Information Intelligent Design Origin Of Life

An encounter with a critic of biological semiosis

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RoyalSociety3

For those who are unfamiliar with The Royal Society, it’s an academic organization whose membership includes many of the world’s most eminent scientists, and is “the oldest scientific academy in continuous existence”. In loose terms, they are a British forbearer to many of the various Academies of Science sprinkled throughout the nations of the world. From their mission statement:

The Society’s fundamental purpose, reflected in its founding Charters of the 1660s, is to recognize, promote, and support excellence in science and to encourage the development and use of science for the benefit of humanity.

This article isn’t necessarily about the Royal Society, except for the fact that it serves as the genesis of the story, and also a proper backdrop to frame the issues at hand.

What is at issue is the void that seems to exist between the average working biologist and the fundamental reality that DNA (the genome) is a genuine representational medium. It operates in a system that translates the representations it uses to encode biological information into long-term memory. It is not sort-of-like information; it is not kind-of-like information. From a physics perspective, it functions exactly like the words you are reading right now. In fact — again from a physical systems perspective — only genetic encoding can match the variety and open-ended content of the words on this page. The genetic code and recorded language are the only two physical systems like this in the entire cosmos. They use spatially-oriented representations and a reading-frame code. It is the organization of arbitrary constraints that enables the combinatorial encoding of effects. In the total sum of human knowledge, they are a set of two    – with no others.

Royal-Society-March-2016

In their March 2016 volume, the Philosophical Transactions of the Royal Society published a special collection of papers under the no-nonsense heading “DNA as Information”. The content of those papers reflect the fact that the study of information remains a huge subject in the sciences, with an array of research opportunities in every direction. Contributions among the twenty-odd papers in the collection include such topics as semantics, mathematics, physics, encoding, measurement, complexity, and the role of meaning in biology.

This issue of Philosophical Transactions is where this story begins. More specifically, it begins with a particular paper (presented in that collection) by a well-respected Italian professor and researcher, Marcello Barbieri, who has for many years promoted a paradigm shift to biological semiosis (biosemiosis) and who is currently advancing this effort under the moniker “Code Biology”.

In opening his paper, Dr Barbieri addresses the central issue of this article:

Molecular biology is based on two great discoveries: the first is that genes carry hereditary information in the form of linear sequences of nucleotides; the second is that in protein synthesis a sequence of nucleotides is translated into a sequence of amino acids, a process that amounts to a transfer of information from genes to proteins. These discoveries have shown that the information of genes and proteins is the specific linear order of their sequences. This is a clear definition of information and there is no doubt that it reflects an experimental reality. What is not clear, however, is the ontological status of information, and the result is that today we have two conflicting paradigms in biology. One is the ‘chemical paradigm’, the idea that ‘life is chemistry’, or, more precisely, that ‘life is an extremely complex form of chemistry’. The other is the ‘information paradigm’, the view that chemistry is not enough, that ‘life is chemistry plus information’.

A link to Marcello Barbieri’s abstract is available on the Royal Society website here.

We pick up the story on the reaction side of its publication; the reaction to these observations by an average American scientist — a published biologist — who voices his point of view on the World Wide Web.

In this article it will not be necessary to perform any critical review of the biologist’s comments; one can tell within just a few words the gist of his position. He clearly has no questions about the “life is chemistry” paradigm he was taught at his university, and he clearly finds any other suggestion to be simply absurd. In his critique of Barbieri’s paper, he begins on his left foot:

Critic: “The first thing that I need to point out is that the author is not a biologist. He is a semiotician (someone who studies symbols and meanings). This will readily explain some of his more idiotic claims …”

I entered the conversation to say that he was tremendously misinformed about Marcello Barbieri’s qualifications, and I posted a short passage of text copied from Barbieri’s webpage about his background. I was also little surprised by the complete disregard for the source of the publication itself – the world’s “oldest scientific academy in continuous existence”. Not only can Barbieri be ignored, but the Royal Society is publishing “idiotic claims” about biology – or so it seems.

code-biology-conf

But there is certainly more to this. I believe there are possibly three things at work in the reaction presented above. First and foremost are the material facts themselves; i.e. the observation of genuine representations and arbitrary constraints (formalized in memory) inside the cell are difficult things to explain by the physical properties of matter. After all, the very essence of genetic translation is that it systematically decouples the production of effects from sheer determinism (physicalism), making possible the full range effects necessary for biology to exist. In other words, a system that functions only by locally eliminating your favorite explanation is a difficult nut to crack.

Secondly, Barbieri’s paper was presented (in this particular instance) under the rubric of philosophy, which (as a general rule) is often looked down upon by certain classes of scientists. Not surprisingly, these often include those sciences (like evolutionary biology and theoretical physics) that promote the notion that they are answering mankind’s biggest questions. As I wrote on Biosemiosis.org, this is cavalier conduct in light of the actual evidence. In any case, for many people, the idea of systematic learning without philosophical grounding is a cart without a horse. The practice of systematic learning is itself a philosophy.

But thirdly, there is something even more central to this critic’s comments; he isolates the lowly “creationist” as the key figure in his response. They are, as it turns out, the real impetus for his comments. He begins “So, it seems that creationists have been spamming this article so I’ll analyze it”. By using the word creationists here, some might suggest the critic intends to attack only those who believe such things as the earth being six thousand years old, for instance. But I think we can fairly assume he intends to attack anyone who believes that life on earth is the product of a creation, and of course, anyone who could believe such a thing obviously deserves to be attacked. The mere appearance of the word provides sufficient license to trivialize both the observations being made, as well as any outfit that publishes them.

Now, I have no evidence one way or another that anyone or any group has piled on to Barbieri’s paper – and it makes not one ounce of difference either way. The real issue here is that verifiable physical evidence is being routinely belittled and ignored simply because it doesn’t conform to the personal metaphysics of proper-thinking biologists — and clearly this is about metaphysics. It’s about the treatment and teaching of metaphysics in science. While the self-appointed defenders of science posture about the provisional nature of science, make no mistake; no physical evidence is allowed to take root if it leads to the unimaginable proposition that today’s biologists could be wrong in their personal beliefs about ultimate reality.

And this view doesn’t merely exist among anonymous biologists posting on the web; it is the dominant view found throughout biology at all levels. For instance, Larry Moran is a respected Professor of Biochemistry at the University of Toronto, and has written multiple textbooks on the subject. But four and a half years ago, I asked him for a clear statement as to whether or not the genome (DNA) actually contained information. He replied:

In common parlance we refer to these sites as containing “information” in the form of specific nucleotide sequence. It’s a very useful analogy and I think everyone knows what we mean when we use it. Nobody expects it to conform to the meanings of “information” in other disciplines. Nobody, that is, except some IDiots who like to play semantic word games instead of addressing real science. I hope you’re not one of those people.

The problem with this, of course, is that investigator expectations are a secondary concern; the genome functions exactly like language, and vice versa.

In any case, the war on outcast metaphysics is made evident again and again. It’s a socio-political enterprise, and when it rises to the level of ignoring valid evidence, it becomes an enterprise aligned against reason itself. This critic of semiosis had no idea that semiosis was physically identifiable, and he doesn’t want to know.

–Upright BiPed

 


 

The remainder of my exchange with the critic follows below. What it lacks in debate it thankfully makes up for in brevity. The critic clearly threw in the towel, rather than show any interest in the science.

UB:  (posted Barbieri’s extensive background…)

– – – – – – – – – – – –

Critic:  Thank you for the correction. From the references that immediately jumped, he seemed to study biosemiotics. That’s very disappointing that he actually has conducted research because he is so wrong-headed in his article.

With regards to my name, I’m a published biologist. I’m a scientist and my name is Sam.

– – – – – – – – – – – –

UB:  Hi Sam. Good to know. Take care.

By the way, he is entirely correct in his paper, you are just unaware of the issues. It happens.

– – – – – – – – – – – –

Critic: No he isn’t. I gave very good reasons. This is far closer to my area of research than his.

– – – – – – – – – – – –

UB: Barbieri states that the code is not reducible to physics. He is correct. Like all code systems ever known to exist, the genetic translation system contains a natural (and necessary) discontinuity between the arrangement of the medium and the determination of its effect within the system. This local discontinuity is what makes it possible for a spatial arrangement of bases in a codon to specify a particular amino acid during synthesis. It is what establishes combinatorial permutations and enables open-ended heredity. I can appreciate the fact that this all sounds foreign to you, but that is only because you are unaware of the data – which has been documented in physics literature starting about half a century ago by physicists such as Howard Pattee and others.

– – – – – – – – – – – –

Critic: “Like all code systems ever known to exist, the genetic translation system contains a natural (and necessary) discontinuity between the arrangement of the medium and the determination of its effect within the system.”

There is no discontinuity. You must’ve never taken molecular biology.

“This local discontinuity is what makes it possible for a spatial arrangement of bases in a codon to specify a particular amino acid during synthesis.”

How so? This is just a bald assertion.

“It is what establishes  combinatorial permutations and enables open-ended heredity.”

Again, bald assertion.

“I can appreciate the fact that this all sounds foreign to you, but that is only because you are unaware of the data – which has been documented in physics literature starting about half a century ago by physicists such as Howard Pattee and others.”

How about you stop condescending to someone who wrote his Master’s thesis on the dynamics of the genetic code? Please make an argument rather than bald assertions you supercilious imbecile.

– – – – – – – – – – – –

UB: “There is no discontinuity.”

Like I said, the local discontinuity is an organizational necessity. The arrangement of bases in a codon does not determine which amino acid is presented for binding. I would think this should be obvious to someone of your training.

– – – – – – – – – – – –

Critic: “The arrangement of bases in a codon does not determine which amino acid is presented for binding.”

Strictly speaking, that is true, but there are a lot of contingencies built into the structure of the code. For example, we have the third base wobble. We also have the fact that more similar amino acids correspond to more similar codons. Thus, there seem to be contingencies built into the code. But, even if I grant you this, where does it get you in an argument?

– – – – – – – – – – – –

UB:  “where does it get you in an argument?”

This is one of the empirical markers a physicist would use to identify the organization of a semiotic code, i.e. the preservation of the discontinuity between the arrangement of the medium and the determination of its effect. The cell accomplishes this by isolating the establishment of the code from the reading of the codons, i.e. the amino acid-to-anticodon association is temporally and spatially isolated from the codon-to-anticodon association. This discontinuity is a physical necessity for translation to occur, and is evident in all instances of semiotic translation.

But that is just the first marker that a physicist would look for. There are others. For instance, genetic translation employs a reading frame code using combinatorial permutations. This requires the arrangement of the bases in each codon to be independent of the minimum total potential energy state of the medium. In other words, a pheromone (for instance) is an informational medium that is recognized in its system by its three-dimensional structure, and that structure is determined by its minimum total potential energy. But in order to enable combinatorial permutations, the arrangement of the medium must be independent of minimum total potential energy – which both DNA and RNA are. This is what physically enables the system to have the informational capacity it requires to describe itself into memory (i.e. to begin the cell cycle, and heredity). It is also what enables the efficient transcription of that high-content information from one medium to another.

These are the types of empirical observations that a physicist (like Pattee and others) would be acquainted with, as well as someone like Barbieri. Or John von Neuman. Or Francis Crick.

You are not acquainted with them, and it’s a sure bet they didn’t appear in your masters thesis on the dynamics of translation. No sweat. I am sure your thesis described other areas of interest in a competent manner. But when you step out and rant on areas of empirical findings that you are uninformed about, you make a mistake. In order to organize the heterogeneous cell, you must first be able to specify a thing and place it under temporal control. This is what protein synthesis does, and the translation of an informational medium is the means to accomplish that effect. But the translation of an informational medium requires one arrangement of matter to serve as a representational medium (codons), and another arrangement of matter to establish what is being represented (aaRS). After all, no object in the material universe inherent specifies any other object in the material universe. Nucleobases do not represent or specify amino acids. They have to be organized in a discontinuous translation system (i.e. semiosis) in order to do so. And that is exactly what is found inside the cell. The material observations that identify the system aren’t even controversial.

– – – – – – – – – – – –

Critic: Thanks for the tripe.

“This discontinuity is a physical necessity for translation to occur, and is evident in all instances of semiotic translation.”

The discontinuity isn’t a physical necessity. You could easily imagine a scenario where amino acids were necessarily assigned to anticodons by chemical properties of tRNAs. I’m sorry but if you can’t get that right, you’re pretty hopeless, idiotically pedantic, and a navel gazer. Goodbye.

– – – – – – – – – – – –

UB: In logic, that’s called “special pleading”. Your imagination, frankly, doesn’t mean diddly. It doesn’t provide you with any exemptions.

The minimum requirement for the origin of the system is established by what is physically necessary to record and translate the amount of information that the system needs to successfully describe itself into memory. On this front, there is very little room. A cell that cannot provide a record of itself cannot begin the cell cycle. A cell that cannot translate a record of itself also cannot begin the cell cycle.

To accomplish what must be accomplished, several of these individual associations (generous estimates typically run between 12 to 15) will need to occur at the same time and place, while the details of their construction are simultaneously encoded in the very information that they make possible.

Odd, isn’t it. Nature passed up on the fully determined (comparatively easy) associations lurking in your imagination, and instead (already faced with an almost vertical face to climb) picked an unnecessary system that preserves the discontinuity between the arrangements and their effects. And even odder still, every system of translation that has ever been examined has followed that same pattern.

Special pleading indeed.  Goodbye.

This article was posted from ComplexityCafe.com

179 Replies to “An encounter with a critic of biological semiosis

  1. 1
    Mung says:

    But Sam did a master’s thesis and is published. Therefore you are wrong.

  2. 2
    Dionisio says:

    UB

    Interesting OP. Thank you.

    I don’t understand why the discussion had to include an offensive sentence like this:

    […] if you can’t get that right, you’re pretty hopeless, idiotically pedantic, and a navel gazer. Goodbye.

    What does that mean?
    Ran out of arguments or patience?

  3. 3
    Dionisio says:

    UB

    Please, help me. My reading comprehension is poor.

    In your brief chatting your interlocutor does not seem to present any arguments backing his position.

    Did I miss something?

  4. 4

    Sam, like many people would, reacted with hostility when faced with evidence that his fundamental worldview is wrong. Best case scenario is that he fumes for a while then later examines the evidence UB provided him.

    Biosemiosis is the smoking gun of the creator in biology, just as fine tuning is the smoking gun of the creator in astrophysics.

    UB – great post. However, you repeated most of paragraph 5 in paragraph 6. I’m not sure that was your intent.

  5. 5

    WJM…oops…copying error.

    Fixed.

    (and Thanks!)

  6. 6

    Hi Mung,

    It’s one of the interesting things about this overall situation – the range of different people and identities involved along the way.

    On one end you have so much as Von Neumann, who all but predicted what would be required for self-replication (long before the genome was even known). Then you have people like Crick, Watson, Zamecnik, Hoagland, Nirenberg, and others, whose experimental results demonstrate the system that Von Neumann predicted. Then there are those like Pattee, and even Barbieri, who have documented the systematic reality of it all. And on the other end you have professors (like Moran) whose capacity to teach a suitably neutral metaphysic is obviously in question, and also the students of biology themselves (like our critic here) who are often completely clueless that there are systematic realities about genetic translation that are required for the system to function. And then you have browser-enabled outsiders – average citizens — like many of us here, who can take the time to read deeply enough into the literature to understand the situation at hand.

  7. 7

    Hello Dio,

    As WJM said, he reacted because he was being challenged. I think he heard just enough to know he didn’t want to hear any more.

  8. 8
    kairosfocus says:

    UB, it is patent that when we look at the D/RNA system and its associated effectors, we are looking at machine code implemented in a molecular system. Proteins, especially, are assembled in a numerically controlled molecular machine the ribosome, through a string data structure that has in it start, sequence and halt conditions, key elements of an algorithm. Prior to that in key cases the mRNA string is transcribed, may be edited and is arranged to drive that process. There is no mechanically necessary connexion between the codons and the proteins, and the tRNA taxi-position arm components use a standard CCA coupler to hold the AAs. It is loading enzymes that define which tRNA carries what AA and in fact there has been reprogramming of certain codes to carry novel AAs, also. Refusal to face this is not a healthy sign — and it inadvertently testifies as to the strength of the inference to design from such phenomena. KF

  9. 9
    John S says:

    The way of a fool is right in his own eyes, but a wise man listens to advice.
    and
    All the ways of a man are pure in his own eyes, but the Lord weighs the spirit.

    trying to reason with an intelligent fool is harder than to do so with a simple one.

  10. 10
    groovamos says:

    Superb post, thx and onward. I have quite a few materialist FB friends, should be interesting if they take the time when I link.

  11. 11

    Hey Groov,

    Thank You!

    …also, Biosemisosis has a Facebook page. We love likes.

    And especially shares.

    🙂

  12. 12

    Hi KF, I agree on every count.

  13. 13
    REW says:

    Yeah, that guy was a jerk. If he had something worthwhile to say he should have said it and not resorted to insults.

    As for the actual argument I think the two of you were mostly arguing past each other. If you both had taken time to more precisely define terms and ideas and implications you could have had a much more productive discussion. I’d love to see a thoughtful critic take on this topic. I’d do it because I disagree with UP but I don’t have the philosophical background

  14. 14
    REW says:

    Yeah, that guy was a jerk. If he had something worthwhile to say he should have said it and not resorted to insults.

    As for the actual argument I think the two of you were mostly arguing past each other. If you both had taken time to more precisely defined terms and ideas and implications you could have had a much more productive discussion. I’d love to see a thoughtful critic take on this topic. I’d do it because I disagree with UP but I don’t have the philosophical background

  15. 15
    Virgil Cain says:

    This alleged scientist Sam should take up Perry Marshall’s offer. He seems confident that he can win the millions of dollars perry is offering.

    This scientist Sam also thinks that imagination is evidence. Strange what anti-IDists will do to try to save their ideology.

  16. 16

    Hello REW,

    I’d love to see a thoughtful critic take on this topic. I’d do it because I disagree with UP but I don’t have the philosophical background

    Neither do I. 🙂

    By the way, what is it that you disagree with?

  17. 17
    REW says:

    Hi UP

    By the way, what is it that you disagree with?

    OK, well I think it will be difficult to explain myself so this may come out a bit disjointed.

    The dispute was framed as an argument between 2 points of view: life is just chemistry, or life is chemistry plus information. Depending on the discussion you could say both are correct or that both are incorrect. As I see it information is everywhere so the phrase ‘chemistry plus information’ is redundant. You could just as easily describe life as chemistry as Sam did. On the other hand that definition leaves out a lot so that makes both incomplete descriptions. I know this sounds wishy-washy but I think the whole topic is ill-defined. I’d like to see some concrete claims that we could sink our teeth into.

    As far as I can tell you understand theres something unique about the coding in DNA. Where you go wrong is that because you understand this in the abstract and that the ‘abstract’ is something that only has meaning in the context of a mind, you think that gives a kind of magical transcendence to DNA – because what DNA does can only be appreciated in the abstract that means a mind must have infused the DNA with the quality. I just dont think theres any justification for thinking that.
    I think many biologists ( like Sam) appreciate that but cant put it into words ( not that I’ve done much better) so they get frustrated and resort to name calling.

    Anyway, if we have a back and forth on this maybe I’ll be able to explain what I mean a bit clearer

  18. 18
    Mung says:

    Molecular biology is based on two great discoveries: the first is that genes carry hereditary information in the form of linear sequences of nucleotides

    If all you’re looking at is the chemical composition of nucleotides you might in fact miss the relevance of their sequence.

  19. 19
    Mung says:

    The conclusion that the cell is a semiotic system, in short, is based on the experimental evidence provided by the adaptors, but also requires a new theoretical framework where concepts like sign, meaning and code are not put aside as metaphorical entities but are defined by operative procedures and are recognized as fundamental components of the living world.

    http://link.springer.com/chapt.....0-4814-9_8

    Sam’s ignorance about Barbieri was pathetically typical.

    https://en.wikipedia.org/wiki/Marcello_Barbieri

    http://www.marcellobarbieri.website/

  20. 20
    PaV says:

    UB:

    Critic wrote:
    The discontinuity isn’t a physical necessity. You could easily imagine a scenario where amino acids were necessarily assigned to anticodons by chemical properties of tRNAs.

