Scientific Vacuity of ID: Lactose Digestion in E. coli

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In a hilarious posting on UcD, our dear friend Davescot, who is best known for his failed predictions 1, explains why recent research into the Lactose digestion of E. coli, undermines the findings of Lenski regarding E. coli evolving the ability to digest citrate. The reason? Our friend Davescot confused citrate with the Lac Operon

Davescot Wrote:

This is contrary to Lenski’s hypothesis that a series of dice throws, each making a small change towards ability to digest lactose citrate, accumulate until lactose citrate digestion is fully switched on. Darwinian gradualism is denied once again and we see a front loaded genome switch to a new mode of operation through a saltational event.

In other words, Davescot made two mistakes in a single posting: first he confused citrate with the Lac operon and secondly, he incorrectly claims that ‘Darwinian gradualism’ is denied once again, because, after all, a stochastic event affects whether E. coli can digest lactose versus glucose.

According to the ID ‘argument’, since chance and regularity can in fact explain the Lac Operon’s switch, any design inference has been prevented. Which is why Davescot, calls it ‘front loading’ or a ‘saltational’ event.

Let’s first spend some time educating our confused Intelligent Design friends about the two studies, one which involve the work by Lenski et al

Zachary D. Blount, Christina Z. Borland, and Richard E. Lenski Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli, Proc. Natl. Acad. Sci. June 10, 2008 vol. 105 no. 23 7899-7906

Abstract
The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that “replayed” evolution from different points in that population’s history. We observed no Cit+ mutants among 8.4 × 1012 ancestral cells, nor among 9 × 1012 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

This paper was also discussed at Pandasthumb by PZ Myers and by New Scientist.

Note that the paper clearly describes that it is discussing the evolution of E. coli’s ability to digest citrate and not the Lac operon. Then again, scientific accuracy has never been a major concern amongst Intelligent Design Creationists and it help us explore how Intelligent Design fails to gain scientific relevance.

And the second paper which discusses the Lac Operon

Paul J. Choi, Long Cai, Kirsten Frieda, and X. Sunney Xie A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell Science 17 October 2008: 442-446.

Abstract
By monitoring fluorescently labeled lactose permease with single-molecule sensitivity, we investigated the molecular mechanism of how an Escherichia coli cell with the lac operon switches from one phenotype to another. At intermediate inducer concentrations, a population of genetically identical cells exhibits two phenotypes: induced cells with highly fluorescent membranes and uninduced cells with a small number of membrane-bound permeases. We found that this basal-level expression results from partial dissociation of the tetrameric lactose repressor from one of its operators on looped DNA. In contrast, infrequent events of complete dissociation of the repressor from DNA result in large bursts of permease expression that trigger induction of the lac operon. Hence, a stochastic single-molecule event determines a cell’s phenotype.

This paper is also discussed by New Scientist and the reference to the work by Lenski may have confused Davescot. This confusion could have been easily avoided by actually reading the papers involved.

Now that we have established that these were two very different studies: one involving the relevance of historical contingency in the evolution of E. coli’s ability to digest citrate and the other involving the Lac operon switching from Lactose to Glucose digestion, a step which involves a stochastic (chance) component.

So let’s address Davescot’s second flawed argument that the switch is a ‘saltational’ event. Let’s first describe the Lac Operon in a bit more detail so that we can understand the ID creationist’s confusion.

The Lac Operon is an operon which controls the switching between glucose and lactose digestion.

In its natural environment, lac operon is a complex mechanism to digest lactose efficiently. The cell can use lactose as an energy source, but it must produce the enzyme β-galactosidase to digest it into glucose. It would be inefficient to produce enzymes when there is no lactose available, or if there is a more readily-available energy source available (e.g. glucose). The lac operon uses a two-part control mechanism to ensure that the cell expends energy producing β-galactosidase only when necessary. It achieves this with the lac repressor, which halts production in the absence of lactose, and the Catabolite activator protein (CAP), which assists in production in the absence of glucose. This dual control mechanism, along with the ability to use lactose analogues in experiments, has lent itself to be studied in a laboratory setting extensively.

The Lac operon story is pretty straightforward, in the absence of Lactose, a repressor protein, encoded by the Lacl gene, which is always expressed, is allowed to bind with the Lac Operon, inhibiting the expression of the Lac genes. Thus during low Lactose availability, the Lac Operon is turned off. When Lactose is available in sufficiently high concentrations, a lactose metabolite binds with the repressor protein which now cannot block the expression of the Lac operon.

