29 February 2008

Weekly sampler 8

It's snowing again. Cycling seems like a childhood memory. You'd think this would give me more opportunities to work on blog posts. Gah.

1. My friends and colleagues, Debbie and Loren Haarsma, were the subject of a nice local news story, focusing on their work as scientists and Christians. They have a superb new book out, which I've promised to review here sometime soon.

2. Is evolution too difficult or complicated for secondary students to grasp? This is a question that was discussed in the blogosphere recently, and even when religious/cultural debris is cleared away, I think the question is still a good one. (Add the religious/cultural influences back in, and you realize that teaching evolution at any level entails both the careful explication of the relevant principles and the careful dismantling of deliberately-introduced misinformation.) Some of the key concepts in evolutionary theory are decidedly non-intuitive. For example, I have the impression that it's just plain hard for people to get their heads around the notion of different species (let alone different families, orders, etc.) springing from a common ancestor. Maybe it's the ongoing influence of old errors (in this case, I think, orthogenesis), but I do wonder if common descent is one of those ideas that our kludgy brains just don't get straight off.

But of course that doesn't mean evolution can't be effectively taught to high schoolers. Algebra, after all, doesn't come naturally to most people, but I haven't seen anyone seriously propose that it be removed from high school curricula.

In fact, I think evolution is a lot like algebra. It takes time to teach right. It's a demanding subject, but it's within the capacity of high schoolers to understand. Levels of mastery and comprehension will vary significantly. Teachers who are poorly-trained and/or unprepared may do more harm than good. The main difference between evolution and algebra is this: there are no ministries or institutes devoted to hindering the work of algebra teachers. (Well, okay, there's MTV, but you get my point.)

3. And on that subject, PBS (WGBH Boston) has collaborated on the development of some resources for instructor professional development, with the aim of providing "the background and skills they need to counter pressures to present or address religiously based alternatives to the theory of evolution." The tools draw on materials from NOVA's "Judgment Day" episode on ID and Dover. I've only browsed, but there looks to be some very good stuff on the site. Maybe I'll comment further sometime.

4. Until this week, I was unaware of the ministry of Timothy Keller and Redeemer Presbyterian Church in New York City. Redeemer alone is an interesting and encouraging story, but now Keller has published a book in which he discusses (among other things) evolution. He was recently interviewed by First Things, and his comments were discussed extensively on the ASA listserv, where some errors (or simplifications) were dissected. It would be interesting to compare his thoughts with those of Tony Campolo: both accept evolutionary science, but "timidly" as one ASA commenter put it.

5. Oliver Sacks is now blogging (occasionally) at the New York Times, in a blog devoted to migraines. (Subtitled "Perspectives on a Headache." Ouch.) I'm not terribly interested in migraines, but if Oliver Sacks wrote an essay about sawdust, I'd read it with rabid anticipation. A recent piece on patterned visual sensations accompanying migraine auras begins with Sacks' description of his own experiences, and ends with musings on the potential universality of "self-organization," with the typical breathtaking Sacks prose beating the path. (Via Neurophilosophy.)

24 February 2008

What I would do with a time machine

I'd go here. I'm sure I could trade my time machine for a ticket.

The city's a flood
And our love turns to rust
We're beaten and blown by the wind
Trampled in dust

I'll show you a place
Where there's no sorrow and there's no shame
Where the streets have no name.
Sometimes these guys make me cry. It's all I can do.

23 February 2008

Crossing the divide

I recently recommended a very nice new blog by Mike Beidler called The Creation of an Evolutionist. It's subtitled "My journey from young earth creationism to evolutionary creationism," and it's downright fun to read. Mike is engaging and bright. He writes with enthusiasm and joy, so it's hard to imagine that his journey might have been difficult in places. But I'm sure it was.

Others have shared here and elsewhere about the trauma that many experience when considering the abandonment of creationism, an experience I mostly avoided because I never fully embraced creationism, and certainly never adopted a young-earth position. But it's easy for me to understand the emotional environment in which such struggles occur, and that's why I'm glad commenters like David O. have insisted on pointing out that the debunking of crude folk science (like the Reasons To Believe train wreck) is not helpful in the absence of a sound theological framework. Why? Because the obstacles that keep most Christians from embracing evolution and an ancient creation are not merely (or even mostly) academic in nature. They're deeper, much deeper than that: they're emotional, tied to the most basic ways by which Christians define themselves.

In the newest issue of Science, a remarkable News Focus piece tackles this very subject. You need a subscription to access the article online. I'll quote it extensively here, but if you are at all interested in this topic, I urge you to get a copy and read it. I find the article remarkable not just for its coverage of the issue, but for the fact that it is published in Science, one of the most prominent science journals in the world.

The article is "Crossing the divide," written by Jennifer Couzin, and it displays this tagline: "Like others who have rejected creationism and embraced evolution, paleontologist Stephen Godfrey is still recovering from the traumatic journey." Godfrey works at the Calvert Marine Museum in Chesapeake Bay; he was raised in a "fundamentalist" Christian environment but came to a "staunch acceptance of evolution."

Godfrey's "anguished path" began with his study of fossils. 'Anguished' sounds right:
With this shift came rejection from his religious community, estrangement from his parents, and, perhaps most difficult of all, a crisis of faith that endures.
After noting the immense emotional appeal of creationism and the cruel God-or-science choice it typically presents, Couzin observes:
People like Godfrey tend not to advertise their painful transition from creationist to evolutionist, certainly not to scientific peers. When doubts about creationism begin to nag, they have no one to turn to: not Christians in their community, who espouse a literal reading of the Bible and equate rejecting creationism with rejecting God, and not scientists, who often dismiss creationists as ignorant or lunatic.
Gosh, that paragraph about sums up one of my main goals as a Christian biologist: to offer fellow Christians at least one other choice. I hope it saddens you as much it does me, and it oughtn't matter whether you believe or not.

There are some rough spots and simplifications in the piece: Couzin refers to the "fateful apple" in Eden, for example, and seems to suggest that only "biblical literalists" hold that "belief is generally an all-or-nothing proposition." (Though I think I know what she means.) The descriptions of the harrowing journey from YECism to evolutionary creation, however, are raw and jarring. Woven into Godfrey's story are quotes from Denis Lamoureux, Brian Alters, and Christopher Smith, Godfrey's brother-in-law who is a Baptist pastor here in Michigan. But it is Godfrey's "anguished path" that is laid out in disheartening detail. Examination of fossil strata (and footprints therein) finally leads to the "explosion" of his YEC ideas.
Godfrey ran through bitterness, anger, and disappointment about having been deceived for so many years. He sought out creationists and confronted them. Late in graduate school, he and his devout Christian wife, mother-in-law, and mother attended a weekend symposium at a Bible school in New York state, where Godfrey says he angrily stood up at the end of a talk and argued passionately with the speaker.
Well...gulp. That reaction is understandable, even laudable, but I think Dr. Godfrey would agree that it's not the way that things should go for long. Indeed, he identifies at least some times when one ought to let sleeping dogs lie.
But sometimes, former creationists believe, changing minds is not worth the heartache it brings. Godfrey no longer considers evolution worth mentioning to his parents, now 78 and 79 years old, and he asked that they not be contacted for this article. “You can live your life just fine and not know squat about evolution,” he says.
The hardest parts of the story for me to read were those that described his parents' distress, convinced as they are that "their afterlife depends on embracing creationism." But before you conclude that he (or I) would embrace laissez faire, consider his passion here:
Just as he longs for biblical literalists to be more receptive to evolution, Godfrey also wishes that biologists would join the discussion. He was incensed 5 years ago when, participating in an evolution-creationism debate at Bishop’s University, where he once argued against the fossil record, no one from the biology department attended.
Ouch! Not in my house.

