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)?
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.
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)?
I know, but anything over 40 years makes me feel too old :^]
Me too.
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.
"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!!
Be nice. It's a reasonable question.
Do you know anything about cloning and DNA sequencing technology (I just need to know where to start my answer, nothing implied).
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..
Oh brother. Don't bother. The correct answer is: full genome sequencing before and after the alleged "mutational event."
If the cost of keeping the code around is extremely low, then it probably won't get selected out any time soon.
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.
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.
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?
I repeated a falsehood?! Please, quote me so that I may have the chance to correct my error(s), if any.
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...
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?
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.
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.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:
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.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."
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:
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)."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.
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.
Thanks for the ping!
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