NTS LogoSkeptical News for 15 July 2010

Archive of previous NTS Skeptical News listings


Thursday, July 15, 2010

Don't be a dick

http://scienceblogs.com/tfk/2010/07/dont_be_a_dick.php

Category: Culture Wars • Policy and Politics
Posted on: July 14, 2010 6:23 PM, by Josh Rosenau

Over the weekend, the skeptics gathered at James Randi's annual The Amazing Meeting, or TAM. By all accounts, it was a great show. Probably the most buzz came from a talk by Phil Plait, which became known as the "don't be a dick" speech, because, well, he argued that skeptics will be most effective when they aren't dicks.

As I wasn't there, I couldn't comment on the speech, but twitter exploded over it. A surprising number of PZ Myers' fans seemed to think Plait was talking about PZ, though PZ wasn't mentioned. Interesting, that PZ's supporters either think he's a dick, or think other people think he's a dick, but that's a discussion for another day. PZ, who couldn't accompany his wife to TAM, had to sort out what was said from the twatting and blogging going on at TAM, summarizing his view as "Nothing I saw from #tam8 was a personal attack. I just hate the 'dick' meme that's growing--it narrows the range of tactics unnecessarily." This, of course, led to various dick jokes.

Daniel Loxton wrote three days after the talk: "Wow. I'm still thinking about @Badastronomer's amazing #TAM8 speech in Las Vegas this weekend. I could not be more moved and impressed." Which is high praise.

So I'm excited to see that Andrew Arensburger has posted a partial transcript of the talk, and then responds to it, generally agreeing. I'll let you read the transcript yourselves, but I want to address some of the examples and counterexamples Andrew gives to Phil's "don't be a dick" thesis. To be clear, the nickel version of Phil's talk is:

  1. People seem to be getting meaner, and skeptics in particular are getting meaner about debunking things.
  2. "How many of you no longer believe in [woo]…because somebody got in your face, screaming, and called you an idiot, brain-damaged, and a retard? [Very few hands go up]"
  3. Research indicates that it's hard to debunk a claim and have the person being corrected actually remember the right answer.
  4. People are wired for faith: it's easier to believe than not to believe, and people who abandon one set of irrational beliefs often do so by replacing them with new irrational beliefs.
  5. Given the challenges of overcoming irrational belief, why make that work harder?
  6. is your goal to score a cheap point, or is your goal to win the damn game?
  7. I think I can sum up my points like this: first, always ask yourself what your goal is. […] Is this argument necessary? What is your goal? What are you trying to accomplish? Before you talk, before you leave a comment, before you engage a pseudoscientist, before you raise your hand, before you sign that email, ask yourself: is this going to help? Is this going to allow me to achieve my goal? And you also need to ask yourself: will this impede me from achieving my goal? Is this just to make me feel better, or am I trying to change the world?

And second, and not to put too fine a point on it, don't be a dick. … All being a dick does is score cheap points. It does not win the hearts and minds of people everywhere, and honestly, winning those hearts and minds, that's our goal.

Now one is always free to say that they don't care about winning hearts and minds, that Phil's goal of wiping out counterfactual belief is not your goal. Fine. But it's a reasonable goal, one that scientists, atheists, and skeptics of any religious persuasion can endorse. If someone rejects that whole concept, I don't know that we have anything to talk about.

Arensburger replies by noting a series of ideas or fields which he thinks support or undermine the "don't be a dick" thesis. I tend to think that the counterexamples he offers, aren't.

Telepathy: I used to believe telepathy was real… What started me down the road to not believing in telepathy anymore was my science teacher … He didn't insult me or anything, he just told me that it didn't exist.… Point to Phil. The Open-Source movement: …Richard Stallman … believes passionately in open source, and has argued for it for many years.

But it wasn't until Eric Raymond began arguing for it that open source and free software really took off and started being taken seriously in corporate circles. While Stallman was known for berating those who wrote closed-source software as greedy, Raymond preferred to explain to people why open source was in their own best interests and how they could make money off of it. Point to Phil.

The "New" Atheism (and probably also women's suffrage, civil rights, and gay rights): There's nothing new about the "New Atheism". A lot of the arguments atheists use today have been around for decades, centuries, even millennia. Answers to the major ones seem to be part of the standard apologetic curriculum in seminaries ("Why is there no evidence for God?" "He doesn't want to violate our free will." "Why should I believe our scripture and that of other religions?" "Because ours was inspired by God, and theirs were written by humans.") But — at least in this country — it was losing ground to fundamentalist Christianity at least for the second half of the 20th century.

It wasn't until Sam Harris, Richard Dawkins, Daniel Dennett, Christopher Hitchens, and others wrote their surprise best-sellers that atheism became part of the national discourse, to the point where a US president mentions in a speech, and prominent religious figures feel they have to respond. Point against Phil (but provisionally; see below).

I can't endorse this one. First, the analogy to civil rights movements is deeply flawed, and goes unargued here. Indeed, I think examples of civil rights, gay rights, and womens rights actually support Phil's point. Martin Luther King, Jr. brought together a massive movement, across religious and racial boundaries, in favor of civil rights. He got invited to the White House and he used his influence to lean hard on JFK and LBJ on civil rights legislation. He was remarkably politically effective, and his non-violent, inclusive approach was a big part of the civil rights movement's success.

Things broke down a bit after his death. There had always been other factions, but folks like Malcolm X, Black Panthers, African Nationalists, etc. gained visibility. Their off-putting and often violent rhetoric, not to mention occasional violent acts, did a lot to allow Nixon to run his racist Southern Strategy, putting civil rights on hold basically until the Clinton years. Point to Phil.

And in womens rights, are inclusivist feminist groups more effective or are separatist feminists more effective? How often do you see someone like Valerie Soianas and her S.C.U.M (Society for Cutting Up Men) Manifesto cited as proof that feminists are just man-haters, and that groups like NOW, or calls for an equal rights amendment, or equal pay for women, or other simple gender equity measures, can all be marginalized? Again, point: Phil.

In gay rights, how much help was it for ACT UP! to storm St. Patrick's Cathedral in New York, desecrating a communion wafer along the way? LGBT leaders decried that militancy, and generally regarded the action as "utter failure." It raised visibility, but it didn't raise acceptance of LGBT citizens, nor of the importance of resources for people with AIDS. What did the job was thousands of individuals telling their families and friends about their sexual orientation. That took gayness from being "other" to being close. I know people in California who voted against gay marriage in the early 2000s but actively campaigned against Prop. 8 in 2008 because their sons and daughters came out and wanted to be able to marry the same-sex partner of their dreams. The single best predictor of whether someone supports marriage equality is how many close friends or relatives they know who are gay. Point: Phil.

As to the "New Atheists," I'd say that the evidence is not yet available. Yes, the "New Atheists" increased the rate at which atheism was discussed publicly. I don't know, but I suspect that President Obama would have given atheists a shout-out in the inaugural either way, but that's not a testable claim. Religious figures have been responding to atheists forever, though, so that's not really a change in anything. Rates of nonbelief are rising, but that rise began before the New Atheist books started coming out and getting major public discussion.

Futhermore, I am not aware of any consistent agreement about what the criteria for success would be among the "New Atheists." Eradication of religion? A more vocal atheist minority? More representation in political office? WIth the civil rights movement, the repeal of Jim Crow laws was a simple and obvious metric for success. With feminism, equal pay and equal rights were clear measures of success, since there were blatantly discriminatory laws on the books and policies in effect. Similarly with gay rights, there are clear cases of institutional and enforced discrimination. With atheism, the case is murkier. There are undeniable problems to be solved in terms of discrimination against atheism and atheists, but the major legal barriers to atheism were overturned last century, often as a result of activism by other religious minorities. Which tends to argue for conciliation and collaboration, rather than absolute, unyielding, and indiscriminate opposition to all religions. But without a clear metric for success, we can't know if the New Atheist strategy has worked or failed.

Yelled at at the intersection: …I was at an intersection where the traffic light had gone out. The way I learned it, at light-free intersections, one person goes through the intersection at a time, in order of arrival. I was about third in line. Four or five cars went through from the right, and then both cars ahead of me went, so I figured that was the way it was done in Nevada, so I followed. A driver coming the other way angrily yelled at me, "One at a time!" I felt chastised, and that perhaps I had committed a faux pas. Point against Phil.

But you knew the rule to begin with, then violated it, and got chastised for breaking a rule. That's different, I'd say. But I welcome folks thoughts on how enforcing societal norms might be similar to debunking widely-believed but wrong claims.

Getting to people first: … there's a lot to be said for being the first to get your message to people who either haven't heard of the problem you're rebutting, or don't don't have enough invested in it to cling to it tightly. But I also don't know how I would have reacted if these articles had ended with "Given all of the above, the people who still believe this are clearly idiots." So I won't award any points for this one.

How does this argue against Phil. One can try to get a debunking out ahead of the curve without being a dick, and if debunking without being a dick is more effective, then it still works well if you get it out to people before they hear the woo.

Insult vs. explanation + insult: Explaining to people how they're wrong and what the facts are, and insulting them, are not mutually exclusive. You can give an explanation, and then point out that your explanation should be patently obvious to anyone with a passing familiarity with reality, and therefore your opponent is a brain-dead moron. This is different from simply saying "You're wrong, and an idiot to boot" and leaving it at that.

Of course, if you're going to give an explanation anyway, then you might as well suppress your anger and frustration for a few more moments, and leave out the insults. So point to Phil.

The campus preacher: I've mentioned Tom Short before. He's the preacher who used to stand in front of the library when I was college and preach the standard fundie line, such as creationism, damnation, and the inerrancy of the King James Bible. He was so obnoxious and so clearly wrong, that he was the one who convinced me that if this is what Christianity is, then I want no part of it. I've since softened my stance, but still: point to Phil.

A safe place to land: Greta Christina has a piece (good, as usual) called A Safe Place to Land: Making Atheism Friendly for the Deconverting. It's all about showing wavering theists and people who aren't happy with their religion that atheism is a viable option, that it doesn't mean giving up friendship and passion and love and community. It's all about drawing people toward atheism, rather than away from theism. The point goes to Phil.

Lewis Black: One of the clips that plays in my mind when someone says something stupid is Lewis Black saying "You're an idiot!" (the other is Greg House saying "You're an idiot.") … Black isn't making much of a rational, pro-science argument; he mostly just uses derision to discredit creationists, Christian fundamentalists, and George Bush. So I think this is a good parallel to what Phil talked about in his presentation.

