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An Eye Into The Materialist Assault On Life’s Origins

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Synopsis Of The Second Chapter Of  Signature In The Cell by Stephen Meyer

ISBN: 9780061894206; ISBN10: 0061894206; HarperOne

When the 19th century chemist Friedrich Wohler synthesized urea in the lab using simple chemistry, he set in motion the ball that would ultimately knock down the then-pervasive ‘Vitalistic’ view of biology.  Life’s chemistry, rather than being bound by immaterial ‘vital forces’ could indeed by artificially made.  While Charles Darwin offered little insight on how life originated, several key scientists would later jump on Wohler’s ‘Eureka’-style discovery through public proclamations of their own ‘origin of life’ theories.  The ensuing materialist view was espoused by the likes of Ernst Haeckel and Rudolf Virchow who built their own theoretical suppositions on Wohler’s triumph.  Meyer summed up the logic of the day

“If organic matter could be formed in the laboratory by combining two inorganic chemical compounds then perhaps organic matter could have formed the same way in nature in the distant past” (p.40)

Darwin’s theory generated the much-needed fodder to ‘extend’ evolution backward’ to the origin of life.  It was believed that “chemicals could “morph” into cells, just as one species could “morph” into another “ (p.43).   Appealing to the apparent simplicity of the cell, late 19th century biologists assured the scientific establishment that they had a firm grasp of the ‘facts’- cells were, in their eyes, nothing more than balls of protoplasmic soup.   Haeckel and British scientist Thomas Huxley were the ones who set the protoplasmic theory in full swing.  While the details expounded by each man differed somewhat, the underlying tone was the same- the essence of life was simple and thereby easily attainable through a basic set of chemical reactions.

Things changed in the 1890s.  With the discovery of cellular enzymes the complexity of the cell’s inner workings became all too apparent and a new theory that no longer relied on an overly simplistic protoplasm-style foundation, albeit one still bounded by materialism, had to be devised.  Several decades later, finding himself in the throws of a Marxist socio-political upheaval within his own country, Russian biologist Aleksandr Oparin became the man for the task. 

Oparin developed a neat scheme of inter-related processes involving the extrusion of heavy metals from the earth’s core and the accumulation of atmospheric reactive gases all of which, he claimed, could eventually lead to the making of life’s building blocks- the amino acids.  He extended his scenario further, appealing to Darwinian natural selection as a way through which functional proteins could progressively come into existence.  But the ‘tour de force’ in Oparin’s outline came in the shape of coacervates- small, fat-containing spheroids which, Oparin proposed, might model the formation of the first ‘protocell’.

Oparin’s neat scheme would in the 1940s and 1950s provide the impetus for a host of prebiotic synthesis experiments, most famous of which was that of Harold Urey and Stanley Miller who used a spark discharge apparatus to make the three amino acids- glycine, alpha-alanine and beta-alanine.  With little more than a few gases (ammonia, methane and hydrogen), water, a closed container and an electrical spark Urey and Miller had seemingly provided the missing link for an evolutionary chain of events that now extended as far back as the dawn of life.  And yet as Meyer concludes, the information revolution that followed the elucidation of the structure of DNA would eventually shake the underlying materialistic bedrock.          

Meyer’s historical overview of the key events that shaped origin-of-life biology is extremely readable and well illustrated.  Both the style and the content of his discourse keep the reader focused on the ID thread of reasoning that he gradually develops throughout his book.

Comments
Onlookers: The thread has now wended its way back to the original focus, with the above link to the Manrubia-Briones paper by Nakashima-san. Now, In that paper, we may see: -------------- >> The size of the first informative molecules was strongly constrained by the accuracy in replication. [Note the questions of source and means of use of information being begged, at the outset] In an environment where proofreading mechanisms were initially absent [absence of error detection and correction would very likely destroy functionality in raid order], replicating biomolecules [replication is assumed not demonstrated, i.e we have the quiet assumption here of either passive reproduction through autocatalysis on templates etc, or the von Neuman architecture for active self-replication] had to be necessarily short. This represented a strong limitation in the amount of genetic information that could be stored and reliably transmitted to subsequent generations [dubiously assumes the existence of information and means of applying it], as well as to the functional capabilities of the evolving molecules. That process likely led to the appearance of molecular quasispecies (Eigen 1971) [i.e imagines a quasi-life based on Dawkinsian or similar replicators], large and heterogeneous populations of replicating molecules that initiated Darwinian evolution. [thus ducks the issues of what life is and how it works per OBSERVATION (i.e cells), and introduces "function" through paper chemistry at best] One of the most popular scenarios for molecular evolution [i.e effectively wholly speculative] prior to the appearance of cellular life is that of the RNA world [Cf below on Shapiro's remarks on that world from his recent article] (Gilbert 1986; Joyce 2002), where small populations of replicating RNA molecules would simultaneously encode information and perform catalytic activity. [smuggles in catalytic activity into the ideas of function and information] Mutation (inherent to the replication process) and recombination should have promoted the appearance of variants. Selection, defined through the characteristics of the environment where evolution proceeded [fallacies of mutation and selection before credible life forms multiplied by galloping hypotheses where speculation ever so soon becomes assumed "reality"], would have favored the replication of certain molecular types. Different microenvironments (characterized by their physicochemical conditions, including ionic strength, pH, metal concentration, or temperature) would then induce different selection pressures, and eventually a spectrum of independent populations of functional replicators might have been simultaneously available [Dawkins' replicator arrives on the scene]. In a favorable situation, it is possible that each molecular quasispecies selected in that way specialized in performing a single, simple function, as a step prior to the emergence of genetic or metabolic reaction networks. [the hypotheses gallop on] This scenario has received steadily increasing experimental support in the last two decades. [hurling the elephant: claiming a weight of evidence that is not justified in details -- note absence of even a link to a survey article here] Although there is no known natural ribozyme that catalyzes the template-directed polymerization of nucleotides, in vitro evolution experiments have shown that RNA-dependent RNA polymerization can be performed without the help of proteins [cf Shapiro on this!] (Johnston et al. 2001; Joyce 2004; Orgel 2004). However, the details of how such a process could have taken place in the RNA world are as yet unknown (Joyce 2002; Joyce and Orgel 2006). Advances in experimental research indicate that the appearance of complex functions in RNA molecules could have been linked to the independent selection of molecular motifs or domains rather than to the de novo selection of complex molecules [speculations gallop on] (Knight and Yarus 2003; Joyce 2004; Wang and Unrau 2005) . . . ---------- In short the paper in question is a mass of galloping hypotheses that soon take on the aura of "fact." Shapiro's strictures on the RNA world are apt . . . [ . . . ]kairosfocus
July 29, 2009
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Adel, you disappointment us.
"What books, other than Scripture, does the other shelf contain?"
This comment is so cheap and stupid. (Clive ban me if you wish) I remember GP and you having a long discussions several months ago, and you never cheapened the topic by this level of utter stupidity. It is sad that you chose to do so now. Adel, if you'd like to discuss ID then I am happy to oblidge. I know for a fact you are smart enough to know the difference in the quality of observations that can be leveled in both directions. I also know that you can see the triviality of your last post. If you simply want to give up on reason and make this level of comment in its place, then please consider keeping your cheap shots to yourself - where they should be.Upright BiPed
July 28, 2009
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"functional complexity" I wonder whatever that could be.jerry
July 28, 2009
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Adel, If the actual substance of the discussion does not interest you, you could always go do something else.ScottAndrews
July 28, 2009
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What books, other than Scripture, does the other shelf contain?Adel DiBagno
July 28, 2009
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Adel, It was more of an illustration than an analogy I suppose, but it was a solid one. If you have a shelf full of books and one is missing, that's a gap. If a few are missing, you have gaps. By comparison, if there are no books on the shelf, we wouldn't call that a gap.ScottAndrews
July 28, 2009
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Scott Andrews, Sometimes, analogies are helpful. Sometimes they are not.Adel DiBagno
July 28, 2009
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My point was simply that it is not possible to commit a "god of the gaps" fallacy when dealing with OOL. For that to be possible, we must fill the void with knowledge and presumably leave some gaps. (Perhaps you were equating my 'books' analogy to knowledge. I was talking about literal books on a shelf.) We have some experimental knowledge, but it may or may not have any connection to the actual events we seek to explain.ScottAndrews
July 28, 2009
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Not amazing, just the distiction between 'how it was' and 'how it could have been'.Nakashima
July 28, 2009
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I wonder what you thought my point was. It must have been really, really amazing! :)ScottAndrews
July 28, 2009
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You give me too much credit.ScottAndrews
July 28, 2009
