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Missing link in origin of life confirms Mike Behe’s thesis?

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Irreducible complexity

From Yahoo News:

The new research — which involves two studies, one led by Charles Carter and one led by Richard Wolfenden, both of the University of North Carolina — suggests a way for RNA to control the production of proteins by working with simple amino acids that does not require the more complex enzymes that exist today.

This link would bridge this gap in knowledge between the primordial chemical soup and the complex molecules needed to build life. Current theories say life on Earth started in an “RNA world,” in which the RNA molecule guided the formation of life, only later taking a backseat to DNA, which could more efficiently achieve the same end result. Like DNA, RNA is a helix-shaped molecule that can store or pass on information. (DNA is a double-stranded helix, whereas RNA is single-stranded.) Many scientists think the first RNA molecules existed in a primordial chemical soup — probably pools of water on the surface of Earth billions of years ago. More.

So this would support RNA World, the five-star hotel of origin-of-life theories

Physicist Rob Sheldon writes to note the remark,

We also looked at the structure of the autocatalytic sets our algorithm identified. Contrary to Kauffman’s original argument that autocatalytic sets emerge as a giant connected components, it turns out that autocatalytic sets can often be decomposed into smaller subsets, which themselves are autocatalytic. In fact, there often exists an entire hierarchy of smaller and smaller autocatalytic subsets. The smallest autocatalytic sets, which cannot be decomposed any further, are called irreducible autocatalytic sets.

In recent groundbreaking work, a group of researchers including Kauffman and Hungarian theoretical evolutionary biologist Eors Szathmary convincingly showed that autocatalytic sets composed of multiple small, irreducible subsets can, in fact, evolve. The main idea is that these autocatalytic subsets can exist in different combinations within a compartment (a protocell), thus giving rise to different types of protocells, and, consequently, to competition and selection. This, combined with our own results that one can indeed expect many such irreducible autocatalytic subsets to exist within a reaction network, suggests that autocatalytic sets are likely to arise from sufficiently complex chemical reaction networks and go on to evolve into larger and more complex systems.

Notice that “evolving” operates at the level of moving IC chess pieces.

Yes, we did notice the design assumptions and language. But naw, it all just sort of happened. 😉

Abstract The hydrophobicities of the 20 common amino acids are reflected in their tendencies to appear in interior positions in globular proteins and in deeply buried positions of membrane proteins. To determine whether these relationships might also have been valid in the warm surroundings where life may have originated, we examined the effect of temperature on the hydrophobicities of the amino acids as measured by the equilibrium constants for transfer of their side-chains from neutral solution to cyclohexane (Kw>c). The hydrophobicities of most amino acids were found to increase with increasing temperature. Because that effect is more pronounced for the more polar amino acids, the numerical range of Kw>c values decreases with increasing temperature. There are also modest changes in the ordering of the more polar amino acids. However, those changes are such that they would have tended to minimize the otherwise disruptive effects of a changing thermal environment on the evolution of protein structure. Earlier, the genetic code was found to be organized in such a way that—with a single exception (threonine)—the side-chain dichotomy polar/nonpolar matches the nucleic acid base dichotomy purine/pyrimidine at the second position of each coding triplet at 25 ̊C. That dichotomy is preserved at 100 ̊C. The accessible surface areas of amino acid side-chains in folded proteins are moderately correlated with hydrophobicity, but when free energies of vapor-to-cyclohexane transfer (corresponding to size) are taken into consideration, a closer relationship becomes apparent (paywall) .– Richard Wolfenden, Charles A. Lewis Jr., Yang Yuan, and Charles W. Carter Jr. Temperature dependence of amino acid hydrophobicities. Proceedings of the National Academy of Sciences, 2015; DOI: 10.1073/pnas.1507565112

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52 Replies to “Missing link in origin of life confirms Mike Behe’s thesis?

