One Way of Getting a Link

S. Faux at Mormon Insights gives his perspective on being a Mormon evolutionist. It's a nice read, and my opinion is in no way biased by the fact that he says nice things about me and my blog.

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Great Primate Fossil; Great Hype

Everyone seems to agree that this 47-million-year-old primate fossil, named Darwinius masillae, is a remarkable find. The preservation is fine enough to reveal the stomach contents and the outline of the fur.

But it's also supposed to be a source of revenue--this may be the first fossil whose publication was accompanied by a press conference, a History Channel film, and a book--and is being hyped (i.e. marketed) as a revolutionary find that's going to change everything about our understanding of primate evolution.

For cooler heads, see here, here, and here.

Bottom line: Neat? Yes. Important? Yes. Revolutionary? Not so much.

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Dinosaurs in the Church News

Via S. Faux at Mormon Insights, I was pleasantly surprised to see that the Church News has an article about BYU's Museum of Paleontology and highlights the work of James Jensen.

Once patrons move past the thrill of peering into a "terrible lizard's" jaws they might be even more surprised to learn the Church-owned school operates one of the largest collections of upper-Jurassic period dinosaur fossils in North America.

I think I detect signs of discomfort, as the article seems to spend a little extra effort to assure readers that everything is on the up-and-up, and it neglects to inform when the Jurassic period was. Further, the article does not give any sense of the results of the research--as though making dinosaur displays represents the sum of the "intellectual curiosity" that drives the museum. Nevertheless, it's nice to see a nod to natural history in the Church News.

Note: I've previously written about the North American Museum of Ancient Life, at Thanksgiving Point, which is also based on the work of Dr. Jensen.

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Vital Force Discovered?

This week I was on an airplane, absent-mindedly browsing the SkyMall magazine, when I noticed an amazing device. It's called Aculife, and it is a variation--well, technically a complete re-definition--of acupuncture. It stimulates and helps to unblock qi by delivering mild electrical pulses. But it doesn't just stimulate qi, it can detect it and let you know where the blockages are! I repeat, it can measure qi! That proves that qi exists!

(Click image to enlarge.)

A number of things about the ad caught my attention.

1. It includes a handy (pun) diagram of qi points on the hand. This represents a mixing of pseudosciences. My understanding is that traditional qi points are located all over the body. For convenience, it looks like they've mixed reflexology (which maps the whole body onto the hand or foot) with acupuncture.

2. The map itself is interesting. The heart, liver, and kidneys are depicted in multiple places. And for some reason, the anus is out on the tip of the thumb (?!), along with fatigue, bronchitis, and insomnia--nowhere near the intestines, inflamed colon, diarrhea, or hemorrhoids. True, the spine is represented along the side of the thumb, but it's in the opposite orientation to the anus that you would expect.

3. "The best way to find out if Aculife is right for you and your health is to try it."

4. ...except if you are "pregnant, have a pacemaker, or suffer from malignant tumors, excessive bleeding or tuberculosis." I guess those things have nothing to do with blocked qi.

5. But wait, over at the base of the thumb is "breast tumor." So I guess as long as the tumor is not malignant, it's alright to use Aculife.

6. "FDA Approved" -- Well, okay, that probably just means that the electrical stimulation won't hurt you, not that this actually can be used to diagnose and treat disease.

7. "Diagnose and heal yourself and your family." Oh.

In summary, this is total garbage and if it doesn't technically break any laws governing advertising or medical claims, it should.

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What Separates Humans from Orangutans?

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

Glucocerebrosidase (GBA) is an enzyme that helps break down a fatty molecule that is present in the cell membrane. Mutations that disrupt its function result in Gaucher's disease, which can have a variety of symptoms with varying severity. An estimated 10-20% of disease-causing mutations are due to the fact that the GBA gene has a duplicate but broken copy next to it. In such cases, recombination between the normal GBA gene and its neighboring pseudogene results in the loss of a fully functional gene, leading to disease.

Wafaei and Choy looked at the GBA genes of several primate species, and it should come as no surprise that chimpanzees and gorillas also have one functional GBA gene and a neighboring pseudogene. I've drawn the following figure to represent their findings. (Note: pseudogenes are sometimes indicated by the Greek letter psi.)

(Click image to enlarge.)

