Death Panels: Universal or Private?

A Daily Show panel weighs in on who should run death panels.




Oh, and since we're at it here is a twist on a classic.

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LDS Guys Talk Physics (and other stuff)

If you like physics, then you may be interested in a blog that popped onto my radar a few weeks ago. It's The Eternal Universe, and it's run by several BYU graduates who majored in physics. At least two All of them have gone on to graduate school.

One of the contributors is planning to explain black holes, quarks, and other fun things with an LDS audience in mind. My understanding of physics can always be improved; I'll be watching.

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Fallible Memories and Prophetic Succession

Our memories are surprisingly unreliable. I say surprisingly because they seem so real and concrete. Of course they are accurate enough for us to get by without major disruption, and most of the time there is no way to prove them wrong anyway. But sometimes they can be wrong in a big way.

Discover Magazine has an article titled "How Much of Your Memory Is True?" that discusses how our understanding of memory is changing. Part of it deals with false memories.

Even harrowing memories—the so-called flashbulb memories that feel as if they have been permanently seared into the brain—are not as accurate as we think. Less than a year after a cargo plane crashed into an Amsterdam apartment building in 1992, 55 percent of the Dutch population said they had watched the plane hit the building on TV. Many of them recalled specifics of the crash, such as the angle of descent, and could report whether or not the plane was on fire before it hit. But the event had not been caught on video. The “memory” shared by the majority was a hallucination, a convincing fiction pieced together out of descriptions and pictures of the event.

Reading this reminded me of the famous story in LDS history of the passing of the prophetic mantle from Joseph Smith to Brigham Young. After Joseph was killed it was unclear who should be in charge. A meeting was held on August 8, 1844 where both Sidney Rigdon (counselor in the First Presidency) and Brigham Young (president of the Quorum of the Twelve Apostles) addressed the congregation and explained why they were entitled to lead the Saints. Many people (including one of my own ancestors) said that while Brigham Young spoke he seemed to sound and/or look like Joseph, and this was taken as evidence of divine approval of Brigham Young. Unfortunately, there are no known contemporaneous written accounts of this manifestation. Even Wilford Woodruff failed to mention anything miraculous in his lengthy journal entry for the day.

Of special interest here are Apostle Orson Hyde and John D. Lee (of Mountain Meadows fame), both of whom left retrospective accounts of their experience. Elder Hyde's accounts are pretty detailed. For example, in 1869 he said,

We went among the congregation and President Young went on the stand. Well, he spoke, and his words went through me like electricity. "Am I mistaken?" said I, "or is it really the voice of Joseph Smith?" This is my testimony; it was not only the voice of Joseph, but there were the features, the gestures and even the stature of Joseph before us in the person of Brigham. And though it may be said that President Young is a complete mimic, and can mimic anybody, I would like to see the man who can mimic another in stature who was about four or five inches higher than himself. Every one in the congregation-every one who was inspired by the Spirit of the Lord-felt it. They knew it. They realized it.

I sat myself down in, the midst of the congregation, with my two wives, whom Joseph had given and sealed to me. When President Young began to speak, one of them said, "It is the voice of Joseph! It is Joseph Smith!" The exclamation of the other was, "I do not see him, where is he?"

The problem is that Wilford Woodruff's journal says that Orson Hyde arrived in Nauvoo on August 13 (he is also missing in History of the Church 7:231) and John D. Lee's own diary says that he arrived August 20--five and twelve days, respectively, after the meeting occurred.

If the written journals are correct, it appears that Hyde and Lee unconsciously created memories of the passing of the mantle based on the stories of others. Or giving them more benefit of the doubt, perhaps they transposed a later spiritual experience onto a false memory of attending the August 8 meeting. Whether the other accounts are of a similar nature is the kind of question historians worry about. My own opinion is that there was at least a core group of people who genuinely had the described experience. They wouldn't be the only ones; decades later several people reported a similar experience when Heber J. Grant followed Joseph F. Smith as Church president.

Nevertheless, the examples of Orson Hyde and John D. Lee (and maybe even Wilford Woodruff) raise questions about the nature of religious testimony and witness. Can we be confident, for example, that the scriptures do not contain any false memories? Whatever the case, these examples suggest that the line between truth and fiction can be blurry. That, and if you have a miraculous experience you should write it down quickly.


[Related post: A Case of First Presidency Amnesia.]


