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.

Saturday, June 28, 2008

Cit+ E. coli evolution ignored in Lenski website, NY Times article!

The evolution of Cit+ (citrate-eating) E. coli bacteria in Richard Lenski et al.'s research has been ballyhooed as the greatest thing since sliced bread. One would think that this Cit+ evolution would be treated as a tour de force, the shining centerpiece of the research of Lenski and his colleagues. However, this Cit+ evolution is given no special attention on Lenski's lab's website, and a fairly recent (June 2007) New York Times article on E. coli research -- including Lenski et al.'s research -- does not even mention the Cit+ evolution at all! At the time of the NY Times article, Lenski and his colleagues were aware of the Cit+ evolution and were probably also aware of Cit+ evolution's "historical contingency" (only descendants of unfrozen populations of 20 K generations or later repeated Cit+ evolution). How could this Cit+ evolution be such an earth-shaking event if it is largely ignored on Lenski's website and completely ignored in the NY Times article? The Cit+ E. coli evolution in Lenski's lab was certainly a noteworthy event -- according to researcher Zachary Blount, this evolution was observed only once before.

On this webpage of Lenski's lab's website, titled "Welcome to the E. coli Long-term Experimental Evolution Project Site," several areas of investigation are mentioned but the evolution of citrate-eating bacteria is not mentioned at all:

Summary data from the long-term evolution experiment including relative fitness, cell size, colony morphology (photographic), and molecular genetics.

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BTW, the last time I saw that term "experimental evolution" was in the name of the Station for Experimental Evolution, which merged with the Eugenics Record Office in 1920 to form the Carnegie Institution's Dept. of Genetics. The Eugenics Record Office helped inspire the Nazis' eugenics programs, so maybe Lenski and his colleagues are Nazis.

Also, another webpage on Lenski's lab's website lists "evolution of citrate utilization" at the bottom of the page.

Also, the NY Times article mentions kinds of evolution in Lenski's lab that were far less significant than the Cit+ evolution but does not mention the Cit+ evolution:

. . . . . 12 lines of bacteria have been reproducing since 1989, when the biologist Richard E. Lenski bred them from a single E. coli. “I originally thought it might go a couple thousand generations, but it’s kept going and stayed interesting,” Dr. Lenski said. He is up to 40,000 generations now, and counting.

In that time, the bacteria have changed significantly. For one thing, they are bigger — twice as big on average as their common ancestor. They are also far better at reproducing in these flasks, dividing 70 percent faster than their ancestor. These changes have emerged through spontaneous mutations and natural selection, and Dr. Lenski and his colleagues have been able to watch them unfold.

Maybe Zachary Blount was right when he said that Cit+ evolution was not a "goal" of Lenski's E. coli experiment! LOL The Cit+ evolution is certainly not treated as a particularly important result by Lenski's lab's website and is not treated as even worth mentioning in the NY Times article.
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20 Comments:

Anonymous 'Nonymous said...

"One would think that this Cit+ evolution would be treated as a tour de force, the shining centerpiece of the research of Lenski and his colleagues."

It is a shiny pebble that they paused briefly to admire. But they are after bigger fish.

"... according to researcher Zachary Blount, this evolution was observed only once before."

First time was the charm -- showed the possibility.

You should note, evolution is not a "Gee whiz!" idea for these researchers; it's part of their basic framework:

"They evolved? So?"

Saturday, June 28, 2008 11:01:00 AM  
Blogger Phae said...

However, this Cit+ evolution is given no special attention on Lenski's lab's website

See that special link on the left side, leading to the project webpage for the experiment? Notice how it's the only project linked like that?

What did you expect, a brass band?

and a fairly recent (June 2007) New York Times article on E. coli research -- including Lenski et al.'s research -- does not even mention the Cit+ evolution at all!

First of all, note that dozens of papers have been published on this topic. These bacteria have yielded a huge amount of results, and the cit+ result is only the latest and most striking example. Second of all, you absolute fucking moron, that article is from 2007, before the cit+ paper. Do you think Zimmer, the reporter, was going to magically predict something before it happened and write about it?

