I'm from Missouri

This site is named for the famous statement of US Congressman Willard Duncan Vandiver from Missouri : "I`m from Missouri -- you'll have to show me." This site is dedicated to skepticism of official dogma in all subjects. Just-so stories are not accepted here. This is a site where controversial subjects such as evolution theory and the Holocaust may be freely debated.

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Location: Los Angeles, California, United States

My biggest motivation for creating my own blogs was to avoid the arbitrary censorship practiced by other blogs and various other Internet forums. Censorship will be avoided in my blogs -- there will be no deletion of comments, no closing of comment threads, no holding up of comments for moderation, and no commenter registration hassles. Comments containing nothing but insults and/or ad hominem attacks are discouraged. My non-response to a particular comment should not be interpreted as agreement, approval, or inability to answer.

Thursday, July 03, 2008

My unchanged opinion of the Cit+ E. coli evolution study

I have learned quite a bit about the Cit+ evolution study (no thanks to lead author Zachary Blount and assorted trolls) in the time since I posted my first article about it but my overall opinion about it remains unchanged. I will restate that opinion here.

In one of the lines of bacteria, there was apparently a "silent" (unexpressed) preliminary (or "potentiating") Cit+ mutation that occurred at around 20,000 generations and then there was one or more expressed mutations occurring at 31,500 generations and maybe later. The 20,000th generation figure was determined by repeatedly re-running the experiment starting with frozen populations that were saved at every 500th generation -- generations older than 20,000 showed a strong tendency to evolve the Cit+ trait whereas generations younger than 20,000 showed no tendency to evolve the Cit+ trait. The silent mutation (~ approximately 20,000 generations) must have been extremely unusual, because otherwise the Cit+ trait would probably have appeared in the other eleven lines of bacteria. On the other hand, the expressible mutations (there may be more than one kind) must be fairly common because the Cit+ trait often reappeared in populations descended from frozen populations of the 20,000th generation or later. I assume that the reason why it took so long for an expressible mutation to be expressed the first time (about five years between the 20,000th and 31,500th generations) was that an expressible mutation had to occur on a bacterium that already possessed the silent mutation and such bacteria were rare because the silent mutation conferred no advantage. However, because the expressible mutations were presumably quite common, the occurrence of the expressible mutation on a bacterium possessing the silent mutation was only a matter of time.

Anyway, I agree with Michael Behe's opinion that the Cit+ evolution represents what he calls "the edge of evolution." He wrote of the Cit+ evolution study,
.
The major point Lenski emphasizes in the paper is the historical contingency of the new ability. It took trillions of cells and 30,000 generations to develop it, and only one of a dozen lines of cells did so. What’s more, Lenski carefully went back to cells from the same line he had frozen away after evolving for fewer generations and showed that, for the most part, only cells that had evolved at least 20,000 generations could give rise to the citrate-using mutation. From this he deduced that a previous, lucky mutation had arisen in the one line, a mutation which was needed before a second mutation could give rise to the new ability. The other lines of cells hadn’t acquired the first, necessary, lucky, “potentiating” (1) mutation, so they couldn’t go on to develop the second mutation that allows citrate use. Lenski argues this supports the view of the late Steven Jay Gould that evolution is quirky and full of contingency. Chance mutations can push the path of evolution one way or another, and if the “tape of life” on earth were re-wound, it’s very likely evolution would take a completely different path than it has.

I think the results fit a lot more easily into the viewpoint of "The Edge of Evolution." One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. “If two mutations have to occur before there is a net beneficial effect — if an intermediate state is harmful, or less fit than the starting state — then there is already a big evolutionary problem.” (4) And what if more than two are needed? The task quickly gets out of reach of random mutation. (emphasis added)

To get a feel for the clumsy ineffectiveness of random mutation and selection, consider that the workers in Lenski’s lab had routinely been growing E. coli all these years in a soup that contained a small amount of the sugar glucose (which they digest easily), plus about ten times as much citrate. Like so many cellular versions of Tantalus, for tens of thousands of generations trillions of cells were bathed in a solution with an abundance of food — citrate — that was just beyond their reach, outside the cell. Instead of using the unreachable food, however, the cells were condemned to starve after metabolizing the tiny bit of glucose in the medium — until an improbable series of mutations apparently occurred. (emphasis added)

Also, the conditions of the experiment were unnaturally favorable for Cit+ evolution -- there was carefully controlled daily glucose-cycling (alternating glucose feeding and glucose starvation) in a citrate-rich medium.

Also, regarding the statement, "if an intermediate state is harmful, or less fit than the starting state": there would be a problem even if an intermediate state is neutral, because a neutral state would confer no competitive advantage and hence would not tend to expand in numbers.

Regarding the statement, "about ten times as much citrate" -- the standard recipe for the medium shows that there is twenty times more sodium citrate than glucose by weight, but the glucose might be a more efficient food source by weight.
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75 Comments:

Anonymous Zmidponk said...

Well, as the information you are after has been spoon-fed to you, and you still seemingly don't understand it, it is with a complete and utter lack of surprise I notice that your opinion of the 'Cit+ E. coli evolution study' is unchanged (assuming, of course, you're talking about Lenski's E. coli project, in which case, you've titled it wrong). However, as you are someone who cannot seemingly understand fairly basic information about this 'study', it would seem your opinion of the 'study' is less than worthless.

Thursday, July 03, 2008 2:07:00 PM  
Blogger Larry Fafarman said...

>>>>>> you're talking about Lenski's E. coli project, in which case, you've titled it wrong <<<<<<

No, I didn't title it wrong -- the Cit+ evolution study was part of Lenski's E. coli project.

>>>>>> However, as you are someone who cannot seemingly understand fairly basic information about this 'study', it would seem your opinion of the 'study' is less than worthless. <<<<<

Then you have the same opinion about Michael Behe because we have the same opinions about the study.

Thursday, July 03, 2008 2:37:00 PM  
Anonymous Anonymous said...

Larry poorly reasoned, "there would be a problem even if an intermediate state is neutral, because a neutral state would confer no competitive advantage and hence would not tend to expand in numbers"

If a trait were neutral it would stand to reason that it would replicate at the same rate as any other trait that the organism had, disappearing from some offspring should the trait be recessive, being very present if the trait were dominant (if such simplistic terms would apply at this level).

A potentially OT observation: my brother has a mutation at some level that has caused him not to grow one of his adult teeth. Should he lose his corresponding baby tooth, he will be missing a tooth and will either have a gap or require an implant or some sort of denture. His son has the same mutation, except it has multiplied, as it were, in that he does not have three (3) adult teeth. Again, he will either have a gap (or three!) and will need implants or dentures or something to cover them, should he want to.

Now, my brother's genetic mutation didn't keep him from reproducing, leading his son to inherit the mutation. What about if he had the mutation 5000 years ago? Depends on how strong that one tooth is and the likelihood of keeping his other teeth. If this is something that doesn't affect him until after he reaches child-bearing age, then he would be a suitable suitor and could pass on the mutation. In today's world, the mutation is basically meaningless. Maybe my nephew, if he loses the teeth in high school or college, will suffer from humiliation or shame and develop some anxiety about his gap -- short-lived as it may be -- but the mutation is unlikely to cause his death or, what's more relevant, his ability to procreate. Since he will be able to procreate (if he wants), he'll be able to have kids and pass on the mutation to them -- despite this evolutionary disadvantage.

And we're even talking about a negative trait. For another example of a negative trait (on one hand), see the sickle cell (which conferred an important advantage on the other hand, probably meaningless at this point).

So, I think your reasoning is way wrong (as usual), but you won't change your mind. I only post here to make sure that the few people who agree with you see other opinions.

Thursday, July 03, 2008 5:56:00 PM  
Blogger Phae said...

I'm not sure anyone is surprised that Behe and other creationists have decided that any mutations we would actually be able to observe are the limits of what evolution is capable. When your beliefs are not based on evidence, but on faith, then they're not science and not falsifiable.

In other words: there is no conceivable experiment that could falsify creationism, as Behe was forced to admit in the Kitzmiller v Dover School Board case.

For people interested in a good background on ID in schools and the best test case to date, I highly recommend PBS' "Judgement Day." You can watch it online here.

Larry, as for you: what would it take for you to think evolution is currently the best theory? Additionally, what would it take for you to think creationism is not accurate? And please no vague principles on either question ("it would take them answering my questions duuuur") but instead supply specific items or reasonable experiments that would suffice.

If you can't think of anything, then you should admit you're believing based solely on faith, and stop pretending to debate.

Thursday, July 03, 2008 8:51:00 PM  
Blogger Larry Fafarman said...

Anonymous said...
>>>>>> If a trait were neutral it would stand to reason that it would replicate at the same rate as any other trait that the organism had <<<<<

I am not talking here about "neutral traits," I am talking about "silent mutations," i.e., mutations that are not expressed as traits. And bacteria with a silent mutation or a neutral trait would replicate at the same rate as the other bacteria and hence would not out-reproduce the other bacteria.

>>>>> disappearing from some offspring should the trait be recessive, being very present if the trait were dominant (if such simplistic terms would apply at this level). <<<<<

Dominance and recessiveness of traits apply only in sexual reproduction, where there are pairings of genes from different parents -- dominance and recessiveness do not apply to the asexual reproduction of bacteria. And under natural (or artificial) selection, dominant neutral traits would have no advantage over recessive neutral traits.

>>>>> Now, my brother's genetic mutation didn't keep him from reproducing, leading his son to inherit the mutation. What about if he had the mutation 5000 years ago? Depends on how strong that one tooth is and the likelihood of keeping his other teeth. If this is something that doesn't affect him until after he reaches child-bearing age, then he would be a suitable suitor and could pass on the mutation. In today's world, the mutation is basically meaningless. <<<<<<<

You are saying that this mutation has no effect on the survival or reproduction of individuals -- "my brother's genetic mutation didn't keep him from reproducing," and "in today's world, the mutation is basically meaningless." But how does that apply to this situation where the mutation -- the ability to eat citrate -- does have a big effect on individuals' ability to reproduce?

>>>>> I only post here to make sure that the few people who agree with you see other opinions. <<<<<<

How do you know that few people agree with my opinions here? Have you taken a poll of readers of this blog?

Also, some commenters are protesting too much by disclaiming that they have any desire to read this blog or comment here. One commenter said that he frequently visits this blog but did not want to put it in his list of so-called "favorite" websites because doing so could falsely imply that this blog is a "favorite" website of his and so he links to this blog from the "killfile dungeon" list of banned commenters on Sleazy PZ Myers' Pharyngula blog. Is that something that I really need to know? Meanwhile, while you people express nothing but disdain for this blog, you have no qualms about taking up my time to answer your comments -- indeed, you people demand that I answer your comments.

=======================

Phae said...
>>>>>> I'm not sure anyone is surprised that Behe and other creationists have decided that any mutations we would actually be able to observe are the limits of what evolution is capable. <<<<<<

This Cit+ evolution appears to be close to the limits of evolution's capability. The Cit+ trait appears to be fairly simple -- just the ability to pass citrate through the cell walls -- and requires only two mutations, but this trait appeared in only one of twelve lines of bacteria in 20 years under conditions highly favorable to evolution of the trait: trillions of bacteria, tens of thousands of generations, and closely controlled daily glucose-cycling (alternating glucose feeding and starvation) in a citrate-rich medium.

>>>>> In other words: there is no conceivable experiment that could falsify creationism <<<<<<

So? There is no conceivable experiment that could falsify evolution.

>>>>> For people interested in a good background on ID in schools and the best test case to date, I highly recommend PBS' "Judgement Day." <<<<<

It was a very bad test case. The case was not appealed, so it is just the opinion of a single judge, who also happened to be biased and incompetent. He showed extreme prejudice against ID and the defendants -- regardless of whether or not ID is a religious concept -- by saying in a Dickinson College commencement speech that his decision was based on his notion that the Founders based the establishment clause upon a belief that organized religions are not "true" religions. And the opinion's ID-as-science section was virtually entirely copied from the ACLU's opening post-trial brief.

>>>>> Larry, as for you: what would it take for you to think evolution is currently the best theory? Additionally, what would it take for you to think creationism is not accurate? <<<<<<

And what would it take to convince you that evolution is not a good theory?

I am not a big fan of intelligent design -- I am more interested in non-ID criticisms of evolution, particularly the problems of co-evolution. I have a special post label for non-ID criticisms of evolution (the post labels are listed in the sidebar). The problems of co-evolution have made me especially skeptical of evolution theory.

I had no particular interest in the evolution controversy prior to the Kitzmiller case. I saw in Kitzmiller that Darwinists were trying to misuse the establishment clause and the courts to suppress and discredit scientific (pseudoscientific, if you prefer) ideas that they don't like. There is no constitutional separation of bad science (or pseudoscience) and state.

Friday, July 04, 2008 2:10:00 AM  
Blogger Phae said...

This Cit+ evolution appears to be close to the limits of evolution's capability. The Cit+ trait appears to be fairly simple -- just the ability to pass citrate through the cell walls -- and requires only two mutations, but this trait appeared in only one of twelve lines of bacteria in 20 years under conditions highly favorable to evolution of the trait: trillions of bacteria, tens of thousands of generations, and closely controlled daily glucose-cycling (alternating glucose feeding and starvation) in a citrate-rich medium.

