Posted on 05/18/2006 11:16:00 AM PDT by PatrickHenry
Forcing Darwin's hand: capturing natural selection in a flask
Even with modern genomic tools, it's a daunting task to find a smoking gun for Darwinian evolution. The problem lies in being able to say not just when and how a specific gene mutated but also how that one genetic change translated into real-world dominance of one population over another.
Rice University biologists, using an ingenious experiment that forced bacteria to compete in a head-to-head contest for evolutionary dominance, today offer the first glimpse of how individual genetic-level adaptations play out as Darwinian natural selection in large populations. The results appear in the May 19 issue of Molecular Cell.
"One of our most surprising findings is that an estimated 20 million point mutations gave rise to just six populations that were capable of vying for dominance," said lead researcher Yousif Shamoo, associate professor of biochemistry and cell biology. "This suggests that very few molecular pathways are available for a specific molecular response, and it points to the intriguing possibility of developing a system to predict the specific mutations that pathogens will use in order to become resistant to antibiotics."
Rice's study involved the heat-loving bacteria G. stearothermophilus, which thrives at up to 73 degrees Celsius (163 F). Shamoo and graduate students Rafael Couñago and undergraduate Stephen Chen used a mutant strain of the microbe that was unable to make a key protein that the bacteria needed to regulate its metabolism at high temperatures. They grew the bacteria for one month in fermentor, raising the temperature a half degree Celsius each day.
Over a span of 1,500 generations, the percentage of mutant strains inside the fermentor ebbed and flowed as the single-celled microbes competed for dominance. Eventually, one strain squeezed out almost all the competition by virtue of its ability to most efficiently metabolize food at high temperature.
The metabolic protein required to thrive at high-temperature could only be made in one genetic region of the bacteria's DNA, meaning the researchers had only to characterize that small region of the genome for each new strain in order to measure evolutionary progress.
The researchers sampled the fermentor for new strains every other day. Though millions of mutations in the target gene are believed to have occurred, only about 700 of those were capable of creating a new variant of the target gene. In all, the researchers identified 343 unique strains, each of which contained one of just six variants of the critical gene.
The first of the six, dubbed Q199R, arose almost immediately, and was the dominant strain through the 500 th generation. Around 62 degrees Celsius, the Q199R was unable to further cope with the rising temperature, and a new round of mutations occurred. Five new varieties - themselves mutant forms of Q199R - vied for final domination of the fermentor. Three of the five were driven to extinction within a couple of days, and the final two fought it out over the remaining three weeks of the test.
The research included a raft of additional experiments as well. The team characterized each of the mutant proteins to document precisely how it aided in metabolic regulation. The fermentor experiment was repeated and the same mutations - and no others - were observed to develop again. Three of the six genes - the "winner," it's closest competitor and Q199R - were spliced back into the original form of the bacteria and studied, to rule out the possibility that mutations in other genes were responsible for the competitive advantage.
Shamoo said it's significant that the mutations didn't arise where expected within the gene. Four of the six occurred in regions of the gene that are identical in both heat-resistant and non-heat-resistant forms of G. stearothermophilus . Shamoo said this strongly shows the dynamic nature of evolution at the molecular and atomic level.
Shamoo said the most promising finding is the fact that the follow-up test produced precisely the same mutant genes.
"The duplicate study suggests that the pathways of molecular adaptation are reproducible and not highly variable under identical conditions," Shamoo said.
The research was funded by the National Science Foundation, the Welch Foundation and the Keck Center for Computational and Structural Biology.
Yo, Dave -- you've always demonstrated that you're incapable of understanding the methods of science, but this one is ludicrous even by your usual standards.
Hint: Experiments are set up very carefully in order to *not* influence the particular effect you're studying. Did you not learn this in gradeschool science class?
Yes, they use "human interaction and influence", but to the goal of crafting the experiment to *not* messing with the actual process they want to learn about, *and* of eliminating from the experiment any separate processes (natural or otherwise) that might influence the results outside of the one process being tested.
This is basic Science 101 -- what's your excuse for not having the first clue how it works? Oh, right, you're an anti-evolutionist: You wouldn't want to risk your opinions about science by exposing them to any actual *knowledge* of the topic, right?