BTW, the last time I saw that term "experimental evolution" was in the name of the Station for Experimental Evolution, which merged with the Eugenics Record Office in 1920 to form the Carnegie Institution's Dept. of Genetics. The Eugenics Record Office helped inspire the Nazis' eugenics programs, so maybe Lenski and his colleagues are Nazis.

This is the stupidest thing I ever heard, and it's compounded by the fact that even your stupidity is wrong. It says "evolution experiment," not "experimental evolution." Even your retarded linkage of concepts, which is entirely without validity, doesn't quite manage to work.

Also, another webpage on Lenski's lab's website lists "evolution of citrate utilization" at the bottom of the page.

That's because it's the most recent result. It's a page of scientific data, not a PR website. Have I called you a gibbering moron lately? Yes, no? Well, let's toss that in for good measure.

Also, the NY Times article mentions kinds of evolution in Lenski's lab that were far less significant than the Cit+ evolution but does not mention the Cit+ evolution

It also didn't mention how in 2012, the demon monkeys will take over the planet. That is because the article could not see the future.

Maybe Zachary Blount was right when he said that Cit+ evolution was not a "goal" of Lenski's E. coli experiment!

That might well be true. If you had read the first paper they published instead of heading to the hills with your pickaxe and binky, you would have been able to see that it was not a stated intent. Lenski appears to have simply intended to observe the adaptations that would occur under the conditions he inflicted. Knowing that evolutionary theory is very well-supported, he was able to surmise that the bacteria would indeed evolve in some manner... as they did in very short order. Increasingly, they adapted to their situation. Eventually, after twenty years, they even evolved the ability to consume citrase. If they had instead evolved the ability to consume one of the other substances in the DM0 medium, it would have been equally important and an amazing result.

Listen, Yar, you are seriously out of your depth. Get a twelve-year-old to explain how the passage of times works, or else call the Times and also demand why they didn't report on the 9/11 attacks in their article about the Towers in 2000.

Saturday, June 28, 2008 12:45:00 PM  
Anonymous Darwin B. Leaver said...

My worship of Darwin is dumb?
But listen: I've totally come
To the grand conclusion
That all my confusion
Is caused by that Larry!(Or rum?)

(My friend Leaver complains that he can't understand Larry's points, and is becoming confused. Leaver's wife points out that he can't understand much anyway, since he is fond of Inherit the Wind, the grotesquely distorted propaganda-movie. Both of us hope that his thought processes may improve, if we can get him into AA.--Jim Sherwood.)

Saturday, June 28, 2008 2:50:00 PM  
Anonymous 'Nonymous said...

(June 2007) (!)

Yikes! I overlooked that; sorry. I might have to modify my earlier comment.

Larry often provides worthwhile links and provokes informative commentary, but accompanied by such a storm of disinformation and misinterpretation that it's tough to avoid going off the rails oneself. Hazard zone.

Saturday, June 28, 2008 3:52:00 PM  
Anonymous 'Nonymous said...

"After bigger fish" is still true I'm sure, but they're entitled to savor their achievement.

Saturday, June 28, 2008 3:55:00 PM  
Anonymous 'Nonymous said...

What did you expect, a brass band?

Probably a movie like Expelled -- you know, deep research? ;-}

Saturday, June 28, 2008 4:00:00 PM  
Blogger Larry Fafarman said...

Phae,
Well, I said that I was not going to respond to you anymore, dunghill, but this is a whole new topic.

>>>>>>See that special link on the left side, leading to the project webpage for the experiment? Notice how it's the only project linked like that? <<<<<<

See the list of categories of summary data on the project webpage that the homepage links to? Notice how the Cit+ bacteria category is the only category that is on the linked page "Summary data" but is not in the following list of summary data categories:

Summary data from the long-term evolution experiment including relative fitness, cell size, colony morphology (photographic), and molecular genetics.

