DLL Hell, Software Interdependencies, and Darwinian Evolution

_{Gil Dodgen

June 6, 2009

Intelligent Design}

Share: Facebook; Twitter; LinkedIn; Flipboard; Print; Email

In our home we have six computers (distributed among me, my wife, and two daughters): two Macs, two Windows machines, and two Linux (Unix) machines. I’m the IT (Information Technology) or IS (Information Systems) guy in the household — whatever is is.

A chronic problem rears its ugly head on a regular basis when I attempt to update any of our computer systems: Software programs are often interdependent. DLLs are dynamic link libraries of executable code which are accessed by multiple programs, in order to save memory and disk space. But this interdependence can cause big problems. If the DLL is updated but the accessing program is not, all hell will break loose and the program will either severely malfunction or suffer an ignominious, catastrophic, instantaneous death. On the other hand, if the program is updated and the DLL is not, the same thing can happen.

I’m still trying to figure out how the circulatory avian lung evolved in a step-by-tiny-step fashion from the reptilian bellows lung, without encountering DLL hell, and how the hypothesized intermediates did not die of asphyxia at the moment of birth (or hatching), without the chance to reproduce.

Of course, we all know that this kind of challenge — no matter how obvious or compelling — presents no problem for the D-Fundies (Darwinian Fundamentalists), who are true believers in the clearly impossible, based on materialistic assumptions in which design could not possibly have played a role.

Comments

Hi Dave, I was a little rushed on the last comment, as evidenced by my missing a blockquote and not ending the italics appropriately. I now have more time to continue our discussion, so will take up #150 with this comment. I'll come to your attempted logical judo later. You said,
I noticed you seem to be assuming anabolic pathways require DNA control. Why?
Because it only appears that way to you. I don't start by assuming that anabolic pathways require DNA control. It is indeed theoretically possible that RNA could control those pathways, or even that they need no control or that they control themselves. But never having seen "highly evolved [understood as complex specified] anabolic pathways" without DNA control, it does seem reasonable that the existence of such an entity, if not impossible, is at least problematic. You yourself later recognize that, as far as the possibility of RNA functioning where DNA now is,
Doing this may indeed solve some problems, but it also may bring up others which in the end might be insurmountable. Should the former happen, then the hypothesis itself may need to be abandoned.
Is it not reasonable to make a fallible tentative conclusion that when the dust is settled, such "highly evolved anabolic pathways" without DNA control will turn out to be not realistically feasible? I tend to be a little more careful the way I phrase things. Maybe the authors were too, and they are quoted out of context in this regard. But I would have preferred to say something like, "If our hypothesis is correct, then life . . . employed amino acids that lie at the end of what must have been highly evolved metabolic pathways. . . ." Otherwise, the "must have" switches from a testable consequence of the theory, and a potential liability, to an assertion about reality. But now that I know, I'll be more careful about accepting conclusions drawn from the paper. I can adjust. You say,
Of course, we haven’t seen life designed in the laboratory either, and even if we did, all that would show is that humans can design life—usually after careful study of how nature does it.
Note the implicit assumption that "nature" did it, without any help. You really have a hard time letting go of your assumptions. Or maybe you just misspoke, for you go on to say,
But I am not insisting the genetic code had to have arisen the way Yarus et al’s hypothesis suggests, so design may very well be the answer.
You then finish with
It sure would be nice, though, if you could point out some experimental evidence specifically contradicting the experimental evidence claimed to support the stereochemical hypothesis. That would be the most effective way to knock it out of the running, IMHO.
I'm not sure it would. For practically any theory, one can find supportive evidence. As I noted above (#161), the best way to destroy the theory that GWB's invasion of iraq did not cause 9/11 is not to argue that GWB did not make any Muslims mad. It is to concentrate on the time issue. Just so, for any theory, it is not the evidence that supports the theory that is likely to be most vulnerable; it is the evidence about the "highly speculative aspects" that is most likely to destroy the theory. That's why I do not concentrate on "the experimental evidence claimed to support the stereochemical hypothesis." I take it by your silence that you are agreeing that my statement that in a given evolutionary pathway,
Each step need not have function. But in that case natural selection cannot select for function,
is accurate, as long as the last clause is understood as meaning "for that step", and are withdrawing your previous objection that what I said is "a massive non sequitur.Paul Giem_{June 17, 2009
June
06
Jun
17
17
2009
12:18 PM
12
12
18
PM
PDT}

Arthur Hunt, ------"As I have indicated in this thread, what ID proponents have done is roll out calculations that have no basis in biological or physical reality." As ID has indicated, what evolutionist proponents have done is roll out hypotheses that have no basis in calculations.Clive Hayden_{June 17, 2009
June
06
Jun
17
17
2009
10:46 AM
10
10
46
AM
PDT}

I have made the comment several times before. There are no accepted definitions of life, intelligence, species and science. People cannot agree on just what each is. As regards to life, I do not think anyone in ID holds that the current DNA based system is the only possible form of life. But life is like obscenity, we will know it when we see it but really cannot define it. We have speculated here on silicon based life but someone said it was rejected because silicon does not form as many molecules as carbon does. Is HAL in 2001 a life form even if he could not reproduce? Most of us would agree that the Christian God if He exists would be a life form. So what is life is problematic.jerry_{June 17, 2009
June
06
Jun
17
17
2009
08:34 AM
8
08
34
AM
PDT}

