you missed the point sfs.
i am NOT proposing that ID and similar "theories" have shred of truth.
what i AM saying is that a breakdown in the modern synthesis does 2 things:
it removes a lot of the arguement against said "theories" and gives them a foot in the door.
How?
The modifications that you keep speaking of are as natural and non-intelligent design as the mechanisms that are already a part of theory. How does HGT among bacteria allow ID a foot in the door? How does genetic drift allow creationism a foot in the door?
OTOH, why is ID and other similar "theories" bad?
I can't speak for sfs, but the main problem I find with ID "theories" is that they don't explain anything at best, and ignore what we already know at worst. ID certainly doesn't explain the signatures of selection that sfs sees in genomes. ID doesn't explain the fossil record. ID doesn't explain why we see phylogenies all over the place. What ID boils down to is a malformed argument against evolution that has no intention of gaining new knowledge.
we definitely have ourselves an interesting little dilemma here in regards to life and how it all works.
sure, mendels laws seem pretty simple in operation, but when you move into the mechanics of it all, you move from the simple to a virtual rats nest.
As sfs' own work demonstrates, evolution is a very useful theory for untangling that rats nest.
also, darwin does a fairly decent job with certain select groups of organisms, but when you try to integrate ALL life into this paradigm, it fails.
this is what this "new biology" is all about, to integrate ALL life, not just select groups.
Finding new mechanisms in different groups of species does not mean that the mechanisms in other groups of species goes away. That is what you keep missing. That is what Koonin's email was trying to communicate. The Modern Synthesis isn't being thrown out, just expanded.
a very good analogy would be newtonian physics and relativity.
It isn't the best analogy. Newtonian physics used instantaneous propagation of gravity which is wrong. Darwinian mechanisms aren't wrong. There just happen to be more mechanisms than what Darwin originally proposed.
A better analogy might be Germ Theory. There are some infections that don't perfectly fit Koch's Postulates, but the diseases he studied still do (e.g. Anthrax). Our ideas of what infectious diseases are and what causes them have expanded, but we haven't had to throw out any of Koch's original discoveries. We may consider prions to be infectious diseases even though they aren't truly germs as Koch first described them. However, B. anthracis is still a bacterial species that causes infectious diseases as Koch first discovered.
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