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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.

Monday, June 16, 2008

Co-author of E. coli paper dodges questions

I previously discussed an experiment about microevolution of E. coli bacteria. A scientific paper about the experiment has attracted a lot of attention -- the Internet has several reviews and hundreds of comments about the paper (see the previous article for links to some reviews and comment threads). Darwinist roaders have been claiming that this paper is positive proof of Darwinism and the paper is being used to attack the ideas of ID-proponent Michael Behe.

A co-author of that paper, Zachary Blount, has been dodging some simple, basic questions I have asked about it.

I originally thought that the purpose of growing the E. coli bacteria with lots of citrate and an insufficient glucose supply was to try to promote the evolution of citrate-eating mutants by giving them an advantage over bacteria that can only eat glucose. Carl Zimmer wrote in a blog article titled "A New Step in Evolution":

The experiment was launched by MSU biologist Richard Lenski . . . Lenski started off with a single microbe. It divided a few times into identical clones, from which Lenski started 12 colonies. He kept each of these 12 lines in its own flask. Each day he and his colleagues provided the bacteria with a little glucose, which was gobbled up by the afternoon. The next morning, the scientists took a small sample from each flask and put it in a new one with fresh glucose. And on and on and on, for 20 years and running.

However, in the comment thread under the article, Zachary Blount has been making mutually contradictory statements about whether an original purpose of the experiment was to try to evolve citrate-eating (Cit+) E. coli bacteria:
.
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). (comment #115)

the intent of the experiment was never to evolve a Cit+ E. coli variant (comment #115)

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. (emphasis added) (comment #122)

I tried to get Blount to either poop or get off the can -- was evolving a Cit+ variant a goal (or a hoped-for result or a wished-for result or whatever) of the experiment or not? I also asked him to describe the purpose of the insufficient glucose supply if the purpose was not to try to promote evolution of a Cit+ variant. He dodged the questions, telling me to just read the literature. When the co-author of a scientific paper refuses to give direct, consistent answers to simple, basic questions about the paper, that paper has no credibility.
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71 Comments:

Anonymous Ric said...

He didn't dodge the question, moron. Read his response. It is clear that Assfly only wanted the data to deride the results. He never intended to use it or even read it.

Typical creationist tactic.

Wednesday, June 25, 2008 6:05:00 AM  
Blogger Larry Fafarman said...

Ric barfed,

>>>>>>> He didn't dodge the question, moron. Read his response. It is clear that Assfly only wanted the data to deride the results. He never intended to use it or even read it. <<<<<<<

WHAAAAT? This post has absolutely nothing to do with "Assfly's" (Andy Schlafly of Conservapedia) request for the raw data!

You should at least read a post before commenting.

Wednesday, June 25, 2008 9:00:00 AM  
Blogger The Inoculated Mind said...

This comment has been removed by a blog administrator.

Wednesday, June 25, 2008 12:24:00 PM  
Blogger Larry Fafarman said...

To The Inoculated Mind:

Your comment was censored because it contains gossip about my private affairs. You may repost your comment with the gossip deleted.

Wednesday, June 25, 2008 12:33:00 PM  
Blogger The Inoculated Mind said...

For the record: private affairs are not private when you make them public to try to get attention for yourself. You're funny. :)

Anyway, scientists often make discoveries that are not intended - being able to recognize these things when you see them is a big part of being a good scientist. So your question about whether or not the Cit+ mutant was planned or not is irrelevant. Nowhere in the email quote was the scientist you contacted dodging anything, either. So you are left with... what exactly is your argument then? Oh yeah, trash the science.

This paper has way more credibility than you.

Thursday, June 26, 2008 2:24:00 PM  
Anonymous Zmidponk said...

Not only did he give you a clear answer (it wasn't a goal, but it was seen as something that might happen), but him repeatedly telling you to read the literature was ALSO an answer - the literature answers your question. So why should Zachary Blount spend more time in answering a question that is not only answered in the literature on the project you're asking about, but has also been answered in a plain, straightforward manner by him already? His job is to DO science, not personally teach it to you.

Thursday, June 26, 2008 4:27:00 PM  
Anonymous NightFlare said...

Larry Fafarman, you're clueless, the question was anwered already in a clear and concise way, you would have to deny logic to think otherwise. Thank you and Godspeed!

Thursday, June 26, 2008 5:24:00 PM  
Anonymous jetmags73 said...

"When the co-author of a scientific paper refuses to give direct, consistent answers to simple, basic questions about the paper, that paper has no credibility."

You think you can discard TWENTY YEARS of research and breezily dismiss a paper as having "no credibility" because YOUR idiotic questions were not addressed? Have you ever done peer review before? Get a clue, jerkoff! He did answer your questions...IN THE PAPER!! READ THE PAPER. Even that smacked-down skunk Assfly admitted he has not done so. READ THE PAPER! READ THE PAPER!

Thursday, June 26, 2008 5:30:00 PM  
Blogger Phae said...

It was my impression that Lenski started this project a long while before Zachary Blount arrived on the scene. Isn't Blount his grad student who has helped analyze the results? And his reply would seem to reflect that... he doesn't want to reply to the whole of the information.

Ask Lenski instead, although again, it is pretty laffo to draw conclusions based on your perception of the promptness or completeness of the answers.

Thursday, June 26, 2008 5:52:00 PM  
Blogger luxzia said...

Please take a science course. Or a logic course. Mr. Blount isn't dodging anything - it wasn't a goal to create the citrate-absorbing E. coli, but to see what reaction E.coli would have in the presence of citrate. It was hypothesized (is that word too big? maybe I should say 'guessed') that it might lead to citrate-absorbing E.coli, but it wasn't a goal. Do the world a favor and buy yourself a good dictionary.

Thursday, June 26, 2008 7:24:00 PM  
Blogger Larry Fafarman said...

luxzia:
>>>>> It was hypothesized (is that word too big? maybe I should say 'guessed') that it might lead to citrate-absorbing E.coli, but it wasn't a goal. Do the world a favor and buy yourself a good dictionary. <<<<<<

You're the one who needs a dictionary. A goal does not have to be a sure result. In searches for the Lost Dutchman Mine and the ivory-billed woodpecker, finding them are "goals." A "goal" can be one of many goals, a secondary goal, a longshot goal, or whatever.

Zachary Blount's following statement in comment #115 under the New step to evolution post on Carl Zimmer's "The Loom" blog indicates that Cit+ (citrate-eating E. coli bacteria) evolution was one of the original goals of the experiment:

"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)."

Blount then created confusion by saying that "the intent of the experiment was never to evolve a Cit+ E. coli variant" (comment #115) and that Cit+ evolution was "not a goal" (comment #122).

The following factors also suggest that Cit+ evolution was an original goal of the experiment:

(1) Cit+ evolution had been observed once before. Blount reported in comment #115 under the New step to evolution post on Zimmer's blog, "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.)").

(2) I and others assumed that a purpose of the glucose-cycling (giving the bacteria an insufficient glucose supply so as to create alternating glucose feeding and glucose starvation) was to favor Cit+ evolution. I asked Blount if this was in fact a purpose of the glucose-cycling and he did not answer. I asked what the purpose of the glucose-cycling was if favoring Cit+ evolution was not the purpose, and he did not answer.

Was there a research proposal for this whole experiment that started in 1988, and if so, what does that proposal say, if anything, about my questions?

Thursday, June 26, 2008 9:23:00 PM  
Blogger jeffjrstewart said...

>>>He dodged the questions, telling me to just read the literature.


Wow...HEAVEN FORBID you actually just read the papers in question.

It's really amazing that you and so many others think you can pick apart a series of papers that YOU HAVEN'T EVEN READ.

Friday, June 27, 2008 12:05:00 AM  
Blogger Phae said...

I notice you "dodged my question" about Blount's status. Look at the list of some of the publications related to this experiment. Note how Blount is only in the latest; clearly, he is the co-author and analyst of this latest research. So perhaps, again, you should be demanding your answers from Lenski.

Still, he does speak to the facts you are asking. Your intent seems to be to imply that they designed circumstances that would favor this particular mutation. This does not appear to be the case.