    I’m trying to understand what he’s trying to say. It doesn’t make any sense to me. It seems he’s missed the entire point you’ve tried to make. Could you decipher for me what you think he was trying to say, if that’s possible?

  21. 21

    Hi REW,

    As I see it information is everywhere so the phrase ‘chemistry plus information’ is redundant.

    There are a lot of people who make this statement (“information is everywhere”) but typically upon examination, it just doesn’t hold up. Or, if they are honest about it, they find — at the very least — that their concept of information is significantly different than what is meant when a physicist like Howard Pattee or a semiotician like Barbieri talks about information. And just as often, they cannot really argue with what the physicist/semiotician would describe as information, so if they are intent on holding onto their definition, there comes a point where there are two disjointed concepts of information; one that adheres to a well-defined physical system, and another that is more or less defined as the “state of an object” — any object — which is why “information is everywhere”. Since this latter description applies to everything, it is all but useless. And it is virtually always heavily anthropocentric as well.

    Such conversations are generally not very productive.

    I do not believe the cross-up between myself and the critic had anything whatsoever to do with this latter definition of information. The problem was that the critic had no idea that semiosis is a physically identifiable system – and he simply didn’t want to know.

  22. 22
    Barry Arrington says:

    REW,

    I find your comments very interesting. I will respond:

    The dispute was framed as an argument between 2 points of view: life is just chemistry, or life is chemistry plus information.

    Nope. You have not identified the points in contention. Yes, Sam is arguing that life is merely chemistry. But UB is not arguing that life is “information” in a general sense. He is arguing that DNA is a particular type of information. He says that the genetic code is exactly that, a semiotic code.

    Depending on the discussion you could say both are correct or that both are incorrect.

    This statement is astonishing to me. The claims are mutually exclusive. As with all mutually exclusive claims, it is true that both might be incorrect. But it is not possible for them to both be correct.

    As I see it information is everywhere so the phrase ‘chemistry plus information’ is redundant.

    And as I have pointed out already, your error is in focusing on information generally instead of the specific type of information (semiotic code) that UB claims is present in the genetic code.

    You could just as easily describe life as chemistry as Sam did.

    Yes, and if UB is right, you would be wrong in describing it that way.

    On the other hand that definition leaves out a lot so that makes both incomplete descriptions.

    Yes, it leaves out the semiotic code that UB claims is present.

    I know this sounds wishy-washy . . .

    No, it sounds confused.

    I’d like to see some concrete claims that we could sink our teeth into.

    You are not paying attention. UB has made a concrete claim. He claims that the genetic code is a semiotic code.

    As far as I can tell you understand theres something unique about the coding in DNA

    Then go back and read the post again. UB does not say the DNA code is unique. He says just exactly the opposite. He says it is one of a set of two. Reread this paragraph from the OP:

    What is at issue is the void that seems to exist between the average working biologist and the fundamental reality that DNA (the genome) is a genuine representational medium. It operates in a system that translates the representations it uses to encode biological information into long-term memory. It is not sort-of-likeinformation; it is not kind-of-like information. From a physics perspective, it functions exactly like the words you are reading right now. In fact — again from a physical systems perspective — only genetic encoding can match the variety and open-ended content of the words on this page. The genetic code and recorded languageare the only two physical systems like this in the entire cosmos. They use spatially-oriented representations and a reading-frame code. It is the organization of arbitrary constraints that enables the combinatorial encoding of effects. In the total sum of human knowledge, they are a set of two – with no others.

    Moving on:

    Where you go wrong is that because you understand this in the abstract and that the ‘abstract’ is something that only has meaning in the context of a mind, you think that gives a kind of magical transcendence to DNA

    No, UB’s claims are not abstract. They are very concrete and specific. He says there genetic code is a semiotic code in the exact same way the sentence you are reading at this moment is a semiotic code.

    – because what DNA does can only be appreciated in the abstract

    That is absurd. We can appreciate what DNA does in a very specific and concrete way. How else can you account for the entire field of genetic engineering? Again, I am astonished that you would suggest otherwise.

    that means a mind must have infused the DNA with the quality. I just dont think theres any justification for thinking that.

    OK, how about this for a justification. For every semiotic code whose provenance is known, the origin of the code is “act of an intelligent agent.” Therefore, when one observes another semiotic code identical in every respect, the abductive inference to best explanation for the provenance of that code is “act of an intelligent agent.”

    I think many biologists ( like Sam) appreciate that but cant put it into words ( not that I’ve done much better) so they get frustrated and resort to name calling.

    No, Sam appreciates it well enough and it scares the hell out of him because it challenges his basic worldview so he runs around with his fingers in his ears yelling “la la la la la la la I can’t hear you; and you are stupid to boot; la la la la la la.”

    To your credit you appear to be willing to engage. So let me ask you this question: Do you deny that the genetic translation system contains a natural (and necessary) discontinuity between the arrangement of the medium and the determination of its effect within the system?

  23. 23
    mike1962 says:

    “Life is just chemistry” is like saying…

    “Computers are just hardware”

  24. 24

    Hi PAV, I hope you are well.

    I’m not entirely sure I can decipher it. Frankly, I had just carpet bombed the guy with positions I was prepared to defend, so I think he was just bailing out.

    But if I give him the benefit of the doubt, I think he was setting aside any energy issues associated with binding, and was simply saying he can imagine a world where tRNA’s don’t all have the same acceptor stems, and instead, each had some arrangement that would somehow attract a particular amino acid, and therefore establish a code association.

    That is why I suggested to him what a wonderfully odd thing it was that Nature foregoes any such (comparatively easy) deterministic system, and instead comes to use a system that preserves a physicochemical discontinuity between the arrangement of nucleotides in a codon and their cognate amino acids.

  25. 25

    mike1962.

    That is EXACTLY right.

    Under his position, if I can explain the physics behind every feature on a space shuttle, then there is no need to suggest that it was the result of design.

  26. 26
    REW says:

    UB and BA

    I think everyone would agree that the genetic code is a physical system. The heart of the debate is whether such codes can only be produced by mind.
    My contention is that because codes have certain properties that we appreciate in the abstract, its easy to have a bias that because the abstract only exists in minds, a mind must create a code.
    My definition ( and you can correct me if I’m wrong on any of this) is that a code is the set of rules that relate one set of objects to another set of unrelated objects, and that the rules are arbitrary. So Morse code relates dots and dashes to English letters, and there is nothing ‘R’like about dot-dash-dot, which specifies the letter R. I think peoples error lies in thinking that because the rules are arbitrary and there is no direct physical necessity between them, then there can be NO link and so the rules must be assigned by a mind. I just dont think that follows ( if i’m correct in my assessment!)
    I think it might be useful to talk about codes in detail. For every code there must be some place that the rules reside. For example the rules for the Morse Code can be listed on a piece of paper or in the mind of the operator. For the german ENIGMA machine the code was contained in the pattern of pins and holes on the rotating drums. So my question is; where is the genetic code actually contained…where is the physical manifestation? Considering this might illustrate ( or refute ) my point above

  27. 27
    Dionisio says:

    “Understanding the protein circuits that perform computations within the cell is a central problem in biology.”
    Uri Alon Lab – Design Principles in Biology.
    http://www.weizmann.ac.il/mcb/UriAlon/homepage

  28. 28

    Hi REW,

    I am at the end of my day. I will respond later, after my commute home.

  29. 29
    Dionisio says:

    2014 Systems Biology course by Uri Alon
    Lecture 1: Basic concepts

    https://www.youtube.com/embed/pyqBvxeVtG4

    [Please, note the time marks given here are grossly approximate]

    @7:30
    Goal: Central idea of the class – it gives unity to the discussed topic.

    Complex biological systems can be understood using design principles which can unify different systems in a mathematical framework.

    @8:30
    it’s up to him to be clear and up to the students to tell him when he’s not.

    @14:30
    Suggested textbook: An introduction to Systems Biology: design principles of biological systems.

  30. 30
    PaV says:

    UB:

    I’m doing well. Thanks for asking.

    Here, I believe, is the source of my confusion (and, perhaps, Sam’s).

    You wrote:

    The cell accomplishes this by isolating the establishment of the code from the reading of the codons, i.e. the amino acid-to-anticodon association is temporally and spatially isolated from the codon-to-anticodon association. This discontinuity is a physical necessity for translation to occur, and is evident in all instances of semiotic translation.

    Here’s the distinction I would make: The “amino acid-to-anticodon association is temporally and spatially isolated from the” DNA-to-codon association. The divide–the source of ‘separability’—is at the point of ‘codon’-to-‘anticodon’ contact; i.e., the ‘mechanism’ giving rise to the ‘codon’ is completely separate from the ‘mechanism’ that gives rise to the ‘anti-codon.’ Or, ‘producing’ the message (=nucleotides “coding” for a protein broken down into individual codons at the mRNA/’transcription’ level), is not the same as ‘reading’ the message (=protein constructed from individual codons at the ‘ribosomal’ level).

    Looked at this way, the point Sam was trying to make is meaningless; i.e., he was simply describing a different kind of chemistry for the tRNA molecule. This, of course, has no bearing, no effect, on the ‘separability’ that the genetic code, as a ‘language,’ requires (That’s why Crick predicted tRNAs. He intuitively knew we were dealing with a coding language).

    One can say, looking at the papers in this symposium, that the elucidation of the genetic code is indeed a great achievement. It is, in a sense, the key to molecular biology because it shows how the great polymer languages, the nucleic acid language and the protein language, are linked together.

    — Francis Crick
    ‘The Genetic Code: Yesterday, Today, Tomorrow’, Cold Spring Harbour Symposium on Quantitative Biology, 1966, 31, 9.
    Science quotes on: | DNA (52) | Molecular Biology (19)

    REW:

    If you reduce humans, and all animal life, and life in general, to completely physical forces, then no one, nor no thing, can escape ‘chemistry.’ However, if there is something called ‘spirit,’ or ‘mind’ (nous in Greek), then you can have separability. It is just such separability that can give rise to language, or bird dialects.

    It’s no small wonder, then, the Crick spent the last years of his life probing into the question of consciousness, though remaining an atheist (presumably, to the end.)

  31. 31
    Origenes says:

    Here follows my summary of Upright Biped’s argument. I’m pretty sure that I don’t have a full handle on it, so anyone is welcome to point out what is lacking and/or mistaken.

    1. The system of protein production in the cell ticks all four physical conditions that are fundamental to translation of information. If it walks like a duck … therefor information in biology is real.
    2. The system is irreducible complex, especially because it (necessarily) consists of two distinct parts — one arrangement of matter evokes an effect within a system, and another arrangement of matter establishes what the effect will be.
    3. The system is fundamental to evolution, so it cannot be explained by it.

  32. 32
    kairosfocus says:

    PaV:

    I see your clip from Critic:

    You could easily imagine a scenario where amino acids were necessarily assigned to anticodons by chemical properties of tRNAs

    The CCA tip that couples to AA’s in tRNA is a universal coupler. Chemically any AA could be loaded to any tRNA, and this universality has been used to load with novel AAs.

    Contingency not mechanical necessity, in short.

    KF

  33. 33
    PaV says:

    KF:

    Thanks for the note. I was looking around for that fact; i.e., that of the “universal coupler.” Is this solidly founded?

  34. 34
    PaV says:

    KF:

    I was looking around for something like the “universal coupler” since something like that seemed to be hinted at.

    However, as I’ve turned it over in my mind, I find something wrong, or missing, about all of this. That there is a “universal” amino acid receptor site doesn’t mean that any-old tRNA molecule can accept any amino acid it chooses. Some specificity must be required.

    I think the import of this ‘universality’ is simply that the “language” the cell uses is determined by all the other parts of the tRNA molecule. That is, if you have a particular “anticodon” end, then all the other loops and such are adapted—we may say—to this “anticodon” end. So the tRNA molecule is not ‘determined’ by the amino acid it links to; rather, the amino acid it links to is ‘determined’ by the “anticodon” end.

    Here’s the analogy of language: if I write an phrase in English, a Japanese man or woman can translate that into Japanese if they understand English, and a German speaking person who understand English can translate the phrase into German. The Japanese language, nor the German language, does not, in any way, determine what I write in English; rather, the English phrase I write determines what the Japanese or German interpreter will write down in their native language.

    So, I think the “separability” that I indicated above is, I don’t think, affected by this “universality.” Some kind of specification must exist ahead of time. And something other than the amino acid is making this specification. IOW, the DNA specifies the codons; and the tRNA specifies the amino acid.

    This said, let me add the following:

    There must be some kind of “hand in glove” quantum mechanical action involved here, I suspect, and the only reason for the universality is so that end of the functional tRNA molecule be ‘adaptable’ to whatever amino acid it’s otherwise meant to attach to. IOW, if EACH tRNA molecule had a “specific” end, matching up to whatever amino acid it is intended to link up with, then that linkage has to—biochemically, or quantum mechanically—take priority. Everything else follows from that. However, if some kind of freedom is to be built into the system–and apparently this is what happens—if you wanted the ‘same’ amino acid linking to ‘different’ “anticodons” then you would be in the position of one “end” constraining the opposite “end,” and, effectively almost having the amino acids determine the code instead of having the code determine the amino acid.

    It gets a little murky fast, doesn’t it?

  35. 35
    Anaxagoras says:

    Hi, UB

    If I´m not mistaken, Barbieri proposes (in his book “The organic Codes” for instance) a fully naturalistic account of biosemiosis. In this sense, he considers that the genetic code is not the product of a mind but just the product of the molecular machines that make the translation in the process of protein synthesis (enzymes and proteins as well). He terms them “code-makers”.
    I have always found that puzzling. On the one hand because these “code-makers” are themselves the product of translation and therefore the product of the genetic code they are supposed to “create”. On the other hand because I see the whole process as a manifestation of the cell´s teleological agency; in the end it is the cell that governs the action of translating what is needed, when it´s needed.

  36. 36

    REW, sorry for the delay…

    My contention is that because codes have certain properties that we appreciate in the abstract, its easy to have a bias that because the abstract only exists in minds, a mind must create a code.

    I accept that this is your contention. The issue at hand is how the system works. What properties of the code do we “appreciate in the abstract” that are not actually working properties of the system?

  37. 37

    PAV,

    You wrote:
    “The cell accomplishes this by isolating the establishment of the code from the reading of the codons, i.e. the amino acid-to-anticodon association is temporally and spatially isolated from the codon-to-anticodon association. This discontinuity is a physical necessity for translation to occur, and is evident in all instances of semiotic translation”.

    Here’s the distinction I would make: The “amino acid-to-anticodon association is temporally and spatially isolated from the” DNA-to-codon association.

    Unfortunately we are talking past each other in a big way. The person I was talking to didn’t believe there was a discontinuity in the operation of the system. I was telling him where he could find it.

    Changing the spatial arrangement of nucleotides in a codon changes which amino acid will be presented for binding, but the spatial arrangement of nucleotides in a codon does not determine which amino acid will be presented. Nucleobases do not specify amino acids. That utility — the capacity to specify something in a universe where nothing specifies anything else — has to be physically realized in the organization of the system. The system only functions if it is organized in a way that establishes the arrangement of the codon as a genuine representation, that is, by preserving the natural discontinuity between the arrangement of the codon and the amino acid it specifies. The cell accomplishes this by isolating the establishment the code from the reading of the codons, i.e. the amino acid-to-anticodon association is temporally and spatially isolated from the codon-to-anticodon association. By being organized this way, the arrangement of nucleobases in a codon can actually represent a particular amino acid in the context of the system – thereby making the organization of the heterogeneous cell possible.

  38. 38
    kairosfocus says:

    PaV:

    Wiki on tRNA:

    The tRNA structure consists of the following:

    A 5′-terminal phosphate group.

    The acceptor stem is a 7- to 9-base pair (bp) stem made by the base pairing of the 5′-terminal nucleotide with the 3′-terminal nucleotide (which contains the CCA 3′-terminal group used to attach the amino acid). The acceptor stem may contain non-Watson-Crick base pairs.[5][7]

    The CCA tail is a cytosine-cytosine-adenine sequence at the 3′ end of the tRNA molecule. The amino acid loaded onto the tRNA by aminoacyl tRNA synthetases, to form aminoacyl-tRNA, is covalently bonded to the 3′-hydroxyl group on the CCA tail.[8] This sequence is important for the recognition of tRNA by enzymes and critical in translation.[9][10] In prokaryotes, the CCA sequence is transcribed in some tRNA sequences. In most prokaryotic tRNAs and eukaryotic tRNAs, the CCA sequence is added during processing and therefore does not appear in the tRNA gene.[11]

    The D arm is a 4- to 6-bp stem ending in a loop that often contains dihydrouridine.[5]

    The anticodon arm is a 6-bp stem whose loop contains the anticodon.[5] The tRNA 5′-to-3′ primary structure contains the anticodon but in reverse order, since 3′-to-5′ directionality is required to read the mRNA from 5′-to-3′.

    The T arm is a 4- to 5- bp stem containing the sequence T?C where ? is pseudouridine, a modified uridine.[5]

    Bases that have been modified, especially by methylation (e.g. tRNA (guanine-N7-)-methyltransferase), occur in several positions throughout the tRNA. The first anticodon base, or wobble-position, is sometimes modified to inosine (derived from adenine), pseudouridine or lysidine (derived from cytosine).[12]

    On loading enzymes, Wiki remarks:

    An aminoacyl tRNA synthetase (aaRS) is an enzyme that attaches the appropriate amino acid onto its tRNA. It does so by catalyzing the esterification of a specific cognate amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA.

    This is sometimes called “charging” or “loading” the tRNA with the amino acid. Once the tRNA is charged, a ribosome can transfer the amino acid from the tRNA onto a growing peptide, according to the genetic code. Aminoacyl tRNA therefore plays an important role in DNA translation, the expression of genes to create proteins . . . .

    In some of the aminoacyl tRNA synthetases, the cavity that holds the amino acid can be mutated and modified to carry unnatural amino acids synthesized in the lab, and to attach them to specific tRNAs. This expands the genetic code, beyond the twenty canonical amino acids found in nature, to include an unnatural amino acid as well. The unnatural amino acid is coded by a nonsense (TAG, TGA, TAA), quadruplet, or in some cases a redundant rare codon. The organism that expresses the mutant synthetase can then be genetically programmed to incorporate the unnatural amino acid into any desired position in any protein of interest, allowing biochemists or structural biologists to probe or change the protein’s function. For instance, one can start with the gene for a protein that binds a certain sequence of DNA, and, by directing an unnatural amino acid with a reactive side-chain into the binding site, create a new protein that cuts the DNA at the target-sequence, rather than binding it.

    By mutating aminoacyl tRNA synthetases, chemists have expanded the genetic codes of various organisms to include lab-synthesized amino acids with all kinds of useful properties: photoreactive, metal-chelating, xenon-chelating, crosslinking, spin-resonant, fluorescent, biotinylated, and redox-active amino acids.[5] Another use is introducing amino acids bearing reactive functional groups for chemically modifying the target protein.

    A simple animation is here:

    http://www.phschool.com/scienc.....addaa.html

    . . . and it illustrates how it is the general conformation of the tRNA that is used to slot it into a cleft of the loading enzyme (specific aminoacyle tRNA synthetase) and so code it. Where there is also a slot for the particular AA to be loaded, which can then be varied to give a different loading for the tRNA as noted by Wiki. This underscores the highly contingent, informational nature of the system.

    Another animation with explanation:

    https://highered.mheducation.com/sites/9834092339/student_view0/chapter15/aminoacyl_trna_synthetase.html

    So, yes there is a universal CCA tip to which the AA is loaded, and it is a universal coupler, proved by not only the same tip being there for natural loadings, but its utility with lab induced unnatural loadings.

    In effect the coding is in the loading.

    (coupled to the anticodon sequence that then matches to the mRNA frame of three letters specifying load the AA x here, next.)

    Loading can then be varied, it is contingent as is required for information conveyance.

    KF

  39. 39

    Hello Anax,

    Yes, in his writing Barbieri has made it abundantly clear that he follows a fully naturalistic metaphysics. That is fine by me — I only have a problem with it when he (or anyone else) wants to force that view on the practice of science. For instance, in his “Brief History of Biosemiosis” (I believe was the title) his attempt at putting a natural-only guise on semiosis stuck out like a sore thumb.

