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Although I intended to make a few comments here about Your Inner Fish, by Neil Shubin, I was invited to participate in a discussion/review of the book with Dave over at Times and Seasons. It has now been posted and you may read it there.
Thanks to Dave for including my two cents.
Carl Zimmer's Microcosm: E. coli and the New Science of Life gives an overview of the kinds of questions that the favorite laboratory bacterium, Escherichia coli, has been used to answer, and how those lessons apply to life in general. It's a pretty easy read and I recommend it--especially if you've never been exposed to bacterial genetics before.
In the book Zimmer reviews some classic bacterial genetics experiments--experiments that I learned about in the course of my education but had not thought of in a while. Here I will briefly review two that Zimmer included.
By the middle of the twentieth century, evolution by random mutation and natural selection (Darwinian evolution) generally reigned supreme except among bacteriologists, who believed that bacteria followed Lamarckian principles. That is, new environments somehow induced bacteria to adapt in a directed manner, which adaptation was then passed on to the bacterial progeny.
1943: Salvador Luria and Max Delbrück took a mathematical approach to the question [original paper]. They grew up a large liquid culture of E. coli and then spread the culture on a series of agar plates that contained a virus that would kill the bacteria. They then counted the number of colonies that grew on each plate. These colonies of bacteria were mutants that were resistant to the virus, and each plate had roughly the same number (say, 13-26). Then they did the same thing again, except instead of using a large initial liquid culture they used smaller individual liquid cultures that all received the same innoculum. When those cultures were plated out, the number of resistant colonies on each plate varied dramatically. Many had zero or just a few colonies, while a few plates had many more--e.g. one plate had 107.
If bacteria mutated and became resistant in response to being exposed to the virus, then you would not expect any difference in the variation of colony numbers between the large single culture and the small individual cultures. However, if the resistance mutation occurred randomly before exposure to the virus, then the larger variation in the small culture experiment makes sense. In fact, their observations fit their theoretical calculations quite well. This work helped earn Luria and Delbrück a Nobel Prize in 1969.
1952: Joshua and Esther Lederberg finished off Lamarck by using a technique called replica plating [original paper]. This was done by pushing a piece of velvet onto a plate of bacteria, and then lifting the velvet and pushing it onto a fresh plate. When the bacteria on the new plate grew, the colonies would be located in the same place relative to one another as the first plate, thus providing a replica plate.
The Lederbergs plated bacteria sensitive to an antibiotic (they also used a virus, with the same result) onto a regular agar plate. They then did replica plating onto an agar plate that contained the antibiotic. By comparing the two plates, they could determine which colonies on the regular plate gave rise to the resistant colonies on the plate with antibiotic. They then used the original colonies on the regular plate to start new cultures and do the procedure over again. Eventually, all of the colonies were resistant when replica plated onto the agar containing antibiotic.
The key here is that the pure culture of resistant bacteria came from colonies on the regular plates; they had never been exposed to the antibiotic! How could a pure culture of resistant bacteria be derived from sensitive bacteria, when none of the bacteria in the lineage had ever touched the antibiotic? Again, this makes no sense under a Lamarckian scenario of induced directed mutation, but it makes perfect sense if mutations are random. The Lederbergs had simply identified random mutants and enriched for them until they had a pure culture of clonal mutants. (Joshua Lederberg received a Nobel Prize in 1958 for other work.)
Lamarck may just be unconscious--there have been several attempts to revive him, and occasionally someone thinks they hear a heartbeat. However, most consider him to have died by 1952, and it was E. coli that killed him.
There has been a flare-up over DNA and the Book of Mormon--this time among believing members. I've had a hard time figuring out exactly what Rod Meldrum's scientific claims are. The best I've found so far is apparently the latest essay by Simon Southerton, "How DNA Divides LDS Apologists." Meldrum appears to be making claims about mtDNA haplogroup X. However, I want to discuss the Y chromosome for a moment.
I freely admit that I am not a geneticist, and I'll be happy to be schooled if I'm getting something wrong. Also, my specific criticism should not be construed as general criticism of those making the claims I criticize below. Now let's get down to business.
Some apologists seem to be making the basic following claim: Certain Y chromosome groups are found among Native Americans, people around Siberia, and among some Jewish groups. Although this chromosome grouping may come from Siberia (which is congruent with mtDNA and archaeology), it could come from the Jewish groups instead, and uncertainty in dating increases the plausibility of this interpretation.
