Bible Code; Genome Code

Craig Venter has been working to create an entirely artificial organism. A step toward that goal was achieved when it was announced that a completely synthetic genome has been created. According to the New York Times:

He revealed that the genome had five “watermarks,” sequences of genetic code that would spell words using the letters for the amino acids that would be produced by the DNA.

Wired Science reported Monday that it had ferreted out the messages, with help from government scientists. One watermark said “VenterInstitvte,” using the unusual spelling because there is no amino acid represented by the letter “u.”

The other messages were CraigVenter, HamSmith, GlassandClyde and CindiandClyde for his co-authors Hamilton O. Smith, Clyde A. Hutchison III, John I. Glass and Cynthia Andrews-Pfannkoch. A Venter spokeswoman confirmed them.

Clever, but not all that novel of an idea.

So I'm wondering why Bible Code believers haven't been scouring the human genome for hidden messages from God. Or have they and I just don't know about it? With 3 billion base pairs, there've got to be a few YAHWEH's--in an interesting context, in some language--somewhere.

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Religion, Cladograms, and Mormons Part 2

Thinking about the lineage of religions provides an opportunity to think about another concept in biological relationships: monophyletic vs paraphyletic groups. A monophyletic group consists of a common ancestor and all of its descendants. If some of the descendants are excluded, the group is paraphyletic.

Let's illustrate with reptiles. When you think of reptiles you probably think of turtles, snakes, lizards, and so forth. A 5-year-old would not confuse reptiles with birds. However, birds are descended from a group of dinosaurs, which were reptiles. The term reptile is useful because it carries with it a certain group of characteristics. However, when it comes to taxonomy and relationships, it is paraphyletic because it excludes birds (aves). Including birds would make it monophyletic. Neither method of classification is inherently good or bad; the value depends on what you want to emphasize. The dominant feeling among biologists is that classification should be organized around evolutionary relationships, so groupings should be monophyletic.

It occurs to me that those who exclude Mormons, Jehovah's Witness, Unitarians, etc, from Christianity make Christianity a paraphyletic group because they exclude some religious descendants of original Christianity. Mormons would prefer that Christianity be monophyletic--or at least more inclusively paraphyletic. (Of course religions are not biological organisms, and the whole exercise is an analogy.)

So the next time someone says that Mormons aren't Christians, ask them their justification for making Christianity paraphyletic. If they don't know what you mean, explain using birds and dinosaurs. I think that--chances are--your conversation will become doubly interesting.

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The Passing of President Hinckley

I feel like the blog should officially note the passing of President Gordon B. Hinckley. Perhaps I will eulogize him later. For now I will simply say that I thought he was an inspired man and leader, and I will miss his optimistic voice, his pragmatic attitude, and his self-deprecating wit.

General Conference will never be quite the same. (Who will be the next person to challenge an Apostle to a duel?)

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Religion, Cladograms, and Mormons Part 1

Scott F. Gilbert is a developmental biologist and textbook author. In 2003 he wrote an article in Nature Reviews Genetics on using developmental biology to teach evolution. In order to illustrate how anatomy and developmental biology combined with genetics help us to identify relationships, he uses religion as an analogy.

First, let's define a couple of terms. Homology refers to a trait shared based on common descent (e.g. wings of a robin and ostrich). Homoplasy is a similar trait based on convergence, not common descent (e.g. wings of birds and bats).


A person unfamiliar with the history of Christianity and Judaism might compare the various religions and come up with different relationships, illustrated by the cladograms in the figure. In b the primary division of Christianity is between east and west and emphasizes common liturgy and Bible translation. The loss of papal allegiance evolved more than once. C emphasizes relationships based on allegiance to papal authority, with non-allegiance developing once and giving rise to the Orthodox religions as well as Lutheran and Anglican. Which relationship is based on true homologies and which is based on homoplasy? The use of historical documents would make clear that b is the correct relationship. In a similar way, genetics can help us judge between relationships based on anatomy and development.

Unfortunately the article is not freely available; however, a similar scenario is described here, and a supplemental file is available here. Note #2 of the supplement contains this statement:

Moreover, the argument over whether religious similarities are due to shared ancestry or separate acts of creation is not a straw man argument. There are real controversies about this. Indeed, this argument frames the controversy between orthodox Mormon scholars (who claim that Jesus appeared separately in the United States and that an angel of God gave to mankind a new gospel, the Book of Mormon) and secular scholars (who claim that the similarities between Mormonism and other western religions is because Mormonism is an offshoot of American Protestantism with which it has common ancestry).