According to Couzin, "Godfrey is conflicted about how, and how forcefully, to press his case." He co-wrote a book with his brother-in-law; his father prayed that it would fail to be published at all, and Godfrey seems unconvinced that the book had any impact.

I want to hear voices like Godfrey's, and David Opderbeck's, and others who have traveled this "anguished path." I've explained elsewhere why I don't think laissez faire is always – or even usually – the right approach. But my path was far less anguished, and I never knew the complete isolation that so many of these wise people experienced. (Thank God.) So I'm listening.

Christendom cannot continue to construct and support folk science and desperate dishonesty. It must not continue to employ falsehood in the "defense" of the gospel. But the dismantling of these corrupt and toxic structures has to be done for the sake of the gospel, and not for any other reason.

That's my pledge. Hold me to it.

Weekly sampler 7

I still owe you a summary of Howard Van Till's address at the Grand Dialogue and something about Richard Colling's talk at Calvin. Plus I'm barely halfway through the "junk DNA" series, and I haven't gotten to the part where I show you just how irresponsible Hugh Ross and Reasons to Believe really are. Sorry about that; here are some of the things that have been distracting me.

1. Illusions can be creepy and exhilarating, as we discover the limits of the reliability of our own senses. More than that, they are useful tools in the construction of models of sensory processing by the brain, and thereby of theories of consciousness. At the excellent blog Cognitive Daily, Dave Munger presents a jaw-dropping optical illusion, and explains what it tells us about how visual information is handled by the brain. If you have built your worldview around the perfection of your sensory input, you might want to skip this one.

2. I've just started exploring this site, Comparative Mammalian Brain Collections, with the marvelous URL of brainmuseum.org. The section on brain evolution starts with a cool little march through mammalian brains, increasing in size. Look for the bat brains! There's even a link to a manitee brain site.

3. Speaking of the Colling lecture, you can find audio and Collings' slides on the Christian Perspectives in Science series site.

4. Anyone else considering a glimpse into their recent evolutionary past? I'd love to be able to afford the ~$200 for a trip down genetic memory lane, but it's not happening now. Someday, though, I'm sure I'll do it, since there's no way I can resist participating in something called the "Matheson Surname DNA Project." (Click on Results to see the interesting part.)

5. If this blog occasionally sails over your head, or gives you vertigo, here's a well-regarded online biology textbook, created by a community college in Arizona. What I've seen looks very good.

6. Genetic diversity among humans should be important and interesting to anyone who is concerned about human evolution, regardless of his/her viewpoint. Humans were once thought to be relatively poor in the genetic-variation department, but new findings (in the last 4 years or less) are painting a new and different picture. An entire supplemental issue of Nature Genetics was recently devoted to this subject, and Nature has just made that supplement freely available. Check out the commentary by Jonathan Sebat ("Major changes in our DNA lead to major changes in our thinking") and consider how these developments might be relevant to creationists.

20 February 2008

Tangled Bank and Encephalon

Two excellent new carnivals have gone up in the last day or so.

Yesterday it was Encephalon at SharpBrains. Encephalon is a neuroscience and psychology carnival that had been in hibernation for some months, and it's nice to see it back. My post on endocannabinoids is included in yesterday's edition.

And just posted on Greg Laden's Blog is Tangled Bank #99. It's loaded, as usual, with excellent and varied contributions.

18 February 2008

There goes the neighborhood.

Hide your valuables: my good friend and colleague Kevin Corcoran has invaded the blogosphere. His new blog is Holy Skin and Bone, and he's already out of the closet on evolution. Check out this post on the idiotic Darwin fish wars, and read his profile. Kevin and I hang in real life, and after a while on his blog (or immediately, if you read his published work) it will be clear why I have a label here called "Christian materialism." I learned it all from Kevin!

My 13-year-old daughter has a one-week-old blog as well, and I'll happily provide the URL when you've filled out a few forms.

17 February 2008

This is your fetal brain on drugs.

We interrupt this series on "junk DNA" and rampant folk science to bring you a months-overdue Journal Club.

I wonder how many of my readers remember this little tidbit of American genius:

I remember some very funny spoofs, mostly on T-shirts. (Back then, I think the Internet was still a toy for geeks at the NCSA.) "This is your brain. This is your brain on drugs. This is your brain on drugs with a side of bacon. Any questions?"

Marijuana, as I recall, was typically included as one of the frying pans that could turn your central nervous system into a not-very-heart-healthy staple at Denny's. It was – and probably still is – easy to get the impression that smoking pot would hollow out your skull and make you into the inspiration for a character played by Keanu Reeves.

But that's baloney. Long-term marijuana use is certainly not without effects on the brain (duh), but its most abundantly-documented pathological outcome is, well, stupidity. (Mild stupidity. How such an effect is detected in ResearchBlogging.organ American population is not so clear to me.) And gosh, if we intend to stamp out stupidity-enhancing behavior through legal action, we'd better send the Marines to Hollywood right now. Seriously, there are few well-established long-term negative effects of using cannabis, and most of those are associated with smoking marijuana and not with the neurological impact of cannabis itself. (Full disclosure: I have never had a joint to my lips, and the closest I've come to inhaling is second-hand at the occasional concert. It would seem that my stupidity has a different cause.)

The rules are different, though, when developing brains are the subject, and it doesn't matter whether the neuroactive substance is legal or not. Maybe pot doesn't mess up a young adult's brain, but that doesn't mean it won't affect a fetal brain. And in fact, some recent studies indicate that we should pay close attention to the possibility that fetal brain development is affected by cannabis. One of those studies, "Hardwiring the Brain: Endocannabinoids Shape Neuronal Connectivity" by Paul Berghuis and colleagues, published in Science last May, suggests that mammalian prenatal brain development is likely to be significantly impacted by cannabis. It's an interesting paper for that reason, and because it deals with two of the subjects of my own research: neuronal growth cones and Rho GTPase signaling. I'll briefly explain those terms later.

