Thursday, November 30, 2006

Free Book: Evolutionary Science and Society

I don't know much about the organization that put out this book, and I haven't been able to give it a thorough reading, but it looks great! I recognize the names of several of the contributors as being prominent in science.

Topics covered include: the origin of life, constructing the tree of life, placing humans in the tree, history and philosophy of science, science and theology, basics of how evolution works, and practical applications.

You can download the whole book, or individual chapters, as pdf files. Did I mention it's free? So go get it, and then you can print out chapters to read at your leisure.

Once again, here is the link.

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Friday, November 17, 2006

DNA and BofM: Signature Response to Stewart's Article

Signature Books posted a response (Nov 16, 2006) to David Stewart's article published at FAIR and FARMS. I previously commented on the article here and here.

Most of the writing is unattributed, but it does contain a response from Simon Southerton on the specific issue of Y chromosome haplotype Q. Even better, there is a link to this paper on Jewish genetics. I'll have to digest it when I get a chance.

There is a history of bad blood between FARMS and Signature Books, so the somewhat snide tone (of the unattributed writing) is not unexpected, although unfortunate. But I can't say that FARMS doesn't deserve it on this one; the writer picked up on some of the same issues I raised before.

Also, I just ran across this page on the Signature Books website. It looks like a hypothetical migration scenario--like that of the Book of Mormon--was posed to several scientists and their comments have been posted. They are worth reading through; most of the answers boil down to 'it depends.' The answer that Henry Harpending (a National Academy of Sciences member) gave should look pretty good to an apologist's eyes.

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Monday, November 13, 2006

Jeffrey Meldrum on Bigfoot

Jeffrey Meldrum has been in the news recently. He is a professor of anatomy at Idaho State University and is a co-author, with Trent Stephens, of Evolution and Mormonism as well as a FARMS article on DNA and the Book of Mormon. He is also a star in Bigfoot research. (I kind of wish I didn't have to write 'Book of Mormon' and 'Bigfoot' in the same paragraph, though of course some would say it's appropriate.)

AP news article: here
NPR Science Friday interview: here. (In the interview, Meldrum maintains that the university faculty are generally not as negative as the AP story sounds.)

He has also authored a new book on the topic: Sasquatch: Legend Meets Science. I'd be interested to read the book at some point. There's a chapter on DNA, but from the NPR interview I understand that they really don't have any yet (other than samples that have turned out to be bison, or some such). I'm on the skeptical side, but it would be really cool to be wrong.

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Thursday, November 09, 2006

Science Investigating Religion; Speaking in Tongues

There is a post over at The Panda's Thumb about science investigating religion, that I think makes some good points. I noted this paragraph:

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Modern medical science is based precisely on comparing the outcomes of different interventions in order to choose the most effective to maximize quality and/or quantity of life. And once the data are known, it is standard medical practice to allow every patient to follow the course of intervention that most satisfies one’s individual preferences and goals. Most of us would consider having the choice between more or less aggressive cancer therapy options, weighing quality of life and survival expectancy issues, to be an absolute positive. I see no reason why the very same should not apply to the option of choosing between different religious practices based on similar parameters, should they be shown to indeed significantly affect life expectancy. In fact, assuming the health benefit of religious practice could be satisfactorily demonstrated, even if the effect of changing one’s religious practice were just marginal on an individual level (say, one month’s longer lifespan on average), the cumulative effect at population level could be enormous, giving the vast numbers of faithful. Just from a public health perspective, it should arguably be considered unethical not to investigate the issue and disseminate the results.
It strikes me that while Mormons are pretty cautious about science and scholarship proving the Book of Mormon or other particular doctrines, we do seem to like touting the 'fruits' of the gospel, which usually include such things as good health (thanks to the Word of Wisdom), somewhat lower divorce (thanks to temple marriage), and so forth.


Also in the news is a neuroscience study on speaking in tongues. He is an atheist, so you would expect him be a little sour about such things, but I think PZ Myers makes good points.
This is a paper that reports quite ordinary changes in the level of brain activity during glossolalia; there are no traces of possessing spirits or other extra-cranial meddling entities, and there is no provision in the work for detecting them if there were.
Mormons tend to be more practical about speaking in tongues; these days our conception of it bears little resemblence to how other Christians view it. But the larger point is that if you want to show that the brain is being acted upon by an outside influence, you're going to have to have a compelling model system.

I think that, ideally, verifiable intelligence would be communicated. That sounds like criteria that Brother Joseph would support.

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Thursday, November 02, 2006

Blogger Reaches Milestone; Sees Promised Land

I met with my dissertation committee a few days ago. They critiqued some of my work, and they have a few more things that they want me to do, but they gave me the green light to start wrapping up my benchwork and write my dissertation. My blogging will therefore be rather light for the next few months. Rather than kicking around blogging ideas, I need to spend the time and mental resources on being an expert in my field, and getting the @#$% thing written. Oh, and finding a job too.

