The second episode of the new Cosmos series is Some of the Things That Molecules Do.
It's about evolution and it's not bad. I have four comments.
A missed opportunity. Natural selection is important and Neil deGrasse Tyson did a pretty good job of explaining it. It wouldn't have taken a big effort to mention that there's more to evolution than natural selection. He could, for example, have pointed out that some breeds of dogs are prone to certain genetic diseases or health problems because some bad mutations were accidentally fixed alone with the good ones. He could have pointed out that our eyes have a blind spot.
The Theory of Evolution is not a fact. Neil deGrasse Tyson said that the theory of evolution is a fact. This is not correct. Evolution is a fact. Evolutionary theory attempts to explain how evolution occurs. Some of the explanations, like natural selection, are facts but many aspects of modern evolutionary theory are still hotly debated in the scientific community.
We don't understand the origin of life. The episode closed with deGrasse Tyson saying the we don't understand how life began and there's nothing wrong with admitting that we don't know something. Excellent!
There are better ways of drawing DNA. I don't like the way DNA is pictured in the first two episodes, especially in the opening sequence. It looks like the bases grow out of the backbone and fuse to form base pairs. They could have drawn a more accurate representation without losing any visual appeal.
I give the episode a B+.
It's been almost a year since I commented on an Nature article by Philip Ball [see DNA: Nature Celebrates Ignorance]. Here's part of what I wrote back then ...
The main premise of the article is revealed in the short blurb under the title: "On the 60th anniversary of the double helix, we should admit that we don't fully understand how evolution works at the molecular level, suggests Philip Ball."
What nonsense! We understand a great deal about how evolution works at the molecular level.
The worst thing about the Nature article was the misuse of the Central Dogma of Molecular Biology. The second worst thing was the "revelation" that genes are regulated by regulatory sequences as if that was a new discovery. (He mentions the ENCODE results.)
I recently described a really bad paper published in Science by Stergachis et al. (2013). The principle investigator is John Stamatoyannopoulos of ENCODE notoriety [see The "duon" delusion and why transcription factors MUST bind non-functionally to exon sequences].
The group mapped millions of transcription factor binding sites in the human genome and discovered that 1.8% of them were in exons (coding regions). They assumed that these were functional—they play a role in regulating gene expression. Thus the nucleotide binding sites are also codons meaning that the sequence specifies two different kinds of information. The workers named these sequences "duons."
Nothing could be wrong until you realize that Science writer editor Elizabeth ("Liz") Pennisi is behind it. That changes things entirely.
To find out why you have to read Dan Graur's latest at: A Dog on the Cover of @ScienceMagazine: Sins of Omissions.
At some point, the big bosses at Science magazine are going to have to wake up to the fact that they're publishing a lot of bad papers and commentaries. Something is seriously wrong.
David Klinhoffer likes Elizabeth Pennisi: Shooting the Messenger: Elizabeth Pennisi. He says ...
As we frequently hasten to emphasize about daring writers and researchers in science, I have no reason to think Pennisi is a Darwin skeptic much less a proponent of ID. Still, she's a reporter who is open to promoting "evolution heresy." She's unafraid to challenge the old guard. More than once she has stuck her finger in the eye of ancient régime. Now you know why she ticks off guys like Graur and Moran.
Yep. He got that right. Graur and I are definitely part of the old regime and we don't like people who promote evolution heresy ... or their sycophants.
I was looking through my copy of Nature the other day trying to take seriously all the special reviews on "Transcription and Epigenetics." One article caught my eye ...
Gut, P. and Verdin, E. (2013) The nexus of chromatin regulation and intermediary metabolism. Nature 502:489-498. [doi: 10.1038/nature12752]
Living organisms and individual cells continuously adapt to changes in their environment. Those changes are particularly sensitive to fluctuations in the availability of energy substrates. The cellular transcriptional machinery and its chromatin-associated proteins integrate environmental inputs to mediate homeostatic responses through gene regulation. Numerous connections between products of intermediary metabolism and chromatin proteins have recently been identified. Chromatin modifications that occur in response to metabolic signals are dynamic or stable and might even be inherited transgenerationally. These emerging concepts have biological relevance to tissue homeostasis, disease and ageing.
The authors argue that, among other things, methylation of histones is regulated by changes in the concentrations of some citric acid cycle metabolites. I find it difficult to imagine that the concentrations of the citric acid cycle intermediates could change significantly enough to act as allosteric effectors but that's not what grabbed my attention.
It's the figure showing the citric acid cycle (TCA cycle) that shocked me.
Textbooks show that the products of the citric acid cycle are ...
