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.]
Mike Elzinga,
I think that he means “it will no longer be protected by natural selection from randomizing degradation.”
I also think that he is guilty of dichotomous thinking, viz: “either it is subject to selection, or it isn’t”, with a bright line between the two categories that cannot be traversed.
It would be nice if he would address criticisms and requests for clarification, but that does not seem to be his style
😮
If iit is neutral it passed through selection. How hard is that to understand?
If only there was some way to test the concept of neutral mutations, some component of the genome that was passed on to each generation “as is” except for the rare mutation(s). Then it would simply be a matter of compiling the mutations and analyzing their impact on function — real world data! Why oh Y is there not such a chromosome?!
Hey, wait a minute . . .
ok, the OP mentions, by name, OMagain.
So I thought perhaps OMagain might produce a substantive response.
No kidding. So?
How can we test this claim? A change in DNA might lead to the expression of more or less of a protein. Or it might not.
A change in code would on average lead to “no protein”. Sez who? Or it might not.
Neil Rickert:
Cells are based on logic gates. Does it follow that they are very brittle?
Isn’t this exactly what we see with cells?
Neil Rickert:
How fortunate are we then, that neither philosophy,. nor mathematics, nor science, are based on logic.
There is a famous (and apparently true) story about the mathematician G. H. Hardy. When he heard of Gödel’s proof (that one could not prove a set of axioms to be consistent) he remarked that we should have realized that. He pointed out that when axioms are inconsistent, they can be used to prove anything, true or false (including that the axioms are consistent).
A listener said “Wait a minute, do you mean that if I grant you that 2+2=5, that you can prove that McTaggart is the Pope?” Hardy said, of course. “2+2=5, but we also know that 2+2=4. So 5 = 4. Now we subtract 3 from each side and we have that 2 = 1. Now McTaggart and the Pope are two, so McTaggart and the Pope are one”.
Hardy’s argument is not a verbal trick, but is a rigorous proof.
Yes, Mung, mathematical proofs are fragile, as Neil Rickert quite correctly said. Extremely fragile, as Hardy pointed out.
Neither mathematics nor science is based on logic. Both use logic as a tool, but not as anything like a basis.
I don’t know about philosophy, though I do sometimes wonder whether many of the problems of philosophy are due to philosophers trying too hard to base their work on logic.
Why are they so demanding when it comes to exacting detail when answering their questions and so lax about even recognizing any questions asked of them, let alone answering them, detailed or not? Doesn’t this constitute a form of bad faith all its own? I know Lizzie demands we not disparage what they know but that isn’t the only way to show bad faith.
One can’t help noticing that his ID/creationist arguments avoid all biology, chemistry, and physics. He doesn’t even acknowledge the existence of these sciences.
He just asserts that whatever happens to the computer code in his “analogy” also happens to the molecules of life.
I have yet to see an ID/creationist “argument” that isn’t about inert things acting as stand-ins for the properties and behaviors of atoms and molecules.
So I am pretty sure that ericB’s knowledge of any science doesn’t extend beyond middle school level – if it even approaches that level. He is totally blind to any science; he doesn’t even recognize a science question.
EricB:
Start with a single sequence, and assume it well-adapted: most changes to it will be detrimental. If, on the other hand, it is poorly adapted, but there are better adapted versions lying as neighbours, random exploration of that neighbourhood will push it in the ‘adapted’ direction. So it depends. You seem to be looking for a universal scenario to something that is very contextual.
Once it has got to an adaptve peak (though I, too, would prefer to reverse the landscape, uphill fitness improvement is the convention) it is severely constrained, because most movement is in a less-adapted (even if historically successful) direction. So if you start from A****, and the best adapted version is ABCDE, AB*** would outcompete on the way up, but would be detrimental when ABCDE is fixed in th’population.
Suppose you now duplicate it. This does not mean you have twice as much ABCDE, which could in any case be disastrous. The reason is the feedback control that accompanies gene expression. Part of adaptation is the dosage control by substrates or other downstream/upstream products. They work to keep the total number of catalyst molecules or net reaction rates constant, regardless whether one or two prime sequences is supplying the raw material.
