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To dream the impossible dream: the quest for the 50-bit life form

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Aleksandr Oparin and John von Neumann. Courtesy of Russavia, Beelaj and Wikipedia.

In two separate comments (see here and here) on a recent post of mine, Intelligent Design critic Dave Mullenix posed a question to ID supporters, which often comes up on this blog:

[W]hy do you ID people insist that the first living thing was complex? 500 to 1000 bits of information? Try 50 to 100. Think of a single polymer whose only capability is reproducing itself, and which is possibly imbedded in the kind of droplets that form naturally…

A simple self replicating molecule isn’t much compared to modern life, but if it self-replicates and allows evolution, it’s all the start we need and a small polymer would do it. Don’t worry about proteins, they come later. Don’t worry about metabolism – that’s also for advanced life. For first life, reproduction with the possibility of Darwinian evolution is all we need and a short polymer will do the trick.

Dave Mullenix confesses to not yet having read Dr. Stephen Meyer’s Signature in the Cell, although he has purchased a Kindle version of the book. I realize that he is a very busy man, and I also realize that other Intelligent Design critics have voiced similar objections previously, so I’ve written this post in order to explain why the scenario Dave Mullenix proposes will not work.

What motivates the quest for a 50-bit life form?

Dave Mullenix is surely well aware of the research of Dr. Douglas Axe, which has shown that the vast majority of 150-amino-acid sequences are non-functional, and that the likelihood of a single protein – that is, any working protein, never mind which one – arising by pure chance on the early earth is astronomically low. Nor can necessity account for the origin of DNA, RNA or proteins. All of these molecules are made up of biological building blocks – nucleotides in the case of DNA and RNA, and amino acids in the case of proteins. Just as the properties of stone building blocks do not determine their arrangements in buildings, so too, the properties of biological building blocks do not determine their arrangements in DNA, RNA and proteins.

If neither chance nor necessity can account for the appearance of fully functional RNA, DNA and proteins, then evolutionists have no choice but to assume that these molecules arose from something even simpler, which was capable of evolving into these molecules. This is the logic which underlies Dave Mullenix’s proposal regarding the origin of life.

Why a 50-bit life form wouldn’t work

Actually, a similar proposal was made by origin-of-life researcher Aleksandr Oparin in the late 1960s. In his original model, put forward in the 1920s and 1930s, Oparin had assumed that chance alone could account for the origin of the proteins which make cellular metabolism possible. However, the discovery of the extreme complexity and specificity of protein molecules, coupled with the inability of his model to explain the origin of the information in DNA, forced him to revise his original proposal for the chemical evolution of life on earth. Dr. Stephen Meyer continues the story in Signature in the Cell (HarperOne, New York, 2009), pages 273-277:

As the complexity of DNA and proteins became apparent, Oparin published a revised version of his theory in 1968 that envisioned a role for natural selection earlier in the process of abiogenesis. The new version of his theory claimed that natural selection acted on unspecified polymers as they formed and changed within his coacervate protocells.[5] Instead of natural selection acting on fully functional proteins in order to maximize the effectiveness of primitive metabolic processes at work within the protocells, Oparin proposed that natural selection might work on less than fully functional polypeptides, which would naturally cause them to increase their specificity and function, eventually making metabolism possible. He envisioned natural selection acting on “primitive proteins” rather than on primitive metabolic processes in which fully functional proteins had already arisen….

[Oparin] proposed that natural selection initially would act on unspecified strings of polypeptides of nucleotides and amino acids. But this created another problem for his scenario. Researchers pointed out that any system of molecules for copying information would be subject to a phenomenon known as “error catastrophe” unless these molecules are specified enough to ensure an error-free transmission of information. An error catastrophe occurs when small errors – deviations from functionally necessary sequences – are amplified in successive replications.[14] Since the evidence of molecular biology shows that unspecified polypeptides will not replicate genetic information accurately, Oparin’s proposed system of initially unspecified polymers would have been highly vulnerable to such an error catastrophe.

Thus, the need to explain the origin of specified information created an intractable dilemma for Oparin. If, on the one hand, Oparin invoked natural selection early in the process of chemical evolution (i.e. before functional specificity in amino acids or nucleotides had arisen), accurate replication would have been impossible. But in the absence of such replication, differential reproduction cannot proceed and the concept of natural selection is incoherent.

On the [other] hand, if Oparin introduced natural selection late in his scenario, he would need to rely on chance alone to produce the sequence-specific molecules necessary for accurate self-replication. But even by the late 1960s, many scientists regarded that as implausible given the complexity and specificity of the molecules in question…

The work of John von Neumann, one of the leading mathematicians of the twentieth century, made this dilemma more acute. In 1966, von Neumann showed that any system capable of self-replication would require sub-systems that were functionally equivalent to the information storage, replicating and processing systems found in extant cells.[16] His calculations established an extremely high threshold of minimal biological function, a conclusion that was confirmed by later experimental work.[17] On the basis of the minimal complexity and related considerations, several scientists during the late 1960s (von Neumann, physicist Eugene Wigner, biophysicist Harold Morowitz) made calculations showing that random fluctuations of molecules were extremely unlikely to produce the minimal complexity required for a primitive replication system.[18]…

As a result, by the late 1960s, many scientists had come to regard the hypothesis of prebiotic natural selection as indistinguishable from the pure chance hypothesis, since random molecular interactions were still needed to generate the initial complement of biological information that would make natural selection possible. Prebiotic natural selection could add nothing to the process of information generation until after vast amounts of functionally specified information had first arisen by chance.

References

[5] Oparin, A. Genesis and Evolutionary Development of Life, New York: Academic, 1968, pp. 146-147.

