Can Anyone Answer This Question?

 
Check out the new look of Uncommon Descent, the blog by Dembski, O'Leary, and friends. It almost looks as though someone intelligent designed it.

Isn't it interesting that the best they can come up with is a bacterial flagellum—a structure whose evolution is getting to be fairly well understood?

While you're there, read Every day biology is looking more and more designed and see if you can answer the question posed by the author,

I receive Nature E-Alerts in a number of biological research fields. Almost every time I read the abstracts and even the titles, or spend more time delving into the detail, I hear “Intelligent Design” silently screamed from the pages. Am I deluded ...?

Update: Joshua Rosenau has an answer at [Simple answers to stupid questions (now with bonus answer to bonus question!)].

The Evolution of Gene Families

The genes for olfactory receptors are part of a gene family. A gene family, by definition, means that there's two or more related genes in a genome. In the case of olfactory receptor genes there are hundreds of different genes spread out over many chromosomes. All the copies are closely related (homologous). They clearly descend from a common ancestor following a gene duplication event.

The evolution of gene families has been studied for over 50 years. We now recognize three different modes of evolution. The two simplest modes are shown below.

Imagine a gene duplication event occurring in a common ancestor at the left-hand side of these trees. Two genes, A and B, are now present in the genome of every species that descends from this common ancestor. In divergent evolution, each of the genes evolves independently after the duplication. Thus, we have two separate phylogenies: one for the A genes and one for the B genes. The two phylogenies will be identical. This is the most common mode of evolution for gene families, especially if the A gene and the B gene are separated in the genome (i.e., on different chromosomes). The classic example is evolution of the α- and β-globin genes in vertebrates.

In concerted evolution, the trees looks like the one on the right. If we assume that the gene duplication event occurred in the last common ancestor of fish, chickens, mice, and humans, then the pattern we see looks very strange. Instead of showing two independent phylogenies, the A and B genes in each species are much more closely related to each other than to family members in any other species. The prototypical example is the evolution of ribosomal RNA genes in all species.

This form of evolution is termed concerted evolution because the pair of genes (A and B) evolved in a concerted manner. They talk to each other. When a mutation occurs in one gene it is transferred to the other so that both genes change in the same direction. The only differences between family members within a species are those that have only become fixed in the very recent past.

The most important mechanism of concerted evolution is gene conversion. This is a form of recombination where the sequence of one gene "converts" the other. It explains how the two genes can communicate. Gene conversion can take place between any two homologous genes in the genome but it is much more common between two homologous genes that are adjacent to each other, especially if they are transcribed in the same direction as a result of a tandem duplication. Gene conversion has been well studied. It is known to produce the results shown in the figure.

There's another way to explain the result in the right-hand tree without invoking concerted evolution. It's possible that our initial assumption is wrong. Perhaps the common ancestor had only a single gene and gene duplications occurred independently within each lineage. This would give a result similar to the tree shown. While this is possible, it seems very unlikely that for a single pair of genes the same duplication would occur in every lineage. With larger genes families such multiple duplication events are more probable.

The third mode of gene family evolution is a combination of the patterns seen in divergent evolution and in concerted evolution. If duplications of family members occur frequently then this gives rise to the birth of new genes. Newborn genes will closely resemble one another, as in concerted evolution. The number of family members does not keep expanding because some of the genes become inactivated—they become pseudogenes and they die. The resulting pattern of evolution will look like a mixture of divergent and concerted evolution. The mode is called "birth-and-death."

The figure below is from a review by Nei and Rooney (2005). Masatoshi Nei is one of the discoverers of birth-and-death evolution (Nei and Hughes, 1992).

Note that in birth-and-death evolution some genes survive in a lineage and some genes are lost. The birth and death of genes can be random or it can be under selection. The point is that not all members of the gene family in the ancestor will show up in all species descending from the common ancestor, and that sometimes several members of the gene family will be much more closely related than you would expect from divergent evolution.

Niimura and Nei (2006) studied the evolution of olfactory receptor genes. In order to study the evolution of gene families you have to be sure you have included every copy of the gene in your study. If you're going to test birth-and-death hypotheses, you also have to include all the pseudognes.

