Haven't read it yet but plan to. Sure has me thinking though.
stuff clipped
> The reason this is so shattering to evolution is that people like
>Dawkins have been saying for years that life LOOKS designed, but there are
>naturalistic explanations for it. Even further, Dawkins has said if he were
>ever shown even a SINGLE case of a complex organ that could not have been
>formed by "numerous successive slight modifications," he would cease to
>believe in evolution.
>
> Now, Behe has provided Dawkins with a whole bunch of them! What we see
>at the biochemical level is "irreducible complexity," which means something
>"composed of several well-matched, interacting parts that contribute to the
>basic function, wherein the removal of any one of the parts causes the system
>to effectively cease functioning."
>
> But how did these exceedingly complex systems, which look even more
>intelligently designed than what Darwin or Dawkins saw, arise? It challenges
>credulity to think that gradualism could do it (and Behe explains why), and
>you can rule out punctuationism altogether.
>
> And you can do another thing: you can scan the scientific literature
>till the cows evolve (ahem), and you won't find ANY paper offering a testable,
>Darwinian scenario for the evolution of these complex systems. (Behe has an
>entire chapter on this).
>
> This is truly where the "naturalism of the gaps" meets its OK Corral.
>Post Behe, it can no longer plausibly be maintained that nature could have
>done this. As Glenn Morton likes to say, we can't dismiss "what we see with
>our eyes." And what we see is design, without any naturalistic explanations.
This whole idea of biochemical complexity intrigues me
and I had been thinking about it the past couple of months but
after yesterdays post and the reading I have been doing just the
last two days the timing is remarkable. I have recently begun
sequencing of a plant mitochondrial gene (small subunit of the
rDNA) and have run into several interesting problems that are
associated with the analysis of such data.
A particular phenomenon has been known to occur in the
mitochondria of plants (as well as in animals and others but
apparently by a different mechanism) that broadly fits under the
description of RNA editing. Here is what happens (as best as I
can describe it, there are several papers on this but I don't have
them in front of me, I can provide more complete references
later). After the DNA has been transcribed and the messenger
RNA (mRNA) has been produced the mRNA sequence can be
edited usually in the form of a Cytosine being converted to a
Thymine (T). Not all Cytosines are converted only those in
particular positions that restore the original conserved sequence
and which can then produce a normal functional protein with the
T replacing the C.
something like:
AGT CCT ACT converted to
AGT TCT ACT which then results in a different amino acid in
the second position
In this way mutation that would have effected the eventual
polypeptide are corrected not at the level of the DNA but in the
mRNA itself. Some genes have been found to have up to 10
edited sites.
What is very unusual (if not disturbing to those of us who like to
know why things happen) is that in the mitochondria of plants
30% of these edited sites occur in the third base position where
they have no effect on the resultant polypeptide.
Many many questions are raised but such a bizarre biochemical
process.
1) how did such an function as RNA editing of this type arise?
How did a system evolve to acknowledge that the original DNA
sequence was mutated in such a way that the direct translation
of it would result in a nonfunctional polypeptide?
2) Even given that some RNA editing has a beneficial effect
what about editing of site which are seemingly insignificant with
respect to the final product (amino acid chain)?
RNA editing has now been identified in several chloroplast
genes.
(more and more cases of editing arise each day as the
technology to identify such phenomenon is increasing. In
general RNA editing is identified first by sequencing the original
DNA strand and comparing it to the sequence of the mature
mRNA which can now easily be sequenced by using reverse
transcriptase to reconvert the mRNA back into DNA - with the
edited RNA sites being maintained)
This has some possibly interesting consequences on much of
the sequence analysis done over the past 10 years. Chloroplast
genes such as rbcL have been widely used in phylogenetic
analysis to look at the relationships of plants to one another by
comparing their DNA sequence. If sites are edited it means that
many of the assumptions written into the formulas used in
analysis of this data are not necessarily based on reality. It has
always been assumed that looking at the DNA sequence is
looking at the code itself in its most basic and purest form.
Although not thought to be serious for studies based on cpDNA
genes anyone studying plant mitochondria (I would note that
animal mitochondria are a whole different ball game in that they
have a very different structure and have been used widely as a
source of phylogenetic data and for population genetic studies)
has to be aware of this potential problem.
Getting back to the point. The whole mechanism, the
reason for it, and most of all how it could have evolved to begin
with is a very difficult question. It is mindboggling to think that in
the case of nuclear genes that the DNA in the nucleus can be
transcribed the mRNA transferred out to the cytoplasm and
there some "factor" edits very particular nucleotides (seemingly
without being able to have any reference to an actual proper
sequence) to essentially fix the errors that the organisms may
have acquired millions of years in the past.
To top it all off there are now reported cases of
reinsertion of the edited mRNAs back into the DNA genome.
This would work approximately like this:
1: mRNA is edited
2: edited RNA is reverse transcribed back into DNA (called
complementary DNA or cDNA)
3: cDNA is then reinserted into genome (much like a retrovirus
inserts its DNA into its host)
- The cDNA representing a particular gene now called
paralogous DNA doesn't even have to reinsert into the same
genome but may be moved to a different organelle or for that
matter could move from one cell to another and insert
somewhere else.
- This has dangerous consequences for phylogenetic studies
because it is possible that the paralogous sequence now (which
can act a duplicate of the original gene and may even end up
replacing the previous "bad" version because the other is lost
since it isn't necessarily needed) may be sequenced by
someone thinking that sequence truly represents that organism
and that it can be directly compared to other sequences from
related organisms. The end result is that a false signal is given
and two samples may look more divergent than they really are.
Things like the evolution of RNA editing boggle my mind,
they seem so unlikely to have occurred by "chance" (note: I
don't believe in chance). At the same time I wonder if even
though these things might seem to extraordinary to have
evolved and thus created, it may be that this is just my first
encounter with this material. We are just on the front edge of
seeing how incredibly complex life is. At first it was adequate to
sequence a gene and compare sequences, then we had to
produce a secondary structure either for the RNA or the
polypeptide, now I have encountered the fact that secondary
structures for ribosomal RNAs are just the beginning because
one has to know the tertiary interactions of the molecule with
itself and the quaternary interactions with other molecules bound
to the ribosome. All of this is necessary to really understand
why certain nucleotides are invariant from bacteria to humans
while other base positions are free to vary. Amazingly though
what was perplexing when one only had the DNA sequence is
remarkable simple when the interaction of the whole molecule is
considered.
Sorry can't think of a catchy sign off.
Joel