What are the limits of Random Variation? A simple evaluation of the probabilistic resources of our biological world

_{gpuccio
October 31, 2017

Intelligent Design

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Coming from a long and detailed discussion about the limits of Natural Selection, here:

What are the limits of Natural Selection? An interesting open discussion with Gordon Davisson

I realized that some attention could be given to the other great protagonist of the neo-darwinian algorithm: Random Variation (RV).

For the sake of clarity, as usual, I will try to give explicit definitions in advance.

Let’s call RV event any random event that, in the course of Natural History, acts on an existing organism at the genetic level, so that the genome of that individual organism changes in its descendants.

That’s more or less the same as the neo-darwinian concept of descent with modifications.

A few important clarifications:

a) I use the term variation instead of mutation because I want to include in the definition all possible kinds of variation, not only single point mutations.

b) Random here means essentially that the mechanisms that cause the variation are in no way related to function, whatever it is: IOWs, the function that may arise or not arise as a result of the variation is in no way related to the mechanism that effects the change, but only to the specific configuration which arises randomly from that mechanism.

In all the present discussion we will not consider how NS can change the RV scenario: I have discussed that in great detail in the quoted previous thread, and those who are interested in that aspect can refer to it. In brief, I will remind here that NS does not act on the sequences themselves (IOWs the functional information), but, if and when and in the measure that it can act, it acts by modifyng the probabilistic resources.

So, an important concept is that:

All new functional information that may arise by the neo-darwinian mechanism is the result of RV.

Examining the Summers paper about chloroquine resistance:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035986/

I have argued in the old thread that the whole process of generation of the resistance in natural strains can be divided into two steps:

a) The appearance of an initial new state which confers the initial resistance. In our example, that corresponds to the appearance of one of two possible resistant states, both of which require two neutral mutations. IOWs, this initial step is the result of mere RV, and NS has no role in that. Of course, the initial resistant state, once reached, can be selected. We have also seen that the initial state of two mutations is probably the critical step in the whole process, in terms of time required.

b) From that point on, a few individual steps of one single mutation, each of them conferring greater resistance, can optimize the function rather easily.

Now, point a) is exactly what we are discussing in this new thread.

So, what are the realistic powers of mere RV in the biological world, in terms of functional information? What can it really achieve?

Another way to ask the same question is: how functionally complex can the initial state that for the first time implements a new function be, arising from mere RV?

And now, let’s define the probabilistic resources.

Let’s call probabilistic resources, in a system where random events take place, the total number of different states that can be reached by RV events in a certain window of time.

In a system where two dies are tossed each minute, and the numbers deriving from each toss are the states we are interested in, the probabilistic resources of the system in one day amount to 1440 states.

The greater the probabilstic resources, the easier it is to find some specific state, which has some specific probability to be found in one random attempt.

So, what are the states generated by RV? They are, very simply, all different genomes that arise in any individual of any species by RV events, or if you prefer by descent with modification.

Please note that we are referring here to heritable variation only, we are not interested to somatic genetic variation, which is not transmitted to descendants.

So, what are the probabilistic resources in our biological world? How can they be estimated?

I will use here a top-down method. So, I will not rely on empirical data like those from Summers or Behe or others, but only on what is known about the biological world and natural history.

The biological probabilstic resources derive from reproduction: each reproduction event is a new state reached, if its genetic information is different from the previous state. So, the total numbet of states reached in a system in a certain window of time is simply the total number of reproduction events where the genetic information changes. IOWs, where some RV event takes place.

Those resources depend essentially on three main components:

The population size
The number of reproductions of each individual (the reproduction rate) in a certain time
The time window

So, I have tried to compute the total probabilistic resources (total number of different states) for some different biological populations, in different time windows, appropriate for the specific population (IOWs, for each population, from the approximate time of its appearance up to now). As usual, I have expressed the final results in bits (log2 of the total number).

Here are the results:

Population	Size	Reproduction rate (per day)	Mutation rate	Time window	Time (in days)	Number of states	Bits	+ 5 sigma	Specific AAs
Bacteria	5.00E+30	24	0.003	4 billion years	1.46E+12	5.26E+41	138.6	160.3	37
Fungi	1.00E+27	24	0.003	2 billion years	7.3E+11	5.26E+37	125.3	147.0	34
Insects	1.00E+19	0.2	0.06	500 million years	1.825E+11	2.19E+28	94.1	115.8	27
Fish	4E+12	0.1	5	400 million years	1.46E+11	2.92E+23	78.0	99.7	23
Hominidae	5.00E+09	0.000136986	100	15 million years	5.48E+09	3.75E+17	58.4	80.1	19

The mutation rate is expressed as mutations per genome per reproduction.

