A computer programmer noticed that he was not able to type very much in a single day. But he mused that if there were a large number of software bots working on his code, then they might be able to proceed via totally blind trial and error. So he decided to try an experiment.
In the initial version of his experiment, he established the following process.
1. The software was reproduced by an imperfect method of replication, such that it was possible for random copying errors to sometimes occur. This was used to create new generations of the software with variations.
2. The new instances of the software were subjected to a rigorous test suite to determine which copies of the software performed the best. The worst performers were weeded out, and the process was repeated by replicating the best performers.
The initial results were dismal. The programmer noticed that changes to a working module tended to quickly impair function, since the software lost the existing function long before it gained any new function. So, the programmer added another aspect to his system — duplication.
3. Rather than have the code’s only copy of a function be jeopardized by the random changes, he made copies of the content from functional modules and added these duplicated copies to other parts of the code. In order to not immediately impair function due to the inserted new code, the programmer decided to try placing the duplicates within comments in the software. (Perhaps later, the transformed duplicates with changes might be applied to serve new purposes.)
Since the software was not depending on the duplicates for its current functioning, this made the duplicates completely free to mutate due to the random copying errors without causing the program to fail the selection process. Changes to the duplicated code could not harm the functionality of the software and thereby cause that version to be eliminated. Thus, in this revised approach with duplicates, the mutations to the duplicated code were neutral with regard to the selection process.
The programmer dubbed this version of his system N.E.C.R.O. (Neutral Errors in Copying, Randomly Occurring). He realized that even with these changes, his system would not yet fulfill his hopes. Nevertheless, he looked upon it as another step of exploration. In that respect it was worthwhile and more revealing than he had anticipated, leading the programmer to several observations as he reflected on the nature of its behavior.
Under these conditions of freedom to change without being selected out for loss or impairment of current function, what should we expect to happen to the duplicated code sequences over time and over many generations of copying?
And why?
[p.s. Sincere thanks to real computer programmer OMagain for providing the original seed of the idea for this tale, which serves as a context for the questions about Neutral Errors in Copying, Randomly Occurring.]
I agree with these statements, so I’m not sure why you think your statement threw any curve. The scenario I set out explicitly recognizing that selection can occur if the walk hits on a configuration that is reproductively advantageous (e.g. point 8). So I don’t see a disagreement about this.
Perhaps you have misunderstood the point I was making, but what you have written here is not correct.
The phrase “dysfunctional degradation” specifically refers to degradation that causes loss of function, but there is no necessary connection to becoming less reproductively fit. Notice the explicit use of the example of the vision system of cave fish. Their vision system undergoes dysfunctional degradation, i.e. loss of function — they go blind. But this does not mean they become less reproductively fit. Since the vision system is not providing a selectable reproductive benefit, it is not protected by selection and can be lost without sacrificing reproductive fitness.
The point is that this is true of any system that is not currently providing selectable reproductive benefit — even if the system is operational or functional. Just as the vision system can be lost, so too any other such system including any Triplet-Reading System prior to providing selectable reproductive benefit.
Since selection cannot consider any future potential selective advantage, your statements assume the system has already begun to provide a real selective benefit. Since my points are examining the entire history prior to the operational system producing that first selectable reproductive benefit, “the acknowledged ability of random factors to change sequence when there is no relative advantage/disadvantage” is “an issue” during that entire span.
If I understand your intended meaning, you’ve switched the meaning of “system” to make your point. My points about “the system” are in reference to the origin of a working and beneficial Triplet-Reading System. Obviously, along the journey from an organism that has no T-RS to one that does, there must be a long period during which there is no operational T-RS and then a point at which the first T-RS becomes operational.
I will guess you may have missed the intended meaning of “system” in my statements. In any case, in order to make your claim about never needing to become operational, you appear to have switched out the intended meaning of “system” and have substituted “the entire system”, which apparently is a reference to the fact that the organism as a whole is operational — which is true but irrelevant to the point I was making.
Keep in mind that nothing in my points assumes or requires the idea that the organism has any loss of differential reproductive fitness. The issue is the ongoing randomization of sequences that are not currently contributing to differential reproductive fitness.
Informally, one sense is the ability to perform some task. Specifically in this case, the function of the TRS would be to read a nucleotide sequence as a sequential series of triplets, matching each (until termination) and performing some action according to the sequence of matches. As was true for the function of vision in fish, to be preserved it is not enough for the system to function. It must also contribute to the reproductive success of the organism.
The journey from not having a TRS to having one that eventually produces what you identified as the “one accidental success to fix the basic system” — this is not a “small step”. Since this is concerning the origin of the TRS, there is by definition no previous working and beneficial TRS from which to take a “local random walk” through “nearby space” to find a new and better TRS.
Now, if you actually could justify the hope and faith that there is a long chain of intermediate wayside rests with increasing benefits to reproductive success all along the journey — even through each of the many hypothetical intermediate stages of construction and orientation experimentation of the components of the TRS, despite the fact that it is not yet even operational — then you really could be dusting off that spot on your piano for that Nobel Prize.
Notice what Hoffmann said:
Sincerely and without any sarcasm, if you were to find such an answer, you could be that genius.
Nevertheless, neither you nor anyone else has found a way to reduce the construction of molecular machinery and systems to a series of small steps that only need to take short local random walks through nearby space to find the next immediate reproductive benefit throughout the chain of construction.
They don’t give Nobel Prizes for solving small problems or making obvious applications of evolutionary ideas that everyone could see. Unless and until someone finds an answer that no one else has found, it remains a major problem for the hypothesis that undirected processes produced such molecular machines.
[If anyone does not consider this to be evidence against that hypothesis, then they are not treating it as a hypothesis that can fail. It is when someone operates as if it is axiomatic, a truth that only is missing explanation, that any apparent implausibility can be dismissed as only appearance and not evidence against the proposition.]
