The platypus genome

Blogging on Peer-Reviewed Research

Finals week is upon me, and I should be working on piles of paper work right now, but I need a break … and I have to vent some frustration with the popular press coverage of an important scientific event this week, the publication of a draft of the platypus genome. Over and over again, the newspaper lead is that the platypus is “weird” or “odd” or worse, they imply that the animal is a chimera — “the egg-laying critter is a genetic potpourri — part bird, part reptile and part lactating mammal”. No, no, no, a thousand times no; this is the wrong message. The platypus is not part bird, as birds are an independent and (directly) unrelated lineage; you can say it is part reptile, but that is because it is a member of a great reptilian clade that includes prototherians, marsupials, birds, lizards and snakes, dinosaurs, and us eutherian mammals. We can say with equal justification that we are part reptile, too. What’s interesting about the platypus is that it belongs to a lineage that separated from ours approximately 166 million years ago, deep in the Mesozoic, and it has independently lost different elements of our last common ancestor, and by comparing bits, we can get a clearer picture of what the Jurassic mammals were like, and what we contemporary mammals have gained and lost genetically over the course of evolution.

We can see that the journalistic convention of emphasizing the platypus as an odd duck of a composite creature is missing the whole point if we just look at the title of the paper: “Genome analysis of the platypus reveals unique signatures of evolution.” This is work that is describing the evidence for evolution in a comparative analysis of the genomes of multiple organisms, with emphasis on the newly revealed data from the platypus.

[Read more…]

A few things that amused me

Here’s a bizarre miscellany.

  • Well, it’s just Wisconsin.

    Two people have been arrested after a Juneau County Sheriff’s deputy found one of them and her two children living in a home with the body of a 90-year-old woman decomposing on the bathroom toilet.

    Tammy D. Lewis, 35, and Alan A. Bushey, 57, both of Necedah are each charged with two felony counts of causing mental harm to a child, according to a criminal complaint filed Friday. Lewis also faces one count of obstructing police.

    The body was decaying for two months in their bathroom. How could they do that? It takes religion to be that crazy!

    Lewis told the deputy that “God told her Alvina would come back to life if she prayed hard enough.” Bushey told the deputy that “Lewis was obedient and served the Lord just as she should.”

    The 12-year-old boy later told investigators that after Middlesworth died, Bushey told him her appearance “was the result of demons attempting to make it appear that Alvina would not come back to life. The boy also reportedly said that Bushey told him that if Middlesworth’s death was discovered, he and his sister would have to go to public school and get jobs because the woman, whom the boy referred to as his “grandmother,” was paying the bills.

  • The ICR has put out an enemies list. There are three people on it: Richard Dawkins, Eugenie Scott, and … me! They noticed <sniff> — I’m so touched.

  • Adnan Oktar, aka Harun Yahya, the notorious Turkish creationist, has been convicted of “creating an illegal organization for personal gain”, and has been sentenced to 3 years in a Turkish prison. Hooray! Justice at last!

When will they learn? Another internet poll

The town of Frankenmuth, Michigan likes to flaunt their crosses — they’ve put them up on signs, and they’ve got one on the city logo. I suspect the town contains a Christian majority, so their local news probably felt safe putting up an online poll asking,

Should Frankenmuth remove its cross from the city shield?

They don’t expect a horde of ravening godless atheists to descend on them and vote “YES!” — they never do. Mount up, internet warriors, and assault their poll with fire and sword and level it until they reel back crying for mercy.

Frankenmuth won’t know what hit them.*

*Literally; most probably won’t even notice. It’s just a pointless internet poll.

Shiny. Pretty. Slimy.

Wired has a pretty gallery of images from the recent Colossal Squid necropsy. If you’ve ever wondered what a pile of squid guts would look like on a table, here you go.

i-8e7802c0c7cc4151566d81f9a2db01e8-squid_guts.jpg

It’s too bad the images aren’t quite large enough to use as wallpaper on my laptop.

Oh, and those colors—that’s exactly what slug guts look like, too. We natives of the Pacific Northwest have many opportunities to get familiar with those.

Pinellas County, Florida expels science

This is the Friends of Brooker Creek Preserve website — it looks exactly like the kind of organization I would support, a community effort to protect a local wildlife area. They lobby, they educate, they offer opportunities to hike and experience nature.

One problem: it’s in Florida. That seems to mean the organization is infected with stupidity and cowardice.

As part of their educational mission, they were going to have a speaker come in next last Febrary, Dr Lorena Madrigal of the University of South Florida. She studies genetics and human evolution, and was going to speak on 12 February, Darwin Day. To the Pinellas County bureaucrats, this is a problem.

“Biology without evolution is not biology,” she suggested, which obviously explains, at least in the mind of William Davis, the Pinellas County director of environmental services, why the professor’s speech would be problematic.

“Her topic was about evolution,” Davis said. Well, yeaaaaaah! “I flinched on that.”

“I canceled her out after discussing it with my supervisors,” he said. “We are not the platform for debate on creationism versus evolution.”

Right. Talking about evolution might annoy the creationists, so the county’s response is to shut down and silence efforts to educate and inform by an environmental institution which relies on evolutionary biology to perform its mission. This is a perfect example of how creationists work to keep people ignorant, and create an environment free of legitimate information about a subject that contradicts their absurd literalist beliefs.