Then what? Well, ABCDE function could be compleletly disabled in one copy. Drift of this copy then allows probing of parts of the adaptive landscape unavailable to ABCDE alone. Or, there could be a complementary coupling of the two copies, which again opens up the landscape to amemdments unavailable to either alone. And this is an important ‘role’ of drift – it allows a landscape to be probed, even from a well-adapted position. Such ‘random’ processes ensure that evolution is much more likely than it is in a beneficial/detrimental dichotomy. Benefit is relative, a continuum, and ever shifting.
Note also that drift is not confined to the neutral zone. Drift is sample error, which can occur even with nonzero selection coefficients. It acts alone at zero (and when population size makes a given s value effectively zero) and plays a diminishing role as s values increase and selection comes into play. Once an adaptation becomes fixed, the population is almost back where it started – there is no reproductive differential. But it is a little higher up the nearest available peak, which reduces the landscape available to mutation.
Drift, and duplication (and not-discussed-above recombination), stop it getting stuck on such local maxima.
Correct. That is a central point of this thread about Neutral Errors in Copying, Randomly Occurring. Natural selection has no ability to weed out copying errors that do not negatively affect reproductive success.
Add the importance of this observation would be what?
ETA:
Actually, there is a way that natural selection can “weed out” neutral mutations. Five points if you can figure out what it is.
Post post post script:
More than one way. Of course no trait is positive or neutral or negative in and of itself. Everything depends on environmental context.
Perhaps with that hint you can figure out how a mutation that is neutral at the time it occurs might eventually be weeded out by selection.
[My original response to the following comment failed to post when TSZ was temporarily suspended.]
You were the first to recognize the cumulative degrading influence of random copying errors. Nevertheless, there are a couple points about what I’ve been saying that you’ve not understood quite correctly. For starters, consider the bolded parts of my earlier response to you below.
Regarding the first error you supposed, it’s clear in the response I had previously given to you that I did understand the idea that the two copies could function equivalently, at least until one of them is changed. As I said to you, either one of the copies could be the one that changes. I didn’t assume the duplicate is the one to change.
Similarly, the second error you supposed was about reduced selective pressure vs. zero selective pressure. However, nothing in my argument depends on assuming there is necessarily zero selective pressure for a duplicated gene. (My argument isn’t even primarily about biological evolution in the completed cell, though there can be applications in that context as well.) My argument considers any context where some form of natural selection is taking place. The argument is focused on “what happens to a sequence while under the influence of random neutral changes.” So I am specifically looking at the cases where any sequence does not contribute to (or significantly detract from) the reproductive success of the “organism.” When that is the case, then consider what happens according to the principles of natural selection regarding Neutral Errors in Copying, Randomly Occurring.
Finally, regarding the third error that you supposed, it’s clear I did not suppose that the copying errors must always remain neutral. Rather, I explicitly allowed that a copying error could occur that would result in a change that is either “detrimental or advantageous to reproductive success”.
I hope that clears up any misunderstandings on those points. Thanks for raising those concerns.
EricB,
It would help if you could precis your argument, as it is not clear.
There is a significant literature on neutral evolution. Are you asking a question about an aspect of it, or telling people what you think happens? There are many pseudogenes that no longer function, and most of them can be traced to duplication of other sequences. Nonselective evolution has disabled them. But are you saying that you expect all duplicated genes to become disabled pseudogenes? If so, why?
Nope, you are repeating your error. The two copies are equivalent, and both can accumulate neutral changes. They would still be equivalent. As they start to accumulate non-neutral changes, or as context changes to make previously neutral changes non-neutral, then both copies diverge.
This highlights the incoherence of your “what happens to a sequence while under the influence of random neutral changes.” If the changes are neutral, then drift occurs. In your “cases where any sequence does not contribute to (or significantly detract from) the reproductive success” changes in that sequence can still be non-neutral. “Neutrality” is a property of the change, not the starting sequence, and it is highly context-dependent.
Below is the text of the post that you are replying to:
In your response, you removed the second and third sentences, and gave a reply that indicates that you did not understand those sentences.
Please read the text that you edited out carefully; when the context changes, a particular mutation may move from any category to any other category.
Context is important, in text as in genes.
To repeat, just because the landscape is locally flat(ter), it does not follow that it is flat everywhere.
Focus on the numbered Observations. They are the step by step foundations. The aim of this progression is to debunk certain mythical tacit assumptions about natural selection that tend to frequently creep into thinking about origins and evolution.
