The Third Way

This is what Larry is talking about Yes? What you think? And in turn the new advances in evolutionary theory?

The neutral theory of molecular evolution holds that at the molecular level most evolutionary changes and most of the variation within and between species is not caused by natural selection but by random drift of mutant alleles that are neutral. A neutral mutation is one that does not affect an organism's ability to survive and reproduce. The neutral theory allows for the possibility that most mutations are deleterious, but holds that because these are rapidly purged by natural selection, they do not make significant contributions to variation within and between species at the molecular level. Mutations that are not deleterious are assumed to be mostly neutral rather than beneficial. In addition to assuming the primacy of neutral mutations, the theory also assumes that the fate of neutral mutations is determined by the sampling processes described by specific models of random genetic drift.[1]
So it is all assumption, where is the empirical anchor so to speak?

According to Kimura, the theory applies only for evolution at the molecular level, and phenotypic evolution is controlled by natural selection, as postulated by Charles Darwin. The proposal of the neutral theory was followed by an extensive "neutralist-selectionist" controversy over the interpretation of patterns of molecular divergence and polymorphism, peaking in the 1970s and 1980s. The controversy is still unsettled among evolutionary biologists.
At the molecular level it gives more power to drift than selection which is blind to it. Certainly cuts Darwin out here. You have to give up the awesome power of NS. Or maybe you just want a little when it suits? I guess that would be nearly neutral theory.

Then at the phenotype we are back to Charlie again from 150 years ago. Much longer than the hardened modern synthesis. Oh oh.

With no explanation on how genotype relates to phenotype. And certainly no answer to the questions of novelty. It is also not the consensus view and is argued over it's validity.

The modern synthesis is the concensus view!

I knew neutral theory was a move away from NS. I must say, that again makes you look a bit silly Paul, giving all that amazing power to natural selection just to give it up in support of Neutral theory. That is a puzzle!
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The modern synthesis is the concensus, neutral theory is not. They are incompatable on the molecular level. One relies on NS the other does not.
It is all that other stuff that demands a new theory! You can't just keep ading adhoc because the contradictions build up. Which is exactly what has happened.

Stuffing it one bag and calling it the Theory of evolution is not a theory. It is you hiding in the safety of vagueness.

But all you are doing is regurgitating Larry and PZs neutral position.

You could have just stated that in the beggining.
Professor Larry Moran has graciously responded to my five questions on the neutral theory of evolution in a recent blog post at Sandwalk, titled, Answering creationist questions about Neutral Theory(6 May 2014). I’ve highlighted Professor Moran’s responses below.
1. Do you agree or disagree with the view expressed by Motoo Kimura that natural selection is necessary to explain evolution occurring at the morphological level?

Professor Moran:
Some evolution at the morphological level can be attributed to natural selection and some is due to random genetic drift. The latter category includes neutral morphological changes and a small percentage of detrimental morphological changes.

I was influenced in this view by Masatoshi Nei’s book Molecular Evolutionary Genetics (1987). [Professor Moran then proceeds to quote a passage from Nei's book, in which he acknowledges that "there is no question about the importance of natural selection in the formation of intricate morphological characters," but then goes on to add that "in some morphological characters a substantial part of genetic variation is nonadaptive."]

So, the answer to your question is “yes;” natural selection and random genetic drift are both necessary to explain evolution at the morphological level.

2. How do you respond to Dr. Gert Kothof’s Korthof’s claim that the neutral theory “is not a theory of evolution,” because it “is not sufficient to explain complex life and adaptations”? If not, why not?

Professor Moran:
I respond by saying that Gert Korthof – whoever that is — doesn’t understand the definition of evolution [What Is Evolution?]. Neutral Theory and random genetic drift are integral parts of evolutionary theory. They are not very good at explaining most adaptations but there’s a lot more to evolution than adaptations.

In a footnote to his post, Professor Moran seems to have taken back his criticisms of Dr. Korthof, implying instead that I had “quote mined” Korthof. I’ll say more about that below.