  40. 40

    Hello Origenes at #31 … no doubt, those are some of the key observations. Thank You.

  41. 41
    kairosfocus says:

    PS: Note from NCBI:

    http://www.ncbi.nlm.nih.gov/books/NBK22356/

    >>Jeremy M Berg, John L Tymoczko, and Lubert Stryer, Biochemistry. 5th edition, NY: W. H. Freeman and Company, 2002.

    Section 29.2Aminoacyl-Transfer RNA Synthetases Read the Genetic Code

    The linkage of an amino acid to a tRNA is crucial for two reasons. First, the attachment of a given amino acid to a particular tRNA establishes the genetic code. When an amino acid has been linked to a tRNA, it will be incorporated into a growing polypeptide chain at a position dictated by the anticodon of the tRNA. Second, the formation of a peptide bond between free amino acids is not thermodynamically favorable. The amino acid must first be activated for protein synthesis to proceed. The activated intermediates in protein synthesis are amino acid esters, in which the carboxyl group of an amino acid is linked to either the 2?- or the 3?-hydroxyl group of the ribose unit at the 3? end of tRNA [–> the CCA tip]. An amino acid ester of tRNA is called an aminoacyl-tRNA or sometimes a charged tRNA (Figure 29.7).>>

    In short there is all we need here, but the way it is discussed in various sources does not outright acknowledge the key points. Thermodynamic unfavourability suggests that something has to be done to get there, which in this case is also highly specific to the given code linked requisites for protein synthesis. Where the existence of a universal coupler CCA tip is not something that is going to be emphasised — it will be acknowledged then there will be a predictable passing on without underscoring of significance — and the words “universal coupler,” for sure are going to be very scarce because of direct import.

    If a Chinese paper that accidentally uses Creator in translation is so sharply challenged, what do we think will happen to something that says too much too explicitly about the CCA coupler?

    And, the coding is in the loading.

  42. 42
    Dionisio says:

    KF @8

    […] it is patent that when we look at the D/RNA system and its associated effectors, we are looking at machine code implemented in a molecular system. Proteins, especially, are assembled in a numerically controlled molecular machine the ribosome, through a string data structure that has in it start, sequence and halt conditions, key elements of an algorithm. Prior to that in key cases the mRNA string is transcribed, may be edited and is arranged to drive that process. There is no mechanically necessary connexion between the codons and the proteins, and the tRNA taxi-position arm components use a standard CCA coupler to hold the AAs. It is loading enzymes that define which tRNA carries what AA and in fact there has been reprogramming of certain codes to carry novel AAs, also. Refusal to face this is not a healthy sign — and it inadvertently testifies as to the strength of the inference to design from such phenomena. KF

  43. 43
    Me_Think says:

    The clear indication that ‘code’ evolved and was not designed, is the fact that codons encode for ‘essential aminoacids’ (V-Valine,T-Threonine,I-Isoleucine,M-Methionine,W-Tryptophan etc). ‘Essential aminoacids’ means the body cannot synthesize it and must be obtained from the diet. Obviously code cannot encode for what the body doesn’t make! So the code evolved after the body started ingesting the essential aminoacids in diet.

  44. 44
    Virgil Cain says:

    Well Me Think, if you can actually demonstrate such a thing you would win a Nobel Prize plus millions of dollars from Perry Marshall.

    The mere fact that codons encode/ represent amino acids is evidence for ID as nature cannot do such a thing. But hey there are millions of dollars for someone who can demonstrate otherwise. So what are you waiting for?

  45. 45
    Me_Think says:

    Virgil Cain @ 44

    The mere fact that codons encode/ represent amino acids is evidence for ID as nature cannot do such a thing. But hey there are millions of dollars for someone who can demonstrate otherwise. So what are you waiting for?

    Intersting.You mean even the codons for the ‘essential amino acids’ (‘Essential aminoacids’ means the body cannot synthesize it and must be obtained from the diet)were there before we started ingesting the essential amino acids?!
    Do you really think Perry Marshall has enough brain to understand the reasoning ? After all he is essentially a marketing guy! ( despite being an Electrical Engineering)

  46. 46
    Virgil Cain says:

    Me Think:

    Intersting.You mean even the codons for the ‘essential amino acids’ (‘Essential aminoacids’ means the body cannot synthesize it and must be obtained from the diet)were there before we started ingesting the essential amino acids?!

    Yes, the entire genetic code is evidence for ID. The codons that represent the essentials are part of the code.

    Do you really think Perry Marshall has enough brain to understand the reasoning ?

    What reasoning? And you have to actually demonstrate that stochastic processes can do it. Imagination gets you nothing.

    After all he is essentially a marketing guy! ( despite being an Electrical Engineering)

    And what are you, a bag boy and the grocery store?

  47. 47
    gpuccio says:

    REW at #26:

    Excuse me if I get late into the discussion: I have just come back and seen this very interesting OP.

    I think you raise some interesting questions, and I would like to propose some answers.

    I think everyone would agree that the genetic code is a physical system. The heart of the debate is whether such codes can only be produced by mind.

    Absolutely correct.

    My contention is that because codes have certain properties that we appreciate in the abstract, its easy to have a bias that because the abstract only exists in minds, a mind must create a code.

    I don’t think this is the real argument here. Please, see later.

    My definition ( and you can correct me if I’m wrong on any of this) is that a code is the set of rules that relate one set of objects to another set of unrelated objects, and that the rules are arbitrary. So Morse code relates dots and dashes to English letters, and there is nothing ‘R’like about dot-dash-dot, which specifies the letter R.

    Absolutely correct.

    I think peoples error lies in thinking that because the rules are arbitrary and there is no direct physical necessity between them, then there can be NO link and so the rules must be assigned by a mind. I just dont think that follows ( if i’m correct in my assessment!)

    OK, I think that UB will answer this for himself, but I give you my personal idea abut this.

    The fact that arbitrary codes derive only form conscious activity, for me, is not a logical necessity, as you seem to suggest. In principle, the simple fact that a physical system has the properties of something which is usually generated by a mind is not a logical guarantee that it originates from a mind. I agree with that.

    But the point is, here we are not making pure logic, or proving a mathematical theorem. What we are doing here is empirical science.

    So, for me, the point is: all cases of codes that we know of, and whose origin is independently known with certainty, are generated by conscious activity

    This is an empirical argument, one which is very similar to the argument for design inference from functional complexity (all cases of functional complexity that we know of, and whose origin is independently known with certainty, are generated by conscious activity).

    Another related point is: if biological codes were truly an exception, is there some reasonably detailed, and credible, theory if how that kind of organization came into existence? And the answer is a very strong: no!

    I think it might be useful to talk about codes in detail.

    Perfect. Let’s do it.

    For every code there must be some place that the rules reside. For example the rules for the Morse Code can be listed on a piece of paper or in the mind of the operator. For the german ENIGMA machine the code was contained in the pattern of pins and holes on the rotating drums.

    Absolutely correct. That’s really the core of the question.

    So my question is; where is the genetic code actually contained…where is the physical manifestation? Considering this might illustrate ( or refute ) my point above

    Very good question. You can easily find the answer at UB’s very good site, but I will try to sum it up for you here.

    The rules for translation in the case of the genetic code are in the whole physical system of translation itself. But, very interestingly, the essential part of the coupling rules is “written” in the 20 Aminoacyl tRNA synthetases.

    Here’s the Wikipedia page for them:

    https://en.wikipedia.org/wiki/Aminoacyl_tRNA_synthetase

    And here is, even better, the PDB “Molecule of the Month” page for them:

    http://pdb101.rcsb.org/motm/16

    What are they? They are 20 very biog and complex proteins. Interesting, isn’t it? The structure which holds the key to the genetic code is nothing else than a set of 20 proteins, which are obviously synthesized from their genes by the translation system itself, with its code. Moreover, as said, they are very bog and complex proteins, each of them hundreds of AAs long, up to more than one thousand, IOWs, a lot of functional complexity of the best kind.

    What do these proteins do?

    It’s simple. They recognize, independently, two things:

    1) The tRNA, with its anticodon

    2) The aminoacid which has to be bound to that tRNA

    I will quote form the PDB page:

    When a ribosome pairs a “CGC” tRNA with “GCG” codon, it expects to find an alanine carried by the tRNA. It has no way of checking; each tRNA is matched with its amino acid long before it reaches the ribosome. The match is made by a collection of remarkable enzymes, the aminoacyl-tRNA synthetases. These enzymes charge each tRNA with the proper amino acid, thus allowing each tRNA to make the proper translation from the genetic code of DNA into the amino acid code of proteins.

    Here we have the discontinuity at its best. The tRNA and its anticodon are coupled to the corresponding aminoacid in the symbolic code only because 20 complex proteins exist, each of them able to recognize separately the correct tRNA and the corresponding aminoacid, and to bind them together.

    IOWs, it’s the specific structure of each of the 20 proteins which has the information about which tRNA (and anticodon) is linked to which aminoacid. Each of the 20 proteins has that information for one coupling, in its specific structure of hundreds of aminoacids.

    Now, for the moment I leave it to you to comment on how the above information relates to your last statement:

    “Considering this might illustrate ( or refute ) my point above”

  48. 48
    Dionisio says:

    John S @9

    The way of a fool is right in his own eyes, but a wise man listens to advice.
    and
    All the ways of a man are pure in his own eyes, but the Lord weighs the spirit.

    Good reminder.

    Maybe that’s one important reason to ask simple questions at the beginning of a discussion, in order to let the potential interlocutors reveal their real motives (by the way they react to those questions), thus helping us to determine whether it’s advisable to continue the discussion or stop it right there to avoid squandering precious time. The genuine humility (or lack of it) displayed by the potential interlocutors while trying to answer the initial “warm up” icebreaking inquiries may be an important parameter to consider for accurate discernment. Let’s always keep in mind that the same rule applies to us too.

    For example, this morning my mother-in-law said her opinion on certain issue. I asked her why she had such an opinion on that given subject and she just responded that she doesn’t know why. No one had asked her that simple question before. But it made her think carefully and realize she had no solid reason to back her position. Most relatives just argue with her to exhaustion, talking past each other indefinitely. 🙂

    I think it’s important to keep in mind that understanding someone else’s point does not mean agreeing with it. But that mutual understanding is necessary for a productive discussion. Also all parties involved in a discussion must be genuinely interested in the truth above anything else. Obviously time should be available for relaxed discussions and the conditions should be conducive to discuss quietly -no background noise, no external interruptions, comfortable sitting, pleasant illumination, etc. Also I think it’s important to have a common language and communication protocol, which also includes the adjustment of the discussion speed to the slower participant in the discussion. Very important is the mutual respect.

  49. 49
    Me_Think says:

    Virgil Cain @ 46

    Yes, the entire genetic code is evidence for ID. The codons that represent the essentials are part of the code.

    I think you didn’t get it – there are codons for essential and non-essential aminoacids. How do you account for the fact that the codon encoding for essential acid existed before we started ingesting essential amino acids?

    And what are you, a bag boy and the grocery store?

    Unfortunately , No! bag boy at grocery store is a better job than hoodwinking people – which is what marketing is.

  50. 50
    gpuccio says:

    Me_Think:

    Again with this nonsense of essential aminoacids? What do you mean? The genetic code is obviously older than any such consideration.

    Sometimes you really stick to completely wrong concepts with a loyalty which would be better used for other things.

  51. 51
    Dionisio says:

    Posted @27:

    “Understanding the protein circuits that perform computations within the cell is a central problem in biology.”
    Uri Alon Lab – Design Principles in Biology.
    http://www.weizmann.ac.il/mcb/UriAlon/homepage

    Posted @29:

    2014 Systems Biology course by Uri Alon
    Lecture 1: Basic concepts

    https://www.youtube.com/embed/pyqBvxeVtG4

    [Please, note the time marks given here are grossly approximate]

    @7:30
    Goal: Central idea of the class – it gives unity to the discussed topic.

    Complex biological systems can be understood using design principles which can unify different systems in a mathematical framework.

    @8:30
    it’s up to him to be clear and up to the students to tell him when he’s not.

    @14:30
    Suggested textbook: An introduction to Systems Biology: design principles of biological systems.

    Note that this professor does not seem to be an ID-proponent at all. Given his academic tenure, he doesn’t seem to be ‘sprinkling’ Darwinian terms here and there just for the sake of securing funds for research projects, as it might be in other cases.

    Here’s a very interesting part of professor Alon’s first lecture in the referenced course:

    Very early in his first lecture, at the time mark 2:30, he introduces himself to his students.
    He said he has been a professor at that institute 14 years (the lecture seems to be from 2014). He worked for a PhD in Physics, hence he was used to systems obeying very precise mathematical laws. Then a friend gave him a biology textbook and it was like a shock for him. He said it was like reading a thriller, because he saw this matter that was behaving completely different than what he was used to: [it was] dancing, amazing structures created and then destroyed almost magically, working very precisely under very strong thermodynamic noise and I had to find out how this works.
    That personal event changed his academic and scientific career radically. Apparently he earned a PhD in biology at Princeton University.

  52. 52
    Dionisio says:

    Glad to see gpuccio is back in town.

  53. 53
    Dionisio says:

    gpuccio @47

    […] all cases of codes that we know of, and whose origin is independently known with certainty, are generated by conscious activity

    […] all cases of functional complexity that we know of, and whose origin is independently known with certainty, are generated by conscious activity

    […] is there some reasonably detailed, and credible, theory if how that kind of organization came into existence? And the answer is a very strong: no!

    The rules for translation in the case of the genetic code are in the whole physical system of translation itself. But, very interestingly, the essential part of the coupling rules is “written” in the 20 Aminoacyl tRNA synthetases.

    The structure which holds the key to the genetic code is nothing else than a set of 20 proteins, which are obviously synthesized from their genes by the translation system itself, with its code.

    […] they are very big and complex proteins, each of them hundreds of AAs long, up to more than one thousand, IOWs, a lot of functional complexity of the best kind.

  54. 54
    Mung says:

    Today theoretical biology has genetic, developmental, and evolutionary components, the central connective themes in modern biology, but also includes relevant aspects of computational biology, semiotics, and cognition research, and extends to the naturalistic philosophy of sciences.

    Series Forward
    The Vienna Series in Theoretical Biology

    Sorry Sam.

  55. 55
    Dionisio says:

    #51 disclaimer

    Please, note that the text is what I think I heard in the video, hence it may not be as accurate as I wanted.

    Everybody is welcome to correct any error in the version of the video transcript posted @51. Thank you.

  56. 56
    Mung says:

    gpuccio: Again with this nonsense of essential aminoacids? What do you mean? The genetic code is obviously older than any such consideration.

    Exactly. It’s just a red herring.

  57. 57
    Dionisio says:

    gpuccio @47

    The tRNA and its anticodon are coupled to the corresponding aminoacid in the symbolic code only because 20 complex proteins exist, each of them able to recognize separately the correct tRNA and the corresponding aminoacid, and to bind them together.

  58. 58
    kairosfocus says:

    MT, so do you mean to suggest proteins in humans should not use essential AAs that can be obtained by simply eating? KF

  59. 59
    Me_Think says:

    KF @ 58

    MT, so do you mean to suggest proteins in humans should not use essential AAs that can be obtained by simply eating? KF

    No, I am saying the the codons which encode for that essential protein evolved after we started ingesting the essential protein because DNA would not have coded for something which is not in the body!
    For example how would the DNA when it evolved know that the organism will start ingesting Isoleucine in future and have code ATT/ ATC/ ATA for Isoleucine?

  60. 60
    Me_Think says:

    KF @ 58

    MT, so do you mean to suggest proteins in humans should not use essential AAs that can be obtained by simply eating? KF

    No, I am saying the the codons which encode for that essential protein evolved after we started ingesting the essential protein because DNA would not have coded for something which is not in the body!
    For example how would the DNA when it evolved know that the organism will start ingesting Isoleucine in future and have code ATT/ ATC/ ATA for Isoleucine?
    Edit: Sorry for double Post

  61. 61
    gpuccio says:

    Me-Think:

    “No, I am saying the the codons which encode for that essential protein evolved after we started ingesting the essential protein because DNA would not have coded for something which is not in the body!”

    Are you serious????

    Codons and the DNA code evolved billions of years ago, when we did not exist, least of all ingest anything. First living beings were certainly autotroph. Proteins are not essential, only some AAs are essential in some species, like humans. What has all this to do with the evolution of the genetic code?

    Frankly, I can’t understand if you are serious and confused, or if you are simply playing tricks.

  62. 62

    What has all this to do with the evolution of the genetic code?

    Absolutely nothing whatsoever.

    🙂

  63. 63
    Dionisio says:

    gpuccio @47

    Now, for the moment I leave it to you to comment on how the above information relates to your last statement:

    “Considering this might illustrate ( or refute ) my point above”

    After your explanatory ‘blitzkrieg’ that leaves little room (if any) for counterarguments, what else can your interlocutor say? 🙂

  64. 64
    bill cole says:

    Me Thinks

    No, I am saying the the codons which encode for that essential protein evolved after we started ingesting the essential protein because DNA would not have coded for something which is not in the body!
    For example how would the DNA when it evolved know that the organism will start ingesting Isoleucine in future and have code ATT/ ATC/ ATA for Isoleucine?

    If you think deeply about the question you are asking, you will realize why there are so many skeptics that random change, natural selection, and neutral theory can account for the diversity we see. The story of life has many chicken and egg paradoxes just like the one you have identified here. Another is how did we get protein production when proteins require amino acids and amino acid production requires proteins. It appears that these systems arrived simultaneously. The simple to complex “story” was made up to explain a mystery. The only real evidence for life we have is that it started as a very complex system. Any other story is pure speculation.

  65. 65
    juwilker says:

    Me_Think @ 45

    “Intersting.You mean even the codons for the ‘essential amino acids’ (‘Essential aminoacids’ means the body cannot synthesize it and must be obtained from the diet)were there before we started ingesting the essential amino acids?!”

    Humm? Maybe we were created! 🙂

  66. 66
    Dionisio says:

    #51 addendum

    At the time mark 43:20 professor Alon apparently said that everything in biology is an invitation to a question.

    [whatever that means]
    🙂

    However, haven’t we heard that there are things in biology that are settled hence unquestionable?

    Are we seeing a contradiction here?

  67. 67
    PaV says:

    UB:

    My point was perhaps more subtle than I thought. Again, here’s what you said up above:

    Changing the spatial arrangement of nucleotides in a codon changes which amino acid will be presented for binding, but the spatial arrangement of nucleotides in a codon does not determine which amino acid will be presented.

    Here’s how I see this (subtly different): DNA “determines” (via RNA processing) the “codon.” It does NOT, however, “determine” the “anticodon.” The “anticodon” determines (via aa-tRNA-synthetase) the amino acid that is associated with that particular “anticodon.” Two, separate systems.

    In your earlier remark to “Sam” you blurred this line a little bit. “Sam”‘s remark about a chemical link between the anticodon and the amino acid misses the mark. The ‘anticodon’ is ‘free’ to associate with any amino acid. The chemistry doesn’t really change that freedom. It’s just a different way of configuring things. This ‘freedom’ is what makes “translation” possible, and which gives us the language of life. And, yes, as KF has posted (I had already read that prior), you can fiddle with the aa-tRNA-synthetase, and so “change” the language.

    If you look at how the aa-tRNA-synthetase operates, the ‘naked’ (without an amino acid) tRNA molecule, which is bound directly to the synthetase, already possesses the ‘anticodon’. I think it’s fairly clear that the presence of the amino acid–already bound to aa-tRNA-synthetase prior to the tRNA being bound—determines the “configuration” of the aatrnasynthetase, and, thus, makes it specific for the tRNA molecule with the “corresponding” (corresponding to the a.a.) “anticodon.”

    Bottom line: it is the aa-tRNA synthetases that determine the language of translation.

    From wiki:

    Both classes of aminoacyl-tRNA synthetases are multidomain proteins. In a typical scenario, an aaRS consists of a catalytic domain (where both the above reactions take place) and an anticodon binding domain (which interacts mostly with the anticodon region of the tRNA and ensures binding of the correct tRNA to the amino acid). In addition, some aaRSs have additional RNA binding domains and editing domains[2] that cleave incorrectly paired aminoacyl-tRNA molecules.

