Home » Adminstrative » What happened to “Colson Praises PETA”?

What happened to “Colson Praises PETA”?

I deleted this thread because I found the comments offensive. Let’s keep postings and comments germane to ID.

Addendum by DaveScot: For the same reason I deleted the “Sterling Example of Anti-Religionists” thread due to many complaints that it was offensive. I want to extend my apologies for my own vulgar contributions that many found to be offensive. When I find myself among the crude and vulgar I tend to participate at the same level rather than rise above it as I should.

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200 Responses to What happened to “Colson Praises PETA”?

  1. Let’s keep postings and comments germane to ID.

    An excellent idea, Dr. Dembski. Perhaps you could bring things back on topic by posting that list of Intelligent Design predictions you have.

    It’s been a month since that post, and the suspense is killing some of us!

  2. vesf: your link seems not to work.

  3. Dr Dembski’s ID predictions? Yes, we’re all keen to hear those. After all, one key thing that a scientific theory – like ID so totally is – does is to make testable predictions.

  4. Apologies, Dr. Dembski. My html skills must have taken a wrong turn at Albuquerque. Semprini’s link is working, though.

    I’m glad I’m not the only one who has been waiting for this.

  5. Here’s what I had FTE’s PR people pass on to Keith Olbermann’s producer:

    —————-

    Dear SNIP,

    Please pass the following examples of ID’s predictive prowess on to [Keith Olbermann's producer]:

    (1) ID predicts that although there will be occasional degeneration of biological structures (both macroscopic and microscopic), most structures will exhibit function and thus serve a purpose. Thus most organs should not be vestigial, and most DNA should not be “junk DNA.” ID proponents have been saying this from the start, and they are now being vindicated. The human appendix, just in the last months, has been found to serve as a repository of friendly flora to keep the gut healthy. Similarly, seemingly useless “junk” DNA is increasingly being found to serve useful biological functions. For instance, James Shapiro and Richard Sternberg (2005) have provided a comprehensive overview of the functions of repetitive DNA–a classic type of junk DNA. Similarly, Roy Britten (2004) has outlined the functions of mobile genetic elements–another class of sequences long thought to be simply parasitic junk. In this case, ID has made potentially falsifiable predictions and neo-Darwinian theory has shown itself to be a science stopper.

    (2) Many systems inside the cell represent nanotechnology at a scale and sophistication that dwarfs human engineering. Moreover, our ability to understand the structure and function of these systems depends directly on our facility with engineering principles (both in developing the instrumentation to study these systems and in analyzing what they do). Engineers have developed these principles by designing systems of their own, albeit much cruder than what we find inside the cell. Many of these cellular systems are literally machines: electro-mechanical machines, information-processing machines, signal-transduction machines, communication and transportation machines, etc. They are not just analogous to humanly built machines but, as mathematicians would say, isomorphic to them, that is, they capture all the essential features of machines. ID predicts that the cell would have such engineering features; by contrast, Darwinian theory has consistently underestimated the sophistication of the machinery inside the cell.

    (3) Conservation of information results (also referred to as No Free Lunch theorems, which are well established in the engineering and mathematical literature — see http://www.EvoInfo.org) indicate that evolution requires an information source that imparts at least as much information to evolutionary processes as these processes in turn are capable of expressing. In consequence, such an information source (i) cannot be reduced to materialistic causes (e.g., natural selection), (ii) suggests that we live in an informationally open universe, and (iii) may reasonably be regarded as intelligent. The conservation of information counts as a positive theoretical reason to accept intelligent design and quantifies the informational hurdles that neo-Darwinian processes must overcome. Moreover, ID theorists have applied these results to actual biological systems to show that they are unevolvable by Darwinian means. ID has always predicted that there will be classes of biological systems for which Darwinian processes fail irremediably, and conservation of information is putting paid to this prediction.

    Best wishes,
    Bill Dembski

  6. Semprini, you should chill a bit on your tone. Rude sarcasm will get you banned very quickly.

    I like hearing from evos, so I don’t want to see you go…just take my word as a friend and be a little more polite.

  7. 7
    sagebrush gardener

    Atom,

    Agreed. It has been my experience that the true effectiveness of one’s message is inversely proportional to the sense of cleverness one feels while writing it.

  8. Thank you, Dr. Dembski. You are without peer when it comes to The Argument Regarding Design.

    I must say, I was also curious about the TV show you would be on. To be honest, I was hoping it would be one of the more credible programs like Glenn Beck or Bill O’Reilly, and not an America hating liberal windbag like that Olbermann idiot.

    I certainly hope you will publish this in the next issue of Progress in Complexity, Information, and Design. When is the next issue coming out, anyway?

  9. “Rude sarcasm will get you banned very quickly.” I’m sure rudeness will get people banned, but I don’t understand why you think this applies to me. After all, ID (despite attempts to brand it as a crude repackaging of creationism) is totally a proper scientific theory, right? And Dr Dembski mentioned specific predictions a month ago.

    “ID predicts that … most structures will exhibit function and thus serve a purpose.” Isn’t there another slightly longer-established theory which says that things must serve a purpose to remain in the population?

    “Moreover, ID theorists have applied these results to actual biological systems to show that they are unevolvable by Darwinian means.” Please elaborate, Dr Dembski. We are agog.g ag

  10. Semprini: Let me encourage you to start by looking at the later chapters of The Design of Life and follow the references there (go to http://www.thedesignoflife.net). That said, I don’t like your tone, so unless you find another way in, you won’t be posting at UD any longer.

  11. but I don’t understand why you think this applies to me. After all, ID (despite attempts to brand it as a crude repackaging of creationism) is totally a proper scientific theory, right? And Dr Dembski mentioned specific predictions a month ago.

    (sigh)

    I can only do so much.

  12. 12

    Dr Dembski: I love the idea of conservation of information, but I’ve been having difficulty demonstrating it. I wrote a program which starts with a letter (‘a’) and then applies three kinds of random mutations (point, duplication, and deletion).

    I’ll show you a quick example…

    a
    aa (duplication)
    ab (point mutation)
    aba (duplication of just the first letter – it selects a random range to duplicate)
    abb (point)
    bb (deletion)
    bbbb (duplication)
    bdbb (point)
    bdbdbb (duplication of the ‘db’)
    bdb (deletion of the 3rd, 4th, 5th letters)

    It makes a lovely string of characters, but I really feel I’m missing the point – these can’t be informationally equivalent can they? I mean, I haven’t yet found out how to calculate information, but if all these strings are equivalent, won’t any string be?

  13. Venus Mousetrap,
    A suggestion, if you will. I think you have a very clever idea, but you are missing the standard darwinist objection. You have no selection. I think you can get somewhere if you figure out a way to have somekind of selection without any intelligent foreknowledge or insight to the process or its conclusion. Perhaps you could start with a small paragraph (100 letters?) and then show it to a child who is just old enough to have moderate reading skills but too young to realize you are testing something. Eight to eleven seems like a good range. Get them to pick a paragraph they like and then do the mutations to it, then have them pick another paragraph and so on. I am very courious to know how this might turn out.

    sincerely,
    d. grey

  14. I was incomplete.
    After you are done, you will probably still notice that there is not any informational difference in the any strings of letters. But ask a poet of Whitman’s caliber to write a string of 100 letters and you will have real information.

    d. grey

  15. Interesting. Suppose the next two events are

    bdd (point mutation of the b)
    bad (point mutation of the middle d)

    Now we have a word.

    Does this word contain information that the original “a” did not? If so, where did the information come from? If not, why not? Surely “bad” has a different meaning than “a”?

  16. “ID predicts that … most structures will exhibit function and thus serve a purpose.” Isn’t there another slightly longer-established theory which says that things must serve a purpose to remain in the population?
    No, Semprini. That one actually predicted junk DNA and vestigial organs.

  17. “It has been my experience that the true effectiveness of one’s message is inversely proportional to the sense of cleverness one feels while writing it.”

    Awesome comment. And so true.

  18. So did he feel clever writing it? :-)

  19. What happened? Oh well.

  20. They are not just analogous to humanly built machines but, as mathematicians would say, isomorphic to them, that is, they capture all the essential features of machines.

    Isn’t claiming isomorphism going a bit far? All machines we know about were designed by humans, so that would imply that the bacterial flagellum is also designed by humans.

    Ah, another ID prediction: time travel is possible!

    More seriously, the isomorphism is clearly not exact, so what tools do we use to decide what aspects of the analogy are correct, and what aren’t?

    Bob

  21. Venus Mousetrap -

    I believe your mistake is in considering the strings produced by your program only and not the program itself (including the pseudo-random number generator) which, as part of the system in question, must be taken into account when calculating the initial information content of that system.

    No new information can be generated by the program because all of the possible strings were defined, in germinal form, in the program’s code.

  22. “Surely ‘bad’ has a different meaning than ‘a’?” – Jack Krebs

    Not within the scope of the system in question. Such meanings arise only when you include a human interpreter as part of the system – but that human observer (and the information he brings with him) must then be counted as part of the initial information content of the system, and therefore nothing new arises.

  23. 23

    GR: that’s interesting, I didn’t look at it like that. But you know what evolutionists are like: they’ll just say ‘well, in that case the environment is capable of causing a mutation to any area of an animal’s DNA, therefore all possible animals are encoded in the environment without violating CoI’. It’s not a good argument for ID because it makes the worth of CoI effectively zero.

  24. Suppose the next two events are

    bdd (point mutation of the b)
    bad (point mutation of the middle d)

    One of the obvious problems with Darwinism is the assumption mutations lose their power with the arrival of something useful. Even in this simple example, the odds are exponentially higher than the next mutation will take bad to bcd than from “bad” to “good”.

    Now, obviously serendipitous mutations can occur and be frozen via natural selection but it requires a belief system akin to the expectation of daily miracles for one to conclude that this process can explain the development and diversity of life. There really is an “edge to evolution”.

  25. “…you know what evolutionists are like: they’ll just say ‘well, in that case… all possible animals are encoded in the environment without violating CoI’ ” – Venus Mousetrap

    Except for two things:

    First, they would still have to demonstrate that the environment is a sufficient (and not just a necessary) cause of what we see and know, which is an exceptionally far-fetched idea akin to perpetual motion or spontaneous generation: the periodic table of the elements plus the basic laws of nature are woefully inadequate to account for life in all its manifestations (even without including consciousness, conscience, moral concepts of good and evil, etc).

    Secondly, they would still have to explain where those cleverly designed elements and those flawlessly integrated laws originated.

    Bear with me.

    The form of our arguments, I think, are the same in the small and the large. We deny both perpetual motion and spontaneous generation on thermodynamic gounds, at any scale. And the notions we have of both specified and irreducible complexity, which are more-or-less “built in” to our psyches, tell us that any sufficiently complex functioning system (whether a microscopic flagellum or a humongous universe) is the result of design and purpose.

    Misunderstanding of thermodynamic principles may be excusable, but denial of our built-in faculty for recognition of “artifacts” is neither a logical nor a scientific problem; it is a manifestation of a spiritual defect (called “depravity” or “original sin”) that cannot be cured by anything short of a miracle (called “regeneration” or “rebirth”). Such obstinate deniers of the obvious are “without excuse”, Romans 1:20, and will be converted only through “the foolishness of preaching”, 1 Cor 1:21.

  26. To tribune7: the issue is merely whether new information has been added. Extrapolating that issue to the power of evolution is far beyond the intent of my remark.

    Also, Gerry writes,

    Secondly, they would still have to explain where those cleverly designed elements and those flawlessly integrated laws originated.

    This also is taking the issue too far. One doesn’t have to know why the universe is as it is in order to explore and explain how it works. You are confusing science with metaphysics, I think.

    And I have to object to your idea that my, or anyone else’s, objections the aspects of ID that you describe is a product of original sin that will be remedied only by spiritual rebirth.

  27. One doesn’t have to know why the universe is as it is in order to explore and explain how it works.

    Experience tells us that it matters a great deal to an investigation whether or not that which is being investigated arose via agency involvement or nature, operating freely.

    However when it comes to origins then we know that nature, operating freely cannot account for the origins of nature.

    Therefor something beyond nature is required. IDists say that something is an intelligent source. The other guys just ignore it all together.

    And now they want to use that ignorance as some sort of leverage to the disadvantage of ID.

  28. 28

    “When I find myself among the crude and vulgar I tend to participate at the same level rather than rise above it as I should.”

    One thing that I have always admired about Dr. Dembski is his humility. He seems like someone who thinks about his actions and cares about how they effect others.

    Three cheers for Dr. Dembski. Hooray!

  29. Hey Bob,

    We could take your line of thought a step further: every machine we know of has been produced by specific people born before 2009. Will this, therefore, imply that the machines of the future (clearly an isomorphic group) were also produced by these same individuals born before 2009? Clearly not.

    We could also widen the criteria instead and say that all known machines produced have been produced by intelligent, animated agents (which is what allows them to build machines in the first place.) Even beavers and bees build simple machines, designed for a contrived purpose, but they are not human. They are, however, animated intelligent creatures.

    I’m sure ID advocates would be comfortable with the conclusion that whatever designed the biological machinery we see must have been an animated intelligent being.

  30. “When I find myself among the crude and vulgar I tend to participate at the same level rather than rise above it as I should.”

    One thing that I have always admired about Dr. Dembski is his humility. He seems like someone who thinks about his actions and cares about how they effect others.

    Three cheers for Dr. Dembski. Hooray!

    It was actually DS who wrote that part. But he equally deserves credit for admitting his behavior was wrong and manning up to it.

  31. 31

    Sorry Dave, this is the second time I didn’t give credit to you when credit was due.

  32. Jack

    If letters are not designed to transmit information, there is no more information in “bad” than there is “bcd”

    If letters are designed to transmit information in highly specified sequences, then then the mutation to “bad” conceivably decreased clarity (information) since bad has a predetermined meaning, and if used in an improper context, would distort reality.

  33. Bob O’H wrties “Isn’t claiming isomorphism going a bit far? All machines we know about were designed by humans, so that would imply that the bacterial flagellum is also designed by humans.”

    I like Atom’s response in 29. Similarly, suppose a human designed and built a machine; let’s call it a human widget (HW). Suppose an alien built a machine that is identical to the HW in all respect. Call it an alien widget (AW).

    Now AW is identical to HW, and the two machines are therefore quite literally isomorphic (which means “equal form”). But under Bob O’H's formulation of isomorphism we cannot say they are isomorphic. Conclusion: Bob’s wrong.

