Ed Brayton has discovered pure hilarity from the American Family Association’s news outlet, OneNewsNow.  The site apparently has a policy of never using the word “gay” in any of its stories, and it utilizes an automated algorithm to replace it with the word “homosexual”.  As Ed points out, that doesn’t work so well for a story about a sprinter named Tyson Gay:

Tyson Homosexual was a blur in blue, sprinting 100 meters faster than anyone ever has.

His time of 9.68 seconds at the U.S. Olympic trials Sunday doesn’t count as a world record, because it was run with the help of a too-strong tailwind. Here’s what does matter: Homosexual qualified for his first Summer Games team and served notice he’s certainly someone to watch in Beijing.

“It means a lot to me,” the 25-year-old Homosexual said. “I’m glad my body could do it, because now I know I have it in me.” (…)

Wearing a royal blue uniform with red and white diagonal stripes across the front, along with matching shoes, all in a tribute to 1936 Olympic star Jesse Owens, Homosexual dominated the competition. He started well and pulled out to a comfortable lead by the 40-meter mark.

This time, he kept pumping those legs all the way through the finish line, extending his lead. In Saturday’s opening heat, Homosexual pulled way up, way too soon, and nearly was caught by the field, before accelerating again and lunging in for fourth place.

OneNewsNow has since fixed the article, but thankfully someone saved a copy:

I wish the AFA knew how much of a laughing-stock they are.

This week I give you a crappy CGI frog extorting lifelong devotion at gunpoint. I’m not sure if this guy is trying to sound like Kermit the Frog, but if not, then he inadvertently picked an appropriate video avatar, because he sounds like Kermit on Quaaludes. Anyway, I find his presentation of God as the godfather extremely fitting. A deity who punishes those who refuse to worship him with eternal damnation is behaving exactly like a criminal kingpin demanding protection money. Not sure why anyone would worship such a self-obsessed entity.

As a consequence of the Lenski affair, I’ve spent some time over the last week or so peeking around Conservapedia.  Yes, I am a glutton for punishment.  Anyway, I noticed that on Conservapedia’s front page, it touts the entry on atheism as the “Article of the Year”.  It’s interesting that atheism is so threatening to them that they consider their hit piece on it to be the crowning achievement of Conservapedia.  Apparently the biggest concern of people like Andy Schlafly is that some of their home-school kids might stray from their religious instruction and become-gasp!-nonbelievers.

It probably goes without saying, but the Article of the Year has some serious problems.  Foremost of these, the article largely depends on ad hominem.  Several sections of the article attack atheism by impugning the character of atheists.  There is a section called, “Atheism and Communism”, and another implies that atheists have mental health problems.  Atheists are presented as suicidal, deceitful proponents of mass murder.  Such accusations are false, of course, but even if they were true, it would have no bearing on the truth or falsity of atheism.  For the most part, then, the article is substance-free fluff meant to inflame the emotions of readers against atheism.

There are, though, some places where Conservapedia attempts to engage atheism on substance.  I thought I would use the opportunity to write about some of the issues raised in the article because, in contrast to the simplistic presentation provided by Conservapedia, they are actually interesting.  The first of these issues is the definition of atheism.  The Conservapedia article defines atheism as the denial of the existence of god.  According to this definition, an atheist believes that god does not exist.  Conservapedia also defines an agnostic as one who “neither believes or disbelieves” in the existence of god.  So, according to Conservapedia, atheists believe that god does not exist, while agnostics simply do not believe that god exists.

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You might not be familiar with John Coleman, but he’s becoming quite the hero among the global warming denialist set.  Coleman is a meteorologist, and his big claim to fame is his founding of the Weather Channel.  He has since retired, but still holds a postition at a television station in San Diego.  He is also a huge denier of global warming, and his popularity with the right-wing has been growing since his threat to sue Al Gore for fraud.  Well it seems that Mr. Coleman spoke before the San Diego Chamber of Commerce the other day about global warming, giving a speech which included the following howler:

Let me illustrate. I estimate that this square in front of my face contains 100,000 molecules of atmosphere. Of those 100,000 only 38 are CO2; 38 out of a hundred thousand. That makes it a trace component. Let me ask a key question: how can this tiny trace upset the entire balance of the climate of Earth? It can’t. That’s all there is to it; it can’t.