You don't appear to be a fan of finding answers, only of asking questions, so I did you the favor of doing your research for you. The first paper on the subject, published three years after the start of the experiment, makes it fairly clear that the objective was to induce the daily starve and plenty cycle in order to apply survival pressure. He intended to observe the adaptations that would evolve to comply and better fit this environment, and in fact in a short time observed increases in efficiency and size in the strain and a more rapid response time to medium transfer, mentioned also in the recent paper. The citrase is part of a standard medium for cultures known as the "Davis Minimal Broth," one example of which you can see here. You will note the citrase within this medium. The variety referred to as the "DM25" medium is a specific standard of growth medium.

To all appearances, the plan was to observe change in the population as it adapted to the feast and famine conditions with the daily medium transfer. While his original intentions are not easily available, and thus a grad student who only recently began working on this twenty year experiment might not be aware, three years afterward there is little indication of any shaping of the experiment towards that specific end. A citrase-based medium may have been chosen with that potential in mind, but E coli is a highly adaptive bacteria; during hard times, it hyperproduces DNA Polymerase IV, which makes it harder for it to accurately copy itself and rapidly increases the rate of mutation. It has mutated to all appearances to consume other food sources as well, previously, all of which were also in its culture. It is not, therefore, as if citrase was a preferred second food for this bacteria - which, short of an adaptive mutation which essentially changes its species, evolving to meet current needs, cannot consume the material. You can find out more information about this in "Error-prone DNA polymerase IV is controlled by the stress-response sigma factor, RpoS, in Escherichia coli," Molecular Microbiology, vol. 50, no. 2; pp. 549-561


See, you didn't have to do all that darn reading and research, after all! Still, it is highly recommended that you read some of the papers before you criticize them.

Friday, June 27, 2008 12:10:00 AM  
Blogger Larry Fafarman said...

jeffjrstewart barfed,
>>>>> Wow...HEAVEN FORBID you actually just read the papers in question. <<<<<

You lousy dunghill, nothing that the papers say could change the fact that Blount posted bullshit on Carl Zimmer's blog, as I showed above.

Friday, June 27, 2008 12:13:00 AM  
Blogger Larry Fafarman said...

Phae said (Friday, June 27, 2008 12:10:00 AM) --
>>>>>>I notice you "dodged my question" about Blount's status.<<<<<<

What do you mean, I "dodged" your question? It was just a rhetorical question: "Isn't Blount his grad student who has helped analyze the results?"

You accuse me of not reading what I write about. Have you read I have written here?

>>>>>> So perhaps, again, you should be demanding your answers from Lenski. <<<<<<

I would be embarrassed to ask Lenski, because Blount is supposed to answer the questions. Also, Lenski can hardly be unaware of my questions -- his blog links to Carl Zimmer's blog post where I repeatedly ask the questions.

>>>>> Your intent seems to be to imply that they designed circumstances that would favor this particular mutation. <<<<<<

The glucose cycling does favor Cit+ evolution -- (1) the glucose feeding time allows silent mutations during reproduction of the bacteria that can eat only glucose and (2) the glucose starvation time gives an adantage to citrate-eating bacteria.

>>>>> The first paper on the subject, published three years after the start of the experiment, makes it fairly clear that the objective was to induce the daily starve and plenty cycle in order to apply survival pressure. <<<<<

Wow -- so now I not only have to read the paper I am discussing, but I also have to read other papers as well.

"Survival pressure" is too vague a term -- more detail is needed.

>>>>>> The citrase is part of a standard medium for cultures known as the "Davis Minimal Broth," one example of which you can see here. <<<<<<

Blount discussed other reasons for using citrate, but that does not answer my questions of whether Cit+ evolution was a goal and whether favoring Cit+ evolution was a purpose of the glucose-cycling.

>>>>>> it is highly recommended that you read some of the papers before you criticize them. <<<<<<

What if the authors present this paper at a conference? Should people in the audience who hadn't read the paper not ask questions?

Friday, June 27, 2008 3:52:00 AM  
Anonymous NightFlare said...

Larry Fafarman, your thinly veiled attempts at having the last words fool no one. Conservatives usually attempt to have the last word to make it seem as if they had won the debate.

Friday, June 27, 2008 4:45:00 AM  
Blogger Larry Fafarman said...

NightFlare driveled,
>>>>> Larry Fafarman, your thinly veiled attempts at having the last words fool no one. <<<<<<

Wrong -- my adversaries are the ones who are trying to have the last word. I am merely refuting their specious arguments.

>>>>>> Conservatives usually attempt to have the last word <<<<<<<

Wrong again -- I don't consider myself to be a conservative.

Friday, June 27, 2008 8:19:00 AM  
Blogger Larry Fafarman said...

BTW, there is a good name for the practice of sending people on wild goose chases through reams of literature. It is called "bibliography bluffing."

Friday, June 27, 2008 8:46:00 AM  
Blogger Phae said...

What do you mean, I "dodged" your question? It was just a rhetorical question: "Isn't Blount his grad student who has helped analyze the results?"

Well, shucks, sure looks like a question to me. See the squiggly thing on the end there? Luckily for you, in my actual next post I went and did your research for you, so you don't have to wrassle with them punctuation marks.

You accuse me of not reading what I write about. Have you read I have written here?

Yes. That's why I was able to reply to it, after reading the relevant papers. Funny how that works. Try it sometime.

I would be embarrassed to ask Lenski, because Blount is supposed to answer the questions. Also, Lenski can hardly be unaware of my questions -- his blog links to Carl Zimmer's blog post where I repeatedly ask the questions.

He can hardly be unaware of your questions because... he linked to the blog post where you are asking them? He's already had to deal with one Random Internet Guy lately about this matter, I doubt he really spends that much of his time desperately seeking out opinions from laypeople.

The glucose cycling does favor Cit+ evolution -- (1) the glucose feeding time allows silent mutations during reproduction of the bacteria that can eat only glucose and (2) the glucose starvation time gives an adantage to citrate-eating bacteria.

No. The manner in which you phrase that implies a specificity to cit+ mutation. In point of fact, the methodology also would tend to reward decreased lag time in medium accommodation, storage and utilization efficiency by size increase and cytoplasmic alteration, and a variety of other things. It's not hard to see the conclusion you are trying to imply ("Oh, so they designed the experiment to create this result?"), and it's an incorrect one that reflects a basic misunderstanding of... well, of how words work. You didn't quite manage with question marks previously, so I guess that's not surprising.

Wow -- so now I not only have to read the paper I am discussing, but I also have to read other papers as well.

I know... it's almost like if you want to know the answer to a specific question about the background of an experiment that you have to read about the background of the experiment! Total bummer!

"Survival pressure" is too vague a term -- more detail is needed.

...really? You read good on bright magic-box?

By creating a set of circumstances where there is a patterned scarcity of food and a variety of opportunities to increase niche advantages, the E coli was put under duress to increase Poly IV and engage the tendency towards bacterial mutation that leads to rapid evolution under such circumstances so that it could be observed within a manageable timeframe. The survival pressure applied pressure on the bacteria to survive, to put it succinctly.

Blount discussed other reasons for using citrate, but that does not answer my questions of whether Cit+ evolution was a goal and whether favoring Cit+ evolution was a purpose of the glucose-cycling.

...no, but the text I posted above did. Did you read it? I'll repeat for you: A citrase-based medium may have been chosen with that [mutation] potential in mind, but E coli is a highly adaptive bacteria; during hard times, it hyperproduces DNA Polymerase IV, which makes it harder for it to accurately copy itself and rapidly increases the rate of mutation. It has mutated to all appearances to consume other food sources as well, previously, all of which were also in its culture. It is not, therefore, as if citrase was a preferred second food for this bacteria - which, short of an adaptive mutation which essentially changes its species, evolving to meet current needs, cannot consume the material. You can find out more information about this in "Error-prone DNA polymerase IV is controlled by the stress-response sigma factor, RpoS, in Escherichia coli," Molecular Microbiology, vol. 50, no. 2; pp. 549-561

What if the authors present this paper at a conference? Should people in the audience who hadn't read the paper not ask questions?

Generally the people at conferences would be biologists with an understanding of the meaning of things like "survival pressure," questions marks, and so on.

Friday, June 27, 2008 9:41:00 AM  
Anonymous Conservative said...

