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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"Stop creationists undermining school science"

A New Scientist magazine opinion piece titled "Stop creationists undermining school science" says,

Say that you are in charge of developing a state-wide high-school curriculum in French-language studies, and that you need the advice of a group of experts on how to put together the ideal programme. Is it better for officials to appoint these people, or for the public to vote on who they regard as the most attractive candidates for the job?

To put it another way, should you need minimum qualifications to be eligible to serve? Should you be required to know some French? Should you be disqualified if you openly profess that French is not a useful language, and that the curriculum should focus on Italian instead?

"Yes" is surely the sensible answer to the last three questions. Yet in the US, we are taking exactly the opposite approach in allowing elected officials who are both ignorant and biased to define the science curricula for public-school students.

I greatly prefer the fundies of the former Dover school board to the stupid scientists and science educators who put the statement "evolution is the fundamental concept underlying all of biology" in the new Florida state science standards.

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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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Judge "Jackass" Jones still on lecture circuit

I think that Judge John E. "Jackass" Jones III's fifteen minutes of fame were probably up a long time ago. There will be no more listing in Time magazine's list of the world's 100 most influential people. No more listing as one of Wired magazine's 10 sexiest geeks. No more honorary degrees. And the ex-celebrity judge who once got more speaking requests than he could handle is probably getting few speaking requests today. But he is giving occasional public speeches. I previously noted that he is scheduled to be a keynote speaker at Hofstra University's "Darwin's Reach" conference. And a NY Times article titled "Philadelphia Set to Honor Darwin and Evolution" says,

Nine academic, scientific and cultural institutions around the city are holding a Year of Evolution, a series of exhibitions, seminars and lectures to celebrate the 200th anniversary of the birth of Charles Darwin next February, and the 150th anniversary of the publication of his seminal work, “The Origin of Species.”

Events will include a talk by John E. Jones III, a federal judge who ruled in 2005 that teaching intelligent design — the belief that some aspects of nature are so complex that they must be the work of a higher power rather than of evolution — in public school science classes was unconstitutional.

I wonder if Judge Jones will continue to violate his pledge to not speak publicly about the specifics of the Kitzmiller v. Dover case.

Also, I wonder why Philadelphia, of all places, is holding a "Year of Evolution" celebration.

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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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Judge "Jackass" Jones to blame for crosses burned into students' arms by creationist teacher

Well, maybe I am exaggerating a little. But Judge John E. "Jackass" Jones III set himself up to be a scapegoat here by greatly intensifying the culture war by issuing his extremely activistic pro-Darwinist Kitzmiller v. Dover decision.

A news report in a Columbus, Ohio newspaper says,

A Mount Vernon teacher undermined science instruction in the public school district by discrediting evolution in his classroom and focusing on creationism and intelligent design, a probe has found

Eighth-graders who were taught by John Freshwater frequently had to be re-taught in high school what they were supposed to have learned in Freshwater’s class, according to outside investigators hired by the district.

For 11 years, other teachers in the school district and people in the community complained about Freshwater preaching his Christian beliefs in class and slamming scientific theories, a school administrator told investigators . . .

Freshwater had been told to stop teaching intelligent design and creationism, but he continued, the report found . . .

The report confirms that Freshwater burned crosses onto students’ arms, using an electrostatic device, in December.

The technique that was used to burn the crosses onto students' arms is described in another news article.

It is ironic that this incident happened in Ohio, because in 2006 the Ohio Board of Education, intimidated by lawsuit threats that were based on the Dover decision, decided to repeal an Ohio evolution lesson plan that included the weaknesses of evolution. This Ohio BoE decision is discussed in a group of articles under the post label "Ohio controversy" on this blog.

As ye sow, so shall ye reap.

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Darwinist roaders go off deep end

Picture is courtesy of the Uncommon Descent blog.

This has got to be the living end. This puts the "I love Darwin" knick-knacks and "Friend of Darwin" certificates (given to the Dover plaintiffs team) to shame.

Also, this Jesus-Darwin smooching logo is being sold on T-shirts, caps, stickers, and mugs.

What we need is a Hitler-Darwin smooching logo.

Another example of Darwinist roaders going off the deep end is the Clergy Letter, which treats criticism of Darwinism as blasphemous or sacrilegious. The Clergy Letter says,

We believe that the theory of evolution is a foundational scientific truth, one that has stood up to rigorous scrutiny and upon which much of human knowledge and achievement rests. To reject this truth or to treat it as “one theory among others” is to deliberately embrace scientific ignorance and transmit such ignorance to our children. We believe that among God’s good gifts are human minds capable of critical thought and that the failure to fully employ this gift is a rejection of the will of our Creator. To argue that God’s loving plan of salvation for humanity precludes the full employment of the God-given faculty of reason is to attempt to limit God, an act of hubris.

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Many "standing to sue" rules should be dumped

I think that a lot of the restrictions on standing to sue should be abolished. The argument that particular such restrictions are necessary to prevent the courts from being "swamped" with lawsuits does not hold water -- the time and expense of suing are sufficient deterrents against frivolous lawsuits. Often restrictions on standing are not definite deterrents because of uncertainty over whether the courts will apply restrictions or recognize exceptions to the restrictions -- for example, in my federal lawsuits against the smog impact fee, my proposed exception to general federal-court tax-suit immunity -- that California had "left the sphere that is exclusively its own" (Parden v. Terminal Railway) by basing the fee entirely on the state's special status under federal auto emissions laws and regulations -- should have been accepted by the courts. Arbitrariness and capriciousness in the restrictions on standing and in applying the restrictions on standing result in unfairness and gross iniquities. Often standing is lost because of mootness caused by lapse of time, and the courts' own delays are often responsible for this particular cause of loss of standing. The right to judicial review should be treated as a very strong right. Some restrictions on standing to sue are arguably unconstitutional because they restrict the federal courts' jurisdiction in areas where the Constitution grants jurisdiction to the federal courts. Following a rule of standing at the expense of violating the Constitution is straining at a gnat and swallowing a camel. The time and resources that are lost because of disputes over standing to sue exceed the time and resources that are saved by having restrictions on standing to sue. There is not even consistency in the rules of standing to sue -- for example, despite the "injured-in-fact" rule supposedly based on the "cases and controversies" rule of Article III of the Constitution, the "citizen suit" provisions of environmental laws do not require allegations of actual or potential harm to anyone or anything. I am not saying that all restrictions on standing to sue are bad, but many are.