Interestingly, orangutans appear to have two functional copies of GBA, while squirrel monkeys (a New World monkey) have a single GBA gene. The pseudogene is not found in non-primates, including mice, rats, and chickens, either. This suggests that a gene duplication event occured sometime after the lineages leading to squirrel monkeys and orangutans (and other apes) diverged.

The pseudogenes shared by humans, chimpanzees, and gorillas are not exactly the same. Each has some unique mutations that are not shared by the others. However, they all have at least one mutation in common: all three have a 55 base pair deletion in the same place, which appears to be the primary cause for the gene being broken. This is shown in a portion of Figure 4, which is an alignment of part of the various GBA genes and pseudogenes.

(Click image to enlarge.)

The human GBA sequence is at the top and is used as a reference. In the comparison sequences, differences are indicated by the changed letter. If the sequence is the same, it is indicated with a period. Missing sequences are represented with dashes. I've boxed the dashes, which are only in the pseudogene sequences.

This is like three copies of text missing the same run of 55 letters, and suggests that the deletion occurred in a common ancestor rather than three times independently. Unlike us, it appears that Orangutans are unlikely to get Gaucher's disease.

Reference:

Wafaei JR, Choy FY. Glucocerebrosidase recombinant allele: molecular evolution of the glucocerebrosidase gene and pseudogene in primates. Blood Cells Mol Dis. 2005 Sep-Oct;35(2):277-85. (Subscription Required)

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Something For Your Time Machine (and/or Handcart)

This is pretty clever (click for large):


It sparked some further thoughts:

1. Something like this should be included in your food storage or something, so that when civilization collapses we can still have air conditioning in Missouri. (We'll need it, from what I hear.)

2. Perhaps the best place to put it is in your scriptures. Because we all know that whatever the disaster, you grab your scriptures first.

3. Say, why isn't something like this already in the scriptures? Deuteronomy has its share of practical advice (e.g. "Thou shalt not plow with an ox and an ass together." Believe me, it's more trouble than it's worth.), but this would have been nice. (Maybe it was in Moses's first set of tablets?)

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FARMS: Of Science, Scripture, and Surprise

The FARMS Review (2008, Volume 20, Issue 2) contains a thoughtful and articulate essay by Duane Boyce titled, "Of Science, Scripture, and Surprise." It is ostensibly a review of Evolution and Mormonism: A Quest for Understanding, by Trent D. Stephens and D. Jeffrey Meldrum. However, discussion of the book is so superficial that I can't help but think that the book is mentioned simply to serve as justification for including the essay in a review publication. In fact, the essay gives much more attention to Stephen Jay Gould's The Structure of Evolutionary Theory.

Most of the essay can be boiled down to this: science is a messy process that is subject to all manner of human foibles.

To one degree or another, these [foibles] are all inevitable realities of intellectual inquiry. They are unavoidable. But recognizing and explicitly acknowledging such tensions and discontents is preferable to ignoring them. By ignoring them we are apt, in our naïveté, to ascribe more certainty than is warranted at any given moment to a particular discipline's range of intellectual conclusions (as happened with psychoanalytic theory, for example) and to risk developing an attitude of dogmatism and defensiveness as a result.

Recognizing such factors, on the other hand, we can be saved from such dogmatism and instead attain something approaching wisdom: a lingering tentativeness and humility about many of the beliefs we hold at any one time. In other words, we can be sure we are mistaken in one way or another even if we cannot be sure exactly where.

This is all well and good, though it can be taken too far. As Timothy Ferris has written,

The empirical spirit on which the Western democratic societies were founded is currently under attack, and not just by such traditional adversaries as religious fundamentalists and devotees of the occult. Serious scholars claim that there is no such thing as progress and assert that science is but a collection of opinions, as socially conditioned as the weathervane world of Paris couture. Far too many students accept the easy belief that they need not bother learning much science, since a revolution will soon disprove all that is currently accepted anyway. In such a climate it may be worth affirming that science really is progressive and cumulative, and that well-established theories, though they may turn out to be subsets of larger and farther-reaching ones--as happened when Newtonian mechanics was incorporated by Einstein into general relativity--are seldom proved wrong. As the physicist Steven Weinberg writes, "One can imagine a category of experiments that refute well-accepted theories, theories that have become part of the standard consensus of physics. Under this category I can find no examples whatever in the past one hundred years." Science is not perfect, but neither is it just one more sounding board for human folly.