Even though a clear understanding of the limitations of natural selection is available, nevertheless it is easy for the reasoning of evolutionists about origins and evolution to neglect to consider the severe limitations on what natural selection provides. Sometimes, when they are not being careful, they reason in a vague manner as if natural selection always generally encouraged everything to become “better” or as if natural selection would always keep working systems working.
It is easy, for example, to suppose that because sequences are expressed and are essential to the continued operation of some mechanism, e.g. the system for vision, that they will therefore be protected and preserved by natural selection. As stated, this is false.
For example, if the shifting environmental context becomes one without light (e.g. fish in caves) so that the vision system no longer provides any selectable reproductive benefit, then those sequences are not protected and preserved by natural selection from the randomizing effects of accumulating random copying errors — even though they are being expressed and even though they are essential to the continued operation of the vision system. The lack of selectable reproductive benefit means natural selection will not prevent the formerly working vision system from being degraded such that it ceases to function and the fish become blind.
Since the idea of “probing” can carry connotations of intention, it is worthwhile to consider more specifically the nature of the “probing” done by a sequence that does not provide a selectable reproductive benefit.
a) Copying errors occur… (since the copying is not perfect — else change would be impossible)
b) … and accumulate … (cf. Observation #2)
c) … randomly … (There is no intention to the “probing.” Obvious, but worth stating. cf. Observation #3)
d) … with a trajectory over time of randomizing the contents of the sequence regardless of their former content, continuing in this manner so long as the sequence does not provide a selectable reproductive benefit (i.e. changes remain neutral), … (cf. Observation #4)
e) … even if that original sequence was essential to the continued operation of some system that is not currently providing a selectable reproductive benefit. (cf. Observation #5 and Observation #6 and the example of cave fish becoming blind).
All of the observations understand that there is an environmental context (that can change), even when they do not repeat the point again explicitly. Nevertheless, for the sake at least of symmetry and to remove any doubt, I’ve added “within the current environmental context” to Observation #1.3.
In light of some expressed unclarity about Observation #6, I’ve also edited that for better clarity to say “a sequence that is redundant due to duplication” rather than “a duplicate sequence” (which was not meant to refer only to the newer sequence, but to either copy that is duplicated) and to say “protected by natural selection from randomizing degradation” rather than “protected from randomizing degradation by natural selection”.
My previous comment was made before I saw your latest comment (excerpts below), but I hope you find the clarifications to the wording of the Observations beneficial to remove misunderstandings.
No objections. My examination of duplication is mostly focused on what happens after either copy receives a change such that it no longer contributes a selectable reproductive benefit. I don’t think you are disagreeing that that can happen, and so I don’t see a disagreement here.
You insist on many good points that I don’t disagree with. So I’m not sure how to respond. You seem to think I don’t agree. Since I don’t disagree, it becomes difficult to “correct” anything, except to try to point out that I don’t see any significant disagreement in the points you are insisting upon.
I’ve indicated many times that context is vital, that it can change, and that selectable reproductive benefit is context dependent (e.g. the illustration of blind cave fish).
I’ve never maintained that changes to a sequence that provides no selectable reproductive benefit must always remain neutral. I’ve explicitly included statements indicating that the continued randomizing of the sequence is conditional on the changes continuing to be neutral.
I would have to say that as far as I can see, you are objecting to a straw man, not to my actual position.
You are making good points. I’m not objecting to these good points.
ericB,
I’m glad we agree on so much, but in that case your scenario appears to be devolving (heh) into a truism, as pointed out by Allan Miller. I will try to explain.
If one stipulates that a total loss of function for one copy as no selectable effect, then one copy is free to drift, become a pseudogene, gradually turn into total “space junk”. See parts of the Y chromosome. No dispute here.
However, this stipulation may or may not be true immediately following the duplication (copy number matters), and it becomes increasingly unlikely to continue to hold true as time passes and the two copies diverge.
NECRO appears to be merely a VLFLA for drift.
Eric has repeatedly ignored requests to explain the importance of all this.
The only importance I see is it enables new IC sequences, as in the Lensky experiment, where two “neutral” mutations accumulated and enabled a new function. Not exactly squirrel to bird, but not bad for a tiny lab population.