I will try to explain why I think this is wrongheaded. Of course it should be obvious that if scientists thought there were good grounds to connect Native Americans with Jewish groups, we would not be having this discussion. And multiple lines of evidence point to Asia over 10,000 years ago, so why should we try to interpret the Y chromosome data in a way that runs counter to the other lines of evidence? But aside from these more philosophical objections, I think that the progressing science is casting additional doubt on the above claim.
The nomenclature of the Y chromosome groupings is quite a hurdle in itself, which is not helped by the fact that it has undergone several revisions. Originally, several researchers were using their own designations and things became a mess. In 2002 the Y Chromsome Consortium established a nomenclature for everyone to use. (It has recently been updated, but I'll get to that in a minute.)
Jeff Lindsay pointed out that haplogroup 1C is found in both Native Americans and some Jews. However, as of 2002 the designation 1C does not exist anymore. This figure shows the Y chromosome haplogroups and how they relate to each other. On the right are colored columns that show the different designations used by different researchers. If you look at the pink column toward the bottom, you will find two labels of 1C. By comparing that to what is on the left, it looks to me that in retrospect, 1C was not very well defined and even included groups not actually closely related. In other words, as additional details and groupings were filled in, it became apparent that the 1C designation was not helpful any more. So much for 1C.
Others make the same claims for M242 or P-36 (which is roughly equivalent to 1C), however similar issues are at play. Below are the latest haplogroup Q designations and relationships (click for bigger image) [1]. You can compare it with the Wikipedia Haplogroup Q page, which is helpful.
Everything to the right of M3 is known exclusively in Native Americans. If you work your way left to P36.2 (formerly P36) and then M242, you will see that the M3 grouping constitutes only a part of what is now included under P36.2 and M242. So to say that P36.2 is also found in Jews is not very informative. If I read this correctly, the closest relative to the M3 group is Q1a3*, which is found in Pakistan and India. If you look at the Wikipedia page, you'll see that if you move up another level you'll find that Yemeni Jews are related, but so are people of Asia and Siberia. The relationship to Jews is at best ambiguous here.
But it looks like we can go a step further. Some apologists point out the uncertainty in dating distinguishing mutations and hint that if we simply adjust time frames, then it all makes sense. Unfortunately for that argument, human remains from On Your Knees cave in Alaska, that radiocarbon dated to 10,300 years ago, yielded Y chromosome DNA falling in the M3 group. This independent dating puts a minimum time on the entrance (or origination) of M3 into North America.
Your head, like mine, is probably spinning by now. In summary, I think apologists should stop trying to link Native American Y chromosomes with that of Jews. Haplogroups represent somewhat arbitrary groupings. The question is not whether Native American genes are related to Jews (of course they are), but how close is the relationship and what time frames are we dealing with? So far it looks like the answers to those questions continue to be that most Native American DNA originated in Asia over 10,000 years ago.
Notes:
1. Tatiana M. Karafet, Fernando L. Mendez, Monica B. Meilerman, Peter A. Underhill, Stephen L. Zegura, and Michael F. Hammer. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res., May 2008; 18: 830 - 838.
Unfortunately I cannot access this paper, but it will become freely available in November. However, the haplogroup chart from which I made the image above is available for download (28MB pdf).
I am almost certainly projecting my own ignorance onto others, but when I was an undergraduate the concept of punctuated equilibria (or equilibrium) was occasionally discussed (in non-paleontological circles), but without anyone really understanding what it meant. At least it wasn't clear in my mind. Then again, given the confusion that has surrounded PE over the years--including among professionals--my sense may have been accurate. My recent casual reading has led me to revisit PE, so I will summarize what I have found below and provide some links for reading.
The idea was put forth by paleontologists Niles Eldredge and Stephen J. Gould in 1972. Although on a popular level Gould's name is probably more closely associated with it, the idea was really Eldredge's. Punctuated equilibria was the paleontological extension of Ernst Mayr's hypothesis of allopatric speciation.
Let me pause and explain. For convenience here is Wikipedia on allopatric speciation:Allopatric speciation, also known as geographic speciation, is the phenomenon whereby biological populations are physically isolated by an extrinsic barrier and evolve intrinsic (genetic) reproductive isolation, such that if the barrier breaks down, individuals of the populations can no longer interbreed. Evolutionary biologists agree that allopatry is a common method by which new species arise.
In other words, some kind of barrier prevents two populations of a single species from interbreeding. Over time, changes occur such that, even if the barrier is removed, the two populations do not interbreed. Thus, one species has become two. Peripatric speciation is basically the same, except there is more asymmetry (i.e. a small population branches off of a larger one and becomes a new species).