The active ingredient in pot is a chemical called Delta(9)-tetrahydrocannabinol, or THC. THC affects the brain by activating receptors on particular types of neurons in the brain, causing these neurons to release less of their neurotransmitters (the normal chemical signals used for communication among neurons). While a serious intelligent design proponent might need to claim that the "purpose" of these receptors is to help people respond to pot (to suppress nausea while on chemotherapy, for example), scientists instead sought and found the chemicals within the brain that normally act on these receptors. These chemicals are called endocannabinoids, signifying that they are cannabis-like but originate from within. (After biologists discovered the endocannabinoids, they subsequently discovered the receptors, but that's not an issue here.)

This means that a first step toward discovering the potential roles of endocannabinoids in brain development is the identification of the parts of the developing brain that display the receptors. If you know where the receptors are, then you know where the chemicals are likely to act. And those are the areas that are likely to be affected by cannabinoids like THC, that come from outside.

Neurons are the brain cells that send and receive electrical signals. A typical neuron has many (perhaps thousands) of dendrites, which receive signals from other neurons, and one axon, which transmits signals to other cells, often a great distance away.
A typical neuron. Image credit: NIH, NIDA

During brain development, neurons have to develop their magnificent and specific architectures. Beginning as a boring little round ball, a neuron has to sprout and extend dendrites and (typically) a single axon. The axon must somehow migrate to its final position, which may be in a completely different part of the body or right next door.

When Berghuis et al. looked for endocannabinoid receptors in the developing brain, they found them in the cerebral cortex, and specifically they found them in the growing axons of the cerebral cortex. In case you haven't been introduced to the cerebral cortex, it is thought to be responsible for "all forms of conscious experience."

Layers of the developing cerebral cortex of a mouse. The red streaks are developing axons that are displaying endocannabinoid receptors. From Berghuis et al., Figure 1D.

They found the receptors in other developing brain regions, too, and they showed that the endocannabinoids are likely to be produced in those regions at those times. The somewhat surprising result raises the possibility that cannabinoids affect how the brain develops, by affecting how the axons develop.

What might these effects be? The authors found that the receptors were clustered right at the growing tips of these developing axons. This region is called the growth cone, and it's one focus of my own research, because it's obviously the place where the axon is continuously elongating, and it's a place where the skeleton of the cell must be always remodeling.

The growth cone of a mouse neuron. The red indicates structural elements of the growth cone; the green blobs are endocannabinoid receptors, and the yellow smudges indicate where the red and green overlap. From Berghuis et al., Figure 2C.

If endocannabinoid receptors are located right on the growth cone, then they are positioned to influence speed and direction of axon outgrowth. Yikes!

Okay, so endocannabinoids (and, of course, THC from pot smoke) are uniquely positioned to affect growing axons in the brain. But what's the effect? The authors show that one effect is the inhibition of steering mechanisms in the growth cone. In my favorite experiment, they put neurons into an electric field, where the growth cones tend to steer toward the negative pole. When the neurons were treated with an endocannabinoid, they failed to show this preference.

Axon growth in an electric field. Each black tracing represents the behavior of one axon. On the left, notice that untreated axons tend to grow toward the negative pole (left side), and many of those that are growing toward the positive pole are turning away from it. On the far right, notice that axons treated with the endocannabinoid grow in every direction and don't care about the electric field; the center shows how they grow when there's no electric field at all. From Berghuis et al., Figure 3D .

The authors went on to show that this effect seems to result from the activation of a well-known signaling system inside cells, mediated by a protein called RhoA. RhoA is a Rho GTPase, and I'll spare you the details since you've probably read all my papers already. :-) What matters is this: Rho signaling is known to be involved in axon growth, and is generally a negative influence on axon growth. In fact, some attempts to stimulate axon growth in the spinal cord after injury (and paralysis) are focused on the inactivation of RhoA and its partners. So this connection between endocannabinoids and Rho GTPases is further evidence of a specific – and likely negative – influence of cannabinoids on axon outgrowth in the developing brain.

But is there any evidence of a specific effect on brain development, in an animal? The final experiment presented in the paper is a genetic experiment, in which the authors examined the brains of mice in which the endocannabinoid receptor (one in particular) was genetically deleted in certain parts of the brain. And they found that certain neurons in the cerebral cortex of these mutant mice had lost almost half of their inputs, presumably due to the inability of the incoming axons to find their way to the recipient neurons. In other words, when the receptors were deleted from a subpopulation of neurons, those neurons evidently had trouble making their normal connections.

What this means is that to whatever extent the human brain resembles the mouse brain with regard to expression of cannabinoid receptors and their function in growth cones, the developing human brain is potentially vulnerable to damage, or at least alteration, by exposure to THC. And as the authors note, this may partly explain recent findings (in rats) that point to permanent alterations in brain function in pot users – alterations that may predispose these people to much more serious addictions.

I've long been inclined to skepticism regarding anti-pot hysteria, and I strongly support efforts to legalize and legitimize medical use of cannabis. But these data should make us look hard at the potential implications of cannabis exposure during human development.
Article(s) discussed in this post:

  • Berghuis, P., et al. (2007) Hardwiring the Brain: Endocannabinoids Shape Neuronal Connectivity. Science 316:1212-1216.

14 February 2008

Weekly sampler 6

I suppose I should report on the activities I mentioned in last week's sampler. Phil Keaggy was fun: the first set was a complete – and, I'm told, "verbatim" – rendition of the 1978 instrumental album The Master and the Musician. I'm neither an audiophile nor a musician, but I liked Keaggy's guitar and especially liked the band behind him. The second set included a little too much Christian pop for my taste.

U23D was great, but we all thought it was too short. And we wished the folks running the IMAX theater would have turned the sound up. (Way up. It's rock and roll.) But that just means we loved it. "Streets" was a high point, and the transition from "Love and Peace or Else" to "Sunday Bloody Sunday" (via Bono on a solo drum) was vintage U2 melodrama.

Saturday's Grand Dialogue keynote lecture by Howard Van Till was superb, and I'll post separately on my impressions of his talk. For now, I'll just note that while I'm a "traditional theist" who happily affirms creeds and confessions of historic Christianity ("tribal orthodoxy" to some) and therefore quite theologically distinct from Howard (or so it seems), I find myself in passionate agreement with just about everything he says. And besides, he reminds me of Bono:
The more you see the less you know
The less you find out as you go
I knew much more then than I do now.
– U2, "City of Blinding Lights"

I don’t know as much as I used to.
– Howard Van Till, 9 February 2008
Howard's remark, part of his response to an incoherently rambling "comment" from the audience after his lecture, drew significant applause. My post will include his extensive outline along with my impressions, and I'm told that audio and/or video will be posted on the Grand Dialogue site at some point.

Now some new morsels.

