I thought I would give a comment by a poster with the handle “ericB” a little more publicity as it was buried deep in an old thread where it was unlikely to be seen by passing “materialists / evolutionists”.
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Calling all evolutionists / materialists! Your help is needed! Alan Fox has not been able to answer a particular challenge, but perhaps you know an answer.
The issue is simple and the bar is purposely set low. The question is whether there exists one or more coherent scenarios for the creation of a translation system by unguided chemicals.
The translation system in cells indicates intelligent design. I would submit that, regardless of how many billions of years one waited, it is not reasonable to expect that unguided chemicals would ever construct a system for translating symbolic information into functional proteins based on stored recipes and a coding convention.
[I realize people have thoughts about what happened earlier (e.g. that might not need proteins, for example) and what happened later (e.g. when a functioning cell provides the full benefits of true Darwinian evolution). For the purposes here, attention is focused specifically on the transition from a universe without symbolic translation to construct proteins to the origin of such a system. Whatever happened earlier or later, sooner or later this bridge would have to be crossed on any path proposed to lead to the cells we see now.]
One of the key considerations leading to this conclusion is that a translation system depends upon multiple components, all of which are needed in order to function.
+ Decoding
At the end, one needs the machinery to implement and apply the code to decode encoded symbolic information into its functional form. (In the cell, this is now the ribosome and supporting machinery and processes, but the first instance need not be identical to the current version.) Without this component, there is no expression of the functional form of what the symbolic information represents. The system as a whole would be useless as a translation system without this. Natural selection could not select for the advantages of beneficial expressed proteins, if the system cannot yet produce any. A DVD without any player might make a spiffy shiny disk, but it would be useless as a carrier of information.
+ Translatable Information Bearing Medium
There must be a medium that is both suitable for holding encoded information and that is compatible with the mechanism for decoding. Every decoding device imposes limitations and requirements. It would be useless to a DVD player if your video was on a USB thumb drive the DVD player could not accept instead of a suitable disk. In the cells we see, this is covered by DNA and ultimately mRNA.
+ Meaningful Information Encoded According to the Same Coding Convention
One obviously needs to have encoded information to decode. Without that, a decoding mechanism is useless for its translation system purpose. If you had blank DVDs or DVDs with randomly encoded gibberish or even DVDs with great high definition movies in the wrong format, the DVD player would not be able to produce meaningful results, and so would have no evolutionary benefit tied to its hypothetical but non-functioning translation abilities. In the cell, this information holds the recipes for functional proteins following the same encoding convention implemented by the ribosome and associated machinery.
+ Encoding Mechanisms
This is perhaps the least obvious component, since the cell does not contain any ability to create a new store of encoded protein recipes from scratch. Indeed, this absence is part of the motivating reasons for the central dogma of molecular biology. Nevertheless, even if this capability has disappeared from view, there would have to be an origin and a source for the meaningful information encoded according to the same coding convention as is used by the decoding component.
(For the moment, I will just note in passing that the idea of starting out with random gibberish and running the system until meaningful recipes are stumbled upon by accident is not a viable proposal.)
So there has to be some source capable of encoding, and this source must use the same coding convention as the decoding component. To have a working, beneficial DVD player, there must also be a way to make a usable DVD.
+ Meaningful Functional Source Material to Represent
It would do absolutely no good to have the entire system in place, if there did not also exist in some form or other a beneficial “something” to represent with all this symbolic capability. If you want to see a movie as output, there needs to be a movie that can be encoded as input. If you want functional proteins as output, there needs to be access to information about proper amino acid sequences for functional proteins that can serve as input. Otherwise, GIGO. Garbage In, Garbage Out. If there is no knowledge of what constitutes a sequence for a functional protein, then the result produced at the end of the line would not be a functional protein.
+ Some Other Way To Make What You Want The System To Produce
If we supposed that the first movie to be encoded onto a DVD came from being played on a DVD player, we would clearly be lost in circular thinking, which does not work as an explanation for origins. Likewise, if the only way to produce functional proteins is to get them by translating encoded protein recipes, that reveals an obvious problem for explaining the origin of that encoded information about functional proteins. How can blind Nature make a system for producing proteins, if there has never yet been any functional proteins in the universe? On the other hand, how does blind Nature discover and use functional proteins without having such a system to make them?
The core problem is that no single part of this system is useful as a translation system component if you don’t have the other parts of the system. There is nowhere for a blind process to start by accident that would be selectable toward building a translation system.
The final killer blow is that chemicals don’t care about this “problem” at all. Chemicals can fully fulfill all the laws of chemistry and physics using lifeless arrangements of matter and energy. Chemicals are not dissatisfied and have no unmet goals. A rock is “content” to be a rock. Likewise for lifeless tars.
The biology of cells needs chemistry, encoded information, and translation, but chemicals do not need encoded information or biology. They aren’t trying to become alive and literally could not care less about building an encoded information translation system.
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I’m hoping ericB will find time to respond to any comments his challenge might elicit.
He has all the ID/creationist talking points down pat; but he doesn’t have a clue what he is saying. He apparently thinks he is being original and that he is not responsible for knowing anything about the science he is “challenging.” I see he is a Hoyle fan.
This is always a peculiar phenomenon to watch. But I’m bored now.
Yes, you have been right about this all along. Creationism and ID are built on top of the Dunning-Kruger effect.
What “non sequitur”? You being a Creationist (of the ID kind, but of course an ID-kind Creationist is still a Creationist), I can see why you might not follow the reasoning, because that reasoning is based on a principle that, while very important to real scientists, is at the same time honored by Creationists rather more in the breach than the observance. That principle is called ‘parsimony’. When you’ve got a theory which adequately explains a given thing (as the mindless, unguided laws of chemistry and physical provide an adequate explanation for the workings of living cells), you don’t spotweld extra crap onto that theory. Since mindless, unguided physics-and-chemistry do such a great job of accounting for the workings of living cells, including their reproduction, invoking
godThe Designer contravenes the principle of parsimony.Given the plain fact that ‘information’ storage in computers is a physical process, which involves fiddling with tiny magnetic domains, I see no reason to think that anything happens inside computers which cannot be described by the boring, mindless laws of physics (with the laws of chemistry being involved to a significantly lesser extent than the laws of physics). Why do you ask?
And here you display yet another Creationist ‘tell’: The arbitrary distinction between ‘origins’ science and ‘operations’ science. Yeah, you ID-pushers aren’t Creationists…
“material processes alone would never create it”: Yes, you have repeated this bald assertion a number of times already. Are you ever going to support said assertion? Or will you, instead, continue to treat it as a locked-in presupposition for which you don’t need to provide any support?
Don’t bullshit us, ericB. You know very well that ID-pushers have disgorged mass quantities of argumentation about what Nature can do in the absence of intervention from
godThe Designer. It’s not that people are assuming that ID posits a supernaturalgodDesigner; rather, it’s that people are paying attention to what ID-pushers say.One more Creationist ‘tell’ to throw on the pile of Creation ‘tells’ you’ve already displayed…
Correction: “apart from artifacts created by biological intelligent agents“. If you know of any “artifacts” of any kind that weren’t created by biological intelligent agents, please clue us all in!
You just can’t stop yourself from leaving a gap in your argumentation that you can fill with your
godDesigner, can you?ericB,
The real ‘motivation’ is the physical nature of the molecules. Protein cannot be readily unfolded at cellular pH, and its amino acid side chains do not lend themselves to serial chemical ‘reading’ the way the base pattern of a single xNA chain does. Even if there were 61 amino acids and 61 used triplets – it’s not a mapping problem. But I think the unidirectionality may be fundamental for another reason: a strong circumstantial pointer to the historic sequence of molecular origins.
No, it doesn’t. The ‘lifeform’ I presented is a fully functional ‘nucleic acid organism’. It has no need of proteins; it gets by perfectly well without them (otherwise it wouldn’t be a fully functional organism). It only has to compete with other xNA life. But if one stumbles across them – by, initially, stumbling across a mechanism for peptide bond formation – and they give it an evolutionary edge, we might expect the xNA organisms to be outcompeted by the protein coders. With hindsight, protein was just what they needed!
