The Basis for ABO Blood Typing Undermines Common Design

When Darwin first proposed the idea of common descent there seemed to be no evolutionary connection between humans and apes. Then the bones and fossils of extinct Neanderthals and other human/ape-like creatures began to come forth--some more like humans, some more like apes--providing confirmation that Darwin was on the right track. Meanwhile scientists began to discover that the proteins of humans and other apes were similar. When the structure and coding of DNA was worked out, scientists began determining the sequence of genes, culminating in the sequencing of whole genomes in the last 15 years or so, including that of Neanderthals. What scientists found in genetic sequence solidified the inferences already arrived at by other means: that among living species, humans are most closely related to chimpanzees and gorillas, with which they share a common ancestor. The evidence for common descent contained in our DNA is rich and multi-layered.

Creationists, however, counter that similarity of DNA is not evidence for common descent. Rather, it is evidence of common design. The basic idea is that since humans and chimpanzees (or any other grouping of species) have similar anatomy and physiology, it makes sense that the Designer would use similar genetic sequences. This assertion certainly has a commonsensical appeal since it casts biology as an extension of human experience in the modern era of mass production, computer programming, and bio-engineering.

The central paradox of this assertion is that in attributing commonalities to common design, one must also attribute to design many ordinary and mundane genetic characteristics that are otherwise explainable on principles of microevolution. Those who make the common design assertion rarely address the patterns of both similarities and differences.

The ABO blood system makes for an interesting case study. The system is a classic example of genetic co-dominance that is often taught in high school biology class, and is also a classic example of the need for matching in blood transfusions or organ transplants. The basis for the system is the pattern of certain molecules expressed on human blood cells and other organs and tissues. Everyone expresses the basic molecule called the H antigen, and if your blood type is O, that's the end of the story. People with A, B, or AB blood-type also have genes for glycosytransferases, which are enzymes that add an extra sugar molecule onto the H antigen--kind of like topping off a Christmas tree with a star, or adding a cherry to an ice cream sundae. The difference between A and B is the type of sugar molecule added to the H antigen. The A enzyme adds one kind, the B enzyme adds a different one. People with type O don't technically lack the transferase genes, they just have versions that are broken due to mutation, though there are no known diseases associated with this. The immune system of people with O or A type will react against type B antigen as a foreign invader, and the same applies to people with O or B in relation to A antigen. People with both genes (A and B) will make both antigens (A and B), and therefore their immune system will not react against A antigen, B antigen, or H (O) antigen.

The A and B glycosyltransferases are actually extremely similar. In fact, there are only four amino acids different between them, and only two of those determine which sugar the enzyme adds to H antigen. I have aligned the protein sequences [1] of the A and B transferases in the following figure. Letters are standard abbreviations for different amino acids (building blocks of proteins), and periods represent identical amino acids. I have highlighted the four differences, and the blue arrows point to the two key amino acids that determine which sugar is added:

If we were to look at the DNA sequence we would see seven differences, instead of just four. However, three of those differences do not change the amino acid sequence. The reason is that many amino acids have several three-letter DNA codes (codons), so changing one of those DNA letters may simply change the three-letter codon to an equivalent codon. Such mutations are called silent because they have no effect on protein function. In contrast, in the four highlighted examples the change in the underlying DNA resulted in a codon for a different amino acid.

These two sequences are so similar that it shouldn't surprise you to learn that scientists believe that one of them originated from the other. At some point one of the genes was duplicated (a common occurrence), and mutations gave one of the two copies a different specificity. And the changes didn't stop there. What I have shown are the two most common sequences for A and B, but some people have variants (alleles) that have other mutations. Most of those mutations are silent, but some of them do change amino acids in various parts of the protein.

The ABO blood groups have been looked at in other animals, and primates have the same basic system. The following (modified) figure shows the evolutionary relationship of various primate species and the blood types that have been found [2]. (Click for bigger image.)

The ABO types are found in varying combinations among hominoids, old world monkeys, and new world monkeys. Previously it was thought that the B alleles were re-created from the A allele in several different lineages. However, a more recent study [2] found that the A and B alleles of the various species are more closely related to one another (A to A, B to B) than any of the A alleles are to the B alleles (with the apparent exception of orangutans). This implies that both A and B were present in the ancestor of primates, and that in some lineages one or the other has been independently lost. In contrast, the O alleles are not all closely related to each other (since there are many ways to break a gene).

Remember, the part of the protein that determines whether the transferase acts as type A or B is dependent on those two amino acids. Interestingly, some primates have a silent mutation in their A gene at one of the important amino acids. I have illustrated this difference with the following figure (compare to the blue arrows in the first figure above):

For each transferase gene, A and B, the DNA sequence is given with the amino acid translation below. The A gene has two versions of the DNA sequence, with the silent mutation (T) in red. Although you might expect CTG and TTG to code for different amino acids, a quick consultation of a codon table shows that both code for leucine (L).

Now here's where things get interesting. Let's look again at the figure showing primate evolutionary relationships, but this time I'll show it without modification [2].

It turns out that the silent mutation in the A gene is only found in old world monkeys; hominoids and new world monkeys have the other version (CTG). Overall, hominoids are more closely related to old world monkeys than new world monkeys, as shown in the figure. But for this piece of the A gene, old world monkeys are different. The simple evolutionary interpretation is that the silent mutation, which is probably selectively neutral, occurred in the lineage of old world monkeys just after they split away from the hominoid lineage. An alternative explanation is that there were multiple independent mutations in the old world monkey lineage. Clearly, several different species independently having the exact same mutation arise and become dominant in the population is of much lesser probability.

So What?

With all of that as background, let's turn our attention to the assertion that similar DNA represents similar design rather than an evolutionary relationship. If the Designer was using similar genetic sequence to make similar organisms, why make a silent DNA change only in old world monkeys?

There are three basic creationist responses that I can think of. First, it could be that each old world monkey species with type A independently had that mutation arise and become fixed in the population. This is essentially the same alternative that was rejected above.

Second, a creationist might argue that the pattern of A alleles represents a sense of whimsy and artistry by the designer. After all, sometimes we do things just because we feel like it. That such alleged artistry happens to also fit an evolutionary scenario might give us pause. At any rate, if the defense of someone's hypothesis when contradicted by the data is simply to assert that the Designer just felt like it, they clearly are not engaged in a scientific discussion and are instead simply seeking to rationalize a conclusion they have already made.

A third creationist argument is more subtle. He/she might note that silent mutations can have an effect on the efficiency with which a protein is made. So perhaps that silent mutation in the A gene actually plays an important role in the context of old world monkey gene expression and physiology. This argument contains at least a grain of legitimate science. That this one silent mutation affects the efficiency of gene expression is highly doubtful, but is testable in principle. However, the notion that it is important for the long-term survival of old world monkeys becomes absurd when you consider that:

1. Like humans, not every member of a particular old world monkey species will have the A gene. Whatever effect the mutation has is irrelevant for those individuals.

