Do you understand this Nature paper on transcription factor binding in different mouse strains?

I've published a few papers on the regulation of transcription of a mouse gene and students in my lab have done the standard promoter-bashing experiment to define transcription factor binding sites. I did ny Ph.D. in a lab that specialized in DNA binding proteins. I've kept up with the basic ideas in eukaryotic gene expression in order to teach undergraduate courses on that topic and in order to write appropriate information in my textbook.

I've been interested in genome organization for several decades and I've been following the literature on pervasive transcription and transcription factor binding in whole genome studies. I'm reasonably familiar with the techniques although I've never done them myself.

I'm not bragging; I'm just saying that I know a little bit about this stuff so when I saw this paper in one of the latest issues of Nature I decided to look more carefully.

Heinz, S., Romanoski, C., Benner, C., Allison, K., Kaikkonen, M., Orozco, L. and Glass, C. (2013) Effect of natural genetic variation on enhancer selection and function. Nature 503:487-492. [doi: 10.1038/nature12615]

Jason Rosenhouse defends Chris Mooney

Jason Rosenhouse read Chris Mooney's article on 7 Reasons Why It's Easier for Humans to Believe in God Than Evolution and liked it. Mooney was arguing that it's easier to believe in god(s) than in evolution because our evolutionary history selected for traits that predisposed us to think more like IDiots than like scientists.

I disagreed [Why don't people accept evolution? ]. Here's what I wrote last week ....

Cherry picking and the safety of low level electromagnetic radiation

While I was researching the previous article on the safety of GM foods, I came across the website of Magda Havas. Here's how she describes herself ...

Magda Havas is Associate Professor of Environmental & Resource Studies at Trent University where she teaches and does research on the biological effects of environmental contaminants. Dr. Havas received her Ph.D. from the University of Toronto, completed Post-Doctoral research at Cornell University, and taught at the University of Toronto before going to Trent University in Peterborough, Canada.

...

Dr. Havas’s research since the 1990s is concerned with the biological effects of electromagnetic pollution including radio frequency radiation, electromagnetic fields, dirty electricity, and ground current. She works with diabetics as well as with individuals who have multiple sclerosis, tinnitus, chronic fatigue, fibromyalgia and those who are electrically hypersensitive. She also conducts research on sick building syndrome as it relates to power quality in schools.

Since the mid 1990s Dr. Havas has taught about electromagnetic pollution in several courses at Trent University and has supervised Reading Courses and Honours Thesis Projects in this area. One of the courses deals specifically with the biological effects of electromagnetic fields and electromagnetic radiation. This is one of the few courses available in North America at a senior undergraduate level critically examining the effects of non-ionizing radiation.

Here comes the fun part. She has made a video in which she explains why we need to pay attention to all the scientific studies showing harmful effects of power lines, cell phones, WiFi etc. She uses Popper's criterion of falsifiability to justify her rejection of all articles that show no harmful effect and she turns cherry-picking completely upside down to support .... cherry-picking!

Don't you just love the title of this video?


In case you don't get it, here's a bit of extra reading.
Magda Havas’ New EHS Study Has Serious Flaws
Trust Me, I’m A Doctor: Magda Havas And WiFi

---

Is there any reliable scientific evidence that genetically modified food poses a health risk?

I recently had a discussion about the safety of food derived from genetically modified organisms. My opponent, whose identity I will conceal (hi Rachel!), argued that GM foods are unsafe and that there's scientific evidence to back this up. Naturally, this evidence is being concealed by Monsanto and other private companies in the same way that tobacco companies tried to hide the evidence that smoking causes lung cancer.

My position is that I'm not aware of any reliable scientific studies showing that GM foods are dangerous to your health and, furthermore, in a free and open democracy with a free press it seems highly unlikely that such evidence is being suppressed. It seems even more unlikely that scientists would be part of this conspiracy.

Michael Eisen defends 23andMe against the FDA

The US Food and Drug Administration has asked 23andMe to stop marketing their genetic test product. The company will test your DNA for the presence of several genetic markers that might indicate a predisposition to disease. The FDA is concerned that 23andMe is not doing enough to ensure that its tests are accurate and the advice it gives is medically sound.

Michael Eisen is on the Scientific Advisory Board for 23andme. He responds to the controversy: FDA vs. 23andMe: How do we want genetic testing to be regulated?.

I think some of his points are worth discussing. My position is that the links between certain diseases and certain SNPs are not well-established. The scientific literature on this topic is not all that great and many of the published results have not been repeated. What this means is that private companies like 23andMe are under pressure to be the first to include a new link in their database but may not be exercising the appropriate amount of skepticism.