  34. BarryA
    Neither Atom’s answer in 29 nor yours in 33 shows that Bob is wrong. There is very good visible evidence that leads to an inference that humans born after 2008 will have the same ability to create machines that earlier born humans do.

    The evidence for the aliens you suppose, or any other non-human machine creator is not quite so clearcut.

  35. congregate wrote:

    There is very good visible evidence that leads to an inference that humans born after 2008 will have the same ability to create machines that earlier born humans do

    Yes, but they are not the same humans. All human design observed thus far has been designed by humans born before 2009. According to Bob’s logic, we’d have to conclude that for the future machines machines to be truly isomorphic they would also have to be produced by people born before 2009. This is clearly not the case.

    I also included the example of non-human design: bees (hive structures), beavers (artificial dams and homes), and let’s not forget spiders (food trapping nets).
    This again shows that Bob’s stringent requirements for “isomorphism” are mistaken, since we have literal examples of non-human design by intelligent, animated agents. So the human factor he requires is not a fundamental or relevant feature to the isomorphism.

  36. When is the interview with Keith Olbermann scheuled? I don’t watch his kind but in this case I’ll make an exception.

    Lou

  37. Atom – I’m not sure I would describe what beavers and bees build as machines. They’re structures, yes, but they don’t have any moving parts. And are they really dissimilar to, say, corals?

    I think you’re actually strengthening my point. The mapping from human machines to the working of the cell is not exact (i.e. it’s not an isomorphism), and the question is where do we draw the line? And how do we find a rule for drawing the line?

    BarryA – Have you ever seen an alien construct a machine? If you have. please report to Area 51 for debriefing.

    Let me repeat what I wrote, and emphasise the bit you missed:
    “All machines we know about were designed by humans”
    So, if I’m wrong, you have an interesting story to sell to the papers.

    Bob

  38. Don’t confuse subjective and objective information.

    BAD might mean something to Jack Krebs but it’s just three letters that hold the same amount of information as any other three letters as far as the universe is concerned.

    Objective information cannot be created nor destroyed. It only changes form. Stephen Hawking spent years trying to prove that information could be destroyed and made a famous bet that it could be. His assertion is that information is destroyed when matter passes through the event horizon of a black hole. He conceded that he was wrong recently. The information enters the observable universe again by way of “Hawking” radiation.

    See

    http://en.wikipedia.org/wiki/B.....on_paradox

    for more on the subject.

  39. OK – so two questions:

    1. Does a four letter “word” have more information than a three letter “word”? I assume the answer to this is yes – if it’s not, please explain.

    2. So suppose a three letter word in the program above gains a letter through duplication, thereby gaining information. If, as you say, “information cannot be created nor destroyed. It only changes form.”, I would conclude that something else must have lost information in order for the word to have gained information. What information was lost? Can you explain?

    Thanks.

  40. Bob

    The genetic code is, well, a code.

    Explain how codes can arise without a coder.

    It wouldn’t be hard to convince me that simple machines can arise without a machinist but not codes. Codes by definition have an abstraction layer which serves to translate coded information from one form to another. In this case from DNA triplets (codons) to amino acids.

    We know that humans can invent codes. Is there anything else in nature that can invent codes that you can name?

    If you can’t name anything then a question that follows is what property of humans gives them the ability to invent codes?

    That’s a rhetorical question. The property is intelligence. It doesn’t require a human to invent codes. It requires intelligence to invent codes.

    Prove this wrong and you’ll have convinced me that intelligent agency is unneccessary in the origin of life.

  41. Speaking of nano-machines, I was browsing “New Scientist” magazine online last night when I came across an article that claimed to explain how the bacterial flagellum evolved. Unfortunately, as I’m not a subscriber, I was only able to read the first paragraph or so online. Has anyone read the article, and is there anything new in it, or is it just the same old stuff?

    By the way, I just had a thought regarding nano-machines. If the universe is the product of a superior but finite intelligence, then as our scientific knowledge advances over the course of time, the complex designs we observe in the universe should become more comprehensible to us, and the ratio of explained to unexplained phenomena should gradually increase. We would thus expect to observe a “God of the gaps” trend in science, as advances lead us to flashes of insight: “Ah, so THAT’S how the intelligence did it!” Our awe of this intelligence would therefore decrease over the course of time.

    If, however, the universe is the product of an Infinite Intelligence, as Jews, Christians, Muslims and Hindus believe, AND if the universe is a reflection of the wisdom of this Intelligence, then as our scientific knowledge advances, we would expect to discover more and more examples of bafflingly complex structures that leave us scratching our heads and wondering, “Who ordered that?” Also, the rate at which we discover new and unexplained complex structures should exceed the rate at which we find explanations for previously known structures. Thus the ratio of explained to unexplained phenomena should DECREASE, and the gaps should grow, not shrink. In the meantime, our awe and bafflement at the kind of mind that could come up with designs that we would never have thought of in a million years should increase.

    I would suggest that what we are now beginning to learn about the complexities of DNA and the human brain may just be the tip of the intelligent design iceberg.

  42. Jack

    Information requires some form of media to contain it. The word isn’t just a word. It’s a pattern of matter and energy. So yes, if you move particles around to add a letter to a word then those particles had to come from somewhere. Another pattern had to be changed in order to change the pattern of the word. The total amount of information remains the same. It merely changes form. If you want to talk about the meaning of a word changing by adding or dropping letters that’s subjective, not objective. There is no meaning unless there’s a subject to which it’s meaningful. Meaningful information can be created and destroyed but only in the eye of a beholder. The unconscious universe is not a beholder.

  43. Jack Krebs:

    “Does a four letter “word” have more information than a three letter “word”?”

    A four letter word has more complexity that a three letter word, but not necessarily the same specification. Just for instance:

    a) cat is a three letter word, with complexity = 1:26^3, and a functional specification due to trhe fact that, in english, it is recognizable as the word for the specific animal.

    b) cart is a four letter word with higher complexity (1:26^4), and similarly specified, but with a different meaning.

    c) catt is a four letter word with the same complexity as b), but not functionally specified, at least in the context of english lauguage.

    Please note that it is easy enough to pass from a) to b) ot from a) to c) through a random process of adding a random letter in a random position, because the search space is not so big. None of these examples is CSI. The first two are non complex, specified infromation. The third is non complex, non specified information. Anyway, the passage from a) to b) indeed destroys some information and creates a different one. That’s perfectly possible, because the information we are considering is trivial, in the sense of non complex, and it can randomly emerge from random processes.

    But consider the same example, but with a) and b) being two different english sentences, of the same length, let’s say 100 characters, which is not a long sentence at all. The two sentences have a specific meaning, but thwy are saying two completely different things with completely different words. In this case the two sentences are CSI (complexity higher than 1:10^150, which is Dembski’s UPB, and functional specification), but it is completely impossible, for all empirical purposes, to pass from one to another through a random process of character substitutions, unless the searching algorithm already knows the target solution and can fix single correct characters (the “Methinks it’s like a weasel” model), or anyway has some other specific knowledge about the target solution which can facilitate the search.

    These examples are just to show that the information in ID discussions should always be considered related to a specification, and not in general as a bit content. Besides, only if you add complexity of sufficient level the difference between random events and designed events becomes evident. At low complexity levels, anything can happen randomly. That’s why languages are complex and we use words and sentences and paragraphs, and not just simple sounds, to express ourselves. That’s why passwords have to be long enough and complex enough to be safe. If you have a 4 bit password, you are doomed, but if you have a 256 bit password you can sleep safely. Unless someone alredy knows it: then the pre-specification of your complex password is shared with another being, and if someone steals from your account, you have not to think long before knowing who is responsible. That’s called design inference…

  44. Bob O’H,

    Spider webs and Beaver dams are both:

    Materials arranged in a pattern which fulfill a specific purpose, due to their properties and physical interactions.

    I don’t know what your definition of a machine is, but an electrostatic food net should probably qualify, no?

    Either way, you are again trying to restrict the isomorphism, this time by adding the “moving parts” requirement. Fine. But let us go all the way and use my “born before 2009″ restriction as well, ok?

    You wrote:

    The mapping from human machines to the working of the cell is not exact (i.e. it’s not an isomorphism), and the question is where do we draw the line? And how do we find a rule for drawing the line?

    In what relevant ways are they different?

    As for your won questions, we draw the line at relevant features, meaning ones that are essential to a) being a machine and b) their construction.

    All three classes of machines (human buiolt pre-2009, human built post-2299, and cellular) share the following traits:

    1) All are material objects.

    2) All use laws of physics and interactions among the parts to seemingly accomplish a goal.

    Now, if there is alien life (as BarryA uses in his thought experiment) or Strong AI in the future, they could also build machines that fit these criteria.

    Again with BarryA’s thought experiment:

    If a non-human intelligence (alien, robotic, etc) were to build an exact replica of a human device, it would be both isomorphic and non-human built. So this thought experiment shows that it is not logically necessary for a machine to have been built by a human in order to be isomorphic to human machines.

    Your bringing up of “we have no proof of alien life” is a distraction and doesn’t do anything for your case; it is irrelevant, as we are discussing what is logically necessary to qualify as an isomorphic machine.

    You might as well argue that Schrödinger never actually had a cat.

  45. I just wrote:

    You might as well argue that Schrödinger never actually had a cat.

    I apologize…that comes across mocking and I’m sorry for writing it. Please disregard that part.

    What I meant to say, more kindly, was that BarryA’s example and mine both show is that “who built it?” is not a logically necessary or relevant requirement for isomorphic relationships among machine classes. Barry’s was a thought experiment only, so finding proof of teh situation actually occuring is irrelevant.

    Again, sorry for my tone of the Schrödinger comment…it sounded better in my head and less mocking.

  46. Atom, don’t be too hard on yourself. I thought the cat comment was funny and not at all harsh. Humor does not equal mocking.

  47. Thanks Barry. It is Bob, however, that may have been offended. If he didn’t see anything wrong with it, then I’m good. But if he was offended by it, then I will apologize to him (as I did).

  48. 48

    DaveScot, isn’t the genetic “code” kind of a metaphor, at least at some levels? (For example, it might be more like a cipher than a code.) Thinking of it as a code can be useful but might also constrain.

  49. larrynormanfan:

    I don’t understand well what you mean with “metaphor”. As far as I know, the genetic code is exactly what the word says: a code.

    Here is a defin ition of code from the internet:

    “A system of symbols and rules used to represent instructions to a computer; a computer program” (from “the free dictionary”).

    Well, the genetic code is exactly that: a system of symbols (the triplets or codons) used to represent instructions to a computer (the translation system in the ribosomes). The codons are symbols, because they represent both the 20 aminoacids and some important punctuation instructions. Each codon has no biochemical relationship with the aminoacid it represents: in other words, the relationship is merely symbolic, acoording to a code established in the beginning (indeed, as we know, it is not even really universal).

  50. 50

    gpuccio, here’s a piece from an article in Modern Drug Discovery that explains what I’m getting at:

    By mid-1954, Gamow had accepted that his diamond code was not accurate, yet he and others continued to deliberate over the various codes presented by disparate researchers. In truth, the notion of a “code” as the key to information transfer was not articulated publicly until late 1954, when Gamow, Martynas Ycas, and Alexander Rich published an article that defined the code idiom for the first time since Watson and Crick casually mentioned it in a 1953 article. Yet the concept of coding applied to genetic specificity was somewhat misleading, as translation between the 4 nucleic acid bases and the 20 amino acids would obey the rules of a cipher instead of a code. As Crick acknowledged years later, in linguistic analysis, ciphers generally operate on units of regular length (as in the triplet DNA scheme), whereas codes operate on units of variable length (e.g., words, phrases). But the code metaphor worked well, even though it was literally inaccurate, and in Crick’s words, “‘Genetic code’ sounds a lot more intriguing than ‘genetic cipher’.” Codes and the information transfer metaphor were extraordinarily powerful, and heredity was often described as a biological form of electronic communication.

    Here is the link. Obviously the code metaphor is important and helpful, but is may be misleading when compared to things like (for example) languages.

  51. 51

    Sorry: I should have added “and computer programs” after “languages” at the end of the previous comment.

  52. larrynormanfan:

    Thank you for the clarification. Frankly, I was not aware of that kind of difference between “codes” and “cyphers” acoording to the fixed-length – variable length issue. And probably, most people don’t use those words in that technical sense.

    The important thing, I believe, is that the genetic code is fully symbolic, and that is a very strong argument for ID. But I fully agree tlat it is a simple enough symbolic system, and should not be called “a language”.

    On the contrary, the genetic code which is responsible for the global control of cell functions, as soon as we understand how it works, will certainly have, in my opinion, all the characteristics of a language.

  53. 53

    I’m not sure I would believe everything LarryNormanFan says.

    He has vested interests as a Darwinists.

    Hail Darwin.

  54. As Crick acknowledged years later, in linguistic analysis, ciphers generally operate on units of regular length (as in the triplet DNA scheme), whereas codes operate on units of variable length (e.g., words, phrases)

    Some codes, however, like assembly language in certain computers, actually use the same format and length for all instructions. So codes can also be of fixed length (computer code is still code, right?)

    See: RISC (Reduced Instruction Set Architecture)

    Other features, which are typically found in RISC architectures are:

    * Uniform instruction format, using a single word with the opcode in the same bit positions in every instruction, demanding less decoding.

  55. 55

    PannenbergOmega, You’re correct that I’m a Christian evolutionist (I don’t use the term “Darwinist” myself). But I’m not sure what you’re trying to say in the comment above except “booga-booga! beware the Darwinist!” The principle of caveat lector applies in all Internet conversation — in fact, in all conversation generally!

    Atom, thanks for that clarification. I don’t really know much about computer langauges. I do think we can use computer codes to help understand genetic codes (I think evolutionary computing has a lot of promise, actually). So to the degree that a computer language can look like the genome, good. But I also think we’ve got to be when we map one kind of domain onto another. There are always limitations when we compare genes with natural languages with computer languages, just as there are problems when we understand the mind in terms of software.

  56. larrynormanfan

    A code is a code. The definition is simple. There are many examples of codes created by humans. There’s only one other example of a code that’s been observed – the genetic code – and it’s in every living thing so far observed and it’s the same code (with some very trivial variations) in every instance.

  57. As gpuccio has said the genome also has instructions which are probably not codon oriented and for which no one yet has a whiff of what it is. That 98.5% of non coding DNA is probably coding for something or executing instructions somehow that affects the use of proteins.

    What encodes the RNA that is used in the cell that is not messenger RNA? Is any of it coded by DNA or is all of it built by proteins?