  1. 1
    bornagain77 says:

    From Chemicals to Codes at the Origin of Life: A Bridge Too Far? – June 5, 2015
    Excerpt: This paragraph undercuts everything that came before. It deflates all the hype in the report. They just admitted they don’t know how to connect the protein code to the genetic code. They tossed out some speculations by other researchers. They tried to “revive a possibility” that something lucky happened. Then they attributed “anticipation” to blind molecules in a soup. Then there is that pregnant phrase, “according to a message.”
    That, the only use of the word message in the paper, is exactly the issue. A message, written in DNA, is transcribed into messenger RNA. The mRNA carries that message to the aaRS family of enzymes, which faithfully translate the message into the protein code. The acylated transfer-RNAs carry both translations to the ribosome, which reads the mRNA and simultaneously assembles the amino acids into proteins that convert message into function by folding into molecular machines. And that’s not all: those machines interact in systems, regulated by layer upon layer of specifications, messages, and functions. Throughout the cell, error-correction systems work to keep the message from getting lost or corrupted.
    “According to a message.” With those four words, they give away the store to intelligent design.
    http://www.evolutionnews.org/2.....96611.html

  2. 2
    harry says:

    What are the odds of the environment the laboratories provide, in which all this is demonstrated, coming about mindlessly and accidentally?

    A completely automated laptop PC factory would demonstrate the mindless production of laptop PCs. But the environments provided by automated factories do not come about mindlessly and accidentally. Nor does an environment that allows for the production of self-replicating, digital-information-based nanotechnology the functional complexity of which is light years beyond our own — nanotechnology that makes laptop PC technology seem crude in comparison.

    As unlikely as it would be for an automated laptop PC factory to come about accidentally, it is far, far more unlikely than an environment that could produce much more sophisticated technology would come about mindlessly and accidentally. And all that had to happen just to get that first single-celled, metabolizing, self-replicating life form. The notion that that extremely unlikely environment would then not only be sustained but also mindlessly and accidentally adjust itself such that ever-increasing functionality would develop and be maintained in the descendants of that first life form, is beyond absurdity.

  3. 3
    Zachriel says:

    harry: But the environments provided by automated factories do not come about mindlessly and accidentally.

    A complete theory of abiogenesis would entail a plausible primordial environment. Many such experiments have already been done, though there is as yet no complete theory.

    harry: Nor does an environment that allows for the production of self-replicating, digital-information-based nanotechnology the functional complexity of which is light years beyond our own — nanotechnology that makes laptop PC technology seem crude in comparison.

    RNA World, along with this result, largely bridges that gap. RNA can act as both memory and replicator, and can also manipulate amino acids.

  4. 4
    Curly Howard says:

    Need upright biped’s take on this and needed it five days ago when I first asked for it!

  5. 5
    ppolish says:

    Andreas Wagner (Arrival of the Fittest) imagines 1st Life sparking up all over the globe at about the same time. Different kinds of 1st Life. But then one version/clan/tribe of 1st Life defeats all other versions, leaving us a single universal common ancestor.

    I think others believe 1st Life sparked in only one place at one time, and spread.

    How long did it take for a unique 2nd kind of life to emerge? 3rd “species” and 4th? Was there an “inflationary” era when new kinds of life were popping up quickly?

  6. 6
    REC says:

    “a group of researchers … convincingly showed that autocatalytic sets composed of multiple small, irreducible subsets can, in fact, evolve.”

    “autocatalytic sets are likely to arise from sufficiently complex chemical reaction networks and go on to evolve into larger and more complex systems.”

    I think the most devastating argument against Behe’s concept of irreducible complexity is that what he calls “IC” systems could evolve, and that the failure of a system with removal of a part is NOT necessarily an indicator of design.

    You seem to quoting Sheldon on exactly that, although I’m not really sure how his comment relates to the paper.

    KF should also read the paper (or at least the Yahoo summary).

    The notion that tRNAs can discriminate between chemicals and while matching to RNA in a NON_ARBITRARY manner dependent on structure destroys that FSCIO semiotic/arbitrary code of his that has been repeated ad nauseum in “comments closed” posts.

    So—-double own goal?

  7. 7
    Mung says:

    REC: the failure of a system with removal of a part is NOT necessarily an indicator of design.

