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Giardia Bares All: Parasite genes reveal long sexual history
Science News Online ^ | Jan. 29, 2005 | Christen Brownlee

Posted on 02/07/2005 1:15:22 PM PST by js1138

Giardia Bares All: Parasite genes reveal long sexual history

Christen Brownlee

While it hasn't yet been caught in the act, a single-celled parasite has been ready for sex for billions of years. A new research finding provides evidence that sexual reproduction started as soon as life forms that have nuclei and organelles within their cells branched off from their structurally simpler ancestors.

The parasite Giardia intestinalis is well known for causing a diarrheal disease that animals and people contract after drinking contaminated water. Many researchers consider this species to be one of the most ancient living members of the eukaryote, or true nucleus, lineage. However, unlike most eukaryotes, G. intestinalis and its relatives have been long considered to reproduce only asexually—by division into two identical cells.

To determine when reproduction via sperm and eggs originated, John Logsdon of the University of Iowa in Iowa City and his colleagues took a close look at G. intestinalis' mysterious reproductive life. They focused on the hallmark of sexual reproduction known as meiosis, the process that halves the number of an organism's chromosomes to make gametes such as sperm and eggs. Among available data on the G. intestinalis genome, the researchers searched for genes similar to those that control meiosis in other eukaryotes, including plants, animals, and fungi.

The researchers' analysis revealed that G. intestinalis possesses genes similar to those used for meiosis by other eukaryotes. At least 5 of those genes function only in meiosis, and 10 others have roles both in meiosis and other functions, Logsdon's team noted in the Jan. 26 Current Biology.

Although the researchers didn't establish that G. intestinalis reproduces sexually, Logsdon notes that a discreet sex life might turn up after further study. "Lack of evidence is not evidence of lack," he says.

On the other hand, the findings suggest that meiosis was established early in eukaryotic evolution, making sexual reproduction "a very central feature of being a eukaryote," says Logsdon. Bacteria and other simple-celled life forms, or prokaryotes, don't make eggs and sperm.

All living eukaryotes, including G. intestinalis, share numerous cellular features and processes that aren't seen in prokaryotes. According to Andrew Roger of Dalhousie University in Halifax, Nova Scotia, establishing that all eukaryotes are capable of meiosis could "make the evolutionary transition from prokaryote to eukaryote even more difficult to sort out.

"A lot had to happen when eukaryotes evolved. Why aren't there any intermediate stages of this process alive today? Did all the intermediate forms go extinct, and why?" Roger asks.

Logsdon says that he and his team plan to continue their research by looking for meiosis genes in other eukaryotes thought to be asexual.

References:

Ramesh, M.A., S.-B. Malik, and J.M. Logsdon Jr. 2005. A phylogenomic inventory of meiotic genes: Evidence for sex in Giardia and an early eukaryotic origin of meiosis. Current Biology 15(Jan. 26):185-191. Abstract available at

http://dx.doi.org/10.1016/j.cub.2005.01.003.

Sources:

John M. Logsdon Jr. University of Iowa Department of Biological Sciences 310 Biology Building Iowa City, IA 52242-1324

Andrew Roger Department of Biochemistry and Molecular Biology Dalhousie University Halifax, NS B3H 1X5 Canada

http://www.sciencenews.org/articles/20050129/fob1.asp

From Science News, Vol. 167, No. 5, Jan. 29, 2005, p. 67.


TOPICS: Culture/Society; Miscellaneous; News/Current Events; Technical
KEYWORDS: crevolist; evolution
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To: js1138

I like your vancomycin expose'. However, I would quibble with one point. Penicillin and all other beta-lactam antibiotics (such as cephalosporins) act by inhibiting new cell wall formation. This causes the cell to explode, since it has no osmotic protection.


51 posted on 02/07/2005 5:34:33 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: Southack

I did answer it, both frivolously and seriously. Sorry you don't see it.


52 posted on 02/07/2005 5:38:41 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: furball4paws; Southack
That should be: "Sorry you don't won't see it."

Just correcting an obvious typo. Moving right along!