    As to “Sam,” he seems to fail to see that it is not DNA that determines the amino acids; rather, it’s DNA that determines the codon. That’s all it does. Then the aa-tRNA-synthetase takes over and “translates,” a process independent of the DNA. Hence, the two systems operate independently of each other. Any “chemical” determinations of the DNA system cannot reach across the codong-anticodon divide. It’s a wall that separates the two systems.

  68. 68
    PaV says:

    KF:

    Loading can then be varied, it is contingent as is required for information conveyance.

    Yes, I would agree. The “anticodon” doesn’t determine the amino acid, the synthetase does.

  69. 69
    PaV says:

    Me_Think:

    No, I am saying the the codons which encode for that essential protein evolved after we started ingesting the essential protein because DNA would not have coded for something which is not in the body!
    For example how would the DNA when it evolved know that the organism will start ingesting Isoleucine in future and have code ATT/ ATC/ ATA for Isoleucine?

    The simplest answer would be this: the capacity to code for these amino acids was present from the beginning. Once organisms began ingesting these amino acids in high quantities, this capacity was shut down, the machinery needed to make them being eliminated.

  70. 70
    PaV says:

    UB:

    I read over my latest post above, and it seems to me we’re saying the same thing but simply with different points of emphasis. The bottom line: DNA does not directly determine the amino acid through a series of chemical interactions. There’s an independence that the aminoacyl-tRNA-synthetases provide.

  71. 71
    forexhr says:

    All relationships between biological structures are semiotical which means that arrangement of molecules or cells forming the bio-structure A is predetermined by the bio-structure B. Otherwise functional biological interactions would be impossible.

    Examples:

    a) intron-exon gene structure predetermines that specific arrangement of molecules is nedded for editing of the nascent pre-messenger RNA transcript in which introns are removed and exons are joined together. This specific arrangement of molecules is called “rna splicing machinery”.

    b) The structure of an egg cell predetermines that specific arrangement of molecules is nedded in order to initiate the development of a new individual organism. This specific arrangement of molecules is called “sperm”.

    c) The structure of the substrate predetermines that a specific arrangement of molecules is nedded in order to accelerate or catalyze chemical reactions. This specific arrangement of molecules is called “enzyme”.

    So, you can’t just throw random bags of chemicals into the cell and expect splicing, fertilization or catalytic function to emerge. Specific arrangement of molecules is nedded. Since this specific arrangements are not predetermined in the laws of nature or in the properties of matter(like snowflakes are) and since all possible arrangements of molecules for ordinary collections of matter are inconveniently large it is physically impossible to achieve even theoretical semiotic relationship via random rearrangements of nucleotides in the dna, let alone temporary and spatially coordinated semiotic relationship, because biological structures are needed at the same time and place to interact functionally. Below I will explain why.

    Given a bio-structure (e.g., a heart valve), we view it as built from some elementary constituents(molecules, cells). Each constituent has a set of possible spatial states it can be in relation to another constituent. The collection of states of all the constituents is the microstate and it forms an identifiable collection of matter which may be more or less constrained to move together by translation or rotation, in 3-dimensional space. The semiotic microstate of the bio-structure represents the number of distinct biologically functional microstates versus and all possible microstates. For a system of a large number of constituents, like a bio-structure, the overwhelmingly probable microstate would be non-semiotic microstate. In other words, overwhelmingly probable microstate or random arrangement of elementary constituents that form a heart valve would be non-functional – not able to close off the atrium or not able to prevent the back flow of blood from the ventricle to the atrium when blood is pumped out of the ventricle.

    The specific arrangement of cells or semiotic microstate, allowing the valve to function properly is predetermined by the structure of the heart the same as the specific arrangement of the mobile phone battery is predetermined by the structure of the mobile phone. Now, we know that there is no natural tendency for atoms to move towards arrangements that would form the mobile phone battery because the mobile phone exists. The same is true for the heart valve or any other bio-structure – there is no natural tendency for nucleotides to move towards arrangements that would form a heart valve because other heart structures exists. So, the obvious question arises: how then semiotic relationship is achieved?

    From the perspective of evolutionary theory the only possible way to achieve semiotic relationship is via random mutations. But viewed from that perspective, one physical problem arises: where would you get the transitional resources to search for semiotic microstates in the in the vast sea of non-semiotic microstates. The heart valve for example consists of many millions of cells. Given the poly-3D*enumeration mathematics, only one thousand cells can be arrangement into approximately 8.37×10^3271 different microstates.

    *2^(n-7)n(n-9)(n-4)(8n^8-128n^7+828n^6-2930^5+7404^4-17523n^3+41527n^2-114302n+204960)/6

    To put this into perspective. Using fast mutation rates and total number of organisms that have ever lived on Earth published extreme upper limit estimates puts the maximum number of transitional resources at 10^43. If we make a generous assumption that there are 10^1000 functional semiotic microstates in our collection of thousand cells, we have only 10^43 opportunities to find semiotic microstates, and that would, on average, require 10^2271 transitional resources. In other words, the entire sum of transitional resources operating over four billion years, would fall short by more than 2228 orders of magnitude in producing functional heart valve.

    Since all components of biological systems are in semiotic relationships and since the number of cells in the human body is 3.72×10^13 it is physically impossible that evolutionary transitions from one microstate to another via random mutations would produce semiotic relationships.

    Of course, ad hoc alibi in the form of natural selection does not work. Natural selection is NOT semiotic microstate search mechanism, but semiotic microstate spreading mechanism. Once semiotic microstate(bio-function) is found and enters the gene pool, natural selection can spread this microstate through the population. But the search for the semiotic microstates in the vast sea of non-semiotic microstates is completely random.

    p.s.
    Mechanical gears discovered on planthopper insects provide an opportunity to recognize semiotic relationship between bio-structures. Gear is a structure for transmitting rotational motion while leg is a locomotive structure. As such they are connected through their relation to a concept of motion. Evolution is not an intelligent agent to be able to conceive concepts. So the only available way to achieve mentioned semantic relationship is by pure chance. But, believing that semiotically undirected transformations from one microstate to another would create semiotic relationship is like believing that erosion processes would turn a piece of clay into clay replica of the Statue of Liberty. This replica would then represent specific arrangements of clay particles predetermined by a colossal neoclassical sculpture on Liberty Island in New York City just like arrangement of cells forming mechanical gears is predetermined by animal’s legs.

    We all know that erosion processes can shape and reshape various physical objects(hence causing transitions from one microstate to another) the same as mutations can shape and reshape various bio-structures(e.g. causing tumors), but no rational person would claim that this processes are able to create predetermined arrangements of clay particles represented in the of Statue of Liberty. The reason nobody would believe that undirected transformations of matter could produce semiotic microstates, lies in the unimaginably huge number of different accessible arrangements of clay or particles. The same is true for bio-systems, but people believe the opposite because they have a prior commitment to materialism and atheism. And that commitment trumps all of the logical, mathematical or scientific reasons.

  72. 72
    PaV says:

    forexhr:

    Nice summary. A slightly different narrative, but ID through and through.

    A is predetermined by B. There’s the crux of the matter. Call it ‘complimentarity’.

  73. 73
    Me_Think says:

    forexhr @ 71

    Since all components of biological systems are in semiotic relationships and since the number of cells in the human body is 3.72?×?10^13 it is physically impossible that evolutionary transitions from one microstate to another via random mutations would produce semiotic relationships

    You don’t believe in common descent? You are assuming body was created as a whole ? In fact you are assuming every part was as it is today ! What is the difference between semiotic microstates and microstate? A microstate can be calculated by N!/(N1!x(N-N1))!, where N is the Number of Microstate, N1 is the macrostate for which you want to calculate the microstate.

  74. 74
    gpuccio says:

    forexhr:

    Very good work! 🙂

    Me_Think:

    Don’t you think that you should clarify your nonsense about essential aminoacids, before engaging in new creative nonsense?

  75. 75
    forexhr says:

    @Me_Think
    No, I believe in common designer.

    I am assuming absolutely nothing about the body. I stated three simple facts that are so obvious that nobody can deny it:

    a) any bio-structure is built of elementary constituents(atoms, molecules) like any other physical object.

    b) each constituent has a set of possible spatial states it can be in relation to another constituent. The collection of states of all the constituents is the microstate – one of the unimaginably huge number of different accessible arrangements of the constituents.

    c) pre-existing bio-structures are predetermining the microstates for subsequent bio-structures (e.g. intron-exon gene structure predetermines microstates of constituents forming rna splicing machinery(this is called semiotic relationship).

    Hence, the difference between semiotic microstates and microstate is the difference between the arrangements of molecules that are able to edit the nascent pre-messenger RNA transcript and the arrangement of molecules that are not able to perform that task.

  76. 76
    Me_Think says:

    GP @ 74

    Don’t you think that you should clarify your nonsense about essential aminoacids, before engaging in new creative nonsense?

    There is nothing to clarify. Those who have understood have replied. In fact PaV’s reply @ 69 is reasonable.I haven’t replied because I don’t have enough data about the ingestion of non-essential amino acid or the critical threshold which would change the non-essential aminoacid pathway to make the ‘non-essential’ pathway ‘essential’.
    Neither microstates (statistical mechanics) nor Common descent is ‘new creative nonsense’. If you think ‘semiotic microstates’ is nonsense, then I can’t help because I have no clue about anyone using it scientifically either !

  77. 77
    Dionisio says:

    UB,
    A few recent papers related to tRNA and translation referenced @ 1597-1600 here (linked 1600):
    http://www.uncommondescent.com.....ent-600563

  78. 78

    PaV,

    Thanks. Changing the arrangement of a codon changes its amino acid effect, but the codon does not physically determine which amino acid is presented — that determination is made solely by the structure of the aaRS (i.e. instant local discontinuity).

    Forexhr,

    Thank you for the contribution.

    Dio,

    Thanks, I’ll try to look them over.

  79. 79
    Origenes says:

    Upright Biped,

    The fact that there is a ‘natural local necessary discontinuity’ strengthens the argument for irreducible complexity. Second it is one of four conditions that are fundamental to translation, which strengthens the argument that we are dealing with genuine (translation of) information.
    Those are the sole two reasons as to why you stress the discontinuity often. Do I understand this correctly?

  80. 80
    gpuccio says:

    Me_Think:

    If you still believe that your discourse about essential aminoacids makes any sense, I suppose there is no hope.

  81. 81
    PaV says:

    Me_Think:

    It would be helpful if you simply stated your position on all these things. You have come to UD and taken a position none of us, I believe, have ever seen before. You are insisting that some “intelligence” is needed for “signalling” and this and that.

    You come here, then, with some presuppositions. The best thing to do, would be to simply state these presuppositions and then give evidence for their validity.

    We’re all sort of scratching our heads a bit, especially gpuccio; and he is usually the most gracious of the bunch of us.

    IOW, you seem absolutely convinced of something that we, OTOH, can’t even seem to figure out. Your certainty is not shared. No one has argued in the way you’re seeming to argue. So, state your case directly, and try to convince us.

  82. 82

    #79

    Hi Origenes, sorry for the delay.

    The fact that there is a ‘natural local necessary discontinuity’ strengthens the argument for irreducible complexity.

    It is natural because no object in the universe inherently specifies/represents any other object in the universe. In this case, it is the contingent organization of the system that enables the arrangement of a codon to specify an amino acid.

    It is local because the organization of the discontinuity is context specific. A codon specifies an amino acid in this system, and nowhere else.

    It is necessary because, again, nucleobases do not represent amino acids. The system must be organized in a way that allows the pragmatic utility of specification to be realized in a material system. If amino acids had to be determined by the surface properties of three nucleobases, we would not be here to contemplate the issue. Yet with a system of discontinuous translation in place, the system becomes limited only by what is physically possible.

    So … “present leucine now” is not an effect that can be derived from any arrangement of three nucleotides in a codon. The “now” part of it can be derived from the placement of a signifying codon (a representation) within a linear sequence. But the “leucine” part requires a second arrangement of matter (the aaRS) to systematically establish what is being represented. The requirement of irreducible complexity is therefore demonstrated under inexorable law, and the function that is lost in its absence is the capacity to specify a thing and place it under temporal control — i.e. the capacity organize the heterogeneous living cell.

    sidenote: My argument about semiosis was never intended to be an argument in favor of IC. It just turns out to be the case that a semiotic system is necessarily IC.

    Second it is one of four conditions that are fundamental to translation, which strengthens the argument that we are dealing with genuine (translation of) information.

    Yes.

  83. 83

    GP,

    Can I ask you a question? What is the shortest aaRS in the database, and how many aaRS does it take to produce it?

  84. 84
    Me_Think says:

    PaV @ 81

    We’re all sort of scratching our heads a bit, especially gpuccio; and he is usually the most gracious of the bunch of us.
    IOW, you seem absolutely convinced of something that we, OTOH, can’t even seem to figure out.

    I agree about GP – he is the most gracious, but he is confused about essential aminoacids, not about need for Designer’s intervention. In fact he stated in some other thread that the Designer would use Quantum mechanical interface to control ‘improbable’ body processes. I, of course, don’t agree as QM is too probabilistic to be used as an interface.

  85. 85
    PaV says:

    Me-Think:

    In fact he stated in some other thread that the Designer would use Quantum mechanical interface to control ‘improbable’ body processes. I, of course, don’t agree as QM is too probabilistic to be used as an interface.

    Your interest in this area of how the Creator/Designer interacts deals with a different kind of interface. But, to have a discussion about this requires leaving science behind and entering the realm of theology.

    Why? Because you’re looking at one side of a “dual” reality. The Bible speaks of angelic powers. It speaks of “Wisdom,” etc. Think of Michelangelo’s Sistine Chapel painting of the Creation: two different types of reality with a single point of contact; only at the fingertips.

    It’s sort of like the Big Bang: Pope Pius XII said that this theory confirms what the Bible teaches about creatio ex nihilo, while Fr. Georges LeMaitre, a Belgian Jesuit priest, said that this linkage must not be made. The mind wants to link these two together, but from a strictly scientific point of view, one must leave off. (Let me just add that nowadays physicists have become “theological” themselves, asking us to “believe” in multiverses.)

    Nevertheless, how do we answer the question: what came before the Big Bang? IOW, what’s the ‘Big Bang’ connected to? How the Creator/Designer interacts with “creation” is a similar matter.

    Frankly, I have a great interest in QM. I’m intrigued with ways in which QM and GR can be united. And I even have my own pet theory. It is a theory that ultimately arises from a comment by Greg Lisi concerning his Very Simple E8 (IIRC) theory. However, it immediately gives rise to theological implications; deeply provocative ones from the standpoint of a believer. In terms of these ideas, if I’m correct, the kinds of questions you pose might have ready answers. However, first these ideas must be somehow established; and, if and when verified, there is again a necessary, though easy, step that has to be taken to arrive at the ‘theological.’

    Put another way, the Bible says: “The heavens proclaim the glory of God.” How do you prove this, exactly, in your nearby laboratory?

    Maybe a better example: the body of St. Rosalia was found in a cave three or four centuries after she died. Her body was, and I suppose still is, incorrupt. Science would say this is impossible. But it happened. So, now what do we do? Do we deny reality, or do we accept that science is NOT the source of ultimate knowledge? What will we decide?

    ID is at the intersection of all of this. One side is apparent–intelligence is at work in biological reality—while the other side—how does this come about exactly?—is not, and may never be. Again, the Bible says: “The God in whom we live and move and have our being.” When we’re dealing with “life,” then we’re dealing with God. And, oh, BTW, St. Paul is quoting the ancient Greeks in the quote above.

  86. 86

    At the end of his post at #22, Barry Arrington asked REW a question:

    To your credit you appear to be willing to engage. So let me ask you this question: Do you deny that the genetic translation system contains a natural (and necessary) discontinuity between the arrangement of the medium and the determination of its effect within the system?

    I didn’t see that REW ever answered that question.

    REW?

  87. 87

    #84,

    Frankly, I am as confused as GP about your post at #43. Wha?

  88. 88
    JDJones says:

    Back to Uncommon Descent! Where are the dissenters? Where are all the objectors?

  89. 89
    REW says:

    UB
    I’ve been reading the posts when I had time but I thought the convo had kinda left me behind.
    I’ll post something tomorrow from work

  90. 90
    Mung says:

    Mike Behe makes The Vienna Series in Theoretical Biology:

    For example, systems of many complex interdependent parts can appear unevolvable – especially when any small change in the system causes the system to cease functioning (Behe 1996).

  91. 91

    Heavens to Betsy !!!

    First, PLOS allows someone to utter foul language in the scientific literature, now KLI and MIT Press have gone off the rails as well. Michael Behe himself is cited without reference to his blasphemy towards Chuck.

    Off with their heads.

    🙂

  92. 92

    REW,

    You suggested that I (and others) are biased because there are properties of the code that we “appreciate in the abstract”, and as such, it is clouding our judgement — that more or less, we are seeing things that are not there.

    I was hoping you might return and clarify what property or properties are these that are not actual working properties of the code system?

  93. 93
    Evolve says:

    UB and all others supporting him are wrong.
    I have told this here before, but UB continues to tout this as the killer argument for ID. It isn’t. Now, new studies are helping to further show why.

    UB’s model is problematic on two counts:

    1) He says that the codon does not determine the amino acid, it merely represents it. By this he implies that a codon could potentially represent any amino acid, but it was assigned to represent a particular one by, er, the intelligent designer. However, a paper from last year by Carter & Wolfenden shows that tRNA can discriminate between amino acids based upon its nucleotide sequence. The sequence at the acceptor stem of tRNA sorts amino acids by size, while the sequence at the anticodon end sorts amino acids by polarity.
    See:
    http://www.pnas.org/content/112/24/7489.long
    Non-technical press release:
    http://news.unchealthcare.org/.....nct-stages

    This means that a codon is forced to code for a particular amino acid because its cognate tRNA is limited or constrained by physical interactions with that particular amino acid. This is unlike Morse code or language, where symbols merely stand for something. UB fatally ignores the role of chemistry in biology, which is lacking in man-made semiotic systems. He thinks that chemical interactions are only occurring at the codon-anticodon interface. Nope.

    2) UB assumes that the present-day translation system (DNA-RNA-Protein) held true right from the beginning. Therefore, someone (i.e. the intelligent designer) had to create the genetic code in the first place, then create tRNAs, aaRSs, ribosomes etc to set translation of that genetic code in motion. However, new studies suggest that the primordial translation system could have been different.

    For instance, in 2013 Carter reconstructed ancestral versions of the two superfamilies of aaRS enzymes, called Urzymes. They retain 60% of the catalytic activity of present-day aaRSs:

    http://www.jbc.org/content/288/37/26856.abstract

    These Urzymes only recognise the tRNA acceptor arm, but not the tRNA anticodon part. Yet they can carry out aminoacylation of the tRNA. This suggests that initial tRNA precursors lacked the anticodon end altogether. A ‘stereochemical code’ based on size may have risen first and codon-anticodon based translation may have risen only later.
    Now, one can still ask how did Urzymes or proteins, in general, arise in the first place. In the following review, Carter argues for a model he proposed along with Kraut back in 1974:

    http://www.mdpi.com/2075-1729/5/1/294/htm

    (see Figs: 1, 2 and also 10)

    In this model, physicochemical interactions between RNA and peptides promote reciprocal autocatalysis, i.e, RNA can be polymerised by peptides and peptides can be polymerised by RNA. This is possible if early tRNA precursors bound amino acids based on their size and branching. Alternatively, it has been suggested that lateral association of tRNA molecules can bring their attached amino acids close enough for peptide bond formation on an ancestral ribosome (which is essentially a ribozyme), without the need for an mRNA. See:

    http://www.ncbi.nlm.nih.gov/pu.....t=Abstract

    Of course, many of these models and suggestions await experimental verification and refinements. More studies are definitely needed. But the take home message is that we have not exhausted all possible physicochemical explanations for the origin of the genetic translation system as we know it. Far from it. UB ignores or misses many papers in the literature to reach his ill-defined conclusion.

  94. 94
    Evolve says:

    UB @ 39 disses the naturalistic route taken by science:

    “Yes, in his writing Barbieri has made it abundantly clear that he follows a fully naturalistic metaphysics. That is fine by me — I only have a problem with it when he (or anyone else) wants to force that view on the practice of science. For instance, in his “Brief History of Biosemiosis” (I believe was the title) his attempt at putting a natural-only guise on semiosis stuck out like a sore thumb.”