Gould has explained that invertebrate paleontologists were trained in geology departments and often did not get much training from biologists. They therefore did not think of their work in connection with concepts that came out of the modern evolutionary synthesis. Their vision of evolution was anagenesis--i.e. that the whole species gradually changes to become different enough to warrant designation as a new species.
Niles Eldredge and Stephen J. Gould applied allopatric speciation to paleontology. They pointed out that fossil species seemed to appear suddenly (geologically), live for millions of years largely unchanged, and then disappear. In other words, they did not see smooth transitions from one species into another, as was often assumed to occur. At the time, most paleontologists attributed this to imperfections in the fossil record. Eldredge and Gould argued that the pattern of the fossil record was not just a result of imperfection, but that it actually said something about how evolution proceeded. New species were formed as an isolated minority over a few tens of thousands of years (which is why the ongoing change was often not reflected in the fossil record), after which they persisted relatively unchanged until they went extinct. They did not claim that anagenesis never occurs, only that the pattern of PE was more frequent.
So to sum it up, PE holds that the formation of new species occurs in isolated populations in brief geological time periods (i.e. tens of thousands of years), and that the species remains relatively unchanged until extinction several million years later. This is in contrast to anagenesis, where the whole species gradually becomes a new species.
PE launched some esoteric debates that I am not qualified to get into. (As if I am qualified on the rest.) Now I turn to common myths.
Myth #1: Punctuated Equilibria is saltationism, where a new species is formed suddenly by a discontinuous jump. Apparently many people held this misconception, but Gould denied it again and again.The saltationist canard has persisted as our incubus. The charge could never be supported by proper documentation, for we never made the link or claim. All attempts collapse upon close examination.
Myth #2: PE is not falsifiable because it relies on the absence of fossils as its evidence. There are two parts to PE: the formation of species, and the stasis once formed. Certainly the stasis part is testable because it does rely on fossils. But what about the formation of species; if the evolution of new species occurs too quickly to be recorded in the fossil record, isn't that just an appeal to missing evidence? Eldredge and Gould have discussed tests for PE. Although they are rare, one of those includes sediments that capture a finer time scale so that the relatively rapid evolution can be seen. In fact, in some cases the pattern of PE has been observed alongside anagenesis; in other words, both patterns have been seen in the same series of sediments.
Myth #3: PE was proposed in order to explain the Cambrian Explosion. I certainly would not characterize my reading on the topic as extensive, but I have not seen anything to substantiate this notion. The original paper describing PE makes no such claim, and anyway PE is about the formation of species, not higher taxa.
Myth #4: PE is just a naturalistic justification for lack of transitional fossils, which pattern really supports divine creation. First it should be kept in mind that the lack of transitional fossils is in reference to the formation of species, not major groups. Failure to keep that straight results in distortion of PE. Second, I think it might be helpful to take a step back and remember what kind of fossils we are dealing with. It is easy to think that we are talking about some kind of mouse-like creature and then (BAM!), there's something like a horse, with no hint of transition between. Niles Eldredge recently reviewed how he came up with the idea in the first place. His work involved different species of trilobites, which he distinguished by a subtle difference in the structure of the eye--i.e. the number and arrangement of lenses. Gould's original contribution to PE was a group of Burmudian land snails. Essentially we are talking about subtle changes between species, the likes of which a lay person would probably not notice, and that even young-earth creationists are willing to cede to evolution "within kinds." It is therefore contradictory to allow evolution "within kinds" while trying to turn PE into evidence for divine creation. However, if you think that PE is just naturalistic rationalizing against God creating 17,000 species of trilobites, you are welcome to it.
Further Reading:
1. Niles Eldredge explains how he came up with the idea.
2. Evolution 101: This is a very simple explanation and illustration of PE.
3. The Unofficial Stephen J. Gould Archive has a number of resources on PE. In particular I recommend the following:
4. Punctuated Equilibria: An Alternative to Phyletic
Gradualism: This is the original paper that coined the term punctuated equilibria. Don't let it scare you, most of it is pretty readable and not too technical.
5. Punctuated Equilibrium at Twenty (pdf): In 1992 paleontologist Donald Prothero provided a non-technical overview of the history and effect of PE.
6. If you are really brave, you can consult Gould's The Structure of Evolutionary Theory, or the chapter that was published as a separate book, Punctuated Equilibrium.