I hope that the MA administrators won't be too quick to kick me out of my cozy spot on the aggregator. (I suspect that more than one of them will be quite empathetic, having done--or preparing to do--the same thing.) I imagine that I will do some quick posts from time to time for diversion, but I will probably be mostly ignorant of what is going on in the bloggernacle. Feel free to email me if I'm really missing something.

But don't worry, I plan to pick up the pace again after defense day. Because...

I'll be back, when the day is new, And I'll have more ideas for you, And you'll have things you'll want to talk about. I will too.

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Monday, October 30, 2006

Rainbow of Colors: Monkey See

Color vision is something I take for granted. I forget that a significant portion of the population does not see the range of colors that I can. And I have no way of appreciating the range of colors that birds and bees can see. The natural history of primate color vision makes for an interesting story.

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We see color because the cones in our retinas make three different versions of proteins called opsins. These proteins are responsible for initiating impulses to the brain, and they have differing sensitivities to different wavelengths of light. It is by comparing the signal strength between the three opsins that our brains are able to interpret color. Since we have three types of opsin proteins (S, M and L), we are trichromats.


(Figure shows spectral sensitivities of the opsins in different organisims [1].)

Although there are several types and causes of color blindness, the most familiar cause is genetic and mainly affects men. This is because two of the three opsin genes are located on the X chromosome. Since females have two X chromosomes it doesn't matter if one of them has a defective opsin gene. But if a male has a defective opsin on the X chromosome, he's out of luck.

Color vision appears to have been the norm for most animals--including fish--but most placental mammals are dichromats, apparently because they lost two unnecessary opsins while adopting a nocturnal lifestyle early in their evolution. Most primates are different, however, and this is where the story gets interesting.


There is a basic divide among the monkeys and apes: there are the Old World Monkeys (OWMs) and Apes (including humans), and then there are the New World Monkeys (NWMs). NWM males are dichromats, but some females are trichromats. How can this be? Well instead of having two different opsins on the X chromosome, there are different variants (allels) of the one opsin gene on the X chromosome circulating in the population. Since females have two X chromosomes, they can have two variants of that opsin at once. Such females are called 'allelic trichromats'. Males are stuck with either one or the other variant, and thus remain dichromats. The exception is the howler monkey, which at some point had a gene duplication occur such that the X chromosome has two copies of the opsin gene. One of the opsins mutated such that it has a slightly different wavelength sensitivity, making howler monkeys 'true trichromats,' like us.

OWMs and Apes are true trichromats. The reason for this is similar to the howler monkey. At an early point after the split from NWMs, a gene duplication occured on the X chromosome leading to the existence of two opsin genes of slightly different peak sensitivity. However this was an earlier and separate event from that of the howler monkey. (In the figure above and to the left [2], the arrows indicate lineages that are true trichromats. Red lineages indicate those with a high precentage of OR pseudogenes, as explained below. Click to enlarge.)

All of this is interesting for a number of reasons, including issues of phylogeny, biogeography and so forth, but the story goes one step further. A group of scientists were studying the olfactory receptors (ORs) in primates. These proteins are to smell, what opsins are to vision--except that there are a greater variety of ORs. Specifically, they looked at the proportion of OR genes that are broken (pseudogenes) in a variety of primates and found something interesting. OWMs and Apes have a higher percentage of OR pseudogenes than NWMs, with one exception: the howler monkey. The figure to the right (click to enlarge) shows the percentage of OR pseudogenes in different primate species [2]. Humans have the highest percentage, but note that the only species above 20% are true trichromats. It is too early to say whether there is a causal relationship, but the correlation is striking and suggests that as primates gained better color vision, selective pressure for smell was relaxed, which allowed increasing numbers of ORs to become broken and unused.

As I look out my window, fall colors are on full display. Limited as they may be in comparision to some other animals, I'm grateful for my senses.




1. Vorobyev, Ecology and Evolution of Primate Colour Vision (pdf), Clinical and Experimental Optometry, 2004, 87:4-5. The same issue of this journal has several additional articles on color vision, freely available here.

2. Gilad et al., Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates, PLoS Biology, 2004, Vol. 2 Issue 1.

See "The Howler Monkey's Tale" in Richard Dawkins' Ancestor's Tale for a popular-science treatment of primate color vision.

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Friday, October 27, 2006

Failures of Alternative Medicine go Unnoticed

I touched on alternative medicine a couple of posts ago. NBC's Robert Bazell recently published a commentary titled, "Ignoring the failures of alternative medicine."