However, there is an intermediate condition where both Lactose and Glucose are present. How does E. coli efficiently deal with this situation: if all E. coli switched to Glucose, an important energy source, Lactose, would remain unused, and if all E. coli maintained Lactose, the Glucose energy source would remain unused. But how to achieve this since all the bacteria are copies?

Terry at Prometheus Untenured explains

That grey widget shaped like a bone binds the DNA and prevents the operon from being expressed into mRNA. Occasionally one end of it will unbind, and you’ll get a short burst of expression - but even more occasionally, it’ll escape entirely, and once it does it takes a while before it can again “find” the DNA it binds to (by diffusing about randomly), and there are very few of these grey repressors about in the cell. Because of this, there’s an element of chance involved - only some of the cells will have a complete escape followed by a large burst of mRNA. Cleverly, the cell proteins made during that burst of mRNA to tie up the grey repressor so that the cell continues to be lactose-munching.

So, no saltational events, and in fact no ‘front loading’ either, just an example of a common repressor gene, with a twist that allows the bacteria to benefit in situations where both glucose and lactose are present. Thus resolving a question mentioned on Wikipedia

The repressor is an allosteric protein, i.e. it can assume either one of two slightly different shapes, which are in equilibrium with each other. In one form the repressor is capable of binding to the operator DNA, and in the other form it cannot bind to the operator. According to the classical model of induction, binding of the inducer, either allolactose or IPTG, to the repressor affects the distribution of repressor between the two shapes. Thus, repressor with inducer bound is stabilized in the non-DNA-binding conformation. However, this simple model cannot be the whole story, because repressor is bound quite stably to DNA, yet it is released rapidly by addition of inducer. Therefore it seems clear that repressor can also bind inducer while still bound to DNA. It is still not entirely known what the exact mechanism of binding is.

As the authors describe

Why do complete dissociation events give rise to large bursts? Our group has recently shown that if a repressor dissociates from DNA, it takes a time scale of minutes for the repressor to rebind to the operator because the repressor spends most of its time binding to nonspecific sequences and searching through the chromosomal DNA. In addition, there are only a few copies of the tetrameric repressors . Such a slow repressor rebinding time, relative to transcript-initiation frequencies, would allow multiple copies of lacY mRNA to be made following a complete repressor dissociation event. Furthermore, in the presence of inducer, the nonspecific binding constant remains unchanged, but the affinity of the inducer-bound repressor to the operator is substantially reduced, rendering specific rebinding unlikely. The large burst that results from slow repressor rebinding is an example of how a single-molecule fluctuation under out-of-equilibrium conditions can have considerable biological consequences, which has been discussed theoretical- ly in the context of cell signaling and gene expression but has not previously been experimentally observed.

In other words, once a rare occurrence of full disassociation happens under lactose/glucose conditions, it takes significant time for the repressor to ‘find’ the LacZ site and rebind. During this period of time, the Lac operon expresses significant bursts which then can cause additional binding of the lactose metabolite with the repressor protein and thus the cell switches to Lactose.

And thus, science advances our knowledge while ID? Well, ask yourself how does ID explain this? By confusing it with citrate? Or by calling it ‘saltational’ or even ‘front loading’? What better term to hide one’s ignorance. But remember that they cannot call it ‘design’ since chance and regularity very well explain the Lac Operon’s behavior.



1

Davescott Wrote:

Judge John E. Jones on the other hand is a good old boy brought up through the conservative ranks. He was state attorney for D.A.R.E., and Assistant Scout Master… extensively involved with local and National Boy Scouts of America, political buddy of Governor Tom Ridge (who in turnis deep in George W. Bush’s circle of power), and finally was appointed by GW himself. Senator Rick Santorum is a Pennsylvannian in the same circles (author of the “Santorum language”) that encourages schools to teach the controversy) and last but far from least, George W. Bush hisself drove a stake in the ground saying teach the controversy. Unless Judge Jones wants to cut his career off at the knees he isn’t going to rule against the wishes of his political allies. Of course the ACLU will appeal. This won’t be over until it gets to the Supreme Court. But now we own that too.

Source: Davescott comment on UcD here

82 Comments

They should have stuck with politics-rabble rousing is easier than science. But seriously-the Lac Operon is now standard High-School biology:

http://books.google.com/books?id=RR[…]y+Lac+Operon

To confuse the switch between the expression of genes (present in the E. coli genome) for glucose vs. lactose consumption, and the evolution of citrate metabolism is really telling.….

