Saturday, January 31, 2009

Parley's Mountains

In 1837 Parley P. Pratt published A Voice of Warning wherein he specified the condition of the Earth as originally created. Like Mary Poppins miraculously pulling a multitude of items out of her modest bag, Parley unpacked many details from a few words of scripture.

Second, We hear the Lord God pronounce the earth, as well as every thing else, very good. From this we learn that there were no deserts, barren places; no stagnant swamps, no rough broken rugged hills, no vast mountains covered with eternal snow; and no part of it was located in the frigid zone, so as to render its climate dreary and unproductive, subject to eternal frost or everlasting chains of ice.

Where no sweet flowers, the dreary landscape cheer;
Nor plenteous harvests crown the passing year:

But the whole earth was one vast plain, or interspersed with gently rising hills, and sloping vales, well calculated for cultivation; while its climate was delightfully varied, with the moderate changes of heat and cold, of wet and dry, which only tended to crown the varied year, with the greater variety of productions: all for the good of man, animal, fowl, or creeping thing; while from the flowery plain, or spicy grove, sweet odours were wafted on every breeze: all the vast creation of animated being, breathed naught; but health and peace, and joy.
On the subject of mountains, he continued:
But how far the flood may have contributed to produce the various changes, as to the division of the earth into broken fragments, islands, and continents, mountains and valleys, we have not been informed; the change must have been considerable.
John Taylor approvingly quoted this passage in Government of God. However, perhaps this passage's biggest fan was Joseph Fielding Smith, who quoted it in at least three books, and alluded to it in at least one other publication. Bruce R. McConkie re-iterated Pratt concerning mountains in Mormon Doctrine under "Restoration of All Things":
When the earth was first created all the land was in one place and there were no mountains and valleys of the kind that now exist.
Although he may not have realized it (though perhaps he did), by denying the existence of mountains before the Fall, Parley was entering into a discussion that had been carrying on in Western civilization for over two hundred years. It turns out that mountains have historically been viewed rather negatively. Up until the 17th and 18th centuries, mountains were generally (though not exclusively) viewed as warts or scars on the face of the earth because they were dangerous and forbidding, but also because they lacked classical properties of symmetry, regularity, and proportion. It was hard to believe that God would create such things, so they were often regarded as products of either God's curse following the Fall, or the Flood, and were generally ignored by artists.


In the 17th century, mechanistic theories of the earth's origin began to take root. A landmark publication was Thomas Burnet's Sacred Theory of the Earth, published in 1681. Burnet was a clergyman, but he realized that the Flood could not possibly have covered the mountains. Drawing on Descartes, he proposed that the Earth originated as a dead star, which had water at the core and a perfectly smooth surface above. As described by historian Peter Bowler [1],
"This surface was the paradise on which Adam and Eve and their children had lived. When they turned away from God, they were punished by the great flood--but the theory provided a natural explanation for this event in the form of a collapse of the crust into the waters beneath. Only irregular fragments of the original surface were left standing out of the water, forming the mountainous terrain of the present landmasses. Our punishment thus became permanent, because Noah's descendants were forced to live among the ugly and dangerous mountains (few as yet anticipated the romantic view that mountains are beautiful). In Burnet's view, we live on a ruined planet that matches our sinful state."
At the same time, Burnet found that mountains gave him a sense of awe and turned his thoughts to God. Over the next century mountains would come to be viewed as sublime, and even beautiful, and artists reflected this change of attitude in their works. With this change came a resistance to the idea that the earth was ruined, and nature became the evidence of God's power. By the time Parley wrote, the change was more-or-less complete; however, for whatever reason Parley viewed mountains as less than "very good."

To Mormons, mountains represent a place of refuge and safety, as well as a sacred place of God's presence, either because temples have been built among them, or because in scripture they have served the function of temples on occasion. I don't know how President Smith and Elder McConkie reconciled their view of the non-creation of mountains with that depicted in the endowment, where God specifically commands the formation of mountains as an element of beauty. Parley P. Pratt wrote before the endowment existed, and I speculate that the explicit mention of mountains was added after the saints made their home among them. Whatever the case, all of this serves to remind me that although we are a restoration movement, we are still tied to our culture, which includes the culture and traditions of mainline Christianity, and that can affect how we interpret scripture.

