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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

Comments
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
Dionisio
April 19, 2017
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#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.Dionisio
April 6, 2016
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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.Dionisio
April 6, 2016
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Upright BiPed: It’s irrational. So?Mung
March 26, 2016
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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.Upright BiPed
March 25, 2016
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Mung: Unreasonable is an euphemism, in this case. Evolve is really trying to outcompete Alicia, although I think Alicia is smarter. :)gpuccio
March 25, 2016
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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/dictionary/plausibleAndre
March 24, 2016
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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.Mung
March 24, 2016
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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.Dionisio
March 24, 2016
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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.Evolve
March 24, 2016
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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.Dionisio
March 24, 2016
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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.Evolve
March 24, 2016
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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)Evolve
March 24, 2016
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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/content/48/1/269.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.Evolve
March 24, 2016
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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.Dionisio
March 24, 2016
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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”.Upright BiPed
March 24, 2016
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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/science/article/pii/S0923250809001028 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/2075-1729/5/4/1687Evolve
March 24, 2016
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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.Evolve
March 24, 2016
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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. :)Dionisio
March 24, 2016
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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. :)Dionisio
March 24, 2016
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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!gpuccio
March 24, 2016
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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! :)gpuccio
March 24, 2016
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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.gpuccio
March 24, 2016
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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.
Upright BiPed
March 23, 2016
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#153 addendum tRNA genes? https://ghr.nlm.nih.gov/geneFamily/trna aaRS genes? https://ghr.nlm.nih.gov/geneFamily/aarsDionisio
March 23, 2016
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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/ :)Dionisio
March 23, 2016
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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?Dionisio
March 23, 2016
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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?Dionisio
March 23, 2016
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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"?Origenes
March 23, 2016
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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. :)Dionisio
March 23, 2016
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