Friday, November 23, 2007

The Appendix is Still Vestigial

I was reminded of a recently published paper that argues that the human appendix has a function--that it acts as a kind of storage area for commensal (helpful) bacteria. I have not read the paper, but apparently it really only contains a hypothesis (ie. no experiments or data collection), and anyway, even if this hypothesis is correct, it does not change the vestigial nature of the appendix.

Douglas Theobald explains at The Panda's Thumb and in his article at talk.origins--the two should be read together.


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Wednesday, November 21, 2007

Meldrum and Bigfoot in Scientific American

The December issue of Scientific American has a feature article on LDS anthropologist Jeffrey Meldrum and his belief in Bigfoot.

Meldrum’s principal critic from his own field is Daegling, who concludes that the “evidence doesn’t look better on deeper analysis, it looks worse.” He adds that “this isn’t about Bigfoot—it is about how scientists go about doing their work and how we should be self-reflective and self-critical.”

Meldrum responds by saying that most people do not see him critically sifting through all the evidence that comes his way—and discarding most of it. But if he is at times frustrated and beleaguered by skeptics, it appears some in his community are beleaguered by his exhortation that more researchers accept his interpretations or become involved. In reviewing Meldrum’s and Daegling’s books in the American Journal of Physical Anthropology, Matt Cartmill of Duke University concludes that if the chances of Bigfoot’s being real are one in 10,000 (his admittedly wild guess), then having one physical anthropologist on the case seems a reasonable allocation of professional resources and that Meldrum does not deserve scorn or abuse. But Cartmill, who notes that he is “mortally certain” there is no Sasquatch, is irked by Meldrum’s trying to guilt-trip those who do not do Bigfoot work and his disparaging them as lazy or aloof.
See also my previous post on Jeffrey Meldrum.


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Tuesday, November 20, 2007

No Wonder I Hate This Guy

Adam's T&S post on stem cell research provided several links, one of which was described as "crowing."

As I read that particular essay, I found myself more and more unhappy with it. President Bush gets the credit for bringing this success through his leadership? Even though one of the two groups in the news today is in Japan? Even though scientists (like James Thompson, leader of the other group) typically pursue multiple strategies because you never know what will pan out?

Then, to top off my negative view of the essay, I saw this:

Wesley J. Smith is a senior fellow at the Discovery Institute
Well that explains some things!

(My rule of thumb: when someone from the Discovery Institute starts talking, be on the lookout for (at a minimum) distortion. If you doubt my rule, see today's example.)


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Playing Who's God?

You have probably heard by now that a method of obtaining stem cells that does not involve embryos looks promising. I think it's great, although it does not change what I think about the obstruction of embryonic stem cell research (I guess because I'm what's wrong with America). But stem cells are peripheral to this post.


The New York Times has an article on the influence of religion on people's worries about scientists "playing God." Here is the sum up:

Christians: God dispenses souls to humans, so don't mess with them. Do what you want to animals and plants, because (a) they don't have souls and/or (b) humans have been given dominion.

Western post-Christians: Not that worried about embryos, but don't screw up Mother Nature (eg. genetically modified crops).

Asian religions: There is no master plan for the universe, what matters is karma, and reincarnation happens. So, less objection to human, animal, and plant research.

These clashing perspectives produce friction.

It is not so easy, though, to defend supposedly self-evident truths about human nature that are not evident to a large portion of humanity.




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Sunday, November 18, 2007

McConkie Non-literalism

From the conservative wing of scriptural commentators: something I agree with (which is not to say that I usually do not agree.)

In Prophets and Prophecy, Joseph F. McConkie (BYU professor of religion--and yes, a son of Bruce R. McConkie) puts forth several myths about scripture.

Myth number three: Revelations are inerrant and infallible.

