Tuesday, December 14, 2010

Iconic Delusions

I don't have much time for blogging these days 'cause I'm in the middle of writing a textbook—trying to be as accurate as possible.

Watch Paul Nelson making comments about the authors of biology textbooks. He sounds very sincere. I think he actually believes that biology textbook authors are deliberately lying. Poor deluded Paul Nelson. That's why we call them IDiots.

Friday, December 10, 2010

A Test for True Christians

Denyse O'Leary doesn't think Theodosius Dobzhansky was a true Christian. She's angry at all those so-called "Christians" who accept evolution because, in her mind, science and Christianity are incompatible [If you are a Darwinist, can you be a Christian if people just say so ... ?].

What do you do about all those fake Christians who believe in theistic evolution? You develop a litmus test, of course.
... if you ask me whether someone is a Christian, I say, "Let him recite the Apostle's Creed and affirm that he believes it and renounces contrary doctrines."
Sounds like a plan. I'll quote the English Language Liturgical Consultation (ELLC) version of the Apostle's Creed and we can discuss whether believing it is compatible with science as a way of knowing. Doesn't look like it to me. Denyse is right!
I believe in God, the Father almighty,
   creator of heaven and earth.
I believe in Jesus Christ, God's only Son, our Lord,
   who was conceived by the Holy Spirit,
   born of the Virgin Mary,
   suffered under Pontius Pilate,
   was crucified, died, and was buried;
   he descended into hell.
   On the third day he rose again;
   he ascended into heaven,
   he is seated at the right hand of the Father,
   and he will come to judge the living and the dead.
I believe in the Holy Spirit,
   the holy catholic Church,
   the communion of saints,
   the forgiveness of sins,
   the resurrection of the body,
   and the life everlasting. Amen.

Thursday, December 09, 2010

Sign a Petition on CIHR Funding

Are you a Canadian researcher who cares about the dismal CIHR funding situation?

Sign the petition at: The CIHR Individual Grants Program. It may not do much good but at least you'll have 700+ friends (latest count).

Wednesday, December 08, 2010

The Cause of Speciation

Jerry Coyne is an expert on speciation. That's why it's always informative to read his latest thoughts on the problem. In spite of what many people might believe, the main cause of reproductive isolation—the actual speciation event according to the biological species concept—is due to accident, not adaptation. It's just one more example of the importance of random genetic drift in evolution.

Here's how Coyne puts it in his latest posting [“Reinforcement” and the origin of species].
Genetic barriers aren’t thought to arise for the purpose of keeping species distinct. Rather, they are usually thought to be evolutionary accidents: geographically isolated populations diverge genetically under natural selection or other evolutionary forces like genetic drift, and that divergence leads to the evolution of genetic barriers (mate discrimination, the sterility of hybrids, ecological differences, etc.) as byproducts of evolutionary change. For example, populations could adapt to different environments (one dry, one wet, for example), leading to them becoming genetically different. When these populations meet each other again, this genetic divergence could result in hybrids that don’t develop properly because the parental genomes are sufficiently diverged that they can’t cooperate in building a single individual.
I wish more people would assimilate this message. It seems to be the overwhelming consensus among the experts in speciation but the average scientist still has an adaptationist view of speciation (and of evolution in general).

Speaking of adaptationists, Coyne also likes the idea that some examples of reproductive isolation can be reinforced by natural selection. You can read about those cases on his blog.

Let Oprah know that Kim Tinkham died of cancer

Kim Tinkham died of cancer today. Orac wants you to Let Oprah know that Kim Tinkham died of cancer. I've already sent my message to Oprah. Why don't you send one?

Watch the video. Oprah sends very mixed messages. On the one hand she advises following the advice of doctors but at the same time she supports The Secret.

DNA, Phosphorus, and Arsenic

Most of you know that DNA strands have a sugar-phosphate background. The bases in each strand are covalently linked to each other by phosphodiester linkages between the 5′ and 3′ carbon atoms of the deoxyribose sugar.