53 posted on 02/07/2005 5:42:07 PM PST by AntiGuv ()
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To: js1138

Compared to most plastic like things nylon is easy. It is a polyamide and finding an enzyme that can cleave a polyamide is not too tough (natural amides are very common). If you like this kind of thing and have a university library close, read the papers of E.C.C. Lin on enzyme recruitment. They date back to the 60's and 70's, before the cloning rage, but they will explain in great detail the natural modification of existing enzymes to use unnatural substances as substrates.

The bugs that eat halogenated hydrocarbons are even more interesting!


54 posted on 02/07/2005 5:45:07 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: Southack
Completely unused code requires more energy for genetic copying, yet delivers, by definition, no benefit to the organism.

So what? If the organism has no problem reproducing and nothing pressuring it to extinction, it will abide. Just because something would be preferable doesn't mean evolution will force it into existence so long as what is already the case is sufficient for the task at hand. Evolution doesn't have a structural objective independent of a functional one..

However, might I add that you just gave an excellent argument for why an intelligent designer would be expected to design differently..

55 posted on 02/07/2005 5:48:57 PM PST by AntiGuv ()
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To: AntiGuv

The Intelligent Designer was the low bidder.


56 posted on 02/07/2005 5:50:48 PM PST by js1138
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To: AntiGuv

Unless evolution was the design objective, in which case it's pretty amazing stuff.


57 posted on 02/07/2005 5:51:55 PM PST by js1138
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To: dljordan
They probably have lots of taxpayer dollars to burn.

Of course they do. It's more of that "free money" that grows on trees and a 'Bush.' LOL!

58 posted on 02/07/2005 5:52:05 PM PST by NRA2BFree (NO AMNESTY, NO UN, NO PC, NO BS, NO MSM, NO WHINY @SS LIBERAL BEDWETTERS, NO LIBERAL JUDGES! YEAH!)
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To: js1138
Unless evolution was the design objective, in which case it's pretty amazing stuff.

Well, that is absolutely correct!

59 posted on 02/07/2005 5:53:09 PM PST by AntiGuv ()
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To: Southack

" And then lets mention: it appears as though genes not only interact with each other, but also that they have multiple functions rather than the old perception (true or not) that each gene did only one thing."

The first part of this is quite true (think of a bacterium as a very complex clock like mess of gears - anything that happens has the potential to affect any other function of the cell), however, the old perception of one gene one thing has been gone out of biology for at least 40 years. The last part of the statement is now widely accepted. It is true that some enzymes are extremely specific in their function, but many are very "loose" such as some that have both proteolytic and esterolytic activities at the same active site.


60 posted on 02/07/2005 5:57:41 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: furball4paws
A lot has changed in 40 years, and a lot has remained the same. Creationists don't care a hoot about molecular biology and the infighting that takes place among those at the bleeding edge.

What the creationist/ID crowd cares about is common descent, which has only been strengthened in the last 145 years.

61 posted on 02/07/2005 6:02:09 PM PST by js1138
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To: js1138; Southack
The Nylon Bug
62 posted on 02/07/2005 6:02:13 PM PST by jwalsh07
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To: AntiGuv; Southack

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

Actually, Guv, Southack is right, only very marginally, on this. I can think of some environments where blowing ATP on conserving DNA that is not used would put a real squeeze on an organism (thermophilic organisms growing at the expense of coal gas combustion emmissions, for example). However, this would not be true of Giardia - it's got plenty of plenty when it's inside you. And that goes for the vast majority of organisms. 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. It would take something more substantial.


63 posted on 02/07/2005 6:05:18 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: All

Guy (and ladies, too, of course):

It's a rare day when I can discuss with friends things that I really know a lot about.

Thank you all; it has been a wonderful afternoon/evening.


64 posted on 02/07/2005 6:15:02 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: jwalsh07
A couple of things: one, natural selection alters the frequence of alleles regardless of their origin; The probability estimate at your source is bogus. It relies on the (missing) certainty that all the alleles had to mutate, and no intermediate step confers any advantage.

It seems to me that many of these altered amino acids are essential to the catalytic effect of the enzyme. How many, I don't know.

65 posted on 02/07/2005 6:15:09 PM PST by js1138
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To: furball4paws; Southack
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. By illustration, that is ultimately the same kind of nonsense as the illogic behind this question: If humans descended from monkeys, why are there still monkeys?