And yet, I think it works. It works because he's funny, which makes him likable, and the audience wants to agree with him. This is not a rational approach, but an emotional one. Granted, the vast majority of bloggers aren't as funny as Lewis Black, but if it succeeds in discrediting creationism, then it works. So although Phil talks about "what is your goal?", I still think the point goes against him.

To award points either way, you'd have to know whether Lewis Black (or the Daily Show, which PZ Myers mentioned in a similar context) actually changes minds in his audience, or if they just figure he's an asshole. I doubt many people leave a Lewis Black set, or finish an episode of the Daily Show, and think: "My thinking about George Bush has totally reversed itself." Their audiences are quite small, and self-select from political liberals who generally agree with the politics of the shows. That Black's approach works for someone who agrees with Black simply isn't dispositive.

This brings me rather neatly to Playing to Win: …if you take the moral high road in an argument (say, by patiently explaining the nuances of your position instead of calling him retarded) and lose, then you've still lost.

This ties in neatly with Phil's chess analogy: is he willing to sacrifice the moral high ground (analogous to the queen), if that's what's necessary to achieve the greater goal? Now, I understand that his goal is not just to bring people to the truth, but also to get people to believe things for the right reasons, to give them the tools to think for themselves. Do insults and vitriol ever work better than polite, rational discussion at achieving that goal, perhaps by spurring them to read up on critical thinking? I can't award this point to Phil. Sorry.

I'm not seeing the argument here. It seems circular.

People will be insulted anyway, so go for it: There are people in the world who are offended at the very existence of atheists (or of evolutionists, or gays, or of pictures of Mohammed, or whatever), so why not give up on the whole "try not to offend anyone" thing altogether, and say what you want? I suspect that Phil's response would be something along the lines of: those people who are offended by your very existence are not the ones who should be setting the bar for what's acceptable and unacceptable discourse. Rather, it should be about how the wider audience will perceive you. And that you can start with your own standards: how would you react to someone who said that, say, democracy is a bad idea? To someone who said you were an idiot for liking democracy? I think imaginary Phil has rebutted this argument, so the point goes to him.

Yes, but it's worth emphasizing that the goal is not to make Deepak Chopra into the next James Randi. It's to make it less likely that people who don't have strong feelings about Chopra will side with him, and make it more likely that people who don't know much about Randi still want to side with him and against Chopra. The undecideds are often much quieter than those with made-up minds, but those are the people we need to reach.

Santa Claus: Matt Dillahunty of the Atheist Community of Austin has pointed out that while many children stop believing in Santa Claus because they catch their parents putting presents under the tree, others stop believing because they get teased about it by the older kids on the school bus. Or at least, this can start them on the road to doubting Santa Claus and figuring out the truth. More generally, people don't want to feel foolish. If they think their opinion will get them laughed at, they're more likely to keep quiet. Now, this doesn't stop them from believing foolish things, but it does help keep them out of the way when you're trying to teach someone else. There are still people out there who believe in flying saucers, the Loch Ness Monster, Bigfoot, crop circles, and the CIA conspiracy to kill JFK, but they have no real sway in society because at this point they're little more than a punchline. 9/11 truthers are, I think, rapidly heading down that road as well.

Along the same lines, while there's still a lot of racism in the US, at least it's gotten to the point where it's no longer socially acceptable. This doesn't stop people from being racists, but it does mean that anyone who wanted to, say, reintroduce segregated schools would quickly be booed out of the town meeting. If we could get to the point where creationism and ID are widely perceived as being a joke, then that would at least stop people from trying to subvert the teaching of science in public schools, which in itself would be a step forward. So I'll score this as a point against Phil.

This can work well for truly fringe things, but gets much harder for things where strong majorities are against you. That's why creationists rebrand their arguments as "intelligent design" or whatever's next, but they don't go away. People don't want to teach "creationism," but they do want "arguments against evolution" taught, for instance. You can damage the brand through mockery, but I don't think that doing so roots out the underlying mental errors.

The straight man and the comedian: In a lot of comedy sketches, there's a straight man, who isn't funny at all, but just sets up the situation for the audience, so that the comedian can give the funny punchline. The comedian gets all the laughs, but the straight man plays a necessary part. Or, as one person put it, Dean Martin's job is to make Jerry Lewis funny. Another analogy might be game hunting, where some people have the job of beating the bushes to drive rabbits and other game toward the hunters. So perhaps those of us without proper credentials or a knack for clear explanation can shame the people who believe in woo, and drive them toward teachers, people who can explain the facts. Where this analogy breaks down is that beating or being the straight man are things that anyone can do, but that are also unrewarding. It's much more glamorous to be the comedian, or the hunter. Whereas in this discussion, anyone can fling insults, and that's also the fun part. It's the difficult job of calm, patient education that is the thankless one, or at least the one that doesn't deliver immediate visceral gratification. So this analogy doesn't really work, and the point goes to Phil. Have you ever changed your mind because someone called someone else an idiot? This was my original question to Phil after the talk, and he said he considered it, but didn't really have a good answer to it. Basically, if you believe in, say, homeopathy, and hear someone call a third person an idiot and a retard for believing in homeopathy, will that make you more or less likely to stop believing in it?

This sounds similar to the beater/hunter analogy above, but I think it's slightly yet significantly different, and closer to the chess analogy. It's also related to something I learned on talk.origins: you don't argue with creationists to convince your ostensive disputant. Rather, you're playing to the audience, the lurkers who have stumbled onto the discussion but aren't posting because they don't have anything to add, or because they're afraid of being ripped to shreds, or whatever.

Now, this may just be a rationalization for why a bunch of us nerds kept going back and slapping down the same bad arguments again and again and again, because SIWOTI. But I don't think so, so I'll tentatively score this as a point against Phil.

On the evidence offered, I don't see why this goes against Phil. It's hard to know how lurkers react to discussions on internet forums or blogs in any systematic way. Yes, there are anecdotes everyone can dredge up, whether it's the person who was forwarded PZ's shredding of some creationist and thereby became pro-evolution, or the creationist who was almost convinced to switch thanks to careful and polite interaction, only to be scared off when someone started name-calling. Absent more comprehensive data, I don't see how this argues either way. In some cases this effect might work, in others it'll backfire, but how can we say more than that?

So I think that Phil scores on all points (points raised by someone generally supportive, note). If I'm wrong, say so in the comments. If I'm right, say so in the comments, too, but do it really nicely so the folks who think I'm wrong will change their minds.

About that ad predicting the fall of Darwinism in 2013…

http://scienceblogs.com/pharyngula/2010/07/about_that_ad_predicting_the_f.php

Category: Creationism
Posted on: July 14, 2010 10:33 AM, by PZ Myers

I know, I know already. We're getting creationist and religious ads appearing on the right sidebar.

Seed has farmed out some of their ad space to a generic ad provider, which doesn't pay us much and which stuffs in ridiculous ads from any old desperate wanker who wants to buy some attention. In this particular case, I know the guy behind the ad: he was one of those obsessed cranks who, for a while, was sending me nagging emails every day demanding that I read his ReVoLuTiOnArY ThEoRy. I guess he got tired of the cold shoulder and decided to buy space on the web, a sure measure of exactly how much validity we should assign to his claims, i.e., none.

Anyway, I read his site so you don't have to. Really, you don't: these are ads paid for by impressions, not clicks, so every time you load this page and get served up that ad, you are costing him money. So don't click on the ad at all, that's what gives him a sense of accomplishment. The best thing you can do is visit Scienceblogs over and over again, bleeding away the money he sunk into the ad and transferring it to my pocket, and never once click on it.

Anyway, his schtick is really clumsy. He wants you to visit his page in which he makes lots of dramatic claims, and then in order to go on and read more, you have to give him a name and address and get on his mailing list. Don't do it. It's like signing up for a subscription to have moldy maggoty tapioca poured in your ear every day.

Here's what he says if you were to waste your time clicking on his ad. It's a prediction that Darwinism will expire in a few years.

It's no different than the Berlin Wall in 1986, Enron in 2000 or the US financial markets 3 years ago: It's a bubble propped up by academic theorists, atheist zealots, politics and shell games - not hard science.

All that needs to happen is for the right 3-5 scientists to step forward and expose the evolution industry for what it is.... and it's not a question of "IF", it's only a question of WHEN. Darwinism has about 2-5 years left. And when the !@#$ hits the, fan it's it's gonna be quite a spectacle.

But that's not the important part! The real crime is that the "evolutionists" never bothered to tell you how evolution REALLY works. The evolutionary process is neither random nor accident. It's purposeful, it's pre-programmed, it's so ingenious and elegant it takes your breath away.

In fact the evolutionary paradigm I'm about to share with you was first proposed more than 60 years ago. It was an object of derision and ridicule until it won the Nobel Prize for Science in 1983.

No, he doesn't actually share the secrets with you. You have to sign up for his ego-serving mailing list, and then he'll tell you. Maybe. He was dunning me with email for a long time, and he never managed to say anything that made sense or even revealed a speck of biological knowledge. He's an electrical engineer and he's an idiot. Surprise!

By the way, there is no Nobel Prize for Science. There is a Nobel Prize in Physics, which was won in 1983 by Chandresekhar and Fowler for work on stellar evolution and the formation of elements; I don't think that's it. There's a Nobel Prize in Chemistry, won by Henry Taube for work on electron transfer reactions; even less likely. Then there's the Nobel Prize in Physiology or Medicine, won by Barbara McClintock for the discovery of mobile genetic elements; BINGO. McClintock's work was certainly surprising, amazing, wonderful…and also difficult to understand, and I can tell you that I've always been dazzled by the astounding insight she brought to that work, but no, it doesn't revolutionize evolution in any way. It's all pure genetics, no magic, and certainly has no implication of a designer.

As for his claim that Darwinism is in trouble and will end in 2013 — <snore>. It's a creationist cliche, and they've been saying this since before Darwin. Predictions that evolution is doomed have been collected by Glenn Morton in The Imminent Demise of Evolution: The Longest Running Falsehood in Creationism. The funniest one there is Dembski's prediction in 2004 that "molecular Darwinism" will be dead in the next five years. The only interesting thing about these predictions is that they set a date for the next creationist-mocking party. See you in 2013!

Local News Anchors Confess Their Chupacabra Report Is Only For The Ratings

http://www.mediaite.com/tv/local-news-anchors-confess-their-chupacabra-report-is-only-for-the-ratings/

by Frances Martel | 8:07 pm, July 14th, 2010

It's a summer Wednesday at your local news office and nothing particularly spectacular has happened in the area, but, as news anchor, you've still got a half-hour to fill and the script shows nothing but dead air for a good five minutes. What do you do? At WOAI San Antonio (an NBC affiliate), anchors Randy Beamer and Elsa Ramon resurrected a decade-old alien story, and felt too guilty not to admit it was a shameless attempt to raise ratings.