Maybe it's necessary to invoke a concept like lateral gene transfer, because I don't think Mormonism fits neatly in the boxes of derived or new creation.

Reference:
Scott F. Gilbert, Opening Darwin's black box: teaching evolution through developmental genetics. Nature Reviews Genetics 4, 735-741 (September 2003)

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What is Homeopathy?

I am currently recovering from a cold. I felt it coming on last Friday, and I didn't feel so great on Saturday and Sunday. It was nothing dramatic, but I did need a nap each day and I occasionally bordered on chills. A member of my ward recommended an over-the-counter (OTC) medicine that is alleged to help colds. I was skeptical, so I did a little internet searching and found that the product is homeopathic. What does that mean?

Homeopathy was developed around the time of the Revolutionary War by a German physician named Samuel Hahnemann in response to some of the unsavory treatments that were part of mainstream medicine at the time (e.g. bloodletting). Hahnemann developed an idea called the law of similars, which holds that symptoms of an illness represent the body's healing mechanism, so treating with something that would cause those symptoms in a healthy person is the way to cure the illness. Hahnemann also developed the law of infinitesimals, which held that the effectiveness of the treatment substance was stronger the more it was diluted. The substance was repeatedly diluted by powers of 10, with vigorous shaking at each step. In some cases, this repeated dilution results in a preparation that does not contain a single molecule of the original substance. Homeopathy proponents claim that the diluting solution (which often contains high levels of alcohol) retains some kind of imprint of the original substance, that aids healing.

To say that this departs from our current understanding of chemistry and pharmacology would be a great understatement.

Given this background, it may surprise you that the FDA regulates homeopathic drugs. FDA was given this responsibility in 1938 in a bill that was sponsored by NY Senator Royal Copeland, a homeopathic physician. FDA does not treat homeopathic drugs the same as other drugs. In contrast to other OTC drugs, homeopathic drugs do not undergo thorough testing for saftey and efficacy. Although there are some labeling requirements, they are not as strict as other drugs because, well, homeopathic drugs don't really have anything in them. So FDA doesn't really worry about reports of adverse reactions either because--again--there's hardly anything in them. (Here's a policy question for you: should insurance companies or medicare/medicaid cover homeopathic drugs?)

By Monday I was feeling better, although I still have some residual congestion. If I had purchased the recommended product, I might be convinced that it helped.

Note: Everything I have written about homeopathy comes from the FDA or the National Center for Complementary and Alternative Medicine (the NIH institute created at the behest of some congressional fans of alternative medicine). For a more critical analysis, see Quackwatch.

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Florida and Texas Race to the Bottom

A couple of weeks ago it looked like Texas was aching to be the next battleground over evolution. But it appears that Florida is not content to live in Texas's shadow. There were rumblings in December. Florida's science education standards are up for review and the draft treats evolution in a straightforward manner. Now various school boards are adopting resolutions that call on the state Board of Education to treat evolution as one of several "theories." Clay and St. John's counties are the latest.

Tommy Allen, District 2 board member, talked for about 6 minutes before members of the public were invited to speak. He explained that he was taught both evolution and other theories in school, and he found that another theory, that of a grand clock-winder, stood out to him. He explained that it was impossible that “things could just happen” and that when he gardens, he never plants a seed for it to grow into a different type of plant than it should. He wants the standards to include other theories which are “just as logically likely”.

The resolution passed unanimously. As a pragmatic matter, given the court history, do you think the Board of Education should listen to them?

I don't get these people, and yet I do. Florida is my native state and I can testify that there are strong Bible belt (esp. Baptist) currents there. (At my high school graduation, the commencement speaker, a local news anchor known for her religious devotion, made clear New Testament references and received a standing ovation.) On occasion I, too, was caught up in the war-on-Christians mentality.

But don't worry, Texas isn't going down without a fight. They are considering whether to give certification to the Institute for Creation Research's graduate degree in science education. You read that right.

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A Case of First Presidency Amnesia

One of my Christmas gifts was the book Can Science Be Faith-Promoting? by Sterling Talmage. Sterling was the son of Apostle James E. Talmage and a professional geologist. Most of the book consists of a series of previously unpublished essays that Sterling wrote, some of which were submitted to the Church for use as a MIA class manual but were rejected. I'm still working my way through the essays, but the real goodies are a number of letters between he and his father, Joseph Fielding Smith, Heber J. Grant, and John A. Widtsoe. I may have more to say about the book later, but I want to highlight one story here.

