A Gene Wiki

 
The prevalence of errors and omissions in sequence databases is one of the ugly little secrets of molecular biology [Errors in Sequence Databases]. We know how to fix the problem; it requires careful annotation by knowledgeable experts. Unfortunately, this is time-consuming and expensive since you have to hire annotators. One other possibility is to allow open access to all existing records in databases such as GenBank, RefSeq, or PDB. This ain't gonna happen because here's no way to verify the changes to make sure they are valid. The people who control these databases are very reluctant to allow open access and the authors of the database entries are uneasy about allowing others to insert annotations into their records.

But there are other models that might work. A recent paper by Huss et al. (2008) in PLoS Biology describes a possible solution. They point out that Wikipedia seems to be a successful model of collaborative effort to ensure accuracy. Why not adopt this model for gene annotation?

Some examples of human genes already had Wikipedia entries and these entries were updated and annotated by various users. In order to stimulate and encourage this process, Huss et al. (2008) created stub entries on Wikipedia for every human gene. Here's how they describe it in their paper.

In principle, a comprehensive gene wiki could have naturally evolved out of the existing Wikipedia framework, and as described above, the beginnings of this process were already underway. However, we hypothesized that growth could be greatly accelerated by systematic creation of gene page stubs, each of which would contain a basal level of gene annotation harvested from authoritative sources. Here we describe an effort to automatically create such a foundation for a comprehensive gene wiki. Moreover, we demonstrate that this effort has begun the positive-feedback loop between readers, contributors, and page utility, which will promote its long-term success.

Today, anyone with access to Wikipedia can contribute to annotating human genes. Two examples of well annotated genes are HSP90 and NF-κB.

Let's look at some examples of stub entries to see how the process might work. I've chosen the human members of the HSP70 multigene family because I'm familiar with these genes. All members of the family function as molecular chaperones, helping to ensure that proteins are properly folded [Heat Shock and Molecular Chaperones].

There are two major inducible genes called HSPA1A and HSPA1B. They are adjacent to one another on chromosome 6. The database entries for these genes are confusing and in most cases it's almost impossible to discern which gene is being referred to.

Here's the Wikipedia stub for HSPA1A. Clearly there's an opportunity to modify this entry in order to make it clear that there are two very similar genes and to point to the proper sequence records for this gene. The second gene, HSPA1B, has its own entry in EntrezGene so I was expecting to find it on Wikipedia. Unfortunately, it's not there. A search for HSPA1B redirects you to HSPA1A. So right away we have a problem. Someone made a decision to merge these entries on Wikipedia making it very difficult to correctly annotate the separate genes.

HSPA1L is an intronless gene closely linked to HSPA1A and HSPA1B. HSPA1L is not heat shock inducible, instead it is developmentally regulated. The gene is expressed exclusively in the testes. The stub entry for this gene [HSPA1L] includes an RNA expression profile that beautifully illustrates the developmental regulation but there's nothing in the annotations that mentions this. This is an excellent opportunity to correct an omission in the existing databases.

Let's look at one more example to see how useful the Wikipedia effort might be. The HSPA4 gene is identified on all databases as a member of the HSP70 gene family. It's usually called "Heat shock 70kDa protein 4." The Wikipedia stub reflects the GenBank annotation [HSPA4]. However, it has been known for a long time that this gene is NOT a member of the HSP70 gene family. The annotation is incorrect. Instead, this gene is Apg-2 an HSP100 homologue not related to HSP70. The original error is due to Fathallah et al. (1993) who sequenced the first example. They mistakenly called it a novel hsp70 gene due, in part, to sequencing errors and partly to an overactive imagination. Mistakes such as these are extremely difficult to remove from the database but we now have an opportunity to correct the error on the Wikipedia entry.

Putting the human genes on Wikipedia is almost as good as allowing open access to the primary sequence databases. The effort will only be successful if scientists make the effort to edit the Wikipedia entries. It's unlikely that most gene entries will be modified but even if only a subset is annotated, it's better than none at all. It would be nice if the RefSeq records could point to the Wikipedia records. That will encourage people to make comments on Wikipedia.

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Huss III, J.W., Orozco, C., Goodale, J., Wu, C., Batalov, S., Vickers, T.J., Valafar, F., and Su, A.I. (2008) A Gene Wiki for Community Annotation of Gene Function. PLoS Biol 6(7): e175 [doi:10.1371/journal.pbio.0060175]

Flatfish

 
Flatfish are strange looking animals that live sideways. One of their eyes has migrated to one side of the fish so that when it lies on its "side" at the bottom of the ocean both eyes point upwards. This is an interesting example of the evolution of a change in development.

Fossil relatives of modern flatfish have recently been described and they confirm much of what was surmised about the evolution of these strange creatures. Several bloggers have written about this and it's well worth the effort to read their postings.

Christopher Taylor at Catalogue of Organisms wrote The Ugly Stick in Action.

Ed Yong at Not Exactly Rocket Science wrote 'Missing link' flatfish has eye that's moved halfway across its head.

GrrlScientist at Living the Scientific Life wrote The Mysterious Origin of the Wandering Eye.

Carl Zimmer at The Loom wrote Dawn of the Picasso Fish.

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[Image Credit: The drawings are by Georgi Pchelarov from The Classification of Fishes.]

Good Science Writers: G. Brent Dalrymple

 
G. Brent Dalrymple is a geologist at Oregon State University (now retired). He received the National Science Medal in 2005. This is the USA's highest award for scientific achievement.

