The Third Way

This response to Shapiro pretty much nails it on the protein issue.

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.
I think the history of science can give a great deal of insight into the science itself. where and how certain hypothesis formed can be very revealing. If students were more thoroughly exposed to the history of thought we could then ask more intelligent questions of science IMO.

This little video is excellent, it briefly outlines where the central concepts of the modern synthesis emerged. Remember it was well before the age of genetics and DNA. The modern synthesis is not modern at all. It also hints at the immunology model explaining how mutations are directed to form an antibody. Consider it as a micro model on how evolution could work. Of course it still does not answer everything. But this seems to be what the evidence is pointing to. Shapiro's site has tonnes of examples. Mutations are not random. A targeted search or directed randomization may be more apt.

Eugene Koonin, also a member of the third way. Reviews the very current modern synthesis as it stands in todays modern times on the 150th anniversary of The Origin of Species.
In the year 2009.

The edifice of the Modern Synthesis has crumbled, apparently, beyond repair.
The summary of the state of affairs on the 150th anniversary of theOrigin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution (Box 1). So, not to mince words, the Modern Synthesis is gone. What’s next? The answer that seems to be suggested by the Darwinian discourse of 2009: a postmodern state not so far a postmodern synthesis. Above all, such a state is characterized by the pluralism of processes and patterns in evolution that defies any straightforward generalization.
Last edited:
That's a change of subject!

Or perhaps you've got some other rule violation in mind?

~~ Paul
Oh, I see. Other stuff is open? How unfortunate.

The modern synthesis is the current paradigm Paul.

As I said earlier, in the last couple of decades or more we have discovered a number of new mechanisms that are at work. As it stands these are just adhocs to the modern synthesis. Many of them breaking the very fundamental rules. This has been decades in the making, and it is ongoing. It has been these very things that have prompted many to call for a rethink. There is no formalized post modern synthesis. That is what Koonin is saying.

If you disagree, I'm am quite sure you can provide some scientific reference outlining this new formalized theory. I must have missed it in the media? Are they teaching it in schools yet? Boy, I download and study lots of related papers, must have missed the revolution eh?

Christian apologists? WTF? You just can't help yourself can you? The subjects of religion and evolution are completely inseparable to you. Must be just terrible to have naturalists such as third way folks dumping on "evolution" as you put it. You can't just cry creationist! 99% of your argument is voided and the the other 1% is just plain wrong.

Quit your pissing contest and try to add something of substance. Till then I will ignore your bizarre unrelated posts and erroneous opinions.
Last edited:
Even wikipedia gets it right.

The modern evolutionary synthesis is a 20th-century union of ideas from several biological specialties which provides a widely accepted account of evolution. It is also referred to as the new synthesis, the modern synthesis, the evolutionary synthesis, millennium synthesis or the neo-Darwinian synthesis.
The synthesis, produced between 1936 and 1947, reflects the consensus about how evolution proceeds.[1] The previous development of population genetics, between 1918 and 1932, was a stimulus, as it showed that Mendelian genetics was consistent with natural selection and gradual evolution. The synthesis is still, to a large extent, the current paradigm in evolutionary biology.
To make it a little shorter, I have just included the last exchanges between Shapiro and the Biological institute. Which is pretty much the sum of the issues over proteins.

Shapiro responds to Gauger and Axe.
Gauger responds, why protein domains are not easily combined.
Why protein domains are not easily combined part 2.

Thanks, this is great! Should have some time this weekend, will definitely read through this. I remember from reading Meyer's book that he referenced some more "mainstream" alternatives to evolutionary biology that folks were coming up with due to a recognition of the shortcomings of NS and Neo-Darwinism. Just couldn't remember if Shaprio was one of them, but seems like a likely candidate.
Last edited:
Thanks, this is great! Should I have some time this weekend, will definitely read through this. I remember from reading Meyer's book that he referenced some more "mainstream" alternatives to evolutionary biology that folks were coming up with due to a recognition of the shortcomings of NS and Neo-Darwinism. Just couldn't remember if Shaprio was one of them, but seems like a likely candidate.
Yep, he's mentioned. I think Shapiro gives some great insight into the mechanics of many aspects of evolution. But I still don't see solutions for the central problems laid out in Darwin's Doubt. He is really in the microbiology area. I can't recall him remarking on body plans or the cambrian actually. He certainly doesn't have all the answers.
Yes I know you have learnt evolutionary theory from the new atheist bloggers. Yeah I don't think adding neutral theory. Which avoids Natural selection by defintion. Or near neutral makes a lick of difference to the foundation of the modern synthesis.. Yet more just so stories. it is no different. Just another adhoc. You still got the all fundamentals.

Watch the lectures I posted to see the true state of affairs. They are not IDers or creationists.

As for the disco tute listed as apologist, umm.... big surpise there. See you just can't help yourself. Completely out of the blue. Even when the thread is about another way.
I have nothing against Christians, but I am not one. I know you are trying to taunt me but It really makes no difference at all to me.

Fear the Banned 7? Lol. Nah, I just prefer an intelligent exchange of ideas.
So, what is your view point Paul?

Could you give a summary in your own words? Or is it what PZ said? That is an obsolete view as far as I am concerned. Watch the videos.

The modern synthesis is a union of ideas, genetic drift, a newer adition has been part of that for some time. Neutral and near neutral theories are of minimal significance and are by no means any sort of departure from the modern synthesis. Even if it marginalized it. I mean big deal. Selection of any type relies on the function being in existence, it does not address that.. They have to be present to be selected! No matter drift or neutral. It answers none of the hard questions.