Ramon and Beamer went on air tonight and reported on the possible discovery of the mythical Chupacabras, most recently seen also helping to fill up dead air time on VH1's "I Love 1999." "You know, what would it be if we didn't have a story about a 'chupacabra?" Ramon asks Beamer, who responds earnestly: "It would not be a ratings month– I'm sorry, did I say that? I can't say that."

Beamer then continues to report to story on the verge of laughter, letting another cynical comment slip mid-report: "[the finding] has many people, especially on TV, wondering: Is the Chupacabra for real?"

Let it never be said that news anchors are not honest people.


Wednesday, July 14, 2010

Federal Appeals Court Rejects Chris Comer's Lawsuit Alleging Discrimination Against Evolution

http://www.evolutionnews.org/2010/07/federal_appeals_court_rejects036601.html

In 2007, Chris Comer was forced to resign from her job at the Texas Education Agency (TEA). She then filed a lawsuit alleging she was forced to "stay neutral on creationism," and claimed that TEA's "neutrality" policy violated the First Amendment. We reported last year when Comer lost on summary judgment at the federal district court level. Comer then appealed her case to the Fifth Circuit Court of Appeals, which filed its ruling on July 2 upholding the district court's decision and tossing Comer's case. The Fifth Circuit held, "we find no evidence to support the conclusion that the principal or primary effect of TEA's policy is one that either advances or inhibits religion, we conclude that the policy does not violate the Establishment Clause" and thus "the decision of the district court is AFFIRMED." While Comer's case was initially favorably pushed by New York Times in two articles and an editorial from NY Times editors, somehow the NY Times and the rest of the national news media have (as-of-yet) completely ignored the dismissal of her lawsuit.

Chris Comer and her attorneys argued that the First Amendment requires the government to allow her to take an affirmative stance against creationism (a religious viewpoint), and that any requirements to remain neutral in matters of creationism are unconstitutional. In reality, as the Fifth Circuit noted, the U.S. Supreme Court has required the government to remain neutral on matters of religion:

Government in our democracy, state and national, must be neutral in matters of religious theory, doctrine, and practice. It may not be hostile to any religion or to the advocacy of noreligion; and it may not aid, foster, or promote one religion or religious theory against another or even against the militant opposite. The First Amendment mandates governmental neutrality between religion and religion, and between religion and nonreligion.

(Epperson v. Arkansas, 393 U.S. 97, 103-04 (1968).)

Since creationism is a religious viewpoint, this long-standing precedent dictates the government must remain neutral with respect to creationism. Not so, argued Chris Comer. In fact, she essentially argued that it's unconstitutional to NOT be neutral with respect to creationism; in essence she argued that the First Amendment requires the government to oppose creationism — or to at least permit opposition towards it. Apparently this twisted, backwards understanding of First Amendment religious freedom is what drives Darwin lobbyists like Chris Comer. The reality is that if TEA were to adopt Chris Comer's non-neutral position on creationism, it's likely that such a policy would be unconstitutional.

But even entering into the above-discussion falls into Comer's trap, because it's actually irrelevant to resolving Comer's case. Both the federal district and appellate courts saw right through Comer's baseless argument since the TEA's "neutrality" policy in fact had nothing to do with creationism or religion. I noted last year:

Comer equivocated over the meaning of the word "neutral." Comer claimed that the TEA illegally required her to remain "neutral" on creationism, when in reality the TEA's policy simply required its staff to remain "neutral" on unsettled curricular matters (regardless of the subject matter in question). The former type of "neutrality" is legal neutrality and is violated only when there is a lack of religious neutrality, whereas the latter type of neutrality simply means avoiding taking a position on an unsettled curricular policy. The latter type should be considered distinct, as far as the law is concerned, from questions about religious "neutrality." Thus Comer's entire lawsuit was based upon equivocating over the legal meaning of "neutrality," conflating the TEA's benign (and statutorily mandated) policy requiring staff "neutrality" on unsettled curricular questions, with the constitutional requirement of religious "neutrality."

The Fifth Circuit also concluded that Comer's claims have little to do with Establishment clause neutrality, but rather require a different type of neutrality. As the court wrote: "Noticeably absent from the present case are the common elements that ordinarily implicate a violation of the Establishment Clause. In First Amendment constitutional jurisprudence, TEA's neutrality policy is much more akin to a policy regulating speech than a policy advancing any specific religion." The Fifth Circuit accurately described TEA's neutrality policy as follows:

In accordance with this neutrality policy, TEA staff can describe the contents of Board policy to others in neutral terms, if their jobs call for it, but they may not express opinions on the wisdom of any particular policy option in their capacity as TEA employees.

(Comer v. Scott, Case No. 09-50401 (5th Cir. 2010).)

Thus, TEA's neutrality policy does not have a primary effect which advances religion:

Upon review of the record and applicable law, we cannot conclude that TEA's neutrality policy has the "primary effect" of advancing religion. The fact that Comer and other TEA employees cannot speak out for or against possible subjects to be included in the curriculum—whether the considered subjects relate to the study of mathematics, Islamic art, creationism, chemistry, or the history of the Christian Crusades—their silence does not primarily advance religion, but rather, serves to preserve TEA's administrative role in facilitating the curriculum review process for the Board. ... we find it hard to imagine circumstances in which a TEA employee's inability to publicly speak out for or against a potential subject for the Texas curriculum would be construed or perceived as the State's endorsement of a particular religion.

(Comer v. Scott, Case No. 09-50401 (5th Cir. 2010).)

The court also observed that "[t]he record also reflects that the neutrality policy has been enforced across a variety of different curriculum issues subject to decision by the Board" — an important point since Comer had in fact violated TEA's neutrality policy with respect to a number of curriculum decisions made by the Texas State Board of Education, as seen below.

Check the Facts Before Hitching Your Wagon to a Lawsuit

In 2008, the National Center for Science Education (NCSE) was desperate for a response to "Expelled: No Intelligence Allowed," the documentary which exposed the epidemic of intolerance, persecution, and other forms of academic discrimination against proponents of intelligent design (ID). Aside from creating an error-filled website that unwittingly validated Expelled by encouraging persecution of ID proponents, the NCSE's primary response was touting a single incident of alleged persecution of a Darwin-lobbyist — that of Chris Comer. According to a YouTube video touted on the NCSE's website, Comer was "expelled for real" from the TEA because she allegedly refused to "stay neutral on creationism." Really?

Fast forward to 2009. No sooner had the California Science Center (CSC) been sued for cancelling a contract of a group seeking to show a pro-ID film than did local Southern California-area evolutionists started e-mailing the NCSE asking for guidance on how to react to the situation. In December, after a lawsuit had been filed against the CSC alleging viewpoint discrimination and breach of contract, NCSE executive director Eugenie Scott gave the following advice to one SoCal evolutionist:

I don't know what the regulations are for renting space to outside parties, so I don't know if the CSC followed its regs or not, so we should be cautious about what we say. I'll get back to you on that later.

(E-mail obtained through public documents request on Natural History Museum of Los Angeles County)

I understand Eugenie Scott's reasoning: If you know that you don't know the facts of a case, it's probably best not to comment on it.

However, as noted, when Comer's case first hit the media in early 2008, it was being widely touted by the New York Times and other media. I received multiple e-mails from individuals seeking a comment on her case. Some of those e-mails came from evolutionists who were basically harassing me to issue a statement supporting Comer. Of course it would be a travesty if an evolutionist was fired due to his or her beliefs on evolution, but much like Eugenie Scott felt about the CSC lawsuit, I told them I didn't feel it was prudent to issue any statement until I knew more about the facts of the situation.

Dr. Scott and the NCSE should have applied this cautious methodology and investigated the facts more carefully before jumping on the bandwagon of Chris Comer's case.

Later in 2008, more facts about Comer's case came out after Texans for Better Science Education (TBSE) filed a public documents request on the Texas Education Agency (TEA) requesting documents pertaining to Chris Comer's performance as a TEA employee. TBSE obtained many internal documents showing that Comer's history of employment at the TEA wasn't exactly exemplary. To summarize some of the problems Comer encountered while working the TEA, consider the following, adapted from TBSE's "Summary and Timeline of Chris Comer's Disciplinary History at the TEA":

(1) June 2003: Comer receives a "Letter of Reprimand and a Notice of Disciplinary Probation" after evidence surfaced that she may have illegally used her position to gain paying contracts with TEA clients outside-of-work. The Letter noted that if she had done this, such actions would actions violate the Texas Penal Code—i.e. they would constitute a crime.

(2) November, 2006: Monica Martinez (Comer's supervisor) instructs Comer not to communicate with anyone outside the TEA about fourth-year science requirements, a curricular matter that was unsettled at the time. But later that same morning, Comer violated this directive in an e-mail she sent to various Texas educators. Martinez later recounted that she "specifically asked" Comer "not to communicate with anyone outside the agency regarding the State Board of Education item on the fourth year of science requirements and asked that you notify George or me immediately if anyone, including board members asked you for information on this topic." Because Comer violated Martinez's directive, Martinez reprimanded Comer stating, "This email was sent in direct violation of the directive not to communicate with anyone regarding these issues" and therefore Comer's actions constituted "insubordination."

(3) February 3, 2007: TEA rules require that "Each employee or official authorized to travel must prepare a travel itinerary for his or her trip" and that this itinerary "is to be approved by a traveler's manager prior to the trip." Comer participates in a science conference, but contrary to TEA policies, did not receive prior approval to attend the conference.

(4) February 12, 2007: Comer attended 2 off-site meetings but again, contrary to TEA policies did not receive prior approval to attend.

(5) February 23, 2007: Monica Martinez sent Comer a "Letter of Counseling," stating that "Over the past several months I have developed serious concerns regarding your job performance with respect your involvement with work outside the agency and failure to follow supervisory directives." Martinez cited the Nov. 16, 2006 e-mail subordination incident, and the Feb. 3 and Feb. 12, 2007 non-approved meeting incidents, as evidence supporting her charges. Martinez warned Comer that some of Comer's actions "constitutes insubordination … and will not be tolerated." Comer was given the following direct orders from her supervisor:

(6) August 14, 2007: Comer sends an e-mail to Monica Martinez notifying that she had recently given a presentation at a meeting of Texas educators. In violation of the February 23 Letter of Counseling ordering Comer to obtain "prior approval" when traveling to conferences, and to "obtain approval on the content" when giving presentations, Comer had neither received approval to travel and give this presentation, nor did she seek or receive approval for her presentation content. Martinez stated that Comer's failure to receive approval and violation of the directives in the Feb. 23 Letter of Counseling, constituted "insubordination."