But, Lenski failed to surround its apparatus with GOD KEEP OUT signs, or to put it inside a pentagram.

How can we know the CIT+ mutation wan’t caused by gods, angels or demons ?

The really bizarre part is that someone has pointed out to DaveScot that it was citrate not lactose in the Lenski experiment, which he accepts, but then fails to change anything else about the post. The false link between the two experiments has been pointed out and it doesn’t change his ‘reasoning’ one bit ? He just replaces lactose with citrate and it’s all good again. Weird

Yes, Davescot should have just withdrawn his foolish posting but then again, this way it serves a much better purpose.

Sunspiker said:

The really bizarre part is that someone has pointed out to DaveScot that it was citrate not lactose in the Lenski experiment, which he accepts, but then fails to change anything else about the post. The false link between the two experiments has been pointed out and it doesn’t change his ‘reasoning’ one bit ? He just replaces lactose with citrate and it’s all good again. Weird

Breathtaking inanity strikes again.

I’m usually not one to throw insults around, but DaveScot has to be the most ignorant ID proponent out. He was the one who kept posting on UcD about the lame Obama birth certificate conspiracy theory. It’s like he has no critical thinking skills at all. Who thought that it was a good idea to let him write on their blog?

DaveScot has managed something that many thought to be impossible, namely dragging down the quality of Uncommon Descent. Notice that this is hardly a simple task given the nature of the contributors who historically contributed at UcD such as Denyse O’Leary and William Dembski.

Note how there is little science left. Much of the space is wasted on silly topics regarding Global Warming and the recent political race. Even Dembski seems to have started to get annoyed by how these participants have dragged down UcD.

Sad really, but such seems to be the fate of so many ID sites.

Worth repeating for the sheer amusement:

DaveScot made an absolute fool of himself here too:

http://www.uncommondescent.com/inte[…]nce-because/

Can you beleive that?! If I had been William Dembski, I would have said to DaveScot: “You idiot! You just blew away our whole legal and scientific case! YOU’RE FIRED!!!”

Hey Dale, please clean up your act.

I wouldn’t be surprised if he was fired from Dell, but there is no evidence of that. His official story is that he is a “self-made millionaire”.

Truth is, he sat on his ass while Dell threw stock options at him and the rest of the company’s employees during the halcyon days of the mid-90s when Dell’s stock price went stratospheric. There were a load of such Dellionaires around Austin at the time, so Mr. Springer is certainly nothing special in that regard.

Best thing you can say about DaveScot is that he sold his stock options at the right time – I guess that makes him a legend in his own lunchtime.

PvM said:

DaveScot has managed something that many thought to be impossible, namely dragging down the quality of Uncommon Descent. Notice that this is hardly a simple task given the nature of the contributors who historically contributed at UcD such as Denyse O’Leary and William Dembski.

Oh. My. Word.

It really does demonstrate the ignorance one is dealing with at UcD on biology.

Dale Husband Wrote:

“Can you beleive that?! If I had been William Dembski, I would have said to DaveScot: ‘You idiot! You just blew away our whole legal and scientific case! YOU’RE FIRED!!!’”

Huh? Are we reading the same thing? It sounds like Dave is pulling the exact bait-and-switch that Dembski wants him to:

DaveScot Wrote:

So what is it. Is ID science or not science? It seems our opponents want to have their cake and eat it too by saying: “ID is not science because it cannot be falsified or verified. And by the way, ID has been repeatedly tested and shown to be false.”

That’s a perfect example of why I have been complaining for 5+ years when people carelessly say that ID “is” creationism. While most critics, and many fans, of anti-evolution activism agree that “creationism” ought to be defined to include ID, the fact is that most people still think of creationism as concluding a 6-day, ~6000 year ago abrupt appearance of many “kinds.” That of course is easily falsified, as are old-Earth variants. ID, however, in Dembski’s own words “accommodates all the results of Darwinism.” Nothing can falsify it.

Where Dave is taking a risk is with the “front loading” and “saltation” language. But Behe already got away with that. ID’s YEC and OEC fans are so desperate to hear only what they want to hear that such YEC-unfriendly language is just tuned out. What really amazes me, though, is how little it is exploited by critics. The first thing I would ask Dave is when he thinks those “front loading” and “saltation” events occurred, and whether Behe agrees or has competing hypotheses. I wouldn’t even bother asking whether he thinks that it’s designer intervention or just a yet-undiscovered “natural” process.