Eric,
Pointing me at your prior ‘observations’ does not consitute a ‘precis’. Credit me with a basic familiarity with programming, evolutionary theory, genetics and molecular biology, and explain succinctly (as if for a published Abstract) what your point is.
Ta
Allan
Since the idea of “probing” can carry connotations of intention, it is worthwhile to consider more specifically the nature of the “probing” done by a sequence that does not provide a selectable reproductive benefit.
Whatever connotations particular linguistic options carry is not particularly important. Random variation demonstrably shakes evolutionary algorithms out of local maxima. This fact is used in real applications. What you call what it is doing is, as I say, unimportant.
If you can’t do science using apologetics, what good is science?
If they are the “foundations” of anything, it is of word-gaming and evasion.
Blunt fact #1: That statement is absolutely false. Since you don’t know anything about basic science, you are only “arguing” from your ID/creationist talking points.
Blunt fact #2: This is a caricature of “evolutionists” that you are in no position to make since you don’t even understand high school level science. You don’t know what “evolutionists” think.
Blunt fact #3: This is pure projection on your part. This caricature of evolution goes right back to Henry Morris and Duane Gish starting in 1970.
Blunt fact #4: You don’t know what scientists suppose; and you are projecting your own misconceptions and misrepresentations onto the scientific community. You yourself don’t know any science; you can’t even use scientific concepts and terms properly. And you certainly can’t recognize when others actually do know things.
Blunt fact #4: You have absolutely no idea what any of that means.
Blunt fact #5: We have already demonstrated for certain – directly, here on this thread – that you don’t even know how to calculate probabilities of molecular assemblies. You don’t even have a clue what those memorized “calculations” that you presented mean, or if they have anything to do with atoms and molecules. You don’t even know if your ID/creationist leaders understand any science.
Blunt fact #6: Any conclusions you attempt to assert from your memorized “calculations” are meaningless. You are deluding yourself if you think anyone here buys such vacuous nonsense.
Blunt fact #7: Your only recourse is to constantly repeat yourself because you aren’t presenting anything based on an understanding of basic science. All you are able to do is word-game everything. You are mindlessly repeating memorized ID/creationist talking points over and over and over and over.
Blunt fact #8: Your “lesson plan” about evolution will get you laughed out of even a high school science class. Bright high school students don’t put up with such crap. Imagining yourself as a teacher standing in front of naive students and filling their heads with ID/creationist talking points will not only get you hauled into the head master’s or principal’s office; it will also very likely get you fired for gross incompetence because of your total lack of scientific knowledge.
Blunt fact #9: If you are the best that ID/creationism can come up with – and you are quite typical of an ID/creationist, by the way – then science has nothing but sectarian socio/political antics to be worried about. You don’t present any alternative to science except a sectarian pseudoscience.
Blunt fact #10: Your “discussion” on this thread is a perfect example of why ID/creationism will never go anywhere. It never converges to anything except endless word-gaming and evasion. In the 50 years that ID/creationism has been pushing its political agenda, ID/creationism has produced absolutely nothing in the way of scientific understanding. However, in that same 50 year period, as it did in the centuries before, science has converged onto an increasingly precise understanding of the universe. There is nothing you can “argue” or word-game that can dismiss that fact.
Science leads to steady progress; ID/creationism is nothing but endless haggling and word-gaming over nothing. You are an ID/creationist.
This goes beyond being merely incorrect. It is so wrong that it is contradicted by nearly anything written for the layman in the last 40 years.
You certainly won’t find it in Gould or Ernst Mayr, the two most popular writers for the layman.
Things do not get “better.” They change. If working systems always remained working there would be no extinction, but 99 percent of known species are extinct.
I’d appreciate someone fixing my close blockquote tag.
I hope I did that correctly. It wasn’t clear where it ended.
Crossposting this, which has some relevance to this thread regarding the pathways of selectable divergence available to a duplicated gene:
Rumraket,
Not in Eric’s scenario, of course, since that specifically excludes parallel evolution where both products continue to contribute to fitness.
An important part of my observations is that, in the general case, the degrading randomizing effect is not limited to cases of a prior loss of function. The vision system of cave fish was originally completely functional.
The pivotal issue is not “does it function” but “does it provide a selectable reproductive benefit.” This is a crucial distinction. Something can be functional and still not provide a selectable reproductive benefit.
