30 August 2007

Skeptics' Circle #68

In other biweekly blog carnival news, the 68th Meeting of the Skeptics' Circle is up at Aardvarchaeology. I highly recommend you check it out. Some of my favourites: Greta Christina compares religion to self-referential Twister, Sieow at Skeptical Personal Development dismantles a quote sometimes mistakenly attributed to Einstein, and Evangelical Realism uses an anti-atheist joke to show how God really works.

Tangled Bank #87



The 87th edition of the Tangled Bank is up and running over at Balancing Life. Be sure to head on over and check out a samplin' of fine science blogging from the last fortnight. (Yours truly even has a submission this time around!)

28 August 2007

Everyone loves a good follow-up

I just saw something that absolutely made my day.

At Borders, I saw three shiny copies of Michael Behe's The Edge of Evolution displayed prominently on a bookshelf, the front cover in plain view right at about eye-level.

In the Christian Fiction section. Right where I had left them two and a half weeks ago.

The best part is, the display has obviously been changed. Behe is now sitting between a pretty lady and a dragon, and his books have been turned to proudly face the customer (Sara and I originally re-shelved them with just the spines visible). Given this kind of treatment, he must be thrilled not to be crammed in the science section anymore.

Glad I could help, Mike. ;-)

27 August 2007

Texas Education Threatened By Creationists

[This entry was originally written as a diary for the Daily Kos. It goes into more detail than my last post regarding education in Texas, so I'm reposting it here as well.]

The Houston Chronicle reported on 24 August that a majority of the current members of the Texas State Board of Education opposed requiring Intelligent Design be taught in public classrooms. This report comes a little over a month after Texas governor Rick Perry (R) appointed Don McLeroy, a vocal creationist, to chair the SBOE. According to the Chronicle, of the 15 members of the board, ten claimed they "wouldn't support requiring the teaching of intelligent design." One member, Pat Hardy, said she would be open to teaching ID. Four members (Rene Nuñez, Cynthia Dunbar, Terri Leo, and Ken Mercer) declined to be interviewed. Many people see this report as a sign of hope for science education in Texas. But I don't buy it for a minute.

What we're seeing now is a word game; the new name for creationism is going to be "evolution" (with the modifier "strengths & weaknesses").

It's a game the creationists have played before. In 1987, the Supreme Court ruled in Edwards v. Aguillard that creationism (or "creation science") was founded in religion, not science, and was therefore unconstitutional to include in public school science curricula. The creationist movement responded by rebranding creationism as "intelligent design." However, in 2005 Judge John E. Jones III ruled in Kitzmiller v. Dover that intelligent design was also unconstitutional to include in school curricula. Expert witnesses like Barbara Forrest successfully demonstrated (using evidence such as the Discovery Institute's "Wedge Strategy" and the Foundation for Thought & Ethics' "textbook" Of Pandas and People) that intelligent design was rehashed creationism, promoted with the intent to drive a wedge between scientific materialism and education to the benefit of a religious worldview. Now, once again, they're changing their rhetoric instead of reanalyzing their argument.

The Discovery Institute, the creationist "think-tank" responsible for the Wedge Strategy, is now promoting a new book entitled Explore Evolution: the Arguments For and Against Neo-Darwinism. They also issued a video in 2005 entitled "How to Tech the Controversy Legally." The video offers five strategies for teachers who want to criticize evolution:
1. Keep the focus ON science
This is the creationists' most basic and most dangerous tactic. Creationists are desperate to have their views accepted as part of the scientific discourse. But any hack can write a book. Real science means having your research and interpretations pass peer review. Not one creationist claim has passed scrutiny by the scientific community. They're trying to bypass that process and gain scientific legitimacy by taking their false facts straight to the impressionable minds of students.
2. Keep the focus OFF religion
Creationists know they need to distance themselves from the religious rhetoric, which means covering their tracks and denying connection to terms like "creation science" and, in the wake of Dover, "intelligent design."
3. Teach MORE about evolution, not less
Here we see the strategy of rebranding the same old creationist talking points, not as a separate hypothesis of creation or design, but rather as supposed "weaknesses" of evolution.
4. Link the teaching of evolution to existing school district policies about teaching controversial issues
This is the "present both sides and let the kids decide" approach favored by those who don't count on students to be well enough trained to see through the false facts being presented by the creationist side.
5. Defend the academic freedom of teachers who want to teach the controversy
And when all else fails, threaten legal action against any school administration that gets in your way.

The Discovery Institute isn't the only one pushing this strategy. Sal Cordova of the major ID weblog Uncommon Descent writes:
As much as I advocate that ID is correct, it is not the time to teach it in the public schools. Creationist Don McLeroy, chairman of the Texas School board, agrees.
. . .
There are individuals who may be pro-ID out there who want to lobby to teach ID in the public schools. I think this is ill advised. I encourage rather than lobbying for the teaching of ID or creation science, one should lobby for teaching MORE evolution, and in the way Darwin would have wished it taught. The was beautifully accomplished in the book: Explore Evolution.
But do we have to worry about this strategy coming from the Texas SBOE? I fear we do. McLeroy is certainly in on the strategy; let's look at the rest of the board.

The Texas textbook curriculum was last up for review in 2003. At the time, McLeroy and others were fiercely advocating replacing the biology text with one more critical of evolution. The board eventually voted 11-4 to approve the existing text. The minority vote consisted of McLeroy, David Bradley (the current vice-chairman of the board), Gail Lowe, and Terri Leo, all of whom still sit on the board. (Note that McLeroy, Bradley, and Lowe all claimed not to advocate teaching ID in the Chronicle interviews.)

However, according to a CNN article, the textbooks for all subjects were approved in a batch vote. McLeroy wanted to vote on each textbook separately, presumably because he felt other members' disapproval of the treatment of evolution was outweighed by approval of other texts. In 2005, McLeroy gave an address on intelligent design at the Grace Bible Church in Bryan, TX. In his speech, he was quite open about the association between intelligent design creationism and religion, and said of the 2003 textbook decision:
[Quoting Phillip Johnson] "This is not to say that the Biblical issues aren’t important, the point is the time to address them will be after we have separated materialistic prejudice from scientific fact."

And let me say it again: in the 2003 biology book adoption in Texas this principle was followed strictly. There wasn’t a board member that wasn’t trying to get the weakness of evolution into the debate. We never brought up religion. We never brought up intelligent design. All we brought up was evidence.
"Evidence," of course, meaning creationist talking points--anything from gaps in the fossil record to slow mutation rates--refuted by the scientific community.

Besides the four minority voters in the 2003 decision, six other current board members were also serving in 2003: Geraldine "Tincy" Miller, Mary Helen Berlanga, Mavis Knight, and Bob Craig (all of whom said "no" to advocating teaching ID); Pat Hardy (who is open to teaching ID); and Rene Nuñez (who declined interview). According to McLeroy in 2005, any or all of these members could be sympathetic to the creationist strategy of highlighting "weaknesses" in evolution.

The next round of textbook review for Texas is scheduled for 2011. With McLeroy now chair of the Texas SBOE (and Bradley vice-chair), it's entirely possible that creationists will manage to smuggle their agenda into public schools. We'll have to be on guard. The real danger of the creationist movement isn't in terms like "creation science" or "intelligent design", but rather in the false facts that these terms encompass and their corruption of the scientific method. Science means unbiased, reproducible research and rigorous, continuous peer review. We need to be prepared to repel not just the creationist name, but their false facts. As Darwin himself wrote:
"False facts are highly injurious to the progress of science, for they often endure long; but false views, if supported by some evidence, do little harm, for every one takes a salutary pleasure in proving their falseness; and when this is done, one path towards error is closed and the road to truth is often at the same time opened."
--Charles Darwin, The Descent of Man p. 385

26 August 2007

Evelyn's Adventures

Our friend Evelyn is back from a two-month expedition studying volcanic activity in the Indian Ocean. She has posted about some of her adventures over at Memoirs of a Skepchick... you should all check it out!

25 August 2007

Creationists rule the Texas Board of Education

It's been two whole weeks since I've had to write about creationists. But duty calls.

From the Houston Chronicle: The Texas State Board of Education appears to be against including Intelligent Design in school curricula. 10 of 11 board members interviewed (the board has 15 members) claim they "wouldn't support requiring the teaching of intelligent design." The 11th interviewee, Patricia Hardy, openly advocated teaching ID.

Phil Plait (of Bad Astronomy) thinks this is good news.
In fact, [McLeroy's stance] is standard creationist rhetoric, and it’s a lie. This is all part of the leaked Wedge plan to get religion taught as science; first they try to show the weaknesses of science, then they make the "if not A then B" argument, which is bad logic (the only kind most promoters of creationism are capable of). If one scientific explanation is weak, why then, creationism must be right!

