Looking for an article…

So…anybody with an institutional subscription care to send me a copy of this paper? My university’s subscription only lets me see articles in this journal after they’ve aged for a year.

Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W (2009) Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. J Evol Biol. 2009 Aug 12. [Epub ahead of print]


Already got it, thanks everyone!

Microsoft owns bioinformatics?

I hope not, but they have filed one of those ridiculously broad, sweeping patents that covers a big chunk of basic techniques in the field:

The patent, filed by Microsoft researcher Steve Ozer in July 2007 and recently discovered by a graduate student at the University of Texas in Austin, claims ownership of several common phylogenetic methods. At its most basic, however, it seems to patent identifying any evolutionary relationship from sequences: “receiving a plurality of sequences across a plurality of species [and] mapping at least a portion of the plurality of sequences to an evolutionary tree.” 

The patent hasn’t been approved, and there’s a good chance it won’t be…but keep an eye on that evil empire in Washington state.

Witch hunt in Illinois

The Illinois Family Institute — they actually italicize the word in their name to emphasize the hypocrisy — is out to get Hemant Mehta. He’s an atheist, you know! And a school teacher! Shun him! You’ve got to appreciate the quality sliming while acknowledging his right (for now, until they get more power) to not believe in gods.

He absolutely has a First Amendment right to promote any feckless, destructive, offensive, and immoral ideas he wants via his blog, but, as I mentioned in my earlier article, parents have the right not to have him as a teacher and a role model for their children.

Yeah, right. Remember, Hemant is the friendly atheist, the nice gentle guy with a blog, and they want to see him fired. There is absolutely no incentive to not be the snarly loud atheist, is there?

Among the trumped up reasons to call him immoral is that some of his commenters discussed polyamory (again, they should witness the decadent discussions about bacon that go on here to acquire some perspective), and that he once linked favorable to Dan Savage. Like I just did. I think Dan Savage is terrific, and I would hope any gay students anywhere would be reading him regularly to get a healthy, positive perspective on their sexual orientation. Should they be getting advice from Tony Perkins or Ted Haggard?

So this Family institute is calling on parents to yank their kids out of Mehta’s classes. If you’re a parent in Neuqua Valley district 204, maybe you should call up the district and throw some praise his way…or try to get your kids in his math classes.

Nice letter

A short letter in this week’s Science echoes a point I made in my last article: lying to students will not win them over to your cause. It’s what will eventually lead to the defeat of creationism, which prompts them to lie ever more in order to drown out that damning evidence.

I was always a mediocre student, especially in high school. I never really knew what I wanted to do, and nothing seemed to excite me. This changed in my senior year, when a creationist visited my biology class.

On that fateful day, all the science students were herded into the school auditorium, where we listened to a long and richly illustrated lecture describing literal creationism. We were informed that in an effort to “balance” our education, we would soon hear an equally long lecture on evolution. This, like many things I heard that day, turned out to be false. The evolution lecture never materialized. Remarkably, I graduated from senior biology having learned only about creationism.

School had finally gotten my full attention. I wanted to know what we were missing, and why. For the first time in my life, I willingly (eagerly even) picked up my textbook and studiously read it. With growing interest, I realized that evolution made an awful lot of sense, and that I was being hoodwinked by my biology class.

It’s hard to overestimate the appeal of rebelling against the system to a teenaged boy, and that day marked the beginning of my path to a career in evolutionary biology. We learned other things in science class that year, too–for example, that all actions have an opposite reaction. For at least one sulky teenager in the small town of Owen Sound, Ontario, it took a creationist to make him into an evolutionary biologist.


Keeling P (2009) Creationists Made Me Do It. Science 325(5943):945.

Yes, millions of years!

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That Answers in Genesis crackpot, Terry Mortenson, is speaking on “Millions of Years” at the Creation “Museum”. Those of us who visited that circus of charlatanry know that this is one of their obsessions — the idea that the earth is more than 6000 years old is one of the wrecking balls atheists use to destroy faith.

He’s right, of course. It’s a very useful tool. When fundamentalists tie their faith absolutely to a claim that is easily refuted, that contradicts the evidence, and that requires them to constantly escalate their denial and delusions in order to sustain their belief, it makes it really easy for atheists to demolish their religion. We don’t even need to attack religion in the classroom at all — we just calmly lay out the facts, let the students work out the conclusions, and sometimes…it’s epiphany time! They realize their pastor lied to them, or was just really ignorant, and suddenly their respect for Christian authority begins to crumble away.

It’s not the atheist’s fault, though. The lesson should be, “Don’t lie to your kids,” not “Silence the people who would reveal that you lied to your kids,” or worse, “Lie harder.”

This is not a lesson that Mortenson has learned. He is apparently planning to babble about revisionist history in his talk, claiming that the evidence for the age of the earth is the product of an atheist conspiracy among geologists.

