or decreasing binding)”

    Well, what does that mean? What is the cause of those changes? I suppose the same as point 1) (single point mutations), or 2) (deletion and insertion (“frame shift”) mutations), or 3) (inversion and translocation mutations).

    So, what is McNeill saying in point 4)? Nothing. He is saying that the usual random variation mec hanisms that we have always known can randomly change the genome, and that the variation is not restricted to protein coding genes, but can affect regulatory sequences. And so? Who had ever though that random variation is restricted to protein coding genes? That would be really silly.

    So, if MacNeill wants to consider also the non coding regulatory parts of the genome, all he has to do is to include the other 98.5% of our genome in the equation, or at list that good part of it (including introns) which has very likely a regulatory function. And then try to compute how probabilistic resources apply to random variations of these components. Good luck to him. And I thought that 20000 protein coding genes were already a bit of a problem for darwinists…

  254. 255

    If anyone wants to know whereAlewn MacNeill’s sympathies lie, go to his weblog and examine at his evolution links. Here are some.

    The Austringer, Wesley Elsberry
    Pharungula, P.Z. Meyers
    Panda’s Thumb, Myers and Elsberry
    The Loom
    Darwinian conservatism.

    Darwinism through and through.

    Guess what is missing – Uncommon Descent.

    Get the picture?

  255. Nakashima-san,

    Thank you for the info.

    Turing machine in a CA of 64 states and 158 cells.

    The rote probability then would be 1 in

    64^158, 64^158 is a very large number!

    I don’t think they say anything about whether our cells are Turing machines. I have yet to hear someone argue that being a Turing machine was of differential survival value to some organism.

    If Turing machines are not favorable to selection, then natural selection should not be selecting in a way that creates computers.

    The Speigelman experiment suggests that selection (if it is present at all) would select for increasing simplicity rather than complexity.

    See: Spiegelman Monster

    Spiegelman introduced RNA from a simple virus (Q?) into a solution which contained the RNA replication enzyme RNA replicase from the Q? virus Q-Beta Replicase, some free nucleotides and some salts. In this environment, the RNA started to replicate. After a while, Spiegelman took some RNA and moved it to another tube with fresh solution. This process was repeated[1].

    Shorter RNA chains were able to replicate faster, so the RNA became shorter and shorter. After 74 generations, the original strand with 4,500 nucleotide bases ended up as a dwarf genome with only 218 bases.

    The reason the selection favored simplicity is for metabolic efficiency. We see the same phenomenon possibly with the blind cave fish. I speculate the same is true of other blind creatures or creatures losing features (like wingless beetles).

    It would appear that there is no reason for selection to exist which would favor the emergence or maintenance or the increase of complexity of a Turing machine.

  256. 257

    Dr. Davison, I know where you’re coming from with regard to the site administration. Certainly when I was moderated, I complained about it vociferously, as many here can attest. Yet I never let it become the major focus of my posts. That may be one reason my comments were eventually freed. In short, and just as a friendly suggestion, I’d advise writing more about things other than your opponents.

  257. If anyone wants to know whereAlewn MacNeill’s sympathies lie, go to his weblog and examine at his evolution links. Here are some.

    The Austringer, Wesley Elsberry
    Pharungula, P.Z. Meyers
    Panda’s Thumb, Myers and Elsberry
    The Loom
    Darwinian conservatism.

    Darwinism through and through.

    Guess what is missing – Uncommon Descent.

    Get the picture?

    John,

    Do you have anthing to say about Abel’s paper or the science surrounding it.

    Allen doesn’t share my views. Are you advocating I suppress viewpoints that don’t agree with mine? [that's a rhetorical question, don't answer that, just offer something of relevance to the discussion].

    This thread is not a forum for personal vendettas, complaints about UD, complaints about Allen. This thread is about David Abel’s paper and its implications.

    You’ve used up plenty of postings talking about everything but the topic at hand.

  258. By the way John, this sort of derailment by your comments doesn’t allow the ID advocates on this forum to argue their case very well when they are confronted with questions by their opponents.

    The readers want to hear our theoretical and empirical defense of our ideas rather than to listen to your complaint list. It’s a waste of time. And I’ve wasted too much comment space already trying to explain to you why your postings aren’t being helpful in this discussion. Do railings against myself or Allen MacNeill or Alan Fox help make David Abel’s case?

    You would do better to put forth arguments that support ID or the content of Abel’s paper.

    Trying to make a case about my character or that of Allen MacNeill or anyone else will do little to inspire confidence in the hypothesis of ID.

  259. 260

    Scordova has become an arrogant tyrant who rules his thread with an iron fist. This is not the first time this sort of thing has happened at Uncommon Descent and I am sure it will not be the last. Check my “Why Banishment?” thread for the documentation.

    jadavison.wordpress.com

  260. I do not respond to ad hominem attacks, character assassination, or other childish rants by megalomaniacs. However, I do respond to outright lies. In the “LINKS” section of the right-hand sidebar at The Evolution List

    http://evolutionlist.blogspot.com/

    anyone who goes there will find the following:

    LINKS: Intelligent Design

    * Design Paradigm
    * Discovery Institute
    * Evolution & Design
    * Evolution News
    * ID The Future
    * IDEA: Intelligent Design & Evolution Awareness Center
    * IntelligentDesign.org
    * The ID Report
    * Telic thoughts
    * Uncommon Descent

    Furthermore, these links have been there since I set up the blog in February 2006.

    Ergo, JohnADavison is either a liar or seriously mentally deranged and/or hallucinating, as all can verify for themselves.

  261. P.S. If anyone here would like to see more links at The Evolution List (from either side of the debate, of course), I will be happy to consider adding them. Simply go to

    http://evolutionlist.blogspot.com/

    pick a thread and insert the URL for the suggested website in the comment box, along with any information you might want me to know, and I’ll take a look.

    There is only one person’s websites that will never be added to the linkslist at The Evolution List. I leave the identity of the author of those lists as an exercise for the reader.

  262. As a courtesy to Dr. Davison, here is a link to Dr. Davison’s weblog.

    Readers interested in what Dr. Davison has to say can read it straight from the source:

    JDavison.wordpress.com

    Derailing of a discussion that UD is hosting about David Abel’s paper is an infringement on our ability to have a discussion in the way we choose.

    Discussion of David Abel’s work and that of Kirk Durston, David Chiu, Eric Anderson, and Michael Behe is being drowned out by sideshows. This is one of the few times and places that this information can be discussed on the net. Yet this discussion is at risk of being spammed into oblivion by posting whose main intent are to make complaints about me and Allen MacNeill.

    I have now provided the readers a place where they can read all about those complaints from Dr. Davison.

    Dr. Davison is invited to say something of scientific substance pertaining to David Abel’s paper. Even peripherally related topics such as platonic forms is admissible.

    Direct and lengthy postings about people’s character is unproductive in the defense or criticism of ID.

  263. Scordova has become an arrogant tyrant who rules his thread with an iron fist.

    Even granting that is true, what does that have to do with Abel’s paper?

  264. Please do not banish John A Davison from either this thread or this website. Nothing anyone could write could be more illustrative of his complete lack of respect for civility, courtesy, or the ancient traditions of the academy than the virtual lack of actual content in his numerous, pointless, increasingly maniacal rants. Everyone here should now be aware of the “quality” of his arguments and the “depth” of his character. Let his own words stand as an admonition to the rest of us.

    I will say no more about him from this point on, nor will I ever again respond to anything he posts, except for outright lies. I recommend that the rest of you do the same, regardless of which side of this debate you are on.

    There are limits to tolerance, but no limit whatsoever to stupidity.

    “Mit der Dummheit kaempfen Goetter selbst vergebens” – Friedrich von Schiller

  265. Allen,

    That was a bit harsh, but I’m trusting we will henceforth try to talk about the topics at hand.

    If you wish to allow more of JDavison’s participation here, that can be arranged.

    But as you can see, these sort of flame wars have a way to destroying discussion of the topics at hand.

    Anyway, thank you for engaging in this discussion..

    For what it’s worth, the irony is that you and Dr. Davison were among the few professors to ever teach ID related courses at the University level. You at Cornell and Dr. Davison at University of Vermont.

    Sal

  266. In comment #254 gpuccio wrote:

    Dr. McNeill’s “mechanisms” are a complete enigma for me. I can’t see how any of them is a mechanism, in the sense of an explanatory model.

    The list of mechanisms located at

    http://evolutionlist.blogspot......awman.html

    were not intended as a list of mechanisms for either evolution or natural selection. On the contrary, they were (and are) intended as a list of the mechanisms that have been shown (through repeated empirical investigation) to cause variations in phenotypes. I honestly do not think that anyone on this thread would like to argue that the mechanisms listed are not capable of causing such changes, nor that the changes they can cause can be quite significant.

    As I have pointed out repeatedly (and as many ID supporters have agreed), if ID actually happens at all (I believe that this is an open question, BTW), it will almost certainly do so via alterations in one or more of the listed mechanisms of phenotypic variation.

    Furthermore, given that much is already known about many of these mechanisms, it should be possible (and certainly will be possible in the near future) to examine the patterns of variation produced by these mechanisms using widely accepted methods of statistical analysis. The results of such analysis should lend credence to one side or the other of the EB v ID debate, and I for one would like to see the outcome to such a resolution.

    “Dr. McNeill [1] just says: that can happen, but never explains why that should happen or how likely it is that it happen.”

    That’s because it’s a list, not an encyclopedia. You can copy each of the mechanisms listed and paste them into Google or Wikipedia and get a reasonably good idea of how they work and how they relate to the overall question of phenotypic variation. I intend to do this eventually, by converting each of the listed mechanisms into a hotlink to relevant explanations. That will take time, however, as I am currently working on four books, two research projects, and a series of videos on the “Darwinian revolutions” for Cornell’s CyberTower program (while teaching my three courses at Cornell and getting ready to teach three more this summer).

    gpuccio then goes on to critique a specific mechanism from the list:

    “4) Changes in promoter or terminator sequences (increasing or decreasing binding)

    Well, what does that mean? What is the cause of those changes? I suppose the same as point 1) (single point mutations), or 2) (deletion and insertion (“frame shift”) mutations), or 3) (inversion and translocation mutations).”

    It is not the case that changes in promoter and/or terminator binding necessarily involve point mutations, deletion or insertion (“frame shift”) mutations, or inversion and/or translocation mutations. On the contrary, changes in promoter and/or terminator binding (i.e. binding by activator or inhibitor proteins or signaling molecules) can happen without any kind of genetic mutations whatsoever.

    As just one example, recent research has shown that the diet consumed by a pregnant mouse can significantly alter the expression of the genes in her offspring in utero, and that such changes are heritable among her affected offspring.

    To give a specific example, a diet high in lysine (or some other methylated amino acids) can alter the expression of an allele called “agouti” in such a way as to produce offspring with markedly different phenotypic characteristics distributed over multiple anatomical and physiological characteristics (see
    http://www.nature.com/ng/journ.....9_314.html )

    We are only just beginning to investigate the myriad ways in which alteration of gene expression (with or without concomitant genetic changes) can alter phenotypes, and how rapidly such changes can occur, and to what extent they alter phenotypes (and to be heritable via various mechanisms).

    Again, if one is interested in verifying that some kind of ID exists, investigating these kinds of mechanisms might very well bear fruit. The only way to find out would be to do the hard, slogging, tedious labor of actually doing the empirical testing. Until this has been done, arguments about what can and can’t happen are certainly premature (and in my opinion constitute a failure of both imagination and faith in the generally accepted methods of doing science).

    [1] Point of information: I am simply Allen MacNeill. I hold no doctoral level degree from any university (yet; I’m working on it). Like Charles Darwin, I’m just “Mr.” Allen MacNeill.

    Personally, I prefer to let my arguments speak for themselves, and avoid any “arguments via authority”.

  267. Sal:

    I agree that I was a little harsh in that last comment, but there are limits even to the patience of a long-time Friend. And please rest assured, I will not respond any further to anyone who attacks my character, but will to the best of my ability defend what I believe (on the basis of the evidence) to be the case.

    And please, if you think that it would help to maintain focus on the issue at hand, delete this comment. I will completely understand, and drop the issue forthwith.

    BTW, I think you have handled this whole situation as well as it could be handled under the circumstances. Hannah and I had the same kind of problem when we were collaborating in the Evolution-Design seminar. We had worked out a system by which we each moderated the comments of people on our own “side”. Sadly, I found myself moderating many more evolution supporters than she did ID supporters. I say “sadly”, because I honestly found that the EB supporters were often much more disrespectful and disruptive than the ID supporters (such as yourself).

    Maybe, if we can continue to respect the tradition of academic collegiality, we can finally get closer to an understanding of just how these fascinating and puzzling things actually happen.

    ‘Tis a consummation devoutly to be wished!

  268. if ID actually happens at all (I believe that this is an open question, BTW), it will almost certainly do so via alterations in one or more of the listed mechanisms of phenotypic variation.

    There is a spectrum of thought in the ID community:

    1. special creation
    2. front loaded variation
    3. extra terrestrial ID
    4. directed natural selection

    I personally accept some combination of the first two.