A long — almost interminable thread — devoted to a point that has been stipulated.
It’s still a god of the gaps argument.
Now tell us what research proposals can be derived from incredulity. Are you saying the work of OOL researchers doesn’t need to be done because you already know the outcome?
Pick one! Work backwards!
In any case, it appears that the work has been done/is being done just presumably not to your required level of detail.
http://www.pnas.org/content/104/17/7116.full
But yes, it’s as you say, we’re totally ignorant of how these things came to be. Or, rather, as ignorant as you make yourself. Given that paper is 5 years old you’ve had plenty of time to find it for yourself. But no doubt it is not considered responsive to your point for some reason.
And no, nobody’s yet solved the origin of life. And so?
ericB,
Sorry Eric, I simply don’t understand your response. Perhaps there is an issue with my ability to cogently express the scientific viewpoint (for which failing, I apologise to scientists everywhere!).
You shouldn’t apologize, Allan; it’s not your fault. You have been more than fair and patient with him; but as long as you keep trying to explain any real science, you lose. That’s the way the ID/creationist debating game is set up. Remember, they don’t do science; they want to debate.
It appears that ericB is employing all the usual ID/creationist misconceptions and misrepresentations about biology, chemistry, and physics and that he thinks in the language of ID/creationist pseudoscience. There is no common language with which to communicate science to him. He is simply mindlessly following a memorized shtick, and he has been exactly on script all along.
Note that ericB’s very meticulous quote-mining of Peter Hoffman’s response to a question was designed to misrepresent what Hoffmann said and meant. EricB has no clue what Hoffmann meant; he hasn’t read Hoffmann’s book, and he doesn’t care what researchers in this field know and believe. EricB’s tactic of quote-mining Hoffmann was for emotional effect in a debate.
What ericB is really trying to “prove” with this debating tactic is what every ID/creationist wants to believe; namely, “if science can’t stipulate exactly every atom-by-atom, molecule-by-molecule step from an ideal gas of non-interacting atoms (i.e., from “spontaneous molecular chaos”) to a specified complex molecular assembly, then science is wrong and ID/creationism is right.”
It is really that simple-minded; that’s how they think.
There will never be any effort on his part to understand any real science. He is following the old, hackneyed ID/creationist debating tactic, right out the Duane Gish playbook; ignore the real science and keep throwing out more crap. Then declare victory at the end of the debate.
His mathematics is a dead giveaway to the way he thinks about atoms and molecules. Everything else he asserts simply confirms what his math already tells us.
Sit back and study the misconceptions rather than trying to correct them. They aren’t correctable.
Ah, Mike, I’m a glutton for punishment!
I just don’t get what you don’t get, Eric. It’s not a random walk from one TRS to another, but a set of shorter walks, giving things that you would not call a ‘TRS’, but each of which provides its own benefit. They ultimately lead to the basic TRS.
Let’s look just at the first step. Suppose an organism possessing transcription but no TRS produces a ‘useful’ dipeptide’ using ribozymes. Sure, if they find themselves in an environment where peptides are of no use, the system could go the way of cave fish vision. So why do you think I suppose it might persist? Are all systems doomed to go the way of cave fish vision? Is there a mechanism that prevents this?
Hee hee. Then as long as there is a masochist to jump in and stir the pot, others can sit back and watch. It’s still data. Carry on. 🙂
Me:
Eric:
This is the kind of thing that is the source of my bafflement. I say something that you have apparently misunderstood, so I try and explain, and you say “yes, yes, I know that”. It appears that you get the same impression. OK, so you understand evolutionary theory, and I understand evolutionary theory; we can tread the path to enlightenment together, and … Eric? Eric! Over here!
If an allele does not provide an advantage it will randomise. Got it. If it does provide an advantage, it will persist. So one needs to postulate an advantage to each incremental step. Which I have. Yet you still, many posts later, seem to think I haven’t grasped the fact that superfluous systems will degrade, and that ‘function’ (a somewhat slippery concept) does not correlate universally with fitness.
Allan,
I think Eric’s problem is that he is locked in some strange dichotomous thinking: either the TRS is ‘operating’ or it is not. Only a fully functional(tm) TRS can provide any benefit. Once you make that assumption, then it does seem unlikely that drift alone would bring you to a place that is one ‘lucky accident’ away from a fully-functional(tm) TRS.
It’s the “what use is half a TRS?” argument.
On the previous thread, you provided a very cogent description of how RNA replicators could arrive at a TRS by small, beneficial steps.
When Eric read those posts, it appears that he was unable to understand them; the best he could manage was to seize upon a phrase or two that he thought supported his argument e.g. “one accidental success” [made in reference to the first mRNA, rather than the TRS] and repeat it out of context.
I do not believe that this quote-mining had any intention to deceive. Rather, I think Eric is completely unable to conceptualize a somewhat functional nascent TRS. Making conversation difficult.
But we can keep trying.
Eric, what is the minimum number of different codons that your “functional(tm), operating, reproductively beneficial TRS” must recognize?
Interesting that Darwin anticipated both the “what good is halfa” argument and the response.
I also find it interesting that ID advocates who accept some bits of evolution seem to be split between vitalists like Eric, who place the moment of inception at the time of first code translation, and those who worry about the inception of the human soul.
Between Paley and Darwin, there is nothing new in the ID movement.
While it may be that full agreement about the conclusion is a bridge too far, I think that mutual understanding is certainly attainable, and may not even be that far off.
The above description doesn’t describe my own position and departs from it in multiple significant respects, but for the sake of discussion, just suppose that I don’t know anything at all. [Yes, I know, some of you may already be operating under that assumption. 😉 So you have a head start with this exercise.] It may help people to consider the matter more objectively if they consider a different question.
Does Peter M. Hoffmann both understand and believe “the basics of evolutionary biology” that are alluded to above?
