Cavalcade of Mammals

Interesting letter about the evolution of the glucocorticoid receptor from Joe Thornton, a biologist at the University of Oregon. Thornton’s lab has figured out some of the details on how this receptor evolved. Thornton’s writing this because creationist Behe is passing off a mangled version of his work as evidence for ‘intelligent design’.

The first Discover magazine blog post gives a good overview of what Thornton’s lab learned about the glucocorticoid receptor.

A UK Bible study group hosted a talk tonight by Dave Eakin, an Associate Professor in the Department of Biological Sciences at Eastern Kentucky University (EKU). I didn’t know quite what to expect coming in to the talk–was Eakin going to explain some biology to the Bible study group or was this going to be bog standard creationism? The talk turned out to be standard old Earth creationism. What an embarrassment he is to EKU!

An MP3 recording of the talk is available here.

I made notes during the talk, they give a flavor for it. My comments are in brackets:

3 groups: biblers, people with set minds…

Comments about apoliticalness and open mindedness.

Cartoon: candle representing science, “Hit it with the Bible”.

Chain of being cartoon.
He mentions he had a creationisty poster at the KAS meeting and no one gave him guff about it.

3 theories of evolution:
1. chemical evolution (abiogenesis)
2. general evolution “an extrapolation of Darwin’s natural selection”
3. natural evolution = special evolution [seems to be a ref to microevolution]

Behe’s Black Box book. [Darwin’s black box: the biochemical challenge to evolution
By Michael J. Behe]

It’s hard to tell if things are designed.
Creationists are blackballed, McCarthyism-type environment for creationists.

Paley-like are arguments are too simple/wrong, but Behe is more sophisticated [not clear how].
Watch, mouse trap, flagellum
[clotting cascade, eye, Krebs]
Eye
Trials for cats. [????]

Graduate of U. of Louisville! [figures!]

No one can solve these problems

Color blindness slide?
Can make it clear by increasing contrast…
“Evidence doesn’t support theories, theories support evidence” –Dr Dave.
Big Bang not current, has been replaced by String Theory

CSI example, making the point that evidence can be made to support whatever theory a person wants.

If 60,000 people believe a lie, it’s still a lie.

All his sick evolutionist friends ask him to pray for them.

Quote: when fossils are known all no more guessing. [missed the cite]

We doesn’t know everything so we know nothing.

Absence of life in pre-Cambrian, organisms suddenly appear, and…

Picture of single-celled microfossils, asks if anyone believes them.
Makes fun of certainty of Ph.Ds.

Something new from Discover mag, image of tree of life from single-celled organism.
Pisoliths from pre-oxy atmosphere Earth (pre 2.3 billion years), but they only occur in presence of oxy.
[Casting doubt on what we know.]

Stephen Jay Gould had a young Earth Creationist student. [meaning unclear…]
Quote from Gould, from Evolution’s Erratic Pace, Natural Hist May 1977, at 12, 14. about no transitional forms.

Erase all the lines from tree of life because we don’t know anything for sure.

Never presented Creationism in class. Wants student to think for themselves.
Quote from Colin Patterson (April 10, 1979) on how we don’t have any transitional fossils.
Quote by Tom Bethell in Harper’s February on how no one is willing to publicly talk about ‘questions’.

But what about Archaeopteryx? Small, unimportant. Just a reptile.
Eakin has reviewed many/most biology textbooks.
Says Archaeopteryx is often misrepresented, over interpreted.

Some point about lack of learned behavior in reptiles.
Figures of bird physiology. Pectoral muscles in bird/reptiles.

How did scales evolve into feathers? Unknown, too hard to imagine. [Evo-dev has been providing answers about this.]

How did birds start to fly? An irreducible jump.
We know in our hearts that transitional forms can’t happen.

Faith is… “the substance of things hoped for, the evidence of things not seen.”

My battery ran down at this point and the sound cut off the last minute or two of his talk and the extended Q&A afterward. He mentioned the audience was very respectful and had given him his say. Bible groups must usually be a rough audience!

In the Q&A, he also said that he had talked to many biologists and that 10-20% were creationists of some variety but unwilling to publicly talk about it. This is quite silly, an argument from popularity. Also it’s nonsense. Anonymous surveys of biologists have been done and almost no biologists are creationists. A 1987 Newsweek article reports a survey found 0.14% of earth scientists and biologists are creationists, and a survey reported in CSI pegs the number at 1-2 in about 2000, about 0.1%.

