Signature in the Cell?

There is much abuzz in the ID-o-sphere regarding Stephen Meyer’s new book, “Signature in the Cell: DNA and the Evidence for Intelligent Design”.  The book is a lengthy recapitulation of the main themes that ID proponents have been talking about for the past 15 years or so; indeed, there will be precious little that is new for seasoned veterans of the internet discussions and staged debates that have occurred over the years.

Long though the book is, it is built around one central theme – the idea that the genetic code harbors evidence for design.  Indeed, the genetic code – the triplet-amino acid correspondence that is seen in life – is the “Signature in the Cell”.  Meyer contends that the genetic code cannot have originated without the intervention of intelligence, that physics and chemistry cannot on their own accords account for the origin of the code.

It is this context that a recent paper by Yarus et al. (Yarus M, Widmann JJ, Knight R, 2009, RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code, J Mol Evol  69:406–429) merits discussion.  This paper sums up several avenues of investigation into the mode of RNA-amino acid interaction, and places the body of work into an interesting light with respect to the origin of the genetic code.  The bottom line, in terms that relate to Meyer’s book, is that chemistry and physics (to use Meyer’s phraseology) can account for the origin of the genetic code.  In other words, the very heart of Meyer’s thesis (and his book) is wrong.

One interesting highlight from this review is the discernment of a set of rules (of sort) for RNA-amino acid interactions.  These rules follow from the structures of several RNA-amino acid complexes, specifically the structures of riboswitches* that bind methionine derivatives, lysine, and arginine.  Based on these structures, Yarus et al. propose that RNA recognizes primarily polar groups (including aromatic rings, that can “bond” with positively-charged groups via cation-pi interactions) in amino acids.  As stated in the paper:

Summary of a Polar Profile, Based on Met–, Lys–, and Arg–RNA Complexes

1. RNA fixes polar features of its ligands, often restraining them at the intersection of multiple directional bonds. Such restraint likely includes aromatic and heteroaromatic rings.

2. RNA can measure the distance between such polar features, possibly allowing substantial freedom in apolar bridging constituents by stacking them loosely.

3. RNA can also sterically limit the size, disposition, and/ or shape of apolar groups close to the specifically bound polar elements cited in item 1.

Of course, other specificities may be added as more RNA-ligand structures are studied. This is particularly true because this analysis is based on only a few amino acid side chains and a few high-resolution co-structures.

The authors then summarize many years of work involving the identification and characterization of RNAs that bind amino acids.  These RNAs have been identified using in vitro selection, usually starting with collections of RNA of random sequence.  Eight such amino acids have been studied to some extent in this regard.  What has been found is that, for six of the eight amino acids (arginine, histidine, phenylalanine, phenylalanine, tryptophan, and tyrosine), RNAs that bind with high affinity are very likely to possess either the cognate codon or anticodon triplet that is associated with the respective amino acid in the genetic code.  For two amino acids (glutamine and leucine), this is not the case.  Put more plainly, 75% of tested amino acids associate with their anticodon (in some cases, along with their codon) in these studies.  This is remarkable, as it is demonstrative of an underlying stereochemical basis for at least some of the genetic code.  As summarized in the abstract:

By combining crystallographic and NMR structural data for RNA-bound amino acids within riboswitches, aptamers, and RNPs, chemical principles governing specific RNA interaction with amino acids can be deduced. Such principles, which we summarize in a ‘‘polar profile’’, are useful in explaining newly selected specific RNA binding sites for free amino acids bearing varied side chains charged, neutral polar, aliphatic, and aromatic. Such amino acid sites can be queried for parallels to the genetic code. Using recent sequences for 337 independent binding sites directed to 8 amino acids and containing 18,551 nucleotides in all, we show a highly robust connection between amino acids and cognate coding triplets within their RNA binding sites. The apparent probability (P) that cognate triplets around these sites are unrelated to binding sites is [approximately] 5.3 x 10-45 for codons overall, and P [is approximately] 2.1 x 10-46 for cognate anticodons. Therefore, some triplets are unequivocally localized near their present amino acids. Accordingly, there was likely a stereochemical era during evolution of the genetic code, relying on chemical interactions between amino acids and the tertiary structures of RNA binding sites. Use of cognate coding triplets in RNA binding sites is nevertheless sparse, with only 21% of possible triplets appearing. Reasoning from such broad recurrent trends in our results, a majority (approximately 75%) of modern amino acids entered the code in this stereochemical era; nevertheless, a minority (approximately 21%) of modern codons and anticodons were assigned via RNA binding sites.