References and Notes:

1. Bowler, Peter. Evolution: The History of an Idea, p. 32.

For more on the changing perception of mountains, see Marjorie Hope Nicolson's Mountain Gloom and Mountain Glory, which I can only claim to have browsed on Google Books.

For one brief treatment of Thomas Burnet (of many on the internet), see here.




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Wednesday, January 28, 2009

FARMS Reviews "The Case for Divine Design"


The Case for Divine Design: Cells, Complexity, and Creation, by Frank B. Salisbury, is reviewed in the most recent FARMS Review (2008, Volume 20, Issue 1). The review article is "The Clockmaker Returns," by James L. Farmer. Dr. Salisbury is an emeritus professor of plant physiology, and Dr. Farmer is a BYU emeritus biology professor.

I have read The Case for Divine Design completely through once, mostly through a second time, and bits and pieces even more. I think the review is pretty straightforward and even-handed, and I generally agree with it. My one quibble is that toward the end Dr. Farmer seems to see Intelligent Design (ID) as only associated ("guilty by association") with Creationism. However, the fact is that ID grew out of creationism in response to court decisions that prevented the teaching of creationism in public schools.

Now for some of my own comments on The Case for Divine Design:

The main point of the book is to argue that science does not disprove God--not that there is scientific evidence for God (Salisbury rejects ID as legitimate science), but that the history of life is not known in sufficient detail to rule out divine intervention. It is in that sense that he seems to feel affinity toward ID.

He describes his worldview as follows (pg 22):

My belief also includes the idea that an Intelligent Creator, God, played a critical role in this process. I have no conclusion about what that role might have been. Did he engineer the first life on Earth and then let evolution take over, as deists and others believe? Or did he intervene in other ways intelligently creating every species? My attitude is that we simply lack enough information to speculate at this time.
It comes as no surprise that science cannot refute such a position.

Although I am less attracted to ID than Salisbury (and I am repelled by the ID movement), my own view is actually quite similar. Yet in spite of that core agreement, I have a few reservations about the book. First let me say that I appreciate the thought that Dr. Salisbury put into the book. There are a shortage of public LDS-scientist role models and his effort to communicate his years of thinking to another generation is to be commended, and his arguments are worth considering.

In a different FARMS Review article that was written by Dr. Salisbury, he suggested that the authors "are so busy defending evolutionary theory that it never seems to occur to them that there might still be problems with the theory." I think I would turn that around here: Dr. Salisbury is so busy trying to find problems with evolution that he misses some of its strengths. To be clear, he assures us that he is not a "bitter anti-evolutionist," and in an interesting end note, he writes that he "was personally deeply troubled" by Joseph Fielding Smith's book, Man, His Origin and Destiny. (He later met with then-Apostle Spencer W. Kimball, who told Salisbury "that he knew little about the science...and had no personal convictions on the matter," and that President Smith's book was "not to be considered Church doctrine" [quotations from the book, which paraphrased Elder Kimball].) Nevertheless, in my opinion his treatment of evolutionary theory is incomplete, as the following two examples illustrate.

1. Adaptationism and genetic drift. Salisbury repeatedly expresses concern that plausible "just-suppose stories"--especially in regard to the power of natural selection--are accepted too readily as final explanations. You could argue that holding a provisional position (and rejecting others) based on existing knowledge and pending additional information, is not a bad thing--and science is not about achieving metaphysical certainty anyway. But that aside, he seems unaware that scientists such as Stephen J. Gould have made similar criticisms. Probably the most famous example is a paper Gould and Richard Lewontin wrote in 1979 called, "The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme," in which Gould and Lewontin argued for a pluralistic approach to evolution that does not entail explaining every detail in terms of natural selection.