This hypothetical nucleic acid organism would have had a genome much like ours. Any triplet in any genome can be interpreted by a triplet-reading system, even if it is there for a completely different reason (taking part in an RNA fold, for example). This genome could be processed by any modern protein coding system (and presumably by any historic one). Among its many random sequences will be sequences that happen to be incorporated into and improve a protein. You only call it ‘encoded’ as a post hoc declaration – if a ‘useful’ protein arises from processing such random sequence, it must have been ‘encoded’? Classic Texas Sharpshooter fallacy.
Well, I hope I didn’t give even the slightest sniff of such teleology in my posts.
Protein, peptide, polypeptide, polyschmeptide … these aren’t hard categories, and they are all made the same way. As I’ve tried to emphasise, you display the common ID perception that ‘protein’ is somehow synonymous with ‘enzyme’. These tend to be large (in modern organisms), and must be repeatably folded, which demands a library of hydrophilic and hydrophobic amino acids in a pattern that is sensitive to disruption. But they are not the sum of useful proteins. Proteins can bind other molecules to neutralise, mask or transport them, they can act as structural components, or affect osmotic pressure … take your pick. Not all of these functions need a large library of acids, nor a large peptide molecule, nor tight specificity. The origin of protein coding is not (necessarily) the origin of enzymes.
Enzymes do require their own explanation, of course. But they are modular. The same motifs appear again and again. Encountering one useful structure – a small fold, for instance – provides the raw material for others. Finding a rich proteome all mining an arcane corner of protein space would be a surprise if there were no mechanism by which protein coding sequence could be duplicated and shuffled. With such a mechanism – common descent at the subgenome level – it’s pretty obvious why such proteins might conform to a set of common patterns. Getting a toehold in this space might be an issue – but one needs a good reason to set the lower limit of acid library and length at particular values. 20 acids and hundreds of residues in modern proteins is not a good reason.
Sorry Eric, but I think you are departing from the terms of the challenge. You wanted an ‘in-principle’ origin of protein coding, and were prepared to make concessions as to precursors such as RNA and DNA. Yet now you object to this ‘in-principle’ scenario because Real Ribosomes Are Big! What can I say? Ribosomes are composed of several subunits, and those subunits themselves reveal, on phylogenetic analysis, serial accumulation and agglomeration of function. You’ll be asking me to make an RNA organism next! There is no in-principle problem with small ribosomes with reduced function. There might be an in-practice one, but you can’t just rule it out due to lack of an actual working example.
The chemistry that requires no real code is the source of the code, so while you might wish to bundle it out the door, it is entirely germane. A system that, on encountering a particular nucleic acid triplet, peptide-bonds a particular amino acid to an exposed N terminus will, when it encounters that triplet, peptide-bond that amino acid to said exposed N terminus. In random RNA, each triplet occurs in 1/64th of the positions on average. It does not need to be put there. [eta: this does, of course, require some mechanism of boxing off the genome such that only the translation you want actually occurs]
Well, funnily enough I have given this some thought (though note my comments above: the origin of protein coding is not necessarily the origin of folded enzymes). If you find time, this may help flesh out my view on the commonly asserted position that function is vanishingly rare in protein space, and that folding is a problem that has to be solved afresh for each new enzyme. It’s long, and it’s a response to vjtorley (hardly economical with words himself 🙂 ) in response to an earlier piece of mine. The significant part lies in the section headed “the relevance of synthetic peptides”.
Regards
I assume your view is that protein space is not necessarily sparse in potentially functional proteins. I don’t know if you spotted a thread at Uncommon Descent where Kirk Durston responds to queries in the comments. Here and onwards.
I wonder if a topic on how rare functional proteins might be as a fraction of all possible theoretical proteins (and how we might demonstrate it rather than assume it) would make a good thread topic. Probably needs a snappier title.
Unsnappy titles are kind of my thing.
My view is that the corner of protein space occupied by functional folded enzymes is explorable by a mechanism that is penalised when it goes outside it. And that gaining a toehold in that space is possible with a catalyst much smaller than a modern one. And … yeah, I have a problem with unsnappy prose too. 🙂
Demonstrations of the functional richness of protein space are legion. How many papers one has to adduce in support of that basic assertion may, of course, be up for grabs. Which renders it tricky, as an assignment. Go for overkill? Do one to death?
Sounds great. Let’s give Axe, Durston and Gauger something to think about! 🙂
Regarding papers, would you be thinking of Szostak, The Hecht Lab, Janet Thornton?
This post may be of interest to any who hold out faith and hope that “Science” will eventually come to the rescue, i.e. that the enterprise of Science can be counted on to eventually vindicate their expectation for a law+chance explanation for the translation system.
This is incorrect in at least two respects.
1. I’ve been consistent in pointing out that an inference to intelligence for the translation system does not directly imply that the intelligence is God or even supernatural. For instance, I gave the example of Sir Fred Hoyle. I don’t endorse or agree with his position, but the relevant point is that he and others infer intelligent design and yet do not infer that the intelligence was God. See also Fred Hoyle – An Atheist for ID.
Therefore, even if one thinks this is a “gap” argument, it would still be incorrect to call it God-of-the-gaps. To think clearly, one must recognize that ID is inference to intelligent design. Anything else is a confusion of concepts.
2. I’ve also been consistent in pointing out that it would never be sufficient to merely argue from ignorance or just from the fact that “we don’t currently have any well-supported answers.”
Rather, it is based on the undeniable fact that there exists a nonempty set of Artificial objects whose observed properties are such that they cannot be reasonably explained as the result of undirected natural processes. What is needed, as I’ve pointed out and as cubist nearly described, is to have reasons based on what we know for thinking that the translation system is beyond what we can reasonably expect from unguided chemicals. In other words, is the translation system itself a member of the nonempty set of detectably Artificial objects?
The problem is that we do know much about chemicals that conflicts with the idea that they would undertake to build a translation system. The point of this challenge is to highlight that fact and the inability to even construct a hypothetical scenario that explains how and why unguided chemicals would do such a thing — without obviously conflicting with what we already know about chemicals.
It’s not possible to understand the issue when conceived of in these terms. The relevant distinction is between the Artificial and the Natural (i.e. what can be produced by the law+chance natural processes alone, without any guidance from intelligent direction).
The great success that the enterprise of Science has had depends upon at least two foundational features of that enterprise.
1. Science as an enterprise succeeds because it is willing to abandon ideas that fail.
Therefore, it does no good to appeal to the success of Science (the enterprise) to defend any particular claim or hypothesis. That idea may be trashed, even while the enterprise of Science succeeds by abandoning the failed idea.
The idea that unguided chemicals can reasonably be expected to produce a translation system that created coded instructions for generating functional proteins can certainly fail — provided it is treated as a hypothesis, rather than a dogma. Science can go on successfully, even while the failed idea is abandoned.
2. Science as an enterprise has succeeded because and only because it has never undertaken to explain the Artificial as the result of natural law+chance.
Throughout the history of Science, we have no examples of ever being able to explain artificial objects as the result of natural law + chance. We don’t consider that a “failure” for Science because no one thinks it is reasonable to even expect natural law+chance to account for such things. No one expects the processes of geology to explain a Rosetta stone or the pyramids. No one expects chemistry to explain the origin of cave drawings.
The point here is that throughout the history of Science, it has always been “a useful and productive” policy to distinguish between Artificial and Natural. Scientists handle each by different methods. Science succeeds and proceeds effectively when we use the appropriate methods for each type of object.
Notice in particular that encoded information is exactly one of those features that has never been successfully attributed to natural law+chance. Thus, the weight of historic precedent is in favor of the hypothesis that encoded specifications for proteins that must be translated via a code are in fact another case of the Artificial.
