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Ready, set, mutate... and may the best microbe win
Rice University ^ | 18 May 2006 | Staff (press release)

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.


TOPICS: Culture/Society; Philosophy
KEYWORDS: crevolist
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To: Right Wing Professor
For each point mutation, there were about 25 instances per generation. The key is, that if the population is large enough to be mutationally saturated, the element of chance is eliminated.

That *is* my point. The design of this experiment seemed to limit other environmental factors. If this had been done in vivo (whatever *THAT* means in this context) with the same number of bacteria, maybe the coverage wouldn't have been 25 point mutations per site; and the rate of change would've slowed down.

Or maybe if they'd just dropped a pair of nylon panty hose in the vessel, there's not telling *what* might've happened :-)

Full Disclosure: You've got a private freepmail coming...

Cheers!

121 posted on 05/18/2006 8:47:45 PM PDT by grey_whiskers (The opinions are solely those of the author and are subject to change without notice.)
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To: Almagest
But I was not referring to criticism from other scientists -- but criticism from religious folks who did not like the "implications" that the movements of the planets could be explained without recourse to the supernatural.

'Tis odd you should've said that.

Do you know where I could pick up a copy of C.S. Lewis Discarded Image cheap? I was led to believe it touched on this topic.

...or for that matter, look at Out of the Silent Planet and Perelandra.

Cheers!

122 posted on 05/18/2006 8:49:52 PM PDT by grey_whiskers (The opinions are solely those of the author and are subject to change without notice.)
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To: onewhowatches
Darwin Central -- Its real!

Cool.

Surely you meant: "Darwin Central -- It's real cool."

123 posted on 05/18/2006 9:06:17 PM PDT by dread78645 (Evolution. A doomed theory since 1859.)
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To: mjolnir

<< The theological assumption that God made the universe to make sense on every level may have made Leibniz an easy target for caricature by Voltaire, and it did lead him on the wrong path regarding Newton's theory, but on the whole that assumption we're talking about one of the most brilliant and productive men who ever lived in too many fields to count. >>


"All is for the best in this best of all possible worlds."

I agree with your admiration of Liebnitz. But -- with all his genius..... after reading up for years on the great Liebnitz/Newton calculus controversy, and recognizing Newton's bad behavior in that whole affair -- I am pretty convinced that Liebnitz probably did see a copy of Newton's work in London and fudge a little from it.


124 posted on 05/18/2006 9:07:19 PM PDT by Almagest (The rules of baseball are anti-god. Teach the controversy!)
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To: DaveLoneRanger

Dave, Dave, Dave.... you silly creationist you. You should know better after all this time on crevo threads. To think that what goes on in the lab is an example of intelligent design. You mean to say that setting up (designing) an experiment takes intelligence? Really now..... You need to go back to school and learn what science is really all about before you join in this discussion.


125 posted on 05/18/2006 9:09:50 PM PDT by metmom (Welfare was never meant to be a career choice.)
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To: Almagest
Heisenberg angels!

The more certainly you can determine how many are dancing, the less certainty you have of which pin.

126 posted on 05/18/2006 9:11:15 PM PDT by dread78645 (Evolution. A doomed theory since 1859.)
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To: dread78645

<< Heisenberg angels! >>

<< The more certainly you can determine how many are dancing, the less certainty you have of which pin. >>


BWAAAAA-HAAAAAA-HAAAAAAA!!


127 posted on 05/18/2006 9:18:32 PM PDT by Almagest (The rules of baseball are anti-god. Teach the controversy!)
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To: dread78645
Heisenberg angels!

The more certainly you can determine how many are dancing, the less certainty you have of which pin.

Gott würfelt mit dem Weltall nicht. ...Aber eine kleine Simulation von Monte Carlo verletzt nie irgendjemanden.

Cheers!

128 posted on 05/18/2006 9:18:52 PM PDT by grey_whiskers (The opinions are solely those of the author and are subject to change without notice.)
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To: grey_whiskers


<< Sorry, I was going for the pun on a well-known phrase also involving interruptus. >>


I'm a real stickler for correct form -- but a good pun always takes precedence!