A little oversight, maybe?

>>>>>> What did you expect, a brass band? <<<<<<

Maybe some triumphant recorded background music.

>>>>>> Second of all, you absolute fucking moron, that article is from 2007, before the cit+ paper. <<<<<

You abominable dunghill, the researchers have been aware of the Cit+ evolution for about 5-6 years (44 K generations minus 31.5 K generations at about 2.2 K generations per year). The Cit+ evolution was supposed to be a big event because it had been observed only once before. Also, the researchers were probably also aware of the Cit+ evolution's "historical contingency" (only descendants of unfrozen populations of 20 K generations or later repeated Cit+ evolution) -- another big result -- at the time of the NY Times article. Anyway, I guess I should have mentioned that the researchers knew or likely knew about these things at the time of the NY Times article.

>>>>> It says "evolution experiment," not "experimental evolution." <<<<<<

The link says "evolution experiment," but the big title on the webpage is "Welcome to the E. coli Long-term Experimental Evolution Project Site."

>>>>>>Also, another webpage on Lenski's lab's website lists "evolution of citrate utilization" at the bottom of the page.

That's because it's the most recent result. <<<<<<

There is no indication that this is a chronological list. IMO Cit+ evolution should be at the top of the list because it is really the most important result, especially in consideration of the discovery of historical contingency. But this is just a minor point.

>>>>> It also didn't mention how in 2012, the demon monkeys will take over the planet. That is because the article could not see the future. <<<<<<

See above.

>>>>>If you had read the first paper they published instead of heading to the hills with your pickaxe and binky, you would have been able to see that it was not a stated intent. <<<<<<

For starters, "intent" is not the right word, because "intent" means only what one plans to do but one cannot plan to have an uncertain result.

Zachary Blount, the lead author of the paper, was answering questions on Carl Zimmer's blog but did not give straight answers to my following simple, basic questions: (1) Was Cit+ evolution a goal of the experiment (I noted that a "goal" does not have to be a sure result and may even be an unlikely result), and (2) was favoring Cit+ evolution a purpose or one of the purposes of the glucose-cycling (alternating glucose feeding and glucose starvation) -- he gave no answer at all to this second question.

Saturday, June 28, 2008 6:20:00 PM  
Anonymous Voice in the Urbanness said...

"There is no hole so deep that Larry will not continue to dig."

Borrowed from Anonymous.

Saturday, June 28, 2008 7:22:00 PM  
Blogger Phae said...

Well, I said that I was not going to respond to you anymore, dunghill, but this is a whole new topic.

A whole new chance for you to humiliate yourself and reuse the same insults over and over. Bravo!

See the list of categories of summary data on the project webpage that the homepage links to? Notice how the Cit+ bacteria category is the only category that is on the linked page "Summary data" but is not in the following list of summary data categories:

Summary data from the long-term evolution experiment including relative fitness, cell size, colony morphology (photographic), and molecular genetics.

A little oversight, maybe?

Well, to me it looks like it has been specifically set aside as a matter of interest. But what are you saying? Are you trying to claim they're... hiding their results? The results they published a groundbreaking paper on and that have been in the news?

YOU BROKE THE CASE! Quick, call out the gendarmes!

You abominable dunghill, the researchers have been aware of the Cit+ evolution for about 5-6 years (44 K generations minus 31.5 K generations at about 2.2 K generations per year). The Cit+ evolution was supposed to be a big event because it had been observed only once before. Also, the researchers were probably also aware of the Cit+ evolution's "historical contingency" (only descendants of unfrozen populations of 20 K generations or later repeated Cit+ evolution) -- another big result -- at the time of the NY Times article. Anyway, I guess I should have mentioned that the researchers knew or likely knew about these things at the time of the NY Times article.

And they hadn't published their paper yet, you cretin. I'm honestly not sure how you think it works. Do you think that they go running down the hall and start shouting their results... before they're finished examining them and prepared a paper? You truly have no idea how this whole "science" thing works, do you? It's some sort of magnificent mystery to you.