Onlookers Passed back for a moment. Simply look above for yourself, and then follow the link to Mr Wisker's blog post. Esp consder the remarks in his linked blog post that:
Ask a high school bio student (e.g., perform a sort of “toddler test”) if these [I add: excerpted below . . . ] characteristics would qualify something as being alive, and the answer very likely would be yes. But in spite of this, OOL research has largely (but not entirely) moved on from these “creatures”. Why is this, if we are so close to (or even at) the point of having created cellular life from little more than amino acids? The answer is simple – there isn’t a very good conceptual link between protocells and life as we know it – e.g., the “DNA+RNA+protein” world.
What's the list? He claims that these microspheres show:
electrotactism (the ability to sense an electrical field) aggregation (the ability to collect into colonies) mobility (the ability to move more or less at will) osmosis (the ability to absorb material from the environment) permselectivity (the ability to selectively pass materials across a semi-permiable barrier) fission (the ability to break about into smaller functional units) reproduction (the ability to create functional copies) conjugation (the ability to join directly to another) communication (the ability to pass information directly to another) excitability (the ability to generate and utilize energy, especially electrical fields)
This list is based on a most patently superficial comparison to real life cells, in turn through a lot of equivocation of key terms and meanings. Of the above list "ability to move AT WILL" are "reproduction" are the most tellingly misleadingly equivocative, I think. So, the problems I have highlighted clearly relate to BOTH Mr Hunt and Mr Wisker. Onlookers, you will get a much clearer idea by simply reading TMLO chs 9 - 10, from 25 years ago. Sad, really. But instructive -- oh, ever so instructive -- on just how absent the tap root of the evolutionary materialist account of the origins of life is. GEM of TKIkairosfocus_{June 17, 2009
June
06
Jun
17
17
2009
08:07 AM
8
08
07
AM
PDT}

Um...
"1 –> We have identified that life forms exhibit FSCI."
Actually, no one anywhere has actually ever established, by direct experimental measurement, that FCSI (or CSI, or whatever) actually exists, in nature or in biology. Rather, those experimental measurements that have been done pretty clearly establish that FCSI (or CSI, or whatever) is a fictional concept. As I have indicated in this thread, what ID proponents have done is roll out calculations that have no basis in biological or physical reality. This is a big stumbling block for ID - math that is disconnected from reality is no way to explore the nature of something.Arthur Hunt_{June 17, 2009
June
06
Jun
17
17
2009
04:52 AM
4
04
52
AM
PDT}

Onlookers, two things: 1)Had kairosfocus read the comments between Paul Giem and me more carefully, it would be obvious he should be having this conversation with Paul. 2) Had kairosfocus read subsequent posts more carefully he would not be so thoroughly confusing me with Art Hunt.Dave Wisker_{June 17, 2009
June
06
Jun
17
17
2009
03:37 AM
3
03
37
AM
PDT}

PS: Onlookers, again, the case of proteinoids and protocells etc 9as raised again in mr Wisker's essay) was already solidly answered 25 years ago, as summarised by thaxton et al in TMLO. Cf Chs 9 - 10 here. Proteinoids, microspheres et al only very superficially resemble the realities and processes of recognisable life; in particular the step by step programmed processes of metabolism and of reproduction of cells simply find no parallel in the simplistic bullet points Mr Wisker lists. (And If I were wrong on the point, Mr Wisker could very easily refute point by point. But, as a look at he linked work will illustrate,a nd as a basic knowledge of cell processes of say protein formation and cell division will illustrate, I am not) That such superficialities and equivocations should still be trotted out 25 years later, tells us a lot, and not in the favour of those who advocate such.kairosfocus_{June 17, 2009
June
06
Jun
17
17
2009
02:45 AM
2
02
45
AM
PDT}

Onlookers: The just above by Mr Wisker is an unfortunately apt illustration of refusing to accept that circumstantial evidence of a typical variety encountered in science is evidence, and that induction on the balance of the empirical evidence is the fundamental method of science. (Insofar as science can be said to have a method as such.) It therefore manifests selective hyperskepticism, and leads to the improper attempt to turn around the burden of proof and to dismiss that which would otherwise be manifestly well warranted. Without simply repeating what has already been pointed out, let us note: 1 --> We have identified that life forms exhibit FSCI. 2 --> It is known (on millions of instances) that the only observed source of FSCI is intelligence. 3 --> It is also known on the search space and statistical weight reasons that ground say the 2nd law of thermodynamics, that there will be maximally low probability that chance processes will be able to get us tot he shores of islands of such complex functionality; on the gamut of our observed universe. 4 --> On inference to best explanation per observed evidence, intelligence is the best explanation for the FSCI we see in life. 5 --> This conclusion is of course provisional: should someone succeed in showing that FSCI is credibly and with reasonable probability produced by undirected mechanical necessity and chance, then the postulated clam will be withdrawn. (Note: where probabilities are sufficiently low, that which is logically possible is often not empirically credible; which is the foundation of the statistical mechanical form of the 2nd law of thermodynamics.) 6 --> And, that holds, whether or not we have directly observed such intelligences actually in the act of creating life de novo. 7 --> That instead of putting up a case where lucky noise creates complex, functionally specific information, we see an attempted -- but improper -- turnabout of the burden of proof in the teeth of massive empirical observation, simply shows that the true burden of proof has not been met, and that we are not up against a scientific issue, but a worldview commitment. GEM of TKIkairosfocus_{June 17, 2009
June
06
Jun
17
17
2009
01:19 AM
1
01
19
AM
PDT}