That's three NADH, one QH2, and one GTP (or ATP) for a total of ten ATP equivalents. The new version, published last week in the most prestigious science journal in the world, shows that there are six NADH produced per cycle for a total of 15 ATP equivalents. It must be correct because this is a paper about intermediary metabolism and it was reviewed by experts in the field. Unfortunately, the authors don't give a reference to this new information. I assume that it's common knowledge among the top metabolism researchers so they didn't bother citing the papers.
Can anyone out there direct me to the revolutionary papers that I missed?
P.S. I'm not even going to mention that FADH2 is NOT a product of enzyme-catalyzed β-oxidation.
Attanasio et al. (2013) published a paper in Science where they identified several thousand possible enhancers that were active in the facial area of developing mouse embryos. About 200 of them appear to be controlling genes that determine the size and shape of the face. (Recall that there are about 20,000 protein-encoding genes in mammals.)
Lynn Yarris of Lawrence Berkeley National Laboratory in California (USA) wrote up the press release [What is it About Your Face?]. It's a really good press release that fairly represents the published work and explains some of the significance. There's no mention of junk DNA in the press release or the published paper.
This is what it looks like when science correspondent Alok Jha published it in The Guardian.
Faces are sculpted by 'junk DNA'
Though everybody's face is unique, the actual differences are relatively subtle. What distinguishes us is the exact size and position of things like the nose, forehead or lips. Scientists know that our DNA contains instructions on how to build our faces, but until now they have not known exactly how it accomplishes this.
Visel's team was particularly interested in the portion of the genome that does not encode for proteins – until recently nicknamed "junk" DNA – but which comprises around 98% of our genomes. In experiments using embryonic tissue from mice, where the structures that make up the face are in active development, Visel's team identified more than 4,300 regions of the genome that regulate the behaviour of the specific genes that code for facial features.
It's pretty clear that science correspondent Alok Jha doesn't understand what he's writing and it's about time we started publicizing the names of those science writers who mislead the public about science. The consensus among knowledgeable scientists is that at least 80-90% of our genome is junk. It's time for science writers to admit that the science favors junk.
Scientists have known for decades that a lot of noncoding DNA is functional. The idea that all noncoding DNA (98%) is junk is false. No knowledgeable scientist ever made such a claim. It is a myth perpetuated, in part, by ignorant science writers; albeit, aided and abetted by ignorant scientists. Scientists have known for fifty (50!!) years that gene expression is controlled by regulatory sequences in noncoding DNA. Scientists have known for at least that length of time that during embryogenesis different genes are turned on and off and that this is due, in part, to binding of transcription factors to those regulatory sequences (enhancers). Scientists have known for one hundred years that the morphological features of mammals, including humans, are controlled by genes.
Move along folks. There's nothing to see here.
Attanasio, C. et al. (2013) Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers. Science 342: Oct. 25, 2013 [doi: 10.1126/science.1241006]
UPDATE: The title is facetious. I don't believe for one second that most so-called "dark matter" has a function. In fact, there's no such thing as "dark matter." Most of our genome is junk. I mention this because one of the well-known junk DNA kooks is severely irony-impaired and thought that I had changed my mind.
A few hours ago I asked you to evaluate the conclusion of a paper by Venters and Pugh (2013) [Transcription Initiation Sites: Do You Think This Is Reasonable?].
Now I want you to look at the Press Release and tell me what you think [see Scientists Discover the Origins of Genomic "Dark Matter"].
It seems pretty clear to me that Pugh (and probably Venters) actually think they are on to something. Here's part of the press release quoting Franklin "Frank" Pugh, a Professor in the Department of Molecular Biology at Penn State.
The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.
"These non-coding RNAs have been called the 'dark matter' of the genome because, just like the dark matter of the universe, they are massive in terms of coverage -- making up over 95 percent of the human genome. However, they are difficult to detect and no one knows exactly what they all are doing or why they are there," Pugh said. "Now at least we know that they are real, and not just 'noise' or 'junk.' Of course, the next step is to answer the question, 'what, in fact, do they do?'"
Pugh added that the implications of this research could represent one step towards solving the problem of "missing heritability" -- a concept that describes how most traits, including many diseases, cannot be accounted for by individual genes and seem to have their origins in regions of the genome that do not code for proteins. "It is difficult to pin down the source of a disease when the mutation maps to a region of the genome with no known function," Pugh said. "However, if such regions produce RNA then we are one step closer to understanding that disease."
I'm puzzled by such statements. It's been one year since the ENCODE publicity fiasco and there have been all kinds of blogs and published papers pointing out the importance of junk DNA and the distinct possibility that most pervasive transcription is, in fact, noise.