Dalrymple has published two books on the age of the Earth: The Age of the Earth (1991), and Ancient Earth, Ancient Skies: The Age of Earth and Its Cosmic Surroundings (2004). The first book grew out of his preparation for the 1981 creationist trial in Arkansas that resulted in overthrowing the "equal time" law. Michael Ruse writes of his testimony at that trial [in Science and Creationism, see NCSE Supporter Dalrymple receives National Medal of Science]

Rounding out the science witnesses was G. Brent Dalrymple of the U.S. Geological Survey. He gave a quite brilliant disquisition on methods of dating the earth. One would not think that such a topic could be all that intrinsically interesting, but Dalrymple gave this assumption the total lie. He held us absolutely spellbound as he talked of various dating techniques and how geologists compensate for weaknesses in one direction by strengths from another. My sense was that Dalrymple was so good and so firm that he rather broke the back of the State's case. He had checked all of the Creationist arguments and showed in devastating detail the trail of misquotations, computational errors, out-of-date references, and sheer blind stupidity which allows the Creationists to assign the earth an age of 6000 years. After Dalrymple, the State seemed far less ready to tangle with witnesses.

The following except is from The Age of the Earth. It can only give a bit of the flavor of Dalrymple's writing. In my opinion this book is one of the classic science books of the 2oth century. Richard Dawkins did not include G. Brent Dalrymple in The Oxford Book of Modern Science Writing.

Four and one-half billion years. That figure, which represents the current estimate of the age of the Earth, is so large, so far outside of our normal everyday experience that it is difficult to comprehend its true scope and meaning. Even scientists who deal with numbers of that magnitude on a daily basis often find it difficult to grasp the full significance of that span of time. If a piece of string 2.4 cm long (about an inch) represents one year, for example, then a 183-cm length (about 6 feet) is equivalent to the average lifetime of a person living in the United States. A string representing all of recorded human history would be fully a kilometer long, but a piece representing 4.5 billion years would be 114,280 km long! Four and one-half billion quarters would form a stack nearly 8,000 km high. Can anyone fully visualize a string that would wrap around the Earth nearly three times, or a stack of quarters that would reach from here to the center of the Earth and halfway to the other side? ...

As staggering as these numbers may seem, the evidence clearly shows that the Earth's age is, indeed, 4.5 Ga, and the universe is probably three to four times older. Yet humans are relatively recent inhabitants of our planet and have witnessed only an infinitesimally small percentage of Earth's history. No man, no creature, no plant was present when Earth, her sister planets, and the Sun condensed from a shapeless cloud of primordial matter. How then can we peer back into these seemingly infinite reaches of time and calculate an age for the Earth that requires ten digits?

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Good Science Writers: Jacques Monod

 
Jacques Monod (1910 - 1976) received the Nobel Prize in Physiology or Medicine (1965) for his work on the regulation of the lac operon (with François Jacob). While best known as a biochemist, Monod was also well respected for his many articles on politics and philosophy.

Dawkins didn't select anything from Monod for The Oxford Book of Modern Science Writing because his selections were limited to books written initially in English. Monod's most famous work is Le Hasard et la Nécessité first published in France in 1970. It is well known in the English version: Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology (1971). The excepts below are from the translation by Austryn Wainhouse.

Various mutations have been identified as due to

1. The substitution of a single pair of nucleotides for another pair;
2. The deletion of addition of one or several pairs of nucleotides, and
3. Various kinds of "scrambling" of the genetic text by inversion, duplication, or fusion of more or less extended segments.

We call these events accidental; we say that they are random occurrences. And since they constitute the only possible source of modification in the genetic text, itself the sole repository of the organism's hereditary structures, it necessarily follows that chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact. And nothing warrants the supposition—or the hope—that on this score our position is ever likely to be revised.

I believe we can assert today that a universal theory, however completely successful in other domains, could never encompass the biosphere, its structure, and its evolution as phenomena deducible from first principles....

In a general manner the theory would anticipate the existence, the properties, the interrelations of certain classes of objects or events, but would obviously not be able to foresee the existence or the distinctive characteristics of any particular object or event.

The thesis that I shall present in this book is that the biosphere does not contain a predictable class of objects or of events but constitutes a particular occurrence, compatible indeed with first principles, but not deducible from those principles, and therefore essentially unpredictable.

Let there be no misunderstanding here. In saying that as a class living beings are not predictable upon the basis of first principles, I by no means intend to suggest that they are not explicable through these principles—that they transcend them in some way, and that other principles, applicable to living systems alone, must be invoked. In my view the biosphere is unpredictable for the very same reason—neither more nor less—that the particular configuration of atoms constituting this pebble I have in my hand is unpredictable. No one will find fault with a universal theory for not affirming and foreseeing the existence of this particular configuration of atoms; it is enough for us that this actual object, unique and real, be compatible with the theory. This object, according to the theory, is under no obligation to exist; but it has the right to.

That is enough for us as concerns the pebble, but not as concerns ourselves. We would like to think ourselves necessary, inevitable, ordained from all eternity. All religions, nearly all philosophies, and even a part of science testify to the unwearying, heroic effort of mankind desperately denying its own contingency.

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Nobel Laureate: Peter Agre

 

The Nobel Prize in Chemistry 2003.

"for the discovery of water channels"


Peter Agre (1949 - ) received the 2003 Nobel Prize in Chemistry for discovering the water channel protein known as aquaporin (AQP1).

Aquaporin is a membrane protein that forms a channel in the membrane. The channel specifically allows water molecule to diffuse across the membrane. No other ions or molecules can pass through the channel. Aquaporin is important in kidney cells where it plays a role in taking up water from the urine. Homologous channel proteins are found in other eukaryotes and in bacteria.

The discovery of aquaporin is related in Peter Agre's Nobel Lecture. It's an example of serendipity coupled with the fortune that favors a prepared mind. Peter Arge is a hematologist who was studying red blood cell antigens. Although aquaporin is a major component of red blood cell membranes its existence was not suspected until the late 1980s because it does not stain with the standard protein stains used to detect proteins on SDS polyacrylamide gels.

The prize was shared with Roderick MacKinnon.

The presentation speech was delivered by Professor Gunnar von Heijne of the Royal Swedish Academy of Sciences on December 10, 2003.