2. At least two old world monkey species have apparently lost the A gene altogether! Clearly the mutation has no relevance for those species.

3. As mentioned above, there are other alleles of the A gene found in humans that contain other mutations, and the same holds for old world monkeys. Natural mutations clearly do occur in the A gene. How can naturally occurring mutations be differentiated from designed ones?

Conclusion

Here we summarize and circle back to the paradox of the common design argument. Considering the variability of the presence of A and B genes within individuals, populations, and species, and considering the fact that various polymorphisms exist within each species (some of which are silent, some of which are not), can the difference of a single silent nucleotide really be justified on principles of common design?


Notes:
1. Source of sequences: Human A - http://www.ncbi.nlm.nih.gov/nuccore/58331215; Human B - http://www.ncbi.nlm.nih.gov/nuccore/AB844269.1

2. Ségurel L, Thompson EE, Flutre T, Lovstad J, Venkat A, Margulis SW, Moyse J, Ross S, Gamble K, Sella G, Ober C, Przeworski M. The ABO blood group is a trans-species polymorphism in primates. Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18493-8. Figure 1 from the paper contained a mistake; the corrected version is here.

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The Evolutionary History of Whales Is Doing Fine, Thank You Very Much

Recently I became aware that the evolutionary history of whales is based on fraudulent information. At least that seems to be the common belief of creationists. We might expect them to be resistant to the fossil and genetic evidence for whale evolution, but what makes it fraudulent?

Some Background

First we need to step back a few decades to get some historical perspective. Prior to 1979 very little was known about the early evolution of whales. Mammals evolved on land long before whales appeared in the fossil record. Therefore, since whales are mammals, you would expect whales to have their evolutionary roots in land mammals. However, there wasn't much fossil evidence to go on. That started to change when, working in Pakistan, paleontologist Philip Gingerich discovered the skull of a land mammal that was similar in form to a wolf. Gingerich noticed a couple of grape-sized bones of the middle ear that were only known to exist in cetaceans (whales, dolphins, etc). This strongly suggested that the newly discovered animal, Pakicetus, was a relative of whales. Over the next few decades, Gingerich and his former student, Hans Thewissen, discovered a number of other related fossils showing various degrees of adaptation to water, and each with the distinctive cetacean middle ear bones.

Scientists initially believed that whales were most closely related to a group of extinct mammals called Mesonychids, which are related to Artiodactyls (cattle, pigs, hippos, etc). However, most experts now believe that whales are more closely related to Artiodactyls based on two principle lines of evidence [1]. First, in the late 1990s a Japanese group found that whales and hippos share some common genetic markers (LINEs and SINEs) that are not shared by other Artiodactyls, suggesting that they share a common ancient ancestor that is not shared by other Artiodactyls or Mesonychids. Second, some of those fossils discovered by Gingerich and Thewissen turned out to have an ankle bone (double-pulley astragalus) that is a defining feature of Artiodactyls.

Let's pause for a moment to make this clear. We have fossils that have one feature diagnostic for cetaceans, and another feature diagnostic for Artiodactyls. Also, modern whales share some unique genetic markers with hippos (which are Artiodactyls). It's almost as if...whales....evolved from....a group of ancient Artiodactyls [2].

The Fraud

So where does the fraud come in? A creationist named Dr. Carl Werner (apparently a physician by training) interviewed some of the paleontologists that study cetacean evolution, especially Gingerich (2001) and Thewissen (2013). Werner produced an anti-evolution video series and published an accompanying book titled, Evolution: the Grand Experiment, with one chapter devoted to whales. For the 2014 third addition of his book, Werner produced a press release that breathlessly lays out the main charges, even though much of it pertains to information over a decade old. During his filmed interviews, Gingerich and Thewissen spilled the beans on how shaky the whale evolutionary scenario is. These amazing revelations included the following:

1. Although the tail of the ancient cetacean Rodhocetus has not been found, Gingerich initially speculated that it had a fluke at the end of it. Also, initially the limbs were not recovered so he speculated that Rodhocetus had flippers. Limbs were later recovered, leading Gingerich to doubt that they were flippers, and ultimately doubt that it had a tail fluke. However, various museums were still displaying drawings of Rodhocetus with flippers and a fluke. Somehow all of this disqualifies Rodhocetus as a transitional fossil and serves as evidence that evolutionary scientists freely spread misinformation.

2. When Thewissen discovered the skeleton of Ambulocetus, part of the upper jaw was missing, along with the nasal opening. The remaining lower jaw allowed him to judge how long the upper jaw would have been. However, the location of the nasal opening is not known. Thewissen's model placed the nasal opening a few inches back from the end of the snout. Since the actual location of the nasal opening isn't known, Thewissen's model is biased and misleading.

3. In discussing the middle ear of Ambulocetus, Thewissen acknowledged that a part called the sigmoid process, which was previously thought to be diagnostic for cetaceans, was 'questionable'. This admission revealed that there was no basis to consider Ambulocetus a cetacean. When combined with #2 above, it was clear that Ambulocetus as a transitional whale fossil was a figment of wishful thinking.

More to the Story

When I first came across these claims I did some Internet searching to see if there was any response. These charges were clearly popular because all kinds of creationist websites dominated my search results. Eventually I found an anonymous message board where one of the participants claimed to have contacted Dr. Thewissen and received a reply, which he posted. Thewissen confirmed that Werner did interview him.

He had me answer the same question a number of times. Usually journalists do this when the answer that a scientist gives is too technical, so usually the scientist rephrases the answer in a more simple way. When Werner shot in my lab, he would ask the same question multiple times, and I simplified my answers more and more each time he repeated a question. He then put my answers together in a creative way that makes it all look pretty silly....

The written piece that you sent me, I had never seen before. It does not discuss the critical piece of information that shows that Pakicetus and Ambulocetus are whales: the thick inner part of the tympanic bone of the ear, called the involucrum. It is not clear to me why this is not presented, as scientists agree that this is the most critical feature. Instead, the video focusses on another part of the tympanic bone, the outer part, which indeed is different in shape in different whales, and occurs in some whale relatives too (artiodactyls are the closest relatives to whales, no wonder that their ears have similarities). So, that feature needs to be qualified when it is explained. In a simple sound bite such as the ones that Dr. Werner presents, those qualifiers are not present and that causes that particular feature to look pretty inconclusive in the way it is presented there.

Since this comes from some unidentified person on a message board, you might be skeptical that it actually came from Thewissen, as you should be. However, the response also drew attention to a video that Thewissen made to help clarify the issues around Ambulocetus, though without direct reference to the creationists. Indeed, the YouTube video does exist! And it's worth watching.



Let's return to the issue of the sigmoid process and the involucrum for a moment. Werner's website quotes a 1998 publication by another whale expert (Zhe-Xi Luo) as follows.