Thus, if I am correct in saying that the translation system is Artificial, that does not in any way mean that Science has failed. Notice also that it does not even mean that the enterprise of Science needs to be radically changed to accommodate that realization. Science already has ways of dealing with the Artificial.
Coming to the conclusion that the translation system is Artificial only means that it is fruitless to try to explain the Artificial through law+chance (as we are seeing), and that Science needs to employ its standard methods for dealing with the Artificial.
Your original premise that cells use “encoded symbolic information” has not been established. As such every other inference you draw from your assumed but not demonstrated premise may be ignored.
Sure, but you’re either deluded or lying about the logical implication of a designer origin for Earth’s DNA-RNA translation. Even you, as illogical as you are, have to admit that the origin of translation was not intended/designed/guided by a natural intelligence which had already arisen within our planetary system, because there was no such intelligence here, not 3billion years ago. Ah, but, you sputter, what about something from space, what about natural aliens?
Don’t be more of a fool than you have to be.
Natural aliens from space leave you with the exact same problem just at one remove. Where did their necessary intelligence come from? Are they an alien lifeform, not like us of course, but recognizably “life”? In which case, how did their exobiological reproduction arise in the course of their life’s evolution in their original home solar system? What’s their exobiological-information-storage translation systme? Did that evolve naturally and unguided in accordance with physics, chemistry, and chance – or was it designed? Okay then, who was their designer? Do you really think their designer was yet another natural, not supernatural, alien kind? Okay then, where did that prior non-supernatural designer come from? Who designed them?
Remember, you can’t have an infinite regress. Not in this real universe. We only have a fourteen or so billion year span. There’s a limit.
At one remove, or at two, you have to admit that the hypothetical natural (alien) designing species themselves evolved naturally [without intention/guidance/design by some pre-existing “natural designer”] from non-life in their home solar system. At some point that logically had to have happened, absolutely must have happened, because there simply could not have been any previously-existing natural lifeform which could design and implement the very first life form in the universe, wherever that might have arisen.
It’s a simple fact.
You can obfuscate, you can claim that’s not the scope of your challenge, you can cry “Hoyle, Hoyle” as much as you want. Won’t change the simple fact. The only way you can escape is to admit that you need a supernatural designer to step in at some point in time.
When you’re honest enough to admit that, we can see if there’s anything left worth discussing in your dishonest “challenge”.
Oh, yeah? This should be good…
The former does not directly imply the latter, no. Are you stupid or ignorant enough to think that there is no such thing as indirect implication? Or do you merely think everyone else is that stupid or ignorant? Look: According to you, this Designer thingie is capable of feats which are just plain impossible for ‘unguided Nature’ to accomplish… so how the pluperfect hell can this Designer thingie of yours not be ‘supernatural’?
Which neatly explains why ID-pushers give talks in churches, not in scientific conferences; and why ID-pushers don’t even publish ID-supportive papers in ID-friendly journals…
Oh… wait. it doesn’t explain that at all. Quite the opposite, in fact. Feel free to stop bullshitting at any time, ericB.
Bullshit. First off, it’s not just that people “think” it’s a gap argument; it damn well is a gap argument. And the essence of a God-of-the-Gaps argument is exactly and precisely “I don’t know, therefore [my favorite cause-of-choice]”. Which is exactly and precisely what your argument is, for cryin’ out loud!
Second off, while it may be true that you generally haven’t used the word ‘god’, the God-of-the-Gaps argument isn’t about the presence or absence of any specific character-string(s).
Bullshit. Now, I can certainly conceive of an “ID” which genuinely is the disinterested scientific study of intelligent design… but that ain’t the “ID” which actually exists and is being pushed by the Discovery Institute. The “ID” which actually exists, the “ID” in support of which the lying pseudo-documentary Expelled: No Intelligence Allowed was made, is exactly and precisely a wholly-owned subsidiary of good old Creationism
Which is exactly and precisely why your ID-pushing arguments, which are exactly and precisely arguing from ignorance on the exact and precise grounds that “we don’t currently have any well-supported answers”, are not sufficient.
I don’t believe anyone has disputed the existence of such a class of entities. The question is whether or not the ‘translation system’ actually is a member of that class. You ever gonna get around to demonstrating that the ‘translation system is one of those ‘Artificial objects’ you speak of, as opposed to asserting that it is on the basis of your multiply-repeated
god-Designer-of-the-gaps argument?Yes. Those ‘reasons’ you speak of are, indeed, needed, and the reason why they’re needed is because there are no such ‘reasons’.
That is, indeed, the question. Good on you for recognizing it! Not-so-good on you for relying exclusively on fallacious bullshit in ‘support’ of your chosen answer to this question.
Bullshit.
Oh, fuck off. You were presented with exactly and precisely a ‘hypothetical scenario’ for how the ‘translation system could arise, and you rejected it out of hand for bullshit non-reasons.
Yeah, you’re not arguing that Intelligence is supernatural, not in the least…
Yep. And this is why Creationism (ID included), which is flatly incapable of abandoning the failed idea of a ‘Creator’, is not science.
Now, what is the scientific theory of Intelligent Design, and how can we use the scientific method to test this theory?
Alan Fox:
Indeed. And the many things one can access simply through Googling such terms as “artificial protein function”. (Proper scientists tend to use more sophisticated literature searches, of course! 🙂 And they don’t bias their literature towards the free-online end of the market)
That Fisher/McKinley/Bradley/Viola/Hecht paper popped up from such a search. One has to winnow such lists to take out those proteins that were designed in their entirety. But I suspect IDers would insist that we winnowed out all papers that had any design in ’em! Leaving us with little as a direct demonstration of The Random Generation of Function. This is simply practicality. My Fisher paper, for example, generated random structures on a 14-residue repeating pattern. This pattern was itself pretty loose, but did ensure folding. So the ID-er will shout “Cheat!. Not random enough”. How random is ‘enough’? For my money, the ability of a restrictive algorithm to generate a theme, variations on which provide 4 different replacement functions in a modern cell, is testament to the ability of randomness to shake out functional novelty from the neighbouring search space. The functional assay meant that search space target density was experimentally restricted by the need to find analogues of tuned modern proteins. But they still succeeded. Early protein coders had no such restriction, which give grounds to think their search space may have been substantially more densely functional then. ‘No worse than the competition’ is the key criterion.
I’m particularly interested in the role of recombination. One worker (can’t find the paper at the mo) devised a method to join the exposed C and N termini of a peptide and create new ones by specific hydrolysis elsewhere within the sequence. Not a single acid was changed, just 2 linkages, but clearly this changes the restraints involved in folding. This would be a pointless thing to do if the result was a denatured, nonfunctional protein – there are much less sophisticated methods available for denaturing protein in any kitchen. But contrary to ID intuition, it produces different functional products a significant proportion of the time. Try doing that with a jumbo jet!
ericB,
But for the fact that arguing on the internet is a voluntary activity I undertake for my own entertainment, I might find that a little frustrating! I thought I had explained how and why unguided chemicals might do such a thing. I do not claim to have offered the answer, but an answer … it does not obviously conflict with what we know about chemicals, and codes, as far as I ever understood those things in my pursuit of qualifications and a job. To the extent which it does, you have not clearly articulated why. Conforming to the constraints implied by the data, rather than sweeping them under the carpet, is kind of the point of scientific model-building.
I may not have spelled it all out in painful detail, but I’ve accounted for the role of energy, the directionality of the system, a plausible sequence in which coded peptide synthesis arises from noncoded peptide synthesis, potential functions available to a system with an initially limited amino acid alphabet and poor control of specificity, and the capacity of this system to subdivide the triplet set in a manner that gradually replaces STOPs with acids (there much less constraint in that direction than the reverse, for reasons one can mathematically defend), and/or subdivides degenerate codon groups between two chemically similar acids (there is much less selective restraint against that than against chemical dissimilarity of substitutions), but suffers a gradually increasing restraint on any further evolution. The question is not what motivates chemistry to evolve a system, but what motivates life.