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen,

In the days of Alfred Nobel, the learned academies used to entertain and educate the public by holding open demonstrations explaining the latest scientific advances. This tradition has been largely – and perhaps unfortunately – forgotten. So let us try to revive the public demonstration of science, if only for a brief moment.

The demonstration I have in mind is a simple one, and only requires that you do something that is in any case particularly fitting for a Nobel Prize ceremony: to think. But only for exactly 5 seconds!

So, please start thinking, for 5 seconds ... Thank you!

Let us now reflect briefly on what has just happened, in each and every one of us. First, a sudden increase in the activity of the brain when you started to wonder what this is all about – should I really think at this point in the ceremony? – then, cascades of nerve signals when you were actually thinking, and finally a return to the normal resting state. And all this thinking ultimately relied on one of the simplest chemical compounds you can imagine: ordinary salt – sodium, potassium and chloride ions – streaming back and forth across the walls of your nerve cells, thereby generating the signals that activated your mind. And not even very much salt – a rough estimate is that the total amount of salt spent during these five seconds in each one of us was no more than a few grains. Only a fistful of salt to set a whole Concert Hall thinking!

And while all this brain activity was occupying our minds, our kidneys worked on quietly, as they always do, reabsorbing water from the urine to the blood. But in this case, the volumes of water transported are too big, even during five seconds, to be suitable for a demonstration from the podium.

This year's Nobel Prize in Chemistry is all about salt water, and the biochemical mechanisms that control where, when, and how often ions and water are let into or out of the cells in our body. Mechanisms that the two Laureates – Peter Agre and Roderick MacKinnon – have elucidated down to the atomic level.

Agre's was a "serendipity discovery": while working on a completely different problem, he stumbled across a protein in red blood cells that he could soon show was the water channel researchers had been looking for in vain for well over a century. His unexpected discovery opened a whole new field of study.

MacKinnon, on the other hand, decided at an early stage that he should try to do what was then thought impossible: to determine the three-dimensional structure of ion channels at atomic resolution. He bet his career on this vision – and succeeded to an extent that probably surprised even himself.

THEME: Nobel Laureates
There is a lesson here, I believe: There is no one way to do science, and our support system must be sufficiently well funded and versatile to prepare the ground for both unexpected serendipity and focused, often risky, attacks on central scientific problems.

Peter Agre and Roderick MacKinnon stand for decisive contributions to the biochemistry of cell membranes, but their discoveries also have an almost tangible aesthetic component. Their work has uncovered an amazing "economy of design" in the atomic structures of the water and ion channels that is breathtaking in its simplicity and perfection. Indeed, after seeing these molecular machines, you find yourself thinking, "Of course, this is how it must be, this is how it must work!" What more could we ask of science?

Professor Agre, Professor MacKinnon, your fundamental discoveries concerning water and ion channels are singular achievements that have made it possible for us to see these exquisitely designed molecular machines in action at the atomic level. The biochemical basis for the transport of water – the most abundant and primordial substance of life – and ions – these tiny, mundane and yet absolutely essential constituents of the living world – can now be understood in unparalleled detail. On behalf of the Royal Swedish Academy of Sciences, I wish to convey to you our warmest congratulations, and I now ask you to step forward to receive the Nobel Prize in Chemistry from the hands of His Majesty the King.

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The Three Fatal Flaws in the Theory of Evolution

Thanks to PZ Myers for finding an important new website called Darwin Conspiracy. It highlights the three faltal flaws in the Theory of evolution.

You have never read about any of these fatal flaws before. Evolution scientists know about these flaws, but they have successfully covered them up with the help of a worldwide Darwin Conspiracy that actively suppresses the fact that Darwinism is not scientific but just an atheist doctrine.

We have discussed the three fatal evolution flaws with scientists and doctors we know and they have all agreed we have found real flaws in the Theory of Evolution.

Each of the three fatal flaws revealed on this website proves that Darwin was wrong.

Wow! Scientists and doctors agree. I'll have to change my position on evolution after reading about these three fatal flaws.

Here they are ...

Evolution is Missing a Mathematical Formula

Mathematical formulae make up the VERIFICATION LANGUAGE of science. Formulae are the only reliable way to test a theory. Every scientific theory has a formula, except the Theory of Evolution. Darwinists have never been able to derive a working Evolution Formula because Evolution theory does not work.

There is No Genetic Mechanism for Darwinian Evolution

Darwinists claim we evolved from the simplest form of bacterial life to ever more complex forms of life. The most basic bacteria had less than 500 genes; man has over 22 thousand. In order for bacteria to evolve into man, organisms would have to be able to add genes. But there is no genetic mechanism that adds a gene. (Mutations change an existing gene but never add a gene.) This means there is no mechanism for Darwinian Evolution and this is a fatal flaw in the Theory of Evolution.

Every Helpless Baby Born Proves Darwin Was Wrong

The Theory of Evolution in a nutshell is "Survival of the fittest." But most mammals and birds give birth to helpless babies - instead of strong and fit ones. Neither Darwinism nor Neo-Darwinism can explain infantile helplessness. Every baby that is born contradicts Evolution Theory and this is a fatal flaw.

Sometimes I think the term "IDiot" is being too kind.

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Good Science Writers: Steven Vogel

 
Steven Vogel is a Professor in the Biology Department at Duke University (N.C., USA). His main research interest is comparative biomechanics. He studies things like the design of fly wings and how organisms adapt to fluids (air and water). His secondary interest is science writing and he has published four books: Life's Devices: The Physical World of Animals and Plants (1988); Cats' Paws and Catapults: Mechanical Worlds of Nature and People (1999); Prime Mover: A Natural History of Muscle (2001); Comparative Biomechanics: Life's Physical World (2003).

The excerpt is from Life's Devises. Here, Steven Vogel gives as balanced a description of the use of "design" and "adaptation" as I've seen anywhere.