129 posted on 05/18/2006 9:24:00 PM PDT by Almagest (The rules of baseball are anti-god. Teach the controversy!)
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To: Almagest
...recognizing Newton's bad behavior in that whole affair -- I am pretty convinced that Liebnitz probably did see a copy of Newton's work in London and fudge a little from it.

Perhaps, and it's definitely disheartening to think of such a talented guys being so petty, not mention imagining that one of them might have been downright dishonest!

Still, even if Leibniz really did steal the calculus-- he didn't just steal it-- he inproved it, too, replacing the fluxions with dx. It's too bad that Britain out of loyalty to Newton and (given the way things are today, I'm tempted to say commendable)anti-continental bias put themselves behind the curve by stubbornly keeping with Newton's system and notation.

130 posted on 05/18/2006 9:27:44 PM PDT by mjolnir ("All great change in America begins at the dinner table.")
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To: DaveLoneRanger
OK, I promised you a reply.

Got caught up with dinner then watching HGTV.

The whole idea of this experiment was to limit the environment al variation to as specific a change as possible, in order that (with any luck) the change would provide selection pressure, so some mutations would become more favorable.

And then with more luck, that the mutations that did so would be few enough and small enough, to enable the researchers to follow what happened.

The reason this does not *prove* intelligent design, is twofold.

1) The researchers did not predict in advance which mutations would result at which temperature of the vessel. So while they *DID* design the experiment, they did not design the "final results" in the population of surviving organisms. In other words, they helped it along, but couldn't predict or guarantee *WHICH* mutations would work.

2) The laws of physics (and indirectly, chemistry, and then again more indirectly, biochemistry) being what they are, a population of microbes subject to any particular environmental stress (provided the population survives) are *probably* (+) only going to have so many available changes in their proteins or other biochemicals, which will be of any difference. If the environmental changes are severe enough, but not TOO severe, then if you give things enough time for trial and error to work, then sooner or later the mutations which help are going to be stumbled across, and the population *will* change. This is true "whether or not" the environmental changes are done on purpose. The advantage of planning the experiment is that one can take care that the environmental changes are not TOO sudden, and that other things don't interfere, like someone dropping 100 gallons of Pine-Sol into the mixing vessel.

Cheers!

131 posted on 05/18/2006 9:28:29 PM PDT by grey_whiskers (The opinions are solely those of the author and are subject to change without notice.)
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To: grey_whiskers
"Einstein, stop telling God what to do with his dice."
-- Niels Bohr
132 posted on 05/18/2006 9:32:58 PM PDT by dread78645 (Evolution. A doomed theory since 1859.)
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To: mjolnir


<< Perhaps, and it's definitely disheartening to think of such a talented guys being so petty, not mention imagining that one of them might have been downright dishonest! >>


Well -- it's possible they both were. Newton was, at the least, devious -- writing the final report of the English investigation himself, while concealing that fact!


<< Still, even if Leibniz really did steal the calculus-- he didn't just steal it-- he inproved it, too, replacing the fluxions with dx. >>


A vast improvement!


<< It's too bad that Britain out of loyalty to Newton and (given the way things are today, I'm tempted to say commendable)anti-continental bias put themselves behind the curve by stubbornly keeping with Newton's system and notation. >>


It certainly did slow Britain down for a while.

One good outcome of the controversy is that it led to the convention that the first to publish gets the credit -- thus stopping scientists from keeping their discoveries secret.


133 posted on 05/18/2006 9:34:01 PM PDT by Almagest (The rules of baseball are anti-god. Teach the controversy!)
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To: Doctor Stochastic

The original cellular organism from which life evolved would reproduce asexually. As it populated, and the environment changed, it would mutate for survival. If it's mutating to maintain survival according to the environment, then would all of the mutations be the same until it is populated to a degree that it begins to compete with it's self and the environment for survival? Is that when divergence would begin according to evolution?


That was my original post. I know that any change indicates evolution, but I'm thinking in terms of evolving for survival. Darwin, from what I've read, based his theories on the premise that life is engaged in a struggle for survival. It sounds like that's what this study in the article was also about. The article also said it's results were reproducible, so does that mean that they are now about to predict the mutations of the bacteria they used, given the same controls? So, this is what I was tinking. 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. This is assuming they are mutating to maintain survival within the environment. If the environment is the only obstacle presenting a challenge to survival, then would they all have the same mutations until another obstacle to survival emerges? Could this possibly be a competition with each other for survival?