    Behe didn’t say it was.

  8. 8
    REC says:

    @7

    “To this let me add: A system is irreducibly complex in Behe’s sense if all its parts are indispensable to preserving the system’s basic function”

    William A. Dembski, 2.17.03

    http://designinference.com/doc.....sponse.htm

    I’ll add: there is no definition of IC meaningful to ID that is supported by the quotes in my post.

  9. 9
    Mapou says:

    Re: Origin-of-Life Story May Have Found Its Missing Link

    The Mapou rule of science news:

    You know a science story is crap if the title has the word ‘may’ in it.

    There are exceptions, of course. You can replace the word ‘may’ with other substitutes such as ‘would’ or ‘could’ if you wish. Now that I think of it, the same rule holds true for peer-reviewed articles, especially articles about evolution and parallel universes.

  10. 10
    REC says:

    Mapou,

    If the “may” wasn’t there, you’d accuse the writer of over-hyping the results. If it is there, then the results must be weak.

    I don’t think there is ANY science in this area you’d like.

  11. 11
    REC says:

    Back to the original article, are those quotes following Rob Sheldon’s name his, or from some other unnamed source?

    What is he working on?

  12. 12
    Mung says:

    Curly Howard:

    Need upright biped’s take on this and needed it five days ago when I first asked for it!

    What does this have to do with Upright BiPed?

  13. 13
    Mung says:

    Notice that “evolving” operates at the level of moving IC chess pieces.

  14. 14
    Box says:

    Instead, it is inherently implausible to think that the specificity necessary to coordinate the movements and arrangements of the billions or trillions of cells present in adult animal forms could be established by the interactions of one or two simple chemicals, even if they formed autocatalytic cycles. Kauffman himself seems tacitly to acknowledge the difficulty of generating biological specificity from the reactions of chemicals alone. He notes, in critique of his own model, that patterns of molecular diffusion produced by chemical autocatalysis would depend crucially upon “the initial conditions.”16 In other words, getting a biologically relevant information-rich arrangement of morphogenic proteins would require starting with a very specific (presumably information-rich) arrangement of autocatalyzing molecules.

    Kauffman encounters this same problem in attempting to explain the origin of the first life as the result of autocatalytic reactions starting from a prebiotic soup. In The Origins of Order, he acknowledges that generating an autocatalytic, or self-reproducing, set of molecules—a crucial step in his origin-of-life scenario—would require “high molecular specificity”17 in the initial set of peptides or RNA molecules. In other words, it would require specificity of arrangement and structure, that is to say, functional information.
    (…)
    Getting a law-governed system to generate repetitive patterns of flashing lights, even with a certain amount of variation, is interesting, but not biologically relevant. A system of lights flashing “Vote for Jones,” on the other hand, would model a biologically relevant outcome, at least, if such a functional sequence of letters arose without intelligent agents programming the system with equivalent amounts of functionally specified information.

    [Stephen C. Meyer, Darwin’s Doubt, Ch.15]

  15. 15
    ppolish says:

    “Szathmary convincingly showed that autocatalytic sets composed of multiple small, irreducible subsets can, in fact, evolve.”

    Evolve? Certainly not NS & RM evolve. What kind of evolve are we talking about? Guided or unguided? Lucky evolve? Magic evolve?

    This is clear cut Design evolve right? Right?

  16. 16
    REC says:

    I think I figured out the original post.

    News quotes one Yahoo article reviewing work that is fully devastating to Kairosfocus’s argument that the codon-amino acid relationship is physically arbitrary. Semiotic? Maybe no.

    Sheldon’s response must then be the line “Notice that “evolving” operates at the level of moving IC chess pieces”? In response to the paragraphs from an article “News” does not provide the citation of, which I found via google here:

    http://www.the-scientist.com/?.....iving-Set/

    The article makes it clear they are talking about the emergence and evolution of IC sets. So, no to Mung on reprinting that little quip. And no to the original post saluting Behe on this study.