This is only a tentative estimate, and of course a gross one. I have tried to get the best reasonable values from the sources I could find, but of course many values could be somewhat different, and sometimes it was really difficult to find any good reference, and I just had to make an educated guess. Of course, I will be happy to acknowledge any suggestion or correction based on good sources.

But, even if we consider all those uncertainties, I would say that these numbers do tell us something very interesting.

First of all, the highest probabilistic resources are found in bacteria, as expected: this is due mainly to the huge population size and high reproduction rate. The number for fungi are almost comparable, although significantly lower.

So, the first important conclusion is that, in these two basic classes of organisms, the probabilistic resources, with this hugely optimistic estimate, are still under 140 bits.

The penultimate column just adds 21.7 bits (the margin for 5 sigma safety for inferences about fundamental issues in physics). What does that mean?

It means, for example, that any sequence with 160 bits of functional information is, by far, beyond any reasonable probability of being the result of RV in the system of all bacteria in 4 billion years of natural history, even with the most optimistic assumptions.

The last column gives the number of specific AAs that corrispond to the bit value in the penultimate column (based on a maximum information value of 4.32 bits per AA).

For bacteria, that corresponds to 37 specific AAs.

IOWs, a sequence of 37 specific AAs is already well beyond the probabilistic resources of the whole population of bacteria in the whole world reproducing for 4 billion years!

For fungi, 147 bits and 34 AAs are the upper limit.

Of course, values become lower for the other classes. Insects still perform reasonably well, with 116 bits and 27 AAs. Fish and Hominidae have even lower values.

We can notice that Hominidae gain something in the mutation rate, which as known is higher, and that I have considered here at 100 new mutations per genome per reproduction (a reasonable estimate for homo sapiens). Moreover, I have considered here a very generous population of 5 billion individuals, again taking a recent value for homo sapiens. These are not realistic choices, but again generous ones, just to make my darwinist friends happy.

Another consideration: I have given here total populations (or at least generous estimates for them), and not effective population sizes. Again, the idea is to give the highest chances to the neo-darwinian algorithm.

So, these are very simple numbers, and they should give an idea of what I would call the upper threshold of what mere RV can do, estimated by a top down reasoning, and with extremely generous assumptions.

Another important conclusion is the following:

All the components of the probabilistic resources have a linear relationship with the total number of states.

That is true for population size, for reproduction rate, mutation rate and time.

For example, everyone can see that the different time windows, ranging from 4 billion years to 15 million years, which seems a very big difference, correspond to only 3 orders of magnitude in the total number of states. Indeed, the highest variations are probably in population size.

However, the complexity of a sequence, in terms of necessary AA sites, has an exponential relationship with the functional information in bits: a range from 19 to 37 AAs (only 18 AAs) corresponds to a range of 24 orders of magnitude in the distribution of probabilistic resources.

Can I remind here briefly, without any further comments, that in my OP here:

The amazing level of engineering in the transition to the vertebrate proteome: a global analysis

I have analyzed the informational jump in human conserved information at the apperance of vertebrates? One important result is that 10% of all human proteins (about 2000) have an information jump from pre-vertebrates to vertenrates of at least (about) 500 bits (corresponding to about 116 AAs)!

Now, some important final considerations:

I am making no special inferences here, and I am drawing no special conclusions. I don’t think it is really necessary. The numbers speak for themselves.
I will be happy of any suggestion, correction, or comment. Especially if based on facts or reasonable arguments. The discussion is open.
Again, this is about mere RV. This is about the neutral case. NS has nothing to do with these numbers.
For those interested in a discussion about the possible role of NS, I can suggest the thread linked at the beginning of this OP.
I will be happy to answer any question about NS too, of course, but I would be even more happy if someone tried to answer my two questions challenge, given at post #103 of the other thread, and that nobody has answered yet. I paste it here for the convenience of all:

Will anyone on the other side answer the following two simple questions?

1) Is there any conceptual reason why we should believe that complex protein functions can be deconstructed into simpler, naturally selectable steps? That such a ladder exists, in general, or even in specific cases?