In the wake of the controversy over B.H. Roberts's book, The Truth, The Way, The Life, James Talmage gave a talk, "The Earth and Man", that expressed views in opposition to published remarks of Joseph Fielding Smith. The speech was given at the suggestion of the First Presidency. However the Quorum of the Twelve were divided over whether the Church should publish it, although both Elders Talmage and Smoot recorded in their journals that a majority favored publication.

After revisions of the speech failed to produce unanimity, Anthony Ivins of the First Presidency finally withdrew the matter from consideration of the Twelve, and the First Presidency approved publication. The approval was noted in Talmage's journal, as well as the diary of Heber J. Grant:

[17 November 1931] At 11:30 Brother James E. Talmage called, and we went over his address delivered in the Tabernacle a number of weeks ago, and authorized its publication and also gave authorization for it to be printed in the same form as the radio addresses, for distribution.

Several years later, and following the death of James E. Talmage, Sterling Talmage was engaged in public and private debate, and naturally referred to "The Earth and Man" in support of his position. In a letter to Sterling, Joseph Fielding Smith denied that the speech carried the weight that Sterling attached to it.

Since you have referred in similar terms to this discourse before, I am writing to say that I hapen to know it was not issued by authority of the Church, but arbitrarily, in the absence of the President of the Church, and over the protest of the majority of the Council of the Apostles.

Sterling protested the implication that his father had somehow been disobedient, and further claimed that he was given to understand, by Anthony Ivins, that publication of the speech had been approved by the First Presidency. He also wrote the First Presidency to seek clarification.

In reply, a letter dated December 19, 1935 from the First Presidency (Heber J. Grant, J. Reuben Clark, and David O. McKay) stated:

...the sermon was brought to the attention of the Council of the Twelve, where it was the unanimous view, minus one, that the sermon should not be published. ...

At this point President Ivins withdrew the sermon from the consideration of the Council and himself decided that it should be published. It was printed within two or three days thereafter. At the time this final decision was made, President Grant was not at home and was not consulted.

The reason for the First Presidency's amnesia remains a mystery. J. Reuben Clark apparently handled much of the First Presidency's correspondence and had not been a General Authority at the time of the speech. David O. McKay had been a member of the Quorum of the Twelve. In the introduction to the book, Stan Larson writes:

Ronald W. Walker and Duane E. Jeffery, both professors at BYU, suggest that "what might have happened was that J. Reuben Clark and Joseph Fielding Smith wrote the letter and piled it with routine letters for President Grant to sign, which he did unknowingly.

Elder Smith later cited the First Presidency letter in his reply to Henry Eying's negative review of Man, His Origin and Destiny.

That the First Presidency approved the speech is supported by the BYU Studies article, "The Story of The Truth, The Way, The Life" by James Allen, which does not mention the later denial of approval. Allen seems to have been pretty well informed; footnote 31 states:

Many of the sources for what follows are generally restricted. They include extracts from the minutes of the Council of the First Presidency and the Quorum of the Twelve; excerpts from the minutes of the Quorum of the Twelve; the journal of President Heber J. Grant; B. H. Roberts papers; committee reports of the Council of the Twelve; miscellaneous correspondence in the papers of the First Presidency; and the Rudger Clawson collection. With the permission and cooperation of the LDS church archives and its advisors in the Quorum of the Twelve who recognized the unusual need for accuracy in writing this history, BYU Studies had special access to these restricted documents.

And so the mystery lives on.



(For a fuller treatment of this story, see The B. H. Roberts/Joseph Fielding Smith/James E. Talmage Affair, by Richard Sherlock and Jeffrey E. Keller.)

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Let Us Speak of Giraffes

I've come across interesting information about giraffes from a couple of different sources recently, so I think a post is in order.

First is a new paper in BMC Biology. (I was going to wait until the final, formatted article was published, but the BMC journals seem to be taking for-ever formatting their articles.) Whereas giraffes are currently considered a single species with several subspecies, the authors reveal that:

"By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies may potentially represent different species. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations."

