27 March 2012

The Clergy Project

In the video below you will find Richard Dawkins speaking with the former pastor Michael Aus, who, rather bravely, came out as an unbeliever at the Reason Rally.
His transition has been facilitated with the help of The Clergy Project (the website, and project of which you can check out by clicking on the title of this blog). The Clergy Project owes its existence, in ways both large and small, to Dan Dennett and two major works of his in recent years. The first is his excellent book, Breaking the Spell: Religion as a Natural Phenomenon and the second is the study he and Linda LaScola did, "Preachers who are not Believers." In both places Dennett describes considerable emotional malaise among priests, pastors who have lost their faith, but essentially have no where to go. The Clergy Project (made possible by a large grant from The Richard Dawkins Foundation for Science and Reason) is an organization that exists to help such pastors with resources, a place to network, and, perhaps just as important, a place to affirm that they are not alone.

If you are a pastor, or know a pastor that might benefit from The Clergy Project, do pass on the link.


Here is the mission statement of The Clergy Project:
The Clergy Project

The purpose of The Clergy Project is to provide a safe haven for active and former clergy who do not hold supernatural beliefs.

The purpose of this “Public Page” is to announce our existence and to reach out to current and former clergy who want to be a part of the group.

The Clergy Project launched a private, invitation only, website on March 21, 2011 with 52 members. Currently it has nearly 200 members.

It originated from a growing awareness of the presence of these clergy and a concern about their dilemma as they moved beyond faith. There were three sources of this awareness and concern:

Stories of the life experiences of former clergy that Dan Barker of the Freedom from Religion Foundation has been collecting over the years;

A preliminary study of “Preachers Who Are Not Believers,” by philosopher Daniel Dennett and researcher Linda LaScola, published in March, 2010 in Evolutionary Psychology and The Washington Post;

Ongoing discussions between Dan Barker and Richard Dawkins, author of “The God Delusion” about the need to help clergy who want to leave the ministry.


The Clergy Project is an on-line meeting place where former and active clergy can talk freely among themselves. “Adam” and “Chris,” still in the ministry, are the moderators; Dan Barker, former evangelical preacher, is the facilitator.

The Clergy Project was made possible through a donation from The Richard Dawkins Foundation for Reason and Science.


A link to Dennett and LaScola's study: http://newsweek.washingtonpost.com/onfaith/Non-Believing-Clergy.pdf

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23 December 2009

A Brunch Film Review: Avatar Part II: A biologist examines Pandora


If Avatar is a film that works for the viewer, a large part of that will be because of the convincing ecology found on Pandora (easily the most stunning creation in science fiction cinema to date). Unlike many sci-fi world creators, it is hard not to think of George Lucas here, Cameron, and his partners at Weta Workshops, ILM and Stan Winston studios (to name just the three large effects houses involved) have put in the time to properly attempt the creation of an entire ecosystem, as well as a convincing anthropology of its native intelligent lifeform. There is certainly a great deal of biological mystery on Pandora (I don't understand its ecosystem fully for instance) however Pandoran ecology all seems so plausible -no surfeit of ecologically inexplicable giants here thank you very much- that even a well trained biologist shouldn't be required to suspend her disbelief in the service of a rewarding two and half hours. And a film that leaves a biologist (like myself) wondering about the evolutionary history of a make believe world without needing to make allowances, and giving passes, is a film going reward in itself.

Pandora is an Earthlike world, though not so Earthlike that humans can breath without aid. (For a detailed account of why this is click here) It is a warm world, or at least the part dominated by the story is and it orbits a gas giant very much like our own Jupiter. The gas giant is probably too much like our own Jupiter, but I will leave all non-biological observations for the astronomically inclined. Pandora is not quite as large as Earth, but large enough to hold an atmosphere capable of trapping heat.

Avatar takes place in what appears to be forests of high photosynthetic productivity. Pandora may have arctic and temperate biomes, but our story takes place in something very like a rainforest. There is a vertical structure to the system, massive canopy trees, and then below a massive complexity to the understory producers. No doubt the books that discuss the planet for other fans will dwell on the film's spectacular fauna, but the structure of that forest is the first step of anchoring the film in reality. Because the makers gave the forest a convincing and diverse understory, as well as the majestic canaopy for its wide shots the world created has a believeable biological depth. It is the brief, or undetailed glimpses of the epiphytes, and ephemerals, of the small game and the creatures of the undergrowth and detritus that will be the unsung heroes of Avatar.