"Other diagnostic characters, such as the sigmoid process as discussed below, are now open to question in the wake of the new fossil evidence from Pakicetus...[The] sigmoid process [in Pakicetus] is a simple plate [and is] equivocal, [since it is also] present in the artiodactyl Diacodexis...compromising its utility as a "dead ringer" apomorphy [unique trait] for cetaceans."

However, this editing leaves out an important preceding sentence from the original publication (a book, by the way, that was edited by Thewissen) (bolding added).

Cetaceans including pakicetids have only one unambiguous bullar synapomorphy that is absent in all noncetacean mammals--the involucrum, or the pachyosteosclerosis of the medial margin of the bulla. Other diagnostic characters, such as the sigmoid process, as discussed below, are now open to question in the wake of the new fossil evidence from Pakicetus and Ichthyolestes.

Luo's argument is rather technical, but the gist seems to be that the sigmoid process should not be considered a definitive sign that an ancient fossil is a cetacean. However, as stated by Luo, that still leaves the involucrum! I wonder if Werner missed that sentence.

Summary and Conclusion

So let's summarize the answers to the supposedly devastating admissions by Gingerich and Thewissen, numbered as above.

1. So far as I know, Gingerich never responded to Werner. Paleontologists often do not recover all of the bones of a fossil skeleton, so their reconstructions sometimes contain some guesswork based on other information. Carl Zimmer's book, At the Water's Edge, which profiled Gingerich's work, stated that most of the tail of Rodhocetus was missing, "preventing [Gingerich] from knowing whether it had grown flukes at its tip." Zimmer's book was published two or three years before Werner interviewed Gingerich, so Gingerich was hardly making a new admission to Werner. Werner's complaint has some justification as far as accuracy of reconstructions go. However, that does not negate the features that make Rodhocetus a cetacean that could function both on land and in water. Rodhocetus retains its place in the evolutionary transition of cetaceans from land to water.

2. Although Thewissen did not know exactly where the nasal opening of Ambulocetus was, its close relation to another fossil suggested that the opening had migrated a bit from the tip of the snout. The exact location of the opening is not important. When you look at the broad picture of cetacean evolution, you see the nasal opening migrate back from from the tip of the snout toward the eyes, where we know it in modern cetaceans as the blowhole.

3. The sigmoid process is a strong indicator of being a cetacean, but is apparently now considered not entirely definitive. However, the involucrum is considered definitive, and all of the fossils in question have an enlarged involucrum.

There are other issues I have not addressed, on both sides. Werner and other creationists have a few other criticisms that I haven't run down, some of which are rooted in a cartoon version of how evolution or science works. Similarly, there are other evidences derived from both living and ancient cetaceans that yield further evidence of, and insight into, cetacean evolution.

In conclusion, the notion that evolution, both in general and as applied to whales, has fallen like a house of cards remains a creationist fantasy. Nor is there any evidence of actual fraud; only some perhaps ill-advised artistic license. In this case, Werner has employed classic creationist tactics of selective quotation and ignoring important context. The evolutionary history of whales remains in good shape.

Further Reading:

These three are easy reading:
Understanding Evolution: Whales - Source of the images above.
National Geographic: Valley of the Whales
Evolution of Cetaceans - Wikipedia

This one is a little more challenging, but more detailed.
From Land to Water: the Origin of Whales, Dolphins, and Porpoises

Notes:

1. There are actually a number of other characteristics that support the relationship, but they are more subtle.

2. Either that, or God created whales on the fifth day of creation, some with a distinctive ankle bone they hardly used, if at all. And then, for some reason, He created a bunch of land Artiodactyls on the sixth day of creation with that same ankle bone, and in a few cases threw in the whale-like middle ear for good measure.

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EVEs Are Bone of Our Bones and Flesh of Our Flesh

When we think of the human genome, we generally have in mind the collection of genes that make us human. What most people don't realize is that a significant portion of their genome (at least 8%) actually comes from viruses, and these parts are called endogenous viral elements (EVEs). EVEs, and other genetic elements like them [1] (which all together make up around half (!) of the human genome), can help establish genetic relationships because they are like molecular fossils. In fact, the term 'paleovirology' has been coined to describe their study. A paper from 2010, aside from being interesting in its own right, has a great illustration that helps to convey this concept [2].

The left side is not very important for our purposes, but basically it shows various types of viruses and the pathways that can land their genetic material into a host genome. The box in the middle-bottom represents double-stranded DNA where the viral sequence has integrated into a host genome.

The right side of the figure represents what happens after that. When the virus integrates into a host genome, it doesn't instantly become part of the genome of the whole population. At first, only one individual in the population has the virus in its genome in a particular spot. However, when that individual has offspring it can pass on the viral element as if it was just another gene. Simply by chance (or perhaps due to selection) the new genetic variant containing the EVE can become more common in the population. (That exact scenario is currently happening in koalas.) Not every individual has it, just like not every human has color blindness, type A blood, blue eyes, or blond hair. Eventually, though, the variant may go extinct, or it may become fixed, which means that every member of the population has it. From that point on, all descendants will have the viral element in the same spot of the genome (unless it is secondarily deleted, which generally leaves a genetic scar).

So looking again at the right side, we can see a rabbit-like species that eventually gave rise to three daughter species. The population giving rise to species C branched off before the EVE invaded the genome, so it is clean (in that specific genetic location). When the EVE first invaded the host genome, it was passed along to descendants until it became fixed--present in all members of the species. So when species A and B branched off, both were marked by the EVE. If you knew nothing about how species A, B, and C were related to each other beforehand, the presence of the EVE in identical spots in the genome would tip you off. After all, the genome is a large place and the likelihood that two EVEs would independently end up in the exact same location are pretty small. This also works for populations within a species as well.

With improvements in technology over the last 10-15 years, scientists have been sequencing the genomes of all kinds of animals to see what is in them. It turns out that EVEs are all over the place. Scientists looking for the presence of one type of human EVE in other primates got results like what is shown below. In case it isn't obvious, the entry of each virus group is mapped onto the primate family tree, and it communicates much of the same information as the figure above, with humans and chimpanzees most closely related because they share the most EVEs [source].

Probably most of the EVEs are just genomic junk hanging around. Sometimes they can cause problems by disrupting a needed gene or its regulation (see: cancer). However, occasionally they can be helpful. For example, in mammalian evolution retroviruses have repeatedly, and independently, donated a gene that is used in placenta formation.

Their critical role in fetal development, their ability to reveal common ancestry, and the fact that they are an integral part of us--all of this makes EVE a fitting name.


Notes:
1. Things like transposons, LINEs, and SINEs (especially Alu elements).
2. Katzourakis A, Gifford RJ (2010) Endogenous Viral Elements in Animal Genomes. PLoS Genet 6(11): e1001191.