66 posted on 02/07/2005 6:16:10 PM PST by AntiGuv ()
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To: furball4paws
If you ever get it, YOU will.

I DID get it. LOL I got it from drinking water from a fountain in a 'state' recreation park. It was absolutely horrible. I lost 14 pounds in a week, and that was all water. They had a hard time diagnosing it because it was not common to the area that I lived in.

When they couldn't find the cause they asked me if I had been camping anywhere that I might have got into water that was bad. When I told them where I had been they tested me to see if I did have Giardia, and I did. The medicine cleared it right up. You would think since it's known to be in that area that they wouldn't put water fountains for people to drink from. Needless to say, I NEVER want to have that experience again. :)

67 posted on 02/07/2005 6:28:52 PM PST by NRA2BFree (NO AMNESTY, NO UN, NO PC, NO BS, NO MSM, NO WHINY @SS LIBERAL BEDWETTERS, NO LIBERAL JUDGES! YEAH!)
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To: js1138
"His second point is just wrong. It seems that he did not read what I wrote about the number of mutations that have to occur. He thinks that I wrote that 47 amino-acid differences separate the nylon bug from its evolutionary predecessor. Far from saying that all 47 have to be precisely specified, I said, “…if only 6 of these 47 mutations were essential for the evolution, the probability of achieving it in 30 years is about 3 x 10^-35.”

He also mistakenly thought that my calculation required all 6 to occur simultaneously. The calculation only assumes that they occurred within 30 years and that there is no selection for any combination other than the correct 6." Spetner

68 posted on 02/07/2005 6:35:27 PM PST by jwalsh07
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To: Southack; js1138; PatrickHenry; furball4paws
["If you read the page at my source, you will find a discussion of bacteria that eat nothing but Nylon. Find that in your pre-existing genes."]

Pilgrims had nothing about eating corn in their genes either,

Sure they did. They had genes which enabled them to eat and digest a wide range of sugars, proteins, and fats.

Since corn consists of these same materials, the Pilgrims' genes most certainly *did* "have something about eating [lots of stuff, including corn] in their genes". (If you still want to disagree, feel free to point out the "corn-eating gene" which indigenous Americans have which Europeans don't have...)

The same can't be said about genes for eating nylon, however, especially since nylon didn't even *exist* before the 1930's (it's a man-made substance). And that's by no means the only example (e.g. Evolution of Enzymes for the Metabolism of New Chemical Inputs into the Environment).

69 posted on 02/07/2005 6:39:30 PM PST by Ichneumon
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To: Ichneumon

I just set up the pins. I rely on you to knock 'em down.


70 posted on 02/07/2005 6:43:03 PM PST by js1138
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To: Ichneumon
They had genes which enabled them to eat and digest a wide range of sugars, proteins, and fats.

The fact that the pilgrims could live off the land supports the theory of common descent. Otherwise, if we crossed an ocean and encountered a whole new continent of "specially created" life, it should be expected that much of it would be totally inedible. Granted, this isn't "strong" support, but if things had turned out otherwise, it would be strong evidence against common descent.

71 posted on 02/07/2005 7:02:24 PM PST by PatrickHenry (<-- Click on my name. The List-O-Links for evolution threads is at my freeper homepage.)
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To: PatrickHenry
"Granted, this isn't "strong" support, but if things had turned out otherwise, it would be strong evidence against common descent."

Oh please. Such "evidence" would be widely disputed by today's Darwinists, lets not go there.

Instead, lets go for evidence that *won't* be disputed: code skipping.

Pick 3 species. Find genetic code that exists in what Evolutionary Theory would say have been in both an earlier and a modern species, but that skips entirely a species that Darwinists claim came in between the two.

Evolutionary Theory completely and totally breaks down in the face of genetic code skipping. DNA that skips an entire intermediate species falsifies Evolution...and it can't be argued otherwise by even the most rogue-ish and obstinate of Darwinists.

72 posted on 02/07/2005 8:10:14 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: AntiGuv

I know, I know, but he's better than most.


73 posted on 02/07/2005 8:15:31 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: furball4paws; AntiGuv

I take that back.


