Klinghoffer talks about red herrings ... I mean heifers

David Klinghoffer, a senior fellow at the Discovery Institute, has a blog on Beliefnet where he specializes in, amongst other things, making grandiose claims for intelligent design creationism and then completely ignoring the counter-evidence offered by commenters. In today's post, he starts off by letting you know this is his M.O.:

... believers in Darwinism can't open their eyes and see when presented with scientific evidence of design in nature. (Note to Darwinist commenters: This is not a blog concerned with presenting that evidence...

No kidding. Although he is kind enough to direct us to where we can find such a response, and it doesn't come from him.

However, if you'd like additional information on the subject, why don't you read Stephen Meyer's new book, Signature in the Cell. After you have read it, then I would be very curious to hear your thoughts about the evidence of intelligent design in DNA.)

Never mind that some of his commenters have read Meyer's new arguments (which are the same as the old arguments), Klinghoffer chooses to remain mum on the subject.

But I digress.

My point is that in today's post, Klinghoffer delineated the difference between god-made laws (chok) and those that laws that were revealed by god but man very well may have come up with on his own (mishpatim). The difference; god's laws are irrational. Sort of:

Sometimes a chok is called a "suprarational" law. That doesn't mean it's irrational. Instead, the rationale behind the law, its significance when considered rationally, can only be perceived from within the system of Torah thought -- the worldview of the Hebrew Bible. From outside, it indeed appears irrational. An alien worldview, like secularism, blinds a person to being able to see the law's sense, the insight and beauty it reflects -- "worldview-induced blindness."

I know that such "statutes" aren't irrational because Jewish tradition has much to say about their meaning.

And, because he is David Klinghoffer, he has to wonder what this has to do with the gays.

The verse doesn't tell us which laws are which, but maybe we can speculate that the laws against incest would fall under the former category [mishpatim or ordinances], and against homosexuality, under the latter [chok or statutes].

I'd like to point out that this is an often used, though little recognized, logical fallacy called the genetic fallacy. By providing a rationale for his argument, Klinghoffer hasn't really answered any criticism against his argument; he has only deflected the issue and presented a red herring. In this case, he claims that there is some special knowledge that we are lacking. However, that special knowledge is not something that is relevant to the topic, which (apparently) is "Should there be moral prohibitions on sexual behavior, in our present day society?". Klinghoffer says yes, because god told him so. And if you don't hear the same thing, you aren't listening hard enough.

'A New Hope' for Texas board of Education?

There is at least one ray of light for the continuing saga that is the Texas Board of Education's fight to completely effup students. A University of Texas math professor, Lorenzo Sadun, has decided to run for the board.

If Sadun is elected, he will be the only scientist on the board. He said that even though he may encounter opposition from members of the board, he will find a common ground with his colleagues and will pursue agreement without sacrificing the quality of education for Texas students.

“Despite my taking a fairly hard line, I am a conciliator,” Sadun said. “I have not met a person who knew so much I couldn’t teach them something, and I’ve never met someone who knew so little that they couldn’t teach me something.”

And the best part about it:

The board has allowed politics and philosophy to influence its decisions regarding science textbooks. The theory of evolution was contested by conservative board members who insisted that the theory of intelligent design, or creationism, be taught alongside the theory of evolution.

“Intelligent design is fake science,” Sadun said. “It is a religious belief about the creation of the earth and humanity, dressed up in the language of science.”

Image via Topic Agnostic

Things are getting busy

The second year of grad school is the worst. Expectations that you will be starting your own research and applying for funding in addition to finishing your coursework(1) really put a crunch on the time a student has. Not to mention that dirty word ... qualification. The quals, the competency test, the BFE. Call it what you will, it's very mention sows in the mind images of medieval torture and carnal abomination. But, of that which we cannot speak, ...

But first a bit of fun.

I have discovered that Family Radio broadcasts in my area, which should not be of too much interest to anyone. However, they do have two titillating short segments called Beyond Intelligent Design with Mel Mulder(2) and Creation Moments with Ian Taylor. Both follow the same sort of format:

A) Scientists have discovered some interesting new fact.

B) Scientists aren't completely sure of the mechanism.

C) Therefore, IT MST TOBE THE JEBUS!!!! ELEVENTEE ONEE !!!!