  58. Atom, thanks for that clarification.

    You’re welcome. I’m happy to help.

    But I also think we’ve got to be [careful] when we map one kind of domain onto another.

    I agree, we should be careful. But I do see DS’ point: every code (symbolic system, if you prefer) of known origin has originated from intelligence. So the best current hypothesis is that the genetic code did as well.

    The thing about codes and symbols in general is that they seem to carry “something” beyond their mere physical description. For example, a fire could be just a fire or it could mean “Get ready, the enemy is coming!” The fires are both fires…but one of them is a code. What made one a code and one not?

    That is why intelligence is needed to give meaning. (A “coder” if you will.) I don’t claim to understand how it all works; it is an area I meditate on and wonder about a lot. (What exactly gives “intention”? What does “intention” or “meaning” consist of?) But I can say that the physical descriptions of the two fires are the same, so the “meaning” cannot consist merely of the physical components.

    And adding other merely physical objects to the equation (the sand around the fire, the trees, the wind, etc) can’t seem to give me the meaning I’m looking for. No, some “meaner” must be inserted into the equation somewhere. If not, it is simply a lump of matter, arranged nicely.

  59. 59

    Atom, you and DaveScot both know a lot more than me about this stuff. But still, it seems more complicated than that. DaveScot says “A code is a code. The definition is simple,” but then jerry points out (rightly) that most of the genome is non-coding, apparently. So it’s a code — simply! — except when it’s not, which may be most of the time. Not so simply a code from that perspective. I don’t know much about computer codes, but inasmuch as the code refers to symbol systems in human communication, it’s got a lot of differences which may be quite important.

    Here’s something I don’t understand about the code metaphor: if a code is intricatel connected to “meaning,” and the “meaner” is the designer, then who is the recipient of the communication? The organism does not “understand” in any “intelligent” sense. In human codes such as language, there is usually intelligence at both ends of the transmission. But the genetic code is only characterized by necessary intelligence, if it is, at the transmitting end.

    (As a Christian, I would be more favorably disposed to ID if it quit pretending that the author of the genetic could be material. If a code is required for material life, and a code needs an intelligent coder, then no intelligent coder is going to be a product of material life. I just don’t get it. None of the published ID people take the idea of a material designer seriously, although they pay lip service to it.)

  60. In human codes such as language, there is usually intelligence at both ends of the transmission

    You’re right, there usually is.

    However, when I think about it, a system that is built to “accept” certain characters mechanically, while needing an intelligence to specify the coding convention and system, is already one we’re familiar with: an deterministic finite accepter, or dfa. What the dfa does is completely mechanical and the dfa is not “intelligent” in the sense we usually mean it; but the both “codes” that it accepts as well as the dfa itself are designed by intelligence. Hence the intelligence at only one end of the transmission.

    A password log-in system is maybe a more familiar example. An intelligence transmits a string of symbols and the machine (lacking intelligence) either accepts or rejects the string.

    Anyway, some good food for thought. I too feel like there is a lot to this whole equation I don’t understand, so I won’t throw stones at you for being honest about your questions.

  61. Speaking of “codes” what do you guys think of the bible code?

    -Lou

  62. Larrynormanfan

    “As a Christian, I would be more favorably disposed to ID if it quit pretending that the author of the genetic could be material.”

    ID does not need to identify the “substance” of which the designer is made. ID applies to archaeology where the designer may be homo erectus or modern man. The exact identity of the designer depends on the available candidates. 2700mil years ago, when life started here, and 500mya when the Cambrian explosion happenned, the candidates are limited to alien space beings or another extant being, God for example.

    For those who say the physical cosmos is all there is, the designer, if ther is one, must by definition be physical. Christians and other Theists are not restricted and may consider whether a transcendent God is the more likely.

    ID detects design. It does not necessarily name designers. Theology and world view provide the candidates.

  63. When I spoke of the non coding region of the genome, I did not mean that it does not code for something. I believe it must but the instructions are not likely to be codons. So the non coding regions are probably mostly code but not in the same sense as the 3 nucleotide codons are.

    I have no proof or evidence for such but there must be some instructions for how and where the proteins are placed and how much. It is interesting that the so called junk DNA is so large in the human genome when other smaller genomes such as a yeast have more coding proteins but a smaller genome. Where is the yeast’s junk DNA? It is older than humans and thus has a long time to accumulate junk.

  64. idnet.com.au:
    “ID detects design. It does not necessarily name designers. Theology and world view provide the candidates.”

    I’m inclined to think differently but not in an arguementive way. Here are my reasons:

    I don’t think theologians will ever discover the designer, or tell us much outside of their own tradition or the study thereof. They’re not any closer now than they were thousands of years ago. New or updated versions of old ideas.

    I’m more inclined to think that instead it will be ID scientists who make a break through scientific discovery and are able to identify (by scientific evidence and not tradition) the actual attributes and “nature” of the designer. I think they stand the best chance of identifying/discover “Him” through scientific methods.

    Take for instance the “Killroy was here” graffiti (design?) which most every American is familiar with. We saw the evidence on American aircraft and people became interested in knowing who, why, how, etc. They did a little digging and now there’s quite a history. The “Killroy” designer was discovered and identified.

    So if ID scientists see a biological “Killroy was here” (IC? bacterial flagellum?) it stands to reason their research will not stop there and they will continue their pursuit of science which I think will lead to new discovies in detecting design and better understanding the designer.

    I’m not argueing this, mind you. It just stands to reason in *my* mind. Time and research will tell.

    -Lou

  65. idnet.com.au, no offense, but I just don’t buy it. As I said before, none of the major ID theorists takes the space-alien theory seriously. Not one. They may say “It could be a space alien,” but I don’t think they mean it. I am willing to be corrected on this, but I don’t think the idea is actually taken seriously by Dr. Dembski, or Dr. Behe, or Prof. Johnson. or Dr. Wells, or Dr. Nelson, or Ms. O’Leary, or anybody who’s published an ID friendly book.

    On the similarity with archeology, there could be a lot to discuss. But I don’t think most professionals in the field of archeology think of themselves as doing intelligent design work. They think of themselves as doing archeology.

  66. just a correction on what I posted. The yeast genome has a relatively small number of proteins that is no where the size of the human genome in terms of proteins.

  67. larrynormanfan,

    I think many here and those prominent in ID hope or wish the designer to be the Judeo Christian God but there is zero scientific evidence to support this.

    So how can they say the science points to this God when in fact there is nothing that does. They would just look like religious zealots when they mix their religious beliefs with science and as such it would undermine their science. The best they can say is that it is an intelligent being while in their hearts they hope it is their God.

    Pushing for such an admission as to Who the designer is has no scientific purpose. Now for the designer of the universe that is a different proposition but even here one is limited to the designer being an immense intelligence that is outside of the natural world. Whether that is the Judeo Christian God is again only conjecture and outside of the realm of science.

  68. As for your won questions, we draw the line at relevant features, meaning ones that are essential to a) being a machine and b) their construction.

    Well, DNA is essential for the construction of biological machines. It directly encodes for the primary structure of the proteins. What encodes the primary structure of your car?

    Bob
    P.S. No worries on the Schrödinger’s cat comment. I like comments like that, because they summarise the point you’re trying to make.

  69. larrynormanfan:

    I appreciate your constructive discussion. Just some comments:

    “DaveScot says “A code is a code. The definition is simple,” but then jerry points out (rightly) that most of the genome is non-coding, apparently. So it’s a code — simply! — except when it’s not, which may be most of the time”

    We are speaking here of two different things. The known genetic code, the one discovered about 50 years ago, is a simple three nucleotide code which essentially codifies the aminoacid sequence of proteins, that is their primary structure. In the human genome, only 1.5% of the genetic information has tha purpose. That is the “coding DNA”, which is made of about 20000 genes, coding for an unknown number of proteins.
    But that does not explain how transcription regulation is achieved. Transcription regulation is the key point in all impotant procedures in the cell and the organism, and it is indeed very intelligent, efficient and robust, otherwise no living being could exist. It is usually felt, by us in the ID field, but now also by many in the darwinist field, that the remaining 98.5% of the genome can have much to do with that. The problem is nobody really understands how. There are now many empirical evidences of that, and we are almost certain that many regulatory functions are achieved by the transcription (but not translation) of segments of the “non coding” DNA, like introns. The relative RNA probably stays in the nucleus, and acts by linking to other DNA segments. Little is known about that anyway, and the bulk of the “non coding” DNA, with its apparent repetitive structure, remains a huge mystery.
    So, my assumption (and not only mine) is that the non coding DNA, in most or all of its aspects, is a form of genetic information written in a code that we simply don’t understand. That, obviously, has nothing to do with the traditional genetic code, of which we understand practically everything.

    “if a code is intricatel connected to “meaning,” and the “meaner” is the designer, then who is the recipient of the communication? The organism does not “understand” in any “intelligent” sense”

    That’s right, but it’s exactly what happens in computer programs. The programmer writes different parts of the software, and they communicate one with the other, and with the hardware, to perform the general function. In the case of the genetic code (the traditional one), the same codon code has been utilized for two different things:

    a) The writing of the information for protein sequences in DNA, which has to be transmitted through reproduction, and which is passed to the cytoplasm by a mirror molecule, messenger RNA.

    b) The syntesis of the specific RNA tranfer molecules, each of which has both a site for a specific aminoacid and a recognition triplet which corresponds to the right symbolic triplet codifying for that aminoacid in the messenger RNA.

    So, as you can see, a symbolic codification is necessary so that the abstract information of the protein sequence may have, at the effector site of the ribosome, the right effect: the correct protein. Indeed, the term “translation” for protein syntesis is perfectly right: the rybosome indeed “translates” the symbolic triplet information in DNA into a real structure written in another language (aminoacids). That is possible only because the aminoacid-triplet link in each RNA transfer molecule is exactly the one used in the symbolic code of DNA.
    Again, we can see here that functionally specified information is recognizable only in the specific context. the nucleotide sequence of a DNA gene would have no meaning, if there were no translation system. Indeed, we have deciphered the code that way, studying the translation system, and not in any other intrnsec way.

    “None of the published ID people take the idea of a material designer seriously, although they pay lip service to it”

    The possibility of a material designer is not just lip service. That is a major misunderstanding by darwinist commenters. Considering the possibility of a material designer is a cognitive necessity, which is implicit in the ID approach, in its foundations and methodology. In other words, ID would not be consistent if it did not consider the possibility of a material designer.

    Why? Because ID infers design in biological information, and the design inference in itself does not tell anything about the nature of the designer. Believe me, that is not a political or strategic affirmation. It is the simple truth.

    So, we have this situation: we infer design in biological information from the presence of CSI in it, and the only other example of CSI observable in nature is in human artifacts, the products of (partially) material beings. Therefore, it is a cognitive imperative to consider the possibility of a material designer. As human beings, as far as we know, were not there when life started on our planet, the only other possibility is aliens, or something like that.

    But, obviously, considering a possibility does not mean believing it is the right solution. Only in the intolerant world of darwinists considering a logical possibility becomes a crime against reason!

    As I have explained in a recent post, there are all the logical reasons to believe that the model of a creating God is the best explanation for biological information, even from a scientific point of view. But, unfortunately, our scientific understanding of reality, and in particular of the living world, is still too superficial to really support that point of view with real evidence.

    On the contrary, the design inference “can” absolutely be supported with striking evidence. That’s why ID, at present, concentrates on the design inference. That’s no strategy and no agenda: only the reasonable behaviour according to the state of facts.

  70. jerry

    Current estimate of protein coding genes in yeast is roughly 5000. In humans the number is 25,000.

    As a general rule of thumb genome size is proportional to cell size and to reproductive speed. Yeast cells are much smaller than mammalian cells (3.5 microns vs. 14 microns average respectively) and divide much faster as well.

    DNA with no other discernable functionality may very well serve as a regulator of cell size and a throttle for replication speed.

  71. larrynormanfan

    You’re wrong about not a single published ID author taking an alien designer seriously.

    Mike Gene who wrote “The Design Matrix: A Consilience of Clues” is one such person. In fact he describes a front-loaded scenario where we envision a human-like intelligence designing a single cell as a seed for life on earth.

    For those here who have read me for very long know that is the exact same scenario that I take quite seriously.

  72. Spider webs and Beaver dams are both:

    Materials arranged in a pattern which fulfill a specific purpose, due to their properties and physical interactions.

    If you want to define a machine that widely, then I think you’ll have to conclude that bacteria and polyps are capable of intelligent design (think stromatolites and coral). Do you want to go that far?

    Your can take your arguments about thought experiments are irrelevant: see my reply to Barry at 37.

    Bob

  73. Bob

    Spider webs and beaver dams aren’t good examples. They’re built by instinct not by invention. As such they’re quite different in kind from man-made machines.

  74. The genetic code is, well, a code.

    Explain how codes can arise without a coder.

    It just needs someone or something that can “interpret” the code. If slime molds excrete cAMP when they get stressed, that can be “read” as a code to say “panic”.

    Indeed, antigens can be viewed as carrying codes. So, if anything, a codee is what is needed (i.e. someone or something that can recognise the sign).

    Bob

  75. Dave @ 74 – I agree. I think that’s an argument for their irrelevance to the issue of the comparison of human-made and cellular machines.

    Bob

  76. Bob

    It just needs someone or something that can “interpret” the code.

    So you’re saying that people understood the morse code before the code was invented. Fascinating. Could you go a little bit more in depth on that?

  77. Dave,

    I meant to say rice, not yeast in my post #64. So I retracted the yeast comment in #67. But then I found out rice which has around 35,000 coding genes also has a fairly large non coding area of 430 million base pairs which did not make the point about the non coding regions.

    I was trying to make the point that there are genomes that have more coding genes than humans but much less non coding genes. If mutation processes are creating this non coding junk then why are some genomes so much smaller. So rice is not a good example. Maybe there are some. If there are some then then that might say something about the necessity of non coding genes. But at the moment I do not have a good example so I will drop it for the time being.

  78. If you want to define a machine that widely, then I think you’ll have to conclude that bacteria and polyps are capable of intelligent design (think stromatolites and coral). Do you want to go that far?–Bob O’H

    I do. I say that any living organism has design capabilities.

    Some single-celled organisms form colonies- that doesn’t happen by chance.

    Spider webs and beaver dams aren’t good examples. They’re built by instinct not by invention.–DS

    I hate that word- “instinct”. Just what exactly is it?

    In a UCD scenario did the alleged ancestors have that instinct or did it “evolve” along with the population?