1. In a past Journal Club, I described work by Joe Thornton's group in which they "resurrected" ancient proteins and examined their properties, thereby assembling an evolutionary history of steroid receptors. Ian Musgrave at Panda's Thumb reviews a recent report that employs a similar strategy, looking much deeper into life's history.

2. Steve Martin at An Evangelical Dialogue on Evolution posts some typically thoughtful and informed reflections on Tony Campolo's Darwin/Hitler piece last month. He doesn't say what he thought of the exchange I had with David Opderbeck in the comments after my own post on the topic. I'm curious.

3. One way to avoid making a fool of oneself while discussing evolution is to understand the concept of a phylogenetic tree. Ryan Gregory has just published an article on the subject, in the online journal Evolution: Education and Outreach. Read it, and promise me you'll never claim that biologists believe that humans have chimps as ancestors. (Image on right: Darwin's first tree, from an 1837 notebook.)

4. Tuesday was Darwin Day, on the occasion of his 199th birthday. How did I celebrate? I think I spent much of that day working with cells and wrestling with DNA sequence analysis, but hey, every day is Darwin Day. :-) Last week's issue of Nature includes a somewhat more substantive tribute, an article by Kevin Padian, "Darwin's enduring legacy," in which he "looks forward to a season of celebration by outlining how Darwin’s ideas changed scientific thinking." The article touches on 10 topics that "hint at the magnitude of the man's legacy," and it's worth the trouble to get a copy if you're looking for an overview of the big ideas that are legitimately attached to Darwin's name.

I was drawn to the last topic: gradual change. Some of the most vituperative disputes in evolutionary science surround this concept. (Witness the recent eruption of rancor after Olivia Judson's piece on "hopeful monsters" and saltationism.) Padian notes that Darwin is correctly remembered as a proponent of gradual evolutionary change. Then:
But what did he mean by ‘gradual’? Most dictionary definitions have it as ‘slow and steady’, and this is indeed one meaning that Darwin used. There is another.
What is the other meaning? Well, consider the word: gradual. As in graded. Padian describes how Darwin noted the graded, stepwise aspects of geologic history as recorded on cliff faces. He described these transitions as "gradual," but did not mean that they were "slow and steady." Padian concludes that Darwin understood – and meant to highlight – both senses of the word 'gradual.'
This conceptual tension between ‘slow and steady’ and ‘step-like’ is the basis of one of the most important evolutionary ideas of the twentieth century: punctuated equilibria. This generalization is based on myriad fossil examples showing that the morphology of species may not change appreciably for much or most of their history, then alter relatively rapidly. If this turns out to be the predominant pattern of evolution in well-preserved fossil sequences, as now seems to be the case, Darwin’s view of the plurality of evolutionary tempos and modes will be vindicated.
Punk eek as Darwin's idea? I like it.

5. Just announced: the 2008 schedule for the Michigan Shakespeare Festival. All's Well That Ends Well and Julius Caesar. All's Well will be a new one for me. We're talking about a family vacation in Jackson. No joke!

11 February 2008

Talking trash about "junk DNA": lies about "function" (part I)

Look, in short, at practically anything – the coot's feet, the mantis's face, a banana, the human ear – and see that not only did the creator create everything, but that he is apt to create anything. He'll stop at nothing.

There is no one standing over evolution with a blue pencil to say, "Now that one, there, is absolutely ridiculous, and I won't have it." If the creature makes it, it gets a "stet." Is our taste so much better than the creator's?
– from Pilgrim at Tinker Creek by Annie Dillard. Harper & Row (1974), p. 135.
God's creative work is ideal. If (as the songwriter David expressed in Psalm 8) the all-powerful, all-knowing Creator made the universe and all that's in it, then people can expect to see superior designs throughout the natural realm.

For those who agree with Darwin's view, any example of nature's imperfection contradicts the notion of a divine creation. As a result, many naturalists regard "junk" DNA as among the most potent evidences for biological evolution.
– from Who Was Adam? by Fazale Rana with Hugh Ross, NavPress (2005), p. 227.
Several weeks ago, I started this series on "junk DNA" by noting that the shoddy nature of anti-evolution folk science is rarely more clearly displayed than in discussions of genomic and genetic findings that are aptly explained by common descent. In that introduction, I noted three overall ways in which creationists – as typified by the apologists at Reasons To Believe (RTB) and the Discovery Institute (DI) – distort and/or ignore the facts about non-coding DNA. The first and most important of these errors regarding "junk DNA" is the claim that "junk DNA" is functional and that this therefore falsifies evolutionary hypotheses regarding its origin.

Hacking through the thicket of disinformation is going to be messy. We're not dealing with a single bogus idea or an isolated pseudo-factoid. We're approaching a quagmire of folk science, some of which is so grotesquely flawed that it's not even wrong. Like most well-designed folk science, the creationist "junk DNA" fables contain just enough factual information to give off the aroma of scientific credibility. As Obi-Wan once said [wink], "We must be cautious."

So what is "junk DNA"? It's a confusing term, and I am one of many scientists who never liked it and never used it. I'll have more on the history of the term elsewhere, but for now we'll use it the way anti-evolutionists (RTB/DI/AiG) use it: "junk DNA" is non-coding DNA, meaning that it is DNA that does not directly specify the code for making proteins. Here is a map of the makeup of the human genome, indicating the relative abundance of various categories of DNA:

Image from Molecular Biology of the Cell online, Alberts et al., 2002.

It's worth taking a few minutes to look at the diagram carefully. Notice that more than half (53%) of the human genome consists of "repeats," meaning certain types of sequences that occur multiple times in the genome. Notice also that relatively little of the genome is identifiably devoted to genes (pink + red in the diagram), and a very tiny proportion (1.5% or so) is devoted to the encoding of proteins (red).

Now, that means that 98.5% of the human genome is non-coding DNA. When creationists define "junk DNA" as non-coding DNA, they're referring to 98.5% of the human genome.

In the next two posts, I will comment extensively on this main error: the claim that "junk DNA" is functional and that this therefore falsifies evolutionary hypotheses regarding its origin. There are actually two falsehoods in that claim. This post, part I, will focus on the first one, and the next post will tackle the second.

Falsehood number 1. Evolutionists said that "junk DNA" has no function. But new evidence shows that "junk DNA" has important functions.

This kind of obfuscatory crap really annoys me. It's all over RTB and DI, and it's rampant in creationism in general right now. Both aspects of this claim are bogus.

