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To: Southack; js1138; AntiGuv; furball4paws; PatrickHenry
Southack: [Natural Selection *should* favor those without the unused code...]

js1138: [On what basis?]

Southack: [Completely unused code requires more energy for genetic copying, yet delivers, by definition, no benefit to the organism.]

furball4paws: [Actually, Guv, Southack is right, only very marginally, on this. [...] However, [...] The minor "waste" of energy (since that what it all boils down to) would probably not put any organism out of existence in competition with other organisms in its niche.]

AntiGuv: [To be sure, I didn't say Southack wasn't right. I said: "So what?" Southack was wrong by his insinuation that this undermines or contravenes the premise of natural selection - through his elliptical hinting that natural selection would predict a different outcome.]

This may be a first on a "crevo" thread -- *everyone's* correct. ;-)

Southack is correct that selection favors "trimming" unused junk from the genome. However, AntiGuv and furball4paws are correct in that the amount of selection would be *very* slight, and that ordinarily evolution would not be expected to seriously "prune" genomes, except in the very rare cases where the tiny amount of extra energy required to copy "junk" DNA (relative to the far larger ordinary metabolic demands of an organism) becomes a "make or break" issue for a given organism -- and it seldom is.

Another factor (perhaps an even greater one than the "evolutionary laziness" described above due to nearly-nonexistent selective pressures "pushing" for such "housecleaning" in order to save negligible amounts of metabolic energy) is the following: There probably aren't any good ways for nature to separate the "wheat from the chaff" in the genome in order to "decide" which parts can be excised.

Nature has a hard enough time just reliably maintaining and copying the genome as a whole (junk and all) with a minimum of errors in order to allow life to proceed reasonably effectively. The evolution (by any means) of a mechanism to CHOP OUT parts of the genome randomly (or even semi-randomly) in the "hopes" of removing a portion of useless DNA and "saving" a tiny amount of energy in the long run would be HUGELY outweighed by the obvious risks and harm inherent in such a "genetic chainsaw" randomly roaming the genome and going, "let's slice *this* piece out and see if maybe we can do without it..." Better to just keep it all and pay the negligble "rental price" on the useless portions than to risk "throwing out" something that actually *is* vital.

Furthermore, in evolution "yesterday's junk" can become tomorrow's genetic innovation, as various bits of DNA get reshuffled, recombined, and mutated. There may be a short-term (and again, *tiny*) energy benefit in taking out the genetic trash, but keeping it around for future adaptive "spare parts" is probably well worth it in the long run.

So for the most part, genomes just carry a lot of "junk" in them. The human genome, for example, is at least 90+% trash that nature never bothered to carry out to the curb.

There are a few interesting exceptions, though. While most vertebrates have a genome size in the 1-5pg range(pg=picogram or one-trillionth of a gram, which by coincidence is just about a billion DNA basepairs, so "Xpg" can be read roughly as "X billion basepairs"), and humans have a 3.50pg genome, the various species of fish in the puffer-fish family have a markedly smaller genome. The Fugu, for example (the fish famous as a sushi delicacy, which can kill by neurotoxins if the meat is improperly prepared), has a 0.40pg genome, less than an eighth the size of humans (and most mammals), and far smaller than even that of most other fish (1.2pg ± 0.02 average for bony fish in general, pufferfish genome is a third of that), so it's not just a fish-vs-mammal difference.

Furthermore, although fish and mammals may seem very far apart biologically, they actually have very similar numbers of individual *genes* (as do all vertebrates), and most genes in any vertebrate have counterparts in the genomes of the other vertebrates -- our fundamental "gene plan" is more alike than different, at least in its basics:

Over 30,000 Fugu genes have been identified in our analysis. The great majority of human genes have counterparts in Fugu, and vice versa, with notable exceptions including genes of the immune system, metabolic regulation, and other physiological systems that differ in fish and mammals.

[from: http://genome.jgi-psf.org/fugu6/fugu6.home.html]

The main reason for the difference between the size of the pufferfish genome and the genomes of most other vertebrates is that for some reason, the pufferfish genome contains far less "junk" DNA than most other vertebrates. For this reason, the Fugu fish was high on the priority list of species to have their entire genome sequenced early, because as this good news article puts it:

In contrast to the epic human DNA strand, the fugu has a mere 400 million chemical letters - and a lot less junk.

"I call it the discount genome," joked the 73-year-old Brenner, who divides his time between research posts at the Salk Institute in San Diego and the Molecular Sciences Institute in Berkeley. "You get about 90 percent of the genes of interest for about 10 percent of the effort."

[...]

Uncovering the genetic sequence of the fugu, which is thought to have a much greater density of useful material, will make it possible to spot not only the genes, but also the regions of the genome that control genes, switching them on or off.

[...]

But Elgar believes that the junk DNA doesn't have any particular purpose. Instead he is of the school that believes junk results from copying errors - transpositions, repeated sections, or stray genetic material that gets incorporated into the genome during reproduction. These errors neither help nor hinder the organism, Elgar said.

"More likely the expansion of junk DNA in our genomes may be tolerated by natural selection. (In other words), there is no pressing advantage to not having it there," Elgar theorized.

[...]

In the meantime, quipped Brenner, "What you have to learn to live with is the fact that your genome is full of junk."

The question remains whether the pufferfish genome just never accumulated so much "junk" in the first place for some reason, or whether unique and extreme evolutionary pressures (or a novel biochemical "cleaning mechanism") in this family of fish managed to excise most of the "junk" that was pre-existing in its ancestors.