74 posted on 02/07/2005 8:19:23 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: Ichneumon; jwalsh07; js1138
Pilgrims had nothing about eating corn in their genes either...

"Sure they did. They had genes which enabled them to eat and digest a wide range of sugars, proteins, and fats. Since corn consists of these same materials, the Pilgrims' genes most certainly *did* "have something about eating [lots of stuff, including corn] in their genes" ... The same can't be said about genes for eating nylon, however, especially since nylon didn't even *exist* before the 1930's..."

Oh please. Nylon is just a polyamide, and finding an enzyme that can cleave to a polyamide is not surprising since natural amides are reasonably common.

75 posted on 02/07/2005 8:19:50 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: AntiGuv
Completely unused code requires more energy for genetic copying, yet delivers, by definition, no benefit to the organism. - Southack

"So what?" - Antiguv

So...technically, an organism would be genetically superior if it had all of its functionality without also having unused genetic code as baggage. Natural Selection *should* favor those without the unused code...

76 posted on 02/07/2005 8:23:27 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: furball4paws

I taught genetics over 40 years ago. There was no "one gene, one function" perception at that time. The mapping from "function" to "gene" was varied; sometimes one-to-one, sometimes many-to-one, sometimes one-to-many.


77 posted on 02/07/2005 8:23:32 PM PST by Doctor Stochastic (Vegetabilisch = chaotisch is der Charakter der Modernen. - Friedrich Schlegel)
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To: Doctor Stochastic
"The mapping from "function" to "gene" was varied; sometimes one-to-one, sometimes many-to-one, sometimes one-to-many."

Interestingly enough, we find precisely that same situation when analyzing database keys and computer programming code today...

78 posted on 02/07/2005 8:25:56 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: furball4paws

Perhaps they'll develop an oral contraceptive to prevent it's replication in your intestines- could prevent the over-prescribing of antibiotics.


79 posted on 02/07/2005 8:26:31 PM PST by midnightson (Mama-the ultimate prognosticator- said there'd be days like this.)
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To: jwalsh07; js1138

Depending on the bug, I could do those 47 amino acid changes in about 6 months, so 6 is a piece of cake. This would use modern molecular biology techniques. To use only "natural" mutational events, it might take a year or two.

The point is well taken that you cannot determine probability based on 6 mutations all occurring at one time in one bug. However, given that the average bacterial culture contains 1,000,000,000 bacteria per ml, a liter would have 1,000,000,000,000 bacteria. An average mutational rate of 1/1,000,000, means that there are 1,000,000 mutants in a liter of bacteria. Digest these numbers and you will see how easy it is to get to a nylon eating bug in a short period of time.


80 posted on 02/07/2005 8:27:30 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: furball4paws
"To use only "natural" mutational events, it might take a year or two."

How do you conclusively show that a change is due to a "mutation event" rather than to an existing gene simply delivering different output functionality (perhaps based upon environmental changes or on differences from other genes)?

81 posted on 02/07/2005 8:31:49 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: Doctor Stochastic

I know, but anything over 40 years makes me feel too old :^]


82 posted on 02/07/2005 8:33:17 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: furball4paws

Me too.


83 posted on 02/07/2005 8:35:10 PM PST by Doctor Stochastic (Vegetabilisch = chaotisch is der Charakter der Modernen. - Friedrich Schlegel)
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To: js1138
"A lot had to happen when eukaryotes evolved. Why aren't there any intermediate stages of this process alive today? Did all the intermediate forms go extinct, and why?" Roger asks.

Sounds like a most bracing, vigorous problem to me, js1138!

May I ask for your ideas regarding how such a problem ought to be conceptualized and organized in the first place, such that all suitable, direct evidence might be qualified in the first place?

It seems we have got one tough epistemological problem raging here; or so it seems to me. Thanks so much for writing, dear js1138.

84 posted on 02/07/2005 8:35:28 PM PST by betty boop
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To: Southack

"How do you conclusively show that a change is due to a "mutation event" rather than to an existing gene simply delivering different output functionality (perhaps based upon environmental changes or on differences from other genes)?"

LAMARK LIVES!!


85 posted on 02/07/2005 8:36:45 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: furball4paws

Be nice. It's a reasonable question.

