Blue Collar Scientist

I’m checked in for TAM and waiting for the first workshop to start. As twitter bar readers will note, things have not started off well here. My vintage 1950 room has a lack of grounded outlets, and I had to remove a six-plug extender to get a place to plug in my laptop. Then I discovered the desk was coated in a mysterious brown sticky substance. When I went to the sink to clean it up, I discovered ants. The list goes on, but suffice it to say that I don’t recommend you stay at the plantation hotel and conference center.

The internet is so irresponsibly bad here that I’m posting from my blackberry.

Hopefully things will improve. The first workshop starts in about 15 minutes - and signs are hopeful that it willturn the tide.

The Panda’s Thumb summarizes some discussion that is occurring on various science blogs lately, a result of a new instance of the old intelligent design creationist ignorance about junk DNA.

The discussion makes pretty clear that historically there have been two camps about the effect of evolution and selection on the genome. From my lay perspective, I’ve identified those camps as the “strict Darwinians” on the one hand, and the “neutralists” on the other. This is my own terminology - maybe I borrowed it from somewhere and it might just possibly mean something to an expert in the field - but it has been a convenient way for me to think about competing hypotheses in some of the sub-disciplines of evolution.

Strict Darwinists, to my mind, would not expect junk DNA to be conserved. If this hypothesis were true, junk DNA would be “rare” - although it is well to note that rare can mean different things to different people, and that what is considered “rare” to an evolutionary biologist might look common to a layperson.

The neutralists, to my mind, would say that since mutations are random, and since some of the genome is redundant, and since some mutations can destroy the ability of a gene to code for a protein, junk DNA should be “common.” One of the ideas here is that junk DNA is not necessarily maladaptive, and its presence wouldn’t necessarily be selected against.

This means, incidentally, that the concept of junk DNA is not Darwinian. And that in turn means that when intelligent design creationists use the term “Darwinian” when they mean “evolutionist,” they are either lying¹ or ignorant².

This is, in any case, a thumbnail view of how I’ve been explaining this issue to people who ask. (I don’t really concentrate on evolution in my instruction activities - I’m more of an astronomer than a biologist.) I’m glad to find some support and some additional clarity for this oversimplified way of explaining these issues in the current round of discussion.

1. And therefore you shouldn’t pay any attention to them [↩]
2. You shouldn’t pay any attention to them in that case either. [↩]

I’m sitting in Jacksonville International Airport, which I’ve discovered has free wireless, and was catching up on my blog reading when I came across Bay of Fundie’s brilliant takedown of some intelligent design creationist ideas involving cows and buffalo.

Not to be missed.

In a few minutes, I’m leaving for TAM 5.5. I’ll hop a flight from Jacksonville, Florida (where I’m currently visiting) to Ft. Lauderdale and return to Jax on Monday. If everything goes well - meaning if the hotel internet is working right - I should be able to post an update each day from the conference. If not - see you Monday!

The LIGO team recently reported that LIGO, the Laser Interferometer Gravitational-Wave Observatory, has failed to detect gravitational waves from a gamma ray burst. Gamma-ray bursts are the most luminous phenomenon in the universe since the big bang. The favored hypothesis for the cause of most GRBs is the collapse and merger of two compact, massive objects; but there are many other possible explanations.

On February 1, 2007, the Konus-Wind, Integral, Messenger, and Swift satellites, each carrying gamma ray burst detection instruments, reported a short-duration burst in the direction of one of M31’s spiral arms. The high energy and brief duration of the burst suggested that the GRB was caused by a merger of neutron stars or black holes, and the direction suggested it had occurred in a nearby galaxy. If these hypotheses were true, the event should have led to gravitational waves that LIGO should have easily detected.

But LIGO, the Laser Interferometer Gravitational-Wave Observatory, failed to detect gravitational waves at the time of this event. This means that either:

1. the burst actually occurred in a distant galaxy in the same direction as M31;
2. the burst did occur in M31 but was not the result of a compact massive object merger.

