[ExI] Essential Upload Data

[Re Rose]

 I tookl John's last post apart this time, so I can focus on points as I
have some time to respond.

So first of all, its not a limitation of "life" in ANY WAY that only a few
elements are used in biological processes. It's a limitation on reality
imposed by thermodyanimc considerations. Instead of giving a course in
physical chemistry and organic chemistry, which as a chemist I certainly
recommend people should take, I'll just say, biology is basicallylimited by
chemical potentials. Reaction in biochemical systems need to be reversible
in order to ;participate in biochcmical cycles. Bones cannot be made of
diamond because bones remodel dynamically, and also the bone tissue evolved
to be part of and participate in other biochchemical mechanisms (as a store
of calcium, for example, or its marrow being part of the immune system).
Diamond is not reactive and would not be a biochemically versatile.

DNA repair is my thing, in fact I am about a month away from a publication
on this topic which I'd be happy to share (note: saying that here gives me
incentive to me complete that damn paper, which is taking a very long
time...!). So - I completely disagree, DNA repair systems are amazing. DNA
is being replicated constantly, it is under constant siege by radicals and
other reactve molecules, it is sitting in an aqueous environment at around
100 degrees depending on the creature, it is subject to constant
environmental attack -- and yet its data stays intact for at least 70 years
and probably can stay intact for hundreds of years. It is robust to
exogenous atttacks such as by mutagens or radiation. There are a number of
interacting repair mechanisims which detect any error or damage to the DNA
within microseconds, and they quickly recruit the correct repair systems to
these lesions. In worst case situations, when data is missing (like over a
double strand break), these repair systems can even recreate missing data -
a strategy which can fail but it is a last ditch effort and often succeeds.

So DNA repair is a huge evolutionary sucess which relaibly carries precious
biological information forward in time, and the inherent chemical and
physical problems evolution solved in order for that relaibility to occur
are tremendous. Each type of DNA damage - base adduct, strand scission,
oxidation, dimerization, there are many more - all have completely
different chemistries, and each DNA repair system deals with each one of
these chemistries eparately. It is truly an amazing feat, one which you (or
any living organisim) literally could not live without.

Please. Respect for DNA repair!

-Regina


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There are 80 stable elements but life only figured out how to use 25 of
them, I fail to see why such a extremely limited repertoire is a virtue. We
have managed to find lots of very useful things that Aluminum can do,
whycouldn't life do the same thing?  And it's all just carbon so why
don'ttigers have carbon fiber skeletons and diamond teeth? Because
Evolution isan incompetent designer that's why, and it's why the retina of
every vertebrate eye is backwards and has a blind spot as a result.

And proteins oversee DNA replication and do a crummy job of it. The typical
error rate for DNA reproduction is about one error per 100 million
nucleotides.

https://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-mutation-409

Each nucleotides contains 2 bits of information so that?s one error per 50
million bits, and one error in 50 million bits is bad, its LOUSY! Your
computer wouldn?t work it it had an error rate that huge, the internet
would not work, our entire information economy would collapse. But it
hasn?t collapsed because Claude Shannon showed us 70 years ago how to
encode information so it can be transferred and duplicated with arbitrary
low error rates, vastly lower than anything biology managed to come up with.

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