There's been a lot of talk recently about the discussion on reddit concerning the ENCODE publicity fiasco.
Here's the forum ...
AskScience Special AMA: We are the Encyclopedia of DNA Elements (ENCODE) Consortium. Last week we published more than 30 papers and a giant collection of data on the function of the human genome. Ask us anything!
It's interesting to see how some of the consortium members are responding to criticism. My personal view is that none of them seem to be very knowledgeable about genome biology and the work that has been published over the past 40 years.
Last week's molecule was N-formylmethionyl-tRNAfMet [Monday's Molecule #188]. Only three people came close. The winner was Mikkel Rasmussen.
Name these molecules. One of them has a well-known common name that you have to include in your answer. The other one also has a common name but you don't have to find it. You have to give the complete formal names of each molecule. Do you know the significance of these two molecules?
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.)
There are several dozen scientists and graduate students in my department studying various aspects of protein evolution, structure, and folding. They've published dozens of papers but, apparently, they never realized that what they're studying is impossible. Douglas Axe, a leading Intelligent Design Creationist, sets them straight.
[Hat Tip: Evolution News & Views: Axe: Vive la Différence]
My granddaughter, Zoë, took a picture of me getting a hot dog. Can you guess where I am?
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?
Ms. Sandwalk and I are in Las Vegas with our friends. Posting may be a bit light for the next few days.
Here's another clue. Where am I today? (Click to embiggen.)
Can you guess where I am today? (Click to embiggen.)
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.)
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.
[Hat Tip: Bad Astronomy]
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.
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.
The end is approaching. See you in Ottawa on November 30th!
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.