Feh.

But let’s be positive here: Other board members who said they believe the curriculum should continue to include evolution and not be changed to accommodate intelligent design were:
Geraldine “Tincy” Miller, R-Dallas; Barbara Cargill, R-The Woodlands; Gail Lowe, R-Lampasas; Bob Craig, R-Lubbock; Mavis Knight, D-Dallas; Rick Agosto, D-San Antonio; Lawrence Allen, D-Houston; and Mary Helen Berlanga, D-Corpus Christi.
Show them your love, folks. They need our support, for surely they have an uphill battle.

But as much as I admire Phil's optimism, I don't buy for an instant that these school board members are really opposed to ID.

Case in point: Sal Cordova (of UncommonlyDense) also thinks this is good news:

As much as I advocate that ID is correct, it is not the time to teach it in the public schools. Creationist Don McLeroy, chairman of the Texas School board, agrees.
. . .
There are individuals who may be pro-ID out there who want to lobby to teach ID in the public schools. I think this is ill advised. I encourage rather than lobbying for the teaching of ID or creation science, one should lobby for teaching MORE evolution, and in the way Darwin would have wished it taught. The was beautifully accomplished in the book: Explore Evolution
Don McLeroy, the creationist appointed to head the Texas SBOE, said the following in his 2005 lecture at Grace Bible Church in Bryan, TX:
According to Johnson, the first thing to do is to get the Bible out of the discussion. Remember, even if you don’t bring the Bible into the discussion, the naturalist has already put it into the discussion. And Johnson states “it’s vital not to give any encouragement to this prejudice and to keep the discussion strictly on the scientific evidence and the philosophical assumptions. This is not to say that the Biblical issues aren’t important, the point is the time to address them will be after we have separated materialistic prejudice from scientific fact.”

And let me say it again: in the 2003 biology book adoption in Texas this principle was followed strictly. There wasn’t a board member that wasn’t trying to get the weakness of evolution into the debate. We never brought up religion. We never brought up intelligent design. All we brought up was evidence.
That's the same speech wherein he quite plainly connected ID to religion, asserting (among other things) that evolution must be wrong because it contradicts the Bible.

Note that remark in the second paragraph: there "wasn't a board member" in 2003 who wasn't trying to highlight the weakness of evolution. Of the current board members, who was serving on the board in 2003? Don McLeroy (current chair), Geraldine "Tincy" Miller (chair in 2003), Rene Nuñez, Mary Helen Berlanga, Patricia Hardy, Mavis Knight, Terri Leo, Gail Lowe, David Bradley, and Bob Craig. 10 out of 15 current members, 8 of whom were interviewed by the Houston Chronicle.

So I'm sorry, Phil, but these other people are not on our side. Texas is doomed.

This is further warning that the new name of creationism and intelligent design is going to be "evolution." (These people have some serious legitimacy envy!) But as one of Phil's commenters pointed out, maybe it's a good thing this is happening in Texas. The success of actions to keep creationism out of schools thus far has largely been leveraging of the separation between church and state. And though the creationists try to play linguistic games, their religious motivations are ever-present, especially in Texas.

Cordova has linked to a Discovery Institute video about circumventing the law to teach ID. So I'm going to have to watch that next... if you don't hear back from me within the next few days, don't worry, the brain hemorrhaging probably won't be too severe.

UPDATE: New post up with more details on the 2003 textbook vote.

Star Wars and Skepticism

The other night, Ben and I watched Star Wars: A New Hope. It was the original theatrical release (Ben has it on VHS), a cool balm after years of increasingly sacrilegious prequels and "special" editions.

And of course, with a movie like this, there are certain things an atheist blogger must address.
Han Solo: "Kid, I've flown from one side of this galaxy to the other, and I've
seen a lot of strange stuff. But I've never seen anything to make me
believe that there's one all-powerful Force controlling everything.
There's no mystical energy field that controls MY destiny."
Why do skeptics in the movies always end up being wrong about this sort of thing? Because it's a movie, doy! Han might not have seen anything to make him believe in the Force, but by this time in the movie we've already seen Darth Vader choke a dude and Obi-Wan Kenobi mindfuck some stormtroopers. The medium is ill-suited for skeptics; thanks to movie magic, we can visualize things that we want to believe but can't see evidence for in real life.

That said, there's a lot more room for skepticism in the first Star Wars film than I had ever realized.

In A New Hope, the Force is completely psychological, and therefore could very well have a natural explanation. It's all about knowing things you shouldn't be able to know (like "oh snap a planet just blew up") or convincing people to do things they don't want to do (like "stop breathing"). It isn't until the later movies that stuff starts levitating and whatnot. Then we can see Obi-Wan's ghost (to go with the voices in Luke's head), Yoda can lift an X-wing, and Emperor Palpatine can shoot lighting out of his goddamn hands! ("I've got blisters on my fingers!")

Who are you more likely to believe has ties to the supernatural: a dude who tells you he hears voices, or a dude who can actually electrocute you with his mind?

So good on Han for being a skeptic at this point in the game. For all we know, Obi-Wan is senile, Luke is lucky and/or schizophrenic, and Vader is just plain scary.

Scary Violent Insane Soldier Person

Sara and I had a bit of a scare the other night. We were walking home late at night from a friend's house, and there was someone a ways behind us shouting violence into the night.

At first I figured he was just raving on a street corner somewhere. But as we continued walking, his voice grew neither louder nor quieter; he was keeping a fairly constant distance behind us. So he was at least walking in our direction, if not necessarily following us. A group of electricians were working in Harvard Square, and a police officer was hanging by watching. I hoped that perhaps the officer would take the guy in for disturbing the peace. But as we kept walking, his voice kept following us, getting more violent, perhaps even getting closer. We cut across to the opposite side of the park, and that seemed to lose him.

He was shouting about "jihad" and "holy war." About how many they had killed, and how they would kill again. About how many he had killed, and how he would kill again. All while barking other threats and obscenities.

The man was a United States Marine. He was singing the Marines' Hymn and everything.

I thought our soldiers were supposed to be defending our country. Instead, innocent people are dying in Iraq and the whole world hates us. And on top of it, our soldiers are coming home with a bouquet of psychological disorders that society must now deal with.

Larry Moran posted this video yesterday, and it raises some of the same questions that have bothered me about supporting the troops, so I think I'll stop there and let A. Whitney Brown take over:

24 August 2007

Keeping up with the coming storm

I'm not saying we're necessarily on the doorstep of a Christofascist theocracy. But at the very least we're on the right block.

It's important for a rising dictatorship to be able to silence dissent at public events, whether by forcibly removing demonstrators or just organizing supporters to drown them out, to give the President and the country the illusion of approval.

Meanwhile, there need to be continued means of more permanently undermining the efforts of political enemies. How about screening charities and nonprofits to search for "terrorism" connections? It gives you the added benefit of securing the moral high ground for noble (read: "Christian") charitable works. Say goodbye to any Muslim charity, no more aid to Palestine or Lebanon, and look forward to secular charities being either squelched or assimilated further into faith-based initiatives.

With all this and more going on, people are going to start getting defensive of their Constitutional rights. But the government isn't taking away our rights... they're just modifying the expression of those rights for our own good. To placate the public and remind them that the government has got their back, declare Constitution Day and Citizenship Day on September 17, followed by Constitution Week through September 23.

Most importantly, the administration can't take all the power for itself; some power must still be given them by the people. That's why it's so critical to have people on the outside. Stu Bykofsky wants another 9/11, so everyone will forget about the crimes committed by the administration and go back to giving President Bush unlimited power. Family Security Matters has been openly advocating genocide in Iraq as a way to unite America and pave the way for George W. Bush to become "President-for-Life." And these people have audiences.

And don't forget how many people want us to go to war with Iran.

I know where my passport and my towel are.

19 August 2007

Intellectual vs Social roles of atheism

Michael Shermer, the publisher behind Skeptic magazine (where I first heard about intelligent design creationism in 2001), has a new editorial up on Scientific American discussing what's next for the atheist movement. He says some familiar good things in the familiar bad tone. From the first sentence:
Since the turn of the millennium, a new militancy has arisen among religious skeptics...
(Damn to the depths whatever man what thought of the phrase "militant atheism"!)
Since the turn of the millennium, a new militancy has arisen among religious skeptics in response to three threats to science and freedom: (1) attacks against evolution education and stem cell research; (2) breaks in the barrier separating church and state leading to political preferences for some faiths over others; and (3) fundamentalist terrorism here and abroad. Among many metrics available to track this skeptical movement is the ascension of four books . . . that together, in Dawkins’s always poignant prose, “raise consciousness to the fact that to be an atheist is a
realistic aspiration, and a brave and splendid one. You can be an atheist who is happy, balanced, moral and intellectually fulfilled.” Amen, brother.