2) Is there any evidence from facts that supports the hypothesis that complex protein functions can be deconstructed into simpler, naturally selectable steps? That such a ladder exists, in general, or even in specific cases?

Comments

To all interested: Now, as a follow-up to my previous comment to forexhr, I will give here a clear example of what I mean when I say that complex functions cannot be deconstructed into simpler, naturally selectable steps. I will use a well known scenario, that we have discussed in depth here and in the previous OP about NS, and that is very well documented: chloroquine resistance. Chloroquine resistance is a "relatively" complex function (about 8 bits). And, as we know, it cannot be deconstructed into two simpler naturally selectable steps of 4 bits each. Why? Because we know well (from Summer's paper) that two individual substitutions are necessary to confer basic chloroquine resistance: either 75E and 76T or 76T and 326D IOWs, no single substitution can confer any resistance, and therefore be naturally selected. IOW, the ladder: 75E -> NS -> 76T -> NS or any other equivalent, simply does not exist. What exists is the sequence: 75E -> 76T -> NS where NS comes into play only after the two mutations occur by RV. IOWs, the function: chloroquine resistance has 8 bits of complexity, and cannot be deconstructed into two 4 bit steps. Now, ATP synthase beta chain, just to use an old friend, has a functional complexity of about 600 bits, as proven by its evolutionary conservation. If even such a simple function as choroquine resistance cannot be deconstructed into simpler naturally selectable steps, how can anyone imagine that a complex, specific function like the function of ATP synthase beta chain can be deconstructed that way? Such an explicit scenario should help my kind interlocutors to try to answer my challenge, and explain if there is any reason to believe such a strange idea, except for blind faith in a wrong theory.gpuccio_{November 13, 2017
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forexhr: True! :) "Function" is a very vague concept, if it is not defined with precision. In my old OP here: https://uncommondescent.com/intelligent-design/functional-information-defined/ I have tried to give a precise definition of function, which includes all possible aspects and is very basic. I paste it here:
I define a function for an object as follows: a) If a conscious observer connects some observed object to some possible desired result which can be obtained using the object in a context, then we say that the conscious observer conceives of a function for that object. b) If an object can objectively be used by a conscious observer to obtain some specific desired result in a certain context, according to the conceived function, then we say that the object has objective functionality, referred to the specific conceived function.
In that sense, any function can be freely defined, because it is not the concept of function which is important in itself. The important concept is not function, but the amount of information that is necessary to implement the defined function. Simple functions can arise, and do arise, all the time in non designed objects: as I often say, a stone can be used for many purposes, and therefore many functions can be defined for it. But all those functions are simple, because no special configuration is necessary to implement them, beyond the few requirements that a lot of stones present (some generic dimensions, weight, and so on). Neo-darwinists love to equivocate on the concept of function, never trying to quantify the functional information linked to a function. That's the case, for example, in Szostak's famous paper, where the generic concept of "functional" sequences is used to make very ambiguous statements. Indeed, as many times said in this thread, the original function found in Szostak's library: a) "Any protein sequence 80 AAs long that can weakly bind ATP, and therefore be selected by ATP columns in the lab" is rather simple, about 40 bits, as demonstrated by the fact that he found 4 such sequences out of 6×10^12 random sequences 80 AAs long. That is the complexity linked to that specific definition. But, as often said here, and as you very correctly remind, there is only one definition of function which is pertinent for the neo-darwinian algorithm. And that definition is: b) "Any function that confers a detectable reproductive advantage in a specific biological context, so that it can be the object of NS" That definition of function is very strict. Now, the correct question is: can we find functions that satisfy that definition and are still simple? The answer, of course, is yes. Antibody resistance, of the simple type, is a good example. It can arise by a single aminoacid substitution (about 4 bits) or by two AAs substitutions (about 8 bits), like in the case of chloroquine resistance. All the known cases of microevolution are cases where a simple new function is found by RV. But, of course, no complex function, satisfying the basic definition given in b), can be found that way! Now, neo-darwinists will argue, at that point, that complex functions can arise as a gradual sum of simpler, naturally selectable functions. That is the lie. Because it is simply not true. And if anyone on the other side thinks differently, he is again invited to take my challenge, and answer the following two questions, that nobody at all, up to now, has even tried to answer:
Will anyone on the other side answer the following two simple questions? 1) Is there any conceptual reason why we should believe that complex protein functions can be deconstructed into simpler, naturally selectable steps? That such a ladder exists, in general, or even in specific cases? 2) Is there any evidence from facts that supports the hypothesis that complex protein functions can be deconstructed into simpler, naturally selectable steps? That such a ladder exists, in general, or even in specific cases?
gpuccio_{November 13, 2017
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Corey Delvine: "Who are you to be defining function and to say what’s selectable and what’s not?" If the theory of evolution teaches that the process of mutations and natural selection create and preserve traits that are fitted to the selection pressures of specific environments, then it is no brainer to define 'function' and to say what’s 'selectable' and what’s not: function is such an arrangement of nucleotides that codes for traits which are beneficial in a specific environment, while selectable is that which is functional. Thus, nobody here needs to define function or selection - the theory itself implicitly defines these terms precisely and it is really funny how those who preach evolution as their gospel are ignorant of what the evolution theory actually teaches. Such paradoxical situation can be explained by the fact that the term 'function' implies something that is too uncomfortable for preachers to accept and as a result they are forced to a priori reject all definitions of 'function'. Of course, they will never provide their own definition because any such attempt would result in anxiety and unacceptable impulses that are experienced when a person simultaneously holds two contradictory beliefs or ideas. In our case, the first belief arises from the dogmatic acceptance of the evolution theory. The second belief arises from the empirical observation of the huge search space(10^810 for average gene size), on which it is impossible to find any evolutionary selectable(functional) instance with only 10^43 mutations which have occurred during the entire evolutionary process. That is why it is impossible to have a rational discussion with an evolution preacher. His belief that evolution must be true is so deep that it trumps any logic or reason.forexhr_{November 13, 2017
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KF @174 & @175: Good points. For example, the fascinating morphogenesis is associated with 4D signaling profiles that form and are interpreted following beautiful spatiotemporally choreographed procedures with multilevel coding beyond anything ever dreamed by the best design engineers. Both the spatial concentration of the morphogens and the duration of their presence may affect the fate determination of the surrounding cells. This is beyond any science fiction ideas ever imagined by the most prolific writers of the genre. But sadly many people are unaware of that.Dionisio_{November 10, 2017
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Corey:
Your claim is that evolution could not arrive at these proteins by a random walk through amino acid sequence space, but nowhere in any literature does anyone claim that this is how protein evolution occurs.
Ummm, no one knows how evolution by means of blind and mindless processes works. That is why the need for the dogma. Look, Corey, if you and yours actually had some experimental evidence of blind and mindless processes producing proteins from scratch you would have presented it. As it is you and yours don't have a clue. Can Corey even support his claims of "strawman"? I doubt it.ET_{November 10, 2017
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Is it clear? Wait. You mean new proteins don't just appear de novo?Mung_{November 10, 2017
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Corey Delvine: c) You say:
You claim that in order for evolution to be possible, the search space must be explored in all its parts.
No. I claim that in order for a specific target to be found, enough probabilistic resources are needed to find it, given its probability to be found. It's a completely different idea.
But there is no evidence that suggest this to be true and the fact that function can be happened upon easily as Szostack shows, disagrees with this.
As I have discussed, Szostak found a simple and useless function using approapriate probabilistic resources: "Let’s take the case of weak ATP binding, a ridiculously simple function, and by far not selectable. There should be no problem to get such a simple function: just a string of AAs that can bind ATP, even at very low levels, so that we can separate the corresponding protein by ATP columns in our lab. That’s what Szostak has done in his famous paper. And, while his results have nothing to do with NS and neo-darwinism, as discussed many times, they can still give us some idea about the functional space for an extremely simple function. Let’s see: I have already computed the functional information for the basic simple function selected by the authors: about 40 bits. That means that, for that function, while the search space (for 80 AAs) is huge (1.2E+104), the target space is very big too: 8.06E+91. The ratio: 6.66667E-13, 40 bits, is the functional complexity for that function in a 80 AAs long sequence. Now, we can easily see that such a simple function is well in the range of what can be found by the total bacterial system, which has a capacity of finding about 138 functional bits per genome, and in particular 123,4 bits for a 80 AAs sequence. So, 40 bits are a piece of cake." This is completely consistent with my reasoning. Indeed, it is an integral part of it. Then you say:
(again this is thinking of function in a biological context, and not using Gpuccio’s personal definition of function).