[14] Joyce, Gerald F. and Leslie Orgel, “Prospects for Understanding the Origin of the RNA World.” In The RNA World, edited by Raymond F. Gesteland and John J. Atkins, I-25. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1993. See especially pp. 8-13.

[16] Von Neumann, John. The Theory of Self-Replicating Automata. Completed and edited by A. Burks. Urbana: University of Illinois Press, 1966.

[17] Pennisi, Elizabeth. “Seeking Life’s Bare (Genetic) Necessities”. Science 272(1996): 1098-99.
Mushegian, Arcady, and Eugene Koonin, “A Minimal Gene Set for Cellular Life Derived by Comparison of Complete Bacterial Genomes”. Proceedings of the National Academy of Sciences USA 93 (1996): 10268-10273.

[18] Wigner, Eugene. “The Probability of the Existence of a Self-Reproducing Unit.” In The Logic of Personal Knowledge: Essays Presented to Michael Polyani, edited by Edward Shils, pp. 231-235. London: Routledge and Kegan Paul, 1961. [But see here for a critique by physicist John C. Baez. – VJT]
Morowitz, Harold J. “The Minimum Size of the Cell,”in Energy Flow in Biology: Biological Organization as a Problem in Thermal Physics, New York: Academic, 1968, pp. 10-11.

(Emphases mine – VJT.)

In conclusion: there are good reasons for thinking that a 50-bit life-form would never work. Since it would not be capable of accurate self-replication, it would be unable to evolve into larger molecules such as RNA, DNA and proteins. Intelligent Design critics who attempt to overcome the astronomical odds against these molecules forming naturally by hypothesizing a simpler, 50-bit life-form that generated them are, like the man of La Mancha, dreaming the impossible dream.

Let me finish my essay by quoting the beautiful lyrics of the song, The Impossible Dream. The song was composed by Mitch Leigh, and the lyrics were written by Joe Darion. It was written for the 1965 musical, “Man of La Mancha”:

To dream the impossible dream
To fight the unbeatable foe
To bear with unbearable sorrow
To run where the brave dare not go

To right the unrightable wrong
To love pure and chaste from afar
To try when your arms are too weary
To reach the unreachable star

This is my quest, to follow that star
No matter how hopeless, no matter how far
To fight for the right, without question or pause
To be willing to march into Hell, for a Heavenly cause

And I know if I’ll only be true, to this glorious quest,
That my heart will lie will lie peaceful and calm, when I’m laid to my rest

And the world will be better for this:
That one man, scorned and covered with scars,
Still strove, with his last ounce of courage,
To reach the unreachable star.