Whenever religious beliefs conflict with scientific facts or violate principles of political liberty, we must respond with appropriate aplomb. Nevertheless, we should be cautious about irrational exuberance. I suggest that we raise our consciousness one tier higher for the following reasons.
He then goes on to talk about how we need to be positive and pro-something, not just anti-religion, and how we need to reinforce our commitment to freedom, and other stuff like that. Nothing really heavy to argue with. My question is, what makes Shermer think our exuberance is irrational?

EDIT: After having slept on it, it occurs to me that Shermer isn't coming down upon Dawkins et. al. so much as he's coming down on those who risk taking Dawkins too far. There are those who take the platform given them by rational atheists like Dawkins and use it to lash out unjustly against the religious, and they should be discouraged. There's a difference between telling the religious that they're wrong, and threatening to take away their rights because they're wrong. I urged for us to pick our battles and play it smart, and I now realize Shermer is pretty much doing the same (hence his advocacy of "rational atheism").

There are, however, those who
would have even the most rational atheists shut up for their own good. And you can expect me to say more about them in the future.

Islam's Jesus, and finding Islam outside the Qur'an

Via Hemant, it appears Great Britain is set to air a TV documentary on the role of Jesus Christ in Islam. This all sounds fairly well and good in theory. But I'm skeptical. From The Guardian:
There was no manger, Christ is not the Messiah, and the crucifixion never happened. A forthcoming ITV documentary will portray Jesus as Muslims see him.

With the Koran as a main source and drawing on interviews with scholars and historians, the Muslim Jesus explores how Islam honours Christ as a prophet but not as the son of God.
I'm hoping this is just bad journalism on behalf of The Guardian, and that it doesn't reflect the documentary. Because it's wrong.

True, Muslims do not believe Jesus to have been the Son of God (they consider the Trinity to be a form of polytheism), and the majority don't believe Jesus was put on the cross (but they do believe someone was crucified; some say the Romans put a phony up there so it looked like they caught Jesus, others say God pulled the ol' switcheroo to get Jesus out of it). But Islamic doctrine DOES hold that Jesus is the Messiah. The general consensus among Muslims is that Jesus ascended to Heaven instead of being crucified, where he lives on today and from whence he will return to Earth in the end times. They believe in the virgin birth; there are regions where Muslim women hold the Virgin Mary in as high regard as do those in any good Catholic village in Latin America. (Fun Trivia: the angel Gabriel who delivered the "good news" to Mary is the same angel who revealed the Qur'an to Muhammad!)

Frankly, if this documentary really is using the Qur'an as its primary source, then I'm highly skeptical of its worth.

A hint to would-be religious anthropologists: no one gives a damn how you interpret their holy texts, we want to know how they interpret their holy texts. It takes more than reading a holy scripture to understand a religion. We saw that clearly enough when Ben showed us how the West misunderstood Buddhism. If you want to know what Muslims believe, you don't rely on the Qur'an, you ask Muslims.

Imagine if I were to read the Bible and use that knowledge to start telling Catholics what they believed. You can imagine my analysis would be somewhat... incomplete. Heck, even if I studied every scrap of official Vatican doctrine, that wouldn't tell me what the average everyday real-life Catholic believed or practiced.

The documentarians apparently hope to bridge some cultural gaps between Christianity and Islam with this show. But there's already some tension among Christians who feel Muslims are getting special treatment, and if this article is any indication then there's some reason to believe Muslims might not find the documentary entirely accurate. So, we might just be asking for trouble here.

Or maybe it'll be a good show. Hopefully it'll pop up on Internet eventually, I wouldn't mind seeing it for myself.

(Thanks to Sara for helping me with some background on Islam)

18 August 2007

Here come the bloody Christian Soldiers

Coming soon to a country near you: members of the clergy are being prepared by the US military to quell public dissatisfaction over martial law armed only with Romans 13 and a smug sense of moral superiority. Read the full story here and pay special attention to the second- and third to last paragraphs, which read:
Such clergy response teams would walk a tight-rope during martial law between the demands of the government on the one side, versus the wishes of the public on the other. "In a lot of cases, these clergy would already be known in the neighborhoods in which they're helping to diffuse that situation," assured Sandy Davis. He serves as the director of the Caddo-Bossier Office of Homeland Security and Emergency Preparedness.
For the clergy team, one of the biggest tools that they will have in helping calm the public down or to obey the law is the bible itself, specifically Romans 13. Dr. Tuberville elaborated, "because the government's established by the Lord, you know. And, that's what we believe in the Christian faith. That's what's stated in the scripture."
So, in summation: the government, which is preparing to enforce martial law on its own soil with Army regulars (not even MPs), is now preparing to employ members of the clergy to placate a populace upset about the revocation of its civil rights with platitudes about submission to Jesus. For those of you keeping score at home, that's a reversal of both the 1878 Posse Comitatus Act and the First Amendment.

I would like to reiterate, because it never gets old, a phrase out of Sinclair Lewis' book It Can't Happen Here, because it never ever gets less true:
“When fascism comes to America, it will be wrapped in the flag and carrying the cross."
Every American should read this book. If you're in the Cambridge area and don't have a library card, well, shame on you, but you can borrow my copy anyway if you promise you'll read it. Remember, under Hitler, the Germans still thought they were free. I don't want to be an alarmist, because I do feel that martial law is still a far way off. But the best way to keep it there is for more people to be outraged at the way it would be coming.

UPDATE: Aaron has just sent me this link to the Heiligewehrmacht training manual. It gives tips on how to use a national crisis as an excuse to proselytize, and do gunpoint missionary work right in your own back yard! Oh goody! Not only will we have the army coming to our doors telling us to accept Jesus as our personal lord and savior (and you thought the Jehovas were bad), but if you refuse to cooperate they can haul you off for disturbing the peace!

(Hat-tip to Friendly Atheist)

17 August 2007

I'm going to hell

Perhaps you're familiar with Ze Frank's social media playground, the ORG. (If not, you should check it out and look me up!) A number of active members have been using the ORG's map function to "flock" to a member who's all alone on the map. That member then joins the flock in visiting someone else the next week, and we traverse the globe in virtual fashion.

Last week, we visited "roni" in Jerusalem. As is the custom, our hostess was kind enough to make a note of where we each chose to land. I happened to land in the Valley of Gehenna:



Looks gorgeous, eh? Well, apparently it's hell. Fancy that.

I know I shouldn't be, but for some reason I'm always just a little surprised when I come across a place referenced in mythology. Perhaps it's because a place can change so much over time, it's odd to think it can keep the same name.

Maybe it's just a funny angle, but I don't see in this photograph any of the sulfur fires or mounds of garbage and corpses for which Gehenna was apparently once known. Looks like they left behind some nice fertilizer, though. If I'm wrong about this whole atheism thing, this is the hell I want to go to. (Unless I get into secular heaven!)

Next stop for the flock is Great Britain. Maybe this time I'll land in an ancient druid shrine or something.

16 August 2007

Ignorance-Only Sex Ed DOES NOT WORK

Time and again, abstinence-only sex education has been shown to reduce neither unwanted pregnancy nor spread of STDs. But Jane Jimenez at One News Now wouldn't have you believe any of that:
Opponents of abstinence education have spent the past ten years denouncing these important health education programs. Their attacks are relentless and ignore the fact that abstinence education works.
Funny, she doesn't give any evidence that it works. Lucky for her, commenter Barbara Ferraro came through with critical evidence:
As a member of CWA, I too have been working to promote the fact, that Abstinence Education is working. I have talked to at least one person who has actually used abstinence in her personal life along with her fiance before they married; she also knows of many others that have done the same.
Ah. Anecdotal evidence. Of "at least one person." I don't know about you, but I'm instantly convinced.

It can't be said often enough: Yes, it's important to inform teens that abstinence is the only 100% sure way to avoid pregnancy/STDs, but that's not enough. They're going to engage in sex anyway, and we need to make sure they're prepared to deal with it intelligently and maturely. Abstinence-only sex education is ignorance-only sex education. And ignorance will screw us over.

I never cease to be amazed by this degree of fingers-in-the-ears-la-la-I-can't-hear-you denial of reality. How can you reason with people who have built up such a strong resistance to reason?

15 August 2007

Evolution of the X and Y Chromosomes, Part 3

Last time, we looked at how Lahn & Page determined the evolutionary ages of various regions of the X chromosome. Since then, more refined techniques have distinguished the following evolutionary strata in the X chromosome:



PAR stands for pseudo-autosomal region. This is a tiny region of DNA that still allows recombination between the X and Y chromosomes; that means the PAR retains high homology between the X and Y. The strata are numbered in order of evolutionary age; S1 is the oldest (in terms of divergence from Y), S5 is the youngest.