It's possible that Pugh and his postdoc are not aware of the controversy. That would be shocking. It's also possible that they are aware of the controversy but decided to ignore it and not reference any of the papers that discuss alternate explanations of their data. That would be even more shocking (and unethical).
Are there any other possibilities that you can think of?
And while we're at it. What excuse can you imagine that lets the editors of Nature off the hook?
P.S. The IDiots at Evolution News & Views (sic) just love this stuff: As We Keep Saying, There's Treasure in "Junk DNA".
Venters, B.J. and Pugh, B.F. (2013) Genomic organization of human transcription initiation complexes. Nature Published online 18 September 2013 [doi: 10.1038/nature12535] [PubMed] [Nature]
Some freelance science writer named Philip Ball has published an article in the April 25, 2013 issue of Nature: Celebrate the Unknowns.
The main premise of the article is revealed in the short blurb under the title: "On the 60th anniversary of the double helix, we should admit that we don't fully understand how evolution works at the molecular level, suggests Philip Ball."
What nonsense! We understand a great deal about how evolution works at the molecular level. Perhaps Philip Ball meant to say that we don't understand the historical details of how a particular genome evolved, but even that's misleading.
I've commented before on articles written by Philip Ball. In the past, he appeared to be in competition with Elizabeth Pennisi of Science for some kind of award for misunderstanding the human genome.
SEED and the Central Dogma of Molecular Biology - I Take Back My Praise
Shoddy But Not "Junk"?
Let's look at what the article says ...
PZ Myers has just given his students a take-home exam. Here's one of the questions [It’s another exam day! ] ...
Question 1: One of Sarah Palin’s notorious gaffes was her dismissal of “fruit fly research” — she thought it was absurd that the government actually funded science on flies. How would you explain to a congressman that basic research is important? I’m going to put two constraints on your answer: 1) It has to be comprehensible to Michele Bachmann, and 2) don’t take the shortcut of promising that which you may not deliver. That is, no “maybe it will cure cancer!” claims, but focus instead on why we should appreciate deeper knowledge of biology.
That first restriction is going to make answering the question a real challenge 'cause you have to take into account the mentality of someone who is not just scientifically illiterate but scientifically anti-literate. 
Nevertheless, this is exactly the sort of thing you want your science graduates to know.
There are now been four papers in the scientific literature criticizing the way ENCODE leaders hyped their data by claiming that most of our genome is functional [see Ford Doolittle's Critique of ENCODE ]. There have been dozens of blog postings on the same topic.
The worst of the papers were published by Nature—this includes the abominable summary that should never have made it past peer review (Encode Consortium, 2012).
The lead editor on the ENCODE story was Brendan Maher and he promoted the idea that the ENCODE results showed that most of our genome has a function [ENCODE: The human encyclopaedia]
The consortium has assigned some sort of function to roughly 80% of the genome, including more than 70,000 ‘promoter’ regions — the sites, just upstream of genes, where proteins bind to control gene expression — and nearly 400,000 ‘enhancer’ regions that regulate expression of distant genes.
Jonathan Eisen is becoming one of my favorite bloggers. He alerts us to a horrible press release published recently by the National Science Foundation (USA):How to Thrive in Battery Acid and Among Toxic Metals.
It talks about a strain of red algae called Galdieria sulphuraria that has apparently inherited many genes from bacteria by lateral gene transfer. Here's how the press release hypes the result ...
The scientists made an unexpected discovery: Galdieria's genome shows clear signs of borrowing genes from its neighbors.
Many genes that contribute to Galdieria's adaptations were not inherited from its ancestor red algae, but were acquired from bacteria or archaebacteria.
This "horizontal gene transfer" is typical for the evolution of bacteria, researchers say.
However, Galdieria is the first known organism with a nucleus (called a eukaryote) that has adapted to extreme environments based on horizontal gene transfer.
"The age of comparative genome sequencing began only slightly more than a decade ago, and revealed a new mechanism of evolution--horizontal gene transfer--that would not have been discovered any other way," says Matt Kane, program director in the National Science Foundation's (NSF) Division of Environmental Biology, which funded the research.
"This finding extends our understanding of the role that this mechanism plays in evolution to eukaryotic microorganisms."
Galdieria's heat tolerance seems to come from genes that exist in hundreds of copies in its genome, all descending from a single gene the alga copied millions of years ago from an archaebacterium.
"The results give us new insights into evolution," Schoenknecht says. "Before this, there was not much indication that eukaryotes acquire genes from bacteria."