One thing that we need to get rid of is this "taxpayer" standing crap. Ironically, under the stupid taxpayer standing rules, there would be standing to sue over a religious symbol on public property if the symbol were privately funded but not if the symbol were government funded!

In the establishment clause lawsuit against the UC-Berkeley evolution website, the issue of taxpayer standing should not apply because the lawsuit is over the way the tax funds are used, not over the allocation of tax funds. The plaintiffs are not demanding that the National Science Foundation or the state stop funding the evolution website. The issue of whether there should be taxpayer standing because of a potential reduction in taxes or a potential refund in taxes does not apply to this lawsuit.

Judges are often afraid to make exceptions to general rules because of a fear that being overruled by a higher court, particularly a supreme court (federal or state), will damage their reputations. However, it is doubtful that a well-reasoned exception to a general rule would be overruled by a supreme court, because overruling the exception would (1) require the supreme court to overturn a precedent that was the basis of the exception and/or (2) make the rules even more complicated than they already are. For example, if the lower court judges had ruled in my favor in my lawsuit against the smog impact fee, the US Supreme Court could have reversed their decision only by repudiating the Supreme Court's own ruling that a state loses its immunity against federal lawsuits when the state "leaves the sphere that is exclusively its own" (Parden v. Terminal Railway) by trespassing into areas that are exclusively under federal jurisdiction.
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Behe slams Judge "Jackass" Jones

In a review of Ken Miller's new book "Only a Theory: Evolution and the Battle for America’s Soul," Michael Behe says,

At a number of points he lovingly quotes Dover trial Judge John Jones, either not recognizing or purposely ignoring the fact that Jones’ opinion was pretty much copied word for word from a document given to him by the plaintiff’s attorneys; there’s no evidence that Jones comprehended any of the expert testimony at the trial — even Miller’s own testimony. Miller even quotes the passage from “Jones”’ opinion which blatantly mischaracterized my testimony, placing in my mouth words that the plaintiff’s attorney had actually spoken. But even that has been gone over many times; if you read the newspaper and some blogs, all this is very old hat.

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Update on establishment clause lawsuit against UC-Berkeley website

I previously reported that an establishment clause lawsuit against a UC-Berkeley evolution website (Caldwell v. Caldwell) was dismissed in a federal district court on the absurd grounds that the plaintiffs lacked taxpayer standing to sue. The Evolution News & Views website reports that last month the 9th Circuit federal court of appeals heard oral arguments on an appeal of the lawsuit. What surprises me is that the oral arguments described in the report only concerned the merits of the lawsuit and did not even mention the dismissal. The district court opinion did not even make a ruling on the merits:

In view of the above holding, the court need not, and does not, reach the parties' arguments on the merits of the Establishment Clause claim. This conclusion is further buttressed by the fact that the court, as described above, is currently unable to take judicial notice of defendants' website. As such, the court does not have access to what defendants argue is the necessary and relevant context in which to evaluate plaintiff's claim.
Accordingly, consideration on the merits is premature at this juncture, and is better suited for resolution if and when the case is again before this court.(page 13)

So there is no decision on the merits for the appeals court to review, no decision on the merits to affirm or reverse. So why is the appeals court listening to arguments on the merits of the lawsuit? And why is the dismissal not mentioned in the EN&V report?

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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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Bizarre parasitisms a challenge to evolution

A caterpillar of the geometrid moth Thyrinteina leucocerae with pupae of the Braconid parasitoid wasp Glyptapanteles sp.

Full-grown larvae of the parasitoid egress from the caterpillar and spin cocoons close by their host. The host remains alive, stops feeding and moving, spins silk over the pupae, and responds to disturbance with violent head-swings. The caterpillar dies soon after the adult parasitoids emerge from the pupae. Photograph by Prof. José Lino-Neto. Picture courtesy of Universiteit van Amsterdam

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Previously my arguments about co-evolution were restricted to the evolution of obligate mutualism (i.e., total co-dependence of two different kinds of organisms) because I thought that only co-evolution of obligate mutualism could require that a mutation in one kind of organism be immediately answered by a corresponding mutation in another kind of organism at the same geographical location in order to produce a benefit or even just for survival. I didn't see parasitism per se as a problem for evolution because I assumed that mutations involving parasitism do not require an immediate corresponding mutation in the other organism. However, I have just discovered literature about bizarre parasitisms that may require changes in the traits of the host and so also may be a problem for evolution.

The abstract of a scientific article titled "Parasitoid Increases Survival of Its Pupae by Inducing Hosts to Fight Predators" says,

Abstract
Many true parasites and parasitoids modify the behaviour of their host, and these changes are thought to be to the benefit of the parasites. However, field tests of this hypothesis are scarce, and it is often unclear whether the host or the parasite profits from the behavioural changes, or even if parasitism is a cause or consequence of the behaviour. We show that braconid parasitoids (Glyptapanteles sp.) induce their caterpillar host (Thyrinteina leucocerae) to behave as a bodyguard of the parasitoid pupae. After parasitoid larvae exit from the host to pupate, the host stops feeding, remains close to the pupae, knocks off predators with violent head-swings, and dies before reaching adulthood. Unparasitized caterpillars do not show these behaviours. In the field, the presence of bodyguard hosts resulted in a two-fold reduction in mortality of parasitoid pupae. Hence, the behaviour appears to be parasitoid-induced and confers benefits exclusively to the parasitoid.