There is more in the review that is provocative.  Yarus et al. explain that, while 75% of tested amino acids have an affinity of sorts for cognate anticodons/codons, only 21% of the possible anticodon/codon triplets that we can get from the genetic code are identified in these studies.  Thus, we can discern that the genetic code as we understand it today likely evolved in several steps – a stereochemical era wherein a core set of triplet-amino acid correspondences was first established, followed by subsequent expansion of the assignments of other triplets and recruitment of other amino acids (typified by gutamine and leucine) via other mechanisms.

So what does this have to do with Meyer’s book?  The argument is best illustrated using Meyer’s own words.  Early in the book, Meyer lays out his challenge:

(pp 134-5)

“The picture of the cell provided by modern molecular biology has led scientists to redefine the question of the origin of life.  The discovery of life’s information-processing systems, with their elaborate functional integration of proteins and nucleic acids, has made it clear that scientists investigating the origin of life must now explain the origin of at least three key features of life.  First, they must explain the origin of the system for storing and encoding digital information in the cell, DNA’s capacity to store digitally encoded information. Second, they must explain the origin of the large amount of specified complexity or functionally specified information in DNA,  Third, they must explain the origin of the integrated complexity – the functional interdependence of parts – of the cell’s information-processing system.”

Later, in Ch. 11, Meyer argues that the genetic code transcends or is apart from physics and chemistry.  Early in this chapter, Meyer invokes Polyani to argue that “reductionism”, that is, chemistry and physics, cannot account for the origins of the genetic code:

(pp 238-40)

“Consider an illustration.  A 1960s vintage computer has many parts, including transistors, resistors, and capacitors.  The electricity flowing through these various parts conforms to the laws of electromagnetism, for example, Ohm’s law (E=IR, or volateg equals the current time resistance).  Nevertheless, the specific nature of the computer, the configuration of its parts, does not result from Ohm’s or any other law.  Ohm’s law (and, indeed, the laws of physics generally) allows a vast ensemble of possible configurations of the same parts.  Given the fundamental physical laws and the same parts, an engineer could build many other machines and structures: different model computers, radios, or quirky pieces of experimental art made from electrical components.  The physical and chemical laws that govern the flow of current in electrical machines do not determine how the parts of the machine are arranged and assembled.  The flow of electricity obeys the laws of physics, but where the electricity flows in any particular machine depends upon the arrangement of its parts – which, in turn, depends on the design of an electrical engineer working according to engineering principles.  And these engineering principles, Polyani insisted, are distinct from the laws of physics and chemistry that they harness.”

And later:

“Polyani argued that, in the case of communications systems, the laws of physics and chemistry do not determine the arrangements of the characters that convey information.  The laws of acoustics and the properties of air do not determine which sounds are conveyed by speakers of natural languages.  Neither do the chemical properties of ink determine the arrangements of letters on a printed page.  Instead, the laws of physics and chemistry allow a vast array of possible sequences of sounds characters, or symbols in any code or language.  Which sequence of characters is used to convey a message is not determined by physical law, but by the choice of users of the communications systems in accord with the established conventions of vocabulary and grammar – just as engineers determine the arrangement of the parts of machines in accord with the principles of engineering.

