More thoughts on the Cit+ E. coli evolution experiment

Prospector A: What are you looking for?
Prospector B: The Lost Dutchman Mine. But finding it is not a goal.

I have established a new post label for the Citrate-eating E. coli evolution experiment. Post labels are listed in the sidebar.

Whether evolution of Cit+ (citrate-eating) E. coli bacteria was an initial "goal" (I use the standard definition of "goal," and there are such things as secondary goals, longshot goals, incidental goals, etc.) when the long-term E. coli evolution experiment began in 1988 has not been established, but it occurred to me that Cit+ evolution must at least have become a "goal" sometime along the way because the experimenters must have been checking for the appearance of Cit+ bacteria because the Cit+ bacteria were detected when they were only 0.5% of the population at about 31,500 generations.

Also, someone suggested that the popular name for the first mutation (~20,000 generations), the "potentiating" mutation, is wrong, because the name implies that this first mutation was a pre-requisite for the second mutation and there is no evidence (at least so far as I know) that it is a pre-requisite. Below is part of a comment that I posted on another blog in response to another comment:
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"If the cit+ mutation had occurred first, wouldn't we be calling the later potentiating mutation the cit+ mutation instead? "

I prefer saying that a mutation "became established" as opposed to saying that a mutation "occurred" -- some mutations, particularly mutations that occurred in one of the last generations of a daily population, might have been lost when only one percent of each daily population was used to start the next day's population.

The first mutation, the so-called "potentiating" mutation, was a "silent" (unexpressed) mutation that became established at around 20,000 generations (~ 9 years); the second mutation, which was expressed as the Cit+ trait, became established at around 31,500 generations (about 5 years later). The "potentiating" mutation is apparently very unusual because the Cit+ trait appeared in only one of the 12 lines of bacteria -- the second mutation is apparently relatively common because the Cit+ trait appeared repeatedly when the experiment was re-run starting with frozen samples from generations containing the "potentiating" mutation (generations numbered 20,000 or later). Because the second mutation is fairly common, the Cit+ trait probably would have appeared in the other 11 lines of bacteria if the first mutation were common. IMO there is no evidence that the first mutation was really a "potentiating" mutation in the sense of being a pre-requisite for the second mutation, so IMO you are right in questioning use of the term "potentiating" to describe the first mutation.

It also occurs to me that it was wrong to call the first mutation "silent" and the second mutation "expressed," because either mutation would be silent in the absence of the other. So maybe it would be best to use the names "mutation A" and "mutation B," respectively, for the first and second mutations.
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Darwinists' bad theory that they own the word "theory"

Update: I have been checking the definitions of "theory" in different places and it is apparent that this idea that a "scientific theory" is by definition well-supported and widely accepted has been concocted solely for the purpose of promoting the theory of evolution.

Darwinists are under the illusion that they can change people's perception of Darwinism by changing changing or restricting popular meanings of the word "theory." In the abstract of an article ironically titled "'Theory' in Theory and Practice," Glenn Branch and Louise S. Mead of the National Center for Science Education say,

Abstract A central obstacle to accepting evolution, both among students and the general public, is the idea that evolution is “just a theory,” where “theory” is understood in a pejorative sense as something conjectural or speculative. Although scientists and textbooks constantly explain that the scientific use of “theory” is quite different, the pejorative use continues to cause confusion, in part because of its deep roots in a popular, Baconian, understanding of science. A constructivist approach, whereby students are helped to examine the adequacy of their preconceptions about “theory” for themselves and to revise or replace them appropriately, is recommended.

For one thing, trying to change change or restrict popular meanings of a term, even just within a particular context such as a scientific context, is an unrealistic task and is going to create or increase confusion. Also, the level of confidence represented by the word "theory" is highly variable even within the scientific meaning of the word -- there can be "strong" scientific theories and "weak" scientific theories. Also, I think that this flexibility in meaning is necessary because otherwise there would be no terms to cover "theories" at all levels of confidence. Also, even if the word "theory" is just colloquially interpreted as meaning "guess," the word can be interpreted in a specific instance as meaning a "good guess" or a "bad guess" or anything in between. It is foolish to try to manipulate people's views of evolution by trying to create a special definition of the word "theory." When a word has a broad meaning or different meanings within a given context, people who want to convey a particular meaning need to do so by means of elaboration rather than by assuming that other people are going to interpret the word as having the intended meaning.
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BTW, in mathematics, the term "theory" often means a branch of mathematics that has been rigorously proven. Some well-known mathematical theories are probability theory and set theory. A related word, "theorem," often means something in mathematics that has been proven, e.g., Pythagorean theorem and binomial theorem, but "theorem" does not always mean something that has been rigorously proven.

