Where Am I?

My granddaughter, Zoë, took a picture of me getting a hot dog. Can you guess where I am?

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Where Am I?

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Ewan Birney: Genomics' Big Talker

My copy of Science arrived in the mail last week and I wasn't surprised to see the article by Elizabeth Pennisi on ENCODE Project Writes Eulogy for Junk DNA. Pennisi has long been skeptical about junk DNA. She advocates the position that what makes us human is hidden in the "dark matter" of the genome. She has never lost an opportunity to promote those scientists who claim to have discovered function in junk DNA so it was natural for her to fall hook-line-and-sinker for the recent ENCODE publicity campaign [see Science Writes Eulogy for Junk DNA].

What did surprise me was a three-page spread on Ewan Birney: Genomics' Big Talker, written by Elizabeth Pennisi. This is extraordinary. I don't know of another example where a leading science journal has promoted a young scientist in this manner. Of course, it's doubly extraordinary because, in this case, Science is promoting a scientist who just made some serious mistakes interpreting his own data! The man who is so prominently featured in the Sept. 7, 2012 issue of Science magazine is coming under serious criticism for letting publicity rule his science. He has almost single-handedly¹ damaged the reputation of 400 scientists in the ENCODE Consortium and he did it, in part, because he was not knowledgeable about his own field of expertise! [see ENCODE Leader Says that 80% of Our Genome Is Functional and The ENCODE Data Dump and the Responsibility of Scientists]

UPDATE:A reader has reminded me that Science published two pages (online) on Felicia Wolfe-Simon at the time of the arsenic affair. Hmmmm ... is this the beginning of a pattern?

Viva Las Vegas!

Ms. Sandwalk and I are in Las Vegas with our friends. Posting may be a bit light for the next few days.

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Where Am I #2?

Here's another clue. Where am I today? (Click to embiggen.)

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Where Am I #1?

Can you guess where I am today? (Click to embiggen.)

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Monday's Molecule #187

Last week's molecule was the core nucleosome complex [Monday's Molecule #186] and nobody who was eligible for a win got it! That's quite shocking. Here's an easy one for today.

Name this molecule, including the name of the "R" group. You'll have to guess but there's really only one possibility in living cells. Don't forget, I need the full name of the most likely molecule given the partial structure that you see.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post 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 comment.)

On the Reasoning Ability of Most Creationists

Here's an excellent example of the difference between a scientific way of knowing and the other kind. Follow this link to the full story. I'm told that reddit user jerfoo wrote the story and took the photos.

I've often admired the jigsaw puzzle analogy to understanding the evidence for evolution. It's as though we have a picture of evolution that's missing but a few pieces yet the creationists steadfastly refuse to see the image and insist that we concentrate on the missing pieces.

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[Hat Tip: Bad Astronomy]

Boudry vs Plantinga

Alvin Plantinga is a famous philosopher who is widely respected and seems to be able to publish in all the right places. He is a theist (Calvinist) and for a long time he was at the University of Notre Dame in Indiana (USA). Since his retirement from there, he has taken a position at Calvin College.

Plantinga has long advocated the accommodationist position from the perspective of Christian apologetics. I bought his latest book, Where the Conflict Really Lies, because I'm interested in the conflict between science and religion.

I've been struggling for weeks with how to explain Plantinga's case. My problem was that I found the whole book quite ridiculous and it seemed to me that Plantina's idea of logic and rationality was much closer to kindergarten philosophy than to something one might expect from a distinguished scholar. I hesitated to say that out loud because it sounds very condescending coming from a scientist.

I had to be missing something. There must be some sophisticated philosophy in there somewhere and I just wasn't getting it. I couldn't post.

Are All IDiots Irony Deficient?

As I'm sure you can imagine, the Intelligent Design Creationists are delighted with the ENCODE publicity. This is a case where some expert scientists support one of their pet beliefs; namely, that there's no such thing as junk DNA. The IDiots tend not to talk about other expert evolutionary biologists who disagree with them—those experts are biased Darwinists or are part of a vast conspiracy to mislead the public.

You might think that distinguishing between these two types of expert scientists would be a real challenge and you would be right. Let's watch how David Klinghoffer manoeuvres through this logical minefield at: ENCODE Results Separate Science Advocates from Propagandists. He begins with ....

"I must say," observes an email correspondent of ours, who is also a biologist, "I'm getting a kick out of watching evolutionary biologists attack molecular biologists for 'hyping' the ENCODE results."

True, and equally enjoyable -- in the sense of confirming something you strongly suspected already -- is seeing the way the ENCODE news has drawn a bright line between voices in the science world that care about science and those that are more focussed on the politics of science, even as they profess otherwise.

Apocalypse in Ottawa!

The end is approaching. See you in Ottawa on November 30th!

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Athena Andreadis Writes for Scientific American: Junk DNA, Junky PR

Quite a few science journalists have clued in to the fact that they were massively conned by the ENCODE publicity machine. Turns out that the death of junk DNA was greatly exaggerated.

Here's what Athena Andreadis has to say on the Scientific American website: Junk DNA, Junky PR. Athena is a professor in the Department of Cell and Developmental Biology at the University of Massachusetts Medical School.

Chris DiCarlo on the Sandwalk

My friend Chris DiCarlo recently visited Down House with his family. Here's a photo of him on the Sandwalk. Chris is a philosopher and it looks like he's trying very hard to strike a philosophical pose.

In fact, he just can't figure out which way to go to get out of there!

Chris joins 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

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Priceless Idiot

UPDATE: The woman in the picture, Kim Stafford, was making fun of the Tea Party with this sign [Internet FAIL: The truth about that Tea Party sorority girl you saw on Facebook.

This photo is everywhere on the internet but it's so perfect that I just have to post it even though spelling is not one of my own strengths.

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Stephen Jay Gould and Sydney Brenner Agree on Junk DNA

It's no secret that I'm a big fan of Stephen Jay Gould. I'm also a big fan of Sydney Brenner. Here's Gould writing in The Structure of Evolutionary Theory (pages 1269-1270). This is long and complicated but if you want to understand junk DNA and why it conflicts with Darwinism, then you've got to make the effort. I especially like the idea that Gould understands the difference between junk DNA, which can't be explained by any adaptive mechanism, and "selfish DNA," which isn't junk and has a Darwinian explanation. Many people don't get this.

Gould and Brenner are talking about repetitive DNA. This includes highly repetitive sequences of simple repeats and moderately repetitive sequences that include the transposons.