Comments
And the kicker dmullenix??? 'science' is not even possible within your atheistic/materialistic worldview of neo-Darwinism!!! Should You Trust the Monkey Mind? Excerpt: Evolutionary naturalism assumes that our noetic equipment developed as it did because it had some survival value or reproductive advantage. Unguided evolution does not select for belief except insofar as the belief improves the chances of survival. The truth of a belief is irrelevant, as long as it produces an evolutionary advantage. This equipment could have developed at least four different kinds of belief that are compatible with evolutionary naturalism, none of which necessarily produce true and trustworthy cognitive faculties. http://www.firstthings.com/onthesquare/2010/09/should-you-trust-the-monkey-mind What is the Evolutionary Argument Against Naturalism? (‘inconsistent identity’ of cause leads to failure of absolute truth claims for materialists) (Alvin Plantinga) – video http://www.youtube.com/watch?v=5yNg4MJgTFw Can atheists trust their own minds? – William Lane Craig On Alvin Plantinga’s Evolutionary Argument Against Naturalism – video http://www.youtube.com/watch?v=byN38dyZb-k “But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?” – Charles Darwin – Letter To William Graham – July 3, 1881 It is also interesting to point out that this ‘inconsistent identity’, pointed out by Plantinga, which leads to the failure of neo-Darwinists to make absolute truth claims for their beliefs, is what also leads to the failure of neo-Darwinists to be able to account for objective morality, in that neo-Darwinists cannot maintain a consistent identity towards a cause for objective morality; The Knock-Down Argument Against Atheist Sam Harris – William Lane Craig – video http://www.youtube.com/watch?v=tvDyLs_cReE “Atheists may do science, but they cannot justify what they do. When they assume the world is rational, approachable, and understandable, they plagiarize Judeo-Christian presuppositions about the nature of reality and the moral need to seek the truth. As an exercise, try generating a philosophy of science from hydrogen coming out of the big bang. It cannot be done. It’s impossible even in principle, because philosophy and science presuppose concepts that are not composed of particles and forces. They refer to ideas that must be true, universal, necessary and certain.” - Crevo Headlines This following video humorously reveals the bankruptcy that atheists have in trying to ground beliefs within a materialistic worldview; John Cleese – The Scientists – humorous video http://www.youtube.com/watch?v=-M-vnmejwXo ============ Materialism simply dissolves into absurdity when pushed to extremes and certainly offers no guarantee to us for believing our perceptions and reasoning within science are trustworthy in the first place: Dr. Bruce Gordon – The Absurdity Of The Multiverse & Materialism in General – video http://www.metacafe.com/watch/5318486/ This following site is a easy to use, and understand, interactive website that takes the user through what is termed ‘Presuppositional apologetics’. The website clearly shows that our use of the laws of logic, mathematics, science and morality cannot be accounted for unless we believe in a God who guarantees our perceptions and reasoning are trustworthy in the first place. Proof That God Exists – easy to use interactive website http://www.proofthatgodexists.org/index.php THE GOD OF THE MATHEMATICIANS – DAVID P. GOLDMAN – August 2010 Excerpt: we cannot construct an ontology that makes God dispensable. Secularists can dismiss this as a mere exercise within predefined rules of the game of mathematical logic, but that is sour grapes, for it was the secular side that hoped to substitute logic for God in the first place. Gödel’s critique of the continuum hypothesis has the same implication as his incompleteness theorems: Mathematics never will create the sort of closed system that sorts reality into neat boxes. http://www.faqs.org/periodicals/201008/2080027241.html etc.. etc.. etc..bornagain77
July 25, 2011
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dmullenix, I noticed after you sneered at the Theistic beliefs of Meyer (you threw sneers at Wells theistic beliefs for good measure), you failed to provide ANY empirical evidence for your atheistic materialistic beliefs themselves. For instance,,, here is 'your scientific evidence' 'Assume you have a shortish polymer,,, 'Now suppose that before it reproduces itself, it makes several defective copies.' Now suppose that the polymer makes a copy of itself that is almost accurate, So basically dmullenix you make a extremely bad Theistic argument to support your atheism, as if this refutes Theism, and then you appeal to your imaginary conjectures to support your atheistic beliefs. But this is all just as well for this is precisely the type of argumentation that infuses Darwinian thought ever since Darwin wrote his book, and as this recent peer-reviewed paper pointed out; Charles Darwin, Theologian: Major New Article on Darwin's Use of Theology in the Origin of Species - May 2011 http://www.evolutionnews.org/2011/05/charles_darwin_theologian_majo046391.html From Philosopher to Science Writer: The Dissemination of Evolutionary Thought - May 2011 Excerpt: The powerful theory of evolution hangs on this framework of thought that mandates naturalism. The science is weak but the metaphysics are strong. This is the key to understanding evolutionary thought. The weak arguments are scientific and the strong arguments, though filled with empirical observation and scientific jargon, are metaphysical. The stronger the argument, the more theological or philosophical. http://darwins-god.blogspot.com/2011/05/from-philosopher-to-science-writer.html ,,,Moreover dmullenix, science owes absolutely nothing to Darwinian thought,,, Materialists like to claim evolution is indispensable to experimental biology and led the way to many breakthroughs in medicine, Yet in a article entitled "Evolutionary theory contributes little to experimental biology", this expert author begs to differ. "Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming's discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin's theory was wrong. The responses were all the same: No. Philip S. Skell - Professor at Pennsylvania State University. http://www.discovery.org/a/2816 Podcasts and Article of Dr. Skell http://www.evolutionnews.org/2010/11/giving_thanks_for_dr_philip_sk040981.html Darwinian Medicine and Proximate and Evolutionary Explanations - Michael Egnor - neurosurgeon - June 2011 http://www.evolutionnews.org/2011/06/darwinian_medicine_and_proxima047701.html Science Owes Nothing To Darwinian Evolution - Jonathan Wells - video http://www.metacafe.com/watch/4028096bornagain77
July 25, 2011
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“Dave Mullenix confesses to not yet having read Dr. Stephen Meyer’s Signature in the Cell, although he has purchased a Kindle version of the book. I realize that he is a very busy man…” Hardly a confession. Meyer is a known quantity due to his work with the Discovery Institute and ARN. He seems to see the world through an ID Reality Distortion Field and, judging by his past output, I really don’t expect to ever find anything useful in anything he writes. “Signature” is basically a compilation of things he’s written elsewhere with some added autobiographical passages. Some casual browsing I did right after I downloaded it gave me the distinct impress that he was trying to put one over on the reader. I mean really, a Bible believing young man graduates from a conservative religiously affiliated college with a degree in earth science and gets a job as a geologist for an oil company and never thinks it’s worth mentioning that he’s a YEC? I’ve heard that there are YECs working as oil company geologists and I would have been very interested to see how he balanced his belief in a young earth with modern geology, but apparently he’s utterly incurious about how the two mix. At least that’s the impression he tries to give in the book. It reminds me very much of Wells writing about his growing suspicion that there’s more to life than Darwinism as he was toiling away in graduate school and then coming across his blog post where Reverand Wells, Moonie pastor and theologian, says that “Father” (Reverend Moon) ordered him to go to graduate school and paid him to attend so that Wells could learn enough to disprove Darwinism. And then there’s this gem from page 24: “Even so, like many scientists I had never really thought about where DNA – or the information it contained – came from in the first place. If asked, I would have said it had something to do with evolution, but I couldn’t have explained the process in any detail.” A Young Earth Creationist thinks it might have had something to do with evolution? Tell me another, but make it a little more realistic please. And what am I to make of this from page 34? “The Rotary scholarship I had received allowed me to attend any one of five overseas universities, provided I could gain admittance. Several of them offered programs in the history or philosophy of science, but in a pre-Internet era it was difficult to extract detailed information from them about the specializations of their faculties. In the end, I set my hopes on Cambridge, since it had more of a reputation for science than the other universities on my list.” The mind boggles! He couldn’t find information on Cambridge because the Internet wasn’t invented yet? Pull the other one now. So it’s not surprising that, “Signature in the Cell” kept getting pushed down on the stack by more useful or at least more interesting books until you brought it up. Having now read your quotations from the book plus some surrounding material, I am sorry to say that the main mistake seems to be both Meyer’s and yours. Oparin’s theory called for some pretty elaborate and high information chemicals to be in place before any evolution could start. On pg 272 Meyer mentions amino acids, sugars and other building blocks producing proteins, carbohydrates and other complex polymers and all those chemicals getting trapped in some sort of crude proto-cell membranes and THEN beginning Darwinian evolution. This is way too much information to be assembled randomly. This was all published in the 1920s. Frederick Griffith first discovered that there was an inheritance molecule in 1928. Oswald Avery finally figured out that DNA was the molecule in the early 40s. This gave Oparin the additional problem of getting the information needed to reproduce all of the above and somehow putting it into the DNA and he never figured out how to do that. But then Meyer assumes that even if he had been able to get the initial information into the DNA somehow, the reproductive machinery would have been too simple to do high fidelity reproduction and the organisms would have been killed off by ever mounting errors, or the “error catastrophe”. This doesn’t affect the simple polymer theory of OOL. Assume you have a shortish polymer – a molecule that is a string made of smaller molecules - monomers. Polymers are constantly forming and being torn apart with each new one being different from its predecessors. Finally, one is formed that manages to reproduce itself at least once before it’s torn apart. This would be the first molecule of life. Now suppose that before it reproduces itself, it makes several defective copies. Too short, wrong sequence of monomers, folded over on itself, whatever. They don’t reproduce, so they are slowly torn apart like all the other polymers. So long as the original polymer manages to make at least one good copy before it’s destroyed, life goes on. Now suppose that the polymer makes a copy of itself that is almost accurate, but contains one or two errors – and that mutated copy also manages to copy itself before it is destroyed. Now we have two, slightly different, polymers reproducing – and Darwinian evolution is off and running. And error catastrophes can’t stop it. I notice that you say, “In conclusion: there are good reasons for thinking that a 50-bit life-form would never work. Since it would not be capable of accurate self-replication, it would be unable to evolve into larger molecules such as RNA, DNA and proteins.” Why do you say this? Not because of the error catastrophe. It doesn’t apply. Not because of anything John von Neumann said – the polymer is the information storage and whatever it’s using to reproduce itself – electrostatic attraction bringing in new monomers to add to the polymer under construction or whatever - is the replicating and processing “system”. I also noticed Meyer wrote this: 269 “ … I saw no reason to accept this prohibition against considering the design hypothesis. To me, it seemed like an unnecessary restriction on rational thought.” As we’ve been discussing on the “No Good Theology…” thread, any thinking Being is orders of magnitude more complex than anything discussed here and consequently is orders of magnitude less likely to exist.dmullenix
July 25, 2011
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Neil Rickert, You make a very good point. In my own defense, however, I made it quite clear at the beginning of my post, when I was quoting Dave Mullenix, that I was addressing a replicator first hypothesis, because that was the one he proposed when he wrote:
[W]hy do you ID people insist that the first living thing was complex? 500 to 1000 bits of information? Try 50 to 100. Think of a single polymer whose only capability is reproducing itself, and which is possibly imbedded in the kind of droplets that form naturally... A simple self replicating molecule isn’t much compared to modern life, but if it self-replicates and allows evolution, it’s all the start we need and a small polymer would do it. Don’t worry about proteins, they come later. Don’t worry about metabolism – that’s also for advanced life. For first life, reproduction with the possibility of Darwinian evolution is all we need and a short polymer will do the trick. (Italics mine - VJT.)
I am of course familiar with metabolism-first scenarios for the origin of life. Dr. Stuart Kauffman is a leading proponent of such scenarios, and Meyer devotes a whole chapter of his book (chapter 12) to Kauffman's proposal, and he carefully explains why he doesn't think Kauffman's scenario - or any other metabolism-first scenario - will work. Here are a few highlights from pages 262-264:
...Kauffman claims that an ensemble of relatively short and "low specificity" catalytic polypeptides and RNA molecules would together be enough to establish a metabolic system. He defends the biochemical plausibility of his scenario on the grounds that some proteins can perform enzymatic functions with low specificity and complexity. To support his claim, he cites a class of proteins known as proteases (including one in particular, called trypsin) that cleave peptide bonds at single amino-acid sites? But is he right? Kauffman himself acknowledges that as yet, there is no experimental evidence that such autocatalysis could occur... In fact, Kauffman's model has at least three significant information-related problems. First, it does not follow , nor is it the case biochemically, that just because some enzymes might function with low specificity, that all the catalytic peptides (or enzymes) needed to establish a self-reproducing metabolic cycle could function with relatively low levels of specificity and complexity. Instead, modern biochemistry show that most and usually all of the molecules in a closed interdependent metabolic system of the type that Kauffman envisions require high-complexity and -specificity proteins... Second, I discovered that even the allegedly low-specificity molecules (the proteases) that Kauffman cites to illustrate the plausibility of his scenario are actually very complex and highly specific in their sequencing. I also discovered that Kauffman confuses the specificity and complexity of the parts of the polypeptides upon which the proteases act with the specificity and complexity of the proteins (the proteases) that do the enzymatic acting. Though trypsin, for example, acts upon - cleaves - peptide bonds at a relatively simple target, trypsin itself is a highly complex and specifically sequenced molecule. Indeed, trypsin is a non-repeating 247-amino-acid protein that possesses signiicant sequence specificity as a condition of function... Third, Kauffman acknowledges that for autocatalysis to occur, the molecules in the chemical minestrone must be held together in a very specific spatial-temporal relationship to one another. In other words, for the direct catalysis of integrated metabolic complexity to occur, a system of catalytic peptide molecules must first achieve a very specific molecular configuration (or what chemists call a "low-configurational energy state"). This requirement is equivalent to saying that the system must start with a large amount of specified information or specified complexity... In short, Kauffman merely transfers the information problem from the molecules into the soup. In addition to these problems, Kauffman's model ... does not explain (a) how the proteins in various metabolic pathways came into association with DNA and RNA or any other molecular replicator or (b) how the information in the metabolic system of proteins was transferred from the proteins into the DNA or RNA. And it gives no account of how the sequence specificity of polypeptides arose (given that the bonding affinities that exist among amino acids don't correlate to actual amino acid sequences in known proteins)... Robert Shapiro, a leading chemist at New York University, has recently proposed that origin-of-life researchers begin to investigate metabolism-first models of the kind that Kauffman proposed... Though Shapiro favors these metabolism-first approaches, he acknowledges that researchers have not yet identified what he calls a "driver reaction" that can convert small molecules into products that increase or "mobilize" the organization of the system as a whole. He also notes that researchers on metabolism-first models "have not yet demonstrated the operation of a complete [metabolic] cycle or its ability to sustain itself and undergo further evolution." In short, these approaches remain speculative and do not yet offer a way to solve the fundamental problem of the origin of biologically relevant organization (or information).
I submit that the metabolism-first scenario which you and Matzke propose suffers from the same defects as the replicator-first scenario: it utterly fails to account for the origin of biological information. In short, Meyer has done his homework. He makes a very formidable case that Intelligent Design is required to account for the origin of life, and scientists working in the field have yet to answer Meyer's case. His arguments stand unrefuted.vjtorley
July 24, 2011
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vjtorley (#15) I am not a biologist either. Research into origins seems to be divided roughly into metabolism first and replicator first hypotheses. Your post mostly seems to apply to replicator first hypotheses. Both Nick Matze and I, in the first two comments, were suggesting that metabolism first is an alternative to be considered. As best I can tell, you seem to have answered this with more objections to replicator first hypotheses. It seems to me that you have missed the point being raised.Neil Rickert
July 24, 2011
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llion:
How much did you make? Send it …
Actually, the first line is redundant, considering the second, so you can condense that to: "Send everything" which, of course is the same as "how much you made" ... So maybe life is simple, after all.SCheesman
July 24, 2011
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Hehe, 1) How much did you make? 2) How much do you think we should let you keep? 3) Signature. I get three lines, Ilion. xpmaterial.infantacy
July 24, 2011
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"Looking for a 50-bit lifeform is like looking for a single-line tax form." ------------- How much did you make? Send it ... ------------- Yep, even the simplest seems to take two lines.Ilion
July 24, 2011
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'Science' is a toy for little boys ... men do philosophy. And theology.Ilion
July 24, 2011
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"Having said that, I utterly reject your charge that ID proponents “can’t be bothered to inform themselves of the actual state of affairs in science, and instead quote decades-old work as if it was definitive.” My own post refutes this very charge. ..." At the same time, it hardly matters even if the accusation were true. For, as we all know, "'science' is not about belief and doesn't require belief" ... or, to put it more directly, "'science' isn't about truth and does not necessarily deliver us truth". And, we can't use 'science' to determine which scientific statements are true and which are not. So, when Mr Matzke falsely accuses anti-Darwinists of "not keeping up with the literature", he's making an accusation of absolutely no importance, and of very little meaning. He's accusing: "You haven't wasted vast amounts of your time poring over the picayune details of this stuff that we who believe it cannot honestly say to be true".Ilion
July 24, 2011
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Looking for a 50-bit lifeform is like looking for a single-line tax form.SCheesman
July 24, 2011
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Nick Matzke, Thank you for your post. Let me make one thing clear up-front: I'm a philosopher. I make no claim to being a biologist, and I therefore welcome criticism from qualified specialists like yourself. Having said that, I'd now like to address the criticisms you put forward in your post. You write:
But, if someone is going to claim scholarly support for the notion that prebiotic natural selection is impossible, and that there is just no conceivable way to get to a self-replicating sytem, should they be aware of, and cite, major recent work by Harvard biologists that directly contradicts their premise? Heck yes! Did you or Meyer do it? Nope.
The paper you cited by Nowak and Ohtsuki was published on July 14, 2008. Meyer's book came out shortly afterwards, in 2009. As you are doubtless well aware, preparing a book for publication is a process that takes several months. It is highly likely that Meyer was not aware of Nowak and Ohtsuki's paper until some time after his book had been sent to his publisher, HarperOne. As for myself, all I can say is that I am not a regular reader of PNAS, the journal in which Nowak and Ohtsuki's paper was published. Perhaps I should be. Having said that, I utterly reject your charge that ID proponents "can't be bothered to inform themselves of the actual state of affairs in science, and instead quote decades-old work as if it was definitive." My own post refutes this very charge. You want proof? Have a look at the list of references from Meyer that I cited. Go on, take a look! Do you notice something interesting in reference 18?
