Friday, June 11, 2004

As Jon Stewart would say, "Wha...???!?"

I just got around to reading this link that Les Lane left in the comments. It's hilarious. A creationist website has a URL that's a little to close to the Raelians for comfort, so they've created this disclaimer:

RAELIAN DISCLAIMER

The Revolution Against Evolution, http://www.rae.org is not associated with the Raelians http://www.rael.org. The Raelians claim to be creationists, but not in the Biblical sense. Instead they believe that life was imported from outer space by aliens. Their god is a UFO driver. Our group, Revolution Against Evolution, is made up of traditional Biblical Christians who believe in a supernatural creator God, and his son Jesus Christ. We in no way believe that this Christ was a space alien. We do suspect, however, that the god the Raelians serve and believe in is a counterfeit, either of their own imagination, or demonic in nature. Our creator God of the Bible is not a super-technological god; He is a supernatural God.

In addition, the Raelians are strong advocates of cloning. We have sincere reservations about the practice, as we believe that this is messing with God’s natural order of things, and too little is known about the effects of the procedure.

We hope to expand upon this page as we research this further. I used to think that this was too bizarre to be taken seriously. Judging by some of the e-mail we get by mistake, we have to rethink this.

A creationist complaining that another loon was "too bizarre to be taken seriously"? I laughed out loud.

Springtime on the prairie...

Jaquandor, author of THE Buffalo blog, the one, true, only high priest of Buffalo blogging, has a comment on those lovely crepuscular rays of sunlight, which prompts me to toss up my own recent picture.

It's been a less-than-lovely week for weather here in Morris (where I, and I alone, am the master of the Morris blog, not that I seem to have much competition), with thunderstorms blowing in for an hour or three just about every day, and much of the rest of the day we're sitting under gray, damp, gloomy skies. I'm routinely strolling into the lab around 6 or 7 every morning to tend to my fish, where I pray to the piscine fertility deities, play a little Barry White, yadda yadda yadda, do whatever I can to get the horny little rascals to go into an orgy of egg and milt spewage, which means I get to see spectacularly oblique early light playing tangentially across extremely angry skies. And of course, it wasn't stationary—it was all writhing in excruciating slow motion. If this photo has captured "god light", I'm not sure what to call this ominously spiky, tormented flocculence, with it's scattered swirls of eye-like vortices. "Cthulhu's Unholy Spunk," maybe?

Casey Luskin and the evolution of an IDEA

I've written before about Casey Luskin and his IDEA club, which exists to promote Intelligent Design on college campuses. I've criticized it for having purely religious motivations (which Luskin tries desperately to conceal), and for their very poor understanding of the science they claim to criticize. Jack Krebs and Wesley Elsberry at the Panda's Thumb have also ripped into Luskin over both of these issues.

Luskin, as you might guess, is indignant. In particular, he is irate that he was caught with a current listing at a conference that describes the IDEA club as a "ministry". It wasn't his fault, he protests. At length. At extravagant length.

At http://www.pandasthumb.org/pt-archives/000246.html, there are some comments being made about the description of the IDEA Center. Namely, at "http://www.idconference.org/html/youth_conference.html", my bio was given as: "Co-president of the Intelligent Design and Evolution Awareness (IDEA) Center, a ministry focused on equipping students to promote Intelligent Design." I never gave them a bio for me nor did I ever instruct them to say anything about me. Quite frankly, I agreed to speak at this conference a long time ago and my name wasn't even up on the site until very recently, much less this description of the IDEA Center.

Obviously the word "ministry" implies we are a religious organization. Let me say that I was very shocked to see this wording, and as soon as I just read over the PandasThumb thread and found out about all this, I e-mailed Sondra Lantzer, a staff member at the church hosting the conference, and I asked her to change it to: "Co-president of the Intelligent Design and Evolution Awareness (IDEA) Center, a non-profit organization focused on helping students to understand and debate intelligent design theory." The latter is an accurate description of what we are. I don't think it is fair to call us a "ministry" because quite frankly, we spend the vast majority of our time talking about scientific issues and a very small minority of our time talking about religious matters. When IDEA Clubs form, we encourage them to register as educational organizations because that is what they are: they host debate forums where people can have friendly, informed, and informal discussion about ID and evolution with individuals of various viewpoints.

He was shocked. Shocked, I tell you, that anyone would assign a religious intent to his organization.