    Also to box, thanks for establishing why this new study is so significant, and a direct answer to previous ID criticisms. As the author of the article I linked put it:

    “In light of all these results, it seems that the main criticisms against the plausibility and evolvability of autocatalytic sets have now been largely resolved.”

    So, Meyer now has some better work to consider….

  17. 17
    Mung says:

    The map is not the territory. Still waiting to see something relevant to Upright BiPed’s argument.

  18. 18
    Mapou says:

    REC:

    Mapou,

    If the “may” wasn’t there, you’d accuse the writer of over-hyping the results. If it is there, then the results must be weak.

    No. I accuse the writer and the researchers of engaging in materialist/atheist propaganda knowing well that they have nothing truly scientific to talk about.

    I don’t think there is ANY science in this area you’d like.

    So true. Calling this crap ‘science’ is a travesty of some big principle somewhere, IMO.

  19. 19
    Curly Howard says:

    Cmon Mungy, are you serious? You’ve been here a lot longer than I have.

    Every time I talk to upright, his argument is that there is no “physicochemical” link between nucleic acid sequence and amino acid sequence. He of course dresses it up with his usual psychobabble wordiness, but either way these findings seem to fly in the face of his semiotics argument. Which is why I would like to hear what he has to say.

  20. 20
    Mapou says:

    It’s almost amazing how the Yahoo article is full of design language:

    Also, proteins have to be shaped a certain way in order to function properly. That means RNA has to be able to guide their formation — it has to “code” for them, like a computer running a program to do a task.

    And so here we go again, quickly descending into the usual abject and shameless silliness for which they are famous the world over: coding without a coder, task performing without goal and a task performer and, of course, programming without a programmer.

  21. 21
    Mung says:

    Curly Howard:

    Every time I talk to upright, his argument is that there is no “physicochemical” link between nucleic acid sequence and amino acid sequence.

    Actually, that’s not what he says. So I’d not be surprised at all if he doesn’t respond to you. He probably has much better things to do.

    What is it from the paper that you find so relevant, or are you just reading the reporting?

  22. 22
    Curly Howard says:

    Actually Mungy, that is pretty much word-for-word what he has said to me at least a few times.
    I’ve only read the science daily blurb, but that was enough to know that the research directly contradicts one of upright’s main selling points.

  23. 23
    EugeneS says:

    ‘Guided evolution’ is not evolution at all. Evolution is unguided by definition. I think the oxymoronic ‘guided evolution’ needs to be dropped altogether because it obscures things.

    Once everyone agrees to this simple and clear terminology usage, the mental picture will be clearer as well, i.e. evolution cannot achieve functional organization. It cannot achieve organization in principle, not just because of limited probabilistic resources. Probabilities are astronomically small, but that’s not the point. Probabilistically, there is always a loophole – ‘however minuscule but greater than zero’ kind of reasoning – that our evolutionist friends we’ll be using. So I think that, by and large, plausibility arguments on their own are a distraction.

    The point is, functional organization (as opposed to trivial order-chaos phase transitions) absolutely requires intelligence to produce. Organization is a prerequisite to evolution, not the other way around. Evolution is but a second-order phenomenon critically dependent on organization.

  24. 24
    Silver Asiatic says:

    EugeneS

    Interesting points.

    The point is, functional organization (as opposed to trivial order-chaos phase transitions) absolutely requires intelligence to produce.

    And this organization is not merely found at the cellular level. There is the functional organization of the earth’s biosphere as a whole – the interaction of all organisms from bacteria to plants to animals to humans, all built on a physical structure that also exhibits levels of organization – and thus fine tuning.

  25. 25
    EugeneS says:

    Silver Asiatic,

    Thanks. I was talking about organization in the narrow sense of biological systems and other linguistic machines (i.e. in the sense niwrad and others have used the term on this blog). I am not that familiar with fine-tuning (the anthropic principle) so I can’t see how fine-tuning may be described in terms of functional organization and irreducible complexity. Fine-tuning is a strong argument but of a different nature, in my opinion.

