Monday, June 30, 2008

Punctuated Equilibria

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.




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Tuesday, June 24, 2008

Richard Lenski Hands Conservapedia Their Backsides

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.


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Collapsing NOMA - Ensign, June 2008

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.

With this in mind, the June Ensign has an article, The Spiritual Component of Healing, by Elder Alexander B. Morrison, an emeritus Seventy. The section, "The Role of Medicine," caught my attention. After explaining that we should consult and follow the advice of qualified professionals (which I was glad to see), Elder Morrison writes:
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."

Presumably we all want our medical care based on the best evidence available. I don't know what spiritually oriented interventions Elder Morrison has in mind--particularly for physical illness, but should physicians make such recommendations unless they have evidence to support their use? And how can such evidence be obtained without rejection of NOMA and opening up to the possibility of falsification? If there exist effective spiritually oriented interventions, there are also, presumably, some that are less effective or worthless. How can the good be separated from the worthless without rejecting NOMA? Are we willing to subject our favored interventions to such tests? How does this square with teachings that spiritual things are not meant to be validated scientifically?

Aside from these interesting (to me) questions, I have two principle concerns with how this paragraph may be perceived. First is that some may think that LDS religious 'spiritual' practices are supported by science. I'm not aware that such practices have even been evaluated, much less supported. Second, I fear that some will interpret this as endorsement of alternative health practices or philosophies that could be interpreted as spiritually based (e.g. chiropractic, therapeutic touch, acupuncture) because they make claims about vital forces, healing energies, etc, but that have no basis in modern science, and do not hold up to scrutiny. But then, that takes us back to the question of NOMA.



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Friday, June 20, 2008

Miles Per Gallon Misjudgment

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.


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Monday, June 16, 2008

Book Review: By the Hand of Mormon

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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Saturday, June 07, 2008

Intelligent Design: Context Matters

[This post is part of a series: (Super) Naturalism, ID, and the Book of Mormon.]

If an intelligent designer was involved in the creation of life, how might we know of their involvement? Certainly one way would be for the designer to publicly announce their involvement. But what if we only consider the world around us, how could we tell? Natural theology and its descendant, Intelligent Design, posit that complicated features of life that appear to have purpose bear the hallmark of thoughtful design. Darwin upset the applecart by coming up with a convincing way for apparent design to arise naturally, without recourse to intelligent intervention.

And here we come to a problem: science, which employs methodological naturalism, takes nature as its guide to reveal what nature is capable of. Leading ID proponents have sought to put a cap on the abilities of nature by asserting that certain features are 'irreducibly complex' or contain 'specified complexity.' They have sought to plant these conceptual flags on various biological features, not because any designer has specified direct involvement in the creation of those features, but precisely because such a designation is lacking. Only if the designer does things that cannot be done in the ordinary course of nature can his works be identified. ID proponents assert that nature as we know it cannot produce some of the things that are found--in nature. They justify their position by appealing to archaeology, forensics, and SETI, each of which are accepted scientific disciplines or ventures that seek to uncover the works of intelligent beings. At the same time, they deny that any knowledge about the designer, his methods, or intentions are needed to justify judging something found in nature as intelligently designed.

The problem is that archaeology, forensics, and SETI each operate with a large background knowledge, not only of what kind of things intelligent beings do, but of what kind of things nature does in the absence of organisms with intelligence levels approaching human. They look for the artificial, which is judged against the background of nature [1]. In my opinion, ID proponents have not yet produced sufficient justification for distrusting nature, and without a more thorough knowledge of the universe with which to make comparisons, science can only employ methodological naturalism to probe life's mysteries. Unless the designer decides to speak up in a clear and open manner, nature is all we have.

ID stands in contrast to the Book of Mormon, for which supernatural claims were made from the beginning, and for which scholarly apologetic arguments depend on knowledge of the circumstances of its production.

Notes:
1. For purposes of simplicity, I am not taking up the argument over whether human intelligence is itself a product of nature.



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Thursday, June 05, 2008

What Happens When You Grow Bacteria for 20 Years?

I've been pretty busy lately, so I will refer you to Carl Zimmer's post about this. I look forward to learning the molecular genetics involved. Anyway, it would seem to be a clear refutation (among other examples) of the bogus claim that mutations are only harmful or only corrupt genetic information.