Oh, but of course when you don't understand the answers to questions, it's the other guy's fault!

The link says "evolution experiment," but the big title on the webpage is "Welcome to the E. coli Long-term Experimental Evolution Project Site."

...my God. My God. You're right. They're... they're Nazis! WHY AREN'T THOSE GENDARMES THERE YET?!

There is no indication that this is a chronological list. IMO Cit+ evolution should be at the top of the list because it is really the most important result, especially in consideration of the discovery of historical contingency. But this is just a minor point.

Absolutely. No indication it is a chronological list. None at all. Except for the dates, listed on the publications page for the experiment in chronological order, you flaming assclown.

For starters, "intent" is not the right word, because "intent" means only what one plans to do but one cannot plan to have an uncertain result.

Yaaaaaar! Where be my dictionary and blankie! Look up my use of the word, yaaar, and see how I used it while being modified by "stated" and as the object of "was not," the negating and past form of "to be." Yar! It was not a stated intent is grammatically correct, except in the prospectin' hills! :D

Zachary Blount, the lead author of the paper, was answering questions on Carl Zimmer's blog but did not give straight answers to my following simple, basic questions: (1) Was Cit+ evolution a goal of the experiment (I noted that a "goal" does not have to be a sure result and may even be an unlikely result), and (2) was favoring Cit+ evolution a purpose or one of the purposes of the glucose-cycling (alternating glucose feeding and glucose starvation) -- he gave no answer at all to this second question.

I can answer those, just like he did, only in smaller words for you:
(1) Nope. Because like all literate people, I am capable of reading the first paper published about it with the stated intentions and noted that such was not among them. You should try that "reading" jazz sometime. It's a hip new fad.
(2) Nope. He appears to have used, again if you read the latest paper, Davis Minimal Broth (DM) zero and twenty-five, alternately, by way of implementing the cycle and without mention of citrase in the first paper.

Inasmuch as I can see, he told you to read the papers after mentioning the protocol. To any normal person, capable of that whole "reading" thing, that would have been sufficient. You're like a three-year-old who can't understand Einstein's accent and who therefore concludes relativity must be wrong.

See, I know that in the high science of holocaust denial, one of your apparent hobbies (at least from some of your previous posts), there are somewhat slacker requirements. You don't have to read or think, for example. Alas, in science things are different.

Saturday, June 28, 2008 7:24:00 PM  
Blogger Larry Fafarman said...

Phae driveled,
>>>>>>Well, to me it looks like it has been specifically set aside as a matter of interest. <<<<<<

WHAAAT? Ignoring something important is specifically setting it aside as a matter of interest? You lunatic.

>>>>>> And they hadn't published their paper yet <<<<<

So what? That doesn't mean they couldn't mention important results. Maybe they didn't want to mention the historical contingency because they were still analyzing it, but I can't see why they would not have reported the Cit+ evolution, an important event because it had been observed only once before.

>>>>> No indication it is a chronological list. None at all. Except for the dates, listed on the publications page for the experiment in chronological order <<<<<<

You dunghill, I wasn't talking about the publications page, I was talking about this page. I said that my observation that Cit+ evolution is listed last is a minor point -- I will drop it if it bothers you so much.

>>>>>>It was not a stated intent is grammatically correct <<<<<<

You stupid fathead, I didn't say it was grammatically incorrect, I only said that the usage of the word "intent" was inappropriate.

>>>>> I am capable of reading the first paper published about it with the stated intentions and noted that such was not among them. <<<<<

There is nothing wrong with asking about something that is not mentioned or discussed in the paper. And it is possible that an omission from the paper was an oversight. Anyway, why did Zachary Blount refer me to the paper when it did not answer my questions?