Recently there has been a claim by NASA-funded scientists that a certain bacterium can replace those phosphates with arsenic. Close examination of the Science paper has revealed that, at most, a few percent of the phosphorus atoms are replaced and even that amount is challenged. It has become abundantly clear from reading the paper that the bacteria absolutely required phosphorus and sufficient quantities were present in the media as contaminants.

I've already linked to Rosie Redfield's critiques of the paper and the press conference. Now I want to add Carl Zimmer's take on the whole affair—the title tells all: "This Paper Should Not Have Been Published".

Carl raises an issue that has cropped up in many of the comments sections of various blogs. Is criticizing a scientific paper appropriate outside of the peer-reviewed scientific literature? Is it ethical to cast doubt on the integrity of scientists when questioning the quality of their science?

Felisa Wolfe-Simon1 is the lead author of the study and she was the main spokesperson in the video below. Carl Zimmer asked her if she wanted to respond to the criticism of her paper and here's what she said, according to the Slate article,
"Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated," wrote Felisa Wolfe-Simon of the NASA Astrobiology Institute. "The items you are presenting do not represent the proper way to engage in a scientific discourse and we will not respond in this manner."
Carl asked some other scientists about this and the best quote comes from Jonathan Eisen,
But Jonathan Eisen of UC-Davis doesn't let the scientists off so easily. "If they say they will not address the responses except in journals, that is absurd," he said. "They carried out science by press release and press conference. Whether they were right or not in their claims, they are now hypocritical if they say that the only response should be in the scientific literature."
My own impression of this fiasco is that the scientific authors of the paper can be accused of bad science and the lead author, Felisa Wolfe-Simon, is guilty of grossly misrepresenting her work at the press conference. There really can't be any excuse for that behavior if you want to call yourself a scientist. Those who think this is impolite and unethical are dead wrong. It's an absolute requirement of good science that we point out to the general public when scientists are behaving badly, otherwise we lose all credibility.

As you watch this video keep in mind that the bacteria absolutely require phosphate in the media in order to grow and that only a few phosphorus atoms, at most, are replaced by arsenic in DNA. If you think that's what Felisa Wolfe-Simon is telling you then you need to work hard on your listening comprehension skills.

1. The name of the bacterial strain is GFAJ-1. Rumor has it that this stands for "Get Felissa a Job." I wonder how that's working out? Do you think the job offers are pouring in?

John Lennon (1940 - 1980)

John Lennon died on Dec. 8, 1980 when he was shot four times in the back by Mark David Chapman. His ashes were scattered by Yoko Ono in Central Park in New York at the site of the Strawberry Fields Memorial.

That was thirty years ago today. A whole new generation has grown up since then and I fear we are in great danger of forgetting what Lennon and The Beatles did to help change our culture for the better.

Monday, December 06, 2010

The Value of Blogs

Many people have questioned the significance of blogs and bloggers. Some think that science blogs have no useful purpose and that they are undermining the peer review process of publication in scientific journals. Science journalists resent the fact that amateur writers can throw up something on a blog and claim that it's contributing to science education.

Over the years I've come to appreciate that science blogs do at least one thing that's new—they provide instant commentary on science news and that helps to serve as authoritative fact-checking. Science blogs monitor science journalism in the same way that political blogs monitor FOX news and the New York Times.

This role has been illustrated in spades over the past few days as we monitor the response to the NASA hype over bacteria that grow in the presence of arsenic. The weaknesses of the Science paper are now well-known thanks to many science bloggers. In the past, this kind of analysis would have had to wait for the publication of an appropriate critique in a scientific journal and that was very unlikely to happen for a number of very good reasons. Thus, in the past shoddy, over-hyped work got a free pass and science journalists who fell for the hype never even realized that they had been duped.

Read David Dobbs on Wired for a thoughtful analysis of the episode and the lesson we need to learn [Is That Arsenic-Loving Bug — Formerly an Alien — a Dog?]. It's interesting that even Nature News got sucked into promoting the hype. This shows that even journalists at the premier science journals are not very skeptical.