This book is mainly about organisms, so we will be concerned with a level of biological organization upon which the invisible hand of the selective process should incur fairly immediate consequences. It is the immediacy of operation of that unseen hand that makes organisms appear well designed—as a colleague of mine put it, "The good designs literally eat the bad designs." But it must be emphasized that we mean "design" in a somewhat unusual sense, implying only a functionally competent arrangement of parts resulting from natural selection. In its more common sense, implying anticipation, "design" is a misnomer—it connotes the teleological heresy of goal or purpose. Still, verbal simplicity is obtained by talking teleologically—teeth are for biting and ears for hearing. And the attribution of purpose isn't a bad guide to investigation—biting isn't just an amusing activity incidental to the possession of teeth. If an organism is arranged in a way that seems functionally inappropriate, the most likely explanation (by the test of experience) is that one's view of its functioning is faulty. As the late Frits Went said, "Teleology is a great mistress, but no one you'd like to be seen with in public."

We functional, organismic biologists are sometimes accused of assuming a kind of perfection in the the living world—"adaptationism" has become the pejorative term—largely because we find the presumption of a decent fit between organims and habitat a useful working hypothesis. But the designs of nature are certainly imperfect. At the very least, perfection would require an infinite number of generations in an unchanging world, and a fixed world entails not only a stable physical environment but the preposterous notion that no competing species undergoes evolutionary change. Furthermore, we're dealing with an incremental process of trial and error. In such a scheme, major innovation is not a simple matter—features that will ultimately prove useful are most unlikely to persist through stages in which they are deleterious or neutral. So-called hopeful monsters are not in good odor. Many good designs are simply not available on the evolutionary landscape because they involve unbridgeable functional discontinuities. Instead, obviously jury-rigged arrangements occur because they entail milder transitions. In addition, the constraints on what evolution can come up with must be greater in more multifunctional structures. Finally a fundamentally poorer, but established and thus well-tuned, design, may win in competition with one that is bascially better but still flawed.

I make these points with some sense of urgency since this book is incorrigibly adaptationist in its outlook and teleological in its verbiage. The limitations of this viewpoint will not insistently be repeated, so the requisite grain of salt should be in the mind of the reader as well as the author. Incidentally, the ad hoc character of many features of organisms are recounted with grace and wit in some of the essays of Stephen Jay Gould, not just as an argument against extreme adaptationism but as evidence for the blindly mechanical and thus somewhat blundering process of evolution. His collection entitled The Panda's Thumb (1980) is particularly appropriate here.

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Evolution Education

Last year the McGill Journal of Education published a special issue on teaching evolution. One of the most interesting articles was by Craig Nelson on TEACHING EVOLUTION EFFECTIVELY: A CENTRAL DILEMMA AND ALTERNATIVE STRATEGIES.

Nelson points out that much of the blame for the evolution/creation controversy stems from poor teaching of evolution in the high schools. The two most obvious failed strategies are:

TEACH THE SCIENCE AND IGNORE STUDENTS’ PRIOR BELIEFS

This is the most common approach to teaching evolution. Students are exposed to the factual material on evolution from a strictly scientific perspective. The fact that most students may have conflicting religious beliefs is not taken into consideration and no time is spent discussing possible conflicts between religion and science. Nelson points out that this strategy is ineffective at getting students to change their minds about evolution. He adds, "However, when students make direct comparisons of their naïve misconceptions with scientifically better-founded schemes, change is frequent. These approaches can lead to greater acceptance of evolution (e.g., Ingram & Nelson, 2005; Scharmann, 2005; Scharmann et al., 2005; Verhey, 2005; Wilson, 2005, 2007; Alters, 2005 reviews earlier work). Thus, naïve views predominate publicly with regard to evolution, perhaps even more than elsewhere in science, at least partly as a predictable consequence of post-secondary pedagogical choices that ignore naïve views and are otherwise sub-optimal."

He's saying that it's better to confront creationism and intelligent design than to ignore it.

AVOIDING AN EVEN WORSE APPROACH: TWO EQUAL MODELS

One alternative is to teach both evolution creationism but to treat them as equivalent theories of origins. This is not appropriate.

Nelson advocates the teaching of creationism and intelligent design in school, but not as science. Instead, they should be used as examples of what science is not. It would be an excellent way of confronting the misconceptions of students head-on to show them why these false ideas are wrong. He echoes a similar call by Bruce Alberts writing in Cell [A Wakeup Call for Science Faculty].

For all those who teach college biology, the current challenge posed by the intelligent design movement presents an ideal “teachable moment.” I believe that intelligent design should be taught in college science classes but not as the alternative to Darwinism that its advocates demand. It is through the careful analysis of why intelligent design is not science that students can perhaps best come to appreciate the nature of science itself.

Alberts is talking about college courses but Nelson wants to use these "teachable moments" in high school. He suggests three possible strategies.

• Discuss common misconceptions, like the second law of thermodynamics or missing links, without explicitly mentioning creationism or religion.
• Make the nature of science a central theme and use evolution as the prime example of how science is supposed to be done. Countering creationist claims would be used as examples of non-scientific arguments.
• Discuss creationism and intelligent design directly in order to make it clear that creationist arguments fail when considered from a scientific perspective.

I agree with Nelson. He is talking about American schools but I think it would be much easier to implement a "teach the controversy" strategy in Canada. If the goal is to teach critical thinking then this is the way to go.

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"Rational" Arguments for the Existence of God

 
The current issue of Christianity Today contains an article by William Lane Craig entitled God Is Not Dead Yet: How current philosophers argue for his existence. Craig is a Professor of Philosophy at the Talbot School of Theology of Biola University, an evangelical Christian college near Los Angeles. His website is Reasonable Faith.

The article is a defense of theology in the face of attacks by "New Atheists."