    At least two authors at UD had been sympathetic to extra-terrestrials. The others accept either front loading, special creation, directed natural selection, or simply leave the matter open.

    I think the objection is valid that direct empirical evidence of these hypothesis may not be accessible to empriical science even if true. The most that can be done is to argue a circumstantial case.

    The segment of the ID community that accept pre-programmed variation have put forward various hypotheses:

    1. Front Loaded Evolution (various like Mike Gene, possibly including Behe)
    2. Prescribed Evolution (Davison)
    3. Directed Evolution (Denton)

    I myself have argued that a very large degree of variation may be pre-programemd. See: Marsupials and Placentals: a case of front-loaded, pre-programmed, designed evolution?

    There are a segment of creationists who think there was a large amount of front loaded evolution. So the once simple camps of “special creation of fixed species” and “Darwinian evolution via common descent” has been blurred considerably now.

    Even myself, being a creationist, I would be reluctant to be too critical of mutational mechanisms. I think there are large degrees of phynotypic variation possible.

    Perhaps the most astonishing variation is that found in butterflies and moths. We basically see to radically different body plans in one creature’s lifetime!!!! You have a walking creature basically sprouting wings!

    In light of such astonishing transformations, I think caution on the part of creationists is in order. We really don’t know how fixed species may have been!

    One area where there seems to be agreement among all the ID camps is the difficulty in the origin of life. It seems this is where there is the most accessible knowledge and observation as far as actually trying to observe life spontaneously emerge.

    Hence, there is an abundance of papers and books such as those by Abel, and far less about organic evolution and supposed mechanisms.

    I’ve suggested if any succeed in being able to trigger or re-create the supposed placental/mammalian divergence (if such a thing realy happened), they would be famous forever.

  269. There are to be more twists to the question of variation and intelligent design. At least one very well-respected scientist at U-Chicago proposes a supposed third alternative: intelligent creatures re-engineering themselves.

    See: Who are the (multiple) designers? James Shapiro offers some compelling answers

    Is there only one Designer of life or are their multiple designers? Here is James Shapiro’s take: Bacteria are small but not stupid:
    Cognition, natural genetic engineering, and sociobacteriology

    Bacteria as natural genetic engineers….

    This remarkable series of observations requires us to revise basic ideas about biological information processing and recognize that even the smallest cells are sentient beings.

    In the case of engineered products we often might think of designers (plural) versus a designer (singular). It may be that some Ultimate Intelligence created the universe and (by way of extension) engineers. But even for those of us who accept that there is an Ultimate Intelligence, it is not customary to say that God made automobiles and airplanes and genetically engineered food.

    Can we find proximal sources of intelligent design of life without appealing directly to the Ultimate Intelligence? Even though I personally believe God was the Ultimate Creator of the universe and hence even the creator of the Wright Brothers, I generally still identify airplanes as the proximal intelligent design of the Wright Brothers. A similar issue may arise in identifying the Designer or designers of life on Earth

    So the issue of ID is more complex than one supposes.

    How does all this relate to OOL? Even granting that bacteria can re-engineer themselves and that there are mutations capable of inducing body plan evolution, how much ID would be needed for the first life?

    Darwin didn’t even really touch upon that question, but OOL is one the focus of ID proponents of all stripes.

    Darwin, perhaps under some duress, wrote in the 6th edition:

    the first creature, the progenitor of innumerable extinct and living descendants, was created

    Charles Darwin

    To be fair, that quote may not represent what Darwin really believed. However, the focus on the question of OOL is whether the first life had to be created.

    My understanding is that Abel’s partner, Jack Trevors (an atheist) simply leaves the question open. Yockey (no friend of ID) thinks the answer to OOL lies outside empirical science. I would speculate Abel’s views are similar to Trevors and Yockey, he is reluctant to commit to ideas that are formally un-provable. Myself, I’m willing to accept a circumstantial inference to intelligent design (even if formally unprovable), but that is just me, and that is not necessarily science formally defined.

  270. As an FYI:

    One does not need DNA changes in order to facilitate radical changes in body plans. The following link has pictures of two body plans created by one set of DNA. See the photo of “how one genome can create two proteomes” here: Michael Lynch: Darwinism is a caricature of evolutionary biology.

    I think creationists are too quick to rule out macro-evolution. First of all theology is not science, and secondly, I’m not so sure, even granting the “Genesis kinds” that all forms of macro evolution are ruled out.

    Here is a dyed-in-the wool Young Earth Creationist by the name of Chris Ashcraft supporting at least the some of the mechanisms of variation which Allen listed:

    Evoluion: God’s Greatest Creation

    and
    What’s Driving Evolution Mutation or Genetic Recombination

    Allen lists these as:

    Genetic Recombination

    28) the exchange of non-identical genetic material between two or more individuals (i.e. sex)

    29) lateral gene transfer via plasmids and episomes (especially in prokaryotes)

    30) crossing-over (reciprocal and non-reciprocal) between sister chromatids in meiosis

    31) crossing-over (non-reciprocal) between sister chromatids in mitosis

    32) Mendelian independent assortment during meiosis

    33) hybridization

    Chis Ashcraft writes:

    Genetic recombination is not random. Offspring survival following genetic recombination is just short of 100% among all sexually reproducing organism substantiating these reaction as highly controlled and specific. We can also not predict the ability of these reactions to modify an organism.

    This sort of variation is circumstantially evidence of ID, but not direct. However, if Ashcraft is correct that the variation is not “random with respect to fitness” than the variation might not be the sort that Darwin envisioned. Allen would be in a better position to comment on this than I however.

    Finally, to throw more monkey wrenches into the discussion, DNA does not even need to change to create extreme phenotypic variation. The book Developmental Plasticity lists the astonishing changes accomplished independent of DNA.

    All these considerations to me suggest why the question of OOL is so central to ID. If even ID proponents and some creationists can accept some macro evolution, then where and when is the actual ID?. I would argue that the question of OOL is the best place to argue a circumstantial case for ID, at least for now.

    I don’t think the ID issues are quite so clean cut for macro-evolution.

  271. Allen,

    I prefer John Davison refrain from his complaints too but he does have some interesting things to say in some of his papers. One of them is the Blind Alley thesis that evolution has essentially stopped.

    http://www.uncommondescent.com.....ind-alley/

    Maybe when things have quieted down, this seem like an interesting topic to pursue. It is loaded with facts and reasoning. And it flows from the same assessment you have made that Darwinian evolution is dead as a theory. John thinks a different mechanism is responsible than what you have espoused. It would be interesting to compare the two.

  272. 273

    Get this folks. Scordova has asked MacNeill for MacNeill’s permission before Scordova intends to let Davison continue here. Is it any wonder that have described them as the dynamic duo?

    It is hard to believe isn’t it?

    In the meantime, Scordova has deleted the vast majority of my comments which were directed not at individuals but at the Darwinian fairy tale. It is not my fault that MacNeill is a devout Darwinian and if you don’t believe me just visit his weblog and see for yourself. And while you are there check the links he lists on the side bar. I already sent that here but it was promptly deleted. You will find it with every other message “blogczar Scordova” has deleted. Scordova makes DaveScot look like Shirley Temple. Now delete this one too Sal.

  273. MacNeill is a devout Darwinian

    and

    Scordova makes DaveScot look like Shirley Temple.

    But even if true, John, what relevance has this to the questions David Abel has raised? Your objections here are derailing an otherwise productive discussion.

    Not to mention you said in Comment 222:

    You now have my permission to continue deleting every new message I present without a word of explanation.

    So perhaps I’m preventing you from making intemperate remarks that you’ll later regret.

    I point the readers to your weblog:
    JADavison.wordpress.com.

    I see you posted a thread, and then let loose with about 500 responses to something you said. Isn’t that monologue a bit monotonous John?

    In any case if you can relate Shirley Temple, DaveScot, myself to Abel’s paper, your comments are welcome. The only thing slowing me down from exercising the permission to delete your comments (permission that you granted), is the fact Allen would like others to hear what you have to say.

    So please stay on topic. Whether Allen MacNeill or I are vile scoundrels is irrelevant to the question of ID.

    See: Scoundrel? Scoundrel…I like the sound of that, and you’ll understand why your objections to people’s actions and character are largly irrelevant to the topic of ID.

  274. 275

    My quarrel is with you shabby tactics .I don’t give a fig about Abel or the subject of this thread. I think you should be deprived of you position as “author” because you have abused that position by the manner you have allied yoyrself with a devout Darwinian and treated this scientist with the utmost contempt. Got that Sal? Write that down!

  275. 276

    So much for my suggestion above.

  276. In #270 Sal wrote:

    “Yockey (no friend of ID) thinks the answer to OOL lies outside empirical science.”

    Me, too. I’ve commented several times that I don’t think that the OOL is actually a question of evolutionary biology. After all, “biology” requires life as a pre-requisite, right? And Darwin never even hinted at a mechanism (“warm, little ponds” are not a mechanism, they’re just a setting; like the difference between a plot and a backstory).

    Even if it is possible to “create” life in a laboratory, there is absolutely no guarantee that that is how it happened in nature.

    Like the old joke says,

    “Very interesting, but that’s not the way I did it” – God ;-)

  277. People who don’t care about the topics of threads should go away and not come back. Staying here to simply fling invective is pointless, demeaning, and discourteous.

  278. My quarrel is with you shabby tactics.

    That’s fine, John, but this thread isn’t the place to quarrel about my behavior. This thread is about Abel’s paper.

    I don’t give a fig about Abel or the subject of this thread

    That’s obvious John, so the question is why then comment about me on a thread about Abel’s paper?

    Wow, after 275 posts, this is your first mention of the Abel.

    you have abused that position by the manner you have allied yoyrself with a devout Darwinian

    I consider Allen my friend. His views about ID or anything else do not automatically disqualify him from being my friend.

    and treated this scientist with the utmost contempt.

    Perhaps the unkind thing to do is to let your intemperate remarks continue to be posted for all to see.

  279. For the reader’s benefit, Will Provine at Cornell was Allen MacNeil’s good friend and mentor.

    Phil Johnson has been widely viewed as the father of modern ID. In that regard, some of my intellectual heritage traces to Phil Johnson.

    Both Phil Johnson and Will Provine have debated each other. They refer to each other as good friends (even in their video taped debates).

    I see no reason that Allen and I have to treat each other as sworn enemies in light of the example that Phil Johnson and Will Provine have given us.

  280. 281

    “I’ve commented several times that I don’t think that the OOL is actually a question of evolutionary biology. After all, “biology” requires life as a pre-requisite, right?”

    How convenient, and ridiculous.

    It may be more ridiculous than convenient, but then again, it may be more convenient than ridiculous. On that point we can be certain; it’s a very, very fine line.

    In any case, the toner must have been out on the mimeograph machine. I am almost certain I’ve come across an evolutionary biologist who claimed that chance and necessity did it. Hell, perhaps all of them do. Has anyone ever done a poll? Does biology require biology, so materialist ideologues don’t have to address the issue?

  281. I’ve commented several times that I don’t think that the OOL is actually a question of evolutionary biology. After all, “biology” requires life as a pre-requisite, right?”

    How convenient, and ridiculous.

    But to be fair, the separation of Darwinian Evolution and OOL was suggested by Abel himself in his quotation of Chang

    ‘Chemical evolution’ should not be confused with Darwinian evolution with its requirements for reproduction, mutation and natural selection. These did not occur before the development of the first living organism, and so chemical evolution and Darwinian evolution are quite different processes.

    David Abel quoting Chang
    page 267

  282. The question is “why Abel would support the distinction between OOL (chemical evolution) and Darwinian evolution?”

    It appears the distinction actually argues against naturalistic evolution of life. He tries to argue that natural selection cannot be appealed to as a mechanism in OOL, therefore, one is only left with chance and necessity.

    The task of arguing against naturalistic OOL is easier if one invokes only chance and necessity and is not burdened with issues of natural selection.

  283. Mr Cordova,

    I think if you go to Sayama-sensei’s Evoloops site, you can see some movies of evoloop OOL and evolution of new species.

    As you noted, if the only selection pressure is raw metabolism, things get simpler instead of more complicated. I think the same thing occurs in Tierra simulations when parasites appear, and get smaller over time. So to me an interesting question is – have there been other necessary pressures (or environmental context) operating on Earth to drive complexity higher?

    I’m sorry I can’t participate more fully in the conversation. It is like being at a party where there are many loud conversations going on at once.

  284. As you noted, if the only selection pressure is raw metabolism, things get simpler instead of more complicated.

    Actually selection pressure for raw metabolism might only have to be stronger, not necessarily the only pressure for simplicity to be the final outcome.

    It follows from Fisher’s Fundamental Theorem of Natural selection that diversity will be reduced. For example, let us say we have two favorable traits:

    Trait A: Intelligence
    Trait B: Speed

    It is possible that a faster creature will out-compete an intelligent creature and thus an otherwise good trait(intelligence) is sacrificed in favor of another good trait (speed). This is called interference selection.

    Ideally the traits will blend rather than one being snuffed out, but this happens only if the selection pressures are comparable and/or sufficiently weak. The irony is that strong selection pressure might actually damage the ability of natural selection to construct something!