Niimura and Nei (2006) were able to do this for the mouse and human olfactory receptor genes because the complete genomes have been published. By examining the sequences of all genes and pseudogenes, they were able to determine that the most recent common ancestor (MCRA) of mice and humans had 754 functional genes (see figure below). Of these ancestral genes, 691 are still functional in the mouse genome but only 326 remain functional in the human genome.

This study can now be extended because there are complete genome sequences of chickens, frogs, and fish. In addition, there is enough sequence information from lampreys to estimate the number of olfactory receptor genes in that species.

The result is shown above in (b). The ancestor of jawed and jawless fish had two olfactory receptor genes: one type 1 gene and one type 2 gene. Each of these genes gave rise to subfamilies in fish so that the MCRA between fish and tetrapods had six type 1 genes and three type 2 genes. Various members of these subfamilies expanded or contracted in number in the lineages leading to modern fish, amphibians, birds, and mammals. This is birth-and-death evolution.

The patterns produced by birth-and-death evolution look much more like random fluctuations than something produced by sustained directional selection. Niimura and Nei (2006) caution against adaptationist explanations of the differing numbers of genes in various species of mammals. For example, it is widely assumed that the reason mice have more functional olfactory receptor genes than humans is because mice have a better sense of smell. But Niimura and Nei (2006) point out that dogs are supposed to have an excellent sense of smell even though they have fewer OR genes than rodents. The number of genes could be due to chance and not selection. (Or, most likely, a combination of accident and selection.)

Nei, M. and Hughes, A.L. (1992) Balanced polymorphism and evolution by the birth-and-death process in the MHC loci. In 11th Histocompatibility Workshop and Conference, ed. K. Tsuji, M. Aizawa, and T. Sasazuki, pp. 27-28. Oxford, UK: Oxford Univ. Press

Nei, M. and Rooney, A. P. (2005) Concerted and Birth-and-Death Evolution in Multigene Families. Ann. Rev. Genet. 39: 121-152.

Niimura, Y. and Nei, M. (2006) Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates. J. Hum. Genet. 51: 505-517.

Evolution and Religion According to John West

 
John West, one of the leading IDiots at the Discovery Institute, continues his defense of religion (his version) with A Further Response to Larry Arnhart, pt. 4: Darwinism, Religion, and Intelligent Design. He says,

In the section of my book on religion, I make clear that “evolution” can be compatible with theism in general and Biblical theism in particular—depending on how one defines the term “evolution.” If all one means by “evolution” is “change over time,” or “microevolution” through natural selection, or even biological “common descent,” then evolution would seem perfectly compatible with most forms of theism. Only if one insists that evolution is an undirected Darwinian process of chance and necessity, with no particular end in view, does there seem to be a serious problem with traditional theism.

Personally, I wouldn't use the term "Darwinism." I would say. "According to science, evolution is an undirected process with no particular end in view." In a rare example of intelligent insight, West has recognized a truth that many evolutionists and appeasers overlook. The scientific version of evolution is not compatible with theism.

Basic Terms and Concepts

 
Coturnix over at Blog Around the Clock has proposed an explanation of Basic Terms and Concepts. This seems to be an idea hatched by the ScienceBlogs group, but I'm going to assume that anyone can play. John Wilkins has started it off with his expanation of CLADE.

The post below is my definition of Evolution and I'll follow up with The Central Dogma of Molecular Biology tomorrow Monday.

What Is Evolution?

Most non-scientists seem to be quite confused about precise definitions of biological evolution. Part of the confusion is because the word "evolution" has many different meanings, depending on the context. When we talk about biology we are thinking about biological evolution and that's the term I want to define here. What do biologists mean when they refer to biological evolution?

One of the most respected evolutionary biologists has recently defined biological evolution as follows:

Biological (or organic) evolution is change in the properties of populations of organisms or groups of such populations, over the course of generations. The development, or ontogeny, of an individual organism is not considered evolution: individual organisms do not evolve. The changes in populations that are considered evolutionary are those that are ‘heritable' via the genetic material from one generation to the next. Biological evolution may be slight or substantial; it embraces everything from slight changes in the proportions of different forms of a gene within a population, such as the alleles that determine the different human blood types, to the alterations that led from the earliest organisms to dinosaurs, bees, snapdragons, and humans.