So you are saying “the two things [the computer that beats the master chess player by executing a look ahead algorithm to evaluate future positions and the consequences of different moves, and (emphasis added) “mindless chemicals that only respond to the current situation according to material laws and chance”] are not distinct at all”?
You really think this? Not distinct at all?
Should I conclude you believe all chemicals execute look ahead algorithms before making their next move? Or should I conclude that you think computers do not do this (since they are made of chemicals)? Or should I conclude you think that whether chemicals do this or not makes no difference at all and therefore they are “not distinct at all”?
You say, “They are merely two different ways of conceptualizing.” So, should I conclude there is no point in manufacturing computers and programming them, and we could save a lot of money since they are “not distinct at all” from other far less expensive chemical objects in how they behave? We only need to conceptualize the less expensive chemical objects differently?
If all chemicals employ look ahead algorithms to decide how they will behave, that would be interesting news indeed. Or if none do, that would be equally interesting. But I confess I don’t know how to make relevant applicable sense out of your stated claim that…
When you have clarified that, please be sure to clearly indicate whether or not you are claiming that prebiotic chemicals could have employed look ahead algorithms to aid them in building a translation system based on the future consequences of their present interactions. That is obviously quite relevant to the current challenge.
Once again, your initial premise that DNA is “a system for translating symbolic information into functional proteins based on stored recipes and a coding convention.” is an unsupported assertion. There is no “symbolic” information anywhere in the process. Codons to not “symbolically represent” functional proteins. They are just a step in an ongoing complex chemical process that results in functional proteins.
Your initial premise is not supported so all of your subsequent inferences are meaningless.
Is that really so hard a concept to grasp?
If you thought that I was comparing computation to chemistry, then you missed the point entirely.
When we describe what happens in a computer with the terminology of computation (algorithms, logic, etc), we are using teleological language to describe. We can, alternatively, describe with a mechanical language, where we would use terms such as “electrical charge”, “current”, “resistance”, “magnetic field”. Both teleological language and mechanical language can be used to describe the same thing.
Your whole argument amounts to describing biology with teleological language, and then saying that mechanism can’t do it. It’s an absurd argument. Describe what happens in mechanical language, and then you might have a basis for determining whether mechanism can do it.
If you are going to insist on teleological language, then you are probably right, that an intelligent agent is required. But the only intelligent agent required is you, to form that description in teleological language. It is your choice to interpret what is happening as a translation system. Looked at mechanically, we don’t see a translation system. We see mechanical operations that you are choosing to interpret as translation.
There’s nothing wrong with teleological language, provided that you understand its limitations. Our description of computers is heavily based on teleological language. Yet we can build computers out of entirely mechanical systems and mechanical operations. The kind of argument that you are pushing — mechanism can’t do teleology – should imply that computers cannot exist. Yet they do.
I genuinely appreciate that you are a rare exception (one of only two) who has actually undertaken to provide a proposal for the challenge. I doubly appreciate that your posts are among those that have a commendably high light to heat ratio.
Please keep in mind that with the limited snatches of time that I have, I am often not caught up on reading through and responding to the posts.
I will point out one possible misunderstanding on your part that may help. The challenge that has been presented is not “… what motivates life.” Rather, “The question is … what motivates chemistry to evolve a [translation] system.”
If you miss this foundational point, even if you succeeded completely in providing a finely detailed explanation for the origin of a kind of “life” that did not require a translation system, by itself that would still be an epic fail with regard to this challenge. I’m not asking for the origin of “life”. I am asking about the origin of a translation system.
(As a side point in passing, to the extent you were to succeed in defending the plausibility of a kind of “life” without translation and codes, you would in fact be simultaneously cutting the ground out from under all of those who want to deny even the logical possibility of a natural undesigned designer that could have preceded our own translation-based form of life. I wonder if they have noticed this.)
The challenge is tied to the claim that the translation system is Artificial, i.e. not reasonably attributable to an origin by unguided chemicals acting only according to natural law + chance. Therefore, for obvious reasons, the primary scrutiny of proposed natural scenarios must be upon the steps leading to the translation system itself.
If your proposal takes key steps for granted, or vaguely hand waves away difficulties of the kinds I’ve already identified, those are the points of failure to meet the challenge that must be examined. When you see the nature of the challenge, it’s plain why those steps are the crucial considerations, regardless of how much detail you have provided for the scenarios that don’t involve translation or codes at all.
There have had some pretty direct answers that you have apparently been avoiding because you won’t even look, let alone try.
There is that little high school physics/chemistry calculation that scales up the charge-to-mass ratios of protons and electrons to kilogram-sized masses separated by distances on the order of a meter.
There is this video that lays out a specific and very important mechanism that has been actually observed.
And there are Allan’s very explicit examples which you apparently haven’t read or understood.
You are still demanding that others explain away a “problem” that arises because of your misconceptions and misrepresentations that follow from your insistence on reifying a metaphor.
Nobody in the scientific community is obligated to explain things that don’t exist in nature. Try addressing a real problem; and stop ignoring the answers you have been provided.
Perhaps more than a few would benefit from clearing up a possible misunderstanding.
Sorry, but that is not correct. I’ve never said or claimed anything like the idea that mechanisms cannot execute algorithms. For example, consider Babbage’s engines. One can even Google and find articles on an implementation of the difference engine made out of LEGO parts (YouTube). One could consider further the generalized concept of a Turing machine.
You are mixing two distinct claims, one false and one true.
Possible Claim #1: Mechanisms cannot be arranged to perform algorithms (i.e. to “do teleology” in the sense that computers routinely “do teleology”).
This is the version that “should imply that computers cannot exist. Yet they do.” This is obviously a false claim. Obviously intelligent hardware designers and programmers (including Ada Lovelace) can so arrange materials such that they will perform in this manner. NOTE: All such arranging of material substances by intelligent agents is Artificial.
Possible Claim #2: Unguided chemicals cannot be reasonably expected to arrange themselves into configurations that will execute a translation system (i.e. to “do teleology” in the sense of creating such a translation system where no such system existed before — something that designers can do when they “do teleogy“).
If unguided chemicals could do this without intelligent direction, that would meet the challenge that has been set. (Side note to cubist, et al: cellular reproduction obviously cannot be used to explain the origin of the translation system without reasoning in a circle.)
It does not matter what language you use to describe the system. You can change the labels and it will still perform translation regardless. The stored specification in DNA is converted via a code to realized functional proteins. It happens.
Notice that nothing in the challenge depends at all on denying that the cell is “mechanical” in its operation, just as you could call a computer “mechanical”. There is no issue at all regarding the material it is made out of or the fact it operates according to the laws of chemistry and physics. For that matter, the challenge does not require that materialism is false, which would imply everything can be conceptualized mechanically/materially.
That said, notice that a pile of sand is silicon just as a circuit can be made of silicon and both operate according to the laws of chemistry and physics. Yet, everyone realizes it would be silly to claim that the computer and the sand are not distinct at all. Or that they are merely two different ways of conceptualizing. Something relevant to its function is true about the computer that is not true about the sand.
Nor do I think anyone would consider it reasonable to attribute the origin of silicon based computer circuits to the explanation that it is “just silicon” and that sand operating according to the laws of chemistry and physics would explain the origin of the computer without intelligent agency.
Therefore, if we can agree that such ideas are truly silly, there is then a real and legitimate question. Is it reasonable that prebiotic chemicals would create a translation system (however described or conceptualized) without the help of intelligence that can anticipate and build toward future benefits?
There is also this housekeeping question: Does anyone believe that the prebiotic chemicals could execute any kind of look ahead algorithm (however described or conceptualized) to help them build the system in light of the future consequences of present actions?
Nobody is obligated to explain things that go on in your imagination.
It is not possible to explain chemistry and physics to someone who refuses to learn.
Why are you avoiding the real science?
When do you think you will get around to looking at what people here have already pointed out to you?
Now, all we need is a definition of “intelligent direction.” Perhaps you will surprise us. My experience is that ID proponents are never clear on what they mean by intelligent.