To really understand what is wrong with belief in millions of years, we need to go back to the early 19th century and study the origin of this idea. This unique and interesting lecture, based on Dr. Mortenson’s PhD research, will clearly show that the idea was not the result of just letting the rocks and fossils “speak for themselves” but rather comes from anti-Biblical worldviews (or philosophical assumptions) being imposed on the geological evidence. The talk explains the key men who helped develop the idea of millions of years, one of the geologically competent Christians who opposed those theories, and the subsequent consequences of the church’s compromise with millions of years. Even non-Christians would find this lecture thought-provoking.

Hah! The only thought it would provoke in me is to wonder where they kept the straitjackets. Looney-tunes revisionist history is not thought-provoking in a good sense.

I actually spend a fair amount of lecture time on the early history of geology in my introductory biology course. One reason is that, if you talk to most people, you will discover this fallacious belief that evolution leapt fully-formed from the brain of Charles Darwin, and there’s an anachronistic idea that ideas about the age of the earth, which are built on independent evidence from geology and astronomy, are somehow rooted in biology. It’s not so! Darwin’s antecedents had already laid the foundations in working out that the earth was old, that life had undergone many transitions, and that maybe species were mutable. Evolution was an inevitable conclusion of the evidence; Darwin and Wallace were just the clever fellows who managed to pull the whole story together.

I find it very useful to give students a quick overview of 18th and 19th century geology before we talk about Darwin, since the creationists in the classroom usually have this image of Darwin as Satan who foisted a false belief on the world because he hated god (hey, sounds like Terry Mortenson!). It’s very useful to be able to show how views of the world evolved, not by ideology, but by the growth of a body of evidence.

Let’s begin with Robert Hooke (1635-1703). He dabbled brilliantly in many things, but one subject of particular interest was the origin of these curious fossils that people kept digging up, which were thought to be either creatures turned to stone by some miraculous process, or were the expression of an intrinsic nature of stone to mimic life. Hooke examined the details of fossils microscopically, and determined that they had once been alive, and also worked out how the transformation had occurred — by the perfusion of minerals into buried or immersed dead organisms. He also examined the distribution of fossils; finding fossilized clams on mountaintops, for instance, says something about the prior state of that environment.

Most of those Inland Places. . . are, or have been heretofore under the Water. . . the Waters have been forc’d away from the Parts formerly cover’d, and many of those surfaces are now raised above the level of the Water’s Surface many scores of Fathoms. It seems not improbable, that the tops of the highest and most considerable Mountains in the World have been under Water, and that they themselves most probably seem to have been the Effects of some very great Earthquake.

These conclusions were evidence-driven. Almost no one in the late 17th century would have been interested in opposing religion, so you can’t pin that heresy on Hooke. He is simply describing the natural world and finding certain conclusions inescapable, including some to which creationists today still can’t adjust — and note that he is writing this more than 300 years ago.

There have been many other Species of Creatures in former Ages, of which we can find none at present; and that ’tis not unlikely also but that there may be divers new kinds now, which have not been from the beginning.

And then there’s Baron Cuvier (1769-1832) and Alexandre Brongniart (1770-1847) who studied the rocks of the Paris Basin. There were many quarries situated around Paris that cut deep into the hills to provide building stone, and they gave these two the opportunity to look into the structure of the rocks. They identified five major layers, and by examining the fossils, worked out what kinds of animals and plants lived there when the layers were deposited. They found that layers with saltwater species were interleaved with layers containing freshwater species — Paris had been under the sea at least twice!

Cuvier was not an atheist. In fact, he was even adamant that the earth was relatively young, but in a way that contradicts what Answers in Genesis would tell you. He had worked out that there were different assemblages of animals in each layer, and proposed an explanation: a series of ages, each very different, with the most recent major catastrophe occurring five or six thousand years ago (to bring it in line with the literal interpretation of the Bible) and sweeping away prior forms to allow for the flourishing of human beings.

It is certain that we are now at least in the fourth succession of terrestrial animals. The age of reptiles was followed by that of the palaeotheres [primitive mammals], then the age of mammoths, mastodons, and megatheria. Finally we arrive at the age of the human species together with domestic animals. It is only in the deposits subsequent to the beginning of this age, in turf-bogs and alluvial deposits, that we find bones all of which belong to animals now existing…None of these remains belong either to the vast deposits of the great catastrophe or to those of the ages preceding that wonderful event.

If you want someone who was willing to assert that the earth was very, very old, we have to look to the Scottish geologist James Hutton (1726-1797), who was accused of atheism for his ideas, but they were backed up entirely by hard-earned evidence. He postulated that the geology we see was created by multiple cycles of sedimentary deposition, volcanic uplift, and erosion, and he mapped and documented complex unconformities and intrusions that demonstrated that the history of the earth was complex and required great time for the formation and distortion of rock. He also found that the evidence of the time was insufficient to even show the history of the beginning of the earth, which is why he closed his book, Theory of the Earth, with the famous line, “The result, therefore, of our present enquiry is, that we find no vestige of a beginning,—no prospect of an end.”