Look, the whole *point* of an experiment is to clear away all the things that might contribute to the results beyond the one thing you're trying to study in isolation, in order to learn how *it* works -- and one of the things specifically eliminated from interaction with the "test subject" is the experimenter's "intelligent design" itself.
So your "point" is, in a word, stupid.
A study would just be a hands-off observance. Will they then turn around and tell us "ha, TOLD YOU it doesn't take intelligence"? What does this say about their opinion of themselves?
It tells us that they know a lot more about how to do science than you do.
Dave, don't you ever get tired of constantly misreading science articles like that?
Why don't you go educate yourself on the subject before you try again?
We are the biomass that cares.
I like it!
Note to self for later reply. :-D
I probably care a lot more than you.
Who cares?
Why don't you go educate yourself on the subject before you try again?
Embarrassing oneself by proudly displaying ignorance...it's the Creationist way.
Answering the rest of your post is a bit more complicated.
Would a single cell that reproduces asexually and creates a community of other like organisms that are exposed to the same environmental conditions ended up having the same mutations across the population.
What we tend to see if we culture a starting strain of bacteria and run it through multiple generations is the emergence of multiple strains due to small differences in a number of genes. In this experiment one gene was put under heavy selection pressure. Higher variation tends to emerge in genes that are not under great selective pressure. Genes with high selection pressure are more likely to have highly conserved sequences across species and perhaps even across kingdoms. For instance, our ribosomes have regions that are conserved fairly well across eukaryotes, bacteria, and archae. But it's impossible to put every gene under high selective pressure, so a variety of alleles (possible sequences for a gene) will eventually arise. This is one way we can estimate how old a population is--if it has low variation in alleles, it probably arose from a bottleneck event not too long ago. On the other hand, Africa is thought to be the region that humans first appeared in partly because Africans have a much higher genetic variation than people from other regions, indicating an old population. So my prediction is that if they repeated this experiment they would again have the same mutations appear, and one (possibly not the same one as last time because there's a certain margin of chance if the top two variants aren't very different in effectiveness) would become prevalent. If they then continued the experiment they would see this strain diverging into multiple strains that have the same allele for the gene required for life at high temperatures, but they would have different alleles for other genes. Unless one of these happened to have some other advantage (better at segregating rare metal ions, for instance) disappearance of various alleles would be driven by random genetic drift and new ones due to mutation would replace them.
Darwin tended to emphasize competition, but sometimes lack of competition can kickstart the process of evolution. Some of the most dramatic radiations we see occurred after mass extinctions emptied a variety of niches and allowed replacement by new species.
Good catch! Thanks for the ping.
Your comments, Moth, inspired me to go and look at Dave's profile. In it I found this shimmering prose:
"DLR appears to have a severe short-term memory problem, to go with his reading comprehension and simple logic difficulties." - Thatcherite, FreeRepublic.com
Dave, I see you are including my words on your profile page. In fact I am delighted, in principal, that you find my words quotable, though I am perplexed by your motivation in demonstrating the fact that so many Freepers and posters on other sites have an extremely low opinion of you. If I attracted as much open contempt as you do I would ponder whether or not the fault lay in me rather than my correspondents.
However, I respectfully request that if you wish to quote me that you include a link to the post where I wrote those words. That will give readers the opportunity to see whether or not the comments I made about your memory, comprehension, and logical skills are warranted by the evidence of your posts that I was replying to. If you do not wish to include such a link then please remove my words from your profile page.
What mechanism are you suggesting for slowing the point mutation rate?
Now a question for you, out of curiosity. :-) I looked at your profile just now, and you have a very nice essay on the purpose of the science threads on FR. I loved it, but I'm curious... you seem to be from the UK... why do you choose to speak from the perspective of an American?
My profile page is a copy of PatrickHenry's. It used to just contain a short vanity piece about me that would have been of no interest to anyone.
PatrickHenry has gone to great trouble to compile his profile page which is a fantastic crevo resource from the science point of view; packed with interesting articles and evidence. A few months ago his homepage was mysteriously deleted. He restored it from a text backup, and it was deleted again a few hours later. Queries to the mods about what was going on elicited no response (as far as I am aware). Quite a few of the pro-science Freepers, including me, decided to duplicate PHs homepage. I've kept it there out of laziness.
Incidentally, hence my tagline.
I was wondered why people were mirroring his profile page.
??
Some Christians on this site must be very, very correct indeed.
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