The Merriam-Webster online dictionary defines "parasitoid" as "an insect and especially a wasp that completes its larval development within the body of another insect eventually killing it and is free-living as an adult."

Here are some excerpts from the article (the numbers are reference numbers) --
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Diseases, parasites and parasitoids can induce spectacular changes in the behaviour of their host [1]–[11]. Some of these changes, such as behavioural fevering [12] and exposure to cold temperatures [13], are thought to benefit the host, but others have been suggested to result in increased transmission of parasites [1], [3], [4], [14]–[17] or increased survival of parasitoids [18]–[22]. One of the most famous examples is the parasitic trematode Dicrocoelium dendriticum, which induces its intermediate host, ants, to move up onto blades of grass during the night and early morning, and firmly attach themselves to the substrate with their mandibles [3]. This is believed to enhance parasite transmission due to increased ingestion of infected ants by grazing sheep, the final host [23]. In contrast, uninfected ants return to their nests during the night and the cooler parts of the day. Other examples of such spectacular behavioural changes include parasitoid larvae (Hymenoepimecis sp.) that induce their spider host (Plesiometa argyra) to construct a special cocoon web in which the larvae pupate [7], rodents infected by Toxoplasma that lose their innate aversion to odours of cats, the parasite's final host [9], and hairworms that induce their terrestrial arthropod hosts to commit suicide by jumping into water, after which the hairworms desert the host to spend their adult stage in their natural habitat. [6], [8]

Regarding the caterpillar and wasp,

Parasitoid larvae are known to interfere with host endocrine functions, causing the host to stop feeding before parasitoid larvae egress [10], [28], [31]–[35]. Levels of juvenile hormone, ecdysteroids and neurotransmitters (e.g. octopamine) have been found to increase shortly before parasitoid egression [33]–[35]. However, it is not clear whether parasitoid larvae produce these substances in sufficient quantity to change host behaviour [10], [34]. Moreover, the most important behavioural changes in the present study occur only after the parasitoids have egressed. The egression usually takes about 1 hour, and the caterpillars do not respond strongly to disturbance during egression, but only 1–2 hours after the event. This casts doubt on the role of the parasitoid larvae in the behavioural changes. However, when we dissected caterpillars from which parasitoids had egressed 3–4 days before, we found 1–2 active parasitoid larvae that had remained behind in the host, as has been found in another system [36]. We hypothesise that these parasitoid larvae are responsible for the changes in host behaviour. A similar mechanism has been described for the trematode D. dendriticum [37] and the liver fluke Brachylecithum mosquensis [23], which both use ants as an intermediate host. One or two of the parasites migrate to the ant's brain, where they encyst and are believed to affect the ant's behaviour. These so-called brainworms are not transmitted, and appear to be sacrificed to enable transmission of their kin [38]. If the parasitoid larvae of the system described here also stay behind to manipulate the host and do not pupate later, this would represent a cost of host manipulation: some offspring are sacrificed for higher survival of their kin [39]. This hypothesis needs further investigation.

Amazing.

The paper is discussed in ScienceDaily.

Another bizarre example of parasitism is described on the blog of science writer Carl Zimmer. To him, it's all just a simple matter of evolution:

Scientists don't yet understand how Ampulex manages either of these feats. Part of the reason for their ignorance is the fact that scientists have much left to learn about nervous systems and metabolism. But millions of years of natural selection has allowed Ampulex to reverse engineer its host. We would do well to follow its lead, and gain the wisdom of parasites.

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Creationists take gloves off and come out swinging

Fed up after years of being pushed around by hardline Darwinist roaders and their running dogs, John E. "Jackass" Jones III and other federal judges, creationists have finally taken the gloves off and come out of their corner swinging. These creationists are mad as hell and they are not going to take it anymore! In an article titled "Should evolutionists be allowed to vote?", Tom Willis said in the newsletter of The Creation Science Association for mid-America,

Claim #3: At least a million new biological structures have formed in the last 500 million years. The only "proof" of this claim takes the form of the Petri dishes above. Bacteria are subjected to some chemical, or other treatment. The change in environment is designed to kill, and many die, but some develop resistance to the new environment. Evolutionists shout, "Evolution is just change, change is everywhere, evolution is a fact!" This is a bit like noticing dents in your child's wagon, and deciding that rocks change wagons, therefore more rocks might turn it into a car. Pause and consider that evolution is sold as a process capable of producing Man from bacteria, but what is demonstrated is bacterial resistance to some chemical. Of the million or so biological structures that evolutionists need, not one has ever been observed, much less demonstrated! It is a simple fact that, in the entire history of man, not one new biological structure has ever been observed. Thus, their theory is an absurd religious insanity. But it gets worse.

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Darwinist bigotry

I found this gem of a comment on Panda's Thumb:

When one thinks about how biology could be taught, it would be possible to make evolution the central theme of such a course. It could be a very exciting and interesting course.

If the fundamentalist anti-evolutionist political activism had not kept biology courses from developing over the last century, we could have had some extremely good courses evolving from the experiences of teaching, learning and administering such courses. As it is, the first major attempt by BSCS met with political resistance and we were set back another 40 years.

I hope we learn from these experiences with ID/Creationism and stop treading lightly in the presence of fundamentalist activism. They need their toes stomped on and their asses kicked. Biology could be really fun.

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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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Both Louisiana houses pass similar academic freedom bills!