(Martinez also found that the content of Comer's presentation was problematic because they included "comments on policy implications that are inappropriate for Ms. Comer to make" including information that "had not been approved by the SBOE." Martinez thus concluded that this presentation as "inappropriate to share publicly" and that Comer "lacks an adequate understanding of her appropriate role as Science Director.")

(7) October 9, 2007: Comer allegedly stood up in front of a meeting of the Texas Regional Collaborative Science Directors, who represent educators from all over Texas, and publicly badmouthed her boss, acting TEA Commissioner Robert Scott, saying that "there was no real leadership in the Agency." Martinez found that Comer's actions constituted "misconduct" under the TEA's stated definition of "Conduct that negatively impacts TEA."

(8) October 26, 2007: Comer receives an e-mail from an NCSE staff member advertising a lecture by Barbara Forrest on November 2, 2007, sponsored by the Center for Inquiry's Austin branch entitled "Inside Creationism's Trojan Horse" on the "history of the 'intelligent design' movement." Comer replies to the e-mail promising "Thanks so much Glenn. I will help get the word out." Later that day Comer used her TEA e-mail account to forward the e-mail advertising Forrest's lecture to about 36 science educators in the Austin area.

(9) October 29, 2007: Comer attends another meeting without obtaining approval. Martinez found that this again "violates the directive Ms. Comer was given not to travel in-state or out-of-state to represent the agency as the Director of Science, whether on her own time or on agency time, unless she obtained prior approval."

(10) Nov. 5, 2007: Monica Martinez drafted a memo of "Proposed Disciplinary Action" and sent it to Susan Barnes and Sharon Jackson. The memo alleged that Comer engaged in "a series of incidents evidencing a serious lack of good judgment and failure to follow agency policies and supervisory directives." Martinez thus wrote, "I request that you approve this recommendation for the termination of Ms. Comer's employment. This action is necessary due to Ms. Comer's repeated incidents of insubordination, the seriousness of her misconduct, and the extent to which she has demonstrated poor judgment." The next day, Comer resigned.

(Adapted from "Summary and Timeline of Chris Comer's Disciplinary History at the TEA")

In case you weren't keeping count, in the year leading up to her departure from the TEA, Comer was charged with insubordination on three separate occasions. Counting her full term at the TEA, she experienced eight separate disciplinary incidents — seven of which had nothing to do with evolution. The final incident — which did touch upon evolution — was just the proverbial straw that broke the camel's back. Thus, it seems that Comer's oft-repeated insinuation that she was "getting fired over evolution" is not entirely accurate. In fact, as the Fifth Circuit notes in its ruling, the final evolution incident was not the first time that Comer had violated TEA's curricular neutrality policy:

Martinez's previous directive to Comer had prohibited Comer from communicating with anyone outside TEA in any way that could imply endorsement of a position on any curriculum issue that may be considered by the Board. Thus, on November 7, 2007, in response to Comer's act of forwarding the Branch email, Martinez drafted a memorandum recommending Comer's termination.

The reality is that Chris Comer appears to have been a difficult employee all along who continually offered her opinion on curricular matters where she was supposed to remain neutral. In one instance, she even went so far as to publicly castigate her boss about a month before her departure, violating TEA's rules of employee conduct. (As General McChrystal recently learned, publicly criticizing your boss is not a good way to keep your job.) The Fifth Circuit rightly rejected her claims.

The moral of this story is this: Whether the case ultimately wins or loses in court, don't speak out publicly on a case until you know the facts. The NCSE is understandably reticent to speak out about a case that shows persecution against ID when it doesn't know the facts. But in early 2008, it was eager to tout a lawsuit allegedly showing persecution against an evolutionist, even though I'm not sure if they knew how weak her case was at the time. It seems that when faced with the avalanche of evidence of persecution against ID as documented in Expelled, the NCSE was desperate to find a rhetorical rebuttal and hitched their wagon to Comer's case.

Chris Comer's case was the one answer that the Darwin-lobby had to Expelled in the spring of 2008 when Expelled came out. Now their rhetorical rebuttal has gone belly up, and their martyr has been shown to more an unruly employee with baseless legal claims, than a victim of discrimination.

Posted by Casey Luskin on July 13, 2010 11:54 AM | Permalink


Monday, July 12, 2010

[Editor's note: Oops! Creationists don't like it when people call a spade a spade.]

Sneers and Double Standards Pass for Scholarship in Evolution: Education and Outreach

http://www.evolutionnews.org/2010/07/sneers_and_double_standards_pa036551.html

Pop quiz: Did the following quote come from (A) Panda's Thumb, or (B) An article in a scholarly journal published by Springer science publishing?

"An especially good example of silliness is the ID assertion that natural processes cannot create new genetic information. ID advocates have recently been pushing this line heavily as of late (Meyer 2009)…"

If you answered (A), then…

…you're wrong. It came from a recent article former by NCSE staff-member Nick Matzke in the journal Evolution: Education and Outreach — an NCSE-aligned outfit, where apparently such language passes for scholarly argument. In the words of Jay Richards "a sneer is not an argument."

Of course Matzke's reference in the quote from his recent paper is to Stephen Meyer's 2009 book Signature in the Cell: DNA and the Evidence for Intelligent Design. The extent of Matzke's technical response is to call the book's argument "silliness" and to later bash the book for allegedly alluding to Rick Warren's "The Purpose Driven Life":

Meyer's reference to a "purpose-driven life" is of course a direct reference (though without citation) to the massively popular book of the same name(Warren 2002) authored by Rick Warren, a megachurch pastor and one of the leading evangelical voices in America today. In any standard scientific book on the origin of life, this would be quite the odd reference, but with creationist works, even ID works, it is par for the course.

But exactly how does Meyer allude to the "purpose-driven life"? Matzke's paper garbles a passage from Signature of the Cell (SITC) as follows:

As a teenager in the mid-1970s, I sensed this absence of meaning in modern life...What heroism, thought or feeling, labor, inspiration, genius, or achievement will last, if impersonal particles are all that ultimately endure? …Though the theory of intelligent design does not identify the agent responsible for the information—the signature—in the cell, it does affirm that the ultimate cause of life is personal...The case for intelligent design challenges the premise of the materialist credo and holds out the possibility of reversing the philosophy of despair that flows from it. Life is the product of mind; it was intended, purposed, "previsioned." Hence, there may be a reality behind matter that is worth investigating.

If the conscious realities that comprise our personhood have no lasting existence, if life and mind are nothing more than unintended ephemera of the material cosmos, then, as the existential philosophers have recognized, our lives can have no lasting meaning or ultimate purpose. Without a purpose-driven universe, there can be no "purpose-driven life." (Meyer 2009)

Using Matzke's quote as a guide, the second paragraph from SITC in this quote is extremely difficult to locate because it appears two pages before the first paragraph. Of course, this reflects the fact that Matzke took the liberty of engaging in a significant amount of re-arranging of Meyer's words, leaving out much context. Had Matzke continued with the actual context after the first paragraph, as his quote wrongly implies the second paragraph ought to be, one would have discovered the following prose from Stephen Meyer:

These implications of the theory are not, logically speaking, reason to affirm or reject it. But they are reasons—very personal and human reasons—for considering its claims carefully and for resisting attempts to define the possibility of agency out of bounds. (p. 451)

The context of Meyer's discussion indicates that he's is talking about the larger implications of ID, and not the arguments for ID. But Matzke's argument implies that discussing larger philosophical or theological implications or alluding to religious topics is inappropriate for "any standard scientific book on the origin of life." Ironically, Matzke is doing exactly what Meyer warns against: trying to define ID as "out of bounds" without actually addressing the argument. Hence, Matzke is reduced to calling SITC's arguments "silliness" and making irrelevant complaints about Meyer's discussion of theological implications.

But is Matzke correct that mainstream scientific books never engage in discussions of the larger implications—even religious implications—of the science? I pulled a few scientific books dealing with origins off my bookshelf, and this is what I found:

Contra Matzke, it seems that standard scientific books on origins — by leading scientists — commonly discuss the implications of their scientific arguments at the end. After spending 400+ pages laying out the scientific evidence for ID, and explaining why this argument is scientifically based, Meyer has more than earned the right to spend a few pages talking about the larger religious implications he draws personally from that evidence.

Nick Matzke is well-accustomed to treating ID proponents with a different standard than that to which he holds evolutionary scientists: Evolutionary scientists are given freedom of speech to discuss the greater philosophical or theological implications of their scientific ideas and still have their ideas called scientific. In my view, that's fine, and that's how it should be. But he applies a double-standard to ID proponents, claiming that if they explore the theological implications of their scientific arguments then they "are engaging in religious apologetics in the guise of science."

Posted by Casey Luskin on July 12, 2010 10:38 AM | Permalink


Saturday, July 10, 2010

Review: Stephen Jay Gould: Reflections

http://ncse.com/rncse/30/1-2/review-stephen-jay-gould-reflections

Reports of the National Center for Science Education
Volume: 30
Year: 2010
Issue: 1–2
Date: January–April
Page(s): 30, 35
Reviewer: Kevin Padian
This version might differ slightly from the print publication.
Work under Review
Title: Stephen Jay Gould: Reflections on His View of Life

Author(s): Edited by Warren D Allmon, Patricia H Kelley, and Robert M Ross
Oxford: Oxford University Press, 2008. 416 pages.
Purchase this book online

At scientific meetings, Steve Gould was usually as mobbed as he was at his public lectures. Everyone had something to discuss with him — a point, a quibble, an idea, a request for help. Whenever we spoke, usually after the throng had dispersed, we would talk about Darwin, dinosaurs, Owen, punctuation, homology, species, and adaptation. But first, we would talk about baseball. As diehard American League fans, we had the endless vicissitudes of pitching, hitting, strategies, and injuries to rehash. Steve was a very public person, and his observers have often been puzzled by his fascination with baseball — as with cathedrals, choral music, and antiquarian books. But the answer is obvious, really, encapsulated in the T-shirt motto: "Baseball is Life." The players have different ecological roles, for which they are selected, but few players are good at everything. There are constraints of the rules of the game, contingencies of the consequences of a fielding error or an unintentional fat pitch hit for a homer. The dynamics change with every hesitation before the next ball is thrown; and just when you think nothing is happening, that's often when the most is happening.