This thread is motivated in part because evolutionists are prone to lose sight of that distinction. While this does have application within biological evolution, it has even more application in the realm of origin of life scenarios.
As long as one is only discussing theme and variations, such as when a duplication of existing sequence and function wanders off to fortuitously land on some other role supported by similar structures, then NECRO might be viewed as a Very Long Five Letter Acronym for drift. (However, even there, I would submit that many do not think seriously about the trajectory of drift, i.e. toward randomizing sequences.)
But at some point, one must contend with the origin of new functionality that is not merely a slight variation on a feature already present and already protected by natural selection. Yet, even in origin of life scenarios, one will typically still appeal to principles of natural selection.
Therefore, it becomes essential to be clear about the critical distinctions regarding the principles of natural selection, e.g. that mere “function” or being able to “operate” or “being expressed” per se is not sufficient to provide protection by natural selection against the degrading randomizing influence of NECRO.
If there are no serious objections to the Observations about the principles of NECRO, I hope to find time this weekend to get to some applications of the principles.
Natural selection does not protect against drift, but you have not conceptually given any reason why it doesn’t protect against degradation.
I can assure you, they are not. When two alleles function differently, but do function, they can still be neutral with respect to each other. This should be news to no-one who has done elementary evolutionary theory.
No-one should be offering Natural Selection as a causal mechanism prior to the origin of competing replicators. Tell me who these people are and I’ll go round and duff ’em up.
If you talk about ‘degrading’ you must be referring to some sense in which the changes render the individuals less fit. Else by what criteria do you define ‘degradation’? What, other than survival/reproduction, adjudicates upon sequence ‘quality’? The notion of degradation that is invisible to selection seems incoherent. Purifying selection will offer protection against incursion by deleterious sequences (although statistical effects – drift of non-neutral alleles – mean that this is not guaranteed in any specific instance). Non-deleterious changes (including neutral ones) will not be subject to such selection, but nor are they degradative.
Just cut to the chase, Eric.
Based on the history of ID claims, there is no chase. Just another installment of “it’s so complicated, therefor goddidit.”
I think Eric has meltdown in mind, but he can’t say that because he know it’s bullshit.
So he pushes the problem back to an era which has no fossils, OOL.
Yes, perhaps the argument will prove to be a cousin of Sanford’s (we must speculate in the absence of the actual argument!).
Indeed. This pattern of attempting to lead one’s interlocutors up the garden path is common among creationists and demonstrates gross lack of respect.
Eric, if you have a point or an argument to make, make it as clearly and concisely as possible in a single post. You might not convince anyone, but you’ll at least demonstrate some intellectual integrity.
I fear he already has made his point and can’t figure out why it isn’t devastating.
On the contrary, I don’t expect anyone to seriously disagree with any of the Observations that I’ve been making, once they think it through.
What I do observe, however, is a tendency to treat ability to function (or the expression or operation of some feature) as being more or less interchangeable with reproductive benefit, as if they are the same concept, or as it there is only one concept to consider. Yet they are not the same.
I have indicated through the Observations exactly why natural selection will not protect any function (or the sequences that make such function possible) against degradation — leading ultimately to the loss of that function as the supporting sequences are randomized — whenever that function no longer provides a selectable reproductive benefit. In caves without light, the vision systems of fish (and the sequences that made vision possible) degrade because they are no longer protected by natural selection.
It’s not the case that I “must” be thinking about degradation in the sense that you supposed, or that this is the only possible meaning of the term.
As soon as one makes the clear distinction between the ability of a system or mechanism to operate or function and the question of selectable reproductive benefit, then it becomes clear and obvious how one can meaningfully talk about the fact that natural selection does not necessarily protect against degradation. This can be so whenever the degradation of the function does not adversely affect selective reproductive benefit.
Notice that is not a claim that the organism is thereby less “fit” with regard to selection and reproductive fitness. The suggestion of an equality between those concepts comes from your question and its assumptions, not from my position, which in part is to try to point out the distinction between those concepts.
A central point of mine throughout is that sequence integrity with regard to function or ability to operate in any fashion is not protected by natural selection — unless that function also provides a current selectable reproductive benefit. Without that, degradation of the sequences and the associated function will occur over time. Cave fish will go blind. That is the sense in which I have referred to degradation throughout the thread.