Not exactly the most rigorous example of logical thought, but at least it is concise. Of particular interest to me is that they sometimes cover topics in the neurosciences. Interesting. I feel that I must go through at some point and confirm the high exacting standards they almost assuredly employ.

Image via Strollerderby

(1) It doesn't help when the course master schedules your course to run four weeks longer than the length of the semester.

(2) Who is, I am convinced based on the lack of prosody in his voice, a robot.

I'm teaching a new generation of medical students

At least indirectly. It's interesting what you find when you google your name.

Thank you, Dr. Puglielli, for including me in your lecture. Though, to be honest, this does raise the specter of something that haunts me; uncredited images. I try to credit when possible, but I'm usually in too much of a hurry.

Beer Wars movie

I had no idea this movie was coming out. I may just have to Netflix it. If it is good, I will forgive them for hiring Ben Stein to promote it.

Spring cleaning

I spent the other day going through my blogroll, adding blogs I frequent and getting rid of the old ones. Unfortunately, I don't think Bohemian Scientist and Angry Lab Rat are coming back. The list now better matches my Google Reader subscription list.

I have to get a case of Molson Gold

I can't believe it took me this long to find this out. The NHL Network, on DirecTV channel 215, broadcasts Hockey Night in Canada.

They have changed the name, but it will always be Molson Hockey Night to me. And here is a clip of my very first exposure to Hockey Night and Don Cherry, complete with lamentations about the end of the Campbell's and Wales's conferences. Of course back then, I used to watch the French version.

Peggy O'Mara misrepresents statistics

I have a sort of love/hate relationship with Mothering magazine. While they do have interesting articles, they have a tendency to twist scientific results to support their idealization of parenting. Take for instance Peggy O'Mara's recent editorial in the January/February 2009 issue titled 'The assault on freedom of conscience'.

Sometimes people will characterize the magazine as pro-homebirth or anti-vaccine because of our frequent coverage of these issues. In fact, we are pro-informed consent; we publish both sides of the story so that parents can be aware of all angles before they make a decision.

That's all well and good; but then Ms. O'Mara and shows her misinterpretation of scientific data regarding measles cases and the decline in vaccinations.

According to the Centers for Disease Control and Prevention (CDC), 63 of the 131 new cases of measles from January to July 2008 were among those unvaccinated. The majority of the cases (68), however, were among those vaccinated.

Face, meet palm. Okay people, a chi-square test really isn't that hard to understand. If you have two populations that are not evenly distributed, say vaccinated and unvaccinated, you would expect the outcome, say disease manifestation, to be similarly distributed unless there is something fundamentally different between the two populations. So, if you have about 95% of children vaccinated (which most states do based on the Healthy People 2010 guidelines), you would expect 95% of children with disease to have been vaccinated. But that is not what you see. Here, I will put it in table form (with hypothetical numbers).

Population size; Disease Prevalence ; Expected Prevalence
Vacci 95,000 (95%) ; 52 (52%) ; 95 (95%)
Unvac 5,000 (5%) ; 48 (48%) ; 5 (5%)
Total 100,000 (100%) ; 100 (100%); 100 (100%)

A majority of patients may have been vaccinated, but it is still significantly less than what it should be. Conclusion: unvaccinated children are more likely to come down with measles. Not complicated. The same sort of stuff they used to find out smoking causes cancer. Understand? Maybe not.

Interestingly, according to the CDC, 89 percent of the 131 new measles cases were "imported from or associated with importations from other countries, particularly countries in Europe, where several outbreaks are ongoing."

You mean countries like the UK, France, and Italy which have lower vaccination rates than those in North America?

Measles is depicted as a life-threatening disease instead of the mild illness that my friends and I all had as children. In the Private Practice episode, the child dies from measles, an occurrence that is so rare that, based on the current incidence levels (42 in 2007), a death from measles would happen once every 119 years. Even if the incidence of measles were to quadruple, we would not see a death for 30 years. The current death rate from measles is 1 in 5,000, yet it is portrayed in the show as though it happens frequently.

This of course ignores a very real problem. The occurrence of measles is now so rare that doctors may be inadequately trained to recognize it, meaning that the disease may reach a more severe stage before it is treated. And what can we thank for such a rare occurrence?

Vaccinations.

If you choose not to vaccinate, you can thank something else.

Herd immunity.

You're welcome.