Some scientists seem to favor the second explanation. Neil Gehrels, the lead scientist of the SWIFT mission, says “We are still baffled by short GRBs. The LIGO observation gives a tantalizing hint that some short GRBs are caused by soft gamma repeaters. It is an important step forward.”

Some reports seem to suggest that LIGO’s result means that short-duration, high-energy GRBs are never caused by massive compact object mergers. That’s overstating the significance of these results. This represents an important incremental step forward, but it will take many such observations before it becomes clear whether any hypotheses have to be abandoned or upgraded.

Still, this is the first science from a brand new frontier - gravitational waves. We can expect in the coming years that this new discipline will have a big impact on the science of GRBs.

I was driving through Orlando, Florida the other day and saw a billboard advertising the Orlando Science Center, so, on a whim, I decided to go. (When you are nearly 4,000 miles from home, you might as well take advantage of these opportunities.)

On the night I went (January 20), the Center was having a big video game convention, so it was crawling with hyped-up overstimulated teenagers who were, by and large, not interested in the exhibits proper. But this didn’t bother me too much - the gaming was going on mainly in the large atrium and in some meeting rooms and hallways, and the exhibit halls were just fine - in fact, it was as though I was there on a slow night.

The Center has the usual exhibits pitched at kids that seek to demonstrate forces, material strength, elastic rebound, electricity, conversion of energy, and other physical concepts with ingenious hands-on devices. They do a nice job with that, and I have nothing bad to say about them.

They also have an excellent cabinet of partial fossils, including some very old mammal skulls, which was absolutely fascinating. I’ve never seen mammal fossils that old before.

But what really stood out was their dinosaur hall. It was absolutely outstanding.

They do not have an especially large space devoted to the topic, but they’ve made very good use of what they have. Most of the mounted skeletons are high-quality casts. They have a cast of Stan, the the Tyrannosaurus rex (BHI 3033), and it is sufficiently good to easily discern the broken ribs and fused cervical vertebra that this skeleton is famous for. It stands as a tribute to the Black Hills Institute’s work (who I presume provided the cast). It is mounted in what I understand to be a more or less proper theropod posture - the spine and tail are roughly horizontal, and although the head is elevated nobody will confuse the posture with that of the old tripod pose with the animal balanced on its tail. It is mounted with a Triceratops in way that suggests interaction.

Remarkably, they also have a cast of the Pachycephalosaurus wyomingensis called “Sandy” (the original is on display at the Rocky Mountain Dinosaur Resource Center. Sandy’s skeleton was partially preserved, making it unique in the genus, and this apparently makes Orlando Science Center’s display more up-to-date than the Wikipedia entry on this dinosaur. In any case, it was a great thrill to see a mounted cast of this very interesting dinosaur.

Other mounts include a cast of the hadrosaur Edmontosaurus annectens, a cast Xiphactinus audax (a big teleost fish, not a dinosaur, this specimen found flattened in the fossil bed and laboriously pieced back together in 3-D), a cast Platecarpus ictericus (a mosasaur, a very long, serpentine marine reptile), a cast Elasmosaurus platyurus (a plesiosaur, another long-necked marine reptile), a Clidastes propython (another mosasaur), and a cast Hesperornis gracilis (a late Cretaceous bird). I may be overlooking a few mounts, but just what is mentioned here makes the exhibit very impressive indeed.

(I am, by the way, very much in favor of the disclosed use of casts, particularly in a museum that attracts a lot of kids. Not that casts are cheap by any means - but they are at least not irreplaceable. The culture of mounting skeletons has at times resulted in exhibit curators conning the viewer by completing a partial skeleton with bones from other specimens, and sometimes even other species. I recall seeing an Allosaur once that had at least ten bones in the leg and foot that were out of place. My observation with casts is that exhibits tend to be - on average - more honest, with replacements more likely to be noted. But this is also true of recently-updated mounts of skeletons, so it may just be a “standards and practices” thing.)