I really don’t think it’s necessary to say anything about how ridiculous that statement is.  I trust that that’s pretty self-evident.  You might expect such a remark from a child, but from a grown man who is supposed have been educated (at least a bit) in atmospheric science?  Of course, it also says something about the credibility of many global warming skeptics that they treat this man as a qualified voice deserving to be heard on the issue of climate change.

Today is lab clean-up day for us, and it’s looking like an all-day affair.  So I might not get to post anything until this evening.  If you’re looking for stuff to read, though, I suggest checking out e! Science News, a scientific news aggregator put together by a Canadian grad student. I just learned of it this morning, but so far it looks pretty good.

The intolerable Michael Medved has penned a response to a recent pro-gay op-ed by Jonathan Rouch in the Wall Street Journal, and it’s on par with the rest of his fatuous catalog.  His thesis is that gay marriage lacks a “magic ingredient” that only heterosexual couples possess:

It’s not “marriage” – some magical status granted by the government – that serves to make people “healthier, happier and wealthier.” It’s the behavior associated with the marital ideal that brings benefits to couples and their children. That behavior doesn’t require official sanction – any more than official sanction guarantees such behavior. (…)

The problem with the Rauch argument and the biggest threat from same sex marriage itself involves flagrant distortion of the “magic ingredient” for lasting, socially beneficial relationships.

That ingredient isn’t governmental authorization or support. It is, rather, the uniting of male and female strengths and values in a durable combination.

He then treats us to much blather about the astounding, innate differences between the sexes, and how each sex brings unique characteristics into heterosexual relationships, concluding that, “a couple that blends male and female is fundamentally different from a couple with two men – just as that male-only relationship is distinct from a partnership of two women.”  Well, no shit.  But difference does that make?  According to Michael Medved, it means that gay and lesbian couples are ill-suited to be parents:

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Ads for scientific products tend to be forgettable, straightforward affairs.  After all, scientists aren’t exactly a huge market, and some of the items advertised run into the $30K or higher range.  From an advertisers prospective, you really just want to present your product and it’s advantages succinctly and be done with it.  Well, Eppendorf, manufacturers of everyone’s favorite 1.5 mL plastic tubes, has thrown that strategy right out the window and produced a music video for their newest product.  It’s some sort of automated pipetting system, and you can see the video here.  Here’s to hoping that this is the start of a new trend in scientific advertising.

Andy Schlafly has finally posted the text of Richard Lenski’s reply to the second request for his data.  It’s absolutely brutal (emphasis mine):

Dear Mr. Schlafly:

I tried to be polite, civil and respectful in my reply to your first email, despite its rude tone and uninformed content. Given the continued rudeness of your second email, and the willfully ignorant and slanderous content on your website, my second response will be less polite. I expect you to post my response in its entirety; if not, I will make sure that is made publicly available through other channels.

I offer this lengthy reply because I am an educator as well as a scientist. It is my sincere hope that some readers might learn something from this exchange, even if you do not.

First, it seems that reading might not be your strongest suit given your initial letter, which showed that you had not read our paper, and given subsequent conversations with your followers, in which you wrote that you still had not bothered to read our paper. You wrote: “I did skim Lenski’s paper …” If you have not even read the original paper, how do you have any basis of understanding from which to question, much less criticize, the data that are presented therein?

Second, your capacity to misinterpret and/or misrepresent facts is plain in the third request in your first letter, where you said: “In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000.” That statement was followed by a link to a news article from NewScientist that briefly reported on our work. I assumed you had simply misunderstood that article, because there is not even a mention of proteins anywhere in the news article. As I replied, “We make no such claim anywhere in our paper, nor do I think it is correct. Proteins do not ‘appear out of the blue’, in any case.” So where did your confused assertion come from? It appears to have come from one of your earlier discussions, in which an acoltye (Able806, who to his credit at least seems to have attempted to read our paper) wrote:

“I think it might be best to clarify some of Richard’s work. He started his E.Coli project in 1988 and has been running the project for 20 years now; his protocols are available to the general public. The New Scientist article is not very technical but the paper at PNAS is. The change was based on one of his colonies developing the ability to absorb citrate, something not found in wild E.Coli. This occurred around 31,500 generations and is based on the development of 3 proteins in the E.Coli genome. What his future work will be is to look at what caused the development of these 3 proteins around generation 20,000 of that particular colony. …”

As further evidence of your inability to keep even a few simple facts straight, you later wrote the following: “It [my reply] did clarify that his claims are not as strong as some evolutionists have insisted.” But no competent biologist would, after reading our paper with any care, insist (or even suggest) that “3 new and useful proteins appeared in the colony around generation 20,000” or any similar nonsense. It is only in your letter, and in your acolyte’s confused interpretation of our paper, that I have ever seen such a claim. Am I or the reporter for NewScientist somehow responsible for the confusion that reflects your own laziness and apparent inability to distinguish between a scientific paper, a news article, and a confused summary posted by an acolyte on your own website?