I don’t see any reason to doubt that Hoffmann both understands and believes the principles of evolutionary biology, including but not limited to everything thorton alluded to above.
Yet, even though Hoffmann understands all of that and is an expert on the operation of those molecular machines, nevertheless when it comes to the question before us of the origin of the molecular machines, this same expert also says the following.
Obviously, if basic principles of evolutionary biology provided the “good answer” for this question, Hoffmann would not say that no one has a good answer for the question of the origin of the molecular machines.
Likewise, if his own research into the operation of these molecular machines provided a “good answer” to their origin, he wouldn’t say what he says. After all, who understands the significance of Hoffmann’s own work with regard to this question better than Hoffmann himself? Thus, those who want to say the answers for the origin question are in Hoffmann’s book are clearly mistaken — according to Hoffmann himself.
On all sides of this issue, everyone is able to see and agree that if there were in fact a chain of neighboring states, each one only a small number of modifications from the other, each one successively beneficial to reproductive success compared to preceding steps, then it would be reasonable to think that an evolutionary process could climb up this gentle stairway. Understanding this has never been the issue.
So how can it be that Hoffmann both understands how evolutionary biology works and believes it can work as described, and yet explicitly observes that no one has a good answer for “Where did the machines come from?”
The obvious answer is that it is not evident — not even to Hoffmann himself, an expert on molecular machines — how there could be such a gentle stairway of successive reproductive benefits to the origin of complex molecular machines.
To be more precise, what is the significant reproductive benefit gained from 10% of a TRS, or 12%, or 14%, … 90% etc. Even at 98% of what would be needed for a TRS to operate, it is still not yet operating. All of the stair steps through that sequence would need to come from supposing some other benefits at every step that by definition cannot come from the operation of the first working system. These various other benefits would have to occur progressively throughout that construction sequence.
Yet, even though the other benefits cannot come from the operation of the future molecular machine, we must suppose they reinforce a path of development that has lead up the stairs to that machine.
The significant point not to be missed is that Hoffmann knows that no one has found this yet. No one has found a good answer for this yet. This is the missing piece that we are waiting for some genius to figure out. The fact that no one, not even Allan, has done this is signified by the fact that no one is expecting (at least not yet) for Allan’s name to be submitted to the Nobel committee. (But maybe someday…)
A core stumbling block is one that I mentioned in the previous thread. Either or both of these problems will occur.
So, for example, if the organism gets some benefit from doing something that does not in any way involve reading a sequence as successive triplets, then it becomes problematic to suppose that this leads to a system for reading a sequence as triplets or to “reading” sequences at all by matching any grouping of nucleotides.
Nor does it help to observe (as we can after the fact) that a triplet reading system would work better than trying to read and match nucleotides two at a time or four at a time. The problem is that we don’t have a stairway leading in an unbroken fashion by small steps to any sequential matching reading system at all.
In the absence of the genius answer, i.e. stairway of reproductive benefits at close intervals leading to the assembly of reproductively beneficial molecular machines, I think most people reading this thread see that the expected result of Neutral Errors in Copying, Randomly Occurring would simply be a randomizing process acting on the underlying sequences (a main point of this thread).
It’s not consistent with what we observe, so no, I don’t think so.
ericB,
Eric,
I’d be wary of appealing to experts. I simply have to quote my pet expert who disagrees. We might as well make glove puppets of them and have at it a la Punch and Judy.
I’ll read your post in more detail later. But it does look on skim as a lengthy repeat. I don’t think you know nothing, but nor do I think you are actually getting my – ahem – drift.
Allan
Despite being corrected a dozen times ericB continues to demonstrate his lack of understanding of science in general and evolutionary biology in specific.
Having a scientist say “we don’t understand yet all the natural steps in how this phenomena occurred” still doesn’t mean “it’s impossible through natural processes therefore GAWDDIDIT”.
Claiming all genetic variations are degrading errors without any consideration for their effect in a changing environment is still the mistake of a scientifically ignorant and clueless neophyte.
ericB, is there a reason why you keep repeating these beginner’s blunders?
I will mention my own speculation on the origin of ‘molecular machines’. I hesitate somewhat, because I don’t think it relevant to this discussion and is more OT-bait. Eric constantly wants to push it back. If I explain X, how do I explain pre-X. If I explain that, how do I explain pre-that? And so on. Which is why I argued that the sensible starting point was an organism with transcription. Such an organism could evolve translation, provided it was viable without. Whence transcription? is not the question that Eric originally asked, though I think in his view he did. He thinks of transcription as ‘for’ translation.
As to that origin, I think that the earliest ribozyme arose not directly as a single strand from a soup of monomers, but from a stable double stranded RNA constructed by hybridisation from short single strand polymers. Nucleic acids have an almost magical property of complementarity. It underlies just about everything significant about Life (including triplet recognition). A strand in 3′-5′ orientation will locate and align with one in 5′-3′ with a strength depending on the complementarity of the base sequence.
To my mind, double stranded RNA has to come first, as a mechanism of purifying the bases for complementary pairs and fixing on a single isomer of sugars – problems which without that step seem very intractable, but with it seem solvable. In principle, out of a mixture of single strands with many more than ‘our’ 4 bases (incuding those with no complementary partner, and those attached to L-sugars), complementary enantiopure short strands will ‘find’ each other more readily than anything else. Such paired strands cannot replicate, but they are ‘selected’ for stability. The sequence is stochastically dependent on the single strands present in the mix – it’s random. By unpeeling a strand from such a pair, and rough-repairing the exposed strand by further hybridisation, it would be possible to produce a folded ribozyme – very primitive transcription. Then, it obviously depends on whether this ribozyme’s activity enhances the survival of the parent sequence.
Eric, you wrote
In which case, you have completely and utterly failed to describe your own position.
Hoffman is not saying what you think he is saying. I suggest you find something that Hoffman has written that supports your characterization of his position, and quote that, with context.