In several articles, Evolution News & Views reports today (June 11) that both houses of the Louisiana state legislature have passed academic freedom bills by veto-proof -- and maybe even Dover-proof (LOL) -- margins. The differences in the two bills need to be reconciled, which appears likely.

Something was needed to counteract the intimidating effects of the Kitzmiller v. Dover decision. Considering the lopsidedness of the votes in both houses of the Louisiana legislature (94-3 in the House, 35-0 in the Senate), it is amazing that no state has enacted an academic freedom law in the 2-1/2 years since the Dover decision or the 3-1/2 years since the Selman v. Cobb County decision. I assumed that fear of taxpayer wrath over the real or imagined legal costs of defending an academic freedom law was a major factor in intimidating state legislators, but it is obvious that the Louisiana state legislators were mostly not intimidated.

Both houses of the Florida state legislature recently passed academic freedom bills, but the two bills were so different that they could not be reconciled.

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The Great Satan in Dover

I previously wrote about the new book The Devil in Dover: An Insider's Story of Dogma v. Darwin in Small-town America. Now a review of the book, written by Wesley "Ding" Elsberry, has appeared on Panda's Thumb. Ding says of the book's author Lauri Lebo, a former newspaper reporter,

. . .there is the personal struggle with those in her profession who misconstrue journalistic “objectivity” perversely as a charge not to speak the truth when a situation indicates that a “side” is plainly in the wrong.

It's part of something called journalistic ethics, Ding -- something that an unscrupulous BVD-clad blogger like yourself can't understand (I prefer "BVD-clad" to "pajama-clad" because Hugh Hefner considers pajamas to be formal wear). When reporting the news, journalists are supposed to present only facts and are not supposed to analyze or interpret the facts. Imagine how stupid a news report about a lawsuit would look if that report labeled one side as wrong. The Code of Ethics of the Society of Professional Journalists says that journalists should,

— Distinguish between advocacy and news reporting. Analysis and commentary should be labeled and not misrepresent fact or context.

Ding Elsberry wrote,
.

Lauri’s descriptions of Buckingham’s frailties and foibles don’t gloss over or diminish his truly monstrous behavior, but they do lend a humanizing touch to someone otherwise known primarily or only for his unswerving intolerance of the religious views of others.

"Truly monstrous behavior"? The only truly monstrous behavior was by his persecutors. Buckingham and other members of the school board agreed to adopt a heavily pro-Darwinist main biology text on condition that the ID book "Of Pandas and People" be adopted as a supplemental text. The Dover science teachers agreed to the compromise. Copies of "Of Pandas and People" were placed in the school library and the teachers were required to read to the science classes a one-minute evolution-disclaimer statement that announced the books. The Pandas book was not required reading. Only Darwinism was actually taught. The science teachers then reneged on the compromise by refusing to read the one-minute statement (the statement was read by administrators instead) and some parents of students sued the school board over the one-minute statement.

Ding Elsberry wrote,

The courtroom provided the denouement for the tragi-comic story of the principal “intelligent design” advocates on the school board who chose to lie rather than expose their policy to a possible temporary restraining order. The depositions of those people taken in early January, 2005 provided clear evidence that Bill Buckingham and Alan Bonsell purposely concealed information pertaining to the purchase of 60 copies of the “intelligent design” textbook, “Of Pandas and People”.

The money to purchase the books was collected at a church. In a comment thread under a previous post on this blog, I said,

The donors' identities and motives should not have been a factor in the case and in fact the questioning about them should have been ruled out of order. In describing her new endorsement test, Justice O'Connor said, "The Establishment Clause prohibits government from making adherence to a religion relevant in any way to a person's standing in the political community." Fundies had the same standing as anyone else to anonymously donate money for the books.

Ding Elsberry is so badly deluded that he still thinks that perjury charges against Buckingham and Bonsell are a possibility -- Ding wrote in the comment thread under his article,

About the perjury issue… AFAIK, that’s still “under investigation”. It will be news, briefly, if it is announced that they have dropped it or will prosecute.

The list of the book's endorsers on the book's official website looks like a who's who of Darwinist bigots. There's Judge John E. "Jackass" Jones III himself -- his endorsement of this biased book speaks volumes about his own bias (he said in a commencement speech that his decision was based on his notion that the Founders based the establishment clause upon a belief that organized religions are not "true" religions). There are endorsements from arbitrarily-censoring fact-fabricating BVD-clad bloggers Fatheaded Ed Brayton and Wesley "Ding" Elsberry. Edward Humes, author of another pro-Darwinist (though less biased) book about the trial, "Monkey Girl," is also there (there is a post label "Monkey Girl" in the sidebar of this blog).

Amazon.com customer reviews of the book are off to a very slow start, even slower than "Monkey Girl"s -- only four reviews have been posted in the first month or so. One of those reviews is the review that Elsberry posted on Panda's Thumb. There have also been relatively few responses to the question "Was this review helpful to you?" and only one outside comment in response to the customer reviews, my response to John Kwok's review (Kwok's response to my comment of course does not count as an outside comment). It looks like the "The Devil in Dover" is going to turn out to be an even bigger flop than "Monkey Girl," which was once touted as the definitive book about the "trial of the century." "Monkey Girl" has had comparatively little customer-review activity on Amazon.com. I don't think that customer-review activity on Amazon.com is in general the sole indicator of a book's popularity, but I think it is a pretty good indicator for non-fiction books on controversial subjects. I think that most people don't care about the Dover case anymore -- to most people, it's yesterday's news, even in the Dover area. Lauri Lebo said in a recent interview,

Q. Where do things stand in Dover now? Has the issue died down?

A. People don’t talk about it much. Folks there have to get along with each other. But one thing is pretty clear. I doubt that anybody’s mind was changed by the trial. Bill Buckingham still calls Judge Jones’ decision “a case of unjustifiable homicide.” And he still forwards me chain e-mails urging me to accept Jesus Christ as my savior.

