Posted on 08/25/2004 10:14:24 AM PDT by Michael_Michaelangelo
DNA mutates, and it's a good thing it does. If it didn't, there could only be one kind of life, not the millions there are today, and species could not adapt to new challenges. This is because mutations in genes—the coding portion of DNA—are the raw material for evolution. However, genes make up a surprisingly small fraction of our DNA. If the genome were a cookbook, its 30,000-odd genetic recipes would be scattered among millions of pages of apparently meaningless nonsense.
Mutations affect all DNA, not just the genes, and this provides population geneticists with a veritable toolbox of methods useful, for example, in DNA profiling. Importantly, all these methods rely on the idea of a “molecular clock,” the notion that mutations rain down on noncoding DNA like a fine drizzle, so constantly that genetic similarity is a good measure of evolutionary time. Thus, if orangutans diverged from humans twice as long ago as did chimpanzees, on any given piece of DNA we would find twice as many differences between the orangutan sequence and the human sequence as between humans and chimps. The mutations are marking time.
If the molecular clock works, scientists can do wonderful things like estimating how long ago it was that the common ancestor of all humans lived, or when birds evolved from dinosaurs. The clock assumes that mutations occur independently of each other and at a constant rate. By analyzing thousands of noncoding DNA sequences scattered throughout the human genome, Edward Vowles and William Amos have found that the clock is anything but constant. Instead, a mutation in one spot in the genome affects the chance of getting another mutation nearby.
Not all noncoding DNA is made up of benign tracts of random letters. Some sequences appear to be more difficult to copy than others, and these trouble spots can give rise to alphabetic stuttering. DNA is made up of four component chemical units, called nucleotides, which are often referred to by their initial letters: A, C, G, and T. Stuttering occurs when the same pairs or triplets of letters occur together, for example ACACAC. Such regions are called microsatellites, and instead of mutating by swapping one letter for another, as most nucleotides do, these sequences evolve mainly by gaining and losing triplets or pairs like “AC.”
In this study, Vowles and Amos used the published sequence of the human genome to track down and compare thousands upon thousands of microsatellites. If the molecular clock ran smoothly, they would expect to find no similarity at all between the DNA sequences surrounding any pair of unrelated microsatellites. To their surprise, they found the complete reverse, with entirely unrelated microsatellites showing widespread and obvious similarities in their flanking DNA. This meant that mutations near microsatellites were not random, but favored certain letters in certain positions. Just as a new shipwreck will attract its own special community of marine life, so microsatellites appear gradually to change the surrounding DNA towards a common pattern. The result is convergent evolution, an unusual state of affairs where, as time goes by, DNA sequences become more similar, not less.
As yet, the exact mechanisms remain unclear, though it probably has something to do with how comfortably different combinations of letters sit next to each other. In English, “U” always follows “Q” and “B” never follows “V.” Similar rules may apply to DNA, albeit on a much subtler level. For example, if a microsatellite contains alternating As and Cs, the flanking regions also tend to have As at alternate positions, in phase with the As in the microsatellite. It is as if the DNA prefers the pattern in the microsatellite to extend into the flanking DNA, rather than abruptly stopping at the end of the microsatellite.
These findings suggest that it may be wise to take the notion of a molecular clock at face value. With a perfect clock, two or three identical mutations would be highly unlikely, but we now know that this may be possible near microsatellites. Vowles and Amos estimate that as much as 30% of the genome may show evidence of convergent evolution, simply because microsatellites are so common. These mutation biases probably exist to a lesser extent in most sequences. Once scientists understand more fully how and where these biases operate, they may be able to estimate more accurately the risk of any given mutation occurring, be it one that causes human disease or makes a virus more virulent. These findings represent yet another windfall from the Human Genome Project, and act as a powerful reminder that unexpected results always lurk around the corner as we delve deeper into the secret world of the genome.
Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH
Back to the old drawing board I guess...
Ping
Science continues to self-correct with further information. Evolution remains the sole reasonable explanation of speciation, and is refined.
These two hypotheses are NOT contradictory, and in fact tend to support one another. I would surmise that a variation in the "tick time" of the molecular/DNA clock is what controls "punctuated equilibrium".
My own take on the subject is that in times of increased stress, the rate of DNA change increases.
Don't disagree, you'll be banished to the cornfield. (Apologies to Rod Serling)
That's a good theory to have if you're interested in defending an existing theory which is apparently flawed.
On the other hand, if you want to look dispassionately at the evidence and engage in science based on that, then such "surmizing" seems contra-indicated.
Researchers find clues about how antibodies specialize
From the article:
"The AID-RPA interaction must be regulated to bring about the specificity of the mutation," Chaudhuri says. "If this regulation is impaired for some reason, then the B cell would incur a lot of random mutations and that might lead to tumors."
Is it unreasonable to believe in God?
“U” always follows “Q” and “B” never follows “V.”
I guess this guy never went to a musical revue. (Some may claim the gay gene derived from just such a pairing).
Mantra: Long ago and far away we had 99% divergent evolution, despite what we see today.
This also brings incite to the idea that married people begin to look more alike. (-|;|Þ "Americans are just a bunch of cowboys".
“B” never follows “V.”
Can I just slink away in shame before the barrage starts? Please?
For techies who do programming, this is most certainly not true. :-)
That's not what the article says, try again.
and a wildly fluctuating molecular clock.
That's not what it says either.
Does anybody know what time it is?
Yes, but you might need some assistance.
Course, problems with the molecular clocks *have* been reported before:
...and are well known. That doesn't make them useless, however, as you and other creationists often try to imply. Why don't you leave science to people who know something about it?
No need.
Thanks for the ping.
That statement is false, unless the "on any given piece of DNA" is changed to indicate DNA which would not be "adjusted".
I'm a scientist---I do that for a living. Based on thirty years of experience in science, I have yet to see any scientific evidence that contradicts evolution (and I include all the "evidence" that shows up on the evolution/creationism threads here).
DNA is a chemical system (I'm a chemist). Chemical systems are influenced by the environment in which they happen. Stress changes the chemical environment within living systems--therefore, the rate at which DNA changes SHOULD change. I have long felt that the idea of a "constant" molecular clock was not valid (based on chemical considerations). The best one can do is develop an AVERAGE rate of change of DNA change based on kinetic rates in systems we have evidence for today. I also expect that they will find (when enough evidence has been collected), that the "clock tick rate" will vary from one species to another.
It's only "apparently flawed" to creationists, because they frantically grasp onto articles like this and misunderstand them and their consequences.
On the other hand, if you want to look dispassionately at the evidence and engage in science based on that, then such "surmizing" seems contra-indicated.
...because...?
...and you've misunderstood/misrepresented *that* article, too.
Disclaimer: Opinions posted on Free Republic are those of the individual posters and do not necessarily represent the opinion of Free Republic or its management. All materials posted herein are protected by copyright law and the exemption for fair use of copyrighted works.