You might think from the recent spate of atheist best-sellers that belief in God has become intellectually indefensible for thinking people today. But a look at these books by Richard Dawkins, Sam Harris, and Christopher Hitchens, among others, quickly reveals that the so-called New Atheism lacks intellectual muscle. It is blissfully ignorant of the revolution that has taken place in Anglo-American philosophy. It reflects the scientism of a bygone generation rather than the contemporary intellectual scene.

Craig defends the idea that there are rational arguments for the existence of God. In other words, believers do not need to fall back on revelation as their only defense of superstitious beliefs.

The renaissance of Christian philosophy has been accompanied by a resurgence of interest in natural theology, that branch of theology that seeks to prove God's existence apart from divine revelation. The goal of natural theology is to justify a broadly theistic worldview, one that is common among Christians, Jews, Muslims, and deists. While few would call them compelling proofs, all of the traditional arguments for God's existence, not to mention some creative new arguments, find articulate defenders today.

What's interesting about this claim is that the arguments (see below) are the very ones that Dawkins discusses in The God Delusion. You might recall that there are many theists who argue that there are much better, more sophisticated, arguments that Dawkins ignores.¹ I thought it would be fun to list the arguments here so we can see how the modern theist justifies belief in God. You'll have to read the article to see how Craig deals with objections to each one.

The cosmological argument

1. Everything that exists has an explanation of its existence, either in the necessity of its own nature or in an external cause.
2. If the universe has an explanation of its existence, that explanation is God.
3. The universe exists.
4. Therefore, the explanation of the universe's existence is God.

The kalam cosmological argument

1. Everything that begins to exist has a cause.
2. The universe began to exist.
3. Therefore, the universe has a cause.

The teleological argument

1. The fine-tuning of the universe is due either to physical necessity, chance, or design.
2. It is not due to physical necessity or chance.
3. Therefore, it is due to design.

The moral argument

1. If God does not exist, objective moral values and duties do not exist.
2. Objective moral values and duties do exist.
3. Therefore, God exists.

The ontological argument

1. It is possible that a maximally great being (God) exists.
2. If it is possible that a maximally great being exists, then a maximally great being exists in some possible world.
3. If a maximally great being exists in some possible world, then it exists in every possible world.
4. If a maximally great being exists in every possible world, then it exists in the actual world.
5. Therefore, a maximally great being exists in the actual world.
6. Therefore, a maximally great being exists.
7. Therefore, God exists.

There you have it. These are the rational arguments for the existence of God from a Professor of Philosophy at a Christian college. Read 'em and weep, all you heathen atheists!

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1. We are never told what these arguments are, only that they exist somewhere.

[Hat Tip: Jason Rosenhouse]

Monday's Molecule #79

 
What is this protein doing and what is its name? You don't need to identify the species.

There's a direct connection between today's molecule and a Nobel Prize. The prize was awarded for discovering this molecule and recognizing that its function was exactly what had been long predicted.

The first person to correctly identify the molecule and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are three ineligible candidates for this week's reward. You know who you are.


THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: The protein is aquaporin, a transporter that moves water molecules from outside the membrane to inside. The Nobel Laureate is Peter Agre. This week's winner is Maria Altshuler of the University of Toronto. Honorable mention to Michael Fraser who answered before Maria but gave the Nobel Laureates and MacKinnon and Agre. We've already done Roderick MacKinnon.

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[Image Credit: Kozono D, Yasui M, King LS, Agre P. (2002)Aquaporin water channels: atomic structure molecular dynamics meet clinical medicine. J Clin Invest. 2002 Jun;109(11):1395-9. [comlete article]]

The Evolution of Flowering Plants

 
A lot more is known about the evolution of flowering plants than most people realize. Christopher Taylor over at Catalogue of Organisms¹ has done the homework and posts a must-read article on the subject [The Origins of Flowers].

He begins by asking the questions, "... what exactly makes flowering plants so distinct? What do they have that no other plant has?" Think of the answers, then get on over to his blog to find out why you are wrong!

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1. One of the top ten biological science blogs, in my humble opinion.

Good Science Writers: Richard Lewontin

 
Richard "Dick" Lewontin (1929 - ) is Alexander Agassiz Research Professor at Harvard University (Boston, USA). He is a well-known geneticist and the discoverer of extensive variation in organisms at the molecular level, with John Hubby [Citation Classic]. (See The Cause of Variation in a Population.)

Lewontin is also one of the authors of the textbook Modern Genetic Analysis. It's impossible to tell who wrote what in that textbook but I strongly suspect that Lewontin is responsible for the material on Random Genetic Drift and Population Size that I quoted last year.

He is the co-author (with Stephen Jay Gould) of The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist program, one of the most important papers in evolutionary biology [Citation Classic]. If you haven't carefully read that paper then you should do so right now.

In addition to his genetics textbook, Lewontin has also written books on The genetic basis of evolutionary change (1974), Human diversity (1995) and The Triple Helix: Gene, Organism, and Environment (2000). He is probably best known for his crusade against genetic determinism as described in Not in Our Genes: Biology, Ideology and Human Nature (with Steven Rose and Leon Kamin) as well as other books. Like several of his colleagues, Lewontin is a frequent contributer to the New York Review of Books and some of his best work has been republished in It Ain't Necessarily So: The Dream of the Human Genome and Other Illusions (2000).

Richard Dawkins did not choose anything from Richard Lewontin for The Oxford Book of Modern Science Writing. I can't imagine why.

The first selection is from Biology as Ideology: The Doctrine of DNA (1991) based on a series of lectures he gave at the University of Toronto in 1990. I was there.

The subject is sociobiology and genetic determinism. He has just finished explaining why there's no such thing as universal human nature—at least not the sort that is postulated by evolutionary psychologists and sociobiologists.

