Understanding Trichotomy

Are you more closely related to a sibling or a first cousin? The answer is obvious, but the question is not as silly as it sounds. If you were trying to determine the relationship of three people (two siblings and a first cousin) based on their DNA sequence, you would get contradictory information. For most informative loci, you would make the correct conclusion. However some of the time you would erroneously group the cousin and one of the siblings together because they shared genes that were absent in the other sibling. So overall, you are more closely related (genetically) to your sibling, but there are parts of your genome where your cousin is your closest relative.

Applying this scenario to a larger scale helps us to understand the trichotomy problem in determining species relationships, such as the relationship between humans, chimpanzees, and gorillas. You've probably heard that our genome sequence is very similar (94-98.5%, depending on how you measure) to chimpanzees. The problem is that both genomes are also very similar to gorilla. Depending on where you look, you might group gorillas and humans together, or gorillas and chimpanzees together. The problem is illustrated in panel A of the the following figure [1]. (Click for larger image.)



The meaning of PI-characters and RGCs is not important here. All you need to know is that, along with genes, these are characteristics in genomes that can be compared. As the figure shows, in most cases the human-chimpanzee relationship is supported, however in a minority of cases other relationships are supported.

Why is there support for alternative relationships? The answer is analogous to the sibling/cousin relationship scenario above. 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.

The concept is illustrated in the following figure [2]:



Here, the broad lines represent what the true relationship of humans, chimpanzees, and gorillas is thought to be. The colored lines represent hypothetical gene polymorphisms. Notice that the true species relationship can differ from that inferred by looking only at the polymorphisms (esp. HG and CG, which give results as in panel A of the first figure).

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1. Rokas A, Carroll SB (2006) Bushes in the Tree of Life. PLoS Biol 4(11)

2. Hobolth A, Christensen OF, Mailund T, Schierup MH (2007) Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model. PLoS Genet 3(2): e7

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Weird People in Utah

Of course there are weird people everywhere. However--

The September 2006 issue of Survey Notes, a publication of the Utah Geological Survey, contains a list of odd questions that their geologists have been asked. I've put the best ones (in my opinion) below.

“As many as 13 black helicopters land, become bright, and then fly away…. They have stolen most of a 350-foot cliff called the Lace Curtain (a black basalt volcanic feature)…. What would be the best way of stopping them?”

“My horse found a gold nugget but now I can’t find the location. Is it possible the Green River has moved its course several miles in the last decade?”

“I am looking for some very, very remote land…. I want it so remote that I will have to walk for three days to get to it. Will you please send me the information I need? The gentleman in Washington told me that the states would have this information….”

“Do you have a map to the Lost Rhodes gold mine?” ( The Lost Rhodes gold mine is a mythical Spanish gold mine allegedly located somewhere in the Uinta Mountains.)

“I found a carving from Spanish explorers (who were in Utah over 200 years ago) on an aspen tree (individual trunks have an average lifespan of less than 100 years)…. Can you help me find the Lost Rhodes gold mine?”

“I was talking to this guy the other day…. He said that everyone knows that the whole Salt Lake Valley sits above a large cavern and that downtown is going to fall about a quarter mile during an earthquake. When I heard this I just laughed. Then, the next day I was reading some stuff on the Internet about very large caverns, occupied by colonies of lizard people, that extend deep beneath the Western Rockies as well as beneath the Bonneville basin…. Can you give me more information?”

“Are you aware of a submarine village under the Great Salt Lake? It belongs to a fine American family that shares it with hundreds of other Utahns….”

“I am very happy to declare that there is an exact relationship between launching of satellites and natural disasters like volcanic eruptions, earthquakes, El Niños, and hurricanes…. Would you like to know more? I am very excited and happy to discuss this data with you because our southern region is in danger of earthquakes after launching from Cape Canaveral….”

“I have been quarrying Cambrian-age quartzite dinosaurs….Can you verify the authenticity of my many astounding discoveries?”

That last one may have more than one thing wrong with it, but I know one thing: there were no Cambrian-age dinosaurs.

Oh, and do a little Google searching using terms in the lizard-people paragraph, and you'll find some treats.

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Genesis and Generation

Having just finished Generation, I had another look at Genesis 1. I think that a pre-seventeenth century reader would have little to quarrel with. The water and earth bringing forth life-forms fits quite nicely with spontaneous generation, which makes me wonder if anybody referred to Genesis in defense of the concept. Another curiosity is that only plants are described as having "seed after [their] kind". Animals do too, so why is it only mentioned for plants? (Plants also have sex, you know. And what we call a seed is actually a plant embryo.)

Once again I am reminded of James E. Talmage's statement:

The opening chapters of Genesis, and scriptures related thereto, were never intended as a text-book of geology, archeology, earth-science or man-science.

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I've got an AIDS cure I want to sell you.

Would you like the Iranian-national pride version or the Gambian-pray-and-paste version?

"Whatever you do, there are bound to be skeptics, but I can tell you my method is foolproof....Mine is not an argument, mine is a proof. It’s a declaration. I can cure AIDS and I will." --Gambian President, Yahya Jammeh

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Book Review: Generation

I just finished reading Generation: The Seventeenth-Century Scientists Who Unraveled the Secrets of Sex, Life, and Growth, by Matthew Cobb. The title is descriptive of the book, though it is not totally confined to the seventeenth century. In the book, Cobb introduces the reader to a number of researchers and scientists including: Jan Swammerdam, Reinier de Graff, Niels Steno, Francesco Redi, Anton van Leeuwenhoek, and others. The book offers a facinating opportunity to put yourself in the place of these men.

For a topic as fundamental to life as reproduction is, it is remarkable how little humanity understood it until recently. Even the concept of fixity of species is a modern one.

Although people all over the world knew that in general 'like breeds like', nobody knew why, and everyone was prepared to accept that there might be exceptions....In this world where like did not necessarily breed like, and where mice could be generated from wheat, there was no space for the idea of 'reproduction'. The word...was not used in its current sense until the second half of the eighteenth century. (pg. 10)

Until the 1600's, understanding of generation was dominated by ancient Greek ideas, particularly those of Aristotle and Galen. But things began to change as people paid closer attention to anatomy and were willing to discard the wisdom of the ancients in favor of observation and experimental results.

However, the scientific method is not a guarantee to an immediate and full understanding, and Cobb details places where these early scientists (an anachronistic word) went wrong in spite of clear experimental results and good logic. By the end of the seventeenth century people were polarized into spermist and ovist camps. For ovists, the egg was the source of generation; something in semen merely activated the egg. (Some dismissed sperm as parasites.) Spermists, on the other hand, thought that the female just provided a nurturing environment for sperm. It would not be until the mid-1800's that this divide would begin to disappear.

There were a number of difficulties in bridging the divide. For one thing, better technology was needed. Before the microscope was invented it was impossible to even see sperm and difficult to see the egg. Cobb also argues that technology provides a conceptual framework with which to understand nature. The frontier of discovery requires new language and analogies to common life.

Because it was thought that organisms were like [divinely designed] clocks, a correct understanding of generation would require people to imagine two clocks splitting in half, and then each pair of half-clocks somehow coming together to make a new clock. This would have required not only an unimaginably complex process, it would also have raised the question of how the two half-clocks 'knew' which bit went where. In the seventeenth century this would inevitably have meant a return to Aristotle's 'final cause' explanation. The search for a mechanical analogy would have led right back to a supernatural mind-set--exactly what the scientific revolution was trying to replace. (pg. 226-227)

There are those who are agitated over the materialist assumptions inherent in science, however the history covered in this book serves as a reminder of the remarkable success materialist explanations have had. Materialism may or may not ultimately explain all of life and nature, but its success in displacing mystical or supernatural explanations--a displacement we often take for granted--should serve as a reminder of its importance to science.

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Valentine's Day Science: Replacing Romance with Discovery

I am reading Generation: The Seventeenth-Century Scientists Who Unraveled the Secrets of Sex, Life, and Growth, and came across a humorous passage last night.

Anton van Leeuwenhoek (lay-wen-hook) was a seventeenth-century Dutchman, who is remembered as the 'father of microbiology' for his improvement of the microscope and resulting discovery of microorganisms. He eventually turned his interest toward bodily fluids, including semen. Using his own, he was the first to observe spermatozoa.

As he later reassured the Royal Society, this semen 'was not obtained by any sinful contrivance on my part', but was 'the excess which Nature provided me in my conjugal relations.' What this means is that a few seconds before making one of the most surprising discoveries in the history of science, Leeuwenhoek had been making love to his wife, Cornelia....Corelia's opinion is not recorded. (pg. 202)

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Comments on Sherlock's FARMS Essay

Sherlock's essay begins with a thought experiment that underlies the rest of the essay.

Let us suppose that at some future date Voyager lands on a distant planet inhabited by beings with intelligence and knowledge much like our own.

When the Voyager craft lands on this faraway world, a team of scientists immediately begins to examine this unfamiliar object. Upon close inspection, what would be the most reasonable conclusion for our distant scientists to reach? Would it be that the random action of physical forces came together in a strange new way to create it, or would it be that it was designed and constructed by an intelligent agent or agents?