    So if pressure for metabolism is sufficiently stronger over other pressures, this pressure could wipe out the favorable benefit of more complex traits. The case of cavefish is an example. The ability to see would generally be regarded as useful, but selection for metabolism thwarts maintenance of an otherwise useful trait. My personal speculation is that selection may do good but it also does a lot of harm to the human genome (one example is sickle cell anemia).

    As far as whether selection operated in the past to create complexity is an open question. We could consider whether selection is increasing complexity in the present day.

    Are their new proteins? Well, maybe single-nucleotide novelties such as Nylonase. Beyond such small nucleotide changes, I personally believe that the number of unique proteins is actually decreasing quite rapidly especially because of extinction.

    It would appear that nature is under no obligation to favor the maintenance of complexity, it does not prevent man, natural disasters, or any other agency from creating extinction.

    Further, these extinctions for the most part appear non-Darwinian. The idea is that the less fit creatures die, but it appears that extinction for the most part is more a product of bad luck than bad genes. I pointed out that there is a general misconception that the fittest survive. See: Gambler’s ruin is Darwin’s Ruin.

    If we had the power to do so, I suppose we could catalogue all the existing proteins and estimate whether the number is decreasing or increasing. I speculate the number is rapidly decreasing. I don’t know how we might possible test the hypothesis through sampling rather than being exhuasive, but that would be a worthy exploration.

    I have a personal interest in seeing empirical exploration of the hypothesis of Genetic Entropy by one of the world’s top Genetic Engineers from Cornell. The hypothesis might be empirically testable as DNA sequencing technogies become cheaper (such as Solexa and Illumina technologies).

    If the Genetic Entropy is correct, and if the number of proteins in the world is rapidly decreasing (such as must be the case in the Amazon rain forrest), then that would lend support to Abel’s hypothesis that it is improbable for new proteins to evolve.

  285. Nakashima-san,

    I forgot to express my thanks for you pointing this out:

    I think if you go to Sayama-sensei’s Evoloops site, you can see some movies of evoloop OOL and evolution of new species.

    Thank you!

  286. 287

    http://jadavison.wordpress.com...../#comments

    # 475.

    There is no point in trying to post it here because it will be deleted by blogczar Sal.

  287. 288

    For some reason my “Why banishment?” thread cannot be read. I wonder why. Naturally, I suspect chicanery but that won’t surprise anyone I am sure.

  288. 289

    Incidentally folks, creative evolution is finished with not a new genus in two million years and probably not a new verifiable species in historical times. Extinction is all that remains.

    “A past evolution is undeniable, a present evolution undemonstrable.”
    John A. Davison

  289. Sal in #285:

    Your discussion of Fisher’s fundamental theorem of natural selection highlights one of the most important ways in which Fisher’s assumptions do not model reality and are therefore of limited value for analyzing how evolution happens in real poulations. For Fisher’s theorem to work, one must assume that there is no linkage between alleles at all (this is also necessary for Wright’s original theory of genetic drift). That is, alleles undergoing positive selection (i.e. increasing in frequency) are not linked in chromosomes with alleles undergoing neutral or negative selection.

    However, we know this is contrary to the underlying biology of chromosomes and DNA. That is, genes are linked together, and so the possibility for genetic “hitchhiking” is very large. If two different genes are located on the same chromosome (and especially if there is no chiasma/recombinatory “hot spot” in between them), they will be inherited together, regardless of the selection acting against each of them separately. This means that linkage groups (i.e. chromosomes) should be considered as whole units, not separately, but the latter is the only way that genetic evolution can be modeled using Fisher’s mathematical formalisms.

    Furthermore, and contrary to one of the basic premises of the “modern synthesis”, selection does not (indeed, cannot) act against single alleles, or even single chromosomes. Selection (or, to be more precise, the prerequisite mechanisms of selection – variation, inheritance, and fecundity) acts at the level of individual phenotypes, and many alleles (especially selectively neutral alleles) “go along for the ride”.

    This is why Stephen Jay Gould’s view of biological evolution is in many ways superior to the one at the heart of the “modern synthesis”, and why evolutionary theory as a whole is slowly (and sometimes painfully) moving closer to Gould’s model of evolution.

  290. 291

    And where are the responses to the challeneges I presented on this thread to the Darwinain hoax? Where are the new species with their known ancestors? Where is there evidence that any creature now extant is capable of leaving ancestors fundamentaly different from itself? Where is there any evidence for the Darwiniann fairy tale? I will tell you where – nowhere, that’s where. It was never anything but a pipe dream.

    “Silence is golden.”
    Thomas Carlyle

  291. One might also ask why Gould’s model of evolution appears to be closer to reality than the one at the heart of the “modern synthesis”. One answer would be that, as a paleontologist rather than a “bean counter” (Mayr’s term for theoretical population geneticists), Gould was a committed empiricist. That is, he based his model on actual physical evidence, rather than abstract mathematical models. It is, of course, impossible to do theoretical population genetics using fossils (G. G. Simpson notwithstanding), and so Gould and other paleontologists (such as Eldredge, Stanley, and Vrba) were and are not “seduced by the dark side of the Force (of theoretical modeling)”.

    The same is true for field ecologists (like my good friend Harry Greene) and other naturalists, who (like paleontologists) are constrained by the actual physical stuff they study to ground their models in reality.

  292. Speaking of the OOL, check this out:

    http://arxiv.org/abs/0904.0402

  293. Sal in #285:

    Your discussion of Fisher’s fundamental theorem of natural selection highlights one of the most important ways in which Fisher’s assumptions do not model reality and are therefore of limited value for analyzing how evolution happens in real poulations. For Fisher’s theorem to work, one must assume that there is no linkage between alleles at all (this is also necessary for Wright’s original theory of genetic drift). That is, alleles undergoing positive selection (i.e. increasing in frequency) are not linked in chromosomes with alleles undergoing neutral or negative selection.

    Allen,

    Thank you. I was not aware of that. I’m indebted to you for the correction.

    Sal

  294. Allen,

    In the cell’s cytoplasm there are amino acids in close proximity.

    Yet unless they are ferried to a ribosome they do not spontaneously form polypeptide chains.

    If they do not form chains when being in such close proximity, what makes you think that any OoL scenario can account for polypeptide chains forming without a ribosome?

  295. Mr. Scordova about John’s blog:

    I see you posted a thread, and then let loose with about 500 responses to something you said. Isn’t that monologue a bit monotonous John?

    It depends. I find the discussion here more monotonous. Secondly – John’s critism of neodarwinism and their proponents is more acute and precise than here.
    Thirdly – John has given me a lot of space to inform others about great work done by such prominent antidarwinian scientists like Heikertinger, Adolf Portman, Zdenek Neubauer, Wilhelm Troll or Jakob von Uexkull. Unless you can read German or Czech you will miss the whole tradition of anti-selectionists thinking. Darwinists pretend those scientists do not exist.

    And last but not at least – this blog is much more slower and it is a real torture to write here a message. It takes a lot of time.

    John’s blog is not as that produced by doctor Myers – and him alike – who releases his void neodarwinian articles every 2 hours (unless he sleeps).

  296. Joseph wrote:

    In the cell’s cytoplasm there are amino acids in close proximity.

    Yet unless they are ferried to a ribosome they do not spontaneously form polypeptide chains.

    And that is a good thing, otherwise we would be dead!

    Sal

  297. What is the goal of the OOL community? Let me give my take.

    The OOL community is trying to find ways to demonstrate that the past conditions which made life were not so extra-ordinary. That is their real goal, imho.

    If OOL researchers synthesize life in the lab, the goal is not to say that the way they did is how life emerged, but rather to show that life is feasible with non-extraordinary conditions.

    But everything we know empirically and theoretically suggests that the emergence of life was an extraordinary event.

    The problem for the OOL community is not that they can’t recreate in exact detail the conditions of the early earth, but that they can’t create any thing truly resembling life without invoking extraordinary conditions, conditions so remote they are indistinguishable from statistical miracles.

  298. —-John A Davison: “And where are the responses to the challeneges I presented on this thread to the Darwinain hoax? Where are the new species with their known ancestors? Where is there evidence that any creature now extant is capable of leaving ancestors fundamentaly different from itself?”

    I have noticed in some of my own debates that Darwinists tend to avoid the really hard questions by reframing the issue and laboring incessantly over the less challenging questions.

    Under the circumstances, I recommend two standards for moderation and deletion, each designed to balance the other:

    [A] Remove from the thread anyone who [repeatedly] practices the sin of verbal abuse.

    [B] Remove from the thread anyone who [repeatedly] tempts the verbal abusers to sin by refusing to answer their questions.

  299. 300

    I see I finally have a supporter here in the person of VMartin. Thank you Martin. I am surprised they let you speak.

    “The applause of a single human being is of great consequence.”
    Dr. Samuel Johnson

    It is not just the scientists you list that the Darwinians have pretended do not exist. They have traditionally pretended that they they have NO critics whatsoever, that anyone who might question the “one true faith” must be deluded or a Bible-banging fundamentalist or an ignorant Philistine or maybe clinically insane. I know that many Darwinian fanatics are on record that I am “crazy as a loon.” Of course they are all anonymous cowards except for Paul Zachary Myers. Visit his “Dungeon” for verification.

    The truth is that there has been a steady stream of great minds that exposed the Darwinian fable, a stream which began with Adam Sedgwick, Darwin’s geology professor and has continued unabated to this very day, a veritable torrent of some of the greatest biologists of the post Darwinian era, not one of whom was either a professed atheist or a religious fanatic.

    As for Darwinism, the most ridiculous suggestion in the history of human thought, let me quote Sir Winston Churchill on that subject -

    “Never in the history of human confict have so many owed so little to so many.”

    As for my own feelings towards those who still embrace the Darwinian fairy tale, I will let Elizabeth Barrett Browning speak on my behalf -

    “How do I loathe thee? Let me count the ways.”

    I realize that “sounds a little harsh” so I will ameliorate it a little with the appropriate words of Christ our Savior -

    “Forgive them Father for they know not what they do.”

    It really isn’t their fault as they were “born that way.”

    “EVERYTHING is determined …by forces over which we have no control.”
    Albert Einstein, my emphasis.

  300. In #295 joseph wrote:

    “Yet unless [amino acids] are ferried to a ribosome they do not spontaneously form polypeptide chains.”

    I’ve taken several biochemistry courses,and read (and in one case wrote a detailed review of) biochemistry textbooks, and I’ve never seen anything on this subject either way. Do you have a reference that confirms this assertion? I am not aware of any, and consider the possibility that amino acids might indeed polymerize in cells without the participation of ribosomes to be an intriguing, but as yet unstudied possibility.

    BTW, it is not sufficient to simply assert that it makes sense that this would not happen. Please provide a reference that indicates that there is empirical evidence that it does not happen.

  301. In #298 Sal wrote:

    “…everything we know empirically and theoretically suggests that the emergence of life was an extraordinary event.”

    Actually, as far as the empirical claim goes, we know nothing of the kind. We only know of one planet on which life has originated. Until (and only if) we can survey other planets similar to Earth, can this question be answered empirically.

    Furthermore, I am not aware of any systematic attempts to determine if life has originated only once or multiple times on Earth. Indeed, I don’t think anyone has systematically laid out exactly how one would go about validating or falsifying this hypothesis. Where would one look, and how. Most importantly, how would one distinguish newly originated living things from those already here?

    Lamarck asserted that life has been continuously originating in various forms over the ages, but this was an assertion, not an empirical discovery.

    And, as should be clear from my skepticism of the utility of the mathematical models at the core of the “modern evolutionary synthesis”, I give very little credence to theoretical models on either side of the OOL debate.

  302. As for the supposed impossibility of spontaneous polymerization of amino acids, see:

    http://www.springerlink.com/co.....836w7v051/

    Rather than invoking “extraordinary” conditions, the researchers in this case have shown that simple adiabatic cooling (“quenching”) of amino acid mixtures in conditions normally found in geysers and hot springs can, indeed, “…oligomerization of glycine up to decamer (Gly10)…”

    So, spontaneous polymerization of amino acids is neither “impossible” nor “unlikely”. It has, in fact, been empirically demonstrated under conditions closely mimicking those found in nature.

    Does this mean that I now believe that such experiments will somehow “prove” current theories of abiogenesis? Nope; it only means that the hypothesis that abiogenesis is both theoretically and practically impossible have been at least partially falsified.

  303. If anyone here does not like something somebody else wrote, they can easily choose not to read it. Alternatively, they can choose to read it, but not believe it. Personally, I think it is very educational to people on both sides of the issue to see certain individuals attempting make arguments via unsupported assertions, ad hominem attacks, and verbal ridicule and abuse. Under such circumstances, those individuals have very clearly demonstrated that:

    • they do not respect the intelligence nor the judgment of the rest of us on this list;

    • they do not actually have any arguments to make that are supported by evidence;

    • they have neither the creativity nor the courage to actually engage in an intellectual debate;

    • they believe that insults and invective, rather than rational arguments, are the basis for deciding scientific issues; and therefore

    • they are to be simultaneously pitied and ignored by compassionate, rational people.