  26. 26
    harry says:

    Zachriel @3,

    Take a look at:

    http://www.panspermia.org/rnaworld.htm

    There you will find criticism of the RNA World hypothesis from the perspective of one who believes it is far more likely that life arrived here somehow from outer space than it is that a transition from from lifeless matter to life took place here on Earth.

    What do you think?

  27. 27
    Silver Asiatic says:

    EugeneS

    Michael Denton has a paper on this in a recent edition of BioComplexity. He talks about “the fitness of the environment”. Within physics itself, there are organizing principles that act on properties of matter — all of these created an environment that made life possible, and which sustains life.

    These things are “organized by” something – since they can’t organize themselves. Laws are constant, when they could have been totally unpredictable.

    It depends on what one means by “organization” though. If the term means that there is necessarily an information feedback process, then ‘organization’ can only refer to living organisms.

    But I’m using the term in the sense of “hierarchical ordering principles and forces that enable function”. That wouldn’t be limited to biological systems.

  28. 28
    Mung says:

    Curly Howard:

    I’ve only read the science daily blurb, but that was enough to know that the research directly contradicts one of upright’s main selling points.

    Well, don’t leave us all in suspense, lol.

    Post the quote and your analysis of how it “directly contradicts one of upright’s main selling points.”

    But if it’s based on your misunderstanding of Upright BiPed’s argument it is probably not going to convince anyone.

  29. 29
    EugeneS says:

    Silver Asiatic,

    I understand. I have absolutely no objections to using ‘organization’ in this sense.

    Thanks for the pointer to the paper. It looks like different researchers are approaching the same issues from different perspectives. As far as I know (I did not read the full paper though so may be wrong), Stuart Kauffman recently was advocating for his old holistic thesis that life could not help emerging (self-organizing); however, according to him, there are no specific laws of life (in other words, the basic physical parameters are such that life is not only possible but inevitable in some form). So the conceptual divide between different perspectives appears to be essential but very thin 😉

  30. 30
    Zachriel says:

    harry: What do you think?

    As abiogenesis is an open question, it’s important to consider a wide range of alternative explanations. It is quite possible organic molecules rained down on the Earth from space. We could even fancifully suggest that a passing intergallactic spaceship dumped their garbage into the solar nebula, both seeding the formation of planets and the beginnings of life. Of course, this only pushes back abiogenesis to some other place and time.

    The evidence tentatively supports an RNA World, but whether RNA World was first, or preceded by something else, no one knows.

  31. 31
    Querius says:

    REC @ 6 speculated,

    It’s amazing how anyone could think that a possibility of a speculation built on an imagination of an assumption can be “devastating” to anything, much less Behe’s successful predictions in IC and malarial resistance.

    You have amazing faith in the supernatural!

    -Q

  32. 32
    Curly Howard says:

    If you understood upright’s argument, Mungy, then I wouldn’t have to explain it to you.

  33. 33
    Mung says:

    Gee Curly, how long did it take you to come up with that response?

    Curly Howard:

    I’ve only read the science daily blurb, but that was enough to know that the research directly contradicts one of upright’s main selling points.

    But you can’t say how. I hope you can understand then why I take what you say for exactly what it’s worth.

    If you can’t articulate the “problem” I doubt Upright BiPed will be able to articulate if for you.

    Do your best. You seem to think it’s important. [Or rather you say that it is and act like it isn’t.]

  34. 34
    wd400 says:

    I’m pretty sure if you understood Upright BiPed’s arguments you’d be Upright BiPed.

  35. 35
    Curly Howard says:

    Look Mungy, upright rants and raves about how their is no “physicochemical” relationship between nucleic acid sequence and amino acid sequence in the translational system. He says, and I quote, “there is nothing you can do to the nucleic acid pattern GCA to relate it to alanine.” Upright calls it a “chemical discontinuity,” however in these few recent papers, a relationship has been uncovered between amino acid sequence and genetic code. Bases favor certain amino acids due to hydrophobics and nucleic acid sequences were found to have tendencies for a specific amino acid. This flies in the face of upright’s “you cannot derive the amino acid from the nucleic acid sequence simply through chemical interactions.”