Again, his conclusion was dictated by the evidence, not some atheistic philosophy.

At the same time Cuvier and Brongniart were exploring the Paris Basin, William Smith (1769-1839) was walking all over England, building up his geological map. We know what his motivation was: it was economic. He worked in mines, and was eager to capitalize on the opportunities opened up by the Industrial Revolution. Railroad and canal cuts exposed the strata of English geology all over the place, and being able to assess good locations for coal mines was a profitable skill — much like petroleum geology now. Smith observed consistent features of geology, like the way rocks were layered, and what fossils were present in specific layers, and could see that a layer was a slice of time, and that each slice contained different animals (which led to his Principle of Faunal Succession). He worked out the first geological map of Britain on the basis of his surveying.

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There is a pattern to geology: we can see that the strata are not purely local phenomena, but part of formations that often extend continent-wide. These strata also have a predictable order that reflects the timing of their formation. These observations are not reconcilable with the simplistic dogma of the creationists.

Charles Lyell was also an important geologist, who was also very influential on Charles Darwin. He was not an atheist, but rather, a devout Christian, which caused him considerable discomfort since he was never able to accept the full implications of Darwin’s work. Lyell’s key dictum was that the present is the key to the past, that what you needed to do was work out mechanisms in action right now and use those to explain what must have happened in the past.

Darwin himself applied this principle to estimate a minimum age for the earth. He knew from published observations that a rapid rate of sedimentary deposition was 600 feet in 100,000 years; he also knew that the known strata in England had a depth of over 72,000 feet, which implied that the earth had to be at least 12 million years old.

It’s so widely accepted that even creationists use it — it’s the basis for their arguments that the ocean sediments and moon dust say the earth is young. Unfortunately, the way they accomplish that is by either using the wrong numbers for accumulation or ignoring the multiple processes that affect the rate.

It is simply ludicrous to claim that 18th or 18th century geologists bent their interpretation to fit some imaginary godless worldview — in general, the scholars of that period were more concerned with avoiding conflicts with religion, since the majority of them were doctrinaire church-going Christians themselves. What led them to the conclusion that the earth was millions, and then billions of years old was the evidence, not their ideology.

And now, of course, the evidence is even more overwhelming, and it’s mostly physics at its heart. Trying to salvage Bishop Ussher’s weird numerological and biblical 17th century chronology in the 21st century by invoking the incomplete understanding of 19th century scholars is exactly the kind of inanity we’ve come to expect from creationists.

Run away, Tom, run away!

Speaking of intellectual cowardice from creationists, we have another shining example: Pastor Tom Estes. You remember Pastor Tom; squirrelly fella who darted up to shake my hand at the Creation “Museum” before running away to hide behind the creationist staff, shrill commenter, proud owner of a very silly blog? Well, he has just declared his blog an atheist-free zone. All you annoying people who wouldn’t simply accept his patriarchal authority finally compelled him to restrict his readership, and you had to register to comment. Somebody was trying to register under my name (I suspect his troll-pal Shaun), too, so I’ve received a few snide emails from Pastor Tom crowing about how he wasn’t going to let me in.

Anyway, while atheists drive him insane (OK, insaner) and won’t be allowed to criticize him, he’s still ranting away about us. Here’s an example of his inadequate tirades.

This is why Biblically based logic and rationality will always work. It begins with God. It has a foundation that cannot be shaken. And before I get into that, let me explain how ridiculously simple the atheist logic is, when it comes to God. Atheists often say, “Well, if God created the universe, than who created God?” They actually believe this logic is sound enough to dismantle the argument that God created everything. But let me share with you a quote I found at EveryStudent.com, made by Aristotle:

there must be a reality that causes but is itself uncaused (or, a being that moves but is itself unmoved). Why? Because if there is an infinite regression of causes, then by definition the whole process could never begin.

Do you see what I’m saying? It’s all circular. If God was created, then someone had to create who created God, etc, etc, etc. And if that logic were true, nothing would exist.

Yes, Pastor Tom. We know. We knew it all along. That’s the point.

There has to be an uncaused starting point to the universe, or it’s an exercise in infinite regression (which it may be; it’s as good a proposition as saying it had a beginning). But let’s just assume that there was something that popped into existence without a causal agent behind it. Now the question is, what was that first something? I think it’s perfectly fine to suggest it was a singularity, that first tiny pinpoint of incipient mass and energy. We gain nothing from saying the first cause was a ‘god’, which is an undefined and inconsistent being of significant complexity with human-like qualities of intelligence, who then by mechanism unknown initiates the singularity. It’s an unnecessary complication, especially when one of your reasons for bringing it into the equation is that you can’t comprehend how matter and energy came into being, so you’re going to invoke magic and push the problem back onto a superman.

Pastor Tom completely misses the point of the argument. What he has to answer is why he thinks the first thing to exist has to be an Old Testament Patriarch with some cranky obsessions about fabrics, diet, and sex rather than a simple expanding sphere of hot space-time.