Structure, contingency, and history were three major evolutionary themes that also resonated in Steve's non-scientific preoccupations. None of the authors in this tremendously informative and accessible volume talks much about baseball or Steve's other passions, though. That's interesting, because he saw much of evolution — although in strictly analogical terms — through the lenses of his favorite pursuits. But the essays in this indispensable book are less about style than substance, and they comprise a collection of lasting value for any evolutionist.

Do the authors, many of whom are Gould's former students, come to praise him or to appraise him? The latter, although it is difficult not to celebrate the man who was not only the most publicly visible and influential paleontologist of the last half of the 20th century, but also the most publicly visible and influential evolutionary biologist. The only scientist who even came close was Henry Fairfield Osborn, who died in 1936 but used the American Museum of Natural History and a slew of books and articles to keep interest focused on the history of life (Rainger 1991, Regal 2002). Osborn's notions about evolutionary progress, vitalism, and teleology are long dustbinned. Will Gould's ideas about punctuated equilibria, species selection, exaptation, and the hierarchy of evolutionary levels meet the same fate?

The authors of this collection don't think so, on balance, although they are clear-eyed about the reception of Gould's ideas in various corners of the field of evolution. The perspectives of a cadre of leaders in paleobiology, all of whom grew up hearing Gould's ideas straight from the source, trying to test and elaborate upon them, are invaluable as an historical record of one of the most original evolutionary theorists of the century. Yes, Gould had his quirks, his inadequacies, and his blind spots, like any scientist. But how many scientists would merit this kind of theoretical analysis?

At the heart of most assessments of Gould's work is punctuated equilibria, which he originated with Niles Eldredge. Several authors (Allmon, Geary, Kitcher, Lieberman) discuss it with great insight. In particular, they note that the critical issues of PE are whether stasis in evolutionary lineages is predominant, and what causes morphological stasis. These are not only central to PE but to all of evolutionary biology. If stasis really is predominant in evolutionary lineages, then most of what we have been taught about population genetic models of tempo and mode, and the tracking of small-scale environmental change by selection, might just be wrong — or at least due for a revision, as Gould suggested in 1980 and explored at length in The Structure of Evolutionary Theory (2002).

The authors in this compilation seem to accept Gould (and Eldredge's) contention that PE is a hypothesis about the deployment of speciation through time. But is it? All that the fossil record shows is morphology; speciation has to be inferred. That would be easy if one lineage clearly divided into two through time, but does it usually? In the classic formulations of PE, including coordinated stasis (Brett and Baird 1995) of many lineages simultaneously, no clear splitting is found. Rather, in classic PE form, one rather stable, vacillating lineage swiftly gives way to another. Is this speciation (cladogenesis) or simply rapid anagenesis? If the former, then competitive replacement of one lineage by another must be geologically instantaneous. In either case, how will diversity increase, as it clearly has through the Phanerozoic Era?

There are many perceptive and useful essays in this collection, and anyone interested in the development of 20th-century evolutionary thought will be fascinated by their insights. They explore the implications of Gould's theories for mass extinction (Kendrick), systematics (Yacobucci), creationism and evolution (Kelley), and ecology (Allmon and others, with the conclusion that Gould never cared about it anyway), among other subjects. Dick Bambach contributes a very useful historical chronology of Gould's ideas, which has the effect of limning clearly the various phases in his intellectual development. Philip Kitcher provides a fascinating and well argued essay on the logic of Gould's major ideas. Lewontin and Levins explore Gould's status as a "radical," by which they mean one who returns to the roots of the field (missing only his "radical" emphasis on original historical literature to dispel the myths of evolutionary history). And Warren Allmon contributes both a sweeping perspective of Gould's contributions to the field and an exhaustive (can it be complete?) bibliography of Gould's work (it runs to 44 pages). The elegant final essay by Robert Dorit, on how the promise of evolutionary developmental genetics has (and hasn't) borne out Gould's perennial theme of the importance of ontogeny to evolution, is a masterpiece not only of content but of writing.

The only thing really missing from this book, apart from assessments by Niles Eldredge, Elisabeth Vrba, David Raup, and other close co-authors of Gould, is an appraisal of his debates with the principal critics of his later years, such as Daniel Dennett, Richard Dawkins, and John Maynard Smith. There will be other essays, tribute volumes, and biographies that assess Gould's work historiographically and scientifically, but as a survey of Gould's contributions to the field, this volume is an instructive and indispensable beginning.

References

Brett CE, Baird GC. 1995. Coordinated stasis and evolutionary ecology of Silurian to Middle Devonian faunas in the Appalachian Basin. In: Erwin EH, Anstey RL, editors. New Approaches to Speciation in the Fossil Record. New York: Columbia University Press, New York. p 285–315.

Gould SJ. 2002. The Structure of Evolutionary Theory. Cambridge (MA): Belknap Press.

Rainger R. 1991. An Agenda for Antiquity: Henry Fairfield Osborn and Vertebrate Paleontology at the American Museum of Natural History, 1890–1935. Tuscaloosa (AL): University of Alabama Press.

Regal B. 2002. Henry Fairfield Osborn: Race and the Search for the Origins of Man. Aldershot (UK):Ashgate.

About the Author(s):
Kevin Padian
Department of Integrative Biology
Museum of Paleontology
University of California
Berkeley CA 94720-3140

Kevin Padian is Professor of Integrative Biology at the University of California, Berkeley; Curator of Paleontology at the University of California Museum of Paleontology; and president of NCSE's board of directors.

Caustic Government Report Deals Blow to Diabetes Drug

http://www.nytimes.com/2010/07/10/health/10diabetes.html?th&emc=th

By GARDINER HARRIS
July 9, 2010

WASHINGTON — A federal drug official on Friday dealt a severe blow to the popular diabetes drug Avandia, issuing a scathing review of a major clinical trial that its manufacturer has been using to argue that the drug was safe.

The reviewer, Dr. Thomas Marciniak of the Food and Drug Administration, found a dozen instances in which patients taking Avandia appeared to suffer serious heart problems that were not counted in the study's tally of adverse events.

Such repeated mistakes "should not be found even as single occurrences" and "suggest serious flaws with trial conduct," Dr. Marciniak wrote.

The detailed report could prove crucial next week, when a panel of experts will meet to consider whether to recommend to the F.D.A. that the manufacturer, GlaxoSmithKline, withdraw Avandia from the market or restrict its sale.

The panel's decision will have broad consequences for the company, the F.D.A. and perhaps even the entire process by which medical products are approved. The agency almost never does clinical trials on its own, depending on drug companies to conduct them appropriately.

Avandia, which helps patients get better control of blood sugar levels, has already come under intense criticism. It has been shown to increase the risks of bone fractures and to cause swelling that can lead to heart failure and eye problems.

And a number of studies, including some by GlaxoSmithKline, suggest that it could increase the risks of heart attacks, strokes and death. But the company has relied heavily on the major clinical trial, nicknamed Record, to demonstrate that those risks are exaggerated.

Dr. Marciniak's review of the Record study calls that assertion into question. He found one case in which a seizure patient was hospitalized for bleeding in the brain, but all mention of the episode was deleted from records. Another patient was hospitalized for 67 days after a severe stroke, but the study record showed no sign of a cardiovascular problem.

Still another died after being hospitalized for a serious heart problem, but the death was listed as arising from an unknown cause and not heart-related.

Correctly interpreted, he concluded, the study actually supports critics' contentions that Avandia may cause heart attacks and strokes. "One does not have to be a mathematician or to perform calculations," he wrote, to come to the conclusion that a combined look at all the trials of Avandia would demonstrate that it causes heart attacks.

Mary Anne Rhyne, a spokeswoman for GlaxoSmithKline, said the study demonstrated that Avandia is safe and added, "The Record study was conducted according to good clinical practices and the data are reliable."

Dr. Marciniak's review is part of a reassessment of Avandia's safety by F.D.A. medical officers to educate the panel, who will meet Tuesday and Wednesday in Gaithersburg, Md., to advise the agency whether Avandia should be withdrawn from the market — after millions of prescriptions, billions of dollars in sales and 11 years of wide use.

The agency's initial review of the Record trial, in 2007, found no problems. But independent researchers who have examined the health records of thousands of patients taking Avandia have found strong hints that the drug is more dangerous than GlaxoSmithKline has claimed. So Dr. Marciniak took an unusually close look at the Record study, demanding to see records that the agency rarely examines.

Only then did he turn up the study's many problems. If given more time, he wrote, he would probably have found still more.

Debate about Avandia's safety and how to handle reports of its dangers has split the food and drug agency and led to fierce recriminations, staff departures and questions from Congress.

It was the F.D.A.'s delay in issuing stronger warnings about Avandia that led Congress in 2007 to give the agency greater powers over drug makers.

Within the F.D.A., some officials insist that the evidence is mixed and others say it is strong enough to merit the drug's withdrawal. An advisory meeting in 2007 concluded that Avandia did increase heart attack risks but that it should stay on the market.

In response, Avandia's sales fell sharply, to $1.2 billion last year from a peak of $3.2 billion in 2006. But while endocrinologists have advised against its use, Avandia remains popular — with nearly two million prescriptions last year. If the drug is withdrawn, GlaxoSmithKline — already facing lawsuits claiming Avandia caused injuries — would see its liability soar.

In that 2007 advisory meeting, the Record trial — specifically devised to assess Avandia's heart risks — was a significant source of reassurance for Avandia's supporters. GlaxoSmithKline insisted the trial had proved that the drug was safe. In a news conference on Thursday, Dr. Janet Woodcock, director of the F.D.A.'s drug center, called the Record trial one of the "most germane because it's a study of cardiovascular outcomes."

Conducted at 338 sites in 23 countries, the Record study involved 4,447 patients with Type 2 diabetes who were recruited between April 2001 and April 2003 and followed for nearly six years. Half of the patients received two older diabetes medicines while the other half were given Avandia in combination with an older diabetes medicine.

The study was paid for by GlaxoSmithKline and conducted in part by Quintiles, a clinical trials company. A spokesman for Quintiles declined to comment.

Avandia's critics have long asserted that the Record study was both weakly designed and too short to prove anything. And an inquiry by the Senate Finance Committee found that GlaxoSmithKline may have improperly influenced the independent experts in charge of the study.

An editorial in The New England Journal of Medicine on Friday accused GlaxoSmithKline of interfering with the trial and said the system for hiring trial safety experts should change.

In an interview on Friday, Dr. Jerome P. Kassirer, a former editor of The New England Journal, said the Record trial raised the question "whether the entire system is corrupt." "To the extent that we can't trust the data," he added, "we are in jeopardy of giving patients the wrong drugs."

One reason Dr. Marciniak's critical review of the Record trial is so important is that he works at the F.D.A.'s office of new drugs, which has long defended Avandia's safety against criticism from a separate safety office.