  304. I have responded to Stephen’s post at 299 here because that is where he and I have been discussing things.

  305. The OOL community is trying to find ways to demonstrate that the past conditions which made life were not so extra-ordinary. That is their real goal, imho.

    They are motivated by religion it seems.

  306. Personally, I think it is very educational to people on both sides of the issue to see certain individuals attempting make arguments via unsupported assertions, ad hominem attacks, and verbal ridicule and abuse. Under such circumstances, those individuals have very clearly demonstrated that:

    • they do not respect the intelligence nor the judgment of the rest of us on this list;

    • they do not actually have any arguments to make that are supported by evidence;

    • they have neither the creativity nor the courage to actually engage in an intellectual debate;

    • they believe that insults and invective, rather than rational arguments, are the basis for deciding scientific issues; and therefore

    • they are to be simultaneously pitied and ignored by compassionate, rational people.

    Agreed Allen. With respect to rude comments from ID proponents directed your way, especially with respect to your scientific questions, it does not reflect well for my side of the aisle. In such case they are just expressing aggravation rather than dealing with scientific questions.

    In my judgement, the challenges you put forward are the variety that any student of science would have, thus your questions are worthy of reasoned answers rather than ridicule or glib dismissals.

  307. StephenB:

    —-John A Davison: “And where are the responses to the challeneges I presented on this thread to the Darwinain hoax? Where are the new species with their known ancestors? Where is there evidence that any creature now extant is capable of leaving ancestors fundamentaly different from itself?”

    I have noticed in some of my own debates that Darwinists tend to avoid the really hard questions by reframing the issue and laboring incessantly over the less challenging questions.

    This thread isn’t about Davison’s questions about Darwinism, it is about David Abel’s papers which deals with OOL. The distinction is relativley important.

    The topic of the thread restricts the sort of questions that are generally admissible. Davison’s questions, by his own admission, have little relevance to Abel’s paper, the topic at hand.

    Davison’s derailments haven’t strengthened the ID case one iota. Rather his attitude has expressed disdain for the work of the 5 fellow scientists mentioned above, 4 of whom are ID proponents.

    This is Davison’s attitude toward the work of the above mentioned individuals:

    I don’t give a fig about Abel or the subject of this thread

    Rather than trying to deal with objections which people on the fence might want answered, I saw ridicule and irrelevancies spamming this thread. I hardly consider that a defense of ID. It’s more of the bluster appropriate for a pep rally, not the sort of thing that really inspires empirical and theoretical confidence.

    Now, for the ID proponents here, Allen has put forward a legitimate objection about amino acid polymerization. Any takers?

    How about JohnADavison, scientist, taking a crack at a legitimate scientific question. I’m a grad student in science. I’d like to hear a reasoned, rational, scientific response to Allen’s objection about amino acid polymerization.

    And, no, I won’t find arguments about Allen’s characters or his motivations convincing.

    StephenB suggested:

    [B] Remove from the thread anyone who [repeatedly] tempts the verbal abusers to sin by refusing to answer their questions.

    Ok StephenB or JohnADavison, how about a response to Allen’s objections about polymerization. I think I have an answer, but how about you provide one rather than me having to shoulder the burden of most of the techincal questions put forward so far.

    I might be tempted then, whenever techinical questions are put forward by:

    Nakashima-san
    Sal Gal:
    Skeech Plus:
    Allen MacNeill:

    to keep referring them to you. If you can’t answer them, it hurts our side (the ID side), and by your standard, responses by you that don’t answer important questions should be removed.

  308. Scordova: In all honesty, after having read the entire thread, I repent. I missed th context entirely.

    Indeed, this is the first time I have ever started late in a thread without paying close attention to everything which had preceeded or even bothered to focus on the theme which has been presented. I allowed my compassion for JAD to get the best of me without zeroing in on the subject matter in context.

    It is clear have done you a injustice, and I am ashamed of my thoughtless eruption. It will not happen again—-ever! Whatever loss of credibility that comes my way as a result of this is all but due justice.
    I have been doing to many lighting round postings and I definitely need to take some time off. I hope between now and the time I come back you can overlook my mistake and pretend it never happened.

  309. 310

    The assertion about polymerization is utter nonsense. Amino acids don’t have to be “ferried” to ribosomes to produce polymers. If you take a bunch of dry amino acids and just heat them they will spontaneously polymerize through dehydration synthesis to form what Sidney Fox called “proteinoids.” The interesting thing about these proteinoids is that they have some enzyme activity. Thus it is wrong to claim that amino acids have to be “ferried” to ribosomes to become proteins. This has been known for fifty years. Of course it has absolutely nothing to do with evolution at all. It is just another manifestation of the well known property that most chemical reactions are reversible. Dehydration synthesis of proteinoids is the reverse of protein hydrolysis driven in that direction by the application of dry heat. In principle any chemical reaction can be reversed by applying a product of the reaction.

    This has nothing to do with the question of how either proteins or ribosomes first appeared. It is my opinion that all intracellular organelles appeared first in their present configuration with no ancestral transitional forms preceeding them. I tend to reject Lynn Margulis’ endosymbiotic hypothesis because it has not been demonstrated experimentally. Mitochondria are not modified bacteria and flagella are not flagellate protozoa that somehow got trapped inside an aflagellate ancestor. The Prescribed Evolutionary Hypothesis does not require such an assumption and as far as I know there is no evidence for it anyway.

    I hope this helps.

  310. My apologies to you StephenB for being a little snippy.

    I have found on technical matters the critics are often scientists who have gone through school, have taught classes, and are extremely versant in science. At least two outspoken critics were my professors in school (Robert Ehrlich and James Trefil at GMU), Ehlrich has even written books critical of ID. See: Eight Preposterous Propositions. You can guess what one of those eight propositions is!

    So I don’t hold all critics of ID with so much contempt that I dismiss them. In fact, I don’t hesitate to say it was an honor to learn from them. Any ID sympathetic student of science will deal with these issues since the majority of good science is still taught in secular universities generally hostile to ID.

    The objections that Allen and others put forward are the sort of things an ID proponent should be able to answer on scientific grounds.

  311. The assertion about polymerization is utter nonsense. Amino acids don’t have to be “ferried” to ribosomes to produce polymers. If you take a bunch of dry amino acids and just heat them they will spontaneously polymerize through dehydration synthesis to form what Sidney Fox called “proteinoids.” The interesting thing about these proteinoids is that they have some enzyme activity. Thus it is wrong to claim that amino acids have to be “ferried” to ribosomes to become proteins. This has been known for fifty years.

    Thank you John, I will offer my responses subsequently.

  312. 313

    You know what happens to a flagellate protozoan when it gets trapped inside an Amoeba? It gets digested! So much for the Margulis hypothesis!

    I love it so!

  313. Scordova, thanks for being so gracious. I will try to get out of the way so as not to be any further distraction. Originally, I had thought that Allen was not responding to JAD and that was what prompted my premature post. Obviously, things are not as simple as all that. It was in no way a commentary on your moderation policy or your sense of fairness, which is, in my judgment, as good as it gets.

    In any case, it appears that John in now getting in the game, which is what I was hoping for.

    Meanwhile, I will take time out to read the paper thoroughly, which is what I should have done in the first place.

    Thanks again.

  314. Allen MacNeill:

    I’ve taken several biochemistry courses,and read (and in one case wrote a detailed review of) biochemistry textbooks, and I’ve never seen anything on this subject either way. Do you have a reference that confirms this assertion?

    and

    Allen MacNeill:

    As for the supposed impossibility of spontaneous polymerization of amino acids, see:

    http://www.springerlink.com/co…..836w7v051/

    Rather than invoking “extraordinary” conditions, the researchers in this case have shown that simple adiabatic cooling (”quenching”) of amino acid mixtures in conditions normally found in geysers and hot springs can, indeed, “…oligomerization of glycine up to decamer (Gly10)…”

    So, spontaneous polymerization of amino acids is neither “impossible” nor “unlikely”. It has, in fact, been empirically demonstrated under conditions closely mimicking those found in nature.

    and

    John Davison:

    Amino acids don’t have to be “ferried” to ribosomes to produce polymers. If you take a bunch of dry amino acids and just heat them they will spontaneously polymerize through dehydration synthesis to form what Sidney Fox called “proteinoids.” The interesting thing about these proteinoids is that they have some enzyme activity. Thus it is wrong to claim that amino acids have to be “ferried” to ribosomes to become proteins. This has been known for fifty years.

    There are subtleties here that bears some elaboration.

    The problem is that it is highly undesirable for the polymerization to be:

    1. polymerization of racemic (non-homochiral) amino acids
    2. polymerization with non alpha-peptide bonds

    Functional proteins such as those found in life are prevented from formation if the polymerizations involve the above characteristics.

    Biotic polymerizations inolve the peptid bond. From Wiki about Peptide Bonds:

    A peptide bond can be broken by amide hydrolysis (the adding of water). The peptide bonds in proteins are metastable, meaning that in the presence of water they will break spontaneously, releasing about 10 kJ/mol of free energy, but this process is extremely slow. In living organisms, the process is facilitated by enzymes. Living organisms also employ enzymes to form peptide bonds; this process requires free energy.

    Thus free energy is required to fuse the bond together, and on top of that it is only metastable.

    Metastability:

    Metastability is a general scientific concept which describes states of delicate equilibrium. A system is in a metastable state when it is in equilibrium (not changing with time) but is susceptible to fall into lower-energy states with only slight interaction.

    The issue with Fox’s work and others is as follows:

    1. High heat is need for polymerization, but high heat causes racimization. Futumura’s article said:

    Once aqueous solutions of monomers were treated at high temperature
    and pressure,

    This will cause racemization, and it did so in Fox’s work (and fox started off with homochiral soy bean derivatives).

    2. Further, thermal fusing of peptide bonds does not result generally in alpha-peptide bonds.

    But the problem with pre-biotic soups is that water dissociates peptide bonds. In such case, time is the enemy. It is well known, Fox’s protocells easily dissolved!

    The reason free roaming amino acids in the body don’t easily bond into existing proteins is the temperature is too low for heat polymerization. Formation of the peptide bond is an endothermic reaction. For that reason, Fox had to raise temperatures to very high levels (that would probably kill most life) to induce polymerization.

    Also, Morowitz, a professor at Yale and GMU was among the first to point out that thermodynamically closed systems will not spontaneously polymerize amino acids because the bond formation is endothermic.

    These ideas were laid out in the 1984 book widely regarded as the beginning of the modern ID movment. The book was Mystery of Life’s Origin.

    Here are some exceprts:

    Mystery of Life’s Orign page 169:

    Folsome points out that Fox used 15 grams total weight of amino acids in 375 ml of artificial seawater…Thus Fox’s synthesis uses a molar ratio of amino acids to salts that is “10 million times less in the geologically plausible world”

    Stanley Miller and Orgel write of proteinoids:

    The degree of nonrandomness in thermal polypeptides [Fox's proteinoids] thus far demonstrated is minute compared to nonrandomness of proteins. It is deceptive, then, to suggest that thermal polypeptides are similar to proteins in their nonrandomness.

    Stanley Miller and Leslie Orgel don’t have kind words for Fox’s work, neither did Fox’s rival Folsome.

    The central question is where did all those pure, dry, concentrated, and optically active amino acids come from in the real abiological world.

    Fox got his pure concentrated amino acids from the chemical manufacturers who in turn got them from soybeans.

    Then Oparin joins in:

    Fox’s microspheres, since they are obtained thermally, do not present very promising results from this view. Their structure is static. This…creates difficulties when it comes to converting them into dynamic systems which could be used for modeling the evoluton of metabolism.

    Miller and Orgel write:

    It seems unlikely…that the division of microspheres is related to the orgin of cell division

    Temussi refers to protenoids as

    the preferential formation of unnatural peptide bonds.

    That means Fox’s proteinoids aren’t proteins, not even close. They don’t have exclusively alpha bonds and are not homo-chiral. What little catalytic abilities exist are from the amino acids themselves, not any coordinated action like a real enzyme.

    Thaxton writes:

    Actually, microspheres posess only outward likenesses and nothing of the inward structure and function of a true cell. They contain no information content, no energy utilizing system, no enzymes, no nucleic acid, no genetic code, and no replication system. They contain only a mixture of polymers and amino acides, the so-called proteinoids.

    People make microspheres today (like Fox’s protocells) for drug delivery.

    It seems from literature that a protocell’s tendency to dissolve is actually being exploited:

    http://www.siu.edu/~protocell/ACS.htm

    We have developed a novel drug delivery system composed of thermally condensed amino acids (proteinoids). These proteinoids have unusual properties in that they undergo a phase transition that is pH determined. For the oral delivery of therapeutic compounds we have developed a family of proteinoids that at acidic pH values manifest themselves as hollow microspheres ranging in size from 0.3 to 10 microns. At neutral or basic pH values, the microspheres spontaneously dissolve.

    This reinforces the view that water tends to dissociate proteinoids. So themrally formed amino acid polymers are vulnerable to dissoaciation. Time is the enemy.