    I wonder if he’ll read this paper or just continue to babble like an idiot.

  36. 36
    Mung says:

    Curly Howard:

    Look Mungy, upright rants and raves about how their is no “physicochemical” relationship between nucleic acid sequence and amino acid sequence in the translational system.

    That was false the first time you said it and it’s still false.

    …a relationship has been uncovered between amino acid sequence and genetic code…

    No one denies there’s a relationship between nucleic acid sequences in DNA and amino acid sequences in proteins.

  37. 37
    Curly Howard says:

    Mungy, wrong on all accounts as usual. Not only do you barely have a basic understanding of biology, but you are apparently clueless when it comes to upright’s arguments. I’ve chatted with upright a number of times here, always about the same thing and what I have written above is pretty much word-for-word what he argues. I would like to hear what upright has to say about the research, not your ignorant, asinine self. Goodbye.

  38. 38
    harry says:

    Zachriel @30

    The evidence tentatively supports an RNA World …

    The evidence supposedly supporting the “RNA World” hypothesis, coming as it does from highly contrived, completely unrealistic laboratory experiments (unrealistic in terms of the real environment that was available), actually indicates, more powerfully than it indicates anything else, the necessity of the involvement of an intelligent agent in the origin of life.

  39. 39
    Zachriel says:

    harry: The evidence supposedly supporting the “RNA World” hypothesis, coming as it does from highly contrived, completely unrealistic laboratory experiments …

    The most important evidence comes from the study of mitochondria; that, and the discovery of ribozymes. The experimental research follows from these findings.

  40. 40
    Mung says:

    Curly Howard,

    If you could actually come up with a quote from Upright BiPed showing him actually saying “there is no ‘physicochemical’ relationship between nucleic acid sequence and amino acid sequence in the translational system” you might be worth taking seriously.

    Until then, cheerio.

    For onlookers who might be inclined to think Curly [or REC – who can’t even get the argument associated with the right person] is worth listening to:

    Upright BiPed acknowledges the system is a physical system and that the relationship is established by physical entities.

    The actual argument is that the relationship is not one of physical necessity, not that no relationship exists. Duh.

  41. 41
    Curly Howard says:

    He calls it a “physicochemical discontinuity,” or a “physicochemically arbitrary relationship.” And he says that “there is nothing about the [nucleic] pattern that determines the amino acid.”

    The research we have been talking about flies in the face of all of these claims as I mentioned above.

    From what I can tell, he is trying to prove that the translational system needs a “coder” to set and preserve the initial relationship between nucleic pattern and amino acid, but according to this research, this is unnecessary. They have shown that there is a chemical relationship between nucleic pattern and the corresponding amino acid, which means it is not arbitrary and the system can be directly traced back to the underlying chemistry.

    I don’t think I can make it any more clear. If you’re still going to argue, then you’re just being a stubborn ignoramus.
    Toodaloo!

  42. 42
    Mung says:

    Curly Howard, who still can’t come up with a relevant quote.

    Am I missing something?

    If you could actually come up with a quote from Upright BiPed showing him actually saying “there is no ‘physicochemical’ relationship between nucleic acid sequence and amino acid sequence in the translational system” you might be worth taking seriously.

    Or are you actually now admitting you were wrong, that Upright BiPed never said any such thing, and that you were misrepresenting his argument?

  43. 43
    Zachriel says:

    Mung: If you could actually come up with a quote from Upright BiPed showing him actually saying “there is no ‘physicochemical’ relationship between nucleic acid sequence and amino acid sequence in the translational system” you might be worth taking seriously.

    Perhaps this will help.
    http://www.google.com/#q=site:.....cochemical

    Here’s a typical example: “the genetic translation system maintains the physicochemical discontinuity between the arrangement of the nucleotides and the binding of amino acids.”

  44. 44
    Mung says:

    Zachriel: Here’s a typical example: “the genetic translation system maintains the physicochemical discontinuity between the arrangement of the nucleotides and the binding of amino acids.”

