Sean Eddy is a bioinformatics expert who runs a lab at the Howard Hughes Medical Institute (HHMI) Janelia Farm Research Campus in Virginia (USA).1 Sean was one of the many scientists who spoke out against the ENCODE misinterpretation of their own results [ENCODE says what?].
Most people now know that ENCODE did not disprove junk DNA (with the possible exception of creationists and a few kooks).
Sean has written a wonderful article for Current Biology where he explains in simple terms why there is abundant evidence for junk (i.e. nonfunctional) DNA [The C-value paradox, junk DNA and ENCODE] [preprint].
Here's a quotation from the article to pique your interest.
Recently, the ENCODE project has concluded that 80% of the human genome is reproducibly transcribed, bound to proteins, or has its chromatin specifically modified. In widespread publicity around the project, some ENCODE leaders claimed that this biochemical activity disproves junk DNA. If there is an alternative hypothesis, it must provide an alternative explanation for the data: for the C-value paradox, for mutational load, and for how a large fraction of eukaryotic genomes is composed of neutrally drifting transposon-derived sequence. ENCODE hasn’t done this, and most of ENCODE’s data don’t bear directly on the question. Transposon‑derived sequence is generally expected to be biochemically active by ENCODE’s definitions — lots of transposon sequences are inserted into transcribed genic regions, mobile transposons are transcribed and regulated, and genomic suppression of transposon activity requires DNA‑binding and chromatin modification.
The question that the ‘junk DNA’ concept addresses is not whether these sequences are biochemically ‘active’, but whether they’re there primarily because they’re useful for the organism.
1. More importantly, he's an alumnus of Talk.origins.
This month's Carnival of Evolution is hosted by Ryan Somma at ideonexus. Read it at: Carnival of Evolution #54: A Walkabout Mount Improbable
I hope everyone enjoyed their holiday dinosaur this Thanksgiving, and thank you joining me in this delightful excursion out into the wide wonderful world of ideas and expressions in evolution.
As it turns out, I did enjoy eating dinosaur on Thanksgiving but it was so long ago (Oct. 8) that I've forgotten what it tasted like.
Enjoy your tour of Mt. Improbable!
The next Carnival of Evolution (September) will be hosted by Genome Engineering. If you want to volunteer to host others, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before. 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.
Last week's molecule was N-(2-aminoethyl)glycine, a molecule that has been used to build artificial DNA molecules. The winner was Michael Rasmussen [Monday's Molecule #193].
This week's molecule is a real pisser. You'll have to give the complete, unambiguous, formal name AND explain why we don't make it.
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.)
It's really hard to maintain one's reputation as a curmudgeon. John Wilkins is having a particularly tough time these days since most of his poss are quite reasonable and rational. I even agree with him on most days.
In an effort to correct this problem, John has decided to defend evolutionary psychology [Eww, I stepped in some evolutionary psychology and other crap]. I posted a comment explaining why he was wrong.
Those of you who are fans of this crap discipline might want to jump on over to Evolving Thoughts and help him out.
He needs you.
One of the highlights of Eschaton 2012 was taking PZ Myers to the Elgin Street Grill for poutine. He had the plain, ordinary version diluted with a chicken burger. I had the chili poutine.
Other highlights included his two talks. The one on Saturday morning was about the sorry state of science education in the United States. That was depressing.
PZ's talk on Saturday evening was at the Canadian Museum of Natural History, just around the corner from the hotel. There were about 200 people in the audience. He tackled a very difficult topic, the role of chance in evolution. Naturally he covered random genetic drift but most of his talk was about coalescent theory because he wanted to explain some recent results from the sequence of the gorilla genome (Scally et al. 2012).
The authors of that paper report that, "In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other." PZ explained why this is exactly the result you would expect. (See his blog post at: A tiny bit of knowledge is a dangerous thing.)
He also pointed out that the Intelligent Design Creationists got all excited about this result, thinking that it overthrows the theory of evolution and proves the existence of God. (I exaggerate slightly, but you get the point!) What this means if that the IDiots really don't understand evolution.
While we don't expect everyone to see immediately why 30% of our genes could be more similar to gorilla genes than to chimp genes, we do expect those who criticize evolution to have a better understanding. Instead, what we see is that those "experts" who post at Evolution News & Views (sic) don't even have an introductory college level understanding of evolution. Their ignorance of evolution produces some remarkably stupid posts on that blog—the website of the Discovery Institute.
