Ready, set, mutate... and may the best microbe win

Rice University ^ | 18 May 2006 | Staff (press release)

[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.

[2nsdammit]

..... I'm stumped.

[jwalsh07]

"The duplicate study suggests that the pathways of molecular adaptation are reproducible and not highly variable under identical conditions," Shamoo said.

Kinda takes the random out of random, no? One would expect the same adaptation response to the same point mutation. But what directs the same point mutations to occur in regions that were identical in both heat resistant and non heat resistant critters?

The article is unclear about how many mutations took place versus the number of possible mutations that could have taken place. Perhaps that info would help me understand the significance a bit better.

[Quark2005]

Of course they are setting up the experiment on purpose - that's how science works.

If you don't reproduce it in a lab, some people will complain it can't occur in nature because it's never been seen by intervening intelligent observers.

Reproduce it in a lab, some people will complain it can't occur in nature because seeing it required intelligent observers to intervene.

You can't win with some people.

[PatrickHenry]

Creationist internal thought processes about this thread:

Lemme see here ... I know there's no evidence for one species -- even a microbe -- evolving into another, and it certainly can't be done in a lab -- everybody knows that! -- so this can't be an example of anything like speciation. Besides, mutations are always harmful. This kind of thing just doesn't happen. It can't happen. Not ever. I read it in a Jack Chick comic.

So what is this article all about? It's a lie, that's what it is! Scientists always lie, according to Chick. This is just another Piltdown Man! Now that I think about it, it's a flat-out attack on my religion! Ooooooooooo, I'm gonna hit the abuse button! Yeah.

[UCANSEE2]

"The duplicate study suggests that the pathways of molecular adaptation are reproducible and not highly variable under identical conditions," Shamoo said.

Interesting.

Almost like it was planned...

[Antonello]

Kinda takes the random out of random, no?

Only anti-evolutionists have ever claimed that selection is random.

One would expect the same adaptation response to the same point mutation. But what directs the same point mutations to occur in regions that were identical in both heat resistant and non heat resistant critters?

The article is unclear about how many mutations took place versus the number of possible mutations that could have taken place. Perhaps that info would help me understand the significance a bit better.

Nothing 'directed' the mutations to happen at all. The mutations occurred randomly, but only those that granted a benefit regarding the changing environment were selected. Therefore only a few of the thousands of mutations that were observed made the cut. And it was those same few in each execution of the experiment.

[jwalsh07]

Only anti-evolutionists have ever claimed that selection is random.

Which confirms the fact that I am not a dreaded "anti-evolutionist", though to be clear I am a creationist, since I never suggested selection was random. I though it was clear I was speaking about the point mutations but sometimes clear just isn't enough.

Nothing 'directed' the mutations to happen at all.

You can prove this statement? I am stuned.

The mutations occurred randomly, but only those that granted a benefit regarding the changing environment were selected. Therefore only a few of the thousands of mutations that were observed made the cut. And it was those same few in each execution of the experiment.

How many point mutations could have occurred? How many did occur? Did the same number happen in the same locii in both iterations? If you can't answer those two questions then you are pretending to know more than you do. Why?

[2nsdammit]

At least you should read the initial post:

"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,"

[js1138]

Kinda takes the random out of random, no? One would expect the same adaptation response to the same point mutation. But what directs the same point mutations to occur in regions that were identical in both heat resistant and non heat resistant critters?

What makes you think this isn't just a case of only a few kinds of mutations being useful? There are countless examples of variation not producing the outcome necessary for the survival of a species. It's called extinction.

[jwalsh07]

Perhaps you should have read the article?

"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."

Millions or 20 million. Estimate or guesstimate?

The conclusion reached by the researchers seems to be that " "The duplicate study suggests that the pathways of molecular adaptation are reproducible and not highly variable under identical conditions," Shamoo said.

Why?

[jwalsh07]

I think undoubtedly you are correct. Most point mutations are either neutral or harmful, the former being the dominant. But my question is not why only one path lead to the Superbowl but how the beneficial mutations duplicate in each iteration of the experiment. There is undoubtedly an answer but it has nothing to do with my being a creationist or a dreaded "anit-evolutionist".

It just hasn't been answered here yet.

[PatrickHenry]

For those who may be struggling to challenge this article, we offer the Evolution Troll's Toolkit.
Another service of Darwin Central, the conspiracy that cares.

[mysterio]

microevolution * 3,500,000,000 = macroevolution

[js1138]

Answer my question. What reason do you have for thinking this isn't just a case of water running downhill and finding the path of least resistance.

The experiment was designed to provide one very narrow and specific environmental challenge. It was also designed to create a winner in a competition.

When you provide a narrow criterion for success, you get the same results from any stochastic process.

I'm not asserting this has to be the case here. I'm just saying there isn't any reason to believe it isn't.

[jwalsh07]

Answer my question.

I answered your question.

Now a few for you.

How many base pairs in the target gene?

What is the mutation rate per generation?

How many bases were impervious to mutation?

Question authority js. :-}

[Conservative4Ever]

My refrigerator and under my sons bed has been doing this for years. Big deal.

[DennisR]

Another waste of money on this "study." Hm...any time you put two living things together that are disparate in strength and/or size, the stronger one will win, will it not? Okay - unless the weaker one has weapons. But barring external things like that, natural selection will favor the stronger. Do not really need a study to reach that conclusion!

[js1138]

Question authority? That sounds odd coming from someone who appears to be religious. Do you apply this motto to all your intellectual efforts, or is it just a plattitude you whip out when it's convenient?

I don't have any answers for your technical questions. What thought is behind your asking them?

[Antonello]

Which confirms the fact that I am not a dreaded "anti-evolutionist", though to be clear I am a creationist, since I never suggested selection was random. I though it was clear I was speaking about the point mutations but sometimes clear just isn't enough.

Since your post #22 specifically referenced a quote that said 'The duplicate study suggests that the pathways of molecular adaptation are reproducible and not highly variable under identical conditions', and since those pathways are a result of selection, perhaps you were not quite as clear as you may have thought. Nevertheless I accept that it was an honest misunderstanding.

If I am understanding correctly now, this means you believe that somehow the statement you quoted said that the mutations themselves were not random. I would ask that you explain that conclusion.

>Nothing 'directed' the mutations to happen at all.

You can prove this statement? I am stuned.

I assume you are implying that God directed the mutations, and are daring me to disprove supernatural intervention in the experiment. My only answer is to clarify that my claim that nothing directed the mutations was only meant to cover the parameters of the experiment, and doesn't address possibilities not in evidence.

How many point mutations could have occurred?

That number is not only indeterminable, but also irrelevant. If you think differently feel free to explain how the number of mutations that didn't occur affect the results of ones that did.

How many did occur?

According to the article, millions.

Did the same number happen in the same locii in both iterations?

I would highly doubt it, since the actual occurrence of the mutations was random both in location and in timing.

If you can't answer those two questions then you are pretending to know more than you do. Why?

So conversely, since I have answered your two - well, three but who's counting ;-) - questions, does that mean you are saying I am not pretending to know more than I do?

[js1138]

There are at least three posters on evolution threads who spend an inordinate amount of time suggesting that mutations are somehow directed. Some seem to suggest that the direction comes from an intelligent agent within the cell itself.

I would love to see an ID advocate produce an actual hypothesis based on this conjecture, or at least tell us what thought is lurking behind their posts.

It really sounds like a revival of Lamarkianism.