Basics: Synteny

Let’s play the most boring card game in the universe!

Here are the rules. We start with a fully sorted deck of 52 cards, and we deal out four hands. We don’t deal in the ordinary way, either: we give the top 13 cards to the first player, then the next 13 to the second, and so forth. (We could also do the usual deal, but it makes the illustration and logic a little more difficult to see. We’ll keep it simple for now.)

This is what the table will look like.

Hand 1 Ai-233f23e2a2ca8059264849e39e1760d2-heart.gif Ki-233f23e2a2ca8059264849e39e1760d2-heart.gif Qi-233f23e2a2ca8059264849e39e1760d2-heart.gif Ji-233f23e2a2ca8059264849e39e1760d2-heart.gif 10i-233f23e2a2ca8059264849e39e1760d2-heart.gif 9i-233f23e2a2ca8059264849e39e1760d2-heart.gif 8i-233f23e2a2ca8059264849e39e1760d2-heart.gif 7i-233f23e2a2ca8059264849e39e1760d2-heart.gif 6i-233f23e2a2ca8059264849e39e1760d2-heart.gif 5i-233f23e2a2ca8059264849e39e1760d2-heart.gif 4i-233f23e2a2ca8059264849e39e1760d2-heart.gif 3i-233f23e2a2ca8059264849e39e1760d2-heart.gif 2i-233f23e2a2ca8059264849e39e1760d2-heart.gif
Hand 2 Ai-94f8cf214b78029e2cd1e9398229dda0-club.gif Ki-94f8cf214b78029e2cd1e9398229dda0-club.gif Qi-94f8cf214b78029e2cd1e9398229dda0-club.gif Ji-94f8cf214b78029e2cd1e9398229dda0-club.gif 10i-94f8cf214b78029e2cd1e9398229dda0-club.gif 9i-94f8cf214b78029e2cd1e9398229dda0-club.gif 8i-94f8cf214b78029e2cd1e9398229dda0-club.gif 7i-94f8cf214b78029e2cd1e9398229dda0-club.gif 6i-94f8cf214b78029e2cd1e9398229dda0-club.gif 5i-94f8cf214b78029e2cd1e9398229dda0-club.gif 4i-94f8cf214b78029e2cd1e9398229dda0-club.gif 3i-94f8cf214b78029e2cd1e9398229dda0-club.gif 2i-94f8cf214b78029e2cd1e9398229dda0-club.gif
Hand 3 Ai-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif Ki-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif Qi-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif Ji-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 10i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 9i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 8i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 7i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 6i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 5i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 4i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 3i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 2i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif
Hand 4 Ai-37cc42c4042ea4372806e327e67b2e42-spade.gif Ki-37cc42c4042ea4372806e327e67b2e42-spade.gif Qi-37cc42c4042ea4372806e327e67b2e42-spade.gif Ji-37cc42c4042ea4372806e327e67b2e42-spade.gif 10i-37cc42c4042ea4372806e327e67b2e42-spade.gif 9i-37cc42c4042ea4372806e327e67b2e42-spade.gif 8i-37cc42c4042ea4372806e327e67b2e42-spade.gif 7i-37cc42c4042ea4372806e327e67b2e42-spade.gif 6i-37cc42c4042ea4372806e327e67b2e42-spade.gif 5i-37cc42c4042ea4372806e327e67b2e42-spade.gif 4i-37cc42c4042ea4372806e327e67b2e42-spade.gif 3i-37cc42c4042ea4372806e327e67b2e42-spade.gif 2i-37cc42c4042ea4372806e327e67b2e42-spade.gif

Next, we play the game, whatever it is. It really doesn’t matter, since we know exactly what hand everyone has, right? So don’t worry about the rules for that. What’s important is that next the dealer carefully picks up each hand in reverse order and stacks them, restoring the original arrangement of the deck.

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Ray Comfort answers a question

I had no idea Ray Comfort was running an Agony Aunt column, but here you go. He got a rather snarky question:

There’ve been several hundred gay marriages enacted in California in the past few days. Maybe a couple of thousand by now, I haven’t checked the numbers. And in the non-gay-marrying Midwest, they’re fighting floods, while in California it’s fair and dry. How is The Golden State managing to escape the wrath of your imaginary friend, I wonder?
Weemaryanne

And then he answered it. Seriously. Isn’t it nice how God has arranged that there is pain and suffering in every part of the world, just so His preachers have something to point to and say “Sinners!”?

Maryanne. At present there are 840 wild-fires that are burning at once in California, destroying many homes. The fires were started by lightning strikes. Guess who’s in charge of the electrical department? These are from thunder storms that have no rain. Guess who gives the rain? You said “while in California it’s fair and dry.” We are having the worst drought in our recorded history. Last year 1,155 homes were destroyed.

It’s always nice to see these kooks get explicit and credit rain to the actions of a god rather than natural meteorological processes. It’s so primitive.

Ah, if only we had stoned those gay people, fire insurance rates in California would be so much lower.

But wait! There’s more! Quick, remove those irony meters from the circuit, because Comfort’s closing will definitely cause them to blow!

You live in an imaginary world. I suggest you get out more.

Right now, my yard is littered with a couple of tons of twisted, smoking scrap irony.

Lenski gives Conservapædia a lesson

Once again, Richard Lenski has replied to the goons and fools at Conservapædia, and boy, does he ever outclass them. For a quick outline of the saga, read this summary at A Candid World; basically, Andy Schlafly has been demanding every bit of data from Richard Lenski’s work on the evolution of E. coli, despite the fact that Schlafly doesn’t have the background to understand it and doesn’t have any plan for what he would do with it if he got it. Lenski has been polite and helpful in his replies; his first response is a model for how to explain difficult science to a bullying ideologue. Now his second response is available, and while he has clearly lost some patience and is unequivocal in denouncing their bad faith efforts to discredit good science, he still gives an awfully good and instructional discussion.

I’ve put the whole thing below the fold, in case you’d rather not click through to that wretched hive of pretentious villainy at Conservapædia.

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Gordy Slack replies

Yesterday, I ripped into Gordy Slack and the NY Times for bad articles on creationism. Now Slack has responded, and in the interest of fairness, I urge you to look at that comment and browse down to several others he has also made.

He’s still wrong, and I still find his article incredibly bad.

Slack’s article is titled “What neo-creationists get right: an evolutionist shares lessons he’s learned from the Intelligent Design camp“. I chewed him out because nothing in his list is anything that creationists got right — it’s a litany of common scientific arguments and complaints — and all he’s doing is falsely pandering to their self-esteem. He says he didn’t try to claim that the creationists came up with these common questions first; OK, he didn’t. He says he wasn’t trying to give creationists credit for being right; OK, I think he’s on shaky ground with that one, but I’ll concede the point to him. Now we’re left with a problem: what the heck was his article about, then? It’s reduced to a shallow attempt at finding coincidental similarities, with no thought put into them.

For instance, his first point of similarity is that creationists say that we haven’t answered the big questions of abiogenesis, and scientists say the same thing. Gosh, we’re in agreement! But no, we’re actually not. Creationists like to point to places where we don’t have all the answers, because they see that as a flaw, as a way to discredit evolution — they like to pretend that they have absolute, perfect knowledge in their holy book, even if all they do is fill the gaps with an unsatisfying and pathetic “god did it.” Scientists are comfortable with uncertainty and change, and they see those gaps as research opportunities — places where information is admittedly deficient, but where new work can be done. What Slack treats as a similarity is actually a fundamental philosophical difference.

And this is precisely where Slack is most unsatisfying. He claims to be trying to understand the creationist mindset, yet all he offers is credulous tripe in which he demonstrates that he hasn’t thought things through. Here, for example:

It surprises me that PZ is so pissed off by my efforts to understand why so many Americans reject evolution. If you ask them, and I have bothered to ask hundreds or thousands over the past two years, many will tell you that more than anything else, it’s the arrogant zealotry of cocksure ideologues that turns them off to evolution. They see people calling their intuitions and worldviews retarded and corrupt, and they march the other way. That’s one reason why we evolutionists have done such an abysmal promotions job even though we’re armed with the most delightful and seductive and potent theory ever. If we can’t sell evolution, we must be doing something wrong. Right? I’m just saying that we might start by resisting the urge to spit bile in the face of potential buyers.

Slack has chewed out most supporters of evolution as doing so without much depth of understanding — they don’t know about genetic drift, for instance. Yet here he is discussing a group who believe the earth is less than ten thousand years old, who are abysmally ignorant of all of evolutionary theory, including drift, who believe with the utmost certainty that Darwin is burning in hell and that all scientists will be following him, and he accuses the scientists of arrogance, on the word of the creationists.

Here’s a clue: Slack got it backwards. It is simply absurd to claim that they are turned off by “the arrogant zealotry of cocksure ideologues”, since that is a more apt description of their own than of scientists. Creationists love arrogance. Their whole schtick is about obedience to the precepts of meddling, pushy busybodies, either the phantasmal kind of their imaginary deity or the sadly real kind of the ranting big-haired zealots who lead their churches. You have to learn fundie-speak to understand what these informants are actually saying.

To them, “arrogant” means “competing authority with an intimidating amount of real-world evidence”.

And of course they resent that. They believe in irrelevant nonsense that requires them to constantly descend deeper and deeper into lunatic rationalizations to maintain that willful suspension of disbelief. And we come along with that “delightful and seductive and potent theory” that they have to close their eyes to, and which merely demands that they reject the temporal authority of their leaders, who threaten them with hellfire and the loss of their children’s love and morality if they accept the evidence. That really is a serious problem, and I know how difficult many people find it to abandon those beliefs, but to call our side “arrogant” while treating their side as humble is not helping. It is reinforcing falsehoods. It is also not going to resolve the problem, because it is a simple fact of the matter that scientists are a competing authority, and they do have an overwhelming amount of evidence that the creationists are wrong, wrong, wrong. Those are not points that we will surrender.

Slack is also unhappy that he has been vigorously criticized and insulted and shredded up one side and disemboweled down the other, all without regard for his genuine appreciation of good science. That’s all true. Comment threads here are not for the temperamentally delicate, that’s for sure, and everyone gets the rhetorical knife all the time (and that includes me: if Slack is appalled that he is being insulted, he ought to spend some time in my shoes. At least no one has threatened to shoot him over this argument yet.) Complaining about that is pointless. It’s like whining that the crucible is hot; of course it is, that’s what they’re for.

As for the complaint that we’re an angry, hostile bunch here: in a country where the enterprise of science and education are seriously threatened by the activist religiosity of ignorant creationists, where politicians defer to religious lunacy, where the craven media has abandoned the concepts of adversarial and investigative journalism, we’re mad as hell and aren’t going to take it anymore*. I propose that there is something wrong with you if you aren’t angry.

*That’s a quote. Look it up, it seems rather appropriate here.

Word salad, with math

I guess most of us missed a bizarre poster at the Evolution 2008 meetings tonight. It was basically a paper titled The Evidently Imminent Phyletic Transition of Homo sapiens into Homo militarensis (the military hominid), by Richard H. Lambertsen. It’s garbage from the first page, I’m afraid, in which the author tries to demonstrate that there must be direction and intent in the evolution of life, and that “Earth’s largest blue whale (Balaenoptera musculus)
swimming at peak velocity most precisely represents the
central tendency of evolution.” This is followed by many pages of oddball math in which the author cites Einstein, Feynman, and himself quite often.

And then it gets weird.

The science of LAMBERTSEN and HINTZ
(2004) and LAMBERTSEN (2007) holds that the
key morphological innovation enabling maximization of free will in the organic domain was a
novel craniomandibular articulation (the MMA).
The MMA trigger enables high dEk/dt events to
be accomplished with precision. Furthermore,
the cosmological constraint confirmed implies
that maximization of free will by means of trigger
action will lead to self-destruction.

Get that? A novel jaw mechanism in whales is the pinnacle of free will.

And then it gets weirder.

Noting the apparent chiral kinematical
symmetry between the MMA and the specialized
trapeziometacarpal, or “saddle” joint of the
hominid thumb, LAMBERTSEN (2007) therefore
warned…

“[In view of that apparent chiral] symmetry we now
must expect trigger actions referable to extremely
powerful individuals that do not lead to self-
destruction, but instead cause the wanton
destruction of others. This is to say that there has
been a paradigm shift in the realization of individual
power. The means to that power is different. The
direction of evolutionary change is not. It thus is to
be expected that aged individuals suffering the
effects of senescence will use the more vigorous
young to achieve their base intention… that mentally
adept if egregious individuals of age will exploit
skillfully the combined naiveté and strength of near
juveniles.”

Because there is a resemblance in the shape of hominid thumbs and whale jaw joints, people are going to do bad things. This is then confirmed by Bush’s invasion of Iraq.

This is literally insane stuff. That interpretation is confirmed by the end of the paper, which contains a series of questions addressed to George W. Bush, including a demand to know if he was the one who sent a sniper to his house at 2:00pm on 28 January, and whether he personally stole Lambertsen’s driver’s license. There was also a bizarre incident in which Lambertsen was arrested for disrupting a flight.

This is just sad. Lambertsen actually does have some scientific qualifications, and has published respectable papers on baleen whales, and you can see buried in this one a foundation of serious work on whale anatomy and physiology. He clearly needs psychiatric help now, though.

Alas, it just goes to show that having something presented at a science conference does not necessarily imply that it is scientific, or even sensible. Keep this in mind when you see the creationists striving to get a single paper published…

And please, I hope somebody gets Lambertsen the help he needs. He isn’t an evil man or a stupid man — he’s got something organically wrong with his brain, I fear, and needs psychiatric intervention.

Denver Pharyngufest

I’m never this organized, so I don’t know what’s wrong with me. I’m going to be in Denver on 3-4 July, and we’re actually getting it together to plan a meetup at the RockBottom Restaurant on 16th and Curtis in downtown Denver. I’ll be there around 5ish on Thursday, 3 July, and I’ll leave when you stop buying me beer.


We have changed the location to Wynkoop Brewing Company. Don’t get lost!

Mark your calendars!