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Sunday, June 01, 2008

The Book of Mormon and the Supernatural: Context Matters

[This post is part of a series: (Super) Naturalism, ID, and the Book of Mormon.]

Suppose that the Book of Mormon came to light as a single copy discovered in a stack of old books. The book states that it was published in 1830 (assume that you know this to be correct), but there is no information as to who published it--it is an orphaned book. Nevertheless, it attracts the attention of a group of sincere Christians who wonder if it is actually a divine and historical (i.e. miraculous) text. What kind of evidence might they point to?

I don't think there is any. Off the top of my head, I can't think of any semi-scientific/scholarly argument for the historicity of the Book of Mormon that is not fundamentally rooted in the history of Joseph Smith--his claims about the book, what he knew, who his associates were, his timeline, etc [1]. (I would be happy to consider counter-examples if anyone thinks of one.) Remove all knowledge about him, and the miraculous origin and historicity of the Book of Mormon become less plausible by orders of magnitude.

This is implied in the argument by Terryl Givens (among others) that the circumstances surrounding the production of the Book of Mormon eliminate any middle ground regarding its historicity and value as scripture. It is made more explicit in a passage in By the Hand of Mormon (pg. 87).

What distinguishes the Book of Mormon as a religious document...has little to do with its internal claims. In this regard, the Book of Mormon well exemplifies the principle laid down by Wilfred Cantwell Smith and William A. Graham, and endorsed by Shlomo Biderman: 'the element of content is not the major factor in establishing scripture.... Because of the enormous diversity of what is said in scripture, it cannot be defined or characterized by its content.'
Philosopher David Hume wrote that "no testimony is sufficient to establish a miracle, unless the testimony be of such a kind, that its falsehood would be more miraculous than the fact which it endeavors to establish." Hugh Nibley sought to meet such a challenge, and his argument is captured in his parable of the diamond (and it is not hard to find General Authorities that echo it):
A young man once long ago claimed he had found a large diamond in his field as he was ploughing. He put the stone on display to the public free of charge, and everyone took sides. A psychologist showed, by citing some famous case studies, that the young man was suffering from a well-known form of delusion. An historian showed that other men have also claimed to have found diamonds in fields and been deceived. A geologist proved that there were no diamonds in the area but only quartz: the young man had been fooled by a quartz. When asked to inspect the stone itself, the geologist declined with a weary, tolerant smile and a kindly shake of the head. An English professor showed that the young man in describing his stone used the very same language that others had used in describing uncut diamonds: he was, therefore, simply speaking the common language of his time. A sociologist showed that only three out of 177 florists' assistants in four major cities believed the stone was genuine. A clergyman wrote a book to show that it was not the young man but someone else who had found the stone.

Finally an indigent jeweler named Snite pointed out that since the stone was still available for examination the answer to the question of whether it was a diamond or not had absolutely nothing to do with who found it, or whether the finder was honest or sane, or who believed him, or whether he would know a diamond from a brick, or whether diamonds had ever been found in fields, or whether people had even been fooled by quartz or glass, but was to be answered simply and solely by putting the stone to certain well-known tests for diamonds. Experts on diamonds were called in. Some of them declared it genuine. The others made nervous jokes about it and declared that they could not very well jeopardize their dignity and reputations by appearing to take the thing too seriously. To hide the bad impression thus made, someone came out with the theory that the stone was really a synthetic diamond, very skilfully made, but a fake just the same. The objection to this is that the production of a good synthetic diamond 120 years ago would have been an even more remarkable feat than the finding of a real one.
The judgment of whether the making of a synthetic diamond is a remarkable feat depends on knowledge of the context (technology available, etc). Despite Nibley's call for "well-known tests for diamonds," I am not aware of any for the Book of Mormon that can be employed without reference to Joseph and his circumstances.

Notes:
1. Of course, multiple specific references to people and places yet undiscovered at the time of publication would count, although judgment would revolve around how specific, and therefore unlikely, the references were. In the case of the Book of Mormon--taken on its own--Nahom and Alma are suggestive, but not overwhelmingly convincing, in my opinion.


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