The populations have distinct genetics, but also distinct fur patterns (i.e. pelage). Looks like speciation in progress. (BMC Biology 2007, 5:57)

Meanwhile, I have been reading Evolution: What the Fossils Say and Why it Matters by Donald Prothero. The closest living relative to giraffes is the okapi (left). However, the fossil record attests to other extinct relatives, although most are more like the okapi than giraffes. However, a yet to be published fossil apparently does show a neck of intermediate length (p. 317-18).

And speaking of the neck, in discussing the oddities of anatomy that occur through evolution, Prothero brings up the recurrent laryngeal nerve (p. 37-38).

Even more peculiar is the course of the recurrent laryngeal nerve, which connects the brain to the larynx and allows us to speak. In mammals, this nerve avoids the direct route between brain and throat and instead descends into the chest, loops around the aorta near the heart, then returns to the larynx. That makes it seven times longer than it needs to be! For an animal like the giraffe, it traverses the entire neck twice, so it is fifteen feet long (fourteen feet of which are unnecessary!).

He goes on to explain that this odd route is a result of historical constraints in evolutionary development based on fish anatomy.

I am also reminded of the last time I saw a giraffe at the zoo. I watched it chew its food, swallow, then regurgitate and continue chewing. The cool part was following the wave of peristalsis up and down the neck.

So there are a few things to think about (aside from tigers) the next time you go to the zoo.

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Happy Birthday, LDSSR

Today marks three years since I began this blog. The bloggernacle was smaller then; Times and Seasons and BCC were already running, but Millenial Star would be created later that month. In those days links on the sidebar were the lifeblood of traffic. Thankfully Mormon Archipelago and LDSelect came along and gave the blog broader visibility. Thanks especially to the MA powers-that-be for giving the blog a prominent position.

I have no idea how much traffic this blog gets relative to other solo blogs in the bloggernacle--my sense is that the relatively narrow focus of the blog results in a correspondingly narrow audience--but it did get a mention in the Salt Lake Tribune once. Not too shabby, I think.

I started the blog because I thought scientific topics were not getting enough coverage in the bloggernacle, and I had some thoughts I wanted to get out. I started out with ambition and have settled into a more comfortable pace. A look at my archives reveals the number of posts each year:

2005 - 224
2006 - 147
2007 - 91

I expect that the future will look more like 2007, but I intend to keep going as long as I enjoy it. Here's hoping it will be worth reading.

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The Mayan Market

From the New York Times:

Scientists using improved methods of analyzing the chemistry of ancient soils have detected where a large marketplace stood 1,500 years ago in a Maya city on the Yucatán Peninsula of Mexico.

The findings, archaeologists say, are some of the first strong evidence that the ancient Maya civilization, at least in places and at certain times, had a market economy similar in some respects to societies today. The conventional view has been that food and other goods in Maya cities were distributed through taxation and tributes controlled by the ruling class.

Also:

Dr. Dahlin was the lead author of a report on the discovery in the current issue of the journal Latin American Antiquity. Richard E. Terry, who conducted the tests, is a soil biochemist at Brigham Young University and an expert in the analysis of soils at archaeological sites.

I'm always glad to see BYU represented well. As to the elephant in the room--does this have any bearing on the Book of Mormon?--I don't really know. I guess at face value it looks somewhat supportive, but I don't know enough context to comment knowledgeably.

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Sciencedebate 2008

There is a growing movement calling for a presidential debated focusing on science and technology. The organizers and supporters of Sciencedebate 2008 include a number of high-profile scientists or science supporters. I recognized probably a dozen of the names among a selection of signers.

This week's Science contains an editorial by Editor-in-Chief Donald Kennedy that argues that if presidential candidates are compelled to tell us about their private faith, then they ought to be compelled to tell us their views on science and technology. The magazine contains profiles of a number of the candidates. Unfortunately it requires a subscription to read, but on the other hand there wasn't much to work with. As Science reported:

"Although none of the campaigns afforded us direct access to the candidates themselves - a telling indicator of the importance of science in the campaign, perhaps - we've talked to some of their advisers, as well as to colleagues, friends and foes alike, who are familiar with their careers."

MSNBC.com has a summary of Science's findings, along with some helpful links. There are a couple of surprises.

It might be fun to watch such a debate, but I don't know if it would be useful. (New topic, same old political spin.) I would hope that some knowledgeable high-profile scientists would moderate it in order to prevent candidates that make ignorant or wrong statements (eg. Giuliani on cancer) from going unchallenged.

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