Analyses of Avandia's safety from other reviewers in the office of new drugs that were posted on the agency's Web site on Friday were not as critical as Dr. Marciniak's, but his defection suggests that Avandia's support within this crucial office has weakened.

Another issue the expert committee will be asked to resolve is whether a GlaxoSmithKline study being done at the F.D.A.'s request, comparing the safety of Avandia with Actos, a similar drug made by Takeda, is ethical. Some agency officials argue that the trial must be stopped, because observational studies — which use health records to measure how patients fared while taking a particular drug — have already proved that Avandia is dangerous.

Others within the F.D.A. say that observational studies are not good enough and that a well-controlled "prospective" study, like the one being conducted by GlaxoSmithKline, is the only sure way to answer whether Avandia is truly dangerous.

In a report released Friday, the Institute of Medicine, the nation's leading medical advisory group, seemed to side with those who have argued that observational studies are adequate. Indeed, the group seemed to describe almost exactly a study of 227,571 Medicare patients conducted by an F.D.A. reviewer and published June 28 in The Journal of the American Medical Association concluding that Avandia increased the risks of stroke, heart failure and death compared with Actos.

The institute concluded that such studies "can sometimes provide higher-quality safety evidence than randomized controlled trials."


Friday, July 09, 2010

Evolution education update: July 9, 2010

The first year of Randy Moore's "People & Places" column is now available on-line. Chris Comer's appeal failed -- the Texas Education Agency's policy requiring "neutrality" of its employees when "talking about evolution and creationism" is not unconstitutional. And NCSE's Eugenie C. Scott is profiled in the Capital Times.

MAKING THE ROUNDS WITH RANDY MOORE

In 2009, Randy Moore began to write a regular column for Reports of the NCSE in which he introduced the people and places of the creationism/evolution controversy. Now the first year of his "People & Places" column is available on-line. Moore visits Siccar Point, "arguably the most important geological site in the world"; the Temple of Serapis, which appears on the frontispiece of Charles Lyell's Principles of Geology; Dayton, Tennessee, which hosted the Scopes trial in 1925; William Paley, whose Natural Theology influenced Darwin's thought; and the Creation Evidence Museum in Glen Rose, Texas -- both before and after its remodel.

A long-time member of NCSE and a recipient of its Friend of Darwin award, Moore is Professor of Biology at the University of Minnesota. If you like his "People & Places" column, you'll be sure to love More than Darwin: An Encyclopedia of the People and Places of the Evolution-Creationism Controversy (Greenwood Press, 2008; University of California Press, 2009), coauthored with Mark Decker. NCSE's Glenn Branch praised it as "[a] marvelous trove for the curious browser, who will be constantly tempted to pull the book off the shelf to read a random entry and discover a new fact or two." And you'll also want to subscribe to Reports of the NCSE!

For the first year of Moore's column, visit:
http://ncse.com/rncse/29/1/siccar-point
http://ncse.com/rncse/29/2/temple-serapis
http://ncse.com/rncse/29/3/dayton-tennessee
http://ncse.com/rncse/29/4/william-paley-1743-1805
http://ncse.com/rncse/29/5/creation-evidence-museum
http://ncse.com/rncse/29/6/going-back-to-glen-rose

For Branch's review of More than Darwin, visit:
http://ncse.com/rncse/29/1/review-more-than-darwin

And for information about subscribing to Reports of the NCSE, visit:
http://ncse.com/membership

COMER LOSES APPEAL

In a decision issued on July 2, 2010, the United States Court of Appeals for the Fifth Circuit upheld a lower court's decision that the Texas Education Agency's policy requiring "neutrality" of its employees when "talking about evolution and creationism" is not unconstitutional. The case, Comer v. Scott, was filed by Chris Comer, the former director of the Texas Education Agency, who was forced to resign from her post in November 2007 after she forwarded a note announcing a talk by Barbara Forrest. In June 2008, Comer filed suit, arguing that the agency's neutrality policy violates the Establishment Clause. Her lawsuit was dismissed in March 2009, but she appealed the decision, and oral arguments were heard in April 2010.

Writing for a three-judge panel of the Fifth Circuit, Fortunato Benavides explained (pp. 11-12), "Upon review of the record and applicable law, we cannot conclude that TEA's neutrality policy has the 'primary effect' of advancing religion. The fact that Comer and other TEA employees cannot speak out for or against possible subjects to be included in the curriculum ... does not primarily advance religion, but rather, serves to preserve TEA's administrative role in facilitating the curriculum review process for the Board. ... Thus, we find it hard to imagine circumstances in which a TEA employee's inability to publicly speak out for or against a potential subject for the Texas curriculum would be construed or perceived as the State's endorsement of a particular religion."

For the Fifth Circuit's ruling (PDF), visit:
http://ncse.com/webfm_send/1390

For NCSE's collection of documents from the case, visit:
http://ncse.com/creationism/legal/chris-comer-docs

NCSE'S SCOTT PROFILED IN CAPITAL TIMES

NCSE's executive director Eugenie C. Scott was profiled by Phil Haslanger in the Madison, Wisconsin, Capital Times (July 1, 2010). "In a place like Madison, it's easy to think about the battles over teaching evolution in schools as something from another time and place," Hanslanger writes. But -- as Scott, who was born and raised in Wisconsin, told him -- "You don't have to go far to find a teacher afraid of teaching evolution or who is teaching creationism ... Teachers will often soft-pedal evolution or skip over it if there is a chance of a confrontation." Additionally, as attempts to have creationism taught explicitly have faltered, the new trend is to require or encourage teachers to present what are billed as the "weaknesses of evolution" -- which, Scott explained, would be "wasting time teaching students a bunch of erroneous information." Haslanger, a regular columnist for the Capital Times, is pastor of Memorial United Church of Christ in Fitchburg, Wisconsin.

For the profile, visit:
http://host.madison.com/ct/news/opinion/column/phil_haslanger/article_954cba6d-1b37-53b5-85ed-d0bc1496cb1b.html

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Blowing in the Wind

http://www.huffingtonpost.com/david-horton/blowing-in-the-wind_b_638696.html

David Horton.Posted: July 8, 2010 04:30 PM

Science, what is it good for? Absolutely nothing these days, it seems.

If you had asked me a few years ago the answer was absolutely clear. No, not the technology, that's just the side effect, a little bonus, cream on top.

The real importance of science, for the last 500 years, was that it was the one aspect of human endeavor that constantly advanced, constantly improved, built on previous work, and earlier understanding, it didn't take a backward step. Each scientist stood on the shoulders of giants, as Newton said.

Up until the Renaissance humans had taken one step forward and two steps back in their understanding of the world around them. Some glimmering of understanding about the nature of the real world would be smashed down again by religion or war or cynical politicians or charlatans. But once the scientific method of hypothesis, experiment, modified hypothesis, became established by people focused on investigating the real world instead of accepting the imaginary world of wishful thinking, the human race never looked back. Or not for long anyway.

The age and structure of the universe was established; the form and relationships of different chemical elements; the development of life on earth (and the place of Homo sapiens in that development); the history and geology and climatology of the Earth; the anatomy and physiology and psychology of the human (and other animals) body. All of this was a long way from superstition, and folk medicine, and mythology, and religion, and the last vestiges of those early and primitive beliefs were gradually being swept away as the twentieth century came to an end. At last the human race was on the move into the twenty first century, after 500 years of steady advance, with a clear vision of reality unencumbered by the past detritus of failed human beliefs.

That was a scary prospect, it seems, for some people. It couldn't be allowed to happen. And suddenly all the junk thought from past millenia (with some additions) was back in the mix, spurred on by politicians and religious leaders and the media. Suddenly there were miracles, and magic remedies (homeopathy just the most egregious), and prayer, and creationism, climate change denialism, belief in ghosts and the afterlife, and heaven and hell, and mysterious forces, and supernatural beings, and faith healing, and magnets and crystals, and human domination over nature, and witches, and spirituality, all flooding back into human society and culture like an oil leak flooding into the Gulf. Just as poisonous to the human condition as oil is to seabirds.

Both of them need a big clean up effort. We need decent science education in schools again, free of the baneful influence of religious followers. And we need a media that again accepts the scientific method and its findings, and refuses to give air time or column inches or internet bandwidth to charlatans, and religious leaders, and the deliberate deceptions of the anti-science self-proclaimed mystics and healers, and the no-nothingism of those determined to let the corporations destroy the planet. Big task to clear all this rubbish out, but once it is gone science can again get on with the task of illuminating the real world. And after the damage that has been done by the charlatans and con men and crooks in the last few years we have lost time to make up, urgently. The answers have been blowing in the wind of nonsense and lies for a decade now.

You with me?

[Editor's note: The following entries are back referenced. Read down to the McLatchie entry for the complete story.]

Ken Miller may face more embarrassing facts, Behe's DBB vindicated

http://www.uncommondescent.com/intelligent-design/ken-miller-may-face-more-embarrassing-facts-behes-dbb-vindicated/

11 July 2007
scordova
[slight correction and update follows]

[update: I had previously taken a second hand quotation from Paul Nessleroade of Ken Miller here (2003 Wedge Update). Below I give a quote by Miller by a better source document here: Life's Grand Design.

However, the more accurate quotation still demonstrates Miller made an embarrassing assessment about the architecture of DNA. I apologize to him for the inaccuracy, however, it was not a material inaccuracy as can be seen in the quotation from his website.

The greater burden is on Miller to retract his mistaken ideas from the public sphere. Further, he owes an apology to many in the ID movement for misrepresentations and errors of fact which he has promoted currently, over the years, and even under oath.]

the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles.

Ken Miller, 1994

Empirical evidence 13 years later is putting some egg on Miller's face [remember Ken Miller is the guy who made misrepresentations under oath in the Dover trial].

Encyclopedia Of DNA: New Findings Challenge Established Views On Human Genome

The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. "Our perspective of transcription and genes may have to evolve," the researchers state in their Nature paper, noting the network model of the genome "poses some interesting mechanistic questions" that have yet to be answered.

Other surprises in the ENCODE data have major implications for our understanding of the evolution of genomes, particularly mammalian genomes. Until recently, researchers had thought that most of the DNA sequences important for biological function would be in areas of the genome most subject to evolutionary constraint — that is, most likely to be conserved as species evolve. However, the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution, at least when examined by current methods used by computational biologists.

According to ENCODE researchers, this lack of evolutionary constraint may indicate that many species' genomes contain a pool of functional elements, including RNA transcripts, that provide no specific benefits in terms of survival or reproduction.