A 2005 paper by Carrel et. al. looked at a whole bunch of genes on the X chromosome, where they were, and whether they escaped X-inactivation. This resulted in the following figure, which shows the amount of escape from inactivation for each stratum:



The red end of the spectrum represents inactivated genes; the purple end represents genes that escape inactivation. Basically, the further away you get from the PAR, the fewer genes you'll find that have escaped X-inactivation.

It's important to note that the genes that escape X-inactivation don't necessarily have high Y-homology themselves; sometimes they just hang out with other genes that have high homology and ride their coattails.

So finally, what does this all tell us about how dosage compensation evolved in mammals? Recall that the active X is hyperactive compared to autosomes. When genes started decaying on the inverted pseudo-Y, the male cells started ramping up expression from their other X chromosome to compensate. But this heightened X expression carried over to females, too. That meant the female cells were getting too much X expression; to compensate, they evolved a mechanism for silencing one of their chromosomes.

Conclusion:
We noted that, though dosage compensation in mammals occurs via inactivation of one of the two X chromosomes in XX cells, some genes escape X-inactivation. Furthermore, expression from the active X is twice as great as expression from the autosomes. We wanted to know how this ties into evolution of the X and Y chromosomes.

X and Y homology experiments have demonstrated that the X chromosome can be broken into a pseudo-autosomal region plus five evolutionary strata based on time since divergence from the Y chromosome.

It turns out that genes found in regions with higher Y-homology are more likely to escape X-inactivation. This tells us that gene silencing likely evolved as a response to up-regulation of X expression, which in turn evolved in response to degradation of homologous genes on the pseudo-Y.

This is, of course, a fairly general model. There are exceptions, genes with homology that are silenced and genes without homology that escape silencing. But we still see a profound evolutionary trend. It goes to show that evolution isn't just about inventing genes for new proteins; it's also about changing regulation of the genes you already have.

14 August 2007

Evolution of the X and Y Chromosomes, Part 2

Let's turn to research on X and Y chromosome evolution to explain some of what we saw in Part 1. Once upon a time, the Y chromosome used to be just another X chromosome. But at some point, the X-that-would-be-Y (I'll call it pseudo-Y for now) suffered a major inversion; that is, a big chunk of the chromosome was broken off, flipped around, and stuck back on. This causes a problem with recombination. During meiosis, homologous chromosomes line up and swap pieces of DNA. This can only occur if the pieces being swapped are pretty much the same. Recombination is an important means of swapping around alleles (different versions of genes) and therefore a big player in evolution.

The inversion event threw a wrench into X chromosome recombination. The un-inverted sections could still recombine, but the inverted section couldn't, and therefore these formerly homologous stretches of DNA diverged, each gradually mutating in different ways. The pseudo-Y experienced a number of other inversion events, each time taking another chunk of the homologous region and rendering it incapable of recombination with X.

How do we know this? Because the inversion events left behind fingerprints:



This image is from a 1999 paper by Lahn & Page. We would expect that inverted sections of the pseudo-Y would diverge from the corresponding regions on the X. The more time has passed since the inversion, the more divergence we should expect.

Lahn & Page looked at 19 X-linked genes that were known to have homologous sections of DNA on the Y chromosome. For each of these DNA regions, they measured the differences between the X and Y versions. The x-axis in the figure shows location on the chromosome. The y-axis shows the estimated mean number of substitutions per synonymous site. What we see are four main age blocks; genes in Group 1 are more diverged from their Y counterparts than those in Group 2, which suggests the Group 1 region of DNA inverted earlier.

Next time, we'll look at how these evolutionary regions of the X chromosome relate to which genes escape X-inactivation.

Evolution of the X and Y Chromosomes, Part 1

So far we know that dosage compensation in humans and mice involves silencing one of the two X chromosomes in XX (normally female) animals (see Part 3 of the Development Primer). But that isn't the whole story.

Dosage compensation requires either up-regulation of X expression in cells with one X chromosome, or down-regulation in cells with two X chromosomes. At first, we just compared the two Xs to each other, and saw that one was silenced while the other was expressed. But when we compare expression from the active X chromosome to a normal autosome, we see that the active X is twice as active as any autosome.

Next, consider Turner syndrome (XO women) and Klinefelter's syndrome (XXY men). These syndromes are caused by a rare event called nondisjunction. Normal human cells are diploid; that is, they have two copies of each chromosome (one from Mom, one from Dad). Gametes (sperm and egg) need to be haploid, having one copy of each chromosome. So as the cell prepares to divide during meiosis, the chromosomes are lined up in the center of the cell and are pulled in opposite directions. Normally, one chromosome of each pair goes to each side. But sometimes nondisjunction occurs; a pair of chromosomes get stuck together, so one gamete gets no copy and the other gets an extra copy (like those old Twix commercials: "Two for me, none for you!"). If those gametes then get to become part of a zygote, then the zygote will have an abnormal number of chromosomes.

If the inactive X chromosome were completely inactive, then we should expect to see no difference between XO and XX females, nor between XY and XXY males. But since Turner and Klinefelter's are syndromes, the lack of X in the former and extra X in the latter must be doing something.

As it turns out, not all the genes on the inactive X are silenced; some escape inactivation. Recall from the Development Primer that Xist-RNA forms a transcription-free zone in the nucleus, and the inactive X crawls inside. But it seems that, like a loose bundle of yarn stuck hastily in your pocket, some loops of DNA dangle out of this zone, and the genes on those loops get expressed. But which genes, and why?

At this point, we turn to research on X and Y chromosome evolution.

Stay tuned.

13 August 2007

Pensée Pins for your Good Cause

Back when we were discussing atheist/humanist/freethought symbols, the pansy was mentioned as a potential candidate. From Wikipedia:
The pansy has long been the symbol of freethought, originally being used in the literature of the American Secular Union in the late 1800s. The reasoning behind the pansy being the symbol of freethought lies in both the flower's name and appearance. The pansy derives its name from the French word pensée, which means "thought"; it was so named because the flower resembles a human face, and in the month of August it nods forward as if deep in thought.
Well, regardless of what you think of the pansy as an adequate symbol, these pins that Ben pointed out to me are gorgeous:



We highly recommend that atheists consider buying one of these real pansy pins. Best of all, it's for a good cause, and (in the true spirit of freethought) you have options as to what that good cause is: your purchase can go towards saving the rainforest, feeding the hungry, providing child health care, preventing breast cancer, or caring for rescued animals. Personally, I'm leaning towards improving child literacy. After all, as The Literacy Site says, "Open books, open minds."

One of the big ways religion tries to promote itself is through charity work. This is a great opportunity for the secular community to show that we're here to help, too. And as a side benefit, we get a little way to display our solidarity.

Enlightened Despotism and Liberal Religion

Consider the conundrum posed by the phenomenon called “Enlightened Despotism” – on the one hand, if you’re going to have a despot I suppose you want him at least to be a nice guy so that things are at least not as bad as they could be (death squads are at a minimum, habeas corpus suspended only on alternate Tuesdays, etc.). But on the other hand, if life under said despot isn’t really so bad, then the likelihood that he’ll be overthrown is incredibly small, whereas if he were a brutal, ruthless, bloodthirsty dictator, then although life under him would be completely unbearable, it is precisely this unbearability that would precipitate his timely overthrow. Hence the dilemma: is it better to live with an attenuated, weak evil that people are willing to tolerate, or is it better in the long run to have a strong, virulent evil that pushes people to eradicate it altogether?

Now, what if I told you that the Enlightened Despot was none other than modern Religion itself? Let me explain. Liberal religion essentially started (in the west) with the Protestant Reformation and continues until today: it has come to welcome all or most changes to the zeitgeist – feminism, LGBTQ, civil rights, human rights, and so on – and strives ardently to make these modern forms compatible with an ancient system of beliefs by a series of ad hoc quasi-intellectual band-aids we call ‘theology’.

On the surface, there’s nothing I can object to here, because one of my biggest quarrels with religion is that it is so characteristically intolerant of the modern ethical zeitgeist – and if the religion is willing to bend to accommodate it, there should be no problem, right? Well, the trouble with this ‘liberal religion’ is the same with the enlightened despot: it is a series of concessions that keeps the people complacent and the dictator in power. In the case of religion, liberal theology prevents the modern middle-of-the-roaders and skeptics from walking away entirely, keeping them instead under the umbrella of the religious to perpetuate the flawed first premise. Many of the modern religious are actually humanists, but because the theists in power are willing to bend over backward, ideologically, to make their superstitions jive with the zeitgeist, when push comes to shove the moderates are more willing to throw down on the side of religion than of their ideologically more-closely related atheo-Humanists.