DaveScot is an idiot!

In other breaking news, the sun rose in the east this morning!

PvM, you keep referring to DaveScot and various others of the ID crowd as “foolish,” and I think that’s not the right word. I don’t think they’re “foolish” at all – DaveScot has a very nice sinecure on the wingnut welfare circuit, is far more famous than someone of his calibre would have been in actual science, has legions of adoring fans, and in all cases feels like he’s actively shaping the public discourse (without having to be elected, educated, or even really know what he’s talking about). That’s hardly a “fool”; that’s a skilled operator who knows just what he wants and has managed to achieve at least the most important parts of it (the stuff that pertains to enriching himself and stroking his ego). And as long as there’s a paycheque and self-gratification in it for him, he’s going to continue to push the ID line.

About the only thing that is going to stop guys like him is to defund them. Since they’re largely funded by private donors, that is, the same billionaires who fund most of the religious right, I don’t see how to do that.

Frank J said:

Dale Husband Wrote:

“Can you beleive that?! If I had been William Dembski, I would have said to DaveScot: ‘You idiot! You just blew away our whole legal and scientific case! YOU’RE FIRED!!!’”

Huh? Are we reading the same thing? It sounds like Dave is pulling the exact bait-and-switch that Dembski wants him to:

Note I said “if I had been William Dembski”. If DaveScot is pulling a bait and switch at Dembski’s bidding, then they are both liars. If not, DaveScot committed an EPIC FAIL! Either way, an honest person should have tossed him out.

Another weird thing is that Mr. Scot himself is responsible for almost half of the contributions to his own articles

Dale Husband Wrote:

Note I said “if I had been William Dembski”. If DaveScot is pulling a bait and switch at Dembski’s bidding, then they are both liars. If not, DaveScot committed an EPIC FAIL!

Got it.

I have no doubt that Dembski not only approves, but encourages what DaveScot says. Even the “front loading/saltation” language probably helps ID distance itself from YEC and OEC. As long as it’s in low doses, that is, too much might backfire. In 2005 DaveScot defended common descent on UcD and practically sounded like he was blowing the whistle on the DI’s “don’t ask, don’t tell” policy. All he got from Dembski was a polite “knock it off.” I would guess that the relevant archives have been long deleted, however.

This was my favorite Davescot moment, where he claimed the return of the ice measures to the global warming regression line somehow disproved global warming because it wasn’t as catastrophic as the last few data points had indicated. It was such an idiotic display of someone seeing what he wanted to see, instead of what the data clearly showed, I still wonder to this day if he was really serious.

It’s nice to see that site sink into total irrelevancy. They’ve earned it.

I’m constantly puzzled why the likes of Dembski, a senior fellow at the Discovery Institute cannot get somebody with actual bona fide scientific qualifications to write on his blog. Instead we have this amazing motley crew of DaveScot, apparently some kind of former computer engineer who is at best an amateur, and by all accounts regularly shows serious gaps in his scientific understanding - and lately is using the blog as his own personal sounding-off platform against Obama; we have Denyse O’Leary - a self-described “journalist” and Coulter-wannabe, but without the wit or writing skills, and who really has absolutely nothing to say expect her constant & repetitive whining about the evils of “Darwinism”.

Seriously, doesn’t Dembski have the clout or influence to get somebody like Wells or Behe contribute to his Blog? At least these people are in possession of actual science degrees. It would at least lend some semblance of credibility to the site.

And the people who are allowed to comment (and they are very, very tightly controlled - I’ve been personally “expelled” at 3 times) not only do not in anyway provide a balanced viewpoint, but frequently quote Biblical scripture (and yet don’t anybody dare to post a comment that criticises ID for being a faith-based initiative - if you do, you would be expelled from UD in heartbeat!)

Timcol Wrote:

I’m constantly puzzled why the likes of Dembski, a senior fellow at the Discovery Institute cannot get somebody with actual bona fide scientific qualifications to write on his blog.

They don’t need anyone with bona fide scientific qualifications, only one who can spin feel-good sound bites to a very forgiving audience. And I don’t mean the hopeless fundamentalists who don’t need groups like the DI and AIG, but the ~70% of the public that falls for some or all anti-evolution propaganda.

With any science-pseudoscience issue the sad fact is that defenders of science need to be as clear as possible, but peddlers of pseudoscience can afford to be careless.

Timcol said:

I’m constantly puzzled why the likes of Dembski, a senior fellow at the Discovery Institute cannot get somebody with actual bona fide scientific qualifications to write on his blog.