It was sad to find out that EKU has a creationist teaching biology. Oh, the poorly served students!

Most surprising was that Eakin gave his whole talk without ever describing the theory of evolution, in any of its forms, either the simple Darwinian version or the Modern Synthesis. His talk was instead the poorly thought out basket of criticisms of evolution with no case made for anything else. I’ve heard this described as common in creationist talks.

Eakin started his talk saying that evidence is never conclusive, that there’s always doubt, and that we can’t be sure of anything. I thought that would be the theme of his talk before he swerved into ordinary creationism.

Eakin’s talk was at least a decade out of date. One topic was Behe’s book and the argument of ‘irreducible complexity’. Eakin doesn’t seem to know that Behe’s featured examples, the flagellum and the eye, have been shown to have evolutionary precursors where part of the ‘irreducible’ structure exists and functions.

Eakin mentions Archaeopteryx and then makes an extended argument that the evolution of reptile ancestors into birds is impossible but doesn’t seem to know that additional transitional birds have been discovered, or the recent evidence of the relationship between scales and feathers.

Eakin also briefly mentioned his impression that few transitional horse fossils are known, and mentioned that the linear, gradual depiction of horse evolution was admitted by biologists to be false. This hoary creationist canard leaves so much out as to be plain dishonest. Eakin should known better.

In the early part of the 20th century, depictions of horse evolution presented a linear, gradual picture of horse evolution, but soon after more and more horse fossils were discovered and filled in a picture of horse evolution as a branching bush with over a score of Genera, many coexisting and all but a few now extinct. Talkorigins.org has a good page on this, though Stephen Jay Gould’s essay “Life’s Little Joke” collected in Bully for Brontosaurus is a better read. There are many transitional horse fossils, and the branching tree of horse evolution has been widely known for 70+ years.

The talk ended with a series of quotes from evolutionary biologists about the lack of transitional fossils and the difficulty of drawing conclusions. This was standard creationist quote mining, quite a laugh.

Eakin is a graduate of U of L. I know that won’t surprise anyone at UK.

I was listening to the NPR food show, The Splendid Table, and they ended the show with by having Dean Radin from the Institute for Noetic Sciences on to talk about how ‘thinking at’ chocolate makes it better. No, I’m not joking, and it wasn’t April Fools’ day. Ordinary fools day, I guess.

Looking at the Institute for Noetic Sciences (IONS) web site, it looks like this is the place where the California nuts collect. They are still doing psi studies, lots of ‘intentional’ studies which test various ways thinking at something changes it, from prayer and healing to remote viewing to psychokinesis. Not too surprisingly, Deepak Chopra is ‘associated faculty’.

The chocolate study guy, Dean Radin, is an interesting nut. He was a real engineer, then got a Ph.D in psychology from U of Illinois at Urbana-Champaign, then went off the deep end. It’s odd, he uses methods that look quite respectable–the chocolate study was double-blinded–to come to nutty conclusions, and publishes them in nutty niche journals. IONS has its own journal, “Explore: The Journal of Science and Healing”, and disturbingly the NIH’s Pubmed article indexing service includes its articles (see http://www.ncbi.nlm.nih.gov/pubmed/17905358). This is by far the craziest journal I’ve ever seen in Pubmed.

I’d heard before that marijuana is the biggest cash crop in California …in Kentucky …in the US. Online you can see a 2006 estimate that puts marijuana on top by Jon Gettman. It always sounded patchy, and here Kevin Drum links to a critical site that estimates the retail value of the cannabis sales at $10 billion.

Even this seems high according to my estimate. I recently (can’t lay my hands on the figure) saw a graph of pot smoking by age in the US within the past month. Highest for people in their 20’s, then about 10% until people hit 60. Older folks smoke very little. So let’s say 10% of people from 15-60 (roughly 24 million people) smoke twice a month:

24 million people x 24 joints/year / 40 joints/ounce x $100/ounce = $1.5 billion retail per year.

By comparison, the US corn crop is $24 billion/year. $1.5 billion/year is about the size of the US tobacco or orange crop. But then we are comparing retail prices to farm prices. So figure growers are getting at best 1/5 or 1/10 or the retail price, and now the marijuana crop is tiny, smaller than the peach crop. Also, considerable marijuana in the US is imported, so the US crop is even smaller.

Running the estimates in the other direction, the $10 billion estimate of spending on marijuana has the monthly US smokers lighting up every other day. This sounds too high, most smokers are occasional smokers. Estimating pot spending at $35 billion as Jon Gettman does has monthly pot smokers averaging eleven joints a week, or every man, woman, and child in the country lighting up once a week. Way high.