This is relevant because Salisbury seems unaware of a significant alternative to natural selection: genetic drift, which is where the frequency of a particular gene can become the norm (or driven to extinction) due to chance events. Imagine an animal hunted to near-extinction; that species will have restricted genetic diversity going forward. In many cases, the reason certain genes will be most frequent in the recovering population will have nothing to do with natural selection. They will be predominant simply because animals with alternate versions happened to get killed by hunters.

This failure to consider genetic drift, in turn, leads him to puzzle over what in my opinion are probably non-existent problems. For example, Salisbury seems to wonder how natural selection can account for the gene that causes Huntington's disease, which kills people in mid-life (i.e. post-reproduction). Although I can imagine a genetic scenario that could lead to the Huntington's gene being spread by natural selection, it is also quite possible that natural selection has nothing to do with it. The gene might simply have spread by chance (i.e. genetic drift). Likewise, Salisbury worries about how a selectively neutral mutation in cytochrome c can spread until it becomes fixed (i.e. present in all individuals of a population). Again, this is the domain of genetic drift, which becomes a dominant factor in small populations.

Salisbury might accuse me of spinning just-suppose stories--which I guess I am, since I haven't looked into the scientific literature concerning the evolution of these genes. However, the point is that once we release ourselves from explaining everything in terms of natural selection and turn to other established evolutionary principles, some otherwise perplexing problems evaporate. Moreover, scientists have devised various statistical tests for differentiating between natural selection and genetic drift.

2. Genetic relatedness. Before genes were understood to be coded by DNA, copies of which are inherited by offspring, evolutionary relationships were determined primarily by comparative anatomy. In the second chapter Salisbury uses a literary device to express his internal deliberations and pondering by putting arguments in the mouths of "the Biologist" and "the Skeptic." The Biologist discusses the relationships inferred by anatomy and the fossil record, but the Skeptic argues (at least twice) that anatomical similarities do not prove genetic relatedness. Inexplicably, the Biologist never points out the evidences of genetic relatedness! The closest we get is a brief treatment of an evolutionary tree generated from cytochrome c sequences in the fourth chapter. He writes:
The conclusion is that, because humans and chimpanzees have identical sequences, they must be closely related, while humans and higher plants must be distantly related, since they have the fewest sequences in common. Stories such as this are compelling and are among the most impressive and plausible evidences that an evolutionist can produce, which is not to say that an Intelligent Creator could not have designed things that way.
This is quite unsatisfactory. Genetic sequences contain treasure troves of evidence suggesting common descent and genetic relatedness, and by and large the inferred relationships match those that were previously determined by comparative anatomy. He may be correct (for now) that we cannot demonstrate a genetic relationship between us and other hominans (for lack of surviving genetic material to study), but if the genetic trail goes cold at Homo erectus, it gets rather hot again with chimpanzees and gorillas. A genetic relationship with a cousin implies a genetic relationship with a common grandparent, even if the exact identity of the parents or grandparents remain uncertain.

In summary, I think that The Case for Divine Design makes some interesting points that are worth considering. However, in the examples I have discussed, as well as some I have not, I think the book raises needless doubt as to why evolution is the central organizing principle of biology. Given the wide range of material that the book covers in so short a space, readers should use the book as a springboard rather than an ending point.



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Friday, January 16, 2009

In Praise of FAIR

I've been meaning to do this for a while, but I just want to praise FAIR for their handling of DNA evidence in the dust-up over Rodney Meldrum's alternate geography of the Book of Mormon. Specifically, it warmed my heart to see a forthright defense of molecular clock. (I also appreciated their treatment of haplogroup X).

The idea of a molecular clock is simple enough: If you can determine how often mutations occur on average, then given differing sequences you should be able to estimate how long ago those sequences diverged from one another. Unfortunately it is more tricky than that in practice. About 10 years ago one study using mitochondrial DNA (mtDNA) turned up a problem with dating the most recent common ancestor (MRCA), sometimes called 'mitochondrial Eve,' when it came up with a date of 6,500 years ago.