Rounding out the collection is an excellent cast of the famous Oviraptor nest that contained a preserved embryo (see “A Theropod Dinosaur Embryo and the Affinities of the Flaming Cliffs Dinosaur Eggs” by Mark Norell et al, in Science, sometime in 1994). Oviraptor was discovered on a dinosaur nest by Roy Chapman Andrews in 1924, and was famously presumed to have been an eater of eggs. By 1977, someone had noticed that the jaw was awfully strong for such a purpose, and discussion ensued about what the diet of Oviraptor really was; but the 1994 paper really blew the lid off things and established that Andrews’ Oviraptor was actually caring for its eggs. The nest that is cast for the Orlando Science Center, with its embryo, established that Oviraptor embryonic development was strikingly similar to that of birds. Oviraptor is considered the most bird-like non-bird dinosaur and therefore its existence is a significant confirmation of evolutionary theory.

They’ve also got a cabinet of small specimens that includes a Pterosaurid skull (labeled Tapejara wellnhoferi, and not a cast, though I thought only one skull of the species had been found). It also included two bird skulls, one toothed (Hesperornis gracilis, again), the other toothless and slightly hook-billed (Paleospheniscus). This is not entirely surprising, since Hesperornis is Cretaceous, or 65+ mya, while Paleospheniscus is from the Miocene, 20 to 5.3 mya. As the theory of evolution predicts, the more recent bird shares more attributes with modern specimens. So right there in that cabinet were two of the “transitional fossils” that the religious extremist evolution deniers swear by the name of their alleged god don’t exist. *

They also had one of the most kick-ass posters I’ve ever seen (A Correlated History of Earth, published by Pan Terra) positioned in the cabinet to provide a context - geographic, deep timeline, and and evolutionary - for the various specimens. I’ve rarely seen a more information-dense tool and I’ve already ordered a copy for myself.

The exhibit was unashamedly evolutionary. There must be a lot of temptation to buckle under to the so-called “controversy” and soft-pedal evolution in a museum that sits in the middle of one of the most backwards states since Kansas, but the people that run the Orlando Science Center are doing the right thing. Interpretive signs discuss in some detail the evolutionary implications of the specimens on exhibit, and explain what elements of the specimen’s anatomy has led to which conclusions by the paleontologists and multi-disciplinary scientists who study these creatures. For someone who is a bit of a lay expert, or at least a lay enthusiast, there is sufficient information to put the specimens in context and think about them intelligently. (Being a real geek, I also looked up some details on a couple of the specimens on my Blackberry.)

Anyway - if you are ever in or near Orlando - go visit the Orlando Science Center. This one room is well worth the price of admission. (Which I think was fifteen bucks - this, in the city of the $120 ticket that gets you into entirely artificial corporate-built “attractions.”)

* The Blue Collar Scientist accepts cladistics and the implications of that discipline on the concept of transitional forms.

An asteroid, 2007 TU24, will shortly pass close to Earth, with closest approach taking place on January 29, at 7:33 PM Alaska standard time. It will be 334,000 miles away at closest approach (about 1.4 lunar distances), and has no chance of hitting the Earth, contrary to what the doomsayer cranks are saying.

The asteroid is about 150 meters across, so should reach about 10th magnitude. From a dark sky, it should be visible in a big pair of binoculars to a well-prepared observer, and will certainly be visible in a small telescope. Orbits and ephemerides are available at the usual places.

Seriously - it does. Just not in the way today’s intelligent design creationists think.

Over at Post-Darwinist, Denyse O’Leary has written some pablum about the scientific predictions made by intelligent design creationism (hat tip to Pharyngula). The entry starts out by citing a question posed on another forum:

can [anyone] provide any samples of things that intelligent design theory has predicted, which researchers have later determined to be true?

O’Leary attempts to respond:

No good theory will be found for a random origin of the universe….

No good theory will be found for a random origin of life….

Complete series of transitional fossils will not usually be found….

Discovering the true mechanisms of bursts of natural creativity may be of immense value to us….

No account of human evolution will show a long slow emergence from unconsciousness to semi-consciousness to consciousness….

O’Leary seems to have a problem understanding the simplest of questions - she was asked for examples of things that intelligent design creationism predicted, and were later found to be true. But she’s actually making up a laundry list of things that intelligent design creationism supposedly predicts that will never be found to be true. And somehow this supports intelligent design creationism.