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Discovery Institute hardly knows the half of it

The New York Times has a news article with the misleading title "Opponents of Evolution Adopting a New Strategy" and a related editorial with the title "The Cons of Creationism" (which should be titled "The Cons of Darwinism" -- the Darwinists are the ones who are conning us).

Robert Crowther said in Evolution News & Views,

Let's review. In 1998, the Texas Board of Education adopted the current set of science standards calling on students "to analyze, review, and critique scientific explanations, including hypotheses and theories, as to their strengths and weaknesses using scientific evidence and information . . . .This is the language that the New York Times now insists is a new development!

John West said in Evolution News & Views,

As previously pointed out, the New York Times botched its recent story about the science standards debate in Texas, implying that support for covering the “strengths and weaknesses” of evolution is supposedly a new strategy on the part of Darwin critics. The only problem is that the “strengths and weaknesses” language in the Texas Science Standards was adopted some 10 years ago in 1998, and so there is nothing new about it.

Then John West said in another article, titled "Message to New York Times Editorial Page: Hire a Fact-Checker,"

The Times apparently hasn’t been paying attention to Texas during the past decade, because (as we pointed out last week) the “strengths and weaknesses” language the Times’ editorialists so fear has been part of the Texas science standards since at least 1998! In short, the Texas State Board of Education isn’t considering whether to add “strengths and weaknesses” language; it’s the Darwinists who are trying to remove the language that has been in the Texas science standards for a decade.

You dummies, the New York Times news article itself says that the "strengths and weaknesses" language was added to the Texas science standards "in the late 1980's":

The “strengths and weaknesses” language was slipped into the curriculum standards in Texas to appease creationists when the State Board of Education first mandated the teaching of evolution in the late 1980s.

Steven Schafersman of the Texas Citizens for Science says that the "weaknesses" language in the Texas science standards may have been first adopted as early as the mid 1980's --

I was present at the very SBOE meeting in the mid to late 1980s (I have not had time to search long-stored records to find the correct date, but the experience is still vivid in my memory) when the "weaknesses" language was first adopted for a textbook proclamation that included biology texts.

So it looks like the Discovery Institute needs a fact checker, too.

Also, John West says in one of the articles,

As for whether “other states are likely to follow” Texas’s example: the Times’ editorial writers clearly haven’t been paying attention to what has been happening in those other states over the last decade. Six states already call for the critical analysis of evolution in their science standards—Minnesota, New Mexico, Pennsylvania, South Carolina, Alabama, and Missouri. Contrary to the Chicken Littles at the Times, the sky hasn’t fallen in any of them.

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Alabama has even had evolution-disclaimer textbook stickers of the kind banned in Selman v. Cobb County.

It is disgraceful for such a prominent reference as the New York Times to spread such misinformation. Who do they think they are, Wikipedia?
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A deserving recipient of the "Friend of Darwin" award

"Friend of Darwin" certificates were distributed at a reunion of the Dover plaintiffs team.

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Darwinists try to dogmatize Texas science standards

I decided to drop the "a" because some people found "Darwinistas" to be offensive. It is against my principles to disparage anyone on the basis of race, color, sex, national origin, etc..

A NY Times article erroneously titled "Opponents of Evolution Adopting a New Strategy" says,

DALLAS — Opponents of teaching evolution, in a natural selection of sorts, have gradually shed those strategies that have not survived the courts. Over the last decade, creationism has given rise to “creation science,” which became “intelligent design,” which in 2005 was banned from the public school curriculum in Pennsylvania by a federal judge.

The term "creation science" (sometimes called scientific creationism) appeared much longer ago than the last decade -- the term appears in the McLean v. Arkansas Board of Education district court decision of 1982 and the Edwards v. Aguillard Supreme Court decision of 1987. Also, creationism did not directly give rise to "creation science" and intelligent design," because the latter two disciplines are based on scientific observations and reasoning and not on religious sources. Finally, the federal judge did not ban ID "from the public school curriculum in Pennsylvania" -- he only banned it from the Dover Area school district.

The article continues,

Now a battle looms in Texas over science textbooks that teach evolution, and the wrestle for control seizes on three words. None of them are “creationism” or “intelligent design” or even “creator.”

The words are “strengths and weaknesses.”

Starting this summer, the state education board will determine the curriculum for the next decade and decide whether the “strengths and weaknesses” of evolution should be taught. The benign-sounding phrase, some argue, is a reasonable effort at balance. But critics say it is a new strategy taking shape across the nation to undermine the teaching of evolution, a way for students to hear religious objections under the heading of scientific discourse.

That's ridiculous -- it is like arguing that teaching evolution is an underhanded way of introducing atheism into public schools.

The NY Times article says,
.

The “strengths and weaknesses” language was slipped into the curriculum standards in Texas to appease creationists when the State Board of Education first mandated the teaching of evolution in the late 1980s. It has had little effect because evolution skeptics have not had enough power on the education board to win the argument that textbooks do not adequately cover the weaknesses of evolution.

How can the words "strengths and weaknesses" be a "new strategy" (as claimed by the article's title) if the words have been in the Texas science standards since the late 1980's? It is certainly not new in Texas.

The NY Times article says,

“Serious students will not come to study in our universities if Texas is labeled scientifically backward,” said Dr. Dan Foster, former chairman of the department of medicine at the University of Texas Southwestern Medical Center at Dallas.

There we go again with that tired old familiar "scaring them away, denying us opportunities, making us a laughingstock" bogeyman again.

The NY Times article says,

Although the state education board is free to set aside or modify their proposals, committee members will recommend that the “strengths and weaknesses” phrase be removed, said Kevin Fisher, a committee member who is against the teaching of creationism.

