Field of Science

Roy Moore is still running for governor

A friendly commenter on an older post of mine reminded me that Roy Moore is running for governor in Alabama. Thanks.

Here's Moore's view on education.

Moore thinks that what's wrong with the American education system is that there isn't enough freedom:
By freedom, I mean the freedom within our education system to allow other schools to compete with public schools, freedom of parents to control the education of their children, freedom of teachers to do their job without burdensome restrictions, and freedom of both students and teachers to express their belief in God and moral standards.
As governor, I will fight to allow parents greater freedom to choose the proper education for their child, whether public school, private school, Christian school, or home school.
Muslim school, Jewish school, Scientology school, FSM school.
Finally, we must remember that God is the true source of wisdom and understanding. As governor, I will protect the freedom of teachers and students to recognize God in prayer and our Pledge of Allegiance.
I wonder if he'll protect the freedom of teachers and students to recite Muslim, Jewish, Hindu, and Buddhist prayers in school.

In other news:
Roy Moore disrespects the non-religious.

Quantitative evolution school in Okinawa, 2010

At the winter school I'm at in Japan, I've just learned of an interesting summer school they will be having here next year in May:

Quantitative Evolutionary and Comparative Genomics.

It will be at OIST in Okinawa May 24 to June 4, 2010.

The theme is ultra-conserved sequences:
The theme of the 2010 Summer School is the phenomenon of strong (or extreme) sequence conservation, which will be explored from a quantitative and multidisciplinary perspective, and connections forged with parts of biology outside of genomics.
Students can apply to have all travel and accommodation costs covered. Application deadline is February 15.

Speakers:
  • Nadav Ahituv, UCSF
  • Peter Arndt, MPI Berlin
  • Gill Bejerano, Stanford
  • Emmanouil Dermitzakis, Geneva
  • Takashi Gojobori, National Institute of Genetics, Japan
  • Ueli Grossniklaus, Zurich
  • Jotun Hein, Oxford
  • Jonathan Miller, OIST
  • Erik van Nimwegen, Basel
  • Howard Ochman, Arizona
  • Anirvan Sengupta, Rutgers
  • Gasper Tkacik, U. Penn
  • Byrappa Venkatesh, IMCB Singapore
  • Ting Wu, Harvard Medical School

Sex is too weird for this blog

Sexual selection. Mmmm. No field matches biology, with lab meetings full of discussions about the benefit of sex, details of reproduction, and anatomical wonders of private parts.


From PartiallyClips.com.

Sexual selection is - apparently, and to my amazement - contentious. Not really, but someone think's it doesn't fit the bill. I find that... [just, no comment].

1 fucked-up weird trick, indeed

Has anyone else seen this advertisement?



I watched the whole video (almost), and the basic idea - though wrapped in escapades and ennuendos* - is very interesting.

It is this.

Back in time when we (they, really) were all cavemen and up for group photos, we were all slim and beautiful not despite but exactly because we ate whatever we wanted whenever we wanted to. Steak for breakfast and brie at tea-time. It was all a big mess, and that's precisely why it worked. Not because food was scarce (come on, it was the days of the giant sloths), but because one day you'd eat breakfast at IHOP and Denny's at the same time, and then nothing until the afternoon two days later, when you stumbled upon a truck-load of zebras who had fourtuitously died right in your back-yard, and the only thing you ate were the fat dripping off their zebra ears. Point is, that food came irregularly, and somehow eating irregularly then made us stay slim and beautiful. It had nothing at all to do with our genes, the fact that food was scarce (because zebra live in flocks, don't you know), or that estrogen-like compunds were in all sources of food, or even that you lived in America, which is God's chosen people for the obese-experiment.

Cavemen stayed slim because they followed this 1 wierd old trick: eat irregularly (but do, FOR GOD'S SAKE, buy my book priced at $39.99 for your benefit) and follow this detailed plan of what to eat when (because that's what the cavemen would do).