If you get any kind of a kick out of the science side of the culture wars, you'll want to see this. I recently drew attention to a 20-year E. coli experiment. Here is some quick background:
Richard Lenski, a new member of the National Academy of Sciences, has been growing E. coli for 20 years. His lab has a recent paper where they report that around generation 30,000 the bacteria gained the ability to grow on citrate. A defining characteristic of E. coli is their inability to get citrate across their membranes, but these bugs have evolved a way to do so. That's a very bare-bones description, so please follow the link in my original post.
This result is threatening to creationists who refuse to allow that random mutations can do anything but destroy. The yahoos at Conservapedia (i.e like Wikipedia, but without all the liberal bias, like science) had the gall to write Lenski and demand that he release his data (reminding him of his taxpayer support) for them to examine. Lenski responded with a polite letter that corrected some of their misconceptions, and suggested that they actually read the paper. The yahoos demanded again.
Lenski has responded again, and it's a doozy. I want to touch on part of it in another post, so for now I will simply urge you to read it.
Addendum: The correspondence back and forth is posted at RationalWiki.
The late Stephen J. Gould is known, among other things, for his view of how science and religion relate to each other. He called it Nonoverlapping Magisteria (NOMA) and argued that
"the magisterium of science covers the empirical realm: what the Universe is made of (fact) and why does it work in this way (theory). The magisterium of religion extends over questions of ultimate meaning and moral value. These two magisteria do not overlap, nor do they encompass all inquiry (consider, for example, the magisterium of art and the meaning of beauty)."This is a controversial idea; some agree with it, while others argue that the two sides cannot be honestly separated--that many religious teachings and practices do, in fact, touch on the empirical realm and therefore constitute scientific questions.
Wise health professionals—whatever their academic training or orientation, be it primarily medical or psychological—increasingly are aware that spirituality is a significant component of their therapeutic resources. As recently as a decade ago only a handful of medical schools in the United Sates offered courses in spirituality and healing, but now more than half do. Particularly with religiously devout patients, evidence is beginning to show that spiritual approaches to the psychotherapy of depression, for example, are at least as effective as those that are purely secular. A growing number of physicians and psychotherapists now use spiritually oriented approaches and interventions in treating patients with both physical and mental illnesses.No references are included. A little internet searching appears to confirm that more medical schools are offering courses in spirituality and healing. Religion--or other forms of spirituality--certainly play an important role in the lives of many people, and will impact treatment decisions, attitude, and overall mental health. I think it is entirely appropriate that physicians and counselors have an understanding of how these issues impact the health of their patients, and use them to their advantage--in ethical ways, of course. What spiritual approaches to healing are--and ought to be--used by health professionals are not specified by Elder Morrison. Nevertheless, it seems to me that he is implicitly rejecting NOMA; he even refers to unspecified "evidence."
This week's Science has an article about why thinking about cars in miles per gallon (mpg) can be misleading. It may seem counterintuitive, but small increases at the lower end of mpg efficiency are more effective than larger increases at the higher end. In other words, increasing from 12 mpg to 15 mpg saves as much gas as increasing from 30 mpg to 60 mpg. The relationship is illustrated in the following graph from this AAAS news release:
The moral of the story is that small increases in the mpg of SUVs, trucks, etc. should not be dismissed, and that in making consumer decisions you are better off comparing the gas used per distance unit (e.g. 10,000 miles). (To calculate, simply take 1/mpg X 10,000.)
For more information, including a nice little video, see the AAAS news release.
A couple of weeks ago I finished reading By the Hand of Mormon by Terryl Givens. I'm only six years late, but better late than never. In my opinion portions of the book should be required reading, especially the first chapter which gives a frank and thorough overview of how the Book of Mormon came to be. Beyond that, the book serves as a nice review of intellectual issues surrounding the Book of Mormon.
Rather than review the book myself, I will refer you to two useful reviews: one from the FARMS Review, and one from Dialogue. I have just a few observations to add.
1. The DNA issue is not discussed, however the treatment of geography is such that it should not be difficult to see how the issue fits in.
2. Perhaps no supporting evidences are uncontested, but some are more contested than others. For example, whereas Givens highlights 2 Nephi 12:16 (cf. Isaiah 2:16), even LDS scholars have urged caution regarding its use. Givens's score-keeping on evidences for or against the Book of Mormon should be used as a guide for getting up to speed on the arguments rather than as a definitive judgment.
3. Don't ignore the endnotes. There are interesting comments and references (some of which can be read online) to be found.
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