However, there were a number of problems with this estimate and the method behind it, and using better methods mitochondrial Eve is currently estimated at about 150,000 to 200,000 years ago. But as you might expect, creationists seized upon the finding as evidence supporting the Ussher chronology of the Bible. Never mind the fact that it didn't hold with all groups of people and disagrees with radiometric and other forms of dating, as well as molecular clock dating of the X and Y chromosomes, creationists have accused scientists of rejecting the six thousand-year figure simply out of bias against the Bible--an accusation that Rodney Meldrum apparently agrees with.

So thank you, FAIR, for explaining and defending the science.



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Tuesday, January 13, 2009

Autism's False Prophets

"Book Is Rallying Resistance to the Antivaccine Crusade" is a New York Times article about Paul Offit's book, "Autism's False Prophets." Dr. Offit is a pediatrician and chief of infectious diseases at the Children’s Hospital of Philadelphia.

Dr. Offit’s book traces the history of autism theories, starting with the child psychologist Bruno Bettelheim’s blaming “refrigerator mothers.” It describes early false cures, including “facilitated communication,” in which assistants helped mute children type their thoughts; head-squeezing by osteopaths; cod liver oil; diets; and a 1998 fad for secretin, a pig hormone. It sums up 16 epidemiological studies showing no link between autism and either measles or thimerosal, a vaccine preservative [which was removed from most vaccines as a precaution in 2001 -- LDSSR].

To the newer argument that vaccines overwhelm babies’ immune systems, Dr. Offit notes that current shots against 14 diseases contain 153 proteins, while babies cope with thousands of new foreign proteins daily in food, dirt and animal hair, and that the smallpox vaccine that nearly every American over age 30 got as a child contained 200 proteins.
I'll be putting this on my to-read list. I've followed the controversy at a more popular level, and my own training is in microbiology and immunology, so I am pretty familiar with the concept of vaccines and how they work. However, I am not a physician so I don't know the clinical side well, and I could use some more information on the history of the movement as well as the epidemiological studies.

You can read an excerpt from the book here. Also, Dr. Offit was interviewed on the podcast, "The Skeptic's Guide to the Universe," which is available here.


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Saturday, January 10, 2009

What Separates Humans from New World Monkeys?

[This post is part of a series, What Separates Humans from the Animals?. This addition of the series comes from the archives and was originally posted as 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.

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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Wednesday, January 07, 2009

Miller, Matzke, et al. Dissect ID Revisionist History

Kitzmiller v. Dover Area School District (2005) was a serious blow to the Intelligent Design movement, and Brown University biologist (and active Catholic) Ken Miller played an important role as an expert witness for the plaintiffs against the ID claims. (If you are unfamiliar with the Kitzmiller case, or need refreshing, may I recommend this review article?) The Discovery Institute has found things to complain about the trial ever since (see the above referenced article), and lately they've attacked Ken Miller's testimony, particularly about 'irreducible complexity,' as "smoke-and-mirrors." This is not just a nerd-fight over history; the Discovery Institute and other ID/creationists are still at work--not doing science, mind you--and they would love for the public and education officials to think that the case was wrongly decided.

Ken Miller has now responded in a three-part guest post on Carl Zimmer's blog, The Loom, and he is great--as usual. Part 1, Part 2 (I found this post particularly juicy), and Part 3.

Nick Matzke, who helped on the plaintiff's side, also responded with a lengthy but informative and entertaining must-read rebuttal (God of the Gaps...in your own knowledge. Luskin, Behe, & blood-clotting). Here is a money quote:

This is exactly the problem with ID/creationism – invoking God into gaps in knowledge is pretty troublesome, but creationists do something even worse. They insert God into gaps in their own knowledge, assuming, usually without even a vaguely serious attempt at a literature search (!!!), that whatever tidbits of biology they happen to have picked up represent the sum total of scientific knowledge on a topic.

And then for some icing on the cake, see While we are piling on Casey Luskin....


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