How do creationists interpret Lenski's long-term evolution experiment?

Lenski's long-term evolution experiment has resulted in dozens of publications in high quality journals. It has led to significant insights into evolutionary processes [e.g. Lenski's long-term evolution experiment: the evolution of bacteria that can use citrate as a carbon source]. You may be wondering how Intelligent Design Creationists react to these results since most IDiots have a natural aversion to evidence.

Denyse O'Leary wasn't impressed [The Latest From Lenski’s Lab]. She doesn't know very much about science so she has to rely on the opinions of other IDiots. In this case, she relies on Ann Gauger who published a comment on the website of The Biologic Institute [Inovation or Rennovation].

Lenski's long-term evolution experiment: the evolution of bacteria that can use citrate as a carbon source

Richard Lenski set up twelve flasks of E. coli B back in 1988. They were allowed to grow overnight in minimal medium containing 139μM glucose and 1,700 μM citrate. The glucose was the only carbon source that the parent strain could use and it limited growth of the cultures. The citrate was present as a standard chelating agent. The bacteria could not take up citrate and use it as an additional carbon source.

Every day the culture was diluted by transferring one ml to 99 ml of fresh medium (1/100). There were 6.64 generations per day or 2,423 generations per year (slightly more in a leap year).

These cultures were under strong selective pressure. Individual bacteria that could grow faster would out-compete other bacteria in the culture and take over. Lenski expected that each culture would show a variety of different solutions to the selective pressure with many common mutations and many that could be unusual.

Ask a stupid question ... can anyone guess the answer?

I just love the IDiots. They never cease to amaze, and amuse, me. Here's the latest from David Klinghofer at: Intelligent Design as an Orange Flag.

The mention of ID seems to give many writers and commentators what they regard as a green light to blather on without taking a moment to grasp what they're writing about. Denouncing ID is one thing. Denouncing it without comprehending what the phrase refers to, which is amazingly common, is quite another.

I continue to find this amazing. What other subject, both controversial and somewhat recondite, seems to license apparently smart people to write and speak in such an uninformed way?

Gee, I wonder what other subject causes apparently smart people to behave like IDiots? What other subject gives people a green light to blather on when they don't have the slightest clue what they are talking about? Is there another subject that some people denounce without comprehending what it means? Hmmm .....

Can anyone think of such a subject?

---

Was Louis Agassiz better in the concrete?

Back in the nineteenth century (i.e. more than one hundred years ago) there was a biologist named Louis Agassiz who didn't like Darwin's radical ideas about evolution. Agassiz, a very famous professor at Harvard, thought that there were major gaps n the fossil record and he lamented the apparent lack of transitional fossils. What he was looking for were fossils of direct ancestors of modern species and not their close cousins.

Stephen Meyer thinks this old debate is still relevant today so he writes it up in Darwin's Doubt as if nobody in the past one hundred years ever thought of an explanation. It fooled Denyse O'Leary (not hard) so she blogged about it today [Louis Agassiz: The selective incompleteness of the fossil record].

This reminds me of a famous photograph of the statue of Louis Agassiz embedded upside down in the courtyard in front of the zoology building at Stanford University. The statue tumbled from its place above the entrance during the San Francisco earthquake of 1906.

According to legend, a passing scientist remarked that,

Louis Agassiz was great in the abstract but not in the concrete.¹

Actually, it would be even better to say that Agassiz looks better in the concrete than in the abstract [see Agassiz in the Concrete and Persecution of Religious Scientists]. By the 1920s (earlier in Europe) Agassiz's reputation had been severely damaged by his willingness to let religious convictions dictate his science.²

---

1. The story is apocryphal (a polite word for "false"). The quotation has been attributed to several men, including the President of Stanford, but all have denied it. Nevertheless, it's too good a story to abandon just because it happens to be untrue!

2. Stephen Jay Gould held the Alexander Agassiz Professor of Zoology Chair at Harvard from 1982 until his death in 2002. Alexander Agassiz was Louis Agassiz's son. Alexander served as President of the National Academy of Sciences.

Monday's Molecule #225

Last week's molecule was EF-Tu (elongation factor-thermo unstable). EF-Tu binds to all tRNA molecules in the cell and helps position them in the A-site of the ribosome-mRNA complex during protein synthesis. Its release is coupled to GTP hydrolysis. Eukaryotes contain homologous proteins with different names (e.g. EF-1α). The winner was Jon Nuelle from Texas. The undergraduate winner was Ariel Gershon for the second week in a row.