Dave W, perhaps this capsule version will help: If life could be created by scientists / designers can create life / therefore ID. If life could not be created by scientists / life is more than chemistry / therefore ID. See how easy that is? ID no matter what.David Kellogg_{June 16, 2009
June
06
Jun
16
16
2009
09:47 AM
9
09
47
AM
PDT}

Hi kairos, You still haven't rescued Paul from declaring ID false by his own argument. There is zero evidence of any intelligence ever having designed and created life. No matter how convincing or plausible any inferences and probability calculations are, ID is false because there is no evidence for one of its central tenets.Dave Wisker_{June 16, 2009
June
06
Jun
16
16
2009
09:43 AM
9
09
43
AM
PDT}

Mr Wisker: As I jut pointed out in steps, we have seen designers and have warranted signs of design; e.g. FSCI. (For simple working purposes, take this as: as a case of functionally specific information, especially algorithmic or linguistic information, comprising at least 500 - 1,000 working bits. [More formal definitions exist but this is good enough for practical purposes. this post is good enough as it passed 143 7-bit ASCII alphanumeric characters.] ) There is no case of observed chance + necessity spontaneously giving rise to FSCI, on a base of literally millions of test cases. It is those who assert or assume that C + N ("lucky noise" as I have termed it; cf the Welcome to Wales exercise) can reasonably give rise to FSCI who have a burden of proof to meet. If met, it would knock the central pillar out from Design theory. Just as, a perpetuum mobile -- if credibly demonstrated -- would destroy thermodynamics. The ball is in your court. GEM of TKIkairosfocus_{June 16, 2009
June
06
Jun
16
16
2009
06:45 AM
6
06
45
AM
PDT}

"You haver it precisely backwards. As Thaxton et al summarised in chs 9 & 10 of TMLO — all of 25 years ago — Fox’s proteinoids (which are not proteins) and microspheres (which are not cytoplasm-containing bilipid layer-enclosed cells) only very superficially resembled life, and even proteins."
KF, if you don't read and understand my essay, you really won't be able to make any substantive contribution to this discussion, I'm afraid. I am not claiming that Fox's proteinoids were the geneological precursor to proteins as we know them. But that's irrelevant when it comes to the place of Fox's critters in the OOL. Of course, this does make another point that ID proponents have a hard time swallowing - not only do the basic properties of life not require DNA, they don't even require proteins as we know them. That's two very big strikes against the need for a code in these processes.
"(Not to mention, as others objected at the time: where did all those optically active pure amino acids come from to be heated to form the non-protein bonded proteinoids in a plausible pre-life world?)"
Similar protocells can be had from Urey-Miller-type mixtures. Which makes this objection irrelevant as well.
"These entities undergo no step-by step controlled biochemical metabolic processes, and what is called “growth” and “reproduction” is a matter of simple physical processes."
In other words, many of the features of living things are "matter(s) of simple physical processes". Thank you for making my point. No code. Just chemistry. We're making some progress here.
"Insofar as proteinoids are chemically active as catalysts, much of that is rooted int eh activity of amino acieds, and they bear no resemblance to the activity level or complex key-lock fitting structures of enzymes."
Another irrelevant objection. As I explain in my essay.
"To proffer such long since adequately rebutted superficial lists still as in any way comparable to life, is to show the utter bankruptcy of the evolutionary materialist origin of life paradigm that they were suggested for in the first place."
KF, I would argue that your unwillingness to even begin to address any of the issues I raise in my essay shows that this essay in fact makes some points that are very threatening to the ID perspective.
"And that conclusion is neither circular reasoning nor self-refuting. "
You don't get it. But I'll keep trying to epxlain.Arthur Hunt_{June 16, 2009
June
06
Jun
16
16
2009
05:13 AM
5
05
13
AM
PDT}

Mr kairos: 1 –> This is of course a turnabout rhetorical resort: That is exactly what it was, to show Paul a problem with his argument.Dave Wisker_{June 16, 2009
June
06
Jun
16
16
2009
04:05 AM
4
04
05
AM
PDT}