* Look, you fucker, number one I am typing on a Japanese keyboard that's got all these funky characters from outer space and number two I've had a truck-load of pseudobeer and number three fuck commas and number four I am watching Eddie Izzard on youtube, so you can bloody well substitute my attemps at being the proper grammarian (yes, that's a word) with the proper britshit.

Computational modeling in Okinawa

I have just arrived at Okinawa Institute of Science and Technology to participate in Winter School on Computational Modeling in Biology - Data and model sharing by SBML and insilicoML. I expect it will be a hugely advantageous learning experience, and that attending the program will increase my bargaining power enormously. I've never been to Okinawa before, but I must say it's really nice here. I have a room with a ocean view, but absolutely no time to go outside at all for the four days I am here.

The school will present and train participants in these technologies:
SMBL - a markup language for describing systems biology models
SBGN - visualizing biological and models
insilicoML - XML based language for describing hierarchy and modularity of physiological functions in multiple levels
insilicoIDE - model editor working in conjunction with insilicoML
CellDesigner - biochemical networks modeling

What does this all mean? I'm not quite sure, but I just might tell you when I find out.

Carnival of Evolution 18



Carnival of Evolution number 18 is up at Biochemical Soul. Irradiatus, founder of CoE, has been managing the carnival really well for a long time, but now he has decided that the time has come to let it go, so he can get some serious research done. He has asked me to take over CoE, which I have happily accepted.

More news to follow on carnivalofevolution.blogspot.com.

Dog speciation

Great post on skepticblog by Daniel Loxton revealing (I think that's the right word) that AiG-type creationists actually think Darwin was right.
creationist leaders share Darwin’s belief that species routinely change (and even originate) through mutation and natural selection.
Indeed, according to Answers In Genesis’ (AiG) current web feature “Top 10 Myths About Creation,” it’s a straw-man to suppose creationists think otherwise:
A popular caricature of creationists is that we teach the fixity of species (i.e., species don’t change). And since species obviously do change, evolutionists enjoy setting up this straw-man argument to win a debate that was never really there in the first place.
Weird, right? But wonderful, that they believe in evolution after all. Or not?
Creationists have long been amazed by the diversity within each created kind (or baramin, roughly on the family level). We know that species do change—but only within the original kinds God created roughly 6,000 years ago.

Species changing via natural selection and mutations is perfectly in accord with what the Bible teaches. Such changes are not evolution—they remind us that God put enough information in the genome of each original kind to live and flourish in a cursed world.
Oh, what scientists call evolution they do not. But they do allow (again, I think that's the right word) changes within families - which would then allow for speciation. But not change at taxonomic levels higher than that.

My reply to John Heininger in the comments of skepticblog:

John, at what hierarchical level of taxonomy do you require observed bifurcation before you will accept macroevolution? Bacteria are a domain, amphibians (tadpoles) are a class, finches are a family, pigeons are a family, monkeys are two pavorders, humans are a species, fruit flies are two families, and viruses are completely off the charts.

The point is that what you are asking for as the only evidence you'll accept for macroevolution is something that we know takes many times the life-span of humans. Speciation, which has arguably been directly observed (e.g. in E. coli, Podarcis lizards, certain plants, finches), is macroevolution by everyone else's definition, and yet the examples you apparently crave have raised the bar intolerably.


Same species, really?

Suppose you were an alien visitor to Earth, and you have to classify species by the same criteria that biologists today use. Surely you would say that ruby throated tigers and lions are different species, right? Sure, they can actually interbreed, and yet it is common sense that they are different, based on their morphology, behavior, etc. Next look at dogs. If at first you only see a great dane and a chihuahua, SURELY you would say they are at least as different from each other as lion and tiger are from each other. My point is that the two dogs, though both characterized as dogs (which is normally considered a species), are different enough to be labeled as two different species (in fact, I challenge the common notion that they can interbreed, which if true would rule them different species), and we know that those two dogs share a common ancestor.


More chihuahua.