Yup, that's virtually exactly what Behe said, all right.

And just like I am not surprised about his conclusion, I'm not surprised about yours. Because I notice you couldn't name anything that would make you believe in evolution, leading me to believe you are opposed to it as a matter of faith. You should stop pretending you care about reasons.

So? There is no conceivable experiment that could falsify evolution.

That is... that is almost absurdly ignorant. We are talking about an experiment that could have falsified evolution. If Lenski had run this experiment for twenty years and not seen any significant results, it would have been impressive evidence against evolution!

How stupid are you, honestly?!

It was a very bad test case. The case was not appealed, so it is just the opinion of a single judge, who also happened to be biased and incompetent.

I actually think the single judge and the clear-cut nature of the case makes it more illustrative, not less. It does make it less conclusive, perhaps. I guess for conclusiveness, I'd point to the half-a-dozen other such cases over the years.

I also trust you will back up your assertions about incompetence and bias.

He showed extreme prejudice against ID and the defendants -- regardless of whether or not ID is a religious concept -- by saying in a Dickinson College commencement speech that his decision was based on his notion that the Founders based the establishment clause upon a belief that organized religions are not "true" religions.

That would seem to have absolutely no bearing on the case at all - unless of course you are admitting that ID is creationism, in which case his ruling was impeccably correct. Otherwise, I am hard-pressed to see how this paraphrased, out-of-context quote of yours has anything to do with the matter. Explain.

And the opinion's ID-as-science section was virtually entirely copied from the ACLU's opening post-trial brief.

In point of fact, only the section on whether or not intelligent design was science (about 6,000 words) was taken from the ACLU amicus curiae. And to use sections of briefs is not unusual at all in findings. The content is what you should be attacking, rather than the judge involved. I can't help but notice all you can muster are attacks on him.

And what would it take to convince you that evolution is not a good theory?

Well, the Lenski experiment not yielding results would be a great first step. Similarly, if paleontological evidence were found that called into serious question the evolutionary tree in some manner. In fact, since most of biology, paleontology, botany, and so on are all based on evolution, there are literally millions of possibilities to build up evidence against the theory.

I am not a big fan of intelligent design -- I am more interested in non-ID criticisms of evolution, particularly the problems of co-evolution. I have a special post label for non-ID criticisms of evolution (the post labels are listed in the sidebar). The problems of co-evolution have made me especially skeptical of evolution theory.

So you don't think it's a good theory, but you don't know of a better one? I guess that's reasonable, although your criticisms appear unfounded in general.

I had no particular interest in the evolution controversy prior to the Kitzmiller case. I saw in Kitzmiller that Darwinists were trying to misuse the establishment clause and the courts to suppress and discredit scientific (pseudoscientific, if you prefer) ideas that they don't like. There is no constitutional separation of bad science (or pseudoscience) and state.

I do prefer "pseudoscientific." Now, please explain to me why scientists SHOULDN'T discredit pseudoscientific ideas, please. Because to anyone who is not a raging moron, that would seem like a very reasonable thing to do.

Observer should note that:

(a)Larry has decided to answer my question about proof by repeating it back to me. So I repeat it again, since he has always had trouble with reading: What would it take for you to believe evolution is the best theory? What evidence would be required?

(b)Rather than addressing the substance of the Kitzmiller decision, he attacked the judge. That is pretty interesting.

Friday, July 04, 2008 6:24:00 AM  
Anonymous Zmidponk said...

Larry blurted...

>>>>>>No, I didn't title it wrong -- the Cit+ evolution study was part of Lenski's E. coli project.<<<<<<

No, it wasn't. He may have started studying the cit+ E. coli that evolved during his project, but, as Zachary Blount clearly stated, creating cit+ E. coli was NOT a goal of the project, so it wasn't part of the project.

>>>>>>Then you have the same opinion about Michael Behe because we have the same opinions about the study.<<<<<<

You don't seem to understand something - I am attacking your reasoning and opinions because they stem from utter ignorance and/or lack of comprehension about Lenski's project. If Michael Behe's reasoning and opinions mirror yours exactly, all that means is that his reasoning and opinions are just as flawed and worthless. If you try to link Behe's opinions with yours, it doesn't bolster yours up - it undermines his.

Friday, July 04, 2008 10:43:00 AM  
Blogger Larry Fafarman said...

Zmidponk barfed,
>>>>>>No, I didn't title it wrong -- the Cit+ evolution study was part of Lenski's E. coli project.<

No, it wasn't. He may have started studying the cit+ E. coli that evolved during his project, but, as Zachary Blount clearly stated, creating cit+ E. coli was NOT a goal of the project, so it wasn't part of the project. <<<<<<<<<

Idiot, Blount et al.'s paper about the historical contingency in Cit+ E. coli evolution is listed on the website of Lenski's E. coli Long-term Evolution Experiment.

As the saying goes, don't feed the trolls.

Friday, July 04, 2008 11:08:00 AM  
Anonymous Zmidponk said...

I said...

>>>>>>No, it wasn't. He may have started studying the cit+ E. coli that evolved during his project, but, as Zachary Blount clearly stated, creating cit+ E. coli was NOT a goal of the project, so it wasn't part of the project.<<<<<<

Given your extreme lack of intelligence, I think I should clarify this, as you may get confused. What I mean is that there was not, specifically, a plan to study the resultant cit+ E. coli when the project began, as they were not trying to make E. coli evolve to eat citrate. They have, undoubtedly, studied the cit+ E. coli, but that comes uder the heading of 'studying and recording what happens during your project', which, just to make sure you realise, is a normal part of every scientific project. So, to title this as a 'Cit+ E. coli evolution study', as if this was something especially conceived and planned by them, is incorrect - it is merely what they will do as their project happened to cause the evolution of cit+ E. coli. If, instead, the E. coli had evolved to eat glass, they would be studying glass-eating E. coli instead.

Friday, July 04, 2008 11:12:00 AM  
Anonymous Zmidponk said...

And, as I was typing my last comment, I notice you did get confused, as I thought you would. Guess I'm better at forseeing what utter morons will do next than I thought I was.

Friday, July 04, 2008 11:15:00 AM  
Anonymous Jim said...

"while you people express nothing but disdain for this blog, you have no qualms about taking up my time to answer your comments -- indeed, you people demand that I answer your comments."

Just like you express nothing but disdain for Zachary Blount and Lenkski's study, you have no qualms taking up their time to answer your comments-indeed you demand that they answer your comments.

"so it is just the opinion of a single judge, who also happened to be biased and incompetent."

This isn't what the ID proponents thought going into Dover. They figured it was in the bag when the case was assigned to a Republican appointed Christian judge. It wasn't until he showed he had the integrity to do his job properly and not rule based on his personal beliefs and faith that ID proponents turned and attacked what they originally thought would be their ally.

Friday, July 04, 2008 12:51:00 PM  
Blogger Larry Fafarman said...

Jim said,
>>>>> Just like you express nothing but disdain for Zachary Blount and Lenkski's study, you have no qualms taking up their time to answer your comments-indeed you demand that they answer your comments. <<<<<

Not true -- I did not show disdain for Blount before he started ignoring my simple, basic questions about the study.

>>>>>> They figured it was in the bag when the case was assigned to a Republican appointed Christian judge. <<<<<<

Judge Jones bent over backwards in an attempt to show that he was not influenced by his background as a Bush-appointed Republican churchgoing judge. Just look at his Dickinson College commencement speech where he showed extreme prejudice against ID and the Dover defendants -- regardless of whether or not ID is a religious concept -- by saying that his decision was based on his notion that the Founders based the establishment clause upon a belief that organized religions are not "true" religions.

Friday, July 04, 2008 1:09:00 PM  
Anonymous Zmidponk said...

Larry frivolously stutters...

>>>>>>Not true -- I did not show disdain for Blount before he started ignoring my simple, basic questions about the study.<<<<<<

Questions which he answered.

>>>>>>Judge Jones bent over backwards in an attempt to show that he was not influenced by his background as a Bush-appointed Republican churchgoing judge. Just look at his Dickinson College commencement speech where he showed extreme prejudice against ID and the Dover defendants -- regardless of whether or not ID is a religious concept -- by saying that his decision was based on his notion that the Founders based the establishment clause upon a belief that organized religions are not "true" religions.<<<<<<

...which is utterly irrelevant if ID is not religiously based, but science based on evidence, as ID proponents constantly claim. So either you are admitting ID is, indeed, religiously based, or you're saying that the judge made a comment that is utterly irrelevant to ID as supposed 'proof' that he was biased against ID. Which is it?

Friday, July 04, 2008 1:52:00 PM  
Anonymous brossa said...

I can think of any number of observations that would tend to disprove evolution:

1)If there was only one example of any 'baramin' of animal: one raptor, one canid, one feline, one beetle, one ant, one lizard, etc.

2) If there were significant niches in the ecosystem that were not filled: plants with no herbivores, herbivores with no carnivores, etc.

3) If traits were not inherited; if offspring had no more resemblance to their parents than to any random adult.

4) If the 'genetic' mechanism of every species turned out to be unique, with no features in common with others - one based on DNA, one on RNA, one on proteins, one on quartz crystals, one on complex lipids, etc.

5) If, even if all organisms shared the same underlying genetic mechanism, organisms that appear to be similar (like humans and great apes) had little genetic information in common. Or if the genetic information of all organisms was exactly the same, with phenotypic differences only arising from differential expression patterns.

6) If there were no examples of 'primitive' traits like pelvic bones in whales or vestigial legs in snakes.

7) If there were fossils of modern animals mixed in with all the dinosaur and trilobite fossils.

8) No drug resistance, no new infectious diseases, no immortal cell lines.

9) No chloroplasts or mitochondria

10) An utterly error-proof genetic information system - perhaps with built-in error detection via check sums for individual genes, or palindromic genes, etc.

11) If amino acid substitution in all proteins inevitably led to immediate decomposition of the protein rather than to varying degrees of alteration of function - that is to say if there were true irreducible complexity of protein structure.

The list can go on and on if need be.

Now, credit where credit is due: Larry is correct that dominant/recessive alleles don't really apply to an asexual organism. He is also partially correct about neutral mutations, by themselves, not tending to spread throughout a population due to selection for the neutral mutation. But he forgets about cases of linkage, in which a neutral mutation is associated with another trait that does confer selection advantage, and the effects of genetic drift. Drift is a significant factor in the LTEE because 99% of the population is discarded every day and a single mutation can go from one millionth of the population to one thousandth of the population overnight just by the luck of the draw.

Friday, July 04, 2008 1:55:00 PM  
Blogger Phae said...

Observers should note that:

(a)Larry has decided to answer my question about proof by repeating it back to me. So I repeat it again, since he has always had trouble with reading: What would it take for you to believe evolution is the best theory? What evidence would be required?

(b)Rather than addressing the substance of the Kitzmiller decision, he attacked the judge. That is pretty interesting.

(c)He keeps repeating quotes that imply the Judge disliked organized religion, and doesn't seem to understand that this should have no bearing on the point... if ID is religion, organized or not, his decision was right. Another ad hominem.

(d)CowardLarry is refusing to answer more and more questions from myself and now others. That's because he has no answers, but is too yellow to admit it.

Friday, July 04, 2008 5:48:00 PM  
Anonymous Voice in the Urbanness said...

>(d)CowardLarry is refusing to answer more and more questions from myself and now others. That's because he has no answers, but is too yellow to admit it. <

I think even the cretin Larry knows that he has made a fool out of himself this time but as you say, he is too yellow to admit it.

Friday, July 04, 2008 8:54:00 PM  
Blogger Larry Fafarman said...

brossa said (Friday, July 04, 2008 1:55:00 PM) --

>>>>>> But he forgets about cases of linkage, in which a neutral mutation is associated with another trait that does confer selection advantage <<<<<<

A good example of "linkage" is the linkage of the "silent" Cit+ mutation (at about 20,000 generations) to the expressed Cit+ mutation (at about 31,500 generations).

Phae driveled,
>>>>> CowardLarry is refusing to answer more and more questions from myself and now others. <<<<<

I am not allowed to discuss co-evolution at all on the Panda's Thumb blog and the blog of the Florida Citizens for Science. Fatheaded Ed Brayton kicked me off his blog permanently because he disagreed with my literal interpretation of a federal court rule, and he did not give me a single chance to respond to his disagreement. So who's the coward, dunghill?

Friday, July 04, 2008 9:57:00 PM  
Blogger Phae said...

I am not allowed to discuss co-evolution at all on the Panda's Thumb blog and the blog of the Florida Citizens for Science. Fatheaded Ed Brayton kicked me off his blog permanently because he disagreed with my literal interpretation of a federal court rule, and he did not give me a single chance to respond to his disagreement. So who's the coward, dunghill?

I have no notion of those circumstances, so it's kind of hard for me to judge them based on their enemy's secondhand account.

But are you proposing that two wrongs make a right? That if they had done the same as you, that would make your own cowardice justified? What an interesting moral principle, you gutless idiot.

Saturday, July 05, 2008 1:10:00 AM  
Blogger Larry Fafarman said...