First, it's just not true that biologists have ever claimed or assumed that 98.5% of the human genome has no function. Ryan Gregory is an evolutionary genomics researcher who has explained just how inaccurate this insidious claim really is, and his blog is required reading for anyone who wants to know more about "junk DNA" and evolutionary genetics. The short story is that biologists have adopted a range of stances toward non-coding DNA, from assuming that it is mostly functional to assuming that it is mostly parasitic. Those biologists, past and present, who would claim that it is mostly functional will readily note that useless parasitic DNA is likely to be abundant in most genomes; those who would emphasize the parasitic or artifactual nature of much of the human genome will readily (and eagerly) note the fact that such elements can and do get co-opted and put to work by the organism. To claim, as Hugh Ross does in Creation as Science (p. 168), that biologists assumed that the "non-protein-coding part of the genome served no purpose" is to promulgate a falsehood.

It's a falsehood, and it's not just irresponsible. It's downright silly. Biologists knew, for example – from very early on – that genetic control regions in the genome are not typically found in protein-coding segments. Only an ignoramus would have assumed or postulated that only protein-coding regions of a genome were functional.

Much worse, though, is this: many of the creationists cited here add another layer of dishonesty to this sick fable. They claim (DI / AIG) that because "Darwinists" assumed that much of the human genome had "no function," biologists failed to study it, and progress in understanding the genome was impeded. At DI, Casey Luskin even claims that this assumption hindered "research into understanding cancer and diabetes." This is how Hugh Ross puts it in Creation as Science (p. 192):
The assumption that naturalistic evolution governs the the history of life on Earth, for example, led to the deduction that the genomes for advanced species predominantly contain useless junk – the accumulation of millions of generations' worth of genetic accidents. This inference led to the 30-year abandonment of research into possible functions of non-protein-coding DNA, the so-called junk DNA.
I believe it is important for folks to understand that Ross and Luskin – and other creationists making this claim – are not telling the truth. If you take only one thing from this post, let it be this: the creationist claim that biologists ignored non-coding DNA for 30 years – because of the assumption that it was all non-functional – is a shameful lie.

Now, that's a pretty serious allegation, so you should expect me to present evidence. First, if you haven't already read Ryan Gregory on the history of the idea of "junk DNA," do it soon. Then, if you're interested and/or skeptical, check out this recent post in which I have a look into the scientific literature over the past 30 years.

The second aspect of this grand creationist lie is the claim that "junk DNA" is functional. And here's where things get a little sticky. Look carefully at a typical creationist argument of this type. It goes like this:
  1. Evolutionists say (or said) that "junk DNA" has no function. (This is a lie, but we already covered that.)
  2. But here is a paper describing a non-coding DNA element that has a biological function.
  3. Therefore, "junk DNA" is functional.
The error here is pretty simple, but I think the argument typically exerts its influence first by virtue of the dishonest first premise, and then by an impressive-sounding (and usually perfectly accurate) discussion of a recent discovery in biology. The bogus conclusion is thus easier to smuggle in, especially if the audience isn't thinking carefully or is otherwise overly credulous.

Here's how to see the error (if it's not already obvious):
  1. Insurance companies say that any 1989 Yugo is worthless and has no utility of any kind. They were crap when they were new, and they're worse than that now.
  2. But let me tell you a story about a 1989 Yugo that is being used as a perfectly good mailbox (or church confessional, or shower).
  3. Therefore, 1989 Yugos are valuable and useful.
Think about it: that first statement can't be right. Insurance companies probably don't say it just like that, and certainly they don't mean that an old Yugo can't be put to some good use. If you showed them one that actually runs, and proved that you drive it to work once a week, they would happily admit that it has some value. But who cares about that anyway? It's a red herring, and it's wrong to boot. Just forget about that silly first claim for a second, and follow the rest of the argument.

It's plain ludicrous. Of course some 1989 Yugos are valuable and useful, but that hardly means that 1989 Yugos are generally valuable at all. If you met someone who asserted that 1989 Yugos were "functional," and who claimed that those who say otherwise are involved in a nefarious conspiracy, you would probably take careful note of the locations of the exits.

There are several interesting types of non-coding elements found in animal genomes, existing in hundreds to thousands to millions of copies. Many of them have well-known properties (the subject of a future post), and many are like Yugos, or rocks, or logs, or roadkill: they're junk, but junk that may, occasionally, be put to use. Biologists have long known this, and suspected from the very beginning that even parasitic DNA elements would occasionally be co-opted by their hosts.

Once you understand what scientists really know about non-coding DNA, and how the history of its study has been systematically misrepresented by Hugh Ross, Casey Luskin, and other careless or unscrupulous creationists, you should see the "junk DNA" fable as inexcusably dishonest. And if you're a Christian, you should worry about your reputation.

I know I do.

10 February 2008

Talking trash about "junk DNA": lies about genomic research

In another post in this ongoing series, we looked at creationist distortions of the nature of research into non-coding DNA, or "junk DNA." There I mention how creationists of all stripes are quite fond of the claim that "Darwinist" assumptions led to the labeling of all non-coding DNA as non-functional, and thereby to the neglect of research in the field for three decades. I've been in biology for most of those 30 years, and I know this claim to be dishonest. But if you want to see for yourself, it's easy enough to determine whether the claim is true (or reasonable, at least). One way to check is to ask someone who actually knows the field (as opposed to, say, a lawyer or a former physicist). Another approach is to look at the evidence in the scientific literature. That's what I did, and here's how it went.

I used PubMed, the standard online (free) database of the biomedical literature, to search for various terms during different time frames. I limited the searches to articles written in English. In each graph, the vertical axis indicates number of unique scientific articles containing the phrase, and the horizontal axis indicates publication date, in five-year intervals. First, let's see how often we find the phrase 'junk DNA' and the related phrase 'selfish DNA.'

Things to notice about this graph:
  1. Neither phrase appears at all before 1970, and the phrase 'selfish DNA' doesn't appear till 1980.
  2. The use of both terms has steadily increased over time.
  3. The terms are extremely rare in the scientific literature. Total number of uses of 'junk DNA' in the past 40 years: 73.
Now, you might think this is pretty strong evidence in favor of the claim that the 'junk' assumption shut down research. Well, let's see. Ever heard of "satellite DNA?" That was an early term for a particular kind of non-coding DNA, composed of lots of small repeated sequences. Contrary to the dishonest claims of Ross and Co., satellite DNA was thought to be functionally relevant from its first description, and hypotheses regarding its roles were being vigorously tested before 1979. Folks, if all you did was read up on satellite DNA, you'd know enough to realize that neither RTB nor DI are telling you the truth about non-coding DNA. But let's see if it gets worse. (It does, of course.)

How much research has been focused on satellite DNA? Here's the graph:

If you look really hard you can see the little blue bars that show you the use of the term 'junk DNA.' And now you know why I am baffled as to why an honest person (much less a responsible Christian) would make a big deal out of the term 'junk DNA.' Biologists sure haven't. And now you know something else: research on satellite DNA was robust, and growing, throughout the 30 years following the first references to 'junk DNA.' Total number of papers that use the term: 4214. We could stop there. But we're just getting started.