< Conservatives usually attempt to have the last word to make it seem as if they had won the debate. >

Here's a "conservative" who does not have any word when the argument is being so deftly handled by Phae.

< Total bummer! >

:-)

Friday, June 27, 2008 11:53:00 AM  
Anonymous Conservative said...

< during hard times, (E. Coli) hyperproduces DNA Polymerase IV >

Fascinating.

As an aside, it becomes clearer how life has penetrated every conceivable niche as well as inconceivable ones.

Friday, June 27, 2008 12:09:00 PM  
Blogger Larry Fafarman said...

Phae:
>>>>> Well, shucks, sure looks like a question to me. See the squiggly thing on the end there? <<<<<<

Rhetorical questions have a "squiggly thing" on the end, too. Another rhetorical question: "See the squiggly thing on the end there?"

>>>>>You accuse me of not reading what I write about. Have you read I have written here?

Yes. That's why I was able to reply to it, after reading the relevant papers. <<<<<<<

The scientific papers are not relevant to my questions. As I said, nothing that those papers say can change the fact that Blount is posting bullshit on Zimmer's blog and not giving straight answers to my questions. As I said, you folks are just trying to send me on a wild goose chase through reams of literature -- that is called "bibliography bluffing."

>>>>> He can hardly be unaware of your questions because... he linked to the blog post where you are asking them? <<<<<<

OK -- let's just say that I would be embarrassed to ask Lenski the questions, because Blount is supposed to be answering them.

>>>>> I doubt he really spends that much of his time desperately seeking out opinions from laypeople. <<<<<

Remember the story of the little boy who said that the emperor had no clothes.

>>>>>>"The glucose cycling does favor Cit+ evolution -- (1) the glucose feeding time allows silent mutations during reproduction of the bacteria that can eat only glucose and (2) the glucose starvation time gives an adantage to citrate-eating bacteria."
The manner in which you phrase that implies a specificity to cit+ mutation. <<<<<<

I didn't say that the glucose-cycling could not possibly have had purposes or effects other than favoring Cit+ evolution.

>>>>>> In point of fact, the methodology also would tend to reward decreased lag time in medium accommodation, storage and utilization efficiency by size increase and cytoplasmic alteration, and a variety of other things. <<<<<<

Please use plain English, not unintelligible high-falutin gobbledygook.

>>>>> Generally the people at conferences would be biologists with an understanding of the meaning of things like "survival pressure," <<<<<

"Survival pressure" is a meaningless term. For example, the environmental "pressure" from ionizing radiation could produce mutations that do not increase survival rates under high radiation but increase survival rates under some other environmental stress, e.g., antibiotics or pesticides. Anyway, I asked for more detail.

Friday, June 27, 2008 12:12:00 PM  
Anonymous Zmidponk said...

Larry, it amazes me that you're still banging on about this. I'll see if I can explain this as simply as possible. When the experiment was set up, they were trying to see what would happen if they applied survival pressure to several different colonies of E. coli. They used a standard growth medium recipe excepting that it lacked glucose, so they could control the amount of food present for the E. coli to munch on. When they looked at their techniques, they realised that it was theoretically possible that E. coli may evolve some method to use citrate as a food source, but were not specifically setting out to make this happen, bearing in mind that E. coli mutating in this way is extremely rare, to such a degree that the lack of the ability to use citrate as food is actually considered one of the defining characteristics of E. coli. Just recently, they realised that this had, in fact, happened, not as a result of them deliberately trying to make this happen, but simply as something that they realised, in passing, could theoretically happen.

Now make a wild guess as to where I got the information that allowed me to explain this to you? I'll give you a clue - the answers provided by a certain gentleman who you claim is 'dodging your questions' and 'posting bullshit on Zimmer's blog'. In addition, your last reply to Phae, which includes such comments like 'Please use plain English, not unintelligible high-falutin gobbledygook' seems to indicate that the problem here is not the answers you've been given, but your ability to comprehend them. Sorry, but, frankly, that's not our problem, it's yours.

Friday, June 27, 2008 12:25:00 PM  
Blogger Phae said...

Rhetorical questions have a "squiggly thing" on the end, too. Another rhetorical question: "See the squiggly thing on the end there?"

Ah, I see the problem. You are not very bright. I was actually asking if you saw it; it's hard to assume you understand much at this point.

The scientific papers are not relevant to my questions. As I said, nothing that those papers say can change the fact that Blount is posting bullshit on Zimmer's blog and not giving straight answers to my questions. As I said, you folks are just trying to send me on a wild goose chase through reams of literature -- that is called "bibliography bluffing."

Well gee golly gosh, and here was me thinking you actually wanted the answer to your questions, which is why I provided those answers. If you're just trying to play "gotcha" to sate your own ideological wishes, then I can tell you I have it on very good faith that Lenski eats Irish babies. So you can ignore his results. Yay! And you didn't even have to learn any science or read anything!

OK -- let's just say that I would be embarrassed to ask Lenski the questions, because Blount is supposed to be answering them.

I would be embarrassed to be asking your questions, too.

Remember the story of the little boy who said that the emperor had no clothes.

And yet the emperor didn't go around knocking on doors, asking every child what that kid thought of his clothes. You know, it might be different if you had some manner of actual substantive point, but inasmuch as I can see all you have are simple questions you could have answered yourself if you'd bothered to read the papers.

I didn't say that the glucose-cycling could not possibly have had purposes or effects other than favoring Cit+ evolution.

No, you didn't say that. But it was pretty clearly where you were going with that. Unless you actually didn't know that, and couldn't figure out how to read the first paper published on the subject. If you're just ignorant, I guess that's an acceptable excuse.

Please use plain English, not unintelligible high-falutin gobbledygook.

Cell go hungry. Cell get BIIIIGGGGER to accommodate more storage. How big? Soooooo big! Sooooooo big! Yes, yes it did!

"Survival pressure" is a meaningless term. For example, the environmental "pressure" from ionizing radiation could produce mutations that do not increase survival rates under high radiation but increase survival rates under some other environmental stress, e.g., antibiotics or pesticides. Anyway, I asked for more detail.

I gotta admit, I am not sure what you want at this point. When you ask for detail and I give it to you, you aren't able to understand and call it "gobbeldygook." I mean, you seem to understand the meaning of the term "survival pressure," giving another example of potential pressure, yet you also say you don't understand.

Wait a second... is this you, Ray? Ray, are you doing that whole "pretend to be a gibbering moron pushing his own ideological point and determined not to understand the alternative because it doesn't suit his beliefs" thing you do? You prankster!

Friday, June 27, 2008 12:59:00 PM  
Blogger Larry Fafarman said...

Zmidponk said...
>>>>> Larry, it amazes me that you're still banging on about this. <<<<<

It amazes me that you trolls are still banging on about this! Please read my original post and this comment thread again -- they show that I have gotten only vague, ambiguous, inconsistent, and unintelligible answers to my questions.

>>>>>> When the experiment was set up, they were trying to see what would happen if they applied survival pressure to several different colonies of E. coli. <<<<<<

I have already pointed out that "survival pressure" is a vague if not meaningless term. In contrast, I was very specific about the ways in which the glucose-cycling favors evolution of citrate-eating E. coli -- see my comment of Friday, June 27, 2008 3:52:00 AM.

>>>>> they realised that it was theoretically possible that E. coli may evolve some method to use citrate as a food source, but were not specifically setting out to make this happen, bearing in mind that E. coli mutating in this way is extremely rare <<<<<<

But Cit+ evolution was observed once before, so maybe Lenski hoped that if he created conditions that were favorable for Cit+ evolution, e.g., glucose-cycling, and he waited long enough, maybe there was a good chance that it would happen again. As I said, a "goal" does not have to be a sure result -- it can even be an unlikely result. For example, in searches for the Lost Dutchman Mine, finding it is a "goal."

>>>>> In addition, your last reply to Phae, which includes such comments like 'Please use plain English, not unintelligible high-falutin gobbledygook' seems to indicate that the problem here is not the answers you've been given, but your ability to comprehend them. <<<<<

No one can understand that crap.

