Yes, full disclosure, I have become skeptical of Darwin's mechanism once I realize the improbability of it all. I used to be fine with the idea of evolution I was taught in school, but looking into the basic combinatorics makes it all seem highly implausible. Then, I thought if Darwin was correct, his work should at least show up in the mathematically rigorous areas of biology that rely on evolution and need to get results. Not the speculative portions of biology. Bioinformatics, with its reliance on homology, seems to fit the bill.
So, I'm not saying that Lamarkianism, or any of these other mechanisms are common. I am saying that Darwin's mechanism do not seem to be useful for getting actual bioinformatics work done. For example, look at BLAST's substitution matrix. They started with PAM that is explicitly based on Darwinian assumptions, and it worked badly. The more they made Darwinism less explicit and relied more on the actual data to compute the matrices, the better BLAST performed. And, reading through a bioinformatics book it is full of observations that contradict what one would expect if Darwin were correct. So, I have been unable to find a significant impact of Darwin's work in an area where results matter.
Let me know if you are aware of any area of biology that is mathematically rigorous and relies explicitly on Darwin's mechanisms of random mutation and natural selection to make discoveries and get results.
Of course using natural selection and random mutation is a pretty dumb method when you can artificially select and selectively mutate instead.
It's why we don't use genetic algorithms when we have a better method. It's really expensive to simulate a "natural environment" and run it for hundreds, thousands, or even millions of generations.
Like I said, if nature found a shortcut - and it has, in the case of HGT or CRISPR - it will use that shortcut. It's just more efficient. The same goes for sexual selection, which Darwin didn't pay special attention to, but which is clearly a very important part of "natural" selection.
In my view, those shortcuts could have developed through Darwinian processes alone, in simpler lifeforms. If you can't conceive of that being possible, that's fine. We can't exactly prove it right through a simulation that is accurate to life on earth.
It's not a disagreement over whether Darwinian processes maybe happened somewhere at some time. The question is what is the primary process driving evolution, and what do we see in the lab. Darwinism isn't there, as far as I can tell. So, why some irrelevant processes are taught as the big guiding mechanisms of evolution is a mystery to me. Darwinism, insofar as it's a major part of evolution, is clearly dead. And with certainty it is dead insofar as it proposed to be #the# fundamental explanation of origin of species, as Darwin originally proposed.
> The question is what is the primary process driving evolution, and what do we see in the lab.
As far as the "state of the art" is concerned, it's still primarily random mutation and natural selection. I highly doubt that Koonin would disagree on this, by the way.
> Darwinism isn't there, as far as I can tell.
What do you mean by "we don't see it in the lab"? Of course you don't see natural selection in the lab, that's oxymoronic.
We can see randomness in the offspring of, say, lab rats. We can selectively breed them to e.g. make them more susceptible to certain diseases. I'd rather call this Mendelian than Darwinian, but the difference is only in how the selection happens.
What happens in nature over billions of years obviously can't happen in a lab. It's obviously not sensible to use natural selection as a tool when you can just artificially select or even directly manipulate the genome.
> So, why some irrelevant processes are taught as the big guiding mechanisms of evolution is a mystery to me. Darwinism, insofar as it's a major part of evolution, is clearly dead. And with certainty it is dead insofar as it proposed to be #the# fundamental explanation of origin of species, as Darwin originally proposed.
It's not irrelevant at all. Again, the fact that you don't observe the effects of natural selection in lab, or that it isn't useful for bioinformatics doesn't make Darwinism irrelevant as an explanation for the origin of species.
Even if we accept that known processes like HGT or CRISPR aren't Darwinian and that it may have accelerated some evolutionary processes in some of our ancestors, they couldn't be the primary driver of evolution because so far we haven't observed it in any "higher" species beyond bacteria.
If you want to speculate that there are more such processes hitherto unknown, that's fine. That doesn't mean a eulogy for Darwinism is warranted at this time.
I'm not sure how to line up what you are saying above, and my observation that bioinformatics algorithms work better the further they are from the RM+NS assumption, plus all the other discrepancies I see between theory and practice in bioinformatics.
Sure, Koonin and others can say RM+NS is primary, but I don't see this in the actual work people do that is quantitative and rigorous vs speculative stories.
Also, I'm not talking about genetic engineering, although the fact we can do genetic engineering vs just randomly jamming nucleotides together in the hopes something happens is also fairly surprising if it was all just RM+NS.
So, I'm not saying that Lamarkianism, or any of these other mechanisms are common. I am saying that Darwin's mechanism do not seem to be useful for getting actual bioinformatics work done. For example, look at BLAST's substitution matrix. They started with PAM that is explicitly based on Darwinian assumptions, and it worked badly. The more they made Darwinism less explicit and relied more on the actual data to compute the matrices, the better BLAST performed. And, reading through a bioinformatics book it is full of observations that contradict what one would expect if Darwin were correct. So, I have been unable to find a significant impact of Darwin's work in an area where results matter.
Let me know if you are aware of any area of biology that is mathematically rigorous and relies explicitly on Darwin's mechanisms of random mutation and natural selection to make discoveries and get results.