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.

Arthrodires got penises!

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This is the skull of an arthrodire, an armored placoderm from the Devonian.

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Somehow, 20 foot long predatory fish with a mouth lined with razor-edged bony shears has never made me think of sexy time…until I ran across this comparison image.

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Oh, schwiiing. It really doesn’t take much to get a mammal to associate just about anything with sex. And then, what do you know, the latest Nature has a short article on an interesting fossil: it’s the pelvic region of an arthrodire, Incisoscutum ritchiei, and look what it’s got: an ossified clasper, comparable to the erectile organ of modern sharks. This is a bony rod that would have been the core of an intromittent organ in the living animal, so what we have here is a small relic of the sex life of a big fish from a few hundred million years ago.

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a, Pelvic girdle in dorsal view; b, pelvic girdle restored.

Think about this, you over-sexed apes: what will be left of your manhood 300 million years from now?


Ahlberg P, Trinajstic K, Johanson Z, Long J (2009) Pelvic claspers confirm chondrichthyan-like internal fertilization in arthrodires. Nature 460:888-889.

Gene regulatory networks and conserved noncoding elements

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We miss something important when we just look at the genome as a string of nucleotides with scattered bits that will get translated into proteins — we miss the fact that the genome is a dynamically modified and expressed sequence, with patterns of activity in the living cell that are not readily discerned in a simple series of As, Ts, Gs, and Cs. What we can’t see very well are gene regulatory networks (GRNs), the interlinked sets of genes that are regulated in a coordinated fashion in cells and tissues.

[Read more…]

The future is roaring your way…

Edge hosted an amazing session that described the looming future of biology — this is for the real futurists. It featured George Church and Craig Venter talking about synthetic genomics — how we’re building new organisms right now and with presentiments for radical prospects in the future.

Brace yourself. There are six hours of video there; I’ve only started wading into it, but what I’ve seen so far also looks like a lot of material that will be very useful for inspiring students about the future of their field. There is also a downloadable book (which is a dead link right now, but I’m sure will be fixed soon) if you don’t want to watch the talks…but the talks are pretty darned good. Somehow, I’m going to have to make time to soak these up. Here’s the overview of the six sessions:

  • Dreams & Nightmares
    Overview, safety/security/policy, nanotechnology, molecular manufacturing

  • Smaller than life
    What is life, origins, in vitro synthetic life, mirror life, computing and DNA, computing with DNA

  • Engineering microbes
    Bio-petrochemicals & pharmaceuticals, accelerated lab evolution

  • Engineering humans
    Electronic-biological interfaces, bioengineered personal stem cells, humanized mice, bringing back extinct species

  • The sorceror
    The diversity of life, constructing life, from Darwin to new fuels

  • The near future, big questions
    Terraforming earth, creating extraterrestrials, the singularity, human nature

There goes your weekend.

The evolution of Hedgehog

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PLoS has recently published a highly speculative but very interesting paper on how a particular signaling pathway, the Hedgehog pathway, might have evolved. It’s at a fairly early stage in hypothesis testing, which is one of the things that makes it interesting — usually all you see published is the product of a great deal of data collection and experiment and testing, which means the scientific literature gives a somewhat skewed view of the process of science, letting the outsider mainly see work that has been hammered and polished, while hiding the rougher drafts that would better allow us to see how the story started and was built. It’s informative in particular for those who follow the creationist “literature”, which often crudely apes the products of actual working science, but lacks the sound methodological underpinnings. In particular, creationism completely misses the process of poking at the real world to develop ideas, since they begin with their conclusion.

So take this description as a work in progress — we’re seeing the dynamic of building up a good working model. As usual, it starts on a sound foundation of confirmed, known evidence, makes a reasonably hypothesis on the basis of the facts, and then proposes a series of research avenues with predicted results that would confirm the idea.

[Read more…]

Brian Goodwin, 1931-2009

It’s sad to see that we’ve lost Brian Goodwin, one of the genuinely original (but not always right!) thinkers of our time. There aren’t many left of the old structuralist tradition in biology, the kind of non-genetic purists who tried to analyze development in terms of the fundamental physical and chemical properties of the organism—they’ve been swallowed up and lost in a triumphal molecular biology research program.

Edge has a nice interview with and essay by Goodwin — they’re good places to start. If that whets your appetite, you should also read his book, How the Leopard Changed Its Spots : The Evolution of Complexity(amzn/b&n/abe/pwll), which is aimed at general audiences and is a good overview of why we should look at more than just genes to explain form.

He was an advocate for one view of nature, and I think he missed the mark by neglecting genes as much as he did; we know now that a lot of details of morphology are directly affected in subtle and not-so-subtle ways by the genetics of the organism. But I think we can also make a case that the modern molecular biological approach is also missing a significant element. Every biologist ought to read a little Goodwin, just to leaven their picture of how biology works with his special perspective.

Good TV

I must thank the reader known to me only as CAC for sending me DVDs of the Inside Nature’s Giants programs. I’ve been enjoying the dissections of an elephant and a whale in the evening — most of the organisms I cut into are millimeters long and require very sharp, thin instruments, so it’s interesting to see ones that require hip waders and backhoes.

You should all lobby your local PBS stations and tell them these would be wonderful additions to the lineup! You might also suggest that broadcasting them during the dinner hour might not be recommended.

What caused the Cambrian explosion? MicroRNA!

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No, not really — my title is a bit of a sensationalistic exploitation of the thesis of a paper by Peterson, Dietrich, and McPeek, but I can buy into their idea that microRNAs (miRNAs) may have contributed to the pattern of metazoan phylogenies we see now. It’s actually a thought-provoking concept, especially to someone who favors the evo-devo view of animal evolution. And actually, the question it answers is why we haven’t had thousands of Cambrian explosions.