Behe 10 years ago, in Darwin's Black Box (DBB) suggested junk DNA may not be junk after all. Behe has been vindicated by the facts, Miller refuted.

Finally, there is at least one other interesting fact in this article: "the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution". This means these designs NOT attributable to natural selection. Features in the genome have been shown not to be likely products of "slight successive modifications". How I love science!

Junk DNA: A Problem for the Evolutionary Paradigm?

http://www.reasons.org/design/bad-designs/junk-dna-problem-evolutionary-paradigm

12/6/2007
by Dr. Fazale ("Fuz") Rana

New Discoveries Raise Questions about Molecular Evolution

One of the most significant challenges to the Christian faith comes from the problem of evil. If God is all-powerful, all-knowing and all-good, why do evil, pain, and suffering exist in the world? In logical terms:

God is all-good.

God is all-powerful.

Evil, pain, and suffering exist in the world.

For skeptics and atheists, the last statement is incompatible with the first two. This inconsistency translates into one of two possible conclusions: either God is not all-powerful or all-good, or God does not exist.

Could it be that a statement is missing from the syllogism? God could have a basis for allowing evil, pain, and suffering to exist. Christian apologists have identified several reasons why God might allow evil, pain, and suffering and still maintain His status as all-good and all-powerful. (See Ken Samples' book Without a Doubt for a detailed Christian response to the problem of evil.)

While it is necessary to explain how God's sovereignty and goodness cohere with the existence of evil in the world, a more fundamental consideration involves the absence of the categories of good and evil within an atheistic worldview and the philosophical position of naturalism. If God doesn't exist, then nature is indifferent. There is no good and evil. When skeptics raise the problem of evil, they inadvertently undermine the very argument they're trying to make because, for the atheist, evil cannot exist.

A couple of recent scientific discoveries expose a similar problem when skeptics bring up "junk" DNA as a challenge to intelligent design and creationism. These advances provide new insights into the behavior of junk (a noncoding type of) DNA that raise fundamental questions about the validity of molecular evolution.

Evolutionary biologists consider the existence of junk DNA as one of the most potent pieces of evidence for biological evolution. According to this view, junk DNA results when undirected biochemical processes and random chemical and physical events transform a functional DNA segment into a useless molecular artifact. Junk pieces of DNA remain part of an organism's genome solely because of its attachment to functional DNA. In this way, junk DNA persists from generation to generation.

Evolutionists also highlight the fact that in many instances identical (or nearly identical) segments of junk DNA appear in a wide range of related organisms. Frequently the identical noncoding DNA segments reside in corresponding locations in these genomes. For evolutionists, this clearly indicates that these organisms shared a common ancestor. Accordingly, the junk DNA segment arose prior to the time that the organisms diverged from their shared evolutionary ancestor.

The challenge represented by junk DNA takes on a similar logical form to the problem of evil.

God is all-good.

God is all-powerful.

Junk DNA exists.

For skeptics and atheists, the last statement is incompatible with the first two. Evolutionists ask, "Why would a Creator purposely introduce nonfunctional, junk DNA at the exact location in the genomes of different, but seemingly related, organisms?"

Proponents of intelligent design and creationism respond to this objection by highlighting recent discoveries that attribute function to junk DNA. The recognition that junk DNA has function weakens the best argument for biological evolution and common descent. It also explains why identical junk DNA sequences appear in corresponding regions of the genomes of related organisms.

Two recent studies raise much more fundamental questions about junk DNA and, as a consequence, the evolutionary paradigm. One study appeared in a recent issue of PLoS Biology. This work examined the functional significance of a class of junk DNA referred to as ultraconserved elements (UCEs). UCEs don't code for proteins. Because they are noncoding, evolutionary biologists in the past would have considered these DNA elements to be junk. In the genomes of humans, rats, and mice, however, these DNA elements display virtually identical sequences. (There are approximately 480 UCEs in the human genome.)

Biologists immediately regarded this level of sequence identity as evidence that the UCEs must be functional, though they had no idea about the specific utility of these sequence elements. From an evolutionary standpoint, conservation of DNA sequences serves as a powerful indicator for function, since any change in these sequences via mutations would be weeded out by natural selection. From an evolutionary perspective, rats, mice, and humans share a common ancestor. As these lineages diverged from one another, the UCEs presumably remained unchanged because of their functional importance.

The idea that functional DNA sequences resist change and nonfunctional DNA sequences vary freely is one of the central tenets of molecular evolution. If the UCEs were nonfunctional, then mutational changes should be inconsequential. Over time, changes in the DNA sequences should accrue as rats, mice, and humans evolved along different evolutionary trajectories. As a consequence the sequences of the UCEs in these species should differ.

Biologists have speculated that UCEs regulate gene activity. For example, these sequence elements cluster near developmental genes. Researchers confirmed the functional importance of UCEs by deleting four carefully selected UCEs in the mouse genome. The deleted UCEs otherwise reside near key developmental genes. Presumably, their close proximity to these genes reflects the regulatory influence that these UCEs exert on the developmental genes.

To everyone's surprise, the mice with deleted UCEs were perfectly healthy. This result suggests that UCEs are not functional.

It is still possible that UCEs are functional. For example, if the UCEs are redundant within the genome, disabling a limited number of them would not harm the mice, since back-up copies of the UCEs would take over the function of the deleted sequences. The experimental design did not take into account this possibility.

Apart from this caveat, taken at face value the deletion experiments indicate that UCEs are not functional. This, of course, is troubling for intelligent design and creationism models, which maintain that all of the classes of junk DNA will ultimately turn out to be functional. Ironically, however, this discovery is much more troubling for the evolutionary paradigm.

One of the cornerstone ideas supporting molecular evolution is the notion that conserved DNA sequences are functional. But this recent study raises the very real possibility that this is not the case at all. If so, then the deletion result makes absolutely no sense. Why would evolutionary processes preserve UCEs if their loss has no significant impact on the mice? Could it be that fundamental deficiencies exist in the evolutionary paradigm?

Equally problematic are the results from the pilot phase of the ENCODE project, published in the summer of 2007. The ENCODE project is a multi-million dollar international effort to catalog all of the functional sequences in the human genome. The initial stage of the project involved a detailed search for every functional element contained in a 1% sample of the human genome.

Based on this survey, researchers discovered that parts of the human genome previously viewed as nonfunctional junk are transcriptionally active, signifying function. Surprisingly, these sequences show little conservation in the genomes of other mammals. In other words, functional sequences freely vary without any evidence for evolutionary constraint.

This recognition runs contrary to the central ideas of molecular evolution and, too, raises fundamental questions about the validity of the evolutionary paradigm.

Consequently, junk DNA is not just a problem for intelligent design proponents and creationists. It is a problem for evolutionary biologists as well.

If skeptics bring up the problem of evil as a way to challenge God's existence, they must also be willing to explain how the categories of good and evil fit within a naturalistic framework. In like manner, if evolutionary biologists bring up junk DNA as a challenge to the work of a Creator, they must be willing to explain the new understanding of junk DNA behavior within an evolutionary framework. Based on these new discoveries, the fundamental ideas about molecular evolution and the behavior of functional and nonfunctional DNA sequences no longer hold.

Simple Logic (and the Data) Refute PZ Myers on 'Junk DNA'

http://www.evolutionnews.org/2010/07/pz_myers_on_junk_dna036321.html

A few weeks ago, PZ Myers commented on so-called 'Junk DNA'. Under the headline, 'Junk DNA is still junk', Myers wrote:

The ENCODE project made a big splash a couple of years ago – it is a huge project to not only ask what the sequence of a strand of human DNA was, but to analyzed and annotate and try to figure out what it was doing. One of the very surprising results was that in the sections of DNA analyzed, almost all of the DNA was transcribed into RNA, which sent the creationists and the popular press into unwarranted flutters of excitement that maybe all that junk DNA wasn't junk at all, if enzymes were busy copying it into RNA. This was an erroneous assumption; as John Timmer pointed out, the genome is a noisy place, and coupled with the observations that the transcripts were not evolutionarily conserved, it suggested that these were non-functional transcripts.

But is it accurate to say that apparently non-constrained elements are always functionless? Evolutionary conservation seems to be a legitimate reason for predicting functionality of genetic elements. As the reasoning goes, if a sequence of DNA performed no useful function, it would accumulate neutral mutations at random. If its sequence remains constant over time, however, this implies that some sort of stabilizing selection is occurring to preserve its function. Conservation of sequence implies function. This is sound reasoning.

However, why must non-conservation imply non-function? The simple rules of logic say the inverse need not be true. Consider the following:

If it's raining outside then the front lawn will be wet.

Now consider the inverse:

If it's not raining outside then the front lawn will not be wet.

Of course, this need not be true. For example, the lawn could be wet due to causes other than rain, such as sprinklers or a water fight on a hot summer day. The fact that it's not raining does not imply that the lawn must be dry.

So simple logic implies that PZ's reasoning could be flawed. But the most important question is, what do the data say? Should the supposition linking non-conserved elements with non-functionality be considered a watertight inference?

It turns out that leading researchers would also disagree with PZ.

A report on research by Kunarso et al. in Nature suggests: "Although sequence conservation has proven useful as a predictor of functional regulatory elements in the genome the observations by Kunarso et al. are a reminder that it is not justified to assume in turn that all functional regulatory elements show evidence of sequence constraint."

These are not isolated results. Another paper was published in 2007 by the ENCODE Project Consortium detailing the results from the ENCODE project, the public research consortium that has been seeking all the functional elements in the human genome.

This research similarly reported,

At the outset of the ENCODE Project, many believed that the broad collection of experimental data would nicely dovetail with the detailed evolutionary information derived from comparing multiple mammalian sequences to provide a neat 'dictionary' of conserved genomic elements, each with a growing annotation about their biochemical function(s). In one sense, this was achieved; the majority of constrained bases in the ENCODE regions are now associated with at least some experimentally derived information about function. However, we have also encountered a remarkable excess of experimentally identified functional elements lacking evolutionary constraint, and these cannot be dismissed for technical reasons. This is perhaps the biggest surprise of the pilot phase of the ENCODE Project, and suggests that we take a more "neutral" view of many of the functions conferred by the genome. (emphasis added)

And so, it seems, while evolutionary constraint may be used to infer function, there is no reason to think that the inverse is true –- that non-constraint implies non-function.

Commenting on what seems to be the almost universal transcription of DNA into RNA (according to the research of the ENCODE project), Myers further remarks,

Creationists thought it was wonderful. They detest the idea of junk DNA – that the gods would scatter wasteful garbage throughout our precious genome by intent was unthinkable, so any hint that it might actually do something useful is enthusiastically seized upon as evidence of purposeful design.