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Updating Sexual Development

One of the things I have always liked about biology is the propensity of nature to violate rules that people think are inviolable. This week's example comes from a news article, Sex Redefined, in the journal Nature. It covers current understanding of sexual development in humans--something most of us thought we understood by the time we finished high school biology. But it turns out that there are multiple stages to it, each of which can produce a variety of results. The basic outline is as follows:

That the two sexes are physically different is obvious, but at the start of life, it is not. Five weeks into development, a human embryo has the potential to form both male and female anatomy. Next to the developing kidneys, two bulges known as the gonadal ridges emerge alongside two pairs of ducts, one of which can form the uterus and Fallopian tubes, and the other the male internal genital plumbing: the epididymes, vas deferentia and seminal vesicles. At six weeks, the gonad switches on the developmental pathway to become an ovary or a testis. If a testis develops, it secretes testosterone, which supports the development of the male ducts. It also makes other hormones that force the presumptive uterus and Fallopian tubes to shrink away. If the gonad becomes an ovary, it makes oestrogen, and the lack of testosterone causes the male plumbing to wither. The sex hormones also dictate the development of the external genitalia, and they come into play once more at puberty, triggering the development of secondary sexual characteristics such as breasts or facial hair.

Not having a developmental biology background, I found that my understanding was a little out of date in that I was still under the impression that female development is the default track. That the developmental process can be altered and lead to surprising results isn't particularly new, but some of the examples given in the article are still impressive (e.g. womb discovered in 70 year old man).

As for how any of this fits (or doesn't) with Church doctrine, I previously laid out a few thoughts here. As a side note, I've only ever heard vague hearsay that special gender cases have gone to the First Presidency. Given the statistics involved (at least 1 in 4500 people), I would imagine that disorders of sex development are not uncommonly considered by Church leadership, but that's just my guess. I would also guess they are handled on a case-by-case basis, but if anyone out there has insight into that aspect, please chime in.


Notes:
For more, see Duane Jeffery's article, "Intersexes in Humans," for a nice LDS-oriented discussion of this topic. It seems to have held up well since it's publication in 1979. See also Jeffrey Keller, "Is Sexual Gender Eternal?"

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The Case for Junk DNA

Most of our DNA probably doesn't really do anything and could be dispensed with. Some may find that statement to be surprising, but there are good reasons to believe it. "The Case for Junk DNA," published a couple of months ago at PLoS Genetics, explains some of the history behind the idea of junk DNA as well as experimental and observational support. (A layman's explanation is provided by Carl Zimmer here.) The argument rests on a few basic facts:

1. Much of our (and other organisms') genome is made up of repetitive sequences, broken genes, bits and pieces of viruses and other self-replicating virus-like elements. A few may have secondarily taken on function in helping to regulate genes, or even create new genes, but attributing some kind of essential function to most of it would be like saying that the phrase "copy and paste me" peppered throughout Shakespeare's works serves a narrative function.

2. There is no correlation between genome size and organismal complexity. As illustrated by the image below, genome size can vary widely, even between closely related lineages. (Millions of bases shown on a log scale, with the star indicating humans.)

Let that sink in for a second. Salamanders have genomes that are over 10 times as large as ours. (Insert joke about the salamander's letters.)

3. If you assume that most of the genome is functional, then the mutation rate in humans (or other organisms) ought to be causing 'mutational meltdown' because our collective genomes are being hit with deleterious mutations faster than natural selection can remove them.

There is also experimental support, such as a 2004 experiment where a large section of a mouse's genome was deleted with no apparent effect.

When you put it all together, I think the evidence strongly suggests that much of our genome is expendable. T. Ryan Gregory, one of the authors, has blogged and published on this issue for a long time. If you think of a reason for why we need all that 'junk' DNA, Gregory asks that you submit it to 'the onion test,' which is simply:

...if most eukaryotic DNA is functional at the organism level, be it for gene regulation, protection against mutations, maintenance of chromosome structure, or any other such role, then why does an onion require five times more of it than a human?

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The Mayans and the Neanderthals

Last week I was reading a news article about a new study that determined that Tibetans inherited a gene that gives them high-altitude tolerance from ancient Denisovans. Denisovans, you may recall, are an extinct human species known primarily by their DNA, that are genetically closer to Neanderthals than us. That Denisovan DNA made it into modern humans is not anything new, but apparently this particular gene variant went extinct except for among Tibetans and some Chinese.

That's interesting in and of itself. However, at the end of the article I read this:

The discovery is the second case in which modern humans have acquired a trait from archaic humans, notes paleogeneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, whose team discovered the Denisovan people. Earlier this year, another team showed that Mayans, in particular, have inherited a gene variant from Neandertals that increases the risk for diabetes.

Wait, what? How did Neanderthal DNA get into Mayans?

A paper published last February reported the results of researchers looking for genetic associations with type 2 diabetes in Mexicans and other Latin Americans. They looked at 9.2 million single nucleotide polymorphisms (SNPs) from 3,848 Mexicans with type 2 diabetes, compared with a similar number of non-diabetics. The scientists found a chunk of the genome where a certain variant containing 5 particular mutations was associated with diabetes. When they looked at other populations, they found the following:

I have simplified their table a little bit. It shows the percent of samples that had the most common version of the gene compared with the version associated with diabetes. You can see that it is hardly found anywhere except among east Asians and Mexicans. Further, when they looked at samples with over 95% Native American DNA, they found the mutant version in about half.

So let's summarize what they found so far: A gene variant associated with type 2 diabetes that is commonly found among Native Americans can also be found among east Asians, but only rarely in Europeans and Africans. That makes sense since Native Americans are descended from east Asians. But what does that have to do with Neanderthals?

Well, in looking at the variant the scientists determine that it diverged from the European version about 800,000 years ago. Modern humans didn't even exist back then, and Africans don't have it, so how could these differences have arisen? It turns out that an unpublished Neanderthal genome has a nearly identical match. Thus, it appears that ancient Asians picked up the gene from Neanderthals. It was then carried into America, and for some reason it is now common among Native Americans.

I didn't find any reference to Mayans in the paper (although I didn't look in the supplementary material) so I'm not sure where that came from, but many Mayans probably did have this gene. Lest you think that Native Americans are special in their inheritance of Neanderthal DNA, the authors point out,

...whereas this particular Neanderthal-derived haplotype is common in the Americas, Latin Americans have the same proportion of Neanderthal ancestry genome-wide as other Eurasian populations (2%)

In other words, many of us have about the same amount of Neanderthal DNA [1], just different parts.

