Pierre-Paul Grassé, Daydreaming, and Darwinian Depression

_{Gil Dodgen

January 7, 2010

Intelligent Design}

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melancholia

What gambler would be crazy enough to play roulette with random evolution? The probability of dust carried by the wind reproducing Durer’s “Melancholia” is less infinitesimal than the probability of copy errors in the DNA molecule leading to the formation of the eye; besides, these errors had no relationship whatsoever with the function that the eye would have to perform or was starting to perform. There is no law against daydreaming, but science must not indulge in it.

Comments

40 GilDodgen 01/10/2010 8:42 pm I was warned about the consequences of this heresy by You Know Who, and I’m prepared to suffer it. Voldemort? : ) Just kidding. I don't read that pagan stuff.feebish_{January 13, 2010
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48 GilDodgen 01/13/2010 11:36 pm P.S.: A thought about my namesake, Gilbert Newton Lewis. Isaac Newton was one of the greatest scientists and mathematicians of all time, and he was a devout believer who “saw God as the masterful creator whose existence could not be denied in the face of the grandeur of all creation.” C.S. Lewis was an atheist into his middle years, as was I, but became arguably one of the greatest Christian apologists of the 20th century. I owe a great debt of gratitude to both Newton and Lewis for opening my eyes in so many ways. What a strange coincidence of names.
Do you intend front-loading?osteonectin_{January 13, 2010
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P.S.: A thought about my namesake, Gilbert Newton Lewis. Isaac Newton was one of the greatest scientists and mathematicians of all time, and he was a devout believer who "saw God as the masterful creator whose existence could not be denied in the face of the grandeur of all creation." C.S. Lewis was an atheist into his middle years, as was I, but became arguably one of the greatest Christian apologists of the 20th century. I owe a great debt of gratitude to both Newton and Lewis for opening my eyes in so many ways. What a strange coincidence of names.GilDodgen_{January 13, 2010
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It is allways appreciated if someone tries to learn biology. However, you should check things before copying them from your personal blog and pasting them here:
At this point decisions have to be made. Where to start, where to stop and although it may seem counterintuitive the mRNA goes to the non-coding strand in order to reconstruct the proper codon sequence (nucleotide triplets which code for an amino acid) for the protein to be formed.
The mRNA doesn't go anywhere on the DNA but is synthesized at the DNA.
Both sides of the parent DNA are exposed yet the mRNA “knows” to only form on one.
The mRNA doesn't know anything. It is actually the pre-initiation complex forming at the promoter which directs transcription.
There is only one start codon which also codes for an amino acid (met) and therefore all amino acid sequences start with methionine.
There are indeed other initiation codons.
The stop codons don’t code for an amino acid.
You may look up how seleno cysteins are encoded or what suppressor mutants are. In addition, it is a good tradition to properly cite ones sources especially if you is quoting verbatim. Joseph cited Batiza AF: Bioinformatics, Genomics, And Proteomics: Getting the Big Picture (Biotechnology in the 21st Century) (rated 2 stars at Amazon for ages 12+)osteonectin_{January 13, 2010
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StephenB:
Retroman, I have observed the extreme vilification that Gil is referring to in other places; he is not talking about the pettiness and irrationality demonstrated on this thread.
Google GilDodgen and IDiot or Gil Dodgen and IDiot for a small sample, and you'll see what Stephen means. I apparently have a 100% unique name. My father named me after Gilbert Newton Lewis, the great chemist with whom my father worked during WWII on the Manhattan Project. On another topic, which I will blog here soon: While Googling my name I ran across a scienceblogs item concerning a poll question: "Do you, personally, believe in the theory of evolution, do you not believe in evolution, or don't you have an opinion either way?" This is an utterly stupid and meaningless question. http://scienceblogs.com/strangerfruit/2009/02/gallup_poll_on_belief_in_evolu.php Commmenter DaveW quoted me with this:
Gil Dodgen proposed the following: 1) Do you believe that all living things came from a universal single-celled common ancestor? 2) Do you believe that random mutation or random variation and natural selection explain the origin of all life and its complexity? 3) Do you believe that humans evolved from a primitive ape-like ancestor in the last several million years, and if so, does the Darwinian mechanism in question 2) explain how it happened? DaveW: An improvement in critical thinking in this country would end stupidly phrased poll questions such as this one.