By "creationist," Myers presumably means anyone who's skeptical of the traditional neo-Darwinian dysteleological understanding of the mechanics of evolution. I find this labeling to be misleading at best. But let's leave that aside.

Myers fails to accurately represent the position and predictions of ID (and Darwinism) regarding so-called "junk DNA." It is a prediction of Darwinian (and most dysteleological) thought that the genome should exhibit islands of meaning in a vast ocean of non-meaning. After all, if the genome has been cobbled together by a process of undirected, mindless chance and necessity, is it not reasonable to expect the presence of a large amount of noise in the genome? Moreover, it is the homologous distribution of supposed "junk DNA" which is often presented as one of the leading arguments for common ancestry. Every time function is ascribed to these elements, the Darwinian argument has to retreat, taking refuge in the ever-shrinking gaps in our knowledge of the genome.

Myers follows this up by citing a paper that appeared just over a month ago in PLoS Biology by Bakel et al. The abstract reads,

The human genome was sequenced a decade ago, but its exact gene composition remains a subject of debate. The number of protein-coding genes is much lower than initially expected and the number of distinct transcripts is much larger than the number of protein-coding genes. Moreover, the proportion of the genome that is transcribed in any given cell type remains an open question: results from "tiling" microarray analyses suggest that transcription is pervasive and that most of the genome is transcribed, whereas new deep-sequencing based methods suggest that most transcripts originate from known genes. We have addressed this discrepancy by comparing samples from the same tissues using both technologies. Our analyses indicate that RNA sequencing appears more reliable for transcripts with low expression levels, that most transcripts correspond to known genes or are near known genes, that many transcripts may represent new exons or aberrant products of the transcription process. We also identify several thousand small transcripts that map outside known genes; their sequences are often conserved and are often encoded in regions of open chromatin. We propose that most of these transcripts may be by-products of the activity of enhancers, which associate with promoters as part of their role as long-range gene regulatory sites. Overall, however, we find that most of the genome is not appreciably transcribed.

Even if we grant Myers his premise (that the majority of DNA is not transcribed into mRNA), it still does not follow that the non-transcribed elements are "junk". In a 2008 paper by Swinburne and Silver, published in Developmental Cell, research uncovered evidence that introns can have function even when they are not transcribed. The paper argues that transcriptional delays may contribute to the timing mechanisms, which are necessary during development.

The bottom line is this: Caution is warranted when one starts making generalizing claims that a DNA element is never transcribed into mRNA. It cannot be ruled out, of course, that a region is transcribed in a few select instances or cell types.

Functions for DNA that was once thought to be junk are being uncovered on a daily basis. Wouldn't it be more scientific to take a wait-and-see approach on the "junk DNA" question?

Posted by Jonathan McLatchie on July 8, 2010 5:05 AM | Permalink

Junk DNA is still junk

http://scienceblogs.com/pharyngula/2010/05/junk_dna_is_still_junk.php

Category: Molecular Biology
Posted on: May 19, 2010 2:05 PM, by PZ Myers

The ENCODE project made a big splash a couple of years ago — it is a huge project to not only ask what the sequence of a strand of human DNA was, but to analyzed and annotate and try to figure out what it was doing. One of the very surprising results was that in the sections of DNA analyzed, almost all of the DNA was transcribed into RNA, which sent the creationists and the popular press into unwarranted flutters of excitement that maybe all that junk DNA wasn't junk at all, if enzymes were busy copying it into RNA. This was an erroneous assumption; as John Timmer pointed out, the genome is a noisy place, and coupled with the observations that the transcripts were not evolutionarily conserved, it suggested that these were non-functional transcripts.

Personally, I fall into the "it's all junk" end of the spectrum. If almost all of these sequences are not conserved by evolution, and we haven't found a function for any of them yet, it's hard to see how the "none of it's junk" view can be maintained. There's also an absence of support for the intervening view, again because of a lack of evidence for actual utility. The genomes of closely related species have revealed very few genes added from non-coding DNA, and all of the structural RNA we've found has very specific sequence requirements. The all-junk view, in contrast, is consistent with current data.

Larry Moran was dubious, too — the transcripts could easily by artifactual.

The most widely publicized result is that most of the human genome is transcribed. It might be more correct to say that the ENCODE Project detected RNA's that are either complimentary to much of the human genome or lead to the inference that much of it is transcribed.

This is not news. We've known about this kind of data for 15 years and it's one of the reasons why many scientists over-estimated the number of humans genes in the decade leading up to the publication of the human genome sequence. The importance of the ENCODE project is that a significant fraction of the human genome has been analyzed in detail (1%) and that the group made some serious attempts to find out whether the transcripts really represent functional RNAs.

My initial impression is that they have failed to demonstrate that the rare transcripts of junk DNA are anything other than artifacts or accidents. It's still an open question as far as I'm concerned.

I felt the same way. ENCODE was spitting up an anomalous result, one that didn't fit with any of the other data about junk DNA. I suspected a technical artifact, or an inability of the methods used to properly categorize low frequency accidental transcription in the genome.

Creationists thought it was wonderful. They detest the idea of junk DNA — that the gods would scatter wasteful garbage throughout our precious genome by intent was unthinkable, so any hint that it might actually do something useful is enthusiastically siezed upon as evidence of purposeful design.

Well, score one for the more cautious scientists, and give the creationists another big fat zero (I think the score is somewhere in the neighborhood of a big number requiring scientific notation to be expressed for the scientists, against a nice, clean, simple zero for the creationists). A new paper has come out that analyzes transcripts from the human genome using a new technique, and, uh-oh, it looks like most of the early reports of ubiquitous transcription were wrong.

Here's the author's summary:

The human genome was sequenced a decade ago, but its exact gene composition remains a subject of debate. The number of protein-coding genes is much lower than initially expected, and the number of distinct transcripts is much larger than the number of protein-coding genes. Moreover, the proportion of the genome that is transcribed in any given cell type remains an open question: results from "tiling" microarray analyses suggest that transcription is pervasive and that most of the genome is transcribed, whereas new deep sequencing-based methods suggest that most transcripts originate from known genes. We have addressed this discrepancy by comparing samples from the same tissues using both technologies. Our analyses indicate that RNA sequencing appears more reliable for transcripts with low expression levels, that most transcripts correspond to known genes or are near known genes, and that many transcripts may represent new exons or aberrant products of the transcription process. We also identify several thousand small transcripts that map outside known genes; their sequences are often conserved and are often encoded in regions of open chromatin. We propose that most of these transcripts may be by-products of the activity of enhancers, which associate with promoters as part of their role as long-range gene regulatory sites. Overall, however, we find that most of the genome is not appreciably transcribed.

So, basically, they directly compared the technique used in the ENCODE analysis (the "tiling" microarray analysis) to more modern deep sequencing methods, and found that the old results were mostly artifacts of the protocol. They also directly examined the pool of transcripts produced in specific tissues, and asked what proportion of them came from known genes, and what part came from what has been called the "dark matter" of the genome, or what has usually been called junk DNA. The cell's machinery to transcribe genes turns out to be reasonably precise!

To assess the proportion of unique sequence-mapping reads accounted for by dark matter transcripts in RNA-Seq data, we compared the mapped sequencing data to the combined set of known gene annotations from the three major genome databases (UCSC, NCBI, and ENSEMBL, together referred to here as "annotated" or "known" genes). When considering uniquely mapped reads in all human and mouse samples, the vast majority of reads (88%) originate from exonic regions of known genes. These figures are consistent with previously reported fractions of exonic reads of between 75% and 96% for unique reads, including those of the original studies from which some of the RNA-Seq data in this study were derived. When including introns, as much as 92%-93% of all reads can be accounted for by annotated gene regions. A further 4%-5% of reads map to unannotated genomic regions that can be aligned to spliced ESTs and mRNAs from high-throughput cDNA sequencing efforts, and only 2.2%-2.5% of reads cannot be explained by any of the aforementioned categories.

Furthermore, when they looked at where the mysterious transcripts are coming from, they are most frequently from regions of DNA near known genes, not just out of deep intergenic regions. This also suggests that they're an artifact, like an extended transcription of a gene, or from other possibly regulatory bits, like pasRNA (promoter-associated small RNAs — there's a growing cloud of xxxRNA acronyms growing out there, but while they may be extremely useful, like siRNA, they're still tiny as a fraction of the total genome. Don't look for demolition of the concept of junk DNA here).

There clearly are still mysteries in there — they do identify a few novel transcripts that come up out of the intergenic regions — but they are small and rare, and the fact of their existence does not imply a functional role, since they could simply be byproducts of other processes. The only way to demonstrate that they actually do something will require experiments in genetic perturbation.

The bottom line, though, is the genome is mostly dead, transcriptionally. The junk is still junk.

van Bakel H, Nislow C, Blencowe BJ, Hughes TR (2010) Most "Dark Matter" Transcripts Are Associated With Known Genes. PLoS Biology 8(5):1-21.

"Monkey Trial" 85 Years Old Today

http://www.cbsnews.com/8301-501465_162-20010011-501465.html

July 8, 2010 3:07 PM
Posted by Charles Cooper

Later this month Dayton, Tenn. will host a weekend festival capped off by a dramatization of the trial which engraved this small town's name into the nation's cultural narrative. Exactly 85 years ago today, a Dayton schoolteacher named John C. Scopes went on trial, accused of violating a state law prohibiting the teaching of the theory of evolution.

What came to be known as the "Monkey Trial" (subsequently immortalized by journalist H.L. Mencken), the case was a showdown between progressives and creationists, who wanted to ban the teaching of Charles Darwin's writing about evolution from local schools.

William Jennings Bryan, a three-time candidate for president, led the prosecution. He was pitted against the famous Chicago attorney Clarence Darrow. The trial lived up to the hype, but it ended on a flat note.

Toward the end of the trial, Darrow asked the jury to find Scopes guilty because he intended to appeal the verdict to the state's Supreme Court. The jury complied and Scopes was fined $100.

The following year, Tennessee's Supreme Court reversed the decision on a technicality.

Writing for the majority, the court's chief justice dismissed the case, saying "We see nothing to be gained by prolonging the life of this bizarre case. On the contrary, we think the peace and dignity of the State, which all criminal prosecutions are brought to redress, will be better conserved by the entry of a nolle prosequi herein. Such a course is suggested to the Attorney-General."

But the battle over evolution continues. Only last month, a federal court prevented the Institute for Creation Research's plans to award master's degrees in science education from "a Biblical scientific creationist viewpoint."