ID proponents are fond of these type of thought exercises; the problem is that they do not mirror the situation in biology. Our judgment on such an issue would depend upon our prior knowledge and experience, and here the object is "unfamiliar." Similarly, SETI researchers look for signals that are different from what they usually find (like pure tones amid all the noise) and forensic investigators and archaeologists use what is known about the natural world and human activities to inform their studies.

Contrast that with life on this planet, which has been in existence for more than 3,500,000,000 years with vast numbers of life-forms having come and gone. We come along at the tail end and decide that certain complexities of life were designed by outside intelligence--that what we find in nature could not have come from nature. Are we really in a position to make such a scientific judgment, particularly when in some cases we have some plausible answers? When he writes that "The claim of design is not made on the basis of ignorance but, like our distant scientists, on the basis of our knowledge of nature and of action of natural causes," it is hard for me not to see it as begging the question.

One of Sherlock's fundamental assumptions is that "God acts in nature and we can recognize it." Perhaps those who have 'eyes to see' will, but the scientific enterprise is about open knowledge and testing. If God's ways are open to such things then how exciting such research would be! Unfortunately it appears that they are not, hence statements from various commentators, including Church leaders, that gospel truths are to be known by the Holy Ghost rather than scientific evidence.

This leads me to Sherlock's claim that ID is not a science-stopper. Regarding the imaginary planet on which Voyager crashes, he writes:

If those scientists ignore design as a relevant hypothesis and just assume randomness—for example, "this is just another meteor"—they will ignore a vast and relevant line of investigation. How was it designed? Who designed it? What was it designed for?

Other than what is in the scriptures, these are exactly the kinds of questions that cannot be answered if the designer is God. Trying to understand why God would do something is a certain recipe for Sherlock's dreaded 'just-so' stories.

Sherlock thinks that scientists should use the model of "faithful history" in their studies. An important difference, of course, is that historians deal with subjects who make claims (sometimes specific) about their inspiration. He asks,

If one accepts God as part of the reality of the cosmos, why should one ignore that in studying order in nature?

I think one answer that many scientists would give is, "because it isn't helpful." Indeed, young-earth creationists take God's involvement in the cosmos very seriously.

Toward the end Sherlock gets into things that have more to do with legal issues. The connection between ID and creationism was quite relevant in the Dover trial. The first ID textbook was originally about 'creation' rather than 'intelligent design,' and some of the central ID arguments were first formulated by creationists. Furthermore it was shown that the Discovery Institute's pushing of ID around the country was part of a calculated cultural/religious revolution, while mainstream scientists disavowed ID. ID was being used as a disguise for religion--a Constitutional issue.

I have some other misgivings about the essay. For example I am suspicious of the invocation of Stephen J. Gould and punctuated equilibrium--a controversial and much misunderstood concept. Also, the reference to the list of scientists who support ID is a farce. And this passage is essentially meaningless as written (though he apparently is getting at this):

Let us consider a relatively uncomplicated protein made up of a chain of amino acids with what biologists call "left and right hands." The probability that this protein could have come into existence by the random combination of amino acids is 1 chance in 10^–125. This is a number so small that it is effectively zero.

I'm running out of steam, but let me recommend TalkOrigins (especially An Index to Creationist Claims) and the review of The Politically Incorrect Guide to Darwinism and Intelligent Design at The Pandas Thumb (See the chapter 10 review for irreducible complexity and the blood clotting cascade) as helpful resources. For those interested, transcripts and the decision from the Dover trial are available here. I should also point out that Thomas Schneider, an actual scientist that uses information theory in molecular biology, has no love for William Dembski (scroll toward bottom).

[Note added: For treatment of several points raised in the essay, see "The Evolution of Biological Complexity."]

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FARMS Review: Intelligent Design

The most recent FARMS Review is out and it contains an article by Richard Sherlock titled, "Mormonism and Intelligent Design." It is not a book review, rather it is an extended opinion piece wherein Sherlock defends ID.