GilDodgen_{January 13, 2010
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Retroman, I have observed the extreme vilification that Gil is referring to in other places; he is not talking about the pettiness and irrationality demonstrated on this thread.StephenB_{January 13, 2010
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Gil, your response that "the material atheists are persecuting me because every time I post something, they criticize me heavily" seems to be nothing but a defense mechanism. For one thing, I am not an atheist. Second, I am criticizing your post because you posted something materially false, then tried to deflect criticism from it. Honestly, have you ever said to yourself that maybe the reason your posts draw heavy criticism is that there is something wrong with your posts? I mean that with all due respect.Retroman_{January 11, 2010
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Zachriel:
If you define “code” as a correspondence, then genes do constitute a code. But there’s no teleology indicated.
The teleology is indicated in the transcription and translation processes: Transcription and Translation- Transcription: You start with a tightly wound piece of DNA. Enzymes called RNA polymerases, along with other transcription factors, begin the process by unwinding a portion of DNA near the start of a gene, which is specified by sequences called promoters. Now there are two strands exposed. One strand is the coding strand- it has the correct sequence information for the product- and the other strand is the non-coding strand. That strand contains the complimentary layout. At this point decisions have to be made. Where to start, where to stop and although it may seem counterintuitive the mRNA goes to the non-coding strand in order to reconstruct the proper codon sequence (nucleotide triplets which code for an amino acid) for the protein to be formed. Both sides of the parent DNA are exposed yet the mRNA "knows" to only form on one. This process is unidirectional (5’-3’). There is only one start codon which also codes for an amino acid (met) and therefore all amino acid sequences start with methionine. The stop codons don’t code for an amino acid. Transcription actually starts before the “start” codon and continues past the stop codon. Before the mRNA leaves the nucleus any/ all introns are cut out and the remaining exons spliced together. A chemical cap is added to the 5’ end, the non-coding stuff at the end is cut off by a special enzyme (endonuclease) and a string of A’s is added in its place. You now have a processed mRNA. So now we have this piece of processed mRNA which leaves the nucleus and has to rendezvous with a ribosome-the protein factory within the cell. On to translation: A ribosome consists of over 50 proteins and 3-4 different kinds of rRNA (ribosomal), plus free-floating tRNA (transfer). Each tRNA has a 3 nucleotide sequence- the anti-codon to the mRNA’s codon plus it carries the appropriate amino acid molecule for its anti-codon. To attach the appropriate amino acid to the correct anti-codon an enzyme called amino-acid synthetase is used.
There, large workbenches made of both protein and nucleic acid grab the mRNA so the correct amino acids can be brought up to the mRNA. Each amino acid is escorted by a module called tRNA or transfer RNA. It is important to note that the escort molecules have three bases prominently exposed on their backsides and that these molecules also use the base U instead of T. The kind of amino acid is determined precisely by the tRNA escort’s anticodon, or triplet set of bases on the escort’s backside.-pg 23
And then the chain starts forming until the stop codon terminates the process. Next is the folding process. That is what allows the protein to be useful- its spatial configuration. That is just the basics of what one is introduced to when reading biology textbooks. And it doesn't include the proof-reading and error correction that accompanies the process. So the bottom-line is if biology textbooks got rid of the biased, untestable and unscientific leanings toward non-telic evolution students reading the books would come to the design inference just based on the data.Joseph_{January 11, 2010
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Zachriel:
RNA can evolve and doesn’t require a code.
Designed RNA can evolve. That is all we have evidence for. There isn't any evidence that RNA, arising without agency involvement, can do anything.Joseph_{January 11, 2010
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You’ll note the extreme vilification to which I’ve been subjected, and the number of comments that follow my posts at UD.