I made a similar point in my talk except that I focused on the IDiot's lack of knowledge of mutation [see Breaking News: IDiots Don't Understand Genomes or Biology].
PZ took on a challenging task but he succeeded better than I could have imagined. While the audience didn't follow all of the explanation, they could see that it was based on solid evidence and theory. Many of them learned for the first time about chance in evolution and that's a plus, in my opinion.
Now let's work on the IDiots.
Scally, A, Dutheil, J.Y., Hillier, L.W., Jordan, G.E. et al. (2012) Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-175. [PubMed]
The hobbit is coming to Toronto. I knocked on the door but there was no answer.
He's not here yet.
Can't wait to meet him.
[Photo Credit: I took this picture in the commuter train concourse at Union Station, Toronto, Ontario, Canada]
Just when you think they couldn't get more stupid, along comes some IDiot to prove you wrong. Here's the latest from an anonymous contributor at Evolution News & Views [Your Genome? Which One?].
A new finding about DNA differences in somatic cells overthrows a common assumption and might have dramatic implications for evolutionary studies.
Young's Law (from Murphy's catalog of perverse tendencies in nature) states that all great discoveries are made by mistake. A corollary is that the greater the funding, the longer it takes to make the mistake, but we won't go there. Anyway, a team of Yale scientists wasn't looking to overturn a huge assumption in genetics -- but they did. The ripple effects of their discovery remain to be seen.
We've all been told that every cell in our body has a copy of our unique genetic code. That's one of those simplistic beliefs that sounds sensible but is almost impossible to check. Doesn't the whole body arise from cell divisions of a single zygote with its unique genetic code? Yes, but it doesn't necessarily follow that the genes in cells downstream don't get modified. That was just assumed....
"Somatic mosaicism" is jargon for the finding that genomes differ from cell to cell -- not only in copy number variations (CNV's), but in single nucleotide polymorphisms (SNP's). The assumption that you have one genome is thus falsified. You have lots of genomes!
Okay, let's take a poll.
How many of you thought that mutations such as nucleotide substitutions, deletions, and insertions, could never take place during the thousands of generations that give rise to our somatic cells? (How were they supposed to be suppressed?)
How many of you thought that all of our cells, including red blood cells, contain copies of our unmodified genome?
How many of you thought that there were no polyploid cells in our liver?
How many of you thought that B cells, and T cells (and others) contain the same identical copy of our genome that's found in germ cells?
How many of you thought that spermatocytes and ovaries have exactly the same genome as our original zygote?
How many of you thought that cancer-causing gene rearrangements and mutations in somatic cells were impossible?
How many of you are completely ignorant of any medical problems due to genetic mosaicism?
If you answered "yes" to all of those questions then, congratulations!, you're as smart as an IDiot.
Sheeesh!
One thing is clear at this stage: the assumption that each individual has a unique genome has been overthrown to some extent. Think how this might impact common evolutionary studies. For years, evolutionists have claimed small differences between human and chimpanzee genomes. What if the percent difference is a function of the source cells used? Remember, the Yale team found differences between cells in the same organ -- human skin. If the percent difference grows or shrinks depending on the source, any conclusions about human-chimp similarities would prove unreliable.
The nameless people at Evolution News & Views (sic) didn't like my comments about Michael Behe. Naturally they focus right in on defending the IDiot science (not!) [Giving Thanks for Minority Opinions]. (The reference to "thanks" is in honor of today's American Thanksgiving holiday.)
When in the future they write the history of modern biology, if it turns out that contemporary ID theorists were onto something big, then Michael Behe's name will figure very prominently as one who helped launch the intelligent-design revolution.
When that history is written, whatever fate holds in store for ID, no one thinks that University of Toronto biochemist Larry Moran's name will figure prominently in any account as a thinker of great stature or influence.
So there's some irony in Moran's patronizing three-part series, at his blog Sandwalk blog, about meeting Mike Behe when the latter came to visit and speak recently in Toronto. Moran is full of condescension and, sticking to the science as always, carefully points out the discrepancy in physical stature between himself and Behe where Moran does have the advantage -- "He's a lot shorter than I imagined but otherwise looks just like his photos." Moran includes a photo of himself leaning over Behe with a smirk to prove the point. Well then!