This should tell you something about being a senior fellow at the DI. Even among creationists.

Timcol said:

Seriously, doesn’t Dembski have the clout or influence to get somebody like Wells or Behe contribute to his Blog? At least these people are in possession of actual science degrees. It would at least lend some semblance of credibility to the site.

See above.

I’m constantly puzzled why the likes of Dembski, a senior fellow at the Discovery Institute cannot get somebody with actual bona fide scientific qualifications to write on his blog.

Well, the obvious answer is that the vast majority of those so qualified have better sense than to believe that stuff, and lack the motivation to pretend to believe it.

Henry

Maybe Dave Scott is arguing that the CIT+ trait is due to a CIT-Operon, without any supporting evidence ?

I expect evidence will come in its own time, with the DNA sequencing of Lenski’s Ecoli strains. What will the Uncommon Dissenters do when the evidence show that the new CIT+ trait require multiple mutations, that were absent in the original (common) strain, and that are still absent in 9 of the 10 separate strains ? Acknowledge they were wrong ? That would be a first.

What will the Uncommon Dissenters do when the evidence show that the new CIT+ trait require multiple mutations, that were absent in the original (common) strain, and that are still absent in 9 of the 10 separate strains ?

Maybe claim that some infinite wavelength photons somehow imparted some new stuff to one of those ten strains? :D

Well, the obvious answer is that the vast majority of those so qualified have better sense than to believe that stuff, and lack the motivation to pretend to believe it.

It’s also to note too that despite all the hoopla about the Discovery Institute’s “Dissent from Darwin” list, not a single person on the list (other than Dembski)is a listed contributor to Uncommon Descent. Pretty sad that Dembski can’t even persuade his DI buddies to contribute to his web site, but as Frank J said the people they are targetting don’t care about such things. When you have a retired computer engineer who is both patriotic and sounds a little sciency, who needs real scientists? He doesn’t even have to use his real name!!!

Frank J said: They don’t need anyone with bona fide scientific qualifications.…

With a few sad exceptions (science apostates such as Dembski, Behe, Luskin, etc.) “anyone with bona fide scientific qualifications” and a shred of ethics would refuse to participate in such a bogus operation as the Dishonesty Institute and its pitiful creation, intelligent design creationism. But the money must be good. I just wonder how they can sleep at night, or face themselves in the mirror. Waitaminute: Behe’s got a beard.…

Paul Burnett said:

Frank J said: They don’t need anyone with bona fide scientific qualifications.…

With a few sad exceptions (science apostates such as Dembski, Behe, Luskin, etc.) “anyone with bona fide scientific qualifications” and a shred of ethics would refuse to participate in such a bogus operation as the Dishonesty Institute and its pitiful creation, intelligent design creationism. But the money must be good. I just wonder how they can sleep at night, or face themselves in the mirror. Waitaminute: Behe’s got a beard.…

As far as I can tell, the only person affiliated with the DI doing any sort of valuable scientific research is Scott Minnich, and of course this work has nothing to do with intelligent design. Behe used to do interesting work in the 90’s (ironically, research that was somewhat related to my own at the time), but he’s hasn’t published experimental data since 1997. Douglas Axe has moved from experimental work to a trickle of theoretical/computational work, but again, it mentions nothing about intelligent design, although it makes for good PR for the DI. I can’t think of anyone else affiliated with the DI who does actual scientific research. Anyone? Anyone?

Science Avenger said:

This was my favorite Davescot moment, where he claimed the return of the ice measures to the global warming regression line somehow disproved global warming because it wasn’t as catastrophic as the last few data points had indicated. It was such an idiotic display of someone seeing what he wanted to see, instead of what the data clearly showed, I still wonder to this day if he was really serious.

It’s nice to see that site sink into total irrelevancy. They’ve earned it.

I sometimes wish they would get rid of the “hockey stick” graph that has been such a lighting rod for denialist attacks.

http://circleh.wordpress.com/2008/1[…]stick-graph/

I would expect better accuracy than that from a graph that has gotten so much publicity. Look at how wide the grey areas are before the 19th Century! I can’t accept that. Could we not do better? We know there was a Medeival Warm Period and a Little Ice Age, so why doesn’t the hockey stick graph make that clear?

