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Major Evolutionary Shift Observed in Bacteria

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Description: E. coli strain evolves new dietary capability with traceable history
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Mefiante
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« on: June 11, 2008, 12:09:02 PM »

[T]he experiment stands as proof that evolution does not always lead to the best possible outcome. Instead, a chance event can sometimes open evolutionary doors for one population that remain forever closed to other populations with different histories.

Lenski’s experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. “The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events,” he says. “That’s just what creationists say can’t happen.”


The expected creationist shouts of “No true evolution!” have already begun, one commentator asking for a demo of a bacterium sprouting legs and/or wings.  Maybe one day a species of goalpost will evolve to the point where it starts walking backwards all by itself.  The survival advantage of such a capability should be self-evident.

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« Last Edit: June 11, 2008, 12:10:57 PM by Anacoluthon64 » Logged
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« Reply #1 on: June 11, 2008, 14:06:54 PM »

This I find especially interesting:
...Lenski turned to his freezer, where he had saved samples of each population every 500 generations. These allowed him to replay history from any starting point he chose, by reviving the bacteria and letting evolution "replay" again.
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Teleological
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« Reply #2 on: May 11, 2010, 15:37:54 PM »

While trauling through this section, I stumbled across this thread. Wouldn't exactly say it is a evolutionary shift, more like an evolutionary stutter Undecided.

E. coli are facultative anaerobic organisms, meaning that in the presence of oxygen, pyruvate (from glycolysis) will enter the Krebs (citric acid) cycle to produce energy and in the absence of oxygen, pyruvate will ferment to form lactate and/or ethanol (depending on the organism). Thus, E. coli can metabolize intracellular citrate just fine. All the machinery necessary to metabolize citrate is present in E. coli and the biochemical processes/reactions are highly coordinated and complex. Therefore, the evolutionary "leap/jump" cited is not an example of a suddenly acquired ability to metabolize citrate as E. coli posses the necessary intracellular machinery to metabolize citrate. What did evolve then? The bacteria just lacked membrane proteins to import citrate, that is all. Hardly a major shift.

The E. coli (subtype B) bacteria where grown in DM25, a minimal salts medium that has 139microM glucose and 1,700microM citrate for about 20 years. Meaning a lot of extracellular citrate and little extracellular glucose. This specific strain did not have a citrate symporter to import the extracellular citrate. Other strains of E. coli posses such membrane proteins (e.g. citT), however some of them are situated on plasmids and the researchers made sure that horizontal transfer of plasmids was not possible in this experiment. Basically, the bacteria were swimming in an ocean of food but could only use a fraction of it because they could not get their "hands" on the goods. At around the 31000-31500th generation the first citrate "importers" arose. It will be fascinating to see the actual mutations that gave rise to this function and it is probably more than one (article speculates on possibly three genetic events related to citrate imprt over many generations). E. coli has many other symporter membrane proteins for dicarboxylic acids and other molecules with similar properties to citrate (e.g. Tartrate or alpha-ketoglutarate). Citrate is a tricarboxylic acid and it is possible that a few key mutations from an existing symporter protein allowed citrate to be imported by an existing protein. If so, it would be interesting how the mutations affected the properties of the original symporter system.

30 000 generations is the equivalent of +-600 000 years of evolution in a species with an average generation of 20 years (like primates). Is this an example of a shift? If you are lactose intolerant, it might very well take 600 000 years before a mutation makes your descendants lactose tolerant (lactase gene beneficial mutation if all your descendants are also lactose intolerant). So in the end it is more like an evolutionary stutter Tongue. Much like nylonase evolution, which was a a pre-existing esterase with B-lactam folds that had minimal nylon hydrolysis activity from the start. Another good example a preadaptation being co-opted into a new function.
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Julian
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« Reply #3 on: May 11, 2010, 18:07:13 PM »

While trauling through this section, I stumbled across this thread. Wouldn't exactly say it is a evolutionary shift, more like an evolutionary stutter Undecided.

Phenotypically, this is a big shift. Previous generations were unable to utilise citrate, these ones were. That is a significant difference, because it means these organisms can outcompete the wild type bacteria in citrate rich environments. The (possible) fact that this change was caused by a mere three point mutations in a related transport protein is irrelevant.

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« Reply #4 on: May 11, 2010, 18:10:31 PM »

Maybe one day a species of goalpost will evolve to the point where it starts walking backwards all by itself.  The survival advantage of such a capability should be self-evident.

 Grin Grin
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Mefiante
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« Reply #5 on: May 11, 2010, 18:10:55 PM »

IDiot soft-pedalling lifted wholesale from comment here or possibly here, and then posted and reposted by Teleological (as Phronesis) before ending up here, in each case without any attribution whatsoever.  At least this IDiot/cretinist had the decency to reference the source and thereby avoid unbridled plagiarism.

And they wonder why IDiots and cretinists have a reputation for being unabashed liars.  These are the same kinds of people that would have you believe that their god/creator/designer is the source of human morality.  Flame Wars, here we come.  Once again.

'Luthon64
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Julian
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« Reply #6 on: May 11, 2010, 18:21:28 PM »

IDiot soft-pedalling lifted wholesale from comment here or possibly here, and then posted and reposted by Teleological (as Phronesis) before ending up here, in each case without any attribution whatsoever. 