Harvey Mudd Conference on mathematics of environmental sustainability

Harvey Mudd College, located minutes away from Keck Graduate Institute where I work, is holding a conference in the end of January. If you're interested in the topic, the Mathematics of Environmental Sustainability and Green Technology, then there is the option for students to apply for travel funding (see below).
The conference will begin on Friday evening January 29th with a panel discussion featuring representatives from the colleges and the Claremont community working on issues of sustainability.

On Saturday there will be four speakers from a variety of disciplines posing problems of interest to mathematicians and scientists:

Harry Atwater (California Institute of Technology) Light-Matter Interactions for Solar Energy Conversion

Ken Golden (University of Utah) Climate Change and the Mathematics of Transport in Sea Ice

Julie Lundquist (University of Colorado at Boulder) Harnessing the Power of the Wind

Ron Lloyd (Fat Spaniel Technologies) Modeling Problems in the Green Economy.

We invite students and faculty to submit posters. There is travel funding available for students. Please see website for more details.

http://www.math.hmc.edu/conferences/2010
I'll probably drop by on Saturday 30th.

Darwin wasn't really a gradualist

John Taylor, dept., og biology, University of Victoria, sent this email today to the EvolDir mailing list:
The title of Richard Bateman's upcoming lecture is "Gradualism: Darwin's big mistake?".

I may be jumping the gun, the question mark hints at a lecture debunking this myth (though the abstract suggests something else), but I can't help but express some frustration over the habit of evolutionary biologists of enhancing their research programs (or presidential lectures) by claiming to address mistakes or solve difficulties in the Origin of Species.

Darwin had no problem with rapid evolution.

Page 148: ".... a new and improved variety might be quickly formed on any one spot, ...."

Page 310: "I may here recall a remark formerly made, namely that it might require a long succession of ages to adapt an organism to some new and peculiar line of life, for instance to fly through the air; but when this had been effected, and a few species had thus acquired a great advantage over other organisms, a comparatively short time would be necessary to produce many divergent forms, which would be able to spread rapidly and widely throughout the world."

Page 318: "There is some reason to believe that organisms, considered high in the scale of nature, change more quickly than those that are low: ...."

And then there's the first chapter, Variation under domestication. It sets up the whole argument and it is a discussion about variation between different sheep herds and about dog breeds. Darwin remarks (page 93) that "King Charles's spaniel has been unconsciously modified to a large extent since the time of that monarch".

Let's give the man a little rope. The common view in 1859, according to Darwin, was the immutability of species. That gradualism was emphasized shouldn't be surprising in this context.
Kevin Padian has pounded this myth before, too.

9 December 2009 - 6.00pm
The President's Talk
Professor Richard Bateman, RBG Kew
Gradualism: Darwin's greatest mistake?
The Linnean Society, Burlington House, London, UK

December 8 1980

Died 29 years ago today.

My favorite atheist singer. Had lots of faults. Had lots of insight.

Arseholegate

More evidence that those climate science people use foul language! If they can cuss on TV, what won't they do with the raw data?



But seriously, one Peter Kelemen has written very nicely on the hacked CRU emails and the implications, as well as making it clear on what grounds it is thought that 1) human activity has caused a steep increase in CO2 emissions, and that 2) increased CO2 emissions leads to a warmer atmosphere (on page 4).
For these reasons, and based on carbon isotope data, it is all but certain that the present, unprecedented rise in CO2 is due mainly to human output. But one cannot rule out with complete certainty other factors, for example, global warming itself, that could also be significantly contributing to the atmospheric CO2 increase.

CO2 (and methane) in the atmosphere are nearly transparent to UV and visible radiation, but absorb in the infrared, creating a "greenhouse." If it were not for this, the surface of the Earth would be much colder. This leads to the inference that increasing CO2 will lead to increasing warmth. Also, high CO2 concentration in the air leads to ocean acidification, which is probably bad for coral and perhaps also for plankton that make their shells from calcium carbonate (soluble in acid) and form the base of the ocean food chain.

Get a B.S. in biology without taking evolution

At Southwestern Adventist University in Texas, Biology majors don't have to take a single class of evolutionary biology. In fact, as far as I can see there are no evolution classes offered at all. They do require the students to take religion classes ("religion elective").


[Click for larger image - also to enjoy the Lorem ipsum dolor sit placeholder still going strong.]

This shouldn't come as a surprise, given the recent push from the Seventh-Day Adventists to force the Adventist universities to teach creationism.

Iranian government threatens Swiss

The government in Iran, of all countries, think it reasonable to threaten Switzerland with consequences because of a ban to build minarets. In Switzerland, that is.
An East-West clash over a Swiss referendum last week banning the construction of mosque minarets heated up today as Iran's foreign minister warned of unspecified "consequences" if the ban were enforced.
I was going to write that they are hypocrites, but apparently Iran actually allows Christians to build churches.
Iran's population is 90% Shiite Muslim. But it permits construction of Christian churches and Jewish synagogues, though some Sunni Muslims have complained they have a tough time building houses of worship in some parts of the country.
And yet, they are bloody hypocrites, because they dare talk lecture the Swiss government on human rights:
But Mottaki had harsh words for Switzerland, saying enforcement of the ban on new minarets was “against the prestige of a country which claims to be an advocate of democracy and human rights" and would "damage Switzerland’s image as a pioneer of respecting human rights among Muslims' public opinion," according to a report by the official Islamic Republic News Agency, or IRNA.
All true, perhaps, that the choice made the the Swiss voters will damage Switzerland's image among Muslims. But seriously, clean up your own house because you threaten other with unspecified consequences and urge them to care about human rights. This was easy to find:

An Afghan citizen was executed in a prison in northern Iran
One man was flogged 80 times and then hanged in a prison west of Tehran
30 people have been executed in the southwestern Iranian province of Khuzestan

Shermer/Prothero vs. Meyer/Sternberg continues

The debate between Shermer/Prothero and Meyer/Sternberg still has everyone in flames.

Now there's an audio of the debate available (I still have to find the time to hear it all).

Prothero rebuts the criticisms listed on the Discovery Institute's site.

And Michael Shermer has written his review of the debate, too, in which he points out the IDists convoluted debate tactics:
The problem, of course, is that evolutionary theory primarily deals with how life changes, not how it originated in the first place. No matter, because in the entire 25 minutes allotted for Meyer and Sternberg, they never once even mentioned the origin of life, and instead attacked “neo-Darwinism,” population genetics, rates of mutation, etc., none of which has anything whatsoever to do with the origins of life. By contrast, Don devoted his 15 minutes to instructing the audience on where the science of life’s origins is today, basically covering his 15-week college course in one minute per week’s worth of material.

(...)

Unbelievably, Meyer opened by accusing us of dodging the debate question!
Robert Crowther has a reply to Shermer, which contains this jewel:
In our uniform and repeated experience, information only comes from minds (read: intelligence). So why should we attribute the information in DNA to a mindless process like natural selection? Meyer doesnt' think we should. Obviously, ID is an inference from the evidence, not from religious scriptures or practices.
Bad, bad, bad inference.
Second, it is clear that Darwinists are unable to demonstrate that the mechanism they champion, natural selection acting on random mutation (the subject of the debate), is capable of accounting for the complexity and diversity of life. On the contrary, it is clear that it is incapable, a point made repeatedly during the debate by Sternberg and Meyer.
How is it clear? By what evidence? That Meyer et al. repeat that it is so does not make it so.

Still no word about the debate from Meyer/Sternberg to be seen anywhere. They are probably just busy doing science...

Evolution highlights IX

Yet another study of the evolution of bird beak size. This time in England, where a smaller fraction of some warbler population don't migrate to southern Spain every winter anymore (fools!), but stay in England eating an abundance of food provided by humans. Incipient speciation, I'd say. And also, yet another possible example of domestication. All in only 30 generations.

Under the headline of Evolutionary Bullshit, we get yet another rant against evolutionary psychology based on the assumption that all human behavior and preferences are learned, and on the tired tenet that if the science can be used to justify immoral behavior, then it is wrong. Good grief!

Comment moderation

The time has come when I am too annoyed with the spam. I get links to dating-sites and bots posting Viagra advertisements.

Comment moderation is on for posts older than seven days, and I've added a captcha image for commenting.

Supremely incompatible accounts of an ID/evolution debate

This is really strange.

It's not that I don't know that when two opposing sides debate, they will often walk away with different observations of what went down. We are human, and we are biased. We will naturally focus on the wins we get in, and automatically downplay our losses. So when Shermer/Prothero debates Meyer/Sternberg on Nevember 30th, it is not unsurprising that they will each report that the debate went well on December 1st.

But this is just waaaay over the top in that category. The accounts are parsecs apart.

Jonathan Wells and Robert Crowther each posted victory cries on the discotute's website, Evolution New & Views.

Crowther:
It was all shaping up to be a serious heavyweight bout. And then Meyer and Sternberg simply KO'd the competition in the opening round. If I were being generous I might say that Prothero tripped over his own arrogance and impaled himself on his condescension, but let's be honest; he was completely knocked out by Sternberg. I think Sternberg earned a third degree tonight, one in evolutionary bulldozing.
I read this first, and though to myself that surely he is exaggerating, but perhaps Prothero did somehow trip and make a fool of himself, perhaps misspeaking on some factual issue.

More Crowther:
To call the debate a massacre would be a discredit to Sitting Bull. The only thing I can say is that Shermer needs to add a point to his booklet on how to debate "creationists" — namely, leave Donald Prothero at home in his van by the river.

This guy is to be taken seriously? I had to remind myself not to laugh every so often during his presentation — it was so pathetic and ill-informed. Basically, Shermer and Prothero blathered on about supernaturalism, and Meyer ceded his time to Sternberg, who made an interesting presentation about whale evolution

(...)

Some of the best points came later in the debate, when Sternberg slammed Prothero with factual put down after factual put down, citing the current literature time and again. His command of the subject matter — from population genetics to junk DNA — was so far and above beyond Shermer and Prothero's knowledge, so far above their pay grade, that it was almost painful to watch him school them point after point.
Wow, right? Even if we expect the "winners" to exaggerate somewhat more than slightly, this is as far as I can tell an account of rare kind of resounding victory in a creationism/ID vs. evolution battle.

So, I looked around after an account from Shermer or Prothero, and found Prothero's on Panda's Thumb.
My subjective summary of it is that our side did very well: I caught them off-guard with new arguments they had no answer for;
Wait, what? I had to double-check that there weren't two different debates, but no.

More Prothero:
we both pushed them hard on the fact that neither of them ever addressed the topic of the debate, “Origins of Life.” I could tell that they were rattled a number of times, and I definitely shook up Meyer and got under his skin with my answers.

(...)

We both chastised them on ignoring the debate topic entirely, but to their minds, the debate was about Neo-Darwinian gradual selection.

(...)

At another point, I tried to get in a complete rebuttal to Sternberg’s weird whale argument, highlighting his invalid assumptions about population size, reproductive rates, and the constancy of point mutations, and arguing that a lot of people are looking at evo/devo to explain the suite of soft-tissue modifications that whales show. Somewhere in there, Meyer used the “condescending” sympathy line but their rebuttal to evo/devo was so garbled that they ended up arguing with each other about those hypothetical reconstructions of 12-winged dragonflies and completely missed the point of evo/devo. (I never got a chance to set that one straight). I knew they were desperate when they suddenly pulled out their “junk DNA” kit of lies, and I slammed them with endogenous retroviruses, pseudogenes, and the onion argument — and then Sternberg got all tangled up admitting these were real but trying to dismiss their importance. Even though the moderator let them get away with more time and interruptions, I feel like we held our own, and most of their garbage got a least a partial challenge and rebuttal from our side.

We then each took a few questions from the audience and moderator, and most were a piece of cake to answer.

(...)

We must have done something right to rattle Meyer as we did, getting under his skin so that he tried to question my qualifications to talk about molecular biology (and then I cut in with “I have a degree in biology”), pull out his “condescension” sympathy line, and now the DI flacks are now busy trying to spin and lie their way out of the debacle.

(...)

Several of the fence-sitters in the audience said I’d convinced them and beat the creationists soundly.
I mean, can these two accounts, supposedly of the same event, really be more at odds? I don't know who the heck Crowther is, but I do know Prothero. I read his book, I heard him talk, we've emailed, and he commented here. This gives me some feeling that he knows what he is talking about, that he isn't some kind of lunatic paleontologist, and that his words carry some weight. (I also know Shermer quite well, and can say the same things about him and his area of expertise.) But Crowther? I have no clue. I hesitate to Google him before I have written this... may I'll do it later. Stephen Meyer is a philosopher. Perhaps you see what I am getting at...?

But, do read both accounts and compare them yourself. And if we're real lucky, a video of the whole debate will go up in the near future, and we can all see for ourselves (that is the plan). I'll for sure see it and write about the experience.

Lecture on why it doesn't matter that Nidal Malik Hasan is Muslim

Here's a little lecture I would very much like to go to. It is, incidentally, right in my hood, but I am afraid I most likely won't be able to go.

Responding to the Fort Hood Tragedy
Imam Zaid Shakir will be presenting a talk to the Claremont College community to address the Fort Hood tragedy: the events asssociated with it as well as those ensuing from it. He will also explain how and why the crime perpetrated by Major Nidal Malik Hasan can not and should not be attributed to Islam.
Date: Wednesday, December 9, 2009
Time: 7:00pm - 8:00pm

"Should not" - sure, I can see why a Muslim would say so.
"Can not" - why not? I'd go to find out what his reason is.

Funny ad

I'm looking intensively for a postdic job for when (if) I graduate in the end of Spring 2010, and today I came across one of the funnies at the Broad Institute:
Job Title: Associate Computational Biologist - Infectious Disease Initiative

General abilities required: multi-task, work independently, collaborative skills, adapt to changing priorities, work in face paced environment, analytical skills, verbal communications skills, written communication skills, presentation skills

[Emphasis added.]
I'd love to work in a face paced environment. I'd also love to try a fast paste environment.

But, I am not going to apply. While EVERYTHING is evolution, this position requires only a Master's degree. What the hell would have been the point of the last four years, then? If my next job doesn't require a Ph.D., I'd much rather write a creationist handbook, slap "Ph.D" after my name on the cover, and go for the Templeton Prize.

Skeptic to save money and lives

Bruce M Hood is a writer and blogger from England, and he has come across information about a bomb-detection device used in Iraq. Bruce raises a lot of doubt about whether this device, the ADE651, works at all.

How To Make A Killing With the Woo Bomb Detector
The “ADE651 device” costs around £35,000 ($60k). It appears to be a telescopic car aerial attached to a black box. Inside there is a plastic card that is supposed to be ready programmed with an electromagnetic ‘resonance’ of what needs to be detected. It is claimed to be based on the principles of nuclear quadrupole resonance but from what I understand that would require generating a magnetic field and sending out a strong pulse – something that seems to be absent in the ADE651 – its powered by body energy! Even if it does use NQR then it seems highly implausible that it can work from an airplane 3 miles up as claimed in the product details. Still, they have already sold an unbelievable £51 million’s worth to Iraq.
The really interesting news here is that Bruce lives close by the company that manufactures the ADE651, and he is in the process of arranging a visit to see the device for himself, together with a physicists friend.

That would be highly interesting however it turns out. If the device doesn't function, then this is a major scandal. If Bruce and his friend goes away unconvinced, then one wonders how the company could get away selling for £51 million of them. If, on the other hand, the device works, then I can't wait to hear how that is. If so, then how could it be that
when a guard and a driver for The New York Times investigating this story, both licensed to carry firearms, drove through nine police checkpoints that were using the device, none of the checkpoint guards detected the two AK-47 rifles and ammunition inside the vehicle. Later, it even failed to detect a grenade and pistol in plain view on the table of the General in charge of the checkpoint, who replied that the operators needed more training.
Do check back with Bruce later on. I'll keep you posted here as well.