Allan cogently described a plausible scenario. That was the challenge, if you recall.
If Allan were able to demonstrate that his scenario was historically accurate, then he could start planning the trip to Stockholm. Currently, they do not award science Nobels for mental masturbation, however elegantly done.
But for the best s&g, Eric, after I point out your problem with dichotomous thinking, you write
So either a step is so similar that it merely shifts the difficulties off screen, OR a step is so great that it creates new difficulties. There’s no in between? Really? How can you be so sure?
Again, to try to get a actual conversation going:
Eric, what is the minimum number of different codons that the first “functional(tm), operating, reproductively beneficial TRS” must recognize?
DNA_Jock,
Umm … I’d go for ‘speculation’, meself’! 😉
This is the problem with trying to give ID/creationists something to read. They never read for comprehension; instead, they engage in trying to extract and justify the meaning they want from the text. For example:
This is typical of the way sectarians argue to justify their presuppositions. ericB continues to engage in exegesis and hermeneutics of Hoffmann’s response to a question without understanding anything about the knowledge base in this field and without any understanding of biology, chemistry, and physics. This debating tactic drags the debate into mud-wrestling over the “TRUE” meaning of the words of the writer; and it attempts to put thoughts into the mind of the writer that are not there.
This debating tactic is one of the behaviors that betray the sectarian nature of ID/creationism. ID/creationists think science is done by exegesis, hermeneutics, and word-gaming in exactly the same way that these ID/creationists engage in sectarian apologetics. With no knowledge of science, this is the only tactic available to ericB. He continues to avoid addressing direct questions that require knowledge of the concepts of science, instead, going directly into exegesis, hermeneutics and word-gaming.
When scientists say that nobody understands the recipe(s) leading to life, they are saying this in exactly the same way they say that nobody understands Saturn’s mysterious hexagon.
Any bets on how ericB will try to word-game this?
ericB:
Hoffmann by his own admission is neither biologist nor chemist. His expertise in the physics of molecular machines (such as actin crawlers) gives him no special insight into their evolution, any more than a cardiologist would know how hearts came about.
Heh heh. What’s 10% of a TRS look like? What does that even mean? Either the system has tRNA anticodons and mRNA docking or it doesn’t. Yet if it doesn’t, why is it no use? What makes you think that the only worthwhile peptide is a coded peptide of a particular minimum subunit variety and length?
Er … yeah. I think we’ve established that. Except for that ‘first working system’ thing – they’re all working systems. The benefits come to the system at the stage it is at. If a ribozyme produces a dipeptide by carrier activation, the organism has evolved aminoacylation and peptidyl transferase activity. Why would that not, in any conceivable milieu, be a useful thing to do?
You want to go to a vote? 😉 I don’t think most people would agree that even primitive peptide synthesis can be assumed neutral.
Let me throw in this consideration. A specific enzymatic sequence stands or falls according to the benefit that enzyme does or doesn’t provide. If it increases an organism’s hairiness, and it’s cold, the sequence may be favoured. If it gets warmer, the benefit will be lost and breakage of the function is lilkely.
However, with the kinds of system we are talking of here, there is much less likelihood of such loss, so long as the system produces more than one product. Suppose, for example, a precursor of the full-blown TRS was capable of producing two products, both useful, by some degree of substrate specificity. Circumstances change and one is disfavoured. This does not lead to cave-fish-eye degradation of the system, however, because it is still needed for the other. We can multiply up for the modern 20,000-gene TRS system and see that the system is very much pinned in place. But this protection starts to become an evolutionary force with a much smaller number of peptide products, and potentially with a much rougher mechanism. It’s not just going to drift into oblivion the moment one product stops being useful.
Sorry…I didn’t mean to imply…
I’ll get me coat.
ericB, your whole argument here is built around neutral “copying errors”. Not beneficial “copying errors”, not deleterious “copying errors”, but neutral “copying errors”. This is why your acronym is NECRO, not BECRO or DECRO.
Why are you ignoring non-neutral “copying errors”? Is it your position that non-neutral “copying errors” don’t/cannot exist, or is it your position that the existence of non-neutral “copying errors” doesn’t affect the degree to which your conclusion actually does apply to Reality, or… what, really?
Mike Elzinga:
Of course, Mike ignores any evidence which contradicts his stereotype. He’s a “true skeptic.”
Mike Elzinga:
Pretty sure you’re lying. But I don’t track all the crap you write that I respond to (or chose to ignore due to the infantile content).
So just in case I didn’t say it earlier, but I probably did:
Mike Elzinga:
Who knows? What is the source and what is the probability of each symbol in the sequence? If you’re talking about biology, I suggest you read Information Theory and Molecular Biology.
Mike Elzinga:
It depends. You managed to type them up and post them online. Did you manage that without the behaviors of atoms and molecules? How so?
Is there something about atoms and molecules that forced you to post those exact sequences rather than some other sequences?
Those were such tough questions Mike.
I answered them, and the best you could come back with was:
You’re pathetic, Mike. It’s not hatred, it’s pity.
They are not ignored. See Observation #1, for example, which mentions them explicitly. Likewise, most other Observations (e.g. #2, #3, #4, and #5) are explicitly conditional on making their claims for the case where the sequence is not providing a selectable reproductive benefit. They don’t claim that this will always be the case. You will also notice the my use of phrases such as “so long as this remains true” (e.g. Observation #6).
When I answered Allan’s “Why not?” question point by point, I was explicit in point 8 about a successful blind walk terminating by hitting upon “real selectable reproductive benefit.” That is a reference to a copying error that is advantageous rather than neutral or disadvantageous.
Likewise, I reminded Allan of this in my response, when he seemed to think otherwise.
The problem isn’t that this is not a possible result of a copying error. (Thus, when people suppose that I am depending on assuming a copying “error” is “bad”, they are mistaken, and have not read my posts carefully. But a copying error is random and that is important.)