Douglas J. Futuyma (1998) Evolutionary Biology 3rd ed., Sinauer Associates Inc. Sunderland MA p.4

Note that biological evolution refers to populations and not to individuals. In other words, populations evolve but individuals do not. This is a very important point. It distinguishes biological evolution from other forms of evolution in science (e.g., stellar evolution). Another important point is that the changes must be genetic, or heritable—they must be passed on to the next generation. Evolution is the process by which this occurs and it is spread out over many generations. Thus, the short minimal definition of biological evolution is,

Evolution is a process that results in heritable changes in a population spread over many generations.

This is a good working scientific definition of evolution; one that can be used to distinguish between evolution and similar changes that are not evolution. Another common short definition of evolution can be found in many textbooks:

In fact, evolution can be precisely defined as any change in the frequency of alleles within a gene pool from one generation to the next.

Helena Curtis and N. Sue Barnes, Biology, 5th ed. 1989 Worth Publishers, p.974

One can quibble about the accuracy of such a definition, but it also conveys the essence of what evolution really is. When biologists say they have observed evolution, they mean that they have detected a change in the frequency of genetic variants (alleles) in a population. (Often the genetic change is inferred from phenotypic changes.) When biologists say that humans and chimps have evolved from a common ancestor, they mean there have been successive heritable changes in the two separated populations since they became isolated.

Unfortunately, outside of the scientific community, the common definitions of evolution are quite different. For example, in the Oxford Concise Science Dictionary we find the following definition:

evolution: The gradual process by which the present diversity of plant and animal life arose from the earliest and most primitive organisms, which is believed to have been continuing for the past 3000 million years

This is inexcusable for a dictionary that's supposed to be a dictionary of science. Not only does this definition exclude prokaryotes, protozoa, and fungi, but it specifically includes a term "gradual process" that should not be part of the definition. More importantly the definition seems to refer more to the history of evolution than to evolution itself. Using this definition it is possible to debate whether evolution is still occurring, but the definition provides no easy way of distinguishing evolution from other processes. For example, is the increase in height among Europeans over the past several hundred years an example of evolution? Are the color changes in peppered moth populations examples of evolution? The definition of evolution in the Oxford Concise Science Dictionary is not a proper scientific definition of evolution.

Standard dictionaries are even worse.

evolution: ...the doctrine according to which higher forms of life have gradually arisen out of lower.. (Chambers)

evolution: ...the development of a species, organism, or organ from its original or primitive state to its present or specialized state; phylogeny or ontogeny (Webster's)

These definitions are simply wrong. The problem is that it's common for non-scientists to enter into a discussion about evolution with such a definition in mind. This often leads to fruitless debate since the experts are thinking about evolution from a different perspective. When someone claims they don't believe in evolution they cannot be referring to an acceptable scientific definition of biological evolution because that would be denying something that is easy to prove. It would be like saying they don't believe in gravity!

Anti-evolutionists often claim scientists are being dishonest when they talk about evolution. The anti-evolutionists believe that evolution is being misrepresented to the public. The real problem is that the public in general, and anti-evolutionists in particular, do not understand what evolution is all about. Their definition of evolution is very different from the common scientific definition and, as a consequence, they are unable to understand what evolutionary biology really means. Scientist are not trying to confuse the general public by using a rigorous definition of evolution. Quite the contrary, saying that evolution is simply "a process that results in heritable changes in a population spread over many generations" is a way of simplifying discussions about evolution.

Note that I have described the minimal scientific definition of biological evolution. Nobody believes that this is all there is to evolution. There are other processes, such as speciation for example, that are clearly important parts of the process of evolution. [Macroevolution]

Objections to the Minimal Definition

Some people, including some scientists, are uncomfortable with this minimal definition because they think it excludes some important parts of evolutionary biology. I'll try and discuss the various objections in a short while but first let me explain why we need a strict minimal definition in the first place.