Thus, Polyani concluded, communications systems defy reduction to physics and chemistry for much the same reasons that machines do.  Then he took a step that made his work directly relevant to the DNA enigma: he insisted that living things defy reduction to the laws of physics and chemistry because they contain a system of communications – in particular, the DNA molecule and the whole gene-expression system.  Polyani argued that, as with other systems of communication, the lower-level laws of physics and chemistry cannot explain the higher-level properties of DNA.  DNA base sequencing cannot be explained by lower-level chemical laws or properties any more than the information in a newspaper headline can be explained by the chemical properties of ink.16  Nor can the conventions of the genetic code that determine the assignments between nucleotide triplets and amino acids during translation be explained in this manner.  Instead, the genetic code functions as a higher-level constraint distinct from the laws of physics and chemistry, much like a grammatical convention in a human language.”

In other words, Meyer is claiming that the genetic code is arbitrary, that there are no chemical or physical underpinnings to the codon-amino acid correspondence that we see in life.  It is because the code is arbitrary, Meyer implies that it must be designed:

(pp240-1)

“Polyani’s argument made sense to me.  DNA, like other communication systems, conveys information because of very precise configurations of matter.  Were there laws of chemistry or physics that determine these exact arrangements? Were there chemical forces dictating that only biologically functional base sequences and no others could exist between the strands of the double helix? After reading Polyani’s essays, I doubted this.

I realized that his argument also had profound implications of self-organizational theories of the origin of life.  To say that the information in DNA does not reduce to or derive from physical and chemical forces implied that the information in DNA did not originate from such forces. “

Note that all of this, which, I must emphasize, lies at the very heart of Meyer’s book, is grounded in the idea that the genetic code has no underlying chemical basis.  The experimental work that is summarized by Yarus et al. contradicts Meyer’s assertion, in that it suggests a clear stereochemical basis for at least part of the genetic code.  In other words, the information in DNA may indeed reduce to chemistry and physics.

In closing, I would point out a few things that are likely to arise when discussing things in the context of the ID controversy.  First, it is true that Yarus’ ideas, and the underlying experiments, are far from a direct and complete demonstration of the origination of the complete RNA decoding system that we see in modern cells.  However, the body of work discussed by Yarus et al. constitutes a significant and compelling set of positive experimental support for the hypothesis that the genetic code has an underlying chemical basis.  As such, it far outstrips the entire body of positive experimental support (there is none) for Meyer’s claim that there can be no way to explain the genetic code (the Signature in the Cell) in terms of chemistry and physics.  On a strictly evidential basis, Meyer’s thesis is found wanting.

Second, Yarus’ ideas are quite apart from the larger issue of the origin of life.  It is natural to insert the model into an RNA World context; indeed, the RNA World model is the inspiration for these studies, and these studies provide significant support for this model.  However, the probability of a stereochemical basis for the genetic code applies just as well to design models of the OOL.  In other words, we can consider Meyer’s assertion, that there is no chemical basis for the genetic code, in a design light.  Thus, Meyer’s claim would be that intelligence (a designer, or whatever) assigned triplets to amino acids in an arbitrary fashion.  The opposing design hypothesis would be that the genetic code has an underlying chemical foundation, and that design was implemented at some point before or after the origination of the genetic code.  The work summarized by Yarus et al. argues against Meyer’s claim, but is agnostic as to other possible design scenarios.  In other words, when viewed solely in terms of ID theory, Meyer’s assertion, the heart of his book, would seem to be wrong, and certainly less well-supported than other possible ID models.

The paper:  Yarus M, Widmann JJ, Knight R, 2009, RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code, J Mol Evol  69:406–429

The interesting first few paragraphs:

Introduction

I am particularly struck by the difficulty of getting [the genetic code] started unless there is some basis in the specificity of interaction between nucleic acids and amino acids or polypeptide to build upon. (Woese 1967)

Nonetheless, it is clear that at some early stage in the evolution of life the direct association of amino acids with polynucleotides, which was later to evolve into the genetic code, must have begun. (Orgel 1968)

Part I: The Observed Mechanism of RNA–Amino Acid Interaction

Just above, Carl Woese and Leslie Orgel, writing at the dawn of molecular biology and coding, suppose that chemical interactions between nucleotide sequences and amino acids are an indispensable basis for the genetic code. It is the conclusion of the present narrative that such interactions are easily demonstrated, utilize plausible, simple chemistry, and can indeed be shown to echo part of the genetic code.