[18] Wigner, Eugene. "The Probability of the Existence of a Self-Reproducing Unit." In The Logic of Personal Knowledge: Essays Presented to Michael Polyani, edited by Edward Shils, pp. 231-235. London: Routledge and Kegan Paul, 1961. [But see here for a critique by physicist John C. Baez. - VJT]
Yes, there's a link to a paper entitled, "Is Life Improbable?" by John C. Baez, in Foundations of Physics, Volume 1, No. 1, 1989. Baez attacks the reasoning contained in Eugene Wigner's argument. I deliberately listed Baez's critique right next to the reference provided by Meyer, precisely because I wanted to stimulate an open and honest discussion on this thread. You failed to even notice the link I provided. Mullenix would not have made that mistake, I can assure you. And now to matters of substance. I had a look at Nowak and Ohtsuki's paper, and I have to say that I was underwhelmed. Why? First, the paper contained absolutely no chemistry. There was only mathematics. Second, the mathematics was not terribly sophisticated. Even I could understand it - and I'm a philosopher who hasn't studied maths for 30 years. (Full disclosure: I have a B.S. in maths, but that was a long, long time ago.) There were no references in the paper to amino acids. There were no references in the paper to nucleotides. There were no references in the paper to polypeptides. There were no references in the paper to polynucleotides. There was one reference in the paper to RNA. There were no references in the paper to DNA. You call this a serious origin of life paper? I wouldn't even call it a science paper. There's no real world connection here. Where's the chemistry? One sentence illustrates the problem with this paper:
The theoretical prediction for this threshold, u_c=1?[(d+2a)/r]^(1/n)=0.058, is illustrated by the vertical broken line and is in perfect agreement with the numerical simulation.
The authors are patting themselves on the back because their theoretical prediction is in perfect agreement with a numerical simulation? Funny. I always thought, with Francis Bacon, that a fundamental criterion for good science was agreement with real-world observations. How silly of me. My second substantive criticism of Nowak and Ohtsuki's paper is that it fails to address Meyer's "error catastrophe problem" head-on. In his book, Meyer wrote:
[Oparin] proposed that natural selection initially would act on unspecified strings of polypeptides of nucleotides and amino acids. But this created another problem for his scenario. Researchers pointed out that any system of molecules for copying information would be subject to a phenomenon known as “error catastrophe” unless these molecules are specified enough to ensure an error-free transmission of information. An error catastrophe occurs when small errors – deviations from functionally necessary sequences – are amplified in successive replications.[14] Since the evidence of molecular biology shows that unspecified polypeptides will not replicate genetic information accurately, Oparin’s proposed system of initially unspecified polymers would have been highly vulnerable to such an error catastrophe.
Notice that in his book, Meyer cites research involving real chemicals: polypeptides. He points out that "the evidence of molecular biology shows that unspecified polypeptides will not replicate genetic information accurately." You refer me to a paper in which the authors make no reference to polypeptides, and hypothesize that for some polymers, the mutation rate is less than a certain critical value:
There is also competition between life and prelife. Life is selected over prelife only if the replication rate is greater than a certain threshold (Fig. 3). Mutation during replication leads to an error threshold between life and prelife. Life can emerge only if the mutation rate is less than a critical value that is proportional to the inverse of the sequence length (Fig. 4).
There is no attempt here to rebut Meyer's observations regarding the error-proneness of polypeptide replication, just a mathematical model that suggests competition can emerge if the error rate is below a certain critical value. Seriously? My third and final criticism is that the proposals put forward by Nowak and Ohtsuki fail to account for the specified complexity of life and of proteins. (I'm using the phrase here in the same sense as it was coined by Leslie Orgel.) There is nothing in Nowak and Ohtsuki's paper that explains how we get to a protein. All it explains is how we get giant polymers in which a "master sequence" is replicated again and again, with a low error rate. That would generate a molecule containing a sequence that was repeated again and again, with slight variations. But that's not what a protein is like. A protein possesses the property of specified complexity, as does a DNA molecule. You may object that a smaller polymer need not possess the property of specified complexity. Fine; but don't expect me to be impressed when you tell me that a molecule lacking the property of specified complexity can somehow magically explain the emergence of a molecule possessing it. And that, as I see it, is what is wrong with your hypothetical scenario, which invokes "the possibility of a chemical system in which monomers flow in from the general environment, drying or freezing or some such increases the concentration of monomers leading to polymerization, followed by polymers degrading at a certain rate. Make this system cyclical (day/night or seasonal cycles) and continue for a few million years." A protein is not a simple repeating polymer, like polyethylene. Unless your fitness landscape is configured in such a way that it favors the production of ever longer non-repeating polymers leading up to the production of the first protein, it is utterly powerless to account for the emergence of specified complexity. But the existence of such a "nice" fitness landscape that allows for the stepwise emergence of proteins and other molecules exhibiting specified complexity would itself be a miracle. Of all possible fitness landscapes that one can imagine, the vast majority will lack this property. But hey, I'm not a biologist. Doubtless you can think of 101 flaws in my argument, Dr. Matzke. So let's hear them. And now, over to you.vjtorley
July 24, 2011
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The bottom line is that people like Matzke assume that once self-replication appeared, in whatever form and by whatever means, that random errors filtered by natural selection could take care of the rest and produce Mozart and his piano concerti in about 10^17 seconds. Any software engineer knows that as the complexity and functional integration of his code increases, the more understanding about how it all works is required, and the less effective trial and error becomes as a developmental strategy. This represents the problem of probabilistic resources. There are lots of bacteria, but very few higher life forms in comparison. Simple logic dictates that as the complexity of functionally integrated life forms increased, the probabilistic resources must also have increased, in order for the Darwinian mechanism to have had any potential creative power. But the exact opposite is the case. The more sophisticated the system, the fewer the opportunities for Darwinian mechanisms to wave their imaginary magic wands. This is why the Darwinian hypothesis is transparently absurd. It is mathematically ludicrous.GilDodgen