I have finally attained a certain age

Postings are lean in part because of academic demands. I just finished a midterm in my course on the physiology of the synapse. It took me four hours, and I was the first to leave.

I was telling my current supervisor about the test and how amazed I was by the tenacity of the other, younger, students. Maybe it's just because I'm lazy, but I feel there is no reason to write a three paragraph answer if one sentence will suffice. Also, there is no point in staring at a question for half an hour if you don't know the answer; accept that you don't know, put down your best guess, and move on. Then my supervisor told me something I wasn't prepared for, something I thought I was not yet of age to have.

"I think that is what they call wisdom ..."

Regulation in animal research

The Huffington Post has already made it clear that they are not exactly pro-science, so I was not too surprised to see the opinion piece by Simon Chaitowitz about her opposition to animal research. However, this story is personal for Ms. Chaitowitz:

I have full-blown leukemia and the chemotherapy I'm taking doesn't seem to be working all that well. And even if it does kick into high gear soon, it's not a cure, only a brief delay of the disease's progression. One way or another, my odds aren't good.

Still, I keep popping pills each morning and night, sitting for many hours each week with an IV in my arm, dealing with all the side-effects of treatment, hoping for a miracle. Some people may call me a hypocrite -- to take advantage of the benefits of animal research.

I can understand the conflict Ms. Chaitowitz must have and could find less dire analogies in my own life. So I wouldn't extend the word hypocrite to include her. Although I disagree with her assessment of the utility of animal research, I know that arguing that battle is not something anyone could win. However, I do take issue with one statement Ms. Chaitowitz makes:

Despite what the research community claims, federal regulations are extremely weak and poorly enforced, and some species -- mice, for example -- are completely excluded from any protection. Many investigations have shown just how bad conditions are.

Bullshit.

While there is kernel of truth to this (mice, rats, and birds for scientific use are excluded from the Animal Welfare Act) to say that mice are excluded from protection is bogus.

I work at an institution that, like nearly all scientific institutions, receives federal funds. Any research protocol I want to run has to go through my Animal Care and Use Committee (IACUC). If I do research without approval, I get punished. If I don't ease pain and suffering of my animals, I get punished. If I deviate from my protocol without prior approval, I get punished. Every procedure I want to do is pored over by scientists, veterinarians, and lay people from the community, often resulting in several weeks or months of delay. All to make sure that I am treating my animals humanely.

As part of our oversight, the Office of Laboratory Animal Welfare does periodic, unannounced, inspections of our facilities. If our protocols are not being followed, if our animals are not being treated humanely, if we do not keep conditions sanitary, we lose our funding. Not a slap on the wrist, not 'hey, try to do better next time'. No, NIH has a right and duty to take away funds, effectively shutting down that research lab.

Additionally, many facilities strive for AAALAC accreditation. It shows that your institution holds their research animals in high regard. It also means submitting to multiple inspections per year, higher levels of cleanliness, and additional training for the animal care staff. Accreditation isn't an easy thing to maintain; you can only do it by treating your animals with the utmost care.

So please forgive my small tirade against Ms. Chaitowitz, but I cannot allow such half-truths to stand unchallenged.

Incidentally, at least one famous case of laboratory animal abuse was, allegedly, only possible through the neglect, duplicity, and mendacity of an animal rights activist.

Satire of intelligent design creationism

This satire is a little too good to not link:

What concerns me is that intelligent design as suggested in the Bible goes beyond merely explaining human origins and the complexity of eyeballs. To be both thorough and consistent, advocates should demand that science classes include additional biblical truths presented in Genesis.

I particularly like this:

We must also stop insisting that various trees are indigenous to diverse parts of the earth. Genesis 2:9 reveals that every type of tree in the world today sprang in the Garden of Eden, later revealed to lie near the Euphrates River, presumably in the vicinity of today's Iraq.

The subject of botany should be amended to teach that fact, and also to include two trees that are not even mentioned in today's botanical texts: the tree of the knowledge of good and evil, consumption of whose fruit endows awareness of right from wrong, and the tree of life, consumption of whose fruit assures eternal life.

Assuming our national leaders were capable of distinguishing good from evil, perhaps the real reason for invading Iraq was to seek eternal life.* When discovered, the tree of life will be recognized by the cherubim - beautiful winged humanoids - who guard it, and by a flaming sword nearby which turns in every direction (Gen 3:22-24).