    The problem is science has never ever confirmed supernaturalistic explanations for anything in its entire history. There has been no evidence for it. In contrast, natural explanations have aptly and satisfactorily solved many scientific questions. In fact science has shown, in several instances, that supernatural hypotheses are wrong and natural explanations can better account for the data. Therefore, the confidence in such explanations is pretty much nonexistent from science’s perspective. That’s the reason why science still proposes naturalistic hypotheses for outstanding questions.

  95. 95
    Mung says:

    UB and all others supporting him are wrong.

    I wouldn’t have it any other way.

  96. 96
    Mung says:

    The problem is science has never ever confirmed supernaturalistic explanations for anything in its entire history.

    Everything about science and nature is supernatural. The desire to call it natural is metaphysical, not scientific.

  97. 97
    gpuccio says:

    Evolve:

    Thank you for providing a link to a very interesting paper.

    But… I suspect that you really don’t understand what the paper is about.

    You say:

    “However, a paper from last year by Carter & Wolfenden shows that tRNA can discriminate between amino acids based upon its nucleotide sequence. The sequence at the acceptor stem of tRNA sorts amino acids by size, while the sequence at the anticodon end sorts amino acids by polarity.”

    Where did you get that strange idea?

    The paper is about the properties of the code, not about physical interactions between tRNAs and the aminoacids, as you seem to believe.

    I will quote from the paper:

    Here, we show that acceptor stems and anticodons, which are at opposite ends of the tRNA molecule, code, respectively, for size and polarity.

    From the “significance” box. Emphasis added.

    IOWs. the point of the paper is that the recognition between aaRS and tRNA is symbolic, as we all know, but that the symbolic recognition is achieved at two separate levels: the aaRS recognizes separately two different regions of the specific tRNA, the acceptor stem and the antocodon. Each of those two regions implements a code, and each of the two codes is related to two complementing levels of abstraction about the biochemical properties of the aminoacid: size and polarity.

    IOWs, the code is more complex than we thought, but it is a code just the same, at all its levels.

    Here is the abstract of the paper:

    Aminoacyl-tRNA synthetases recognize tRNA anticodon and 3? acceptor stem bases. Synthetase Urzymes acylate cognate tRNAs even without anticodon-binding domains, in keeping with the possibility that acceptor stem recognition preceded anticodon recognition. Representing tRNA identity elements with two bits per base, we show that the anticodon encodes the hydrophobicity of each amino acid side-chain as represented by its water-to-cyclohexane distribution coefficient, and this relationship holds true over the entire temperature range of liquid water. The acceptor stem codes preferentially for the surface area or size of each side-chain, as represented by its vapor-to-cyclohexane distribution coefficient. These orthogonal experimental properties are both necessary to account satisfactorily for the exposed surface area of amino acids in folded proteins. Moreover, the acceptor stem codes correctly for ?-branched and carboxylic acid side-chains, whereas the anticodon codes for a wider range of such properties, but not for size or ?-branching. These and other results suggest that genetic coding of 3D protein structures evolved in distinct stages, based initially on the size of the amino acid and later on its compatibility with globular folding in water.

    Emphasis mine.

    So, I really can’t understand why you say that:

    “This means that a codon is forced to code for a particular amino acid because its cognate tRNA is limited or constrained by physical interactions with that particular amino acid. This is unlike Morse code or language, where symbols merely stand for something.”

    Emphasis mine.

    I am afraid you did not understand what the paper is discussing. I suggest that you correct your position, before any further discussion can be done on any other aspect you mention.

  98. 98
    Axel says:

    Well said in #96, Mung. Even the joins, the seams, between our integrated and coordinated, personal worlds are established by QM.

  99. 99
    gpuccio says:

    Mung:

    I am still waiting for someone to give a credible definition of “natural”. Never a word so ambiguous was so universally, and sadly, used (except, maybe, “love” 🙂 ).

  100. 100
    Evolve says:

    gpuccio,
    You’re missing the points altogether while making a big deal of the word ‘code’. By ‘code’ they simply mean specific parts of the tRNA molecule select for specific properties of amino acids. This selection happens through structure, conformations and interactions of the molecules involved. If you’re confused by the technical paper, then look at the non-technical press release again:

    “That link suggests to us that there was a second, earlier code that made possible the peptide-RNA interactions necessary to launch a selection process that we can envision creating the first life on Earth.”
    “Thus, Carter said, RNA did not have to invent itself from the primordial soup. Instead, even before there were cells, it seems more likely that there were interactions between amino acids and nucleotides that led to the co-creation of proteins and RNA.”
    http://news.unchealthcare.org/.....nct-stages

    The fact that molecular interactions are involved differentiates biology from man-made semiotic systems. This is the key point.
    For example, in language, the shape ‘A’ can potentially represent any sound. It can represent B,C,D,E etc. It is we humans who randomly assigned the sound A to the shape ‘A’. That’s how semiotic systems work.

    But in biology, a codon does not have the potential to randomly represent any amino acid. It is constrained to code for a particular amino acid that interacts in the right manner with the codon’s corresponding tRNA and associated aaRS. It’s the physicochemical interaction among the tRNA, amino acid and aaRS molecules that determines which amino acid is selected. There’s no freedom of choice here, it boils down to chemistry.

    The implications of this is even more far-reaching especially in light of related previous work, which I discussed above. See the review by Crater, especially.
    Collectively they point to ancestral tRNAs lacking anticodons, ancestral aaRSs that only bind the tRNA acceptor arm and ancestral ribosomes with only the peptide-bond forming rRNA ribozyme. Such a primitive system can join amino acids to produce peptides (short proteins) in the absence of mRNA codons or codon-anticodon pairing. This negates the need for there being mRNA-based code right from the start. That may have evolved later.

  101. 101
    gpuccio says:

    Evolve:

    It’s you who are missing the point. If you’re confused by the non-technical press release, then look at the technical paper. Believe me, it’s better!

    It’s always the aaRS which recognizes both the anticodon region and the acceptor region of tRNA. The paper only analyzes interesting details about how the genetic code is implemented, at two different levels, in the interaction between the aaRS and the two different regions of tRNA. That is done by a regression method which relates the type of AA coded with the nucleotide sequence (code), and there is no evidence of biochemical interactions between the tRNA and the AA.

    So, the interaction is always symbolic, because it depends on the structure and specific configuration of the repository of the code (the aaRS). There is absolutely no evidence in the paper of a direct interaction of the tRNA with the aminoacid, as you seem to believe.

    So, if you are still convinced that such a direct interaction is the basis for the code, could you please point to the facts in the paper which support that belief? Otherwise, your discourse is senseless.

  102. 102
    gpuccio says:

    Evolve:

    By the way, you could also try to explain how the aaRS, even in their urzyme form, came into existence, and how the code worked in their absence? Or are you suggesting that such complex enzymes were there even while molecular information was not yet transmitted by a genetic code?

    Just to understand what you think.

  103. 103
    gpuccio says:

    Evolve:

    This is the level of highest fact independent speculation that you can find at the end of the paper:

    “Although we are not in a position to address the question of how aminoacylated tRNA acceptor stems might have been aligned in accordance with a primordial mRNA without anticodons, Rodin and Ohno suggested that reconstructed tRNA acceptor stems display evidence of complementary sequences (59). Our results revive the possibility that such complementarity and/or lateral-loop-loop base-pairing (60) might have aligned acylated acceptor stems, anticipating the assembly of peptides according to a message.”

    IOWs, the data in the paper are merely about the coding power of the acceptor stem and the anticodon, mediated by the recognition by the aaRS. The paper states that two levels of coding are present when the aaRS interacts with the tRNA: both are symbolic, and together they determine the correct association between the tRNA and the corresponding aminoacid according to the genetic code we all know. The paper is about how the genetic code is implemented by the interaction between the aaRS and the two sequences of nucleotides in the anticodon part and the acceptor part of the tRNA.

    tRNA is a passive vehicle of information in all this process: it’s the aaRS which recognizes the information, and binds the correct AA.

    From the paper:

    “Dual coding for amino acids by tRNA acceptor stem and anticodon bases correlates strongly with experimental values for two linearly independent branches of the thermodynamic cycle of vapor to solvent transfers, Kv>c and Kv>w (SI Appendix, Fig. S1). That cycle (19, 28) affords a comprehensive experimental description of how the 20 amino acids direct folding (Fig. 1 C–E), supporting the view that acceptor stem and anticodon bases compose full, complementary, and independent, specifications for the 20 canonical amino acids by coding, respectively, for size and polarity.”

  104. 104
    Evolve says:

    I’m baffled to hear that you think this is symbolic! No, these are real physical interactions. How else do you think specific parts of the tRNA molecule can select for amino acids? Carter discusses this paper in his review, which I’ve already mentioned more than once. I’m quoting from the review where he mentions acceptor stem coding:
    http://www.mdpi.com/2075-1729/5/1/294/htm

    “Figure 9 illustrates aspects of the Carter and Kraut model consistent with acceptor stem base coding. Large amino acid side chains at inward-facing positions would seriously disrupt peptide–RNA interactions in three ways. Displacing the antiparallel ?-structure to higher radii would (i) eliminate the synchronous periodicity of dipeptides and bases; (ii) break the peptide-sugar phosphate hydrogen bonds; and (iii) break Van der Waals interactions between other inward-pointing side chains and the RNA bases. Accepter stem coding on the basis of amino acid size therefore appears central to preserving such interactions. ?-branched side chains are preferentially observed in extended ?-structure in contemporary proteins [57]. Selectively identifying such side chains would have the advantage of enforcing extended secondary structures, also preserving peptide–RNA interactions by a complementary constraint.”

    Such molecular associations between RNA and peptides were modelled by Carter back in 1974:
    http://www.ncbi.nlm.nih.gov/pm.....PMC387987/
    You seem to be missing all this.

  105. 105
    Evolve says:

    “By the way, you could also try to explain how the aaRS, even in their urzyme form, came into existence,”

    See my first post, #93

  106. 106
    Evolve says:

    The paper states that two levels of coding are present when the aaRS interacts with the tRNA: both are symbolic, and together they determine the correct association between the tRNA and the corresponding aminoacid according to the genetic code we all know.

    Wrong.
    it’s not just the aaRS that interacts with the tRNA, but also the amino acid. The tRNA is anything but a passive vehicle, it actively sorts amino acids based on their properties.
    Figure 4 of the paper shows how stereochemical specification might have worked:

    “Acceptor stem coding may have conferred a selective advantage by distinguishing smaller from larger amino acids and identifying ?-branched, aliphatic, and carboxylate side-chains. Fig. 4 shows how only small side-chains fit between peptide and RNA bases, whereas side-chains pointing away from the RNA are not so constrained. Coding of amino acid size could thus have helped preserve these patterns in transitions from a proposed direct, stereochemical specification (49, 50) to triplet coding. The conformational propensity of ?-branched side-chains could similarly have favored ?-secondary structures”

    The paper is about how the genetic code is implemented by the interaction between the aaRS and the two sequences of nucleotides in the anticodon part and the acceptor part of the tRNA.

    Nope. The paper is about the intrinsic ability of tRNAs to discriminate amino acids, which in turn provides clues to ancestral translation in the absence of codon-anticodon pairing. Initial acceptor stem-based coding may not have allowed production of fully folded globular proteins like today because discrimination on the basis of hydrophobicity was absent:

    “We suggest that genetic coding evolved in distinct stages. Initial discrimination on the basis of size may have allowed coding by tRNA acceptor stems to ensure that the earliest peptides were ?-structures with alternating large and small side-chains, to interact with RNA, and only later encoded globular conformations with greater catalytic activity. The earliest peptides may have included the unstructured peptide tails that stabilize ribosomal RNAs.”

  107. 107
    gpuccio says:

    Evolve:

    Apparently, you cannot distinguish facts from mere speculations.

    In the Carter Wolfenden paper of 2015 there is absolutely no fact about direct interactions between the tRNA and the aminoacid. They are not using the word “code” as a game. They are using it because that’s what they are analyzing: a symbolic code where there is correspondence between the sequence of nucleotides in the acceptor stem and the anticodon region, which are both recognized by the aaRS, and the properties (size and polarity) of the specific AA which will be bound to the tRNA by the aaRS.

    It is a regression study showing association between the two things. It is not a biochemical study showing any kind of biochemical interaction between tRNA and AA. Is that clear?

    Those are the facts. Symbol + symbol equates final symbology (the classic genetic code).

    The rest are the usual speculations, absolutely unsupported by facts.

    For example, these are the conclusions from the Carter review:

    4. Conclusions
    The structural biology of aminoacyl-tRNA synthetases (aaRS) furnishes a platform from which to examine experimentally the steps by which pre-biological chemistry gave rise to the universal genetic code, thereby creating genetics. A key stage in the process was likely driven by “Urzymes,” which are models we developed to represent the core catalysts embedded within two distinct, contemporary aaRS superfamilies. aaRS Urzymes contain only ~15% of the total mass of the largest synthetases. They retain ~60% of their catalytic proficiency [13], but less than 20% of their specificity [20]. These properties match those necessary to produce statistical ensembles of functional peptides, as proposed by Woese. The two distinct classes of aaRS that translate the code today were formerly considered to have arisen independently. We used Urzymes to show that, rather than arising independently, the two classes probably descended from opposite strands of the same ancestral gene [17], as proposed by Rodin and Ohno [8]. Our group has ventured both backward in time [12,20], investigating likely precursors of Urzymes, and forward in time, investigating how Urzymes subsequently developed epistatic mechanisms [25,26] that increased specificity, enabling the evolution of the universal genetic code. As Urzymes cannot recognize the anticodon stem-loop, it is likely that the acceptor stem code preceded the canonical genetic code. The acceptor stem code favors the capacity of polypeptide sequences to interact with double-stranded RNA. We link these numerous biochemical, phylogenetic, and structural observations to the Carter & Kraut structural model to form a credible, testable alternative to the RNA World Hypothesis for the origin of translation and the genetic code. This work does not presuppose an “RNA world,” which we feel is based on the wrong assumptions. Rather, comparison of predictions based on the two hypotheses indicate that a peptide/RNA world is substantially more predictive, and hence a more credible and probable alternative to the prevailing idea that life originated from a single polymer with both catalytic and informational functions.

    Interesting speculations, all centered however on the role of aaRSs. Nothing more.

    While darwinists fight about RNA worlds or peptide/RNA worlds of which we have absolutely no evidence, the genetic code is there, symbolic as ever, and the recognition of tRNA and AA by aaRSs is there, symbolic as ever.

    If you really believe that tRNAs recognize their aminoacid according to biochemical laws, and self-charge themselves with it, please show me the experiments where those facts are observed.

    The only fact is that aaRSs recognize their tRNA symbolically, and charge it with the appropriate AA because their complex structure is organized to do so. This is the simple truth.

    Facts please, if you have them.

  108. 108
    gpuccio says:

    Evolve:

    “The paper is about the intrinsic ability of tRNAs to discriminate amino acids,”

    Nonsense. Can you please show where tRNAs are shown to discriminate between aminoacids? Did they do it in tyhe lab? Do you understand what you are reading?

  109. 109
    gpuccio says:

    Evolve:

    Your quote from the paper.

    “We suggest that genetic coding evolved in distinct stages. Initial discrimination on the basis of size may have allowed coding by tRNA acceptor stems to ensure that the earliest peptides were ?-structures with alternating large and small side-chains, to interact with RNA, and only later encoded globular conformations with greater catalytic activity. The earliest peptides may have included the unstructured peptide tails that stabilize ribosomal RNAs.”

    These are not facts, but mere speculations. The facts are the statistical association between certain sequences of nucleotides in the accepètor stem (a code, by admission of the authors themselves) and the kind of aminoacid which is bound to tRNA by the aaRS.

    Let’s be clear: if you want to affirm “the intrinsic ability of tRNAs to discriminate amino acids”, you must show in the lab that tRNAs discriminate aminoacids by biochemical interaction. Where is that evidence?

    If you just build a regression between sequences and the aminoacid which is bound by an enzyme, what you are analyzing are codes. Indeed, the authors know that very well, and that’s why they always use the word “coding” which you seem not to like at all.

    Again, you are not able to distinguish between facts and mere speculations, or abstract models unsupported by observations.

  110. 110
    Evolve says:

    “It is a regression study showing association between the two things. It is not a biochemical study showing any kind of biochemical interaction between tRNA and AA. Is that clear?”

    But you’re totally missing the fact that association cannot happen without interaction, which Carter elaborates in his review. I find that baffling.
    How else can tRNA distinguish between amino acids based on their size or polarity if there’s absolutely no interaction? What rubbish is that?
    I think you’re confusing interaction to be some kind of biochemical reaction producing a product. No, interactions here mean things like Van der Waal’s forces and hydrogen bonds between the nucleotides in the tRNA and residues in the amino acid or peptide.

  111. 111
    Evolve says:

    “Interesting speculations, all centered however on the role of aaRSs. Nothing more.”

    These are informed speculations, not wild speculations. They’re based on available data.

    “While darwinists fight about RNA worlds or peptide/RNA worlds of which we have absolutely no evidence, the genetic code is there, symbolic as ever, and the recognition of tRNA and AA by aaRSs is there, symbolic as ever.”

    And creationists do nothing more than misrepresent all the hard work of biologists while doing hardly any experiments of their own or to try and falsify their fanciful ideas. Meanwhile, it’s too ignorant of you to claim that there’s no evidence for the RNA world or RNA/peptide world. There is substantial evidence but not conclusive enough to formulate a theory.
    The genetic code is of course there, but increasing evidence suggests that it didn’t exist in the present form right from the beginning. That’s what I discussed above. Ancestral aaRSs, ancestral tRNAs and ancestral ribosomes were all different from modern-day versions. Therefore, alternative modes of rudimentary protein synthesis and RNA replication are likely to have preceded the current mechanisms.

  112. 112
    gpuccio says:

    Evolve:

    I think there is no hope with you.

    An association between the kind of nucleotide sequences which are recognized by the aaRS in the acceptor stem and the aminoacid that the aaRS binds to that tRNA ia a code, not an interaction.

    The interaction would be if the tRNA were able to select the aminoacid by itself, and not because its sequences are recognized by the aaRS. The paper, which you obstinately misunderstand, is all about codes: it just suggests that one part of the code could be older, in particular the acceptor stem code, because the urzymes modeled by the authors can recognize that code, but not the anticodon code. Maybe, or maybe not. Anyway, the simple fact is that there are two levels of code, one in the sequence of the nucleotides in the acceptor stem, and the other in the sequence of nucleotides in the anticodon part. Both are symbolic coding sequences, and together they allow the aaRS to recognize the correct tRNA and charge it with the correct AA.

    Let’s say it this way. The aaRS must recognize the correct tRNA to couple it with the correct aminoacid for which that aaRS is specific (remember, there are 20 of them, one for each aminoacid). Now, the essence of the paper is that the aaRS recognizes the tRNA by two different messages: one is in the acceptore stem, and it informs the aaRS about the size of the aminoacid which has to be charged. So, the aaRS can recognize tRNAs which are coding for the correct size. At the same time, the anticodon part bears a signal which points to the polarity. The sum of size and polarity, as coded in the two different parts of the tRNA, allows the aaRS to recognize the correct, specific tRNAs, and charge them with the correct aminoacid. This system, although complex, allows for precision, because it guarantees that the aminoacid in the end will be exactly the one coded for by the original codon in the DNA gene, minimizing the possibility of errors.

    In no moment of this procedure does the tRNA “select” the aminoacid. The tRNA cannot select any aminoacid by itself. It can only do it by interacting with the aaRS, and exhibiting its two signals to the enzyme. The key to the decoding is in the aaRS, as we have always known.

    These are the facts. All the rest are speculations on how and why such a system could have originated, according to the current dogma of neo darwinism.

    You must make up your mind: do you still affirm that the paper demonstrates the “intrinsic ability of tRNAs to discriminate amino acids”?

    Because, you know, when you just state:

    “The genetic code is of course there, but increasing evidence suggests that it didn’t exist in the present form right from the beginning. That’s what I discussed above. Ancestral aaRSs, ancestral tRNAs and ancestral ribosomes were all different from modern-day versions. Therefore, alternative modes of rudimentary protein synthesis and RNA replication are likely to have preceded the current mechanisms.”

    you are simply considering and sponsoring the speculations in the paper, and you are free to do that, as much as I am free not to believe them at all.

