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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: PatrickHenry

<< Just the man I've been looking for! How would you render the slogan of Darwin Central (the conspiracy that cares) into Latin? The best w've come up with are the following: >>


I like two of them. The connotations of the others are a little too far off:


<< 2. Coniuratio quae sollicita est. "The conspiracy which is concerned." >>


Well -- that word "sollicita" most often carries connotations of anxiety and worry -- but this one rates high.


<< 4. Coniuratio Compatiens "The caring conspiracy." >>


Probably the best one. It's also concise. Take it from the magistro antiquo -- this is the one you want.


101 posted on 05/18/2006 7:38:50 PM PDT by Almagest (The rules of baseball are anti-god. Teach the controversy!)
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To: PatrickHenry

You know I've been researching for the last hour or so...and by just looking at the amount of variation on the planet of various species...we have always been in the Age of Bacteria.

Their numbers are incredible and they live on just about every surface on earth...including inside of us. Amazing.

I wonder if a similar long term experiment on the common cockroach over the course of a 100 years would show significant change? I wonder what the effect of increasing gravity on cockroaches would give us in a 100 years?


102 posted on 05/18/2006 7:42:46 PM PDT by I got the rope
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To: Liberal Classic
Does ToE suggest that all life evolved from the same type of single celled organism, or does it only take it back to a variety, or even just several single cell organisms?

I have been under the impression that it is one single cell organism, which leads me to a question. This organism would reproduce asexually. As it populates, and the environment changes, 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?
103 posted on 05/18/2006 7:43:42 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: Almagest
Probably the best one [Coniuratio Compatiens]. It's also concise. Take it from the magistro antiquo -- this is the one you want.

That's pretty much what's been decided. It wasn't one that I came up with, but if you like it, I'll stop my grumbling about how I suffered with those relative pronouns and the passive voice. Thanks. Much appreciated.

104 posted on 05/18/2006 7:45:11 PM PDT by PatrickHenry (Unresponsive to trolls, lunatics, fanatics, retards, scolds, & incurable ignoramuses.)
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To: mjolnir

<< Before Newton the Cartesian mechanistic model of gravity prevailed. >>


Among scientists.


<< The main criticism of Newton came from rationalists like Leibniz who made the entirely reasonable criticism that his model of gravity contituted "action at a distance." >>


The main SCIENTIFIC criticism -- right.


<< Leibniz's point was that Newton's model was in effect positing a miracle-- hardly an argument that it had "made science atheistic." >>


That's true. 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.

I spent a large part of my life reading religious arguments along with the scientific ones. Can't get all that time back now, but I did pick up a few real gems -- such as Luther and Calvin's criticism of Copernicus, for example. Reading sermons leads to all kinds of unintended discoveries!


105 posted on 05/18/2006 7:46:52 PM PDT by Almagest (The rules of baseball are anti-god. Teach the controversy!)
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To: jwalsh07


<< No problem, I can take the teasing. But what makes you think it wasn't a tyypo? >>


I thought of that -- but it would not be as funny that way!
With my typo-leanings, I'll give you and everyone else plenty of fodder. It'll stune you fer sure!


106 posted on 05/18/2006 7:50:14 PM PDT by Almagest (The rules of baseball are anti-god. Teach the controversy!)
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To: I got the rope
You know I've been researching for the last hour or so...and by just looking at the amount of variation on the planet of various species...we have always been in the Age of Bacteria.

This is definitely a microbe's world. I've read that they are, by far, the great majority of the planet's biomass. Very successful in terms of survival and reproduction. Of course they miss out on a lot, but they don't know about it, or care. We do know, and we care, but we probably miss out on a lot too.

107 posted on 05/18/2006 7:51:31 PM PDT by PatrickHenry (Unresponsive to trolls, lunatics, fanatics, retards, scolds, & incurable ignoramuses.)
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To: Right Wing Professor
I wasn't thinking of the *rate* per se, but of the "coverage" necessary. If you are mainly selecting for one thing, with few other factors coming in to eliminate cells which possess the beneficial mutation, then you won't have to get as lucky so often. If you have other major causes of morbidity/mortality, then some of the cells which otherwise might've given rise to the highly adapted progeny, will die off from other causes before their advantageous genes get passed on.

I assume this would affect the perceived selection pressure, changing the rate at which the particular mutations in question 'take over' the population: and therefore changing the number of times a mutation has to occur at the favored site before things take off...