Phae:
>>>> Cell go hungry. Cell get BIIIIGGGGER to accommodate more storage. How big? Soooooo big! <<<<<

That's more like it. Why can't you translate the rest of your gobbledygook into plain English?

Next question -- if the cell is starving, how can it grow bigger? And what does this have to do with mutations?

>>>>> When you ask for detail and I give it to you, you aren't able to understand and call it "gobbeldygook." <<<<<<

When I ask for details, I obviously mean details in plain English, dunghill. You are just a charlatan who thinks that you are impressing people by spouting high-falutin jargon.

Conservative barfed:
>>>>>> Here's a "conservative" who does not have any word when the argument is being so deftly handled by Phae. <<<<<

How many times do I have to tell you lousy trolls to not clutter up this blog with that kind of crap? If you have nothing worthwhile to contribute to the discussion, then you ought to keep your trap shut.

Friday, June 27, 2008 3:52:00 PM  
Anonymous NightFlare said...

"NightFlare driveled,
>>>>> Larry Fafarman, your thinly veiled attempts at having the last words fool no one. <<<<<<

Wrong -- my adversaries are the ones who are trying to have the last word. I am merely refuting their specious arguments."

You're wrong, and you will not be able to see that unless you open your mind.

">>>>>> Conservatives usually attempt to have the last word <<<<<<<

Wrong again -- I don't consider myself to be a conservative."

It is a common conservative tactic to pretend you're a liberal. Liberals aren't deceitful. Conservatives don't mind being deceitful if that means advance for the conservative agenda.

Friday, June 27, 2008 3:54:00 PM  
Blogger Larry Fafarman said...

Anyway, Phae, even if your answer to my questions about glucose-cycling were good (it is not), it still would not excuse Zachary Blount's failure to answer those questions. So there.

Friday, June 27, 2008 5:43:00 PM  
Anonymous Anonymous said...

"No one can understand that crap."

Anyone who's familiar with biology and is capable of reading the primary literature can understanding that "crap."

"As I said, you folks are just trying to send me on a wild goose chase through reams of literature -- that is called "bibliography bluffing.""

No, they're expecting you to educate yourself and see that most of your questions are answered by reading a little background. The answers that have been provided for you are the answers you'd get if you actually put some effort into understanding the topic and not merely throwing a little hissy bitch fit. My guess is they're not the answers you want to hear so you disregard them and plunge on anyways despite the spanking Phae gave you.

"they show that I have gotten only vague, ambiguous, inconsistent, and unintelligible answers to my questions."

No, just not the answers you want.

Friday, June 27, 2008 6:39:00 PM  
Blogger Phae said...

That's more like it. Why can't you translate the rest of your gobbledygook into plain English?

Because I don't work in your nursery school. If you really needed a translation of what I posted, then I would suggest that you are simply unequipped to be asking the questions you are demanding, since you need the answers explained to you in minutiae.

Next question -- if the cell is starving, how can it grow bigger? And what does this have to do with mutations?

See, this is pretty much what I am talking about. The cell grows larger in order to accommodate more cytoplasm to store more of the glucose from the plenty phase for the starvation time. If you need to know what cytoplasm is, hit up Wikipedia.

When I ask for details, I obviously mean details in plain English, dunghill. You are just a charlatan who thinks that you are impressing people by spouting high-falutin jargon.

I gave you details in plain English. If you show this page to someone capable of understanding it (i.e. someone who is not you) then I assure you that they will confirm that the error doesn't lie in the rest of the world, only with your inability to successfully understand it.

See, microbiology is pretty complex science. It has a lot of terms and information associated with it, to enable people to communicate effectively about topics. When you ask a question about microbiology, people are generally going to reply succinctly, which requires use of the appropriate jargon. Very few people are going to be willing to take you by the hand and start teaching you things from the ground up, especially when you're unwilling to do any work at all to understand it but need it spoonfed to you. You could, at the very least, try reading the papers I have mentioned in order to perhaps improve your ability to understand and speak on this matter. The very fact that you think I'm trying to deliberately confuse you with fairly basic terminology and concepts indicates that you seriously should start smaller. Much smaller.

It also indicates that you should rethink whether or not Blount answered your questions. Is it not possible, since you can't even understand me, that he did and you just aren't able to realize it?

Many community colleges have introductory courses in biology. You should consider taking one.

Friday, June 27, 2008 10:01:00 PM  
Blogger Larry Fafarman said...

>>>>>> Anyone who's familiar with biology and is capable of reading the primary literature can understanding that "crap." <<<<<<

OK, smartypants, let's see if you can translate this high-falutin gibberish into plain English --

In point of fact, the methodology also would tend to reward decreased lag time in medium accommodation, storage and utilization efficiency by size increase and cytoplasmic alteration, and a variety of other things . . . .

By creating a set of circumstances where there is a patterned scarcity of food and a variety of opportunities to increase niche advantages, the E coli was put under duress to increase Poly IV and engage the tendency towards bacterial mutation that leads to rapid evolution under such circumstances so that it could be observed within a manageable timeframe.


Remarkably, Phae, the author of the above sentences, restated the 2nd sentence in plain English:

E coli is a highly adaptive bacteria; during hard times, it hyperproduces DNA Polymerase IV, which makes it harder for it to accurately copy itself and rapidly increases the rate of mutation.

Now if he had initially stated his point in that way, I would have questioned whether the glucose cycling (giving the bacteria insufficient glucose so as to cause alternating glucose feeding and glucose starvation) is the kind of "hard times" that would cause this hyperproduction of DNA. But I never got that far because of his bullshit.

Also, while you're at it, let's see if you can translate the following bullshit, from a previous post:

Evolution of mixed strategies

In this study we present a simple optimization model for the evolution of defensive strategies (tolerance and resistance) of plants against their natural enemies. The model specifically evaluates the consequences of introducing variable costs and benefits of tolerance and resistance and nonlinear cost-and-benefit functions for tolerance and resistance. Incorporating these assumptions, the present model of plant defense predicts different evolutionary scenarios, not expected by previous work. Basically, the presence of an adaptive peak corresponding to intermediate levels of allocation to tolerance and resistance can arise when the shape parameter of the cost function is higher than the corresponding of the benefit function. The presence of two alternatives peaks of maximum tolerance and maximum resistance occurs only when benefits of tolerance and resistance interact less than additive. Finally, the presence of one peak of maximum resistance or maximum tolerance depends on the relative values of the magnitude of costs for tolerance and resistance. An important outcome of our model is that under a plausible set of conditions, variable costs of tolerance and resistance can represent an important aspect involved in the maintenance of intermediate levels of tolerance and resistance, and in favoring adaptive divergence in plant defensive strategies among populations. The model offers a framework for future theoretical and empirical work toward understanding spatial variation in levels of allocation to different defensive strategies.

EVOLUTION OF MIXED STRATEGIES OF PLANT DEFENSE ALLOCATION AGAINST NATURAL ENEMIES, Evolution, Volume 58, Issue 8 (August 2004)


>>>>> No, just not the answers you want. <<<<<

No, they are not the answers I want, dunghill. You are so full of living crap that it is coming out of your ears, you no-good sack of @#*^$#. You lousy trolls just clutter up this blog with your bullshit.

Anyway, as I said, no explanations that anyone can give here can excuse Zachary Blount's failure to give straight answers to simple, basic questions.

Friday, June 27, 2008 10:16:00 PM  
Blogger Phae said...

OK, smartypants, let's see if you can translate this high-falutin gibberish into plain English --

You sound like a mix between an eight-year-old and a grizzled prospector. I imagine you two feet tall, with braces and a bushy beard. "Yar, I lost this here eye in '42, right after I lost my bottle. Yar."

Remarkably, Phae, the author of the above sentences, restated the 2nd sentence in plain English:

Now if he had initially stated his point in that way, I would have questioned whether the glucose cycling (giving the bacteria insufficient glucose so as to cause alternating glucose feeding and glucose starvation) is the kind of "hard times" that would cause this hyperproduction of DNA. But I never got that far because of his bullshit.


Those read like almost the same thing to me. Could you please specify which words you didn't understand, so we can nail down exactly where in primary school your reading level is?