    In his book “Why is a Fly Not a Horse?” geneticist Giuseppe Sermonti has a chapter titled “I can only tell you what you already know”. In it he mentions a source of information that living orgaqnisms tap for knowledge- either knowingly or unknowingly.

    from that chapter:

    An experiment was conducted on birds-blackcaps, in this case. These are diurnal Silviidae that become nocturnal at migration time. When the moment for the departure comes, they become agitated and must take off and fly in a south-south-westerly direction. In the experiment, individuals were raised in isolation from the time of hatching. In September or October the sky was revealed to them for the first time. Up there in speldid array were stars of Cassiopeia, of Lyra (with Vega) and Cygnus (with Deneb). The blacktops became agitated and, without hesitation, set off flying south-south-west. If the stars became hidden, the blackcaps calmed down and lost their impatience to fly off in the direction characteristic of their species. The experiment was repeated in the Spring, with the new season’s stars, and the blackcaps left in the opposite direction- north-north-east! Were they then acquainted with the heavens when no one had taught them?

    The experiment was repeated in a planetarium, under an artificial sky, with the same results!

  79. Dave @ 78 – No I’m not. bililiad’s interpretation of what I meant is correct.

    I do. I say that any living organism has design capabilities.

    Some single-celled organisms form colonies- that doesn’t happen by chance.

    You seem to be ignoring self-organisation. The only alternative, as far as I can see, is that you’re claiming that bacteria are intelligent.

    Bob

  80. do. I say that any living organism has design capabilities.

    Some single-celled organisms form colonies- that doesn’t happen by chance.

    You seem to be ignoring self-organisation.

    What is the evidence for self-organization when it comes to colonies of single-celled organisms?

    How did this ability arise?

    The only alternative, as far as I can see, is that you’re claiming that bacteria are intelligent.

    They are at least one scale above evolutionists.

  81. Bob

    Okay. Sorry. What Bililiad said you said was:

    I think what Bob is arguing is that another system might adapt to understand the code. E.g. a human could decode morse code without knowing what it was first…

    So you’re saying morse codes were zinging along wires carrying messages like “Hi Dad. I need money for books. I got an A in biology. Love, your son.” before anyone knew how to either encode or decode the messages.

    Fascinating. Could you go into more detail on that?

  82. Bob

    I think what Jerry is saying is that bacteria do things by instinct which seem to require intelligence at some point to program the instinct.

    By the way, do you have any ideas about how instincts are encoded by DNA? I’ve always wondered about that and have never seen any research into it. How does a bird that’s never seen another bird know how to build a nest characteristic of its species, for example? Obviously the information about what materials to look for, where to build it, how to weave it, and the dimensions must be inside the egg shell somewhere. The alternative, that the information is somehow transmitted to the bird by mental telepathy or something equally paranormal is not something that a good materialist would consider so I won’t.

    Fascinating. I wish I could go into more detail on how instincts are encoded and decoded but if you google “how are instincts encoded” you get just two hits and I’m one of them last year. It seems I’m the first person to ask the question anywhere accessible to google’s search bots. Is this gap in knowledge another one of those trade secrets of biology that’s just too awkward to talk about?

  83. bililiad

    I think you’ve got a good handle on it. We look at the machinery of life and know it somehow came to exist because it’s staring us in the face. We know that intelligent agents with some expertise in biochemistry and means of turning abstract thought into physical reality can do this. We don’t know of any other way. That’s not to say there is no other way but as it stands now intelligent design is the best explanation.

  84. No, Dave, I’m not. Codes can have designers, but I’m arguing that it’s not strictly necessary. The signal could be sent accidentally. For example, the signal that says “I’m a Brassica” that is received by parasitoids of flea beetles. Flea beetles are pests of Brassicas (things like cabbage and oil seed rape), and the signal is actually a chemical that defends against generalist predators. But specialists (like flea beetles) need the chemical to feed. The fact that the parasitoid (I think it’s a wasp) is attracted by the chemical too is, at one level, incidental, but at another level can be interpreted as an example of communication, and hence as a coded “help”.

    Joseph –
    Dictyostelium discoideum
    self-organises, so we have actual observations. As to how it arose, this is part of the story, but there is much more (and it’s not an area I follow. Although I have looked after the cat of the girlfriend of one of the people working on it).

    I’ll ignore your abuse.

    Bob

  85. bililiad

    The most wikipedia offers in explanation is that neural network wiring is responsible for complex instincts like nest building. I agree but that doesn’t help at all. Where and how is the neural network schematic stored?

  86. Dave (@85) – I don’t know how instincts are encoded, neurobiology is not an area I follow (too grey and squishy). There has been work on the genetics of behaviour – IIRC there was something weird with pika last year.

    Shocking as this may be I’m actually not omniscient. :-)

    Bob

  87. Bob

    Let’s stick to well defined codes that have a rigid structure like the genetic code or the morse code. Both are excellent examples of rigid codes and are very similar in the number of symbols. 22 symbols for the genetic code representing 20 amino acid plus stop and start symbols vs. 36 symbols for the morse code representing 26 letters and 10 numerals. Moreover, each symbol in the genetic code is composed in numerical base 4 (A C T G) and each symbol in morse code is composed in numerical base 2 (dot and dash). Let’s stay focused on these.

    In each there are three basic elements needed. A transmitter, a receiver, and the code itself. We know that for the morse code all were devised in parallel in the mind of an intelligent agent who then translated abstract thought into physical reality. The challenge you face is to explain how, in detailed logical progression, how these three elements came into existence without planning in the case of the genetic code.

  88. bililiad

    That’s the problem alright. Biologists shrug off the engineering requirements with a wave of a chance and necessity magic wand. Engineers know that entropy is an enemy of design not an ally. They also know that the only way to slow down the catastrophic effect of entropy is through careful planning. Chance and necessity is incapable of planning. Planning is something only intelligent agency (as far as we know) can accomplish. Chance and necessity is reactive. Intelligence is proactive.

  89. 1) The DNA code is a rather simple code, but still it is much more complex than a “signal”. It is a set of symbolic correspondences which assign to each of the 64 combinations of four values (the nucleotides) a specific, often redundant, meaning, be it an aminoacid or a punctuation. No surprise that darwinists have really no clue of how it “evolved”, and not even the slightest idea of how it “could” have evolved.

    To make things “easier” for darwinists, just consider that the code is the basis of conservation and transmission of information, and at the same time the instrument of protein synthesis. The only meaning and utility of the code, as far as we know, is to allow protein synthesis according to stored information. Before it “evolved”, how were proteins synthesized? If proteins were not yet there, of what utility would the code be? In ither words, the idea of evolution of the code is simple nonsense.

    Moreover, let’s pretend that the RNA world hypothesis is true. We have to remember that the RNA world hypothesis is, at present, the only way to “solve” the chicken-egg dilemma of what came firt. DNA or proteins, because RNA is the only known molecule which can do both things: store information and, sometimes, act as effector (enzyme).

    Well, let’s suppose that RNA was the carrier of information and the effector. Let’s neglect, for the moment, the craziness of that. But then, how is that supposed to have shfted to the genetic code and the synthesis of proteins? In the RNA world, information is stored and selected to the purpose of syntesizing ribozymes, the RNA effectors. The function of the RNA sequence, in that scenario, is to guide the form of the effector RNA molecule, according to RNA biochemistry. If an hypothetical RNA organism evolves, it will do that in the sense of survival advantage, that is of better ribozymes. There would be no trace, in such a world, in such genomes, of a symbolic code to synthesize proteins, molecules which are still not there, least of all any information about any protein sequence. Remember that any information for a ribozyme has no meaning for a protein, because they are two differnt macromolecules, and their biochemistry is completely different. So, in the RNA world scenario, the appearance of the DNA code and protein syntesis is even less likely than in a pure OOL scenario, because it should not only emerge all at once randomly, but it should emerge in organisms which have already evolved and adapted according to a completely different system. Nonsense, again.

    2) Instinct. That’s really an enigma. DaveScot, you are right: practically nobody speaks of that, perhaps because nibody has the least hint of how to explain it. As for me, I am just awed each time I see a mosquito (it happens quite often at my home!) flying with the accuracy of a sophisticated airplane, indeed much more elegantly, utilizing probably just a bunch of neurons, and realizing what my sophisticated computer would have difficulties in computing. Self-organization? We could better speak of miraculous organization. And yes, I have looked at the links about Dictyostelium, and the only instinct I found there is that of researchers who can convince themselves that they have understood, while they have understood nothing. The concept itself of self-organization, anyway, is much more mystical than I can bear. What is that self-organizes? Can we reason for a moment on the meanings of the two words, “self”, and “organize”?

    3) Are bacteria intelligent? I don’t know. But I know for sure that they behave very intelligently, as do ants, bees, birds, and so on. Whence does that intelligence come? Is it encoded in the genome, or somewhere else? I don’t know. Let’s start with recognizing it. Intelligence. That’s the word. Then, once we get rid of the useless attempts to deny it, we could start studying it.

  90. gpuccio:

    I’m a little confused. In what way to bacteria “behave very intelligently”?

    I think that intelligence implies some sort of cognitive function as opposed to “stimulus X provokes response Y”.

    Please elaborate on your claim.

  91. guppcio:

    We have to remember that the RNA world hypothesis is, at present, the only way to “solve” the chicken-egg dilemma of what came firt. DNA or proteins, because RNA is the only known molecule which can do both things: store information and, sometimes, act as effector (enzyme).

    I think you give RNA world far too much credit. Though it is conceivable that an RNA+Protein world could have migrated to a DNA+RNA+Protein world. (I think it conceivable that DNA were at some point an unwanted parasite in the RNA world, and because of this the RNA world developed some efficiency in manipulating DNA.)

    However, we still have a huge chicken & egg problem in the RNA world model. How on earth did the mechanism to make Protein from RNA develop? There could be no pattern of proteins prior to RNA doing it. You can’t convert directly from an RNA enzyme to a Protein enzyme. The protein machenery necessary to create protein required both code and mechanism to make it. The method of information to make it exists in the RNA world, but the mechanism didn’t exist. You can’t get there from here. RNA world leaves a HUGE chicken & egg problem.

  92. I read this:

    “(1) ID predicts that although there will be occasional degeneration of biological structures (both macroscopic and microscopic), most structures will exhibit function and thus serve a purpose. Thus most organs should not be vestigial, and most DNA should not be ‘junk DNA.’”

    And wonder how compelling it is as an ID prediction. How do we quantify “most structures” exactly? Is it 51%? 75%? And how does one arrive at such a number? Indeed, doesn’t that presume in some way to know the “mind” of the designer? And it seems like it would be hard– if not impossible– to prove this prediction wrong. After all, if after a period of time X we find that, say, only 45% of structures “exhibit function and thus serve a purpose,” the IDist could reply that the “function” of the other 55% (or whatever) just hasn’t been discovered yet.

  93. —–Larrynormanfan writes,” (As a Christian, I would be more favorably disposed to ID if it quit pretending that the author of the genetic could be material. If a code is required for material life, and a code needs an intelligent coder, then no intelligent coder is going to be a product of material life. I just don’t get it. None of the published ID people take the idea of a material designer seriously, although they pay lip service to it.)”

    If the ID scientist focuses on the fact that a design inference is based on observation and has nothing to do with religion, the Darwinist will say, “stop lying, we know that you really think that the designer is God.” That is what happened to Micael Behe two years ago.

    If the ID scientist acknowledges that, in his opinion, God is the designer, the Darwinist will say, “see, I knew all along you were just just doing religion in the name of science. I knew you were lying.” That is what happened to William Dembski last month.

    In other words, the ID scientist is a liar regardless of whar he does or doesn’t say. NOW DO YOU GET IT?

  94. Why would someone not call Mac Johnson a Christian? He calls himself one.

    -Lou

  95. Bob,

    If a fisherman’s net is a machine to catch fish, then so is a spider web. If you want to include coral, I’m fine with that, as long as specific materials are gathered and arranged in a manner that solves a problem and accomplishes a goal.

    Dave, I see your point, but I see animal “instinctual” design as simply transitive intelligence at work. Like AI would be. (Intelligence designs the machine that then “instinctually” solves a problem.)

    Bob, to recap:

    BarryA and I argue that “made by humans” is not a logically necessary requisite of isomorphism. Barry showed that it is possible for a non-human alien to build an isomorphic device, thus showing your “requirement” is not a necessary one.

    You replied by saying we have no evidence that alien device makers exist.

    If you’re happy with that argument, that is fine with me.

  96. 96

    StephenB, I know what you’re saying, and I sympathize. Perhaps we’re caught in opposite conceptual traps: you seem to have a hard time believing that a person can be a Christian and an evolutionist. I have a hard time believing that a person can go for intelligent design without theistic motivations.

    DaveScot, I’ll check out Mike Gene. Thanks for the reference. I haven’t read his work, and I didn’t know that about him.

  97. larrycranston:

    For bacteria, I was referring mainly to the observations by Shapiro, especially his recent “Bacteria are small but not stupid: cognition, natural genetic
    engineering and socio-bacteriology”, which you can easily find online. In general, it seems that bacteria act often as a collective organism, and that’s why that reminded me of the problem of instinct and complex social behaviour in higher organisms. I am not saying that the individual bacterium is intelligent, but that their collective behaviour shows signs of intelligence. But I don’t know how that is realized, as I don’t know how birds collectively migrate or ants build an ordered society. Really, animal instinct is a bigger enigma than usually thought.

  98. larrynormanfan, I am a Christian of the go to church every Sunday variety. Yet I do not find Miller’s theistic evolutionary view to be any less theologically palitable than ID is. (I actually find ID to be at significant tension with my “inspired word of God” upbringing.)

    That said, it is not my faith that has me hold to an “agency” view of evolution — that our development was twiddled with along the way, it is the fact that I develop computer software. Every bone in my software developer’s body says that DNA did not develop as the simple byproduct of a set of laws. Not in a million years.

  99. bFast:

    “You can’t convert directly from an RNA enzyme to a Protein enzyme”

    That’s exactly one of the points I was trying to express. I agree with you that the RNA world hypothesis is crap, but was discussing it because so many people stick to it as though it were revealed wisdom.

    In the same way, I think that the RNA + protein model is even more crap. The problem is not so much how that model could have shifted to DNA + RNA + protein, but rather how RNA, supposededly the precursor molecule of everything else, should have started to produce proteins. In other words, as you have said, here we are talking od two different kinds of information: a direct information stored in RNA which codes for ribozymes and a second symbolic information which, always stored in RNA, should code for proteins. How the second system could have arisen in organisms working by the first, is beyond my imagination. Perhaps I am not trained enough in building just so stories.