*Riboswitches are sites in mRNAs that bind ligands such as amino acids and thereby change conformations; these structural changes affect stability and/or translatability of the mRNAs and thus regulate gene expression.

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30 Responses to Signature in the Cell?

  1. Wayne Robinson says:

    Nick Lane in “Life Ascending” makes most of the same points in the chapter on DNA. Good book to recommend to the ID proponents.

  2. That’s very interesting, and it once again shows the value of evolution as simply explaining what is found. We wouldn’t really think to predict the association of RNA and amino acids, at least not as anything but a possibility, it’s more on the order Dobzhansky’s observation that nothing in biology makes sense, except in the light of evolution.

    Of course this review doesn’t tell us how the RNA originated in the first place, but it does relate to how information arises in organisms.

    Meanwhile, ID continues to say “duh,” or rather, it bloviates all around the issue of explanation in order to cover up the “duhs.”

    Glen Davidson
    http://tinyurl.com/mxaa3p

  3. Dave Wisker says:

    It’s always amusing watching IDC’s choke on Yarus’s elegant work and statistical analysis. They either stop responding or simply try and downplay its importance.

  4. Paul Burnett says:

    Yarus’ detailed science will be utterly ignored by the intelligent design creationists, as they have nobody on board who can understand it, much less refute it.

    I still haven’t gotten responses from any of the fundagelical apologists how the “signature” Meyer claims to have found in the cell was that of Jehovah the creator God of Genesis, as opposed to the “signature” of Odin/Wotan or Zeus Pater/Jupiter or Brahma or Allah or Mumbo-Jumbo Lord of the Congo.

  5. Midnight Rambler says:

    For that matter, as neat as Yarus’ paper is, I don’t see how it matters to Meyer’s argument even if the genetic code was arbitrary. That doesn’t make it any more “designed” than if there is a chemical basis for it.

  6. Wayne Robinson says:

    Midnight Rambler,
    Stephen Meyer’s argument is that the DNA code could not develop by natural causes. Having a chemical basis means that it could develop naturally. Only by not having a chemical basis would that support Stephen Meyer’s position. All we need is a plausible mechanism, not proof (3.8 billion years ago is a very long time, and we’d be hard pressed to find proof either of natural cause or an Intelligent Designer).

  7. Olorin says:

    The arbitrary code is a persistent theme in Meyer’s book. However, he seems to end every argument with a statement about the initial origin of life from “dead” matter.

    It’s as though he consciously built an escape hatch into every argument. When Meyer must finally acknowledge Yarus’ work, he will no doubt retreat to this position.

  8. paul fcd says:

    TGCA

    The Genetic Code: Arbitrary

    Our God has spoken. In english. His signature in the cell.
    :D

  9. Theoretix says:

    Unlike your many posts, I’m glad to see that you have brought some substance to the table.
    However, the content of the article you brought, still argues in terms of biochemical level of the RNA, DNA and not the information-nanobot technology level. Why didn’t the evaluators address this issue? This is the innovative research from which the Intelligent Design scientists postulated an Intelligent Designer as a tentative best explanation for the empirical data that they have discovered.
    Meyer wrote a complete book to help address his critic’s comments and positions during the past 10 years. The biochemical level of the RNA is but a part of that issue, and Meyers did a good job in presenting his case. The book’s evaluators who are Evolutionists no doubt, cannot really approach the information-nanobot technology level at the sub-chromosome level, because that’s where the evolutionist’s premises dissolve. yet, an explanation must be given for such (VH) very-high-level of information technology. The Intelligent Design people proposed a workable thesis/theory – an Intelligent Designer.
    You may also consult Dr. George Grebens’ books: `Which Ones Are Scientific’ and his forthcoming more scholarly book `Evolution-Creation-Intelligent Design-Hybrids’ – they show the insurmountable difficulties that must be overcome when dealing with such complexity. Shoving ‘complexity’ under a run as the National Academy of Science recommends, does not make the scientific issue go away. Yet, because of this directive, understandably, Evolution scientists do not address issues of information-nanobot technological operations at the sub-chromosome level. Grebens approaches the issue not from the biochemical point of view but from the 3D Management Model view. Here it becomes evident that all the debaters (Evolution-Creation-I.D.-Hybrid) must address management issues of: change at three levels of qualitative infrastructures, not only on an expanded micro-change. This means the debaters must address issues of `automatic’ re-engineering, re-design principles, codes and standards. This is just the beginning, yet Evolutionists do not address such issues in measurable scientific means/methods.
    Briefly, when examining empirical data, Evolution scientists are trained to see this data within the materialistic uniformitarian framework. To categorize or make predictions from such empirical data, they limit themselves to a framework that specifies the following points:
    a) Existing processes, rates and trends, which reflect
    b) A simple-to-complex (primitive-to-modern) progression
    c) Within statistical, random or chance parameters
    d) Without the influence of external forces
    e) Over long periods of time – billions, millions and hundreds of thousands of years
    Each of these points is axiomatic. The grouping of these axiomatic points are then identified as being theoretical – in other words, remaining at the `uncertainty’ level awaiting identification/discovery of physical laws that must circumvent existing contrary laws (e.g., entropy, thermodynamics, qualitative infrastructural and macro-change, re-engineering, re-design laws, information/nanobot technology operations at sub chromosome levels, etc.) The 150-year-old theoretical status, i.e., `uncertainty’ has rendered the theory into a belief/faith system. We see this in each of its axiomatic not scientific statements: `existing’ conditions (a); extended over long periods of time (e); which are long enough to allow statistics to work itself out (c), from simple to complex (b), without supernatural forces to guide the process (d). Why use these axiomatic points instead of some other? Well here is where ideology comes in – materialism and anti-Christianity.
    Advocates of the `Hybrids’ view (i.e., `Theistic Evolution’; `Progressive Evolution’; `Old Earth Creation’) redefine point (d) (e.g., `…influence of external forces’) and attribute some unknown supernatural force that acts upon the uniformitarian process at various points in the uniformitarian process, usually where geological gaps emerge. In spite of the redefinition – (d) still remains axiomatic.
    This is why the reviewers of Meyers’ book remain at the biochemical level and never touch the subject of information/nanobot technology operations at sub-chromosome levels. It is at this information level that classical materialism and uniformitarianism evaporate.

  10. Clem Weidenbenner says:

    Theoretix:
    Help me out a little please – I’m not familiar with the term “information-nanobot”. I’ve tried to track it down through Google and am only getting artintl’s blog post at OC (which I suspect you are familiar with).

    I’m thinking artintel is George Grebens, would you know?

    At any rate, there are some philosophical issues here that may be worth consideration. So if a definition for information-nanobot might be proffered, I’ll anxiously await it.

  11. John Stockwell says:

    We need only look at the oft-quoted paragraph from Paley to see that
    Meyer is simply modernizing the Paley argument:

    “In crossing a heath, suppose I pitched my foot against a stone, and were asked how the stone came to be there: I might possibly answer, that for any thing I know to the contrary, it had lain there for ever: nor would it perhaps be very easy to show the absurdity of this answer.

    Translation, Paley and his era is utterly ignorant of geologic processes.

    “But suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place; I should hardly think of the answer which I had before given, that for any thing I knew, the watch might have always been there. Yet why should not this answer serve for the watch, as well as for the stone? why is it not as admissable in the second case as in the first? For this reason, and for no other, viz., that when we come to inspect the watch, we perceive (what we could not discover in the stone) that its several parts are framed and put together for a purpose . . . This mechanism being observed . . . the inference, we think, is inevitable, that the watch must have had a maker; that there must have existed, at some time, and at some place of other, an artificer or artificers, who formed it for the purpose which we find it actually to answer; who comprehended its construction, and designed its use.”