Onlookers: Re Mr Wisker, 164:
We have zero empirical evidence that intelligence has designed and created life ( no created life in any test tubes, as far as I know). It doesn’t matter if we devise hypotheses involving information and irreducible complexity, probability and such– the fact is, we have no empirical demonstrations that intelligence has even done it once. Without this, the truth of the rest of the tenets of the ID hypothesis cannot save it. If there are no clearly demonstrable instances of intelligence designing and creating life, then the ID hypothesis is false. Period.
1 --> This is of course a turnabout rhetorical resort: not having any good evidence that mechanical necessity and chance can give rise fo FSCI, per the information origination and thermodynamics issues that arise, the attempt is to shift rthe burden odf proof. 2 --> In fact, cell based life is from a category of systems that we know very well: finely-tuned, multi-part complex entities that exhibit algorithmic step by step processes that use functionally specific complex coded information. 3 --> Common examples of such systems include PCs and cell phones. And, as these names suggest, we know that such entities are the routine product of intelligent designers. Going further, we are able to identify, following Von Neumann in the '40's, the architectural requisites of a self-replicating automaton; which we observe being met in the cell -- blueprint and replicating factory must be incorporated in the entity. that is, we see that we need to move up to a higher level of complexity; just we have not been technically able to do so as yet from scratch. (Mind you, post Ventner and post recombinant DNA, intelligent design of life forms is a FACT, not a speculation.] 4 --> Furthermore, in ALL cases of FSCI-rich systems where we know the origin directly and independently, we see that these are the product of intelligent designers. 5 --> On consulting the issues of getting to isolated islands of fucntion in vast configuration spaces, we see that chance based random walks, regardless of the presence of hill-climbing rewards, first have to get to the shores of function, before hill climbing selection processes can have any impact. 6 --> But, routinely, intelligences using understanding and creaticity, develop such functional entities. 7 --> So, FSCI etc are reliable signs of intelligent design, and on the same inductive grounds that we used to get to the generally accepted laws of nature, we have every right to treat FSCI etc as reliable signs of intelligence in action. 8 --> Therefore, let us not allow ourselves to be distracted: the real unmet empirical evidence challenge is the one to show that with reasonable odds of success, FSCI etc can be produced by blind chance + mechanical necessity through random walks that get us to shores of function. 9 --> That, after weeks, months and years of putting up this challenge at UD, the anti-design advocates still resort to turnabout rhetorical tactics and the like, tells us most eloquently, that they cannot meet the spontaneous information origination by chance plus necessity only challenge. 10 --> So, we have every reason to be confident that the inference to design on reliable signs such as FSCI etc, is a good one. GEM of TKIkairosfocus_{June 16, 2009
June
06
Jun
16
16
2009
03:19 AM
3
03
19
AM
PDT}

Mr hunt: You haver it precisely backwards. As Thaxton et al summarised in chs 9 & 10 of TMLO -- all of 25 years ago -- Fox's proteinoids (which are not proteins) and microspheres (which are not cytoplasm-containing bilipid layer-enclosed cells) only very superficially resembled life, and even proteins. (Not to mention, as others objected at the time: where did all those optically active pure amino acids come from to be heated to form the non-protein bonded proteinoids in a plausible pre-life world?) These entities undergo no step-by step controlled biochemical metabolic processes, and what is called "growth" and "reproduction" is a matter of simple physical processes. Insofar as proteinoids are chemically active as catalysts, much of that is rooted int eh activity of amino acieds, and they bear no resemblance to the activity level or complex key-lock fitting structures of enzymes. To proffer such long since adequately rebutted superficial lists still as in any way comparable to life, is to show the utter bankruptcy of the evolutionary materialist origin of life paradigm that they were suggested for in the first place. And that conclusion is neither circular reasoning nor self-refuting. It is a simple pointing out of the obvious differences between globules of molecules and well-known processes and characteristics of living cells. GEM of TKIkairosfocus_{June 16, 2009
June
06
Jun
16
16
2009
03:00 AM
3
03
00
AM
PDT}

I refer to a document from 25 years ago to point out that this is nothing really new, and it is not a real answer on OOL dilemmas of evo mat paradigms.
KF, you clearly don't understand why I cited my essay. Paul Giem asked Dave Wisker for experimental evidence for life without a DNA code. I interrupted (with belated apologies) gave him some. Many here will protest that Fox's pets were/are (a few labs work on similar systems today) not alive, but these arguments boil down to circular reasoning and are thus self-refuting. And they are to boot irrelevant. What is quite clear is that one does not need any sort of DNA code to attain any of the life-like characteristics I listed.Arthur Hunt_{June 15, 2009
June
06
Jun
15
15
2009
06:50 PM
6
06
50
PM
PDT}

Dave Wisker:
We have zero empirical evidence that intelligence has designed and created life ( no created life in any test tubes, as far as I know).
The ONLY evidence we have demonstrates that life comes from life. Anything else is science fiction. BTW there isn't any data that demonstrates living organisms arose from non-living matter via unguided processes. That goes against all observations.Joseph_{June 15, 2009
June
06
Jun
15
15
2009
10:48 AM
10
10
48
AM
PDT}