The serious problem is that if you are not within the near neighborhood of a few deviations on already beneficial sequences, the randomization of neutral copying errors in an unselected sequence will accumulate. That is a fact, not speculation. Furthermore, the sparseness of sequence and configurational space makes the chances of hitting a selectable configuration from a randomized sequence implausible.
In other words, the longer that a sequence follows that trajectory, the more any starting sequences necessarily become randomized and it becomes a task of trying various randomized sequences in the hope of hitting on something selectable. That is a blind walk depending on being unbelievably lucky. Any realistic assessment of that prospect is bleak.
This is why it becomes necessary to make it plausible that it never comes to that bleak condition. This depends on the existence of a gentle stairway of many selectable states very near to each other and extending from a plausible starting point all the way to the construction of a molecular machine or system such as the TRS.
The genius answer that we still don’t have is how to do this for molecular machines that don’t provide their ultimate benefit before they are operational. That is why this is still considered problematic and unsolved. How is it that there are many closely spaced stairs of selectable benefit prior to getting the machine’s own benefit from its future operation — yet that lead to a future machine with future benefit after it is operational?
This is the claim that ericB keeps repeating and refusing to justify. He thinks it is N^L.
This is at the very core of ID/creationist pseudoscience; and it is wrong. Repeating it endlessly while ignoring the real science doesn’t make it true.
That isn’t relevant to the reasons I recently highlighted his statements. The question was, first of all, “Does Peter M. Hoffmann both understand and believe “the basics of evolutionary biology” that are alluded to above?” You would agree that he does have at least this level of understanding, correct?
Secondly, he was describing the fact that no one yet has a good answer to the origin of molecular machines. You’ve said yourself that you aren’t dusting off your piano for that Nobel Prize. So again, the fact that the genius answer is still missing is not really a reasonably disputed point.
Finally, it is obvious that the missing piece is not an understanding of what evolution would require to work (i.e. a series of selectable steps to the end result). What is missing is how to make that plausible in the case of molecular machines composed of multiple cooperating parts in specific configurations.
You can’t be seriously suggesting that you can explain the origin of the TRS by assuming you can start from something that already “has tRNA anticodons and mRNA docking”, can you? That isn’t your idea of an explanation of its origin, is it? In theory, one way to “win” a race is to start just before the finish line and then step across, but that would not be a very impressive accomplishment.
The problem isn’t that there could not be any use for something earlier than a TRS.
If I have a broken DVD drive that cannot work as a DVD drive, there still may be plenty of uses for it. It might serve as a paperweight or a doorstop or a boat anchor.
It is reasonable to think that evolution operating on the biological equivalent of a “paper weight” could produce an improved “paper weight.” Or that operating on a biological “doorstop” could produce an improved “doorstop.” Or that operating on a biological “boat anchor” could produce an improved “boat anchor.”
It is not reasonable that evolution would convert any of those things into the biological equivalent of a working “DVD drive.”
Even if there is a similarity to the end benefit provided by both the method of existing operation A and hypothetically better method Z, if the methods used to produce the benefit are fundamentally different, then it is problematic to get to different method Z by evolutionarily refining method A. Evolution cannot say, “You know, there is a much better but completely different way to get this. Let’s start building toward that.”
In the case of molecular machines, no one has found the plausible gentle staircase that gets to the machines with selection preferring steps all along the way for increasing reproductive benefits. To get there incrementally in small steps, one would need benefits that don’t come from the new method, but that nevertheless lead toward the new method (that has never been used and has never been anticipated) with more and more selectable reproductive benefits all along the way at every small step. Yet with no intention and no foresight of the new method.
How does evolution move the organism toward, “Let’s process an mRNA with a sequence of matches of the nucleotides as groups of triplets.”, in numerous small gentle steps of increasing reproductive benefit when there is no docking of mRNA for such a purpose, no prior need for triplets as such, etc. and the organism has never before processed a strand by successively matching its nucleotides in small groups of triplets? It cannot care about what any of that would do in the long run. It only considers immediate reproductive benefit to determine the direction of selected changes.
ericB,
Eric,
You seem to be arguing that ‘TRS function’ is arrived at, in my tiny mind, by a series of random walks by the same sequence, each gradually getting closer to TRS and providing a benefit before (perhaps with duplication) the next step is taken. That’s not it. Full TRS function is a conglomerate of many sequences. The random walk is taken by the entire genome, rather the entire set of the population’s genomes, and novelty can come from anywhere within it (and, indeed, from outside by LGT). Additionally, the adaptive landscape is multidimensional. Benefit can come in any manner of different ways. And changes to the organism change the landscape.
Your apparent mental image equates to an adaptive landscape with no higher ground whatsoever within reach of a random walk. You can make a dipeptide? That’s your lot, buddy. Artificially restricted, I’d say. It’s a shame you didn’t take on board Hoffmann’s message from the talk about randomisation being a great way of shaking novelty out of a system.
A sequence never becomes truly ‘dead’ after it has gone a-driftin’. It can donate a segment to another sequence which will mostly do nothing or be harmful, but will occasionally be beneficial. Like other beneficial mutations, it only has to happen occasionally. The unmutated majority is a placeholder. The detrimental ones are lost. The rest are evolution-fodder. Only if ‘the rest’ is an empty set do you have any hope that adaptive evolution will stall.
well, ericB, since Allan Miller apparently hasn’t read Life’s Ratchet and doesn’t care to defend it’s arguments, and Mike Elzinga claims he has read Life’s Ratchet but doesn’t appear to care to defend it’s arguments, maybe it’s time for you to drop that whole line of argumentation.
The reason I know you haven’t read it is because I had been asked to do a book review of it – which I did – long before you started pretending you read it.
Hoffmann’s book is way over your head.
