Why should enhancer evolution work at all?
I'm not sure I understand exactly what you are asking here...
Did you even read the link?
The
abstract of that paper is already a big helping of misrepresenting the field, seasoned with unsupported claims out of personal incredulity. Doesn't seem to get much better, from the looks I've had at the main text...
Plus I don't see how it is relevant to my question to you, but look how easy I am to derail...
Cserháti 2007 said:
Because of their widespread distribution, conserved non-coding sequences have important implications for the
creation/evolution debate. Such sequences are indeed highly conserved, which means they resist mutational
change.
Like all "conserved" DNA, conserved non-coding elements are conserved to
highly variable degrees.
Here's a figure from another study on enhancer evolution that demonstrates this. CsB, the HoxD control element illustrated in the figure, has bits that are conserved all the way across jawed vertebrates, other parts only across the amniotes, and some that are specific to the mammals. Note also that even with the most highly conserved regions, we're not talking about 100% identity.
Cserháti 2007 said:
Thus, they are design elements in the genetic makeup of organisms that may help to differentiate
between taxa. Moreover, many evolutionists now believe regulatory sequences are the central motor for molecular
evolution, and that evolution of these regulatory regions is what mainly alters protein expression.
Actually, it's becoming increasingly clear that regulatory regions AND protein coding sequences (and RNA genes, let's not forget those) are heavily involved in evolution (and
molecular evolution means something slightly different).
Of course you mainly (or at least often) alter protein expression by messing with the regulatory elements. (Other options include microRNAs, alternative splicing and even
ribosomal proteins.)
He says that like coding sequence evolution was thought to alter protein expression before. (Which, as a matter of fact, it can do. IIRC, bacteria make use of rare codons to slow down translation, and I'm sure there are other examples.)
But regulatory elements are very obviously not the only players.
Cserháti 2007 said:
But this does
not explain molecule-to-man evolution, which requires a continuous supply of new genetic information.
And here our author conveniently omits that NO ONE is proposing that CNEs alone explain everything. Presumably, he's never heard of gene duplication, domain shuffling, HGT, heck,
de novo gene birth from non-coding DNA! (The first is hard to believe given that he discusses it in the main body of the paper...)
Cserháti 2007 said:
It does
however provide an explanation for the origin of variability within the created kinds in the biblical creation
model. In this model, the information content of genes is conserved, while certain regulatory changes bring
about changes in gene expression.
And here, he basically says that enhancer evolution does work. Since morphologically and genetically speaking, we're well within the "ape kind" (unless
domestic dogs are several different kinds...), your "did you read???!!11!!!" source appears to be on my side
A choice quote from the paper itself, for what it's worth:
Cserháti 2007 said:
That is, the
more a pair of genes have diverged from each other, the
larger the differences in TFBS content and expression
patterns. However, a detailed study by Zhang et al. of
202 pairs of yeast genes showed there was only a weak
correlation between TFBS content and expression, and
showed that the 10 most highly co-expressed gene pairs
do not have even half of their TFBSs in common. They
believe other factors, such as motif-motif interactions*,
trans factors, and chromatin structures might be responsible
for differences in expression.
57
It doesn't work that way. Transcription factors work in combinations to activate (or repress) a target gene. We've just seen from the
eve study that quite different sets of TFBSs can sum up to the exact same expression pattern, using the exact same TFs to boot (all enhancers were tested in the same species). It's like 2x2 + 3x7 is the same as 1x5 + 5x4. Thus expecting raw divergence in TFBS content to match expression divergence is probably not a good idea.
What the differences are appears to be more important than
how many there are. Naturally, that's also a far more
difficult situation to analyse.
Who said anything about 20-something million years? And the fruit fly example shows changes over 20 million years? My question did they diverge at all? Still fruit flys right?
They obviously did, or there wouldn't be a paper about it. You do know what "divergence" means, right?
And don't come with that tired trope. Fruit flies happened to be morphologically conservative over that time span. Other things haven't. (Ironically, the "slow-breeding" apes may have changed more in appearance in the last 20 million years than the "fast-breeding" flies!) But that's not why I brought this up at all.
Of course, you didn't seem to get why I did bring it up, so let's have another go at explaining that...
me said:
In any case,
that was not the point of my example. Recall that
you said that genetic switches only make sense with design. In return, I asked you how design explains the differences between certain genetic switches.
you said:
Design says just that the differences did not come about by small changes over long periods of time (as in a hominid). How do I explain different sub routines as a programmer? I designed them that way.
If you were a designer with a thimble of sense,
why would you change a perfectly functional design to something that produces the exact same result?
What was your point about your example?
That question above.
And before you answer "'cuz I felt like it", think about what that implies for the testability of the design hypothesis.