>>>>>He appears to have used, again if you read the latest paper, Davis Minimal Broth (DM) zero and twenty-five,<<<<<

Here is a description of the liquid medium:

The basic medium used for propagating the long-term lines is Davis minimal broth (Carlton and Brown 1981*) supplemented with glucose at a concentration of 25 mg per L, which we refer to as DM25. This medium supports a stationary-phase density of about 5 x 107 cells per ml for the founding strain of E. coli B.

The researchers deliberately supplied an insufficient amount of glucose so that it would be exhausted in a few hours of the 24-hour lives of the populations (the populations started growing in the morning and the glucose would be exhausted by the afternoon). I asked if the purpose or one of the purposes of the glucose-cycling (alternating glucose feeding and starvation) was to favor Cit+ evolution, and Zachary Blount did not answer. I asked if there were any other purposes of the glucose-cycling, and he did not answer. If he can't or won't answer simple, basic questions, he has no credibility.

Voice in the Urbanness barfed,
>>>>> "There is no hole so deep that Larry will not continue to dig." <<<<<

No matter what the circumstances, some trolls are going to clutter up this blog with asinine knee-jerk comments like that. Just shut up, damn you. Just shut up.

Saturday, June 28, 2008 11:55:00 PM  
Blogger Phae said...

WHAAAT? Ignoring something important is specifically setting it aside as a matter of interest? You lunatic.

Those damn expert biologists and their refusal to design their webpages the way you want! How dare they?! Clearly, not putting it together to your specifications must mean they are trying to hide their carefully presented results that they submitted to a world-renowned and world-famous journal. Those jerks!

So what? That doesn't mean they couldn't mention important results. Maybe they didn't want to mention the historical contingency because they were still analyzing it, but I can't see why they would not have reported the Cit+ evolution, an important event because it had been observed only once before.

That's why you think this is important? You really DON'T understand jack crap about this matter, do you?

This is important because Lenski has a single unbroken evidenciary chain tracing the evolution of a species. While a mutant has been observed, trained barimologists at the cutting edge of creation science can say that Jesus Done It. Now we have samples every five hundred generations and know when the mutation occurred and can study the exact evolutionary mechanism. It's not important because we now have E coli that can consume citrate, since it's not like the Exxon Valdez was spilling that everywhere and we needed a cleanup.

You are a rare species yourself, my friend, and your inability to understand basic things might get you classified as a new baramin!

As for the paper, what kind of moron spills their key results before they're sure of them and can get them to paper in a cogent form?

You dunghill, I wasn't talking about the publications page, I was talking about this page. I said that my observation that Cit+ evolution is listed last is a minor point -- I will drop it if it bothers you so much.

Indeed, like every other one of your points, it is unfounded. It's amazing you are trying to draw such conclusions based on their webpage design, but it is almost slanderously moronic to try to think they're... what, hiding the results?

You stupid fathead, I didn't say it was grammatically incorrect, I only said that the usage of the word "intent" was inappropriate.

ATTENTION! NEW INSULT DETECTED! "DUNGHILL" HAS EVOLVED UNDER CONTROLLED OBSERVATION INTO "FATHEAD." NEW SUBJECT DOES NOT UNDERSTAND DICTIONARIES.

There is nothing wrong with asking about something that is not mentioned or discussed in the paper. And it is possible that an omission from the paper was an oversight. Anyway, why did Zachary Blount refer me to the paper when it did not answer my questions?

He referred you to the previous literature, and appears to have had the faith that you would be able to figure out the answer to your questions. He was not familiar with your stunning inability to read things.

Here is a description of the liquid medium:

The researchers deliberately supplied an insufficient amount of glucose so that it would be exhausted in a few hours of the 24-hour lives of the populations (the populations started growing in the morning and the glucose would be exhausted by the afternoon). I asked if the purpose or one of the purposes of the glucose-cycling (alternating glucose feeding and starvation) was to favor Cit+ evolution, and Zachary Blount did not answer. I asked if there were any other purposes of the glucose-cycling, and he did not answer. If he can't or won't answer simple, basic questions, he has no credibility.