Also, while you're at it, let's see if you can translate the following bullshit, from a previous post:

Evolution of mixed strategies

In this study we present a simple optimization model for the evolution of defensive strategies (tolerance and resistance) of plants against their natural enemies. The model specifically evaluates the consequences of introducing variable costs and benefits of tolerance and resistance and nonlinear cost-and-benefit functions for tolerance and resistance. Incorporating these assumptions, the present model of plant defense predicts different evolutionary scenarios, not expected by previous work. Basically, the presence of an adaptive peak corresponding to intermediate levels of allocation to tolerance and resistance can arise when the shape parameter of the cost function is higher than the corresponding of the benefit function. The presence of two alternatives peaks of maximum tolerance and maximum resistance occurs only when benefits of tolerance and resistance interact less than additive. Finally, the presence of one peak of maximum resistance or maximum tolerance depends on the relative values of the magnitude of costs for tolerance and resistance. An important outcome of our model is that under a plausible set of conditions, variable costs of tolerance and resistance can represent an important aspect involved in the maintenance of intermediate levels of tolerance and resistance, and in favoring adaptive divergence in plant defensive strategies among populations. The model offers a framework for future theoretical and empirical work toward understanding spatial variation in levels of allocation to different defensive strategies.


Sure, I'll translate it. It says, "I am not here to teach you basic biology concepts that you don't understand, go and take a class you ignorant moron."

It's not hard. But it is a specialized field, and if you want tutoring, you have to send me a check. Or, alternatively, you can admit your ignorance and ask me nicely to explain it to you, "dunghill."

Anyway, as I said, no explanations that anyone can give here can excuse Zachary Blount's failure to give straight answers to simple, basic questions.

If you've already decided that there can't be any explanation, why even pretend otherwise? Here I was, explaining concepts to you and working on the latter part of the alphabet with you, and you had already decided that no matter what answer you got, your mind was made up.

Hey, are there any other questions whose answers you magically know won't be sufficient ahead of time? Is this a special child-prospector power? Yar.

Friday, June 27, 2008 10:35:00 PM  
Blogger Larry Fafarman said...

Phae barfed,
>>>>>>Here I was, explaining concepts to you <<<<<<

You lousy dunghill, you did not come here to try to explain anything -- you just came here to try to belittle me by showing off your high-falutin jargon. So why don't you just get lost.

Friday, June 27, 2008 11:14:00 PM  
Anonymous Good Commenter said...

"they are not the answers I want"

OK.

You are absolutely correct, and brilliant, to notice that Intelligent Design explains the development of the E. Coli citrate metabolism and maybe even co-evolution.

These alleged scientists should give you the credit you deserve. I nominate you for a Nobel Prize.

Judge Jones should rescind his order and demand that your views be included in the High School curriculum, lest students otherwise grow up ignorant.

PZ Myers, Ed Brayton, Wes Elsberry, and many commenters here are twits and likely to remain so.

Anything else?

(I seem to lack Jim Sherwood's knack for limericks; sorry.)

Friday, June 27, 2008 11:24:00 PM  
Blogger Phae said...

You lousy dunghill, you did not come here to try to explain anything -- you just came here to try to belittle me by showing off your high-falutin jargon. So why don't you just get lost.

Well, really I came here to explain to you why you were an idiot. But you seem to be able to fully grasp that concept. So we'll add it to the list of things you understand.

1. Minin' for gold in them thar hills.
2. Where your binky goes.
3. That you are an idiot.

Not a long list.

So anyway, you're very wrong. The answers you sought were in the papers already publicly available, and Blount seems to have answered you satisfactorily. The only burnt-out circuit is you, Yar.

Friday, June 27, 2008 11:56:00 PM  
Blogger Larry Fafarman said...

Phae barfed,
>>>>>> Well, really I came here to explain to you why you were an idiot. <<<<<

And how did you try to do that, dunghill? By using high-falutin gobbledygook that no one could understand?

Saturday, June 28, 2008 2:59:00 AM  
Blogger Phae said...

And how did you try to do that, dunghill? By using high-falutin gobbledygook that no one could understand?

I think you're the only one who didn't understand. You're kind of like the really drunk older guy at the party who laughs way too loud and follows one of the less pretty girls around, creeping everyone out. You stare at her and bother her, and yet when someone takes you aside and tells you that you're being a tool you just can't quite understand in your besotted brain. Only I guess you're a child-prospector doing all of the above. Your persona is hard to pin down, Yar.

But hey, I'm a forgiving fellow. Go ahead and make your claims again. What questions have you asked that he hasn't answered and that you still don't know? I will explain it to you in my infinite graciousness. In nomine patri, et filii, et espiritu sancti.

Saturday, June 28, 2008 3:09:00 AM  
Anonymous NightFlare said...

Larry Fafarman (is that your real name?) you've been doing nothing but using deliberate ignorance on the subject and feigned disgust at the replies you receive, even though conservatives rarely say the same to genuine actions brought upon by fellow conservatives.

Saturday, June 28, 2008 7:27:00 AM  
Blogger Larry Fafarman said...

First these jerks start coming up with all kinds of crazy definitions of "goal," saying that a goal has to be an expected result, or a goal has to be an intended result, and one definition even says that something is not a goal if the effort doesn't end when the goal is reached! And then Zachary Blount won't answer the question of whether favoring Cit+ evolution was a purpose or one of the purposes of the glucose-cycling (giving the bacteria an insufficient glucose supply in order to create alternating glucose feeding and glucose starvation). I am right and they are wrong. It's as simple as that.

Saturday, June 28, 2008 8:09:00 AM  
Anonymous Good Commenter said...

"I am right and they are wrong. It's as simple as that."

Of course. QED.

Saturday, June 28, 2008 9:57:00 AM  
Anonymous Anonymous said...

Larry Fafarman said,

You lousy dunghill, you did not come here to try to explain anything -- you just came here to try to belittle me by showing off your high-falutin jargon. So why don't you just get lost.

Don't worry, Larry. I don't think anyone really could belittle you.

Saturday, June 28, 2008 10:57:00 AM  
Blogger Phae said...

First these jerks start coming up with all kinds of crazy definitions of "goal," saying that a goal has to be an expected result, or a goal has to be an intended result, and one definition even says that something is not a goal if the effort doesn't end when the goal is reached! And then Zachary Blount won't answer the question of whether favoring Cit+ evolution was a purpose or one of the purposes of the glucose-cycling (giving the bacteria an insufficient glucose supply in order to create alternating glucose feeding and glucose starvation). I am right and they are wrong. It's as simple as that.

So... what, you need to know what a goal is? It's a colloquialism, not a scientific term except in the loosest sense, so naturally the definitions offered by people will differ.

And your question about cycling was answered in the first paper published by Lenski, but as I patiently explained to you earlier, Blount was only the co-author of the most recent one on these results, not there twenty years ago at the inception. Are you like the guy from Memento? Try tattooing it on your chest, along with a reminder that you're a douchebag.

Saturday, June 28, 2008 12:08:00 PM  
Blogger Larry Fafarman said...

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

Saturday, June 28, 2008 12:40:00 PM  
Blogger Phae said...

I haven't met your family, so don't worry, I won't feed them.

Saturday, June 28, 2008 12:51:00 PM  
Anonymous Zmidponk said...

Larry excreted...

>>>>>>>It amazes me that you trolls are still banging on about this! Please read my original post and this comment thread again -- they show that I have gotten only vague, ambiguous, inconsistent, and unintelligible answers to my questions.<<<<<<<

No, they show that you have gotten answers that YOU find (or claim to find, anyway) 'vague, ambiguous, inconsistent, and unintelligible'. Given the responses and comments you have received, a great many other people find them clear and perfectly intelligible.

>>>>>>>I have already pointed out that "survival pressure" is a vague if not meaningless term.<<<<<<<

No, again, you have pointed out that YOU find it a 'vague if not meaningless term'. Again, other people don't.

>>>>>>>In contrast, I was very specific about the ways in which the glucose-cycling favors evolution of citrate-eating E. coli.<<<<<<<

Yes. And? This was probably how Lenski, et al, realised that it was theoretically possible for the E. coli to evolve to eat citrate.

