Re: Incredible evolution


"Glenn" <GlennSheldon@xxxxxxx> wrote in message news:1186867351.900086.19470@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
On Aug 11, 2:17 pm, Ron O <rokim...@xxxxxxx> wrote:
On Aug 11, 12:29 pm, Glenn <GlennShel...@xxxxxxx> wrote:





On Aug 11, 4:58 am, Ron O <rokim...@xxxxxxx> wrote:

On Aug 10, 8:55 pm, Glenn <GlennShel...@xxxxxxx> wrote:

http://www.sciencedaily.com/releases/2007/08/070809130025.htm

"Modification of histones has been studied for some time, now we are
moving to understand the modification of something that modifies
histones," Shen says of INO80.

Shen's research is conducted in yeast, but the pathways involved are
conserved in all forms of life with complex cellular organization,
known as eukaryotes, right on up to humans, Shen notes."

It seems to me that repair mechanisms are essential for life. Are
there any examples of organisms that lack these complex systems?

Repair systems are found in all bacteria and eukaryotes that we have
looked for them in, but they are missing from viruses. Some viruses
do not even use host repair genomic repair systems, although they
might depend on them indirectly for up keep of host translation
systems.

If you are claiming that repair systems might be required for
lifeforms, the claim is untenable at this time. You are just looking
at the extant organisms that have been in competition for living space
and resources for billions of years. We only see the survivors.

Actually I was looking at "the pathways involved are conserved".

The problem is that you probably have no point that you can make
relavent to whatever you want to put forward or defend. If you have
one, make it.

They seem to be talking about conservation among eukaryotes for
histone pathways. Genomes were limited in size for a couple billion
years until one lineage figured out a means to package large amounts
of DNA in multiple packets called chromosomes. All eukaryotes share
this feature, and are descended from that ancestor. Prokaryotes
developed other systems for DNA packaging, but never made the jump
past a certain amount of DNA in their genomes.

The evidence suggests that it may have taken nearly 2 billion years to
evolve this DNA handling system. No one claims that it was easy.
There is the fact that, apparently, it hasn't happened again
independently, or the Johnny come latelies that evolved something
similar could never get a foothold in the turf plowed by the first to
do it. It is a highly conserved system. The chromosomes aren't as
tightly packed in fungi as they are in, say, mammals, but the basic
packing is pretty much the same. This chromatin has to be dealt with
in pretty specific ways. You not only have to keep track of all the
DNA, you have to condense it and open it up for gene transcription and
genome replication. By the time the lineages for plants and animals
was separating the system had evolved pretty much to its present state
and has been fairly conserved since. You can look up the Histone
genes and find that there might only be a single amino acid difference
between the same gene in a pea as in humans. It took looks like it
took hundreds of millions of years to evolve this system to that
point, and there hasn't been much improvement in it for a long time.

"Conserved" is a relative term. It isn't completely conserved, but it
is conserved enough so that we can determine that everyone of our
ancestors since the single celled eukaryotes that were the common
ancestors of both plants and animals had this basic system.


What a waste of bull***.

Glenn, I think you should back up, take a deep breath, and look at this
thread again. Here is how I see it:

You started by quoting some nice research, including the background
information that the repair system they are looking at seems to be
conserved in eukaryotes. You then wrote:
It seems to me that repair mechanisms are essential for life. Are
there any examples of organisms that lack these complex systems?
See the potential ambiguity? Does "these complex systems" mean the
systems that the researchers were investigating? Or does it mean
repair systems in general - which you assume are always complex?

Both Harshman And Ron O were trying to clear up the ambiguity. All
organisms don't have the same kinds of repair systems that the researchers
were talking about. Viruses mostly don't have repair systems in any
real sense. Bacteria do have repair systems, in some sense, but they are
very different from the ones in eukaryotes. They have to be, because
eukaryotes (because the genome is diploid) can practice some kinds of
repair which prokaryotes can't do.

However, there is one common denominator to both prokaryotic and eukaryotic
repair systems. The systems are tied in to a 'checkpoint' system. The
simplest possible checkpoint system is one which says, in effect, "Don't
divide the cell until the DNA has been successfully replicated."

Some logic like this exists in every organism - prokaryote or eukaryote.
This logic almost certainly existed in the cellular LUCA. Different
descendents of the LUCA have elaborated on this simple rule in different
ways. There are lots of different ways to repair DNA because there are
lots of different ways it can become 'broken'. Different organisms
have different repair systems - so different that it may be difficult to
find any homology. But the core system in the eukaryotes is a pretty
complex one which seems to be mostly conserved among eukaryotes. Various
prokaryotes have various different systems of various levels of complexity.
One interesting one is used by this little bug:
<http://en.wikipedia.org/wiki/Deinococcus_radiodurans>
but there is lots of variety.

My own viewpoint is that DNA repair mechanisms are not an absolute
requirement for cellular life. A very desirable add-on, though.
What I think *is* pretty much an absolute requirement is some kind
of cell-division checkpoint system - "Don't divide the cell until the
genome has been successfully replicated." But I don't see that this
checkpoint system needs to *be* especially complex. It is pretty much
a sure thing though that it will *become* more complex over evolutionary
time in just about every successful lineage. And that mechanisms for DNA
repair will provide part of that evolved complexity.

.