Hi Paul,
That may be true. But if one of its central tenets has no evidence for it, and the extant evidence is against it, if that central tenet should fail, the truth of any or all of the other tenets would not save the theory. The theory that GWB’s invasion of Iraq caused 9/11 may have evidence supporting many of its central tenets. But the simple fact that the invasion didn’t happen until after 9/11 means that all those considerations are irrelevant. It doesn’t matter if some Muslims hate GWB for what he did. It doesn’t matter if we find private journals from the hijackers saying, “Bush’s invasion of Iraq must be avenged.” The theory is false. Just so, if there was no life without a DNA code, HY is false. Period. Evidence against life without a DNA code is evidence against HY, and your asking for “experimental evidence” has been fulfilled.
We have zero empirical evidence that intelligence has designed and created life ( no created life in any test tubes, as far as I know). It doesn't matter if we devise hypotheses involving information and irreducible complexity, probability and such-- the fact is, we have no empirical demonstrations that intelligence has even done it once. Without this, the truth of the rest of the tenets of the ID hypothesis cannot save it. If there are no clearly demonstrable instances of intelligence designing and creating life, then the ID hypothesis is false. Period. Have you informed the ID community about this? If not, why not?
i>The problem I have with HY is not with its empirical bases. It is with the “highly speculative aspects”, to use your phrase.
That's fine with me, as long as you consistently apply the same skepticism to intelligent design.
Would you, if all the evidence overwhelmingly pointed to an intelligent designer, join Shapiro in his search for non-intelligent explanations for life, or are you prepared to give this search up at some point, however difficult that point might be to reach?
I'd probably choose the route that has the most viable research program (Baby needs shoes, after all). ;) Seriously, though, it would depend on just how much positive evidence there was for the other side. The scenarios posited above by Shaprio involve 100% negative evidence. Frankly, I'm wary of arguments built entirely on that. If that were all of the "overwhelming" evidence for ID, then I would be driven to suspect that research on neither side would be fruitful.Dave Wisker_{June 15, 2009
June
06
Jun
15
15
2009
10:36 AM
10
10
36
AM
PDT}

Folks: Busy this morning, so I simply point to TMLO online [click the picture to do a download -- FAT] where one may read ch 10 which in part goes into protocell worlds as are imagined by many,including Fox's microspheres, coacervates, proteinoids etc. I refer to a document from 25 years ago to point out that this is nothing really new, and it is not a real answer on OOL dilemmas of evo mat paradigms. GEM of TKIkairosfocus_{June 15, 2009
June
06
Jun
15
15
2009
05:51 AM
5
05
51
AM
PDT}

Can entities that grow, divide, evolve, respond to external stimuli, and are capable of rudimentary metabolism arise from simple beginnings, and without DNA? Sure enough!Arthur Hunt_{June 14, 2009
June
06
Jun
14
14
2009
08:33 PM
8
08
33
PM
PDT}

Hi Dave, Thanks for your replies. You even, IIUC, answered some of my questions, albeit indirectly. I asked,
do you have any experimental evidence of any life without a DNA code?"
Your reply was,
Secondly, when I say this or that hypothesis has experimental backing, I’m not saying (as the wording of your question implies), that this primordial life has somehow been recreated in a test tube. That, frankly, is a naïve expectation (at least at this point), and if that is the only kind of experimental evidence you will accept in order to discuss the hypothesis seriously, please speak up now and save us both the effort.
I take it that the short answer to my question is "No." If the answer is "no", that in itself is evidence against the theory. The theory requires that we have life before DNA, or at least before the current (majority) DNA code. Just as the existence of life without a DNA code would be evidence for the hypothesis of Yarus et al. (HY), the non-existence of life without a DNA code is evidence against HY. You may object that this is very weak evidence, and susceptible to being overturned at a moment's notice, and I would agree that this evidence is the kind backing the "all swans are white" assertion; one black swan effectively refutes it. But you don't have the right to insist that I stop calling it evidence. And it is evidence suggesting that HY is wrong, because it suggests that one of HY's fundamental premises is wrong. You precede this answer with the statement,
First of all, the stereochemical hypothesis for the origin of the genetic code arose from other work which suggested that the genetic code as we see it today is not what life used in its very earliest forms.
Suggested to whom and for what reason? This is beginning to sound like my defense #4: Life must have arisen naturally, the genetic code could not reasonably have been anywhere near its present form if life arose spontaneously, therefore the genetic code must have arisen in a different form. There is experimental evidence for the second clause, and therefore there is experimental evidence suggesting HY. But that is only true if one starts with the premise that life must have arisen naturally. You defend HY by saying,
I’m saying the hypothesis has experimental results which support many of its central tenets.
That may be true. But if one of its central tenets has no evidence for it, and the extant evidence is against it, if that central tenet should fail, the truth of any or all of the other tenets would not save the theory. The theory that GWB's invasion of Iraq caused 9/11 may have evidence supporting many of its central tenets. But the simple fact that the invasion didn't happen until after 9/11 means that all those considerations are irrelevant. It doesn't matter if some Muslims hate GWB for what he did. It doesn't matter if we find private journals from the hijackers saying, "Bush's invasion of Iraq must be avenged." The theory is false. Just so, if there was no life without a DNA code, HY is false. Period. Evidence against life without a DNA code is evidence against HY, and your asking for "experimental evidence" has been fulfilled. You started out by asking, Preferably arguments with some experimental results we can evaluate? Now, you are asking for something else;
I was asking for positive experimental evidence which contradicts any of the reported empirical bases for the hypothesis.
The problem I have with HY is not with its empirical bases. It is with the "highly speculative aspects", to use your phrase. So why should I be asked to provide experimental evidence against the parts that I don't particularly question? You seem to recognize the weakness of HY, for you say,
I suppose I should step in here and say something about what I don’t believe. I don’t believe the stereochemical hypothesis is true. It’s one of many hypotheses coming out of the overarching RNA World idea. But I like it better than others because, as I pointed out above, it has elements conducive to experimental examination. I hope that makes my position a bit clearer.
Yes, I think that does make your position clearer. Now if you will clarify one other point, it will be helpful. Robert Shapiro, in Origins: A Skeptic’s Guide to the Creation of Life on Earth,
Some future day may yet arrive when all reasonable chemical experiments run to discover a probable origin for life have failed unequivocally. Further, new geological evidence may indicate a sudden appearance of life on the earth. Finally, we may have explored the universe and found no trace of life, or processes leading to life, elsewhere. In such a case, some scientists might choose to turn to religion for an answer. Others, however, myself included, would attempt to sort out the surviving less probable scientific explanations in the hope of selecting one that was still more likely than the remainder.
Would you, if all the evidence overwhelmingly pointed to an intelligent designer, join Shapiro in his search for non-intelligent explanations for life, or are you prepared to give this search up at some point, however difficult that point might be to reach? You will be pleased to know that I do not have time right now to combine replies to your last two posts, and so will approximately halve the length of this post, responding only to #146. The response to #150 will have to wait for now.