Third, it is apparent to me, and many others who have followed this exchange and your on-line discussions of how to proceed, that you are not acting in good faith in requests for data. From the posted discussion on your web site, it is obvious that you lack any expertise in the relevant fields. Several of your acolytes have pointed this out to you, and that your motives are unclear or questionable at best, but you and your cronies dismissed their concerns as rants and even expelled some of them from posting on your website. [Ed.: citation omitted due to spam filter] Several also pointed out that I had very quickly and straightforwardly responded that the methods and data supporting the evolution of the citrate-utilization capacity are already provided in our paper. One poster in your discussions, Aaronp, wrote:

“I read Lenski’s paper, and as a trained microbiologist, I thought that it was both thorough and well done. His claims are backed by good data, namely that which was presented in the figures. I went through each of the figures after Aschlafly said that they were uninformative. Actually, they are basic figures that show the population explosion of the bacterial cultures after the Cit+ mutation occurred. These figures show that the cultures increased in size and mass at a given timepoint, being able to do so because they had evolved a mechanism to utilize a new nutrient, without the assistance of helper plasmids. … Lenksi’s paper, while not the most definite I’ve seen, is still a very well-researched paper that supports its claims nicely.”

(As far as I saw, Aaronp is the only poster who asserted any expertise in microbiology.) As further evidence of the absence of good-faith discussion about our research, in the discussion thread that began even before you sent your first email to me, I counted the words “fraud” or “fraudulent” being used more than 10 times, including one acolyte, TonyT, who says bluntly that I am “clearly a fraudulent hack.” In the discussion thread that also includes comments after my first reply, the number of times those same words are used has increased to 20, with the word “hoax” also now entering the discussion. A few posters wisely counseled against such slander but that did not deter you. I must say, it is surprising that someone with a law degree would make, and allow on his website, so many nasty comments that implicitly and even explicitly impugn my integrity, and by extension that of my collaborators, without any grounds whatsoever and reflecting only your dogmatic adherence to certain beliefs.

Finally, let me now turn to our data. As I said before, the relevant methods and data about the evolution of the citrate-using bacteria are in our paper. In three places in our paper, we did say “data not shown”, which is common in scientific papers owing to limitations in page length, especially for secondary or minor points. None of the places where we made such references concern the existence of the citrate-using bacteria; they concern only certain secondary properties of those bacteria. We will gladly post those additional data on my website.

It is my impression that you seem to think we have only paper and electronic records of having seen some unusual E. coli. If we made serious errors or misrepresentations, you would surely like to find them in those records. If we did not, then – as some of your acolytes have suggested – you might assert that our records are themselves untrustworthy because, well, because you said so, I guess. But perhaps because you did not bother even to read our paper, or perhaps because you aren’t very bright, you seem not to understand that we have the actual, living bacteria that exhibit the properties reported in our paper, including both the ancestral strain used to start this long-term experiment and its evolved citrate-using descendants. In other words, it’s not that we claim to have glimpsed “a unicorn in the garden” – we have a whole population of them living in my lab! [ http://en.wikipedia.org/wiki/The_Unicorn_in_the_Garden] And lest you accuse me further of fraud, I do not literally mean that we have unicorns in the lab. Rather, I am making a literary allusion. [ http://en.wikipedia.org/wiki/Allusion]

One of your acolytes, Dr. Richard Paley, actually grasped this point. He does not appear to understand the practice and limitations of science, but at least he realizes that we have the bacteria, and that they provide “the real data that we [that’s you and your gang] need”. Here’s what this Dr. Paley had to say:

“I think there’s a great deal of misunderstanding here from the critics of Mr. Schlafly and obfuscation on the part of Prof. Lenski and his supporters. The real data that we need are not in the paper. Rather they are in the bacteria used in the experiments themselves. Prof. Lenski claims that these bacteria ‘evolved’ novel traits and that these were preceded by the evolution of ‘potentiated genotypes’, from which the traits could be ‘reevolved’ using preserved colonies from those generations. But how are we to know if these traits weren’t ‘potentiated’ by the Creator when He designed the bacteria thousands of years ago, such that they would eventually reveal themselves when the time was right? The only way this can be settled is if we have access to the genetic sequences of the bacteria colonies so that we can apply CSI techniques and determine if these ‘potentiated genotypes’ originated through blind chance or intelligence. But with the physical specimens in the hands of Darwinists, who claim they will get around to the sequencing at some unspecifed future time, how can we trust that this data will be forthcoming and forthright? Thus, Prof. Lenski et al. should supply Conservapedia, as stewards, with samples of the preserved E. coli colonies so that the data can be accessible to unbiased researchers outside of the hegemony of the Darwinian academia, even if it won’t be put to immediate examination by Mr. Schlafly. This is simply about keeping tax-payer-funded scientists honest.”

So, will we share the bacteria? Of course we will, with competent scientists. Now, if I was really mean, I might only share the ancestral strain, and let the scientists undertake the 20 years of our experiment. Or if I was only a little bit mean, maybe I’d also send the potentiated bacteria, and let the recipients then repeat the several years of incredibly pain-staking work that my superb doctoral student, Zachary Blount, performed to test some 40 trillion (40,000,000,000,000) cells, which generated 19 additional citrate-using mutants. But I’m a nice guy, at least when treated with some common courtesy, so if a competent scientist asks for them, I would even send a sample of the evolved E. coli that now grows vigorously on citrate. A competent microbiologist, perhaps requiring the assistance of a competent molecular geneticist, would readily confirm the following properties reported in our paper: (i) The ancestral strain does not grow in DM0 (zero glucose, but containing citrate), the recipe for which can be found on my web site, except leaving the glucose out of the standard recipe as stated in our paper. (ii) The evolved citrate-using strain, by contrast, grows well in that exact same medium. (iii) To confirm that the evolved strain is not some contaminating species but is, in fact, derived from the ancestral strain in our study, one could check a number of traits and genes that identify the ancestor as E. coli, and the evolved strains as a descendant thereof, as reported in our paper. (iv) One could also sequence the pykF and nadR genes in the ancestor and evolved citrate-using strains. One would find that the evolved bacteria have mutations in each of these genes. These mutations precisely match those that we reported in our previous work, and they identify the evolved citrate-using mutants as having evolved in the population designated Ara-3 of the long-term evolution experiment, as opposed to any of the other 11 populations in that experiment. And one could go on and on from there to confirm the findings in our paper, and perhaps obtain additional data of the sort that we are currently pursuing.

Before I could send anyone any bacterial strains, in order to comply with good scientific practices I would require evidence of the requesting scientist’s credentials including: (i) affiliation with an appropriate unit in some university or research center with appropriate facilities for storing (-80ºC freezer), handling (incubators, etc.), and disposing of bacteria (autoclave); and (ii) some evidence, such as peer-reviewed publications, that indicate that the receiving scientist knows how to work with bacteria, so that I and my university can be sure we are sending biological materials to someone that knows how to handle them. By the way, our strains are not derived from one of the pathogenic varieties of E. coli that are a frequent cause of food-borne illnesses. However, even non-pathogenic strains may cause problems for those who are immune-compromised or otherwise more vulnerable to infection. Also, my university requires that a Material Transfer Agreement be executed before we can ship any strains. That agreement would not constrain a receiving scientist from publishing his or her results. However, if an incompetent or fraudulent hack (note that I make no reference to any person, as this is strictly a hypothetical scenario, one that I doubt would occur) were to make false or misleading claims about our strains, then I’m confident that some highly qualified scientists would join the fray, examine the strains, and sort out who was right and who was wrong. That’s the way science works.

I would also generally ask what the requesting scientist intends to do with our strains. Why? It helps me to gauge the requester’s expertise. I might be able to point out useful references, for example. Moreover, as I’ve said, we are continuing our work with these strains, on multiple fronts, as explained in considerable detail in the Discussion section of our paper. I would not be happy to see our work “scooped” by another team – especially for the sake of the outstanding students and postdocs in my group who are hard at work on these fronts. However, that request to allow us to proceed, without risk of being scooped on work in which we have made a substantial investment of time and effort, would be just that: a request. In other words, we would respect PNAS policy to share those strains with any competent scientist who complied with my university’s requirements for the MTA and any other relevant legal restrictions. If any such request requires substantial time or resources (we have thousands of samples from this and many other experiments), then of course I would expect the recipient to bear those costs.