A "new mechanism of evolution" that was only revealed a decade ago by genome sequencing? Jonathan Eisen explains why this is so very wrong. You should read his post: Ugg - story about gene transfer/evolution based on NSF press release has a NASA-esque smell. I agree 100%. We've got to put and end to this kind of ridiculous hype and misrepresentation. It's damaging to science.1
The published results are interpreted as novel but only in the sense that the genes acquired from bacteria are (presumably) directly related to enhanced fitness (Schönknecht et al., 2013). Here's what the authors say in the paper.
Eukaryotic innovations usually arise through gene duplications and neofunctionalizations, which lead to expansion of existing gene families (8). In contrast, archaea and bacteria commonly adapt through horizontal gene transfer (HGT) from other lineages (9). HGT has also been observed in some unicellular eukaryotes (10); however, to our knowledge, horizontally acquired genes have not been linked to fitness-relevant traits in free-living eukaryotes
That point is reiterated in the summary.
These findings for G. sulphuraria mirror the results of a previous systematic study, which showed that proteobacterial adaptation relies on the horizontal acquisition of genes that function at the bacteria's interface to the environment (19). Whereas the importance of HGT for evolution of Bacteria and Archaea is well established, adaptation of a eukaryotic extremophile by gene transfer from Bacteria and Archaea is unexpected and shines a new light on the evolution of unicellular eukaryotes.
There's nothing about a new mechanism of evolution in the actual paper.
[Image Credit: Gerald Schönknecht]
1. Ed Yong gets it right: How the Lord of the Springs Survives Where Most Things Die, demonstrating, once again, that good science writers can cut through the hype and lies.
Schönknecht, G., Chen, W.H., Ternes, C.M., Barbier, G.G., Shrestha, R.P., Stanke, M., Bräutigam, A., Baker, B.J., Banfield, J.F., Garavito, R.M., Carr, K., Wilkerson, C., Rensing, S.A., Gagneul, D., Dickenson, N.E., Oesterhelt, C., Lercher, M.J., and Weber, A.P. (2013) Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote. Science 339:1207-1210. [PubMed] [doi: 10.1126/science.1231707]
Here's a short paragraph containing three sentences from my textbook (page 584). Is there anything wrong with any of these sentences?
Under physiological conditions, double-stranded DNA is thermodynamically much more stable than the separated strands and that explains why the double-stranded form predominates in vivo. However, the structure of localized regions of the double helix can sometimes be disrupted by unwinding. Such disruption occurs during DNA replication, repair, recombination, and transcription.
Having trouble seeing where I went wrong, according to some people? Check out this and this.
Oh, and don't forget this.
Science magazine (published by AAAS) was one of the major news sources that fell hook, line and sinker for the ENCODE/Nature publicity campaign last September [Science Writes Eulogy for Junk DNA]. It even published a laudatory three page profile of Ewan Birney, the man responsible for misrepresenting the ENCODE results as evidence that most of our genome is functional [Ewan Birney: Genomics' Big Talker].
I was somewhat apprehensive when I saw that the editors of Science had picked the ENCODE results as one of the top ten breakthroughs [Genomics Beyond Genes]. Would the editors continue to promote the idea that most of the human genome is functional?
One of the Saturday morning sessions at Eschaton 2012 was on science education. Eugenie Scott started off with a survey of various states (in the USA) that are passing laws promoting creationism. In my presentation I tried to explain the scientific facts that we know for sure then I described an example of Intelligent Design Creationist stupidity showing that they really have no idea what they are talking about. See: Breaking News: IDiots Don't Understand Genomes or Biology. PZ Myers finished of with a depressing summary of the state of science education in the USA.
In my talk I explained that I preferred a broad definition of science, one that emphasizes science as a way of knowing. My definition encompasses the activities of everyone who seeks knowledge and that includes people working in fields outside of the traditional science disciplines.
Eugenie Scott prefers a more restricted definition of science, one that refers to the activities of biologists, chemists, physicists, and geologists. Eugenie thinks there are other ways of knowing and she supports the idea that the actions of scientists are constrained by the rule of methodological naturalism.
I don't know what's happening at Science these days. It got caught up in the arsenic affair last year and it recently made a fool of itself over the ENCODE publicity fiasco where it was completely duped by Ewan Birney.
Now it has published the following "perspective" in the October 12th issue. It reads like a Sokal hoax but it's perfectly legitimate. That's actually how Stuart Neuman proposes to solve the mystery of the Cambrian explosion.