Peter M. Hoffmann:
How so, Mike? Was that covered in your book review?
Maxwell’s Demon 2: Entropy, Classical and Quantum Information, Computing
Poor Peter Hoffmann. His groundbreaking work seems to have been excluded.
That’s right, Mike, I’ve never read it, but if I have read it, I don’t understand it, but if I have read it and I understand it then I’m lying about it, because I’m an ID’ist/Creationist. But you’re the real skeptic here.
Lizzie would be proud of you.
Peter M. Hoffmann:
Shades of “the Elzinga challenge!”
Who wrote:
multiple choice:
a. Mike Elzinga
b. Peter M. Hoffmann, in Life’s Ratchet
c. Some ID/Creationist nutjob.
d. Anyone taking an objective view of the evidence.
Oh, you mean like you claim to have read Darwin’s Doubt but don’t appear to care to defend its arguments. Got it.
I suspect that even that book is way over his head.
He just wants to “debate” over the meaning of the meanings of meanings. He doesn’t have to know anything to do that.
Oh for Chrissakes Mung! Of course I’m not going to defend the arguments of a book I haven’t read. I’m busy defending my own arguments! Make all the feeble capital from that you wish.
I dutifully watched the video because Eric considered Hoffmann’s statements in Q&A to be important. So I spent some time doing Eric the courtesy of watching it. Having done so, I don’t consider it relevant to this argument (though it is interesting, and there is a lot you could learn about the scale dependence of interaction and the role of randomness).
And you have succinctly extracted the reason why. Ya see (as Joe G might say):
Evolved from enzymes. That means after the evolution of the “Triplet Reading System”, at least for those that are protein. So OT for my purposes. If you want to talk of the ribosome … well, we are, at least in part, dunno if you grasped that.
Mung,
Mung
So if we don’t see Origin events on a routine basis, there wasn’t one? Or just not a ‘natural’ one?
Hoffmann clearly states that there was an origin. I heard him say it. Either he’s very inconsistent, or you are taking something out of context.
I missed this which arrived from Eric while I was composing my post of 3:57am Saturday.
ericB,
[snip … Hoffmann Hoffmann Hoffmann …] As I have said, arguing by pet expert is not productive. What am supposed I to make of the fact that someone who knows more than me about the operation of molecular machines does not have an explanation for their origin? That when we talk of a structure, the ribosome, that can be described as a ‘molecular machine’, we can’t possibly have any more idea than Hoffmann? You’re right, Eric. Hoffmann appears stumped. Therefore it’s unanswerable.
You can’t seriously have read everything I’ve written on the matter and conclude that that is what I’ve been saying, can you? The excerpt above is merely saying that a TRS has those characteristics, otherwise the T (triplet) part is meaningless. You can’t have 10% of those characteristics. So when you say “what use is 10% of a TRS?”, it’s meaningless. A system can be intermediate between No-Peptide-Bonds and a TRS, and fully functional for its present role, without being describable as “x% of a TRS”.
In precisely the way I have outlined. Your intuition regarding macro-scale, designed objects is leading you in the wrong direction (a direction I suspect you are only to happy to be led). It’s biology, Eric. Different segments of DNA (or RNA) do something and the possessor of amended versions of such sequence has the same, or a better or worse, chance of survival or reproduction as a consequence. Where there is a multi-part system, this is generated from multiple segments of the RNA/DNA which each find their effect on survival/reproduction affected by the presence of the other (epistasis). It is not necessary that these parts come together in a ‘machine’, but to the extent that they do, it is not a matter of copying working machines and tinkering with them, but copying the genetic sequences and assembling them afresh each time. And again: it’s biology; there is much more lability in these assembled structures than in brittle constructions of metal and silicon, or in computer programs.
1) A simple system joins an amino acid to ATP to produce amino-acyl AMP. This has many potential ‘selectable benefits’, and doesn’t need a molecular machine to do it, but a chemical catalyst. RNA can do this. RNA Sequences just 5 bases long can do this. You want THE selectable benefit? How the hell should I know? Complexing molecules with ATP occurs all over the place, as a step in many reactions. I think we can reasonably surmise that the ability to do this is superior to its absence.
2) Aminoacyl-AMP can donate the acid to a length of RNA. I’m willing to bet that the terminal sequence of this RNA was ACC, and the acid was attached to the A. Doing this via the intermediate of aminoacyl-AMP makes the reaction energetically favourable, and generates a ‘high-energy bond’ between the acid and the terminal Adenosine. Selectable benefit? How about transport?
3) Two acylated ACC-terminal carriers can, if oriented correctly, generate a peptide bond. The amino acid of one remains attached to the ACC, the other, because of the shifting of electrons to make the bond, is detached from its ACC carrier, which becomes free to be aminoacylated once more. Selectable benefit? Simple uncoded peptide manufacture.
I’m going to stop there because I suspect I may be pissing in the wind. The point I am trying to get across is that this is not a machine-for-making-proteins, but 3 or 4 separate ribozymes which pass products between each other by diffusion, and each of which has the potential to be there for reasons other than to contribute to the full 1+2+3 system.
But you might see in 3) the glimmer of a proto-ribosome – the ‘origin’ of the peptidyl transferase centre. I’ll go through the rest if you like, but while you keep on thinking in terms of DVD players and reminding me that the system cannot be preserved for its future benefit, I’m not too sure how productive that would be.
No, actually as I already explained to William people draw conclusions based on your general behavior and not just your specific claims.
For example, you make a claim to have read a particular book but seem unable to engage on points raised by critical reviews of that book either in this thread on linked to externally.
Therefore your claim of having read the book has to be balanced against your inability to actually engage on the contents of the book.
So on balance it does not matter if you’ve read the book or not, only that you are capable and willing to engage on the content. And you are not. So it does not matter if you have or have not read the book, same difference!