* Yes, I realize that is the Tree of Knowledge in the picture. All the ones of the Tree of Life seemed to be lacking flaming swords.

Utah to allow home-brewing

Pending Gov. Huntsman's signature, Utah residents will be able to legally homebrew starting 12 May. The legislation was approved by over 80% of both houses of the state legislature. But not everyone.

"I'm not comfortable with home brewing," [Senate Majority Assistant Whip Gregory] Bell said to the Deseret News. "It seems fraught with mischief to me. Maybe I don't understand it."

Does he think citizens are going to start racing around in '69 Chargers trying to outwit the police at every turn?

Georgia may expand alcohol sales to Sundays

From NPR, a report on a push in Georgia to allow Sunday sales of alcohol.

Says Sadie Fields from the Georgia Christian Alliance:

"You can buy alcohol or wine or beer in Georgia six days a week, so, you know, why this extra day?"

Certainly, if your concern is the deleterious effects of over drinking, wouldn't it make much more sense to ban Friday or Saturday sales, the days where people are more likely to buy large amounts of alcohol for weekend consumption? The question isn't why allow seven days of liquor sales, but why ban sales on this one day?

Chirp, chirp, chirp, ...

Tucker Carlson emphasizes fact-checking, and gets booed for it

Tucker Carlson, of all people, came to the defense of the New York Times by saying "it's a paper that cares about accuracy" at CPAC yesterday. And he got booed for it. Let me say that again:

He stated that checking the facts is important to journalism. And he got booed for it.

Blog Interviewer ... uhh ... Interview

I had forgotten that I did this interview a long time ago. Actually, well over a year ago. I don't know why it took so long to get put up. Anyway, you can read about and rate my blog. Enjoy.

The Vermont Coutry Store is selling what?

I had pointed out this fact last year, but apparently I am ahead of the curve:

For 64 years, it's been a mailbox staple, offering home remedies, kitchen wares, and long-forgotten brands to help consumers solve life's little problems, from spider veins to unwanted nose hair.

But recently, the Vermont Country Store catalog made a surprising addition: sex aids.

The inclusion of an "Intimate Solutions" section selling instructional sex videos, "pleasure gels," and other items has prompted cancellations, irate letters and calls, and a sort of identity crisis for the staid New England brand, which has never been accused of being racy.

For Luskin, some remedial Research Design

There are two caveats that I took home from my many, many, many (1) research design/statistics courses. The first is a caveat concerning the danger of over design:

Replication is the most powerful statistic.

No matter how ingenious your design, no matter how intricate your analysis, it doesn't mean diddly-squat if someone else can't repeat your results.

The second caveat, which is more important to this post, concerns the danger of under design. In a class discussion, one student asked why null results are inherently uninteresting to scientists. Why do we care if we reject the null hypothesis, but not so much if we fail to reject? What the teacher said to us stuck with me:

Anyone can get null results; you just have to do bad research.

Increase your error rate enough, and it doesn't matter how much of an effect you have. You still will never reach p < .05.

Why do I bring this up? It has to do with Casey Luskin's issues with a recent Science paper (2). In this paper, the authors created self replicating RNA enzymes. Great, support for the RNA world hypothesis. What are Mr. Luskin's objections:

1) The system is completely contrived consisting ONLY of catalysts and substrates. No competing materials or reactions were allowed. No natural analog is possible.

Yes, well they did want the experiment to work. I suppose you could have shot yourself in the foot by throwing the catalysts in a slurry of protein. But then, if you saw no replication would that tell you anything?

2) There is a vast gulf between their reaction mixtures and anything that might possibly come from a Stanley Miller type electric discharge experiment. This requires explanation.

Umm, the Miller-Urey experiments took place in 1952. A year before the structure of DNA was deduced. The RNA world hypothesis didn't come out for another 16 years. Miller-Urey took place at time when the smart money was still on protein as being the storage mechanism of genetic information. You do realize that nucleotides and amino acids are different things, right?

3) The 5’-end of the oligonucleotides were primed for the condensation reaction by prior synthesis of the high energy triphosphate form. Simple phosphates fail to react or react at rates orders of magnitude slower. Clearly the reaction only does what the chemist intended.

Again, Mr. Luskin wants to design a study that will fail. Yes the reaction would be slower. And because they wanted the reaction to happen within their lifetime, preferably with some room for publishing, they juiced the system slightly.