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OK, your point was less sophisticated than I thought.Nakashima
July 28, 2009
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And I should add, I'm being rather generous by saying that we have hypotheses. I won't elaborate though, to avoid distracting from the main point.ScottAndrews
July 28, 2009
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Mr. Nakashima: The research explicitly describes a "scenario." It further states:
The results that we present in this section have been obtained from computer simulations in which the evolution and selection of a population of RNA sequences are numerically implemented.
Of course, there's nothing wrong with exploring scenarios through simulations. But my question is, does this paper describe what happened billions of years ago? Does it even claim to? Unless the answer is yes, sorry, no books on the shelf. My claim is that we can't explain or describe how life originated - we have only hypotheses. Presenting a hypothesis does not counter that claim.ScottAndrews
July 28, 2009
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Mr ScottAndrews, Modular evolution and increase of functional complexity in replicating RNA molecules This is the kind of research which I think justifies saying there are a few books on the shelf! ;)Nakashima
July 28, 2009
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Nakashima:
We are past just showing that the components can be synthesized, and there are experiments looking at how they are assembled into larger ensembles.
We know that the components can be synthesized. That's a bit like melting sand and saying we've discovered the natural origins of computers. It's wishful extrapolation. There are experiments to see how those components could be assembled. Obviously it follows that we don't know. Our supposed knowledge of OOL boils down to what the pieces would be and what the finished product looks like. Everything else, where the components came from and how they came together, is hypothetical. That's why I maintain that there are no "gaps" in our knowledge of the OOL. It's just one enormous gaping (redundant) gap.ScottAndrews
July 28, 2009
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Mr ScottAndrews, Our understanding of the chemical makeup of life may not be an empty shelf, but our understanding of how life’s components came to be arranged is. I'm not sure I agree. We obviously don't know the historical reality, but I think you are asking a more sophisticated question. We are past just showing that the components can be synthesized, and there are experiments looking at how they are assembled into larger ensembles.Nakashima
July 28, 2009
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Nakashima @353: Our understanding of the chemical makeup of life may not be an empty shelf, but our understanding of how life's components came to be arranged is. I'm not aware that we know anything at all. We can perform experiments that produce organic molecules, but do we have any idea whether life's actual origins resemble those experiments? In my 'books on the shelf' analogy, I equate the books to knowledge, not to hypotheses. Our understanding of life's origins is a void, not a body of knowledge with a few gaps.ScottAndrews
July 28, 2009
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Mr Hayden, I agree that it is a powerful argument relative to any explanation of OOL. The question is the relative humility and acceptance of that. Scientists who are investigating OOL know how much they don't know. I don't see the same attitude in KF-san.Nakashima
July 28, 2009
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Nakashima at 348, In response to my 336 - you simply should have lef it alone. I never used the word "program". So replacing the word I actually did use, we get: "The revised claim would be that any programming could falsify, not that any programming is a falsification. ...which is idle jibberish (and as trivial as your oroginal post). You are defending a post that was so contorted it only needed no one to notice in order to be forgotten. - - - - - - - - KF at 339, thank you.Upright BiPed
July 28, 2009
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Nakashima, ------"But again, simply repeating an assertion doesn’t make it true. How do we measure function in the pre-biotic world? Upon what objects are measuring function? until you can answer these questions you can’t say anything about the reality of islands of function. Appealing to life today is not helpful." This is really just as powerful an argument against evolution.Clive Hayden
July 28, 2009
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Mr ScottAndrews, I agree with KF-san that the abiotic creation of organic molecules is well demonstrated. There are gaps in our knowledge in how so many of these molecules connect, stay connected, become energised, etc. But I would not call that an empty shelf.Nakashima
July 28, 2009
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SA: Excellent point. Wells' discussion on Miller-Urey here should be a good point of departure. gotta go GEM of TKIkairosfocus
July 28, 2009
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PS: Constitute or contain or imply. DNA molecules and RAM chips or DVD disks as such are not the information itself but encode and store it. PC LCD screens store and display rapidly update-able information. Voltage variation in a chip is not information itself but a signal that bears it. Information is the abstract entity that is so stored or implied or used. (And that is part of the trouble that materialists have with information: it is abstract but real enough to function as the foundation of our technological world. BTW, energy is also pretty abstract . . . we infer it through operational means [that which can be converted into work, i.e forces moving points of application across space] but we do not ever see energy itself, just energy carriers and expressers.)kairosfocus
July 28, 2009
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BillB: As much as I hate to post anything in the middle of this excellent thread, In response to
...you acknowledge that you don’t know anything about the evolution of early life or proteins. Whatever your argument with ID is, you’ve just confessed to having no specific alternative.
You write:
Alternative to what?, you seem to have just proposed a god of the gaps.
When one suggests that life originated via chemical accidents but cannot offer a single specific as to how that happened, that is not a gap. A book missing from a shelf is a gap. An empty shelf is not a gap.ScottAndrews
July 28, 2009