    In the end, we come back, as often happens, to the truth: the only reasonable model for OOL is a heavy intervention by a designer.

  100. bililiad, I was not offended at all by your comments. I was simply asking why one would not consider Mac Johnson a Christian when he himself self-identifies as one.

    -Lou

  101. Every bone in my software developer’s body says that DNA did not develop as the simple byproduct of a set of laws. Not in a million years.

    Go with your bones!

  102. 102

    bFast, I wonder what tihngs will look like in a hundred years, when what we know about software now will seem quaint and primitive. What makes an early 21st century software developer’s perspective the most relevant one?

    I’m not trying to change your mind; far from it. I just don’t know why a particular work should be given sway. ID seems to have a lot of software designers and engineers. But what should I take from that: a lesson about DNA, or a lesson about computer science and engineering?

  103. larrynormanfan:

    ID seems to have a lot of software designers and engineers.

    Yes it does, doesn’t it. However, I think that this statement on your part seriously addresses your earlier statement:

    I have a hard time believing that a person can go for intelligent design without theistic motivations.

    It seems that there is another very valid motive for buying into ID than “theistic motivations.”

  104. 104

    bFast, I should have written that better. I meant that I don’t see how a person could embrace ID without being a theist (or at least a deist) first. Motivation is not really the issue. I admit this is a prejudice of mine, just as others hold a prejudice that I can’t be a Christian evolutionist. It’s just hard for me to understand.

  105. 105

    I do have a version of the alien theory. From Larry Norman’s song “UFO”:

    He’s an unidentified flying object.
    You will see Him in the air.
    He’s an unidentified flying object.
    You will drop your hands and stare.

    You will be afraid to tell your neighbor.
    He might think that it’s not true.
    But when they open up the morning paper.
    You will know they’ve seen Him too.

    Lyrics for all occasions!

  106. larrynormanfan:

    I meant that I don’t see how a person could embrace ID without being a theist (or at least a deist) first.

    Larrynormanfan, please check out panspermia.org. Here is a whole community that is adimantly both ID and non-theist. Its clearly possible.

  107. StephenB, I know what you’re saying, and I sympathize. Perhaps we’re caught in opposite conceptual traps: you seem to have a hard time believing that a person can be a Christian and an evolutionist.

    No, I said I have a hard time believing that a Christian can be a Darwinist. Are you purposely being intellectually dishonest? Or, is it the case that you simply cannot make simple distinctions? Now I understand why you call yourself a Christian evolutionist when you are really a Christian Darwinist. There is nothing like generic terms to cause confusion and muddy the waters is there?

  108. 119 is for Larrynormanfan: the “Christian evolutionist,” whatever that means.

  109. 109

    StephenB, Huh? I really don’t understand. I’m not being dishonest, and I’m not trying to be stupid — but maybe I am.

    I’ve said I don’t use the term “Darwinist” myself, as I don’t think it’s useful and it seems to be used by the ID side to describe a kind of position I don’t really recognize as scientific, like the Richard Dawkins position, which is more philosophical than anything else.

    To lay it on the table, let me tell you what I take for granted:

    1. An ancient age for the Earth (4.5BY) and the universe (13-14 BY or thereabouts).

    2. Descent of humans from earlier hominids.

    3. Universal or near-universal common descent and (therefore) the relatedness of all the major life forms on Earth.

    4. A number of mechanisms which seem to be entirely naturalistic from the scientific perspective (excepting the very recent manipulation of life by humans, which seems to be the exception rather than the rule). Natural selection is one, but only one, of these mechanisms.

    5. A God who controls all by letting the world operate according to the rules he established. Interventions occur, of course — I’d count the resurrection as the most important — but these interventions, being miraculous, are violations of those rules by definition.

    Does that make ma a “Darwinist”? A hypocrite? Stupid? Dishonest? Unsaved? I’m interested in your response though I answer, thankfully, to Another.

  110. Larrynormanfan, you appear to be confused about the general position of the average IDer.

    1 – Though the young earth theory is within the ID camp, those who hold to it usually align themselves with the YEC community, not with ID. In general, those who identify themselves as IDers hold to an old earth.

    2 – The ID camp seems evenly split on the descent of humanoids. Though many hold to the “common design” position, many of us, including Behe, have come to accept common descent even for humans.

    3 – I, like many IDers, recognize that there is a strong case for common descent. There are clearly some twists, as science recognizes, such as HGT. Some wonder if common descent really holds through some of the most radical transformations, such as the cambiran explosion. I, for one, am prepared to accept common descent until there is clearly evidence to the contrary.

    4 – Many IDers, like myself and Behe, recognize that natural selection is a valid force of nature. We also recognize that random variation, such as random mutation, are valid forces of nature. Most of us are highly skeptical of the suggestion that random mutation has done very much good at all, however. Let me strongly suggest to you that the mainstraim scientific community sites all manner of “mechanisms”, MacNeill recently listed a bunch of ‘em, but they all filter down to two — random variation, and natural selection. “Mechanisms” such as genetic drift, molecular clocks, HGT, and on and on are all so summarized, honest.

    5 – Interventions occur. This is the great question. Are all interventions limited to God’s interaction with man, or is there a bunch of evidence in the rock record of interventions. Is the solution to the enigma of the origin of life actually an intervention of God? Is the cambrian explosion an intervention of God? What of the bacterial flagellum? Is it intervention or natural phenomenon?

    What of my favorite, the HAR1F gene? With the exception of 3 nucleotides which wander randomly, it is exactly the same in all mammals but man. In man it differs by 18 point mutations. The three-dimentional gemometry seems to indicate that all 18 had to have happened simultaneously. Is this evidence of an intervention?

    Was there just one super-intervention, the big bang? If you see it as such, then your view is the same as the recognized IDer Michael Denton. It takes only the acceptance of one intervention to to make you into an IDer.

  111. Larrynormanfan: In rereading my last two responses, I find that I have been unnecessarily cynical and a little sarcastic. Maybe, we ought to start over again. I don’t think we have gone past the point of no return. I became a little irked when you suggested that I thought that a Christian cannot be an evolutionist, when I said I don’t believe a Christian can be a Darwinist. To me, and most on this blog, an evolutionist is simply someone who accepts macro-evolution. A Darwinist is someone who posits an unguided evolution. My point has always been that the former is compatible with Christianity, while the latter is not. In any case, I will try to tone it down a little bit. Perhaps you were a little irked with me for questioning your faith. I have been through this same kind of dialogue with others who were not being sincere, and the temptation is to place everyone in the same category. I am all for a fresh start. How about you?

  112. 112

    StephenB, I’m happy for a fresh start. I just wanted to clarify my position.

    bFast, perhaps it was silly of me to mention the age of the earth and universe. I mentioned them just because they seem basic, and to refuse those is to argue with more than evolutionary biology. I’m actually not that interested in cosmological ID, since cosmology of that sort is always more philosophy than science. It’s the history of life on earth that’s interesting to me — and how to explore it scientifically.

    As for common descent, I’m under the impression that, although Behe accepts common descent, most of the others (Wells, Johnson, Nelson, Dembski, etc.) are deliberately silent or skeptical. So I’m not sure it’s “evenly split” even on humans. But I may be wrong. (I was, apparently, wrong on naturalist versions of ID such as Mike Gene’s. But that makes me confused about the complaints about materialism on the top of this very web page!)

  113. I was, apparently, wrong on naturalist versions of ID such as Mike Gene’s

    I think the Mike Gene’s view of biology is fundimentally, well, telic. One can gather this from the name of what has become his website – telicthoughts.com. Gene (a pseudonym) seems to be adimant that he is not part of the “ID movement”. He also repeats that “ID is not science”. I don’t exactly understand him in this. I think he means that it has not risen to the level of theory. In addition, he holds his theological position very tight to his chest — as he does his education.

    Alas, it would appear that you are in the ID camp. Some of us have tried to introduce the title ID Evolutionist, especially for those who hold to common descent. I personally like to see myself as an ID Evolutionist. Though many of the fellows of the Discovery Institute are not clear about there view of common descent, or hold to the “common design” view, I think that this site contains a good number of common descenters.

  114. bFast,

    I myself feel that ID science is moving towards becoming a fully-formed discipline: it has all of Kuhn’s indicators of what he would call a “pre-science” that exists before a fundamental shift in how science is conducted.
    At this point scientists that accept the Intelligent Design continue to work out the underlying principles of the theory. While the philosophical and ethical arguments for ID are currently ahead of the science, Dr. Dembski’s recent groundbreaking work in information theory and Michael Behe’s papers on irreducible complexity lead me to believe that in only a few years Intelligent Design will become the dominant paradigm.

  115. Common descent can have more than one meaning so one should be clear about what one is discussing when using the term.

    In the Darwinian sense, common descent means that all life flows from an original singular celled prokaryote organism. This led to other prokaryote singular celled organisms and to eukaryote singular celled organism and then to multi-celled organism to the phyla and then to every thing else that has existed. This is usually referred to as universal common descent.

    Or it could mean that human beings are descended from apes with similar scenarios for other animals and plants but that not all are descended from the same ancestor. In other words there is no universal common descent.

    None of this says anything about mechanism for descent. It does not imply gradualism as the mechanism though many people equate the two erroneously. Mechanism must be proved independent of whether one thinks common descent has been indicated.

    I don’t think Dembski believes in the Darwinian version of common descent and if anyone has any references on this, please feel to add to it. The last time I saw any reference to it by him was when he discussed Ayala’s book. In the Design of Life the authors are skeptical about how some species could arise through natural selection but certainly not all. If that it is the case then they are questioning universal common descent.

    Personally, I believe the evidence supports some limited form of common descent based on interventions at one or more times by an intelligence after the initial origin of life. If that is the case, then common descent could flow after each intervention but it still begs the question for the mechanism for the origin of some species. Natural selection could explain a lot of it but not all.

  116. larry

    I understand your confusion re; the complaints at the top of the page. It’s materialistic ideology that’s the problem. Material explanations, where they are warranted, are not the problem. It’s the dogmatic belief that everything has a material explanation that’s the problem. Science is supposed to be agnostic about things lacking material explanations. There are many practitioners within it who believe it should be positively atheist about everything, even those things which it cannot explain. We simply don’t believe that material explanations are adequate to explain the origin and diversification of life at this point and they are being presented as factual to a trusting public when they are not at all factual. That’s not to say there is no material explanation. There very well may be one. But maybe there isn’t one either. The evidence for and against any theory of life’s origin and diversification should be presented without prejudice. Many scientists with vested interests in evolutionary dogma are unwilling to give the negative evidence a fair hearing. I’m quite convinced the reason for that is a lot fewer people would uncritically accept the dogma if they were made aware of how weak it really is and the vested interests, whether it be promotion of atheism, funding, or credibility and esteem, would be harmed as a result. In other words, scientific objectivity is playing second fiddle to political and personal self-interest.

  117. larry

    With regard to the term “Darwinist” and who uses it I’d have you read the keynote speaker at the 2005 “Woodstock of Evolution” Lynn Margulis.

    http://www.sciam.com/article.c.....038;page=9

    Michod’s talk was the perfect lead-in for the penultimate lecture of the conference by the acknowledged star of the weekend, Lynn Margulis, famous for her pioneering research on symbiogenesis. Margulis began graciously by acknowledging the conference hosts and saying, “This is the most wonderful conference I’ve ever been to, and I’ve been to a lot of conferences.” She then got to work, pronouncing the death of neo-Darwinism. Echoing Darwin, she said “It was like confessing a murder when I discovered I was not a neo-Darwinist.” But, she quickly added, “I am definitely a Darwinist though. I think we are missing important information about the origins of variation. I differ from the neo-Darwinian bullies on this point.”

    Protests of “Darwinist” only being used by anti-Darwinians is not true. The most famous among them use the term to describe themselves.

  118. DaveScot,

    Hear, hear!
    The problem with ID materialists is that it’s a contradiction of terms: atheistic “science” has finally reached a dead end, and the traditional mores of science just won’t answer the big questions anymore. Those that have accepted ID science and remain materialists are subject to cognitive dissonance – and nothing more. That doesn’t mean that ID scientists must be religious; far from it. Only that scientific naturalism is inherently ineffective, immoral, and absurd.

  119. chuck

    I think it’s premature to say atheistic science has reached a dead end. A road block which may or may not have a way around it is more apt. The only real “dead end” I’m willing to accept without protest lies at the bounds of the observable universe in space and time. That appears to be a dead end for methodological naturalism. There’s a whole heck of a lot of time and material between the beginning of life on the earth and the beginning of the observable universe. We’ve barely scratched the surface of that so far. All one has to do is consider the current popular view in cosmology that only 5% of the “stuff” that makes up the universe is described by current theory. Some 25% is an unknown substance called “dark matter” and another 70%, even more mysterious, is called “dark energy”. We don’t know what this stuff is. All we know is that it interacts with the universe we know about through the force of gravity acting on very large objects over very great distances. The visible tip of an iceberg is 10% of it. So we can’t even say we can see the tip of the iceberg yet. We can only see the tip of the tip. If that doesn’t humble people who think they have all the material explanations for the universe well-in-hand then I don’t know what could possibly humble them.

  120. DaveScot,

    If Darwinism and all other naturalist theories are part of the Big Lie of science, I think it is fair to think that only a revolution that fundamentally changes how we as humans – as scientists and philosophers – observe the world can liberate science.
    Until then, you and I may have our differences on the severity of it being a “road block” or a “dead end”, but I believe the Religion of Atheism has impeded our quest for understanding the wonders of the universe.

  121. chuck

    Whatever you happen to believe about the mechanisms of macro-evolution, whether chance or design, neither belief impairs or improves what science delivers in way of practical things. Macro-evolution, by whatever means, happens too slowly to make any practical difference over the course of mere centuries. As far as practical intervals of time are concerned (tens and hundreds of years) macro-evolution is at a complete standstill. Modern biology is the study of living tissue. Historical biology is the study of ancient imprints in rocks. Practical applications in biology come through the study of living tissues not imprints in rocks.

  122. Science cannot be guided by an ideology, be it materialistic or not. Science can only be defined as any functional way of understanding what is empirically true with empirical methods. Ideologies are vast theories about the global nature of reality. Ideologies are not based on empirical evidence, although they can be inspired by it. That’s why materialistic ideology is not science, in the same way that religion is not science. Materialistic ideology would not be science, even if it were philosophically true.