Stuart A. Newman
Physico-Genetic Determinants in the Evolution of Development
Science 338:217-219 [DOI: 10.1126/science.1222003]
Abstract
Animal bodies and the embryos that generate them exhibit an assortment of stereotypic morphological motifs that first appeared more than half a billion years ago. During development, cells arrange themselves into tissues with interior cavities and multiple layers with immiscible boundaries, containing patterned arrangements of cell types. These tissues go on to elongate, fold, segment, and form appendages. Their motifs are similar to the outcomes of physical processes generic to condensed, chemically excitable, viscoelastic materials, although the embryonic mechanisms that generate them are typically much more complex. I propose that the origins of animal development lay in the mobilization of physical organizational effects that resulted when certain gene products of single-celled ancestors came to operate on the spatial scale of multicellular aggregates.
Neuman was one of the Alternberg 16, a group of scientists who met in Altenberg, Austria in 2008. Their purpose was to develop a new theory of evolution. The proceedings were collected in a book edited by Massimo Pigliucci and Gerd B. M^uuml;ller, Evolution: The Extended Synthesis.
This story has been promoted by a rogue journalist named Suzan Mazur and she has written a book on the subject. Here's her interview with Stuart Newman, The New Master Of Evolution?. Elizabeth Pennisi, a senior editor at Science, helped publicize the Altenberg 16 back in 2008 by publishing an article in Science [Modernizing the Modern Synthesis]. She has been sympathetic to the bizarre views of some Altenberg 16 members so I suspect she's behind the publication of Stuart Newman's article in Science.
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?
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.
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.
One of the good things to come out of this ENCODE/junk DNA fiasco is that I've discovered a number of excellent scientists who aren't afraid to speak out on behalf of science. One of them is Mike White, a systems biologist at the Center for Genome Sciences and Systems Biology, Washington Univ. School of Medicine, St. Louis (USA). He blogs at The Finch & Pea.
Mike published an impressive article on the Huffington Post a few days ago. This is a must-read for anyone interested in the controversy over junk DNA: A Genome-Sized Media Failure. Here's part of what he says ...
If you read anything that emerged from the ENCODE media blitz, you were probably told some version of the "junk DNA is debunked" story. It goes like this: When scientists realized that classical, protein-encoding genes make up less than 2% of the human genome, they simply assumed, in a fit of hubris, that the rest of our DNA was useless junk. (You might have also heard this from your high school or college teacher. Your teacher was wrong.) Along came the ENCODE consortium, which found that, far from being useless, junk DNA is packed with functionality. And so everything scientists thought they knew about the genome was wrong, wrong wrong.
The Washington Post headline read, "'Junk DNA' concept debunked by new analysis of human genome." The New York Times wrote that "The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as 'junk' but that turn out to play critical roles in controlling how cells, organs and other tissues behave." Influenced by misleading press releases and statements by scientists, story after story suggested that debunking junk DNA was the main result of the ENCODE studies. These stories failed us all in three major ways: they distorted the science done before ENCODE, they obscured the real significance of the ENCODE project, and most crucially, they mislead the public on how science really works.
What you should really know about the concept of junk DNA is that, first, it was not based on what scientists didn't know, but rather on what they did know about the genome; and second, that concept has held up quite well, even in light of the ENCODE results.
Way to go, Mike!
In the past week, lot's of scientists have demonstrated that they don't know what they're talking about when they make statements about junk DNA. I don't expect any of those scientists to apologize for misleading the public. After all, their statements were born of ignorance and that same ignorance prevents them from learning the truth, even now.
However, I do expect lots of science journalists to write follow-up articles correcting the misinformation that they have propagated. That's their job.
John Timmer is the science editor at Ars Technica. Yesterday he published the best analysis of the ENCODE/junk DNA fiasco that any science writer has published so far [Most of what you read was wrong: how press releases rewrote scientific history].
How did he manage to pull this off? It's not much of a secret. He knew what he was writing about and that gives him an unfair advantage over most other science journalists.
Let me show you what I mean. Here's John Timmer's profile on the Ars Technica website.
John is Ars Technica's science editor. He has a Bachelor of Arts in Biochemistry from Columbia University, and a Ph.D. in Molecular and Cell Biology from the University of California, Berkeley. John has done over a decade's worth of research in genetics and developmental biology at places like Cornell Medical College and the Memorial Sloan-Kettering Cancer Center. He's been a speaker at the annual meeting of the National Association of Science Writers and the Science Online meetings, and he's one of the organizers of the Science Online NYC discussion series. In addition to being Ars' science content wrangler, John still teaches at Cornell and does freelance writing, editing, and programming.
See what I mean? He has a degree in biochemistry and another one in molecular biology. People like that shouldn't be allowed to write about the ENCODE results because they might embarrass the scientists.