Well, thanks to a tip from Nick Matzke who pointed out that several examples of the IDEA club web page can be found using the Internet Archive Wayback Machine, we can see what the IDEA center has said about itself in the past. Here are several versions of the IDEA mission statement, and we can see how it has (dare I say it) evolved over the years.

From 2001: Formerly the "IDEA Club at UC San Diego", the IDEA Center is officially Christian-affiliated, existing under the auspices of Faith Seminary and is based out of San Diego, California. As seen in our mission statement, some of our primary goals are to: promote, as a scientific theory, the idea that life was designed by an Intelligence, facilitate discussion, debate, and dialogue over these issues in a warm, friendly, and open atmosphere where individuals feel free to speak their personal views, and coordinate student-run IDEA Club chapters on university and high school campuses to achieve these goals among students.

From 2002: The IDEA Center today is a non-profit organization based out of San Diego and existing under the auspices of Faith Seminary. Our mission statement says we aim to: Promote, as a scientific theory, the idea that life was designed by an Intelligent Designer Hold, through other arguments, that the identity of the Designer is consistent with the God of the Bible Educate people about scientific problems with purely natural explanations for the origins and evolution of life Challenge the philosophical assumptions of Darwinism, naturalism, and materialism Facilitate discussion, debate, and dialogue in a warm, friendly, and open atmosphere where individuals feel free to speak their personal views Host lectures, conferences, and other events for churches, educators, and those interested Start student-run IDEA Club chapters on campuses The Center hopes to host classes, conferences, and discussion groups whenever possible to fulfill our mission statement and to include universities, churches, high schools, community institutions, and any other accepting venue in the Center's activities as opportunities and resources avail themselves.

From 2004 (the current statement): The IDEA Center is an autonomous non-profit organization based out of San Diego, California. Our mission statement is as follows: The purpose of the IDEA Center shall be to: Promote, as a scientific theory, the idea that life was designed by an intelligent designer, Educate people about scientific problems with purely natural explanations for the origins and evolution of life, Challenge the philosophical assumptions of Darwinism, naturalism, and materialism, Facilitate discussion, debate, and dialogue in a warm, friendly, and open atmosphere where individuals feel free to speak their personal views, Host lectures, conferences, and other events for churches, educators, and those interested, Help establish and maintain student-run IDEA Club chapters on school campuses or wherever interest exists. The Center hopes to host classes, conferences, and discussion groups whenever possible to fulfill our mission statement and to include universities, churches, high schools, community institutions, and any other accepting venue in the Center's activities as opportunities and resources avail themselves.

It all reminds me of the evolving banners at the Discovery Institute.

Note how it moves from explicitly "Christian-affiliated" to "under the auspices of Faith Seminary" to "autonomous". This is odd, since you can also look at who is on the Board of Directors, which "makes all official decisions about the direction and status of the Center", from the 2001 board to the current leadership. Several new people have been added, but the original core group is still running things: Michaeel Adams, dean of Faith Seminary, Eddie Colanter, Assistant Professor of Apologetics and Ethics at Faith Seminary, H. Wayne House, Distinguished Professor of Biblical and Theological Studies at Faith Seminary, Casey Luskin, Steve Renner, and Scott Uminsky. As Luskin has no doubt noticed, pretending to be a source of scientific information while nestled under the wing of a seminary is not a great idea.

Note also that one rather significant clause in the 2002 document, "Hold, through other arguments, that the identity of the Designer is consistent with the God of the Bible", has been deleted. It's also politically unwise to expose your narrow sectarian religious beliefs while pretending to be scientific, so that had to be jettisoned.

So, yes, I can see why Casey Luskin was shocked that the organizers at a conference sponsored by the Community Bible Church of Highlands, NC would call his organization a "ministry". They were blowing his cover.

Luskin, in his outraged defense against the indignity of being called a "ministry", implores people to call the conference organizer and check that his excuse was valid. I did. She replied with nearly the same words Luskin used, taking all the blame for the mistake, although she didn't say how she came up with the idea that the IDEA club was a ministry.

While I had her on the phone, though, I did ask her one other question. This conference, which has also been mentioned by John Lynch, is titled "Two World Views: what's the difference". Here is its purpose:

Conference Purpose:   To introduce Jr. and Sr. High Youth to two worldviews.
1.   The secular worldview which is humanistic in nature placing man at the center of all philosophy.
2.   The Biblical worldview which looks to the Bible as the ultimate authority of all truth.