Unguided air molecules will never form themselves into a tornado. Yet we have tornados occurring naturally with some frequency. There are natural feedback systems that provide the “guidance” that makes tornados possible. Can we say that those are intelligent?
There are lots of natural systems that provide various kinds of “guidance”. I put “guidance” in quotes because it is a teleological term. You seem to be insisting on a mechanical (non-teleological) account of how there could be a translation system, when the whole idea of a translations system is teleological.
Honest scientific discussion requires clear definitions. If you want to use the word “intelligent” in a scientific discussion, then we need that word to be clearly defined with enough precision that there is no ambiguity.
For all those who question whether a material object or system (e.g. a cell) can meaningfully be considered to process information…
The non sequitur is this. There is nothing about the nature of a system that processes information that implies that the system “cannot be described by the boring, mindless laws of chemistry and physics”. Let’s put it into the obvious reductio ad absurdum that all materialists should appreciate.
So, will materialists accept the conclusion and deny the reality of information and of systems that actually hold and process information? Or will they reject the conclusion? If they reject the conclusion, how many guesses are needed about which premise they will also reject?
I ask because you have just undermined the claim in your own non sequitur. You have just acknowledged that a system can indeed hold and process information and yet this does not in any way lead to the conclusion “that ‘information’ can and should affect the internal working … in ways which cannot be described by the boring, mindless laws of chemistry and physics.”
Reminder to all materialists:
The challenge does not require you to assume that materialism is false. Nothing in the challenge would change if it were the case that materialism is true.
The fundamental reality that the challenge depends upon is simply this. There obviously exists a nonempty set of Artificial objects and systems whose origin cannot be reasonably attributed to undirected natural processes.
Therefore, it is reasonable and meaningful to consider whether the process by which stored DNA specifications are translated via a code into functional proteins is such a system.
Whether materialism is true or not, the very same issue remains.
Good grief; just look at the Gish Gallop!
This kid hasn’t even had a middle school science course.
ericB:
Cheers! This is, as I’ve said, a leisure activity, and people are always at liberty to disagree, even for reasons I find unsatisfactory. I react to goading like most people, but that’s a different issue. Ultimately, you are judge and jury on your own challenge, so I will be neither surprised nor upset if you don’t find my proposal satisfactory!
Well, from where I sit, what motivates Chemistry to produce a translation system is Life. Life (as I’ve defined it: iterated replication) is a means, the only means so far proposed, by which raw unguided chemistry can come to produce such highly complicated structures and processes. By setting up a competition between replicating entities in a finite world, improvement in replicating capacity is guaranteed provided there is a pathway to it. And this is the way I have framed my answer. I start with replicating entities without coded phenotypes, and propose advantages for the serial establishment of the steps of protein coding. Without replication, it doesn’t work. Unless you are in competition, just keep doing what you’re doing.
Of course. I’m surprised you read my answers in that way. I haven’t offered an explanation of the origin of Life (my pre-protein replicating entities). I have offered an explanation as to how such replicating systems may have come to possess a multi-acid codon-mapped translation system. If we are at cross-purposes about What Is Life, I can only ask you to be clear in understanding that when I talk about it, I mean (as a minimal definition) replicating chemical systems, not any of the other things they may do – being cellular, metabolising, gathering energy, excreting, synthesising molecules of type X, Y or Z etc.
I don’t think so. If one is inclined towards denying the role of a designer, there is IMO sufficient warrant in the facts of nucleic acid chemistry to support that – ribozymes provide an uncoded phenotype that is still in use today, quite centrally in protein translation: tRNA, rRNA, and all the other RNA’s, are uncoded. OK, you might argue, they are ‘differently encoded’. Either way, similar arguments can be brought to bear. I should emphasise that I don’t go out of my way to shut the door on the design hypothesis, but I find that the difficulties presented with the ‘natural’ hypothesis can be frequently surmounted.
In the context of talking of hypothetical events some 3.5 billion years in the past, I don’t think I’ve been all that vague or hand-wavy! 🙂 (There is an obvious counterpoint to mention in passing regarding the specific activity of a Designer in any alternative hypothesis.)
But you have been a little vague there yourself. What things have I taken for granted (other than the existence of a noncoding nucleic acid replicator); what difficulties have I handwaved away (other than my contention that a proto-ribosome does not have to be large or multifunctional to do something useful in a cell)?
I certainly don’t deny that there can be other reasons why going from a realized protein structure to an encoded recipe is implausible. I wasn’t intending to impose those obstacles as an assumption (since someone might want to argue in favor of that idea), but if you acknowledge those obstacles yourself, I certainly do not object.
[BTW, the mapping problem I alluded to is not about the need to fill up all 64 possible triplet combinations, but rather the point that others have made that there can be multiple different codons representing one amino acid. Many to one decoding is not a problem, but an encoding mechanism that goes from one to many raises certain difficulties. However that may be, your additional points about the implausibility are well taken.]
You just misunderstood my point is all. I wasn’t saying proteins are needed in the ‘lifeform’ you presented. I was referring in the context of the actual challenge to the requirement of explaining the existence of a populated store of meaningful recipes for functional proteins. Until you can do that without hand waving or unwarranted leaping assumptions, you have not accounted for the translation system and you have not met the challenge.
By acknowledging the implausibility of an encoding process (cf. previous point), you have cut off one theoretical avenue for populating the store of meaningful recipes. Consequently, you have made the store of recipes strictly upstream from the existence of any decoding engine or of the existence of any realized protein products.
Yet we do find that coding DNA does store recipes that — when interpreted according to the coding conventions used downstream by the decoder — do translate into functional proteins with stable structures and effective properties. As I said, it exists.
So part of the challenge is to show that this is reasonable to expect from mindless chemicals. If we are starting from a system that has no need for proteins and sequences that have no intentional relationship to a specification for a stable, functional protein, how and why does there come to be translation at all, rather than something that never utilizes translation to create proteins?
Here is an example of an implicit unwarranted leap in a crucial required aspect.
I don’t mean simply that you suppose chemicals “initially, stumbling across a mechanism for peptide bond formation”, if by “mechanism” you simply mean that sometimes peptide bonds may form between amino acids. Let’s assume for the present that happens. But you go on to reference “the protein coders” as having “an evolutionary edge” over merely “xNA organisms”.
Obviously, how there comes to be “protein coders” at all is at the very heart of the challenge. It would be illegitimate to just assume they come along in some unspecified way and thereby compete at an advantage.
For an organism to gain a consistent advantage from proteins, it would need to have a consistent way of producing the proteins. If this is because the system has learned how to store a coded recipe that is decoded into a protein, you’ve assumed the very thing you were challenged to explain. On the other hand, if you are not assuming this, then how do you propose the system stumbles upon a “mechanism” that consistently produces for the system those proteins which give it an advantage in the competition?
Here again you make the unwarranted leap of just supposing “a triplet-reading system”. There is no need to read any “triplets” in order for an RNA sequence to fold. The fold makes no consideration of “triplets” as such. Even granting a “genome” (a leap we will pass over for the present, provided you are not assuming any “coding” regions in the genome), a transcription process could make RNA transcripts suitable for folding with no consideration of “triplets” or any “triplet-reading system”.
Except that it is illegitimate to merely presume that even “any historical” “protein coding system” exists. That is, after all, at the very heart of the challenge itself.
This is certainly false so long as you do not yet have a working system for converting transcripts from the “genome” into candidate proteins. Again, your logic assumes you already have the vital components that you were challenged to justify.
If you assume that chemicals will build your “historical” “protein coding system” for the sake of the competitive evolutionary benefit that will accrue from the future proteins and future improved proteins, then you would be making that very assumption. As it is, you have been assuming such a reading-and-translation protein coding system will appear without any justifying explanation at all. So the question is whether you can provide suitable justification without falling into those teleological assumptions.
They could be made the same way, once you have your “historical” “protein coding system”. But unless and until you do, what then?