Notes:

1. Africans have little to no Neanderthal DNA because their ancestors remained in Africa and never met Neanderthals.

Source: SIGMA Type 2 Diabetes Consortium, Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico, Nature. 2014 Feb 6;506(7486):97-101

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Scientists: Bigfoot Still Missing

University of Oxford scientists have published--in a peer-reviewed journal--results of DNA tests for 'anomalous primates' (i.e. Bigfoot). They put out a call for people to send in hair samples and received 57. Actually, not all of the samples were hair, so after they discarded those and others from which DNA could not be extracted, they were left with 30 samples. They sequenced the mitochondrial DNA of the remaining samples and compared the sequences to those in databases. They found polar bear, horse, raccoon, porcupine, dog, and even one human. None of the results came back as not-quite-human. It wasn't a total waste of time though, because a couple of samples from the Himalayas came back as polar bear, suggesting a hybrid species of bears.

The authors conclude:

While it is important to bear in mind that absence of evidence is not evidence of absence and this survey cannot refute the existence of anomalous primates, neither has it found any evidence in support. Rather than persisting in the view that they have been ‘rejected by science’, advocates in the cryptozoology community have more work to do in order to produce convincing evidence for anomalous primates and now have the means to do so.

I think that's a diplomatic way of saying put up or shut up.

Notes:
Source: Sykes, Proc. R. Soc. B 22 August 2014 vol. 281 no. 1789

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And God Created Fowl

If you have 3 minutes to spare, have a look at this video. Science writer Carl Zimmer explains the origin of birds and feathers. I don't think I'm spoiling anything if I tell you that there was more to it than God saying, "Let there be..."

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Lead Heads

The Guardian's George Monbiot:

At first it seemed preposterous. The hypothesis was so exotic that I laughed. The rise and fall of violent crime during the second half of the 20th century and first years of the 21st were caused, it proposed, not by changes in policing or imprisonment, single parenthood, recession, crack cocaine or the legalisation of abortion, but mainly by … lead.... It's ridiculous – until you see the evidence.

He's talking about the recent cover story for Mother Jones, "America's Real Criminal Element: Lead," by Kevin Drum. The whole article is worth reading, but here are the highlights:

-Lead was added to gasoline in the 1920s to eliminate knocking and pinging in automobile engines.

-Following WWII, the boom in automobile sales resulted in increasing environmental lead levels from auto emissions, particularly in dense population areas.

-Children in these areas were exposed to increasing levels of lead.

-The rise and fall of environmental lead mirrors the rise and fall of violent crime 20 years later.

-The link between lead and crime holds true in different cities, states, and countries.

-Lead is now known to cause damage to the developing brains of children, particularly in areas involved in control of aggression, attention, emotional control, etc. It also lowers IQ. These effects can be seen at blood levels previously thought to be safe.

-In children followed from birth to adulthood, higher blood levels are associated with arrests for violent crime.

-Residual lead in soil and old paint (especially dust produced) continue to cause damage.

-Areas with the highest levels of residual lead also tend to be the areas of highest crime.

When you put the whole puzzle together you get a compelling picture. Drum:

Needless to say, not every child exposed to lead is destined for a life of crime. Everyone over the age of 40 was probably exposed to too much lead during childhood, and most of us suffered nothing more than a few points of IQ loss. But there were plenty of kids already on the margin, and millions of those kids were pushed over the edge from being merely slow or disruptive to becoming part of a nationwide epidemic of violent crime. Once you understand that, it all becomes blindingly obvious. Of course massive lead exposure among children of the postwar era led to larger numbers of violent criminals in the '60s and beyond. And of course when that lead was removed in the '70s and '80s, the children of that generation lost those artificially heightened violent tendencies.

In a follow-up blog post, Drum is clear that lead was, and is not, the sole driver of crime. Without lead there would continue to be violent crime for a variety of reasons. However the evidence suggests that lead is largely responsible for the epidemic of crime.

Okay, so we have taken lead out of gasoline and paint. Existing environmental lead is still a problem, but at least it's not getting worse. Right? Back to Monbiot:

There is only one remaining manufacturer of tetraethyl lead on earth. It's based in Ellesmere Port in Britain, and it's called Innospec. The product has long been banned from general sale in the UK, but the company admits on its website that it's still selling this poison to other countries. Innospec refuses to talk to me, but other reports claim that tetraethyl lead is being exported to Afghanistan, Algeria, Burma, Iraq, North Korea, Sierra Leone and Yemen, countries afflicted either by chaos or by governments who don't give a damn about their people.

In 2010 the company admitted that, under the name Associated Octel, it had paid millions of dollars in bribes to officials in Iraq and Indonesia to be allowed to continue, at immense profit, selling tetratethyl lead. Through an agreement with the British and American courts, Innospec was let off so lightly that Lord Justice Thomas complained that "no such arrangement should be made again". God knows how many lives this firm has ruined.

Is it just me, or does it seem like those countries don't need a lower violence threshold?

Back to Drum:

Not only would solving our lead problem do more than any prison to reduce our crime problem, it would produce smarter, better-adjusted kids in the bargain. There's nothing partisan about this, nothing that should appeal more to one group than another. It's just common sense. Cleaning up the rest of the lead that remains in our environment could turn out to be the cheapest, most effective crime prevention tool we have. And we could start doing it tomorrow.

I find the whole idea striking! To think that so much hand-wringing about the cause of crime has perhaps been entirely beside the point--it makes me wonder what other of our ills have been entirely misdiagnosed. It's also another example where industrial production of a product has real consequences for society. What makes this one especially interesting is that it affects behavior.

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Another Utah Geology Report

Last month our family took a trip to Utah. I always enjoy my visits there--which sadly seem to be increasingly spaced apart. Having been an easterner for most of my life, I love the change in scenery that Utah offers and I try to incorporate learning a little geology each time I visit. This post is my show-and-tell report, focusing on southeastern Utah again. (Previous reports here, here, and here).

Let me pause to highlight two helpful resources for learning about Utah's geological history. The Utah Geological Survey website has lots of good information that can help you get a general feel for the history. Also, I spent a lot of time with Utah's Spectacular Geology: How it Came to Be, by Lehi Hintze, in my hand. Hintze divides the geological history into nine chapters. But the best part of the book is toward the end where 19 areas are given individual treatment, including photographs with labels. (See modest recreation of one image below.) I found the book to be very helpful and informative. Its one defect is the lack of an index (!).

OK, moving on. We spent a day down at Arches National Park (ANP). But first we stopped at Dead Horse Point (DHP), which is near by and a must-see if you've never been there. When you turn west off Highway 191 onto 313 toward DHP, look to the right and you will see this, (but without labels). (Click for larger.)

The labeling is based on a similar image in Hintze's book. The Wingate Sandstone is pretty easily identifiable at both DHP and ANP, and the Chinle Formation is rather distinct with its green coloring. The Chinle Formation contains uranium--too bad I didn't have a Geiger counter to play with.

