A scientific Caturday felid: how it got its coat

January 9, 2010 • 8:20 am

by Matthew Cobb

We have discussed the evolution of mammalian coat colour several times on this blog, including here, here and here. It still remains a mystery, mainly because although we know a lot about the patterns involved, and can guess about some of their adaptive advantages, their genetic bases are largely unknown. Using a mixture of classic pedigree studies and molecular genetics, a new paper in Genetics (abstract only unless you have a subscription) has examined the genetic bases of stripes and spots in the domestic cat.

Source: Genetics.

Previous attempts to unravel the genetics of coat colour in domestic cats had come up with the following hypothesis, based on tracking coat patterns down the generations. The character(s) producing the classic tabby (like my cat Pepper) – D in the figure above – is/are recessive to all other forms (the is/are ambiguity is because we have (or had) no idea about the number of genes involved). The dominant form is the unmarked (Abyssinian) form (A), which is dominant over the spotted coat (B), which in turn is dominant over the striped coat (like my cat Ollie – C).

To see how many genes are actually involved in determining cat coat patterns,  the researchers, led by Eduardo Eizirik, now at the Pontifíca Uniservidade Católica de Rio Grande do Sul (Porto Alegre, Brazil), set up a series of mating crosses. The figure below shows the way they studied the basis of the spotted and “ticked” (Abyssinian) variants. They crossed homozygous individuals (aa or AA, respectively), then “backcrossed” their heterozygous offspring (Aa – called the F1 generation), to each of the parental types (only aa in this example) and tried to make sense of what happened in the third generation (or backcross – this is the bottom line on the figure). This is essentially the same procedure used by Gregor Mendel with his peas, over 150 years ago, which led to the foundation of genetics.

Source: Genetics

The figure below shows what happened when they tried to work out what genes are controlling the “spotted” coat variant, by crossing it to the tabby version (top line). The offspring (F1) showed a range from stripes to spots to tabby blotches (not shown). The backcross animals sometimes showed complete stripes, including the “mackerel” variant (bottom left).

Source: Genetics

They then used “microsatellite” genetic markers – small sequences of DNA that can be used to track and identify regions of the genome that may be responsible for the character under study. They were able to identify at least three different genes responsible for coat patterns – Tabby, which has two alleles or versions (one producing the mackerel pattern, the other the blotched); Ticked, which has an Abyssinian and a non-Absyssinian version, and one or more genes that alter the mackerel stripes and may also produce the blotched pattern. Furthermore, Ticked can alter the wayTabby is expressed.

In other words, it’s complicated. Which is hardly surprising, in a way – if it was straightforward, cat breeders would have figured it out long ago. What this study has shown is that there are genes involved in coding colour and pattern, that they are not necessarily the same, and that they affect the way each others’ expression. Exactly how this happens – or indeed, what these genes actually do – is unknown. They have yet to be identified at the molecular level.

Intriguingly, some of these genes may have equivalents in other animals, and may help in precisely identifying the genes involved in cat coat colour. For example, a human gene that may be similar to Tabby may be involved in the rare Hermansky-Pudlak syndrome type 2, where patients have reduced skin pigmentation.

Once the genes involved in determining coat colour and pattern in cats have been identified, we will be able to have a stab at understanding how they do what they do what they do. It will also give us the opportunity to study these genes in the 37 felid species that are still roaming the planet. In turn, that may help us understand apparently simpler patterns, such as those seen in tapirs, raccoons and badgers.

Of course, just because different species have similar patterns, that doesn’t mean that they will necessarily use the same genes to produce them. Natural selection “cares” about the phenotype, not the genes that underlie that phenotype. There is more than one way to skin a cat.

[First posted over at the Z-letter.]

Hitchens on blaming the victim

January 8, 2010 • 11:26 pm

by Greg Mayer

Michael J. Totten has an interview with Christopher Hitchens concerning the piece in the Guardian by Nancy Graham Holm, in which she blames Danes for the attempted murder of the cartoonist Kurt Westergaard and his granddaughter.

Money quote:

These people [Holm and her ilk] are saying the grandfather and granddaughter were the authors of their own attempted assassinations. These are some of the same people who say that if I don’t believe in God I can’t know what morality is. They’ve just dissolved morality completely into relativism by saying actually, occasionally, carving up grandfathers and granddaughters with an axe on New Year’s Eve can be okay if it’s done to protect the reputation of a seventh century Arabian man who heard voices.