So there you have it. I know that I’ve been a bit less polite in this response than in my previous one, but I’m still behaving far more politely than you deserve given your rude, willfully ignorant, and slanderous behavior. And I’ve spent far more time responding than you deserve. However, as I said at the outset, I take education seriously, and I know some of your acolytes still have the ability and desire to think, as do many others who will read this exchange.

Sincerely,
Richard Lenski

P.S. Did you know that your own bowels harbor something like a billion (1,000,000,000) E. coli at this very moment? So remember to wash your hands after going to the toilet, as I hope your mother taught you. Simple calculations imply that there are something like 10^20 = 100,000,000,000,000,000,000 E. coli alive on our planet at any moment. Even if they divide just once per day, and given a typical mutation rate of 10^-9 or 10^-10 per base-pair per generation, then pretty much every possible double mutation would occur every day or so. That’s a lot of opportunity for evolution.

P.P.S. I hope that some readers might get a chuckle out of this story. The same Sunday (15 June 2008) that you and some of your acolytes were posting and promoting scurrilous attacks on me and our research (wasn’t that a bit disrespectful of the Sabbath?), I was in a church attending a wedding. And do you know what Old Testament lesson was read? It was Genesis 1:27-28, in which God created Man and Woman. It’s a very simple and lovely story, and I did not ask any questions, storm out, or demand the evidence that it happened as written at a time when science did not yet exist. I was there in the realm of spirituality and mutual respect, not confusing a house of religion for a science class or laboratory. And it was a beautiful wedding, too.

P.P.P.S. You may be unable to understand, or unwilling to accept, that evolution occurs. And yet, life evolves! [ http://en.wikipedia.org/wiki/E_pur_si_muove] From the content on your website, it is clear that you, like many others, view God as the Creator of the Universe. I respect that view. I find it baffling, however, that someone can worship God as the all-mighty Creator while, at the same time, denying even the possibility (not to mention the overwhelming evidence) that God’s Creation involved evolution. It is as though a person thinks that God must have the same limitations when it comes to creation as a person who is unable to understand, or even attempt to understand, the world in which we live. Isn’t that view insulting to God?

P.P.P.P.S. I noticed that you say that one of your favorite articles on your website is the one on “Deceit.” That article begins as follows: “Deceit is the deliberate distortion or denial of the truth with an intent to trick or fool another. Christianity and Judaism teach that deceit is wrong. For example, the Old Testament says, ‘Thou shalt not bear false witness against thy neighbor.’” You really should think more carefully about what that commandment means before you go around bearing false witness against others.

Schlafly is upset about Lenski’s response, telling his readers to “Take a good look at the attitude our tax dollars are paying for.”  Well Andy, you deserve it, and federal funding does not come with a stipulation that dipshit cranks be treated gingerly and with respect. So, kudos to Richard Lenski.  I think most scientists of his caliber would have simply deleted Schlafly’s email.  But instead he replied with appropriate vitriol.  Bravo.

The recently released survey by the Pew Forum on religious beliefs in America has been getting a lot of play in the news today, so I don’t have much to say that hasn’t been said already.  I would, however, like to note that 68% of American adults “believe that angels and demons are active in the world.”  Think about that.  Two-thirds of your fellow Americans believe that world events are being shaped, at least in part, by the actions of angels and demons.  I’ll take that drink now.

Joel Barofsky has written a baffling post at Uncommon Descent. In it, he attempts to argue that naturalism offers no reasons to protect the environment, but intelligent design does. Gag. His post is dedicated to the failure of naturalism to provide motivation for going green. He has a second post planned espousing the need for ID in environmentalism. If the first post is any indication, the follow-up will be a real gut buster.

Barofsky offers three alleged “naturalistic arguments” for addressing climate change. Unfortunately, he never defines what he means by “naturalism”, so it is hard to address his claims without running the risk of putting words in his mouth. With that risk in mind, I will take “naturalism” to be the view that the natural universe is all that exists, that there is no “supernatural” realm. Assuming I have Barofsky’s concept of naturalism correct, let’s take a look at his discussion of these naturalistic arguments for environmental protection.

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