Branch and Mead discuss the controversy over adding the term "scientific theory" to the term "evolution" in the Florida state science standards:

. . . in Florida, just days before the state board of education was scheduled to vote on the new state science standards in 2008, there was a proposal to insert the phrase “the scientific theory of” before mentions of evolution. As the Orlando Sentinel reported, “By adding the word theory, which many opponents of the standards had argued for, the new version may appease those who do not view evolution as a scientific fact or those whose religious beliefs are in conflict with evolution” (Postal 2008). Clumsy, unnecessary, and apparently opposed by a majority of the writing committee, the revisions were accepted anyway, despite a valiant effort on the part of board member Roberto Martinez, who described the revisions as “an effort by people who are opposed to evolution to water down our standards” (Bhattacharjee 2008).

As the dust settled, though, it was increasingly clear that the revisions did not, after all, succeed in materially compromising the scientific integrity of the standards. Evolution was not invidiously singled out for attention: plate tectonics, cell theory, atomic theory, electromagnetism, and the Big Bang all received the same treatment.

Also, the final version of the Florida state standards gives its own non-dictionary definition of "theory," and -- as I indicated -- I think that is a wrong thing to do:

Recognize and explain that a scientific theory is a well-supported and widely accepted explanation of nature and is not simply a claim posed by an individual. Thus, the use of the term theory in science is very different than how it is used in everyday life. (page 50 of document, page 54 of pdf file)

Unfortunately, the debate over using the word "theory" in the Florida science standards completely pushed aside the debate over the outrageous statement "evolution is the fundamental concept underlying all of biology," which remains in the final version of the standards (page 89 of document, page 93 of pdf file).

Controversy over the meaning of "theory" also arose in the Selman v. Cobb County evolution-disclaimer textbook-sticker case, particularly in regard to the phrase, "evolution is a theory, not a fact." The complete statement of the textbook sticker was,

This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully, and critically considered.

Selman noted that a version that was proposed by a teacher and approved by the administration (but ignored by the school board, in large part because the school board had already voted on language that their counsel thought was constitutional) said,

This textbook contains material on evolution, a scientific theory, or explanation, for the nature and diversity of living things. Evolution is accepted by the majority of scientists, but questioned by some. All scientific theories should be approached with an open mind, studied carefully and critically considered.

The statement "Evolution is accepted by the majority of scientists, but questioned by some" is an example of how an intended meaning of the term "theory" can be narrowly specified.

On Evolution News & Views, Casey Luskin is starting a five-part series that discusses the following questions:

1. Are Darwinists correct to define "theory" as "a well-substantiated scientific explanation of some aspect of the natural world" or "a comprehensive explanation of some aspect of nature that is supported by a vast body of evidence"?

2. Under such a strong definition of "theory," does evolution qualify as a "theory"?

3. Is it correct to call evolution a "fact"?

4. Is it best for Darwin skeptics to call evolution "just a theory, not a fact"?

5. All I wanted to say is that I’m a scientific skeptic of neo-Darwinism. How can I convey such skepticism without stepping on a semantic land mine and getting scolded by Darwinists?”

Also, in discussions of the study of evolution of Cit+ (citrate-eating) E. coli bacteria, there was a lot of confusion over the meaning of the word "goal." Zachary Blount, the lead author of the paper on the study, said that he believed that the Cit+ evolution was foreseen as a possible and desirable result of the experiment but it was "not a goal." To me, that is a definition of "goal" -- something foreseen as a possible (or sometimes even virtually impossible) and desirable result. For example, in a search for the Fountain of Youth, finding it is a "goal." So merely saying that Cit+ evolution was "not a goal" can be very misleading. The word "goal" needed to be qualified here, e.g., a secondary goal, a longshot goal, one of many goals, etc..
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My unchanged opinion of the Cit+ E. coli evolution study