This is unusual for a vertebrate, but there are numerous invertebrate and single-celled examples of the same thing. Ordinary brewer's yeast, for example, has a very "lean and mean" genome at 0.008pg, and last time I checked it "held the record" for the smallest genome of any eukaryotic organism. This actually makes *sense* though, since yeast has a "feast or famine" lifestyle that accords well with the kind of thing furball4paws was talking about when he wrote about niches "where blowing ATP on conserving DNA that is not used would put a real squeeze on an organism", causing uncommonly high evolutionary pressures for "streamlining" a genome. But again, for most organisms this just isn't a big issue.

Meanwhile, the slovenly Marbled Lungfish lugs around a whopping 133pg of genome (40-ish times as much as a human's DNA), currently considered the record-holding largest genome of any animal.

For far more data on various genome sizes than you would ever want to know (don't say I didn't warn you), see the: Animal Genome Size Database. I didn't even know this website existed until I went looking for hard numbers while composing this article just now. I had *no* idea such a thing was even available (or that it would have data on over 4000 species already).

And for those creationists who still cling to the notion that most "junk DNA" may actually be useful, we just "don't know" what it does, they might want to read up on the many studies which, by multiple independent lines of evidence and/or experimentation, all indicate that with a few rare exceptions, "junk DNA" is entirely dispensible. For example: Megabase deletions of gene deserts result in viable mice. In short, the researchers snipped over 2.3 *million* basepairs of apparently "junk DNA" out of mouse DNA, then produced offspring mice which were entirely missing that DNA. The resulting mice were normal in all respects. As a press release states:

"In these studies, we were looking particularly for sequences that might not be essential," said Eddy Rubin, Director of the JGI, where the work was conducted. "Nonetheless we were surprised, given the magnitude of the information being deleted from the genome, by the complete lack of impact noted. From our results, it would seem that some non-coding sequences may indeed have minimal if any function."

A total of 2.3 million letters of DNA code from the 2.7-billion-base-pair mouse genome were deleted. To do this, embryonic cells were genetically engineered to contain the newly compact mouse genome. Mice were subsequently generated from these stem cells. The research team then compared the resulting mice with the abridged genome to mice with the full-length version. A variety of features were analysed, ranging from viability, growth and longevity to numerous other biochemical and molecular features. Despite the researchers' efforts to detect differences in the mice with the abridged genome, none were found.

Finally, coming full circle on this discussion -- if our genomes were "designed", why did the "designer" put so much useless junk into his work? On the other hand, accumulating harmless random junk is exactly what one would expect from evolutionary processes, which generate "junk" via random mutations, then via selection the fortuitiously useful parts of the "junk" are preserved and concentrated, the harmful pieces of junk are eliminated -- and the neutral junk is left alone, with no mechanism by which it will be "cleaned out" under ordinary circumstances, except by accident (i.e. further random changes).
98 posted on 02/07/2005 9:12:28 PM PST by Ichneumon
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To: Ichneumon
"Finally, coming full circle on this discussion -- if our genomes were "designed", why did the "designer" put so much useless junk into his work?"

Have you ever looked at large, long-lived software projects such as MicroSoft Windows? Enormous amounts of old, unused code is copied due to lazyness and reducing risk (Oh gee, Bill...we thought that subroutine wasn't used any longer), as well as currently unused code that is inserted or left for "hooks" to anticipated future software. Such projects also tend to leave in some benchmarketing and profiling routines, useful only to the software designers, simply because removing such code would require re-testing before deployment.

"On the other hand, accumulating harmless random junk is exactly what one would expect from evolutionary processes..."

Yes, but here's the rub...we see neither of the two things that we would expect from an unaided, purely Evolutionary system in our currently sequenced genomes.

We would *expect* to see DNA junk code incrementally increase in *every* later species...or else we would expect some genetic mechanism to gradually filter *all* of the junk DNA code away.

We see neither. Some newer species like the Fugu have very little DNA junk code, while some older bacterias have large amounts of junk DNA (while brewers' yeast has very little).

So the junk DNA jumps around. It neither incrementally increases in each newer species, nor does it gradually get incrementally filtered out.

That should be RINGING LOUD ALARM BELLS among serious students of Darwinism.

104 posted on 02/07/2005 9:29:20 PM PST by Southack (Media Bias means that Castro won't be punished for Cuban war crimes against Black Angolans in Africa)
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To: Ichneumon
...if our genomes were "designed", why did the "designer" put so much useless junk...

Perhaps She's just a slattern? (Or a packrat.)

108 posted on 02/07/2005 9:53:25 PM PST by Doctor Stochastic (Vegetabilisch = chaotisch is der Charakter der Modernen. - Friedrich Schlegel)
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To: Ichneumon
Better to just keep it all and pay the negligble "rental price" on the useless portions than to risk "throwing out" something that actually *is* vital.

Reminds me of a science fiction story I read long ago, and I can't remember the title or author. It's the future, of course, and man has gone extinct -- as he so often does in these tales. What remains are androids which we had created. They reproduce and all that stuff, and they know all about man, and they have a cloning program to try to re-create man from old samples.

The androids had been careful to keep all the material and circuitry in their own bodies, and especially their brains, even though they couldn't understand all of it. They figured if man had put it there, it should stay. (And now you see what it was in your post that triggered this response.) Large sections of their brain circuits were a mystery to them, but they seemed harmless and non-functional.

Then they create a man. They had a woman too. (I don't recall why, but these humans were adults, and could speak. Maybe they had been frozen away somewhere.) One of the androids comes into the humans' room, and the man says: "Oh, here comes another one. What do you want?"

The old, mystery circuits in the android's brain click in. He bows his head, low, and responds: "I want only to serve you, master."

131 posted on 02/08/2005 3:06:24 AM PST by PatrickHenry (<-- Click on my name. The List-O-Links for evolution threads is at my freeper homepage.)
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