I know what I'm trying to ask, but I'm having a hard time wording it. Be patient with me. Does it make any sense?


134 posted on 05/18/2006 9:34:45 PM PDT by Conservative Texan Mom (Some people say I'm stubborn, when it's usually just that I'm right.)
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To: Conservative Texan Mom
...would all of the mutations be the same until it is populated to a degree that it begins to compete with it's self ...

I think you have a partly incorrect mental model of what evolutionary theory says. (So do lots of people.) The diversity is among individual organisms. All that happens is that those with more offspring tend to have even more offspring. The source of the diversity is the mutations (due to inexact replication of genetic material). Most mutations are neutral; some are helpful; some are harmful. Helpful and harmful may change depending on the environment.

Mutation proposes; selection disposes.

The measurement of success is offspring (survival of the "species"). Indirectly, this may be due to faster breeding (kudzu), better hunteing (sharks), immunity to danger (sequoias), more efficient long-range planning (primates), etc.

135 posted on 05/18/2006 9:57:16 PM PDT by Doctor Stochastic (Vegetabilisch = chaotisch ist der Charakter der Modernen. - Friedrich Schlegel)
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To: Seamoth; DaveLoneRanger; PatrickHenry
PH didn't use any words that creationists don't use quite frequently. The most common I reason I read for evolution being pushed as a conspiracy despite allegedly overwhelming evidence against it is so scientists & atheists can justify their libertine lifestyles, especially their wild sex lives.

Indeed, DaveLoneRanger has used that exact argument himself, and then confessed that the source he got it from (a famous scientist admitting it in a creationist quote-mine, which had mysteriously transmuted into being "early evolutionary theorists" in DLRs prose) was completely fabricated. But stick around here and you will see that consistency and fairness are not DLR's strong suits. On another occasion he deplored ad hominem while in the same screed using the "argument" that "Haldane was a communist". We are still searching to see if we can find out what DLR's strong suit is. So far it appears to be the vacuous repetition of quote mines.

136 posted on 05/18/2006 11:45:18 PM PDT by Thatcherite (I'm PatrickHenry I'm the real PatrickHenry all the other PatrickHenrys are just imitators)
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To: metmom

:)) good answer......


137 posted on 05/18/2006 11:57:05 PM PDT by tgambill (I would like to comment.....)
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To: Conservative Texan Mom
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.

No, the mutations are random, within the bounds of viable chemistry.

This is assuming they are mutating to maintain survival within the environment.

They don't do that intentionally; differential survival and progeny chances is a side-effect of mutations. The population gets all the mutations spread amongst its individuals, but the individuals with the right mutations (for their current environment) survive to have offspring.

If the environment is the only obstacle presenting a challenge to survival, then would they all have the same mutations until another obstacle to survival emerges?

No, covered above, all the mutations occur, and the beneficial ones (in the current environment) prosper.

Could this possibly be a competition with each other for survival?

Exactly, but not quite in the way you were thinking; I hope that it is clearer now.

138 posted on 05/19/2006 12:00:35 AM PDT by Thatcherite (I'm PatrickHenry I'm the real PatrickHenry all the other PatrickHenrys are just imitators)
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To: tgambill; metmom
Crevo conversation 1

Scientist: We can't do cool evolutionary stuff in the lab.

Creationist: You can't do it in a lab! So you aren't practicing science at all. All you've got is a load of wild assertions. Come back to me when you've got some lab results, loser. Till then I'm running with intelligent design.[scientist shakes head in disbelief]

Crevo conversation 2

Scientist: We managed to do some really cool evolutionary stuff in the lab. You've got to listen to us now.

Creationist: BUWAHAHAHA!!! You've got to be kidding me! All those petri dishes and test tubes, all that intelligence you've used designing your experiment. Idiot, can't you see, all you are managing to prove is Intelligent Design.[scientist shakes head in disbelief]

139 posted on 05/19/2006 12:12:50 AM PDT by Thatcherite (I'm PatrickHenry I'm the real PatrickHenry all the other PatrickHenrys are just imitators)
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To: Thatcherite

:)) I'm keeping this one in my files........:)))


140 posted on 05/19/2006 12:53:25 AM PDT by tgambill (I would like to comment.....)
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