It lists 5 speakers, Mark Eckel, Kenneth Boa, Michael Behe, Chuck Colson, and Casey Luskin. The first two are ministers, Behe is the anti-evolutionist author of Darwin's Black Box, Colson is the crook who found Jesus, and Luskin is...whatever. The obvious question, and the one I asked the organizer, is given the intent of the conference to present two worldviews, and with that list of speakers, who is presenting the secular worldview?

To my surprise, she was very quick with the answer, and even gave me a brief summary of what he'll be talking about. It wasn't Behe, and it certainly wasn't Luskin: it's Eckel. Yes, that's right, the Associate Professor of Educational Ministries at the Moody Bible Institute is going to give an overview of secular humanism to the kids, warning them of what they can expect when they go off to college. That's their idea of presenting the secular worldview.

A question that only Luskin can answer is what the heck he's doing, inviting himself to a bible camp meeting^*, if he's so embarrassed by the religious foundation of his IDEA club.

^*The exact wording of the conference organizer was that they came up with the bio after Luskin "asked to be a part of the conference." So much for the implication that he was invited to participate.

No one here but us fundamentalist, extremist zealots

WorldNetDaily does it again...another ridiculous article, titled "Who are the real fundamentalist, extremist zealots?" Can you guess who? Sure you can. Evolutionists, of course.

Parent Larry Caldwell had an idea to bring more diversity into the education of his child and fellow students of the Roseville, Calif., Joint Union High School District.

Months ago, he observed, the district's biology textbook failed to point out any of the weaknesses of the theory of evolution—teaching it instead as a matter of fact.

How tiresome. How unimaginative. How stale.

Look. There's a simple request I would like to see addressed by the next person who complains that evolution is taught without mentioning its weaknesses.

Name them.

That's right. Rattle off a list of these purported weaknesses for me. Tell me all the stuff that I ought to be explaining in class that I'm hiding. In detail. Preferably with a discussion of your alternative theory, which covers these deficiencies better than evolution. OK?

And please...do your homework. Don't tell me how weak and inadequate the theory of evolution is, how there hasn't been any supporting evidence for it generated in over a century, and then happen to admit that you've never heard of the neo-Darwinian synthesis, as has actually happened here. You don't get to declare that thousands of scholars have been dead wrong while revealing that you haven't even heard of the simplest, most basic, most fundamental points of the theory.

Go ahead and read the rest of the dreary, boring WorldNetDaily article. The author expends a lot of effort complaining about how evolutionists are all religious fundamentalists (and we all know how evil that is)...but look closely. Despite announcing our failure to teach the weaknesses of evolution, he doesn't name one. Not one.

Despite claiming that evolution has become "so sacrosanct that you can't question it", he doesn't ask one question. Not one.

He claims that evolution is "unsupported by facts and unsupportable by facts". All that means is that he doesn't know one thing about the science. Not one.

Dealing with people who wear their ignorance as a badge of honor does get rather depressing. It's also painful to see these constant accusations that scientists are afraid to face problems in the field, when practically every paper published is saying, "here is a problem we are trying to answer" and "here is a new problem that our data has exposed." I can't even imagine what these people think must be in a scientific paper—do they picture something like a church newsletter, with lots of "Praise Darwin!"s and announcements about the upcoming lab social?

Thursday, June 10, 2004

My weaknesses revealed

As long as I'm getting accused of being a socialist, I might as well 'fess up. Yes, I rather like many socialist ideas. Kurt Vonnegut says it better than I could.

Eugene Debs, who died back in 1926, when I was only 4, ran 5 times as the Socialist Party candidate for president, winning 900,000 votes, 6 percent of the popular vote, in 1912, if you can imagine such a ballot. He had this to say while campaigning: As long as there is a lower class, I am in it. As long as there is a criminal element, I'm of it. As long as there is a soul in prison, I am not free.

Doesn't anything socialistic make you want to throw up? Like great public schools or health insurance for all?

Oh, yeah. Those public schools, the idea of helping the poor to better health...I like those ideas. I like them very much. They seem so civilized.

I can even agree with Vonnegut that there are some very nice things in Christianity.

How about Jesus' Sermon on the Mount, the Beatitudes?

Blessed are the meek, for they shall inherit the Earth.
Blessed are the merciful, for they shall obtain mercy.
Blessed are the peacemakers, for they shall be called the children of God. ...

And so on.

Not exactly planks in a Republican platform. Not exactly Donald Rumsfeld or Dick Cheney stuff.