I've already alluded to one of the classic questions that a proper definition can answer—the increased height of Europeans over the past five centuries. Armed with a good definition of biological evolution we can focus on one of the key requirements; namely, heritable change. It turns out that the increase in height is due to a better diet and not to genetic changes. Therefore, this is not evolution according to the scientific definition.

We can also ask whether the development of antibiotic resistance in bacteria is a valid example of biological evolution. In this case the answer is "yes" because a new antibiotic resistance allele has arisen by mutation and subsequently became fixed in the population. Anyone who wants to offer an alternative minimal definition of evolution will have to make sure that it will help answer questions such as these.

Sometimes it's convenient to refer to evolution as "descent with modification." This conveys a different impression of evolution than the minimal definition. Descent with modification refers to the long-term consequences of short-term changes within a population. It incorporates additional concepts such as speciation, which is an important part of macroevolution. Paleontologists are one group of scientists who aren't directly concerned with the minimal definition of evolution since they are mostly interested in the history of life. They have to deduce that evolution, in the sense of the minimal definition, has taken place from evidence of phenotypic change in the fossil record.

The bad thing about "descent with modification" is that it's not a very rigorous definition. It doesn't rule out modifications that are not genetic in origin and it doesn't rule out individuals evolving—as opposed to populations.

Many people are confused about the difference between a definition and an explanation. That's why we often see incorrect "definitions" that describe how natural selection works. This is wrong. In order to be useful, a definition has to enable us to distinguish examples of evolution from non-evolution but the definition should be neutral with respect to how evolution occurs. It should not distinguish, for example, between Lamarckian evolution and Darwinian evolution even though we know that one of these explanations is incorrect.

Attempts to define evolution in terms of natural selection are not only logically flawed but scientifically flawed as well. They exclude change due to random genetic drift when every evolutionary biologist agrees that drift is a mechanism of evolution.

Evolving Definitions

In 1997 a group of twenty scientists chaired by Douglas J. Futuyma issued a working draft of a "white paper" on Evolution, Science, and Society. The paper was written on behalf of eight scientific societies who wanted to make a statement about evolution. The initial draft defined evolution as,

Biological (or organic) evolution consists of change (modification) in the hereditary characteristics of groups of organisms over the course of generations. Such groups of organisms, termed populations or species, are formed by division of ancestral populations or species, and the descendant groups then change independently. Hence, in a long-term perspective, evolution is the descent, with modification, of different lineages from common ancestors.

This is a pretty good definition. It includes the minimal definition but adds the idea that long-term evolution is descent with modification. The initial draft definition was modified [final draft] so that on the current website it now reads,

Biological evolution consists of change in the hereditary characteristics of groups of organisms over the course of generations. From long-term perspective, evolution is the descent with modification of different lineages from common ancestors. From a short-term perspective, evolution is the ongoing adaptation of organisms to environmental challenges and changes.

This last sentence is really unfortunate. These twenty scientists have now agreed to a definition that specifically mentions the mechanism of adaptation. This is not how one should define evolution. One wonders whether they mean to exclude random genetic drift or whether they simply lost sight of their goal in trying to work out a compromise definition.

The Gene Centrist Objection

Ernst Mayr wrote an entire book on the subject of this little essay. One might expect some insight from one of the original founders of the Modern Synthesis but, unfortunately, we aren't going to get any help from Mayr. On page 157 he says,

Evolution in sexually reproducing organisms consists of genetic changes from generation to generation in populations, from the smallest local deme to the aggregate of interbreeding populations in a biological species.

Ernst Mayr (2001) What Evolution Is, Basic Books, New York p.157

This is good stuff. It restricts the changes to genetic changes and it clearly identifies the population as the unit that evolves. There's no mention of any particular mechanism. But—and you knew there was going to be a "but" didn't you?—good things never last. In his chapter on macroevolution Mayr describes the work of his colleagues Rensch and Simpson. These workers were able to study macroevolutionary events without referring to allele frequencies in a population. Mayr coments,

This approach was consistent with the modern definition of evolution as a change in adaptedness and diversity, rather than a change in gene frequencies, as suggested by the reductionists.