Another compelling detail is the day, night switch in forest ecology that appears to occur on Pandora. Pandora isn't earth, but like Earth, its ecology is not dominated by the same players at all hours of the day and night. But that is probably where the similarities between the two worlds end. The change in players and signals among the players seems more like a pelagic switch on Pandora. Bioluminescence dominates the Pandoran biota. Does this make much sense biologically? At first, I thought it might be a bit of Weta, or ILM or some effects house demonstrating their coolness (and as such it works magnificently) but upon reflection I've come to a different conclusion. Bioluminesence makes some sense considering Pandora does not orbit its solar system's star like Earth. It orbits a gas giant on an outer orbital track. This would mean somewhat reduced exposure to sunlight, and maybe selective pressures pushed toward more intense visual signalling apparatus. Stephen Jay Gould would probably say I am crafting 'just so stories' but regrettably I'm unable to go to Pandora and prove my hypothesis, so just you quiet down ghost of Stephen Jay Gould. The point is that this weird morphological trait, shared by much of the biota (notably absent in at least two of its alpha predators) makes plausible evolutionary sense. We could probably infer from the prevelance among the biota, that bioluminescence is evolutionarily ancient. I suspect that if Grace Augustine's (Sigourney Weaver) research lab had its own Genome Project it would reveal that bioluminescence was actually lost in the alpha predators but that the ghosts of those genes still exist hidden in their genomes. Here the creators have crafted a scientifically believable ecological backdrop. The time and effort that this must have taken is extreme, and it is richly rewarded on screen.



Taxonomy is important and Cameron and his team have given this some thought as well. The plants are not dwelled on enough to examine their taxonomy, but among the land based vertebrate type animals we see at least two major evolutionary families, tetrapods and hexapods, that is four and six limbed types. Hexapods enjoy greater representation in the Pandoran biota (at least in the region where the film takes place). Is this a split similar to the marsupial/placental split in mammals? It isn't discussed. From an evolutionary perspective this would be a fascinating development (oh the research we could do!). On Earth only one major body plan emerged among big land animals, it has been greatly elaborated on, but all vertebrates are basicaly tetrapods. Not so Pandora. The Na'vi, the indigenous people of Pandora, are notably tetrapods. While potentially very interesting, Pandoran morphology is not discussed in any detail in the film, but remains an interesting point of mystery for the serious science fiction fan. There are substantial differences in morphology among the tetrapods and hexapods though both share at least one organ, even if they differ in limb number. I don't want to go to deeply into detail about what is shared, and what is not, because to do so would be to violate spoiler protocols. I will say that there are no evolutionary barriers to plausiblity to this state of affairs. What is clear is that Pandora is a planet that has produced a fascinating biota, that has had a different evolutionary history than our own.

It probably goes without saying that the ethology of the organisms is also meticulously and plausibly created. I will dwell on only one example, the megafaunal predator called a thanator. This intimidating, hexapod, alpha predator, resembles in many ways the big cats of our own planet, except of course for the extra limbs, and the ten senosry quills, attached to flat chitinous plates. There is something insect-like in the quality of its body. It's teeth and claws resemble material found in the chelicerae of spiders, or the stinger of a scorpian. The color of a thanator, an inky blue-black, also hints at some insect like evolutioanry roots. When we see it for the first time it attempts to attack a young Hammerhead Titanothere. Through this vinette we see more of its behaviors (it is a surprise predator, and has an impressive threat display of rattling plates and quills, pulled back lip flaps that reveal a strange set of gums, and a toothy maw). Also terribly crucial to establishing biological reality, we don't see many of these alpha predators in the landscape (this was probably the crucial ecological "flaw" of Peter Jackson's excellent King Kong). Big predators sit atop an energetic knife edge. That is to say consumers (animals that eat stuff and do not produce their own food like plants) are not terribly efficient at aquiring nutrients from their food stuffs. From the base of the food chain, the plants and other producers, to the top of the food chain, the alpha predators, lots of energy is lost by animals as they consume food. If plant consumer X has only managed to acquire 10% of the energy available it becomes immediately apparent that any animal that eats consumer X will need to be eating a lot of X to stay alive. An ecosystem can only support a few such predators (especially if they are "warm-blooded") in a given area.


All of this behavior has the feel of things I've seen in the field. If you have ever watched a bird in your back yard, a coyote in the wild, or had to have a face to face with a big black bear, found fresh mountain lion scat on the trail you use, or nearly been run down by elk, watching the thanotar, or indeed any of the nature in Avatar will seem like authentic nature watching. From climate, to taxonomy, to evolutioanry history Avatar works as a very convincing bit of science fiction.

There are some animals in Avatar that will seem too much like analogues of Earth creatures, the Direhorse will seem too much like our own horses, the Viperwolves to obviously like wild dogs found on Earth and so on through much of Pandora's fauna and flora. I suspect that would be one of the major objections for the avid science fiction fan. It is an echo of the old complaint, "Why so many humanoids?" that science fiction fans have been offering for decades. It is an important objection but one that I think evolutionary theory allows us to dispense with, at least in the broad strokes, as we watch Avatar.