Collecting a few more observations for easy reference…
Observation #8: Natural selection operates (or not) according to the current presence or absence of selectable reproductive benefit. It does not consider potential future benefits or past benefits that no longer apply.
The vision systems in cave fish were once beneficial. If the fish or their descendants were to reemerge into lighted conditions, it could become beneficial again. Natural selection doesn’t care. Lack of current selectable reproductive benefit means the sequences supporting vision will accumulate random neutral copying errors. The fish go blind.
Observation #9: Learning from a WEASEL about Artificial Selection vs. Natural Selection
If one wanted to suppose that evolution could create the innovation of a complex new molecular machine or system of multiple coordinated components, here is an ideal property for natural selection to have. It would all work very easily if cumulative selection operated based on nearness to eventual function. But in reality, natural selection doesn’t consider future functionality or benefit (cf Observation #8).
When Richard Dawkins used the famous WEASEL program as an illustration of the power of cumulative selection, he indicated that it was not an accurate modeling of natural selection. It actually models artificial selection.
The program starts with a random sequence of letters and spaces. At each generation, potentially imperfect copies are made. The artificial selection process keeps those sequences that are comparatively nearest to a distant ideal target sequence such as “METHINKS IT IS LIKE A WEASEL” — even if all the preferentially retained sequences are all still meaningless gibberish.
It is this property of artificial selection that allows the program to function at all effectively when faced with multiple sequences, all of which are meaningless and therefore completely without function in the context of meaningful English text.
In contrast, natural selection would not preserve the contents of any sequence that is not currently providing reproductive benefit. So long as this remains true, all such sequences would be randomized by the accumulation of random copying errors.
Observation #9a: If people assume that natural selection will reward and preserve changes just because they bring a molecular machine or system nearer to operation or that nearness to operation itself implies reproductive benefit, they are mistakenly thinking of artificial selection as illustrated by the WEASEL program, not natural selection.
Observation #9b: The actual behavior of natural selection with regard to any sequence that is not currently providing selectable reproductive benefit is exactly the reverse of what the Dawkins WEASEL program illustrates.
Imagine any run of the WEASEL program proceeding from a nonsense random sequence via many generations to an accurate copy of some meaningful sentence. Now consider the lineage of that final descendent copy that arrived at the target, but considered in backwards order from a copy to its immediate ancestor going back all the way to the original random sequence.
Considered in the reversed order, the process is one of accumulating random changes that are degrading the functional integrity of the once meaningful sequence.
This reversed illustration perfectly depicts the trajectory of change by Neutral Errors in Copying, Randomly Occurring for any sequence that is not contributing to reproductive success, including those that formerly made such a contribution (e.g. supporting vision for cave fish). The very real consequences of N.E.C.R.O. are the exact opposite of what is depicted by WEASEL’s artificial selection.
Observation #9c: When considering the origin of a complex molecular machine or system, the only intermediate natural selection options available during its progressive construction are those which, by definition, cannot depend on the completion of the machine or system.
If selection is not operating to preserve the integrity of the sequences that will be required for the new system, they will be continually randomized over time by accumulating neutral copying errors. This would effectively result in the bleak prospects of a blind random walk through a sparse and exponentially vast multidimensional search space using the limited resources of a finite population and linear time.
Yet, natural selection cannot select for the future operation of the system or according to nearness to that future benefit (as can happen for artificial selection). The only selection that can occur is for present real reproductive benefits that are contributed prior to the operation of the completed and working system.
Therefore, the only selectable benefits possible are those that must not need the proposed system to be operational in order to enhance reproductive success.
Observation #9d: This can lead to the paradox of trying to justify the construction of a new complex molecular machine or system by appealing to natural selection for benefits that exist and are provided without any need for that prospective system to become operational.
Example: Any reproductive benefit provided prior to the existence of an operational Triplet-Reading System is necessarily one that does not require that any operational TRS ever exists.
[Anticipatory reminder to any who may have missed it. Observations #9c and #9d are discussing the period prior to the operation of the new system. Since the initial operation of the prospective new system is in the future, it is not yet operating partially or poorly or at all.]
Eric,
If I appear grouchy … well, I am, sometimes! I am very aware that people’s conception of a God matters very much to them, and the neatness of various things in biology is very much a part of that. In a way that would have me drummed out of Atheists’ Club were I to join such a bizarre organisation, I kind of hope I’m wrong and you’re right. Not about the molecular machines, but the broader questions. I love existence! But either way, the fact that a collection of atoms can probe itself, can come to a pretty fair approximation of understanding its own ‘stuff’ … I just find that incredibly … well, cool. I’m not trying to disabuse anyone of anything, just trying to convey the intellectual satisfaction that even our incomplete grasp of the story can bring.
Allan
Earlier I pointed out that degradation of the sequence by random change is an issue prior to the occurrence of your “one accidental success to fix the basic system”.
In addition, this claim of yours, “I have offered a potential selective advantage for all steps,” highlights a couple severe problems that run through your proposal both here and in the full proposal for the earlier thread.
#1. For each “step”, the “potential selective advantage” you offer comes after achieving the step and is based on the assumption the step would be achieved.
This does provide a reason to believe the step of adding system X would be preserved, if it occurred. However, since natural selection is oblivious to future benefit, it cannot provide any reason to justify the assumption that system X would occur. At best, your proposed advantages provide support for the survival of hypothetical organisms that have that system. It provides no answers at all for the questions about the plausibility of the arrival of the system despite all obstacles. (The same problem can be described allegorically.)
Pointing out the value of a destination does not show the destination will be reached. Yet, it is the questions about the plausibility of the undirected origin of these features that are the central ones being raised, both before and now. In short, they provide answers to the wrong questions.
#2. By claiming you have “offered a potential selective advantage for all steps”, it’s clear that you are referring to your large conceptual steps (leaps actually), not to the many small steps of actual change that would be physically required, e.g. to build the first TRS.