It’s a pretty easy sport, and I’d like to play. I hereby confidently predict, based entirely upon what the theory of evolution says about the world, that it will never be found that invisible pink unicorns exist.

Ha! See what I did there? I have single-handedly proved evolution is true.*

Buried amongst O’Leary’s “nine predictions” are some statements that when initially evaluated, might appear to be theoretical predictions in the scientific sense. Such as:

We will discover the functions of many brain areas whose functions we did not know before.

This isn’t a prediction of intelligent design creationism, its a prediction based upon an empirical observation of the progress of human knowledge. Evolution predicts we will discover the functions of previously mysterious brain areas, too, and for two reasons. One reason is that evolution predicts that the phenotype will not be purposeless. The other is that the philosophical and epistemological foundations of evolution (and all scientific theory) presuppose that knowledge can be obtained.

Note that O’Leary disagrees with that last bit - most of her predictions are that knowledge can not be obtained. This is the fundamental weakness of intelligent design creationism - it presumes that answers aren’t available, that because we don’t know something, it must have been god, or little green space aliens, that did it.

The next doozy isn’t even a complete sentence:

Better health care for people with complex illnesses.

Again, I’m pretty sure that every evolutionary biologist for the last century has predicted that a better understanding of evolution (including evolution’s sub-specialties of genetics, inheritance, development, and biochemistry) would lead to better health care.

The problem here is that the intelligent design creationists do not understand how to identify a unique or distinct prediction made by their supposed hypothesis. When scientists evaluate rival hypotheses that seek to explain the same phenomenon, they focus on the predictions that contradict each other. That way, by testing one of them, they can generate evidence that favors one hypothesis over another.

I know I’m only a layman in this field, and I know I’m swimming against the current here and that the mighty PZ Myers says otherwise, but I believe that intelligent design creationism does make predictions. I think O’Leary could have posted some coherent predictions of intelligent design creationism, but that she didn’t, because those predictions have been proven false.

Intelligent design creationism claims (I’m taking this claim from the book Of Pandas and People, which is a generally-recognized as valid source among intelligent design creationists) that different creatures are specially created and are not related.

If that were so, I believe that we would find that these creatures would be made of the most appropriate chemical compounds given their phenotype and environment. But this turns out to not be so - out of a possible thousands of amino acids, all of life’s protein is built by only twenty of them, and all the species in the world can only produce a couple hundred amino acids. Despite this, some amino acids that are not used or made by living organisms would be quite useful to many living creatures today. For example, synthetic amino acids with efficient chelating properties might be quite useful to organisms living in areas with arsenic-contaminated water. Yet such organisms lack such useful amino acids and must make do with less effective chelators.

Evolution, on the other hand, predicts that life will be parsimonious in its building blocks, because, the theory says, a mutation that allows the synthesis of a new amino acid is much less likely than a mutation that repurposes an existing one for a new function or a new piece of anatomy.

More fundamentally, I think intelligent design creationism predicts that all organisms should be able to synthesize all of the amino acids necessary to their life. There’s no reason why, given that so much of an organism’s genotype is noncoding and therefore available to undertake this trivial function, that an intelligent designer would not have given every organism this ability But this turns out not to be the case - in many organisms, some necessary amino acids must be consumed, and cannot be produced.

Meanwhile, evolution predicts that some organisms will lack the ability to synthesize an essential amino acid. One of several ways this might happen is as a result of a deleterious mutation - the species may nevertheless survive as long as the essential amino acid is present in their diet.

Intelligent design creationism predicts that, since insects, fungus, lobsters, snails, and octopus are unique, distinct, unrelated creatures, and since they live very distinct lifestyles with vastly different requirements, that they would not be made of the same substances. What is actually found in nature, though, is that the cell walls of fungus, the shells of lobsters, the teeth of snails, and the beak of the octopus are all made of the same substance - chitin.