Have you ever wondered why there are so many more openly ex-Catholics running around than ex-Protestants? It's probably because Catholics, traditionally, have been theologically stricter, more hierarchical, etc, etc. Until Vatican II made Catholicism into ‘Protestantism Lite’, Protestants had been the only ones to sell out consistently to the changing times, resulting in the curious phenomenon of the so-called "mainline Protestant" who largely subscribes to the belief that some kind of Deist divinity is completely compatible with all the bounty that Science has to offer. Because Protestantism has historically been willing to compromise, not only is it staying around longer but its logical contradictions are getting ever more glossed-over, sugar-coated, and justified. It is now much harder for the average Joe to think his way out of Protestantism than it would be to think his way out of Catholicism. Even the most ‘modern’ Protestant denomination still posits a God: otiose, uninvolved, disinterested, incompetent, natural, or cosmic – however you want to slice it, there is still a God at the center. And because it has adapted itself to still be palatable to the modern person, mainline Protestantism is like a cockroach - it can withstand countless atom bombs of reason and skepticism because it has evolved (oh, the irony!) defense mechanisms against intellectual challenges. Not so with traditional Catholicism. Catholicism, with its smells, bells, rosaries and saints, is somewhat like a bacteria that refuses to mutate: because it refuses to change, it hasn't developed the mechanisms to thwart the things that try to kill it.

Which is why I have such mixed feelings about a recent piece of news my mother sent me a few weeks ago. Apparently Pope Benedict recently decided to lift the sanctions on the Tridentine (Latin) Mass. The Mass had been all but outlawed by the church since the introduction of the vernacular mass after the Vatican II council over 40 years ago. Until now, the decision to permit the conducting of a Latin mass rested in the hands of the local bishop - but with Ratzinger's new decree, that prerogative now rests in the hands of the individual parish priest, and thus many people are predicting a huge upsurge in both the number of Latin masses offered and the numbers of people attending them.

Now, in general, the idea of reactionism bothers me. I’ve always hated the new happy-clappy guitar-playing feel-good vernacular Catholic Mass – even when I was still a Catholic – but what’s done is done, and even though it should never have happened in the first place, it says something rather dangerous about a religious community that would willingly revert to the Dark Ages for an hour every Sunday morning after having lived under rather silly but nevertheless earnest liberal theology for the past four decades.

But after greater reflection, I wonder if it might be possible that this bull will ultimately be beneficial to the cause of organized Humanism? On the one hand, if indeed the Latin Mass becomes more widespread, modern Catholics will probably get even more disaffected because the theology and ritual will be getting stricter. Returning to the Enlightened Despot analogy, the more assertive and dogmatic the religion is, the more likely people are to become disaffected and leave altogether. So score one for Ratzinger for alienating Catholic moderates – I approve wholeheartedly.

But more than this, if the mass is in Latin, that also means the reintroduction of all the cultural and ritual aspects of Catholicism that people are so fond of - the sense of age, mystery, the incense, the rites, the incantations - and gets rid of all the bad things, like folk music and the fact that the people in the congregation can actually understand what’s being said. Perhaps the reversion to the Latin mass is not, as I might fear, a sign of the return of an increasingly authoritarian Church, but perhaps an unwitting admission on the part of the Vatican that it and its religion are otiose bodies, relics of the past. Perhaps this is the first step toward the creation of a Catholic Humanism - much like already exists in Europe - in which God has all but disappeared but the intense and distinct culture of Catholicism remains. Although on the one hand this measure might actually boost church attendance, the fact that the scriptures will be in a language that nobody understands and the rite will be reverting to an earlier form, it will start going back to the days when Mass was Theater. And if Mass is Theater, then that means that truly enlightened 'ethnic Catholics' will be able to come for the cultural pageantry and not be asked to check their minds at the door. People don’t realize it, but they can have their cake and eat it too.

It's a long shot, but I'm hopeful.

A Conflict we Cannot Afford

Lately, a movement calling itself the New Humanism has been challenging what have come to be known as The New Atheists for their argument and for their presentation. The charges most often levied against these alleged (and wrongly so) 'Atheist Fundamentalists" Dawkins, Harris, Hitchens is that they are too dogmatic in their beliefs, that the Atheist utopias they describe are impossible to achieve, and that their public relations need serious help.

The New Humanists prefer to push a friendlier, shinier view of Humanism. They claim to recognize that an atheist society as Dawkins et al. envision it is wholly impossible because even if you get rid of all the God stuff, people still want to keep their cultures, which are largely influenced by religion. Ergo, they say, in order to bring about a Humanist society, we need to have something positive (Humans!) rather than negative (not-God!) to base the system around.

Now I came very close to being sold by this argument for a number of weeks. As an anthropologist, I certainly recognize how much of any given religion's staying power is due to culture (that is to say, all of it), and so the idea of needing to have a positive thing people could rally behind made a lot of sense.

Except that it's impossible. Man can't invent culture - it just doesn't work. All of our attempts to engineer a culture broadcloth have ended in catastrophic failure. Even the most charismatic, inventive, and successful inventors of belief systems (Muhammad, Jesus, L. Ron Hubbard, etc.) have required the additional efforts of a large number of followers over a considerable span of time to take a world-view and a moral creed and mold it into a distinctive way of life. And even then, it survived largely because it as both a) radically new and b) was in drastic in-group/out-group opposition to the prevailing status quo of the place and time.

Is the difficulty of creating a single, universal, worldwide world-view with mankind, sui generis, at its center becoming clearer? As an example of the impossibility of this proposition, let's take the case of modern secular ethics. Yes: it is eminently possible to have morality without a divinity, this has been demonstrated more times than I would care to mention. But here's the trouble with morals: they are inherently boring - especially when they are completely in line with the prevailing zeitgeist (which, incidentally, will never be uniform throughout the entire world anyway). Can you imagine anyone getting excited by a member of the Humanist Clergy getting up on a dais and spouting such self-evident tautologies as "doing bad things to people is bad!" The only way people have so far been willing to stomach having morals preached to them is if there's a threat of hellfire or something equally colorful attached. Without a well-established cultural vessel for the message, humanist morals - true though they are - carry about the same emotional force as a rerun of Mr. Rogers' Neighborhood. Fine for children, but tedious for adults.

Ironically, the man who led me most conclusively to this view is the late and greatly missed Rabbi Sherwin Wine, the founder of organized Humanistic Judaism and a keynote speaker at the recent conference on The New Humanism at Harvard. In his opening lecture on the possibility of an "Abrahamic Humanism," he stressed over and over that the thing that keeps people coming back to their religions - even after they have partially or completely lost faith in the God hypothesis - is allegiance to their parents, to their ancestors, to their culture (I refer you to Blair's comment on one of my prior posts). Simply put, we are cultural animals, and people do not want to abandon their cultural forms because it's a huge part of their lives. It's comfortable for them, and except for the occasional freethinking housecat, people aren't going to defect from their religions wholesale and join a fledgling milquetoast generic 'Humanist' movement that has no real cultural oomph. What they'll join instead, Rabbi WIne seems to suggest, is a group that resembles their old culture but in which the God hypothesis is explicitly absent. Rabbi Wine managed to create an organized form of cultural Judaism that would be appealing to Jews who had lost their faith in God but were still Jews nevertheless. The same is true for other religio-cultural complexes, and the first step is to admit that the culture doesn't have to be thrown out with the God.

So what does this mean for the debate between the New Humanists and New Atheists? For my part, it is precisely because I agree with the New Humanist position that any successful world system has to have a strong, positively-inflected culture that I simply cannot put my faith behind their vision of a unified Humanist culture. Instead, the people who have the Humanists' best interests in mind are in fact the New Atheists. Rather than ask people to abandon their cultures in favor of a new (crappy) one, the New Atheists are asking only that we abandon our faith in the God hypothesis, which many people are already doing tacitly in their own churches and mosques. Only when we give these people a place where they can still be Catholic, Anglican, Presbyterian, Methodist, Sunni, Shi'a, and so forth - without believing in the supernatural will we be able to have a humanist world.

Godwhacker

Have you ever been listening to a song you've heard dozens of times before, only to suddenly realize that you've never paid attention to the lyrics? Yeah, I've got a whole new reason to love Steely Dan now:
In the beginning
We could hang with the dude
But it's been too much of nothing
Of that stank attitude
Now they curse your name
And there's a bounty on your face
It's your own fault daddy
Godwhacker's on the case
. . .
Yes we are the Godwhackers
Who rip and chop and slice
For crimes beyond imagining
It's time to pay the price
You better step back son
Give the man some whacking space
You know this might get messy
Godwhacker's on the case

BEES, by the grace of GOD!