The piece by Holm is a truly execrable piece of nonsense, much worse than I had thought it would be. She believes (among other things) that: (a) the Danish Prime Minister should have apologized for the cartoons; and that (b) this would have prevented adverse reaction. Anyone who believes (a) doesn’t seem to have even a nodding acquaintance with the relationship between the government and the press in a liberal democracy; and anyone who thinks zealous arsonists and attempted murderers would be deterred by an apology has a more sanguine view of their appeasability than seems wise. Do read Russell Blackford’s analysis, linked to earlier by Jerry.

[The Guardian’s editors note two errors in Holm’s column, which they have corrected. One they missed is that she incorrectly describes Westergaard’s cartoon (did she not look at it carefully?); it depicts a fused hollow shell bomb, not a stick of dynamite. Hitchens, in his interview, states the cartoons were published in a “small town press”, which might be true on an international comparative basis, but Jyllands Post is Denmark’s largest circulation newspaper.]

h/t:  Andrew Sullivan

Russell Blackford on blaming the victim

January 7, 2010 • 5:59 pm

A few days ago, Nancy Graham Holm wrote an execrable column, “Prejudiced Danes provoke fanaticism,” in which she held Danish cartoonist Kurt Westegaard and the Danes themselves responsible for provoking an axe-wielding Muslim’s assault on Westegaard and his granddaughter.

Over at Metamagician and the Hellfire Club, Russell Blackford gives Holm a well-deserved spanking:

What utter nonsense! First, people in Western democracies (or, arguably, anywhere else) should have every right to be suspicious of religion, or of a particular religion, and the right to express their suspicion in whatever form they find most natural – including by way of satire or mockery. They should then have the right to stick to their guns and refuse to apologise, even if somebody takes offence. We can argue about whether or not a particular expression of views – once interpreted “correctly” – was wise or justified, or whether it was tainted in some way, but people do, or certainly should, have the right to express what they think and feel. It is not reasonable to demand that they give insincere apologies if someone else responds with violent acts. Even a wildly implausible view, tainted by suspect motivations, and expressed in a highly provocative way, does not provide any excuse for acts of murder. . .

Holm’s entire article is incredible. She would do better to stand up for the right of Danes such as Westergaard to be suspicious of religion – and to express it openly if it’s what they feel. What she has written is worth denouncing – soberly, deliberately, and in all seriousness this time. Let the name of Nancy Graham Holm find its place in every hall of ignominy and shame, indelibly incribed there for posterity.

I wonder if Holm has any regrets about what she wrote.

Francisco Ayala on “Signature in the Cell”

January 7, 2010 • 4:42 pm

by Matthew Cobb

Jerry, on his way to the Galapagos, asked me to post this. Over at Biologos, “Science and the Sacred” has persuaded Francisco Ayala  to write a review of Stephen C. Meyer’s Signature in the Cell. Here it is. There’s a debate going on over there, too.

How should a person of faith respond to Signature of the Cell? I am an evolutionary scientist who would suggest the following considerations.

The keystone argument of Signature of the Cell is that chance, by itself, cannot account for the genetic information found in the genomes of organisms. I agree. And so does every evolutionary scientist, I presume. Why, then, spend chapter after chapter and hundreds of pages of elegant prose to argue the point? It is as if in a book about New York, the author would tell us that New York is not in Europe, and then dedicate most of the book to advancing evidence that, indeed, truly, New York is not in Europe.

Signature of the Cell offers Intelligent Design (ID) as the alternative explanation to chance in order to account for genetic information. This suggestion turns out to be no more convincing than a proposal by the author of the book about New York, who having exhausted all possible ways of telling us that New York is not in Europe, would now offer Peoria as the alternative city to visit. We would rather read about New York’s architecture, splendid avenues, and great parks; about the rich culture and ethnic diversity of the city; about its restaurants, concert venues, theatres, and wonderful sights in and around the city. But regarding natural selection, genetics, ecology, development, physiology, and behavior in the evolution of genetic information, there is nothing substantive in Signature of the Cell.