  315. JohnADavison– good answer at 310!

  316. 317

    Thanks.

    I have no quarrel with Scordova’s reaction at all. I am not a Darwinian and I don’t believe that life ever originated spontaneously. That is why I have been puzzled by the shsbby way I have been treated here by both MacNeill and Scordova.

    I do not “debate” and I don’t even like to discuss very much. My position on evolutionary matters is well known. My Providence, if I may so bold, is to confront the Darwinian fairy tale wherever I am permitted, to challenge it and, when my challenges are not met, to broadcast that reality to the scientific community at large. When I am ignored, insulted, denigrated, deleted or banished I broadcast that too.

    I further believe, with Einstein, that we are all victims in a completely determined scenario in which there was never a role for chance.

    I believe I am an honest man and if others choose to question my integrity as has happened here, it reflects on them not on me. I do not need to be “protected from myself” as Scordova has so gallantly suggested as the excuse to delete several of my messages either.

    Since my challenges will not be met here, I might as well find another venue to invade, to issue challenges that are never met, probably to be further treated with contempt and continue my dedication to the demise of the biggest hoax ever foisted on a naive quasi-scientific public. It is a dirty job, but someone has to do it and it is a most worthy cause which I thoroughly relish.

    “If you tell the truth, you can be certain, sooner or later, to be found out.”
    Oscar Wilde

  317. “spontaneous polymerization of amino acids”

    There is a problem with this even if it easily done and the polymers remain stable. All proteins of length of around 40-45 exhaust the entire matter of the universe. So random polymers generated this way will only represent a small fraction of potential polymers and the likelihood of them being useful and favored for some reason is infinitely small.

    There are I believe 39 possible combinations of amino acids found in nature that are used in life and of these 39, 19 are the wrong chirality but are equally likely to form a bond. Someone with a chemical background can certainly over rule me and give a better explanation but using just the 20 in life in a chemical reaction is not likely to generate many things that are useful. JAD said that some of the ones he referred to were useful as enzymes but how many or what percentage are?

    Then there are other amino acids besides the ones used in life so the odds of spontaneous polymerization seems to be remote as a source of useful proteins. This is one of the arguments I have seen against this source for the generation of proteins but what other ways are there besides creation by a ribosome and then where did the ribosome come from.

    It seems the proteins which ended up in life were somehow selected but how.

  318. 319

    Sal at #282

    But to be fair, the separation of Darwinian Evolution and OOL…

    …is obvious. Yes I know, but that is hardly the issue.

    Sal, you are being very gracious. The idea that your involvement is not to the betterment of the debate is never in question – as least not by me.

    But perhaps there are other ways of looking at the exchange. You seem to see it as a necessary intellectual tea party of sorts, and it is surely that. But being that as it may, it is also a competition of ideas. It is subject to the values that all competitions are subject to. In other words, we know a thing or two about competition, and there are tidbits of that knowledge that rise to the surface. One of those tidbits is about having the will to defend your own territory.

    Evolutionary biology is not separate from the history of life, and the history of life is certainly not separate from its origin. The only dividing line is that evolutionary biologists like nothing more than ruling on the cause of life by means of a neighborly fiat, and they’ve gotten away with it by erecting a paper fence that ID proponents keep haplessly supporting. It’s like a paraphrased Berlinski “it happens so often that it’s almost forgotten that it makes no sense at all.” In this case, the territory that is ceded away is the very territory that Abel is fighting for in the paper at the top of this thread. This is not a trivial point.

    Then to quote (as you do) Abel’s technical acknowledgement that origins research doesn’t include some of the issues in evolution (like mutation, selection, etc.) is like suggesting that it’s a good place to build a fence.

    When your opponent says “I’ve commented several times that I don’t think that the OOL is actually a question of evolutionary biology” please consider how it serves his argument. If our theories are to be the best explanations for life, then he’s assuming the protection of a division within that explanation – which he himself has placed there. Why would he want a divide? He’s then free to tend the fence by passing off papers that are beside the point. The central conclusion of Abel’s work is that chance and necessity cannot coordinate the required function within nucleic sequencing, and that only agency is capable of creating such a pattern. Where has your opponent addressed the stated reasons for this conclusion?

    What you’ve allowed your opponent is that any doubts cast upon the sufficiency of chance and necessity in the origin of life will be kept separate from the explanation of life, given by him and given by science. He’s insulated from the paradox of information, and the language, and the instructions that cause life. And if that is the case, whatever Abel is saying about volitional agency being the only cause known to be suited to the actual evidence, these are then conclusions evolutionary biologists needn’t consider. So have a nice day.

    “After all, “biology” requires life as a pre-requisite, right?”

  319. 320

    jerry

    The proteinoids produced by Sidney Fox have weak enzyme activity, mostly urease I believe. All proteins seem to have some enzyme activity. Fox’s proteinoids have nothing to do with evolution any more than George Wald’s organic soup does. The organic soup hypothesis is a pipe dream. Sidney Fox’s proteinoids are at least solid biochemistry. Neither have anything to do with phylogeny which remains like ontogeny a phenomenon whose origin remains a total mystery.

    Living things violate all known physical laws, yet the individual reactions that drive life all obey physical laws. That is why I cannot accept the notion that an evolving life could ever emerge spontaneously even once.

    I agree with Otto Schindewolf that evolution is not an experimental science. It is an historical reality that cannot be reproduced. It is a fool’s errand to try to produce evolving life in the laboratory. There is no question in my mind that the origin or, more likely, origins of evolving life required (past tense) supernatural intervention. The Creative Age finished long ago. We are now in the Extinction Age, the terminal phase of a planned sequence. Evolution, exactly like development, has proven to be a self-limiting process.

    Davison, J.A. “Evolution as a self-limiting process.” Rivista di Biologia 91:199-220(1998).

    I also understand that many will not agree with me.

    I am not very happy with that conclusion but that is exactly what the facts demand.

    I hate being right!

    “A past evolution is undeniable, a present evolution undemonstrable.”

  320. We are now in the Extinction Age, the terminal phase of a planned sequence.

    If all that mattered was matter that would be quite depressing. Fortunately, it doesn’t.

    Happy Easter, everybody.

  321. Mr Cordova,

    Sorry to be late to the polymerization discussion. It seems to me that the real question is whether there are non-biotic alternatives to the ribozyme that can assist polymerization, even if they are less efficient. If Fox used ‘artificial seawater’, then he was assuming a pelagic origin of life. Perhaps motivated by the failures and criticisms discussed here, theories have moved on to vents, clays, eutectic freezing, etc.

    Let us honor Fox for trying! Science proceeds by the analysis of failure. This to me is the great thing about science. There is no dishonor in failure or success. Wow! There is only dishonor in not trying at all.

  322. John Davison,

    Even the committed atheists and evolutionary biologists admit that Darwin is dead. They are looking towards another explanation. Exaptation not adaptation.

    The theory in its basic terms says that non coding regions mutate and a very small number of them eventually produce a functional element which is then exapted to some use. The main form of mutation is transposition through reverse transcriptase. So gradualism in the Darwin sense is out but a new form of gradualism is taking hold.

    That is why the topic of the arbitrary creation of proteins through a transcription and translation process is of interest. What is the likelihood of an arbitrary polymer of amino acids having some function or being able to fold.

    So Darwin’s adaptive gradualism is dead, natural selection exists but is a destructive and conservative force not a creative one and the heart of Darwin is gone. There is no malthusian competition for resources driving change. Only common descent remains which is why now you have people fighting desperately for that. Once that is gone all of Darwin is gone.

    OOL is related to evolution because most of the abiogenesis theories resort to a competition for resources and a selection process based on some form of fitness. Or a molecular evolution. So while Darwin did separate the two processes, his ideas are dead so why maintain this last bit of charade that what he said means anything. In other words the total problem may come down to how proteins and other functional polymers arise whether before the first cell appeared or afterwards.

  323. Dr Davison,

    So, do you share with Allan MacNeil a distrust of population genetics? Has that field made too many simplifying assumptions to remain relevant?

  324. It is not just the pelagic or any other natural environment that can assist polymerization. There is the finding of useful polymers after such a process starts. As I said above proteins of 40-45 amino acids exhaust the matter of the universe. So how does a small area of a small planet provide enough resources to search for useable proteins and then what makes them useable in such a situation.

  325. jerry,

    you seem to draw a hard line between exaptation and adaptation when none exists. exaptation results in adaptation. it is just a narrower form of adaptation in which the trait under examination existed previously in a different form or performed a different function than it currently does. natural selection is necessary for exaptation and adaptation in general. so in no sense is natural selection “dead.”It remains the only way that adaptation can occur (drift might result in adaptation but without at least some selection it is very unlikely).

  326. ps jerry,
    here’s a nice example of the type of exaptation you describe in action. he third paragraph of the introduction might clarify some things for you:

    http://www.plosgenetics.org/ar.....en.0030166

  327. 328

    jerry

    Sorry but gradualism never had any significant role in the origin of species or of any other taxa. All such origins were instantaneous events exactly as the fossil record shows.

    What in God’s name do mean by exhausting the matter of the universe? That makes no sense at all.

    Nakashima

    It is not only population genetics that I reject, it is all of obligatory sexual (Mendelian) reproduction. Of course you would know that if you had read my papers and I wouldn’t have to respond to your questions because you wouldn’t be asking them.

    “You can lead a man to the literature but you can’t make him read it.”
    John A. Davison

    You can’t make him comprehend it either!

    I have no intention of repeating material that is freely available both on the side bar here at Uncommon Descent and on my weblog.

  328. JAD, I have read some of your work and find it to be refreshingly clear and easy to understand. I do have an idea though. Why not simply disabuse Darwinists of their fantasies by directing them to the appropriate paper. For example, you could simply tell them that they will find the answer to such and such an objection in “The Evolutionary Manifesto,” or in your “Response to Dawkins,” or whatever. Just tell them which paper to read and then ask them to get back to you. That way you don’t have to repeat yourself. What’s wrong with that?

  329. Tribune wrote:

    Happy Easter, everybody.

    Yes of course! Happy Easter!

  330. John Davison,

    People are suggesting proteins arose by random construction of polymers. Just constructing one each of every proteins of 40-45 amino long would require all the matter in the universe. Obviously an absurdity. I am pointing out that random creation of proteins is extremely unlikely to find a useful protein and and a search of all proteins or even an extremely small set of them is a non starter.

    So what I am pointing out that the origin of those proteins used in life can not be due to any random creation of them in whatever primordial condition they want to chose. The origin must lie elsewhere.

  331. John Davison,

    Your are misreading a lot of what I am writing to you. I never said gradualism ever did anything. I am just pointing out that Darwin’s gradualism is dead and Gould’s gradualism is what they are now defending. It will probably die to when enough people scrutinize it.

  332. Cabal wrote:
    I am not yet convinced that we may dismiss self-organization as a relevant subject without taking a closer look first:

    http://plus.maths.org/issue37/…..index.html

    Would Sal care to comment?

    Yes. Sorry for the delay. You raise an important consideration.

    I had commented about Laughlin’s work at UD before. See: Irreducible Complexity in Mathematics, Physics, and Biology

    In that thread I quoted an article from the NY Times, December 4, 2001

    In science’s great chain of being, the particle physicists place themselves with the angels, looking down from the heavenly spheres on the chemists, biologists, geologists, meteorologists — those who are applying, not discovering, nature’s most fundamental laws. Everything, after all, is made from subatomic particles. Once you have a concise theory explaining how they work, the rest should just be filigree.

    Even the kindred discipline of solid-state physics, which is concerned with the mass behavior of particles — what metals, crystals, semiconductors, whole lumps of matter do — is often considered a lesser pursuit. “Squalid state physics,” Murray Gell-Mann, discoverer of the quark, dubbed it. Others dismiss it as “dirt physics.”

    Recently there have been rumblings from the muck. In a clash of scientific cultures, some prominent squalid-staters have been challenging the particle purists as arbiters of ultimate truth.

    “The stakes here are very high,” said Dr. Robert B. Laughlin, a Stanford University theorist who shared a Nobel Prize in 1998 for discoveries in solid-state physics. “At issue is a deep epistemological matter having to do with what physics is.”

    Last year Dr. Laughlin and Dr. David Pines, a theorist at the University of Illinois and Los Alamos National Laboratory, published a manifesto declaring that the “science of the past,” which seeks to distill the richness of reality into a few simple equations governing subatomic particles, was coming to an impasse.

    Many complex systems — the very ones the solid-staters study — appear to be irreducible. Made of many interlocking parts, they display a kind of synergy, obeying “higher organizing principles” that cannot be further simplified no matter how hard you try.

    Carrying the idea even further, some solid-state physicists are trying to show that the laws of relativity, long considered part of the very bedrock of the physical world, are not platonic truths that have existed since time began.

    In the world of solid-state physics, quasi particles abound. In some substances, like the semiconductors used to make computer chips, the displacement of an electron leaves behind a “hole” that behaves like a positively charged particle. An electron and a hole can sometimes stick together to form a chargeless quasi particle called an exciton. Other such ephemera include magnons and polarons.