For some reason, the most vocal Christians among us never mention the Beatitudes. But, often with tears in their eyes, they demand that the Ten Commandments be posted in public buildings. And of course that's Moses, not Jesus. I haven't heard one of them demand that the Sermon on the Mount, the Beatitudes, be posted anywhere.

"Blessed are the merciful" in a courtroom? "Blessed are the peacemakers" in the Pentagon? Give me a break!

Something is wrong in the universe when a cranky curmudgeon of an atheist like me has a soft spot in his heart for ideas like these, while those who rule and invoke God the most often repudiate them.

What did I do to deserve this?

I woke up this morning to a bizarre bolus of hate mail (and fan mail!), all from Texas, and all about my short comments on Reagan. It turns out I've been quoted in the Dallas Morning News (free registration required, bleh), sandwiched in between Andrew Sullivan and James Lileks (and if that imagery gives you nightmares, think how I feel. Shudder.)

Another bothersome thing about it all is that that was a 2-minute, off-the-cuff grump about politics, and it gets cited in a big city newspaper. I spend an hour carefully writing something detailed about biology, and what do you think the odds are that it would get that kind of attention? Oh, well, I've got my priorities straight, if only the media would follow...

Fossil pterosaur embryo

Chinese scientists have found a fossilized pterosaur egg from the early Cretaceous, 121 million years ago, containing a very well-preserved embryo that was probably killed just a few days before hatching. It's well enough preserved that wing membranes and patches of skin can still be seen.

Isn't it beautiful?

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Wang X, Zhou Z (2004) Pterosaur embryo from the Early Cretaceous. Nature 429:621.

A few site announcements...

• Pharyngula will be down most of Sunday, 13 June. They physical plant crew is doing a sustained test of faculty patience by shutting down all the power to campus that day. I don't know why; I suspect it is a demonstration of their power, and will be followed with extortion demands. Similarly, the custodial crew is kicking me out of my lab next week so they can wax the floors, which won't affect any of you guys, but keeps me away from my fish. That'll probably be the day they lay the 2000-egg cohort I need for some long-range experiments I'm working on.
• There will also be some downtime later this month, whenever the new G5 that I'll be using as a server and general purpose lab machine arrives. It won't be one of these brand spankin' new watercooled dual processor beauties (mmmm-baby...<drool>), but it will be significantly faster than the sadly obsolete (but wonderfully reliable) G4 we're running on right now. I should mention that this computer is also the one I use to run some of my time-lapse imaging experiments, and although that's usually a fairly low impact drain on the computer's resources, there may sometimes be slight slow-downs as I play with embryos.
• There's some sweet stuff in this Expression Engine blogware I'm running here, that I'm itching to implement once I've got a server with a bit more oomph. One thing I have done now is to turn on the registration capability, over to the left on the main page. The useful thing about that is that if you register, the software will remember who you are when you are posting...and the silly, pointless thing it will also do is give you the ability to have a little member avatar next to your comments. (You may have noticed the small pumpkin floating around in the article comments: that's supposed to be my head.) The picture needs to be 48x48 pixels in size, all you have to do is provide a url that points to it, and if you don't have one, I tossed a collection of them onto this page of member avatars.

Wednesday, June 09, 2004

Regulatory evolution

Richard Hoppe points out that one of the articles I cited in my discussion of Vernanimalcula has some interesting implications, so I thought I'd expand a bit on some points brought up in a couple of these Davidson papers.

One idea is a general one that we have to keep in mind when studying the evolution of developmentally significant molecules—genes don't necessarily have the simple functions that we assign to them. For example, one of the better known genes in the popular press is BRCA1, named because certain alleles of this gene are associated with a higher frequency of breast cancer. It is not a breast cancer gene, of course; the gene product is a nuclear phosphoprotein with a bewilderingly complex set of functions. We have to be careful not to think that the convenient handle we attach to genes when we name them by the initial description of a phenotype when they are defective is an at all accurate or complete description of their normal function.