>>>>> I have no notion of those circumstances, so it's kind of hard for me to judge them based on their enemy's secondhand account.

But are you proposing that two wrongs make a right? <<<<<<

Aha -- at least you concede that these acts of censoring me and my comments were wrongs. The other trolls here have not even conceded that much.

Saturday, July 05, 2008 3:26:00 AM  
Anonymous Hector said...

> Aha -- at least you concede that these acts of censoring me and my comments were wrongs. The other trolls here have not even conceded that much. <

Perhaps because it never happened. You seem to be the only one who has resorted to censorship.

Saturday, July 05, 2008 7:12:00 AM  
Anonymous brossa said...

A good example of "linkage" is the linkage of the "silent" Cit+ mutation (at about 20,000 generations) to the expressed Cit+ mutation (at about 31,500 generations).

Possible, but not yet proven. Linkage implies that two or more genes are involved; it may be that the potentiating mutation and the Cit+ mutation are in the same gene. If you wish to define linkage as two 'genetic markers', not genes, this still falls short as the 'genetic marker' associated with the potentiating mutation has not yet been identified, nor has the 'genetic marker' of the Cit+ mutation.

I was thinking more along the lines of a scenario in which the clone with the potentiating mutation persisted at some very low level in the population, experiencing no selective advantage, until an unrelated second mutation (like better glucose exploitation) occurred that could increase fitness and therefore boost the potentiating mutation to a larger %age of the population. This is mere speculation, however, and is not required for the Cit+ mutation to arise. If and when the potentiating mutation is identified, it will be interesting to see how how its penetrance tracks over time between the 20k generation and the 31k generation.

Saturday, July 05, 2008 4:39:00 PM  
Blogger Larry Fafarman said...

Brossa said,
>>>>> Possible, but not yet proven. Linkage implies that two or more genes are involved; it may be that the potentiating mutation and the Cit+ mutation are in the same gene. If you wish to define linkage as two 'genetic markers', not genes, this still falls short as the 'genetic marker' associated with the potentiating mutation has not yet been identified, nor has the 'genetic marker' of the Cit+ mutation. <<<<<<

Well, is it a linkage or not? If it is a linkage of genetic markers, what difference does it make whether or not those genetic markers have been identified?

>>>>> I was thinking more along the lines of a scenario in which the clone with the potentiating mutation persisted at some very low level in the population, experiencing no selective advantage, until an unrelated second mutation (like better glucose exploitation) occurred that could increase fitness and therefore boost the potentiating mutation to a larger %age of the population. <<<<<

The bacteria that acquire the citrate-eating ability do not need better glucose exploitation in order to have a big advantage, because these bacteria have many hours of having something to eat -- an abundant citrate supply -- while the glucose-eating-only bacteria have nothing to eat.

>>>>> If and when the potentiating mutation is identified, it will be interesting to see how how its penetrance tracks over time between the 20k generation and the 31k generation. <<<<<<

I suspect that the penetrance of the potentiating mutation was low. I assume that the second, expressible mutation was fairly common because it was frequently expressed when the experiment was re-run starting with frozen populations of 20K generations or later -- that is how it was determined that such frozen populations have a tendency to re-evolve the Cit+ trait. However, it took a long time -- about five years (20K generation to 31.5K generation) -- for the Cit+ trait to appear the first time, and I think that the reason for that was that few bacteria possessed the potentiating mutation. However, presuming that the expressible mutation is fairly common, its occurrence on a bacterium with the potentiating mutation was only a matter of time.

Sunday, July 06, 2008 3:01:00 AM  
Anonymous W. Kevin Vicklund said...

>>>Well, is it a linkage or not? If it is a linkage of genetic markers, what difference does it make whether or not those genetic markers have been identified?<<<

I think Larry's confusion is a result of the ambiguity of the definition Brossa gave for linkage:

a neutral mutation ... associated with another trait that does confer selection advantage

The "association" is by physical location on the chromosome (or other gene storage organelle), not a functional relationship. Larry's interpretation of that definition is logical, though incorrect.

By itself, the potentiating mutation is neutral, but it is beneficial when what Larry calls the "expressive" mutation is present, therefore the definition is not met. I should also note that mildly deleterious mutations can be propogated due to linkage. The process of propogation of mutations linked to beneficial mutations is called hitchhiking.

>>>The bacteria that acquire the citrate-eating ability do not need better glucose exploitation in order to have a big advantage, because these bacteria have many hours of having something to eat -- an abundant citrate supply -- while the glucose-eating-only bacteria have nothing to eat.<<<

But the point you're missing, Larry, is that Brossa is discussing what may have happened during the 11,000 generations between when the potentiating mutation was acquired and the ability to eat citrate evolved. A bacterium with only the potentiating mutation is still a glucose-only bacterium. Thus, a mutation that better exploited glucose would give a big advantage to the bacterium that evoled it. Any neutral mutations in that bacterium would end up being propogated through the population.

I should also note that better exploitation of glucose is still beneficial to the Cit+ mutants, because they still prefer glucose to citrate. This preference is why they almost went extinct - the glucose-only bacteria evolved a better exploitation of glucose, and outcompeted the slow-eating Cit+ mutants. Until a Cit+ mutant gained another mutation, one that allowed it to have more than 6.64 generations while eating citrate in the time allotted.

Sunday, July 06, 2008 9:09:00 AM  
Anonymous Sp said...

propAgated

(You get 3, I guess, before someone objects.)

Sunday, July 06, 2008 12:21:00 PM  
Blogger Phae said...

Aha -- at least you concede that these acts of censoring me and my comments were wrongs. The other trolls here have not even conceded that much.

I very carefully said - and you even quoted me saying! - that I could NOT pass judgment on that censoring. I didn't see it, I don't read those blogs. And I'm certainly not going to go slog through the comments just to find out. I don't care. I was just pointing out that YOU think they're wrong, and asking you that if you do, why you were prepared to do the same. I guess you do think two wrongs make a right.

Sunday, July 06, 2008 5:49:00 PM  
Blogger Larry Fafarman said...

Kevin Vicklund said,
>>>>> By itself, the potentiating mutation is neutral, but it is beneficial when what Larry calls the "expressive" mutation is present, therefore the definition is not met. <<<<<<<<

Where did you get that arbitrary definition? Brossa defined "linkage" (Friday, July 04, 2008 1:55:00 PM) as where "a neutral mutation is associated with another trait that does confer selection advantage." By that definition, the linkage between the potentiating Cit+ mutation and the expressible Cit+ mutation is especially strong, because the potentiating Cit+ mutation always accompanies the expressible Cit+ mutation whenever the latter mutation confers an advantage in selection.

>>>> Larry, is that Brossa is discussing what may have happened during the 11,000 generations between when the potentiating mutation was acquired and the ability to eat citrate evolved. <<<<<

So you are talking about what may have happened. This is all wild speculation.

>>>>> I should also note that better exploitation of glucose is still beneficial to the Cit+ mutants, because they still prefer glucose to citrate. <<<<<<<

Wild speculation.

>>>>>> This preference is why they almost went extinct -- the glucose-only bacteria evolved a better exploitation of glucose, and outcompeted the slow-eating Cit+ mutants. <<<<<<

More wild speculation.

Sunday, July 06, 2008 5:56:00 PM  
Blogger Larry Fafarman said...

Phae said,
>>>>>>I very carefully said - and you even quoted me saying! - that I could NOT pass judgment on that censoring. <<<<<<

Descriptions of where I was censored on Fatheaded Ed's blog and the Florida Citizens for Science blog are here and here.

So now you can pass judgment.

>>>>>> I guess you do think two wrongs make a right. <<<<<<

Where is the second wrong? I am not arbitrarily censoring anyone here.

Sunday, July 06, 2008 7:55:00 PM  
Blogger Phae said...

Phae said,
>>>>>>I very carefully said - and you even quoted me saying! - that I could NOT pass judgment on that censoring. <<<<<<

Descriptions of where I was censored on Fatheaded Ed's blog and the Florida Citizens for Science blog are here and here.

So now you can pass judgment.


Hahahaha YOU ARE SERIOUS! Holy shit! You seriously and honestly think your own opinion and description of something would be sufficient for me to decide you were in the right?!

Hahahaha that is amazing!! You are just ADORABLE!

Where is the second wrong? I am not arbitrarily censoring anyone here.

That would be the one where you have decided to start deleting comments with which you disagree - er, I mean, that you think are "blatantly untrue."

Sunday, July 06, 2008 8:47:00 PM  
Blogger Larry Fafarman said...

>>>>> You seriously and honestly think your own opinion and description of something would be sufficient for me to decide you were in the right?<<<<<<<

You lousy dunghill -- I linked to the blog comments where these things actually happened.

>>>>> that you think are "blatantly untrue." <<<<<<

Things that I know are blatantly untrue. For example, when Judge Jones tells a newspaper that the school board election results would not affect his decision, it is blatantly untrue to say that Judge Jones told the newspaper that he was going to follow the law.

You lousy trolls are only making yourselves look completely ridiculous.

Pretty soon I am going to stop feeding you trolls altogether -- you are just wasting my time.

You hypocrites of course know that your comments would be censored on most other blogs.

Sunday, July 06, 2008 9:00:00 PM  
Anonymous W. Kevin Vicklund said...

>>>Where did you get that arbitrary definition? Brossa defined "linkage" (Friday, July 04, 2008 1:55:00 PM) as where "a neutral mutation is associated with another trait that does confer selection advantage." By that definition, the linkage between the potentiating Cit+ mutation and the expressible Cit+ mutation is especially strong, because the potentiating Cit+ mutation always accompanies the expressible Cit+ mutation whenever the latter mutation confers an advantage in selection.<<<

Neutrality is relative, not absolute, Larry. In the presence of the "expressive" mutation, the potentiating mutation is beneficial. Therefore, Brossa's definition is not met, because there is no neutral mutation present.

It's like being young or old. I'm in my 30s. Does that make me young or old? The answer is that it depends on the situation. In a preschool, I would be quite old, but in a nursing home, I would be quite young. Similarly, what may be beneficial in one environment may be neutral in another, and deleterious in a third environment.

>>>>>> Larry, is that Brossa is discussing what may have happened during the 11,000 generations between when the potentiating mutation was acquired and the ability to eat citrate evolved. <<<<<<

>>>So you are talking about what may have happened. This is all wild speculation.<<<

No shit, Sherlock. Brossa said that up front.

>>>>>> I should also note that better exploitation of glucose is still beneficial to the Cit+ mutants, because they still prefer glucose to citrate. <<<<<<

>>>Wild speculation.<<<

No, proven fact. It's right there in the paper that you still haven't read. The third page, left-hand column. Also, Zachary Blount confirmed in the comments at The Loom that the Cit+ mutants eat glucose when it's present, and only after it is gone do they switch over to eating citrate. In the clones previous to gen 33K, it takes up to 72 hours of being glucose straved before they switch over to rapid growth on citrate. And you didn't even need to read the paper to know that: all you had to do ws pay attention to Zachary!

>>>>>> This preference is why they almost went extinct -- the glucose-only bacteria evolved a better exploitation of glucose, and outcompeted the slow-eating Cit+ mutants. <<<<<<

>>>More wild speculation.<<<

Still haven't read the paper, I see. Same page and column as above.

Sunday, July 06, 2008 9:08:00 PM  
Blogger Phae said...

You lousy dunghill -- I linked to the blog comments where these things actually happened.

You linked to excerpts from what are, knowing you, months of comments and interactions on those blogs. In order to be able to assess whether or not your blocking was justified, I'd have to be familiar with your pattern of interaction there. I'm not willing to go read all that nonsense, and it is unreasonable to expect me to hunt down your previous comments.

Things that I know are blatantly untrue. For example, when Judge Jones tells a newspaper that the school board election results would not affect his decision, it is blatantly untrue to say that Judge Jones told the newspaper that he was going to follow the law.

Do you have some way to consult an arbiter of objective truth? Do you live in Delphi?

And anyway, why would you want to block someone who said something you could concretely prove was untrue? Just respond with a citation to the story and prove him wrong. I'll be the first to say you're right, if you are. Instead you're censoring him and have lost the chance to hold that high ground.

You lousy trolls are only making yourselves look completely ridiculous.

Yup. We sure are. Darn our inability to answer questions and fumbling attempts to repeatedly provide you with arguments and evidence!

And yet you have decided to censor. Must not be quite so ridiculous if you're afraid.

Pretty soon I am going to stop feeding you trolls altogether -- you are just wasting my time.

That's cool. You can stop replying anytime you want. You can even start deleting all critical comments, but I am afraid I will have to report you to the head of the Association of Non-Censoring Bloggers, an extensive organization with MANY members and IRONCLAD rules about censorship.

You hypocrites of course know that your comments would be censored on most other blogs.

Is this another time where you say it's okay for you to censor people because you think it's been done to you? Your unique moral math again.

Sunday, July 06, 2008 9:14:00 PM  
Blogger Larry Fafarman said...

Phae said,
>>>>>> In order to be able to assess whether or not your blocking was justified, I'd have to be familiar with your pattern of interaction there. <<<<<<

Fatheaded Ed Brayton kicked me off his blog permanently because of a single comment I made which gave a literal interpretation of a federal court rule. He did not give me a single chance to respond to his disagreement. All of this is evident from the comments that I linked to.