The final step in the sociobiological argument is to say that the genes we possess for universal human nature have been established in us through evolution by natural selection. That is, once upon a time human beings varied genetically in the degree to which they were aggressive, xenophobic, indoctrinable, male dominant, and so on, but those individuals who were most aggressive or most male dominant left more offspring, so the genes that were eventually left in us as a species were the ones that now determine those traits. The argument of natural selection seems a fairly simple and straightforward one for some kinds of traits. For example, it is argued, the more aggressive of our ancestors would leave more offspring because they would swoop down on the less aggressive and eliminate them. The more entrepreneurial would have appropriated more resources in short supply and starved out the wimps. In each of these cases, it is easy to make up a plausible story that would explain the superior reproductive abilities of one type over another.

There are, however, some traits that are said to be universal and that do not lend themselves so easily to this story of individual reproductive advantage. An example, and one that is discussed a great deal by sociobiologists, is altruistic behavior. Why should we be cooperative under some circumstances, and why should we sometimes give up what appear to be immediate advantage for the benefit of others? To explain altruism, sociobiologists advance the theory of kin selection. Natural selection for a trait does not require that individuals possessing it leave more offspring but only that the genes coding the trait be represented in larger numbers in future generations.

There are two ways to increase the representation of one's genes in future generations. One is to leave more offspring. The other is to arrange that even if one does not leave more offspring, one's relative's do so, since close relatives share genes. So, a person could sacrifice his reproduction completely, provided his brothers and sisters left many more children. Thus, his kind of genes would increase indirectly through his relatives and, in this indirect way, he would leave more offspring. An example of this phenomenon is the occurrence of "helpers at the nest" in birds, in which it is said that nonreproductive birds help out their close relatives, who are then able to raise more than the ordinary number of offspring and in the end more family genes are left. To make kin selection work, a sufficient number of excess offspring must be left by relatives. For example, if an individual gives up its own reproduction, its brothers and sisters must have twice as many offspring as ordinarily, but one can at least tell a story that might make this plausible.

We are then left with those traits that do not even benefit relatives differentially, for example, a general altruism toward all members of the species. Why are we good to strangers? For this phenomenon, the sociobiologist provides the theory of "reciprocal altruism." The argument is that even if we are unrelated, if I do you a favor that costs me something, you will remember that favor and reciprocate in the future, and by this indirect path I will succeed in advancing my own reproduction. An example often given is that of a drowning person. You see someone drowning and jump in to save that person even at the risk of your own life. In the future, when you are drowning, the person whose life you have saved will remember, and save you in gratitude. By this indirect path you will increase your own probability of survival and reproduction over the long run. The problem with this story is, of course, that the last person you would want to depend on to save you when you are drowning is someone whom you had to save in the past, since he or she is not likely to be a strong swimmer.

The real difficulty with the process of explanation that allows direct advantage, or kin selection, or reciprocal altruism when one or the other is useful in the explanation, is that a story can be invented that will explain the natural selective advantage of any trait imaginable. When we combine individual selective advantage with the possibility of kin selection and reciprocal altruism, it is hard to imagine any human trait for which a plausible scenario for its selective advantage could not be invented. The real problem is to find out whether any of these stories is true. One must distinguish between plausible stories, things that might be true, and true stories, things that actually have happened. How do we know that human altruism arose because of kin selection or reciprocal altruistic selection? At the very minimum, we might ask whether there is any evidence that such selective processes are going on at the present, but in fact no one has ever measured in any human population the actual reproductive advantage or disadvantage of any human behavior. All of the sociobiological explanations of the evolution of human behavior are like Rudyard Kipling's Just So stories of how the camel got his hump and how the elephant got its trunk. They are just stories. Science has turned into a game.

The second example is from a review of Darwinism Defended: A Guide to the Evolution Controversies by Michael Ruse. It was first published in The New York Review of Books on June 16, 1983 and reprinted in It Ain't Necessarily So: The Dream of the Human Genome and Other Illusions.

If Darwin's revolution was not in proclaiming evolution as a fact, then it must have been in his theory of its mechanism. And what was that theory? Why, "natural selection," of course, which then makes the theory of natural selection the very essence of Darwinism and any doubt about the universal efficacy of natural selection anti-Darwinian. There is a form of vulgar Darwinism, characteristic of the late nineteenth century and rejuvenated in the last ten years, which sees all aspects of shape, function, and behavior of all organisms as having been molded in exquisite detail by natural selection—the greater survival and reproduction of those organisms whose traits make them "adapted" for the struggle for existence. This Panglossian view is held largely by functional anatomists and comparative physiologists who, after all, make a living by explaining what everything is good for, and by sociologists who are self-consciously trying to win immortality by making their own small revolution. Evolutionary geneticists, on the other hand, who have spent the last sixty years in detailed experimental and theoretical analysis of the actual process of evolutionary change, and most epistemologists take a more pluralistic view of the forces driving evolution.

An occasional philosopher has allied himself or herself with the "adaptationists," who give exclusive emphasis to natural selection., and one such, Michael Ruse, makes a characteristic presentation in Darwinism Defended. Darwinism, the representative of objective modern science, is under ideologically motivated attack. Professor Ruse is alarmed: "'Darwinism,' as I shall refer to Darwin-inspired evolutionary thought, is threatened from almost every quarter." Well, not from every quarter, just the right and left flanks, it seems. First, the fundamentalists, supported by Ronald Regan, make a know-nothing assault from the right. No sooner have real evolutionists wheeled to face this attack than they are fallen upon by subversive elements from the left, "biologists with Marxist sympathies" and their "fellow travelers" among philosophers who argue "that any evolutionary theory based on Darwinian principles—particularly any theory that sees natural selection as the key to evolutionary change—is misleadingly incomplete."