    Evanescent though they are, quasi particles act every bit like elementary particles, obeying the laws of quantum mechanics. This has led some mavericks to wonder whether there is really any difference at all. Maybe elementary particles are just quasi particles — an effervescence in the vacuum.

    But the issue with solid state physics is not one of SELF-organization but one of emergence once an organization is already existing.

    For the phenomenon of electron “holes” to exist, an irreducible organization, like a solid-state transistor has to be created in the first place.

    Note the controversy of immutable platonic forms emerges not only in biology but also physics. Physics has traditionally been defined by the search for elegant platonic forms in Nature. Squalid-state-physics goes against long held traditions.

    The bottom line is that Laughlin’s work does not necessarily imply SELF-organization, it is more an inquiry of what happens when certain irreducibly complex organizations are already put together. A good example might be superconductivity, or even the behaviors of common place appliances like transitors (one of the most well-known products of squalid-state physicists).

    I would actually argue a computer, a cell, and life-itself are emergent phenomenon not reducible to ordinary physics and chemistry.

    Modern science is beginning to deal with the problem of organization (holism) versus pure reductionism, partly because of the discipline of engineering.

    I elaborated the idea here: Darwinism is a Caricature of Evolutionary Biology

    To understand the concept of higher levels of organization, I begin with a down-to-earth example of a public library. Simply speaking, the library is composed of collections of books (and other things), books are composed of chapters, chapters are composed of paragraphs, paragraphs are composed of sentences, sentences are composed of words (and punctuation), words are composed of letters of the alphabet, letters of the alphabet are composed of ink on paper.

    I gave a description of books basically in terms of what is printed. But even beyond that description, how can we describe the notion of books without the notion of themes and ideas? These are also higher levels of organization, and these levels of organization are especially problematic for materialists.

    Does it make sense to try to fully understand a library by studying the alphabet? Of course not. Does it make sense to describe the contents of books, their origin and evolution, in terms of the dynamics of how ink is put on paper? Of course not. Pigliucci is subtly criticizing Lynch for making comparable errors in Lynch’s view of evolution.

    I spoke of books, but let me add one more illustration: spacecrafts. It would be futile to describe spacecrafts merely as conglomerations of atoms (credit Polanyi for that idea). A spacecraft is understood in terms of propulsion, navigation, guidance, control, communications, remote sensing, and a multitude of other “higher levels of organization”. Saying a spacecraft is made of atoms is correct, but the description is deeply incomplete.

    With this in mind, we can appreciate Pigliucci’s critique of Lynch. Pigliucci alludes to the fact separate fields of study have emerged to study higher levels of organization in biology. Like the various specialized fields in the science of spacecrafts, we now have specialized fields in biology. If anything, biology is infinitely more complex than spacecrafts.

    Some of these fields are identified with the suffix of “-omics”, such as proteomics. These fields describe higher levels of organization within biology
    ….

    For example, regarding “-omics” we hear much of genomics (DNA), but what are the other “-omics”. One important “omic” is proteomics. From wiki:

    Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological pathways of cells. The term “proteomics” was coined to make an analogy with genomics, the study of the genes. The word “proteome” is a portmanteau of “protein” and “genome”. The proteome of an organism is the set of proteins produced by it during its life, and its genome is its set of genes.

    Proteomics is often considered the next step in the study of biological systems, after genomics. It is much more complicated than genomics.

    But in addition to genomics and proteomics we have the various other “-omics” transcriptomics, metabolomics, and even phenomics, etc.

    These scientific displines of “omics” are rooted in ideas about organization, not traditional physics and chemistry.

    Layers of organization may not be restricted to engineering and biology, but may extend to irreducibly complex phenomenon in the field of squalid-state physics.

    PS
    I like that term “squalid-state physics”. It suggest something scandalous. :-)

  333. Mr Jerry,

    What does “useful” mean if you are just synthesizing random 45 AA proteins? It sounds like you are attempting a criticism of “metabolism first” OOL theories, such as Stuart Kauffman’s.

  334. Mr Cordova,

    I don’t think you should tell Dell, etc. that computers are not reducible to physics and chemistry! :)

    There are many mathematical systems that are ‘duals’ of each other. Neither is more ‘fundamental’ than the other. So the basic description of the world may come in different choices of “fundamental” particles.

  335. I thought to mention, the notion of organization has little meaning without a very great capacity and tendency toward dis-organization. Hence, self-organizing (as used in OOL) is a bit of a meaningless concept.

  336. Let us honor Fox for trying!

    Dittos to that.

    I don’t think you should tell Dell, etc. that computers are not reducible to physics and chemistry!

    Are you sure of that? :-)

    What is the value of the material components of a computer? What is the value of the computer? Why is there a difference?

  337. Mr Cordova,

    I don’t think you should tell Dell, etc. that computers are not reducible to physics and chemistry!

    Computers may be composed of physical and chemical materials, but laws of physics and chemistry do not sufficiently describe nor can they describe what a computer is.

    This would be about as difficult as describing the experience of color using black and white ink. The concepts are in different worlds.

    Attempting to describe what a computer is by sole reference to the laws of physics (such as classical mechanics, relativity, quanutm mechanics, themodynamics) doesn’t seem possible much less appropriate. The concepts of traditional physics and computation seem very distinct.

    [Although, as I alluded to above (with Landauer and Chaitin), there is a school of thought the laws of physics are compuations. If so then computation may explain the laws of physics, but not the other way around.]

  338. Reductionism is a worthy goal. Much of scientific advancement and mathematics came about through reductionistic explanations.

    But as Chaitin pointed out, pure mathematics is irreducibly complex (ala Godel). Reductionism of everything is not possible even in principle.

    Ironically these philosophical issues have practical importance. When we create compressed files (either exact or lossy compressed files), such as MP3 JPEG, whatever, we are dealing the the limits of reduction. How far can we reduce certain concepts such as musical sounds or photographic images to more compact representations?

    With mechanical processess like data compression, we are actually dealing with issues of reductionism. If complex data were reducible to very simple forms we would have no need of mass storage or large bandwidth communication devices.

    By many lines of thought and technological experience and mathematical proof, we are coming to terms with the limits of reductionistic explanations.

    Black and white photographs of colorful scenes are lossy representations of reality. One cannot reconstruct in exact detail the color properies of a scene from a black and white photo.

    The science of physics and chemistry are lossy compressed representations of reality. It is futile to try to understand compuation in terms of these reduced representations of reality.

    It might be possible to describe physics in terms of computation, but not the other way around, much like we can derive a black and white photo from a color photo, but not the other way around.

    These considerations are at the heart of Abel’s paper.

  339. Nakashima,

    Where do the proteins come from? I am saying they cannot come from amino acids coming together in some chemical reaction unless you are saying that a high percentage of random protein combinations are useful for something. There are just too many combinations to be searched unless a high percentage have some function and any old proteins will do.

    You can define useful in any way that makes sense for life. For example, they have some function in some life process.

    So I am saying that random protein formation in some chemical soup in some environment can not be the origin of those proteins used in life unless a very high percentage of proteins have some functional use.

  340. khan,

    You should read the Vrba and Eldredge book on macro evolution especially the first chapter to understand the debate.

  341. jerry,

    I was just commenting on what you said and pointing out that exaptation requires natural selection to operate just as much as plain old adaptation. how else do you think those mutated gene duplications with new functions become fixed in the population? do you disagree?

  342. oh and jerry,
    here’s another example of exaptation in action:

    http://www.nature.com/nature/j.....04696.html

  343. 344

    jerry

    There s no room for “debate” in science and never has been. There is only discovery of unalterable truth and its dissemination. Name a single issue that was ever resolved thrugh “debate.” You won’t of course because you can’t.

  344. 345

    Stephen B in #324

    There is plenty wrong with that. What real scientist ever had to remind everyone to read his papers. You can’t name one and you know it.

    The atheist Darwinians are well aware of my papers and the manner in which they devastate their silly thesis. Why else do you suppose they have they banished me from their intellectual ghettos?

    I am now holding forth on Dembski’s recent thread. I have little more to offer here where most of my comments have not even appeared thanks to the high handed tactics of the author of this thread. If you have any further comments directed toward me do it there. I’m finished here.

  345. —-JAD: “What real scientist ever had to remind everyone to read his papers. You can’t name one and you know it.”

    I was just trying to provide you with suggestions about how to get off the sidelines and on to the playing field. Why would anybody show up for the game and then decide that they don’t want to play, especially if they are qualified? I am not getting that.

  346. oh and jerry,
    here’s another example of exaptation in action:

    http://www.nature.com/nature/j…..04696.html

    That paper is an example of proof by circular reasoning.

  347. In #319 UprightBiped wrote:

    “If our theories are to be the best explanations for life, then he’s assuming the protection of a division within that explanation – which he himself has placed there. Why would he want a divide? He’s then free to tend the fence by passing off papers that are beside the point. The central conclusion of Abel’s work is that chance and necessity cannot coordinate the required function within nucleic sequencing, and that only agency is capable of creating such a pattern. Where has your opponent addressed the stated reasons for this conclusion?”

    Ever since Darwin’s publication of the Origin of Species, evolutionary biology has been based on four biological mechanisms which, taken together, produce the characteristics we see in living organisms. These mechanisms are:

    1) Variety: There are non-trivial differences between the phenotypes of organisms in populations, produced by the “engines of variation” (listed here: http://evolutionlist.blogspot......awman.html );

    2) Heredity: some of the variations produced by the “engines of variation” are heritable from parents to offspring;

    3) Fecundity: Some of the individuals whose variations are heritable can reproduce and pass on those variations to their offspring (in the “classical” form of this condition, such reproduction is considered to be maximized); and

    4) Demography: Some individuals survive and reproduce more often than others.

    There are two primary outcomes that result from these demographic changes:

    01) Adaptation: Some characteristics become more common among the members of a population; and

    02) Descent with Modification: The characteristics that are present in populations change over time in a way describable using cladograms (i.e. phylogenetic “trees”).

    That’s evolutionary biology in brief. Even a cursory glance at the six numbered points listed above will indicate to almost anyone that the origin of life from non-living materials does not involve a single one of the processes and outcomes listed:

    OOL1) Variety: Yes, if life originated from non-living materials, there would presumably be considerable variation between the materials formed. Indeed, there would almost certainly be much more variation, as there would presumably be racemix mixtures of the chiral molecules formed, which only later in the process became canalized into homochiral forms. But none of the “engines of variation” that produce differences between the phenotypes of living organisms produce the changes we see in spontaneously formed biomolecular building blocks.

    OOL2) Heredity: It should be obvious to anyone on this list that genetic heredity is a consequence of the origin of life and the genetic code, not a prerequisite for it.

    OOL3) Fecundity: Reproduction, even among asexual organisms such as bacteria, is a complex biological process requiring the coordination of multiple biological processes, including the replication of genetic material and the coordinated production of new cells (and tissues, organs, etc. in multicellular eukaryotes). Again, none of this is possible until after the origin of life, the genetic code, and cellular metabolism and reproduction have already occurred.

    OOL4) Demography: Yes, the “sorting” of spontaneously formed biomolecular monomers and polymers show patterns of formation and destruction that could be called “demographic”, but only by stretching the definition of that term virtually to the breaking point.

    OOL5) Adaptation: Same response as for the previous point (OOL4).

    OOL6) Descent with Modification: “Descent” requires reproduction, and the kind of “descent with modification” posited as the outcome of biological evolution also requires genetic heredity.

    Ergo, there is a fundamental dividing line between the purely chemical and physical processes that are invoked to explain the spontaneous origin of life from non-living materials and the biological processes which, operating together, produce the phenomenon we refer to as biological evolution. No amount of unsupported assertion can make this fundamental division go away, no matter how much the people making the assertions (on both sides of the OOL issue) would like it to.

  348. In #323 jerry wrote:

    “The theory [of exaptation]…says that non coding regions mutate and a very small number of them eventually produce a functional element which is then exapted to some use. The main form of mutation is transposition through reverse transcriptase.”

    This is a grossly inadequate description of Gould and Vrba’s definition of the term “exaptation”. First of all, exaptation is not defined genetically (i.e. in reference to “non-coding regions in DNA”). Rather, exaptation refers to alterations in the frequency of particular phenotypic characteristics in populations as the result of changes in the demographic survival and reproduction of individuals with particular phenotypic characteristics. Indeed, in Gould and Vrba’s original definition of “exaptation”, they limited it to characteristics that were adapted to one particular function being altered to produce another, related function.

    However, since Gould and Vrba proposed the term in 1982, evolutionary biologists have recognized that these limitations to exaptation need not necessarily apply, and that it could refer to a process whereby any phenotypic characteristic (adaptive or not) could be altered by the “engines of variation” and subsequent changes in frequency of expression among the individuals in a population to become a significantly different characteristic (and again, not necessarily one that is “adaptive” by the traditional sense of that term, nor one that is related to the original function of the characteristic in any way).

    Furthermore, as Jablonka and Lamb have recently pointed out, such phenotypic characteristics need not be genetically inherited at all, nor do they necessarily have to start out as non-adaptive characteristics.