Ernst Mary (2001) What Evolution Is, Basic Books, New York p.189

Consistency is not one of the hallmarks of Ernst Mayr's writings. That's why he can propose two conflicting definitions in the same book, even a book that's devoted to the topic of defining biological evolution! Nevertheless, Mayr does highlight two different objections to the minimal definition that I am defending.

First, Mayr wants a definition that restricts evolution to the mechanism of adaptation. This is a lost battle. There may have been a time in the 20th century when a majority of biologists rejected random genetic drift and other non-adaptationist forms of evolution but that time is long gone. Mayr was one of the last hold-outs. Besides, as I mentioned above, it isn't appropriate to restrict the definition of evolution to a particular mechanism even if you strongly believe that it's the only possible mechanism. That's not how you define something.

Second, Mayr doesn't like reducing evolution to the level of the gene. This charge of reductionism is more interesting. In spite of the fact that Mayr was one of the founders of the Modern Synthesis, he never had much respect for genes and population genetics, or "bean-bag genetics" as he called it. He makes this point very strongly in the preface to his book.

... most treatments of evolution are written in a reductionist manner in which all evolutionary phenomena are reduced to the level of the gene. An attempt is then made to explain the higher-level evolutionary process by "upward" reasoning. This approach invariably fails. Evolution deals with phenotypes of individuals, with populations, with species; it is not a "change in gene frequencies." The two most important units in evolution are the individual, the principle object of selection, and the population, the stage of diversifying evolution.

Ernst Mary (2001) What Evolution Is, Basic Books, New York p.xiv

I happen to agree with some of those who criticize the extreme reductionist views of scientists like Richard Dawkins but in this case Mayr has it all wrong. When we define evolution as a change in the heritable characteristics of a population we are not reducing evolution to the level of the gene. We are merely stating that populations don't evolve unless they undergo genetic changes. This is not controversial in spite of Mayr's objection. He is confused about the difference between a definition of evolution and a proposed mechanism of change—as was obvious in his attempt to include adaptation. This is a remarkable error in a book called "What Evolution Is."

The Minimal Definition and Macroevolution

The minimal definition of evolution is not inconsistent with Hierarchical Theory and a focus on macroevolution as opposed to microevolution. This point is worth emphasizing since the minimal definition has often been criticized for excluding lots of evolution that takes place at higher levels. Stephen Jay Gould—no fan of reductionism and no stranger to hierarchical theory—addressed this problem in his last anthology.

The Darwinian principle of natural selection yields temporal change—"evolution" in the biological definition—by a twofold process of generating copious and undirected variation within a population, and then passing only a biased (selected) portion of this variation to the next generation. In this manner, the variation within a population at any moment can be converted into differences in mean values (such as average size or average braininess) among successive populations through time.

Gould, S.J. (2002) "What Does the Dreaded 'E' Word Mean Anyway?" in I HAVE LANDED Harmony Books, New York p. 246

The purpose of his essay was to point out the fundamental difference between this biological definition and the common vernacular meaning of the word "evolution." (I wish he hadn't used the word "selected" in his definition since it implies natural selection and Gould knows that there are other mechanisms.) Gould points out that other sciences, such as astronomy, use the word "evolution" in a very different sense—one that is actually closer to the original nineteenth century meaning. The vernacular meaning carries an implication of purpose and direction that is entirely absent from the biological definition of changes in the heritable characteristics of a population over time. This is why Darwin never used the dreaded "E" word.

Gould argues that an understanding of the true importance of the biological definition is absolutely essential to understanding why the general public is confused. He is especially concerned about emphasizing the lack of progress and direction in the definition of biological evolution. He advocates that scientists owe it to the general public to teach the biological definition.

I don't mention these differences to lament, or complain, or to criticize astronomical usage. After all, their concept of 'evolution' remains more faithful to etymology and the original English definition; whereas our Darwinian reconstruction has virtually reversed the original meaning. In this case, since neither side will or should give up its understanding of "evolution"—astronomers because they have retained an original and etymologically correct meaning, evolutionists because their redefinition expresses the very heart of their central and revolutionary concept of life's history—our best solution lies simply in exposing and understanding the legitimate differences, and in explaining the good reasons behind the disparity of use.