But evolutionary theory predicts that many different structures with very different functions in many different organisms will be made of the same substance, because it is easier for variation and mutation to put an existing substance to work in a new way, than to come up with a whole new appropriately designed substance for the task in the way an intelligent designer would.

I could go on, but suffice it to say that I think biologists unnecessarily denigrate the predictive power of intelligent design creationism. The predictions are there - they’re just false. They’ve long since proven to be baloney. I think it is time that the actual experts who walk among us point this out. These ideas have already been tried, they’re not true, and that’s going to have more effect swaying an undecided school board member than making the bland assertion that intelligent design creationism makes no predictions.

* By no means should you believe this claim.

The Panda’s Thumb has helpfully posted several examples of Christian churches and clergy members making statements in favor of evolution. This sort of thing helps to make clear that among the religious, only religious extremists, and those deceived by them, have a problem with evolution.

Currently in Florida, extremists are telling county school boards that teaching evolution violates the Establishment Clause of the constitution. How does that work? They say that teaching evolution demands and establishes an atheistic mindset:

It will demand that the concept of “God” be banished from the mind and replaced by atheism; It will displace any idea that there is purpose for man except to discover what it means to be human; It will demonstrate that other species of animal life have as much value and right as man; and it will require a mind devoid of biblical theism—devoid of any concept of God.

(I suppose that to find this line of argument at all compelling, you’d have to be aware of the extremists’ assertion that atheism is a religion. I guess you’d also have to believe it.) If this is all so, however, how is it that so many Christian churches and clergy accept evolution?

The General Assembly of the Presbyterian Church says:

“[T]here is no contradiction between an evolutionary theory of human origins and the doctrine of God as Creator.”

Pope John Paul II, in a message to the Pontifical Academy of Sciences on October 22, 1996, said:

“In his encyclical Humani Generis (1950), my predecessor Pius XII has already affirmed that there is no conflict between evolution and the doctrine of the faith regarding man and his vocation…. Today, more than a half-century after the appearance of that encyclical, some new findings lead us toward the recognition of evolution as more than an hypothesis. In fact it is remarkable that this theory has had progressively greater influence on the spirit of researchers, following a series of discoveries in different scholarly disciplines. The convergence in the results of these independent studies — which was neither planned nor sought — constitutes in itself a significant argument in favor of the theory.”

Note well - the Catholics have understood for fifty-eight years that evolution in no way contradicts the faith. That’s almost three generations.

The Clergy Letter Project has gathered over 10,000 signatures from Christian ministers, pastors, and priests who agree with this statement:

“We the undersigned, Christian clergy from many different traditions, believe that the timeless truths of the Bible and the discoveries of modern science may comfortably coexist. We believe that the theory of evolution is a foundational scientific truth, one that has stood up to rigorous scrutiny and upon which much of human knowledge and achievement rests. To reject this truth or to treat it as ’one theory among others’ is to deliberately embrace scientific ignorance and transmit such ignorance to our children. We believe that among God’s good gifts are human minds capable of critical thought and that the failure to fully employ this gift is a rejection of the will of our Creator…. We urge school board members to preserve the integrity of the science curriculum by affirming the teaching of the theory of evolution as a core component of human knowledge. We ask that science remain science and that religion remain religion, two very different, but complementary, forms of truth.”

Although it would not do to confuse Judaism with Christianity, it is well to note, given that many extremists loosely couple “Judeo” with “Christian” as a way of co-opting a different tradition to support their own, that the Central Conference of American Rabbis has said:

“[S]tudents’ ignorance about evolution will seriously undermine their understanding of the world and the natural laws governing it, and their introduction to other explanations described as ‘scientific’ will give them false ideas about scientific methods and criteria.”

I’m not apologizing for Christians here. I believe that, too often, mainline churches sit idly by while extremists of their own faith carry on in outrageous ways. By ignoring this, allowing it to go on without comment, they provide the cover of legitimacy to those who lack it. Still - here are some exceptions to this general trend. Some Christians whine and carry on in an attempt to get special rights for their beliefs, government subsidies for religious educational materials, and forced religious education in public schools, but most Christians are against this kind of excess.