Paul Giem_{June 14, 2009
June
06
Jun
14
14
2009
08:27 PM
8
08
27
PM
PDT}

"In short, there is good reason, coming from serious calculation by serious and in some cases even eminent workers, to infer that AH’s estimates on the odds of functional proteins forming by chance are rather too optimistic."
These "serious calculations" would lead one to insist that proteins such as that discussed in this essay cannot possibly exist. When a calculation fails so badly to agree with observation and experimental result, the proper thing to do is to toss the calculation, or at least examine the math to figure out where and why the calculation is so badly in error.Arthur Hunt_{June 14, 2009
June
06
Jun
14
14
2009
09:30 AM
9
09
30
AM
PDT}

Jerry: Let me scoop out a couple of estimates on protein formation, from Bradley's fairly recent presentation, using point 9 in my first appendix the always linked: ______________ Recently, Bradley has done further work on this, using Cytochrome C, which is a 110-monomer protein. He reports, for this case (noting along the way that Shannon information is of course really a metric of information-carrying capacity and using Brillouin information as a measure of complex specified information, i.e IB = ICSI below), that: >>Cytochrome c (protein) -- chain of 110 amino acids of 20 types If each amino acid has pi = .05, then average information “i” per amino acid is given by log2 (20) = 4.32 The total Shannon information is given by I = N * i = 110 * 4.32 = 475, with total number of unique sequences “W0” that are possible is W0 = 2^I = 2^475 = 10^143 Amino acids in cytochrome c are not equiprobable (pi ? 0.05) as assumed above. If one takes the actual probabilities of occurrence of the amino acids in cytochrome c, one may calculate the average information per residue (or link in our 110 link polymer chain) to be 4.139 using i = - ? pi log2 pi [TKI NB: which is related of course to the Boltzmann expression for S] Total Shannon information is given by I = N * i = 4.139 x 110 = 455. The total number of unique sequences “W0” that are possible for the set of amino acids in cytochrome c is given by W0 = 2^455 = 1.85 x 10^137 . . . . Some amino acid residues (sites along chain) allow several different amino acids to be used interchangeably in cytochrome-c without loss of function, reducing i from 4.19 to 2.82 and I (i x 110) from 475 to 310 (Yockey) M = 2^310 = 2.1 x 10^93 = W1 Wo / W1 = 1.85 x 10^137 / 2.1 x 10^93 = 8.8 x 10^44>> Recalculating for a 39 amino acid racemic prebiotic soup [as Glycine is achiral] he then deduces (appar., following Yockey): >>W1 is calculated to be 4.26 x 10^62 Wo/W1 = 1.85 x 10^137 / 4.26 x 10^62 = 4.35 x 10^74 ICSI = log2 (4.35 x 10^74) = 248 bits . . . . Two recent experimental studies on other proteins have found the same incredibly low probabilities for accidental formation of a functional protein that Yockey found 1 in 10^75 (Strait and Dewey, 1996) and 1 in 10^65 (Bowie, Reidhaar-Olson, Lim and Sauer, 1990).>> ________________ In short, there is good reason, coming from serious calculation by serious and in some cases even eminent workers, to infer that AH's estimates on the odds of functional proteins forming by chance are rather too optimistic. As well, the issue of what function is comes into force: unless the relvant proteins are integrated with other relevant macromolecules in a matrix ont eh scope of about 20 microns, they will have no function -- part, wholes and organisation are all implicated. Sir Fred Houyle's 747 in a junkyard remark -- which I elaborate on in the same appendix -- brings this to the fore. That is, even when the proper parts are present, their organisation into a functional, complex whole then needs to be reckoned with. For that, we must face the fact that the configuration space on that is generally well beyond the reach of the search resources of the cosmos we observe. No wonder evolutionary materialistic origin of life theories are at a conundrum. GEM of TKIkairosfocus_{June 14, 2009
June
06
Jun
14
14
2009
01:03 AM
1
01
03
AM
PDT}