References:

Lynne W. Jorgensen and BYU Studies Staff, The Mantle of the Prophet Joseph Passes to Brother Brigham: A Collective Spiritual Witness. BYU Studies 36, no. 4. (1996-1997)

Richard Van Wagoner, The Making of a Mormon Myth: The 1844 Transfiguration of Brigham Young. Dialogue: A Journal of Mormon Thought, vol. 28 no. 4. (1995)

Reid L. Harper, The Mantle of Joseph: Creation of a Mormon Miracle. Journal of Mormon History vol. 22 issue 2. (1996)

Thomas Alexander, Mormonism in Transition, p. 117

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What Separates Humans from Chimpanzees? (Part 1)

[This post is part of a series, What Separates Humans from the Animals?]

In a previous post in this series I explained that transposons are short stretches of DNA that make copies of themselves and insert back into the genome at a different place. Retrotransposons are very similar; the main difference between them is that regular transposons are directly copied as DNA, but retrotransposons are copied into RNA and then back into DNA, which then integrates into the genome. It may come as a surprise that retrotransposons make up about 42% of the human genome! (Regular transposons contribute another ~3%.)



There are several kinds of retrotransposons. Some are disabled viruses that are distantly related to HIV. Here we will focus on Alu elements, of which there are over 1 million copies in the human genome (or about 10% of the genome). Alu elements are only found in primate genomes, but they don't code for any proteins. A mere ~300 base pairs (i.e. DNA 'letters'), they depend entirely on proteins produced by the cell and other retrotransposons, for their replication. When new Alu copies integrate into the genome of a germline cell, the Alu element becomes part of the DNA that is passed on to that person's descendants. In humans they sometimes cause genetic diseases when they integrate into--and thus disrupt--a functional gene.


Scientists have found that Alu elements make great genetic markers, and the reason is pretty simple: for any stretch of DNA that has an Alu element, the ancestral state can be inferred to be the same stretch without the Alu. As an analogy, consider a document that has been photocopied repeatedly and distributed throughout an office. If you compare two copies--one with a nice big coffee stain, and one without--you know that the clean copy is descended from a copy that pre-dates the coffee-stained one. The same reasoning applies here. Further, the chances of two Alu elements independently inserting into the exact same place are low, and it is rare (but not impossible) for an Alu element to be precisely removed.



When Alu elements are copied, mutations can occur which are then propagated to subsequent copies. For this reason, Alu elements can be grouped into families based on sequence differences [1]. Salem et al. compared Alu elements of a particular family in the genomes of humans, chimpanzees, bonobos (pygmy chimpanzees), orangutans, siamangs, green monkeys, and owl monkeys. More specifically, they looked for Alu elements that were located in the same place in the genome of different species. Their overall finding is summarized in Figure 3 of their paper.

(Click to enlarge.)

Figure 3. Primate relationships reconstructed by using Dollo parsimony analysis of Alu elements. Primate relationships were derived from analysis of 133 Alu loci by using maximum parsimony criteria. The number of insertions observed along each branch of the tree is indicated, and bootstrap support values are placed above each node.

The figure is read similar to a family tree. Each node represents a common ancestor of all species to the right of that node. The numbers underneath the triangles indicate how many Alu elements are contained in identical locations in the genome of each species descended from that node. So, for example, humans, chimpanzees, bonobos, and gorillas all share 33 separate Alu elements at the same place in their DNA. Humans have 7 unique insertions, chimpanzees and bonobos together have 14. So for this family of Alu elements, humans and chimpanzees (including bonobos) are separated by 21 unique insertions. (If we consider all Alu families, humans have about 7,000 lineage-specific Alu insertions and chimpanzees have about 2,300.)

Yet, the unifying nature of the Alu insertions is obvious. As the authors wrote,

The patterns observed clearly indicate a stepwise pattern of insertion reflecting the relative divergence of each group in the hominid lineage.

The clarity is impressive, but there is one minor snag. The authors found one Alu insertion shared between humans and gorillas that is not shared with chimpanzees. If you looked only at that insertion you would conclude that humans are more closely related to gorillas than chimpanzees. Is this a problem? No.

The splitting of the lineages that led to gorillas, chimpanzees, and humans are thought to have occurred within a few million years of each other. This has resulted in the trichotomy problem, which I have explained before (see Understanding Trichotomy). As I wrote then,

Humans, chimpanzees and gorillas each have their roots in a common gene pool. However, the sorting of ancestral polymorphic alleles in the diverging lineages is subject to evolutionary processes such as genetic drift. Thus purely by chance, alleles can become fixed in a way that gives a different picture than the true species-branching pattern.