As for my discussions of co-evolution on the Florida Citizens for Science blog, my discussions there were the same as they are here in my articles about co-evolution in the Non-ID criticisms of evolution post-label group. So are you too lazy to read those articles?

>>>>>>> And anyway, why would you want to block someone who said something you could concretely prove was untrue? Just respond with a citation to the story and prove him wrong. <<<<<<<<

I have to do this repeatedly because the lies are told repeatedly. My responses take time and this blog gets cluttered up with lies and corrections of lies. So I finally got fed up and started deleting the lies.

Sunday, July 06, 2008 10:01:00 PM  
Blogger Phae said...

Fatheaded Ed Brayton kicked me off his blog permanently because of a single comment I made which gave a literal interpretation of a federal court rule. He did not give me a single chance to respond to his disagreement. All of this is evident from the comments that I linked to.

So... I tell you that I would need to see the whole pattern to judge this, not just your personal interpretation and a single discussion... and your response is to personally interpret it again and point me to that single discussion a second time?

You do realize that these squiggles generally have meaning. We call them "words," and each signifies a specific set of meanings. When put together, they often express ideas. Well, mine do. Yours don't.

As for my discussions of co-evolution on the Florida Citizens for Science blog, my discussions there were the same as they are here in my articles about co-evolution in the Non-ID criticisms of evolution post-label group. So are you too lazy to read those articles?

So your sum total of interaction is represented in the link? If I go back to previous posts on there besides the one you link, I won't find you commenting?

I have to do this repeatedly because the lies are told repeatedly. My responses take time and this blog gets cluttered up with lies and corrections of lies. So I finally got fed up and started deleting the lies.

That must be convenient to be able to censor things you think are wrong. Oh, wait, sorry, you are infallible and KNOW they're wrong, which makes it different. Thanks for clearing up the fact that you don't like addressing criticism and so you eliminate it.

Sunday, July 06, 2008 10:11:00 PM  
Blogger Larry Fafarman said...

As the saying goes, don't feed the trolls.

Like the boy who cried wolf, your comments won't get answered even when they are legitimate comments.

Sunday, July 06, 2008 10:30:00 PM  
Blogger Phae said...

That's cool. Observers should note that Larry admits my comments and points are legitimate, but he won't answer me because of who I am. It's always an interesting pattern... he argues and argues and argues about every point RIGHT UP UNTIL he is proven immensely wrong. Then suddenly he is short on time.

Shucks ;)

Sunday, July 06, 2008 10:50:00 PM  
Anonymous W. Kevin Vicklund said...

Phae, what happened is that on another blog, ViU gave his interpretation of what Jones meant, in the form of "When he told the reporter X, he was saying Y." Larry commits the exact some act when he states the following:

"He showed extreme prejudice against ID and the defendants -- regardless of whether or not ID is a religious concept -- by saying in a Dickinson College commencement speech that his decision was based on his notion that the Founders based the establishment clause upon a belief that organized religions are not "true" religions."

If Larry were not a hypocrite, he would have to delete all of his posts where he makes that comment.

The problem is, the quote in question appears to be an editor's paraphrase of a reporter's paraphrase of what Jones actually said. On November 14, 2005, the York Daily Record had a "breaking news" story on its website. The relevant sentence originally read:

He considers only what has been offered for the record and won't take into consideration news accounts or that a new Dover Area school board has been elected since the trial.

The next day, the print and online version had been edited to read the following:

Judge John E. Jones III said the election results don't figure into his ruling.

By law and rule, federal judges are only allowed to rule based on information offered for the record. (As always, there are some exceptions) Also, Rule 25 of the FRCP requires that when a defendant being sued in his official capacity is replaced (such as by death, resignation, or election), the trial continues with the replacement officer having the same rights and responsibilities as the original officer.

Normally, my next sentence would start "What Jones was saying was that..." but Larry has banned the use of that idiom by anyone but himself, so I must use a more technically correct phrase. What Jones was explaining was that newspaper reports or the fact that new board members were elected would not alter his decision, and that only those items offered for the record could cause him to alter his decision. An example of something that could be offered for the record is notification that the board had repealed the ID curriculum change. Nothing in either paraphrase indicates whether such a notice would alter his decision, so he is not "giving legal advice" according to Larry's use of the term. Another thing to consider is that a number of people (including Ed Brayton and Larry) assumed or speculated that, because the new board was against the ID curriculum change, the judge might simply dismiss the case without any action by the board being necessary. In fact, the way the initial report is phrased, I would guess he was addressing that exact issue.

Sunday, July 06, 2008 10:50:00 PM  
Blogger Phae said...

Thanks, Vicklund. Good to know the exact background on his lie.

Sunday, July 06, 2008 10:52:00 PM  
Blogger Larry Fafarman said...

Kevin Vicklund said,
>>>>> Brossa's definition is not met, because there is no neutral mutation present. <<<<<

But the potentiating mutation is neutral when the expressible mutation is absent. So it is just a matter of the definition of "linkage." You have defined "linkage" to exclude potentiating mutations accompanying associated expressed mutations.

>>>>>>So you are talking about what may have happened. This is all wild speculation.<

No shit, Sherlock. Brossa said that up front. <<<<<<<

I went back and read your statement and I am not exactly sure what you were saying. Anyway, it was just speculation.

>>>>>> No, proven fact. It's right there in the paper that you still haven't read. <<<<<<

So why didn't you cite your source instead of making strange statements out of the blue? Am I supposed to read minds? Sheeesh. You trolls really waste my time by playing games.

Sunday, July 06, 2008 11:06:00 PM  
Anonymous brossa said...

Where did you get that arbitrary definition? Brossa defined "linkage" (Friday, July 04, 2008 1:55:00 PM) as where "a neutral mutation is associated with another trait that does confer selection advantage."

Let me start off by saying that my meaning might have been clearer if I hadn't put a comma in there by error: my intent was to say 'But he forgets about cases of linkage in which a neutral mutation is associated with another trait that does confer selection advantage...' In other words, I did not mean to define linkage as requiring a benefical mutation. Linkage has nothing to do with whether the genes involved are adaptive, neutral, or maladaptive.

Linked genes are those that are likely to be inherited together; in sexual organisms this normally means that they are physically close enough to each other on a chromosome that the crossing-over events of meiosis are unlikely to separate them. In bacteria, where there is no meiotic crossover, all the (non-plasmid) genes can be thought of as linked because they are all transmitted to the offspring en bloc.

Linkage tells you nothing about whether a functional relationship exists between the involved genes, nor does it address whether they are beneficial, neutral, or maladaptive. In a subset of cases of linkage, a neutral or maladaptive mutation can increase in penetrance because it is linked to a beneficial mutation (hitchhiking, as w kevin vicklund said).

I balked at your statement that the potentiating mutation and the Cit+ mutation were linked because, as I understand it, linkage is between two or more genes - so if both mutations were in the same gene they would not meet the definition. I concede that I may be wrong about this definition, however. It is possible, even likely, that both the potentiating mutation and the Cit+ mutation(s) are passed on together. It is also possible, however, that the Cit+ mutation event(s) altered or eliminated the original potentiating mutation.

Take the following example - imagine that the string of letters represent a string of amino acids in a protein coded for by a single gene.

ABCDEFGHIJKLMNO (original) --->
ABCKJIHGFEDLMNO (potentiated) -->
ADEFGHIJKCBLMNO (Cit+)

In the above, an initial inversion event results in the 'potentiated' state, which is then further altered by a second inversion to form the 'cit+' state. However, the cit+ state does not 'also include' the potentiated state- that mutant form no longer exists. Contrast this with:

ABCDEFGHIJKLMNO (original) -->
ABXDEFGHIJKLMNO (potentiated)-->
ABXDEFGHIJKRMNO (cit+)

In this case, the potentiating and activating mutations both continue to be passed on.

I already pointed out that I was speculating about this - since we don't yet know what the potentiating mutation was, we can't track its penetrance through the population, or even tell whether the potentiating mutation was altered by the second mutation. I agree that it's likely that the penetrance of the potentiating mutation was low, though.

It is not speculation that the Cit+ mutants still prefer glucose to citrate, however. Their growth curves show that they grow rapidly on glucose; then, when the glucose runs out, there is a pause before they begin to grow again (more slowly!) on citrate. In a best case scenario, a citrate molecule offers less than half the energy of a glucose molecule, and the Cit+ bacteria clearly still prefer glucose when it is available.

It's also not speculation that the Cit+ strain nearly went extinct. The earliest Cit+ mutants were very poor utilizers of citrate but they were able to grow to 19% of the population before something else changed which caused them to drop back down to 1.1%. The likely explanation is that they were outcompeted by a better Cit- mutant, and only came to dominate after a third mutation boosted their citrate-utilization further. It will take years to nail this down conclusively.

Sunday, July 06, 2008 11:09:00 PM  
Blogger Larry Fafarman said...

Brossa:

You and Kevin Vicklund can't even agree on a definition of "linkage," which shows how much your definitions are worth (well, they're worth something).

>>>>>> It's also not speculation that the Cit+ strain nearly went extinct. <<<<<<

I never said that was speculation -- it was mentioned on Carl Zimmer's blog.

>>>>>>> The earliest Cit+ mutants were very poor utilizers of citrate but they were able to grow to 19% of the population before something else changed which caused them to drop back down to 1.1%. The likely explanation is that they were outcompeted by a better Cit- mutant, <<<<<<

That seems an unlikely explanation for the big drop in Cit+ bacteria, because the Cit+ bacteria had many hours (~18?) of access to an abundant food source, citrate, that their Cit- neighbors could not utilize.

Sunday, July 06, 2008 11:55:00 PM  
Blogger Larry Fafarman said...

Kevin Vicklund barfed (Sunday, July 06, 2008 10:50:00 PM) --
>>>>>what happened is that on another blog, ViU gave his interpretation of what Jones meant, in the form of "When he told the reporter X, he was saying Y." <<<<<<<

Wrong, dunghill -- ViU was saying that Judge Jones was actually saying Y. ViU was trying to dodge the implications of X.

>>>>>> Larry commits the exact some act when he states the following:

"He showed extreme prejudice against ID and the defendants -- regardless of whether or not ID is a religious concept -- by saying in a Dickinson College commencement speech that his decision was based on his notion that the Founders based the establishment clause upon a belief that organized religions are not "true" religions." <<<<<<<

That's an accurate statement, dunghill. Here is what Jones actually said:

. . . this much is very clear. The Founders believed that true religion was not something handed down by a church or contained in a Bible, but was to be found through free, rational inquiry. At bottom then, this core set of beliefs led the Founders, who constantly engaged and questioned things," to secure their idea of religious freedom by barring any alliance between church and state.

>>>>>>On November 14, 2005, the York Daily Record had a "breaking news" story on its website. The relevant sentence originally read:

He considers only what has been offered for the record and won't take into consideration news accounts or that a new Dover Area school board has been elected since the trial.

The next day, the print and online version had been edited to read the following:

Judge John E. Jones III said the election results don't figure into his ruling. <<<<<<<

I never saw the first statement, dunghill -- I only saw the second statement.

There is a small chance that Jones' statement was just an indiscretion, but I doubt it. The only way that the election of the new school board could possibly affect his decision would be by repeal of the ID policy. So by saying that the election results would not affect his decision, he was essentially saying that repeal of the ID policy would not affect his decision. And he knew that the new school board members were inclined to repeal the ID policy because they had campaigned against it. And it is one thing to say that his statement was possibly just an indiscretion and another thing entirely to say that his statement could not have been a factor in the new school board's decision to not repeal the ID policy prior to judgment.

>>>>> What Jones was explaining was that newspaper reports or the fact that new board members were elected would not alter his decision, and that only those items offered for the record could cause him to alter his decision. <<<<<<<<

But he didn't have to say that because everyone knew that the only thing that could possibly alter his decision -- or cause him to dismiss the case -- would be repeal of the ID policy. In fact, the question of whether to try to moot the case by repealing the ID policy was discussed at the last meeting of the old board and the first meeting of the new board.

>>>>> Another thing to consider is that a number of people (including Ed Brayton and Larry) assumed or speculated that, because the new board was against the ID curriculum change, the judge might simply dismiss the case without any action by the board being necessary. <<<<<<

You disgusting sack of &^*#$@, I never made any such assumption or speculation, and Fatheaded Ed Brayton certainly never did.

Phae barfed,
>>>>> Thanks, Vicklund. Good to know the exact background on his lie. <<<<<

Where's the lie, you disgusting dunghill?

One of the bad things about running a small, low-traffic one-man blog is that I have to make most of the responses to trolls myself (though in many cases the trolls' comments are not even worth answering). This is starting to take too much of my time and I just have to cut back. Other bloggers without my high ethical standards (we all know who they are) would just take the easy way out and censor the trolls' comments, but I can't do that (except for the most flagrant violations).

Monday, July 07, 2008 1:01:00 AM  
Anonymous brossa said...

You and Kevin Vicklund can't even agree on a definition of "linkage," which shows how much your definitions are worth (well, they're worth something).

Well, please don't just take my word for it:

http://en.wikipedia.org/wiki/Genetic_linkage

http://en.wikipedia.org/wiki/Genetic_hitchhiking

http://www.blackwellpublishing.com/ridley/a-z/Hitch-hiking.asp

http://www.jstor.org/pss/1309007

I never said that was speculation -- it was mentioned on Carl Zimmer's blog.

It's mentioned in Lenski's paper, too.

That seems an unlikely explanation for the big drop in Cit+ bacteria, because the Cit+ bacteria had many hours (~18?) of access to an abundant food source, citrate, that their Cit- neighbors could not utilize.

Taken directly from the Blount paper:
"The precipitous decline in the frequency of Cit+ cells just before the massive population expansion suggests clonal interference, whereby the Cit- subpopulation produced a beneficial mutant that out-competed the emerging Cit+ subpopulation until the latter evolved some other beneficial mutation that finally ensured its persistence. The hypothesis of clonal interference implies that the early Cit+ cells were very poor at using citrate, such that a mutation that improved competition for glucose could have provided a greater advantage than did marginal exploitation of the unused citrate.

Indeed, the Cit+ clones isolated from generations 32,500 and earlier grow much more slowly on citrate than those from 33,000 generations and later. After depleting the glucose in DM25, the earliest Cit+ clones grow almost imperceptibly, if at all, for many hours before they begin efficiently using the citrate (data not shown), whereas later Cit+ clones switch to growth on citrate almost immediately."

Monday, July 07, 2008 5:35:00 AM  
Anonymous W. Kevin Vicklund said...

>>>>>>what happened is that on another blog, ViU gave his interpretation of what Jones meant, in the form of "When he told the reporter X, he was saying Y." <<<<<<

>>>Wrong, dunghill -- ViU was saying that Judge Jones was actually saying Y. ViU was trying to dodge the implications of X.<<<

Wrong. ViU was saying that X implied Y, as opposed to the Z that you claimed it implied.

>>>>>> Larry commits the exact some act when he states the following:

"He showed extreme prejudice against ID and the defendants -- regardless of whether or not ID is a religious concept -- by saying in a Dickinson College commencement speech that his decision was based on his notion that the Founders based the establishment clause upon a belief that organized religions are not "true" religions." <<<<<<


>>>That's an accurate statement, dunghill. Here is what Jones actually said:

... this much is very clear. The Founders believed that true religion was not something handed down by a church or contained in a Bible, but was to be found through free, rational inquiry. At bottom then, this core set of beliefs led the Founders, who constantly engaged and questioned things," to secure their idea of religious freedom by barring any alliance between church and state.<<<

Nowhere in that quote does Jones say he based his decision on his notion of the Founding Father's basis for the Establishment Clause. That is merely your own interpretation. Likewise, he did actually say that organized religions are not true religions. That is your interpretation. What he said is that certain characteristics (which may define an organized religion) are not the same as the characteristics that define true religion. The way I interpret that, and the way the book he is quoting interprets that, is that organized religions are not necessarily true religion - but some of them could be! A chair is something you sit on, not something with four legs. That doesn't mean that a chair can't have four legs.

>>>>>>On November 14, 2005, the York Daily Record had a "breaking news" story on its website. The relevant sentence originally read:

He considers only what has been offered for the record and won't take into consideration news accounts or that a new Dover Area school board has been elected since the trial.

The next day, the print and online version had been edited to read the following:

Judge John E. Jones III said the election results don't figure into his ruling. <<<<<<

>>>I never saw the first statement, dunghill -- I only saw the second statement.<<<

Flat-out lie (and neither of them are statements, they are paraphrases, if you want to be pedantic). I have previously presented that to you, and you replied to that portion of the comment.

>>>There is a small chance that Jones' statement was just an indiscretion, but I doubt it.<<<

Where's the indiscretion? He is simply telling them the law - that the fact that a new board was elected does not figure into his ruling.

>>>The only way that the election of the new school board could possibly affect his decision would be by repeal of the ID policy.<<<

But he did not say that the election of a new board couldn't possibly affect his decision. All he said was the fact that there was a new board would not alter his ruling - rescinding the ID policy was not on the ballot. Any action that the new board might take is independent of the election. Besides which, there are several courses of action that the board could have taken that might have affected his decision.

election results = the fact that there is a new board

>>>So by saying that the election results would not affect his decision, he was essentially saying that repeal of the ID policy would not affect his decision.<<<

But he never said that. See above.

>>>And he knew that the new school board members were inclined to repeal the ID policy because they had campaigned against it.<<<

How would he, as the Honorable Judge Jones, know that? As a judge, he can't rely on news accounts when making his decision. It would have to be something offered up for the record. Wait, didn't the original news report paraphrase him as saying something about that? Until and unless the board requested official notice of a change in the policy, his decision couldn't be altered.

>>>And it is one thing to say that his statement was possibly just an indiscretion and another thing entirely to say that his statement could not have been a factor in the new school board's decision to not repeal the ID policy prior to judgment.<<<

It is possible that the poor paraphrasing by the newspaper of what he said, plus the inclusion of that paraphrase in the middle of an article about whether it was possible to moot the case by rescinding the policy, may have impacted the board's decision. However, the blame for that lies on the newspaper, not the judge, who was merely explaining courtroom procedure to reporters as permitted by the official judicial code of conduct. It is far more likely that the fact that the defense lawyers, the plaintiffs' lawyers, and their own independent counsel all told them that the case couldn't be mooted was the deciding factor (especially since the defense lawyers had successfully argued in front of two en banc panels of two Circuit Courts that the presence of nominal damages normally precludes mootness) is what drove the decision.

>>>>>> What Jones was explaining was that newspaper reports or the fact that new board members were elected would not alter his decision, and that only those items offered for the record could cause him to alter his decision. <<<<<<

>>>But he didn't have to say that because everyone knew that the only thing that could possibly alter his decision -- or cause him to dismiss the case -- would be repeal of the ID policy.<<<

But not everyone knew that. A lot of people thought that he could simply dismiss the case simply because the new board was opposed to the policy.

>>>In fact, the question of whether to try to moot the case by repealing the ID policy was discussed at the last meeting of the old board and the first meeting of the new board.<<<

Setting aside the fact that as a judge he couldn't take that into consideration without it being offered for the record, we have no proof that he made his statement after the last meeting of the first board. In fact, I need to make a correction. If you look at the time stamp, the first paraphrase appeared on November 14. I just checked the calendar: the last meeting of the old board was held on November 15, and the story was printed on the 16th, two days later, not one as I previously stated. This means that Jones made his statement before the meeting. I have reason to believe that the statement was actually made the day after the elections (the article in question appears behind a pay wall). Since the board members only refer to what the lawyers were telling them, I assume that that was the causitive factor in their decision, not a poorly paraphrased version of what the judge said. In fact, what the judge said may have been what prompted the attempt to repeal the policy in the first place!

>>>>>> Another thing to consider is that a number of people (including Ed Brayton and Larry) assumed or speculated that, because the new board was against the ID curriculum change, the judge might simply dismiss the case without any action by the board being necessary. <<<<<<

>>>You disgusting sack of &^*#$@, I never made any such assumption or speculation, and Fatheaded Ed Brayton certainly never did.<<<

Oh what a tangled web we weave
When first we practise to deceive
- Sir Walter Scott

On December 25, 2005, Larry made the following comment on Panda's Thumb (emphasis mine):

"As for the district court judge in this case, I don't know what all his options were. For example, instead of immediately throwing out the case as moot after the previous board members were voted out, maybe he could have suspended the case pending suit of the new board members if they did not rescind the ID rule. I don't know."

You certainly speculated about it as a possibility then. I will grant that most of your speculation at the time was whether the board could have mooted the case by rescinding the policy. (By the way, I used a backdoor that allows me to view all comments made on pt under a specific username - the link to the post no longer works and would require additional searching, which I don't have time for right now)

And here is what Ed had to say on his blog the afternoon of November 9, 2005 (the morning after the elections, emphasis mine):

"B. The new board's position. Which is a little ambiguous. Yes, they ran on a platform of being against the ID policy, but they've also said that they were going to wait for the judge's ruling before making any changes in the policy. They are seated on December 5th and will not have an opportunity to actually change the policy until at least January, which will likely be after the ruling is issued. It does not look, at least, as if the new board is going to ask the court to end the proceedings because the issue has been mooted. And I think it's highly unlikely that the attorneys for the present defendants will ask for the case to be mooted. Can the judge himself decide that the circumstances have mooted the issue in the case and decide not to issue a ruling? Good question, and I'm pretty sure the answer to that is no. So there's a good chance that this won't even come up."

Ed speculated that it might happen, even though he was pretty sure that it couldn't. But it was indeed a question that people had. (italics highlight a side issue)

Monday, July 07, 2008 8:56:00 AM  
Blogger Larry Fafarman said...

I have finally realized why you and other trolls spend so much time commenting on this blog, Kevin. It is because you see this blog as a big threat.

>>>>> ViU was saying that X implied Y, as opposed to the Z that you claimed it implied. <<<<<

The implication of Z was much stronger than the implication of Y.

>>>>> Nowhere in that quote does Jones say he based his decision on his notion of the Founding Father's basis for the Establishment Clause. <<<<<<

That was the whole theme of the speech, you stupid fathead.

>>>>> That is merely your own interpretation. <<<<<<

That is the simplest reasonable interpretation. And according to Occam's Razor, the simplest reasonable interpretation is the best interpretation.

>>>>> Likewise, he did actually say that organized religions are not true religions. <<<<<<

I agree.

>>>>>> The way I interpret that, and the way the book he is quoting interprets that, is that organized religions are not necessarily true religion - but some of them could be! <<<<<<

You are reading too much into his speech.

>>>>> Flat-out lie <<<<<<

Wrong, dunghill, it's the truth -- I never saw the first statement.

>>>>> and neither of them are statements, they are paraphrases, if you want to be pedantic <<<<<<

You are not just being pedantic -- you are wrong. They are statements -- the newspaper's statements.

>>>>> Where's the indiscretion? <<<<<<

The statement could easily be interpreted as hinting that repeal of the ID policy would not affect his decision -- and such hinting is improperly giving legal advice.

>>>>>> He is simply telling them the law - that the fact that a new board was elected does not figure into his ruling. <<<<<<

Actually, I think that the election results did figure into his decision -- because he knew that the new school board was not likely to appeal the decision, the decision was less restrained than it otherwise might have been. And if Jones had anticipated an appeal, the opinion's ID-as-science section possibly would not have been virtually entirely copied from the ACLU's opening post-trial brief, because appeals courts frown on such copying.

>>>>>>And he knew that the new school board members were inclined to repeal the ID policy because they had campaigned against it.<

How would he, as the Honorable Judge Jones, know that? <<<<<<

Everyone knew it, idiot.

>>>>>> It is far more likely that the fact that the defense lawyers, the plaintiffs' lawyers, and their own independent counsel all told them that the case couldn't be mooted was the deciding factor<<<<<

You dunghill, the newspaper reported that the plaintiffs' lawyers did not comment (why should they, and why would they be believed) and there was no evidence that the school board got any advice from their independent couusel. And an attorney prepared a report telling the board that they might be able to moot the case by repealing the ID policy.

>>>>> A lot of people thought that he could simply dismiss the case simply because the new board was opposed to the policy. <<<<<<

Some really stupid people might have thought that. And the school board certainly didn't think that, and that is what counts.

>>>>>> This means that Jones made his statement before the meeting. <<<<<<

So what?

>>>>> Since the board members only refer to what the lawyers were telling them <<<<<<

We have no idea what was said at the meetings.

>>>>>>On December 25, 2005, Larry made the following comment on Panda's Thumb (emphasis mine):

"As for the district court judge in this case, I don't know what all his options were. For example, instead of immediately throwing out the case as moot after the previous board members were voted out, maybe he could have suspended the case pending suit of the new board members if they did not rescind the ID rule. I don't know." <<<<<<

I think that you misquoted me. I would not have said something exactly like that, .e.g, "maybe he could have suspended the case pending suit of the new board members," which is a meaningless statement. As I remember, I said that he might have delayed releasing his decision in order to give the new school board a chance to repeal the ID policy before release of his decision (the school board actually had an opportunity to do that in early December but did not take it). A non-activist judge would have welcomed a repeal of the ID policy as a reason to dismiss the case. At any rate, I never said that he might have dismissed the case if the board did nothing.

>>>>>Fatheaded Ed said, "They are seated on December 5th and will not have an opportunity to actually change the policy until at least January, which will likely be after the ruling is issued." <<<<<<

Wrong. They could have repealed the policy at the Dec. 5 meeting or they could have scheduled a special meeting for early December.

>>>>>Fatheaded Ed said, "Can the judge himself decide that the circumstances have mooted the issue in the case and decide not to issue a ruling?" <<<<<

Fatheaded Ed is a stupid idiot. He argued that the judge was not going to dismiss the case even if the board repealed the ID policy, so how could he say that the judge might have dismissed the case if the board did not repeal the ID policy?

Monday, July 07, 2008 11:43:00 AM  
Blogger Larry Fafarman said...

brossa said (Monday, July 07, 2008 5:35:00 AM) --

>>>>>>You and Kevin Vicklund can't even agree on a definition of "linkage," which shows how much your definitions are worth (well, they're worth something).

Well, please don't just take my word for it:

http://en.wikipedia.org/wiki/Genetic_linkage

http://en.wikipedia.org/wiki/Genetic_hitchhiking

http://www.blackwellpublishing.com/ridley/a-z/Hitch-hiking.asp

http://www.jstor.org/pss/1309007 <<<<<<<<

OK, but there must be some disagreement as to what the words "linkage" and "hitchhiking" actually mean.

>>>>>It's mentioned in Lenski's paper, too. <<<<<<

I'm not surprised -- Zimmer's blog was based on the paper.

>>>>>>That seems an unlikely explanation for the big drop in Cit+ bacteria, because the Cit+ bacteria had many hours (~18?) of access to an abundant food source, citrate, that their Cit- neighbors could not utilize.

Taken directly from the Blount paper:<<<<<<

OK, but when you make a statement that seems strange on its face, you should cite your source.

Yes, it does seem that the first Cit+ bacteria were not terribly good at utilizing citrate, because it took them a long time to grow to just 19% of the population.

Monday, July 07, 2008 5:22:00 PM  
Anonymous brossa said...

I'm curious - have you still not read the paper itself?

Tuesday, July 08, 2008 10:45:00 AM  
Anonymous W. Kevin Vicklund said...

Larry Fafarman, July 7, 2008:

"At any rate, I never said that he might have dismissed the case if the board did nothing."

Larry Fafarman, January 1, 2006:

"Actually, I think that the judge should just have declared the case moot when all the pro-ID members were voted off the school board and replaced by anti-ID members, or at least he should have waited to see what the new board was going to do (the first meeting is on Jan. 3)."

Later that day:

"The lawsuit should have been dismissed as moot because the cause of action had ceased to exist."

...and a follow-up:

">>>Neither the action had ceased to exist not the possibility of continued action by another board. The issue was hardly moot.<<<

The new board members had campaigned on a promise to repeal the ID rule."

Are you man enough to admit your mistake, or are you going to continue to lie in the face of evidence?

Tuesday, July 08, 2008 10:56:00 AM  
Blogger Larry Fafarman said...

brossa said...

>>>>>> I'm curious - have you still not read the paper itself? <<<<<<

I have skimmed the paper. And even if I had read it in its entirety, it was a long paper and I likely would forget little details like the one you mentioned. There is nothing wrong with commenting on a paper or asking questions about it without having read it -- for example, suppose that I am in the audience at a presentation of the paper and I haven't read it. I presume that most people who have commented on the paper haven't read it.

Because the paper has been so widely discussed on the Internet, I thought that it was more important to concentrate on the discussions rather than on the paper itself. I got the impression that a lot of people think that the Cit+ evolution was the main if not the sole goal of the experiment, even though Zachary Blount claims that it was not even a goal at all. And I also got the impression that a lot of people think that the purpose of the glucose cycling was to promote Cit+ evolution.

Tuesday, July 08, 2008 11:57:00 AM  
Blogger Larry Fafarman said...

W. Kevin Vicklund said...

>>>>> Larry Fafarman, July 7, 2008:

"At any rate, I never said that he might have dismissed the case if the board did nothing."

Larry Fafarman, January 1, 2006:

"The lawsuit should have been dismissed as moot because the cause of action had ceased to exist."
<<<<<<<<<<

I apologize for calling you names for allegedly misrepresenting what I said earlier. I would not have jumped on you if you weren't such a lousy troll in general.

You watch every word I say so that you can quote-mine me later. You remember what I've said better than I do.

What I was thinking back then was that Judge Jones could have dismissed the case immediately after the elections by saying, "the new school board members ran on a campaign against the ID policy so the case is moot because they are going to repeal the ID policy anyway." A dismissal would not have been irrevocable -- he could have rescinded it if the school board for some strange reason failed to repeal the ID policy at the first clear opportunity. Anyway, IMO this is an intriguing legal question which I will raise in a future post.

Tuesday, July 08, 2008 12:27:00 PM  
Anonymous brossa said...

I have skimmed the paper. And even if I had read it in its entirety, it was a long paper and I likely would forget little details like the one you mentioned.

I'm sorry to hear you say that. As I said in my initial post here, I took at face value your statement that "Right now I am just trying to understand the experiment." It would be one thing to ask questions at a conference, where you presumably had not been exposed to the material before; but to have not read an eight page paper after almost a month while continuing to comment on it indicates that you are not sincere in wanting to understand it.

Tuesday, July 08, 2008 4:05:00 PM  
Blogger Larry Fafarman said...

Brossa said,
>>>>>>to have not read an eight page paper after almost a month while continuing to comment on it indicates that you are not sincere in wanting to understand it. <<<<<<

I didn't say that I didn't read it at all -- I said I skimmed it. There are a lot of little details that I don't need to know. Meanwhile, the lead author of the paper, Zachary Blount, has not helped me to understand the experiment -- he did not give straight answers to my simple, basic questions about the experiment.

Tuesday, July 08, 2008 7:47:00 PM  
Blogger Erin said...

To repeat. Again. Larry, if you want to understand an experiment, the whole paper is probably important. That's why the authors wrote the whole paper. . .so that other people could understand their experiment. If you're not going to read the whole paper, the abstract might be a good place to start. If that doesn't satisfy your supposed "curiosity" then reading the whole (zomg) 8 page paper, would be a logical next step.

Arguing with people who /have/ read the paper and/or demanding answers from the author, having not read the whole paper are NOT acceptable alternatives.

Tuesday, July 08, 2008 10:32:00 PM  
Blogger Erin said...

On another note, skimming doesn't count as reading. Presumably you are capable of reading since you respond to very many comments on your blog.

P.S. skimming doesn't count. (Although on second thought, if you simply skim comments before responding, it could explain some of the idiocy that runs rampant around here.)

Tuesday, July 08, 2008 10:35:00 PM  
Blogger Larry Fafarman said...

Erin said,
>>>>>> If you're not going to read the whole paper, the abstract might be a good place to start. <<<<<<

Of course I read the abstract, idiot. How could I browse through the paper without reading the abstract.

>>>>>> Arguing with people who /have/ read the paper and/or demanding answers from the author, having not read the whole paper are NOT acceptable alternatives. <<<<<<

Zachary Blount has no excuses for not giving straight answers to my simple, basic questions about the experiment: (1) was Cit+ evolution a goal of the experiment (there are such things as secondary goals and longshot goals) and (2) what were the purposes of the glucose cycling (giving an insufficient glucose supply so as to cause alternating glucose feeding and starvation). If the paper answers the questions, he could have quoted the paper or cited the page number(s). And I asked him to clarify ambiguous and inconsistent statements that he made on Carl Zimmer's blog -- not in the paper -- in regard to whether Cit+ evolution was a goal of the experiment. My questions are especially important because I get the general impression that many people -- maybe even most people -- think that Cit+ evolution was the main if not the sole goal of the experiment and that the purpose of the glucose cycling was to favor Cit+ evolution.

Thursday, July 10, 2008 8:55:00 AM  
Blogger Erin said...

"Of course I read the abstract, idiot. How could I browse through the paper without reading the abstract."

I have known you to do things more stupid even than that.

"Zachary Blount has no excuses for not giving straight answers to my simple, basic questions about the experiment: (1) was Cit+ evolution a goal of the experiment (there are such things as secondary goals and longshot goals) and (2) what were the purposes of the glucose cycling (giving an insufficient glucose supply so as to cause alternating glucose feeding and starvation)."

Actually he does. YOU HAVEN'T READ THE PAPER. (Did I forget to say that skimming it doesn't count?) The answers are in the paper, I believe Phae has pointed them out to you, by page number. Researchers are not in the business of hand-holding idiots. They are (somewhat unsurprisingly) in the business of research.

"If the paper answers the questions, he could have quoted the paper or cited the page number(s)."

Again, a researcher's job is not holding the hand of idiots who can't even be bothered to read the whole paper. Additionally, these questions have been answered for you, by people who have read the paper, pages cited, etc. Stop whining.


"And I asked him to clarify ambiguous and inconsistent statements that he made on Carl Zimmer's blog -- not in the paper -- in regard to whether Cit+ evolution was a goal of the experiment. My questions are especially important because I get the general impression that many people -- maybe even most people -- think that Cit+ evolution was the main if not the sole goal of the experiment and that the purpose of the glucose cycling was to favor Cit+ evolution."

Who thinks that and what does it matter?

Thursday, July 10, 2008 2:32:00 PM  
Blogger Larry Fafarman said...

How many times do I have to go over this, dunghill?

I asked him to clarify ambiguous and inconsistent statements that he made OUTSIDE the paper. Nothing in the paper can justify making ambiguous and inconsistent statements OUTSIDE the paper.

Also, he didn't respond to my questions about glucose cycling at all -- not even with bibliography bluffing.

>>>>>> Additionally, these questions have been answered for you, by people who have read the paper, pages cited, etc. <<<<<

No one has cited pages of the Cit+ evolution paper that answer my questions, dunghill. If you continue to tell lies like that, your comments will be deleted.

>>>>>I get the general impression that many people -- maybe even most people -- think that Cit+ evolution was the main if not the sole goal of the experiment and that the purpose of the glucose cycling was to favor Cit+ evolution."

Who thinks that and what does it matter? <<<<<<

Who thinks otherwise aside from a few lousy trolls who have been cluttering up this blog with their crap?

Apparently a lot of people think that Cit+ evolution was the sole or main goal of the experiment, because the Cit+ evolution has been the only result of the experiment that has been widely publicized.

These things matter because they are important in understanding the experiment, bozo. For example, see my post "A reason for glucose-cycling in Lenski's E. coli experiment".

Lousy troll.

Thursday, July 10, 2008 3:14:00 PM  
Anonymous brossa said...

We've been over the issue of 'goal' before, and it doesn't look like there will be any resolution of that issue, in part because you seem to be using a different definition of 'goal' than most other people. No matter. For the sake of argument, let's accept your suspicion that the development of a Cit+ strain was a main goal of the experiment in the first place. Furthermore, suppose that this goal has been a secret since 1988, which is why it is not mentioned in any of the papers published on the LTEE so far. We can even hypothesize that the design of the experiment, from the outset, was specifically tailored to encourage Cit+ mutation over all other adaptive pathways (in real life it can be shown that there would be much better ways to do this, by the way).

Taking all of that as granted, what do you think that this proves? What would the significance of this be? Does it merely reflect on Lenski's character, or is the science affected in some way? Why can't other trained biologists recognize that what was reported as a long-term study of evolution is actually a cleverly designed breeding program with a specific outcome in mind? Now that he has his Cit+ strain, do you think that Lenski will halt the LTEE? I'm asking rhetorical questions, but I'm genuinely interested in your responses here.

Regarding glucose cycling, there are really only three ways in which to culture cells indefinitely:

1) Provide them with a significant excess of nutrients, minerals, cofactors, etc., so their growth basically continues unchecked until the next transfer is made. If you let the population really explode at each transfer, then you will tend to transfer a smaller percentage of the final population. You may be taking only one thousandth or one millionth per transfer. In a study that is trying to monitor mutations, you will be discarding the lion's share of your genetic diversity each time, and genetic drift will play a huge role in how the population develops. In many experiments this is unimportant, but not so much in this one, in which one of the goals was the ability to 'replay' evolution. The bacteria also experience very little change in their environment over the course of the experiment - the temperature is constant, there is always plenty of food, etc. - and an unchanging environment to which the organism is already exquisitely adapted provides no evolutionary pressure. So the LTEE would be hampered by excessive drift, poor repeatability, and little if any observable evolution.

2) Chemostat: keep the concentrations of nutrients at a constant, arbitrary level (high or low) by constantly adding fresh media and removing exhaused media. The number of bacteria in the chemostat is kept constant by removing bacteria at the same rate that they breed. The population dynamics in a chemostat are profoundly different than in serial cultures; you can look it up if you want to, but as an example it would be impossible to have semi-stable subpopulations as have been seen in the LTEE. Chemostats are also much more expensive and labor-intensive than serial cultures. They are a poor model system for following evolutionary changes long-term.

3) Nutrient cycling, in which some essential substance is present in a limited amount that will be exhausted by the time the next transfer is made. In theory you could limit anything; iron, carbon, nitrogen, oxygen, etc. In the LTEE, it is convenient to limit the amount of glucose. This has several effects:

a) As you noted, it limits the total number of bacteria that will grow in the medium in a predictable way. Enough glucose can be added to allow for an arbitrary final population density. Thus the effect of genetic drift can be controlled somewhat, by fixing the percentage of bacteria transferred at an arbitrary number: 10%, 1%, 0.1%, whatever. 1% is a nice round number and strikes a reasonable balance between discarding too much of your genetic diversity and keeping the population too static by not allowing enough cell division. It's a compromise.

b) More significantly, it creates a changing environment for the bacteria. The glucose level falls over the span of several generations, then it is exhausted for a long period. Because this environment is harsher than that of 1)or 2) above, random mutations experience greater selective pressure, both for good and ill. If this is not clear to you, please say so and I can go into greater detail.
For the purposes of the LTEE, this heightened selection pressure is crucial.

c) There are other effects that are basically trivial - it is cheaper in resources, it allows for contamination by citrate-using bacteria to be spotted easily.

If you believe that glucose cycling favors the development of Cit+ over all other possible pathways, please explain why you hold this belief. Before you mention that the trait has been seen once before, and is therefore 'likely' in some nebulous way, I would turn your attention to the many, many, many strains of E. coli that produce toxins.

I get the general impression that many people -- maybe even most people -- think that Cit+ evolution was the main if not the sole goal of the experiment and that the purpose of the glucose cycling was to favor Cit+ evolution.

If that were the case, then many people -- maybe even most people -- would be wrong. Is that so terribly surprising?

Thursday, July 10, 2008 3:14:00 PM  
Anonymous brossa said...

I didn't say that I didn't read it at all -- I said I skimmed it. There are a lot of little details that I don't need to know.

These things matter because they are important in understanding the experiment, bozo.

Do you see the incongruity of these two statements?

Thursday, July 10, 2008 3:21:00 PM  
Blogger Erin said...

"No one has cited pages of the Cit+ evolution paper that answer my questions, dunghill. If you continue to tell lies like that, your comments will be deleted."

Oooh, a threat to ignore the "rules" of your blog. I'm so scared!


In other news:

Wednesday, July 02, 2008, Phae said in reply to post "A reason for glucose-cycling in Lenski's E. coli experiment,"

"p7905 of the newest paper notes methodology, and directs those interested in the details of the overall experiment to the first paper, as I have said to you. Note the reference to the footnote about it, after the first sentence in ''Materials and Methods.'' Following the reference to the '91 paper now on JSTOR, which should have been incredibly easy for you since I have told you where it was previously and linked you there (not that you were willing to read it) - even had it not been in the quite obvious publication list to which I also linked you - we come to the '91 paper, which immediately summarizes the whole of the experiment's intent. On page 1316 is a very clear summary of the intent of the experiment, expressed "metaphorically" rather than technically for the convenience of idiots (hint: you). Notice that citrate is not mentioned."

Glossary:
Methodology: the analysis of the principles or procedures of inquiry in a particular field (aka, "why they did what they did". . .including glucose cycling)

Intent: something that one hopes or intends to accomplish -- See GOAL

Definitions pulled from M-W.com

(Glossary included for such people as find ad hominem attacks to be a convincing mode of argument despite having threatened to delete comments that employ that very same mode of argument)

Thursday, July 10, 2008 5:49:00 PM  
Blogger Larry Fafarman said...

brossa said...

>>>>>>I didn't say that I didn't read it at all -- I said I skimmed it. There are a lot of little details that I don't need to know.

These things matter because they are important in understanding the experiment, bozo.


Do you see the incongruity of these two statements? <<<<<<

Sheeesh -- what is the matter with you? I was talking about two different things -- my first statement was about the paper, my second statement was about the questions that I asked Zachary Blount.

Thursday, July 10, 2008 11:08:00 PM  
Blogger Larry Fafarman said...

>>>>>Oooh, a threat to ignore the "rules" of your blog. I'm so scared! <<<<<

You better be scared.

>>>>>Wednesday, July 02, 2008, Phae said in reply to post "A reason for glucose-cycling in Lenski's E. coli experiment,"

"p7905 of the newest paper notes methodology, and directs those interested in the details of the overall experiment to the first paper <<<<<

I'm talking about what was in the Cit+ evolution paper -- that was not in the Cit+ evolution paper. Anyway, even if the Cit+ evolution paper answered my questions, it would have been courteous of Blount to show me exactly where the questions were answered, or quote the answers, or repeat the answers, etc.. I have to keep repeating myself over and over again, so why shouldn't Blount repeat himself?

Anyway, you are only proving that the Cit+ evolution paper did not answer my questions. So why don't you just shut up already, damn you, because you are not proving anything.

Thursday, July 10, 2008 11:17:00 PM  
Blogger Phae said...

You better be scared.

Hahah yeah, she's shaking in her boots you'll start censoring people and give us even better evidence of your hypocrisy! And of course, I have all responses saved since they're all emailed to me, so it's not like anything would be lost.

I'm talking about what was in the Cit+ evolution paper -- that was not in the Cit+ evolution paper.

The paper directed you to all of that for general background. It would be foolish of them to include so much general information in each of the papers published about this experiment (of which there have been more than a dozen). I understand that reading is hard for you, but I did take you by the hand to show you the really easy way you could have found the answers to your questions, dancing monkey.

Anyway, even if the Cit+ evolution paper answered my questions, it would have been courteous of Blount to show me exactly where the questions were answered, or quote the answers, or repeat the answers, etc.. I have to keep repeating myself over and over again, so why shouldn't Blount repeat himself?

It might have been courteous, but he happens to be a well-respected scientist and you are an ignorant moron on the internet. Surprisingly, I doubt anyone holds it against him that he didn't cater to your ignorance when you wouldn't even read the paper you were trying to criticize.

Anyway, you are only proving that the Cit+ evolution paper did not answer my questions. So why don't you just shut up already, damn you, because you are not proving anything.

"You're just making yourself look worse and dumb and making me look right so why don't you be quiet and SO WHY DON'T YOU PEOPLE STOP TALKING OH JESUS WHY YES I CAN'T READ IS THAT REALLY SO BAD?!"

Thursday, July 10, 2008 11:24:00 PM  
Blogger Larry Fafarman said...

brossa said (Thursday, July 10, 2008 3:14:00 PM) --
>>>>> We've been over the issue of 'goal' before, and it doesn't look like there will be any resolution of that issue, in part because you seem to be using a different definition of 'goal' than most other people. <<<<<

OK, below what level of probability does a hoped-for result or a wished-for result cease to be a goal -- 100%? 90%? 80%? 50%? Please give me a number.

>>>>> For the sake of argument, let's accept your suspicion that the development of a Cit+ strain was a main goal of the experiment in the first place.<<<<<<

I never said it was a "main" goal. Being an improbable event, it should probably be called a secondary goal (if there were primary goals) or a longshot goal.

Even if only a minority of people interpret the way "goal" in the way I do, that could be a hell of a lot of people who are going to be deceived when they are flatly told that something was not a goal at all when it was a secondary goal or a longshot goal.

As I said, in searches for the Lost Dutchman Mine, the Fountain of Youth, the Holy Grail, the ivory-billed woodpecker, etc., finding them are "goals."

>>>>> Furthermore, suppose that this goal has been a secret since 1988, which is why it is not mentioned in any of the papers published on the LTEE so far. <<<<<

What? It is mentioned in the latest paper on the LTEE -- in fact, it is the subject of the latest paper.

>>>>> I'm asking rhetorical questions, but I'm genuinely interested in your responses here. <<<<<

Dammit, I'm asking questions because I want to understand the experiment as well as possible.

>>>>>> The glucose level falls over the span of several generations, then it is exhausted for a long period. Because this environment is harsher than that of 1)or 2) above, random mutations experience greater selective pressure, both for good and ill. <<<<<<

What do you mean by a "harsher environment"? Does a few hours of glucose starvation put significant stress on the bacteria? Does this stress tend to cause mutations? We know that some kinds of stress, such as ionizing radiation and irritating chemicals, tend to cause mutations. And the most obvious "selective pressure" of glucose cycling is the favoring of Cit+ bacteria.

>>>>> If you believe that glucose cycling favors the development of Cit+ over all other possible pathways, please explain why you hold this belief. <<<<<<

I don't know what you mean by "all other possible pathways" -- do you mean other pathways for Cit+ evolution, or pathways for other kinds of evolution? Anyway, it is obvious that glucose cycling strongly favors Cit+ evolution.

>>>>>> Before you mention that the trait has been seen once before, and is therefore 'likely' in some nebulous way <<<<<<

I didn't say "likely" -- but Cit+ evolution was shown to be a possibility.

>>>>>I would turn your attention to the many, many, many strains of E. coli that produce toxins. <<<<<

So what does that have to do with Cit+ evolution?


>>>>>I get the general impression that many people -- maybe even most people -- think that Cit+ evolution was the main if not the sole goal of the experiment and that the purpose of the glucose cycling was to favor Cit+ evolution.

If that were the case, then many people -- maybe even most people -- would be wrong. <<<<<<

That is a reason why it is so important for the experimenters to give straight answers to questions about the experiment -- so people can learn the truth about the experiment.

Friday, July 11, 2008 12:01:00 AM  
Blogger Larry Fafarman said...

As the saying goes, don't feed the trolls. Phae and Erin are just trolls who post nothing but crap here.

Friday, July 11, 2008 12:06:00 AM  
Blogger Phae said...

As the saying goes, don't feed the trolls. Phae and Erin are just trolls who post nothing but crap here.

Aha, the difficult-to-decipher Larrycode! I will put it through my hash converter... yes, here we go. That actually says, "Oh shit, they presented facts again, I better run away." A little more complex than the Caesar cipher, but it works to conceal incredible cowardice for a time.

Friday, July 11, 2008 12:43:00 AM  
Anonymous brossa said...

As I said, in searches for the Lost Dutchman Mine, the Fountain of Youth, the Holy Grail, the ivory-billed woodpecker, etc., finding them are "goals.

If I tell people that I am going to catalog all the holes in the state of Arizona, because I have a theory about how holes form, and I think that maybe holes that form in different places will end up looking alike, or maybe there will turn out to be 'classes' of holes that are very distinct, and maybe if I find a hole and fill it in it will eventually come to be a hole similar to the one I filled in, and holy crap I just fell into a hole and it says "Lost Dutchman Mine" in here!

Or: I tell people that I am setting up a billion monkeys with a billion typewriters and I am going to observe what they type. I will monitor their writing and apply statistical techniques to see whether it changes over time. I will look for patterns in the writing - maybe the monkeys that are related to each other will type in ways that are distinct - and lookit this this monkey just typed the seventh chapter of Moby Dick!

I tell you what: when you use the word 'goal' I will mentally substitute 'possible outcome', and you do the opposite.


What? It is mentioned in the latest paper on the LTEE -- in fact, it is the subject of the latest paper.


You are correct. Cit+ evolution is mentioned in the last paper, after they detected it. Is it mentioned in the forty-one papers previously published on the LTEE? (hint: no)

What do you mean by a "harsher environment"? Does a few hours of glucose starvation put significant stress on the bacteria? Does this stress tend to cause mutations? We know that some kinds of stress, such as ionizing radiation and irritating chemicals, tend to cause mutations. And the most obvious "selective pressure" of glucose cycling is the favoring of Cit+ bacteria.

The glucose starvation does not inherently cause more mutations (a sort-of-exception will be mentioned later). It accentuates the differences in adaptation of the mutations that are already present in the population.

Take three people who can reproduce asexually: one is 'normal', one has a bad clubfoot, and one has Lance Armstrong's stamina. If you put them on an island, up to their necks in food, none of them will starve, and they will all reproduce and pass on their characteristics. On an island with less food, however, when they have to work to find it, the clubfoot will provide a significant disadvantage and that person may not find enough food to reproduce. With even less food on the island, even the 'normal' person can be outcompeted by Lance.
The limited food didn't cause Lance, it merely brought out the difference between Lance and the other two.

Here's the sort-of-exception: some of the mutations that can arise randomly occur in the genes that code for the enzymes responsible for DNA repair. This can lead to more error-prone DNA repair and replication, such that the affected strains are 'hypermutators'. The hypermutator trait can itself be selected for or against - in a stable environment, to which an organism is already well-adapted, it can be a disadvantage because fitness will be decreased more often than it is increased. In a marginal environment, however, you 'want' to shuffle through all possible mutations quickly, and mutations will be more likely to be favorable than in the 'perfect' environment. Note that the difference may be small, but it will be significant - if one in one billion mutations are beneficial in an ideal environment, but one in one million mutations are benefical in a marginal environment, then hypermutation will be selected for in the harsh environment. It won't be caused by the harsh environment, just selected for.

I don't know what you mean by "all other possible pathways" -- do you mean other pathways for Cit+ evolution, or pathways for other kinds of evolution? Anyway, it is obvious that glucose cycling strongly favors Cit+ evolution.

I mean other possible adaptations. Let's use the island example from above, with the three people. When they run out of food, they hibernate until a rescue chopper comes. But now the 'normal' guy has a knife. He stabs Lance and the guy with the clubfoot, and now he's the only one left on the island, and when the rescue chopper comes the island is populated by knife-wielders. Lance's stamina doesn't seem like such a great advantage anymore. Now replay things, only now the guy with the clubfoot has a taste for human flesh. He bides his time until the Lances and normals hibernate, then he sneaks up on them and eats them while they're dormant. Now the stamina and the weapon are both outcompeted. Does the starvation inherently favor one pathway over the other? You could change 'Lance' into a guy who can eat some other limited thing, like grass, but he can still be outcompeted by a guy with a knife or a ghoul.

I didn't say "likely" -- but Cit+ evolution was shown to be a possibility.

So what does that have to do with Cit+ evolution?

Cit+ evolution was shown to be a possibility, and so was toxin evolution. Many times over. So why would Cit+ be more likely or favored than the other? Why not state that toxin formation was a goal of the experiment, rather than Cit+? Why not say that glucose cycling strongly favors toxin?

Friday, July 11, 2008 8:14:00 AM  
Blogger Erin said...