    If that’s typical then I think I’ve made my point.

    Upright BiPed does not claim that “there is no ‘physicochemical’ relationship between nucleic acid sequence and amino acid sequence in the translational system.”

  45. 45
    Zachriel says:

    Upright Biped: there is no physicochemical relationship between specific nucleotides and amino acids

    http://www.uncommondescent.com.....ent-461213

  46. 46
    Mung says:

    Upright BiPed: there is no physicochemical relationship between the specific arrangement C-T-A and leucine

    http://www.uncommondescent.com.....ent-461213

  47. 47
    Mung says:

    Curly Howard @ 19

    Every time I talk to upright, his argument is that there is no “physicochemical” link between nucleic acid sequence and amino acid sequence.

    Zachriel:

    Upright BiPed: there is no physicochemical relationship between specific nucleotides and amino acids

    Yes, but that’s not his argument. At most it’s a statement removed from the context of his argument.

  48. 48
    Zachriel says:

    Mung: If you could actually come up with a quote from Upright BiPed …

    You asked.

    Mung: Yes, but that’s not his argument.

    Affinities may constitute evidence of the origin of the genetic code.

  49. 49
    Mung says:

    Yes Zachriel, I did. And thank you.

    I was wrong when I said that Upright BiPed does not make that claim. But that is not his argument. That is a snipped of his argument.

  50. 50
    Mung says:

    Upright BiPed:

    The mapping of nucleic acids to amino acids is also based on observed regularities. Those regularities do not stem from the dynamic properties of nucleic acids.

    In order to organize the cell, the mapping between nucleotides and amino acids must be established in the translation system while preserving the physicochemical discontinuity between them.

    Otherwise, the system could not function.

    Upright BiPed:

    The core of my argument is not about irreducibility, but about the necessary function of the system. Even so, I do not assume that genetic translation is irreducible. The notion that translation is irreducible to a representation and interpretant was a prediction of logical necessity, and as it turns out, our universal observation of the natural world has borne this out to be true – without exception. People who question this generally seem to do so without addressing the physics involved. Typically the first thing to go is translation itself.

    Upright BiPed:

    Can you derive which amino acid will be presented at the peptide binding site by the spatial arrangement of bases in a codon? If not, why not.

    Upright BiPed:

    Of course you can’t. It’s because the effect of translation is not physically determined by the arrangement of an informational medium, it determined by the arrangement of the translation apparatus that produces the effect.

  51. 51
    Mung says:

    An even more recent statement of the argument of Upright BiPed can be found here.

  52. 52
    EugeneS says:

    Gents,

    For one, I haven’t looked at this research alluded to by Curly Howard. But what I know is that there’s a lot of confusion even at the basic level of information, as regards what information is and even whether it is objective. Full stop.

    Once there is a disagreement at this basic level of assumption, it’s no wonder different research programs arrive at substantially different results. And, what’s more, even the same result may be viewed through different lenses, as it were, and ‘shown’ to demonstrate vastly different things.

    As David Abel noted in his recent paper, the realization that Maxwell’s demon needed to be ‘informed’ in relation to the OOL came at least as early as in 1964.

    Physical/chemical effects cannot produce anything more than a deterministic bias towards certain structures. Period. However, the OOL needs lots more than the right initial conditions. And physicality therefore is not enough. Not only should Maxwell’s demon be informed about the right choices, but it must make those choices in order for life to kick off. But then again, the whole debate rests upon the notion of information.

    Until such time as we have a principle agreement about what constitutes information and what information translation is, it is not worth wasting time in repartee, I don’t think.

    My take on this is, information is real, it is neither matter nor energy, as Norbert Wiener once noted. Information can be encoded in configurations of matter under certain conditions. It can only be possible if there is a multiplicity of equilibrium states, in other words, once the decoupling from the necessity of the laws of nature is provided. There is zero information carrying capacity in anything that is solely due to the determinism of the laws of nature. On top of that though, to transfer information an agent must make concrete choices. Information processing is a result of decision making.

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