    Translation: Instead of concentrating on processes Paley seeks meaning in
    objects he observes. Finding a watch means “designer”. Having made this
    leap, Paley states a correspondence principle, with no corresponding
    process, and leaps further to asserting that anything that “looks purposefully
    designed” imples a “Designer”. (Kind of like astrology, correspondence
    principle with no process.)

    The fallacy of the watchmaker argument is that we know a great deal more
    about watches and their process of origin than we know about biology.
    In 1800 a watch was a high tech wonder inspiring much the same reaction
    as the most high tech computer or cellphone today. Paley could track down
    the location of manufacture, the processes by which the parts were made,
    the very mines where the ores were quarried, and the foundry where the
    metals were smelted from the ore. Furthermore, Paley could find the
    vendor who sold the watch and the person who bought it, and ultimately
    could return the watch to its owner.

    The modern version of all of this all hinges on the unfortunate choice of
    the word “code” to describe DNA. DNA is not a code. It is not a message
    transmitted to a receiver and translated into information for a recipient
    party. DNA is a template. It is a wondrous, complicated template, but
    a template just the same.

    Ignoring the real scientific issue of “processes”, Meyer, as all ID proponents
    do, sees the DNA and asks “what does this mean?” not “how did it get
    here? and proceed to reason from analogy without regard to processes

    Asking “what does DNA mean?” is no more scientific than seeing a flock
    of birds fly over and ask “what does it mean?” in the sense of a fortune teller.

    This is augury, it is not science.

  12. eric says:

    Theotrix: scientists do not discuss the ‘nanobot level’ because nanobots are (so far) fictional critters from the Star Trek and Star Gate TV series.

    As to your claim that mainstream science cannot ‘approach the information-nanobot level at the sub-chromasome level,’ the sub-chromasome level is exactly what this article addresses.

    A chromasome is, roughly speaking, a double helix (DNA) string between ~10^5 and 10^9 base pairs long. This article addresses the interactions of RNA – a single helix – with amino acids – which are about the size of one to two base pairs. In other words this article discusses how the interaction of one biological molecule (which is smaller than a chromasome) with other biological molecules (that are much much smaller than a chromasome) could create a genetic code.

    I.e. the article gives evidence for a chemical basis for the development of a genetic code at the sub-chromasome level. You may wish to bone up on the definitions of RNA, amino acid, and chromasome before responding.

  13. paul fcd says:

    Theoretix

    Your theoretical framework, points a. through e. seem to be a sentence puncuated by letters. It is difficult to understand, especially when you contend that each point is axiomatic. And as clem w pointed out “nanobot-information” is difficult to understand. Your post is opaque. Maybe you could re-state it for laymen like me.

    also, eric, sp. ‘chromosome’

  14. [...] Hunt posted Signature in the Cell? at his blog The RNA Underworld. Art attempts to refute Meyer by citing a paper (RNA–Amino Acid [...]

  15. Naon Tiotami says:

    Wow, that’s an amazing discovery. I can’t wait to bear witness to the discoveries that abiogenesis research is going to uncover in the next ten years.

  16. Joe G says:

    Did the paper demonstrate that the genetic code can arise just via chemistry and physics?

    No.

    Geez there isn’t any data for self-replicating RNAs.

    As for “arbitrary” what Meyer is talking about is that there isn’t any law which decides the way nucleotides are arranged on the Sug-Phos backbone.

    Nucleotides can be arranged any way, yet only certain ways will create/ do something.

    However all that is moot because the “information” isn’t the sequence.

    Rather the sequence is the physical medium for the information just as a disc is the physical medium for a computer’s information. The disc isn’t the info- the info rides on the disc.