Last week’s study showing that the widely touted and sold supplement DHEA does nothing to slow the effects of aging was only the latest major piece of research with powerfully negative results from the National Institutes of Health Center for Complimentary and Alternative Medicine. Previous placebo-controlled trials proved the uselessness of St. John’s Wort for depression and saw palmetto for enlarged prostates, shark cartilage for cancer, echinacea for the common cold and glucosamine plus chondroitin sulphate for arthritis. [emphasis added]

But it doesn’t matter much — few seem to care....

No doubt some of the thousands of products sold as dietary supplements work well, but the industry that sells them has neither motivation nor desire to know which ones work and which don’t.
For one physician-scientist-blogger's view, see Orac's take.

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Thursday, October 26, 2006

Report: David Calderwood and Voices from the Dust

I recently attended a presentation given by David Calderwood, author of Voices from the Dust. Brother Calderwood served a mission in Uruguay and has subsequently lived in, and traveled to, South and Central America throughout his career. After retiring he returned to graduate school at the University of Texas at Austin to study at the Institute of Latin American Studies where he earned an M.A. Over the years he has collected over 70 chronicles written by Spanish and Portuguese explorers, priests, and soldiers. He was apparently a popular speaker at the recent CES Education Week at BYU.

What follows is my report of his talk, according to my notes.

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The main theme of Bro. Calderwood's talk was that Spanish and Portuguese chronicles, written in the 15-1600's but not published until at least the late 1800's, contain descriptions of native history and folklore that correspond with the Book of Mormon.

Early in the talk he said that researchers are tied to "make-believe histories." The first is evolution and that there was no creation. The second is that Native Americans migrated from Asia 15,000 years ago and that there were no significant outside contacts until Columbus. (He did not specify whether he objected to the early migration, or just the isolation.)

He spent most of the time talking about interesting elements in various chronicles. I will provide names (where I have them) and some of the things they described.

Miguel Cabello Valboa (1586): recorded legends of the earth shaking, the sun being darkened, and the graves being opened.

Felipe Huaman Poma De Ayala (1609): legends of natual disasters including volcanoes, fire from heaven, sand flattening a city, earthquakes and tidal waves.

Diego de Landa: described baptism in the Yucatan. Bro. Calderwood said that the practice was more widespread and that the Maya term "caput sihil" means to be born again or anew.

Martin de Murua: described Incan religious cleansing that involved confession. Bro. Calderwood said that they had rules that correspond well with the Ten Commandments, and that some of the punishments also correspond (eg. adultery punished by stoning). As part of purification, people would say, "I have confessed my sins to my father, the Sun."

Fernando de Montesinos: His reports are ignored by many scholars because they seem outlandish. His writings include a reference to a transition from government by kings to wise men (judges). Describes how ancient records were used to eradicate homosexuality from the civilization [apparently through repentance].

Pedro de Cieza de Leon: wrote that the Chachapoya indians were the whitest he had seen, and that their women were beautiful.

Bro. Calderwood described other documents refering to white indians, and said that there are still white Amerindians in some places. He also showed iconography depicting white and dark figures. In the picture he showed, it appeared that the dark figures were conquering the white figure.

Alonso de Ercilla Y Zuniga: Araucanos used implements of war including bow and arrows, swords, and scimitars. Bro. Calderwood made a point of telling us that Alonso had seen Old World scimitars.

He related a story about a Jewish rabbi in the 1600's named Aaron Levi [I think], who lived in South America. During his prayers he kept having the thought that Native Americans were Jewish. He was introduced to a group who claimed Abraham, Issac, and Jacob as their patriarchs and said that Joseph lives in the middle of the ocean, divided in two parts.

He also discussed metallurgy and the skill with which some ancient American cultures could manipulate gold, silver, and copper. He also mentioned their skill with cloth and their ability to make a fiber derived from animal hair that was likened to silk.

All in all I thought that the presentation was interesting. At first glance it seems remarkable that the various chronicles contain things that really seem to reasonate with the Book of Mormon. Yet without having studied the material myself--and again, having not read his book--I was at times a little skeptical of the connections he was making. For example, he showed some complicated iconography and explained the interpretation of many of the elements. Since they were of a religious nature it was pretty easy to draw connections to the Book of Mormon. But beyond that, he then pointed our attention to a figure whose meaning is unknown, and suggested that the meaning comes from a particular part of the Book of Mormon. There were a couple of other instances of the same type of thing, and I found myself skeptical that it is really that easy.

It seems to me that it is rather easy to fool ourselves on an issue like this, and although the intent of his talk was to build faith, I did not see evidence of skepticism except as applied to mainstream thought. But if there are real connections to be made, there must also be a host of false positives as well. If LDS scholarship is to have a credible voice, it must separate out the wheat from the chaff. I look forward to seeing how his book fares in the FARMS Review.

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