    Ergo, what jerry asserts is the whole of “exaptation” is actually only one mechanism from dozens, possibly hundreds, by which the demographic distribution of heritable phenotypes may change over time in populations of living organisms.

  349. khan,

    “exaptation requires natural selection to operate just as much as plain old adaptation. how else do you think those mutated gene duplications with new functions become fixed in the population? do you disagree?”

    Never said it doesn’t. I have been on record at several different places over time on the efficacy of natural selection as a process that causes change in nature. I have never doubted that natural selection processes operates and selects. The problem has always been that natural selection rarely has anything meaningful (in terms of the evolution debate) to select (by the way notice I didn’t say never but that they are rare and so far I haven’t seen how complex novel capabilities could have arisen to be selected.) The origin of new complex capabilities or what we call here macro evolution is where the debate is. Natural selection will often chose a better option in terms of survival which is obviously important to the organism and its gene pool but it can not select what isn’t there.

    My problem is that no one has shown that Allen MacNeill’s 50+ engines of variation ever produced anything meaningful for natural selection to operate on.

    I have no problem with genetics and have said so maybe a hundred times or more. But without the necessary variation natural selection is hopeless as a process that produces novel complex capabilities and only conserves.

    You are getting tiresome with all these attempts at a gotcha. They are getting more feeble as time goes on. Give it a rest. It just makes you look bad when you suggest there is something I believe in when I don’t. It is not good to create straw men to knock down.

    To give you a heads up for futures. I believe in micro evolution which by the way includes natural selection and all the other elements of genetics. That means I also believe in Allen MacNeill’s 50+ engines of variation to the genome which includes gene duplication. I have also pointed you to the latest thinking on genome modification which I do not deny. In fact I, the ID supporter, have to give the anti ID supporters the latest in evolutionary thinking. Which Allen MacNeill provided and verified that I had a correct assessment. I don’t view it as any threat to ID since there is no evidence that source of variation has ever led to anything. I am just saying what is the latest thinking not that it is correct thinking.

    Natural selection only has the power to bring out of the genome what is currently there (repeated for the umpteenth time.) If it is not there, it cannot create it. So the real issue in the evolution debate is the source of new variation to a population gene pool that underlies the origin of complex novel capabilities (repeated for the umpteenth time.) So do you get the picture.

    So far I have not seen any credible evidence that points to any process as capable of producing the variance in a gene pool to get from microbes to man and many of the steps along the way. There are lot of gene pools in that long set of sequences and I have not seen how the new variance could be produced for many of the steps.

    If you want to pick at that, go ahead or want clarification, go ahead but before you attempt your next set of gotchas, you should ask before hand if I believe in something or not. Like when you asked the other day about why I considered natural selection a weak force. Yes it is because all it does is select what is already there (repeated for the umpteenth plus one time.)

    Darwin was misled by artificial selection because he led him to believe thatt there was magic somewhere within the organism that could be brought out by the right combination of conditions. Well he was wrong. There are limits to what is in the organism that eventually can be expressed.

  350. In #332 jerry asserts that Gould’s version of the theory of evolution is a “gradualistic” theory, not different in essence from the one at the heart of the “modern synthesis” (i.e. “neo-Darwinism”). This is clearly a gross misunderstanding of Gould’s theory, especially as presented in his paper coauthored with Niles Eldredge in 1972, in which they presented the theory of punctuated equilibrium. In that paper, they clearly contrasted their theory with what they referred to as “phyletic gradualism” and carefully pointed out how their theory was much better at explaining the patterns of phenotypic changes observed in the fossil record.

    IOW, calling Gould’s theory of evolution (in which punctuated equilibrium is a central explanatory concept) “gradualist” is like calling Mt. Everest a “valley”.

  351. In #333 Sal wrote:

    “I would actually argue a computer, a cell, and life-itself are emergent phenomenon not reducible to ordinary physics and chemistry.”

    I completely agree. This is one of the main reasons that I believe that the question of the origin of life is fundamentally separate from the question of biological evolution. As I have pointed out in comment #348 (assuming that the numbering stays the same after my comments emerge from moderation), biological evolution is the result of four processes, all four of which are emergent properties of living systems.

  352. In #350 jerry wrote:

    “My problem is that no one has shown that Allen MacNeill’s 50+ engines of variation ever produced anything meaningful for natural selection to operate on.”

    This is simply not true. There is a vast and growing literature on precisely this subject. For example, Sean Carroll’s book, Endless Forms Most Beautiful contains hundreds of examples of major phenotypic changes produced by relatively minor changes in homeotic regulatory mechanisms. One need only follow up on the references Carroll provides for each chapter in his book to read the primary literature on this subject.

    BTW, the mechanisms described by Carroll are #8 – 14 and #37 – 39 in my list of the “engines of variation” at http://evolutionlist.blogspot......awman.html

  353. jerry,

    I’ve counted about 8 misconceptions in your posts. here we go

    1)

    Even the committed atheists and evolutionary biologists admit that Darwin is dead.

    assuming you don’t mean physically dead, which everyone agrees is true, I’d like to see some support for this assertion. Natural selection and common descent, the key components of Darwin’s theory are alive and well, and I haven’t heard anyone besides ID people make this claim.
    2) Exaptation not adaptation. Darwin hmself mentioned exaptation as a possible mechanism for adaptation (see chapter 6 of Oo Species). Again exaptation is a form of adaptation so I’m not sure what you mean here. and there is lots of evidence for other kinds of adaptation.. e.g. symbiosis, co-evolution, good old mutation and selection..
    3)

    So gradualism in the Darwin sense is out but a new form of gradualism is taking hold

    there is very nice evidence for gradualism in e.g. the evolution of color vision (series of 3 slightly beneficial mutations leading to a large shift in visual sensitivity). the shift of jawbones to earbones in mammals is nicely documented as a series of gradual changes in the fossil record. feathers evolved in a very gradual manner from simple unbranched rachis to “fuzzy” rachis w branched barbs to rachis w branched barbs and branched barbules and finally to asymmetric flight feathers. so in what sense is it dead?
    4)

    natural selection exists but is a destructive and conservative force not a creative one

    exactly who has ever argued that natural selection is a creative force? speaking of strawmen..
    5)

    There is no malthusian competition for resources driving change

    adaptaion through NS can occur without any competition for resources, which was shown during the modern syntheis 80 years ago. it also happens when there is intense competition. so what is your point?
    6)

    Only common descent remains which is why now you have people fighting desperately for that.

    fighting desperately? even your hero Michael Behe accepts common descent. who is fighting and how?
    7)

    My problem is that no one has shown that Allen MacNeill’s 50+ engines of variation ever produced anything meaningful for natural selection to operate on.

    this is where you need to do more research. you can start by looking at the two papers I linked you to. or the evolution of sex chromosomes: http://www.nature.com/hdy/jour.....8115a.html
    8)

    So far I have not seen any credible evidence that points to any process as capable of producing the variance in a gene pool to get from microbes to man and many of the steps along the way.

    evolution is a bush, not a ladder, asi think you know. but i will repeat something fro the umpteenth time, namely that the origin of chlorplasts and mitochondria by endosymbiosis is a critical example o the formation of new complex capabilities. lots of new “information” is generated as the process proceeds, so this is not just chunking two existing things together. just bc you won’t accept it doesn;t mean it doesn’t exist.

  354. Allen wrote:

    Ergo, there is a fundamental dividing line between the purely chemical and physical processes that are invoked to explain the spontaneous origin of life from non-living materials and the biological processes which, operating together, produce the phenomenon we refer to as biological evolution. No amount of unsupported assertion can make this fundamental division go away, no matter how much the people making the assertions (on both sides of the OOL issue) would like it to.

    Allen,

    [Thank you again for you patience. I was logged off for a while before noticing your comments.]

    I’ve generally been ambivalent to this issue, and in light of the fact David Abel appears to be in general agreement with you, I would have to tentatively agree, thus reversing my slight (and I emphasize slight) bias toward lumping chemical evolution with biological evolution.

    Finally, I don’t see that it helps arguments in favor of ID to try to conflate OOL with biological evolution. It doesn’t clarify ID arguments, and it just results in sideshows about definitions.

    If all sides can agree that Darwinian evolution doesn’t explain the origin of life, I’m content to accept that.

    Sal

  355. Khan wrote:

    the origin of chlorplasts and mitochondria by endosymbiosis is a critical example o the formation of new complex capabilities

    I’m afraid this is an example of proof by assertion. It would be fair to say there is evidence apparently supportive of endosymbiosis. It is quite another thing to assert endosymbiosis is as empirically validated as an accepted law of physics.

    To quote Albert DeRoos, a cellular biologist who studies these things:

    Well, I think the endosymbiotic theories are far from being proven.

    The endosymbiotic theory of the origin of the nucleus is just wild speculation. There are so many mechanistic problems with it that one has to conclude that it is practically impossible. How can people propose such a theory without even discuss how the nuclear mRNA export mechanism was implemented?

    There are also major difficulties with the endosymbiotic theories of the origin of chloroplasts and mitochondria. Their early divergence of the root of the Tree of Life, the mechanism of endosymbiosis, the emergence of their mutual genetic dependence etc. Currently it is like ‘one bacterium swallowed another, and they lived together happily ever after’.

    Just like common descent, we do know that bacteria and mito’s have genes in common. It doesn’t say anything about the mechanism.

    –Albert DeRoos
    Informal Discussion at ARN

    This thread isn’t the place to get into big discussion about endosymbiosis primarily because without OOL, it is a moot point.

    I would point out however, if endosymbiosis is an unproven theory, it might be disqualified as a proof that large scale integrated information can spontaneously evolve.

  356. 357

    Allen at 348.

    Thank you for that recounting of evolutionary biology, but I must say it was uneccesary.

    Unfortunately, you’ve failed to address the issue, and the substance of your post provided nothing but a demonstration of my previous comment.

    You operate under an assumption that is wholly unproven, yet your assumptions are held without even the slightest margin for error.

    The strong (and repeated) inferences being derived from OBSERVATIONS of nucleic information are that a non-agency cause for life is very likely to be 100% dead wrong – and those observationas are ignored by evolutionary biologists (as you have done) or given lip service to discoveries just around the bend (as you’ve done) or flanked by collateral observations that never rise beyond the trivial (as you have done).

    Allen, you are wrong. You cannot be correct in assumming a material cause for functional nucleic sequencing in the face of substantial unanswered counter evidence. Instead, you are obligated to respond to that evidence if you intend to retain your prior assumptions.

    The distinction between non-living matter and functional living tissue is information, written in a language, and forming instructions that have meaning. This phenomena is being studied and understood, and the issues it raises are germane to your assumptions and must be addressed in earnest.

    Metabolism first? Instructions first? It does not matter, you have nothing to assume.

    So, do not attempt to flank the argument with collateral observations that do nothing to impact the evidence being presented, do not attempt to denigrate the evidence or its sources or authors, and do not attempt to play a process game with the various specialties and divisions within biology, instead, MEET the evidence in a straightforward manner, just this once:

    The capabilities of stand-alone chaos, complexity, self-ordered states, natural attractors, fractals, drunken walks, complex adaptive systems, and other subjects of non linear dynamic models are often inflated. Scientific mechanism must be provided for how purely physicodynamic phenomena can program decision nodes, optimize algorithms, set configurable switches so as to achieve integrated circuits, achieve computational halting, and organize otherwise unrelated chemical reactions into a protometabolism. To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it:

    “Physicodynamics cannot spontaneously traverse The Cybernetic Cut [9]: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.”

    A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.

  357. 358

    I see that Allen MacNeill has followed me over to Dembski’s thread to further whine about my imagined incivility. MacNeill reminds me of Alan Fox who also follows me around like a “dog” with one goal in mind – to discredit me whatever the cost. I am flattered by the attention. I find it to be very revealing.

  358. Upright Biped:

    Well said!

    INFORMATION is central to modern life and science.

    But we directly empirically know that information, functionally specific, complex information comes from intelligence. In every case where we can directly track down the source. (And side debates on defns and quantification etc are simply distractive. We have good enough definitions and concepts with instances, and we have simple and more elaborate quantifications, with 35 recently published values of FSC, as the referenced paper cites. [Cf WACs and glossary for more if you want more onlookers.])

    EMPIRICAL CLAIM: There are no known cases of 1,000+ bits worth of functional information originating by chance, whatever some may assert. [To refute this, simply produce a directly observed case. We have been waiting on that for months or years here at UD. A whole Internet full of examples is just Exhibit no 1 on the empirical claim above.]

    On inference to best explanation, FSCI, and its more technical forms, FSC and CSI, are the product of directed, purposeful contingency.

    Indeed, stochastic, undirected contingency on the gamut of our cosmos, is unable to find such targets. for, a space that can sample 10^150 configs, is not going to scratch the surface of a space of 10^301, which is what 1,000 bits specifies. And, credible simplest independent life forms are at about 600 k bits, or 10^180,617 configs.

    Worse, the info in the cell is integrated into a certain known irreducibly complex entity: a computer, a structured digital data storing, step by step algorithm executing, self-replicating computer using informational molecular based nanotech.

    provide an empirically credible explaantion of such per chance + necessity only in any reasonable pre-biotic environment plese Mr Fox et al, or surrender tothe point thqa the only known source odf such systems is irtnelligence.