How embarassing. Or maybe Telly is also a SillyWabbit, and just likes to post the same thing endlessly on different sites?

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Mefiante
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« Reply #7 on: May 11, 2010, 18:30:11 PM »

How embarassing.
No, it’ll just get brushed off with some ruse or simply be ignored.



Or maybe Telly is also a SillyWabbit…
The prose is very clearly several notches above his usual style.



… and just likes to post the same thing endlessly on different sites?
Oh, that he definitely loves doing, and isn’t shy to prove it either.

'Luthon64
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rwenzori
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« Reply #8 on: May 11, 2010, 19:27:34 PM »

IDiot soft-pedalling lifted wholesale from comment here or possibly here, and then posted and reposted by Teleological (as Phronesis) before ending up here, in each case without any attribution whatsoever. 


TeleoPhroners has been caught out in blatant plagiarism before, over on MyBB.

<kotch icon>
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Teleological
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« Reply #9 on: May 12, 2010, 06:51:00 AM »

Oh great, now I am being accused of plagiarizing my own writing. Btw, check the date if you don't believe me. Lol muffles, you are scraping low to try and score a few browny points with the fellow "critical thinkers"? You can do better honestly. Why can't you discuss the actual biology anyway. It is not ID related in any way. I can of course understand why you want to drag yet another thread to the flame-wars section, hardly surprising really. Btw muffles, thanks for giving a positive acknowledgment of my prose Evil.
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« Reply #10 on: May 12, 2010, 06:55:18 AM »

While trauling through this section, I stumbled across this thread. Wouldn't exactly say it is a evolutionary shift, more like an evolutionary stutter Undecided.


Phenotypically, this is a big shift. Previous generations were unable to utilise citrate, these ones were. That is a significant difference, because it means these organisms can outcompete the wild type bacteria in citrate rich environments. The (possible) fact that this change was caused by a mere three point mutations in a related transport protein is irrelevant.

Hardly a big shift really. Even nylonase evolution is more interesting, and that is not even a big shift. Of course this has nothing to do with disproving evolution or making any pro-points for ID, it just shows that the media reports are filled with hyperbole about everyday evolutionary changes (some people gobble it up without any critical thought unfortunately). Nothing spectacular, just simple biology.
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« Reply #11 on: May 12, 2010, 11:01:25 AM »

If I have wrongly accused you then I withdraw the allegation without prejudice and offer you an unreserved apology.  In my defence, though, your own history and my search for evidence (admittedly circumstantial), having failed to turn up your MyBB post of 13/06/2008, strongly suggested such plagiarism, given the variety of locations at which the text was posted and the range of author names under which it appears.

'Luthon64
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« Reply #12 on: May 12, 2010, 11:05:12 AM »

If I have wrongly accused you then I withdraw the allegation without prejudice and offer you an unreserved apology.  In my defence, though, your own history and my search for evidence (admittedly circumstantial), having failed to turn up your MyBB post of 13/06/2008, strongly suggested such plagiarism, given the variety of locations at which the text was posted and the range of author names under which it appears.

'Luthon64
No worries, apology accepted.
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« Reply #13 on: May 12, 2010, 11:09:10 AM »

To me, this part sounds like typical evolution:
Quote
Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities.

Teleological, are you saying that the enzyme necessary to break down the citrate already existed in the bacteria, or that the coding to synthesize the enzyme already existed?

And now for my usual dumb question bit:
You mention intracellular citrate. Was this citrate not outside the cell?
How did the bacteria know about the existence of the citrate?
Or is the "The bacteria just lacked membrane proteins to import citrate, that is all." bit confusing me.
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« Reply #14 on: May 12, 2010, 11:37:40 AM »

To me, this part sounds like typical evolution:
Quote
Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities.

Teleological, are you saying that the enzyme necessary to break down the citrate already existed in the bacteria, or that the coding to synthesize the enzyme already existed?

And now for my usual dumb question bit:
You mention intracellular citrate. Was this citrate not outside the cell?
How did the bacteria know about the existence of the citrate?
Or is the "The bacteria just lacked membrane proteins to import citrate, that is all." bit confusing me.
So, the important things to remember are the following:
1) The bacteria used in the experient are capable of metabolizing citrate via the Krebs cycle. They are able to generate intracellular citrate from pyruvate (pyruvate is generated from glucose via glycolysis in the cell) in order to generate ATP or energy for biological processes.
2) This particular strain of bacteria lacked the ability to import extracellular citrate. There are of course other strains of bacteria that can do this (they possess the citrate symporters). The researchers particularly selected for a strain that did not have this citrate symporter. However, they were still able to import and utilize the glucose.
3) The bacteria where grown in medium that has 139µM glucose and 1,700µM citrate. The citrate and glucose were extracellular, but only the glucose could be used for energy.

My guess is that a few key mutations from an existing symporter protein allowed citrate to be imported by an existing protein. I haven't followed up on the results from the genomic studies of these organism, but it would be interesting to see which mutations resulted in an increase in citrate import. Maybe someone here is interested to look it up?
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