>>>>>>>But Cit+ evolution was observed once before, so maybe Lenski hoped that if he created conditions that were favorable for Cit+ evolution, e.g., glucose-cycling, and he waited long enough, maybe there was a good chance that it would happen again.<<<<<<<

Yes, it was observed once before. And? Yes, you can speculate that 'maybe Lenski hoped that if he created conditions that were favorable for Cit+ evolution, blah, blah, blah. However, this is pure speculation that seems to be discounted by Zachary Blount's answers. As I said, it seems to be that the evolution of E. coli was seen, in passing, as something that could theoretically happen, but was not a goal. To use the 'Lost Dutchman's Mine' analogy your seemingly so fond of, it's as if they were simply walking across a landscape, said to each other, 'hmm, the Lost Dutchman Mine is supposed to be around here somewhere. It is theoretically possible we could blindly stumble across it', then did so. They were not looking to find it, in any way, shape or form, they were simply looking to get from A to B across that particular part of the terrain, it is simply the case they realised it was theoretically possible they could, by sheer chance, find it, before they actually did.

>>>>>>>No one can understand that crap.<<<<<<<

No, again, YOU cannot understand 'that crap', seemingly. Other people can.

I also note that you have utterly ignored the fact I gained the knowledge for my explanation from the very answers you claim are 'vague, ambiguous, inconsistent, and unintelligible'.

As for your comments about you being right and everyone else being wrong, sorry, but everything you have written so far indicates the only reason you believe this is your own lack of knowledge causing to to fail to comprehend the answers you have been given. The fact my own knowledge and expertise in biology stops at the high school level, and yet I can understand what went on from Zachary Blount's answers and you cannot is a pretty clear-cut indication of that.

Saturday, June 28, 2008 1:00:00 PM  
Anonymous Anonymous said...

"OK, smartypants, let's see if you can translate this high-falutin gibberish into plain English --"

What you're asking for is a teacher, not a scientist. Many scientists I have come in contact with are pretty awful at explaining things "in plain English" but are brilliant when speaking to other scientists and people on the same page.

"You lousy trolls just clutter up this blog with your bullshit."

You don't need us "trolls" to accomplish that.

"You sound like a mix between an eight-year-old and a grizzled prospector. I imagine you two feet tall, with braces and a bushy beard. "Yar, I lost this here eye in '42, right after I lost my bottle. Yar.""

HAHA that's great.

Saturday, June 28, 2008 2:04:00 PM  
Anonymous Eric said...

Larry, my man. I'd tell you to STFU, but it's just too funny. We've been laughing at your ass for the last half hour over here.

Saturday, June 28, 2008 7:05:00 PM  
Anonymous That's What I Thought said...

A minor detail, for the record: There are numerous (7) usages of "citrase" in this thread where "citrate" was intended. Citrase is an enzyme for citrate.

Saturday, June 28, 2008 11:47:00 PM  
Anonymous lv said...

You know Larry, you're one of the reasons why I do not go to church anymore though i consider myself a Christian.

It is utterly impossible to have an intelligent discussion with a Christian who already believes they know everything. It's literally as bad as talking to a fundamentalist Muslim. Blount is right. All your commentors are right. Read the research and if you can't understand it, take a real science course.

Honestly people like you are what discredits religion these days. Far as I can tell, Phae has answered you more reasonably than you deserve. You're picking at literal technicalities hoping to tear open a sleeve.

"Wow -- so now I not only have to read the paper I am discussing, but I also have to read other papers as well."

Uh, duh? It boggles my mind that you can even try to hold a legitimate discussion about something without even reading the relevant material, however poor your understanding might be.

Monday, June 30, 2008 5:23:00 AM  
Blogger Larry Fafarman said...

Iv driveled,
>>>>> It is utterly impossible to have an intelligent discussion with a Christian who already believes they know everything. <<<<<<

You dunghill, I am not a Christian. And I don't believe I know everything. It's my detractors who believe they know everything.

>>>>> It boggles my mind that you can even try to hold a legitimate discussion about something without even reading the relevant material, <<<<<

I have read a lot of the relevant material, you stupid dunghill. Otherwise I would not be able to ask the right questions.

Lots of people -- presumably most -- who have commented on the paper have never seen it, you stupid sack of @*&^$.

And as I said, suppose I am in the audience at a presentation of the paper at a scientific conference and that I haven't read the paper. Does that mean that my question(s) about the paper should not be answered?

Answering specific questions by broad references to the literature is aptly called "bibliography bluffing."

Monday, June 30, 2008 5:49:00 AM  
Anonymous Zmidponk said...

Larry blurted...

>>>>>>You dunghill, I am not a Christian. And I don't believe I know everything. It's my detractors who believe they know everything.<<<<<<

No, your 'detractors' believe they know how to gain the answers you seek from the answers provided by Zachary Blount (otherwise known as 'reading them, and understanding what they say'). Something which, seemingly, you cannot do.

>>>>>>I have read a lot of the relevant material, you stupid dunghill. Otherwise I would not be able to ask the right questions.<<<<<<

Well, if you've already read much of the relevant material, what's the big problem about reading the material Zachary Blount pointed you towards? If you're genuinely after an answer to your questions, go read it. If you're not, and simply want an excuse to whine about people 'dodging your questions' simply because they don't have the time and/or inclination to spoon-feed you what you want, well, you're doing an excellent job of manufacturing such an excuse, well, fine, say so, and we'll all leave you to amuse yourself with your whining.

>>>>>>Lots of people -- presumably most -- who have commented on the paper have never seen it, you stupid sack of @*&^$.<<<<<<

So any scientist who even so much as publishes a single paper about anything should spend all their time running around answering questions by random morons who haven't even read the paper, instead of doing science?

>>>>>>And as I said, suppose I am in the audience at a presentation of the paper at a scientific conference and that I haven't read the paper. Does that mean that my question(s) about the paper should not be answered?<<<<<<

Well, if you're at a scientific conference asking questions on a paper, it is simple common courtesy to have at least read the paper. However, I have noted that common courtesy, amongst other things, is something which you seem to utterly lack.

>>>>>>Answering specific questions by broad references to the literature is aptly called "bibliography bluffing."<<<<<<

However, if the answer to that question is in the literature referred to, it is called, 'referring the questioner to the appropriate place to find the answer he's seeking', especially if you've already actually answered the self-same question to the self-same person.

Monday, June 30, 2008 12:03:00 PM  
Blogger Mumphrey Bibblesnæð said...

Sad, sad, sad.
And just for your edification, whether the Holocaust happened is NOT a controversial subject: it did.

Monday, June 30, 2008 1:00:00 PM  
Blogger Larry Fafarman said...

>>>>> Sad, sad, sad. <<<<<

You are sad, sad, sad, dunghill.

>>>>>And just for your edification, whether the Holocaust happened is NOT a controversial subject: it did. <<<<<

And for your edification, I never said that the holocaust did not happen -- I only said that a "systematic" holocaust was impossible because the Nazis had no objective and reliable way(s) of identifying Jews and non-Jews.

Monday, June 30, 2008 1:43:00 PM  
Blogger Larry Fafarman said...

Zmidponk moaned,
>>>>> Well, if you've already read much of the relevant material, what's the big problem about reading the material Zachary Blount pointed you towards? <<<<<<

He didn't point me to anything specific, like a page number. And the reason why he did not is that the paper did not answer my questions. Duh

>>>>> So any scientist who even so much as publishes a single paper about anything should spend all their time running around answering questions by random morons who haven't even read the paper, instead of doing science? <<<<<

As I said: If you can't stand the heat, get out of the kitchen.

>>>>> Well, if you're at a scientific conference asking questions on a paper, it is simple common courtesy to have at least read the paper. However, I have noted that common courtesy, amongst other things, is something which you seem to utterly lack. <<<<<

Often a lot of papers are presented at conferences, dunghill, and the attendees don't have time to read all of them in detail. And how would Blount know whether someone asking a question has read the paper or not, and why should he not answer the question just because the questioner did not read the paper.

As I said, presumably most of the people commenting about the paper have not read it. I have made a much deeper study of the paper than most people who have commented on it -- and that includes my detractors.

Monday, June 30, 2008 2:00:00 PM  
Anonymous Zmidponk said...

Larry belched...