86 posted on 02/07/2005 8:37:48 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: Southack

Do you know anything about cloning and DNA sequencing technology (I just need to know where to start my answer, nothing implied).


87 posted on 02/07/2005 8:48:42 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: Southack

I've already responded to your 'concerns' above. Repeating your falsehood doesn't make you any less wrong, just more stubbornly wrong.

PS. The only genetic "superiority" from the standpoint of evolution is fitness to survive and propagate. Our aesthetic value-judgments are of no consequence whatsoever in that regard..


88 posted on 02/07/2005 8:53:58 PM PST by AntiGuv ()
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To: furball4paws
"Do you know anything about cloning and DNA sequencing technology (I just need to know where to start my answer, nothing implied)."

Oh brother. Don't bother. The correct answer is: full genome sequencing before and after the alleged "mutational event."

89 posted on 02/07/2005 8:57:13 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: Southack
So...technically, an organism would be genetically superior if it had all of its functionality without also having unused genetic code as baggage. Natural Selection *should* favor those without the unused code...

If the cost of keeping the code around is extremely low, then it probably won't get selected out any time soon.

90 posted on 02/07/2005 8:57:27 PM PST by xm177e2 (Stalinists, Maoists, Ba'athists, Pacifists: Why are they always on the same side?)
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To: AntiGuv

Do you have a link to the questions of evolving "up", "higher", "lower". Gould used to persuasively argue that there is not up or down. A trilobite was highly evolved and successful. It is not a lower form (evolutionary speaking) that a human. Both are/were ideally suited for their respective environments and points in history.


91 posted on 02/07/2005 8:57:41 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: AntiGuv
"The only genetic "superiority" from the standpoint of evolution is fitness to survive and propagate. Our aesthetic value-judgments are of no consequence whatsoever in that regard.."

Then you misunderstood my point, which *wasn't* aesthetic; it was caloric.

It takes *more* energy, with more risk, to make genetic copies of DNA that include completely unused code.

Ergo, an organism that was identical in every way except that had less unused genetic code than its (outwardly appearing) twin would have an energy advantage; Natural Selection should therefore favor it.

92 posted on 02/07/2005 9:01:15 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: Southack

Hmmmmmm. With the technology we have today, we can make a one nucleotide change in the DNA of just about any bacterium and look at the change. Is this not a good enough cause and effect for you?

Don't you see how Lamarckian (try a different spelling this time) your question was?


93 posted on 02/07/2005 9:01:45 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: AntiGuv
"I've already responded to your 'concerns' above. Repeating your falsehood doesn't make you any less wrong, just more stubbornly wrong."

I repeated a falsehood?! Please, quote me so that I may have the chance to correct my error(s), if any.

94 posted on 02/07/2005 9:03:24 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: furball4paws
"With the technology we have today, we can make a one nucleotide change in the DNA of just about any bacterium and look at the change. Is this not a good enough cause and effect for you?"

That sort of intelligent programming (well, really "guessing" due to our early stage in all of this) is precisely good enough for me, but I suspect that *your* side might prefer something a bit more unaided for these sorts of debates...

95 posted on 02/07/2005 9:07:22 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: xm177e2
"If the cost of keeping the code around is extremely low, then it probably won't get selected out any time soon."

If we have a fast-changing bacteria, say 100 alleged "mutational events" per day, would 4 billion years be long enough to see some unused code get filtered out?

96 posted on 02/07/2005 9:09:12 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: Southack

There is nothing you can do with molecular biological techniques that does not happen naturally. A mutagen doesn't make mutations that don't happen naturally, it just increases their frequency.


97 posted on 02/07/2005 9:11:10 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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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: Southack

We have a bug problem here.

As I mentioned earlier, it is possible for extra DNA to be a drain on a bug, in certain high risk and tricky environments. However, in a vast majority of cases that extra energy would not be a factor in survival.

However, in lab bugs it won't happen since there is no competition, just plenty of food and great growing conditions.


99 posted on 02/07/2005 9:16:06 PM PST by furball4paws ("These are Microbes."... "You have crobes?" BC)
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To: PatrickHenry

Thanks for the ping!


100 posted on 02/07/2005 9:21:48 PM PST by Alamo-Girl
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