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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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Everybody be nice.
1 posted on 05/18/2006 11:16:02 AM PDT by PatrickHenry
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To: VadeRetro; Junior; longshadow; RadioAstronomer; Doctor Stochastic; js1138; Shryke; RightWhale; ...
Evolution Ping

The List-O-Links
A conservative, pro-evolution science list, now with over 370 names.
See the list's explanation, then FReepmail to be added or dropped.
To assist beginners: But it's "just a theory", Evo-Troll's Toolkit,
and How to argue against a scientific theory.

2 posted on 05/18/2006 11:17:29 AM PDT by PatrickHenry (Unresponsive to trolls, lunatics, fanatics, retards, scolds, & incurable ignoramuses.)
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To: PatrickHenry

Look at that. Evolution in a flask!

And they recorded the chain of mutations.

Great experiment.


3 posted on 05/18/2006 11:23:12 AM PDT by mc6809e
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To: PatrickHenry
"The duplicate study suggests that the pathways of molecular adaptation are reproducible and not highly variable under identical conditions," Shamoo said.

Interesting.

4 posted on 05/18/2006 11:23:21 AM PDT by Liberal Classic (No better friend, no worse enemy. Semper Fi.)
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To: PatrickHenry

Lots of stuff to chew on.

For those critters that reproduce sexually, the ratio of unsuccessful to successful sperm cells is hundreds of millions to one. Lots of room for unhelpful mutations to get weeded out.


5 posted on 05/18/2006 11:25:15 AM PDT by js1138 (Well I say there are some things we don't want to know! Important things!")
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To: PatrickHenry; gobucks; mikeus_maximus; MeanWestTexan; JudyB1938; isaiah55version11_0; bondserv; ...


You have been pinged because of your interest regarding matters of Creation vs. Evolution - from the young-earth Creationist perspective. Freep-mail me if you want on/off this list.



PatrickHenry won't ping threads I ping my list to. I wonder if this means I can dog him and each thread he posts, preclude his ping with mine? Just an idle, amusing thought...

Highlights:
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.

...

"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 ... 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."
The way I read that, it takes an incredibly specialized, highly-tailored "evolution" to take the "right" path. Interesting.

See also:

Argument: Natural selection leads to speciation

Argument: Some mutations are beneficial

Is Bacterial Resistance to Antibiotics an Appropriate Example of Evolutionary Change?

Word to Creationists: Be nice, respectful, no personal attacks, and put your hard hats and kevlar on.
6 posted on 05/18/2006 11:25:58 AM PDT by DaveLoneRanger ("You're not going crazy! You're going sane in a crazy world!" - The Tick)
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To: PatrickHenry

By the way, these guys are forcing this; setting up the experiment with purpose, intent, will, intelligence, etc. in manmade containers with manmade, controlled environments, and human-designed instruments. This is an experiment, which means human interaction and influence. 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?


7 posted on 05/18/2006 11:30:14 AM PDT by DaveLoneRanger ("You're not going crazy! You're going sane in a crazy world!" - The Tick)
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To: PatrickHenry

In before Hitler!

Seriously, interesting article, thanks for the ping. Of course, the deniers will still discount it as "micro-evolution", or something.

Unfortunate name for the scientist, too! I anticipate lots of killer whale jokes.


8 posted on 05/18/2006 11:30:26 AM PDT by 2nsdammit (By definition it's hard to get suicide bombers with experience.)
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To: DaveLoneRanger
The way I read that, it takes an incredibly specialized, highly-tailored "evolution" to take the "right" path. Interesting.

You read that wrong. There was no tailoring done. There were simply millions of random mutations, only a few of which were beneficial.

No intelligence had to alter those genes. No tailoring was done. They mutated on their own and the environment (temperature) weeded out the unfit.

9 posted on 05/18/2006 11:33:49 AM PDT by mc6809e
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To: DaveLoneRanger

You mean like the "hands-off" experiment we are doing daily, building all those anti-biotic resistant microbes in nature (our bodies)?