In this way, at least, we may avoid confusion and the special frustration generated when prolonged wrangles arise from mis-understandings about words, rather than genuine disputes about things and causes in nature. Evolutionary biologists must remain especially sensitive to this issue, because we still face considerable opposition, based on conventional hopes and fears, to our emphasis on an unpredictable history of life evolving in no inherently determined direction. Since astronomical 'evolution' upholds both contrary positions—predictability and directionality—evolutionary biologists need to emphasize their own distinctive meaning, especially since the general public feels much more comfortable with the astronomical sense—and will therefore impose this more congenial definition upon the history of life if we do not clearly explain the logic, the evidence, and the sheer fascination of our challenging conclusion.

(ibid p. 250-252)

I agree with Gould. That's why I think it's important to explain the real biological definition of evolution as a change in the heritable characteristics of a population over time. We can explain that this is a minimal definition, and that there's more to evolution than this, but we shouldn't back away from the real meaning of the term since it conveys some important messages. If we cave into pressure from the general public to make evolution into something they can understand, with all their biases, then we will have lost the battle before we even begin.

The amazing thing about the minimal definition of biological evolution is that it doesn't carry any baggage concerning the history of life or its future. As soon as we try to define evolution in terms of the historical record, we run into all kinds of problems because we confuse evolution as a process with evolution as a history of life. The scientific definition attempts to describe the minimum thing that might be called evolution. We know that the history of life is more complicated than this and we know that evolutionary theory encompasses other things such as the formation and extinction of populations. There is no conflict between the minimal definition of evolution as a change in the genetic composition of populations and macroevolution. Gould understands this.

[This is a slightly modified version of an essay that appears here. An earlier version is on the TalkOrigins Archive.]

My Library Card

 
Everybody else is doing it. Here's my library card. Make your own at Catalog Card Generator.

Canadian Scientists Show that Speaking Two Languages Protects You from Dementia

 
Biology News Net reports that a Canadian study shows bilingualism has protective effect in delaying onset of dementia by four years. It's total nonsense, of course, ... but what the heck, it makes good press, n'est-ce pas?

I'm embarrassed that so-called scientists at my university are allowing such rubbish to be published in a press release. The clear implication is that there's something about speaking two languages that delays the onset of dementia and Alzheimer's. Correlation is not the same as cause and effect. Repeat after me, a correlation does not necessarily identify a cause.

Update: Here's the original press release from the Baycrest Centre.

Little Mosque on the Prairie

 
There's a new sitcom on Canadian television called "Little Mosque on the Prairie." The first show aired on Wednesday and it's already attracting a lot of attention. See Monado's review at Little Mosque on the Prairie starts this week.

Does Disbelieving Evolution Reflect a Lack of Understanding of It?

 
Bill Dembski is troubled by the latest report in Science that shows a correlation between acceptance of evolution and education. [See PZ Myers' summary on Pharyngula.] The data suggests that the more educated you become the more likely you are to accept evolution. In other words, the data suggests that IDiots are, well, idiots.

You can see why Dembski is upset [Does understanding coerce belief?]. The truth hurts. Dembski then goes on to give us a good demonstration of the negative correlation between intelligence and belief in intelligent design.

But why should disbelieving evolution reflect a lack of understanding of it? Alternatively, does understanding evolution automatically force one to believe it? I remember speaking at the University of Toronto in 2002 when a biologist challenged me about how holding to ID renders one a nonscientist. I asked him if that disqualified Isaac Newton from being a scientist. His instant response was, “but he didn’t know about evolution.”

I don't know if Dembki is referring to me or to one of my colleagues who was at the meeting. I recall accusing Dembski of stupidity and of not being a good scientist, but there were so many of us making the same point that I don't know which one Dembski remembers. (Dembski has mentioned this meeting many times. It must have been very traumatic for him.)

At the risk of boring anyone with an IQ over 80, let me make the point that Dembski is deliberately missing. In 2002, if you rejected evolution you were an idiot. That's because the evidence for evolution is overwhelming. The same correlation holds today, only more so.