...within the scriptures we even find the verities of heaven taught with incorrect illustrations. Moses wrote of eagles bearing their young upon their wings (Deutoronomy 32:11), something that eagles simply cannot do, though until the nineteenth century it was thought that they did. ... A number of Old Testament writers make reference to leviathan (thought to be a many-headed, serpent-like sea monster) in contexts which do not suggest that the references are figurative (Job 41:1-10; Psalm 74:14; 104:25-27). Further, it was not uncommon for Old Testament prophets to draw on pagan symbolism in scriptural texts. For instance, Isaiah uses the form of a Canaanite ritual drama in a dual prophecy which describes the fall of the king of Babylon and the ultimate defeat of Lucifer (see Isaiah 14:1-23). Malachi quotes the Lord as saying that the "Sun of righteousness" will arise with healing in his wings (Malachi 4:2). The imagery "is derived from the symbolism of Egyptian religion--a symbolism also found elsewhere in the ancient Near East." ...many an inspired discourse has drawn upon illustrations that are not the equal of the eternal verities being taught. (p. 124-25)

We are all selective literalists.




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Thursday, November 15, 2007

Witch Hunt 2

Somehow it seemed wrong not to separate the contents of this post from the last one.

Here are my two favorite lampoons of witch hunt mentality. (Links may not last.)










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Witch Hunt

The New York Times has an article about children in Africa who have been accused of being a witch by their families. The results play out with some combination of physical abuse, ostracizing, or death. It is one of those articles that depresses me about humanity, but I think that there are lessons here that transcend this specific problem.

They gathered that afternoon in Domingos’s mud-clay house, he said, seized him and bound his legs with rope. They tossed the rope over the house’s rafters and hoisted him up until he was suspended headfirst over the hard dirt floor. Then they told him they would cut the rope if he did not confess to murdering his father.

“They were yelling, ‘Witch! Witch!’” Domingos recalled, tears rolling down his face. “There were so many people all shouting at me at the same time.”

Terrified, Domingos told them what they wanted to hear, but his relatives were not appeased. Ferraz Bulio, the neighborhood’s traditional leader, said seven or eight captors were dragging Domingos down a dirt path to the river, apparently to drown him, when he intervened.

“They were slapping him and punching him,” he said. “This is the way people react toward someone accused of witchcraft. There are lots of such cases.”

------------------
Still, [Domingos's mother] said, she suspects that he was bewitched into murder. “It must be true because he himself confessed,” she said, eyeing Domingos carefully across a table in her two-bedroom house.

At that, Domingos stood up and walked swiftly from the house. Ten minutes later, he reappeared in the doorway, his face red and splotchy. “Mother, from this day on, I am no longer your son,” he declared fiercely.

Ms. Pedro wordlessly watched him go. “I just don’t know why Domingos got so angry,” she said later.





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Monday, November 12, 2007

PBS NOVA: Judgement Day, ID on Trial


PBS NOVA will air a program on the Dover, PA court case from 2005 dealing with Intelligent Design in public schools. The program received a positive review in Nature. This case was a big loss for ID, and if you did not follow the case at the time, you should watch this program to see why. The program airs tomorrow--Tues, Nov 13--at 8 pm (check local listings to be sure), but will be available on the website for viewing as well.

Some ID proponents refused to participate. As the senior executive producer explains:

However, Michael Behe, Scott Minich, and other ID proponents affiliated with the Discovery Institute declined to be interviewed under the normal journalistic conditions that NOVA uses for all programs. In the midst of our discussions, we even offered to provide them with complete footage of the interviews, so that they could be reassured that nothing would be taken out of context. But they declined nonetheless.

In some sense, though, we do hear from both Behe and Minich in the program through our recreated trial scenes; the words that our actors speak are taken verbatim from the trial transcripts. And of course we hear directly in the program from lawyers for the defense—Richard Thompson, Patrick Gillen, and Robert Muise—as well as from Phillip Johnson, who is often credited as "the father of intelligent design." [italics added]



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Thursday, November 08, 2007

Lamanite Claims Scaled-back

As has been covered by other blogs already, an article in the Salt Lake Tribune revealed that the Church is updating the Introduction of the Book of Mormon in a way that scales back claims for Lamanite ancestry.

After thousands of years, all were destroyed except the Lamanites, and they are the principal among the ancestors of the American Indians.
In a comment at Times and Seasons, Kevin Barney points out that there are probably more changes coming based on Royal Skousen's work examining the original and printer's manuscripts.

The new Juvenile Instructor blog also notes another modest change in the Introduction.

I think it is great that the Church is making a change that is more in harmony with compelling scientific findings. I applaud the decision and hope it is a trend that will continue. "That which is demonstrated, we accept with joy."