Onto the field, mounted upon his charger perfectly adapted for the purpose, with weapons carefully shaped by selection to spread maximum confusion among the enemy, not to mention innocent civilians, comes Professor Ruse, "trying to rescue ... from the morass into which so many seem determined to drag them," "Darwin's life and achievements." In all fairness to Professor Ruse, he did not invent this version of events. The theory that evolutionary science is being brutally beaten and cut with crosses, hammers, and sickles made its first appearance in E.O. Wilson's On Human Nature as the only plausible explanation he could imagine for the failure of sociobiology to achieve instant, universal, and lasting adherence. The situation of evolutionary theory, however, is rather more complex and more interesting than Professor Ruse's Manichaean analysis suggests....

What vulgar Darwinists fail to understand, however, is that there is an asymmetry in Darwin's scheme. When adaptation is observed, it can be explained by the differential survival and reproduction of variant types being guided and biased by their differential efficiency or resistance to environmental stresses and dangers. But any cause of differential survival and reproduction, even when it has nothing to do with the struggle for existence, will result in some evolution, just not adaptive evolution.

The Panglossians have confused Darwin's discovery that all adaptation is a consequence of variational evolution with the claim that all variation evolution leads to adaptation. Even if biologists cannot, philosophers are supposed to distinguish between the assertion that "all x is y" and the assertion that "all y is x," and most have. This is not simply a logical question but an empirical one. What evolutionary geneticists and developmental biologists have been doing for the last sixty years is to accumulate a knowledge of a variety of forces that cause the frequency of variant types to change, and that do not fall under the rubric of adaptation by natural selection. These include, to name a few: random fixation of nonadaptive or even maladaptive traits because of limitations of population size and the colonization of new areas by small numbers of founders; the acquisition of traits because the genes influencing them are dragged along on the same chromosome as some totally unrelated gene that is being selected; and developmental side effects of genes that have been selected for some quite different reason.

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[Photo credit: The photograph of Richard Lewontin is from (Photographs of Participants in the Molecular Evolution Workshop)]

Cuss Level

 
Canadian Cynic scored 19.5% on the Cuss-O-Meter [It's all fucking relative, isn't it?]. This isn't a big surprise, although in person (s)he doesn't swear nearly as much as on the blog.

I couldn't resist entering Sandwalk to see how I do.

Hmmm ... 5.2% of my pages have "cuss" words. I wonder what they are? Does "IDiot" count?

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Good Science Writers: Niles Eldredge

 
Niles Eldredge ranks as one of the best science writers among professional scientists, in my opinion.¹ What I like about Eldredge is that he does not disguise his biases by ignoring all those who disagree with him. Instead, he tries to explain why his view of biology is correct. In this sense he is like Richard Dawkins, although he differs significantly from Dawkins because he (Eldredge) is better at correctly describing the views of his opponents.

Eldredge has written 20 popular books on evolution. Dawkins didn't select anything from Eldredge for The Oxford Book of Modern Science Writing. I can't imagine why.

The first example of Eldredge's writing is from Darwin: Discovering the Tree of Life published in 2005. You'll soon see why I choose it.

Imagine for a moment, Charles Darwin taking one of his daily walks along his beloved "Sandwalk"—that stretch of Kentish gravel Darwin had built along the rear edge of his property at Down House. Outwardly, things were normal. It is mid-June 1858. Darwin picks up his walking stick and goes out the back door of Down House. He is a middle-aged man of forty-nine years—a man of regular habits. Strolling along the Sandwalk, a path lined with bits of chalk, flint, and the occasional fossil from the local Cretaceous bedrock of southeastern England, he regularly took the air, inspected his grounds—and mulled over his life and work. He often found peace walking along the path that lay between his expansive field and his neighbor's adjoining property. And he occasionally felt that exhilaration that comes when sudden insight pops into the brain—a solution to a nagging problem that often did not even seem to be uppermost in one's mind at the moment. Darwin was a highly intuitive man, a man whose capacity for creative thought was perfectly matched by his rigor in testing his ideas with observation and analysis, de rigueur in the freshly minted practice of modern professional science.

But things were far from normal that day. For one thing, his two-year old retarded child, Charles Waring, was battling scarlet fever and near death. His fifteen-year-old daughter Etty (Henrietta) had diphtheria, and Darwin had already lost his dear Annie seven years earlier. She had been the second child, Emma and Charles's first daughter, her death from tuberculosis in 1851 had removed what little was left of his religious faith. All this was enough to make him upset. Though another son, Francis, was to write many years later that his father hardly knew a day when his health was robust and normal, that June day his stomach must have been in even greater turmoil than usual.

But there was more, far more, upsetting Darwin's stomach that day. For Charles Robert Darwin had lived the past twenty-two years as a man with a secret. And this was not just any old garden-variety secret like a clandestine love affair, or commission of a crime (although he often thought of it in those terms). He had traveled the globe as a young man in the 1830s, gentleman ship's naturalist and companion to the Beagle's captain Robert FitzRoy, and by the time he reached home in late 1836, not quite twenty-eight years old, he was convinced that life had evolved through natural causes. He saw that human beings were no exception: we are part of the spectrum of life along with all other species of animals, plants, and the then largely unknown microbial world.

....

Darwin had finally begun writing his magnum opus, to be entitled Natural Selection, on May 14, 1856. As he trudged along the Sandwalk that June day in 1858, he had already amassed some ten chapters, and there was still a long way to go. He was cramming in virtually all the examples he had found in his life that supported his ideas: observations he had made as long ago as the Beagle voyage in the 1830s; analysis by experts of some of the plants, animals, and fossil he had brought back from that epic voyage; but also assorted facts on natural history that he had amassed over the past twenty years from the newly emerging scientific literature—and not least, from the dozens of contacts he had made through correspondence with botanists, zoologists, geologists, and plant and animal breeders throughout the world.

His correspondents included a young man named Wallace who, in part modeling himself after Darwin, had been studying the fauna and flora of the far-flung islands of what are now Malaysia and Indonesia. Darwin had written Wallace, encouraging him to pursue his work, including his thoughts on species.