    And, to elaborate first body plan into teh major configs, we have incremets of 10′s – 100″s odf mega bits of information to account for, ocver 500+ mY or so, indeed in a 10 MY window inthat span. Kindly jsutify that origin by chance + necessity, with empirical support.

    We know that intelligences can routinely create designs embedding that scope of functional info.

    We even were able to predict the sort of architecture that a self-replicating entity would require in the 1940′s — a decade before DNA was discovered and subsequently shown to be the blueprint.

    Just, we have not built self-replicating automata yet. [I want to get tht going, as such automata look great for terraforming Mars to me! (Ship out a rocketful of them as seeds, and let them build themselves and then get to work on building the Martian environment for the first colonists to move into.) then, on to the asteroid belt. I want to be talking to my grandson on Mars, with my great grandson born there! So let's get cracking on a 40 year project.]

    GEM of TKI

  359. “Ergo, what jerry asserts is the whole of “exaptation” is actually only one mechanism from dozens, possibly hundreds, by which the demographic distribution of heritable phenotypes may change over time in populations of living organisms.”

    Well If I said “whole” (and I searched the whole thread and it wasn’t in any of my posts – now I used it), I was using it as hyperbole. Allen you are the one who said I got it right and the Brosius article which leads off the Vrba and Eldredge book is essentially about the concept of the exaptation of non coding regions to functional use.

  360. khan,

    Allen MacNeill who is commenting on this thread quite intensely, has said Darwin is dead and not just literally which I think is one thing we all can agree with.

    We all agree that natural selection works but like you said it does not create anything. It just selects what is already there. So we agree it is a weak force, is essentially destructive and does not create. It just selects.

    ID accepts micro evolution so bringing up examples of them does not do your argument any good. If you want to bring up minor changes to the eye which aided color vision. Fine and good but where did the eye come from?

    Story telling may be useful but it is not evidence. Maybe at some future time we can deal with the various stories and assess their relevance.

    Michael Shermer is one who said that natural selection is the heart of naturalistic evolution and I believe someone named Charles Darwin had a similar point of view. Or am I wrong that natural selection is/was a big part of Darwin’s theory.

    Eventually you will find some relevant criticism of what I say and I can learn from it.

    So keep it up but probably not here since this is supposedly about OOL and most of us have been off thread so I will not comment any more here except on that topic.

  361. While Allen MacNeill has built a firewall between OOL and evolution, this has not stopped many who discuss OOL from using things like natural selection, survival of the fittest, more efficient use of resources in a scarce environment in their search for a chain of events from molecules to microbes.

  362. jerry,

    Allen MacNeill who is commenting on this thread quite intensely, has said Darwin is dead

    that’s it? but you said “even hardcore atheists and evolutionary biolgists admit that darwin is dead”, which sounds plural to me, and makes it sound like there is some kind of consensus, when in fact it’s just one guy commenting on a blog. thanks for the clarification.

    Michael Shermer is one who said that natural selection is the heart of naturalistic evolution and I believe someone named Charles Darwin had a similar point of view. Or am I wrong that natural selection is/was a big part of Darwin’s theory.

    of course natural selection is critical to all forms of adaptive evolution. it is a necessary but not sufficient condition for adaptation to occur. but no one ever said it was a creative force, so you seem to be arguing against your own version of it.

    If you want to bring up minor changes to the eye which aided color vision. Fine and good but where did the eye come from?

    i was using that as a simple illustration of gradualism.. the actual evolution of the eye itself is much more complex, as you’ll find when you read this paper:Lamb TD, Collin SP, Pugh EN Jr. (2007) Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nat Rev Neurosci 8(12):960-76.

    ps i still want to know who is furiously defending common descent, and from whom.

  363. If all sides can agree that Darwinian evolution doesn’t explain the origin of life, I’m content to accept that.

    All sides don’t agree Sal. In fact, the determination to separate ool from evo by Darwinians seems to be based more on conditions and expediency rather than with the goal to enlighten i.e. Evolution 101 — from soup to cells– the origin of life

  364. 365

    Stephen B in #346

    It is not I who is on the sidelines and not on the field of play. It is devout Darwinian mystics like Allen MacNeill, Richard Dawkins, Stephen J. Gould, Ernst Mayr and P.Z. Myers that are now on the sidelines. No one even cites them any more because an enlightened evolutionary community has rejected the Darwinian fairy tale as without foundation, a house of cards which never had anything to do with speciation or the origin of any other taxa in either the plant or animal kingdoms.

    Darwinian evolution has achieved the same credibility as Phlogiston and Ether, neither of which even exist! Get used to it as I and countless others already have. Just because Allen MacNeill insists on remaining a Darwinian doesn’t mean anyone else should.

    If you don’t want me to respond here, don’t say silly things like that snd i won’t have to respond.

  365. JohnADavison:

    MacNeill reminds me of Alan Fox who also follows me around like a “dog”

    John,

    Such inflammatory comments have nothing to do with the topic at hand, and you are referencing discussions outside of this thread with no relevance to this thread.

    Sal

  366. If all sides can agree that Darwinian evolution doesn’t explain the origin of life, I’m content to accept that.

    All sides don’t agree Sal. In fact, the determination to separate ool from evo by Darwinians seems to be based more on conditions and expediency rather than with the goal to enlighten i.e. Evolution 101 — from soup to cells– the origin of life

    Thank you for the info Tribune. It demonstrates there may be a variety of viewpoints on the definition.

    But as a matter of principle, it is more important to discuss the plausibility of materialistic OOL. Arguing over whether it should be lumped in or not with evolutionary theory is a sideshow and is therefore a distraction.

    Suffice to say, I will let defenders of evoutionary theories compartmentalize the ideas whichever way they wish, it won’t change the fundamental problems of OOL.

    I have never gotten a complaint for separating the two ideas from the anti-ID side for making the separation. I’ve never improved my defense of ID by lumping OOL and biological evolution together.

    I don’t think there is much to gain by insisting the two concepts be lumped together.

  367. 368

    Sl

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  368. Suffice to say, I will let defenders of evoutionary theories compartmentalize the ideas whichever way they wish, it won’t change the fundamental problems of OOL.

    That’s not a bad policy Sal and you are right with regard to OOL

    Personally, I don’t care if OOL is included with NDE, but if an NDE defender insists that it’s not it is appropriate, and necessary, to point out that he is either speaking for himself or demand that he join us in condemning things like that Berkeley site or museum exhibits or textbooks that conflate them.

  369. 370

    Th prsnc f #368 prvs tht Slvdr Crdv hs n bsnss bng n “thr” t ncmmn Dcsnt. Ths thrd s jst nthr flm pt lk ftr th Br Clss.

    Shm n Sl!

  370. Sl

    r cmmttng prfssnl scd wth r dgnrt tctcs. wll nvr gn b rspctd nd t wn’t b jst b m.

    nj r mmnt n th sn.

    What you write has nothing to do with Abel’s paper and the topic of this thread.

    UD is under no obligation to keep posting numerous off topic comments by repeat offenders.

    Besides John, you said:

    You now have my permission to continue deleting every new message I present without a word of explanation.

    I have a responsibility to the readers to help keep the discussion on topic.

  371. 372

    Scrdv

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    Nw dsmvwl ths n t!

    Now disemvowel this one too!

  372. 373

    Wh dn’t s r nw fnd nflnc hr nd hv m bnshd? Tht s wht DvSct (Dvd Srngr) sd t d.

    N gts n glr.

  373. 374

    nd lk wht hppnd t hm!

  374. 375

    “The one thing we learn from history is that we don’t learn from history.”
    anonymous?

    It is hard to believe isn’t it?

    Not any longer it isn’t!

  375. 376

    To conserve cyberspace -

    http://www.iscid.org/ubbcgi/ul.....108#001620

    my comment April 15, 2009, 8:40 AM

  376. One of the better objections to Abel’s paper was put forward by Olegt, a very fine Condensed Matter Physicist at a very fine school. He posted his comments at TelicThoughts (where this discussion actually began as referenced in the original post).

    Here was my comment 226701:

    My understanding is that much of physcisal law is described by differential equations. Differential equations don’t describe the essential architecture of computer systems.

    Experimental results seem to agree with Abel. Life has not been observed to spontaneously emerge.

    Here was Olegt’s response 226774

    The choice of the mathematical language depends on the physical system. Yes, many physical theories contain differential equations: classical mechanics of a few particles is described in terms of ordinary DEs. But try to extend it to a system of many particles and you’ll quickly find that it is not guaranteed to work. In some cases it will: theory of elasticity and fluid mechanics are based on partial DEs. In others it won’t: you can say that “Differential equations don’t describe” the properties of a gas in thermal equilibrium. We have to use an entirely different mathematical language: statistics.

    One can say that the dynamics of individual molecules in a gas is still governed by Newton’s laws, which are expressed by ordinary DEs. That is the reductionist approach and in this case it fails spectacularly. The DEs of Newtonian mechanics are invariant under time reversal: if you film the motion of a particle or a collision of two particles and then run the tape backwards, the time-reversed motion still obeys all of Newton’s laws. However, we know that gas, a collection of a large number of molecules does not behave in a reversible manner. The entropy of an isolated system tends to increase with time. A broken glass does not spontaneously reassemble and jump back to the table. So the naive expectation of the reductionist (thermodynamics reduces to Newtonian mechanics) is shattered in the relatively simple case of a gas. It doesn’t mean that science fails to describe thermal phenomena. It’s the reductionist approach that fails. That’s why I find Abel’s null hypothesis silly.

    There are of course physical systems where even the basic rules are not stated in the form of DEs. Take the Ising model of a ferromagnet, which played a very important role in the development of the modern theory of critical phenomena. Its variables are binary numbers (a spin points either up or down) and its dynamics is discrete. Kinetics of crystal growth is also modeled by discrete variables. And these models in statistical physics are a short step from cellular automata, a class of mathematical models with discrete states and simple sets of rules governing their dynamics in discrete time. Guess what, one of these cellular automata, known as Rule 110, is capable of universal computation. In this case, trivial rules give rise to highly nontrivial behavior. Does that undermine Abel’s case? I think so.

  377. [Here was my response (226792) to Olegt's very fine critique:]

    olegt,

    Thank you for the insights. Your above paragraph is already the best critique that I have seen regarding Abel’s paper. I will reference your comments at UD because I think the objections you raise are substantial.

    The choice of the mathematical language depends on the physical system. Yes, many physical theories contain differential equations: classical mechanics of a few particles is described in terms of ordinary DEs. But try to extend it to a system of many particles and you’ll quickly find that it is not guaranteed to work. In some cases it will: theory of elasticity and fluid mechanics are based on partial DEs. In others it won’t: you can say that “Differential equations don’t describe” the properties of a gas in thermal equilibrium. We have to use an entirely different mathematical language: statistics.

    Agreed, I retract my earlier statement. I stand corrected.

    There are of course physical systems where even the basic rules are not stated in the form of DEs. Take the Ising model of a ferromagnet, which played a very important role in the development of the modern theory of critical phenomena. Its variables are binary numbers (a spin points either up or down) and its dynamics is discrete. Kinetics of crystal growth is also modeled by discrete variables.

    And my understanding is that even solutions to differential equations may entail discrete states. For example there may be infinite solutions to Schrodinger’s equations in various circumstances, but these solutions occur only in discrete states, i.e. the allowed energy levels of the electron correspond to the solutions of Schrodinger’s differential equation, and these levels occur at discrete level.

    It is because the universes is subject to quantum law that some argue that the universe as a whole is a giant quantum computer. I found passing mention of this here: Church Turing Thesis.

    But the question of OOL is not merely whether a system is capable of computation, but whether the system will compute and construct physical replicas of itself.

    When a stone is thrown in a still pond, a wave is formed, and in a sense a wave “replicates” itself through the water as it travels.

    It is certainly conceivable that Ising’s work would suggest that a configuration of spins could replicate and propagate in a material, but this does not seem at all analogous to the propagation of replicas that we see in bioogical systems.

    It seems the question of what kind of replication constitutes life. I think more work in understanding what is meant by replication is in question.

    The question of what constitutes was indirectly raised by John Baez’s commentary on Eugene Wigner’s paper: Is Life Improbable.

    Baez left open the question of what constitutes replication. I think the question is not whether replication is possible, but the kind of replication taking place, namely the sort involving the materials we see in life. As Baez pointed out, as best as I can tell, one can define what observables one wishes to observe, and one can see a replication if one chooses to. [That's at least how I interpet Baez' paper].

  378. 379

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  379. 380

    a

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  380. 381

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  381. Incidentally, Nobel Laureate Wigner was skeptical of Darwinian evolution.

    The essay by Wigner which was referenced above through John Baez paper was mentioned favorably in the book which founded the 1984 ID movement, Mystery of Life’s Origin.

    Wigner wrote his essay in Polanyi’s book around 1960 just before he was awarded the Nobel prize.

    I don’t believe his essay is beyond repair if we increase the dimensions of H to be non-trivial, but that is just a guess at this point. I have to look into it more.

    Sal