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Jerry: A computer screen and associated display unit constitute a functionally specific complex information based organisation of components that work together at an operating point, to display information. [Think about how exactly the pixels on your screen are organised and controlled, whether LCD or CRT or Plasma or whatever] I am saying that: [1] the display itself expresses FSCI, [2] a screenful of organised imagery and text on it constitutes FSCI -- that is what I spoke of earlier [and made a calculation on 800 x 600 24-bit pixels for], and [3] the info fed in to form an organised image and/or text themselves will as a rule constitute FSCI, once they exceed 500 - 1,000 bits. GEM of TKIkairosfocus
July 28, 2009
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Mr Biped, but your revised sentence says that the hypotheses can be falsified if any successful algorithmic programming can be found. Very nice, Nakashima. Thank you, but no. The revised claim would be that any programming could falsify, no holds barred on technique, not that any program is itself a falsification.Nakashima
July 28, 2009
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As I close off for the day: Evoloops. Hurling the elephant: no details, just a name as if that proves something. On looking up: >> As genes circulate in the loop counterclockwise, copies of them are made [Just how, kindly sir?] and sent [again, just how,a dn how will these copies just happen to program functional protein chains etc?] toward the tip of the arm. The arm grows through repetition of straight growth and left turning. [How is such "folding" initiated and controlled? Is not Right turning just as probable inherently, in a presumed prebioptic soup, and how are the "right" monomers going to be available in step by step sequence to carry out the info storage and onward metaboliic function etc?]. When the tip reaches its own root after three left turns, they bond together to form a new offspring loop. [an algorithm writes itself out of lucky noise -- or is that by an intelligent programmer's input] Then the connection between parent and offspring disappears [[ That is, we have termination here, a nontrivial issue in algorithm design]]. ( In such a way, the loop reproduces its offspring which has a structure identical to its parent's in the right area, in 151 updates. >> Such loops of course are implemented through complex and specifically functional algorithms. D/RNA chains in such loops would have to be self replicating, requiring a handy "soup" that goes well above investigator interference levels of implausibility relative to realistic prebiotic worlds. [Start with homochirality vs racemic energetic equivalence of different handednsss issues.] In short,the image makes a nice looking but again predictably misleading icon. Next rhetorical wave please. GEM of TKIkairosfocus
July 28, 2009
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"Similarly, the screen that displays the output contains FSCI" kairosfocus, I am not sure I agree with you or do not know what you mean here. The screen is a manufactured item but I am not sure where the FSCI is in the screen. It certainly is in the computer program in two separate ways. FSCI is in an entity if that entity is information, complex, and specifies a function in something independent. So I am not sure how a screen fits that. The computer program is FSCI in two completely separate ways. It is FSCI just as any written communication that makes sense in terms of a grammar system or vocabulary makes sense. It is also FSCI in the sense that any computer program that is functional is FSCI. FSCI is in an entity but it requires two other independent entities for it to be so. The simplest illustration is DNA which requires the machinery of the transcription and translation process and the object of the process or protein. Without the latter two the DNA might well as be junk as is probably some DNA. It is only when the the second entity (transcription and translation process) turns something into a third entity that has function that the FSCI arises in the DNA. Similarly a random set of letters probably does not contain FSCI because the vocabulary and grammar system will not produce any meaning in our minds other that this is a useless pieces of letters. So any computer program is FSCI since by definition it presupposes this intermediary machinery that reacts to the binary machine code and produces a screen display or a printed document. The screen display or printed document is not FSCI necessarily. There are some intermediary steps in the computer program and each may be producing some entities with FSCI. For example the binary code itself could be a useless series of 0's and 1's or it could be mediated by the hardware to produce something functional. A good computer programmer should be able to delineate the steps. Now the code of a computer program could also be looked at in terms of any communication. The communication contains FSCI, but the mechanism for mediating that communication, vocabulary and grammar, are the means that turn that communication into another entity, the understanding in our minds. Obviously the example of language is a complicated process but the same three independent entities are there. A. the element with FSCI: DNA, lines of computer code, a sentence in a language or the same thing spoken or put into signs. B. The set of rules that transforms or mediates the original entity with FSCI such as the machinery of transcription and translation; the process that turns the computer program into digital information and then the hardware that produces the output and this is very analogous to transcription and translation; and for language the vocabulary and grammar developed over the years and which we teach our children. C. The entity that is produces by these processes, a protein, a printed page or screen view, an understanding in our minds. So FSCI is as simple as ABC but all three are needed but the FSCI only resides in the A but needs B and C to be FSCI. And B or C may or may not contain FSCI.jerry
July 28, 2009
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Nakashima-san: Again, photographs are an example of observed, functionally specific complexity. Photography is, notoriously, a field of technology. That is, on EMPIRICAL EVIDENCE [tut, tut . . . ] -- and a successful counter example of images produced naturally (e.g. of Mt Rushmore) would be important -- photographs are designed. The differential image on a leaf idea is of course an extension of putting a bit of black paper on a leaf then exposing it to sunlight and "developing" the latent image by using iodine or whatever. [The leaf provides a handy grid that is light sensitive; the image comes from a designed process. Remember we are dealing with photos not "film." (Besides the leaf itself is riddled with FSCI and raises the issues Abel just noted as I excerpted. Can you adequately explain in technical details the origin of chloroplasts with their own DNA chains, on chance + necessity from simple initial components that do not embed FSCI?)] GEM of TKIkairosfocus
July 28, 2009
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