There are transposable elements, templating, splicing codes, genome doubling, adaptive mutations, induced mutations, symbiosis, horizontal gene transfer, epigenetics etc...

Neutral theory? Big f'nn deal.
Last edited:
Well I can only repeat myself at this point.
Random drift, neutral theory that avoids the amazing power of NS. And near nuetral theory that is just as likely to fix bad mutations.
Variations on darwinian population genetics.

There you go, your ñew modern synthesis.

Okey dokey.
My view is that evolution will use whatever works. The Theory of Evolution includes all the mechanisms that we discover. There is no Capitalized Dogma that we need to defend.

I do not believe that design is involved. I look forward to evidence that I am wrong.

~~ Paul
Evolution is a broad term, it does not exclude agency, cellular or other. So I would agree.
No dogma. Wow.
Maybe you should look at the evidence that has been found cited by Shapiro and actually see what evolution is becoming based on the evidence? Watch the videos.

You can believe what you want, and obviously do. The funny thing is you can't prove any of it. Your belief is an act of faith.
As I am talking the third way here, we can leave design out.

The evidence, the observable, testable tangible evidence shows that organized cellular processing rules. The cell can rewrite it's own genome and mutations are not truly random. Since evolution uses what works and includes automatically what we discover then it sure looks like cells are intelligent!
I'm not sure why you keep saying the neutral theory avoids natural selection.

~~ Paul
Natural selection will also sift out bad mutations, they say. Neutral mutations are neither beneficial or deleterious. So it is assumed that mutations can accumulate under the nose of NS without being filtered out. The mutation must have some effect on the organism good or bad for NS to be able to act upon it. Neutral is essentially neutral to NS. No amazing power available here.

It certainly doesn't exclude those things in principle. Now we just have to find some of it.
For the third way the agency is in the cell. There seems ample evidence. We then walk a very fine line.
Well not me, I know exactly why digital semantic code will never emerge from mud. But that is another subject, one we know all too well. Let's stick with the third way.
Right, but neutral theory is in addition to the rest of the theory. You speak as if it replaces it.
No single aspect could be considered to work alone. I thought that went without saying.

I very much doubt you will find any Third Wayers talking about agency in the cell. They will talk about all sorts of cool mechanisms, but I don't think they will assign agency.
James Shapiro who's book the third way is named after refers to cellular cognition and decision making. Small but not stupid are his words. Just watch the videos. Don't be scared. It is really quite fascinating.
I am very familiar with his work and his blogs. I have mentioned him many times since I first starting posting here a couple of years ago. He clearly talks of cellular cognition. Exact words.

You can mix and match your mutations as much as you like, it makes no difference. Different mutations are accumulating, the neutral ones are immune to the amazing power of NS. NS will filter bad ones as long as they don't accumulate too quick. If it were truly random deleterious ones would be the norm, and selection could not keep up. The rate is very limited, 6 per genome in one study.. Most are said to be neutral. This is because crucial genes are protected. This is no accident. Neutral mutation is equal to targeted randomization. You can't claim neutral theory for youself buddy!

You are still stuck in the modern synthesis view that mutations are random and haphazard.

I will try again. In order for natural selection to have an effect, the function must be present and confer some benefit.

To reach the islands of functionality in the genome fitness landscape, multiple steps must be taken. The distances are vast actualy, astronomically so. Like a mountainous landscape as soon as you start the trek for functionality to the next functional peak you descend out of fitness. Blindfolded by the way, even if there were little hopping stones of functionality, which there are not, you could not see them. You can't fly there on the amazing power of NS.

But we have done all this Paul! You had no answers then, do you have something new?
Seriously dude.

It is all assumptions Paul. Assumptions founded on the modern synthesis, and certainly not on any sort of empirical basis.
Last edited:
Who cares what you think?
Organized cellular processes are advantageous that does not explain there origin.
You won't say what your opinion is beyond a couple of vague generic lines.
No not IC. Novelty. Nothing evolves unless it already exists.
Fitness landscape. Yep been there too remember proteins Paul? Dam how many times! There are plenty of experiments and genomic data around this issue, i have read many of them thanks. Unlike you my opinions have basis.

You may have memory issues Paul, I am being quite serious.

I grow weary of you inventing your own just so stories. And having to repeat myself. If you have something of substance then great I will be here.

Your strawman attempt to detatch the modern synthesis, neo Darwinism from evolutionary theory is ludicrous and completely refuted. As far as I can see that is your only single point here.
Last edited:
You require that evolutionary theory = the modern synthesis so that you can continually point out how the theory of evolution is outdated, doesn't tell the whole story, and leaves out important new ideas. I have no such requirement.

~~ Paul
Strawman, it is the consensus view, and it is what is taught in schools all over the world. Àre you saying the modern synthesis is dead? Really? Can I have that confirmed?
Neutral theory has been around for decades. You just want to call it evolutionary theory so you can hide behind vagueness, and include anything you want as you said. How conveniant.
Last edited:
But it is not your argument is it Paul? You are just saying what Larry and PZ say aren't you? That is the entire source of your argument! Wow!

Drift and neutral theory? Is that a complete theory? How? They are trying to distance themselves but neither are willing to give up the main concepts quite clearly.

There has been a debate on this recently with Larry and UD.

I question if there actually is a neutral theory. And Larry by his own words does not even seem sure. He gives no indication of departing from Darwinism at all going by the answers to some questions on neutral theory that were asked of him.
Last edited: