Tuesday, April 19, 2005

Role for BYU in Ancient Text Discovery

I've seen the discovery of the Oxyrhynchus Papyri mentioned on several blogs including Clark at Mormon Metaphysics. However, it wasn't until I saw this discussion by the editors of Scientific American, that I realized that BYU played a role. (The article Clark linked to also mentions BYU about 3/4 of the way down.) Must be the university's Institute for the Study and Preservation of Ancient Religious Texts (ISPART).

Go Cougars!

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The Genographic Project

You may have read about The Genographic Project--I've seen it discussed on a number of blogs. The researchers behind the project are seeking to obtain 100,000 DNA samples from around the world, especially from aborigines, in order to understand ancient population migrations.

This reminded me of the work going on by BYU's Dr. Scott Woodward and the Sorenson Molecular Geneology Foundation, so I contacted them to get their perspective as to how their work compares with GP.

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Their response reads, in part:

The short answer to your question on how we differ from the Genographic Project (GP) is that our study is genealogical in nature, while the GP is anthropological. Our personal feelings on this matter is that the two studies are complementing each other, as the data we are collecting and analyzing is used to reconstruct lineages that are close to us in time (within the last 6-10 generations), while the GP's goal is to link people back 10-60 thousand years ago.

Some of the genetic techniques used in both studies are similar, but they are used to produce different type of data and answer different questions. In addition, GP is not collecting any pedigree information, which is a key point in our study.

The SMGF project has already been going for over four years and has collected 50,000 samples from around the world. The GP is just starting and will collect samples for the next five years.

You can visit the respective websites for information about participation. SMGF will send you a free kit; GP's kit costs $100.

I definately recommend a visit to GP's website. It is pretty slick--in addition to some nice tutorial information, there is an interactive map that shows current understanding of human migrations over time with respect to specific genetic markers. Clicking on elements of the map will allow you to read specific information on that element.

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Sunday, April 17, 2005

Approaches to Quitting Smoking

Dave recently pointed out The Elder Barr Blog, via The Bloggernacle Times. It's an interesting idea for a blog. I didn't read any of it, I just scrolled down and looked at pictures--the same type of pictures that have been taken probably millions of times now. However one picture caught my eye. There is a picture of Elder Barr on the street holding a sign that says "Free Stop Smoking Workshop."

I could be wrong, but I think I have a pretty good idea of what that workshop involves--cinnamon mouthwash, gum, and toothpaste.

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On my mission we had a stop-smoking program, but I always thought it was odd because it didn't have the Church's stamp of approval anywhere on it. In fact it was copyrighted and we technically were not supposed to copy it--it said so right on it. But I just went with the flow--this was what we were supposed to use, so I used it.

As time has passed, I've become more skeptical. Not only do I wonder where the heck that thing came from, I also wonder if it has ever worked. I don't think any of my smoking investigators successfully quit. (My wife says hers did.) If it is the offical way to quit, why aren't the Church's fingerprints anywhere to be found on it?

For as much press and discussion the issue of smoking gets in church, there is precious little in terms of guidance as to how to quit. A quick look on the Word of Wisdom section of Provident Living.org reveals a number of links to talks in the Ensign and lessons from manuals, but none seem to give much advice.

The closest I've seen to scientific treatment of the problem was in the February 2002 Ensign article "Tobacco: Quitting for Good." It provides links to professional and government organizations such as CDC and the Dept. of Health and Human Services. (Interestingly, this article is not included in the list of Ensign articles on ProvidentLiving.org.)

As a missionary, having never battled addiction before, it made sense to me that prayers and cinnamon were the answer to quitting. The push for baptisms perhaps squeezes out more effective or lasting approaches. The above referenced Ensign article states:

Because no single condition leads to tobacco dependence, no single solution cures smokers of their dependence on cigarettes. Some people are able to quit smoking easily, while some find quitting so difficult that they do not quit even when facing tobacco’s serious health problems. Smokers who believe that quitting smoking will be easy or that God will make it easy for them may become disillusioned if they experience the normal withdrawal symptoms or if they relapse back to smoking. Therefore, it is wise for smokers to take time to plan this important change carefully and prayerfully.

Successful treatment can include at least three components: (1) counseling and advice from a skilled, knowledgeable professional, with a focus on developing problem-solving skills, overcoming barriers to quitting, and preventing relapse; (2) support from friends and family members; and (3) the possible correct, careful use of legal stop-smoking medications, including nicotine replacement and other drugs tested for safety and effectiveness.

Can you imagine a missonary suggesting nictotine replacement? Some people quit cold-turkey and are successful. However this approach does not work for eveyone. In fact it is the least successful approach.

So when I hear the missionaries say that they are going to do a stop-smoking program with someone, I can't help but think, "Been there--done that--doubt it'll work." Do I have too little faith, or should we approach smoking from a different angle--a more effective angle? Should we have good evidence that investigators have overcome their WoW addictions before baptism?

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Thursday, April 14, 2005

Richard Dawkins: Friend or Foe?

If there is a single modern person who draws the most ire from critics of evolution, I think it has to be Richard Dawkins. His popular science writings on evolution are pointed and powerful, and his atheism outspoken and unyielding. This makes him controversial both on scientific and philosophical grounds. And yet I quite enjoy his books. I certainly don't agree with his atheism, nor necessarily his politics, but I don't see him as a threat--I see him as a challenge. His writings make you think and introduce you to new perspectives. And sometimes I even make religious connections with his arguments.

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Several years ago I read his well-known book, The Blind Watchmaker. I rather liked the book and thought he made some good points. One passage in particular caught my interest. Near the end he discusses non-Darwinian conceptions of the creation of life on earth and why they fail. In response to theistic evolution--that God used evolution to create--he says:

All that we can say about such beliefs is, firstly, that they are superfluous and, secondly, that they assume the existence of the main thing we want to explain, namely organized complexity. The one thing that makes evolution such a neat theory is that it explains how organized complexity can arise out of primeval simplicity. If we want to postulate a deity capable of engineering all the organized complexity in the world, either instantaneously or by guiding evolution, that deity must already have been vastly complex in the first place.


He says a similar thing in Carl Zimmer's Evolution book:
If you're allowed just to postulate something complicated enough to design a universe intelligently, then you've sold the past. You've simply allowed yourself to assume the existence of exactly the thing which we're trying to explain. The beauty of the theory of evolution by natural selection is that it starts with simple things, and it builds up slowly and gradually to complex things, including things complex enough to design things--brains, in other words. If you allow yourself to use the idea of design right from the start, then you are simply giving up the beginning. You're simply not providing any kind of explanation at all.

When I read the that first passage I thought, "you know, he's got a point here." It also occured to me that Mormon theology comes closer than any other I am aware of, particularly Christian, to addressing this issue.

We don't have any final answers for the issue Dawkins raises, but we have more of a start than anyone else. Joseph Smith broke with strong tradition with his King Follet Discourse, and other similar teachings. The ideas that the elements are eternal, that God progressed to become what and who he is--these are mind expanding and daring ideas. Who else would sing a hymn asking, "Do you think that you could ever, in all eternity, find out the generation where gods began to be?" We don't know much about these issues so we don't emphasize them, but Joseph opened doors that would be unthinkable in other Christian traditions--and we are often criticised for them.

So in some ways, when I read Dawkins, I see him as a kindred spirit rather than the enemy. He is bold enough to ask big questions, and while I don't have the answers, I at least appreciate the questions.

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Review of Evolution: The Triumph of an Idea

I recently finished reading Evolution: The Triumph of an Idea, by Carl Zimmer and want to share a few of my thoughts about it. It is the companion book to a PBS series. (The PBS website is worth browsing as well.)

I think Evolution is a great book for anyone wanting a broad introduction to evolution. It is well written and has many beautiful color pictures, illustrations, and figures. I was suprised at the quality of my paperback version--the paper is not the cheap kind usually used in novels. The book has a textbook feel and look, but with clear, mostly non-technical writing. It gives a broad overview of evolutionary theory using many fascinating examples, along with some discussion of its history and implications. Although a biology background is certainly helpful, I think the writing is clear enough that anyone with rudimentary science education would easily understand the concepts presented. I thought it was also written in a balanced way. For example, I knew ahead of time evolutionary psychology is a controversial area. To its credit, the book presents the views of both proponents and critics.

Here is a basic outline of the content:

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  • Biography of Charles Darwin and how he was influenced in developing his theory.

  • The basic principles of natural selection.

  • Discussion of the history of life on earth including its beginning, and major steps forward in complexity.

  • The role extinctions have played in natural history and their future implications.

  • Coevolution--how evolution of one species affects the evolution of others.

  • The role of evolution in infectious diseases.

  • The purpose of sex and how sexual selection shapes life.

  • The evolution of humans

  • The history of the conflict between science and religion in America, and current issues.