I am not trying to vilify anyone. I am merely trying to understand, as apparently also are Retroman and Zachriel, to what extent you agree with Grasse's statement that you quoted. It isn't a hard question. Could you please answer it?efren ts_{January 10, 2010
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StephenB: "Gil, I don’t know how you do it, but you really know how to set the stage..." Stephen, I was once a Richard Dawkins clone -- a mindless, materialist atheist who hated the God I was sure did not exist. I am certainly not proud of this, and make no apologies for my ignorance and the harm to others I surely caused as a result of my idiocy. I was once a Saul of Tarsus. Needless to say, that changed in a rather dramatic way, once reason convinced me that materialist arguments represented a Himalayan pile of BS concerning everything that matters. Everything I believed was wrong, except for the utterly trivial that matters not in the grand scheme of things. You'll note the extreme vilification to which I've been subjected, and the number of comments that follow my posts at UD. I raise the ire and fuel the passion of my former materialist, atheist brethren. I am a heretic of the worst kind, having not only abandoned, but attacked the Church of Darwin, with which I was not only formerly associated, but in which I was a fervent evangelist. I was warned about the consequences of this heresy by You Know Who, and I'm prepared to suffer it.GilDodgen_{January 10, 2010
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SCheesman: I think it goes beyond an analogy. It is a code, there is transcription, and there is (correct me if I am wrong) universal agreement that, aside from epigenetic factors, evolution cannot occur without the evolution of that code.
RNA can evolve and doesn't require a code. In addition, there is evidence in stereochemical affinities that the genetic code was preceded by a simpler system where proteins had direct contact with DNA bases. (Epigenetics don't appear to persist over generations.) If you define "code" as a correspondence, then genes do constitute a code. But there's no teleology indicated.Zachriel_{January 10, 2010
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GilDodgen: The quote was from Pierre-Paul Grassé, not me. Was this not obvious?
Without surrounding text, the blockquote is far from obvious. Thank you for the clarification. From what I understand Grassé was a Lamarckian. Were you posting the quote because you agree with him that there is a natural mechanism of evolution (albeit one that the vast majority of scientists have all but abandoned)?Zachriel_{January 10, 2010
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Seversky: Thank-you for the clarification on the "eschews"... I was unaware of the quotation. I actually agree with quite a lot of what you say. I don't have much more to say on this, except in regards to the following comment you made: The biological process in a cell at the molecular level can be described in terms of machinery or even factories but is that anything more than a convenient metaphor? While there are certain similarities there are also substantial differences between a microscopically small cell and one of our factories. I think it goes beyond an analogy. It is a code, there istranscription, and there is (correct me if I am wrong) universal agreement that, aside from epigenetic factors, evolution cannot occur without the evolution of that code. Finding out the limits (if any) on how that code can evolve is the key to determining this whole debate.SCheesman_{January 10, 2010
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Gil, I was aware by the indent and light gray color that it was a quote, but that is neither here nor there. The person you quote creates a straw man of evolution, and by quoting him without any objection (or commentary whatsoever), you give the impression that you agree with him. It's an evasion, to say, "well, I was quoting someone else." Sure, but you did so approvingly, carrying on the error of Grasse.Retroman_{January 10, 2010
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SCheesman @ 27
Seversky: If you will not accept the theory of evolution unless it can provide evidence at the “pathetic level of detail” that Intelligent Design eschews then I assume that you demand a similar standard of evidence from ID. [Note: I think you meant "demands", not "eschews"?]
You may not be familiar with the following comment posted to the ISCID bulletin board by William Dembski in 2002:
William A. Dembski Posted 18 September 2002 09:01 Rafe, I wrote, "Please show me in Michael Behe's writings or my own where we deny that IC systems can be made up of subsystems that can be functional in their own right." Both Behe and I have always defined IC with reference to the basic function of the system in question (if we've not said it explicitly -- and I have in NFL -- then a charitable reading would have granted that -- neither Behe nor I are that stupid). We therefore left open the possibility of subsystems having function in their own right. You and Yersinia charge us with a denial. The quotes you give indicate no such thing. As for your example, I'm not going to take the bait. You're asking me to play a game: "Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position." ID is not a mechanistic theory, and it's not ID's task to match your pathetic level of detail in telling mechanistic stories. If ID is correct and an intelligence is responsible and indispensable for certain structures, then it makes no sense to try to ape your method of connecting the dots. True, there may be dots to be connected. But there may also be fundamental discontinuities, and with IC systems that is what ID is discovering. [My emphasis]
Clearly, according to this, Dr Dembski did not believe that ID should be held to the same standard of evidence as other theories such as evolution, hence my use of the word "eschew".