Also note what I wrote at the end:

Denialists have made a great deal about how the global warming “scam” was based on the flawed hockey stick graph. But this is incorrect. In fact, the science behind global warming is based on the known properties of carbon dioxide and other greenhouse gases. It is amazing that denialists have never done experiments to disprove the heat retaining properties of the supposed greenhouse gases, for that is indeed the only way they can discredit the case for the man-made global warming hypothesis. So why have they not done this? Because they can’t!

It’s time to toss out the hockey stick of Dr. Mann and find more accurate data! Ironically, by doing so, we can make the case for doing something about global warming that much stronger!

The case FOR man-made global warming is too strong to be debunked by cherry-pickers with a dishonorable agenda. It can only be made more accurate.

“So what is it. Is ID science or not science? It seems our opponents want to have their cake and eat it too by saying: “ID is not science because it cannot be falsified or verified. And by the way, ID has been repeatedly tested and shown to be false.”

I don’t see that as an issue.

Its pretty simple really, where ID is testable it has been falsified.

Whats left is untestable hence ID is either failed science or untestable.

Not much of a talking point for ID, I think…

Stuart Weinstein said:

“So what is it. Is ID science or not science? It seems our opponents want to have their cake and eat it too by saying: “ID is not science because it cannot be falsified or verified. And by the way, ID has been repeatedly tested and shown to be false.”

I don’t see that as an issue.

Its pretty simple really, where ID is testable it has been falsified.

Whats left is untestable hence ID is either failed science or untestable.

Not much of a talking point for ID, I think…

And, sadly, Intelligent Design proponents prefer not to have Intelligent Design in a position to be tested in the first place.

PvM said:

For a recent paper by Mann on Global Warming, see the article at RealClimate, one of the better climate sites.

The paper

Michael E. Mann, Zhihua Zhang,Malcolm K. Hughes, Raymond S. Bradley, Sonya K. Miller, Scott Rutherford, and Fenbiao Ni Proxy-based reconstructions of hemispheric and global surface temperature variations over the past two millennia PNAS Published online before print September 2, 2008

Thank you, PvM. I will return to my wordpress blog and make an update after seeing this new data. Dr Mann and his colleagues have redeemed themselves!

Glen Davidson said:

It took over 30,000 generations for an e-coli variant to develop the ability to use citrate for nutrition.

If it took this many generations for bacteria to develop something useful-would it take a near infinity for slower-breeding creatures (including us) to innovate?

We have this thing called “sex,” which shuffles genes around. Bacteria do have conjugation, but it is not as good at pairing up genes to “see which combinations work best” as sex is. Conjugation is, however, very good at letting numerous species of bacteria in on the way to avoid the latest shared threat to microbes (viruses take a huge toll on bacteria in the oceans), which likely makes it the better mechanism for bacteria.

In fact, evolution seems to be a major (probably the major) reason for sexual reproduction having evolved, if likely more to counter parasites than to evolve new ways of living–but it worked for the latter purpose.

What is more, your 30,000 generations are in a very small population, compared to wild populations.

Glen D

http://tinyurl.com/2kxyc7

Good point about the population size in this experiment. Larger populations would obviously have larger reservoirs of variation to draw on to “answer” challenges from the environment.

tresmal said:

Another point is that this and similar studies start with a single strain of bacteria (for the very good reason of reducing variables.) This stacks the deck against natural selection by eliminating horizontal gene transfer. Or at least eliminates the point of it. A more natural setup would start with several diverse strains of bacteria all negative for citrate metabolism and allow for genetic exchange. The thinking here is that a larger extended genome would allow for quicker results. This would come at the cost, however, of making the researchers’ job much more difficult.

By reducing the genetic depth of the population the scientists may have handicapped themselves (to an extent) and slowed the citrate evolution? Makes sense.

Mike says:

“But why? Yes, we’re being intolerant, but why?”

Why? Because we want to know the truth about the Universe we inhabit. We are vitally interested in factual knowledge about the real world, as attested by empirical evidence.

And why do we want to know the truth? Well, because it’s the truth, dammit! Jesus of Nazareth remarked that we would know it, and it would set us free. So it does; so it has; so it will. Nevertheless, it is more than merely liberating. Truth is a good and righteous thing in and of itself, and it can be discovered and demonstrated by empirical observation and unfettered reason. Yes, the method of science is cool observation of fact; but at its heart there lies a passion for knowing the truth.

So science is outraged by the lies, disinformation, propaganda, falsehood, prejudice and misrepresentation which are the currency of creationism - and so it should be. Intolerance is the only self-consistent response to such things. It is thus the only ethical response to them.

That’s why.