July 24, 2011
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It was a little jest :) But seriously, I think carbon is the crucial thing. In a carboniferous universe, life may be almost inevitable, given enough planets. But maybe not. A SETI signal would be cool :)Elizabeth Liddle
July 24, 2011
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Liz: "Just add water, and wait for consciousness" The soup was rejected due to insufficient energy source. "Despite bioenergetic and thermodynamic failings the 80-year-old concept of primordial soup remains central to mainstream thinking on the origin of life," said senior author, William Martin, an evolutionary biologist from the Insitute of Botany III in Düsseldorf. "But soup has no capacity for producing the energy vital for life." http://www.sciencedaily.com/releases/2010/02/100202101245.htmjunkdnaforlife
July 24, 2011
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Absolutely right, Mung. To enable Darwinian evolution you have to have a) a self replicator b) that replicates with variance c) the variance has to affect efficiency of self-replication. Some crystal satisfy the first two but rarely the third. And to the third you need to add a fourth: d) the possible variance in self-replicatory efficiency has to be multidimensional. That's quite a tall order, but I don't think it's much taller than that. And organic molecules are pretty special. Personally, I think the stroke of genius on the part of the Designer was: Carbon!!!!! Just add water, and wait for consciousness :)Elizabeth Liddle
July 24, 2011
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Yes Nick, let us keep up to date: Nick's 2008 paper suggests the famous "soup" idea: A binary soup and the tree of prelife. Except what Nick's fails to mention is that 2010 research has dumped his soup idea in the trash: New Research Rejects 80-Year Theory of 'Primordial Soup' as the Origin of Life: http://www.sciencedaily.com/releases/2010/02/100202101245.htm There is a major energy problem that Nick pretends is not a problem. Maybe thermal vents is the new soup as the article suggests? Then again maybe not:
Prebiotic chemistry points to a low-temperature origin because most biochemicals decompose rather rapidly at temperatures of 100 degrees C (e.g., half-lives are 73 min for ribose, 21 days for cytosine, and 204 days for adenine).
http://www.ncbi.nlm.nih.gov/pubmed/11539558 Is it possible the whole entire story is BS and you are blowing smoke up our asses?junkdnaforlife
July 24, 2011
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As to what wiki says: Early research by John von Neumann [2] established that replicators have several parts: A coded representation of the replicator. A mechanism to copy the coded representation. A mechanism for effecting universal construction within the host environment of the replicator. Exceptions to this pattern are possible. For example, scientists have successfully constructed RNA that copies itself in an "environment" that is a solution of RNA monomers and transcriptase. In this case, the body is the genome, and the specialized copy mechanisms are external. It is important to note their 'exception' (which was non-referenced); Biologic Institute Announces First Self-Replicating Motor Vehicle - Doug Axe - Excerpt: "So, advertising this as “self-replication” is a bit like advertising something as “free” when the actual deal is 1 free for every 1,600 purchased. It’s even worse, though, because you need lots of the pre-made precursors in cozy proximity to a finished RNA in order to kick the process off. That makes the real deal more like n free for every 1,600 n purchased, with the caveats that n must be a very large number and that full payment must be made in advance." http://biologicinstitute.org/2009/04/01/biologic-institute-announces-first-self-replicating-motor-vehicle/bornagain77
July 24, 2011
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"Life is that which replicates and evolves." Taken literally, this claim means that individual organisms aren't alive, for they do not "evolve" in the way Darwinists use that term.Ilion
July 24, 2011
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The work of John von Neumann, one of the leading mathematicians of the twentieth century, made this dilemma more acute. In 1966, von Neumann showed that any system capable of self-replication would require sub-systems that were functionally equivalent to the information storage, replicating and processing systems found in extant cells.
Why should we believe that von Neumann was wrong? http://en.wikipedia.org/wiki/Self-replication#TheoryMung
July 24, 2011
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Some notes as to the profound difference between life and non-life that Nick seems to 'innocently' gloss over as if they are not of great concern:; Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information - David L. Abel and Jack T. Trevors - Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8 "No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf First-Ever Blueprint of 'Minimal Cell' Is More Complex Than Expected - Nov. 2009 Excerpt: A network of research groups,, approached the bacterium at three different levels. One team of scientists described M. pneumoniae's transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation. "At all three levels, we found M. pneumoniae was more complex than we expected," http://www.sciencedaily.com/releases/2009/11/091126173027.htm “The difference between a mixture of simple chemicals and a bacterium, is much more profound than the gulf between a bacterium and an elephant.” (Dr. Robert Shapiro, Professor Emeritus of Chemistry, NYU) The Capabilities of Chaos and Complexity - David L. Abel - 2009 Excerpt: "A monstrous ravine runs through presumed objective reality. It is the great divide between physicality and formalism. On the one side of this Grand Canyon lies everything that can be explained by the chance and necessity of physicodynamics. On the other side lies those phenomena than can only be explained by formal choice contingency and decision theory—the ability to choose with intent what aspects of ontological being will be preferred, pursued, selected, rearranged, integrated, organized, preserved, and used. Physical dynamics includes spontaneous non linear phenomena, but not our formal applied-science called “non linear dynamics”(i.e. language,information). http://www.mdpi.com/1422-0067/10/1/247/pdf Yet even though there is a 'universe wide chasm' between life and non-life the first tiny baby steps on any imagined pathway to life from non-life are are block on each side by impenetrable barriers; Nick Lane Takes on the Origin of Life and DNA - Jonathan McLatchie - July 2010 Excerpt: As Stephen Meyer has comprehensively documented in his book, Signature in the Cell, the RNA-world hypothesis is fraught with problems, quite apart from those pertaining to the origin of information. For example, the formation of the first RNA molecule would have required the prior emergence of smaller constituent molecules, including ribose sugar, phosphate molecules, and the four RNA nucleotide bases. However, it turns out that both synthesizing and maintaining these essential RNA building blocks -- especially ribose -- and the nucleotide bases is a very difficult task under origin-of-life conditions. http://www.evolutionnews.org/2010/07/nick_lane_and_the_ten_great_in036101.html