Re: ID and Predictions
- From: lamoran@xxxxxxxxxxxxxxxxxxxxxxx (Larry Moran)
- Date: Thu, 29 Sep 2005 12:59:35 +0000 (UTC)
On Wed, 28 Sep 2005 23:32:20 -0400, catshark <catshark@xxxxxxxxx> wrote:
>
> Because of the recent article about confirmed predictions of evolutionary
> theory where John West was asked to name any made by ID (he came up with:
> an intelligent designer would not fill animals' genomes with DNA that had
> no use, predicted that much of the "junk" DNA in animals' genomes -- long
> seen as the detritus of evolutionary processes -- will someday be found to
> have a function). That interested me if they have any others. A fairly
> comprehensive search of the DI site shows that they are few and far
> between.
>
> However, there was one that was well beyond my scientific understanding
> (ok, so that's not so hard) and I was wondering if anyone could interpret
> and comment. It is from "Irreducible Complexity And Darwinian Pathways
> Guest response to article by R.H. Thornhill and D.W. Ussery" By: Mike Gene
> ARN Forum, June 16, 2000:
>
><http://www.discovery.org/scripts/viewDB/index.php?command=view&id=273>
>
> When we look to eubacteria, the three chaperone components are
> universal. They are found in gm+ and gm- bacteria, thermophiles
> (Thermotoga and Aquifex), spirochetes, Deinococcus, Campylobacter,
> cyanobacteria, Neisseria, and even Mycoplasma. Again, this is most
> likely due to the fact that this chaperone machine is IC (IC
> predicts functional constraint) and other proteins cannot
> substitute through adoption from a different function.
>
> Recently, it was determined that most known Archaea lack this
> chaperone machine. That some have it has been attributed to
> horizontal transfer. Here was a good opportunity to gather more
> positive support for the IC status of such an ancient and highly
> conserved system. I predicted that where we would find the chaperone
> machine in Archaea, we'd find all three components given that it
> is IC. Then, not too long ago, I came across a review paper on
> stress genes and proteins that verified this prediction. The
> authors noted that genomic data demonstrate the following in Archea:
>
> "whenever hsp70 was present in a genome, hsp40 and grpE were also
> found if enough sequencing was done; conversely, genome sequencing
> has demonstrated that if the hsp70 gene is absent, hsp40 and grpE
> are also absent."
>
> IC nicely explains this as the lateral transfer of only one or
> two components of the chaperone machine would be useless and thus
> degrade. That's why you see either all three gene products or none.
> But if adoption from a different function was a common IC generator,
> we should see permutations in Archaea, where a laterally transferred
> dnaK gene would find helpers in the archaeal cytoplasm and evolve a
> new chaperone machine. And all of this is significant because the
> chaperone machine is a very simple example of IC having only three
> parts.
>
> Thus, it would seem that the more complex an IC system is, and the
> less variable it is across phylogenetic lines, the less likely it
> is that adoption from a different function explains its origin.
>
> Thanks.
Hsp70 is the major chaperone in all species. It is probably the most
highly conserved protein in all of biology. Chaperones are responsible
for assisting other proteins to fold into the proper three-dimensional
conformation. Not all proteins require the assistence of chaperones.
Hsp70 forms a complex with at least two other proteins called GrpE and
Hsp40. Hsp70 is a big protein and GrpE and Hsp40 are small proteins that
stick to in to modify its activity. In bacteria, the gene for the Hsp40
homologue is called dnaJ and the gene for Hsp70 is called dnaK.
I know a little bit about hsp70 genes.
http://bioinfo.med.utoronto.ca/HSP70/
If you go to this website and click on "Prokaryotes" you will get to a page
of hsp70/dnaK sequences in bacteria. The archaebacteria sequences are listed
at the top of the page.
The dnaK, grpE, and dnaJ genes are linked in an operon in most bacterial
genomes. You can see a good example of this by clicking on the genome entry
for Methanothermobacter thermautotrophicus [AE000894]. Scroll down the
features table and you will see the genes grpE, dnaK, and dnaJ one after
the other. It makes sense to have these genes in a single operon since they
form a multisubunit complex.
In other genomes the order can be different and sometimes there are additional
small genes in the operon. You can check this out for yourself by visiting the
other genomes on the website. (Parts of the site are under construction as
we speak. If you want to see the human HSP70 genes then follow the link to
"BiP/HSPA5" to see what the entries will look like when I'm finished.)
Here's a picture that shows the organization of the operon in various
species of bacteria.
http://aem.asm.org/cgi/content/full/71/1/487/F1
Some archaebacterial species don't have Hsp70. This was a surprise when it was
first discovered. Those species also don't have genes for GrpE and Hsp40/DnakJ.
This is not a surprise - in fact it's exactly what any good scientist would
predict.
Archaebacteria that lack the grpE-dnaK-dnaJ operon appear to have lost it.
Those species of archaebacteria that still have the operon appear to have
retained it from the common ancestor of all life.
There's nothing remarkable about any of this that would lend support to
intelligent design. In fact, the article suggests that there should be
species that have evolved additional proteins to replace DnaJ and GrpE.
This is not a prediction of any evolutionary theory that I know of. However,
it just so happens that all eukaryotes have replaced GrpE with another
protein and the DnaJ-like protein is only distantly related. Furthermore,
eukaryotes have additional (IC) proteins that are part of the complex and
these proteins are not present in bacteria.
The Discovery website suggests that such a discovery would refute intelligent
design. Consider it refuted.
Larry Moran
.
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- ID and Predictions
- From: catshark
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