I love living in the future.

[theweaselking]

Watching evolution in a lab: scientist observes E.Coli developing a new and extremely complex behaviour in a lab, is able to "replay" the event from previous frozen samples and demonstrate it over and over again with variations.


Edit: Quoth PZ Myers on this,

The citrate+ trait was first observed in the population called Ara-3 at roughly generation 33,000. By looking back at the frozen populations, they determined that the initial mutation that enabled growth on citrate actually appeared sometime between generation 31,000 and generation 35,000. These early generations were not as efficient at growing on citrate, so another mutation is thought to have occurred around generation 33,000 that allowed much more rapid growth. E. coli from generations prior to 31,000 had no significant, detectable ability to grow on citrate.

So they pushed it back further, by taking samples from earlier generations and allowing them to replicate again, replaying history. If the citrate mutation was a rare, unique mutation, they wouldn't expect to see the novel trait arise again. What they saw, though, was that the bacteria sampled after the 20,000th generation re-evolved the citrate capability with a greater frequency — there is something that arose around generation 20,000 in the Ara-3 population that did not make them citrate+, but did make it easier for subsequent generations to evolve citrate+, confirming their hypothesis of a historical contingency.

Quoth Michael Behe on this, "Duh, I eat poop!"

Comments

[elffin.livejournal.com]

I read this while out with my parents, wife, and stepson at a CiCi's pizza, a week and a half ago.

My mother had to thrust quarters at me to have me go play the 'motorcycle game' with my boy to get me to shut up about it.

The part I love is that because they were able to "replay" it over and over again, it discounts the possibility that the e.Coli picked up the genome to do so from eating some other bacterium that can process citrate - which FUCKING WHIPS THE BEHE'S ASS. No new information? HAHAHAHA

[dreamshade.livejournal.com]

I discuss Lenski’s fascinating work in Chapter 7 of The Edge of Evolution, pointing out that all of the beneficial mutations identified from the studies so far seem to have been degradative ones, where functioning genes are knocked out or rendered less active. So random mutation much more easily breaks genes than builds them, even when it helps an organism to survive. That’s a very important point. A process which breaks genes so easily is not one that is going to build up complex coherent molecular systems of many proteins, which fill the cell.

Is there any truth to that?

[theweaselking.livejournal.com]

You forgot to quote the "Duh, I eat poop!" at the end of that. The coda is important whenever you're quoting a Creationist.

And it's a half-truth.
MOST mutations are not useful.
Most DETECTABLE mutations are harmful.

However, while mutation is random, and random events in complex systems tend to lead to failures, failures mean that the mutation does not propagate. Harmful mutations don't get passed along, because the carrier doesn't reproduce as well as the non-harmed siblings.

If the mutation is neutral, the animal is likely to propagate it.

If a second mutation arrives that turns the first one *useful*, suddenly you've had two separate random events that have combined to give you new functionality that required two changes.

If the situation changes, such that a previously neutral mutation is now useful, those with it with thrive over those who don't, and it becomes ubiquitous.

And if the original mutation was useful, it propagates.

A process which breaks genes so easily is not one that is going to build up complex coherent molecular systems of many proteins, which fill the cell. Duh, I eat poop!

See, this is a flat, pure, unsupported lie.

A process that breaks genes so easily *does* build complex coherent molecular systems. It's been shown to, over and over and over again - because if it breaks an important gene, that break doesn't get passed on, and breaking an unimportant gene is just setting yourself up for a second change to turn it into something new and useful.

The creationists are trying to fool you into thinking that evolution describes a random process. It does not. Mutation is random, but the mechanisms by which mutations are tested and either propagated or destroyed are anything but random. There's a reason it's called "selection".

[tyoko.livejournal.com]

I'm an anthropologist rather than a biologist, so I wouldn't claim to be an expert, but I can help pick holes in his argument. If random mutations could only really break things, causing internal processes of the cell to fail and become less complex even as it helps the organism to survive, then I'd wonder why the genomes of living things haven't been hopelessly corrupted by now, and why life hasn't devolved into simple single celled slime.

Loss of complexity does happen in evolution, and is more likely to occur just as he says, it's just that the results tend to be out-competed by organisms that have evolved to be more complex and more specialised. The rarer complexity building mutations tend to out-compete the more common simplifying ones.

[jerril]

With the footnote that sometimes loss of complexity is entirely beneficial, removing some system that was once helpful but is now mostly metabolic dead weight.

A good example is how many subterranean organisms eventually loose complex vision, and eventually even loose basic "eye spots" with crude light detection abilities.

[theweaselking.livejournal.com]

If random mutations could only really break things, causing internal processes of the cell to fail and become less complex even as it helps the organism to survive, then I'd wonder why the genomes of living things haven't been hopelessly corrupted by now, and why life hasn't devolved into simple single celled slime.

You're forgetting, this is Michael Behe. He is a CREATIONIST, and his answer to why we haven't devolved into slime yet is "God doesn't want it to happen. Duh, I eat poop!"