"Does a few hours of glucose starvation put significant stress on the bacteria?"

Uhh, yeah, a few generations of starvation's gonna stress just about anything.

"Does this stress tend to cause mutations?"

Irrelevant. Mutations happen and stress selects between them.

Friday, July 11, 2008 9:03:00 AM  
Blogger Larry Fafarman said...

Brossa,

You still have not answered my question -- what level of probability distinguishes goals from non-goals? 90%? 80%? 50%? I want a number.

>>>>> I tell you what: when you use the word 'goal' I will mentally substitute 'possible outcome', and you do the opposite. <<<<<<

OK, so when Zachary Blount says that Cit+ evolution was "not a goal," you can mentally substitute "not a possible outcome" for "not a goal." BTW, a goal is not only a possible (or sometimes nearly impossible) outcome but is also a desirable outcome -- and usually some effort is involved in pursuing the goal (though as I said, Cit+ evolution could have been a goal in the experiment even if nothing specific was done to favor it -- merely conducting the experiment was an effort).

>>>>>> You are correct. Cit+ evolution is mentioned in the last paper, after they detected it. Is it mentioned in the forty-one papers previously published on the LTEE? (hint: no) <<<<<<

Are you sure? There is a fairly good chance that it was mentioned in the first papers or in the research proposal (if there was one).

>>>>> The glucose starvation does not inherently cause more mutations <<<<<

One commenter (Phae?) said that it causes more mutations -- something about production of Polyamerase IV. And a commenter called the glucose starvation an "environmental stressor" (whatever that is). Anyway, why can't Zachary Blount answer these questions. He ought to be glad that people have enough interest in the study to ask questions about it.

Saturday, July 12, 2008 1:25:00 AM  
Blogger Phae said...

Anyway, why can't Zachary Blount answer these questions. He ought to be glad that people have enough interest in the study to ask questions about it.

"Why doesn't this busy scientists spend more time on the internet answering my questions?! How rude of him! No, of course I won't read the study I am criticizing."

Saturday, July 12, 2008 1:37:00 AM  
Anonymous brossa said...

You still have not answered my question -- what level of probability distinguishes goals from non-goals? 90%? 80%? 50%? I want a number.

Probability does not distinguish goals from non-goals. The goal of the SETI program is to detect a radio signal from space that indicates the presence of alien intelligence. The probability of detecting such a signal is low. Yet it remains their goal, because, among other things, they say that it is their goal, and all of their actions appear directed toward detecting such a signal as opposed to surveying the cosmic microwave background radiation.

If I asked you what speed defines a car race, how would you reply?

OK, so when Zachary Blount says that Cit+ evolution was "not a goal," you can mentally substitute "not a possible outcome" for "not a goal."

No, I said when you said 'goal', I'd substitute 'possible outcome'. I don't have to do that with Blount, because we seem to have the same definition of 'goal'.

Are you sure? There is a fairly good chance that it was mentioned in the first papers or in the research proposal (if there was one).

This one may shock you, but I've actually read the first half-dozen papers. For comprehension. And I'm working through the others as time allows.
Citrate evolution is not mentioned until the last paper. I invite you to cite evidence to the contrary.

One commenter (Phae?) said that it causes more mutations -- something about production of Polyamerase IV.

I already addressed this - one type of mutation results in more error-prone DNA replication, which increases the overall mutation rate. This initial mutation can be selected for in an environment to which the organism is poorly adapted. The mutation that causes the hypermutator phenotype is not caused by the marginal environment, it is selected by it. A number of Lenski's E. coli lines have independently become hypermutators.

And a commenter called the glucose starvation an "environmental stressor" (whatever that is)

Yes. It is a factor in the environment which stresses the organism. Fitness is determined by the organism's reproductive success in the face of stress.

Anyway, why can't Zachary Blount answer these questions. He ought to be glad that people have enough interest in the study to ask questions about it.

Why won't Bill Gates answer my questions about what how a computer works? He should be flattered by the attention that I'm offering him.

Saturday, July 12, 2008 6:47:00 AM  
Blogger Larry Fafarman said...

Brossa said,
>>>>>>> Yet it remains their goal, because, among other things, they say that it is their goal, and all of their actions appear directed toward detecting such a signal as opposed to surveying the cosmic microwave background radiation. <<<<<<<<

You are really painting yourself into a corner. Now you are saying that something is not a goal unless all actions are directed towards achieving it. There are such things as secondary goals and incidental goals.

>>>>>>No, I said when you said 'goal', I'd substitute 'possible outcome'. I don't have to do that with Blount, because we seem to have the same definition of 'goal'. <<<<<<

You and Blount are not the only ones who need to understand what the word "goal" means. When you use the word "goal," you should be darn sure that everyone knows what you are talking about.

>>>>>> This one may shock you, but I've actually read the first half-dozen papers. For comprehension. And I'm working through the others as time allows. <<<<<<

I don't have the time to do that kind of stuff.

>>>>>>> Citrate evolution is not mentioned until the last paper. <<<<<<<

Well, was there a research proposal? Does that say anything about Cit+ evolution?

On Carl Zimmer's blog, Blount said that it was his understanding that Cit+ evolution was a hoped-for or wished-for result of the experiment. To me, that means that Cit+ evolution was a "goal." It might have been one of many goals, a secondary goal, an incidental goal, a longshot goal, or whatever, but it was still a goal. Then Blount created confusion by saying that Cit+ evolution was not a goal. Actually, I was not the one who introduced the question of whether Cit+ evolution was a goal of the experiment -- I just assumed like a lot of people that it was a goal.

>>>>>>One commenter (Phae?) said that it causes more mutations -- something about production of Polyamerase IV.

I already addressed this - one type of mutation results in more error-prone DNA replication, which increases the overall mutation rate. This initial mutation can be selected for in an environment to which the organism is poorly adapted. The mutation that causes the hypermutator phenotype is not caused by the marginal environment, it is selected by it. (emphasis added)<<<<<<<<<

I asked whether the glucose starvation tended to increase the number of mutations. The answer is apparently no.

>>>>>>And a commenter called the glucose starvation an "environmental stressor" (whatever that is)

Yes. It is a factor in the environment which stresses the organism. Fitness is determined by the organism's reproductive success in the face of stress. <<<<<<<

That statement is too vague -- it does not distinguish between glucose starvation's effect on mutations and its effect on natural selection. Anyway, you appeared to state above that glucose starvation does not tend to increase the number of mutations.

>>>>>> Why won't Bill Gates answer my questions about what how a computer works? <<<<<<

Not comparable. I asked Blount very simple questions on a comment thread where he was routinely answering the questions of other commenters.

Monday, July 14, 2008 12:06:00 PM  
Anonymous brossa said...

Well, was there a research proposal? Does that say anything about Cit+ evolution?

For what it's worth, the abstract of the application for the first grant to fund the LTEE does not mention cit+ evolution. The full text of the application is not online. I say 'for what it's worth' because of course I don't have access to Lenski's diary, or personal communications, or thoughts so secret that he dared not commit them to paper. Suffice it to say that the papers on the LTEE which address the carbon sources in the culture medium state explicitly that the only carbon source in the medium was glucose. They weren't hiding the presence of the citrate, because they name the medium as DM, which has a standardized formula that includes citrate. It was simply unthinkable that the E. coli would be able to use the citrate as a carbon source, in the same way that nobody thinks of wood as being a food source for humans.

As a hypothetical, what if Blount looked you in the eye and said 'I was wrong when I said that Lenski thought that the E. coli might become Cit+. Nobody thought that that would happen until it actually did.'?

That statement is too vague -- it does not distinguish between glucose starvation's effect on mutations and its effect on natural selection. Anyway, you appeared to state above that glucose starvation does not tend to increase the number of mutations.

I guess that you really do need this spelled out e-x-p-l-i-c-i-t-l-y: glucose starvation has NO EFFECT on mutation rates. It does not induce them. It does not cause them. It does not promote them. It does not encourage them. It does not favor mutation. Mutations take place in bacteria that have insufficient, adequate, and superabundant
glucose, and at the same rates.

Glucose starvation accentuates the adaptive differences between the mutants that already exist in the population. The mutants already have inherent differences in fitness. Those differences can be insignificant under conditions of plenty but large under stressful conditions. Going back to the island example: a guy with a clubfoot and a normal guy can both get plenty to eat and reproduce if they are up to their necks in food. If the food is scarce enough that they can quickly eat everything that is within reach, they will have to start walking around to find more, at which point the clubfoot starts to be a disadvantage.

There is a class of mutation that does increase the overall mutation rate, by decreasing the fidelity of DNA repair and replication. This class of mutation can increase the mutation rate in the rest of the genome by many hundred percent. In some environments, this class of mutation tends to be selected against, albeit slowly. In stressful environments, the hypermutators can be selected for through a hitchhiking process. So 4 out of 12 of Lenski's strains have become hypermutators; not because glucose starvation induces mutation, but because the starvation conditions indirectly favor the hypermutators. Lenski's paper #147 addresses the mechanism in detail.

Monday, July 14, 2008 10:37:00 PM  
Blogger Larry Fafarman said...

Brossa said,

>>>>>>> For what it's worth, the abstract of the application for the first grant to fund the LTEE does not mention cit+ evolution. The full text of the application is not online. <<<<<<

How do you know so much about the experiment, if I may ask? Are you involved with it in any way?

>>>>>> It was simply unthinkable that the E. coli would be able to use the citrate as a carbon source, in the same way that nobody thinks of wood as being a food source for humans. <<<<<<

"Unthinkable"? Here is a quote from Zachary Blount on Carl Zimmer's old "The Loom" blog --

When Dr. Lenski started, he figured the citrate would provide an opportunity that the populations might or might not figure out a way to exploit, thereby presenting a potential point of divergence between the populations (this is my understanding - I will need to check with him to make certain I understand this properly). However, and unsurprisingly given that there has been only one report of a spontaneous Cit+ mutant of E. coli in the past century (Hall, B. 1982. Chromosomal mutation for citrate utilization by Escherichia coli K-12. Journal of Bacteriology, 151: 269 � 273.), none did (which wasn't a problem -- despite some misunderstanding on the internet, the intent of the experiment was never to evolve a Cit+ E. coli variant)...until, after 31,000 generations of evolution and fourteen years of the experiment, one population we call Ara-3 figured it out.

In the above quote, Blount is already starting to make ambiguous use of the word "intent."

I thought that Cit+ evolution might have been a "goal" (a secondary goal or longshot goal or whatever) because it had been observed once before. And I never got an answer to my question of whether favoring Cit+ evolution was one of the purposes of the glucose cycling -- and I got the impression that a lot of people thought that it was a purpose of the glucose cycling.

Also, Blount further confused the issue by his following statement in another comment, where he said that Cit+ evolution was "not a goal":

The evolution of a citrate-utilizing variant E. coli was seen from the beginning as a possible occurrence, and one that would be pretty neat should it occur (and indeed as it has proven to be now that it has happened), but not a goal.

>>>>>>> I guess that you really do need this spelled out e-x-p-l-i-c-i-t-l-y: glucose starvation has NO EFFECT on mutation rates. It does not induce them. It does not cause them. It does not promote them. It does not encourage them. It does not favor mutation. Mutations take place in bacteria that have insufficient, adequate, and superabundant glucose, and at the same rates. <<<<<<<<

Thank you. That is what I want to know.

I need to have things spelled out explicitly because -- like the title of the blog says -- "I'm from Missouri," in spirit if not physically.

Monday, July 14, 2008 11:45:00 PM  
Anonymous W. Kevin Vicklund said...

>>>How do you know so much about the experiment, if I may ask? Are you involved with it in any way?<<<

Probably did the same thing I did a couple of weeks ago. Read the paper, got to the part at the end called "Acknowledgements," saw who was providing the funding and the grant number, looked up the website for the granting agency, and searched for information on the grant (I ended up doing a search on his name). Lenski received numerous continuation grants from that agency for the project. The grant info includes the abstract for the proposal. None of the abstracts had any mention of Cit+ evolution. Nor did Lenski cite the previous Cit+ paper in any of his papers until the most recent one - there is no evidence that Lenski even knew of the earlier experiment. Also, Lenski was using glucose-limited serial transfer in experiments prior to the start of the LTEE - in fact, one of these previous experiments was how he got the 12 ancestral lines. Couple that with the fact that glucose-limited serial transfer had been used in expiriments for 40 years prior to the start of the LTEE, and there is ample reason to believe that there are other purposes to glucose-limited serial transfer than Cit+ evolution.

P.S. the earlier experiment is available online, but my computer crashed trying to open it (I had a few too many instances of Adobe open - it was my machine that was the problem, not the paper)

Tuesday, July 15, 2008 6:59:00 AM  
Anonymous brossa said...

How do you know so much about the experiment, if I may ask? Are you involved with it in any way?

I am not involved with Lenski's research in any way. His published papers, and an undergraduate degree in biochemistry and microbiology have been my only sources of information in this matter. The papers reference the funding grants, which can be researched online with a trivial Google search. The papers are online and free at Lenski's site. Papers #145 and #147 are particularly good overviews of the goals and procedures of the LTEE, as you have been told before.

Tuesday, July 15, 2008 9:09:00 AM  

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