See point-by-point, below. At 04:54 PM 9/6/2012, Warren Smith wrote:

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From: Henry Baker <hbaker1@pipeline.com> Re biological Rube Goldberg: I disagree vehemently. The more I learn of DNA, RNA, proteins, signalling, etc., the more impressed I am. For example, the process of mere _copying_ of DNA operates very close to the thermodynamic limit -- i.e., it would be very difficult to design _any_ system for copying DNA that produced less waste heat than our own DNA copying.

--Exactly wrong. DNA copying is done with rechecking and with use of ATP->AMP not ADP so it can get extra certainty. In other words it intentionally uses both extra energy and extra chemical steps.

Silly me, relying on papers by Bennett, etc. Yes, there is an energy cost in doing accurate copying, but it can be made smaller by working more slowly, and not doing irreversible operations at every step.

Many biochemical reactions in fact ARE reversible (e.g. fructose <--> glucose interconversion) and hence consume zero energy. But DNA copying is not one of them.

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If our DNA copying were any less thermodynamically efficient, and we continued to copy at the same rate, our dividing cells would fry themselves like a fried egg.

--utter bull. DNA copying is a very small expenditure in human cells compared to other stuff.

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Most evolutionary biologists will tell you that _none_ of the DNA is truly "junk". The proof: if it weren't important, it would relatively quickly disappear after a few generations.

--complete bull. DNA actually is expensive in bacteria and viruses, and they have little or no junk. But in eukaryotes like us, DNA is a tiny expenditure relatively speaking so we can afford lots of junk. By the way, you just "proved" microsoft windows is small and compact, not bloated.

I'm certainly no fan of Microsoft or SW bloating, but the number of bits in human DNA -- on the order of 2^32 -- is incredibly small in comparison with the complexity of the human that is produced. In the near future, we'll be in a position to start randomly (or not so randomly) deleting DNA from mammals to see what the "minimal mammal" is. Of course, just like a random user of Microsoft Windows, we have no idea what insults from the past were alleviated by some particular piece of DNA. In the language of computers, we don't have access to Microsoft's "test suite", that exercises every portion of Windows to make sure that any change in one area doesn't break some other portion of Windows code. So without a _complete_ test suite, we won't be able to determine what is "junk" DNA and what isn't. The bottom line is this: there is clearly strong evolutionary pressure against carrying around too much DNA, because there appear to be very strong reasons for copying the _entire_ DNA into _every_ cell. Since this cost is borne by every single cell on every cell division, the time & energy needed to do a cell division is compromised by having to reproduce too much DNA. It is possible that this idea of having to copy the entire Microsoft Windows system onto every PC in a cluster is not optimum, but nature has so far found this strategy to be extremely robust. This definitely reduces communication costs during the organism's growth & development, and does offer the opportunity for cells--e.g., skin cells--to revert into stem cells again, as has recently been shown.

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Several biologists have proposed that complex organisms have lots of DNA as a form of "diagonalization": all of its siblings with less DNA didn't survive. This is akin to comparing the power of Turing Machines with more or less tape: those with "more" tape can simulate _all_ Turing Machines with "less" tape and do something different.

--you are totally confused. (And if you are right re "several biologists", they are confused too.)

Basically, an organism with more bits of DNA can have more complex behavior than and organism with fewer bits of DNA, and in particular, the organism with more DNA bits can defend against any suite of attacks by organisms with fewer DNA bits.

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For example, some of our DNA encodes experiences with viruses, some of which may be long extinct or at least dormant. Yet if that virus suddenly shows up, there are at least some fraction of humans that will survive.

--some of our DNA encodes viruses that incorporated themselves into our DNA and are now carried along for the ride for free inside us, where they are incurable since part of us.

Yes, viruses can become part of our DNA -- there are a large number of these. But the presence of these viruses also proves that we were successful against them, else we wouldn't be around to still be carrying them. They are sort of "merit badges". They might also be seeds for useful capabilities that we are using now -- e.g., recognizing them or producing some of the proteins that they would have produced.

Further, some our DNA is "self replicating elements" which in fact multiply WITHIN our DNA; they are "out for themselves" not you. Somewhat like cancer but at a smaller size and longer time scale. This is (I suspect) the main reason closely related species have way different amounts of junk and that much of our junk is repeating sequences.

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Plants (which typically don't move) seem to require more DNA than animals (which do move). One can speculate that plants have to sit there and take every insult, while animals can avoid the insult by moving and even emigrating when necessary.

--plants do a lot more chemistry than animals, so they need more genes (which describe chemistry). You can't synthesize many amino acids, fats, and vitamins you need because you lack the genes. Plants do not have that luxury. Animals can't do photosynthesis, even though it'd clearly be beneficial if they could.

I think that the jury is still out on this one. I believe that there have already been experiments showing that photosynthesis is not incompatible with being an animal. I think the big problem with animal photosynthesis is the same reason that putting solar cells on a car is a huge waste of time: there simply isn't enough surface area on a car to make enough electricity to be useful. I would imagine that animals get mutations all the time that lead in the direction of photosynthesis, but since it doesn't improve the animal's life in any way, the mutations immediately get lost. Animals that can store & utilize energy in the form of fat have a huge advantage (nearly 2:1) over the storage of energy in the form of sugars. When you're a warm-blooded mammal, whose basal metabolic rate is upwards of 50% of the animals total daily energy expenditure, fat is clearly the way to go. Energy from photosynthesis at that point is a complete joke.

--In this post I am repeating the usual bio- philosophy & refuting weird myths posted by HB. The alleged new "it aint junk" philosophy to some extent must overthrow the old bio philosophy, but I'd like to know what is wrong with the old arguments, because they sure mostly are not wrong.