“When you consider evolution, there are certainly questions that have yet to be answered,” said Mr. Fisher, science coordinator for the Lewisville Independent School District in North Texas.

But, he added, “a question that has yet to be answered is certainly different from an alleged weakness.”

Mr. Fisher points to the flaws in Darwinian theory that are listed on an anti-evolution Web site, strengthsandweaknesses.org, which is run by Texans for Better Science Education.

“Many of them are decades old,” Mr. Fisher said of the flaws listed. “They’ve all been thoroughly refuted.”

The Darwinists are not willing to just maintain the status quo, but are seeking to roll back the protections of critics and criticism of Darwinism.

“[A] question that has yet to be answered is certainly different from an alleged weakness”? If the question could be answered, it wouldn’t be a weakness. Also, an unanswered question about evolution is a flaw in the theory, so how could alleged flaws in evolution have "all been thoroughly refuted" if unanswered questions about the theory exist?

Also, the Darwinists have a double standard. They say of unanswered questions about Darwinism, “we don’t know the answers now, but we are working on finding the answers and we may find them someday," but they say that no new questions or revisions of old questions are going to be found in the future.

Yes, I remember reading intelligent-design and irreducible-complexity arguments many decades ago, but a lot of the evidence is of recent origin. Recent discoveries have shown that cells are not just amorphous blobs of protoplasm as previously presumed but contain remarkably complex nanomachines (e.g., bacterial flagella), biochemical factories (e.g., the blood-clotting cascade), and data-processing systems (e.g., genetic codes).

The NY Times article has stirred a lot of interest and controversy and articles about it have been posted on Evolution News & Views, Panda's Thumb, Uncommon Descent, etc. (see sidebar for links).

It used to be that Cornelia Dean wrote the Darwinist hatchet jobs for the NY Times. Now it looks like the NY Times has a new hatchet man (or, should I say, hatchet woman or hatchet person?), the author of this article, Laura Beil.

The story was also covered by the San Antonio Express-News.

Also, the National Center for Science Education reported,

Steven Schafersman of Texas Citizens for Science told NCSE, "What Bradley and his colleagues actually plan to do is damage evolution instruction by trying to get the new science standards to mention alleged but false 'weaknesses' of evolution, in order to weaken evolution content, confuse students and make them think science is less accurate and reliable than it really is about biological origins, and intimidate teachers to avoid or minimize the subject (as many of them do now in Texas)." With respect to Bradley's description of evolution as theory not fact, he added, "This banal canard is indulged in by every creationist who thinks he can get away with it. ... Evolution is a fact, if fact is defined as something for which so much reliable evidence exists that it would be irrational to deny it."

Wow -- so evolution is a fact. I guess that settles it, doesn't it?

Steven Schafersman wrote a long article about the controversy for Texas Citizens for Science.

A NY Times editorial says,

The Texas State Board of Education is again considering a science curriculum that teaches the “strengths and weaknesses” of evolution, setting an example that several other states are likely to follow. This is code for teaching creationism.

It has the advantage of sounding more balanced than teaching “intelligent design,” which the courts have consistently banned from science classrooms. It has the disadvantage of being nonsense.

"[W]hich the courts have consistently banned from science classrooms"? Only one judge ever ruled on intelligent design, Judge John E. Jones III in Kitzmiller v. Dover.

Darwinists’ paranoia towards all criticisms of Darwinism is stifling scientific inquiry. For example, the Florida Citizens for Science blog has banned me from discussing co-evolution there.

I discuss co-evolution in several articles in the "Non-ID criticisms of evolution" post-label group in this blog. This post label is also in the sidebar.
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Can Yoko sue "Expelled" under foreign copyright laws?

Famous last words (is he saying "I don't deserve to die" or "I could have kept myself out of this chair if I were a lawyer"?)

A coin-operated, do-it-yourself electric chair. "When a coin is inserted, and the switches are pulled, the condemned man twitches and jerks in the chair. Sparks fly and the odor of burning hair is emitted from the panel."

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

As a result of the lifting of the temporary restraining order in the federal lawsuit against "Expelled," the way is now clear for the movie to open as scheduled in Canada on June 6. Some people are now asking if Yoko can sue the "Expelled" producers under copyright laws in foreign countries.

You will never see me say "I am not a lawyer," often abbreviated "IANAL." In fact, the expression "IANAL" is one of my pet peeves. Telling laypeople that they can't understand the law sends a message to young people that they shouldn't bother to get educations. When I don't know something about the law, I look it up, just like a lawyer would.

Wikipedia says about the Berne Convention,

The Berne Convention for the Protection of Literary and Artistic Works, usually known as the Berne Convention, is an international agreement about copyright . . .

Since almost all nations are members of the World Trade Organization, the Agreement on Trade-Related Aspects of Intellectual Property Rights requires non-members to accept almost all of the conditions of the Berne Convention.

As of April 2008, there are 163 countries that are parties to the Berne Convention

The Berne Convention requires its signatories to recognise the copyright of works of authors from other signatory countries (known as members of the Berne Union) in the same way it recognises the copyright of its own nationals, which means that, for instance, French copyright law applies to anything published or performed in France, regardless of where it was originally created.

The USA became a member of the Berne Union in 1989.

One of the questions that arises is: if "Expelled" is shown or sold in a foreign country, does that country's copyright law apply just to the movie itself or does it also apply to copyrighted works contained in the movie?

I investigated further by looking at the provisions of the Berne Convention.

Articles 5(1) and 5(2) says,

(1) Authors shall enjoy, in respect of works for which they are protected under this Convention, in countries of the Union other than the country of origin, the rights which their respective laws do now or may hereafter grant to their nationals, as well as the rights specially granted by this Convention.