  17. Dolly Sherrif says:

    I think Meyer has done a good job with his book. Judging from the response above, there certainly is a scientific debate going on here. This shows that ID is finally being taken seriously by the Pandas Thumb supporters!

  18. Arthur Hunt says:

    Hi all,

    Thanks for the comments. I’ll add a few brief ones here.

    Theoretix, I’ll add to the other comments that note that “information/nanobot” technologies seem, as I understand the terms, to be quite irrelevant to the inner workings of living cells. I’ll also note that the “biochemical level” is precisely where discussions of the OOL, and DNA, and gene expression should be.

    Joe G, Yarus et al. provide evidence that supports precisely the hypothesis (“that the genetic code can arise just via chemistry and physics”) you are choking on. But you are correct in pointing out Meyer’s cartoon that passes for a discussion of DNA. I won’t elaborate, but any serious biochemist would find it hard to take seriously Meyer’s discussion of the sequencing of bases in DNA, and the revelation he had that base-base interactions could not lead to any sort of genetic code.

    Dolly, I would call you comment faint praise indeed for ID.

    Again, thanks to all for stopping by.

  19. Joe G says:

    Arthur Hunt-

    You are mistaken and you are choking on it.

    The paper takes a look at how things are running now, assumes it is reducible to matter and energy and then extrapolates from that.

    Heck no one can get the RNAs required to form!

    And without that you cannot have a genetic code form.

    Are you saying that the way nucleotides can be arraged down one side of DNA is determined?

    Meyer says it is not and the science supports him.

    So what we have is Art misrepresenting Meyer and posting wishful thinking to support his position.

  20. derwood says:

    Yeah Art!

    If we do not know EVERYTHING about the genetic code and abiogenesis RIGHT NOW, then we can make NO statements about it whatsoever, and therefore, Joe G’s analogy-driven beliefs are TRUE TRUE TURE!

  21. Joe G says:

    derwood,

    I was unaware that I had an analogy-driven belief.

    Please enlighten me.

    Or are you just upset that your position doesn’t have any analogies?

    But anyways why the extreme absolute?

    My wife “argues” like that.

    Heck I say know as much as we can because the more we know the better Intelligent Design looks.

    That said, Yarus et al., are trying to put together a plausible scenario based on the assumption that living organisms can be reduced to basic physics and chemistry- ie matter, energy, chance and necessity.

    Now given that assumption, and understanding the impossibility of a DNA-first world under that assumption, then there had to be some other carrier- RNA is a good candidate- again under that materialistic assumption.

    Ya see that assumption is the problem.

    Living organisms are not just a bunch of blind macro-molecules blindly making other blind macro-molecules that will blindly bind to yet other blind molecules to form chains that will then blindly go into this little chamber that then helps this blind polypetide find its much needed form.

    Living organisms are real-live information processors.

    The information is not the DNA sequence- iow it is not sequence specific. Sequence specificity is just required to carry out the instructions.

    The information in living organisms cannot be reduced to matter and energy- those are just required as carriers.

  22. Theoretix says:

    Nothing new – evoltuionists still present an argument on the bio-chemical (reductionist) level, nothing about the information-nanobot technology level at sub chromosome levels, where statistical methods (change through random processes over time) do not apply.
    Before continuing this debate, please read Dr. George Grebens’ “Which Ones Are Scientific” (Trafford, 2009), and his forthcoming more scholarly book “Evolution-Creation-Intelligent Design-Hybrids” (2010). Many of the issues discussed here are addressed in these two books – the fundamentals

  23. Arthur Hunt says:

    Hi Theoretix,

    I must confess that the readership of this blog is quite tiny, and I suspect that sales of these books would not be much improved if everyone reading this bought one.

    I’m also guessing that readers here are not going to be swayed by reference to ill-defined, vague, and seemingly irrelevant terms such as “information-nanobot technology level at sub chromosome levels”, especially when you seem unwilling to discuss the terms and explain a bit of their authentic relevance to biology. Clem, Eric, and Paul above all ask questions or raise points the answers to which will help greatly in coming to that “buying” decision.