The distance between your conceptual steps for which you’ve “offered a potential selective advantage” is not a small span that could be traversed by a short random search of the local neighborhood of possibilities. Consider the distance between the specific potential selective advantages you’ve offered that bracket the construction of the first TRS.
On one end, you’ve pointed to a subsequent potential selective advantage that could fix the system sometime after it is operational. (Therefore, it does not explain its origin.)
On the other end, you’ve pointed multiple times now to proposed advantages that would precede the TRS, especially the prospect of creating a dipeptide without needing a TRS. For example (my italics added):
Since there is “no TRS” needed for this earlier advantage, and since the TRS has been fully operational for some time to produce the latter advantage you offered, the process of constructing a working system that actually reads triplets falls entirely in between this pair of “step” advantages that you’ve offered.
Yet you claim to have “offered a potential selective advantage for all steps”? How about the steps whereby the organism to actually builds a system for matching a sequence as triplets?
When I asked you “How does evolution move the organism toward, “Let’s process an mRNA with a sequence of matches of the nucleotides as groups of triplets.”, …?”, your response seems to fall back onto vague generalities and hand waving.
What follows is more detail about forming a peptide bond — without using a TRS or needing one. So we still don’t have any real indication that an undirected process would actually lead toward processing a sequence as a series of consecutive triplets, i.e. no real indication that this will “ultimately lead to the basic TRS.” That is a pretty vital missing piece for a Triplet-Reading System where you claim to have “offered a potential selective advantage for all steps”.
Furthermore, the situation is made difficult by the fact that every instance of natural selection that you might appeal to during the construction of the TRS will necessarily be for reproductive benefits that don’t require any TRS to be operational (cf. Observation #9).
How then do you propose to make plausible that the organism would build such a system to read a sequence as triplets?
Eric
eta – we cross posted within a minute. I’ve had a quick squint, but it’s too late here to do more than blink. I may still be blinking when I read it again in the morning. 😉
Not a problem. I welcome your contributions, grouchy or not, and miss them when you are not participating.
Even if I am sometimes harsh in my evaluations of some points in your posts, I value your posts highly. You work to deal with the subject matter itself and therefore you among those who set a positive example. May those that follow that example increase!
No, that’s not how it happens. Eyes and vision take energy. In a lighted environment the energy cost is balanced by the survival benefit vision provides. When the environment changed to zero light, the eyes still cost energy but provided no benefit and became a liability. Mutations to the eyes that shut down vision were therefore beneficial (not neutral) to the fish because those fish who lost didn’t have to expend energy building / maintaining vision. In the other direction, the energy saved on eyes could be used on heightened additional sensory systems such as smell and hearing so those mutations were selected for.
Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish
Yoshizawa et al
BMC Biology 2012, 10:108
“Conclusions: We conclude that natural selection for the enhancement of VAB and EO SN indirectly promotes eye regression in the Pachón cavefish population through an antagonistic relationship involving genetic linkage or pleiotropy among the genetic factors underlying these traits. This study demonstrates a trade-off between the evolution of a non-visual sensory system and eye regression during the adaptive evolution of Astyanax to the cave environment. ”
Once again you flat out refuse to understand that any genetic mutation can only be judged deleterious, neutral, or beneficial with respect to its effects in the current environment. You keep making the same beginner’s mistake over and over and over and over.
This is a perfect description of the misconceptions ALL ID/creationists have about molecular assemblies and evolution in general.
EricB’s misconceptions about genetic algorithms are also consistent with his 1/(n^l) calculations for the probability of an assembly of atoms or molecules. In ID/creationist world, specified molecules are formed directly out of an “ideal gas” of inert atoms and molecules.
The WEASEL program doesn’t need a “meaningful” English sentence in order to work. It could have been any randomly generated string. But not one ID/creationist knows why.
I am quite certain that ericB cannot even conceive of what an ID/creationist “genetic algorithm” would look like, and how he would justify it.
Eric, in response to Allan’s statement:
You wrote
The only interpretation I can put on this exchange is that you are describing an organism that ” produces a ‘useful’ dipeptide’ using ribozymes.” as having a TRS. This is much the same mistake that you made on the previous thread, where you referred to Allan’s “simple peptide bonding ribozyme” as
“a simple ribosome capable of receiving a random non-coded RNA sequence as guidance”.
You appear to be repeating the same misconceptions, even after they have been pointed out to you. Do you understand that a dipeptide could be synthesized via a process that is NOT template-directed? In fact, a specific dipeptide could be synthesized via a non-template-directed process.
Likewise –
You do understand that RNA replicators evolve?
And that Mike’s RNA sequences are not equiprobable?
Your argument seems to consist of endlessly repeating that [evolution cannot consider future benefit], but AFAICT no-one, on either thread, has ever suggested otherwise.
Finally (third time’s a charm)
Eric, what is the minimum number of different codons that your “functional(tm), operating, reproductively beneficial TRS” must recognize?
Eric, what’s wrong with this thought?
I’m not asking you to agree or disagree. Just ponder this concept and tell us what’s wrong.
This assertion is dead wrong; and it is more evidence that ID/creationists don’t understand how scientists can write computer programs that mimic the processes found in nature, thereby producing the results found in nature.
ID/creationists think that scientists put the answer into the program.
Dawkins WEASEL program is so simple that it is easy to program on even a graphing calculator; yet ID/creationists don’t understand it.
Furthermore, ericB cannot tell us what an ID/creationist algorithm programmed on a computer would actually look like and how he would rationalize the algorithm.
Eric,
Perhaps in light of DNA Jock’s comment, you are reading “ribosome” when I say “ribozyme”. That would make more sense of your responses.
I have composed a longer response to your last, but need to give it a bit more thought. From where I sit, you have a number of misconceptions about the roles of variation, selection and drift, and serial pathways of adaptive evolution, but I’m running out of ways to address them.