4) Reactions were carried out at 42 deg C. --> fine-tuning --> fine-tuner!

Yes they could have run the reaction at many temperatures, although 42 C seems like a very reasonable starting point. But, again, to avoid shooting themselves in the foot and to get data in their lifetime...

5) Only one bond is formed by either of the paired enzymes. The rest of the molecule was pre-assembled by Joyce and his colleagues. What this experiment shows is that some clever chemists have spent ten years of their lives re-engineering a pair of RNA-zymes to catalyze ONE reaction. And without a constant supply of pre-fabricated component parts, nothing happens. Indeed, if anything, the road to self-assembly just got longer.

To catalyze one reaction ... over and over again. By itself. Without any input. As I've said, I didn't study the paper in detail. But just from reading the abstract you can at least glean that self-replication is the main point.

I'm not saying that there are not limitations to this study, of course there are. But that is the point of doing controlled experiments. They don't replicate the natural world, but control as many variables as possible in order to best be able to detect an effect if there is one. See caveat two above. To put it another way:

If you don't have an effect with optimal conditions, then you won't have an effect with sub-optimal conditions.

In Mr. Luskin's world, the ideal way to test the RNA world hypothesis is to start out with an Earth-like planet, set up all the conditions that we think the early Earth had, and wait about 3 billion years (3). Not particularly expedient, and not likely to be funded. This is what we would see if the Underpants Gnomes ran the NIH: set up an experiment, variables be damned, and hope that you come out with some useful data at the end (4).

To reuse this gnome metaphor, intelligent design creationists propose a mechanism (a designer) that underlies a phenomenon (complexity of life) and then refuse to test (or even guess) how such a mechanism works. Without that, it's not science. At best it's philosophy; at worst it's just plain bull.

(1) Many. No, I do not consider myself an expert. But every academic institution I go to feels that I could always use more instruction on the topic.

(2) To disclose, I have not yet carefully reviewed the Lincoln and Joyce paper; but Mr. Luskin's dismissal of it has very little to do with the content of the paper and much more to do with how science is conducted.

(3) Of course, intelligent design creationists could insist on an infinite regression, "Well, you designed the Earth-like planet ..."

(4) He he ...

Dentists have a plethora of instruments of torture

I went to the dentist yesterday. I've never liked dentists, and passionately avoided my high school guidance counselor's advice to go into that field. I'm not saying that all dentists are like Orin Scrivello; but they do have access to quite the array of torture devices. But yesterday, I was exposed to the most heinous, pain-inflicting tool yet devised by man.

As I got into the chair, they started to play Air Supply: Greatest Hits.

I particularly like track 6.

More ways to not settle science

Coming up with a list of people who agree with your position. When I heard Sean Hannity on his Tuesday radio program bemoan the proposed $400-500 million dollar funding of climate change research for NASA by claiming that 650 scientists don't believe there is any climate change, I knew something was amiss. Searching for the source of his claim, I was led to (no surprise) the government sponsored website of Oklahoma Senator James Inhofe.

The UN global warming conference currently underway in Poland is about to face a serious challenge from over 650 dissenting scientists from around the globe who are criticizing the climate claims made by the UN IPCC and former Vice President Al Gore.

Look, Discovery Institute publishes a list of people who dissent from evolution. The NCSE has published an even bigger list of biologists named Steve who accept evolution. Take home message: lists don't matter, facts do.

And by the way, the 650 scientists ... turns out to be significantly less than that.

Free trip to Seattle, c/o Discovery Institute

This is not interesting:

Discovery Institute is pleased to announce two intensive summer seminars on intelligent design, science, and culture from July 10-18, 2009 in Seattle. The first seminar is for students in the natural sciences and philosophy of science; the second seminar is for students in the social sciences and humanities (including politics, law, journalism, and theology).

However, this is:

Discovery Institute will pay expenses for students who are accepted into this special program (travel, lodging, meals, books and other course materials).

A free trip to Seattle, and all you have to do is listen to some drones prattle on about biological principles about which they know little and understand even less?

Now, far be it from me to condone unethical behavior; but if a college student wanted to make things more difficult for Discovery Institute by having them waste money and time by preaching to those who know better, this would be a great way.

Plus you could take some time for yourself and explore the underground.