Christians and other people of faith should be troubled about Signature of the Cell for several reasons. One is that Meyer avoids consideration of the negative implications of ID as an explanation of the origin of genetic information, which is his main subject. According to Meyer, ID provides a more satisfactory explanation of the human genome than evolution does. ID’s explanations envision “discrete or discontinuous intelligent activity in the history of life” (p. 481). Scientists have now obtained the complete DNA sequence of the human genome. The genome has a length of about three billion nucleotides, the “letters” of the DNA alphabet. Scientists have also obtained the complete DNA sequence of the chimpanzee genome—also three billion letters long—and of several hundred other species of organisms. How can we envision the “discrete or discontinuous activity” of the Intelligent Designer? The human and chimpanzee genomes differ from each other in just a few percent of the DNA letters, less than two percent in the genes that code for proteins. Did the Designer tweak the chimpanzee genome to make the human genome? Or, perhaps more likely, did the Designer use a preexisting genome and tweak it a bit to make the human genome and tweak it a different way to make the chimpanzee genome? Did the Designer go on tweaking genomes a bit at a time to design the genome of the gorilla and other primates, and more and more tweaking for other animals, all the way down to mice, and even to fruitflies, with which we share a good fraction of the genome?

The human genome includes about twenty-five thousand genes and lots of other (mostly short) switch sequences, which turn on and off genes in different tissues and at different times and play other functional roles. There are also lots and lots of DNA sequences that are nonsensical. For example, there are about one million virtually identical Alu sequences that are each three-hundred letters (nucleotides) long and are spread throughout the human genome. Think about it: there are in the human genome about twenty-five thousand genes, but one million interspersed Alu sequences; forty times more Alu sequences than genes. It is as if the editor of Signature of the Cell would have inserted between every two pages of Meyer’s book, forty additional pages, each containing the same three hundred letters. Likely, Meyer would not think of his editor as being “intelligent.” Would a function ever be found for these one million nearly identical Alu sequences? It seems most unlikely. In fact, we know how these sequences come about: one new Alu sequence appears in the genome for every ten newborns, generation after generation. The Designer at work? Unlikely: many of these sequences damage the genome causing abortion of the fetus during the early weeks of life.

Perhaps one could attribute the obnoxious presence of the Alu sequences to degenerative biological processes that are not the result of ID. But was the Designer incompetent or malevolent in not avoiding the eventuality of this degeneration? Come to think of it: why is it that most species become extinct? More than two million species of organisms now live on Earth. But the fossil record shows that more than ninety-nine percent of all species that ever lived became extinct. That is more than one billion extinct species. How come? Is this dreadful waste an outcome intended by the Designer? Or is extinction an outcome of degeneration of genetic information and biological processes? If so, was the Designer not intelligent enough or benevolent enough to avoid the enormity of this waste?

Meyer asserts that the theory of intelligent design has religious implications. “Those who believe in a transcendent God may, therefore, find support for their belief from the biological evidence that supports the theory of intelligent design” (p. 444). I do think that people of faith may find in the world many reasons that support their belief in God. But I don’t think that intelligent design is one of them. Quite the contrary. Indeed, there are good reasons to reject ID on religious grounds, in addition to scientific grounds. The biological information encased in the genome determines the traits that the developing organism will have, in humans as well as in other organisms. But humans are chock-full of design defects. We have a jaw that is not sufficiently large to accommodate all of our teeth, so that wisdom teeth have to be removed and other teeth straightened by an orthodontist. Our backbone is less than well designed for our bipedal gait, resulting in back pain and other problems in late life. The birth canal is too narrow for the head of the newborn to pass easily through it, so that millions of innocent babies—and their mothers—have died in childbirth throughout human history.

I could go on about human features that betray a design that certainly is not intelligent. I will add only one more consideration. More that twenty percent of all human pregnancies end in spontaneous abortion during the first two months of pregnancy. That is because the human genome, the human reproductive system, is so poorly designed. Do I want to attribute this egregiously defective design to God, to the omnipotent and benevolent God of the Christian faith? No, I don’t. It would not do to say that God designed intelligently the human genome and that it then decayed owing to natural processes. If God would have designed the human genome, surely He would have done it so that this enormous misfortune would not happen. Think of it: twenty percent of all human pregnancies amount to twenty million abortions every year. I shudder at the thought of this calamity being attributed to God’s specific design of the human genome. To me, this attribution would amount to blasphemy.