A more accurate understanding of reality is also a survival advantage. Rather than sacrifice the virgin to the volcano god, let her contribute to the gene pool. :-)

sorry, Sam, it’s never easy to tell whose questions are genuine and whose are the beginning of a troll. I hope your questions are being answered to your satisfaction.

Larry Boy: (Also keep in mind that while we are waiting the half million years necessary to pick up a cit+ phenotype, thousands of other features will be evolving as well.)

Yeah, naturally evolving populations aren’t being force fed one problem largely to the exclusion of all other problems (or as close to that as the researchers can manage). They also have access to a variety of environments, so might “solve” any one problem by moving to where that problem isn’t (or rather, the populations in the other environments become more successful than the ones facing the problem being considered here).

Larry Boy: Meh, I am personally skeptical [of hypothesis that sex is principally to counter parasites]. I favor sex as a genetic repair mechanisms to combat Muller’s Ratchet. (Which can be quite severe in organisms with a large genomic mutation rate)

Maybe it’s some combination of the two?

———-

Dave Luckett: as is the case with the bdelloid rotifers. These have apparently returned from sexual to asexual reproduction.

They probably just got tired of waiting for the phone to ring, and found a strategy that didn’t require dating. :)

———-

Glen Davidson: Conjugation is, however, very good at letting numerous species of bacteria in on the way to avoid the latest shared threat to microbes (viruses take a huge toll on bacteria in the oceans), which likely makes it the better mechanism for bacteria.

I wonder, do bacteria have any mechanism to select what part of their genome gets shared in these conjugal visits? That is, if the primary benefit is defense against parasites, seems like that if the defense-related genes were concentrated in one area, and the conjugation mechanism also concentrated in that area, seems like that would work better than random picking of what to share with the neighbors.

Henry

I wonder, do bacteria have any mechanism to select what part of their genome gets shared in these conjugal visits?

To some degree, yes. They exchange plasmids primarily (or exclusively? Elements often do make it to the chromosome at some point, though), the extrachromosomal elements which often contain useful resistance genes.

I believe that by exchanging plasmids they tend to select genes that would be likely to help in general bacterial (or archaeal) defenses, or probably, also genes that might help in virulence (Bacillus thuringensis is said to be virtually the same as anthrax, except that the two have different plasmids, which I presume encode what are virulence factors for their respective organisms). On the whole, as I understand it, the plasmids are heavy in genes that would be useful to a variety of micro-organisms.

Glen D

http://tinyurl.com/2kxyc7

Henry J said:

Dave Luckett: as is the case with the bdelloid rotifers. These have apparently returned from sexual to asexual reproduction.

They probably just got tired of waiting for the phone to ring, and found a strategy that didn’t require dating. :)

Someone mention “rotifers”?

Semi-microscopic denizens of temporary ponds, such as the bdelloid rotifers and Daphnia tend to be female, and produce daughter-clones of themselves in order to quickly take advantage of resources by crowding out the competition. With bdelloid rotifers, in particular, these clonal generations are all haploid: males (who are also haploid) only appear when the populations are at their peak, or are beginning their decline. The males then mate with their sisters, who, in turn, lay the diploid resting eggs that then hatch after the habitat dries out and remoistens. The populations continue on until the pond dries out, or no more resources are available.

Some rotifers, such as the highly carnivorous species of the genus Asplancha (who are to other rotifers what Hell’s Angels are to go-carters), will produce differentiated generations of clones. With Asplancha, the females feed on herbivorous, freshwater zooplankters, especially protozoa and other rotifers, and accumulate Vitamin E from their prey. As their dietary Vitamin E levels increase, females lay eggs that hatch into successively larger forms, termed “cruciform” for the larger rotifer-eating form, and “campanulate” for the largest rotifer- and crustacean-eating form. This way, each generation can coexist with each other without competing with each other, though, they will readily cannibalize each other given the opportunity. Males often have long, large spines to defend themselves from their sister-girlfriends, though the size apparently depends on how readily their sisters cannibalize each other from one particular generation.

So, in other words, in this case, the strategy for overcoming the heartache of Saturday Night is to lay their dates’ eggs on Saturday Night. Literally, as the average lifespan of the average rotifer is only about a week, barring violence.

Also, Komodo dragons have a similar strategy, in that a lone female can resort to parthenogenesis, and lay eggs that hatch into clonal-sons. And should her sons survive to maturity, they can then mate with their mother, and produce more females. However, the resulting inbreeding makes me cringe.