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Wednesday, November 07, 2007

Opposition Bias or Lehi's Law

Confirmation bias is the tendency to seek confirmation of one's beliefs or ideas, and to ignore or not seek refuting evidence. For example, I have heard--although I don't know how common it is--that Emergency Room staff or police sometimes believe that a full moon = busy night (the lunar effect). Apparently most studies have failed to find an actual correlation, so why would someone think such a thing? The answer seems to be that once they are led to believe it is true, a person will tend to notice the chance correlation of a busy night with the full moon (or perhaps, nearly full), but fail to notice exceptions (ie. a slow night with a full-moon, or an equally or more busy night without a full moon). The same kind of principles can apply to racial stereotypes, or the ubiquitous invocation of "Murphy's Law" when an inconvenient problem arises.

I was reminded of this recently at church when someone said that good things in life are always opposed by problems/bad things. We have all heard such sentiments and supportive stories--such as cars breaking down on the way to the temple, etc--and 2 Nephi 2:11 is often cited for support.

First of all, I think that is a mistaken--if dominant--interpretation of scripture. But more to the point: Do we remember or account for all of the cars that made it to the temple without trouble, or the other times we made it to the temple without incident?

I do not dispute that good and evil struggle for domination, and that struggle may play out in ways I don't appreciate or understand. I do hypothesize that much of the invocation of what we might call "Lehi's Law" is actually confirmation bias.



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Monday, November 05, 2007

Sidney Sperry and Peanuts

I ran across the following quote from Sidney B. Sperry:

Too many persons in every generation, including our own, hope for things—fantastic things—in the name of faith and religion, but give little thought as to whether or not they are based on truth.
I had been kind of hanging on to this quote, but I thought it went well with the Peanuts strip of Nov 1.

Linus complains,
I believed in the "Great Pumpkin" with every fiber of my being!

Charlie Brown:
In all the world there is nothing more upsetting than the clobbering of a cherished belief.


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Friday, November 02, 2007

Transforming the Tree of Life


When you think of representations of speciation, you probably think of a tree--with species splitting off here and there. It's a metaphor that goes back to Darwin. Representing all life, this pattern is often referred to as the Tree of Life, with modern species represented at the tips of the branches, and the last universal common ancestor (LUCA) at the base of the trunk.

At first blush, "Pattern pluralism and the Tree of Life hypothesis" by W. Ford Doolittle and Eric Bapteste looks like one of those papers that is about to upset the apple cart.

...other evolutionists, ourselves included, question even this most fundamental belief, that there is a single true tree.
It turns out that this is not crazy-talk; rather it is a discussion about whether the data support our preconceptions about evolution--especially among prokaryotes. As I read him, Doolittle argues that down at the base of the "tree," there has been so much swapping around of genes (lateral gene transfer--LGT) that there is no one true tree--based on gene sequences--that represents the real relationship of microbial groups. In other words, as he has written elsewhere,
...lateral gene transfer simply means that there is no unique tree that can describe the history of genomes. The lineages of cells harboring those genomes can still be thought of as having a unique, treelike history, even though our ability to reconstruct it may be compromised by transfer.
So the way to the cellular Tree of Life remains guarded, while the genome Tree of Life may not even exist.

Now for some clarification.
To be sure, much of evolution has been tree-like and is captured in hierarchical classifications. Although plant speciation is often effected by reticulation (80) and radical primary and secondary symbioses lie at the base of the eukaryotes and several groups within them (81, 82), it would be perverse to claim that Darwin's TOL hypothesis has been falsified for animals (the taxon to which he primarily addressed himself) or that it is not an appropriate model for many taxa at many levels of analysis.
And,
Holding onto this ladder of pattern is an unnecessary hindrance in the understanding of process (which is prior to pattern) both ontologically and in our more down-to-earth conceptualization of how evolution has occurred. And it should not be an essential element in our struggle against those who doubt the validity of evolutionary theory, who can take comfort from this challenge to the TOL only by a willful misunderstanding of its import. [italics added]
It looks like this is an issue that is still being hammered out. But in the meantime, don't confuse the base of the tree with the branches.

Reference:

Doolittle WF, Bapteste E. Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2043-9.



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