On this trip I experimented with taking images that could be viewed in 3D. This was easily done by snapping a picture, taking a step to the side, and taking another picture. I've put them side-by-side below. Look between the two pictures and relax your eyes, as though you are looking through your screen. With a little practice, you should be able to bring the two images together such that you see three images. You'll be focused on the one in the middle, which should lock into place and become 3D. Once you are successful, should be able to keep the effect while moving through the pictures. You can see slightly larger versions by clicking on them, but you may have more difficulty bringing them together. I find it helps to back away from the screen a little, and then once I have the image I can look closer.

Dead Horse Point

Arches National Park

This next picture is of the Fiery Furnace at ANP. I didn't realize at the time that my life was in danger, but when I looked at the picture I saw that the Grim Reaper was coming after me.

Book Cliffs

On the east side of the road between Price and Green River are what are known as the Book Cliffs. Some Internet sources say that they get their name because they look like shelves of books. However, I have it on pretty good authority that it's actually because of their appearance from above--they look like pages at the edge of an open book. The grey rocks are Mancos shale, which was laid down over 65 million years ago when the interior of North America was covered by sea (picture the Gulf of Mexico stretching up through Canada) with Utah as the western shoreline.

North of Price is a small town called Helper. Just north of the merger of Highway 6 with 191, Highway 6 cuts through rock. That black strip is a coal seam.

We only spent a day in the Moab area, but those are the geological highlights of our trip. I took a lot of pictures that I would like to share, but they just don't do the area justice! Go see it for yourself; I don't think you'll be disappointed. I can't wait to go back.

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What the Big Bang Means for Mormons

Since we're on the topic of the Big Bang, I want to highlight an article from the FARMS Review (now Mormon Studies Review) in 2004: The Big Bang: What Does It Mean for Us? by Hollis R. Johnson, an emeritus professor of astronomy at Indiana University. The essay is a response to an evangelical critique of LDS doctrine, but it serves as a nice accessible introduction to cosmology. You should read the whole thing, but I'll give you the nickel version.

To understand the evangelical critique, you have to know that the original formulation of the Big Big bang envisioned the initial state of the universe as infinitely dense and infinitely small, known as a singularity. This fit nicely with creation ex nihilo, and also implied that if God exists in space and time, then he was a product of the Big Bang.

This notion of singularity has had a lot of staying power in the popular understanding of the Big Bang, but Johnson points out that science has moved on and the singularity has been discarded. For one thing, the notion of a singularity is at odds with quantum mechanics because it would violate the Heisenberg uncertainty principle. (I presume that this holds for black holes as well?) This and other questions gave rise to inflationary cosmology, and the concept of the multiverse.

So what does the multiverse mean for our theology? Well it supports the teaching that matter (i.e. energy) is eternal. It's less clear to me what it means for God or our future in this universe, but Johnson thinks it's premature to take a strong stand on these things anyway. He chastises critics for assuming any particular scientific model as the final truth, especially when dealing with a topic as large and mysterious as cosmology. His frustration with theologians comes through in these two gems:

Creation from nothing is clearly a fantasy devised by certain theologians, perhaps in a misguided attempt to glorify God by making of him a fantastic magician.

How long is eternity? Theologians can speculate forever, while scientists continue to provide a factual time line.

The straightforward and unapologetic explanation of cosmology makes this essay one of my favorite FARMS Review essays.

Note:

I found a minor mistake that is hardly worth bringing up, but I'm going to anyway. Footnote 7 says: "Note that numbers in an exponent simply show the number of zeros after (+) or before (-) the given digits. For example, 10⁵ means 1 followed by 5 zeros (100,000), and 10^—9 means 1 preceded by a period and 9 zeros (.0000000001)." The first part is correct, but the second is not. 10^—9 = .000000001; one preceded by eight zeros.

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The Big Bang: Let's Get Some Things Straight

In the wake of General Conference, I thought we might briefly review the science (which Elder Richard G. Scott has told us, is one of two ways to find truth) of the Big Bang.

What is the Big Bang?

In the mid-twentieth century, astronomers made some observations indicating that distant galaxies are moving away from each other, and that the universe is expanding. This implies that in the past they were much closer together. Astronomers reasoned that at some point in the past (~13.7 billion years ago) the universe was compressed into an extremely hot and dense state--so hot that atoms could not yet form because the high energies would rip them apart. The term Big Bang (initially coined as a term of mockery) refers to the rapid expansion of this compressed universe.

One prediction made based on the theory was that as the universe expanded and cooled, and atoms began to form, electromagnetic radiation should have begun escaping and might still be observable, but at much lower energy. The discovery of the cosmic microwave background in 1965 fulfilled this prediction and gave empirical support to the theory. Although the original Big Bang theory has been modified and added upon, these core features remain.

Was the Big Bang an explosion?

As mentioned above, the universe began in an extremely hot and dense state and rapidly expanded. In this sense, the Big Bang was like an explosion. However, the result of the Big Bang was not like that of explosions. One way of looking at entropy is as a measure of disorder in the universe. When we think of explosions, we think of ordered material being scattered into unordered pieces. From an energy perspective, concentrated energy in the fuel is released and converted into heat and kinetic energy. We end up with scattered pieces of matter, and energy converted into forms that aren't useful. In other words, explosions increase entropy. However, counter to intuition, the result of the Big Bang was a universe of low entropy. As the universe expanded and cooled, matter was able to condense into atoms--especially hydrogen. Hydrogen atoms were attracted to each other by gravity until they reached such density that they began to fuse together, forming stars. Stars have made the heavier elements of which we are composed.

The main point here is that the Big Bang did not use up fuel to scatter material throughout the universe. Rather, it created the raw fuel (hydrogen) from which all else would be made. In other words, the universe created by the Big Bang was one of low entropy and pregnant with potential.

Did the Big Bang create life?

Not directly, no. The Big Bang occurred about 13.7 billion years ago. Earth is only about 4.5 billion years old, so all life on Earth is obviously younger than that. All elements on Earth were created through the birth and death of stars.

Does order require intelligence?

There are many examples of order in the natural world that do not require intelligence. Many of the features of our universe (stars, galaxies, orbits, etc) are the result of simple laws like gravity. Intuition is not a good guide on these matters because nature is cleverer than we are. I covered this topic in a previous post, Order from Chaos. (It includes a couple of neat videos.) Similarly, there does not appear to be any natural law that would preclude the origin and evolution of life on Earth over billions of years by natural processes.

Whether divine intervention occurred in the formation of the universe or life on Earth is a historical question that cannot be ruled out by science, but neither does there seem to be any great need or evidence for it, scientifically speaking.


Further Reading:

Cosmology Primer

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If You Bet Against Einstein, Prepare to Pay Up

Last year physicists in Europe reported the detection of neutrinos that traveled faster than light, which would violate relativity. The prospect was intriguing if unlikely. Further investigation revealed some problems with the experimental setup, including a loose optical fiber connection that would pretty well account for the apparent speed discrepancy. Now measurements from a different detector show the neutrinos obeying the speed limit.

More here and here.


I think this whole episode is a nice example of how science works. An odd result was observed that contradicted well-established science. That being the case, every effort needed to be made to rule out bugs in the system, and it needed to be substantiated by others. In this instance bugs were found, however, and independent measurements fail to support the anomalous result. It's looking like the story essentially ends there.

There are people who seem to constantly lick their lips at the prospect of a major scientific paradigm being overthrown, and they think the resistance of scientists to jump headlong into the new way is simply because of hubris or materialistic blindness. They remind me, especially in this case, of Krusty the Clown, from The Simpsons, who once bet against the Harlem Globetrotters because he thought the opposing team was due for a win.

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XMRV Paper Retracted

Earlier this month I highlighted the drama and controversy surrounding the claim that a virus (XMRV) was associated with chronic fatigue syndrome. The original paper has now been fully retracted by Science.

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Real-Life Science Drama

I'm late on this, but I'm guessing most people haven't paid attention to it anyway, so it's just as well. And as you'll see at the end, it's a story that hasn't finished.

In 2009 a paper was published in Science that reported an association between chronic fatigue syndrome (CFS) and a retrovirus called XMRV. Although it was premature at the time to say that XMRV caused CFS, once it was shown that XMRV was sensitive to anti-retroviral drugs used in HIV treatment, some patients started taking the drugs in an attempt to treat CFS, and patient advocacy groups rallied around the new CFS paradigm. Further, there was concern that XMRV might be in the blood supply, prompting the exclusion of donors with CFS.

However, there is mounting evidence that the claims of the original paper were not correct, with other groups repeatedly failing to confirm the results, the original group unable to reliably identify positive samples, and evidence that the virus itself is a laboratory product. Last May Science suggested that the original paper be retracted, but the authors refused. So the editor, Bruce Alberts, published an "expression of concern" which essentially said that Science no longer had confidence in the paper. Fast forward to September: the authors of the original study retracted several figures from the paper when they determined that the results were based on contaminated samples. A week later lead author Judy Mikovits was fired, apparently over a dispute about sharing of cell lines.

The XMRV history is mostly laid out in "False Positive", published in Science, but it's behind a paywall. However, the LA Times had a good story that covers much of the same material. It's fascinating to read as the evidence for the hypothesis is described, and then to watch the tide turn against what seemed like compelling findings. Mix in Mikovits digging her heels in--going so far as to claim conspiracy against her--and the hysterics of patient-advocacy groups (physically threatening scientists, in some cases), and you've got a real scientific drama.

But beyond the drama, this story helps to illuminate how science works. Philosopher Karl Popper famously argued that science works by falsification. It's not uncommon (at least in Internet discussions) to hear this view strictly applied--that it only takes a single experiment to falsify a theory. But this example shows that it isn't so simple. The impact of a single experiment depends on context, technology, and the state of the field. When contradictory results are obtained, it takes time to gain clarity. Right now it looks like the XMRV link to CFS is dead. However, Mikovits still believes that a link exists and that the difficulties in nailing it down can be attributed to the biology of the virus-host interaction. Is that ad hoc rationalization in an attempt to save a favored hypothesis, or is it perseverance in the face of a complex world that doesn't always give easy answers?

This, in turn, gives us an opportunity to think about Thomas Kuhn's notion of paradigms and what it means to know something based on collected knowledge. Going forward, the notion that XMRV or any other retrovirus causes CFS will be viewed with great skepticism by most scientists, and this collective judgment will dominate the field, while a few dedicated (intransigent?) researchers may soldier on. I don't think that CFS is prevalent enough to catch public attention like, say, vaccines have, but you never know. Will we hear complaints that the dominant view is held by closed-minded defenders of the status quo? Will the minority attempt to wrap themselves in the clothes of Galileo?

The latest is that Mikovits has been charged with two felonies in Nevada and is the subject of a civil suit from her former employer over the removal of laboratory notebooks and attempts to send materials to another lab.

It's been a roller-coaster ride so far, and it looks like the ride isn't over yet.

(In addition to links in the post, also see here.)

[Update, 12/22/11: The original paper has been fully retracted.]

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Archaeopteryx is Still a Transitional Fossil

A research article published in this week's Nature describes a fossil, named Xiaotingia, that comes from the boundaries of birds and (non-bird) dinosaurs. As part of their work the researchers performed a statistical analysis designed to give the best picture of who is related to whom, and the result has led to talk in the press of a fall from grace for the iconic fossil Archaeopteryx.

Archaeopteryx was discovered in 1861 and quickly attracted attention. Darwin's theory, published two years prior, held that new species formed by branching off existing ones, which when viewed backward in time meant that taxonomic divisions of organisms would gradually merge. And if that was the case, it meant that there should be transitional fossils--fossils that show characteristics intermediate between otherwise distinct lineages. Archaeopteryx fit the bill of a transitional fossil as a small dinosaur-like creature that also had feathers and a bird-like opposable toe. It's precise relationship to birds has been controversial over the decades, but it has widely been viewed as an early representative of the lineage connecting dinosaurs to modern birds.

Paleontologists don't generally think of fossil organisms as being direct ancestors or descendants from one another, since such relationships are very difficult, or impossible, to prove. Rather, they group them according to relatedness and as more specimens are collected, the relationships can shift around and be refined. Over the past couple of decades a number of fossils of feathered dinosaurs have been discovered, which has complicated the picture of how different lineages relate to one another. With this new fossil thrown into the mix, it now appears that Archaeopteryx was a sister lineage to the lineage that led to birds.

Whether these results hold up under further scrutiny and as more fossils are found remains to be seen. However, none of this changes the broader meaning for Archaeopteryx. It is still a transitional fossil.

For more authoritative information, see here.

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Order from Chaos

The second law of thermodynamics states that the universe is increasing in entropy. This is often casually interpreted to mean that everything in the universe is tending toward decay and disorder. This may ultimately be true, but our intuition based on our experience with disorder in everyday life is not always a good guide on the matter.

You wouldn't think that a bunch of molecules shaking around could produce any order, but that's what constantly goes on inside every cell of your body. Animations of cellular processes usually depict molecules coming together in an ordered and purposeful fashion, but reality is not as neat. A good example is the assembly of viruses.

Viruses are parasites of living cells; they enter cells, commandeer the cellular machinery and use it to produce more viruses, then leave to find more cells in which to replicate. Many viruses assemble a protein shell that is formed from smaller subunits. This assembly is depicted in the following cartoon (from Alberts, Molecular Biology of the Cell).



The virus is built through self-assembly, a process that is foreign to our daily experience. With that in mind, have a look at these two videos, which model the self-assembly of viruses. (I found them in a post at BioLogos discussing God and randomness.)






Note that the second law of thermodynamics is never violated. The flow of entropy simply takes a route that is not immediately obvious.