    So, the only correct question is: is darwinian evolution a true scientific theory, or is it a non scientific theory (or if you prefer a bad scientific theory) whose general success and diffusion in the scientific world is warranted by the prevailing materialistic ideology?

    Of course, you know my answer.

    By the way, the same question can be made about ID and religious ideologies. Here again, my answer is obvious.

  123. gpuccio,

    I respectfully disagree. Kuhn’s The Structure of Scientific Revolutions is an excellent book about how science is conducted; even if you were a fan of Popper and believe Kuhn gets the history of sceince worng, the lie of evolution clearly doesn’t fit his definition of falsifiability. Regardless of what either you or I may believe, it’s clear that Evolutionary Theory isn’t falsifiable:
    As Karl Popper said in Conjectures and Refutations (1962, p.340),

    There exists no law of evolution, only the historical fact that plants and animals change, or more precisely, that they have changed. The idea of a law which determines the direction and the character of evolution is a typical nineteenth-century mistake. ..

    ID science on the other hand…

  124. 124

    bFast,

    Alas, it would appear that you are in the ID camp.

    Not so fast! ID makes a number of specific claims, pretty much none of which I presently accept. By “interventions” I was referring to miraculous interventions in human history such as the incarnation and resurrection of Jesus.

  125. 125

    DaveScot,

    It’s the dogmatic belief that everything has a material explanation that’s the problem.

    I guess I count myself as a “methodological materialist.” Not everything has a material explanation. But when something is explained in scientific terms, how can that explanation be anything but materialist?

  126. chuckhumphry:

    Maybe I don’t understand. What exactly do you disagree with? I happen to agree with what you are saying, and although I respect Popper, I prefer Kuhn, and even more Feyerabend.
    When I say that “science cannot be guided by an ideology, be it materialistic or not”, I am not meaning that it is not, but rather that ideal science shouldn’t. Even so, I don’t believe in the objectivity even of ideal science: the concept of ideal science, for me, is where honest and sincere people do their best to pursue truth with the best methods they can find, acoounting for their own subjectivity and ideologies.
    In other words, science should not be “guided” by ideologies, but is always influenced by them. A honest and earnest attitude of search for truth and of intellectual confrontation with others is for me the standard of good science. Probably, that standard cannot reasonably prevail in the general community, but it exists, and can be applied by single individuals.

    Regarding darwinian evolution, just to be clear I will reaffirm that, in my opinion, it is a theory which does not meet the standards of a scientific theory, good or bad, by any definition, and not only in a Popperian sense. But the real problem is not the theory itself, which could as well survive in the minds of its enthusisasts. After all, bad theories are not dangerous in themselves. The problem is the general status that such a non theory has gained, becoming one of the strongest dogmas of modern thought, and the incredible number of lies and deformations of truth that feed that status.

    ID, on the contrary, is a beautiful, simple theory, which has more importance than one could suspect, not only in biology, but in all fields of science and knowledge. It is, in my opinion, a truly important advancement of thought, a new paradigm which offers the foundations for great future progress. It is not all, and it is not enough. But it is a great start.

  127. larrynormanfan:

    “Not everything has a material explanation. But when something is explained in scientific terms, how can that explanation be anything but materialist?”

    Why do you say that? The concept of matter is only one of the many concepts of science. Energy, law, conservatio of quantities other than matter, symmetry, and others are a good example of objects of science. And even the concept of matter is not so well defined in science, we should rather use terms like mass or energy. I don’t think that “matter” is a good and precise word.

    Maybe you can express better the fundamentsl dualism of modern science if you consider absolute determinism vs non absolute determinism. That was the true issue between Einstein and Bohr. And that problem, still, is not solved. But, if progress has been done, it is in the direction of non absolute determinism.

    I can’t understand how many religious people can easily accept a completely deterministic view of reality! How can they account for free will, responsibility, purpose, and similar? Here, I am not speaking of divine interventions at all. But, if you accept a completely deterministic theory of “matter”, how can you explain even the simplest human volition? And if you don’t accept absolute determinism, where is the difficulty of conceiving divine intervention, not as a miracle, but as a supremely normal fact? Why shouldn’t an omnipotent God be able to do the same kind of things that we daily do? For instance, imparting design to matter, whatever it is…

  128. larrynormanfan,

    ID has no problem with using whatever tools or methodology that modern science provides and in general assuming that the findings follow natural laws. Or as you express it, the explanation is materialistic. Where it differs is in the interpretation of the results of some studies. Study after study provides explanations that are not supported by the facts. This does not say that all the explanations are unsupported and for the most part most are reasonable. But modern science lets an ideology govern or limit acceptable interpretations in certain areas and this definitely steers what is reported. Whether this is materialistic or not it is bad science.

    One of the knocks against ID is that it does not do any original science. If a scientist did an identical study to one just reported in the journals but suggested a different interpretation of the findings that would support ID, that researcher would quickly find himself without a lab, funds to do research, denial of tenure if applicable, the inability to find a journal to publish his findings and the opprobrium of all his open minded and fair colleagues.

  129. gpuccio,

    Oh, my apologies.
    With a little clarification on your part, I see what you meant. In your case, I agree with you on each of your points, but for me it is a matter of degree. I am convinced that materialism has funamentally scarred our culture in the scientific, philosophical and moral disciplines. Nothing less than its complete failure (through rigorous debate, published papers and the allure of a new paradigm; of course) can possibly redeem America.

  130. jerry,

    I disagree on one small point of interest. Every now and then a significant paper is published in a leading scientific journal that directly counters the Darwinist hegemony. For instance, Han and Warda’s paper Mitochondria, the missing link between body and soul: Proteomic prospective evidence provides a powerful argument against Darwinism.

  131. Chuckhumphry,

    The article in question was withdrawn as much it featured significant examples of plagiarism. I read through a draft, though, and didn’t find it to be quite the “powerful argument” at all.

  132. chuckhumphry,

    There are several who will question Darwinian processes but the paper itself is not pro ID in its conclusions. Your link did not point to anything so I cannot comment on the study you mentioned. As you say, reports appear frequently that question Darwinian ideas but a pro ID interpretation if nearly always verboten. Read Dave’s comment about Lynn Margulis above. She is anything but pro ID.

    But you could take this paper (which I have not read) and probably a lot of others and make some conclusions about ID as if you did the research and what would happen is just what I outlined above. In a way Darwinian processes are working in academia. You would not survive in the current environment but maybe in the future the environment will change.

  133. What is the evidence for self-organization when it comes to colonies of single-celled organisms?

    Bob O’H sez:
    Dictyostelium discoideum self-organises, so we have actual observations. As to how it arose, this is part of the story, but there is much more (and it’s not an area I follow. Although I have looked after the cat of the girlfriend of one of the people working on it).

    Umm as far as anyone knows these cells organize because of their design- IOW these single-celled organisms were designed to colonize in certain scenarios.

    There isn’t any data that this organization arose via culled genetic accidents.

  134. jerry,

    It worked for me when I tried the link; perhaps I made a mistake with the html. If you can, get your hands on a copy of the paper. The middle of it is full of excellent ID propositions. For instance,

    Alternatively, instead of sinking in a swamp of endless debates about the evolution of mitochondria, it is better to come up with a unified assumption that all living cells undergo a certain degree of convergence or divergence to or from each other to meet their survival in specific habitats. Proteomics data greatly assist this realistic assumption that connects all kinds of life. More logically, the points that show proteomics overlapping between different forms of life are more likely to be interpreted as a reflection of a single common fingerprint initiated by a mighty creator than relying on a single cell that is, in a doubtful way, surprisingly originating all other kinds of life.

    It’s a very interesting paper. The Times Higher Education has some neutral background on it (although the disgusting PZ Meyers is quoted in it, trying to discredit the paper’s conclusions).

  135. chuckhumphry,

    I tried the link on two different browsers and all I got was an error at pubmed.

    If you have a full text copy of the article, save it because it sounds like it will disappear from the journal.

  136. jerry, Try this?

  137. Are you aware hat the article has already been retracted? Speak of the efficiency od darwinists…

  138. I cry shenanigans on the editors of Proteomics for retracting the article! They’ve caved under the pressure of the Darwinist agenda.

  139. larrynormanfan: I come in peace, I promise.

    You wrote, “ID makes a number of specific claims, pretty much none of which I presently accept.”

    Which claims about ID do you not accept and why? Place special emphais on the why. Or, if you like, just pick one. It would help if I could know your rationale.

  140. Cunniformist,

    Ah, perhaps I was too strident in my opposition to Darwinism.
    When I read the paper, I found their argument to be very persuasive. I’m sorry they resorted to plagiarism, but that shouldn’t effect their thesis in any way. I stand behind Han and Warda’s theory.

  141. Chuckhumphry,

    You’re right that their arguments aren’t minimized because they copied parts of their article. And perhaps they can resubmit their work with the lifted paragraphs properly cited, etc. I don’t know how such things work, though.

    In any case, from what I read of the article, I wasn’t all that impressed. And I don’t know how we test for the “common fingerprint initiated by a mighty creator” at all. I’m not sure how to test for ID at all, actually. I noted above that Dembski’s predictions seem impossible to prove wrong, and that seems to be to be a problem.

  142. And Bob,

    Single-celled organisms coming together and forming colonies is a sign of cellular intelligence.

  143. Cuneiformist:

    Am i too skeptical if I suspect that the supposed plagiarism could have been an excuse, and the content of the article the real motive? After all, the article has immediately been classified as “creationist” by our usual friends (pharyngula or similar, I believe), and I don’t think the “creationist” approach was plagiarized (otherwise, the original articles would have alredy been retracted, too).

    The sad thing is that now I (and a few million other people, probably) will not be able to judge for myself, because the article is no more available (luckily I saved the abstract from Pubmed, while it is still there), unless someone, maybe the authors, make it available somewhere. But perhaps they’ll try to save their career…

    Anyway, if anybody has news about the text, please let me know.

  144. gpuccio,

    Excellent point!
    While charges of plagiarism are a career-breaker in Big Science’s inner circle, being labeled an ID sceintist is even worse. I think we as Intelligent Design advocates should not condone any work of plagiarism, but we cannot let Dogmatic Evilutionists besmirch two scientists that happen to advocate ID science. Their conclusions are perfectly justified under ID Theory.

  145. Wait, wait– aren’t we getting ahead of ourselves here? Again, there were numerous instances where said authors lifted passages from other articles without citation. Thus, the article was pulled. It’s that simple. There’s no reason to be skeptical of this action and posit some grand, evil Darwinist conspiracy.

  146. Cuneiformist,

    It’s not that the editor’s choice of retraction is proof of an Athistic Conspiracy in science. Simply put, in a larger context of the culture of atheist dogma in science, it confirms what would be observed if there were a grand conspiracy.

  147. chuckhumphry,

    You read the full text article but did not save it? If so then next time just hit the save button.

    I am sure many of our curious as to what it actually said.

  148. jerry,

    Rejoice! I found part of the paper at a Darwinist site here: Pimm. The full paper gave an interesting history of the mitochondria, and I’m sorry to see it gone.

  149. cunneiformist

    I’m not sure how to test for ID at all, actually. I noted above that Dembski’s predictions seem impossible to prove wrong, and that seems to be to be a problem.

    If you can’t prove or disprove the design hypothesis then it follows you can’t prove or disprove the non-design hypothesis. Thus ID and MET are equally pseudo-scientific. Objectivity (no double standards) would then compel us to reject both. In other words, you can’t have your cake and eat it too.

  150. DaveScot,

    That actually makes a lot of sense. I never thought about it that way, but that is a serious argument Darwinists have to deal with. The universe obviously exhibits design; athists keep having to deny the obvious becuase it conflicts with their dogma.

  151. Another way to support ID’s basic assumptions is the Behe model of the Edge of Evolution.

    We do not just have the malaria parasite, bacteria and HIV viruses that do not produce anything, we have several hundred families, thousands of genera and tens of millions of species.

    If we look at the species which according to Darwin are supposed to be the top of the evolutionary tree and an icon for the modern evolutionary theory and if we do the analysis of them and find no creativity in any, then we have destroyed one of the fundamental axioms of MET.

    If in this analysis we find essentially narrower gene pools in each species then existed at the family or genera level, we can say that natural selection works but what it does is cull down the gene pool and will eventually lead to extinction as the reduced gene pools will not be able to deal with some new environments.

    In other words naturalistic evolution works in the complete opposite way of what Darwin predicted. Starting with the Cambrian Explosion we see mostly downward evolution and not upward evolution.

    There has been obviously upward evolution that took place. Then the question becomes was the total package there from the start or was it added to as time and the environment changed the earth. We can only get science and the general population to come to these questions once they learn that Darwinian processes work but only to refine a gene pool and not expand it in any meaningful way. It doesn’t create, it refines and adds no additional complexity or novelty.

    This is ID research with some very solid predictions to be confirmed by research that has already taken place and to be done in the future. One of the comments I have heard by a geneticist was that they have so much data on genomes that most are not being analyzed because it exceeds the capacity of the people now available to do it. ID could put a framework on this data to confirm its predictions and if the predictions fail in some cases then these present new opportunities for meaningful research.

  152. Cuneiformist:

    “Again, there were numerous instances where said authors lifted passages from other articles without citation. Thus, the article was pulled. It’s that simple. There’s no reason to be skeptical of this action and posit some grand, evil Darwinist conspiracy.”

    Are you kidding? Are you so naif, or what? Have you read the general scandal which accompanied the online publication of the article on darwinists’ sites? Are you aware of the intimidating e-mails which, for explicit admission of the same sites, were sent to Proteomics? The “conspiracy” is there, for all to check. Those people were not concerned about the “plagiarism”, they were concerned, and really furious, because a “creationist” article had found a way through “peer review” (read: organized censorship). It’s pretty obvious that the formal charge of “plagiarism”, either there is something to it or not (and I will believe not, until I can evaluate by myself), was only an excuse, because it would not have been elegant to write online: “We have onliged the authors to retract the article because it was a creationist article”. It’s that simple, and that is not my opinion, it is under the eyes of all.

  153. gpuccio,

    I read the Darwinist “evidence” of plaigarism, and I think I must retract what I said in comment # 158: there is no plagairism, and if there were evidence, the article did not deserve to be removed. As one of the authors of the article (Warda) said,

    The problem is that we described in very clear and definite way the disciplined nature that takes part inside our cells. We supported our meaning with define proteomics evidences that cry in front of scientists that the mitochondria is not evolved from other prokaryotes. They want to destroy us because we say the truth; only the truth.