This is a talk by Elizabeth Lloyd from a conference in Italy last May on "Stephen J. Gould’s Legacy: Nature, History, Society." Thanks to Ryan Gregory for posting all the videos [Stephen Jay Gould conference in Italy — full series of talks].
Lloyd explains the problems with the adaptationist approach to the logic of research questions using a case study on the evolutionary origins of female orgasm. She points out that Gould & Lewontin were right 33 years ago when they called attention to the adaptationist bias and that things haven't changed very much.
This is an excellent example of a philosopher of biology, Elizabeth Lloyd, making a substantial contribution to science and the philosophy of science
From The Gazette (Montreal, Quebec, Canada): Man charged with threatening people using social media — again.
A Saint-Laurent man has been charged, again, with abusing social media to threaten people who express their views online.
Dennis Markuze, 40, faces three new charges, including one alleging he violated the conditions of a sentence he received in May for the same offence. He was also charged with threatening the Montreal police officer who was investigating claims from several of Markuze’s past victims. Those victims alleged that Markuze’s threats have intensified in recent months.
In May, Markuze received an 18-month suspended sentence after pleading guilty to uttering threats toward eight people he believed to be atheists. The court was told Markuze’s problems could be attributed to drug consumption, which caused him to believe he was “the Voice of God.” As part of his sentence, he was ordered to “abstain from participating in a social network, blog and discussion forum.” But during the summer, several people contacted The Gazette to report that Markuze appeared to be ignoring the court order.
[Hat Tip: Friendly Atheist]
I went to three of Michael Behe's talk while he was in Toronto [see Michael Behe in Toronto!, Part 1,
Part 2].
The third talk was on Friday morning (Nov. 15, 2012) in the Multifaith Centre. It was sponsored by Power to Change (formerly Campus Crusade for Christ). There were about 150 people in the audience, mostly undergraduates. I estimate that less than half were believers.
Behe gave pretty much the same talk he had given the night before. There was only time for a few questions and most of them were from skeptics. Two students challenged the science but their questions were convoluted and confusing and Behe had no trouble dismissing them. (The standard trick is to say "That's a very good question" and then suggest they could discuss it later on so that others have a chance to ask questions right now.)
One student asked about the philosophical justification for some of Behe's conclusions. It was a valid question but way over the heads of the audience. Behe gave an incorrect answer. I spoke to that student and her friends after the talk. Several of them were taking biology/evolution courses but they weren't really prepared to identify the flaws in Behe's arguments. They just knew that he had to be wrong.
This is the problem. It's just not that easy for the average person to refute the arguments of people like Michael Behe and Jonathan Wells. That's why we need to teach the controversy in school and show why their science is flawed.
Here's a propaganda video produced by the Discovery Institute. It's based on a book called The Magician's Twin edited by John G. West. John G. West is "a Senior Fellow at the Seattle-based Discovery Institute (DI), and Associate Director and Vice President for Public Policy and Legal Affairs of its Center for Science and Culture (CSC), which serves as the main hub of the Intelligent design movement."
In other words, he's one of the chief IDiots.
The video is interesting for several reasons. Not only does it have the look and feel of a 1950's American propaganda film but it mimics the same utter lack of critical thinking that characterized that genre of film. Perhaps this is intentional since the goal is to attack rationality and critical thinking and the last thing you want to do is be accused of using the very tools that lead to evils such as eugenics, evolution, atheism, and Marxism. (But see "doublethink," below.)
Behe's main talk was last Thursday evening at 7pm (Nov. 15, 2012). It was in the lecture theater were we teach medical students. The room holds about 350 students and every seat was taken. There were about 100 people sitting in the aisles and on the floor.
The gist of Behe's talk was that "Darwinism" can't explain macroevolution. The problem isn't common descent—Behe agrees that common descent is "trivial." The problem isn't natural selection—Behe doesn't have a problem with natural selection. The problem is random mutation. It's incapable of generating the required changes in a timely manner.
Last week's molecule was capsaicin, the molecule responsible for the "hot" sensation of chili peppers. There were two winners: Seth Kasowitz and Bill Gunn [Monday's Molecule #192].
This week's molecule is featured in an article that I will (hopefully) blog about in the next few days. There's a common name of sorts but you will need to supply the correct IUPAC name to win the free lunch.
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.)