But, prodigious as this fledgling manuscript on Natural Selection had already become, it was too little, too late. What was bothering Darwin most that June day in 1858 was the arrival a few days before, of yet another letter along with a manuscript from that far-off naturalist and specimen collector, Alfred Russel Wallace. With it came a fresh round in Darwin's own personal "struggle for existence." For Wallace had truly scooped him—outlining a theory of natural selection (though he didn't call it that) so well that Darwin later said he could hardly have written a beter abstract of his ideas himself.

The next example is from Eldredge's excellent book Reinventing Darwin: The Great Debate at the High Table of Evolutionary Theory, published in 1995. This is required reading for anyone who wants to understand the controversies in evolutionary theory.

Eldredge claims, correctly, that the dominant paradigm of the late twentieth century was an over-emphasis on natural selection acting on individuals (or genes). Those who accept this point of view are called Ultra-Darwinians. Richard Dawkins and John Maynard Smith were the ringleaders. The ultra-Darwinians dominated the High Table and only reluctantly invited their opponents to visit on special occasions.

The grand mistake, the cardinal sin that rightly carries automatic suspension of seating privileges at that High Table, is to suggest a theoretical proposition that assumes that the neo-Darwinian paradigm is somehow erroneous. Theories that claim, in some fundamental sense, to be alternatives to the neo-Darwinian paradigm bear an immense (and I believe insurmountable) burdon of proof on their metaphorical shoulders.

Ultra-Darwinians who people the following chapters are fond of accusing their opponents of precisely that crime.: opposing the core of the neo-Darwinian paradigm. That's precisely what Fairfield Osborn did with his theory of "aristogenesis" in the 1920s, and that, too, is the original sin of Richard Goldschmidt. But that's not what the latter day arrivistes at the Table are doing. We are making the milder, far more defensible, claim that one cannot simply take the neo-Darwinian paradigm and extrapolate it all across the board. We simply do not believe in attributing population-level phenomena to such disparate entities as species, higher taxa, social systems, and ecosystems. And that's precisely what the ultra-Darwinians have been up to, claiming all the while that they've actually demonstrated the truth of what was in reality assumed all along: that the neo-Darwinian paradigm of the workings of natural selection within populations is necessary and sufficient to explain evolutionary history. We naturalists agree that it is necessary. But it isn't sufficient.

Naturalists argue that ultra-Darwinians look endlessly at the minutia of population biology, periodically glancing up to apply their principles across the board in simplistic and generally unrealistic ways. Never shy, the ultra-Darwinians persist in telling anyone who will listen that our naturalists' attempts to formulate theoretical propositions on the nature of the evolutionary process are overwrought failures.

It sounds like George Simpson's story of geneticists versus paleontologists all over again. But there has been progress, within both the ultra-Darwinian and modern versions of the naturalist camps. The problem is reconciling the two. Anyone not seated at (or in the immediate vicinity of) the High Table would surely be reminded of the blind men and the elephant. And while the spirit of the present enterprise remains argumentative, I share George Simpson's conviction (and Maynard Smiths' sometime view) that surely someday, somehow a genuine rapprochement will emerge. One day evolutionists will be able to dine in relative harmony at the High Table.

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1. Gould was better when he was alive.

Henry Morgentaler Receives Order of Canada

 
Dr. Henry Morgentaler is a Canadian physician who campaigned for a woman's right to choose abortion. He is responsible for overthrowing the laws against abortion in Canada. Here's the entry in Wikipedia [Henry Morgentaler].

On June 1, 1970, Morgentaler was arrested in Montreal for performing illegal abortions. ... He was acquitted by a jury in the court case, but the acquittal was overturned by five judges on the Quebec Court of Appeal in 1974. He went to prison, appealed, and was again acquitted. Morgentaler first went to the Supreme Court of Canada in an attempt to overturn the country's abortion law in Morgentaler v. The Queen but was unsuccessful.

In 1982, the Canadian Charter of Rights and Freedoms was enacted as part of the Canadian Constitution. Morgentaler was charged again in 1983 in Ontario for procuring illegal miscarriages. He was acquitted by a jury, but the verdict was reversed by the Ontario Court of Appeal. The case was then sent to the Supreme Court of Canada. He was acquitted once again, and the Canadian Supreme Court declared the law he was convicted under to be in violation of the Charter and thus unconstitutional in the case of Morgentaler et al. v. Her Majesty The Queen 1988 (1 S.C.R. 30). This ruling essentially ended all statutory restrictions on abortion in Canada.

Yesterday, Canada Day, Morgentaler was named to the Order of Canada in recognition of his service to women and to the country. Canadian Cynic has a funny posting about the discussion that might have gone on when the committee was making up it's mind about Morgentaler [Fly on the wall, Order of Canada edition]

As you can imagine, not everyone in Canada is pleased about this award. The (Not Progressive) Conservative government under Prime Minister Stephen Harper was among the first opponents of women's rights to speak out as reported in the Globe & Mail [Cheers, jeers greet Morgentaler's honour].

The Harper government was quick to distance itself from the announcement that Henry Morgentaler, the controversial abortion doctor who changed the face of health care in the country, was named on Tuesday to the Order of Canada.

The Tories, no doubt sensing a brewing backlash from their conservative base, issued a brief response outlining how the appointment process has nothing to do with the government.

“The Conservative government is not involved in either deliberations or decisions with respect to which individuals are appointed to the Order of Canada,” the PMO statement said.

On the other hand,

But Liberal Leader Stéphane Dion called for politics to be put aside and asked Canadians to look at Dr. Morgentaler's contributions to society.

“Dr. Morgentaler has stood up for a woman's right to choose for his entire career, often at great personal cost and risk,” Mr. Dion's office said in a statement. “The Order of Canada process has been designed to keep politics out of it and I think we should all respect and celebrate the decisions of the panel and the Governor-General.”

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