Whats the right way? 
I don’t think the current paradigm explains new features. I think it explains genes being passed from one generation to another. New features require new functional information. This information lives in very large sequence space so any change is exceedingly more likely to break it down then generate new information.
Too strange
Can you cite an example of this?
None of that is particularly contentious, we’d just argue that though the sequence space is large, it’s so large as to be innaccessible to the natural process of evolution. I also think fitness landscapes are surprisingly smooth when you take into accout their hyperdimensionality. Have you read Andreas Wagner’s book?
An example of changes in transcription factor binding motifs changing the transcription factor that binds to the motif? I thought that was self-evident. Do I really have to give an example?
Yes. A couple of years ago along with Shapiro’s book.
What did you get out of it?
He had an explanation for the arrival of complexity that involved metabolic networks. I thought it was interesting conceptually but did not address the problem we are discussing which is the arrival of large functional sequences.
Yes. Eukaryotic transcription factors are very complex and I am skeptical you can swap them randomly and not have a catastrophic event.
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Instead of looking at it as changes to a sequence, look at it as beneficial changes to an organism and its descendants.
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The source of that change is?
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Pragmatism.
Yes, there are random changes. But it is pragmatism that makes use of the changes that work well.
I think @colewd was asking how you get changes in the organism.
Once a change is made, pragmatism, aka natural selection can kick in… not before.
The only pragmatism I see to random changes in the cell nucleus is purifying selection.
This issue is what I was getting to above and I’m still confused about it. This could be a sidebar or maybe you don’t even wish to engage, Neil, but, to me (admittedly from the outside, looking in) the beneficial changes to an organism are a description of what we see. As such, they cannot also be the cause or explanation.
When Dr. Lents would describe the mutations, he would also speak as to their acceptability(?) Is it not circular in terms of an explanation to define the mutations as being either neutral of beneficial, but also to point to their being beneficial as causal? Every time I read this kind of statement, it doesn’t feel right to me. But I could be misunderstanding.
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So you agree that transcription factors can be “swapped” by mutations, you’re just skeptical that it could happen and be anything but a catastrophy?
I thought we were talking about functional information as in complex phenotypes.
Change is a commonplace. It does not require explanation. Things are changing all the time.
The concern of @colewd seems to be with long sequences of changes. And that’s where pragmatism comes in.
Actually, I don’t identify pragmatism with natural selection. Yes, natural selection provides a bias toward pragmatism. But this only works if natural selection is some kind of driving force, rather than a mere statistical effect.
Biological system have a built-in drive to survive. And that’s what I see as the main source of pragmatism.
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