To answer the question posed in the title; yes, disbelieving in evolution reflects a lack of understanding of evolution. That's an empirical observation. There are very, very few IDiots who understand evolution. (Don't believe me? Read Uncommon Descent and Evolution News & Views.) Dembski sure aint' one of them. He didn't understand the basic principles of evolutionary theory in 2002 and he's given no indication of having learned anything since then.

Newton didn't know about evolution so he couldn't have rejected it. He wasn't stupid and he wasn't a bad scientist. He also didn't know about general relativity and plate tectonics but that didn't mean he was stupid either. If Newton were alive today you can be sure he would accept evolution, continental drift and general relativity. In the 21st century, anyone who rejects these fundamental concepts in science doesn't deserve to be called a scientist.

Barack Obama Is a Closet Muslim

 
Friday's Urban Legend: FALSE

There's an email circulating that Barack Obama was educated as a Muslim in a Wahabbi school in Indonesia. According to the email message ("The Enemy Within"), his step-father, Lolo Soetoro, was a Muslim who brought up Obama in the Muslim tradition. (The truth is that Obama's mother was an atheist and so was his biological father. His step-father was a non-practicing Muslim.)

Later on as an adult, Obama joined the United Church of Christ in order to convince voters that he was a Christian but he's still an ideological Muslim, according to the email message.

The take-home message is FALSE according to snopes.com [The Enemy Within] but there are elements of truth in the email message. It's worth reading the entire snopes article in order to understand Obama's religious views. This is the sort of thing that's going to come out during the Presidential campaign and if the snopes article is accurate, there's trouble brewing.

Stem Cell Debate in the USA

 
Furriners like me sometimes have a hard time following American politics. Take the debate over funding stem cell research, for example. America doesn't do it. Bush is very much against changing the law to permit development of new lines of stem cells. It's against his religion.

Mathew Nesbit has written an excellent summary of the situation over at Skeptical Inquirer [Political Communication in the 2007 Stem Cell Debate]. He follows up with a report on his blog [STEM CELL BILL PASSES THIRTY-SEVEN VOTES SHORT OF VETO OVERRIDE]. Apparently this is another fight over which "power" (President or Congress) is supposed to make laws. You'd think the Constitution would be clear about those things.

Now, if only someone could explain who's supposed to be in charge of making war ..... people seem to be confused about that as well.

Human Races Populations

 
I get pretty sick of hearing that there's no such thing as "races" in the species Homo sapiens. RPM has revived the controversy in More About Human Populations. Read the comments as well.

Apparently, it's more politically correct to refer to human "populations" and avoid the r-word.

We Really Are Quite Small

 

Olfactory Receptor Genes

 
The human genome contains 388 different olfactory receptor (OR) genes. These genes encode olfactory receptors, the molecules that detect odors [A Sense of Smell: Olfactory Receptors]. Our genome also has 414 olfactory receptor pseudogenes. These are stretches of DNA that resemble functional genes but they have accumulated mutations rendering them non-functional. In some cases, a single mutation has disrupted the open reading frame—these pseudogenes have recently evolved from functional genes. In most cases the olfactory receptor pseudogenes have multiple mutations, including extensive insertions and deletions, indicating that these pseudogene lost functionality millions of years ago.

None of the olfactory receptor genes have introns. This is a huge advantage because it is much easier to recognize functional genes and pseudogenes by scanning the genome.

The human genes and pseudogenes are clustered. Some clusters contain dozens of genes while others have only a few. There are 95 different clusters spread over all chromosomes except chromosome 20 and the Y chromosome. The first figure (below) is from a review by Niimura and Nei (2006). It shows the locations of the OR gene clusters. The vertical lines above the chromosome indicate the number of functional genes at that position—the taller the line the more genes. Lines below the chromosome indicate pseudogenes at that position.


A phylogenetic tree of the 388 functional OR genes reveals two main classes. All 57 class I genes are clustered together on chromosome 11. The class II genes can be subdivided into several subgroups labelled A to S in the figure below (Fig. 2 from Niimura and Nei (2006)). Several clusters are shown in order to illustrate the fact that genes of the same subclass tend to cluster together. Large letters indicate functional genes and small letters indicate related pseudogenes. Genes below the line are transcribed in the opposite direction from those above the line. (X identifies unclassified genes.)

Adjacent, closely related genes that are transcribed in the same direction are said to be tandemly duplicated, indicating that they probably arose by gene duplication. For example, most of the subclass A genes in cluster 11.11 probably resulted from repeated duplication of single A-type gene at that site.

The mouse genome contains 1037 functional genes and 354 pseudogenes in 69 clusters. Almost all of the clusters map to related clusters in the human genome. If we look at the relationship between the clusters on human chromosome 11 (Hs11) and mouse chromosome 2 Mm2), we see that the mouse cluster is larger and parts of it have been split up into four different clusters in humans. Nevertheless, the general order of genes is similar in mice and humans. There are more mouse OR genes, as expected. It has long been known that genes on human chromosome 11 are related to genes on mouse chromosome 2. (The figure is from Niimura and Nei (2006)).

How did this large gene family evolve? It seems clear that the common ancestor of mice and humans must have had many OR genes. It appears that the number of genes has probably changed considerably in one, or both, lineages. Why, and how, do some genes become inactivated? Is evolution of gene families due to natural selection or someting else? See "The Evolution of the Olfactory Receptor Gene Family" in tomorrow's posting.)

Niimura Y. and Nei M. (2006) Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates. J. Hum. Genet. 51:505-17

Cut and Run

 
"Cut and run" is straight talk for a military strategy otherwise known as "strategic redeployment" or "tactical victory." In some circles it's called "defeat" but that's a little too close to the truth to be acceptable.

The cut and run strategy means withdrawing all troops from Iraq and Afghanistan immediately. Not next year, and not next month. Tomorrow would be good. I'd vote for that.

Why should our troops stay in the Middle East? The most common argument in favor of continued occupation is that we broke Afghanistan and Iraq and it's now up to us to stay there and fix them (The Pottery Barn Rule).

This is a strange argument if you think about it for more than a second—a length of time that seems to just about cover the average attention span of neocon war hawks. What we've done in Afghanistan and Iraq is to destabilize those countries by removing a strong central government that provided peace and security to the majority of their citizens—albeit, at the expense of freedom and, in many cases, lives. Not perfect but better than what they've got today. That's why 80% of Iraqis preferred the life they had before the invasion (Iraqis say they were better off under rule of Saddam Hussein).

By staying there and propping up a Quisling "democracy" that's incapable of maintaining law and order, we are encouraging and protecting the local warlords and private militia. We are creating an environment that promotes a low-level civil war that will never produce a victory for either side. In other words, our troops might be contributing to the problem, not the solution. Furthermore, the Pottery Barn Rule runs counter to the stated goal of the invasions, which were supposed to allow the citizens to choose their own form of government. They own it; they should fix it.

The proper strategy is to withdraw. Cut your loses and get out as fast as possible. That's the only honorable way out of a losing strategy. Just like Vietnam. If we don't leave now, we'll be having this debate a year from now, only the countries will be even more broken. (I said the same thing a year ago, and I expect to be saying it in 2008 and 2009 and ....)

Thousands of allied soldiers died during the invasions and the subsequent occupations of Afghanistan and Iraq. Many people are opposed to the idea to admitting we made a mistake because of the extreme sacrifices that these soldiers have made. They ask the tough question, "Does this mean that all those men and women died in vain?"

Yes. That's one of the unfortunate consequences of making a bad decision. While there was some justification for invading Afghanistan in 2001, we have overstayed our welcome and it's time for the Afghanis to settle their own internal squabbles.

But there was never any rational justification for invading Iraq. Most of us know that by now. Everyone who has died there has died in vain—including tens of thousands of innocent Iraqi citizens. It's sad to have to admit this, especially when talking to the friends and loved ones of fallen soldiers, but pretending it ain't so isn't going to help. You can't use the fact that soldiers died unnecessarily as an excuse to send more troops into battle.