>>>>>>He didn't point me to anything specific, like a page number. And the reason why he did not is that the paper did not answer my questions. Duh<<<<<<

The paper he pointed you to most definitely DOES answer your questions. Moreover, in addition, he answered your questions in a more direct and straightforward manner. The reason he doesn't actually 'give you a page number' is because an extremely large portion of the document answers your questions in great detail right at the start, by going into exquisite detail as to how and why they performed their project in the way they did. So, if you had bothered to read it, you would have seen it right away. But, no, instead of actually bothering to even so much as glance at the document in question, you seem to use the excuse that he didn't 'give you a page number' to level the accusation of 'bibliography bluffing', 'dodging the question' and 'posting bullshit'.

>>>>>>As I said: If you can't stand the heat, get out of the kitchen.<<<<<<

Translation: Yes, I think scientists do have to run around answering questions by random morons who haven't even read the paper, instead of doing science.

Not really much to say to that, except that it confirms what my first impression of you was. And that's not very flattering for you.

>>>>>>Often a lot of papers are presented at conferences, dunghill, and the attendees don't have time to read all of them in detail.<<<<<<

Quickly reading a paper, especially if it's a relatively short one, like this one, can be done in a fairly short period of time. As well as being common courtesy, so you are not wasting the author's time by asking questions already answered, it also saves you the embarrassment of doing this.

>>>>>>And how would Blount know whether someone asking a question has read the paper or not,<<<<<<

Well, clue number one might be the questioner posing a question that the paper answers.

>>>>>>and why should he not answer the question just because the questioner did not read the paper.<<<<<<

In a presentation, he probably would (though, if it were me, by saying, 'well, as stated in the paper, blah, blah, blah'). Getting a random question from a random moron on the internet is another matter, though.

>>>>>>As I said, presumably most of the people commenting about the paper have not read it. I have made a much deeper study of the paper than most people who have commented on it -- and that includes my detractors.<<<<<<

Well, if that's true, then your problem is definitely one of comprehension, or lack thereof, as, if you had actually understood all this 'deep study', you wouldn't be continuing to claim Zachary Blount is 'dodging your questions'. You would, in fact, realise the answers were already written down at the point in time you asked them.

Monday, June 30, 2008 2:50:00 PM  
Anonymous Cosmic Comic said...

Are "random morons" bosons or fermions?

Monday, June 30, 2008 3:11:00 PM  
Anonymous 'Nonymous said...

"Mumphrey Bibblesnæð said..."

After many years of ignorance, I finally learned about Upper- and lower-case thorn in a trip to Iceland ... (about a year after learning about 'æ').

Tuesday, July 01, 2008 12:40:00 AM  
Anonymous Anonymous said...

"Often a lot of papers are presented at conferences, dunghill, and the attendees don't have time to read all of them in detail. And how would Blount know whether someone asking a question has read the paper or not, and why should he not answer the question just because the questioner did not read the paper."

More often, work presented at meetings is UNpublished work and therefore the presenter would know that no one has read the paper. However, they would be well assured that those in the audience, and those asking questions in particular, would be familiar with the background material and literature.

If you has asked these questions at a meeting, you would have gotten a similar response: A real answer (as you've been given), if you still didn't understand you'd be referred to their previous papers (which you were) and finally you'd be asked to continue the conversation privately after the session was over if you continued to push it.


"As I said, presumably most of the people commenting about the paper have not read it. I have made a much deeper study of the paper than most people who have commented on it -- and that includes my detractors."

Pure conjecture. It's incredibly obvious that your "detractors" have read the paper and have a much deeper understanding than you do as they have provided answers to you that you would have understood if you'd truly made a "deep study" of the paper. Which brings up another point. If you can even understand the answers given to you, how can you expect anyone to think your "deep study" was actually worth anything? I can deeply study a document written in Greek, but I'm not going to understand a damn thing since I don't speak Greek.

Your problem is common amongst laymen. They read scientific articles (mainstream media usually, sometimes primary literature) and all of a sudden they think they're educated and on the same plane as the scientists they're questioning. Do you honestly believe you are in a position to truly question the integrity of the paper with a laymen's scientific knowledge and reading level when actual scientists, people who have been living and breathing this stuff for years (decades probably), didn't find any fatal flaws? Can you define arrogance for me?

Tuesday, July 01, 2008 9:30:00 AM  
Anonymous LostSailor said...

This has been an utterly fascinating thread. Let's see if I have this straight:

Larry heard about some research on the internet about E.coli. He claims in this post the the paper describing that research "has no validity" because he couldn't understand the answers one of the authors of the paper gave him to questions that indicate he doesn't understand either the research or the science behind it.

He not only hasn't read the paper, but refuses to read the paper. When several commenters explain the paper and the research he doesn't understand them; when further explanations in simpler words are provided he either doesn't understand them or mis-understands them.

I don't see why Blount owes you any explanation or further answers at all. He's provided you with answers and refers you to the specific paper you're discussing but can't be bothered to read.

Why should anyone care about your opinions on this matter when those opinions are not just uninformed, but the result of willful ignorance?

Wednesday, July 02, 2008 12:32:00 PM  
Blogger Larry Fafarman said...

LostSailor driveled,
>>>>> Let's see if I have this straight: <<<<<

No, you don't have this straight, idiot. Either you have not read the post and the comment thread or you don't comprehend them. Zachary Blount has not been giving straight answers to simple, basic questions about the experiment. As I showed above, he made ambiguous and inconsistent statements about whether Cit+ evolution was a goal of the experiment. When I asked for a clarification, he just used bibliography bluffing -- i.e, he told me to just go read the literature. Also, he did not answer my questions about the purpose(s) of the glucose-cycling (giving the bacteria an insufficient supply of glucose so as to cause alternating glucose feeding and starvation).

You really are lost, sailor.

>>>>> He not only hasn't read the paper, but refuses to read the paper. <<<<<

I browsed through the paper, but Blount should give straight answers to my questions whether or not I looked at the paper. Presumably most people who have commented on the paper have not seen it.

You trolls are just full of hot air -- you say that the literature answers my questions but can't show me exactly where my questions are answered. That's just bibliography bluffing.

People have all sorts of reasons for asking questions of papers' authors -- the questions may ask about something that was not covered in the paper, or may ask for a clarification of something in the paper, or may express a disagreement with something in the paper, or maybe the questioner missed something in the paper, or maybe the questioner did not read the paper thoroughly, or did not read the paper at all, or whatever. With all the conditions you are setting up for asking questions of the authors of scientific papers, no one could ever ask them any questions at all.

Wednesday, July 02, 2008 1:29:00 PM  
Anonymous LostSailor said...

You trolls are just full of hot air -- you say that the literature answers my questions but can't show me exactly where my questions are answered. That's just bibliography bluffing.

People have all sorts of reasons for asking questions of papers' authors -- the questions may ask about something that was not covered in the paper, or may ask for a clarification of something in the paper, or may express a disagreement with something in the paper, or maybe the questioner missed something in the paper, or maybe the questioner did not read the paper thoroughly, or did not read the paper at all, or whatever. With all the conditions you are setting up for asking questions of the authors of scientific papers, no one could ever ask them any questions at all.


You can certainly ask questions of the authors, but if you don't read the paper or did not understand it, they are under no obligation to answer you. As this thread ably demonstrated, not only did the author answer you, others have as well, yet you persist in demanding answers that have already been given. As others have pointed out, just because you don't like the answers (or more aptly, don't understand them) doesn't mean that your questions haven't been answered or deserve further attention.

You frequently use the meaningless phrase "bibliography bluffing". I take this to mean a response that generally says "go read all of the relevant literature and then come back." However, when the "relevant literature" is a single paper that is the direct subject of discussion, it is not a "bluff" but a completely on-point answer.

If you haven't bothered to even read the paper (and "browsing" isn't reading, especially since you consider anything above a 5th grade reading level as "gobblydegook") and at least attempted to understand it, why should the authors or anyone else pay any attention whatsoever to your questions. It is not up to others to "point out" where the answers are as the whole paper itself will answer your questions.

Whether you understand or accept the answers is your problem. You can ask questions, but you have no right to an answer.

Wednesday, July 02, 2008 3:15:00 PM  
Blogger Erin said...