But such a level of detail would really clinch it for evolution, and be intellectually satisfying as well, you must admit.
Unquestionably. But, as I am sure you are aware, demanding evidence that both the questioner and the those being questioned know full well almost certainly does not exist is more of a debating tactic than a genuine scientific inquiry. Without doubt, evolutionary biologists would be delighted to find a fully-preserved genetic pathway spanning the millions of years between a parent species and its offspring. Both sides, however, know that the chances of such fragile material fossilizing at all, let alone so extensively, is negligible. The alternative is to continue what Darwin started, namely the construction of a framework theory into which such fragmentary data as is available can be fitted as evidence. As more data is gathered, assuming it can be accommodated within the theory, the firmer the structure becomes. The gaps in the evidence are perforce filled with speculative explanations. There is nothing wrong with that provided there is no attempt to claim that they are more than speculation or, at best, inferences from available evidence. As for clockwork watches, machines, computers and information theory, they may be useful analogies for biological processes but it could be misleading to think of them as anything more than that. In evaluating any analogy you should weigh the similarities against the differences between the two cases being compared. I am no information theorist, for example, but I have quoted philosopher of science John Wilkins who is one of an admittedly small minority who believe that information is best understood as a property of our models and that it is misleading to attribute it as a property of the systems being modeled. The biological process in a cell at the molecular level can be described in terms of machinery or even factories but is that anything more than a convenient metaphor? While there are certain similarities there are also substantial differences between a microscopically small cell and one of our factories. Is the inference warranted that one of those similarities is the property of being designed?Seversky_{January 9, 2010
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Gil, Since you seem to take some degree of pleasure in the fact that two opponents have mistaken Grassé words for yours, I have to assume that you don't agree with at least part of what was quoted. If you agree with it 100% then the distinction regarding who made the statement is meaningless. It would be instructive to understand what part of Grassé statement you don't subscribve to and why. thanks.efren ts_{January 9, 2010
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Gil, I don't know how you do it, but you really know how to set the stage. What could be more fun that watching Darwinists trying to extract timeline sequences from metaphors? Just be glad you didn't use the tornado in a junkyard analogy. Your adversaries would have accused you of misrepresenting the evolutionary pathway and failing to accurately measure the velocity of the wind. You have to love this.StephenB_{January 9, 2010
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#31 Gil rotflmao!!! Of course your the one that doesnt know anything. Vividvividbleau_{January 9, 2010
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Retroman and Zachriel, The quote was from Pierre-Paul Grassé, not me. Was this not obvious? Sigh^1024.GilDodgen_{January 9, 2010
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Retroman: I can only think of two reasons to explain this, since I believe you didn’t willfully lie when you said you understand evolution.
Another possibility is that he was waxing eloquent about what he clearly believes is obvious. (That doesn't preclude #2. We reject #1 out-of-hand.)Zachriel_{January 9, 2010
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ScottAndrews: It’s a tautology.
