The Smithsonian Museums are highly respected but that doesn't mean their website is scientifically accurate [Junk DNA Isn’t Junk, and That Isn’t Really News].
Remember in high school or college, when you learned about all that DNA inside of you that was junk? The strings and strings of nonsense code that had no function? A recent blitz of papers from the ENCODE project have the world abuzz with news that would rip that idea apart.
But, like many things that stick around in text books long after science has moved on, the “junk DNA” idea that ENCODE disproved, didn’t really need disproving in the first place. Even in 1972, scientists recognized that just because we didn’t know what certain DNA regions did, didn’t make them junk.
This is getting very depressing.
A few hours ago I criticized science journalists for getting suckered by the hype surrounding the publication of 30 papers from the ENCODE Consortium on the function of the human genome [The ENCODE Data Dump and the Responsibility of Science Journalists].
They got their information from supposedly reputable scientists but that's not an excuse. It is the duty and responsibility of science journalists to be skeptical of what scientists say about their own work. In this particular case, the scientists are saying the same things that were thoroughly criticized in 2007 when the preliminary results were published.
I'm not letting the science journalists off the hook but I reserve my harshest criticism for the scientists, especially Ewan Birney who is the lead analysis coordinator for the project and who has taken on the role as spokesperson for the consortium. Unless other members of the consortium speak out, I'll assume they agree with Ewan Birney. They bear the same responsibility for what has happened.
I've been trying to keep up with the ENCODE PR fiasco so I immediately click on a link to Michael Eisen's blog with the provocative title it is NOT junk. The article is: This 100,000 word post on the ENCODE media bonanza will cure cancer.
Michael Eisen is an evolutionary biologist at the University of California at Berkeley. He's best known, to me, as the brother of Jonathan Eisen. 
Michael, like me and hundreds of other scientists, is upset by the ENCODE press releases. One of them is: Fast forward for biomedical research: ENCODE scraps the junk.
The hundreds of researchers working on the ENCODE project have revealed that much of what has been called 'junk DNA' in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes. Without these switches, genes would not work – and mutations in these regions might lead to human disease. The new information delivered by ENCODE is so comprehensive and complex that it has given rise to a new publishing model in which electronic documents and datasets are interconnected.
Here's the interesting thing. Many of us are upset about the press releases and the PR because we don't think the ENCODE data disproves junk DNA. Michael Eisen's perspective is entirely different. He's upset because, according to him, junk DNA was discredited years ago.
The problems start before the first line ends. As the authors undoubtedly know, nobody actually thinks that non-coding DNA is ‘junk’ any more. It’s an idea that pretty much only appears in the popular press, and then only when someone announces that they have debunked it. Which is fairly often. And has been for at least the past decade. So it is more than just intellectually lazy to start the story of ENCODE this way. It is dishonest – nobody can credibly claim this to be a finding of ENCODE. Indeed it was a clear sense of the importance of non-coding DNA that led to the ENCODE project in the first place. And yet, each of the dozens of news stories I read on this topic parroted this absurd talking point – falsely crediting ENCODE with overturning an idea that didn’t need to be overturned.
Eisen is wrong, junk DNA is alive and well. In fact almost 90% of our genome is junk.
This is what makes science so much fun.
ENCODE (ENcyclopedia Of DNA Elements) is a massive consortium of scientists dedicated to finding out what's in the human genome.
They published the results of a pilot study back in July 2007 (ENCODE, 2007) in which they analyzed a specific 1% of the human genome. That result suggested that much of our genome is transcribed at some time or another or in some cell type (pervasive transcription). The consortium also showed that the genome was littered with DNA binding sites that were frequently occupied by DNA binding proteins.
THEME
Genomes & Junk DNAAll of this suggested strongly that most of our genome has a function. However, in the actual paper the group was careful not to draw any firm conclusions.
... we also uncovered some surprises that challenge the current dogma on biological mechanisms. The generation of numerous intercalated transcripts spanning the majority of the genome has been repeatedly suggested, but this phenomenon has been met with mixed opinions about the biological importance of these transcripts. Our analyses of numerous orthogonal data sets firmly establish the presence of these transcripts, and thus the simple view of the genome as having a defined set of isolated loci transcribed independently does not seem to be accurate. Perhaps the genome encodes a network of transcripts, many of which are linked to protein-coding transcripts and to the majority of which we cannot (yet) assign a biological role. Our perspective of transcription and genes may have to evolve and also poses some interesting mechanistic questions. For example, how are splicing signals coordinated and used when there are so many overlapping primary transcripts? Similarly, to what extent does this reflect neutral turnover of reproducible transcripts with no biological role?
This didn't stop the hype. The results were widely interpreted as proof that most of our genome has a function and the result featured prominently in the creationist literature.
Ed Yong is a science journalist and usually he's a very good one. This time, however, he should have gotten the other side of the story.
Ed interviewed Ewan Birney for a story on the function of sequences in the human genome [ENCODE: the rough guide to the human genome].