I’ve never maintained that all proteins are enzymes or that all enzymes are proteins, so your assumption in that regard is false.
That said, regarding enzymes I’m glad you acknowledge the size, the need for a repeatable fold, and the sensitivity of the amino acid pattern to disruption.
What I have pointed out is that enzymes are vital for harnessing energy and converting it to useful work for chemical transformations that would otherwise be inaccessible and uphill thermodynamically. If you are proposing to build even your “historical” “protein coding system”, you will need appropriate enzymes to pull that off, as I pointed out among the obstacles.
Therefore, the origin of protein coding is necessarily intertwined with the origin of enzymes.
First, I see that I was not clear enough and you have misunderstood my objection. Sorry about that. When I objected to just assuming “a smaller version of the ribosome”, my reason was not because “Real Ribosomes Are Big!” (so that a smaller one would supposedly not work). No, rather my objection was and is to the idea of just merely assuming any ribosome at all, regardless of size.
Simply shrinking the size of the ribosome does not establish a justification for thinking that any ribosome at all would ever be made. If one is supposing an organism that has no proteins and doesn’t need proteins, that is all the more reason to question the mere assumption of creating any ribosome to make proteins, especially when there does not exist anything for the ribosome to work on other than sequences that are not encoded for protein expression.
The only thing approaching a chemical justification that you’ve provided is the idea that proteins could confer an evolutionary advantage — something only seen in hindsight. So how does hindsight promote the creation of a ribosome, or even of the enzymes that would be needed to build a working system with any ribosome?
Second, I am not at all departing from any of the terms of the challenge, which have been explained here and at UD.
Both at UD and here, I have granted the assumption of the existence of RNA and/or DNA as mediums that would be capable of holding symbolic information. Creating the physical medium for information is not the issue and I don’t want to get sidetracked by irrelevant chemical issues about natural production of DNA or RNA.
However, I’ve also been clear that this does not mean one can merely assume that the DNA or RNA has whatever sequence of nucleotides one may need.
That includes assuming any kind of sequenced enzyme one needs. As you pointed out, they tend to be large and sequence is important. That is a lot of assuming for something that will contribute toward something (a working ribosome) that could make something (“Protein, peptide, polypeptide, polyschmeptide”) that at best would be based on the translation of an effectively random sequence with the eventual possibility that something might have a evolutionary advantage — that is seen in hindsight.
I’m not objecting to the size or the reduced function, per se. I’m objecting to the complete lack of justification for merely assuming any ribosome at all.
Describing how the system would work, once it is created, is not a justification for the implied claim that it would be created at all. Earlier you assumed a triplet reading mechanism in an organism that had no need to consider xNA sequences in triplets. Here you merely assume a system for reading an extended sequence of nucleotides as triplets while inducing a corresponding extension of a polypeptide. That’s simply a description of what a ribosome does. Again, no warrant for its origin is given.
Description is not justification of origin.
In short, when it comes to the core of the challenge, you’ve been assuming the very points you need to justify in order to actually meet the challenge.
That said, I still respect the fact that you are participating and doing so in a courteous manner. I thank you for your posts. Exchanges would be better if more would follow your example.
Best to you.
I’ve written a detailed response to your detailed response. Unfortunately, it appears that the result was long enough that it is being held “awaiting moderation.” So I don’t know when it will appear.
If need be, I could always break it into smaller pieces, but I don’t want to redundantly post it, if the original will be coming out soon. Perhaps in the future I can be more careful about that. I’m new here, so I’m not familiar with how this should go. I appreciate your patience with this newbie on the site.
EricB, I noticed this turd of yours.
Allan Miller and I are not in disagreement with each other. That you have to dishonestly pretend we are, in order to stir your shit, just demonstrates how weak your position is in reality.
I completely agree with Allan Miller that natural unguided/undesigned chemistry is sufficient to explain a simple kind of life as he defines “life” arising. Then, theoretically, becoming more complex as replication-wiith-better-fidelity from not-fully-featured-translation-system overtakes replication-with-low-fidelity from no-translation-system.
Your fault is in pretending that those simple lives upon which Allan and I agree could in by any possible stretch of your imagination be the Natural Designer of a more-complex translation system. They absolutely could not have been capable of that, neither their own deliberate self modification (how would that work, even in your imagination, much less in physical reality?) nor planning or scheming or hoping for their descendants’ improvements. No minds, no fingers, no way to desire, no way to physically implement – it is simply a fact that those lives could not be your Designer.
And if you’re going to pretend that it’s possible that simplest early life just got more and more complicated (but without naturally evolving a more-fit higher-fidelity translation system from its original not-very-fit not-very-capable translation system such as Allan Miller describes), developed the intention to design and the physical means to execute its designs, and then one day woke up and said “what we’re missing is a modern genetic translation system, we need to design a translation system and then we need to go back in time and insert it into the LUCA” so that it will be functioning for the next 3billion years of evolution. Well then, you’re not just dishonest, you’re addled.
You might be able to get away with such turds around the fanbois at UD who slobber over your illogical fantasies, but you won’t get away with it here.
That is the point of error in your reasoning.
I’ve claimed the translation system (codons-to-proteins) is a member of the nonempty set of Artificial objects and systems. It cannot be reasonably attributed to unguided natural processes.
I haven’t claimed that such a translation system is essential to anything called “life”. In fact, Allan Miller has been building a case for the plausibility of a kind of “life” that does not need proteins or codes or translation. So if you think this is impossible, you and he need to work that out. (I’ll watch, preferably with popcorn.)
If there can be a kind of material “life” that doesn’t need a translation system, are you prepared to prove that it could not possibly evolve without having a translation system?
If that type of “life” could evolve without a translation system, are you prepared to prove that it could not at some point gain intelligence?
If that type of “life” could gain intelligence, are you prepared to prove that it could not design the type of life we see?
I don’t believe this is what happened and I’m not defending it as the truth. However, I am pointing out what Hoyle and others have already pointed out, i.e. the concept of a designer does not automatically imply the supernatural, even if one rules out an infinite regression.
[As an aside, I’ve encountered those who avoid God as the designer by appealing to the infinite regression of a loop in time. I don’t buy that, but I mention as another position that some have advocated.]
Therefore, the claim that an undesigned designer automatically implies the supernatural is simply false.
*One type of evidence or “signature” of design would be the presence of dependence on systems that are Artificial and therefore require design, e.g. a translation system.
As I’ve said, nothing in the challenge changes at all even if one supposes that materialism is true.
Released. Sorry about not noticing this earlier.
I didn’t see this response of yours until after my last post.
I agree that what you describe is not coherent. However, that isn’t what Dawkins or Hoyle or anyone else that I know of would claim. They aren’t suggesting anything as bizarre as “then we need to go back in time and insert it into the LUCA” so that it will be functioning for the next 3billion years of evolution.”
What they are describing is that some other form of life created the life we see (at least the LUCA) as an artificial life form. No time travel involved.
Even now, humans are advancing toward the point of being able to create artificially designed life forms, as Craig Ventor et al are doing. Obviously, the day may come when we could potentially plant those life forms in some world. Nothing you’ve offered excludes the possibility that our biology is itself the result of such a process by some other intelligence.
This doesn’t even need to assume that a natural designer started out with exactly the same scenario that Allan Miller has proposed. The point of my reference is to show the error in thinking, “if you don’t have translation, then you can’t have life.” If that were true, then Allan Miller’s proposal fails since it could not get started.
BTW, Allan Miller is not claiming that his precursor form of life depends on having a weak or low fidelity or early translation system. (If he did, his position would fail immediately for a question begging, circular dependence.) His point is that you can have something that is justifiably called “life” even with no translation system at all. The addition of translation would be a later development.
So, if it is true — as Allan Miller claims — that you can have something that is justifiably called “life” even with no translation system at all, your argument against even the logical possibility of what Dawkins or Hoyle or others have described falls apart.
You seem to be missing the fact that every intelligent agent is able to do this, including humans.
Yep, sez you. With zero evidence. And with a theistic bias that you only pretend to rise above.