Homochirality and Darwin: part 2 - Robert Sheldon - May 2010 Excerpt: With regard to the deniers who think homochirality is not much of a problem, I only ask whether a solution requiring multiple massive magnetized black-hole supernovae doesn't imply there is at least a small difficulty to overcome? A difficulty, perhaps, that points to the non-random nature of life in the cosmos? http://procrustes.blogtownhall.com/page3 etc.. etc.. etc.. ,,, and even IF once you had a 'simple' self replicating molecule, the insurmountable 'information problem', faced in any materialistic origin of life scenario, certainly does not just magically go away; "If complex organisms ever did evolve from simpler ones, the process took place contrary to the laws of nature, and must have involved what may rightly be termed the miraculous." R.E.D. Clark, Victoria Institute (1943), p. 63. The GS (genetic selection) Principle – David L. Abel – 2009 Excerpt: Stunningly, information has been shown not to increase in the coding regions of DNA with evolution. Mutations do not produce increased information. Mira et al (65) showed that the amount of coding in DNA actually decreases with evolution of bacterial genomes, not increases. This paper parallels Petrov’s papers starting with (66) showing a net DNA loss with Drosophila evolution (67). Konopka (68) found strong evidence against the contention of Subba Rao et al (69, 70) that information increases with mutations. The information content of the coding regions in DNA does not tend to increase with evolution as hypothesized. Konopka also found Shannon complexity not to be a suitable indicator of evolutionary progress over a wide range of evolving genes. Konopka’s work applies Shannon theory to known functional text. Kok et al. (71) also found that information does not increase in DNA with evolution. As with Konopka, this finding is in the context of the change in mere Shannon uncertainty. The latter is a far more forgiving definition of information than that required for prescriptive information (PI) (21, 22, 33, 72). It is all the more significant that mutations do not program increased PI. Prescriptive information either instructs or directly produces formal function. No increase in Shannon or Prescriptive information occurs in duplication. What the above papers show is that not even variation of the duplication produces new information, not even Shannon “information.” http://www.bioscience.org/2009/v14/af/3426/3426.pdf Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video http://www.metacafe.com/watch/3995248 “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net 'fitness gain' within a 'stressed' environment i.e. remove the stress from the environment and the parent strain is always more 'fit') http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/bornagain77
July 24, 2011
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If anyone here can speak hand-waving and/or literature bluffing, I'd appreciate a translation of Nick@2. Knowing how self-replicating molecules are naturally selected for, and how that correlates/leads directly to natural selection operating at the organismal level would be very valuable indeed. If that problem's been solved, I'd appreciate a reference to the Nobel prize recipient along with references to the correlating empirical results. Thanks in advance! From the paper:
"We have proposed a mathematical theory for studying the origin of evolution."
So the application of the material in the above linked paper should eventually show us how self-replicators evolved. Put another way, we will then fully understand how evolution evolved.
"Life is that which replicates and evolves. The origin of life is also the origin of evolution."
Stupid creationists.material.infantacy
July 24, 2011
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Prevolutionary dynamics and the origin of evolution
Life is that which replicates and evolves. The origin of life is also the origin of evolution.
Why should we believe this?Mung
July 24, 2011
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You have to just love the belief of the evolutionist. All we need is the simplest self-replicating molecule and everything else becomes possible. Well, yeah, it would have to include some sort of variation in order for selection to be possible. And we'll ignore the fact that a simple self-replicating molecule that did not vary might well gobble up all the available resources and evolution would never even have a chance. Can someone tell my why that would not be the more likely scenario? Oh yeah, and not only must it vary, but it must do so in such a way that the variances have a selectable effect. So a simple self-replicating molecule isn't enough. Neither is a molecule that simply replicates with variance. But even assuming you get a population of self-replicating molecules within which the variations that appear somehow cause a variant to increase in number relative to other variants just what exactly does that get you? So consider this as search. At a minimum what does our search have to find? We have at least three targets at a minimum. Of all possible chemical combinations that are energetically feasible how many result in what we need to find? Is a crystal an example of a self-replicating entity?Mung
July 24, 2011
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Surely any vaguely capable summary of this issue would have to include the possibility of a chemical system in which monomers flow in from the general environment, drying or freezing or some such increases the concentration of monomers leading to polymerization, followed by polymers degrading at a certain rate. Make this system cyclical (day/night or seasonal cycles) and continue for a few million years. Then, consider the possibility that some of the polymers catalyze the formation of new polymers that are similar to themselves. This is the beginning of a situation where prebiotic natural selection is *not* a contradiction in terms. The polymerization, monomer inputs, cyclical change in environment, etc., are provided by common natural processes -- only much, much later does biology "take over" these functions, at which point they seem "essential" for "self-replication". Now read: Martin A. Nowak and Hisashi Ohtsuki (2008). "Prevolutionary dynamics and the origin of evolution." PNAS September 30, 2008 vol. 105 no. 39 14924-14927 http://www.pnas.org/content/105/39/14924.full Do we know exactly what the chemistry is that could undergo the transition from prevolution to evolution? No. But, if someone is going to claim scholarly support for the notion that prebiotic natural selection is impossible, and that there is just no conceivable way to get to a self-replicating sytem, should they be aware of, and cite, major recent work by Harvard biologists that directly contradicts their premise? Heck yes! Did you or Meyer do it? Nope. Will scientists ever take ID seriously, when it is the opponents of ID that are forced to do basic literature review work *for* the ID proponents, who can't be bothered to inform themselves of the actual state of affairs in science, and instead quote decades-old work as if it was definitive? Nope.NickMatzke_UD
July 24, 2011
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If life started naturally, then it probably started as zero-bit. It would not have looked much like life as we know it, so would have been some kind of pre-life or proto-life process. Notice that I began that with an "if".Neil Rickert
July 24, 2011
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