(2) The enjoyment and the exercise of these rights shall not be subject to any formality; such enjoyment and such exercise shall be independent of the existence of protection in the country of origin of the work. Consequently, apart from the provisions of this Convention, the extent of protection, as well as the means of redress afforded to the author to protect his rights, shall be governed exclusively by the laws of the country where protection is claimed.

One of "the rights specially granted by this Convention" is "fair use." The applicable parts of Article 10 [Fair Use], say,

(1) It shall be permissible to make quotations from a work which has already been lawfully made available to the public, provided that their making is compatible with fair practice, and their extent does not exceed that justified by the purpose, including quotations from newspaper articles and periodicals in the form of press summaries.

- - - - - - - -

(3) Where use is made of works in accordance with the preceding paragraphs of this Article, mention shall be made of the source, and of the name of the author, if it appears thereon.

Article 10, quoted above, says nothing about applying a foreign country's laws to claims of fair use -- all that is required is that the borrowing of other works be "compatible with fair practice" and that the extent of the borrowing "does not exceed that justified for the purpose." "Expelled"s use of "Imagine" easily satisfies these criteria -- if "Expelled"s use of "Imagine" is not fair use, then nothing is fair use. Also, it is reasonable to expect that countries should give "full faith and credit" to the originating country's determination of fair use, because otherwise chaos would result. Also, Article 10(3) above is satisfied by the credits shown at the end of the "Expelled" movie.

Article 6bis says,

(1) Independently of the author's economic rights, and even after the transfer of the said rights, the author shall have the right to claim authorship of the work and to object to any distortion, mutilation or other modification of, or other derogatory action in relation to, the said work, which would be prejudicial to his honor or reputation.

"Expelled" did not distort, mutilate, or otherwise modify "Imagine." As for "other derogatory action," "Expelled" did not misrepresent John Lennon's actual views, particularly in view of John Lennon's statement -- made several years prior to recording "Imagine" -- that the Beatles were "more popular than Jesus."

Article 19 [Right to Claim Greater National Protection] says,

The provisions of this Convention shall not preclude the making of a claim to the benefit of any greater protection which may be granted by legislation in a country of the Union.

I think that the above loophole would be unavailable to Yoko Ono in all or almost all foreign countries because all or almost all foreign countries would consider this to be fair use. Also, this loophole appears to contradict Article 5(2) -- cited above -- in regard to fair use. And under Article 33 [Disputes among countries], the USA may be able to dispute another country's finding that this is not fair use.

In short, IMO Yoko Ono cannot dispute "Expelled"s fair use claim in foreign countries.
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Welcome, visitors from Sleazy PZ Myers' Pharyngula blog

Sleazy PZ Myers' Pharyngula blog has caused the biggest spike of traffic since I installed Sitemeter in August 2006 (the Sitementer logo is at the bottom of the sidebar). I normally get around 40-60 visits per day (some are repeat visits from the same person), but I got 392 visits yesterday and over 300 visits so far today. The "By Referral" list on the Sitemeter shows that most of the extra visits are coming from Sleazy PZ's "Killfile Dungeon", where I am at the top of the list of banned commenters. Sleazy PZ referred readers to his Killfile Dungeon when he added another commenter ("Kenny") to the list, and readers who saw the link to this blog -- which Sleazy PZ calls "a bottomless pit of stupidity" -- apparently decided to pay this blog a visit out of curiosity.

My most-recommended articles here are my articles about co-evolution, which are under the post label titled "Non-ID criticisms of evolution". My ideas about co-evolution are considered so dangerous that they were banned from Panda's Thumb and the blog of the Florida Citizens for Science.

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Update on state court suit against "Expelled"

The On the Cover Songs blog reports that the defendants have moved for dismissal of the complaint in the state-court suit against "Expelled." The oral hearing on the motion is scheduled for June 9. The plaintiffs in the state court suit are EMI Records and Capitol Records, not Yoko Ono et al.. As I noted before, the name of the court, Supreme Court of the State of New York, is a misnomer -- this is a trial court of original jurisdiction.

The case documents show that no temporary restraining order was issued in state court (the federal-court TRO has now been lifted). Actually, because the US Constitution gives Congress jurisdiction over copyrights and interstate commerce, I question the authority of a state court to take any kind of action to enforce a copyright, including any action that applies just to a state.

Unlike in federal courts, a PACER account is not needed to view at least some of the case documents in this state court (some federal court decisions can be viewed without PACER if the court chooses to post them). I don't see the reason for the following rule: "Except in matrimonial cases, . . . .judgments are not entered by the County Clerk until an attorney for a party to the case appears at the Judgment Clerk's desk (Rm. 141B at 60 Centre Street) and requests entry."

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Evolution and Fatheaded Ed Brayton. Again.

In a blog article titled Evolution and the Texas Board of Education. Again., Fatheaded Ed says,

The Texas State Board of Education may be the single most ridiculous legislative body in America. . . . they're about to take up the science standards yet again, which can only lead to absurdity. Just take a look at some of the quotes from school board members in this article.

Ken Mercer, R-San Antonio, said that standard is clear and worth keeping.

"We want our children to be able to think and understand the strengths and weaknesses of any theory. Some ultra-radical groups have not evolved to the point where they realize that the 'theory of Evolution' is just that -- a theory," Mercer said.

I've got news for you, Mr. Mercer: every single explanation offered in every single scientific subject in Texas schools is "just a theory." . . . . A theory is not a wild assed guess and it's not a step on the way to something else . . . . Theory is the highest level of certainty granted to scientific explanations.

Wrong, Ed -- law is the highest level of certainty granted to scientific explanations. Here I am using the term "explanation" in a broad sense to include explanations of how as well as why. Also, there is no reason why a theory cannot be a step on the way to something else.