Erwin and Davidson discuss some of these misleading conceptual associations we fall prey to in development. Here is a table of a few examples of genes that have a proposed, simple function, and a better alternative function:

Diverse interpretations of some examples of gene use across Bilateria

Gene(s)	Proposed conservation of pathway for:	Alternative proposal: conservation of cell type specification
tinman, nkx2.5, mef2	Heart	Control of cardiac type muscle protein genes, other cell-type specific cardiac genes
pax6 and orthologues	Eye	Control of retinal visual pigment genes, other cell-type specific eye genes
orthodenticle and otx	Anterior brain	Differentiation of specific neuronal cell types, acoustic, ocular olfactory sensory including neurons, neuroblast replication
dachshund	Eyes, central nervous system, many other sites	Control of cell-type specific genes in retinal cells (with pax6 genes); cell-type specific function in ganglionic neurons
apterous and lhx genes	Role in brain, neural tube, olfactory tube	cell-type specific function in sensory neurons and in pathfinding activity of interneurons
caudal and cdx	Gut	Control of cell-type specific intestinal cell function

For example, you will often hear pax6 described as a 'master control gene for eye formation'; I've done that myself. It's a gene that is expressed in a pair of fields at the anterior end of the animal, where the eyes will form, and misexpressing it in other regions of the animal will induce eyes to form in ectopic locations, so it is easy to slip into the habit of thinking of it as the gene that makes an eye. It isn't. It would be better to consider it a component of a regulatory network of genes, characterized by an upstream pattern of regulation that induces its expression in a specifically localized anterior field, which in turn induces a pattern of downstream gene activity that will initiate development of a photoreceptor.

"It's a gene that makes an eye" is a heck of a lot easier to say.

The evolutionary significance of the more complex understanding of its role, though, is that the diverse eyes of multicellular animals may have evolved independently, but all use pax6 because it was part of a conserved module for activating genes needed for an eye.

In development, morphogenetic regulatory programs for pattern formation precede the institution of cell differentiation programs, but it is likely to have been the reverse in the evolution of body parts. This would allow for the continuing selective advantage, at each evolutionary stage, afforded by the respective differentiated cell functions. As an example, consider the famous case of pax6, a transcriptional regulator utilized in the morphogenesis of eyes in both insects and vertebrates. The common view is that this morphogenetic function of pax6 is a pleisiomorphy descendant from the common PDA. The alternative is that what is actually homologous in the role of the pax6 gene in the diversely constructed eyes of various bilaterians is only its function in the control of genes encoding visual pigments. All eyes of all kinds require visual pigment genes, and this is the pleisiomorphic role of pax6; the gene was later coopted for use in the different morphogenetic programs that produce the different structures on which the pigment cells are mounted in different creatures.

A related idea from Peterson and Davidson (2000) is that what was going on in pre-Cambrian metazoan evolution was the assembly of a sophisticated and flexible toolbox of genes that had specific functions in bilaterian ancestors, but could be readily redeployed for novel functions by regulatory changes—that is, the tools were all present and functional, and are still present as common elements in all metazoans, but what has changed is how they get used in development. Here is a pretty figure (click on it for a larger version) they used to illustrate a little bit of the history of major evolutionary inventions; one of their points is that all of these were in place before the Cambrian.

The point is that the genes we've studied to infer common descent are truly ancient, 600 million years old or more. What makes a jellyfish different from a human being isn't that we have Hox genes and they don't (because, as you can see, they do), but that evolution has elaborated on the control circuitry behind them.

By the time the crown group of Bilateria appeared, all signaling pathways and transcription factor families were present, because they are common to all modern bilaterians. The important conclusion follows that evolution of phylum-specific body plans does not depend on invention of new developmental genes but rather on novel gene regulatory circuitry. The advent of this circuitry, that is, of regional specification mechanisms including the Hox gene complex, occurred by the latest Precambrian if not before. In our view, it is likely that this was preceded by a long prior history of bilaterian micrometazoans similar in grade of organization to the primary larvae of modern bilaterians.

What they propose to have been different about those archaic bilaterian metazoans is that they relied more on lineage-dependent developmental processes; that is, that cells are immediately specified for a particular fate upon cleavage or before. This is the kind of pattern of development that generates larval forms in modern echinoderms and lophophorates and molluscs and others...all those animals that have a reasonably invariant embryogenesis to produce a characteristic larva. It's those late features in the diagram above, set-aside cells and regional specification mechanisms, that have increased the versatility of metazoan development. What they suggest is that the 'special' attribute of more complex animals is that they can set aside populations of relatively indeterminate cells in early embryogenesis that can later make decisions on the basis of positional information about how to differentiate.

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Erwin DH, Davidson EH (2002) The last common bilaterian ancestor . Development 129:3021-3032.

Peterson KJ, Davidson EH (2000) Regulatory evolution and the origin of the bilaterians. PNAS 97(9):4430-4433.

My feelings exactly

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