3. Can you point to any complex structures, functions or behaviors which you believe could not have arisen in the absence of natural selection? (You’ve already nominated the change occurring in the human brain over the past few million years as an event in which natural selection played an indispensable role; what else would you put on your list?)

Professor Moran:
The vast majority of complex structures seem to be adaptations of one sort of another. I suspect there are many “functions” and “behaviors” that are neutral, or even detrimental, but it’s difficult to rule out any adaptive component.

4. In which of the following events do you see natural selection as having played a decisive role: the origin of eukaryotes, the origin of multicellularity, the 20-million-year Cambrian explosion, the origin of land animals, the origin of the amniote egg, the origin of angiosperms, and the radiation of mammals immediately after the extinction of the dinosaurs?

Professor Moran:
I think that natural selection played an important role in all of those events.

5. Or is it simply your contention that natural selection, while not playing an important role in the origin of complex structures and novel morphological features, exerts a refining and purifying effect subsequent to their appearance, weeding out non-viable life-forms?

Professor Moran:
No. I have always contended that natural selection plays an important role in the origin of most complex structures and novel adaptive morphological features. There are likely to many “novel morphological features” that are non-adaptive.

It’s also true that negative natural selection acts as a break on evolution by preventing detrimental changes and “weeding out non-vaible life forms.”​

My verdict: An embarrassing climb-down for Professor Moran

Reading Professor Moran’s post, I was struck by its muted tone. Moran believes that “some evolution at the morphological level can be attributed to … random genetic drift,” including “neutral morphological changes and a small percentage of detrimental morphological changes.” He admits that “Neutral Theory and random genetic drift … are not very good at explaining most adaptations,” adding that “the vast majority of complex structures seem to be adaptations of one sort of another.” He then tentatively proposes that “there are many ‘functions’ and ‘behaviors’ that are neutral,” but concedes that “it’s difficult to rule out any adaptive component.” He finally acknowledges that “natural selection plays an important role in the origin of most complex structures and novel adaptive morphological features,” but goes on to suggest that “there are likely to [be] many ‘novel morphological features’ that are non-adaptive.” However, since Professor Moran has already conceded that “the vast majority of complex structures seem to be adaptations of one sort of another,” it is difficult to know what to make of his last suggestion.
In short: Professor Moran’s endorsement of the neutral theory is hedged with so many qualifications that his post might as well have been written by Professor Jerry Coyne, who articulated his views with the utmost clarity, in a post dated December 5, 2012:
The much disputed theory of Neutral Evolution.

This was the sum of a few rather interesting exchanges on Neutral Evolution. Another just so story. Neutral theory = no amazing power from NS.
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You appear to believe that neutral theory eliminates natural selection as an aspect of evolution. That is not the case.
I am quite sure you don't read my posts too well. I quoted the theory from that link already. It is all pretty clear. A bunch of assumptions.. You can't have it both ways. You diminish NS to Drift. This is why Larry thinks he is departing from the modern synthesis. I say whoopdy doo!

So you think that with additional research we can come up with a simpler theory that still takes all the observations into consideration? That would be cool, but there is no reason in principle why that should happen. For example, it is clear that natural selection plays a role and genetic drift plays a role. How would a simpler theory reduce these two aspects down to one?

You don't need to keep playing the personality game. The theory of evolution is not finished, so of course scientists will be arguing with one another. That's how science works.
I said in the beggining of this thread, we have much to learn.
There is no science in your just stories.
Geez Paul the very first sentence in your link that I already quoted is this...

The neutral theory of molecular evolution holds that at the molecular level most evolutionary changes and most of the variation within and between species is not caused by natural selection but by random drift of mutant alleles that are neutral
I agree with the interpretation. Pretty clear I think. It marginalizes selection. It must because of the reason that is evident in it's name. It is neutral to selection!. As I have been saying.The majority of all molecular changes that is, not all. This is the big departure from the modern synthesis you are on about. Yes I know.