I was pleased that toward the end of the essay Boyce balances his critique of scientific certitude with a critique (though brief) of scriptural certitude. His examples are two of my favorites: the degrees of glory described in D&C 76 and the re-definition of eternal punishment in D&C 19. Both revelations fundamentally altered the way previous scripture was understood. In summary,

...we are likely to understand new truths and experience new perspectives that will dramatically inform and revise matters that we think we understand now: subsequent revelations have a way of informing previous ones.

Next, Boyce takes issue with an interpretation advanced by Stephens and Meldrum of 2 Nephi 2:22, the preeminent 'no death before the fall' scripture. Although he tries to be fair, I don't think that Boyce quite does justice to the interpretation of Stephens and Meldrum. But the strengths and weaknesses of alternative interpretations does not concern me here. What I wish to point out is that this wrangling over interpretation concerns a single, short passage concerning a largely figurative story. To paraphrase B.H. Roberts, I think it is a thin thread to hang heavy weights on.

Moving on, toward the end of the essay Boyce expresses two concerns about evolution, and I will consider his questions in turn.

1. What are we to make of Moroni and Jacob, who both speak of the creation as miraculous?

To begin with, we might consider something Brigham Young said about miracles [1]:

The providences of God are all a miracle to the human family until they understand them. There are no miracles, only to those who are ignorant. A miracle is supposed to be a result without a cause, but there is no such thing. There is a cause for every result we see; and if we see a result without understanding the cause we call it a miracle.

It is not clear to me that Jacob and Moroni had special insight into the creation, as Boyce seems to assume. Both passages occur in a context of the prophet extolling the greatness and power of God. Given their scriptural heritage (especially the creation as depicted in Genesis) and the state of their scientific understanding [2], what choice would they have but to see the creation as miraculous? And if you are looking for examples of miracles, what better example could you find than the creation of the earth and life on it? Processes that we might call ordinary (though still wonderous) were apparently unknown to Jacob and Moroni. If our estimation of God is based on the impressiveness of his miracles (rather than his character and attributes), Brigham Young's statement suggests that we eventually may be disappointed.

2. Since the scriptures relate many miracles where God accomplished great feats quickly, why would he use such a long and wasteful method of creation?

In my mind, this is a more difficult question. It plays a role in some people's disbelief in God, and I don't know of an obvious answer to it. Nevertheless, the view that God as been at work for extremely long periods of time has early support in the Church. For example, we have the statement in a letter from W. W. Phelps [3] that,

...eternity, agreeably to the records found in the catacombs of Egypt, has been going on in this system, (not this world) almost two thousand five hundred and fifty five millions [2,555,000,000] of years: and to know at the same time, that deists, geologists and others are trying to prove that matter must have existed hundreds of thousands of years;—it almost tempts the flesh to fly to God, or muster faith like Enoch to be translated and see and know as we are seen and known!

It is unclear exactly what "system" Phelps was referring to, but this passage has been used by commentators such as Elder Bruce R. McConkie as support for God's vast experience, knowledge, and work. And of course there is also the statement in scripture that "all is as one day with God, and time only is measured unto men" (Alma 40:8). Why the quick miracles then? At least one reason might be that God desired results relevant to human timescales rather than his.

I don't know why God would use such a long process of creation. Presumably, God could have created the earth and life on it in six literal days, which would be quite a miracle. We could draw up a list of reasons why one way would glorify God more than the other. However, as I have argued previously, the issue is not what God could do. The issue is what the surviving evidence suggests. Happily, well-represented portions of Mormonism are quite at home with the vast timescale of creation suggested by the evidence.

Ultimately, I fundamentally agree with Boyce: we will continue to be surprised. I would simply ask that we not lose sight of the well-supported surprises that have already come.

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Notes:
1. This sentiment has been echoed by other Church leaders, and the link provided is to Teachings of Presidents of the Church: Brigham Young. This is not an attempt to settle the question by an appeal to authority; it is simply to show that Brigham Young's sentiment is still welcome within mainstream Mormonism.

2. As an example, both prophets appear to believe that God speaking was the direct cause of man's creation from dust, which is a straightforward interpretation of Genesis. Other modern scriptures suggest a more indirect relationship between God's words and the desired result. Further, Brigham Young called the idea that Adam was made from dust "baby stories." It may be that on the topic of the creation, Jacob and Moroni wrote 'pre-surprise.'