    But if you say that the paper demonstrates the “intrinsic ability of tRNAs to discriminate amino acids”, then you are just a fool.

  113. 113
    gpuccio says:

    Evolve:

    Just for further clarification here is a quote from the PDB page for aminoacyl tRNA synthetases:

    Finding the Proper Mate

    As you might expect, many of these enzymes recognize their tRNA molecules using the anticodon. But this may not be possible in some cases. Take serine, for instance. Six different codons specify serine, so seryl-tRNA synthetase must recognize six tRNA molecules with six different anticodons, including AGA and GCU, which are entirely different from one another. So, tRNA molecules are also recognized using segments on the acceptor end and bases elsewhere in the molecule. One base in particular, number 73 in the sequence, seems to play a pivotal role in many cases, and has been termed the discriminator base. In other cases, however, it is completely ignored. Note also that each enzyme must recognize its own tRNA molecules, but at the same time, it must not bind to any of the other ones. So, each tRNA has a set of positive interactions that match up the proper tRNA with the proper enzyme, and a set of negative interactions that block binding of improper pairs. For instance, the aspartyl-tRNA synthetase shown here (entry 1asz ) recognizes the discriminator base and 4 bases around the anticodon. But, one other base, guanine 37, is not used in binding, but must be methylated to ensure that the tRNA does not bind improperly to the arginyl-tRNA synthetase.

    As you can certainly see, the problem is in the coupling of the aaRS to the correct tRNA. The aminoacid has no role, it is simply recognized by the aaRS. Which is not a simple task. Again. from the PDB page:

    Aminoacyl-tRNA synthetases must perform their tasks with high accuracy. Every mistake they make will result in a misplaced amino acid when new proteins are constructed. These enzymes make about one mistake in 10,000. For most amino acids, this level of accuracy is not too difficult to achieve. Most of the amino acids are quite different from one another, and, as mentioned before, many parts of the different tRNA are used for accurate recognition. But in a few cases, it is difficult to choose just the right amino acids and these enzymes must resort to special techniques.

    Isoleucine is a particularly difficult example. It is recognized by an isoleucine-shaped hole in the enzyme, which is too small to fit larger amino acids like methionine and phenylalanine, and too hydrophobic to bind anything with polar sidechains. But, the slightly smaller amino acid valine, different by only a single methyl group, also fits nicely into this pocket, binding instead of isoleucine in about 1 in 150 times. This is far too many errors, so corrective steps must be taken. Isoleucyl-tRNA synthetase (PDB entry 1ffy ) solves this problem with a second active site, which performs an editing reaction. Isoleucine does not fit into this site, but errant valine does. The mistake is then cleaved away, leaving the tRNA ready for a properly-placed leucine amino acid. This proofreading step improves the overall error rate to about 1 in 3,000.

    These are facts. These are biological interactions.

  114. 114
    Evolve says:

    “Let’s be clear: if you want to affirm “the intrinsic ability of tRNAs to discriminate amino acids”, you must show in the lab that tRNAs discriminate aminoacids by biochemical interaction. Where is that evidence?”

    tRNAs discriminate amino acids by physical interaction, not biochemical. If you test this in the lab, you’ll see what you’ve always seen – one tRNA gets charged with one amino acid. The paper here provides an explanation for why that’s the case through regression analysis.

    “If you just build a regression between sequences and the aminoacid which is bound by an enzyme, what you are analyzing are codes. Indeed, the authors know that very well, and that’s why they always use the word “coding” which you seem not to like at all.”

    Codes or not, these associations are the result of molecular interactions which the authors make abundantly clear in the paper (e.g Fig 4) and in the review that followed. It is unbelievably stupid on your part to deny that fact.

    “Again, you are not able to distinguish between facts and mere speculations, or abstract models unsupported by observations.”

    Lol!

  115. 115
    gpuccio says:

    Evolve:

    “If you test this in the lab, you’ll see what you’ve always seen – one tRNA gets charged with one amino acid.”

    Withouth the aaRS? OK, I don’t want to waste any more of my time with you. You are really a fool.

  116. 116
    Mung says:

    Only someone completely ignorant of ID, or someone intent on willfully misrepresenting ID, would say that ID holds to the position that molecules do not interact.

    Sheesh.

  117. 117
    Mung says:

    Evolve: That’s how semiotic systems work.

    No, it isn’t. There has to be something that establishes the relationship between the representation and that which is being represented. Without that you don’t have a semiotic system.

  118. 118
    Evolve says:

    “Withouth the aaRS?”

    What?
    Without the aaRS you won’t see much because it is the tripartite complex involving all 3 molecules – tRNA, amino acid and aaRS that produces the right conformation to carry out the reaction.

  119. 119
    Evolve says:

    “Only someone completely ignorant of ID, or someone intent on willfully misrepresenting ID, would say that ID holds to the position that molecules do not interact.”

    You are fully aware of molecular interactions, you’re fully aware that biology is fueled by such interactions and it is totally unlike man-made systems where molecular interactions don’t apply. But you never acknowledge these facts wholeheartedly, because if you do the whole ID premise will collapse. ID hangs on through bad analogies between biology and man-made stuff.

  120. 120
    Evolve says:

    “There has to be something that establishes the relationship between the representation and that which is being represented. Without that you don’t have a semiotic system.”

    Not necessarily. The word CAR does not relate to a car in any manner. It just so happens that we humans decided to represent a car with that 3-letter word in English.

  121. 121
    Mung says:

    Evolve: You are fully aware of molecular interactions, you’re fully aware that biology is fueled by such interactions and it is totally unlike man-made systems where molecular interactions don’t apply.

    What are those man-made systems made of? Are they immaterial?

    If you push an A on your keyboard an A doesn’t appear on your screen? It does, but no molecules are involved?

  122. 122
    Mung says:

    Evolve: I’m baffled to hear that you think this is symbolic! No, these are real physical interactions.

    The two are not mutually exclusive.

  123. 123
    Mung says:

    Evolve: The word CAR does not relate to a car in any manner.

    Yes it does, and it’s right there in your very next sentence.

    It just so happens that we humans decided to represent a car with that 3-letter word in English.

    IOW a convention was established. A code. Is it your position that this occurred supernaturally?

  124. 124
    Evolve says:

    Convention was established at our convenience. We could have established ANT to mean car with equal value. No constraints are present.

  125. 125
    Evolve says:

    ///What are those man-made systems made of? Are they immaterial? If you push an A on your keyboard an A doesn’t appear on your screen? It does, but no molecules are involved?///

    Not what I meant.
    Let’s say you compare DNA to language – something routinely done by creationists. DNA is a chemical molecule, language has no chemistry whatsoever. DNA reacts, interacts & changes all on its own. Language does not unless humans intervene.

  126. 126
    Evolve says:

    gpuccio @112 & 113

    You’re all at sea here, gpuccio. The paper and the review DO talk about tRNA-amino acid interactions in spite of your vehement denials.
    I even cited a 1974 paper modeling RNA-amino acid interactions!

    By the way, I don’t need lessons on aaRSs.
    You’re forgetting that aaRSs are enzymes which can interact strongly or even form bonds with its substrates.
    But that does not mean tRNAs cannot interact with amino acids. They also interact, albeit at a weaker extent.
    It beats me why you can’t get your head around this.

    First and foremost you must understand the difference between interaction and covalent bonding.
    A covalent bond is strong linkage where the two molecules involved are in very close proximity. Bonds are mostly stable and long lasting.

    Interations, on the other hand, can be strong or weak, with a gradation in strength depending on many factors.
    They can occur at greater distances compared to covalent bonds and could be stable or unstable.
    Van der Waal’s forces, hydrophobic interactions, hydrogen bonds etc are all examples of weak interactions always occurring between molecules.
    When we talk about tRNA interacting with amino acid, we mean those weak linkages occurring at a distance. They’re fleeting, can be easily broken apart and reconfigured.
    Now, all interactions may not be of equal strength. Enzymes like aaRS, for instance, interact much more strongly with their substrates.
    tRNA-amino acid interactions could be weaker than that, but nonetheless they still interact.

    You also have this stubborn idea in mind that aaRS, tRNA, amino acid all exist like solid blocks in one rigid, fixed shape.
    Not the case.
    Molecules are constantly changing shape as they interact with everything in their vicinity. They’re flexible.
    Do you think DNA always exists in the classical double helix form inside the cell? If you think so, you’re wrong. It’s constantly changing shape.

    Like kids’ bumper cars in an amusement park, ALL aaRSs will bump into ALL tRNAs as well as ALL amino acids . No physical barriers exist to prevent these molecules from bumping into one another.
    Everytime they bump into each other, there are interactions, which changes the shape, form and function of these molecules.
    In this sea of interactions, a particular set of aaRS, tRNA and amino acid associate in such a way that the resulting conformation (shape) of the complex favors covalent bonding of the amino acid with the tRNA in that complex.

    Now, this is what the paper is talking about. They don’t say that tRNA selects amino acid all by itself or that aaRS selects tRNA all by itself. Interactions in the tripartite complex involving all 3 molecules determine the specificity of the reaction.
    The paper focuses on previously unexplained tRNA-amino acid associations in this complex. I hope now you can see where you’re going wrong.

  127. 127
    Origenes says:

    Evolve,

    Mung: There has to be something that establishes the relationship between the representation and that which is being represented. Without that you don’t have a semiotic system.

    Evolve: Not necessarily. The word CAR does not relate to a car in any manner. It just so happens that we humans decided to represent a car with that 3-letter word in English.

    Well, we humans establish the relationship between “car” and a car, so Mung is right.
    BTW how about computer code? Is it a real code? Or is it reducible to molecular interactions?

  128. 128
    Dionisio says:

    This seems like an interesting discussion, but there are a few things I may not understand clearly:

    1. Does the “charging”/”loading” of a given tRNA(i) with a given AA(j) occur through the enzymatic catalyzing mediation of a given aaRS(k)?

    2. Does the final “binding” of the given AA(j) to the given tRNA(i) take place at a part of the given tRNA(i) that is not specific to the given AA(j), i.e. it could “bind” a different AA(m) as well?

    3. Is the association between the given aaRS(k) and the given tRNA(i) understood through the anticodon part of the given tRNA(i) which somehow is “recognized” by the given aaRS(k)?

    4. How is the given aaRS(k) associated to the given AA(j)? IOW, how does the given aaRS(k) “recognize” the given AA(j)? By some kind of unique structural features or physicochemical properties of the given AA(j)?

    Please, kindly forgive me if the above questions make no sense, are too ‘dumb’ or have been already answered in this thread. That would just confirm my deep ignorance on this subject. Thank you for any help with this.

  129. 129
    Me_Think says:

    Origenes @ 127

    BTW how about computer code? Is it a real code? Or is it reducible to molecular interactions?

    The code requires an OS for interpretation (which requires flow of electrons through the silicon chips) and once interpreted, at the hardware level again, electrons flow through the circuitary to interpret the code and drive the CPU, so computer code too requires, if not molecular – electron intercation 🙂

  130. 130
    Dionisio says:

    UB and gpuccio

    Please help me with the 4 questions @128.
    Thank you.

  131. 131
    Evolve says:

    ///1. Does the “charging”/”loading” of a given tRNA(i) with a given AA(j) occur through the enzymatic catalyzing mediation of a given aaRS(k)?///

    Yes, contemporarily.
    However, aaRS may not have been involved at the beginning.
    gpuccio posed me the question of how tRNAs can be charged without aaRS, at least without the ancestral urzyme version of aaRS. He hasn’t read enough.
    tRNAs have been charged with amino acids in the lab non-enzymatically:
    http://nass.oxfordjournals.org.....1/269.long
    http://www.sciencedirect.com/s.....3094900434

    ///2. Does the final “binding” of the given AA(j) to the given tRNA(i) take place at a part of the given tRNA(i) that is not specific to the given AA(j), i.e. it could “bind” a different AA(m) as well?///

    Yes

    ///3. Is the association between the given aaRS(k) and the given tRNA(i) understood through the anticodon part of the given tRNA(i) which somehow is “recognized” by the given aaRS(k)?///

    aaRS recognises both the acceptor stem of the tRNA (the part that binds to amino acid) as well as the anticodon end (the part that binds to the mRNA codon). But again, that’s with contemporary aaRSs.
    Ancestral versions of aaRSs have been reconstructed which were found to recognise only the acceptor stem. And ancestral versions of tRNAs have also been reconstructed that lack the anticodon part. These two facts gel well and collectively suggest that primitive translation involved no codon-anticodon pairing. That may have evolved only later.

    ///4. How is the given aaRS(k) associated to the given AA(j)? IOW, how does the given aaRS(k) “recognize” the given AA(j)? By some kind of unique structural features or physicochemical properties of the given AA(j)?///

    aaRS binds the amino acid first, modifies it, then binds to the tRNA and attaches the modified amino acid onto the tRNA. But new studies are showing that the tRNA also sorts for amino acids based on their size, branching and polarity.

  132. 132
    Evolve says:

    ///Well, we humans establish the relationship between “car” and a car, so Mung is right///

    He’ll be right if we use an image of a car to represent a car (e.g., a traffic sign), because the image establishes the relationship. But the word “car” does not establish any relationship, it merely represents a car.

    ///BTW how about computer code? Is it a real code? Or is it reducible to molecular interactions?///

    Computer code is of course a real code, but not involving chemistry in the same sense as codes in life, such as DNA. As such, analogies between the two don’t hold water despite it being a favorite activity of creationists.

  133. 133
    Dionisio says:

    Evolve @131

    ///1. Does the “charging”/”loading” of a given tRNA(i) with a given AA(j) occur through the enzymatic catalyzing mediation of a given aaRS(k)?///

    Yes, contemporarily.
    However, aaRS may not have been involved at the beginning.
    gpuccio posed me the question of how tRNAs can be charged without aaRS, at least without the ancestral urzyme version of aaRS. He hasn’t read enough.
    tRNAs have been charged with amino acids in the lab non-enzymatically:
    http://nass.oxfordjournals.org…..1/269.long
    http://www.sciencedirect.com/s…..3094900434

    ///2. Does the final “binding” of the given AA(j) to the given tRNA(i) take place at a part of the given tRNA(i) that is not specific to the given AA(j), i.e. it could “bind” a different AA(m) as well?///

    Yes

    ///3. Is the association between the given aaRS(k) and the given tRNA(i) understood through the anticodon part of the given tRNA(i) which somehow is “recognized” by the given aaRS(k)?///

    aaRS recognises both the acceptor stem of the tRNA (the part that binds to amino acid) as well as the anticodon end (the part that binds to the mRNA codon). But again, that’s with contemporary aaRSs.
    Ancestral versions of aaRSs have been reconstructed which were found to recognise only the acceptor stem. And ancestral versions of tRNAs have also been reconstructed that lack the anticodon part. These two facts gel well and collectively suggest that primitive translation involved no codon-anticodon pairing. That may have evolved only later.

    ///4. How is the given aaRS(k) associated to the given AA(j)? IOW, how does the given aaRS(k) “recognize” the given AA(j)? By some kind of unique structural features or physicochemical properties of the given AA(j)?///

    aaRS binds the amino acid first, modifies it, then binds to the tRNA and attaches the modified amino acid onto the tRNA. But new studies are showing that the tRNA also sorts for amino acids based on their size, branching and polarity.

    Only the answer to the 2nd question was correctly formatted.

    Questions 1 throu 3 were “Yes”/”No” questions, but in questions 1 and 3 you expanded your answers with hypothetical issues that were not requested by the question and could only add confusing noise to the answers.

    Actually, in question 3 the words “Yes” or “No” are missing.

    The 4th question is not a “Yes”/”No” question, but a “How?” question, hence it demands an explanation. That question was not answered at all or at least not explicitly.

    Please, note that I’ve emphasized the parts of the answers that met the required format and stroke out the parts that did not meet that requirement or were off the exact question focus.

    Please, try answering the 4th question again at your convenience, if you will.
    Thank you.

  134. 134
    gpuccio says:

    Dionisio:

    1) Yes.

    2) Yes.

    3) Not only. The aaRS recognizes both the anticodon part and the acceptor stem part of the tRNA, which are at opposite ends of the molecule.

    4) The aaRS recognizes its specific AA by a specific part of its molecule. Here is a good summary:

    “Aminoacylation must be carried out accurately: the correct amino acid must be attached to the correct tRNA if the rules of the genetic code are to be followed during protein synthesis. It appears that an aminoacyl-tRNA synthetase has high fidelity for its tRNA, the result of an extensive interaction between the two, covering some 25 nm2 of surface area and involving the acceptor arm and anticodon loop of the tRNA, as well as individual nucleotides in the D and T?C arms. The interaction between enzyme and amino acid is, of necessity, less extensive, amino acids being much smaller than tRNAs, and presents greater problems with regard to specificity because several pairs of amino acids are structurally similar. Errors do therefore occur, at a very low rate for most amino acids but possibly as frequently as one aminoacylation in 80 for difficult pairs such as isoleucine and valine. Most errors are corrected by the aminoacyl-tRNA synthetase itself, by an editing process that is distinct from aminoacylation, involving different contacts with the tRNA (Hale et al., 1997; Silvian et al., 1999).”

    An important point is that the process has to be very precise to be of any utility, because errors in translation can scarcely be tolerated. One of the problems with Carte’s hypothesis of “urzymes” is that in no way they can ensure the needed precision and specificity. This is from Carter’s review:

    ““Urzymes” are quite small, highly conserved fragments of the two aminoacyl-tRNA synthetase superfamilies (Figure 3). Our biochemical studies have shown that Urzymes from both classes retain ~60% of the Gibbs energies of catalytic proficiency of fully evolved synthetases [13,14,21] and ~20% of their specificities for amino acid activation”

    By the way, I think that I will not answer any more Evolve’s “arguments”. He is a fool, he does not understand, or simply he does not want to understand.

  135. 135
    Dionisio says:

    gpuccio
    Thank you for the answers.

    Ensuring that I understood the situation implied by the answer to the second question, could any AA chemically bind -at least in theory- to the acceptor arm of any tRNA regardless of the tRNA anticodon loop, provided that some mechanism would bring the AA close to the tRNA acceptor arm?

    Regarding the 3rd question, here are two subquestions:
    3.1) do the tRNA have the same acceptor arm?
    3.2) is their main difference in the anticodon loop?

  136. 136
    Dionisio says:

    #133 error correction
    Part of the first sentence in the answer to the 3rd question was incorrectly stricken out.
    My fault.

  137. 137
    gpuccio says:

    Dionisio:

    I am not a biochemist, but I think that the answer to your question is: yes. The aminoacid binds by an ester bond to the 3′-OH group in the CCA end of the molecule, which is the same in all tRNAs, as far as I understand.

    The anticodon end, in particular, can have no real role in that binding, because it is at the other end of the tRNA molecule.

    The acceptor stem, instead, coould have some role in the biochemical interaction with the aaRS when the aminoacid charging takes place, because it’s the acceptor stem which ends with the CCA sequence.

    However, both the acceptor stem and the anticodon region are recognized by the aaRS because of their specific configuration, which depends on their sequence, which is different in different tRNAs. That’s what is called “code” in the paper linked by Evolve (and not understood by him).

    This acceptor stem code and anticodon code are not the same thing as the genetic code. They are the codes which implement the genetic code.

    The genetic code maps each codon of the DNA gene to an amonoacid.

    The acceptor stem code and the anticodon region code are sequences which are recognized by the specific aaRS. The combined recognition of both regions is symbolically coupled (by the aaRS structure) to the correct aminoacid, realizing so the implementation of the genetic code, because in the end the anticodon in the tRNA which is recognized by the aaRS corresponds symbolically to the aminoacid which is bound by the aaRS and then charged to the tRNA.

    It can be useful to remind, again, that no tRNA can biochemically discriminate between the aminoacids, least of all biochemically interact with its specific aminoacid. That simply does not happen.

    The two simple papers quoted by Evolve at #131 are further evidence of that. They are two examples of artificial charging of tRNA by extremely artificail lab conditions, not certainly because the tRNA spontaneously reacts with the aminoacid.