An hour of radio inanity

I’ve tuned into KKMS, although to be honest, I lost all respect for these evangelical radio cretins when they had that Simmons “debate” and left me out. We’ll have to see if their guest’s attempts to criticize atheists in their absence will be as effective.

I’m trying to grade exams while simultaneously listening — it’s like listening with half my brain tied behind my back.

The host claims that it is important to understand the perspective of the “New” Atheists…so why are they inviting this Aikman clown on, instead of an actual atheist?

Aikman claims the atheists are bringing “pestilence”, and claims that we only pick on Christians (what? What about Hitchens?) because Christians are so good and kind and generous and won’t blow them up. We’re already in stupid territory: the atheists criticize Christians because they are the dominant element in our culture.

We get some whining about how Christianity is portrayed in the media (ubiquitously?), and an uncontested claim that the religion is a benefit to society.

So far, I’m still waiting to hear a real criticism of atheism and atheists.

Oh, yeah…”I used to be an atheist”. I knew he’d say that eventually. It’s amazing how 99% of the evangelical world seems to have been godless, once.

Now we get another predictable claim: atheists have done all the evil of the 20th century, and communists and Pol Pot get dragged out.

Another predictable point: there is no basis for atheist morality. To which I always wonder, if there is no god, then there must be no basis for Christian morality either.

These guys are completely clueless. This isn’t an exercise in learning more about the New Atheists, it’s 3 ignoramuses making up stuff with one another.

Good — August Berkshire called in to criticize, and hit them with a good question: if god is a source of morality, what is the Christian position on the death penalty? On contraception? Would you believe the Aikman clown tried to claim that the death penalty is not a moral issue? The DJs tried to run away and claim that their belief in the crucifixion is the core of their belief…which is not a moral issue, either. Aikman tries to dig up Hitler, and claims everything is about the basis of morality, while avoiding the simple fact that Christianity does not provide simple moral guidance.

Berkshire throws their own claim that the ten commandments are the basis of morality by pointing out that the punishments for violating most of those rules was death. When they try to duck and weave by saying they don’t follow the Old Testament rules anymore, Berkshire hammers on the obvious fact that there has been a rather substantial change in the treatment of moral issues.

Another caller: Jeff from Maple Grove, who babbles a bunch of apologetics for the Old Testament. God Hates Sin. He didn’t change his mind! Dear dog, I’m feeling my brain leaking away as I listen to these idiots.

Now Damon in Las Vegas calls in. Points out that atheists can’t disprove the Christian god, but Christians can’t disprove the other gods, but dismiss them — how do they do that? Aikman answers (?) that Christians believe they can have a relationship with god mediated through Jesus, and that the historical evidence for Jesus is strong, and then makes up a bunch of bullshit about evidence for the resurrection (making it up all the way). Then he claims again that he used to be an atheist.

He doesn’t answer the question!

Bob calls in to address August, and again, he claims god didn’t change, the people did. August clearly hit a nerve with that one.

Tony (Toni?) calls in to explain that she lost her Catholic faith and is an atheist, and her old associates all think she’s going to burn in hell. She asks how a loving and just god could do that. Aikman chickens out and refuses to answer. The DJs try to dig into her Catholic background, and then basically tells her to accept it, and that you have to be perfect to live forever, and that’s Jesus’s gift…they’re essentially telling her that she gets to burn in Hell. Aikman butts in and tells her to read Strobel. Strobel! That guy is awful.

I must apologize for mentioning this radio show to everyone. It’s pathetic. It’s three buffoons babbling on the air. I didn’t learn a thing about atheism (how could I? They had no knowledge between them), but I was reminded once again how foolish theology is.

Ken Miller weighs in on Expelled

Guess what? He didn’t like it, nosir.

“Expelled” is a shoddy piece of propaganda that props up the failures of Intelligent Design by playing the victim card. It deceives its audiences, slanders the scientific community, and contributes mightily to a climate of hostility to science itself. Stein is doing nothing less than helping turn a generation of American youth away from science. If we actually come to believe that science leads to murder, then we deserve to lose world leadership in science. In that sense, the word “expelled” may have a different and more tragic connotation for our country than Stein intended.

That’s timely, since it’s also a theme of Miller’s new book, which argues strongly that creationism has destructive consequences for America’s scientific enterprise.

Seattle is calling me…

After all, the big squid are washing up on Puget Sound beaches, so I, too, feel the call. I’m going to have to make the journey.

It also helps that the Northwest Science Writers Association has invited me to come out and give a talk. I’ll be speaking on 2 June at the Pacific Science Center on communicating science, somehow. I think I’ll also be spending several days visiting family and friends…and maybe some of those poor lovely tentacled denizens of the Sound who find themselves stranded on the shore.

Light…tunnel…end of…going into! The light!

My last class for this semester was today. I’m done with the teaching part, now all that’s left is the dry, husky, tedious, boring administrative part: final exams and grading and the passing of final judgment on the efforts of my students. I get to become a mindless bureaucratic drone unenlivened by creative thought for a little while.

Anticipate continued incoherence, with light and scattered posting for a while. But there is hope, and none too soon.