  154. DaveScot,

    You wrote, “If you can’t prove or disprove the design hypothesis then it follows you can’t prove or disprove the non-design hypothesis. Thus ID and MET are equally pseudo-scientific. Objectivity (no double standards) would then compel us to reject both. In other words, you can’t have your cake and eat it too.

    I’m not sure I agree. As an example, endogenous retrovirus (ERV) sequences serve to confirm common descent. Moreover, what we understand about common descent and primate relationships allows for some predictions about ERV sequences. If humans and orangutans shared an ERV sequence not seen in chimps, it would be a blow to modern evolutionary theory.

    Conversely, I’m still not sure how Dembski’s prediction I noted above could be falsified. It may be possible, even if I don’t see it. That’s why I’m asking.

  155. chuckhumphry,

    I’m confused by your comment re plagiarism. The side-by-side pairings of what Warda and Han wrote versus what came from other articles (several pages’ worth!) without citation is unequivocal evidence of plagiarism!

  156. 156

    StephenB, sorry to have taken so long. I’m really busy these days. But in answer to what claims, I’ll start with the key notions of irreducible complexity and CSI. Both concepts seem to say “here we have a necessary moment of intervention.” But I don’t see why that’s the case.

    Sorry I can’t follow up at more length: I’m getting ready for a business trip and will be out of touch for a couple of days.

  157. gpuccio,

    Are you kidding? Are you so naif, or what?

    So that’s a little hostile, but perhaps expected? Anyhow, there was obviously a backlash against the editors of the journal in asking how such a paper got past peer review. I don’t know how they reacted to that backlash and I don’t know what they were thinking. But it’s impossible to defend the charge of blatant plagiarism– paragraph after paragraph were lifted verbatim from other articles. It would have been interesting to see if the journal had stood by its reviewers, but given the plagiarism, the editors had no real choice. Having work rejected (and careers ruined) because of plagiarism is not uncommon, and happens to “atheist” researchers within both the sciences and the humanities.

    If there weren’t plagiarism and the article were retracted, we could talk about conspiracies and such. But we’ll have to wait and see before that can be tested, I think.

  158. cuneiformist

    As an example, endogenous retrovirus (ERV) sequences serve to confirm common descent.

    I agree and so will lots of other ID proponents here and elsewhere. Michael Behe for instance has no problem with common descent. Obviously you’re a victim of the Darwinist disinformation campaign that ID and scientific creationism are synonymous. They aren’t. I and many others believe the weight of the evidence for common descent such as anatomical and molecular homology, pseudo-genes and ERV remnants, chronological deposition in the sediments over hundreds of millions of years of increasingly complex forms bearing a likeness to past forms, and the law of biogenesis taken together are quite compelling, one might even say overwhelming evidence of common descent with modification. What serves to confirm that random mutation is the source of variation in all that? If random mutation is somehow confirmed as the mechanism driving all descent with modification then that will falsify the intelligent design hypothesis.

  159. Cuneiformist,

    Ahem – while we may part ways regarding, as DaveScot says, the “Darwinist disinformation campaign['s]” forcible retraction of the paper that allegedly plagiarized, I will remian in the same camp as gpuccio and DaveScot: you have given in to atheistic thinking on numerous issues regarding Intelligent Design Science.
    Dr. William Dembski and DaveScot have written extensively on the scientific bona fides of ID theory, and I trust in their work. You have the right to not believe ID theorists, just as you have the right to believe Darwinist propaganda. But we have the right (as DaveScot has promptly done) to call you on your misconceptions.

  160. Cuneiformist:

    You can probably judge about plagiarism because you must have the article. I am not so lucky, and so I have to suspend any judgement.

    Still, I am convinced that the charge of plagiarism would never have been an issue, if the content of the article had been “normal”.

    Anyway, the article could have been re-written, or citations added, if the problem had been only that. Still, and always speaking blindly, not having read the paper, I think that “at least” the “spiritual” or ID perspective had to be original, and an article can very well be a new take at known facts, and still retain its validity.

    The fact is, I am truly interested in what these authors had to say about mithocondria, and at present I cannot read it. Whatever you say, I am sure I have to thank darwinist censorship for that.

    The biggest lie in discussions about ID is that “ID does not do any scientific research” and that “darwinists are always doing research”. That kind of false arguments is completely pointless. It is obvious that most “research” is done by scientists with a darwinian perspective, because that’s the prevailing doctrine in the scientific, and especially biological community, and that’s why most, if not all, of the resources are owned by biologists professing darwinian faith. But that’s not the point.

    The point is that ID and darwinism are different models, different ways to explain and interpret known facts. So, in a way, as I have said often, all research is ID research. Or darwinain research, if you prefer. It just depends on who’s right.

    Research gives us facts. Researchers give us, together with the facts, their interpretation of facts, often in a dogmatic, non realistic way. But we are not obliged to accept that. We can take the facts, and interpret them on our own. Facts belong to all. Interpretations are the responsibility of those who express them.

    So, differently from what many darwinists claim, much work in science consists in reviewing and interpreting facts discovered by others. That’s, indeed, “original” work.

    That’s why, plagiarism or not, I would be interested in Warda and Han’s point of view: I am sure it is “original”, and probably stimulating. Anyway, it deserved to be discussed at the same level at which it was offered: intellectual confrontation in the scientific community. Forced retraction by technical harassment is only a demonstration of fear and cowardice.

    So, please excuse me if I appeared a little hostile (but, after all, “naif” is not a real offense), but I was just indignant. And I think I will stick to my opinion about this shameful fact.

  161. gpuccio,

    You said it far better than I could.

  162. Thanks for that explanation, DaveScot, though I don’t really consider myself a “victim” of any “disinformation campaign.” Any review of the ID material suggests a number of different camps. For instance, over at the DI, there is a featured article where, for instance, common ancestry between humans and chimps is called into doubt. (Of course, later the author is careful to suggest that “intelligent design is not incompatible with common ancestry” but bulk of the article gives one the impression that the question is wide open.)

    In any case, I’ll think more about your comments re random mutation. It’s been a pleasure talking with you!

  163. gpuccio, this post has a link which compares side-by-side the article in question with other published works. The plagiarism is unequivocal. And indeed, even if the article were just about “atheistic” science, it would have been retracted had such plagiarism occurred. (The difference, to your defense, is that were this some typical science article, scores of bloggers wouldn’t have bothered checking!) Indeed, the father of a friend of mine had his career ruined in the pages of the Chronicle of Higher Education when they exposed his rampant plagiarism. This isn’t something “atheists” do to keep out radical proponents of new ideas.

    I honestly don’t know what the options are for Warda and Han. Can they edit their article to fix the plagiarism and re-submit it? I have no idea what the policies are. There’s of course nothing to stop them from making their work available elsewhere.

    Still, I find the suggestion that this is nothing but “[f]orced retraction by technical harassment” to betray a misunderstanding of plagiarism in academia. It really is a big deal, and it usually isn’t solved by a simple “oops, sorry” sort of reply.

  164. cuneiformist

    Please don’t get me wrong about common descent. I believe it’s the best explanation based on the weight of the evidence. That said, it’s still a historical reconstruction of past events which weren’t observed and, so far, can’t be repeated. No one has come even close to observing the creation of novel cell types, tissue types, organs, and body plans by any natural or artificial means.

    One non-Darwinian hypothesis I find intriguing is held out by a biology professor with 50 years experience of comparative physiology labwork under his belt, John Davison, is that speciation is usually, if not always, caused by chromosomal reorganization. One of the more interesting aspects of this is his assertion that, at least in principle, it should be possible to reverse the speciation process and turn some extant organism back into its ancestor by artificially reorganizing its chromosomes. Something like that would really shore up any remaining doubt about common descent. I encourage you to read his papers on organic evolution, many of which can be found at his university webpage before he was “Expelled” in 2000 for his anti-Darwinian heresies.

    http://www.uvm.edu/~jdavison/

  165. DaveScot wrote (178):

    “Please don’t get me wrong about common descent. I believe it’s the best explanation based on the weight of the evidence.”

    I think it’s fair to say you have been very consistent in your assessment that common descent is the best explanation of the evidence.

    But where ID has a problem – and I think Cuneiformist may share this view – is that it is inconsistent on common descent. There are those such as yourself who concur that common descent is the best explanation (also Mike Behe), yet there are many others (Dembski, the DI) who don’t. But those who don’t haven’t really said why they doubt common descent. Unless the ID movement gets to grips with this issue, and accepts that common descent is the best explanation of the evidence, it risks always being associated with creationism.

  166. Clarence,

    Common descent is consistent with creationism or creationism is consistent with common descent. You have to define both terms before you can understand either.

  167. Clarence,

    See my post above at #128 on this topic.

  168. “Common descent is consistent with creationism or creationism is consistent with common descent. You have to define both terms before you can understand either.”

    Why?

  169. But where ID has a problem – and I think Cuneiformist may share this view – is that it is inconsistent on common descent…Unless the ID movement gets to grips with this issue, and accepts that common descent is the best explanation of the evidence, it risks always being associated with creationism.

    1st, let me suggest that we need to get past the idea that ID is a theory. Id is a framework for the development of theories. Irreduceable Complexity is a theory, along with clear and obvious falsification. Specified Complexity is another theory within the ID framework. If someone did come up with a good case against common descent, ID is a framework large enough to accomodate their theory.

    2nd. Lets get rid of the fantacy that those that bow to the god of naturalism are going to accept anything that could be interpreted as supernatural. If an intelligent, possibly supernatural, agent is suggested in the chain of explanation for our development, then, according to naturalists, it is creationism. Plain and simple.

    There is hardly a move afoot to split Behe from the rest of ID, and to welcome him into the scientific fold because he accepts common descent.

  170. bFast: There is hardly a move afoot to split Behe from the rest of ID, and to welcome him into the scientific fold because he accepts common descent.

    What is the precise formal definition of common descent? Would it be correct to say that all modern computers are descended from Babbage’s analytical engine and, as a result, can be said to have a common ancestor? If so, common descent would thus assume an evolution of sorts but not necessarily a gradual Darwinian evolution. Why should the religious among us object to this definiton? It’s perfectly acceptable to me, as a Christian.

  171. Clarence,

    What do you mean by creationism? What do you mean by common descent? There are several definitions of each so before you can make any observations about them, you have to define them.

  172. By the way, several people at ASA consider Behe a TE.

  173. —–Jerry: “By the way, several people at ASA consider Behe a TE.”

    Yes, this is a good example of how the undefined word causes untold confusion. When Christians push darwinism, we should call them Christian Darwinists, and reserve theistic evolution for someone like Behe.

  174. to Mapou: do you believe that human beings have a biological relationship with pre-hominids, as well as with earlier mammals, through an unbroken string of parent-child relationships? That is what common descent means in evolutionary science.

  175. Clarence writes, after agreeing with DaveScot (as I do) that the evidence strongly supports common descent:

    Unless the ID movement gets to grips with this issue, and accepts that common descent is the best explanation of the evidence, it risks always being associated with creationism.

    As far as I know, the alternative to common descent involves some new kind of organism, individually or in groups, somehow immediately coming into existence. Such an event would have to be a supernatural event: special creation is the only alternative I have ever heard anyone offer to common descent. I would be interested to hear what those who don’t accept common descent have to say about this: is special creation the alternative hypothesis, or are there other hypotheses that I am not aware of?

  176. Jack Krebs: do you believe that human beings have a biological relationship with pre-hominids, as well as with earlier mammals, through an unbroken string of parent-child relationships?

    No I don’t. Thanks for asking and for explaining the meaning of the word as used by Darwinists. Having said that, I do believe that the designer of homo sapiens very likely reused some of the existing genes of other animals such as primates. I mean, why redesign the wheel? In that sense, I could say that humans are related to animals. ‘Descent’ has too much historical and emotional baggage attached to it, in my opinion. It’s probably not a safe word to use anymore.

  177. Jack Krebs,

    you said

    “Such an event would have to be a supernatural event”

    No, only a design event. Otherwise you have to believe in fairy tales on how tens of thousands of magical things just happened to the DNA so that birds could fly and have unique oxygen transport systems with four chambered hearts and be warm blooded. And then not really getting much different than that in the next 150 million years.

    Darwinian processes do not create complexity or novelty but just narrow gene pools so how diid bats get their wings and sonar? How did humans become so different so quickly? How did insects get their wings? How did eyes just appear out of no where in the Cambrian Explosion? And where did mammals come from? Lots of fairy tales of magical massive DNA reorganizations.

    Jack, there is no credible theory to handle these changes, only wild a** speculation.

    It is a mystery. As more genomes get mapped and understood we will see either clear paths to all this complexity and novelty or bottle necks that could not be overcome by any naturalistic methods. I am betting on the latter. That is where all the current evidence is pointing.

  178. Mapou,

    Would it be correct to say that all modern computers are descended from Babbage’s analytical engine and, as a result, can be said to have a common ancestor?

    No, computers are not the offspring of other computers. They are not born. Common descent requires being born.

    Let me suggest two definitions: “Common descent”, as Jack Krebs described, is the understanding that my mother’s mother’s mother… was a pre-human of some sort, and that that person/animal’s mother’s mother’s mother… was a fish.

    “Universal Common Descent” extends beyond this. UCD says that if I had complete historical records I could trace my lineage back to the the first self-replicating molecule that started it all. Consider, however, that if the first self-replicating molecular structure was the product of a designer, a simple blue-green algae-like organism, we would still have universal common descent. That organism would then be the first self-replicating molecular structure that started it all.

    Now, within common descent remains significant room for a designer to act as genetic agent. Consider that humans have taken genes from one organism and put them into another, producing interesting offspring, glow-in-the-dark rabbits and such. These glow-in-the-dark rabbits have some genes in them that are received via human-induced horizontal gene transfer. However, they still were the offspring of a rabbit. Therefore, if a designing agent twiddled with genes along the way, causing a human to be born of pre-human parents, both ID and common descent would be true.

  179. Jack Krebs:

    I would be interested to hear what those who don’t accept common descent have to say about this: is special creation the alternative hypothesis, or are there other hypotheses that I am not aware of?

    Though I hold to common descent, I have watched this chatter for a long time. An alternative term used for such an event is “Common Design”. They hypothesis, if I understand, is that the great designer modifies the original sorce code to create something new, then uses the modified source to “recompile” a new creature. I think that this is an attempt to explain why there is much DNA code in common, but it is also an attempt to avoid the disgusting term “creation”.