The evidence suggests the majority of all mutations are not completely random at all. Quite the opposite. Lots of references at Shapiro's site.
I did. Meaning most changes are not under selective pressure! Meaning most changes are not under the influence of the amazing power of NS.

I wouldn't use the word "marginalize." What will happen when a mutation is highly deleterious?

As above. Yes that interpretation of the jumble of assumptions seems accurate, or do you mean how neutral theory is just as likely to fix deleterious mutations? Invoking neutral mutations gives in to randomness. Won't help you build a new protein Paul. You youself have ruled out randomness. You are all over the place.

I'm not on about the modern synthesis. The modern synthesis is obsolete.
Whoot! All right we have some agreement after all. Well that is what they teach in schools all around the world as fact. That is what has been thrust down our throats as truth! That is what is in place when atheists tell us there is no controversey!

Wow. Can I use that in my sig?

It goes much much further than neutral theory Paul. The complete concept of the gene has changed. The central dogma is bust. Cells literally can rewrite their own genome to adapt! Neutral theory is small potatoes.

Does the evidence suggest that the mutations are selected by a designer? If not, then what's the issue?
Well design does not require mutations to be selected by a designer or any magic be happening in the cell at all. However, because I am arguing for the third way, then the cell itself is the arbiter of its design based on the evidence from microbiology. The issue is about the evidence.

As for design.

Everyone agrees that life appears designed, but the design is an illusion. it is just darwinism was said to have shown that illusion to be true. All efforts are about explaining away the obvious appearance of design. You say show me proof? And I do, (non material semantics). You say evolution did it when it did not even exist.

I say show me proof random mutation, neutral or otherwise, selection or drift can be shown to be responsible for even one novel gene. And you can't do it. That is Ok no one else can. How about a new protein fold? Nope. No help there either.

The way I see it. Life's irrefutable appearance of design is not an illusion. The burden of proof is to firmly establish that it is an illusion.
They never were close, and now with the concensus view of the modern synthesis obsolete as you say. Well there is some humble pie to be eaten and some egg on the faces of countless knobs in and outside of science and philosophy throughout the last century who have been speaking out of their ass all because of ideology and not actual science!

Such fun, but time for weekend fun.
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The modern synthesis is the concensus. Neutral theory adds nothing but insisting drift plays a bigger role than selection. And pretty much all the general principles of the modern synthesis have been refuted or replaced as Koonin's paper clearly elucidates. Neutral theory refutes the centrality of selection and gives into random mutation. Something Dawkin's even says is absurd. Yes I know NS is not completely ruled out! So I don't see much removal from Darwinism beyond that.

But I am just repeating myself. Always happens with Paul.

I agree selections role is restricted. But neutral theory answers nothing. Both neutral and selection are all modeled under assumptions with statistical models.

Assumption: synonymous mutations are selectively neutral because they don't modify protein sequence.
Assumption: non synonymous mutations which change the amino acid sequence are preserved because of selection.

We have reason to doubt this. We know that synonymous codons can preferentially bind transcription factors or other molecules, like histones. Meaning they are not neutral!

There is something wrong with Paul no doubt.. He is not a skeptic but just another fundamentalist. he makes a strawman which is equal to saying the modern synthesis is not the concensus view. Bullshit! He then goes on to defend a rewrite of another story such as the neutral theory that answers nothing. Completely contradicting everything he has said in the past. Ignoring what has already been said as can be seen in his last post. He has clearly been shown to be wrong, over and over, again and again when it comes to evolution. But cognitive dissonance is too great.

Evidence for the third way is at Shapiro's site. I may post some.This thread has been derailed with irrelevant rubbish, straw men and baseless opinions leaving the actual subject on the sidelines. That is why we have safe havens from the idiocy.

What is really funny is that for years Paul has been arguing the central role of selection and the standard definitions. Citing evolutionary programs based in this standard definition as proof. Even claiming the amazing power of NS at the beginning of this thread!