Okay, I'll admit it, this post is little more than an excuse to post some pictures I've taken recently. But... bees! All up-close-like!



Aw, it's shy.

Okay, okay, I'll try to make this slightly relevant. Ever hear that old wives' tale that the laws of aerodynamics make bumblebee flight impossible? Ever hear someone use that as an argument for God's existence? As if bumblebees, out of all the animals in the world, were exempt by the grace of God from the laws of physics. Yes, humble Bombus gets to be buoyed about by the hand of the Almighty himself, while every other flying insect has to get itself off the ground the old-fashioned way. So silly.

Silly fundies.

"I'd take the awe of understanding over the awe of ignorance any day." --Douglas Adams

bumblebee flower 20070808

(And while we're posting pictures, why should Bombus get all the fun? Let's throw some Apis mellifera in there, and a touch of Agapostemon for good measure:)

honeybee side 20070808

agapostemon coming in for a landing 20070812

12 August 2007

Development Primer: 3 Models of Sex Determination and Dosage Compensation, Part 3

Mus (mouse)
Of our three models, the mouse (being a mammal) is most closely analogous to humans. Here, as with the flies, XX animals are female and XY animals are male. This time, however, sex determination depends upon the Y-linked gene Sry instead of the X:A ratio. If you have Sry, you become a male. Note the implications of this for individuals with an abnormal number of sex chromosomes. An XO fly would become a (pseudo)male due to the X:A ratio, whereas an XO human would become a female (with Turner syndrome) due to lack of Sry. An XXY fly would be female, whereas an XXY human would be male (with Klinefelter's syndrome).

Overall sex determination in mammals relies primarily on differentiation of the gonad. The embryonic gonad is bipotential (neither male nor female but capable of differentiating into either) and contains both somatic cells and germ cells (the cells that will give rise to the germ line, i.e. sperm or eggs). The somatic cells of the gonad will differentiate into either Sertoli cells (for testes) or Follicle cells (for ovaries); the hormone production of the gonad will then affect development of the rest of the body.

So we're looking for a cellular mechanism affecting gonad differentiation. As it turns out, there are two primary exogenous growth factors (proteins excreted from a cell that affect growth and development) expressed by the somatic cells: FGF9 and WNT4. FGF9 causes the somatic cells to differentiate into Sertoli cells, and inhibits Wnt4 expression. WNT4 causes the somatic cells to differentiate into Follicle cells, and inhibits Fgf9 expression. Initially, the somatic cells express both factors, and they balance each other out. But as development progresses, the balance gets tipped one way or the other.

In mammals, SRY promotes expression of FGF9, thus tipping the balance toward male development. However, a similar mechanism in other vertebrates might not require a single gene like Sry. For instance, for many animals (such as crocodiles) sex determination is affected by environmental factors like temperature. It's entirely possible that these environmental factors could be affecting a balance such as that between FGF9 and WNT4.

This sex determination mechanism takes place primarily in the gonad; a different mechanism entirely is needed for dosage compensation in all the cells of the body. Unlike the worm mechanism of reducing each X by half in hermaphrodites or the fly mechanism of doubling expression of the male X, dosage compensation in mice and humans works by (almost) completely silencing one of the two female X chromosomes.

In both males and female cells, the autosomes produce enough of a certain blocking factor (BF) to bind to one X chromosome and block expression of the gene Xist. In a cell with only one X chromosome (i.e. a normal male), that' the end of the story. In a cell with two X chromosomes (i.e. a normal female), Xist is expressed on the chromosome that did not receive BF. Xist is a gene that does not code for protein; its end product is untranslated RNA. Xist RNA aggregates to form a region in the nucleus that excludes RNA ploymerase II and transcription factors. The X chromosome migrates into this region, thus silencing it.

The paternal X chromosome carried by the sperm is imprinted so it will always be chosen for inactivation in the zygote. Once the embryo reaches the blastocyst stage of development, X-inactivation is temporarily turned off. As the cells then differentiate, X-inactivation is reinitiated. This time, the decision of which X chromosome to deactivate is random. Thus, the adult animal will be mosaic for X-inactivtion; some of the animal's cells will have the paternal X deactivated, and some cells will have the maternal X deactivated.

The location where BF binds to the X chromosome, since the region runs opposite to Xist, is called Tsix. If Tsix is deleted from one X chromosome, then that chromosome will always be chosen for X-inactivation, since BF cannot bind it. A Tsix deletion in an XY cell will result in ectopic (out-of-place) X-inactivation, which is lethal.

Mouse summary:
Two sex chromosomes -- XY male, XX female. FGF9 and WNT4, mutually inhibitory growth factors, are expressed in the gonad somatic cells. Y chromosome carries Sry, which promotes FGF9 and tips the balance to testis development; otherwise, WNT4 tips balance to ovary development. X-inactivation occurs by transcription of Xist RNA, which forms a nuclear domain excluding transcription factors. Autosomes produce enough blocking factor (BF) to rescue one X chromosome from inactivation, by binding Tsix and thereby blocking Xist. The paternal X is imprinted to be always chosen for inactivation in the zygote; at the blastocyst stage, X-inactivation is reset and randomized.


11 August 2007

Development Primer: 3 Models of Sex Determination and Dosage Compensation, Part 2

Drosophila
Drosophila's sex chromosomes are perhaps more familiar-looking, in that it has an X and a Y chromosome, with XX animals being phenotypically female and XY animals being phenotypically male. As we'll see, however, the mechanisms are vastly different from what we see in humans and other mammals.

Sex determination and dosage compensation begin as they did in C. elegans with reading the X:A ratio. This time, however, the X-linked numerator factors (like daughterless and sisterless) drive Sxl (sex lethal) expression from a promoter that results in the code for a fully-active SXL protein (nomenclature note: italics are typically used for the name of the gene, capital letters are used for the corresponding protein). The A-linked denominator factors (like deadpan) bind to the numerator factors to inhibit their activity. Thus, if the fly has only one X chromosome, the denominator factors will titrate out the numerator factors, so Sxl only gets up and running in XX animals.

SXL a protein that alters RNA splicing. Most mRNA when it is first transcribed from DNA must first be processed within the nucleus before it is shipped out for protein translation. This processing includes removing introns, non-coding regions of DNA within a gene. Normal Sxl mRNA has a premature stop codon in its third intron; if the cell tries to make protein from this mRNA, it will stop translation short, resulting in a non-functioning protein. SXL protein is responsible for altering splicing to remove this intron so the cell can make more fully functional SXL.

Thus, SXL drives its own positive feedback loop. Both XX and XY animals express Sxl mRNA from the normal promoter. In XY animals, there isn't ever any SXL around to splice this mRNA, so no SXL is made. In XX animals, the numerator factors drive SXL expression at the beginning of development from a special promoter that doesn't require splicing, so there's enough SXL to kick-start splicing of the normal mRNA and keep generating more SXL long after the numerator factors stop working.

SXL is then responsible for proper splicing of tra to its active form, which in turn (in conjunction with tra-2) alters splicing of the transcription factor dsx, which causes differentiation to the female phenotype.

SXL also inhibits msls, a gene which otherwise would initiate dosage compensation by increasing expression from the male X. Note that in C. elegans, dosage compensation meant scaling down expression in the female, but in Drosophila, dosage compensation means scaling up expression in the male.

Drosophila summary:
Two sex chromosomes -- XX female, XY male. Numerator factors drive expression of fully-functional SXL in XX animal, kicking off SXL positive feedback loop. SXL activates pathway leading to female development. SXL inhibits msls pathway to dosage compensation. In the absence of SXL (i.e. in XY animals), msls drives increased expression from the single X chromosome.


10 August 2007

Development Primer: 3 Models of Sex Determination and Dosage Compensation, Part 1

You're probably aware that a person's sex is typically determined by their combination of sex chromosomes. In humans, females have two X chromosomes, whereas males have an X and a Y. But how do you go from X and Y to boy and girl? And what does the cell have to do to compensate for the chromosome differences between the sexes?

Sex chromosomes pose two interesting questions in the study of development:
  1. Sex determination: How does the cell interpret the data from the sex chromosomes to result in phenotypic sex?
  2. Dosage compensation: The sex chromosomes carry many genes that aren't sex-specific; that is, both male and female cells need the products of those genes in approximately equal amounts. Without dosage compensation, a cell with two X chromosomes will produce twice as much of a given X-linked gene product as a cell with one X chromosome. How does the cell regulate sex chromosome expression so that cells with unequal sex chromosomes express sex-linked genes equally?
The animal kingdom employs a number of different mechanisms for dealing with these two questions. Let's take a brief look at sex determination and dosage compensation in three model organisms: the nematode worm (Caenorabditis elegans), the fruit fly (Drosophila melanogaster), and the common mouse (Mus musculus).