Throughout the book there are many illustrative examples of how evolution has shaped life and they represent a challenge to think of a more reasonable explanation. This is especially true in the strange world of sexual selection. Why do certain male insects allow the female to eat them after mating? Why do peakcocks have such big tails? Why do male lions kill lion cubs that are not their own? Why do some animals display signs of altruism? Why do chimpanzees display such violence but bonobos (another type of chimpanzee) make love, not war? These and other questions, it seems, can only be answered in the context of evolution.

The final chapter deals with religious controversies. It provides multiple perspectives and is done respectfully, I think. At the end is a brief discussion of Darwin's view of religion. He was not a raging atheist--he was rather private in his views and shunned the spotlight. He did move to agnosticism, but this cannot be attributed to his theories alone--personal tragedy, combined with uninspired (in my view) theology played an understandable role. I came away quite sympathetic to him--I do not believe he deserves the personal hostility often shown toward him by critics.

I do have a couple of brief criticisms of the book. First, instead of a footnote or endnote format, the book has a bibliography. This makes looking up references for specific claims or examples a little more difficult. Also, when discussing extinctions and the evolution of resistance in microbes and other pests, the writing seemed a little alarmist to me. They are important issues, but my impression was that these discussions had a little too much doom and gloom to them.

My criticisms are minor. At around twenty dollars, this book is a good buy for the money. I certainly recommend it.

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Wednesday, April 13, 2005

Zimmer and Viral Evolution

Carl Zimmer has a post responding to some criticism that one of his posts received from the creationist organization, Answers in Genesis. The topic was the evolution of HIV, and Zimmer noted that in studying these types of things, nobody uses creationist assumptions. Follow the link and you can catch up on the argument if you wish.

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Zimmer caught a sentence contained in an Answers in Genesis article.
Viruses can have no evolutionary relationship to any other form, and so whatever may have happened to say, the AIDS virus, has no relevance to the supposed history of truly living organisms in any case.
Actually they do. He also correctly notes that sometimes viruses insert themselves into our genome. He then links to several interesting papers.
 
I'd like to add a couple of links of my own. First, I recently posted about co-speciation of simian foamy viruses and their primate hosts. Also, check out this paper--it's free.
 
Now I know you won't understand everything in it. Some of the technical details I don't fully comprehend either, but here is the upshot:
 
Retroviruses replicate by first inserting their genome into the host DNA (as is the case for HIV). If the viral genome is inserted into a germline cell, the viral genome will be passed on to future generations as part of the host genome (assuming the virus is not too pathogenic). A number of these retroviral genomes (or remnants of them) have been identified in primate (and even more broadly, vertebrate) genomes. Looking at the sequence of these viral remnants and where they have integrated allows scientists to make comparisons among related species. If the concept of common descent is true, you would predict that species that share a common ancestor would share the same viral integration events (ignoring a few potential complications). This turns out to be true and is, in my mind, powerful evidence for common descent. The researchers go a step further and show that certain features of these viruses can be used to support the time of divergance.
 
Viral evolution is a topic I'd like to have a better handle on. It is a difficult topic in some respects because we don't have much to go on in terms of studying ancient viruses. We can, however, make comparisons and those comparisons can tell as much.

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Tuesday, April 12, 2005

Marburg Outbreak Continues

There is a big Marburg outbreak going on in Angola (Marburg virus is related to Ebola virus), but locals are apparently scared of the WHO wokers that are trying to help contain it. This article describes the problem.
Fear and ignorance are fuelling the world's deadliest outbreak of Marburg fever in Angola, where locals are too suspicious of medics in "astronaut" suits to let them take away infected loved ones, aid workers said on Monday.
 
Terrified residents stoned World Health Organisation (WHO) workers' vehicles late last week, putting a brief halt to their operations to contain the disease in Uige province, northeast of Angola's capital Luanda.
 
"We no longer have people coming to the isolation ward -- people are hiding their patients at home because they're scared. That means the virus keeps on spreading in the community," Monica Castellarnau, emergency coordinator for Medecins Sans Frontieres (MSF) in Uige, told Reuters by phone from Uige.
 
The outbreak has killed 194 of the 214 known cases, according to the WHO.
One the great blessings of our civilization that often goes unnoticed is the combined effect of education and our public health system.

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Monday, April 11, 2005

Adam and Eve: When and Where?

[The following is a cross-post from Mormons and Evolution.]