khan, You present possible sources of macro evolution (I will continue to use our definition because it is the issue under debate). The question is what actually happened and how. To me you are presenting speculation and I question the speculation and the mechanism behind your claims. To get past the speculation phase one has to present evidence to show how something happened. So far I claim that no one has done that. Has Dawkins done it? Has Ayala done it? Has Carroll done it? Has Ken Miller done it? Has Coyne done it? Has Henry Gee done it? Has Provine done it? Has Allen MacNeill done it on his web site? I have not seen it in these so called experts on evolution. If you disagree then you will have to make a much better argument then they have made. I ask you to lay out in layman's language the arguments and you say you did such and as your example you point to the end of comment #152. I am sorry but those few general sentences don't do it. I suggest you clear your thoughts and make a long comment summarizing your arguments maybe using the hemoglobin article as a starter. Indicate what is hard fact, what is suspected to be true and how it relates to your thesis on how macro evolution (our definition) happened. If you cannot do that then we are at an impasse. You see I have not seen it done with all the authors I have mentioned and you and Dave referencing articles don't accomplish it. Prepare you defense of naturalistic evolution and use as much space as you want. You might want to lay it out in a series of comments so that it is easier to read. Until then all I see is some wishful speculation and the pointing to an occasional study. If it is well thought out and full of logic and facts then it will be read and can be used for future discussions.jerry_{June 13, 2009
June
06
Jun
13
13
2009
06:24 PM
6
06
24
PM
PDT}

"I have never seen a coherent argument for macro evolution (origin of complex novel capabilities)"
Ouch! Talk about a slam! That's worth a five minute major, IMO. (Aside - nice job, Pens!) Help me out, jerry. Send me along questions so that my essay that others have linked to here can be improved, so that readers such as yourself can follow and understand it better.Arthur Hunt_{June 13, 2009
June
06
Jun
13
13
2009
04:20 PM
4
04
20
PM
PDT}

Jerry, I have never seen a coherent argument for macro evolution (origin of complex novel capabilities) and I have read a lot of pro naturalistic evolution books. Hence, I suspect such an argument does not exist or else it would be presented. Since you use a very idiosyncratic definition of macroevolution, I assume you don't look in the macroevolution sections of the books for answers. Here, however, you have been given several concrete examples that address your concerns. Art Hunt gave you the plant examples, and I gave several that addressed some of the ones you specifically suggested, i.e, insect wings, multichambered hearts, and the avian oxygen transport system. Yet, to my recollection, you never responded. Instead, here you are waving a bs meter. I know you saw Art's examples. Since I was under moderation at the time, there is a good chance you missed mine: they can be found in the "human-evolution-the-spin-machine-in-top-gear" thread. I keep pointing you to the Brosious article And I keep asking you what is so new and special about exaptations. It was meant as an up to date review of macro evolution and it is mostly speculation. Actually, it was a discussion of retronuons and exaptations. Again, what makes this article so important? Exaptations are nothing new (they are simply mutations with deferred selective value) and fall easily under modern evolutionary theory. They challenge none of its essential tenets. If there was chapter and verse supporting his beliefs do you not think he would have presented them. Maybe some of his beliefs aren't so well supported-- I noticed he seemed to side with Gould and the "species selection" crowd. That group has never really made much of a case for their point of view. Yet here we are, trying to engage you with nice juicy examples to tear into. And what do we get in return? a bs meter reading! There is are various levels of expertise and after a certain point no more is necessary to assess certain aspects of an issue. The lack of expertise I was pointing to was the knowledge on the functionality of proteins. One does not have to be an expert on protein biology/chemistry to understand many or most of the issues. What I was referring to is that I do not have the information to make a good judgment on what is possible and what is not at the moment to make a functional protein that will work with another functional protein to create a situation that is more functional than either working independently. Yet you have declared Behe's book the "definitive work" on the subject. How on earth would you know, if you don't have the knowledge to come to an informed opinion? Art Hunt makes an assertion and he may be right or it may be couched in some restrictions that I have no idea about at the moment. Over time a discussion on this would get at the issues. Are you planning on engaging in a discussion with him on it?. There have been others on this site who have indicated that the odds of finding a suitable protein island of proteins is much rarer than what was given by Art. Hence, I do not have the knowledge or expertise to assess this at the moment. But I suspect that there are others out there who do have this information. Funny, the only one actually talking numbers from wet bench experiments has been Art. That sets my BS claxon squawking, to tell you the truth. The main thesis of the Edge of Evolution was that these proteins are rare and there is no evidence that they exist in any great number. And funny how none of the reviews called Behe on this. Instead they debated irrelevant issues. Why? The BS meter is detecting something. None? How about Ian Musgraves review at The Panda's Thumb? http://pandasthumb.org/archives/2008/04/behe-versus-rib.html One thing that sets off the BS meter like a Geiger counter in an uranium mind is an attempt to hide behind obscure scientific data. How would you know if it was "obscure" or not? Or are you simply assuming it is obscure because you haven't heard about it?Dave Wisker_{June 13, 2009
June
06
Jun
13
13
2009
03:52 PM
3
03
52
PM
PDT}