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

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

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

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

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

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

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

Regarding the statement, "about ten times as much citrate" -- the standard recipe for the medium shows that there is twenty times more sodium citrate than glucose by weight, but the glucose might be a more efficient food source by weight.
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Andy Schlafly's unreasonable request for raw data of Lenski's E. coli experiment

Conservapedia's Andy Schlafly's unreasonable (IMO) request for the raw data of Lenski et al.'s E. coli experiment has stirred a great deal of interest and controversy on the Internet. Many websites have articles about it, and since mid-June the Conservapedia "project" page (with copies of the Schlafly-Lenski corespondence) has been accessed over 75,000 times and the corresponding Conservapedia talk (discussion) page has been accessed over 50,000 times. For comparison, Conservapedia's Theory of Evolution page, a popular page on Conservapedia, has been accessed about 317,368 times since it began in December 2006.

Who cares about the raw data? Lenski et al. claim to have the Cit+ (citrate-eating) E. coli bacteria, which are extremely rare (Cit+ evolution had been observed only once before), and claim to have E. coli bacteria with a strong tendency to evolve the Cit+ trait (i.e., frozen bacteria of 20,000 generations or later in one line). Using these bacteria, it would be fairly easy to verify or disprove the results of the experiment.

Also, requesting the raw data is wrong because (1) copying all of the raw data to send would be a huge job and (2) the raw data might not even be in a form that could be readily understood by someone who did not participate in the research.

IMO the controversy over Andy Schlafly's unreasonable request is overshadowing worthwhile commentary and discussion regarding the Cit+ evolution.

I would like to post this stuff on Conservapedia but I wore out my welcome there by voluminous answering of trolls' unreasonable criticisms of my legitimate complaint that the Cit+ paper's lead author Zachary Blount ignored my simple and basic questions about the experiment.

Prospector A: What are you looking for?

Prospector B: The Lost Dutchman Mine. But finding it is not a goal.

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A reason for glucose-cycling in Lenski's E. coli experiment

I asked Zachary Blount, the lead author of the paper on the evolution of Cit+ (citrate-eating) E. coli bacteria, if favoring Cit+ evolution was a purpose or one of the purposes of the glucose-cycling (giving the bacteria an insufficient supply of glucose so as to cause alternating glucose feeding and starvation), and he did not answer. What is he trying to hide? Maybe he is trying to hide the fact that the glucose cycling favored Cit+ evolution, because some people might regard that as cheating. Aha -- that must be the reason! Also, he did not answer my question about whether there were other purposes of the glucose-cycling. Now I have found another purpose on my own, and I deserve sole credit for the answer.

Each daily population of the 12 lines of bacteria was raised in 10 ml of medium, and one-percent -- i.e., 0.1 ml -- of each old population is transferred to start the next population. That ratio of the medium transfer allows a 100:1 growth in population to maintain the same final population density in the populations. Assuming a doubling of population with each generation, a 100:1 population growth would be reached in 6-7 (6.64, to be exact) generations. 6-7 generations occur in just a few hours (the populations are started in the morning and the glucose is exhausted by the afternoon). If more generations were allowed, the population density would become too high, which would limit capacity for population growth when the next population is started, so glucose supply is limited to limit the number of generations of glucose-eating-only bacteria. I presume that the 10 ml and 0.1 ml quantities are limited by the physical limitations of the lab equipment, e.g., the incubator size and the means for transferring the medium. If desired, the glucose starvation period could be eliminated by restarting the populations more frequently, but that would make the experiment even more labor intensive and I think it was desirable to have a glucose starvation period, anyway. The medium recipe says that the glucose supply could be varied, and the supply might have been varied to control population growth -- I don't know. The experimental procedure is described here.
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Also, as I noted before, Blount did not give straight answers to my question about whether Cit+ evolution was a goal of the experiment. If, say, Cit+ evolution was a secondary goal or a longshot goal, he would be misleading people by going around flatly telling them that Cit+ evolution was not a goal of the experiment. In a sane world, Blount's failure to answer my simple, basic questions would be widely condemned -- but this is not a sane world.

Another somewhat minor concern I have is the potential loss of mutations during transfer, but that loss is inevitable. Mutations occurring in one of the last generations in a daily population might exist in only one, two, or just a few bacteria and so would have only a small chance of being in the one-percent of the medium that is transferred to start the next generation.

The glucose supply was unbelievably small -- only 25 mg per liter or just 0.25 mg for the 10 ml medium for each population!