What do you mean? I have no "personal definition of function". I accept all functions that can be defined explicitly, as clearly stated here: https://uncommondescent.com/intelligent-design/functional-information-defined/ What I say about what you call the "biological context", but should be rather called the "neo-darwinian scenario", is that: "a function should be naturally selectable to be naturally selected". Which is, I suppose, a tautology. Can you object to that? You say:
“Let’s take the case of weak ATP binding, a ridiculously simple function, and by far not selectable.” Who are you to be defining function and to say what’s selectable and what’s not?
I am not defining function. I am saying that the function found by Szostak is relatively simple (40 bits) for the context we are discussing (biological evolution). I am saying that such a function is not naturally selectable, because of course it cannot confer any reproductive advantage in any known biological context. That point is rather intuitive, but it is also proven by the following experimental article: "A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754611/ So, as far as we can tell, Szostak's ATP binding protein, in one of its most evoluted forms, is not naturally selectable, indeed it is deleterious. If you have reasons to think differently, please state those reasons. I will not object: "Who is Corey Delvine to be defining function and to say what’s selectable and what’s not?" I will simply consider your arguments, for what they are worth.gpuccio_{November 10, 2017
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kairosfocus: "GP, not just coded but executed, and that implies a need for corresponding execution machinery, taking the issue to another whole level, as such machines are also coded for in the system." Of course you are right. I suppose I was again "graciously" understating some aspects. :)gpuccio_{November 9, 2017
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Corey Delvine: b) You say:
High homology across species obviously suggests function, but function does not require high homology. Proteins with the same function can have very different amino acid sequences and experiments have swapped amino acids in proteins, heck they’ve even stripped all 20 amino acids away and rebuilt proteins using only 4 amino acids and the protein was still functional.
Give the reference, please. Then I will answer. More in next post.gpuccio_{November 9, 2017
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Corey Delvine: Hi Corey, welcome to the discussion! :) I was feeling rather lonely: I had never had a thread where nobody from the other side made any intervention. I was beginning to beg for some name calling, at least! :) But here you are, at your best. So, thank you. Answers to your points: a) You say:
Your claim is that evolution could not arrive at these proteins by a random walk through amino acid sequence space, but nowhere in any literature does anyone claim that this is how protein evolution occurs.
No. As you should well know, I have debated in great detail the role of NS and its limits in the previous thread: https://uncommondescent.com/intelligent-design/what-are-the-limits-of-natural-selection-an-interesting-open-discussion-with-gordon-davisson/ to which you have brilliantly contributed. What's happening to your memory? Age? My first statement in this OP is: "Coming from a long and detailed discussion about the limits of Natural Selection, I realized that some attention could be given to the other great protagonist of the neo-darwinian algorithm: Random Variation (RV)." So no, I am not simply "claiming that evolution could not arrive at these proteins by a random walk through amino acid sequence space". Look again (if you have already looked) to my OP here. You will find this clear (I suppose) statement: "In all the present discussion we will not consider how NS can change the RV scenario: I have discussed that in great detail in the quoted previous thread, and those who are interested in that aspect can refer to it. In brief, I will remind here that NS does not act on the sequences themselves (IOWs the functional information), but, if and when and in the measure that it can act, it acts by modifyng the probabilistic resources. So, an important concept is that: All new functional information that may arise by the neo-darwinian mechanism is the result of RV." Now, I will try to explain it better for those who has some difficulties in understanding: NS must act on some already existing new function in its initial form, which must therefore be, of course, naturally selectable. That initial new function must be generated by RV only. Is it clear? So, what I am claiming is that: "evolution could not arrive at these new initial functions by a random walk through amino acid sequence space". Is it clear? More in next post.gpuccio_{November 9, 2017
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GP, not just coded but executed, and that implies a need for corresponding execution machinery, taking the issue to another whole level, as such machines are also coded for in the system. this is part5 of why I always highlight that we must start at the root of the tree of life type icon, OoL. At that level, differential reproductive success is not on the cards as the origin of relevant mechanisms for metabolism and for self-replication is what is on the cards. Design is present at the root of the tree of life as the best explanation, once methodological naturalist blinkers are taken off. If such is there at the root, it is there all along. And in the end, I am astonished at how readily ever so many would account for such systems on blind chance and/or mechanical necessity that is readily shown to be overwhelmed by the challenge of forming 500 - 1,000 bits worth of functionally specific complex organisation and associated information. Appeal to statistical miracle after statistical miracle. KFkairosfocus_{November 9, 2017