    I’ll look forward to further discussion and clarification.

  24. Clem Weidenbenner says:

    Theoretix:
    “Where statistical methods do not apply”… uhh, well, I suppose. If you say so.

    In my humble opinion, the fact that we don’t have all the answers yet is actually quite satisfying. The thrill of trying to figure out how things work keeps me going. So I’ll probably hang on to my college statistics texts for now.

    My experience in biology has centered on whole plants, larger communities of plants, and the other organisms they interact with. So while I read about chemistry, physics, and other fields exploring sub chromosomal space my knowledge of the same does depend upon the insights of others. If you have some insight that shows how statistical methods have no relevance at levels below that of whole chromosomes I’m ready to see it.

  25. Tom English says:

    I’m glad to see you invite gpuccio to come over from UD. I’m working on yet another response (expect it this afternoon) to Dembski’s “scientific” analyses of the Weasel program, and gpuccio is welcome at my blog also.

    BTW, fantastic post. I’m following your blog now.

  26. Arthur Hunt says:

    Hi Tom,

    Thanks for the kind words. Unfortunately (and quite predictably), the moderators at UD have deleted my follow-up to gpuccio, and he clearly isn’t going to pursue things here. So I am afraid that my invitation was an exercise in futility.

    I’ll look forward to your follow-up to Dembski’s analyses of Weasel.

  27. Theoretix says:

    Clem Weidenbenner
    I hope that you have had time to consult the literature I mentioned more than six months ago (specifically ‘info-nanobot operations at sub-chromosome levels’). That literature contains answers to your questions. I understand that people specializing in the various science branches (e.g., biology) may inevitably bypass some specifics. I got some additional literature and excellent DVD science productions, on the subject you had questions – see http://www.discovery.org/ also http://www.intelligentdesign.org/ . I’n not an Intelligent Design member, but these are Intelligent Design websites, they contain the most objectively documented information (both sides of the issue) on the subject.

  28. Astrophysics says:

    Astrophysics…

    [...]Signature in the Cell? « The RNA Underworld[...]…

  29. Anatole says:

    Anatole…

    [...]Signature in the Cell? « The RNA Underworld[...]…

  30. pnyikos says:

    Hunt’s review has recently been reposted in:
    http://darwinsdoubtreviews.blogspot.com/2013/09/signature-in-cell.html

    I have replied to it there as follows:

    Hunt misses out on a much less theoretical objection Meyer had to the genetic code: that ribosomes, shorn of their sophisitcated proteins, are unable to produce polypeptides of appreciable length; branchings soon become inevitable.

    There are two weaknesses in Meyer’s argument. One is that the rRNA component of the ribosome might have degenerated as a result of the addition of these dozens of accompanying proteins. The other is that Meyer nowhere takes advantage of the Achilles’ heel of abiogenesis (of life as we know it): the protein takeover.

    There have been interesting and plausible speculative scenarios for the evolution of the genetic code that take us to the protein takeover. The best I have seen so far is a rather old one:

    AM Poole, DC Jeffares, D Penney, The path from the RNA world. J.
    Molecular Evolution 46: 1-17, 1998.
    http://awcmee.massey.ac.nz/people/dpenny/pdf/Poole_et_al_1998.pdf

    But it stops at the threshold of the heart of the protein takeover, the replacement of almost all ribozymes by protein enzymes. I have never seen any attempt at a scenario for this, not even a highly speculative one.

    The most crucial for the genetic code (READ: the whole protein translation mechanism) is the advent of the highly diverse aa-tRNA synthetases. Their astonishing fidelity is presumably better than that of the hypothetical ribozymes they replaced, but we are in a catch-22 situation: as their conjectural precursors began aa-tRNA binding, they would perforce have had LESS fidelity than the ribozymes their “Darwinian” descendants ultimately replaced. And as such, they would be detrimental to the “fitness” of the cells in which they arose.

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