Anyway, what is the likelihood that anything similar to the carefully controlled conditions in this experiment could occur in nature? Even with these carefully controlled conditions that favored Cit+ evolution, the Cit+ evolution was a rare occurrence, occurring in only one of 12 lines of bacteria in 20 years.

Anyway, unlike Andy Schlafly over at Conservapedia, I see no reason to suspect error or fraud in the claims of Cit+ evolution. Lenski et al. claim that they have the Cit+ E. coli bacteria -- which are very unusual -- and also claim that they have E. coli bacteria that have a strong tendency to evolve the Cit+ trait (bacteria of 20,000 generations or later). It would be easy to verify or disprove the claims about Cit+ evolution.
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I am blocked on Conservapedia

I am now unable to post comments on Conservapedia because my IP address is blocked there. The excuse: violation of the "90/10 rule" -- i.e., large contributions to talk pages in comparison to contributions to the articles. I pointed out that I am new to Conservapedia and therefore have had no opportunity to contribute to the articles. Also, all of my comments on this talk page have been responses to other commenters' responses to my comments, and most of my comments have been defensive. It is outrageous that I am now unable to defend myself against attacks on my positions in that talk page. Conservapedia rules are no better than Wikipedia rules.

The disreputable practice of IP address blocking is often ineffective and often unintentionally blocks other Internet users who share the same ISP proxy. It also discriminates against Internet users who use only one IP address. Anonymous proxies are sometimes -- but not always -- effective in evading IP address blocks, and have not been effective lately.

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Edit war on Lenski talk page at Conservapedia!

Edit wars on talk (discussion) pages on wiki-based (i.e., normally editable by all readers) encyclopedias are rare but one is going on right now on Conservapedia's talk page about Lenski's E. coli experiment! Edit wars on the talk pages are generally considered to be no-nos -- the talk pages are supposed to be free-speech areas (unscrupulous Wickedpedian administrators censored my comments on talk pages). Here is a comment that one user added and another user censored on the Lenski talk page (Aschlafy should be spelled Aschlafly -- it's the username of Conservapedia founder Andy Schlafly):
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Stop the carping and do the right thing

The original hypothesis was that Professor Lenski was being disingenuous in both his paper and his dealings with “the public”. Professor Lenski has, politely and patiently, disclosed his data sufficient for his good intent to be verified. He then, again politely but less patiently, expanded on this. He has offered to share not just his data but also the “real data” contained in the genomes of his various strains of bacteria. Any hypothesis about Professor Lenski’s honesty has been thoroughly refuted.

However Aschlafy appears not to accept this refutation and, instead, appears to be trying to find something that is less than perfect about the various publications, review processes and disclosures to support the “Professor Lenski isn’t playing it straight” hypothesis. If you accuse someone of dishonesty when they have been honest you have done them wrong. The correct action is to stand up, like an adult, and apologise; it is not to desperately scratch around for something, anything, that would make the allegation justified. I would expect a grade schooler who had trespassed to come up with a string of excuses, why little Katy hadn’t lied but it was his turn on the swing anyway and so…. I would expect an adult to simply extend a hand, apologise and carry on.

I would suggest that Aschlafy acts like a man and publishes an apology to Professor Lenski. It does not have to be crawling, it does not have to be humbling. If it were me I would hope that I would write something like:

“I am sorry for the tone and the implication of my letters. As you are probably aware evolution is a big issue with me. I rather let the importance of that issue affect the way I wrote to you. Naturally I am happy to accept that you’ve been both honest and professional in your work and your publications. Again I think the emotive nature of the subject was behind what, in retrospect, are pretty silly accusations that were put on Conservapedia.

I may, in the future, try and organise some research in this area. I’m no biologist but Conservapedia and other organisations I am involved in may be able to organise the Discovery Institute or other organisations that do have the skills needed to perform the research. If so we may take you up on your offer of samples of the various strains. As our main aim will be to test the apparent support of your results for evolution per se I do not think that it would risk overlapping, and thus “scooping”, your research. I’m sure, however, that all the knowledge that you have gained over the years in this specific field could help us in designing the best tests. Who knows we may be able to devise a “critical test” of whether new information can arise in the genome.”

How about it Aschlafy?