Of course they are setting up the experiment on purpose - that's how science works. They come up with a prediction, based on the prevailing science, set up an experiment which they predict will give a particular outcome, then watch it run.


10 posted on 05/18/2006 11:35:20 AM PDT by 2nsdammit (By definition it's hard to get suicide bombers with experience.)
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To: 2nsdammit
Unfortunate name for the scientist, too! I anticipate lots of killer whale jokes.

Yousif Shamoo: Associate Professor of Biochemistry and Cell Biology.

11 posted on 05/18/2006 11:37:34 AM PDT by PatrickHenry (Unresponsive to trolls, lunatics, fanatics, retards, scolds, & incurable ignoramuses.)
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To: PatrickHenry
They grew the bacteria for one month in fermentor, raising the temperature a half degree Celsius each day.

I wonder if they ever cackled evilly as I did when lysing my transfected bacteria before bleaching them and dumping them down the sink.

12 posted on 05/18/2006 11:45:18 AM PDT by ahayes (Yes, I have a devious plot. No, you may not know what it is.)
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To: mc6809e
Look at that. Evolution in a flask! And they recorded the chain of mutations. Great experiment.

But it's still a microbe! Get back to me when you can recreate the entire planetary biosphere in your satanic lab. And don't forget to get your own dirt!
</creationism mode>

13 posted on 05/18/2006 11:47:44 AM PDT by PatrickHenry (Unresponsive to trolls, lunatics, fanatics, retards, scolds, & incurable ignoramuses.)
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To: 2nsdammit
Of course they are setting up the experiment on purpose - that's how science works. They come up with a prediction, based on the prevailing science, set up an experiment which they predict will give a particular outcome, then watch it run. They purposely mutate a microbe to exist in designer environment. Call me when they observe, or even intelligently cause, speciation into a higher lifeform.
14 posted on 05/18/2006 11:47:49 AM PDT by mikeus_maximus (Hey George! Read OUR lips: Build the wall!)
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To: DaveLoneRanger

By the way, these guys are forcing this; setting up the experiment with purpose, intent, will, intelligence, etc. in manmade containers with manmade, controlled environments, and human-designed instruments. This is an experiment, which means human interaction and influence. 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?

What intelligent act actually caused the thousands of mutations to occur? And what intelligent act caused some of these mutations to be selected as more beneficial than the others regarding the changing environment?

15 posted on 05/18/2006 11:49:02 AM PDT by Antonello (Oh my God, don't shoot the banana!)
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To: PatrickHenry

LOL!!!!

I love it! You got this in 5 seconds before the (non-sarcastic) example!!


16 posted on 05/18/2006 11:49:46 AM PDT by 2nsdammit (By definition it's hard to get suicide bombers with experience.)
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To: 2nsdammit

Which is satire, and which is sincere? That's your homework assignment.


17 posted on 05/18/2006 11:51:47 AM PDT by PatrickHenry (Unresponsive to trolls, lunatics, fanatics, retards, scolds, & incurable ignoramuses.)
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To: mikeus_maximus
They purposely mutate a microbe to exist in designer environment. Call me when they observe, or even intelligently cause, speciation into a higher lifeform.

Where did you get the idea that they ever caused any mutation at all, purposely or not? And what exactly is a higher life form? One that can survive in an environment that a preceding life form could not, perhaps?

18 posted on 05/18/2006 11:52:18 AM PDT by Antonello (Oh my God, don't shoot the banana!)
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To: PatrickHenry; furball4paws
This sounds like a really cool experiment. Is this sort of thing up that's right up "furball4paws" alley?

If so, perhaps he can point out the significance of the findings.

19 posted on 05/18/2006 11:52:48 AM PDT by longshadow (FReeper #405, entering his ninth year of ignoring nitwits, nutcases, and recycled newbies)
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To: mikeus_maximus
They didn't "purposely mutate" - they purposely selected for a mutation, which occurred on its own.
20 posted on 05/18/2006 11:53:15 AM PDT by 2nsdammit (By definition it's hard to get suicide bombers with experience.)
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