I believe you have a tendency to misrepresent what biologists say and think. I think you need some citations.
Cave fish genomes do not degrade. They adapt to a changed environment.
ericB,
I would change one word:
By the time “degradation” occurs, however, the functionality of that particular sequence may no longer be necessary.
As in your example of cave fish, eyes that are perfectly functional may not provide any improvement to reproductive success compared to cave fish with limited functioning eyes or missing eyes. If it’s a neutral change (and if the population sufficiently large) then we would expect a mix of eye types to be sustained across generations. It’s only when missing eyes provide an improvement to reproductive success that we would expect it to spread throughout the population.
In other words, the need for a given function can be lost before the genetic integrity of that function.
Natural Selection of the Chemical Elements
Have you read it? The book?
Mung,
Mung, I can only read an abstract. No doubt you have coughed up and read the whole thing, so you can correct my understanding: it seems pretty clear that he is referring to the usage of elements by replicators, not the origin of those replicators. So far Williams, he will be relieved to hear, is spared a duffing-up.
Biochemistry is the study of an intricate interwoven `designed’ use of many elements in cells. It can only be fully appreciated in terms of the patterns of flow of chemicals, of ionic and electronic charge, and of energy directed in space. This requires a knowledge of the selection of the elements not only in analytical terms of uptake and chemical combination but also in terms of their spatial separation and functional specification. Starting from the abundance and availability of the elements an attempt is made here to analyse the roles of the elements, showing that much of the `chosen’ chemistry is an inevitable consequence of atomic properties. Selection has played upon this chemistry, extracting the utmost value from it, as seen in the refinement of functions of individual elements so that each element plays a quite separate and distinct role. Unique qualities dominate comparative similarities through the use of evolved specific small molecule and protein ligands. Proteins provide the evolutionary media for the development of function. It was the recognition and separation of each element in their specific sites (proteins) that allowed elements to be positioned in space. In turn the spatial organization generates, through feedback, the flow of other elements. Biological chemistry is only understandable in terms of the symbiotic use of some 25 elements and should not be related to so-called organic rather than to so-called inorganic chemistry.
I don’t know where you do your observing. Loss of function can provide reproductive benefit.
Well, I did offer the opportunity to actually SAY what alternative criterion you have in mind. That you ‘must’ mean degradation in reproductive terms … or … what?. The available arbiters of a ‘degraded’ sequence are reproductive success and an opinion.
So we have established that NS does not protect against loss of function. You choose to call that ‘degradation’. The hind limbs of the whale, the appendix, the GULOP gene, our feeble covering of hair … NS has not ‘protected’ these functions (and in some instances may actually have participated in their ‘degradation’). Got it.
rhampton, You raise a good point with regard to the wording question between what I said
and what you alternately proposed
I did consider that question, even before I saw your comment. I would suggest that the distinction is not one of kind but one of time. I have a one word suggested change for you. You said…
The idea that the mix is being “sustained” implies or suggests the operation of some principle that would sustain it. Yet, all descendants are subject to the non-zero probability of copying errors, including those that degrade the vision system. It is only a matter of time and probability until vision is lost across the population. When we find blind cave fish, do we still find that some of their sibling fish can see? Early on this would certainly be true but over time it would become less and less likely.
The key is that the process is not limited to transmission of errors through inheritance. It also occurs as the result of independent new copying errors. Of course, the rate that all of this takes place is influenced by many factors, such as by proof-reading to correct copying errors, for example. In pre-cellular systems without proof reading for copying, the error rate would have been much greater.
Applying the Principles of N.E.C.R.O. to the Origin of a Triplet-Reading System for Peptide Synthesis
While the principles of Neutral Errors in Copying, Randomly Occurring do have applications within biological evolution, the primary focus of this thread is their application to origin of life issues, especially the origin of the molecular machines needed for the operation of cellular life. (Hence the new category Origin of Life.)
An example of this is the translation system that decodes the information encoded into protein coding DNA to produce proteins. An essential subsystem of the translation system is the Triplet-Reading System, which reads an RNA sequence as triplets of nucleotides. Each of these triplets is matched by a corresponding tRNA.