    That said, any act of agency is realistically a creation event. I know that this line of reasoning would lead to a validation of the view that ID is creationism. Let me just speak to this obvious line of reasoning before having it raised, if that’s ok.

    Classic creationism is an attempt to confirm a holy text (usually the Bible) within science. ID, weather of the common descent or of the common design variety, does not begin with, or in fact nicely fit, any holy texts. As such, I am happy to consider ID to be “small c creationism”, but it is WILDLY different than the “fundamentally religious” “large C” Creationism that it is accused of being.

  180. I agree with most of what bfast says, but I’d like to make one important clarification.

    bfast writes,

    Therefore, if a designing agent twiddled with genes along the way, causing a human to be born of pre-human parents, both ID and common descent would be true.

    There is no one birth that separates the members of the pre-hominds from the first hominds. Speciation is a gradual process, and it is only when we look from a distance, so to speak, at individuals separated by many generations do we see distinct enough differences to conclude that individual A is a different species than individual Z. There is no one individual K or M or P that marks some type of objective dividing line between two species.

    With that said, I agree that one can, as Behe does, accept common descent and accept this gradual change as the generations go by but believe that the genetic changes (some or all) are caused by an intelligent force other than purely natural forces. I think bfast is correct in saying that there is no conflict between this ID hypothesis and common descent.

    And last -a minor point: Bfast writes, “my mother’s mother’s mother… was a pre-human of some sort.” Let’s be clear that we are talking about someplace in the order 300,000 generations here.

  181. Clarification – when I said “I agree with most of what bfast says” I was referring to post 191 above, not post 192 (which came in as I was writing my post.)

  182. Jack Krebs, “There is no one birth that separates the members of the pre-hominds from the first hominds.”

    True enough. It is really hard to say that a particular mutation pushed humanoids over the line to become human. However, whether naturally caused or agent inspired, each mutation had to have happened in one individual. That individual had to mate with the pre-mutated pre-humans. Some of its offspring would have the mutation, and the mutation would eventually fix in the population. As such, common descent requires that the line between species be extremely fuzzy as you follow your ancestry back.

  183. bFast:

    In general, I agree with most of what you say. As I am completely open minded about common descent, in the sense that I tentatively accept it, but am well ready to evaluate all the evidence, pro and con, I would like to add a few words about the theoretical frame of the problem:

    1) Creation and creationism. I may agree with your discourse about the different meanings of creationism. The only meaning of creationism which cannot be allowed, in my opinion, in a scientific discourse, is the one which proceeds from sacred scriptures as “authority” at the scientific level. That’s exactly what ID is not. (I am not criticizing those who accept that position, only saying that it is not a purely “scientific” position, while ID is). But, obviously, contemplating some form of “creation” as a possible explanation of what we observe is, in principle, perfectly scientific.
    And yet, I don’t think that the concept of “divine intervention” and “creation” are completely the same: that can be true only if we are speaking of “occasional divine intervention”. In that case, the concept is not easily distinguishable form some form of “miracle” or, if you want, “small creation”.
    But there is another possibility. If natural laws, not only those that we know, but higher ones which we still have to discover, and natural just the same, allow for divine intervention, possibly “continuous” divine intervention, exactly as they allow for continuous human intervention (free will, the constant interaction of a spiritual principle with phenomena), then I would not speak, for the origin of biological information, of miracles (if not in the sense that everything is a miracle), or “creation”, at least in a specific sense, but just of the “natural” expression of the Divine Intelligence in Its creation.

    2) Regarding the implementation of biological information, I don’t necessarily believe it had to be gradual. We have no idea of how the genetic change happened, but many evidences are partially against graduality. Whatever the possible mechanism, we have to consider the possibility that speciation, at its higher level (appearance of phyla), may have been a special phenomenon, and required a special mechanism. The same can be said for OOL, which at present is more easily conceived as rather sudden.
    So, if some of these events were not at all gradual, was the implementation made on the existing “hardware” (common descent), or just by “recompiling”, as you say, and existing, modified “software” (common design)? I really don’t know. I think we should admit how that at present we have no clue of how those things happened. And any model we try, we should not forget OOL: what happened at OOL, indeed, can have happened afterwards.

  184. #196 gpuccio

    then I would not speak, for the origin of biological information, of miracles (if not in the sense that everything is a miracle), or “creation”, at least in a specific sense, but just of the “natural” expression of the Divine Intelligence in Its creation.

    That’s correct but then you wrote:

    So, if some of these events were not at all gradual, was the implementation made on the existing “hardware” (common descent), or just by “recompiling”, as you say, and existing, modified “software” (common design)? I really don’t know. I think we should admit how that at present we have no clue of how those things happened.

    Don’t you think that these cases would anyway be non-gradual? In other way, wouldn’t big steps in the evolution of genomic information be regarded as mere miracles?
    After all the possibility that God can do (visible) miracles is what Christians have been accepted for 2000 years.

  185. kairos:

    In my heart, I am at present more for non graduality. But my point is that we really don’t know for certain. Indeed, I am convinced that the refinement of scientific knowledge will give us more clues.

    Here I am speaking from a purely scientific point of view, in a rigorous ID perspective. I try to stay loyal to my commitment to not letting religious “beliefs” have part in scientific discussions. But yes, I agree with you that I am often surprised of how christian scientists, including theistic evolutionists, whatever they are, and including people I deeply admire and respect, like Behe, seem to have so great a difficulty in conceiving God’s interventions in nature, while they should be accustomed to believe in explicit miracles.

    For me, I prefer to believe that everything is a miracle, and that God’s will and intelligence have a perfectly elegant and simple way of “communicating” with physical reality. Again, I insist that it’s not so different from what we are doing any minute, if we believe that we have soiritual souls which interact with reality through our bodies (as, if I am not wrong, christians usually believe).

    About non graduality, my idea is that there are very strong arguments for it.
    First of all, the lack of missing links. Whatever darwinists may say, missing links are just that: missing. And there are indeed billions and billions of missing links, as an ID book states in its title. Because, if we believe that the transitions are really gradual, then you need a lot of transitional states, really a lot. And we have no evidence of them, neither in the fossil record, nor in the surviving genomes we can study. It is absolutely true that species appear to be organized in disctinct and separate entities, and not in a continuum. In other words, species are a quantum entity.

    The second argument is chronological, and again it comes from fossils. It is, obviously, the cambrian explosion (and other similar explosions, like the one which preceded the cambrian). We must remember that the cambrian explosion is really an explosion, it is not a metaphor. Such a number of new complex body plans appearing practically out of the blue. And nobody knows how sudden that was. We can just restrict the period to 20-30 million years, if one is a darwinist trying to defend his own credibility, or 2-3 million years, if one is a more relaistic and unbiased person, but for what we know, it could have been 2-3 days or less. We really don’t know. However, it is certainly a stunning and unexplained phenomenon.

  186. 186

    Personally, I think Universal Common Descent is bogus. Special Creation of organisms out of thin air too though.

    Obviously there are groups of organisms that are related and have undergone evolutionary change. I would even go so far as to say that something is guiding an organism’s development at the *species level.

    To say that we all come from a single cell in the primordial past is hard for me to believe.

    * I finally received my copy of Uncommon Dissent. In the chapter by Michael J. Denton, he describes how Marcel-Paul Schützenberger did not believe Darwinism could account for the biological adaption of organisms.

  187. 187

    In regards to the discussion of ID and theodicy. Here is an article by Jay Richards on Intelligent Design and evil. http://www.salvomag.com/new/ar.....chards.php

    Enjoy

  188. to Pannenburg: if universal common descent is bogus, and special creation out of thin air is also. what are your thoughts about how the different groups of biologically related organisms came out?

    A related second question: what are yuor thoughts about what taxonomic level or organisms are biologically related? That is, if organisms within a species are related but different species are not, then there are hundreds of thousands of groups whose origin needs to be accounted for in whatever way you propose in answer to my first question. On the other hand, if you think that all organisms within a phyla are biologically related, then you have much fewer “coming into existence” events to account for.

    What are your thoughts on these two questions?

  189. bFast: Therefore, if a designing agent twiddled with genes along the way, causing a human to be born of pre-human parents, both ID and common descent would be true.

    Thanks for the clear explanation of common descent and its birth requirement. If that’s the case, I don’t think I can subscribe to common descent. It makes sense to me that any designer who is advanced enough to design and engineer complex life would not be constrained by primitive human-like engineering methods that involves gene-splicing, insemination and birth.

    There is no reason to suppose that such an advanced designer would not have the ability to engineer fully formed creatures. Using copies (“blueprints” or design specs) of genes that were sucessful in other animals would of course be the way to go. However, this would not be common descent, given the accepted definition of the term.

  190. So my next question is this: supposing that the designer could “engineer fully formed creatures,” what would we see when these creatures first appeared in the world? Are they engineered off-site, so to speak, (outside the material world) and then placed in the material world when done? If so it seems we would see the sudden materialization of such creatures. I think this would look to us like creation ex nihilo – special creation.

    Or would all the assemblage be done in the material world? – here I imagine various particles dis-assembling and then re-assembling to form a new creature, in which case we would see massive violations of known physical laws happening.

    Or there may be other hypothises – I am interested in what you think.

    But whatever the case, if birth is not involved, and the creator is making creatures fully-formed, then the question of what happens in the world during this process – what would see as the creature came into existence – is an important question to ask if an alternative to common descent is to be offered.

  191. But whatever the case, if birth is not involved, and the creator is making creatures fully-formed, then the question of what happens in the world during this process – what would see as the creature came into existence – is an important question to ask if an alternative to common descent is to be offered.

    I do not think that common descent or the lack thereof is essential to the design hypothesis, as I understand it.

  192. True, but the topic of at least the last ten or so posts has been common descent. There is nothing about ID that precludes common descent, so I am wondering what alternative hypothesis within an ID framework is offered by those who don’t accept common descent?

  193. so I am wondering what alternative hypothesis within an ID framework is offered by those who don’t accept common descent

    Uncommon Descent

    (Sorry I couldn’t resist…but it is true. Limited common descent, rather than universal. See Walter ReMine’s Discontinuity Systematics for one example.)

  194. So what do you, or Remine, say to the question of what happens – what woud we see – when a new organism comes into existence if it isn’t via common descent?

  195. Krebs: True, but the topic of at least the last ten or so posts has been common descent. There is nothing about ID that precludes common descent, so I am wondering what alternative hypothesis within an ID framework is offered by those who don’t accept common descent?

    I can’t think of any observation that might indicate beyond a doubt that some creatures were engineered fully formed. Not even the Cambrian explosion or any other biological explosion could be used as evidence in my opinion. I choose to reject common descent based solely on my conviction that an intelligent designer who is advanced and powerful enough to engineer complex life would not be constrained to use such a low-tech and inefficient mechanism.

  196. Jack Krebs,

    you said

    “what would we see – when a new organism comes into existence ”

    Probably something similar to what will appear from the biology laboratories at MIT or other institutions when they modify existing organisms. And since they will essentially be modifying current genomes, you could call it a sort of common descent with modification. Except it will be an intelligence doing the modification.

    Jack, how hard is this to understand. I know all your attempts is to try paint a supernatural spin on this so you can then tout ID as religious. But give it a rest and just look at the data for a change and keep away from your ideology.

    You are getting so predictable in your comments.

  197. Mapou:

    I choose to reject common descent based solely on my conviction that an intelligent designer who is advanced and powerful enough to engineer complex life would not be constrained to use such a low-tech and inefficient mechanism.

    Your description of a design event is painfully anthropomorphic:

    It makes sense to me that any designer who is advanced enough to design and engineer complex life would not be constrained by primitive human-like engineering methods that involves gene-splicing, insemination and birth.

    I suggest that the designer uses a very different model than you describe. Consider the HAR1F gene. It has 18 specific mutations that appear to have had to all happen at once. This is well beyond the scope of natural laws. Yet natural mechanisms exist to cause mutations in organisms. If the designer is able to manipulate the timing of these natural mechanisms, he/she/it could pull off this 18 simultaneous mutations in a way that would cause a scientist viewing it to say “hey, I just witnessed 5 royal flushes in a row!”

  198. bFast: I suggest that the designer uses a very different model than you describe. Consider the HAR1F gene. It has 18 specific mutations that appear to have had to all happen at once. This is well beyond the scope of natural laws. Yet natural mechanisms exist to cause mutations in organisms. If the designer is able to manipulate the timing of these natural mechanisms, he/she/it could pull off this 18 simultaneous mutations in a way that would cause a scientist viewing it to say “hey, I just witnessed 5 royal flushes in a row!”

    There is no doubt in my mind that the HAR1F gene would appear highly unlikely if engineered that way. My point is that you cannot show that this is the method that was used to engineer life on earth. After all, even human genetic engineers can build DNA molecules one letter at a time. The life designer that I envision would have the ability to replicate extremely long strands of DNA molecules quasi-instantaneously.

    I’ll go even further. I don’t see the need to work directly with actual molecules at all. At least not initially. Why not use a virtual machine that is powerful enough to simulate an entire organism? It would be like a writer composing and revising an article on a computer before printing out a perfect copy.

    If modern day engineers can use simulations for project design, why must a designer of complex life be forced to manipulate the timing of natural mutation events in order to compose life? Makes no sense to me. As advanced as he is, he should have the ability to use virtual genes to create fully-formed virtual organisms before outputting a fully-formed copy. Heck, he might even be able to do all of this with his mind, depending on how advanced he is.

  199. #199 gpuccio

    Here I am speaking from a purely scientific point of view, in a rigorous ID perspective. I try to stay loyal to my commitment to not letting religious “beliefs” have part in scientific discussions.

    Ok; I’ve understood your position and I too agree about.

    #211 bFast

    If the designer is able to manipulate the timing of these natural mechanisms, he/she/it could pull off this 18 simultaneous mutations in a way that would cause a scientist viewing it to say “hey, I just witnessed 5 royal flushes in a row!”

    This is also my thought about. I don’t see any problem in the the mere fact that a designer would have chosen to create new biological blueprints
    by heavily acting on what was already at disposal. After all, let’s think about the way designers do act in our world. Most of the advancements do require only minor (but INTELLIGENT) modifications of already existant designs; and in some cases the designer does “create” something by heavily modifying current paradigm, but very rarely by completely discarding the older ones.

  200. This hypothesis of coordinated mutations would take place in the context of common descent.

    And to Jerry: I’m not talking here about ID vs. non-ID. I’m talking about common descent vs. something else, and I’m trying to find out what people think that something else might be.

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