And having said that, I now return you to our regularly scheduled program.

Stanton, Komodo dragons, with or without incest, make me cringe just on general principles. And now I have learned a number of things that I would not have learned if I didn’t read and post on this blog. Thank you.

Dave Luckett said:

Stanton, Komodo dragons, with or without incest, make me cringe just on general principles. And now I have learned a number of things that I would not have learned if I didn’t read and post on this blog. Thank you.

On the one hand, Komodo dragons are extremely dangerous animals, even without their Staphylococcus-infected venom, on the other hand, though, it is possible to tame them: this one male + female pair from the Berlin Zoo during the 1960’s was documented as being extremely docile, as the keepers would let children ride around on the female’s back.

He watched “Expelled,” and learned how Charles Darwin directly inspired both Joseph Stalin and Adolf Hitler to commit their respective atrocities.

I did watch Expelled actually. Not so sure about your caricature, but I didn’t know that watching documentaries was funny.

Let’s hit this another way: Suppose there was a Biblical scholar (already known for sloppy scholarship and careless publication) who reported that his research showed that at the Last Supper, Jesus had used milk or orange juice instead of wine. Would such a report be greeted with loving kindness, or with negativity and intolerance?

If there were such a “Biblical Scholar,” his name would probably be Bart Ehrman.

Also, that research sounds very childlike and so I don’t think it should be greeted negatively.

Well this wasn’t very productive, as all it was was elite mockery and PhD-ism. I shall exit from this debate, knowing that my arguments hold up even after all your scrutiny.

BTW one commenter, PvM, said I had “rants” on my blog against relativity, which is a complete fabrication. Check for yourself.

“NotedScholar” said: Also, that research sounds very childlike…

That’s how some of us feel about much of intelligent design creationism’s “research.” I knew you would understand.

NotedScholar said:

He watched “Expelled,” and learned how Charles Darwin directly inspired both Joseph Stalin and Adolf Hitler to commit their respective atrocities.

I did watch Expelled actually. Not so sure about your caricature, but I didn’t know that watching documentaries was funny.

The joke is that Stalin sent many biologists who refused to deny the theory of evolution to die in prison camps in Siberia (e.g. check out Nikolai Vavilov) while Hitler never once wrote or spoke about Darwin or the theory of evolution but ‘The Origin of Species’ was on a list of banned books.

NotedScholar said:

Well this wasn’t very productive, as all it was was elite mockery and PhD-ism. I shall exit from this debate, knowing that my arguments hold up even after all your scrutiny.

BTW one commenter, PvM, said I had “rants” on my blog against relativity, which is a complete fabrication. Check for yourself.

I even provide the link, and yes, your articles show either a sense of humor or a lack of scientific understanding and logic.

PS: What argument?

What the Hell is PhDism? The nutty notion that the more one studies something, the more one tends to understand it? Wouldn’t that the make your position essentially intellectual homeopothism?

NotedScholar said: Well this wasn’t very productive, as all it was was elite mockery and PhD-ism. I shall exit from this debate, knowing that my arguments hold up even after all your scrutiny.

To which PvM replied:

PS: What argument?

I had to relook, but I found it. The only argument NotedScholar has put forward on this thread is that PT posters calling DaveScot an idiot proves that Evolution is the root cause of fascism and terrorism.

And he wonders why we mock. :)

NotedScholar said: The rhetoric here about DaveScot is very negative and intolerant. This merely demonstrates the Creationists’ most striking thesis - that Evolution is the root cause of fascism. Also, of terrorism.

NotedScholar said:

[snip]

If there were such a “Biblical Scholar,” his name would probably be Bart Ehrman.

[snip]

Gee, it’s funny how often your sloppy Biblical Scholar, Bart Ehrman, is cited in the, you know, Biblical Studies literature – unlike any of the Disco dudes.

The other alternative is that the population had some prior enabling characteristic, some quirk in its genome that didn’t really affect survival in one way or another, but that, in combination with some other ordinary mutation of ordinary probability, could predispose the population to acquire the useful citrate characteristic.

Only lacZ and lacY appear to be necessary for lactose catabolism and is inversely proportional to that of glucose. The second control mechanism is a response to glucose. They are oriented in the same direction immediately adjacent and are not produced by the bacterium when lactose is unavailable as a carbon source. In the absence of glucose Cyclic adenosine monophosphate (cAMP) is a signal molecule whose prevalence is inversely proportional.

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This page contains a single entry by PvM published on October 19, 2008 9:00 PM.

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