To hell with your popcorn and your shit-stirring, both.
You wrote that before I refuted your similar turd just above, and I’m not too proud to repeat myself. Allan Miller and I agree on the plausibility of “life” that did not have translation/codons as it first arose in its simplest possible form. Your dishonesty is in pretending that I reject any simple form of life when what I specifically rejected is your putative (alien) form of life complex enough to Design Life without themselves having evolved naturally/unguided/undesigned on its home planet from its own simpler precursors
To hell with that nonsense. If it’s your claim that it could, provide evidence. It’s nonsense to pretend that it’s my job to prove a negative “that it could not”.
To hell with that nonsense. If it’s your claim that it could, provide evidence. It’s nonsense to pretend that it’s my job to prove a negative “that it could not”.
To hell with that nonsense. If it’s your claim that it could, provide evidence. It’s nonsense to pretend that it’s my job to prove a negative “that it could not”.
But it’s bizarrely irrational of you to imagine that (alien) life could naturally/unguided/undesigned evolve to a sufficient point of complexity and intelligence that they would be capable of designing our own kind of biotic life and implementing their design physically on Earth, yet without having any kind of genetic code system of their own through their own billions of years of evolution. And yet again without them having any reason to insert our type of translation system into our LUCA since – by your own scenario – their own non-translation-system had worked just fine for them to get to that advanced level of Design capacity. What are you, their science experiment? Seriously? Seriously, your brain is cooked. See if you can get help!
Good, then you can finally shut your mouth.
No, you’re just trolling. Tell me something I didn’t already know.
Hoyle was bizarrely illogical about some things. No wonder he’s your hero.
Anyone who “points out” that a big-D Designer does not have to be supernatural is either deluded, or lying, once an infinite regression is ruled out.
No need to drag more idiots into your discussion.
Sez you, but you don’t speak truth. And you’ll repeat your duplicity as often as you think you can get away with it.
Circular. That’s not evidence, that’s the un-evidenced premise of your argument.
P1. Artificial things like translation systems are designed.
P2. This is a translation system.
C. Therefore it was designed.
How do we know it was designed? Because it’s an artifical thing!
How do we know it’s an artificial thing? Because it had to be designed to begin with!
You know better, but you keep doing it anyways. Or maybe you’re really not capable of noticing that you’re using a circular argument. In which case I actually feel sorry for you.
So what. You’ve repeated this a half dozen times already, pointlessly.
I’m not arguing because I’m defending “materialism”. I’m arguing because you choose to tell fairy tales about the possibility of it being a natural Designer while you pretend to talk about logic and science. Maybe there was a Designer of our life to begin with, a supernatural one. I don’t think so, and you don’t have a speck of evidence there was one – or even a hypothesis about how there could be one. But maybe just by luck you happen to be on the right track, and there was one. Fine. Thank you god for Designing primitive life so we could evolve to our current happy state.
But what we did NOT have is a Natural Designer. if by some truly weird happenstance, we had an exobiotic alien designer, they themselves were either naturally/unguided/undesigned evolved, OR they themselves had a Supernatural Designer. One, or the other. Because, infinite regression. Which even you aren’t illogical enough to claim is a possible thing.
EricB, you are so dishonest that I will not speak with you again. It’s against my religion to continue to speak with habitual liars and distortionists.
It’s quite likely that this comment will be moved to Guano, and if so, I accept that, but I do hope that it is visible long enough for you (and others) to understand why I don’t respond further to your most recent lies and distortions of what we have already said.
ericB,
I think there is a fundamental issue that you aren’t getting regarding the ‘motivation’ of chemistry to refine. Life, by replicating imperfectly, explores the local neighbourhood of its heritable sequence (DNA or RNA). If this blind stumble encounters a configuration that increases its rate of increase, by whatever means, then this configuration will outcompete the existing (ancestral) structure. This is basic Natural Selection. It’s not about hindsight or foresight, it’s not ‘pure’ chemistry or physics, but it is important. Coded sequence happens to be filtered through its effect on protein, but it is still, ultimately, the xNA sequence that matters.
The existence of a ‘population of meaningful (protein) recipes’ in my model is a modern derivative, not the starting point. My starting point is a simple peptide bonding ribozyme. A single dipeptide, or monotonous sequence of acids, not stored in DNA as such, but made by a ribozyme that is, is perfectly plausibly beneficial to a cell. If you wish to dismiss such plausible scenarios as ‘handwaving’ or ‘unwarranted leaps’, further conversation is pointless, since you can simply play that card at every juncture, tediously, unless I build you an organism and show it competing. You might want to lay off vague suggestions about some designer, sometime, somehow, being involved, if handwaving bugs you.
No, I have placed the origin prior to anything one could meaningfully declare to be a ‘store of recipes (for protein coding)’. There’s just DNA/RNA, and if you doubt that a random piece of DNA/RNA could possibly be functional, ever, when processed by a translation system, I would wonder what you based that on, other than vague surmise. As we’ve discussed elsewhere, random protein space is rich in functional peptides. But it is enormous. If you thought it reasonable to insist that I show you the exact First Sequence, and its selective advantage, I’d think you were yanking my chain.
My ‘store of protein recipes’ builds up gradually from one or a few very simple proteins, with limited complexity and specificity. The formation of the initial one is the payoff for developing early translation, not the subsequent ones. And note my starting point – noncoded peptide synthesis. As soon as a piece of RNA becomes involved in the process, we have the beginnings of a ‘recipe’. But it did not have to be encoded as such. In one scenario I suggested, the RNA could have functioned as peptide length control – it would not have to contain any meaningfiul instructions, just Start and STOP an appropriate distance apart.
What do you think should have happened? If RNA life could exist, is it inconceivable that it could be improved? You presumably see an advantage to protein over no-protein. And you must be able to see the advantage of repeatability and specificity over the ad hoc. These are central to why protein coding is such an ID icon – not just the resemblance to programming, but the fact that its subtleties are useful to life. Therefore, though you would not phrase it so, you accept that there are potential selective reasons for proteins to become prevalent – yet you are reluctant to bite the bullet and agree ‘Natural Selection could do this’, unless I come up with THE advantage, and THE pathway, whereby serial selective advantage accrued.
Gggggnnnnnhhh! I have NOT said ‘in some unspecified way’! Those posts took ages! I’ve presented a detailed pathway with all the necessary steps, and plausible advantages to each. Wasn’t that the challenge? A plausible, hypothetical sequence?
So you think that no poorly or unspecified protein could possibly be advantageous? A potential non-translation way to achieve consistency is to only have one amino acid available! Still, all one needs for an early system is an advantage in doing X however badly in a world where nothing else does it at all. Vague but true.
Mutation, Recombination and Natural Selection. Obviously, this is something that happened in deep time, so I can only surmise as to the details. Which I have, at length. The key point to reiterate is that any functional protein is likely to have neighbours that are also functional. Add in duplication and module shuffling and you can build your entire protein library from those precursor sequences, not by repeat search from scratch.
Groups of three bases obviously exist throughout the genome, overlapping, but ‘triplets’ only become relevant on binding the tRNA, and moving on. Do you know the comparative binding energies between singlet, doublet, triplet and quadruplet Watson-Crick pairs? Or the geometric constraint of binding a folded structure to a linear one? Singlet and doublet binding are too weak and error-prone; quadruplet stronger and hard to keep straight. Triplet also corresponds most closely to the C-N distance of an amino acid. Triplet is just Goldilocks-right. It’s not an unwarranted assumption that even a mere length-control counting system would operate to a triplet frame; it is supported by geometry and physics.
Hah. I was merely saying that if a different code existed in the past (eg 5 acids instead of 20, or even just one), it would still be capable of processing any stretch of nucleic acid, and producing peptides of some length from contiguous non-stops. Clearly, it is the historic protein coding system that one needs to explain first. There are good reasons to suppose it had fewer assignments than the modern one, but had many (not all) of its features.