Caught a story on the Oprah TV show talking about why the people living on the Nicoya peninsula on the Pacific coast of Costa Rica are long lived. And I asked myself, are these people long-lived? I haven’t heard that before and I should know.

So I went looking, and the special on Oprah was touting a book, The Blue Zones: Lessons for Living Longer From the People Who’ve Lived the Longest by Dan Buettner. Buettner first reported the story for National Geographic. So why does Buettner think Nicoyaians are long lived?

Some populations have been studied and found to be long lived–for example, there are four times as many centenarians in Okinawa, Japan compared to Japan as a whole.

Buettner’s source is Dr. Luis Rosero-Bixby, a Costa Rican demographer. The sole published source I can find is The exceptionally high life expectancy of Costa Rican nonagenarians. I haven’t read the paper, but from the abstract national birth registry data was used to establish date of birth and census data was used to monitor survival, and life expectancy of 90-year olds was found to be half a year longer than anywhere else in the world, for males only.

This seems very thin evidence, I can’t find other studies by Rosero-Bixby or evidence that these people were studied by any other groups. It is especially odd that the effect is seen in males but not females–this was the pattern in other areas where long survival was reported but didn’t pan out-the Caucus region of Georgia, northern Pakistan, and the Andean village of Vilcabamba in southern Ecuador. Usually remote areas with poor record keeping.

I read a review of Michael Brooks’s 13 Things That Don’t Make Sense on the Uncertain Principles blog. I haven’t read the book, but the review tickled me enough that I looked around for more info and found Jennifer Ouellette’s review in The New Scientist where Brooks is a contributor.

Both Chad Orzel and Jennifer Ouellette give Brooks weak “this book has some weak parts but also some good parts” reviews. Just from the reviews and blurbs I can tell Brooks book is destructive, part worthless speculation on the meaning of anomalous results that are almost certainly erroneous and part flattering discussion of pseudoscience.

Why are people giving Brooks such gentle reviews? The physics results are typical of the lot. John Webb’s fine-structure result is of the same sort as the Viking experiment result. Interesting if true, but not reproduced and instead contradicted by other experiments and thus uninteresting.

Brooks doesn’t understand that for something to not ‘Make Sense’ it has to be true. Anomalous *verified* results, results that can’t be explained theoretically or seem to contradict existing results are the kinds of things that ‘Don’t Make Sense’ but could be cool. These are the kinds of things that Brooks should be writing about.

One of Brooks’s topics is the mimivirus, a virus with the largest genome known so far (1.2 Mb). I can’t imagine anything particularly Earth shaking about it–it’s really big for a virus, but that’s it. Biology is littered with oddities and weird exceptions. No one tell Brooks about ttn-1, a titin protein 57X larger than the average worm protein. Or about the ostrich.

The placebo effect has two components, self-delusion and a poorly understood mechanism whereby the state of mind can affect the body. The mind->body connection is true and poorly understood, the proper subject of Brook’s book.

In Jennifer Ouellette’s review she says that Brooks includes homeopathy because of its relation to the placebo effect. This is ridiculous–any of the thousands of worthless ‘medical’ treatments known from blood letting to magic spells have this property.

Brooks’s inclusion of homeopathy and death is complete nonsense. Homeopathy is pseudoscience, bunkum. And there well understood evolutionary reasons why organisms die, death (and aging) are not even anomalous.

You would think someone would have caught a photo of bigfoot by now considering how much more common cameras have become in the past decade. Point-and-click cameras and cell phone cameras are in everyone’s pocket. Instead, ‘peak Bigfoot’ was in the 50’s and 60’s, when cheap movie cameras became available to the hoaxing public…

Pepper spray has been around for years now, but there is not commonly available antidote. And we know how the active ingredient, capsaicin acts to active, or hold open, the ion channels that transduce pain signals. In fact, a quick Google shows that capsaicin binds and activates a receptor called the vanilloid receptor subtype 1 (VR1), a member of a group of related receptors called TRP ion channels that are activated by temperature changes.

Capsaicin chemical structure (from Wikipedia)

So an antidote would be an inhibitor of the VR1 receptor, and such a thing should be easy to find, or create, and in fact another Google shows that several have been created. Capsazepine was the first inhibitor discovered, way back in 1994. Activators and inhibitors of this receptor have many potential uses as analgesics and anti-inflammation compounds so there is a lot of research interest.