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CD, on very long and good track record, GP is not on trial. You are. The score does not look so good so far, given the sort of rhetoric you chose above. FYI, your relevant choice on cause is: blind chance and/or mechanical necessity, or intentionally directed configuration. Rule the latter out and you are stuck at the former, where protein sequences (and the codes for them) are patently highly contingent. So, the choice is hitting a needle in a beyond astronomical scale haystack by blind chance -- aka repeated statistical miracles in a huge chain -- or having a small step increment between functional forms; something Dawkins pointed out when he put up his rather misleading Weasel case back in the 80's. GP is pointing out issues with the small step approach. And if you think the genetic code and proteins were written into the laws of our cosmos making emergence of life inevitable, you are looking at a version of cosmological fine tuning that is way beyond what has been claimed. The issue is not oh unless you can show reason that blind chance and mechanical necessity working through evolutionary mechanisms in chemistry of a warm little pond or the like and then onward through whatever flavour of macro-evo you favour then we can pose the magic word evolution and game over, but instead, showing empirically supported credible means. The absence of Nobel prizes for having shown those means speaks for itself as appeal to repeated statistical miracles is utterly self defeating, and appealing to quasi-infinite multiverses to open up possibility explorations is in the end a resort to bald ad hoc unsupported speculation. KFkairosfocus_{November 9, 2017
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Corey Delvine:
Your claim is that evolution could not arrive at these proteins by a random walk through amino acid sequence space, but nowhere in any literature does anyone claim that this is how protein evolution occurs.
Thank you for telling us how protein evolution does not occur. Given your obvious familiarity with the subject matter and your review of all the literature, how do proteins evolve? You left that out.Mung_{November 9, 2017
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Let’s say that, in the fabulous RNA world, sequence A is functional: it has some specific biochemical activity
Let's say that it's function is to fold in on itself, because that's what RNA does. Which makes it sort of hard to copy.Mung_{November 9, 2017
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Your claim is that evolution could not arrive at these proteins by a random walk through amino acid sequence space, but nowhere in any literature does anyone claim that this is how protein evolution occurs. So you're argument is a strawman argument. High homology across species obviously suggests function, but function does not require high homology. Proteins with the same function can have very different amino acid sequences and experiments have swapped amino acids in proteins, heck they've even stripped all 20 amino acids away and rebuilt proteins using only 4 amino acids and the protein was still functional. So again, your argument is a strawman. You claim that in order for evolution to be possible, the search space must be explored in all its parts. But there is no evidence that suggest this to be true and the fact that function can be happened upon easily as Szostack shows, disagrees with this. (again this is thinking of function in a biological context, and not using Gpuccio's personal definition of function). Again. strawman. "Let’s take the case of weak ATP binding, a ridiculously simple function, and by far not selectable." Who are you to be defining function and to say what's selectable and what's not? Do you see everything in black and white or is that just how you view biology?Corey Delvine_{November 9, 2017
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Oh brother Gpuccio, you're still passing out this kool-aid?Corey Delvine_{November 9, 2017
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The OOL + Neo-Darwinian evolution stories are starting to look like a bunch of 'chicken-egg' conundrums mixed with many 'humpty-dumpty' issues. And it seems like getting worse with every discovery. But maybe we just don't understand it. :)Dionisio_{November 9, 2017
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gpuccio @167:
[...] that sequence of AAs, and therefore the structure and function of the protein, depend on the nucleotide sequence only symbolically, through an arbitrary code.
The essence of the problem.Dionisio_{November 9, 2017