Allan Miller made a proposal earlier concerning the origin of the translation system, and of the Triplet-Reading System in particular. In his proposal, initially he supposed a single tRNA, which means the only sequence that could originally be matched would be one in which the same triplet is repeated over and over. That creates problems in itself (e.g. some mentioned here), but passing over that for now, consider the relevance to this thread on Neutral Errors in Copying, Randomly Occurring.
Allan made this comment about suggested early version of the ribosome to promote peptide synthesis.
Notice that even though the system was not designed to provide a benefit, there is an expectation that at some point after it is operating it will produce “one accidental success to fix the basic system”.
This implies that prior to the occurrence of this accidental success, there is an acknowledgement that the basic system is not yet fixed. While it is perfectly reasonable to expect that an undesigned system cannot be assumed (absent teleological assumptions) to be beneficial immediately, the consequence is that even after operation is supposed to have begun in some basic manner, it is not yet providing the accidental selectable success that will come later.
This means that, at best, it is under the influence of Neutral Errors in Copying, Randomly Occurring. (At worst, it could interfere with replication. Natural selection would work to eliminate those cases.)
Those errors occur randomly and they accumulate. The trajectory of that process is to randomize any sequences that are not currently providing a selectable reproductive benefit.
And just as is true for the vision system in cave fish without light, while it is not providing a selectable reproductive benefit even a working system is not protected from degradation and the resulting inability to operate. The random copying errors can happen anywhere, including in any of the many ways that would disable such a system.
Since this is so even after operation has supposedly begun, the much more serious problem is that it is certainly even more true prior to the beginning of operation.
It is necessary to assume there are copying errors (else with perfect copying there would be no change).
Since these are unguided errors, their location is random and not with regard to any plan or concern for future ability to operate or provide a benefit.
The neutral errors will accumulate throughout those sequences that (it is hoped) would be transcribed eventually into the components of a working system.
Since natural selection has no ability to consider possible future benefits, it cannot possibly act to prevent the accumulating randomization of any sequences that don’t yet provide selectable reproductive benefit.
In short, to put it mildly, it is severely problematic to try to use a process that continually randomizes sequences with accumulating random errors as the foundation for trying to build new molecular machines as systems of stable coordinated parts. It will always be far easier for an accidental random change to interfere with its future operation.
It would be unreasonable to expect any such process to ever reach operability, let alone persist in operation long enough to subsequently produce results even later yet that could be selected as beneficial to reproductive success.
Engage with the scientific literature dealing with exactly this or stop wasting everyone’s time.
Eric, you seem hung up on the word error, as if changes to a sequence simply have to be bad.
Consider for a moment that in the Lensky experiment, a small lab bound population had sufficient time and resources to “try” every possible point mutation.
Chemistry simply isn’t analogous to computer programming. There is no grammar or syntax that allows us to read new molecules for meaning (as we can read new utterances in English or COBOL for meaning) .
You cannot know the effect of a new sequence without trying it. Not even in principle. Feel free to offer a counterexample.
DNA is not a language. The analogy fails at its core.
That’s about as clear an example of ericB’s fundamental misunderstanding of how evolution works as one could ask. Changes to the genome aren’t errors, they’re merely variations. Whether on not a particular variation work better, the same, or worse than the original depends entirely on the surrounding environment.
ericB has the same Creationist mentality that John Sanford and many Fundies exhibit. The genome was created “perfect” and any change at all must be a degradation by definition. Of course this naive belief has been disproven 1000X over by the empirical evidence.
I know this basic error has been pointed out to ericB a dozen times but until he grasps the concept – that the effects of mutations are context dependent – there’s just no hope of having an intelligent discussion.
Eric, this is so simple it is impossible that you cannot understand it.
Languages (human and computer) share one interesting property: Novel utterances can be understood by any speaker of the language. Anything I say in English can be understood by anyone who has the vocabulary.
Chemistry does not share this property. If you make the analogy that DNA is coded instructions, you could say that an interpreter of the code can follow completely novel instructions, but that is not the same as reading for understanding.
When you get outside the realm of regular molecules and crystals, and into the realm of complex organic molecules, you simply can’t abstract the code. You can’t determine the properties of a new chemical utterance without making the molecule and trying it.
Hence evolution. Cut and try. Feel free to cite a counterexample.