You might have noticed that satellite DNA research seems to have peaked in the early 90's, and fallen off since. What's up with that? Heh. As methods for analysis of DNA and genomes improved, biologists recognized that satellite DNA could be categorized into two broad types: minisatellites and microsatellites. The technical differences don't concern us, but I think this graph will make it clear why the term 'satellite DNA' has become less prominent in the biomedical literature:
Got it? The new term was catching on, and replacing the old term. And what about microsatellites?

That's quite a different story, now isn't it?
Recapping so far – total numbers of articles, to date, using these phrases:

Junk DNA
Satellite DNA

What about introns? Those are the pieces of DNA interspersed in most genes (of organisms other than bacteria), pieces which are chopped out of the message before it's translated into protein. They're non-coding DNA, and therefore "junk" according to our creationist pundits. Question: how did research on introns fare during those 30 dark years of neglect?
Answer: pretty darn well. Total number of hits: 37,830.

Had enough? We could analyze research on ERVs, LINEs, SINEs, centromeres, telomeres... but I think it's clear enough that the fable about the evil Darwinists who killed an entire area of research, and with it countless victims of colon cancer and diabetes, is just a damned lie.

If you're just a Christian who's been reading this stuff, stop spreading the disease, and either give up the pointless opposition to common descent or find more respectable ways to defend your position.

If you're a Christian who's been writing this stuff, apologize, purge, re-orient, and maybe re-think. Your folk science is toxic, and our faith doesn't need "help" like that.

08 February 2008

Random Design author at Calvin

Some of you might remember the disheartening events at Olivet Nazarene University several months ago: a biology professor's book banned and the professor removed from intro classrooms, due to his authorship of a book that was unpopular with donors and trustees. The professor is Richard Colling, and the book is Random Designer. You'll find a lot of information at Threads from Henry's Web, including a series of blogs on the book and extensive commentary by Colling in response.

Well, Prof. Colling will be visiting Calvin next Friday, speaking in our Christian Perspectives in Science seminar series. Here's his abstract:
The history books of life – fossils and DNA – reveal a most remarkable creation story. Over unfathomable eons of prescribed life and death cycles, single-celled life has advanced as a divine, majestic, and interconnected web. Filling every niche of our dynamic ever-changing planet, evolutionary creation has miraculously culminated in sentient beings capable of self and God-awareness – us! As Christians desiring to remain faithful and culturally credible in our claim that God is the creator and that all truth is God’s truth, we are challenged to work together across faith boundaries seeking ways to effectively integrate knowledge from science into a dynamic and coherent faith. This talk introduces a new creation “logos” – Random (Equal Opportunity) Design. Simple, but ultimately profound, random design reflects a God-ordained and sustained paradigm of astonishing creative genius that produces an integrated network of unrivaled biological development. The talk includes defining appropriate definitions of randomness, the importance of adequate information/dot development, examples of randomness generating remarkable biological order, and a call to expand traditional views of scripture and science to accommodate a bigger, more profound God.
Looking forward to it.

07 February 2008

Weekly sampler 5

Well, the Pats lost, and I was a little disappointed (I'm a huge fan of Tedy Bruschi, Arizona '95), although I've always loved upsets and underdogs. More importantly, I enjoyed seeing my hometown in the spotlight. (I grew up in west Phoenix, just a mile from Glendale, and 8.5 miles from the stadium.) That's all the football you'll get on this blog, though. Pitchers and catchers report in 6 days...now that's blogworthy.

1. David Sloan Wilson has a four-part series on the New Atheists on the Huffington Post, which I discovered while visiting Rationally Speaking, Massimo Pigliucci's blog. Pigliucci is a first-rate evolutionary biologist and a savvy commentator, and I recommend the blog highly. (His review of Michael Lynch's new book is a nice little introduction to the geneticists-vs.-the-world disputes in modern evolutionary science.) I read Pigliucci's critique, but I haven't read through the Wilson series. Anyone? I'll even provide the links: Part I Part II Part III Part IV.

2. I just finished reading Gordon Glover's Beyond the Firmament, and I'll have a review in print in the near future. But here's a freebie for all 156 of my blog readers. I'm frequently asked, "Can you recommend a good book on evolution that would cover all that stuff you were talking about?" And I've never had a good answer. "Well, you can read this, and that, and that, and this, and... well, just go the ASA web site." Or lately: "Try my blog." (Thinking, of course, that they'll follow links to good sites like Steve Martin's or Gordon's.) Well, now I have a great answer: "Get a hold of Beyond the Firmament by Gordon Glover." I'm going to buy a few copies and hand them out. That's how good it is.

3. I'll soon review Deborah and Loren Haarsma's new book here, and will give it similarly high marks. It's called Origins: A Reformed Look at Creation, Design, & Evolution, and it's aimed a little differently than Beyond the Firmament, but provides another very good answer to the question above.

4. At wonderful Park Street Church in Boston, which I've mentioned here before, senior minister Gordon Hugenberger is preaching a significant series on creation and science, and specifically on Psalm 19. The series (available streaming or as a podcast) started on November 25, includes three Sundays in December, and apparently resumed this last Sunday. I'm still working through them, but Gordon's sermons are always worth the trip. (I loathe "Christian radio," but most Sunday mornings in Massachusetts, I turned it on in order to listen to Gordon's preaching. Our family attended the evening service, where we had the privilege of hearing Daniel Harrell, in the flesh.) On the ASA listserv, David Opderbeck recommends some sermons at another fine church in Massachusetts, Grace Chapel. I believe the sermons in question are under "Tough Questions. Honest Answers."

5. An odd story this week: a peer-reviewed science journal, Proteomics, published (online) a paper with this title: "Mitochondria, the Missing Link Between Body and Soul: Proteomic Prospective Evidence." Wait..."body and soul"? The article reportedly includes "sections with language supporting the idea of creationism." PZ Myers is quoted in that Chronicle report, which also mentions plagiarism.

6. A teaser for an upcoming journal club, from a paper published about a year and a half ago:

For now, just enjoy the picture and think about bats. As in flying mammals, Manny. Image from an article in PNAS, 10 October 2006.

7. Larry Moran has started a series on "junk DNA" at Sandwalk. My series will get back underway this weekend, though maybe by then it'll just be a list of links to Larry and Ryan Gregory.

8. This weekend is Evolution Weekend. How am I celebrating? Saturday I'll be at the Grand Dialogue, mostly to hear Howard Van Till, but also hoping to bump into some fellow Michigan-based bloggers (and you know who you are). I'll blog it, live if there's wireless access for visitors. Saturday night it's Phil Keaggy in concert at Calvin. I'm not a Christian music fan but I have it on good authority that this one's not to be missed. Sunday a bunch of us are driving to Lansing so we can see U23D on the IMAX screen. "Now you get to see the lard-arse 40-foot tall." Can't wait! Now that's a weekend.