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Dionisio (and whoever is interested): I would like to be more detailed on this important point. Let's say that we have a sequence of nucletodes A. Let's say that, in the fabulous RNA world, sequence A is functional: it has some specific biochemical activity, for which it has been selected and preserved. The functional information in sequence A is also passed to new generations because, of course, a sequence of nucleotides can be copied by some RNA polymerase activity, effected by the RNA itself. This is, I suppose, the central idea for the RNA world: RNA can be both an effector molecule and an information storing molecule. Now, let's say that we make the transition to an RNA-protein world. Let's say that the function which was effected by A in the RNA world should now be inherited by a protein Ap. Well, there is absolutely no way that the information in A (the nucleotide sequence) can be "transferred" to some other nucleotide sequence (let's call it A1) which can code for the protein Ap. Why? Because the information in A1 for Ap must of course be coded according to the symbolic genetic code. IOWs A1 (which should code for Ap) has absolutely no relationship with A (the nucleotide sequence which effected the function in the RNA world). They are two completely different types of information, because they have information for the same function, but in two completely different ways: a) A has information for an RNA molecule, whose 3d structure and biochemical activity depend directly on the nucleotide sequence, according to objective biochemical laws (IOWs, in the same way that a protein structure and function depend on its AA sequence). b) A1 has information for a sequence of AAs, corresponding to a functional protein, but that sequence of AAs, and therefore the structure and function of the protein, depend on the nucleotide sequence only symbolically, through an arbitrary code. So, there is absolutely no way that the information in A can generate the information in A1 by non design mechanisms. IOWs, the RNA world is no "precursor" to the protein world: all the information in the RNA world will be lost in the supposed transition to the protein world. IOWs, the protein world could as well arise from scratch, as far as functional information is concerned.gpuccio_{November 9, 2017
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gpuccio @155: That seems like an accurate diagnosis of the current hopeless condition of the terminally-ill Neo-Darwinian story. Thanks.Dionisio_{November 9, 2017
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gpuccio @159:
“A regulatory function linked to the biochemical structure of the nucleotide sequence has nothing to do with the potential symbolic function of those same nucleotides to code for functional proteins.” is also the main reason (but not the only one) why the imagined transition from some hypothetical RNA world to a DNA-RNA-protein world (the only one we know to exist) is simply impossible.
The OOL debate is over.Dionisio_{November 9, 2017
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jerry: "This is the point I have been making for years. I have said that shortly the evidence for what is possible will be available to either support or destroy the Neo Darwinian point of view. My guess is that it will reveal some very interesting changes that have happened in species due to natural events but support the edge of evolution thesis." I absolutely agree with you. :)gpuccio_{November 9, 2017
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So, the point remains valid: the best perspective for neo-darwinism, as far as a new functional protein coding sequence must be found, which is sequence unrelated to what already exists, is a random walk on some non coding and non functional DNA sequence, where no intervention of NS can help the walk (and therefore all the probabilistic limits highlighted in this OP definitely apply), and where a lot of lucky events must also happen to allow the (im)possibly found sequence to be translated and selected at the right time.
This is the point I have been making for years. I have said that shortly the evidence for what is possible will be available to either support or destroy the Neo Darwinian point of view. My guess is that it will reveal some very interesting changes that have happened in species due to natural events but support the edge of evolution thesis. If a new protein arises or a new regulatory element arises through some form of random process there should be evidence for it in related species where a similar sequence is present in an incomplete form. Dr Gauger replied to a comment that I made back in May that this is happening on a small scale and pointed to an analysis of some plant genomes and their common proteins and unique proteins. What was amazing about the study she pointed to was the number of unique proteins in these plant species. Or the taxonomically restricted genes that encode for these proteins. https://uncommondescent.com/intelligent-design/do-nylon-eating-bacteria-show-that-new-functional-information-is-easy-to-evolve/jerry_{November 9, 2017
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Mung: OK, you have me! :) The "size of beak" argument is really a game stopper! :)gpuccio_{November 9, 2017
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Origenes: "Another minor detail …" Yes. A lot of "minor" details, indeed, often "graciously" underestimated in the debate. Are we really too kind to our interlocutors? :)gpuccio_{November 9, 2017
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GPuccio: But, as soon as a potentially functional sequence is reached, it must be fully transcribed and translated (and, I would add, correctly regulated) to be able to confer the reproductive advantage that will expose it to NS.
Another minor detail ...Origenes_{November 9, 2017
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To all: By the way, this statement in my answer to jerry at #158: "A regulatory function linked to the biochemical structure of the nucleotide sequence has nothing to do with the potential symbolic function of those same nucleotides to code for functional proteins." is also the main reason (but not the only one) why the imagined transition from some hypothetical RNA world to a DNA-RNA-protein world (the only one we know to exist) is simply impossible.gpuccio_{November 9, 2017