According to ENCODE’s analysis, 80 percent of the genome has a “biochemical function”. More on exactly what this means later, but the key point is: It’s not “junk”. Scientists have long recognised that some non-coding DNA probably has a function, and many solid examples have recently come to light. But, many maintained that much of these sequences were, indeed, junk. ENCODE says otherwise. “Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more,” says Tom Gingeras, one of the study’s many senior scientists.
And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”
The creationists are going to love this.
You blew it Ed Yong. Why didn't you ask him about the 50% of our genome containing DEFECTIVE transposons and the 2% that's pseudogenes, just for starters? Then you could ask him why he believes that all intron sequences (about 20% of our genome) are functional [What's in Your Genome?].
"Almost every nucleotide ..."? Gimme a break. Don't these guys read the scientific literature?
This is going to make my life very complicated.
I thought that people like Chuck Norris were big fans of the idea that America is the greatest country in the world. Apparently I was wrong.
This is an appeal to evangelicals to prevent the triumph of evil and 1,000 years of darkness.
[Hat Tip: Friendly Atheist]
Methodological Naturalism is an a priori argument in favor limiting science to investigations of the natural world. It serves to protect religion from science since most religious questions are concerned with the supernatural and science, by fiat, isn’t allowed to ask those questions. Coincidentally, it also protects philosophy from science since metaphysical questions now become the exclusive domain of philosophy.
There are some philosophers who see through this house of cards but they are few and far between. It’s mostly scientists—and those who think like scientists—who say "What the heck are they talking about?"
Maarten Boudry, Stefaan Blancke, and Johan Braeckman from the Department of Philosphy at the University of Gent (Belgium) represent the heretics and dissenters among philosophers. If you want a summary of posts on this topic go to: Is Science Restricted to Methodologial Naturalism?. Here’s an excerpt from Grist to the Mill of Anti-evolutionism: The Failed Strategy of Ruling the Supernatural Out of Science by Philosophical Fiat (Boudry et al. 2012).
I began this discussion a few days ago by questioning the purpose of some common philosophical arguments. The example I selected concerned the claim that evolution is unguided. A prominent philosopher, Elliott Sober, tells us that even though there’s no evidence that evolution is guided it is still possible to imagine a supernatural being who could control evolution by tweaking molecules at the level of quantum mechanics. If this being was clever enough, and wanted to leave no trace of his activity, then one could imagine a situation where evolution was guided without anyone realizing it. Thus, theistic evolutionists need not despair because the scientific way of knowing can’t legitimately say that evolution is unguided.
I used the analogy of The Flying Spaghetti Monster Steals Meatballs to poke fun at this spurious way of reasoning.
Last week's molecule was raltitrexid, an anti-cancer drug [Monday's Molecule #183]. The winner was Raul A. Félix de Sousa. Raul has won ten times since I restarted Monday's Molecule last November.
This week's molecule is another strange-looking molecule with a very specific purpose. Identify the molecule and its role in mammals.
Post your answers 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.)
Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)
In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.
Winners will have to contact me by email to arrange a lunch date. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.
Comments are invisible for 24 hours. Comments are now open.
UPDATE: The molecule is warfarin or Coumadin®, a rat poison and an anticoagulant. It's a competitive inhibitor of vitamin K reductase and this blocks blood clotting. The winner is Matt McFarlane, one of the few people who can actually collect a free lunch. Please contact me by email.
Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia
July 23: Raul A. Félix de Sousa
July 30: Bill Chaney and Raul A. Félix de Sousa
Aug. 7: Raul A. Félix de Sousa
Aug. 13: Matt McFarlane
Aug. 20: Stephen Spiro
Aug. 27: Raul A. Félix de Sousa
Sept. 3: Matt McFarlane
I try really hard not to ban anyone from commenting on Sandwalk but there are some things I will not tolerate.
Someone named David Roemer recently tested the limits of my patience, and failed. He is now banned.
Here's what happened. I received an email message from David Roemer about a comment of his that did not appear on Sandwalk. I don't know why it didn't appear. I don't remember seeing it.
Shortly after receiving the email message I received a copy of a message David Roemer sent to the chair of my department. Here's the beginning ...
Dear Dr. XXX,
Prof. Moran, I believe, didn't approve of the following comment I made on his Sandwalk blog. He has every right to do so, but he has a moral duty not to coverup the misinformation contained in the AJP article I mention in my censored comment:
Natural selection only explains the adaptation of species to the environment. Not enough is known about the innovations natural selection acts upon to understand how mammals evolved from bacteria in only 3.5 billion years (common descent). The only theory that attempts to explain common descent is ID, but there is no evidence for ID.
IDiots try to make their theory look better by comparing it with natural selection. Atheists go along with this scam because they don’t want to admit that ID is a better theory than natural selection in some sense.