Before the scientific revolution of the sixteenth and seventeenth centuries, earthquakes, volcanic eruptions, and the like were attributed to direct action by God, so that the tsunami that five years ago killed two hundred fifty thousand Sumatrans might have been interpreted as God’s punishment. Now we know that these catastrophes are the result of natural processes. Similarly, people of faith would do better to attribute the mishaps caused by defective genomes to the vagaries of natural selection and other processes of biological evolution, rather than to God’s design.

h/t: Darrel Falk

The tracks of a ghost

January 7, 2010 • 4:48 am

by Matthew Cobb

One-time US Secretary of State Donald Rumsfeld actually got it right about one thing: there are unknown unknowns – things we don’t know we don’t know. A cracking example of an unknown unknown –transformed by discovery into a known known – has just appeared in Nature: the earliest known trackways produced by a tetrapod – a four-limbed animal that is part of the same lineage as dinosaurs, cats and us.

In 2006, Jerry’s Chicago colleague, Neil Shubin, discovered Tiktaalik, a lobe-finned fish that pulled itself out onto the land about 375 MY ago, exactly filling a gap in the fossil record. A year later, Polish paleontologist Grzegorz Niedzwiedzki discovered some traces of footprints in the disused Zachelmie quarry in the Holy Cross Mountains. At first he thought they were made by dinosaurs, but he eventually realised that the rock they were found in was far, far older than the earliest dinosaur.

These exquisitely-preserved traces not only date to 397 MY (22 MY years earlier than Tiktaalik) above all they clearly show the marks of feet and toes. They were not made by a lobe-finned fish. They were made by tetrapods. And big ones at that – some of the traces (there are around a dozen of them) suggest the animals were up to 2 metres long.

Left: Laser scan of trace. Right top: drawing of left hind limb of known fossil, Ichthyostega, bottom of Acanthostega, both of which show similarities to the limb that left the trace.

Some of the traces show clear examples of parallel and alternating limb movement, like those made by modern reptiles or amphibians.

Left: trackways; animal is presumed to be traveling from bottom to top. Middle: graphic representation of traces. Right: generic tetrapod showing how its gait might have created the traces. Source: Nature

We don’t know exactly what made the traces, because there are no skeletons to go with them. But the fact that they show such clear traces of toes shows that the current view that tetrapods evolved at most 385 MY ago is wrong. Behaviour has trumped anatomy – we can see what the animal did, even if we don’t (yet) know exactly what animal made it. For the moment, these animals are “ghost fossils” – they must have existed, but we don’t know what they were.

Evolutionary tree of living and fossil lobe-finned fishes, and tetrapods. The new tracks are given in green. Dashed red lines = “ghost fossils”. 1 = earliest articulated tetrapod skeletons; 2 = earliest isolated tetrapod bones; 3 = earliest known tetrapodomorph fish; 4 = possible earlier tetrapodomorph fish. Source: Nature

It’s not only the date that’s got people excited, it’s also the location where these fossils were found. Not an obscure Polish quarry, but the tropical tidal mud-flats that made up the rock that was eventually dug up nearly 400 MY later. It was previously thought that the first steps onto land – like those by Tiktaalik – were made in brackish ponds. The authors correctly write that their discoveries “force a radical reassessment of the timing, ecology and environmental setting of the fish-tetrapod transition, as well as the completeness of the body fossil record”.

Here is a terrific video produced by Nature to explain the discovery. It includes a great scene where they bring a model of Tiktaalik to the cloud-shrouded gloomy quarry and show that it couldn’t have made the footprints… (For reasons too boring to mention, this is taken from The Guardian website.)