Today's molecule (below) is an intermediate in a very important pathway that's only found in some species. This is one of those times when you need to supply the common name AND the correct scientific name that specifies the exact molecule shown in the figure.

Email your answer to me at: Monday's Molecule #225. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)

Carnival of Evolution #66: The Day of the Doctor

This month's Carnival of Evolution is hosted by none other than John Wilkins. He's a philosopher but don't let that put you off. He blogs at Evolving Thoughts although from time to time he threatens to stop blogging. Encourage John by visiting The Day of the Doctor of Evolution: CoE #66.

The "Doctor" in the title is a reference to Dr. Who. Apparently John watched the first episodes in 1963!! "Who" knew that he was even born in 1963?

I was eight years old in late November 1963. I didn’t pay much attention to the TV news – some guy had been shot or something, and I wasn’t to know that C. S. Lewis had died until much later – but I was instantly taken by the eerie sound of the opening music of a new show. Yes, it was the very first episode of Dr Who, in glorious monochrome! I was a Whovian from the beginning, before it was cool. I’m so hip…

If you can't name the blue thingy on the right then you probably never win trivia games.

If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Bjørn is threatening to name YOU as host even if you don't volunteer! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.

CoE on Facebook
CoE on Twitter

---

Elizabeth Pennisi writes about Richard Lenski's long-term evolution experiment

Elizabeth Pennisi has written about the long-term evolution experiment of Richard Lenski [The Man Who Bottled Evolution]. The experiment is in it's 25th year and it is entirely appropriate that Science magazine devotes several pages to describing the results. There have been some remarkable discoveries.

But I want to focus on a couple of things that Pennisi says in her article. There has also been a discussion on Panda's Thunb: Lenski’s experiment: 25 years and 58,000 generations. Pennisi writes ...

Lenski's humble E. coli have shown, among other things, how multiple small mutations can prepare the ground for a major change; how new species can arise and diverge; and that Gould was mistaken when he claimed that, given a second chance, evolution would likely take a completely different course. Most recently, the colonies have demonstrated that, contrary to what many biologists thought, evolution never comes to a stop, even in an unchanging environment.

Let's talk about two issues in that paragraph.

Why don't people accept evolution?

Chris Mooney (remember spin framing?) is at it again. This time he writes for Mother Jones: 7 Reasons Why It's Easier for Humans to Believe in God Than Evolution.

Before we look at the seven reasons let's remember the poll from 2005 that surveyed acceptance of evolution in 34 countries. Note that the percentage of the population who reject evolution ("false") is somewhere between 10% and 20% in the countries at the top of the list. About 75% of the people in those countries think that evolution is true.

In the USA the percentage who reject evolution is closer to 40% and only about 40% think that evolution is true. Clearly if we're going to ask why it's easier for humans to believe in god(s) than in evolution then we have to take these differences into account. It seems reasonable, doesn't it, to look for something that the USA, Turkey, and Cyprus have in common that makes people not accept evolution?

What do you think of Brian Pallister's statement?

Brian Pallister is the leader of the Progressive Conservative Party of Manitoba. Here's a statement he made the other day. I'm not particularly offended by what he say about atheists. I think it demonstrates that he is really stupid and probably should have kept his mouth shut but that's actually good for secularism, no? It's pretty clear that he doesn't know any atheists, or, even more likely, none of of the atheists he knows want to tell him that they are nonbelievers.

… I wanted to wish everyone a really really Merry Christmas, Happy Hannukah, all the holiday… all you infidel atheists out there, I want to wish you the very best, also. I don’t know what you celebrate during the holiday season — I myself celebrate the birth of Christ — but it’s your choice, and I respect your choice. If you wish to celebrate nothing and just get together with friends, that’s good, too. All the best.

(I think I understand why his parents gave their farm to his brother. )

---

[Hat Tip: Friendly Atheist]

Bill Farrell and Louis C on the Sandwalk

Here's a photo of Bill Farrell ("Doc Bill") and Louis C on the Sandwalk.

They join a distinguished list of people whose visit to the Sandwalk has been recorded here.

Larry Moran
PZ Myers
John Wilkins
Ryan Gregory
The God Delusion
Cody
John Hawks
Michael Barton
Seanna Watson
Steve Watson
Michael Richards
Jeffrey Shallit
Chris DiCarlo
Bill Farrell and Louis C

---