In case you haven’t been keeping up, miRNAs are a hot topic in molecular genetics: they are short (21-23 nucleotides) pieces of single stranded RNA that are not translated into protein, but have their effect by binding to other strands of messenger RNA (mRNA) to which they complement, effectively down-regulating expression of that messenger. They play an important role in regulating the levels of expression of other genes.

One role for miRNAs seems to be to act as a kind of biological buffer, working to limit the range of effective message that can be operating in the cell at any one time. Some experiments that have knocked out specific miRNAs have had a very interesting effect: the range of expressed phenotypes for the targeted message gene increases. The presence or absence of miRNA doesn’t actually generate a novel phenotype, it simply fine-tunes what other genes do — and without miRNA, some genes become sloppy in their expression.

This talk of buffering expression immediately swivels a developmental biologist’s mind to another term: canalization. Canalization is a process that leads organisms to produce similar phenotypes despite variations in genotype or the environment (within limits, of course). Development is a fairly robust process that overcomes genetic variations and external events to yield a moderately consistent outcome — I can raise fish embryos at 20°C or at 30°C, and despite differences in the overall rate of growth, the resultant adult fish are indistinguishable. This is also true of populations in evolution: stasis is the norm, morphologies don’t swing too widely generation after generation, but still, we can get some rapid (geologically speaking) shifts, as if forms are switching between a couple of stable nodes of attraction.

Where the Cambrian comes into this is that it is the greatest example of a flowering of new forms, which then all began diverging down different evolutionary tracks. The curious thing isn’t their appearance — there is evidence of a diversity of forms before the Cambrian, bacteria had been flourishing for a few billion years, etc., and what happened 500 million years ago is that the forms became visible in the fossil record with the evolution of hard body parts — but that these phyla established body plans that they were then locked into, to varying degrees, right up to the modern day. What the authors are proposing is that miRNAs might be part of the explanation for why these lineages were subsequently channeled into discrete morphological pathways, each distinct from the other as chordates and arthropods and echinoderms and molluscs.

[Read more…]

Why do they hate the manimal?

It’s happening again. The Republicans are tilting at one of their favorite windmills, the mad scientists’ dream of creating an unholy union between beast and human to produce a slave race of soulless monsters. They have introduced legislation to ban human-animal hybrids. And it’s even bipartisan! They’ve got 19 Rethuglicans, like Sam Brownback, the ignoramus from Kansas:

What was once only science fiction is now becoming a reality, and we need to ensure that experimentation and subsequent ramifications do not outpace ethical discussion and societal decisions. History does not look kindly on those who violate the dignity of the human person.

And they’ve also got 1 Dimocrat, Mary Landrieu of Louisiana:

Here in the United States, we simply cannot open the door to the unethical blending of humans and animals, which the British government seems intent on doing. It creates an unnatural species and is a clear line we cannot cross.

One teensy little problem: these clowns do not understand the science. We actually aren’t planning to creating a slave-race of beast-men; the technology isn’t there, for one thing, and for another, that’s really not at all an interesting goal. No one is planning on operating on any human persons, or even violating them; the focus is all on cells and molecules. This is routine stuff. In one hand, you’ve got a dish full of human cells — it doesn’t talk, it can’t sign a consent form even if it had the capacity to understand one — and you want to know what makes them tick. In the other hand, you’ve got a collection of hard-won tools you’ve gathered from work in mice or worms or flies; interesting vectors, genes that act as indicators or switches, ways to basically reach into a cell and toggle states. Scientists have had these for years, and we’ve regularly used these tools to manipulate cells and puzzle out what happens.

Another example: we want to know what genes on different human chromosomes do, but it is highly unethical to do random mutagenesis on human gametes, bring them together, and then raise up the fetus in a volunteer’s womb to find out what interesting ways it might go kablooiee. One technique that has been used is to make mouse-human hybrid cells: use a little ethylene glycol to weaken the cell membranes, push a mouse cell next to a human cell, and presto, they fuse. They then recover and go through cell divisions, and the hybrid cell begins to lose pieces of the unnatural excess of chromosomes it’s got. You can then screen the resultant cells and correlate the presence or absence of gene products with the presence or absence of specific human chromosomes.

I know. It sounds so nefarious.

One more example: scientists have made transgenic pigs carrying five human genes. The idea is to create animals that can be a source for xenografts — transplanted organs — in humans with a reduced level of rejection. These pigs would become illegal under the Brownback bill, because they mingle a blessedly human H-transferase gene with pig cells. This is not to argue that there are no ethical considerations in these kinds of experiments, since there certainly are: we can argue about the ethics of creating species of pigs with the specialized purpose of providing organs for human use (it’s about as great a moral dilemma as raising pigs for meat), and there’s also the concern that hybrid pigs will also be dangerous incubators for training viruses to respond to human epitopes. But the ethical debates aren’t the domain of crude science-fiction versions of the science that these clueless lawmakers think them to be.

I’d like Brownback to answer a simple question. Does putting the human insulin or growth factor gene into E. coli violate the dignity of the human person? If it does, he’s suggesting shutting down a good chunk of the pharmaceutical industry. And Ms Landrieu: what is an “unnatural species”? If they’re unnatural and we can’t cross that line, then we certainly don’t need legislation to enforce it.

I don’t know why she bothered to complain about the British government, unless she’s using just plain old conservative xenophobia to stir up votes. American scientists have been using hybrid cells and have been introducing cross-species genes into cells for a long, long time now.