Aside from being interesting in their own right, viruses, and these models, serve as a reminder that we should be cautious about using our intuition as a guide to what is or isn't plausible under the second law of thermodynamics. If you think of the Big Bang as a kind of explosion, you might mistakenly think that the immediate product was a disordered universe with very low entropy. Think instead of a universe filled with hydrogen which, under the attractive force of gravity, condenses to form stars, which ultimately produce the rest of the elements and the earth upon which we live.

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More Viruses in Your Genes

For over a decade we've known that a certain family of viruses--retroviruses--has left remnants in our genome. However, a recent survey has found that this phenomenon extends to a much broader collection of viral families. Although new in its extent, this is not all that surprising when you consider what a jumble of chemical reactions occur in the cell.

For more, see the summaries by these Discover Magazine bloggers:

Carl Zimmer - Your inner viruses: the trickle becomes the flood

Ed Yong - I am virus – animal genomes contain more fossil viruses than ever expected

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Amber Fossils, T. Rex, and YECs

A collection of 50 million-year-old amber fossils from India were in the news last week (see here). Resin secreted by certain plants can trap and preserve insects, microorganisms, plants, and even (rarely) small vertebrates. Some of these amber fossils have survived hundreds of millions of years.

Seeing these amber fossils reminded me of something I had been thinking about regarding how young earth creationists view science. For them, the earth is about 6,000 years old and everything must be interpreted in that light. They claim that they and scientists share the same facts, but simply differ in interpretation. This strategy is especially effective for scientific findings that superficially support their view.

A perfect example of such a finding was published in 2005 in the journal Science. Paleontologist Mary Schweitzer described the recovery of soft tissue from the femur of a fossilized Tyranosaurus rex. This was a surprising finding that the atheist conspiracy failed to suppress, since the fossil was 65 million years old. Moreover, they were later able to recover and sequence some fragments of collagen protein (not DNA). Nobody knew that such preservation was possible, which is why YECs have had a field day with it. They argue that such preservation isn't possible, which is why this finding supports a young earth. They emphasize how delicate biological molecules are and how quick and pervasive decay processes are. Any other interpretation is just evidence of an unwillingness to face the plain facts. In contrast, mainstream scientists consider the age of T. rex to be pretty solid, supported by an array of evidence. To them, the remarkable preservation of the tissue represents nature teaching us that such preservation is possible under the right conditions, even if unexpected.

Same facts, different interpretation, right?

If Schweitzer had simply cracked open the bone and found soft tissue, we might have a legitimate problem. However, putting it in such simple terms distorts reality. There is a whole discipline of science that studies how fossils are formed, called taphonomy, and there are several types of preservation. Some of these involve replacement of minerals or the infusion of minerals into empty spaces. In the case of T. rex, although the precise mechanism of the preservation is not yet known, minerals obviously played an important role in preventing decay because the tissues had to go through an extensive demineralization process in the laboratory. So although the preservation was unexpected and is not fully understood, it isn't totally detached from prior understanding, either [1]. When considered in the context of all of the supporting evidence for the ancient age of the fossil, it is more parsimonious to conclude that such preservation can occur, rather than that it can't and that all of the supporting evidence is wrong too.

This brings me back to the amber fossils. YECs certainly do not believe that such fossils are millions of years old, but as far as I have seen they don't argue their case on the basis of preservation--that it is impossible--like they have done with T. rex. There seems to be an implied admission that if amber fossils actually were ancient, the degree of preservation would still be believable. It seems, then, that their objection is not to preservation per se. Further, they argue that fossilization can take place rapidly, which undercuts their argument that the T. rex preservation is impossible.

So what about DNA--can it be recovered from amber fossils? It depends on the age. A 2005 review article I found does a nice job of explaining the difficulties of working with ancient DNA [2]. Over the last couple of decades there have been a handful of studies that have claimed to recover DNA from samples tens of million years old, some of them from amber fossils. However, according to the authors there is a theoretical/empirical limit of DNA survival on Earth of about one million years, and in each of these cases the results either could not be replicated or were found to be from contaminants. Their Figure 2 summarizes many of the ancient DNA publications over the last couple of decades. (Click to enlarge. Note that the Y axis is actually log scale.)



The YEC view of the earth is compressed enough to fit well within the theoretical limits of DNA preservation. If scientists can get DNA from a mammoth and Neanderthal, they should also be able to get it from a dinosaur--or certainly a comparably aged amber fossil--without much more trouble. We wouldn't want to say that scientists will never recover such DNA because, just as in the case with T. rex, the possibilities in nature can surprise us. Indeed, subsequent to this review article there have been additional claims of DNA recovery from amber fossils older than the theoretical limit, though the reliability of these reports remains to be determined. However, given that deep time inversely correlates with the technical feasibility of recovering ancient DNA, YECs need to explain the disparity in DNA recovery if deep time is actually an illusion.

They have creative minds. I'm sure they will think of something.



Notes:
(Both articles are freely available.)

1. Mary Schweitzer et al., Soft tissue and cellular preservation in vertebrate skeletal elements from the Cretaceous to the present, Proc. R. Soc. B 22 January 2007 vol. 274 no. 1607 183-197.

2. Eske Willerslev and Alan Cooper, Ancient DNA, Proc. R. Soc. B 7 January 2005 vol. 272 no. 1558 3-16.

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An Agent of Misery Dies a Quiet Death

In case you missed it--and you probably did--Rinderpest virus has been eradicated. Rinderpest is a disease of cattle that is extremely deadly--killing upwards of 90% of infected animals. It is closely related to--and thought to be the origin of--Measles virus. If it wasn't one of biblical plagues, it certainly could have been. As explained by the New York Times (Virus Deadly in Livestock Is No More, U.N. Declares),

Rinderpest is thought to have originated in Asia and spread through prehistoric cattle trading; it was in Egypt 5,000 years ago. It never became established in the Americas (though there was a small outbreak in Brazil 90 years ago), nor in Australia or New Zealand. Cattle infected with it would have started dying aboard ship and the herd would be slaughtered or quarantined on arrival.

But it reached Africa in the late 19th century, with devastating consequences. The near total destruction of herds meant widespread famines; in one of those, a third of the population of Ethiopia died, according to the Food and Agricultural Organization.

It was apparently introduced to Abyssinia, which is now Ethiopia, in cattle from India imported by the Italians during their campaign to conquer Abyssinia, said Dr. Jeffrey M.B. Musser, a rinderpest expert at Texas A&M’s veterinary school. Some experts believe it was deliberate, as a form of biological warfare, he said, while others contend that it was accidental.

As a result of a sustained international vaccination campaign, rinderpest has not been detected in the field since 2001. Field surveillance will now cease and the eradication officially declared complete later this spring. This is only the second virus to be eradicated from the earth--aside from remaining frozen laboratory stocks--the first being smallpox.

Thank you, science!

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