    For example, in the second paper, the abstract states:

    This paper shows that the phenylalanine-specific tRNA of Escherichia coli as well as the yellow lupin methionine initiator tRNAMet can be charge specifically with phenylalanine and methionine, respectively, in the absence of specific aminoacyl-tRNA synthetases, under high pressure of a maximum of 6 kbar (1 bar = 105 Pa; 1atm = 1.01 × 105 Pa). The esterification reaction takes places at the 3? end of the tRNA molecules. The yield of Phe-tRNAPhe or Met-tRNAMet at high pressure is ?10 times lower than that of the enzymatic aminoacylation reaction. This reaction seems to be specific, and mis-aminoacylation of tRNAPhe and tRNAMet with serine is negligible.
    It is well known that tRNA undergoes conformational changes during interaction with an aminoacyl-tRNA synthetase. Similarly, on the basis of circular dichroism spectra, we showed that the conformation of tRNA at high pressure differs slightly from its original A-RNA form. Therefore, it can be speculated that the chargeable conformation of tRNA induced by the aminoacyl-tRNA synthetase during enzymatic aminoacylation and the one created at high pressure are similar and are most probably formed by a dehydration mechanism. We think that the ‘unique’ tertiary structure of tRNA existing under high pressure creates an active centre which might itself catalyse ester bond formation. Therefore, the structure of the amino acid stem of tRNA may determine (code) the charging of the particular amino acid to specific tRNA. This code is clearly distinct from the rules of the classical genetic code.

    Emphasis mine.

    IOWs, it is true that the acceptor stem has a structure which is able to help the charging of the correct aminoacid, but in no way it can do it by itself. In the paper, they used extremely high pressures, up to 6 kbars, to change the structure of the tRNA in a way that allows the binding, a way which is similar to what the aaRS does.

    I quote again from the PDB page about these enzymes:

    These enzymes are not gentle with tRNA molecules. The structure of glutaminyl-tRNA synthetase with its tRNA (entry 1gtr ) is a good example. The enzyme firmly grips the anticodon, spreading the three bases widely apart for better recognition. At the other end, the enzyme unpairs one base at the beginning of the chain, seen curving upward here, and kinks the long acceptor end of the chain into a tight hairpin, seen here curving downward. This places the 2′ hydroxyl on the last nucleotide in the active site, where ATP and the amino acid (not present in this structure) are bound.

    Emphasis mine.

    IOWs, the aaRS has a really central role: nothing could happen without it.

    a) It recognizes and binds the correct aminoacid and ATP, generating the aminoacyl-AMP.

    b)It recognizes the correct tRNA at two different sites, binds it and strongly changes its 3D structure (in a way which is similar to what we do with a pressure of 6 kbars).

    c) So, it charges the tRNA with the correct aminoacid, which corresponds to the anticodon in the tRNA according to the genetic code, and all that is done with an extremely low error rate.

    So, while Evolve continues to imagine tRNAs which spontaneously select their aminoacid, and shamelessly conflates bumping molecules with biochemical bindings, these are the facts.

    The myths of primitive beings where aminoacids are spontaneously bound by tRNAs, and then spontaneously form peptides, without any transmission of information by DNA genes, and then by completely imprecise urzymes, so that in the end what we observe could evolve, are myths. Facts are all another thing.

  138. 138
    gpuccio says:

    Dionisio:

    The human genome has 497 identified tRNA genes. They differ both in the anticodon region and in the acceptor arm.

    However, the 3? end of all tRNAs have the sequence CCA, with the amino acid attached by the tRNA synthetase to the terminal adenosine residue.

  139. 139
    Dionisio says:

    gpuccio
    Thank you for the excellent explanation (as usual).

  140. 140

    WOW!

    I had no idea that this thread was still going.

    Let me catch up.

  141. 141

    UB and all others supporting him are wrong.

    In case you haven’t noticed, Evolve, outside of a few kind (and obviously perceptive and brilliant) people who comment here on UD, I don’t have any active “supporters” – at least not in the established ID community, and certainly not in the semiotic community. I very thankfully have some friendly voices here and there, and that’s it. That is, of course, unless you are talking specifically about support for the demonstrated mechanics of genetic translation, then I have the whole world’s collective community of textbook authors on my side. Nice, isn’t it? 🙂

    More seriously Evolve, this isn’t about people, it’s about what can and cannot be demonstrated.

    UB’s model is problematic on two counts:

    1) He says that the codon does not determine the amino acid, it merely represents it.

    On my website (Biosemiosis.org) I state that the aaRS satisfies a necessary systematic role that is found in all semiotic systems. That is; it is an arrangement of matter that “establishes the otherwise non-existent systematic relationship between the (codon) representation and its (amino acid) effect”. This is a demonstrated fact, repeated throughout the whole of biology. The set of aaRS systematically establishes the genetic code. That’s how the system works.

    2) UB assumes that the present-day translation system (DNA-RNA-Protein) held true right from the beginning.

    I do not say that, I say that semiosis has existed on earth at the point that the heterogeneous living cell became organized. I say this because semiosis is the physical means to organize it.

    – – – – – – – – – – – –
    (still reading)

  142. 142

    Thank you GP, Dio, and Mung for commenting.

    GP you are a rock star.

  143. 143
    Evolve says:

    ///I do not say that///

    You don’t say it, but you assume it. You’re talking teleologically as if the DNA code was first set and then a decoding system was established to decode it semiotically (by which you imply design). But emerging evidence suggest that rudimentary peptide synthesis carried out by precursors of today’s aaRSs, tRNAs and ribosomes, originated before the DNA code was even involved in the process. This, of course, is in line with evolutionary principles and predictions.

    ///On my website (Biosemiosis.org) I state that the aaRS satisfies a necessary systematic role that is found in all semiotic systems///

    Teleology again.
    The aaRS’s role is not to establish any relationship with anything. It is the physical & chemical interactions that limit which amino acid can be bound by which aaRS and loaded on to which tRNA. Thus the amino acid a codon can code for is constrained by these interactions. There’s no freedom or choice here as in true semiotic systems. It’s governed entirely by spontaneous molecular interactions and the resulting limitations and constraints, something that doesn’t apply to man-made semiotic systems.

  144. 144
    Evolve says:

    ///GP you are a rock star.///

    In name-calling and fact denials!

  145. 145
    Dionisio says:

    Evolve @143

    …emerging evidence suggest that rudimentary peptide synthesis carried out by precursors of today’s aaRSs, tRNAs and ribosomes, originated before the DNA code was even involved in the process.

    Then how could the current transcription-translation system* have arisen?
    Can you point to any serious literature that describes it accurately, step by step?
    Note this is not about speculating how it could have happened, but about describing in a comprehensive manner how it could be done, regardless of how it actually occurred.
    (*) including the post-transcriptional and post-translational modifications as well as other processes and mechanisms known to be part of the currently observed biological systems.
    Thank you.

  146. 146
    Evolve says:

    If we had all the answers in step-by-step detail, we could have shut down our labs and gone home. We’re trying to figure out something that happened 3.5-4 billion years ago, that too molecular events which have hardly left any trace. It’s a daunting challenge.

  147. 147
    Evolve says:

    Dionso @ 133,
    //Only the answer to the 2nd question was correctly formatted Questions 1 throu 3 were “Yes”/”No” questions.//

    You never said upfront that your queries were only meant to be answered with a Yes or No.
    I only tried to enlighten you with some related info for each of your queries.
    But you reacted in an impolite fashion, quite unbecoming of a gentleman.

  148. 148
    Dionisio says:

    Evolve @146

    If we had all the answers in step-by-step detail, we could have shut down our labs and gone home. We’re trying to figure out something that happened 3.5-4 billion years ago, that too molecular events which have hardly left any trace. It’s a daunting challenge.

    Apparently you misunderstood my message:

    Note this is not about speculating how it could have happened, but about describing in a comprehensive manner how it could be done, regardless of how it actually occurred.

    Forget about natural history. Scientists have the biological systems right in front of their noses. They have the most advanced technology for researching. They have accumulated an enormous amount of information.
    I’m just asking to show me a valid accurate description of how to support what you wrote @143 that was quoted @145.
    That’s all.

  149. 149
    Evolve says:

    And gpuccio,
    I can see that you’re avoiding replying to me directly and instead addressing my points in your reply to others.
    Calling me names and attacking me personally won’t make your moot points any more worthwhile.

    ///I am not a biochemist///

    It shows, because you don’t even understand molecular interactions.

    ///However, both the acceptor stem and the anticodon region are recognized by the aaRS because of their specific configuration, which depends on their sequence, which is different in different tRNAs. That’s what is called “code” in the paper linked by Evolve (and not understood by him).///

    Codes or not, they involve molecular interactions, which you’re adamantly denying.
    I don’t know how many times I have had to correct this.
    For the umpteenth time, look at Figs: 1, 2 & 10 of Carter’s review of his paper and read the relevant text:
    http://www.mdpi.com/2075-1729/5/1/294/htm

    There’s a stereochemical relationship between bases in the RNA and amino acid residues. He calls it the stereochemical code.
    This results from physical interactions of these molecules. He talks about van der Waal’s forces & hydrogen bonds.
    He even proposes that complimentary RNA-peptide hairpins can be formed by these interactions, which facilitate polymerization of both molecules.
    This, he speculates, can account for the origin of both RNA and short rudimentary proteins before the advent of modern genetics.

    ///They are two examples of artificial charging of tRNA by extremely artificail lab conditions,
    not certainly because the tRNA spontaneously reacts with the aminoacid.///

    http://www.sciencedirect.com/s.....3094900434
    You’re missing the crucial point here.
    This work shows that tRNAs can be specifically charged with the correct amino acid in the absence of aaRS.
    They use high pressure to simulate the conformational change normally induced by aaRS in the tRNA.
    And then the tRNA can specifically react with its “correct” amino acid even when the specific aaRS is absent!
    This means tRNA has the ability to select its “correct” amino acid if it is in the right conformation. And the role of aaRS is to induce the right conformational change in the tRNA. So much for your obstinate denial that tRNA cannot recognize its amino acid!

    In a follow-up paper, the same group further show that these pressure-charged aminoacyl tRNAs are indistinguishable from aaRS-charged ones in protein synthesis:
    http://onlinelibrary.wiley.com.....02872/epdf
    They also discuss amino acid recognition by RNA molecules.

    ///The myths of primitive beings where aminoacids are spontaneously bound by tRNAs, and then spontaneously form peptides,
    without any transmission of information by DNA genes, and then by completely imprecise urzymes,
    so that in the end what we observe could evolve, are myths. Facts are all another thing.///

    Whether you like it or not, that’s what a growing body of evidence is suggesting.
    Your biases will urge you to dismiss these as “myths”, but they have emiprical support.
    Molecular interactions between RNA, amino acids and peptides fueled polymerization of both RNA and the first simple proteins. Later, proto-aaRS enzymes catalyzed addition of amino acids to proto-tRNAs, and protein synthesis was carried out on proto-ribosomes in the absence of any codon-anticodon pairing.
    This whole talk of “someone” having to invent a semiotic DNA translation system becomes superfluous.

  150. 150
    Dionisio says:

    Evolve @147

    You never said upfront that your queries were only meant to be answered with a Yes or No.
    I only tried to enlighten you with some related info for each of your queries.
    But you reacted in an impolite fashion, quite unbecoming of a gentleman.

    Well, it was obvious that those were yes/no questions @133.
    Note that gpuccio @134 didn’t have any problem understanding how to answer those same questions.
    Note that I made a correction @136.
    Had this been an exam, you would have flunked it. 🙂
    My questions were clearly about how something works NOW, but you devoted most of your answer to speculate about how you think things might have worked in the past. That’s off topic, to say it politely. 🙂

  151. 151
    Origenes says:

    Evolve: Computer code is of course a real code, but not involving chemistry in the same sense as codes in life, such as DNA. As such, analogies between the two don’t hold water (..)

    Why not exactly? Can you explain the crucial difference? Suppose we design a computer that utilizes the storing properties of DNA, would that make the computer code less “real”?

  152. 152
    Dionisio says:

    Evolve @131

    ///2. Does the final “binding” of the given AA(j) to the given tRNA(i) take place at a part of the given tRNA(i) that is not specific to the given AA(j), i.e. it could “bind” a different AA(m) as well?///

    Yes

    Does that mean that theoretically the given tRNA(i) could be somehow charged/loaded with an AA that does not correspond to the given tRNA(i) anticodon, according to the genetic code?

  153. 153
    Dionisio says:

    Evolve,

    How do the aaRS appear in the scene? Are they the product of gene expression through GRN, signaling pathways, etc.

    How do the tRNA appear in the story?

  154. 154
    Dionisio says:

    Origins @151

    Suppose we design a computer that utilizes the storing properties of DNA, would that make the computer code less “real”?

    https://www.technologyreview.com/s/400727/dna-computing/

    🙂

  155. 155
  156. 156

    Evolve #143

    You don’t say it, but you assume it.

    No, I’ll repeat it for you again: I conclude (after several years of researching the literature) that “semiosis has existed on earth at the point that the heterogeneous living cell became organized”, and I say this because “semiosis is the physical means to organize it”.

    You’re talking teleologically as if the DNA code was first set and then a decoding system was established to decode it semiotically

    I don’t think you quite appreciate the core issue. What I have presented is an inventory of the physical conditions required to organize the heterogeneous cell. I have pulled that data from dedicated and competent researchers (all presumed materialists I might add, some who have spent their entire career on these specific issues). Their research has established the minimum physical requirements for the origin of the system — i.e. what is physically required to record and translate the amount of information that the system needs to successfully describe itself into memory. In short, the cell cycle cannot originate in an entity that cannot create a record of itself -or- translate a record of itself. This should be reasonably self-evident. You have biases that cause you to reject the requirements of coding and decoding (a representational medium) at the origin of the heterogeneous cell, but that is an issue you’ll have to take up with physical reality.

    (by which you imply design)

    I’m not implying design, I am concluding that design is the best explanation based directly on our universal experience (one of the methodological foundations of doing science). Again, personal biases that do not square with our universal experience are something you’ll have to take up with physical reality.

    Teleology again.

    You say this as if “teleology” is a word that should immediately stop your opponents in their tracks — as if the demonstrated physical conditions of the system in question actually suggests a non-teleological source. But they don’t. From an empirical perspective, the inference to teleology is entirely universal. I suspect that your biases have prevented you from grasping that reality yet.

    The aaRS’s role is not to establish any relationship with anything.

    If it is the word “role” you are objecting to here, then you are being unnecessarily pedantic. I can walk up to any biologist on the planet and ask what role the aaRS plays in translation, and he or she will certainly say it establishes the genetic code. However, if it’s the word “relationship” you are objecting to, then you need to educate yourself on how relationships are formed in the context of information and translation systems. The set of aaRS in the cell most certainly establishes a set of systematic relationships inside the cell, which we now call the Genetic Code.

    It is the physical & chemical interactions that limit which amino acid can be bound by which aaRS and loaded on to which tRNA. Thus the amino acid a codon can code for is constrained by these interactions.

    So on your view, if physical history should have it that a particular amino acid is to be indicated and appear in the operation of a translation system, then as a matter of physical law, a particular aaRS and tRNA will also appear in order to limit the system to the specification of that particular amino acid.

    That makes perfect sense. I suppose I should be happy that you’ve at least grasped the irreducible complexity of the system. And I’m sure you’ll be eager to acknowledge this, now that I’ve brought it up.

    There’s no freedom or choice here as in true semiotic systems. It’s governed entirely by spontaneous molecular interactions and the resulting limitations and constraints, something that doesn’t apply to man-made semiotic systems.

    No one is talking about the system not operating faithfully in accordance to inexorable law, so this comment is excessively uninformed Evolve. Ask Hubert Yockey about the information-carrying capacity of a system that has no degree of freedom. Listen to the things you say. Go on the bibliography at Biosemiosis.org” and read Pattee. I’ll join GP and others here who ignore you. I concur; you are foolish.

    Since we know that a heritable genetic memory is an essential condition for life, my approach to the problem of determinism began by expressing the precise requirements for a constraint that satisfies the conditions for heritability. I can do no better than to restate my early argument (Pattee, 1969b):

    “A physical system is defined in terms of a number of degrees of freedom which are represented as variables in the equations of motion. Once the initial conditions are specified for a given time, the equations of motion give a deterministic procedure for finding the state of the systems at any other time. Since there is no room for alternatives in this description, there is apparently no room for hereditary processes. . . The only useful description of memory or heredity in a physical system requires introducing the possibility of alternative pathways or trajectories for the system, along with a ‘genetic’ mechanism for causing the system to follow one or another of these possible alternatives depending on the state of the genetic mechanism. This implies that the genetic mechanism must be capable of describing or representing all of the alternative pathways even though only one pathway is actually followed in time. In other words, there must be more degrees of freedom available for the description of the total system than for following its actual motion. . . Such constraints are called non-holonomic.”

    In more common terminology, this type of constraint is a structure that we say controls a dynamics. To control a dynamical systems implies that there are control variables that are separate from the dynamical system variables, yet they must be described in conjunction with the dynamical variables. These control variables must provide additional degrees of freedom or flexibility for the system dynamics. At the same time, typical control systems do not remove degrees of freedom from the dynamical system, although they alter the rates or ranges of system variables. Many artificial machines depend on such control constraints in the form of linkages, escapements, switches and governors. In living systems the enzymes and other allosteric macromolecules perform such control functions. The characteristic property of all these non-holonomic structures is that they cannot be usefully separated from the dynamical system they control. They are essentially nonlinear in the sense that neither the dynamics nor the control constraints can be treated separately.

  157. 157
    gpuccio says:

    Evolve:

    1) I have neither called you names nor attacked you personally. I have only said that you are a fool, which is a very cool cognitive judgement about the things you say. The only reason that I avoid replying to you directly is that you make foolish arguments, and I don’t want to waste my time where there is no hope of having a serious discussion.

    2) Carter’s review which you obstinately link is about a conceptual proposal of a peptide-RNA world for OOL instead of the classical RNA world hypothesis. It has nothing to do with our discussion here. In no way it shows experimental evidence that tRNA can recognize and bind by itself its specific aminoacid. But you will never understand, or admit, this very simple point, and that’s why I don’t want to waste any more time with you.

    3) You say:

    “This work shows that tRNAs can be specifically charged with the correct amino acid in the absence of aaRS.
    They use high pressure to simulate the conformational change normally induced by aaRS in the tRNA.
    And then the tRNA can specifically react with its “correct” amino acid even when the specific aaRS is absent!
    This means tRNA has the ability to select its “correct” amino acid if it is in the right conformation. And the role of aaRS is to induce the right conformational change in the tRNA. So much for your obstinate denial that tRNA cannot recognize its amino acid!”

    You are a fool (cool cognitive judgement about what you say, not personal attack!).

    So, tRNA can specifically react with its “correct” amino acid even when the specific aaRS is absent if 6kbars of pressure do what the specific aaRS does! Impressing, indeed.

    The simple point is: can tRNA specifically react with its “correct” amino acid by itself? Without the contribution of its specific aaRS? Or of 6kbars of pressure? IOWs, what is the scenario that you imagine, with your fervid zeal, where tRNAs reacted with their correct aminoacid spontaneously, and from which the present scenario evolved? Where your primitive cells living at 6 kbars of environmental pressure?

    Just to understand how your mind works.

    4) You say:

    “In a follow-up paper, the same group further show that these pressure-charged aminoacyl tRNAs are indistinguishable from aaRS-charged ones in protein synthesis:”

    And so? We have already agreed on the fact that 6 kbars of pressure do the same thing that is done by aaRS to charge the aminoacid.

    Regarding the specificity of the process, Iwould like to remind you that the only experimental support to it is that the authors tried to charge the tRNAs for phenylalanine and methyonine respectively with phenylalanine and methyonine, in the presence of increasing amount of serine, which was not charged. That is not enough to say that the effect is specific, at most it shows that those 2 tRNAs cannot easily be charged with serine.

    And I really don’t understand why you are so excited because a tRNA molecule which is designed to be bound to a specific aminoacid by a coded interaction with an aaRS happens to be well designed to be charged with that aminoacid. You are very simply conflating two different statements:

    a) Each tRNA is well designed to be charged specifically with its correct aminoacid by its aaRS. That includes also having the correct anticodon, which corresponds to the correct amonoacid in the symbolic genetic code. (True)

    b) The tRNA can self charge its specific aminoacid by itself. (False)

    Even you should understand that the only point here is where the key to implement the genetic code resides. If b) were true, the key would be in tRNAs. But b) is false, and only a) is true, therefore the key resides in the aaRSs, as I have always said.