That should have been attributed to ScottAndrews above.Zachriel_{January 9, 2010
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Gil, I believe you're an honest person, so I will take your word for it that you understand evolution. But then I am confused as to why you didn't accurately reflect evolution in your original post and instead made a straw man of it. I can only think of two reasons to explain this, since I believe you didn't willfully lie when you said you understand evolution. 1. You are engaging in propaganda, misrepresenting the theory of evolution to get others who have less knowledge than you to reject it. 2. You think you understand the theory but really don't.Retroman_{January 9, 2010
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Seversky: If you will not accept the theory of evolution unless it can provide evidence at the “pathetic level of detail” that Intelligent Design eschews then I assume that you demand a similar standard of evidence from ID. [Note: I think you meant "demands", not "eschews"?] But such a level of detail would really clinch it for evolution, and be intellectually satisfying as well, you must admit. My sceptisism, and likely that of others, is that our experience with coded instructional systems (and written language and computer coding are two) indicates that such systems are inherently non-evolvable beyond strictly "local" bounds, using any type of random mutation (e.g. at the "letter", "word", "sentence" or "paragraph" levels). This is what the "Edge of Evolution" implied, and why the arguments in "Darwin's Black Box" have force. It is why Dr. Dembski and Dr. Marks are working on the statistics of searches. You cannot evolve computer code or written languages by random mutation except for the most trivial of cases. Truly new meaning or functionality calls for wholesale input of intelligence. What you call a "pathetic level of detail" is a standard requirement in geology, where the study of lithogeochemistry tracks the formation of minerals from the original fluids using detailed systems such as CIPW analysis; or in nuclear chemistry, where the progression of radioisotopes in the decay chains is dissected analysed and timed. Each stage is detailed, measured, quantified. We know at each point the chemical or physical reasons why it occurs, and the statistics involved. Evolution really occurs at the code level. Everything else is derivative, and what is derivative (e.g. the changing of forms in the fossil record) can tell you very little (in fact it can tell you almost nothing) about what is really changing at the coding level. There are dozens, perhaps hundreds of molecular machines. So far, not one has been explained. Not even part of one has been explained at this "pathetic level of detail". If there were even any evidence that we have started to explain parts of it, going beyond the "edge", then you've got something that will catch my attention. Everything I've seen, for instance on the evolvability of new binding sites, indicates otherwise.SCheesman_{January 9, 2010
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SCheesman @ 8
You are correct that the theory of evolution does not propose that the eye appeared “de novo”. It would hardly be a theory of evolution then. I don’t believe any of the posts above implied it did, and certainly not Gil’s original post.
The OP only makes sense as a variant of Hoyle's Fallacy in which wind-blown dust is substituted for the tornado in a junkyard. The theory of evolution makes no claim about complex biological structures being created in one step. GilDodgen claims a detailed understanding of the theory yet erects strawmen such as the above which are inconsistent with that claim.
If it can ever be demonstrated that any molecular machine can be “coded” in such an incremental, developmental manner, with working solutions strung like thousands of pearls on a necklace from the “no machine” to the “functioning machine” state then ID has no more case. As a developer myself, I remain sceptical, but I’m willing to be convinced.
Moderate skepticism is a rational position to adopt but it should be even-handed. If you will not accept the theory of evolution unless it can provide evidence at the "pathetic level of detail" that Intelligent Design eschews then I assume that you demand a similar standard of evidence from ID.Seversky_{January 9, 2010
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Gil, I think you don’t believe in evolution because you don’t understand it.
Retroman, I think you believe in evolution because you don't understand it.Mung_{January 8, 2010
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Zachriel: (Supposedly quoting me) SCheesman: It's a tautology. Now you're making up things that I supposedly said? Are you accessing an alternate universe? If you're going to quote me, at least use something I actually said.SCheesman_{January 8, 2010
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"Gil, I think you don’t believe in evolution because you don’t understand it." I understand it thoroughly, unequivocally, and in excruciating detail, which is why I don't believe it. Of course, I believe in "evolution" in a general sense because living things are not now as they once were; therefore, evolution has occurred by definition. I don't believe in the Darwinian mechanism of random errors -- with the bad stuff being thrown out by natural selection -- as explaining anything of any significance. This is a patently absurd proposition, based on what we now know about living systems, which are based on the most sophisticated computational technology ever invented. The notion that this came about by the Darwinian mechanism is simply absurd and represents catastrophic ignorance and denial of everything that has been learned in the last 50 years in biology and information theory. It is Darwinists who are clinging, desperately, to the equivalent of phlogiston theory and geocentrism in the modern era concerning biology.GilDodgen_{January 8, 2010
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Zachriel: "GilDodgen: What gambler would be crazy enough to play roulette with random evolution?" Sigh. God forgive me, but arguing with idiots is a hopeless pursuit.GilDodgen_{January 8, 2010
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A library does not fabricate information, it receives it from without, classifies and stores it. The medieval copyists made mistakes that altered, vitiated the texts they were supposed to reproduce. Who dares assert that their errors are the work itself? ~ Pierre Grassebevets_{January 8, 2010
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