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jerry: OK, I will look with interest to the paper about mammal speciation that you suggested, and will give you my feedback. Regarding the second point, of course variations in regulatory elements in non coding DNA can be selected, if they give some reproductive advantage. But those are sequences of non coding but absolutely functional DNA (or RNA). The issue I was discussing was, instead, the possibility of getting to some functional protein coding sequence from some non functional DNA sequence (like a duplicated and inactivated gene). In this case: a) The starting sequence must be non functional, which is important to allow a non restricted random walk, one that can reach completely new sequences in the search space. b) The intermediate states of the random walk are not functional, too. c) Only when we reach the final state of a basic functional protein coding gene, whose coded protein can give some reproductive advantage, can the result be selected by NS. d) The point raised by Origenes, and supported by me, was that a further difficulty is that the intermediate states are not transcribed, or at least not translated (because the sequence is not yet an ORF, or because it is an ORF that codes for some useless protein). But, as soon as a potentially functional sequence is reached, it must be fully transcribed and translated (and, I would add, correctly regulated) to be able to confer the reproductive advantage that will expose it to NS. Otherwise, any new neutral variation can easily degrade the potential function so preciously (and improbably) reached. e) In the light of the above argument, possible selections of non coding DNA sequences for some regulatory function can have no role at all, or probably a negative role. Indeed, if some part of the sequence which should be a step to the future protein is selected for a regulatory role as DNA or RNA, that would be a final stop to its further "evolution" in the direction of a protein coding sequence, because indeed negative selection would act to preserve the sequence as it is. And a regulatory function linked to the biochemical structure of the nucleotide sequence has nothing to do with the potential symbolic function of those same nucleotides to code for functional proteins. So, the point remains valid: the best perspective for neo-darwinism, as far as a new functional protein coding sequence must be found, which is sequence unrelated to what already exists, is a random walk on some non coding and non functional DNA sequence, where no intervention of NS can help the walk (and therefore all the probabilistic limits highlighted in this OP definitely apply), and where a lot of lucky events must also happen to allow the (im)possibly found sequence to be translated and selected at the right time.gpuccio_{November 9, 2017
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gpuccio:
These huge transitions (OOL, eukaryotes, metazoa, vertebrates, and certainly many others) are really beyond any hope of explanation, even vague, if design is not factored.
Don't we have some very fine and detailed examples of how evolution can bring about minor transitions? Say, from one protein to another. Or a slightly different size of beak in a population of birds.Mung_{November 9, 2017
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Gpuccio, A couple things. I pointed to Brosius because he is considered important in the evolution science community. He was the person given the honor of introducing the tribute to Gould. He is a serious researcher as opposed to Dawkins who is a polemicist. He runs a very respected research lab on evolution. Whether he or his colleagues have produced anything that challenges the ID point of view is what is of interest. I have said for about 8 years, since he was first introduced to UD by Allan MacNeil, that I could not see any real evidence for his overall worldview. But there are some interesting questions which his colleagues are investigating. One recent one is,
Speciation network in Laurasiatheria: retrophylogenomic signals Liliya Doronina, Gennady Churakov, Andrej Kuritzin, Jingjing Shi, Robert Baertsch, Hiram Clawson, and Jürgen Schmitz Genome Res. June 2017 27: 997-1003 Based on my limited understanding of the abstract this is about what are the possible causes for the differences between various mammals and what are the origins of these causes? Certainly an interesting question and one that looks at the edge of evolution.
I don't pretend to understand the science for these differences because the layman's description has not been written. Before you say this issue is not part of your thesis which I agree, it points to how various morphological and adaptive elements arise by apparently possible natural events. And understanding them correctly can only contribute to the ID worldview by showing what is possible and what is not. They don't seem to rise to new complex, functional systems. They are actually nails in the coffin by showing just what the limits are. ------------ On what is selectable in NS, Brosius maintains that it is more than proteins but includes RNA sequences and control mechanisms on the DNA. You said
So, I believe that all the search that happens in non coding DNA cannot be helped by NS, at all. Only if and when an ORF is transcribed and translated it can be detected by NS, and only if it confers some detectable reproductive advantage.
From the abstract above
Raw material for novel genes encoding protein or RNA, or parts of genes including regulatory elements that selection can act on, continues to enter the evolutionary lottery.
So he is looking at a lot more than coded genes. Again, there is no evidence that any of this challenges the ID position.jerry_{November 9, 2017
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