[ronebofh.livejournal.com]

Results 1 - 5 of 5 for "duh i eat poop".

[theweaselking.livejournal.com]

But it's so true!

[elffin.livejournal.com]

I agree with the first two comments above.

Behe is being disingenuous by oversimplifying. Random mutation does not "break" genes. Random mutation changes genes. Those genes either provide more of an advantage or less of an advantage in a given environment than their predecessors.

Often, random mutations destroy some or part of the information on the previous genome, because the genome is (usually) a "fixed length".

Whether the part of the genome was ever expressed - there is a big question.

Table:

If the part of the genome that was overwritten was "junk" or was never expressed, and the new mutation actually does get expressed, then complexity has increased and new information has been created.

If the part of the genome that was overwritten was "junk" or was never expressed, and the new mutation is not immediately expressed, then complexity has not increased and no new information has been created.

If the part of the genome that was overwritten was "junk" or was never expressed, and the new mutation is not immediately expressed BUT another mutation down the line causes it to be expressed, then complexity has increased (as compared to the starting point but not as much as compared to the immediately previous generation) and new information has been created.

If the part of the genome that was overwritten was expressed, and the new mutation is not immediately expressed, then complexity has not increased and no new information has been created. Both have decreased.

If the part of the genome that was overwritten was expressed, and the new mutation is immediately expressed, then complexity has not increased and no new information has been created.

If the part of the genome that was overwritten was expressed, and the new mutation is expressed AND other genes previously unexpressed are now expressed as a result, then complexity has increased and new information has been created.

* Information in the evolutionary / information sciences meaning, which Behe supposedly uses.
--

In a full half of the outcomes listed above, complexity increases and new information is created. In 2/3, there is an increased /potential/ for increased complexity. In 5/6, information/complexity remains neutral or increases. Only in one of the six does complexity/information decrease. That is the key.

Whether or not any or all of these changes provide the resulting organism with an advantage over their predecessors and/or competitors /in a given envrionment/ lets us determine whether it is a beneficial or harmful mutation.

What is beneficial in one environment may be harmful in another, vice versa.

Behe purposefully waves his hands over the fact that evolution is a parallel process going on in billions of billions of billions of billions of cells right now, much less the billions of billions of billions times more cells that it has occurred in, in the past.

Yes, random mutation much more easily "breaks" genes: Rather, it does so much more /often/, in such instances as cancer and irradiative shredding of DNA/RNA and retroviral hijacking: Those organisms, almost by definition of that process, do not survive, are no longer players in evolution - or the cells that /are/ mutated aren't organism-to-organism reproductive cells and the loss of their function kills the organism and/or the changes are otherwise incapable of being transmitted to another generation.

But even by his OWN ADMISSION, random mutation - a single genetic bit at a time - DOES "BUILD" THEM - and if he could stop eating poop for a few seconds, he'd remember that it only has to happen once for the mutant to propagate.

(edited for clarity and insight, like, several times, and I apologise for the multiple comment notifications you're getting.)

[dreamshade.livejournal.com]

I'm amused that Richard Dawkins makes the list.

[peristaltor.livejournal.com]

Behe's speaking in code only Creationists can understand. It helps to recognize the code words. For me, the crazy alarm goes off here: So random mutation much more easily breaks genes than builds them. . . .

For Creationists, this is an important distinction. When God created, he built. The farther one gets from the original creation, the more "degenerate" one gets. "Degenerate" means, essentially, "broken." (I elaborate a bit on the history and meaning of degeneration here.)

For evolutionary scientists and people like me, this distinction between "breaking" and "building" are silly and meaningless; there is no difference between mutations that "break" gene codes and those that "build" them, since this is just how the gene code changes. As long as the organism continues to survive and propagate, the code continues. Genes appear amazingly agnostic to the method of change.

[glitteringlynx.livejournal.com]

You will become famous for that phrase now. :)

[sivi-volk.livejournal.com]

My understanding (though I've been out of school for more than a year now) is that in fact, most mutations are neutral, followed by a smaller number of deleterious ones, followed by a smaller number of beneficial.

I remember reading on The Panda's Thumb, or ERV, or somewhere, more precise numbers, but I don't remember where.

[sivi-volk.livejournal.com]

*cough*

You're forgetting about the high prevalence of neutral mutations in any given genome.

Otherwise, that's a good summary.

[theweaselking.livejournal.com]

Isn't that what I said?

Most are not useful.
Some are harmful, and those are the ones we see most often.
Very few are helpful, simply because of the odds of a random change improving things over a previously working system.

[sivi-volk.livejournal.com]

We only see the harmful ones most often because it's very difficult to detect neutral mutations, if that's what you meant. It sounded as though you meant deleterious ones occur more often, which is incorrect.

I may just have misinterpreted your meaning, which I found ambiguous and potentially misleading. People often put too much emphasis on helpful and harmful mutations while ignoring the presence of neutral ones.

[elffin.livejournal.com]

Thank you. I was indeed leaving out that fact, and it bugged me on the bus on the way home.