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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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"Creationist critics get their comeuppance"

A New Scientist magazine blog article titled "Creationist critics get their comeuppance" attacks Conservapedia's and Michael Behe's responses to Lenski et al.'s paper about the evolution of citrate-eating E. coli bacteria:

A couple of weeks ago we reported on the work of Richard Lenski, who has spent much of the last 20 years maintaining cultures of E. coli to see how they evolve. His paper describes how one of his populations evolved the ability to metabolise citrate, something E. coli cannot do by definition.

It's one of the most dramatic examples of evolution in action ever seen, and because Lenski freezes samples of the population every 500 generations, it is possible to go back and track how the ability developed. Lenski and his team are now doing so, and hope to have a detailed history of the ability developing, mutation by mutation.

All in all we thought it was a pretty excellent piece of research, and plenty of other sites agreed: Pharyngula, for instance, devoted a lengthy post to it. However, such an unambiguous example of evolution in action was always going to bring the kooks out of the woodwork.

First up was Michael Behe, the intelligent design proponent and biochemist, who argued in his Amazon blog that Lenski's work was in fact excellent evidence for intelligent design. His argument is a variant on the usual "it's just so improbable" line: the ability to metabolise citrate required several different mutations (true), which each have a low chance of happening in a given time (true), and it may even have been necessary for them to happen in a particular order (true), therefore Darwinian evolution can't explain it. Er, no, it just means it would take evolution a little while to manage it. 20 years, as it turned out.

However, a far more amusing response came from Andrew Schlafly, the boss of Conservapedia. This, you may recall, is an alternative version of Wikipedia that aims to "correct the biases" of the original site - it has, for example, a young-Earth creationist viewpoint on evolution.

Schlafly wrote a brusque open letter to Lenski, expressing "skepticism" about his claims and demanding to see the data.

Well, the researchers still have not answered simple, basic questions about the paper, so who cares about the data?

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Crazy Conservapedia and Wikipedia rules

"So I'm the bad guy? How did that happen?"
-- D-Fens in movie "Falling Down"
(maybe D-Fens was really sane and it was the world that was crazy)



I have started posting on Conservapedia and have found that the Conservapedia rules are as crazy as the Wikipedia rules. For example, Conservapedia's "90/10 rule" says,

The 90/10 rule, unique to Conservapedia, authorizes the blocking of accounts that engage in excessive talk, bickering, last wordism, and other unproductive activity. Specifically, as has been stated in the rules since soon after the formation of Conservapedia:

Unproductive activity, such as 90% talk page edits and only 10% quality edits to Conservapedia articles, may result in blocking of the account

The 90/10 rule is remarkably adept at discouraging and eliminating the mobocracy or talk pollution that runs rampant on other sites, such as Wikipedia. Implementation is simple and application is swift.

"Last wordism" is defined as follows:
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Last wordism is the belief that victory can be obtained in a debate or discussion by having the "last word." Some argue that last wordism is often a characteristic of "less intellectually robust presentations."[1].

Last wordism reflects a lack of restraint, a characteristic of wrongdoing or sin. The ultimate in last wordism was men asking for Jesus to be crucified and Pontius Pilate stating that Jesus was to be crucified, to which God responded with the resurrection of Jesus Christ.

Wikipedia has what I call the "bears-don't-shit-in-the-woods-unless-a-reliable-nonpartisan-source-says-so" rule:

Editors should not make the mistake of thinking that if A is published by a reliable source, and B is published by a reliable source, then A and B can be joined together in an article to come to the conclusion C. This would be synthesis of published material which advances a position, which constitutes original research. "A and B, therefore C" is acceptable only if a reliable source has published this argument in relation to the topic of the article.

In other words, if a reliable nonpartisan source is found that says that bears shit all the time, and another reliable nonpartisan source is found that says that bears live in the woods, concluding that bears shit in the woods "would be synthesis of published material which advances a position, which constitutes original research," which is not allowed on Wackopedia. I am NOT exaggerating -- I ran into precisely this problem when I tried to add "Of Pandas and People" to the Wackopedia list of banned books.