    5) I stick to what I have said about myths. You are free to stick to your “growing body of evidence”. Cognition is a free will issue.

  158. 158
    gpuccio says:

    Dionisio:

    You ask:

    “How do the aaRS appear in the scene? Are they the product of gene expression through GRN, signaling pathways, etc.

    How do the tRNA appear in the story?”

    You must have been distracted. It’s certainly because of bumping molecules, and the occasional Van der Waals interaction! 🙂

  159. 159
    gpuccio says:

    Dionisio:

    “My questions were clearly about how something works NOW, but you devoted most of your answer to speculate about how you think things might have worked in the past. That’s off topic, to say it politely.”

    That’s the whole point. Evolve has no idea of what scientific epistemology is about.

    It’s certainly easier to debate one’s personal suppositions about what could maybe have happened billions of years ago, and for which there is no observable support, rather then debate and try to explain what we can observe today. IOWs, facts.

    But we know well that some neo darwinists love to explicitly state that theories are facts!

  160. 160
    Dionisio says:

    gpuccio @158

    You must have been distracted. It’s certainly because of bumping molecules, and the occasional Van der Waals interaction! 🙂

    Oh, no! I’ve missed the magic show again.
    You’re right, I better stay alert so I don’t miss the most dramatic episodes of the Darwinian novella.
    🙂

  161. 161
    Dionisio says:

    gpuccio @159

    It’s certainly easier to debate one’s personal suppositions about what could maybe have happened billions of years ago, and for which there is no observable support, rather then debate and try to explain what we can observe today. IOWs, facts.

    Yes, excellent point.
    Biology -perhaps more than other branches of science- is very rich in observable and testable facts demanding serious research in order to be explained accurately, hence there’s not much time left for debating personal presuppositions. We could leave that kind of debating for the social occasions. 🙂

  162. 162
    Evolve says:

    UB @ 156,

    ///I conclude (after several years of researching the literature) thatsemiosis has existed on earth at the point that the heterogeneous living cell became organized///

    Unwarranted conclusion. We don’t know what the first living cell was composed of or what its genetics and biochemistry were.
    However, we are becoming increasingly aware that the present-day genetic translation system didn’t exist as such right from the start, that its origins are rooted in much more simpler systems, that it is indeed reducible. Therefore, your assumption doesn’t sound valid in light of the data. You’re erring right from the start, I’m afraid.

    ///In short, the cell cycle cannot originate in an entity that cannot create a record of itself -or- translate a record of itself.///

    You’re clueless. There’s no need for any cell cycle if simple membrane-bound vesicles can replicate by budding. Prebiotic chemistry could very well have been cooking inside such protocells. Watch:
    https://www.youtube.com/watch?v=PqPGOhXoprU
    https://www.youtube.com/watch?v=CJ5jh33OiOA
    https://www.youtube.com/watch?v=jfq5-i8xoIU

    ///I am concluding that design is the best explanation based directly on our universal experience///

    Design is simply not the best explanation, since we see a simple system preceding the current complex genetic translation machinery.
    Everything from proto-aaRSs to proto-tRNAs and porto-ribosomes capable of carrying out crude protein synthesis in the absence of codon-anticodon pairing flies in the face of the design hypothesis. It screams classical evolution from simpler precursors.

    ///You say this as if “teleology” is a word that should immediately stop your opponents in their tracks — as if the demonstrated physical conditions of the system in question actually suggests a non-teleological source. But they don’t.///

    When sufficient non-teleological explanations are present, invoking teleology is unwarranted, it shows your bias towards design. Design inference should only be made if all other explanations are ruled out.
    In this case, we can easily explain why a codon ends up coding for a given amino acid. It’s because molecular interactions constrain it from coding for something else. And not because someone purposefully made a codon to represent one amino acid and then arranged the system to that effect.

    ///can walk up to any biologist on the planet and ask what role the aaRS plays in translation, and he or she will certainly say it establishes the genetic code///

    Of course, if you ask me I’ll say the same thing. We don’t discuss the underlying intricacies every time we talk about something, we keep it straight and simple in easily conveyable language. But that doesn’t mean that’s all what’s there to it.

    ///The set of aaRS in the cell most certainly establishes a set of systematic relationships inside the cell, which we now call the Genetic Code.///

    The aaRS, in reality, does not establish any relationship. Its interactions with surrounding molecules including the aa, tRNA etc places constraints on the system which we interpret as establishing a relationship. This is unique to molecular interactions and absent from man-made semiotic systems. This is the point you must understand. And then you can free yourself from the teleological mindset that influences all your writings.

    ///So on your view, if physical history should have it that a particular amino acid is to be indicated and appear in the operation of a translation system, then as a matter of physical law, a particular aaRS and tRNA will also appear in order to limit the system to the specification of that particular amino acid.///

    Teleology, yet again!
    Who wants a particular amino acid to be indicated somewhere? Nobody wants that. You’ve got such and such molecular species floating around. They react & interact. Molecular interactions channel reactions down particular pathways, that’s all!
    We’ve already seen that before the current players arrived on the scene, their precursors could drive similar reactions using different mechanisms.

    ///I’ll join GP and others here who ignore you. I concur; you are foolish.///

    Only shows your desperation and reluctance to learn or correct your mistakes when confronted with the facts. I don’t expect you to do that either, otherwise this whole UD site will have to be shut down. There’s not a single conclusive, unambiguous piece of evidence in favour of design. Only rampant misunderstandings & misrepresentations of the science.
    But, don’t worry, I won’t retort to you in the same language, my culture doesn’t allow that.

  163. 163
    Evolve says:

    Dionso @148,

    ///I’m just asking to show me a valid accurate description of how to support what you wrote @143 that was quoted @145.///

    I’ve posted several papers and links which detail how components of the current genetic apparatus is reducible to simpler, ancestral versions and how random molecular reactions preceded the organised decoding we see today. Some more:

    Here are two good papers on the origin and evolution of the ribosome and how reducible it was and how molecular interactions which once served a particular function, were later coopted for a different function. It kinda destroys the theme in UB’s thesis that irreducible machines were set up to decode the DNA code:

    http://www.pnas.org/content/112/50/15396.abstract
    http://www.sciencedirect.com/s.....0809001028

    The following article details evolution of the tRNA molecule, how proto-tRNAs, called mini helices lacked the codon-recognising anticodon ends (which again is central to UB’s flawed semiotic idea), but still was capable of protein synthesis:

    http://www.mdpi.com/2075-1729/5/4/1687

  164. 164

    Unwarranted conclusion

    Ah yes Evolve, why should anyone think to use the observed properties of the object we are trying to explain – in order to explain it. In proper epistemology, it’s apparently “unwarranted” to think that in order to explain the origin of life we will need models that actually achieve the properties that make life possible. Or to borrow a line: ”Who needs facts when we have all the theories.”

    We don’t know what the first living cell was composed of or what its genetics and biochemistry were.

    Which is exactly why we begin with what we do know. And of course, we can ask “on what grounds” do we assume that life is possible without the very specific properties that have been repeatedly demonstrated to make life possible. I suggest that we should have something more relevant than “we can force an amino acid onto a receptor stem under enormous artificial pressure” or “the region of a protein that binds an aa to a receptor stem works even without an anti-codon being present” or “amino acids can be bound together without a nucleic script to follow” or “nucleotides can become trapped inside inanimate membranes”.

  165. 165
    Dionisio says:

    Evolve @163

    Thank you for providing references to specific papers.

    I’ll try to read them later, but for now I took a quick look at one of them and the famous US TV commercial question “Where’s the beef?” came up to my mind.

    This is one reason why I try to make the task easier by requesting a logical, coherent, complete, comprehensive and detailed explanation of how things could (hypothetically) happen, rather than guessing and speculating on how they might have occurred in the remote past.

    I looked at the paper titled “History of the ribosome and the origin of translation” where apparently the authors use “a 3D comparative method” which seems like describing the evolution of transportation by comparing some main components (wheel, pedal, windshield, driver’s seat, engine, etch) of bikes, motorcycles, cars, SUVs, minivans, trucks, boats, airplanes, drones, tramways, trolleybuses, trains, hydro-hovers, levitation trains, yellow submarines, etc.

    There’s not much (if any at all) detailed comprehensive coherent biochemical explanation backing their arguments. How could it go from state A to state B? Why – i.e. what events triggered that transition from A to B?

    Regarding the tRNA – is there any explanation for their synthesis from their corresponding gene expression? I could not see any, but I looked very fast. How did it appear on the scene? Why?

    Here are some pieces of text copied from the paper, which seem to give at least an idea of what the paper is about:

    Here we use information within ribosomes from each major branch of the tree of life to reconstruct much of the emergence of the universal translational machinery.

    tRNA structure. Proto-tRNA is composed of a CCA tail (Fig. 3), which acquires the amino acid acceptor stem and then the T-stem and T-loop to form a minihelix

    tRNAs are optimized to form quasi stable base-pair triplets with proto-mRNAs

    Using sequences of rRNAs as a telescope in time, Woese and Fox (1) sketched three primary branches in the tree of life on earth.

    The transition from the synthesis of noncoded heterogeneous oligomers to proteins by the ribosome conferred advantages, because some reaction products bound to the ribosome.

    Proteinization of the ribosome drove a more general proteinization of other processes, giving rise to modern biology as described by the central dogma. The ribosome spawned the existing symbiotic relationship of protein and nucleic acid.

    Really? How? Why? What triggered such a change?
    How did other parts of the system affect the indicated changes? How did the indicated changes affect other parts of the system and the interaction between them?

    After a more detailed reading perhaps more questions could be raised.

  166. 166
    Evolve says:

    Gpuccio,

    Keep on beating around the bush when confronted with evidence and facts.
    You’re never going to acknowledge your mistakes and blunders, because you can’t in this ID community setting.

    ///Carter’s review which you obstinately link is about a conceptual proposal of a peptide-RNA world for OOL instead of the classical RNA world hypothesis. It has nothing to do with our discussion here. In no way it shows experimental evidence that tRNA can recognize and bind by itself its specific aminoacid. But you will never understand, or admit, this very simple point, and that’s why I don’t want to waste any more time with you.///

    It’s not a conceptual proposal but based on modelling data that they published in 1974 which I’ve already shown you. You’ll sidestep it because it contradicts your blunder that RNA cannot interact with amino acid. That’s nonsensical whichever way you look at it. Only someone who deliberately refuses to acknowledge facts will say so.

    ///The simple point is: can tRNA specifically react with its “correct” amino acid by itself? Without the contribution of its specific aaRS? Or of 6kbars of pressure? IOWs, what is the scenario that you imagine, with your fervid zeal, where tRNAs reacted with their correct aminoacid spontaneously, and from which the present scenario evolved? Where your primitive cells living at 6 kbars of environmental pressure?///

    The simple point is that tRNA can recognise and react with its amino acid as long as it is in the correct conformation – whether that conformation is provided by aaRS or induced thru high pressure. So it’s the conformation of the tRNA that ultimately drives the reaction, not the aaRS per se. This destroys your canard that tRNA cannot associate with the amino acid. That’s it.

    In fact, high pressure provides thermal energy that substitutes for ATP in the aaRS-catalyzed reaction.

    You then talk about primitive cells being at 6 kbars of pressure. But ancestral tRNA was different from the modern one, its catalytic function and requirements would also have been different, something which I have already told you many times over!

    In fact, the second paper I had posted describes aaRS-independent charging of such an ancestral tRNA version (mini helix) using a bridging oligonucleotide:
    http://nass.oxfordjournals.org.....1/269.long
    This was using a prebiotically plausible route without any aaRS. And you conveniently ignored it!

    /// And I really don’t understand why you are so excited because a tRNA molecule which is designed to be bound to a specific aminoacid by a coded interaction with an aaRS happens to be well designed to be charged with that aminoacid.///

    Nice to see your somersaults. You first said that aaRS was indispensable and when confronted with evidence, you kind of acknowledge that the tRNA has the potential to do the job without the aaRS.

    ///Even you should understand that the only point here is where the key to implement the genetic code resides///

    No! The point of all this is that amino acid charging of tRNA, peptide synthesis etc can proceed without the involvement of any genetic code at all! Welcome to non-genetic protein synthesis.
    Your teleological notion of God setting a genetic code and then creating a translation system breaks down under the weight of the evidence, whether you have the guts to stomach that or not.

  167. 167
    Evolve says:

    Dionso @ 150,

    ///Well, it was obvious that those were yes/no questions @133. Had this been an exam, you would have flunked it.///

    No, it was not obvious. If it were an exam, they would have made it clear what kind of answer they expect, but you never said anything of that sort.

    ///Note that gpuccio @134 didn’t have any problem understanding how to answer those same questions.///

    His post (#134) came after yours (#133)

  168. 168
    Evolve says:

    Dionso 165,

    I already told you that you won’t get a complete & comprehensive account of all this. In fact, we may never know entirely how all these events unfolded, most of it may have been lost to history. However, with more investigation we keep on gleaning new information. And I have tried to bring some of that to your attention here.

  169. 169
    Dionisio says:

    Evolve @168

    I’m not asking to guess or speculate on how things happened in the remote past, but how could they happen hypothetically, applying the accumulated knowledge.

    Here’s what I wrote @165

    This is one reason why I try to make the task easier by requesting a logical, coherent, complete, comprehensive and detailed explanation of how things could (hypothetically) happen, rather than guessing and speculating on how they might have occurred in the remote past.

    The first paper you referenced @163 does not seem to meet that requirement. It’s just filled with speculative statements, leaving outstanding questions unanswered and raising new questions.
    I quoted a few parts of the text for illustration. I can indicate the exact page each text was copied from. Did you read the entire paper before referring to it?

    BTW, did you answer the questions @152 & @153? Please, note that additional information is provided @155.

  170. 170
    Evolve says:

    Origenes 151,

    ///Why not exactly? Can you explain the crucial difference? Suppose we design a computer that utilizes the storing properties of DNA, would that make the computer code less “real”?///

    Computers utilizing DNA’s storage capacity is different from life because they do not involve the spontaneous reactions, interactions, replications, conformational changes
    or mutations that DNA undergoes inside a cell. The computer simply reads ones & zeroes assigned to the DNA letters with no chemistry involved in the process.
    In the cell, however, order emerges from a contingent sequence of molecular interactions. For instance, in cells DNA is methylated and acetylated – chemical modifications that change its properties. Nothing of that sort happens with computer code.
    Additionally, the vast majority of DNA in the cell is junk – it codes for nothing worthwhile. No computer code is written with so much wastage built in.

  171. 171
    Dionisio says:

    Evolve @170

    Computers (including software) can’t be compared to biological systems seriously.
    Computers of any level of sophistication can’t produce a red rose (even if it’s not for a blue lady) or a juicy mango from a seed. Neither they can produce a monarch butterfly from a caterpillar.
    Everything about computers is well documented. But there are many things unknown or poorly understood about biological systems.

  172. 172
    Mung says:

    Evolve: You’re never going to acknowledge your mistakes and blunders, because you can’t in this ID community setting.

    This is simply false. gpuccio has repeatedly admitted his error in trying to debate with unreasonable people.

  173. 173
    Andre says:

    Evolve

    When something is plausible it does not make it fact. It is plausible that you have 12 fingers….. do you?

    http://www.merriam-webster.com...../plausible

  174. 174
    gpuccio says:

    Mung:

    Unreasonable is an euphemism, in this case. Evolve is really trying to outcompete Alicia, although I think Alicia is smarter. 🙂

  175. 175

    Computers utilizing DNA’s storage capacity is different from life because they do not involve the spontaneous reactions, interactions, replications, conformational changes or mutations that DNA undergoes inside a cell. The computer simply reads ones & zeroes assigned to the DNA letters with no chemistry involved in the process. In the cell, however, order emerges from a contingent sequence of molecular interactions. For instance, in cells DNA is methylated and acetylated – chemical modifications that change its properties. Nothing of that sort happens with computer code. Additionally, the vast majority of DNA in the cell is junk – it codes for nothing worthwhile. No computer code is written with so much wastage built in.

    Good grief.

    Your entire response is misinformed. Part of it is wrong and the other part is irrelevant. Every medium of information that has ever existed in this universe has been a material object of one type or another, and each must interact with the rest of the world by virtue of its material properties. The capacity to communicate information can be implemented in wood pulp and pigments, electrons, physiological gestures, neural patterns, thermal energy, pheromones, soundwaves, electromagnetic radiation, and an untold number of other various arrangements of the material world. The material stuff that these systems are implemented in is completely irrelevant to the issue. The real problem is that you still just don’t seem to grasp (or want to grasp) that none of these things are mediums of information because of their material properties.

    They only function as mediums of information because they are organized in a system to be so. And in genetic systems, the first consequence that this organized capacity must establish is the set of non-dynamic constraints that form the organization itself. Also in regard to genetic systems, these constraints must enable combinatorial permutations in both the arrangement of the medium and in the translation of that medium. Otherwise, the system would not have the informational capacity to record itself into memory, or the capacity to increase its complexity through open-ended evolution. Nothing you’ve presented even touches (or begins to touch) these fundamental requirements. Instead, you seem to want to cling to the ridiculous notion that there are no immediate physical requirements to life, even as those systems clearly demonstrate what the requirements are (and when they are necessary).

    You are free to believe whatever you wish, and to seek physical evidence to support whatever your beliefs may be — but to pretend that the system isn’t what it is, and doesn’t do what it does, is simply anti-science.

    It’s irrational.

  176. 176
    Mung says:

    Upright BiPed: It’s irrational.
    So?

  177. 177
    Dionisio says:

    Systems biology course (2014) by Professor Uri Alon – lecture 4: Absolute robustness

    @time mark 8:50 he writes on the board:

    Robustness: Biological circuits are designed

    then he paused to clarify that by “defined” in this case he meant that evolution did it (or something like that) – a quick disclaimer for damage control? 🙂

    Here’s the link to the video of that lecture:
    https://www.youtube.com/embed/_dHaZdr0M24

    Anyway, the course is very good and I definitely recommend it to get a nice introduction to Systems Biology in 15 lectures. MIT also offers a Systems Biology course online, also recorded in 2014.

  178. 178
    Dionisio says:

    #177 addendum

    Systems biology course (2014) by Professor Uri Alon – lecture 2

    @time mark 20:45 the professor says “evolution designed…”

    https://www.youtube.com/embed/xo-7m0YnN8o

    PS. Anyone looking for an introduction to Systems Biology may seriously consider watching the entire 15-lecture video course. Professor Uri Alon teaches it very clearly with deep breaths of relief every once in a while.

  179. 179
    Dionisio says:

    UB,
    any comments on this?
    Thanks.

    The 20 aminoacyl tRNA synthetases (aaRSs) couple each amino acid to their cognate tRNAs.

    […] 19 aaRSs expanded by acquiring novel noncatalytic appended domains, which are absent from bacteria and many lower eukaryotes but confer extracellular and nuclear functions in higher organisms.

    AlaRS is the single exception, with an appended C-terminal domain (C-Ala) that is conserved from prokaryotes to humans but with a wide sequence divergence.

    In human cells, C-Ala is also a splice variant of AlaRS.

    Crystal structures of two forms of human C-Ala, and small-angle X-ray scattering of AlaRS, showed that the large sequence divergence of human C-Ala reshaped C-Ala in a way that changed the global architecture of AlaRS.

    This reshaping removes the role of C-Ala in prokaryotes for docking tRNA and instead repurposes it to form a dimer interface presenting a DNA-binding groove.

    This groove cannot form with the bacterial ortholog.

    Direct DNA binding by human C-Ala, but not by bacterial C-Ala, was demonstrated.

    Thus, instead of acquiring a novel appended domain like other human aaRSs, which engendered novel functions, a new AlaRS architecture was created by diversifying a preexisting appended domain.

    Two crystal structures reveal design for repurposing the C-Ala domain of human AlaRS
    Litao Sun, Youngzee Song, David Blocquel, Xiang-Lei Yang and Paul Schimmel
    PNAS vol. 113 no. 50 14300–14305
    doi: 10.1073/pnas.1617316113

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