Sunday, December 05, 2010

Arsenic and Bacteria

The blogosphere is not happy with the recent announcement by NASA of bacteria that are able to "thrive and reproduce using the toxic chemical arsenic." [NASA-Funded Research Discovers Life Built With Toxic Chemical]
This finding of an alternative biochemistry makeup will alter biology textbooks and expand the scope of the search for life beyond Earth. The research is published in this week's edition of Science Express.
I read the paper (Wolfe-Simon et al., 2010) and I can assure you that nothing in that paper is going into my biochemistry textbook. I predict that a year from now we'll have forgotten about this discovery. I'm not even sure it's going to be confirmed but, if it is, the result is pretty trivial.

For a start, even the title of the paper is misleading. The title says "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus" but all of the data show that there was phosphorus in the media and that the bacteria used it for growth and reproduction. This selected strain of bacteria incorporated more arsenic than non-selected species but it by no means did it replace all phosphate with arsenic. Only a few percent (at most) of the phosphorus atoms in DNA, for example, were replaced by arsenic.

The purpose of this posting it to alert you to a fantastic article by microbiologist Rosie Redfield at the University of British Columbia. I strongly urge that everyone read her take-down of the science paper [Arsenic-associated bacteria (NASA's claims)]. The problem is not just that a bad paper was published in Science—it's that the paper was so heavily promoted in the media. We've got to do better when it comes to educating the general public about science.

Wolfe-Simon, F., Blum, J.S., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D., and Oremland, R.S. (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science Published Online 2 December 2010 [DOI: 10.1126/science.1197258]

Saturday, December 04, 2010

Carnival of Evolution #30


The 30th version of Carnival of Evolution has been posted on The Scientific Life (Bob O'Hara).

The Death of the Sniper Scientist


I've just discovered a new blog called Canadian Girl Postdoc in America. Check it out.

You can start by recommending your favorite science book [The One] but be sure to read the wonderful series on Slow Science: The Death of the Sniper Scientist.

The author is interested in evolution and population genetics and she has been blogging for three years! I think she likes plants.

Wednesday, December 01, 2010

Students vs Icons of Evolution

I teach in a second year course on "Scientific Misconceptions and Controversies." In my part of the course we discuss creationism and evolution. The object is to learn to think rationally about the controversy.

Students have to read Icons of Evolution and write an essay analyzing the arguments in one of the chapters (their choice). They have no problem recognizing the flaws in the logic and the outright mistruths in that book. For typical university students with a rudimentary understanding of evolution it's like shooting fish in a barrel.

The Discovery Institute sees it differently but they must live on another planet.

Here's how David Klinghoffer describes Jonathan Wells in a recent posting on Evolution News & Views [Celebrating Ten Years of Icons of Evolution].
A Berkeley PhD in molecular and cell biology, Wells is among the most lucid and accessible scientist-writers devoted to the modern project of critiquing Darwin. When I say the book is sweetly reasoned, I don't only mean that it's well reasoned but that there's an appealing geniality, a sweetness, to the man's writing that stands out in contrast to the donkey-like braying of a Darwinian biologist Jerry Coyne, the sinister coilings of a Richard Dawkins, the ugly "humor" of a P.Z. Myers. Yes, you can get a sense of a person's character, and perhaps too his credibility, from the words he uses.
And here's an example of "sweet geniality" from page 234 of Icons.
What about scientists who knowingly make false utterances or misleading omissions but believe the overall effect is not misleading because they are teaching "a deeper truth"? Does the commitment to a supposed deeper truth excuse conscious misrepresentations? Such an excuse probably wouldn't help a stock promoter. Under federal law, a stock promoter is not justified in mistating the facts just because he or she deeply believes that a company is destined to prosper. The stock promoter commits fraud by misrepresenting the truth, regardless of his or her underlying beliefs. Shouldn't scientists be held to the same standard?

Fraud is a dirty word, and it should not be used lightly. In the cases described in this book, dogmatic promoters of Darwinism did not see themselves as deceivers. Yet they seriously distorted the evidence—often knowingly. If this is fraud when a stock promoter does it, what is it when a scientist does it?


If dogmatic promoters of Darwinian evolution were merely distorting the truth, that would be bad enough. But they haven't stopped there. They now dominate the biological sciences in the English-speaking world, and they use their position of dominance to censor dissenting viewpoints.