Fatheaded Ed continues,
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Once again I am left wondering why in the world we let people who have no expertise whatsoever in science determine the science curriculum in public schools. Doing so is positively irrational. We would not dream of electing a state licensing board for, say, medical schools and putting people on that board without any training in medicine. It is no less absurd to allow people with no background in science to decide what is taught in science classes.

Sheeeesh, Ed, the article said that Ken Mercer has a degree in biology from the University of Texas at Austin.

There once was a blogger named Ed,
who was known as a stupid fathead.
The stuff he did write,
on his blogging site,
was like a balloon filled with lead.

The story is also covered in an article in the NY Times.
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Hamas leader says Darwinism is a Zionist tool

Following are excerpts from an interview with Saleh Riqab, Hamas deputy minister of religious endowment, which aired on Al-Aqsa TV on May 14, 2008:

Saleh Riqab: The goal of the Zionist movement is to establish a state in Palestine, which would become a base for ruling the entire world. Its other goals are to destroy the religions it opposes, particularly Islam; to corrupt values and morality; to spread permissiveness and sex; and to generate moral decline.

They have come up with many means to achieve this, such as inventing philosophical theories that destroy religion and morality . . . . .

. . . . . There are also theories that were invented by non-Jews, but they disseminate them, knowing that they are scientifically false, such as the theory of Darwin. Darwin was not Jewish, but they exploited his theory. Even though new Darwinist theories have appeared, they spread the original theory, because the concept of "survival of the fittest" serves their colonialist needs.

Interviewer: That's what the theory says.

Saleh Riqab: Yes. It serves the goals of global Jewry.

Saleh Riqab is correct to some extent -- some major Jewish organizations, notably the Anti-Defamation League and the American Jewish Congress, have embraced Darwinism with a vengeance. The ADL's embrace of Darwinism is beyond all sense and reason -- for example, the ADL called the rabidly pro-Darwinist Kitzmiller v. Dover decision a "victory for students." The ADL's opposition to anti-semitism may be assumed to represent all Jews, but the ADL's support of Darwinism certainly does not represent all Jews -- many Jews, particularly orthodox Jews, strongly oppose Darwinism.

However, I think that a large part of the interview consists of demagogic nonsense:

Saleh Riqab: By the way, I'd like to say something... I don't want to mention names. The viewers will know what I mean. There is a book called Les Fous de la Paix, which was written by two Jewish journalists. I have a copy. It was translated into Arabic, and I've read it. It mentions that one of the architects of the Oslo Accords was meeting with the Jewish negotiator at a hotel in Britain. According to the book, in an adjacent room, the son of the Palestinian negotiator was with the daughter of the Jews, and they locked the door. That's when the Palestinian negotiator was brought down.

[...]

We see this clearly in the U.S. elections. Both Democrats and Republicans compete to please the state of the Jews. That's why when a Democrat comes to occupied Palestine, he puts on a religious skullcap, goes to the Western Wall, bangs his head against the wall, and says: "Your philosophy and the need to please you is now inside my head." They all compete with one another, but the Jews maintain a balance, and they always prefer the Christian Zionists.

If a Democrat comes to power, like [Bill] Clinton -- who served them well in Oslo and elsewhere, and almost served them in the second Camp David, but then made statements [they didn't like] -- what did Zionism do? It sent him the Jewish Monica, with whom Clinton had sex in the American White House.

Clinton left [the White House], but there are thousands of pages documenting his sexual depravity, because he had sex in the White House. I read a report that Clinton used to call Arab leaders and talk to them while she was having sex with him.

Interviewer: My God!

Saleh Riqab: These things are documented, but the Arabs don't read them.

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I re-installed the Sitemeter

The Sitemeter, at the bottom of the side bar, records visitor data. To see details of the data, just click on the Sitemeter icon.

I temporarily removed the Sitemeter because it was causing loading of the blog to hang up. I re-installed it and everything seems to be working OK again.

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Judge expels Yoko's suit against "Expelled"

JUDGE GIVES TWO THUMBS UP FOR FAIR USE

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In a 23-page opinion, a federal judge has denied Yoko Ono et al.'s motion for a preliminary injunction against the producers of "Expelled" for alleged infringement of the copyright of the song "Imagine." We have not yet heard from the state court judge but I expect him to follow suit.

The ruling is hardly surprising -- Yoko et al. had a very weak case. The only thing that I was worried about was the claim that the movie producers discriminated against "Imagine" because they paid licensing fees for other music in the film, but the judge dismissed that claim.
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Though this ruling is only on a motion for a preliminary injunction, for all practical purposes it is a final ruling -- all significant issues have been thoroughly addressed and there are no additional facts to discover. Yoko et al. can appeal, but IMO they would be wasting their time -- they lost on all of their claims in the district court. They could still lose an appeal even if they win some of their claims.

The Darwinists' invective against the "Expelled" producers for using the song without permission was incredible -- for example, Josh Rosenau, who is on the staff of the National Center for Science Education, titled a post on his Thoughts from Kansas blog, "Expelled steals from the dead".

My prediction that the judge's opinion would be a 100-page dissertation was not far off the mark -- it was 23 pages (actually only about 22 pages if the heading and signature section are subtracted). That is a lot more than I got in my lawsuit against the "smog impact fee" -- I got no oral hearing and no written opinion, even though my argument against defendant California -- that the state lost its federal-court tax-suit immunity by "leaving the sphere that is exclusively its own" (Parden v. Terminal Railway of the Alabama State Docks Dept.) by basing the fee entirely on the state's special status under federal auto emissions laws and regulations -- was so airtight that the state's attorney did not even attempt to answer it.

Comments about the ruling may be left at the following websites: Panda's Thumb, Wall Street Journal Law Blog. I will add other sites that allow commenting when I find them --

Lessig Blog
Pharyngula
Uncommon Descent
.

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