Earlier I discussed some of the issues surrounding how Adam and Eve were created, and listed two tentative suggestions for reconciliation with science. Here I will discuss some of the issues involved in placing Adam and Eve in time and geography. Up front I want to point out that I am not a geneticist, archeologist, or anthropologist. My understanding of the issues involved come primarily from writings for non-expert audiences.

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The LDS Model:

The traditional LDS placement of Adam and Eve is straightforward. Using Biblical chronology and other supportive scriptures, Adam and Eve became mortal around 6,000 years ago. Scriptural statements place the future (and by implication the past) site of Adam-ondi-ahman in Missouri. A number of personal accounts state that Joseph Smith identifed Jackson county as the site of the Garden of Eden, and identified some stones as part of an altar that Adam built after leaving the garden. Some presume that Noah was responsible for transfering the human race to the Eastern Hemisphere.

The Scientific Models:

One of the components of evolutionary theory is the concept of common descent--that all living organisms descend from previously living organisms and that ultimately, all living organisms share common ancestors. For humans this means that our physical bodies share common ancestry with other primates. Long ago it was recognized that the closest living relative, with which we share a common ancestor, is the chimpanzee. This hypothesis is supported by both anatomical, archeological, and genetic evidence. Since chimpanzees are only known to have lived in Africa, the origination of humans was hypothesized to have taken place there.

Accumulating evidence has continued to support Africa as the place of human origins. The oldest hominid (including Homo sapiens) remains are found there. Genetic diversity in humans is greatest in Africa and less diverse outside of Africa, which suggests that populations throughout the rest of the world are descended from a subset of early African populations.

The relatedness of hominid species is still under debate. As I understand it, the current dominant model of human development and expansion is called "Out of Africa 2." In this model, modern humans developed in Africa after other hominids had migrated to Asia and Europe. Modern humans eventually moved out of Africa and replaced other hominids who became extinct. The other main model is called the "Multiregional" model. In this model, early hominids moved out of Africa to colonize Asia and Europe as described above, but modern humans arose gradually through genetic mixing of these populations. Other models contain a mixture of these two models. One recent paper, based on genetic evidence, argues for genetic mixing with several major migrations, including three from Africa.

Below is a rough, brief timeline of significant events in hominid evolution:

>1 million years ago: First hominids leave Africa
200,000 years ago: First anatomical Homo sapiens in Africa
~160,000 years ago: "Mitochondrial Eve"
~60,000 years ago: "Y-chromosome Adam"
40-50,000 years ago: Development of culture (more sophisticated tools, art, ceremonial burial of dead)
15-30,000 years ago: Colonization of North America
10,000 years ago: Development of Agriculture
3-4,000 years ago: Development of written language

Placing Adam and Eve in light of current scientific understanding and without additional revelation is highly problematic. The qualities associated with Adam and Eve in the scriptures include intelligence, writing, and agriculture. Further, the LDS model places Adam and Eve in North America around 6,000 years ago. This timing is reasonably consistent with agriculture and writing, but is inconsistent with genetic or geneological ancestry to all living humans. Placing Adam and Eve in a position of genetic or geneological ancestry is inconsistent with writing and agriculture, as well as with placement in North America. The concepts of "mitochondrial Eve" and "Y-chromosome Adam" are not helpful her because, in spite of their naming, they do not refer to the biblical persons. That this is true is evident from the different times that these two individuals lived.

With scientific debate still surrounding how early hominids relate to each other it seems premature to pose any scenario that accounts for Adam and Eve, much less their placement in North America. Such a proposal would also require revelatory clarification on the timing and geography of Adam and Eve, and whether the identification of stones derived from Adam's altar was a matter of speculation or literal truth. (Duane Jeffery recently pointed out the problem these stones pose for a worldwide flood scenario.) Until information is more forthcoming, on both sides, it seems best not to force a reconciliation. Speculation is all we can do right now.

Further Reading
There are a number of explanations of human development and migration available on the internet. I will list just a few here.
Origins of Modern Humans: Multiregional or Out of Africa, by Donald Johanson
Alan Templeton, Out of Africa again and again
Becoming Human
Out of Africa, EvoWiki
Human mtDNA Migrations

There are a number of books that likely give good general explanations of current scientific thought. Since science moves, sometimes quickly, it is important to seek out information that is as fresh as possible. It is also important to read from multiple sources in order to not mistake one person's opinion for generally accepted conclusions. This advice applies to all scientific fields.

Comment at Mormons and Evolution.

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