Capsaicin inhibitor capsazepine (from Wikipedia)

A spray containing one of these inhibitors should be an effective antidote for pepper spray. But surprisingly no such inhibitor is available! The small quantities of purified inhibitors are available in small quantities for research purposes (i.e. capsazepine, 50mg for $455 but I can’t find anyone who has made an antidote preparation. This should be safe and fairly easy. Safe, because it would be applied mainly externally, and because pepper spray is itself fairly safe–aside from the pain and shock it is used to cause. It doesn’t have other, non-specific side effects. And relatively easy to make because the literature describes the synthesis of inhibitors from capsaicin itself. So the starting product used to make an inhibitor can be capsaicin, and capsaicin is readily available in large quantities!

Ah, health nuttery, a spice that can be added to anything. I’ve heard it many times, that alternative medicine and quack cures have a collection of ideas (all bonkers) that often get combined together. You see all sorts of combinations. Qi magnets, detoxifying magnets, Qi detoxification. Most of these terms mean so little that they can be combined randomly to make a novel-sounding new types of alt. med.

It’s really just like advertising, where there is a pool of non-specific positive adjectives that are slapped on a product to jazz it up. Pick any two or three: new, brighter, improved, best, free, breakthrough, exciting.

That’s all background for describing something that made me bust a gut. Bear Grylls, star of the Man vs. Wild survival show, had caught and gutted a fish. As he often does, he starts chomping on it raw. Then he says it’s high in protein, gives you energy, and helps boost the immune system. Yes, boosts the immune system! One of the universal alt med claims! If you are stranded in the wilderness without shelter, fire, food, or water, ‘Does this boost my immune system?’ is not on your list of priorities. Bear didn’t think through his food options, and think, I could eat a caterpillar, but a fish will boost my immune system more, so I’ll try and catch a fish. No, the choice was a raw fish or nothing, and it is literally true that a fish, being food, would be better for the immune system than not eating for the day. Trivially true, but really, really funny!

In 1997, the Kyoto Protocol agreement to reduce green gases was signed by 30+ nations including (as best I can tell) all the Western countries except the US. So it was clear in 1997 that the world was warming and green house gas emissions needed to be reduced, but *when* exactly did scientists figure this out?

My memory of the issue with a little proding stretches back to the 1992 climate agreement signed by George HW Bush, officially called the U.N. Framework Convention of Climate Change. It called on countries to cut green house gas emissions but didn’t set binding targets. So global warming was understood back in ‘92, and must have been known about years earlier for political action to have been taken then. I didn’t know about research earlier than the 1970s modeling research.

A great talk laying out the history of global warming science by historian Naomi Oreskes is on the web:

She lays out a number of landmarks. She gives an interesting talk–I’ve pared it away and just list the landmarks here:

• 1931, E. O. Hulbert, increasing atmospheric CO₂ 2-3X will lead to 4-7°K increase in world temperature.
• 1938, G. S. Calender, increasing CO₂ leading to increased temps, 1880-1930s
• 1957, Suess and Revelle paper pointing out that dumping back into the atmosphere over a few decades CO₂ stored over millions of years in coal and oil could heat up the world. Calls for detailed research into the world CO₂ budget–where will the CO₂ go, and what secondary effects will there be?
• 1964, NAS committee warns of “inadvertent weather modification” caused by CO₂ from burning fossil fuels.
• 1965, Keeling, about 1/2 of CO₂ from burning fossil fuels will end up in the atmosphere.
• 1965, President’s Science Advisory Committee, Board on Environmental Pollution, by 2000 there will 25% more CO₂ in the atmosphere and marked and uncontrollable changes in climate could occur.
• 1979, JASON committee reports that predicted increases in atmospheric CO₂ will increase world temperature 2.4°C or 2.8°C (two different JASON models). Further, the increase will be much greater at the poles, 10-12°C [Now observed].
• 1979, Charney report summarizes climate science “If CO₂ continues to increase, [we] find no reason to doubt that climate changes will result, and no reason to believe that these changes will be negligible.”
• 1988, IPCC created to study climate and suggest solutions.
• 1988, US National Energy Policy Act, “to establish a national energy policy that will quickly reduce the generation of CO₂ and trace gases as quickly as is feasible in order to slow the pace and degree of atmospheric warming…to protect the global environment.”
• 1992, U.N. Framework Convention of Climate Change
• 1997, the Kyoto Protocol