05 February 2008

Tangled Bank #98

Hey! Welcome to Tangled Bank #98, and thanks for stopping by. If you've never been to Quintessence of Dust, the lobby is below and to the right. I hope you'll poke around a little.

PZ didn't give me a budget for refreshments, but if you come to the house I'll make sure we at least have plenty of guacamole. Chips are here, and beer is over there. Our city was once used by Anne Lamott as a metaphor for plainness, but it's much cooler than most people think. You can get to our house on a nice bus system, and after the carnival we can pick one of two Ethiopian restaurants. My day job is at Calvin College, but right now I'm on sabbatical in the lab of a friend and collaborator at the Van Andel Institute in downtown Grand Rapids.

I know a junior-high science and math teacher who displayed a poster on her classroom wall that read, "Free knowledge: bring your own container." The image, of course, was a human brain. That's how I feel about the blogosphere, and if there's a theme for this Tangled Bank, that's it, although "junk DNA," the plague, heat (you'll see), sex and food are some other keywords. The last two are personal favorites, so...let's eat!

Is that a shrew eating a cephalopod? A shrew gagging on a cephalopod? A grey-faced sengi gagging on a cephalopod? You probably know what it is; if you don't, head over to The Daily Mammal and check out today's special. Ambitious and beautiful. Maybe it'll be beetles next; that'd take, what, 50 years?

Uh, "grey-faced sengi?" Like Matheson knows what that is. But Brian does, despite being "educated" at Rutgers. See one, and read about it, at Laelaps.

"Indisputably cute" is how the pika is described at The Beagle Project. The article is a fascinating lesson on natural selection, and it features the cute pikas and their remarkable colonization of high, cold regions. It's Detecting natural selection: a pika's tale.

Lots of those cute daily mammals have provided hot meals to pit vipers, and especially rattlers. Curious? Of course you are. Rigor Vitae is worth a look just because of the name, but today the article to read is A Serpent's Tail, exploring the rattle and discussing a new member of this charming group of creatures.

If you prefer birds, have a look at the White-Cheeked Pintails at 10,000 Birds. Mike says they "seem perfectly suited to that relaxed West Indies environment." We're expecting 10" of snow in the next 12 hours. Harrumph, Mike. Gorgeous birds, though.

What do hummingbirds and rattlesnakes have in common? Well, some hummingbirds use their tails to make sounds. Cool sounds, too: one species (Anna's hummingbird) makes a "high-frequency chirp...during his display dive." Read more about this Novel mechanism for sound production in birds at Behavioral Ecology Blog.

It's a famous question: "What good is half a wing?" GrrlScientist recaps a very recent paper examining mechanisms of evolution of flight in her post Flying Lessons: Additional Insight into the Evolution of Flight in Birds at Living the Scientific Life. (Warning: Living the Scientific Life is a carnival unto itself, so be sure to read just one article and hurry back.) One of my first posts on Quintessence of Dust reviewed an article on bird evolution and genome size; check it out if you get the chance.

Want weird? How 'bout "cactus animals"? Technically, they're chancelloriids, and they're in the spotlight at Catalogue of Organisms in Scleritome Week: The Cactus Animals.

At Invasive Species Weblog read about how flame retardants are likely to provide assistance to invasive plants, one of which is known to make wildfires worse. We Didn't Start the Fire...or maybe we did will wipe that Tangled Bank smile right off your face.

This should help. Go to PodBlack Cat's Blog and feast on this celebration of science and poetry: Nothing In the 'Verse Can Stop Me. In The Bath should prepare you well for a segue into, um, reproductive biology – read it, then go straight to The Tree of Life and ask yourself, "Is that a sex organ on the cover of Nature?" Check out the comments.

Proceed immediately to Not Exactly Rocket Science and read Sex runs hot and cold. Well, okay, the full title is "Sex runs hot and cold – why does temperature control the gender of Jacky dragons?" but we were on a roll with the sex thing and I didn't want to lose our momentum. The post reviews a recent study that addresses a longstanding question in evolutionary biology regarding sex determination.

Have you "worked up a good sweat" at this point? At Swans on Tea you can learn about how "a good sweat" can be too much of a good thing. Read No Sweat, and bring a towel.

Lemme guess: you're hungry now. :-) Let's carb-load on biblical pasta. No really: our server at VWXYNot? reviews "Ezekiel 4:9 Penne" in Holy Penne, Batman. Best line: "I tend to be in favour of the separation of church and dinner, but this stuff was quite tasty." So you prefer potatoes? Greg Laden writes in The Great Potato Origins Debate May Be Settled that the history of the European potato may need to be rewritten, and along with it our understanding of potato blight. And at rENNISance woman, Cath Ennis reviews recent work on the role of diet in evolutionary divergence (with regard to gene expression). She asks "Are we really evolving, or just eating too many Big Macs?" I'd say both...

I think "negligible senescence" sounds like a great name for a band, but it's also an interesting topic in evolutionary biology. Some organisms just don't age. (Like Mick Jagger. Or not.) Explore recent work on this subject at Ouroboros, in a pair of posts: The evolution of negligible senescence and The evolution of negligible senescence, part II: Organisms that are remotely like us.

Recently, The Black Death was featured prominently on some of the finest science blogs around. But a Black Death Carnival just doesn't sound right, so the plague is here on our house. Aetiology included an entire series on the topic of "What caused the Black Plague?" Retrospectacle ran five posts on the Black Death. And Archaeozoology discusses Yersinia pestis, ancient DNA and the Black Death. It's a sub-carnival of death that's worth a chunk of your remaining time on earth.

After all that heavy Black Death stuff, read about The Galaxy that ate Detroit. Why Detroit? Maybe Phil at Bad Astronomy is a White Sox fan. And is this biology? Well, it involves eating, doesn't it?

Oh, speaking of eating (again), go back to Living the Scientific Life to see how certain parasites make sure that they get from one host to another. Berry butts! Yum!

From red butts on ants to... well, have you ever wondered whether red leaves can still perform photosynthesis? Get to Further Thoughts to find the answer.

Punctuated equilibria made headlines in the blogosphere last week. To learn more about the dustup, and about the issues involved, go to Sandwalk and read Larry Moran on Macromutations and Punctuated Equilibria. Then check out a very interesting follow-up at HENRY, illustrating principles of Punctuated equilibrium and the evolution of languages.

Assessing Diversity in the Past is a detailed examination of another recent discussion of evolutionary biology on the blogs. Mike at The Questionable Authority works through a recent paper on recovery of ecosystems after the end-Permian mass extinction. People pay serious money for education like this.

Creationists make mischief with the term "junk DNA," and I'm working on a series on the subject. But the real work has already been done by Ryan Gregory at Genomicron. On his new blog, DNA & Diversity, he reposts a review of the topic – Junk DNA: function and non-function.
On the same subject, at The Open Helix Blog, you'll find a review of a recent article on non-coding RNA: Non-coding, non-functional or junk ncRNA. Pseudogenes are one kind of "junk DNA," and Science and Reason provides a basic overview in Human gene count drops again.