In other words, as the lineages leading to the different species were branching off from one another, the presence of that particular Alu within each population was in flux. Probably by chance, it was lost from the chimpanzee lineage and retained in the gorilla and human lineages. In support of this, the authors estimated the ages of the conflicting Alu insertions based on mutation rate and found that the anomalous insertion supporting the human-gorilla relationship is 1-4 million years older than those that support the human-chimpanzee relationship.

It is beautifully amazing to me that such short and simple pieces of DNA can provide such a clear picture of evolutionary history.


Notes:

[1] To see how the distribution of Alu families among primates also supports common descent, see Figure 3 in Roy-Engel et al.


References:

Salem AH, Ray DA, Xing J, Callinan PA, Myers JS, Hedges DJ, Garber RK, Witherspoon DJ, Jorde LB, Batzer MA. Alu elements and hominid phylogenetics. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12787-91.

Roy-Engel, A. M., M. A. Batzer and P. L. Deininger (2008) Evolution of human retrosequences: Alu. In "Encyclopedia of Life Sciences".

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What's the Deal with Cattle and Methane?

On my recent vacation, my dad asked me about the science regarding cattle and methane in connection with global warming. As much as I would like others to think that I know everything, I unfortunately do not, so I could only give a vague answer. I've since done a little poking around on the internet to find out more, and I figured I would post it here for anyone interested.

Here is a two-minute summary:

Methane (CH4), of course, is the main component of natural gas and is produced in a variety of places in nature. Like carbon dioxide, methane is a greenhouse gas because it traps heat in the atmosphere. Before the year 1750, methane levels in the atmosphere averaged around 700 parts per billion; now the level is around 1,700 parts per billion.

Ruminant livestock such as cattle, sheep, and goats have a special digestive system that allows them to break down plant material. Methane is a by-product of their digestion (enteric fermentation), and is released into the atmosphere. Livestock account for around 20-30% of human-related methane production; in the U.S. livestock and landfills are the top two human-related sources of methane.

Efforts at reducing livestock methane emissions are focused on better efficiency, genetics, and nutrition, especially in the beef industry.

For more information, see the following links to the EPA: here, here, and here.

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One Giant Leap for Mankind

40 years ago today, Neil A. Armstrong and Edwin E. "Buzz" Aldrin Jr. became the first humans to set foot on the moon, while Michael Collins orbited as the command module pilot. They left a plaque that said,

Here Men From The Planet Earth First Set Foot Upon the Moon, July 1969 A.D. We Came in Peace For All Mankind.

For more incredible pictures, see The Big Picture.

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Moon Landing Sites Photographed by Satellite

NASA's Lunar Reconnaissance Orbiter (LRO) has photographed five of the six moon landing sites. Equipment, and even a trail through the dust, are visible! Even better images are expected once the LRO is settled into its orbit.

Here is the best one, but go see the rest!

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Alternative Medicine Fails; Not That It Matters

I'm back from vacation, and although I'm not exactly awash in free time, I hope to push out some of the blog material that has been accumulating. First up: alt med.

A June AP news story looked at what has been gained by the government's spending of $2.5 billion on research into alternative medicine, much of it through the National Center for Complementary and Alternative Medicine (NCCAM). The answer: almost nothing. But let's back up.

NCCAM, and its earlier incarnation, the Office of Alternative Medicine, has been the personal project of Senator Tom Harkin (D-IA), who became convinced that bee pollen helped his allergies and that another Congressman had been cured of cancer by alternative medicine.

Last February in a Senate hearing, Harkin complained--I am not making this up--that NCCAM was too negative in that it was casting doubt on many treatments but not validating enough of them.

One of the purposes when we drafted that legislation in 1992 . . . was to investigate and validate alternative approaches. Quite frankly, I must say it's fallen short. I think quite frankly that in this center, and previously in the office before it, most of its focus has been on disproving things, rather than seeking out and proving things.

As if the problem is science!

There is a hierarchy of plausibility in alternative medicine. Toward the top are herbal treatments because they are basically unregulated drugs. It is entirely possible that some of them could be useful. Toward the bottom are homeopathy or treatments that claim to alter some sort of vital energy or life force, because they are essentially supernatural claims and are often rooted in pre-scientific notions about physiology and medicine.

I agree with those who argue that the term 'alternative medicine' is really a misnomer. To begin with, some things that are called alternative medicine are encompassed within mainstream medicine (e.g. nutrition, exercise, relaxation, and other healthy lifestyle activities). But beyond that, treatments that are shown to be effective are incorporated into mainstream medicine; those that remain untested or unproven are not, and don't really deserve to be called 'medicine'. I know which group I want when I get sick.

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