Only to refute himself by supporting a non Darwinian neutral theory! That in the very words of it's founder some 45 years ago says the overwhelming majority of molecular changes are neutral to selection! Basically voiding everything he has said in the past. Yeah, Yeah, it does not rule it out. Only in the case of the overwhelming majority of molecular changes based on the assumption that synonymous mutations are selectively neutral because they don't modify protein sequence.

Haha. Classic Paul.

The other funny thing is. I agree that selections role is minimal and most mutations probably are neutral, because mutations are primarily in tissue specific genes and not crucial housekeeping ones. Not random. Neutral theory is random.

Larry says..

The revolution is over and strict Darwinism lost. We now know that random genetic drift is an important mechanism of evolution and there's more to evolution than natural selection. Unfortunately, this blatantly obvious fact is not understood by the vast majority of people and teachers. There are even many scientists who don't understand evolution.
I can certainly agree with this. Except the revolution is not over, it has just begun, And random drift does nothing to answer innovation. And in typical fashion when they disagree, obviously those scientist don't understand evolution. Sheesh! No one does!

Back on ignore you go funny man.
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Cutting to the chase, this is one of the key issues. I re post this for those who may not be aware and yet again for the willfully ignorant with short memories.

Other experiments over the last few decades have also shown this to be true.
In fact it has been suggested based on the evidence that proteins evolve by systems control, regulated cellular processes and not any Darwinian mechanism or Neutral theory. In fact neutral theory requires innovation from random mutation alone. Only when the function is in existence can any selection have an effect. As I keep trying to say, the function must be present for selection to act. It does not matter neutral or not! Nothing evolves unless it already exists!

This is the bottom line, expressed towards both Larry and Shapiro from Doug Axe.

So, to Moran I say, regale us with heroic stories of magically evolvable apes and magically evolvable enzymes if you must, but when you're finished with the stories, be sure to join us in doing the science that should convince everyone one way or the other as to their plausibility.
I know of many processes that people talk about as though they can do the job of inventing new proteins (and of many papers that have resulted from such talk), but when these ideas are pushed to the point of demonstration, they all seem to retreat into the realm of the theoretical. Having followed this debate for some time now, and having made several experimental contributions to it, Ann and I have become convinced that none of the current naturalistic ideas about the origin of protein folds or the functional diversification of existing folds actually works in any general sense.

But of course, as experimentalists we are very willing to see the evidence that might prove us wrong.
Evidence! they whine and complain about this inconvenient fact. But when it comes down to it they fail. Yes this includes Shapiro.
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In case you don't trust this information (even though it has empirical basis) because of the source. Here is the current situation in protein evolution from the mainstream research.

Close to a Miracle

“Once you have identified an enzyme that has some weak, promiscuous activity for your target reaction, it’s fairly clear that, if you have mutations at random, you can select and improve this activity by several orders of magnitude,” says Dan Tawfik at the Weizmann Institute in Israel. “What we lack is a hypothesis for the earlier stages, where you don’t have this spectrum of enzymatic activities, active sites and folds from which selection can identify starting points. Evolution has this catch-22: Nothing evolves unless it already exists.”
Overall, what the field of protein evolution needs are some plausible, solid hypotheses to explain how random sequences of amino acids turned into the sophisticated entities that we recognize today as proteins. Until that happens, the phenomenon of the rise of proteins will remain, as Tawfik says, “something like close to a miracle.
Close to a miracle!

Don't let ideological excuse makers deny the scientific facts. Random Mutation, neutral or not, selection or drift has no solution for the very fundamental and foundational level of protein evolution.

Dick wads want to tell stories because of ideological bias. Just shut up and let science be the arbiter. We have done this argument several times here, there are no answers, but it is soon forgotten and just so stories fill the gaps.

"But of course, as experimentalists we are very willing to see the evidence that might prove us wrong."