All this genomic analysis required DNA sequencing, and that process is becoming far faster and cheaper. Michael White at Adaptive Complexity explains in What Next Generation DNA Sequencing Means For You. And what about the converse – building custom genomes? Jim at from Archaea to Zeaxanthol provides a Synthetic life followup, commenting on the recent announcement of the first human-made genome.

If there's anything left of your brain at this point, drag it over to SharpBrains and read Looking inside the Brain: Is my Brain Fit? to learn some basics about brain imaging and the concept of "cognitive reserve."

At Pure Pedantry, Jake describes How tool use is encoded in the brain, reviewing some very recent and intriguing neuroscience. Turns out the tool is treated by the brain as a part of the body! [joke deleted]

Down Syndrome (Trisomy 21) is well-known for (among other things) its effects on the nervous system. Less widely recognized is apparent resistance to solid tumor formation in Down sufferers. At Guadalupe Storm-Petrel, barn owl discusses a recent report on this topic in Down Syndrome Mouse Models: Trisomy Represses Formation of Intestinal Tumors.

How's this for an interesting question: "Would you vaccinate against drug abuse?" Would you vaccinate against, say, cocaine? This has been recently proposed, and DrugMonkey explains the ins and outs before posing the tough questions.

Vaccination makes me think of homeopathy. (Poo.) Evolved and Rational contributes A skeptical look at homeopathy.

At Effect Measure, Revere patiently explains the potentially alarming but surely complex situation leading to "an unexpectedly high rate of Tamiflu resistance" in European influenza this year. The article is Tamiflu resistance in seasonal flu: the devil is in the details.

Okay, we're almost at the end. But before we hit the bottom, get acquainted with ResearchBlogging.org by reading the introduction at BPR3. Most of the posts in this carnival were flying the ResearchBlogging icon, and the aggregator is a great resource in which to find quality science blogging. Free education!

Deep Sea News belongs at the bottom, I think, although the subject is about The Beginning. Check out Hydrothermal Vents, Life and Everything Else to learn about The Lost City and carbonate chimneys.

Here ends Tangled Bank #98. Thanks for coming by. The 99th Edition will be hosted by Greg Laden's Blog on Wednesday, February 20.
Image credits: star-nosed mole from this post at The Daily Mammal; others created at this sign generator site.

03 February 2008

Call for submissions: Tangled Bank #98

The next Tangled Bank science blog carnival will be here at Quintessence of Dust on Wednesday. Send me your submissions!

The previous edition included articles on cooking & evolution, shower temperatures, dental plaque, and plant identification, all with a theme of keeping warm. (The Mind is a whiner.)

01 February 2008

Weekly sampler 4

This week's theme is, um, "fun with biology." Seemed apropos after all the bickering I did this week. Which I'll mention as well.

1. So I assume you saw that Craig Venter's outfit produced the first "synthetic genome" recently. All this means is that they synthesized a very long piece of DNA, and included within it all the components known to be necessary for bacterial life. The simplistic line is that this is "synthetic life"; the standard scientific caveat is that this human-made genome hasn't been used to direct an actual organism. Yet.

2. And I'm guessing that you heard that the makers of this synthetic genome included within it a "coded message." The message itself is pretty uninspiring. ("METHINKS IT IS LIKE A WEASEL" would have been perfect, but anything would be better than the name of a company and its techies. Boooooorrrrrring!)

3. Well, what kind of message would you put into a genome? And by the way, it's not a completely silly question; it will soon be easy enough to do, and will take the place of name an asteroid/star after yourself/loved one as the latest vanity gift. Want to check it out? First you need to have a look at the alphabet that's available. Don't worry – it's not just A,T,G,C. That's the DNA alphabet, which is translated into the protein alphabet. The means of translation is what is commonly called the genetic code: each three-letter DNA "word" is translated (via RNA) into a single amino acid, a string of which adds up to a protein. There are 20 different amino acids in nature, and scientists have devised a single-letter abbreviation system to facilitate the display of protein sequences. So, here's your alphabet:
LetterAmino acidLetterAmino acid


You may have noticed that we're missing some very useful letters. Two vowels are out (O and U) and you'll have to do without B, J, X and Z. The Venter folks used V in place of U (a neat trick), but I don't know what we'll do for an O. (I guess we can use Q in a pinch.)

Still, you can do a lot with an alphabet like that, starting with "Methinks it is like a weasel." (But not "in the beginning.") And you can search genomes to see if they contain favorite words or secret codes just for you. (Is "ELVIS" in the human genome? Yep. "LIVES"? Yep. "ELVISLIVES"? Alas, no.) Want to try? Go to the Protein Blast page at NCBI, enter your word or phrase in the big box at the top, select "Non-redundant protein sequences (nr)" for your database, and enter "human" (or any other interesting species, or nothing to search all genomes) in the organism box. Click on the Blast button at the bottom, and ignore the window that comes up first; it will probably report that it hasn't found any "putative conserved domains" and will give you an estimate of how long you'll have to wait for results (mere seconds, usually). Then...presto!

You might get nothing of course, or you might get a report of X number of Blast hits on the sequence. Scroll down to see the various alignments, which might only encompass part of your search string.

'STEVE' hits dozens of proteins (some "hypothetical"); here's a partial screen shot of the results for 'STEVE' in the human repertoire, showing what the alignment looks like:
The alignments, perfect in this case, are indicated by the subtle red arrows. When I Blasted 'STEPHEN' the best match I got was 'STEPHE.'

So much more fun than biblical numerology, if you ask me, and Carl Zimmer seems to agree: he's sponsoring a contest to see who can find the longest word embedded in protein sequences. I'm gonna work on it!

4. Another way to waste time: GenePaint, a site full of anatomical maps, for the purpose of revealing gene expression patterns. Just what I need, Shelley.

5. Some of the bloggers at ScienceBlogs are having a book club of sorts, simultaneously reading and blogging on Stephen Jay Gould's hefty opus, The Structure of Evolutionary Theory. I haven't read it yet, and maybe now I won't have to.

6. Instead, I'm reading H.W. Brands' biography of Ben Franklin, The First American. Very interesting; expect some quotes to find their way here.

7. Seen any good science blogging lately? Send me a heads-up – I'm hosting Tangled Bank next week and I'm looking for submissions, especially from bloggers who might not know about this excellent carnival.

8. Some seem to think I've been too hard on Tony Campolo. Well, check out what I wrote about Jerry Coyne in response to his brainless outburst in response to a blog post about "hopeless monsters." (There was a related discussion on Greg Laden's Blog in which I commented further.) See? I'm an equal-opportunity basher.