"No, you don't have this straight, idiot."
>>An ad hominem attack, supremely relevant.

"Either you have not read the post and the comment thread or you don't comprehend them."
>>As far as I can tell, he's summarized the post and the comment threat pretty succinctly.

"Zachary Blount has not been giving straight answers to simple, basic questions about the experiment."
>>He seems not to have given straight answers because you're asking irrelevant questions. Larry, did you walk to school or bring your lunch?

"As I showed above, he made ambiguous and inconsistent statements about whether Cit+ evolution was a goal of the experiment."
>>Larry, you never showed this. Was your "goal" today in going to the store to find a great bargain on. . .cheese? If you'd found one. . .would you have bought the cheese? If you had bought said cheese, and someone had asked you if that was your goal, what would you have answered? Something to the effect of, "Well, not specifically, but I always keep an eye out for great bargains on things I use with regularity." (Which, presumably, in this example, would include cheese.)

"When I asked for a clarification, he just used bibliography bluffing -- i.e, he told me to just go read the literature."
>>To reiterate, have you looked at these sources? It's not bibliography bluffing if the sources exist and explain what you want to know. Just sayin'


"Also, he did not answer my questions about the purpose(s) of the glucose-cycling (giving the bacteria an insufficient supply of glucose so as to cause alternating glucose feeding and starvation)."
>>The purpose of glucose-cycling was (as previously stated by other commenters) to provide survival pressure which has been adequately defined without "gobbeldygook" (a scientific term, I assure you) above by Phae in his comment of June 27.

"You really are lost, sailor."
>>Good use of another ad hominem attack.

"I browsed through the paper, but Blount should give straight answers to my questions whether or not I looked at the paper."
>>Giving straight answers to **Your** questions is not Blout's job. Answering scientist's questions is concievably his job but it is apparent to all involved parties that you are not a scientist. Additionally, "browsing through" the paper is insufficient. Especially considering that you claimed to have undertaken a "deep study" of said paper. "Browsing through" and "deep study" are mutually exclusive.

Presumably most people who have commented on the paper have not seen it.
>>This is potentially true, but irrelevant. The primary commenters have obviously read the paper (or have at least skimmed it, at least as much as you claim to have done) because they have commented on specific features of the paper (notably graphs.)

"You trolls are just full of hot air -- you say that the literature answers my questions but can't show me exactly where my questions are answered."
>>AAAnd we resume with the ad hominem attacks. They have told you **exactly** where your questions are answered, in a scholarly fashion. The answers are **surprise** IN THE PAPERS YOU REFUSE TO TRACK DOWN AND READ.


"That's just bibliography bluffing."
To repeat, it's not bibliography bluffing if the answers are where they tell you to look. Please go look there. Skim the articles, if need be, to isolate the particularly relevant passages AND THEN GO READ THOSE PASSAGES. It's called research.

"People have all sorts of reasons for asking questions of papers' authors -- the questions may ask about something that was not covered in the paper, or may ask for a clarification of something in the paper, or may express a disagreement with something in the paper, or maybe the questioner missed something in the paper, or maybe the questioner did not read the paper thoroughly, or did not read the paper at all, or whatever. With all the conditions you are setting up for asking questions of the authors of scientific papers, no one could ever ask them any questions at all."
>>Scientists may have any and all of those reasons for asking questions. Scientists asked questions (such as yours) that are answered in the paper have a simple recourse. They tell the questioner to READ THE PAPER. If the questioner refuses to take such an obvious step, the scientist has no obligation to repeat the contents of the paper for the questioner. You allude to this kind of responsibility in many posts where you request that the commenters (AKA questioners) have read your post and all the comments.

Wednesday, July 02, 2008 3:52:00 PM  
Blogger Larry Fafarman said...

Answer to trolls:

You can't excuse the inexcusable.

Wednesday, July 02, 2008 4:35:00 PM  
Anonymous Anonymous said...

Larry, I'll assume your last comment was self-referential.

Wednesday, July 02, 2008 5:27:00 PM  
Anonymous Anonymous said...

"Ric barfed"
"NightFlare driveled"
"Phae barfed"
"LostSailor driveled"

These are only a few of the juvenile attacks you've launched on other posters trying to explain this. They're not even original. You're not polite and you're not very smart (calling scientific terms "gobbledygook" doesn't help the image). If you want to play in the scientific arena, you've got to read the paper in question and all related literature, comprehend them, and then make criticisms based on data and your own analysis. It's not bibliography bluffing- it's standard procedure. You can't simply complain that the language is to difficult for you, or that people won't spoon feed it to you (which they have).

The E. Coli experiment and the previous explanations are clear if you want to listen, but if you won't learn to swim then get out of the pool.

Sunday, July 13, 2008 1:56:00 PM  
Anonymous Anonymous said...

last post!

Sunday, August 24, 2008 3:39:00 PM  
Anonymous Anonymous said...

his comments were quite clear. The proffessor was well aware that e coli dont use citrates but the fact they are there provides a potential resource that would be interesting if a mutation occurred to use it.
I would assume that nutrient limitation was used as a stressor to encourage a more robust organism, though that is conjecture. Questions should really be addressed to Proffessor Lenski rather than the other team members .

Friday, September 05, 2008 8:59:00 PM  
OpenID pulnimar said...

Forgot to mention this in my previous comment: I'd originally assumed the minimal media with a very low supply of glucose was used to limit the number of bacterial generations per day - to make it more manageable.

With extremely rich media it's hypothetically possible to get 36 - 72 population doublings (presumably "generations") per 24 hour period. Freezing them down every 500 generations would mean freezing them down every week or two - this would quickly add up in terms of storage space.

Having generations that fast in media that rich would also reduce any selective pressure among the bacteria in forms of competition or niche exploitation, and would mean a greater number of conceivable mutations would have a negative effect on fitness when they would otherwise have a positive effect on fitness in a less utopian environment (ie. you'd be making a large number of evolutionary pathways dead ends given everything is already ideal for the parent strain).

Having generations that fast would also mean that any experimental tests (such as the citrate experiment) would have to be done at breakneck speed, with a speedily written paper, just to get them done in time to do the next experiment or paper the fast generation times demand.

Saturday, January 03, 2009 2:01:00 PM  
Anonymous Anonymous said...

It is amazing that so many people continue to argue with Mr. Fafarman. Young earthers, creationists, anti-evolutionists, IDers, and the like believe they have all the answers in their bible. No amount of evidence, discussion, or name calling will change their minds. They base their arguments on matters that cannot be proven or disproven.

I admire everyone's perseverance but I just get so damn tired and frustrated. Its like holding up a red ball to someone and they continually tell you it’s a blue square. How do you argue with that? Keep up the good fight.

Thursday, February 12, 2009 1:42:00 PM  
Blogger Larry Fafarman said...

>>>>>> They base their arguments on matters that cannot be proven or disproven. <<<<<<

Just like Darwinists.

Thursday, February 12, 2009 1:55:00 PM  
Anonymous Kaonashi said...

Ya know, I know it's an old topic, but I just couldn't resist.
The question was asked whether evolving a strain of E.Coli was one of the "goals" of the experiment.
Let me try to answer this question in a way that perhaps Larry could understand.
When I go to the grocery store, I know from previous experience that it's possible that I may find a $20 bill on the ground while on my way to the store. My GOAL for the trip is to purchase food. Finding a $20 bill on the ground is a lucky chance, one that I knew was possible, but not something I actively set out to achieve.
It's the same thing with the E.Coli. Lenski knew that evolving E.Coli was a possibility, a lucky chance, but it was not an intended goal of the experiment as you seem to think it was.
When you set a goal, you actively work towards achieving that goal (like building a house). If you happen to achieve something else at the same time (like getting stronger), that doesn't make the secondary achievement a goal also.

Tuesday, September 28, 2010 12:47:00 AM  
Blogger Larry Fafarman said...

>>>>>>> When you set a goal, you actively work towards achieving that goal (like building a house).<<<<<<<

I was wondering if the purpose of the glucose cycling was to work towards a "goal" of producing citrate-eating bacteria. I feel that when you take certain actions to make achieving something more likely, that something is a "goal" because you are taking special action to try to achieve it.

Wednesday, September 29, 2010 9:51:00 PM  

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