C. elegans
C. elegans is a tiny invertebrate worm with just one kind of sex chromosome: X. A normal worm with two X chromosomes (XX) is a hermaphrodite, producing both sperm and eggs and capable of self-fertilization. A normal worm with one X chromosome (XO) is a male; they're smaller and capable of mating with hermaphrodites.

The pathway leading to sex determination and dosage compensation is initiated by "reading" the X-to-autosome (X:A) ratio. (Autosomes are any chromosomes that aren't sex chromosomes.) In C. elegans, the first main gene in the signal transduction pathway is xol-1 (XO lethal 1, so named because mutations of the gene are lethal to animals with XO genotype). The autosomes express a number of genes, such as sea-1, that promote xol-1 expression; these are called denominator factors, since they show up on the bottom of the X:A ratio. Each X chromosome carries genes like sex-1 and fox-1 that inhibit xol-1 expression; these are called numerator factors. An XO cell doesn't produce enough numerator factors to "cancel out" the denominator factors, so xol-1 is "turned on." An XX cell has twice as much of each numerator factor, enough to "turn off" xol-1.

Xol-1 is the first in a series of several regulatory genes. Since the genes regulate each other, activity alternates down the chain. If xol-1 is on, then it turns off sdc-2, which means her-1 gets turned on, etc. Alternatively, if xol-1 is off, then sdc-2 gets to turn on, and that turns off her-1, etc. This pathway ultimately leads to expression of transcription factors (gene-regulating proteins) specific for either hermaphrodite or male differentiation.

Loss-of-function mutations of some of the genes in this pathway can cause "transformation" to the wrong sexual phenotype. For example, in XO animals her-1 is normally turned on, and we expect to get a male. But if we mutate her-1 so it can't perform its function, then the rest of the pathway downstream acts as if her-1 is off and we get a hermaphrodite phenotype. (Genes are often named according to the phenotype of the mutation that led to their discovery; thus, her-1 got its name for turning XO animals into hermaphrodites.)

So that's sex determination, but what about dosage compensation? It turns out that dosage compensation is activated by sdc-2. Dosage compensation in C. elegans acts by cutting expression of both X chromosomes in half in XX animals. That way, two X chromosomes at half-expression result in the same amount of product as one X chromosome at full expression. That's also why xol-1 mutations are lethal for XO animals; without xol-1 to regulate it, sdc-2 gets turned on when it shouldn't be. That in turn activates dosage compensation, and with only one X-chromosome at half its normal expression, the cell doesn't have enough X-linked gene product to survive.

C. elegans summary:
One sex chromosome -- XO males, XX hermaphrodites. X:A ratio read by X-linked inhibition of xol-1, affecting downstream chain of regulatory genes. Dosage compensation reduces expression from each X chromosome by half in XX animals.


IDiot Rundown

Dacook of UncommonlyDense quote-mines a recent National Research Council report:
On Page 8 of a Report from the National Research Council there is an interesting admission:
“Natural selection based solely on mutation is probably not an adequate mechanism for evolving complexity.”
Of course the report itself supports the concept of Darwinian evolution. But I think the admission that mutation is an insufficient mechanism is significant. They invoke lateral transfer of genes as the alternate explanation:
“More important, lateral gene transfer and endosymbiosis are probably the most obvious mechanisms for creating complex genomes…”
Of course this begs the question; where did the genes come from that are being laterally transferred?
The genes come from mutation. The report admits that mutation alone is not sufficient for evolution (not a new revelation), but it's certainly necessary. The point is, you're not looking at one single genome being continuously mutated over time. You have a bunch of different genomes mutating, and then mixing and matching the parts that work to create entirely new genomes.

Meanwhile, turnabout is fair play. Several months ago, Time magazine made the insulting decision to have Michael (Fucking) Behe write Richard Dawkins' profile for their list of the year's 100 most influential people. Now, Bruce Chapman of the Discovery Institute is flustered because the New York Times Review of Books chose Dawkins to review Behe's The Edge of Evolution. Let me give it to you straight: Dawkins is respected in the scientific community. Behe is not. It's dishonest enough to pretend that they're equals without going further to say Behe is above Dawkins.

Next, the media made a hubbub over recent hominid fossils, and DI's Casey Luskin wasn't going to let the sensationalism go by untouched. Rather than write about everything that's wrong with his interpretation of the fossils, I'll just let you choose from a few other bloggers: 1 2 3 4 5. I'll just add that I found scordova's (UD) remark on the matter highly ironic:
It [sic] understandable that scientists make mistakes, but one would hope an entire scientific discipline could get at least one fact right once in a while.
Strong words, from someone who thinks ID counts as a scientific discipline.

We've got a transcript of a 2005 speech by creationist Don McLeroy, now head of the Texas State Board of Education. Texas is screwed. That might deserve a post of its own.

William Dembski apparently thinks animated .gifs and Beatles lyrics are accurate representations of evolutionary theory. This is a problem.

Finally, our old friend Michael Egnor still insists that questioning evolution in schools is a federal crime:
It’s a federal crime to violate a federal court ruling, such as the
ruling by federal judge John E. Jones banning criticism of Darwin’s
theory in the curriculum of biology classes in Dover, Pennsylvania
public schools.
There's just one problem with Egnor's logic: Judge Jones' ruling doesn't ban questioning of evolution. Questions are a good thing. It does, however, ban teaching of intelligent design, on the grounds that ID is rehashed creationism bent on sneaking religion into science curricula. (Don't believe that? Check out the Don McLeroy transcript.)

A question of disclosure

Recently, I had an interview for a job at a local bookstore. During the interview, I was asked to name some of my all-time favorite books, those that had had a major impact on my life.

I wanted to name The God Delusion as one of them, but I didn't know how something like that would come across. So I went with The Selfish Gene instead, figuring I could get in my appreciation of Dawkins without necessarily blowing the cover on my atheism.

I am open and honest about my atheism. You'll notice that I blog under my real name. And yet, I felt apprehensive about making my atheism a topic of direct conversation during a job interview. It's not even that I didn't want my prospective employer to know I was an atheist (heck, all he'd have to do is google me). But I didn't want him to think of me as unprofessional for bringing my atheism into the workplace. And I have to wonder, would I have been as worried about appearing unprofessional for sharing an experience as a Christian?

The workplace is hardly the ideal atmosphere for matters like religion and politics, to be certain. But when an interviewer is trying to get a sense of who you are, what do you do? Did I demonstrate good tact, or did I just chicken out?

What would you have said if you were in the same situation? Have you ever had to make similar checks on voicing your opinions on religion?

(And in case you're wondering, I didn't get the job. Apparently they went with candidates who had previous bookstore experience, which is understandable.)

A trip to the bookstore

My fiancée Sara and I happened to be in the vicinity of Border's in downtown Boston today, so we took a bit of a browse. (Sadly, I didn't have my camera with me... I would have liked pictures of what's to follow.)

I took a little wander over to the Science section, and sure enough there were three copies of Behe's "The Edge of Evolution" nestled in the biology section. Inspired by Biologists Helping Bookstores, Sara and I helpfully relocated Behe's books to a prominent shelf in the Christian Fiction section. He's nestled between two books with pretty ladies on their covers, I'm sure he can't be too upset.

I've seen some mention online that bookstores are starting to set up whole displays dedicated to atheism. Well, I'm sorry to say that this Borders had a bittersweet offering for us. There was a shelf dedicated to atheism in the religion section, and there was an aisle display nearby much like the one depicted in the link above. But this aisle display was labeled "assault on faith," hardly a positive spin. Furthermore, their selection of books (or rather, a book) was atrocious. Sure, they had plenty of copies of Hitchens' god is not Great, a bunch of Harris' The End of Faith, and a couple of Dawkins' The God Delusion toward the bottom. But topping the display were several shiny black copies of Alister McGrath's joke of a book, The Dawkins Delusion. I can't imagine how that book found its way on the display; from the scathing critiques I've read, The Dawkins Delusion is one strawman argument after another, completely failing to honestly address Dawkins' arguments.

I didn't know what to do with the McGrath book on display; I wanted to reshelve it, but something told me reshelving it in the only proper place (the trash can) would have gotten me in trouble. So we just obscured a stack of the books with a copy of I Sold My Soul on eBay that Sara had been browsing. Hemant's book is hardly an assault on faith, but maybe it will give someone pause to reconsider how they choose to advertise their books.