[vodpod id=ExternalVideo.913408&w=425&h=350&fv=playerID%3D26396137001%26%40videoPlayer%3D60439973001%26domain%3Dembed%26autoStart%3Dfalse%26adServerURL%3Dhttp%253A%252F%252Fads.guardian.co.uk%252Fhtml.ng%252Fspacedesc%253Dvideo%2526system%253Dvideo%2526title%253D60439973001%2526site%253DScience%2526url%253D%2525252Fscience%2525252Fvideo%2525252F2010%2525252Fjan%2525252F05%2525252Ffirst-tetrapods-walked-earth%2526comfolder%253DEnvironmentConservation%2526keywords%253DFossils%25252B%252528Science%252529%25252CZoology%25252CEvolution%25252B%252528Science%252529%25252CScience%25252CAnimals%25252B%252528News%252529%25252CWorld%25252Bnews%2526bandwidth%253Dcable%2526tile%253D5924007%2526partnerid%3D%2526]

There are some other fascinating points raised by this research.

First, Swedish paleontologist Per Ahlberg, who helped guide the discovery into the pages of Nature, writes: Niedzwiedzki made his amazing finding by looking in the “wrong” place (“everyone” knew that the tetrapod transition to land took place at another time, in different kinds of rocks): “If you’re thinking of applying to a research council for a grant to do that, you are virtually certain to be turned down. But you need to have the opportunity to do what might seem to be crazy things. It’s only by doing this kind of stuff that wildly unexpected things can be discovered.”

Given the current debate in the UK over government proposals requiring research to have social and economic “impact”, this is a telling comment. Many (most?) of the  most stunning scientific discoveries have been made by accident, or without any expected “impact”.

Second, these animals were not the first to venture onto the land. Invertebrates got there first. The earliest know terrestrial arthropods were Trigonotarbids, tiny spider-like animals that ventured onto the land around 400 MY ago, and are now preserved in the Rhynie chert in Scotland. Something clearly happened to the Earth’s ecosystem at this time that made it possible for a wide range of organisms to colonize the land. Within 30 MY or so, the dry surface of our planet was teeming with walking and crawling things.

Finally, as I write this, I have just finished marking some student essays about the evolution of odorant binding proteins (OBPs). These are enigmatic molecules that all terrestrial animals have in their noses (or antennae), and which – in ways we don’t really understand – help us to smell. One of the things these OBPs do is to help smells get through the watery barrier that protects our smell neurons.

Fish, strikingly, do not have OBPs, but they do have a sense of smell, which only works in the water. So we can be pretty certain that when the first animals stuck their noses into the air, they couldn’t smell. Per Ahlberg suggests that the Polish “ghost fossils” would have been coming onto the land to nibble at the flotsam and jetsam left by the tide – dead fish and so on. Maybe so, but if they were, they wouldn’t have been able to smell those rotting fish.

Or, to put it another way, any animal that could produce a molecule that would help to detect those stinking fish would be at an immediate advantage – natural selection presumably led to the rapid evolution of these molecules and of this key sense. Curiously enough, the deep phylogenomics of OBP genes might tell us something important about those first steps onto the land, and about the “ghost fossils” that left these amazing traces.

h/t: Ray Moscow

First posted over at the z-letter

I get mail

January 6, 2010 • 12:31 pm

. . . unfortunately, sometimes it’s from creationists.  Here’s a present that came from Paul Nelson in yesterday’s mail.  Nelson was apparently inspired by my post about this movie (whose showing is causing a bit of a kerfuffle in Los Angeles) to send me my very own copy.  I just can’t wait to see it!

Fig. 1.  Madness on the hoof.

Nelson, who has a Ph.D. in philosophy from the University of Chicago, is a young-earth creationist (YEC) and a fellow of the Discovery Institute. (Not surprisingly, the DI doesn’t mention his young-earther views in its biography, probably because they’re at odds with the views of the DI’s old-earther loons.)  Nelson has written some stuff about the Cambrian explosion, and co-authored a book with two others, including Stephen Meyer, who as far as I know is an old-earther.

I’m baffled about how a YEC can even deal with the Cambrian explosion.  Sure, they might think it was instantaneous (it was not), or that it couldn’t be explained by natural selection, or that God did it, but one thing they must confront is this:  when did it occur? All the available evidence points to around 550 million years ago. Folks like Nelson think that it occurred no more than 10,000 years ago.  To hold that view, they must categorically reject every bit of geological, chemical, and physical evidence that enables us to date fossils.  This is a species of insanity I can’t fathom, even if it comes from a blind adherence to religious dogma.

Anyway, I will watch this movie and report back.  Don’t expect a positive review.