A corollary of the limitations of natural selection is that the second law of thermodynamics doesn’t apply to evolution, just as it doesn’t apply to the evolution of stars. Nevertheless, there is scientific literature about whether evolution violates the second law. Authors on the “does not” side argue that heat energy from the sun accounts for the increase in order (decrease in entropy). Heat, of course, tends to increase disorder.
This nonsense reached an extreme level in an article published by the American Journal of Physics (Entropy and evolution, Nov. 2008). This article actually calculates the entropy of the biosphere using the Boltzmann constant and an estimate of the thermodynamic probability of life. I’m trying to get the AJP to retract this absurd article.
I'm copying David Novak because he is on the Institute Board of First Things, which is refusing to publish my attached essay explaining why the AJP article is absurd. Both Novak and Moran are helping the AJP lie about evolution and thermodynamics.
My chair will be amused by this sort of thing. There's nothing he could do about it even if he wanted to.
This is one of the criteria for banning. Anyone who tries to get someone fired or reprimanded by going over their head to their employer will be banned. Anyone who harasses the family and friends of someone they disagree with will be banned. There are no exceptions.
I've also banned John Kwok for doing the same thing in an attempt to silence Jim Shapiro.
John starts his defense by explaining the correct use of "begging the question." I agree with him 100%. I hate it when people misuse this phrase by thinking it means "prompts me to ask the question."
He then goes on to give an example ... [Begging questions about philosophy, science and everything else]
But we expect better of the educated and cosmopolitan. It comes, therefore, as a continuing pain to me that scientists will often offer this piece of question beggary:
- Science finds out things
- Philosophy does not find out things the scientific way
- Therefore philosophy is a waste of time and effort
The begged premise here is that only knowing things the scientific way is knowledge, or if the philosopher in question doesn’t say that knowledge is what philosophy offers, that only knowing things the scientific way is worthwhile. Some may even hint that only science delivers beauty, too.
It pains me to read this because I expect so much better of an educated and cosmopolitan Australian.
I'm not aware of any scientist who argues like this.
There was a time, not so long ago, when science and philosophy coexisted in (relative) peace and harmony. This began to change when science came under increasing attack from religion and from others who simply denied the knowledge that had been produced by the scientific way of thinking. (The latter group included advocates of parapsychology. The modern versions include those who deny climate change and those who think vaccinations cause autism. These groups are not necessarily religious.)
The rise of anti-scientism provoked a response from scientists, just as you might expect. Scientists began to speak out against the irrational claims of these science deniers. The counter-attack necessarily covered many people with strong religious beliefs. Gradually, many scientists came to the realization that the main problem was not the specifics of evolution or whether ESP could be tested. The real battleground was a war between rationalism and superstition. This led to a number of scientists coming out in support of atheism and focusing their attention on the flaws in religious thinking (i.e. superstition).
Now, you would think that philosophy would be a natural ally in this fight since the most important feature of philosophy is its ability to distinguish logical arguments from ones that are illogical. In other words, philosophy should be on the side of rationalism and not on the side of superstition.
I been watching proceedings at the Republican National Convention in Florida. If you think it's annoying for most liberal Americans, imagine what it's like for us furriners!
Coincidentally, we watched the last episode of The Newsroom a few days ago then decided to re-watch all ten episodes. It's one of the best shows on television. Makes me sad that The West Wing was cancelled. It's not a show that Republicans will enjoy.
Here's the clip from the first episode that sets the tone for a new kind of TV news show. The hero, Will McAvoy, is a cable news anchor who wants to tell it like it is instead of chasing ratings. The excerpt is from a town hall meeting at Northwestern University. A student has just asked why America is the greatest country in the world. (The student shows up again in Episode #10 when she wants to become a "greater fool.")
The short video by Bill Nye ("The Science Guy") attracted a lot of attention [Bill Nye: Creationism Is Not Appropriate For Children ].
Not to be outdone, Ken Ham and the Creation Museum have taped a response ...
We are [responding to Nye] today with a video rebuttal featuring our “science guys” — Dr. David Menton and Dr. Georgia Purdom of our AiG and Creation Museum staff. These two PhD scientists were asked to reply to Mr. Nye, whose academic credentials do not come close to Drs. Menton and Purdom.
I present this for your amusement. I feel a bit sorry for Georgia Purdom since there's a high probability that some of her grandchildren are going to reject creationism. I wonder how she'll deal with that?
Tim Radford reviews The Selfish Gene by Richard Dawkins [The Selfish Gene by Richard Dawkins – book review]. The review is a bit late—the book was published in 1976—but I suppose the old adage of "better late than never" applies.
Actually it's not as bizarre as you might think. Lot's of people don't understand the ideas that Dawkins was pushing. He was mostly pointing out that evolution is a phenomenon that takes places at the level of genes and populations. Dawkins tweets that Rafford "gets it" in his review.
Lovely retrospective review of The Selfish Gene by Tim Radford, the Guardian's distinguished science writer. He gets it.