Dick wads can remember this when they make their excuses. But they usually don't evidently.
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A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.
"Our new theory extends Darwin's model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness."
No, it replaces Darwin's model completely. This is "natural genetic engineering".

"What we have found is that certain kinds of biological structures exist that are able to steer the process of evolution toward improved fitness," said Rabitz, the Charles Phelps Smyth '16 Professor of Chemistry. "The data just jumps off the page and implies we all have this wonderful piece of machinery inside that's responding optimally to evolutionary pressure."
The authors sought to identify the underlying cause for this self-correcting behavior in the observed protein chains. Standard evolutionary theory offered no clues. Applying the concepts of control theory, a body of knowledge that deals with the behavior of dynamical systems, the researchers concluded that this self-correcting behavior could only be possible if, during the early stages of evolution, the proteins had developed a self-regulating mechanism, analogous to a car's cruise control or a home's thermostat, allowing them to fine-tune and control their subsequent evolution. The scientists are working on formulating a new general theory based on this finding they are calling "evolutionary control."
The mechanisms for evolution evolved. Somehow. Note the circular logic.

Chakrabarti and Rabitz analyzed these observations of the proteins' behavior from a mathematical standpoint, concluding that it would be statistically impossible for this self-correcting behavior to be random, and demonstrating that the observed result is precisely that predicted by the equations of control theory. By operating only at extremes, referred to in control theory as "bang-bang extremization," the proteins were exhibiting behavior consistent with a system managing itself optimally under evolution.
Statistically impossible to be random.

"In this paper, we present what is ostensibly the first quantitative experimental evidence, since Wallace's original proposal, that nature employs evolutionary control strategies to maximize the fitness of biological networks," Chakrabarti said. "Control theory offers a direct explanation for an otherwise perplexing observation and indicates that evolution is operating according to principles that every engineer knows."
This part I love.

The scientists do not know how the cellular machinery guiding this process may have originated, but they emphatically said it does not buttress the case for intelligent design, a controversial notion that posits the existence of a creator responsible for complexity in nature.
They don't know but are still quite sure. Of course how could engineering principles ever be connected with intelligent design. Lol.

This is 100% in line with Shapiro's "natural genetic engineering". Slam dunk!
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Seemed relevant:

Evolution depends on rare chance events, 'molecular time travel' experiments show

Tracing these alternative evolutionary paths, the researchers discovered that the protein – the cellular receptor for the stress hormone cortisol – could not have evolved its modern-day function unless two extremely unlikely mutations happened to evolve first. These "permissive" mutations had no effect on the protein's function, but without them the protein could not tolerate the later mutations that caused it to evolve its sensitivity to cortisol. In screening thousands of alternative histories, the researchers found no alternative permissive mutations that could have allowed the protein's modern-day form to evolve. The researchers describe their findings June 16, online in Nature.

"This very important protein exists only because of a twist of fate," said study senior author Joe Thornton, PhD, professor of ecology & evolution and human genetics at the University of Chicago. "If our results are general – and we think they probably are – then many of our body's systems work as they do because of very unlikely chance events that happened in our deep evolutionary past," he added. this fine tuning from biology instead of physics?
Does anybody think natural selection has been shown to be a "unique creative force" or is this just a biased opinion? State why.
OK - I agree with the original quote, which talks about NS being elevated into the unique creative force. You somewhat changed its meaning - probably by mistake.

I mean from time to time, people come up with other mechanisms - such as genetic drift - but they always seem to miss the point somehow. So for example, genetic drift is a mechanism for change - not improvement. The most it can do is to provide some options for NS to operate on.

Another example might be sexual selection. Peacock's tails get longer and longer to attract both females and predators! This seems more like a mechanism of some sort that has simply gone awry. Indeed the tail lengthening may or may not have happened via natural selection!

I guess the real question,is whether someone can come up with a materialist evolutionary 'force' that doesn't amount to NS.

The website looks very interesting!