I think maybe tomorrow I'll have to check to see how some of the bookstores in Cambridge are handling the atheist literature.

06 August 2007

Why Intelligent Design is Creationism

There's been a lot of buzz lately over the distinction (or lack thereof) between creationism and intelligent design.

Casey Luskin at the Discovery Institute wrote last week that ID wasn't just a protestant Christian movement: an orthodox Jew was in on it, too! (I'll give you a second to get over the shock that Xians and Jews could agree on the origins of life.)

Denyse O'Leary once again mumbles praise of the Creation Museum under her breath. Notice how she praises the museum for not aligning itself with ID, rather than condemning it for using false science. That's because O'Leary doesn't give a damn about real science. As long as the CM helps her undermine evolutionary biology, it's okay in her book. She just doesn't want her version of creationism to be

Mike Dunford at the Panda's Thumb agrees (reluctantly) with O'Leary that Creationists and IDiots are different; the difference being, Creationists aren't afraid to admit that their ideas come from their faith, whereas IDiots like O'Leary are afraid to admit to the metaphysical beliefs at the foundation of ID.

Larry Moran doesn't want to let O'Leary off the hook so easily. Creationism, he says, encompasses Young Earthers, Old Earthers, IDiots, and even Theistic Evolutionists (to varying degrees). I agree. If you think God created us, whether you think you can prove it or not, then you're a Creationist.

Meanwhile, Michael Egnor took offense to Dunford's post. Mark Hoofnagle gave Egnor a thorough thrashing.

For my part, I'm convinced that Intelligent Design is a subspecies of Creationism. The only way you can make a reasonable design inference is if you have reason to believe there could have been a designer present. I don't care how unlikely you think a pattern is. If I pour a bowl of alphabet soup and find the phrase "You're a douchebag, and by the way we're almost out of milk," I'm still going to have to chalk it up to coincidence unless you can give me some other evidence that I have pantry gremlins. Suppose we find artifacts such as stone tools and crockery at a new site in Wisconsin, dated confidently to 7000 years old. We could make the reasonable inference that people had left them behind, because we have other evidence that tool-making people existed on Earth 7000 years ago.

Even if you don't have evidence for a designer apart from whatever it is you think has been designed, you sure as hell would normally look for more evidence of the designer to back up your design inference. Imagine if we found what we thought were stone tools dated with all confidence to 125 million years old. We'd variously be questioning our dating techniques, looking for toolmaking dinosaurs, looking for evidence of time travelers, or coming up with natural explanations for the stones' appearance. If we found "tools" on Mars, we wouldn't sit back in our recliners and take that as unequivocal proof of Martians, we'd keep on looking.

The Intelligent Designers time and again deny being interested in who their designer is, how he did it, or why he did it the way he did. Every single thing that humans identify as "designed" has been accompanied by at least a vague guess based on our best evidence as to who the designer was. After all, how can you have design without a designer? No, the truth is, IDiots already have an idea who the intelligent designer is, and they don't want to admit it because that intelligent designer is God (or Rael, or whatever your faith of choice dictates). They have no evidence of the designer, nor will the seek it, because they have their faith. That's why ID is Creationism, and decisively not science.

05 August 2007

Verdammen Politik!

I am so very furious with Congress right now.

It's particularly disappointing to know that I voted for Bob Casey (D-PA). Sure, he was an easy choice against incumbent Rick Santorum (*shudder*) and I wouldn't have cast my 2006 vote any differently, but I still feel partly responsible for having supported Casey.

And just when things were finally starting to look up, what with Gonzales on the ropes and all... but now, hey, why not give the incompetent/dishonest Attorney General even more power in the meantime?

Scheiße.

04 August 2007

I must be a glutton for punishment

I've commented at UncommonlyDense again. The conversation isn't quite as heated this time around... at least not yet, anyway. BarryA referenced a talk at the TED conference by David Bolinski, one of those who worked on the animation The Inner Life of a Cell. He used one of Bolinski's comments to say that, since life needs molecular "machines" to survive, this poses a problem for abiogenesis. I made the case that just because something is necessary now, doesn't mean it has always been necessary:

BarryA: “If no life is posibble without these nano-machines, where did the nano-machines come from?”

Easy. Life as we know it might rely on the these biological machines, but that has not always been the case. As supply evolves, so does demand. Just as these biological machines were evolving to more accurately and efficiently do their jobs, the rest of the cell’s machinery was evolving to more efficiently utilize them.

Consider the automobile: without automobiles, American society as we know it would not be able to survive. But that doesn’t mean American society has always needed automobiles. Nor when the automobile was invented did we instantly plant a nationwide network of superhighways. Transportation technology has been evolving, as has our reliance upon said technology.

I was eventually pressed for evidence that older life forms got by with less sophisticated cellular machinery. In my research, I turned up this pretty impressive kinesin phylogenetic tree. Just imagine how much work went into accumulating and interpreting all that data... and to think the IDiots among us would have us discard all that research as irrelevant!

We'll see if that conversation goes anywhere... but I'm not counting on it.

You know my biggest mistake on the UD comments? Using the name "Hawkeye." Until now, that nickname has been associated solely with friends. It's unnerving to be referred to as "Hawkeye" by people who are most assuredly NOT my friends.

So to balance out that bad mojo... Hello, friends. My name is Aaron, but you can call me Hawkeye. ;-)

03 August 2007

Behe visits the Colbert Nation

You know, it figures. The very day our cable finally ran out, Michael Behe appeared on the Colbert Report. Thank goodness for the Internet:

Considering Colbert's often hit-or-miss interview record, I'm pleased with the way he handled Behe. He obviously did his homework. Behe made some of the same old laughable claims, such as the idea that no one questioned the Gospel of Newton before Einstein. Stephen got in a nice dig at Behe's mousetrap analogy, which is always nice to hear. Kudos to Colbert for bringing God into the discussion so matter-of-factly; it's interesting that Behe didn't bother trying to deny ID's true agenda there.

Hat tip to Science after Sunclipse (click the link for more thorough commentary than I give here).

01 August 2007

Refusing to Identify the Intelligent Designer

Ugh. Yesterday I registered as a commenter on Uncommon Descent and spent most of the day debating a band of ID cranks pretty much single-handedly.

I've done wiser things.

I initially registered to comment on Granville Sewell's absolutely stupid argument from the second law of thermodynamics, but ultimately decided that I couldn't say anything reasonable and productive about that. So instead, I commented on BarryA's post about Indian arrowheads. In his post, BarryA tells a little satire about how the arrowheads in his grandfather's collection must have been produced by natural causes, despite their obvious appearance of design, because no one can tell him who designed them. Hopefully you can see the problem with his little analogy.

Let me say that arguing with ID cranks on their own terms, especially en masse, is difficult, physically draining, and ill-advised. I tried to make a case for needing to investigate the designer even if something looks designed, without addressing other issues (like the fact that life doesn't look designed and that cells aren't completely analogous to machines). I think I very well may have failed.

Bad logic has strength in numbers. I tried to tease one aspect of their argument out into the light where I might tackle it individually, but they wouldn't have it. And in so limiting myself I probably made some bad (or at least incomplete) arguments myself. You can't blame a guy for trying.

Ultimately, though, I'm proud of myself for having been able to end on a strong note:
This discussion is beginning to get too broad, and so for now I will respectfully bow out. I only want to bring attention to my initial comment: BarryA wanted to say that you could tell something was designed without knowing who designed it or how it was designed/manufactured. However, to do so, he made an analogy to something for which we DO know about the designer.

As of yet, no one has given me an example of something (other than life, as ID claims) that is generally accepted to have been designed, but for which we have absolutely no idea who designed it or how. We’ve seen a lot of hypotheticals (computers on Mars, messages from extraterrestrials), but I point out that each of those examples of suspected design would be accompanied by an investigation into the nature of the designer. Why, then, does such an investigation not accompany ID?

Cheers,
–Hawkeye–

As of this morning, there have already been a number of responses but no satisfactory answers. One poster, "nullasalus," says that knowing the designer is "simply outside the scope of things" without justifying why that should be the case. "Jerry" dismisses my question as a "tired cliché." "Atom" responds with such things as Viking artifacts in North America, which of course doesn't answer my question because we do have a clue as to who designed those artifacts (surprise! we think it may have been Vikings!).

I meant it when I said I was bowing out of that discussion... one can only butt heads with the UncommonlyDense for so long before you get a headache (or suffer brain truama). I know I probably didn't sway anyone against whom I was arguing, but I have some small hope that I may have planted some questions in the mind of a passing visitor.

I'll certainly think twice before commenting at UD in the future. There's just too much that's wrong about ID to overcome in a handful of blog comments.