Cheers!

108 posted on 05/18/2006 7:54:09 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: jwalsh07
Is there only one solution set for this temperature increase?

Try again in plain English.

109 posted on 05/18/2006 7:54:49 PM PDT by Right Wing Professor (...founder of African Amputees for Pat Robertson)
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To: PatrickHenry
Given the number of times the threads get moved to the Smoky Backroom, or get hijacked, how about:

8. Coniuratio interruptus

Cheers!

110 posted on 05/18/2006 7:56:18 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
I wasn't thinking of the *rate* per se, but of the "coverage" necessary.

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.

Think stat. mech.. The population was large enough to be thermodynamic (barely). Once you get above the level of fluctuations, the result is inevitable.

111 posted on 05/18/2006 8:02:52 PM PDT by Right Wing Professor (...founder of African Amputees for Pat Robertson)
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To: PatrickHenry; DaveLoneRanger; Michael_Michaelangelo
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.

The killer whale has discovered something Dr. James Shapiro knew many years ago.

A 21ST CENTURY VIEW OF EVOLUTION

In addition to temporal specificity, it turns out that many natural genetic engineering functions show intriguing degrees of selectivity in where they act within the genome. This selectivity appears to be chiefly related to interactions between natural genetic engineering systems and the cellular systems controlling transcription and chromatin formatting. The examples we have of target selection include the action of localized point mutagenesis, retrotransposons and DNA transposons (see 9, 10 for specific references):

...

These few cases of targeting for natural genetic engineering may well be the tip of the iceberg. It is likely that many more instances will be discovered when the target specificity of MGEs and mutators are investigated systematically. The indication that target selection for natural genetic engineering can interact with the transcriptional control apparatus and chromatin formatting provides a realistic basis for thinking about molecular mechanisms that can target mobile regulatory modules (e.g. LTRs or transposons) to a series of functionally related genetic loci. This kind of molecular targeting would greatly enhance the potential for creating novel adaptive multilocus genome systems in response to an evolutionary crisis.
[emphasis mine]

112 posted on 05/18/2006 8:03:55 PM PDT by AndrewC (Darwinian logic -- It is just-so if it is just-so)
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To: Conservative Texan Mom
Is that when divergence would begin according to evolution?

Divergence begins when the system undergoes inexact replication. (Of course, at finite temprature, almost any system undergoing replication will replicate inexactly; it's a consequence of the Second and Third laws of thermodynamics.)

113 posted on 05/18/2006 8:04:05 PM PDT by Doctor Stochastic (Vegetabilisch = chaotisch ist der Charakter der Modernen. - Friedrich Schlegel)
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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.

Those lectures of Calvin and Luther you refer to sound interesting; I do remember reading Calvin on Copernicus. But the problem I had with your statement is that you seemed to be dividing up scientists and believers, whereas the cosmology of Leibniz, is, if anything, more God obsessed than that of Calvin or Luther but certainly just as much so. 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.

114 posted on 05/18/2006 8:05:08 PM PDT by mjolnir ("All great change in America begins at the dinner table.")
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To: grey_whiskers
Coniuratio interruptus

"Coniuratio" is feminine, so it would be "interrupta"

But the thought's good

115 posted on 05/18/2006 8:05:41 PM PDT by Virginia-American
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To: Right Wing Professor

Ok, here goes. If the experiment is done 10^10 times, will any other combination of point mutations cross the finish line?


116 posted on 05/18/2006 8:20:04 PM PDT by jwalsh07
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To: UCANSEE2
Almost like it was planned...

Well, in this particular case, it was. In other situations, it's a result of variable environmental conditions rather than actual planning.
117 posted on 05/18/2006 8:41:51 PM PDT by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: Virginia-American
"Coniuratio" is feminine, so it would be "interrupta"

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

If I had used the correct form the pun would have been lost.

Cheers!

118 posted on 05/18/2006 8:44:23 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: Doctor Stochastic

Would this be a catalyst to produce this divergence?


119 posted on 05/18/2006 8:44:47 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 this be a catalyst to produce this divergence?

What's "this"? I'm not sure I understand the questions.

120 posted on 05/18/2006 8:46:56 PM PDT by Doctor Stochastic (Vegetabilisch = chaotisch ist der Charakter der Modernen. - Friedrich Schlegel)
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