jerry, another great ad hominem coupled with a substance-free non-reply. your stock and trade.
I thank you for the article on hemoglobin and in time I will read it.
great, I look forward to that. just like I look forward to you eventually learning about mitochondria, plants, protein formation, etc. you keep saying you don't know enough about these evidences for macroevolution to make a judgement, yet you never bother to learn about them and then continue in with your assertions that there is no evidence for macroevolution. why is that?
But as I have asked you before, why don’t you lay out the evidence in the article in layman’s language so all might learn.
if you look in 152, it's right there at the bottom.
As an aside, do you think that two mutations that turn a dandelion into an oak is the type of explanation that would explain how microbes turned into man.
behe extrapolates from malaria to everything else in Edge. you seem to accept that logic. why don't you accept the same logic here?
If it is, then why is such an explanation not in the books on evolution?
perhaps bc the paper is from 2008 and textbooks don't move that fast.Khan_{June 13, 2009
June
06
Jun
13
13
2009
03:26 PM
3
03
26
PM
PDT}

khan, Whenever I need reassurance, khan provides. He says: "that there is no evidence for macroevolution is based on one article in a book that you cite incessantly" Are you trying to impugn me or Brosius with this sentence? I use the Brosius article because of who chose it, the context in which it is used and what it says. You use an interesting choice of words and it is one of my cues that there is no evidence. You would not waste a second with what I said and instead present the overwhelming evidence. I thank you for the article on hemoglobin and in time I will read it. I believe hemoglobin is often used as an example of gene duplication and its usefulness and also in common ancestry. But as I have asked you before, why don't you lay out the evidence in the article in layman's language so all might learn. As an aside, do you think that two mutations that turn a dandelion into an oak is the type of explanation that would explain how microbes turned into man. If it isn't, then why mention it? If it is, then why is such an explanation not in the books on evolution? I keep on wondering why the experts on evolutionary biology don't emphasize them or how they missed it. PS - Allen MacNeill pointed me to the Vrba and Eldredge book which is titled "Macroevolution."jerry_{June 13, 2009
June
06
Jun
13
13
2009
03:07 PM
3
03
07
PM
PDT}

"Art Hunt makes an assertion and he may be right or it may be couched in some restrictions that I have no idea about at the moment. Over time a discussion on this would get at the issues."
I agree. But ID proponents choose to avoid substantive discussion.
" There have been others on this site who have indicated that the odds of finding a suitable protein island of proteins is much rarer than what was given by Art. "
To pick up on a theme of yours, jerry, these "others" are using imaginary arguments that are not grounded in chemical or experimental reality. My assertions are backed up by direct experimental measurement and by some pretty obvious and simple chemistry.
Hence, I do not have the knowledge or expertise to assess this at the moment. But I suspect that there are others out there who do have this information.
You suspect incorrectly.
The main thesis of the Edge of Evolution was that these proteins are rare and there is no evidence that they exist in any great number. And funny how none of the reviews called Behe on this. Instead they debated irrelevant issues. Why? The BS meter is detecting something."
jerry, I have called Behe on this. Heck, I even gave Behe an opportunity to review and comment on my Pandas Thumb entry before I posted it. He declined, I suspect because he knows that I am a working biochemist and that my arguments gut the very core of his thesis. He has no response to my various essays because there is no ID- or Behe- friendly one. (Oh, and what does "there is no evidence that they exist in any great number" mean? Are you claiming that there are not very many proteins in the biosphere? Maybe some clarification is in rder.)Arthur Hunt_{June 13, 2009
June
06
Jun
13
13
2009
02:24 PM
2
02
24
PM
PDT}

jerry, to summarize, your conclusion that there is no evidence for macroevolution is based on one article in a book that you cite incessantly and the behavior of some people on a website. the problem is, whenever someone presents evidence for macroevolution, you either say you don't know enough to make a judgement or ignore it. for example, art presented some nice evidence showing that two mutations can turn a herbaceous plant into a woody one (think: dandelion to oak). you said you didn't know enough about plants to make a judgement. have you learned enough in the meantime? and if you're dissatisfied with the lack of examples in the Brosius article, here's one: http://mbe.oxfordjournals.org/cgi/content/full/24/9/1982 the authors show that the d-globin gene (encoding a subunit of hemoglobin that allows for greater oxygen affinity) in amniote vertebrates arose through duplication and divergence of an embryonic globin-like gene. this additional was one of the factors that enables the diversification of tetrapods, so it's a very significant change.Khan_{June 13, 2009
June
06
Jun
13
13
2009
02:17 PM
2
02
17
PM
PDT}

Prev 1 2 3 4 5 6 … 10 Next

You must be logged in to post a comment.

Leave a Reply