Though I am now logged in on Conservapedia, I find that for some strange reason I cannot add more comments to a talk page that I myself started under my username LarryFarma. However, my original comment did get a favorable response from Conservapedia founder Andy Schlafly:

LarryFarma raises an excellent question about whether a goal of Lenski and Blount's project was to generate citrate-eating E. Coli bacteria. (I did not find the answer in the paper.) Did the researchers figure out, after many years of fruitless attempts, how best to promote the percentage of citrate-eating E. Coli bacteria in a population? The details of the data might shed light on how that goal was achieved, if in fact that was the goal. They should turn over the data for public scrutiny so that questions can be resolved.--Aschlafly 19:33, 26 June 2008 (EDT)

Some of the additional material that I wanted to post on Conservapedia is now posted here in this comment.
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Conservapedia requests raw data from Lenski's E. coli study

There has been a tremendous amount of interest and controversy concerning Richard Lenski et al.'s research into the evolution of E. coli bacteria. Now Andy Schlafly, founder of Conservapedia, is asking for the raw data from the research! If he doesn't trust the scientific paper that reported the research, then why should he trust the raw data?

On Carl Zimmer's blog, I am still getting the runaround in response to my questions about the study.

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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:
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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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Lenski's E. Coli bacterial microevolution experiment

A short description of the experiment is here; a longer description is here -- comments may be left in both places. The experiment is being performed by Richard Lenski and colleagues at Michigan State University. The results are being debated on Uncommon Descent [1] [2] and Panda's Thumb . The comment thread under Carl Zimmer's article is probably the best because he provides the most details about the experiment. Michael Behe's response is here. The debate has barely begun and some Darwinists are already rejoicing -- that's very open-minded of them.

I have barely begun to read others' comments about the experiment, but here are my own observations and questions so far:

The mutations appear to have occurred at two or even three stages: the first -- or preliminary -- mutation at around the 27,000th generation (around the 20,000th generation according to some sources), the second at around the 31,500th generation, and possibly a third around the 33,000th generation.

Question: To what extent did the first mutation spread through the population, if it spread at all, considering that it apparently conferred no advantage?

There were around 44,000 generations in 20 years, or about 2,200 generations per year. So assuming that the first mutation occurred at 27,000 generations and the second occurred at 31,500 generations, that would be about 2 years from the first mutation until the second mutation. That seems to mean that the second mutation is rare -- however, on the other hand this second mutation appears to be common because it was repeated numerous times by starting with the unfrozen samples of previous generations. So how could the second mutation be both rare and common at the same time? Maybe the second mutation is really quite common but is rarely expressed because there are relatively few individuals with the first mutation, which confers no advantage.

Carl Zimmer said,
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Blount took on the job of figuring out what happened. He first tried to figure out when it happened. He went back through the ancestral stocks to see if they included any citrate-eaters. For the first 31,000 generations, he could find none. Then, in generation 31,500, they made up 0.5% of the population. Their population rose to 19% in the next 1000 generations, but then they nearly vanished at generation 33,000. But in the next 120 generations or so, the citrate-eaters went berserk, coming to dominate the population.

Carl Zimmer gives the following explanation for the preceding observations:

This rise and fall and rise suggests that the evolution of citrate-eating was not a one-mutation affair. The first mutation (or mutations) allowed the bacteria to eat citrate, but they were outcompeted by some glucose-eating mutants that still had the upper hand. Only after they mutated further did their citrate-eating become a recipe for success.

Actually, the rise and fall at 31,500 and 33,000 generations respectively is not what indicates that the citrate-eating trait is not just a one-mutation affair, because -- as noted above -- it appears that an essential preliminary mutation occurred at around 27,000 generations (around 20,000 according to some sources).

Also, in a sense the citrate-eating bacteria are not really competing with the glucose-eating bacteria, because the two kinds of bacteria have different food sources.

The citrate-eaters were initially getting quite good at competing with the glucose-eaters, rising to 19% before nearly vanishing and then becoming dominant. Zimmer does not adequately explain why the citrate-eaters nearly vanished.

Also, Zimmer said,

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.

As I calculated above, there is an average of about 2,200 generations per year, so if a new population was started each day with a sample from an old population, then there were about 6 generations per population. With only 6 generations, there might be a significant possibility -- depending on the size of the sample -- that a mutation occurring in an old population would not be collected in the sample used to start the next population, particularly if the mutation occurred in one of the last generations of the old population. The populations should of course be well-stirred before collecting the samples to start the next populations - the Zimmer article says that the flasks full of E. coli were placed on a "gently rocking table," and I presume that means that the populations were well-stirred before collecting the samples.
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