3. Times and Seasons, vol. 5 (January 1844-January 1, 1845) No. 24.

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What Separates Humans from Monkeys? (Resurrection Edition)

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

Many of our genes exist as families. Gene families are groups of genes that have been created through duplications within the genome, and individual members often subsequently take on different functions as a result of mutation or alteration in regulation. Gene families can expand and contract over time, resulting in greater or fewer family members. This story is about a family of genes involved in the immune system called Immunity Related GTPases (IRGs). Most mammals have multiple copies of these genes, but humans have only two: IRGC and IRGM. Our focus here is on IRGM; we have a functional gene but Old and New World Monkeys do not.

Bekpen et al looked at the IRGM gene of a number of primate species and compared it to those of mice and dogs. The first thing to note is that dogs, mice, and prosimians have multiple copies of IRGM (although not all are functional). Now, here's where things get interesting.

(Click to enlarge.)

Figure 5. A model for the evolution of primate IRGM genes is depicted. The mammalian IRGM tandem gene family contracts to a single-copy gene after the divergence of prosimians and anthropoids. The single-copy gene is pseudogenized in the anthropoid ancestor due to an AluSc repeat integration into the second exon, disrupting the ORF of the sole remaining IRGM gene. Multiple stop codons and frameshift mutations accrue in all Old World and New World monkey lineages. Three mutation events restore the IRGM gene in the common ancestor of apes and humans: integration of the ERV9 element to serve as a new promoter, a single-nucleotide mutation that introduces a new ATG codon (green arrow) after the Alu repeat and the loss of a stop codon that is shared with Old World monkey species. The latter event is polymorphic in orangutans rendering both functional and nonfunctional copies in this species. (*) of the five gibbon species analyzed, H. gabriellae shows a heterozygote stop codon. In the human and African great ape, the functional copy becomes fixed. Frameshift mutation (Fs) and stop codons are indicated. The genomic loci are not drawn to scale with the exception of the full-length sequence of IRGM ORF.

Step 1 - Death: Around 40 million years ago, the ancestor of anthropoids (i.e. monkeys and apes) lost IRGM when there was a contraction down to one copy, followed by the insertion of an Alu element that disrupted the single remaining gene and turned it into a non-functional pseudogene.

Step 2 - Decay: With the single copy of IRGM now broken, mutations in it could begin to accumulate without resulting in a selective disadvantage, and the relative order of the mutations can be determined by looking at which lineages share them. All Old World Monkeys share a mutation that created a premature stop codon in the gene. Remember, a stop codon indicates the end of a gene and the creation of one in the middle of a gene leads to a truncated protein that may be non-functional. However, in this case the stop codon had no real effect because the beginning of the gene was already broken by the Alu element.

Step 3 - Resurrection begins: At least 8% of our genome consists of endogenous retroviruses (ERVs). Retroviruses are a family of viruses that integrate into DNA as part of their life-cycle. If they find their way to a germ-line cell, they can remain in the genome permanently and be passed on as though they were just another gene. Lucky for IRGM, about 20 million years ago an ERV inserted upstream of the Alu element. The reason this was lucky is because the ERV contains a sequence that acts as a promoter, which is a stretch of DNA that promotes the transcription of a gene. In other words, the ERV helped turn IRGM back on. The ERV insertion was accompanied by an independent mutation just after the Alu element that created a new start codon--a new beginning of the gene.

Step 4 - Resurrection complete: Alright, the gene has been turned back on and has a new start codon, but what about that premature stop codon? A simple mutation turned it from a stop codon back to a codon for an amino acid. The gene was thus restored, though shorter than the original. Interestingly, the version of the gene with the stop codon (still broken) and the version without it (functional) can both be found in a species of gibbon and among orangutans. Gorillas, chimpanzees, and humans appear to have completely lost the broken version; they only have the resurrected IRGM. Analysis of the sequence of the resurrected gene suggests that it has been under positive selection (i.e. natural selection favors it).

So the next time you hear someone claim that mutations only destroy genetic information, remember the mutational resurrection of IRGM.


Reference:

Bekpen C, Marques-Bonet T, Alkan C, Antonacci F, Leogrande MB, et al. (2009) Death and Resurrection of the Human IRGM Gene. PLoS Genet 5(3).

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