He did answer you. I also answered you. You could have even answered this yourself if you had done as he asked and read the previous literature on the subject.

Still, I am sorry to hear he has no credibility. The scientific community is going to be pretty upset that Blount didn't answer the questions of Some Random Internet Asshole sufficiently, when you were a lone voice for justice. Some looked at that exchange and saw a clear answer pointing you to the information, and a jackass who didn't realize the problem was him. Only you had the courage to sit there and cast aspersions. You brave, brave man.

No matter what the circumstances, some trolls are going to clutter up this blog with asinine knee-jerk comments like that. Just shut up, damn you. Just shut up.

If you go crazy, I call your pickaxe and binkie for my trophy case.

Sunday, June 29, 2008 12:21:00 AM  
Blogger Larry Fafarman said...

I don't need to answer, because it is obvious that I have won the debate.

I declare victory.

Sunday, June 29, 2008 2:19:00 AM  
Blogger Phae said...

This comment has been removed by the author.

Sunday, June 29, 2008 2:40:00 AM  
Blogger Phae said...

I don't need to answer, because it is obvious that I have won the debate.

I declare victory.


Typo in that last one.

I was going to write a bitingly sarcastic comment as a reply, but really there's nothing I can say that would highlight your striking lack of a grasp on reality and rhetoric - what more could I add to your perfect summation? You're like a rare bird, beautiful and free, that is also incredibly retarded and after ramming its head into a rock wall for an hour, declares that the wall has lost.

Yaaar!

Sunday, June 29, 2008 2:42:00 AM  
Anonymous Hector said...

Latest round:

Phae 1, Larry 0

Sunday, June 29, 2008 5:28:00 AM  
Anonymous Fever Swamps of ID said...

"barimologist" ... not found by Google. ?

Should say: Baraminologist.

Excerpt:

Polybaramin: A polybaramin is an ad hoc group of organisms where at least one of the members must not be a holobaramin and must be unrelated to any or all of the others. For example:

Humans, wolves and a duck are a polybaraminic group. This term is useful for describing such hodgepodge mixtures of creatures.


Ain't "science" wonderful? :-P

(BTW, Phae, what's the derivation of "Yar"? Is it a literary allusion? OK not to answer if you prefer.)

Sunday, June 29, 2008 10:22:00 AM  
Blogger Phae said...

You're right, I misspelled that particular pseudoscience, as well as "citrate" on the other post. Thanks :)

The "Yar" thing comes from the grizzled statement I picture him making, as some mighty combination of newborn infant, incapable of seeing the world ("didn't answer my questions"), and ancient prospector, withered and knobby ("high-falutin'"). If I was going to make a literary allusion about him, it would be to call him a patchwork Russian, for his maddened and thoughtless loyalty to whatever Michael Behe says.

Sunday, June 29, 2008 11:09:00 AM  
Blogger Larry Fafarman said...

Bart, you lousy dunghill, I decided not to publish your comment because it contains nothing but scoffing. Scoffing is sometimes OK if you are specific about what you are scoffing at and exactly why you are scoffing.

Monday, January 05, 2009 11:39:00 PM  
Blogger Lisa said...

Each year, there are approximately 73,000 cases of E. Coli. This number may seem low in comparison to other infections, but in knowing how preventable it is; it is a big number. After reading through your website, it is clear that your organization has the same passion for E. Coli awareness, as Disease.com. Here, at Disease.com (a non profit website dedicated to the preventions and treatments of diseases) we realize how important establishing awareness is. That is why we have worked with several elite non profit organizations in the past. If you could, please list us as a resource or host our social book mark button, it would be much appreciated. Together, we can turn 73,000 into 0.If you want more information on that please email me back with the subject line as your URL.

Monday, December 07, 2009 10:37:00 AM  
Blogger Larry Fafarman said...

Lisa,

The purpose of this blog article was to discuss evolution of E.coli bacteria, not to promote awareness of E.coli infections.

Thursday, December 24, 2009 5:39:00 PM  

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