Such as? You allowed the pre-existence of nucleic acids. That (and replication) were pretty much all I needed.
Have I not explicitly denied teleology, while covering the immediate selective advantage of each step? Selective advantage is the only possible justification in a ‘natural’ scenario (the advantage of a scenario like ID, of course, being that you don’t have to justify a damned thing!).
You repeatedly talk as if sequence specificity is vital for any coded protein worth the name, so if you drop that, I’ll drop the assumption that you think along those lines. Even if, at one level, you recognise the distinction between protein types, it appears that you are stuck in a viewpoint that regards coded proteins as vital for protein coding, much like Upright Biped.
That is incorrect. The energetic requirements of the cell are almost entirely met by nucleic acid bases, not protein. Proteins utilise these bases in driving reactions in the thermodynamically favourable direction, but the role of protein is to lower activation energies, which is not the same thing. Ribozymes do much the same as proteins, albeit less well. There is, of course, no extant life using a purely RNA based system for charging ATP. But in principle, nothing to stop it. If you allow RNA life, it must necessarily have had its energetic requirements satisfied, non-enzymatically.
I would not even dream of building my proposed system using enzymes. I feel slightly insulted that you would think I would make such an obvious error! The origin of protein coding is (in principle) achievable using only ribozymes and other RNAs, a very different molecule. Enzymes came later, clearly.
The initial function of the ribosome was (in my scenario) peptide synthesis. The heart of the modern ribosome is RNA-catalysed peptidyl transferase activity. This (on phylogenetic analysis) is one of the oldest parts of the ribosome. The organism doesn’t have to need proteins to benefit from them, as I have repeatedly said. Your not grasping this basic fact of mutation/selection makes the whole conversation difficult. It is true that the first sequences passed through any primitive coding ribosome were not designed to be coded from. But it only takes one accidental success to fix the basic system, which may then uncover further novelties, further cementing its role and selecting for its refinement.
Hardly a chemical justification – and it is like saying that higher rates of interest only produce greater returns with hindsight. Evolutionary advantage = differential survival and reproduction. If one type regularly produces more offspring than another, the former will tend to eliminate the latter.
Enzymes are protein. The ribosome is a type of ribozyme – an RNA catalyst. It’s neither hindsight nor foresight – some accidents are fortuitious from the point of view of survival and reproduction.
Which is my point. You wanted an in-principle, hypothetical scenario, but now you want a detailed inventory of the specific sequences involved and their selective advantage in the environmental milieu of 3.5 billion years ago. Don’t want much, do ya?
Tend to be large now. They have been through many millions of years of refinement, and longer does appear to be the rule, which I would propose as favoured by selection – it allows for much more subtle kinetics. Sequence is important, but not acid-by-acid vital. And anyway … I don’t assume enzymes! There is, as I have mentioned, a 5-base ribozyme that aminoacylates ATP. I don’t think I’m assuming too much in thinking that smaller precursors, both of enzymes and ribozymes, are entirely plausible.
Not at all. I have assumed only the existence of an RNA/DNA replicator, with ribozymes, and an advantage for, serially,
(1) noncoded peptide bonding.
(2) RNA control of peptide length and/or base-pairing enhancement of peptide bonding kinetics
(3) Some specificity of subunits against RNA template
(4) Tighter control of specificity
(5) Amino acid library expansion
(6) Duplication and recombination of proteins and domains from among the ‘proven set’ following subsequent rounds of selection.
(7) protein aaRS’s replacing RNA ones
(8) Lengthening, combination and multifunctionalisation of both RNA and peptide macromolecules.
None of this took as a starting point any form of translation, nor any special kind of ‘useful sequence’ just waiting to be uncovered upon passage through a coding ribosome, other than that which would be lying around in a nucleic acid genome. I cannot fill in every blank, but the fact that the modern system can be deconstructed in this way, with evidential support for all the principles invoked, casts doubt upon your insistence that it is IC.
Well, that WAS the challenge, but EricB is not honest enough to concede that you’ve met the original challenge and is compelled to pretend that you haven’t. Sorry.
But at least, you’ve written some wonderfully clear posts that serve to educate the rest of us.
Perhaps when EricB comes back (if he does) to spam this thread with yet another distortion of what’s been clearly said, you can just copy and paste your own responses over again. It’s not as if he’s going to listen any better the second time (or the third, or the fourth …) than the first, but he might get bored and leave. No loss 🙂
Neil Rickert:
In short, your rebuttal is nonsense.
You’re playing word games. A “completely material description of its actions (in terms of electromagnetic signals)” is not necessarily a complete description. And the claim that “that material description completely describes what happens in the computer.” is simply laughable.
Two different ways of conceptualizing WHAT?
Alan Fox:
How, by erecting straw men?
Alan, over in the Durton thread it was patiently explained to you how and why you were mistaken about the argument being made. Yet you show absolutely no evidence that you learned a thing.
So the first question you should have asked Allan is, what is the relevance of protein folds to protein function? Then, perhaps, he might be able to give a relevant response.
Then you might ask about how common protein folds are in sequence space.
But that’s all OT for this thread, I suppose, and I don’t want to detract from ericB’s participation here at UD.
thorton:
It’s true by definition, as has been amply demonstrated to you.
Neil Rickert:
To describe WHAT?
Given that there is a complete description of what goes on in a computer available without using “teleological language,” why on earth would anyone resort to such language?
Neil Rickert:
Then what on earth does the use of “teleological language” add?
Neil Rickert:
And when we describe what happens in a cell with the terminology of computation (algorithms, logic, etc)?
Simply false. Or you’re equivocating, again.
You said:
Is it the teleological description that is superfluous, or the “material” description?
What an odd attempt at a distinction. If it’s teleological it’s not material? Why so?
Neil Rickert:
Therefore, air molecules are not unguided.
Prove it. Show us the math.
How else would they occur?
hotshoe:
ericB, you’ve posted too much. You’re spamming.
OTOH, Mike Elzinga complains that you’ve posted too little.
Neil Rickert:
lol. one for the ages.
1. Lots of “natural” systems provide guidance.
2. Guidance is a teleological term.
It follows that lots of natural systems are teleological.
Or, perhaps, they are not “natural.”
Or, perhaps, they are not mechanical.
But are not “mechanical” systems “teleological,” by definition?
Indeed. And those are the FACTS of the case.
So, is there or is there not, a translations system in the cell?
And if not, why not?
cubist:
ericB responded, but since this was addressed to me, there is no such thing as “extremely complex chemistry.” You are simply misguided.
Perhaps what you meant to say was that all information processing is “just chemistry.” But that’s just absurd.
Alan Fox:
You’re confused.
Me:
Is incorrect. It was late! Nonetheless, my other points stand. The geometry of xNA-xNA interactions disfavours anything much longer, and anything much shorter, than triplet when a folded molecule is ‘attempting’ to align with a linear one.
Mung:
Very relevant to certain classes of proteins, not so much to others, as I’m sure Alan is aware.
Depends how big you make it. Density may go down as subunit variety and length go up. Therefore (up to a point) it must go up as those parameters decrease. One would expect them to be more likely to be small than large on F-Day – the day a critter encountered the First Functional Fold.
A patterning algorithm of 14 residues, with a binary choice of residue at each point, produced functional synthetic folds in one experiment. This space has 16384 members, same as a run of 14 Heads. Even if this is the only fold in the space, 16384 is not that hard for a population to thoroughly explore. End-joining such a discovery into longer modular repeats takes one into spaces where ‘from-scratch’ fold density may be minute. But you didn’t start from scratch, you took a viable fold and repeated it.
Tell me, mung, when is a protein not a polypeptide and when is a polypeptide not a protein?
Thanks for the kind words – I do wonder if I am being clear; part of the point of debating is to try and be so. And it helps one’s thought processes and articulation to see how others see things. I don’t have any beef against Eric, beyond that voiced in mild expressions of exasperation! Credit to anyone who is prepared to discuss. I never expect to persuade.
I’ve got the popcorn!