In the editor's introduction, Daniel Peterson writes that he expects the piece will be controversial and that FARMS will take criticism for publishing it. He further writes:

Candidly, I've been astonished at the consistent inaccuracy with which ID theory, as it's sometimes called, has been depicted in the press, and at the knee-jerk and caricaturizing negativism with which some believing Latter-day Saint scientists have responded to it. It seems to me, whether ID is ever shown to be correct or not, or whether it can even be formulated as a truly scientific hypothesis or not, Latter-day Saints, of all people, should not automatically dismiss it as a possibility. We have no obligation, whatever the surrounding culture may say, to accept the notion that naturalism is the default setting for scientific and scholarly discussion. Why hand such an advantage to critics of the gospel and the restoration without even seriously considering the question? Sometimes, it seems to me, we Latter-day Saints are so terrified of being thought provincial and backward that we are much too quick to signal our submission to reigning cultural and intellectual dogma. But such submission will never convince any of our cultured despisers that we're not backward rubes . . . and a hasty and uncritical zeal to ape our "betters" may only serve to confirm that we are, indeed, insecure provincials.

The motivation for publishing this article may be to begin to address "secular anti-Mormonism," something that Peterson recognizes as a problem with an inadequate response. As far as publication goes, my initial criticism is this: an articulate LDS scientist with a contrary opinion should have been invited to respond. This is something that can be remedied in the next issue, and I hope it will. But let me also say that I am pleased that FARMS is willing to publish material that breaks through the standard creationist paradigm.

For the sake of easier blog-post digestion, I will save many of my comments for at least one more post. For now, I want to get a few things out of the way. First of all, ID can be a difficult issue to discuss because assumptions and agendas concerning science, theology, scripture, and law/politics quickly come into play. The ID concept is intimately wrapped up with a particular group of advocates associated with a think-tank that has been persuing a cultural agenda that involves scientific and legal issues, and must be viewed in the context of the decades-long fight with creationists over evolution in the public schools. It does not necessarily follow that because one dislikes or fights against the ID movement that one is therefore dead-set against God intervening anywhere in the 4.5 billion-year history of the earth.

Let me state up front that I have no philosophical problem with God intervening in the world on occasion. I agree with Sherlock that our theology, scriptures, and history demand such things. However, I am skeptical of our ability to recognize his interventions scientifically (at least yet) and I think that ID advocates have charted a course which, if persued, could do real damage to the scientific enterprise. Furthermore the central claims of ID advocates are at best untested hypotheses that have not yet earned their place in the sciences. The fact that such hypotheses seem intuitive does not make them right.

More to come.

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Symbiosis: Russian Doll-Style

I came across the following abstract today:

A mutualistic association between a fungal endophyte and a tropical panic grass allows both organisms to grow at high soil temperatures. We characterized a virus from this fungus that is involved in the mutualistic interaction. Fungal isolates cured of the virus are unable to confer heat tolerance, but heat tolerance is restored after the virus is reintroduced. The virus-infected fungus confers heat tolerance not only to its native monocot host but also to a eudicot host, which suggests that the underlying mechanism involves pathways conserved between these two groups of plants.

In other words, a virus that infects a fungus that infects a plant allows the plant to live in (Yellowstone) soil at 65 degrees C (149 F). Cool!

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"A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance." Science. 2007 Jan 26;315(5811):513-5

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Francis Collins in National Geographic

Francis Collins, the man who headed the public side of the human genome project, has written a book about science and his faith in God titled, The Language of God. There is an interview with him in the current National Geographic. Below are a couple of passages that caught my eye.

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Horgan: The problem I have with miracles is not just that they violate what science tells us about how the world works. They also make God seem too capricious. For example, many people believe that if they pray hard enough God will intercede to heal them or a loved one. But does that mean that all those who don't get better aren't worthy?

Collins: In my own experience as a physician, I have not seen a miraculous healing, and I don't expect to see one. Also, prayer for me is not a way to manipulate God into doing what we want him to do. Prayer for me is much more a sense of trying to get into fellowship with God. I'm trying to figure out what I should be doing rather than telling Almighty God what he should be doing. Look at the Lord's Prayer. It says, "Thy will be done." It wasn't, "Our Father who art in Heaven, please get me a parking space."

I was a bit surprised by that answer. You would think (or at least I did) that an evangelical Christian physician and scientist would have at least one or two stories of the potentially miraculous.

Horgan: What do you think about the field of neurotheology, which attempts to identify the neural basis of religious experiences?

Collins: I think it's fascinating but not particularly surprising. We humans are flesh and blood. So it wouldn't trouble me—if I were to have some mystical experience myself—to discover that my temporal lobe was lit up. That doesn't mean that this doesn't have genuine spiritual significance. Those who come at this issue with the presumption that there is nothing outside the natural world will look at this data and say, "Ya see?" Whereas those who come with the presumption that we are spiritual creatures will go, "Cool! There is a natural correlate to this mystical experience! How about that!"

I don't think you can say that without taking the science to the next step. And that is, why does the temporal lobe light up? Speaking from the background of Mormon materialism, there must be a physical reason.

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