Stephen Jay Gould rather famously put the problem as follows,

"But if I could rerun the tape of life from the origin of unicellular organisms, what odds would you give me on the reevolution of this complex and contingent insect-flower system? Would we see anything like either insects or flowers in the rerun? Would terrestrial life originate at all? Would we get mobile creatures that we could call animals? Fine-scale predictability only arises when you are already 99 percent of the way toward a particular result -- and the establishment of this 99 percent lies firmly in the domain of unrepeatable contingency."


The notion of historical contingency set ideas about progress in evolution on their ears. There was a tendency among both lay people and many working biologists to think of evolutionary processes as an inexorable march toward humanity. It was a kind of recapitulation, in natural terms, of the idea of the Scala Naturae but without all the angels, or a god. Gould thought his ideas about contingency were fairly radical, but his ideas were often not quite as revolutionary as he made them out to be in his less reserved moments. That isn't to say that contingency is unimportant, clearly accidents of history play huge roles in evolutionary history. Allow me to point out an obvious accident that was a massive biotic regime changer. If, Sixty-five million years ago, a large astroid had managed to slide by Earth, you and I are not here to have this little electronic exchange of ideas. No earth shaking astroid impact in the Yucatan Peninsula, means no age of mammals, and no age of mammals means no humans. Likely it would mean 65 million more years of dinosaurs engaging in the business of being dinosaurs. Contingency is important.

But so is convergence, which Gould simply neglected in his analysis (as does Michael Shermer, Gould's most staunch defender on the point of contingency). The philosopher of evolutionary biology/psychology Dan Dennett, and the evolutionary biologist Richard Dawkins have been most articulate in their (mild) critique of Gould's Radical Contingency. But what is convergence in evolutionary biology? Or to put the question as it may be framed in the reader's mind, "what is convergent evolution and how, Mr. Blogger Fanboy, can it help us see the creatures of Pandora as plausible products of evolutionary processes?"

Convergent evolution is a process whereby organisms only distantly related, in evolutionary terms, exhibit similar morphology, or behaviors because their lineages have been exposed to similar selective pressures. That is to say organisms take on similar traits and come to look like one another because they evolved in either similar environments or engaged in a similar ecology. Below is perhaps my favorite example of evolutionary convergence. This looks like a wild dog. It is not.

This is a marsupial, now very likely extinct, that not only looks like a dog but acts like a dog. The similarities between old world canids and the thylacine exist only because they are the products of similar selective pressures. Evolutionary convergence is not at all uncommon. Another text book example is the form of fish, ichtyosaurs and dolphins. All are only distantly related, but all have converged on a similar form because they evolved in a similar environment. Convergent features are something Dan Dennett has referred to as a "good move" or "forced move" in animal evolution. That is to say certain strategies, forms and structures evolve again and again (not precisely copied mind you and bearing the stamp of contingency) because selective processes favor their discovery. Even the rudimentary stages, it appears, of these evolutionary "good moves" offer such advantages, that selection favors elaboration of the trait, strategy, or behavior.

Eyes have evolved independently on Earth at least forty times. They are not identical, but certainly they are identifiably "eyes." Fin like structures have also evolved dozens of times independently. Insulation, endothermy, parental care, pack hunting, complex problem solving intelligence, chemical warfare have all evolved independently several times on Earth. It is the phenomena of convergence in evolutionary processes that makes the flora and fauna of Pandora more than mildly plausible. The animals have the stamp of their evolutionary history all over them. They are not identical to their earthly analogs, but represent another iteration of a "good evolutionary move." Both contingency and convergence are satisfied.

To return to Gould's famous question, would we be here if we could rewind the tape of life to its unicellular beginnings? If by we Gould means big brained mammalian primates, with opposable thumbs, limited body hair, and a penchant for sweets, then the answer is an obvious no. But if by we he means an intelligent, technology using species then the answer is-given enough time- probably yes. Intelligence, like fins, insulation, and wings, is a good evolutionary move that has been hit upon again, and again by evolutionary processes. So if the presence of horse like things bothers you as you watch Avatar think about contingency, but also convergence and maybe that will resolve your dilema.

The AVATAR program hinges on the genetic hybrid avatar bodies, which are clones of their human "drivers," mixed with DNA of the Na'vi. There is an implication here, wholly unexplored by the film, of quite a bit of extreme genetic similarity between Earth and Pandoran life forms. This is harder to explain. Two hypotheses come to mind, and I will leave it you to essay others.

The first is that our genetic code isn't particularly difficult to make. That is to say, given the right chemical environment, early self-replicating molecules will hit upon nucleic acids regularly. DNA/RNA are simply the most stable of the alternatives. If this is so, we can expect this mechanism of heredity (DNA, RNA)commonly wherever we find life- given a certain set of evironmental conditions.

The second hypothesis belongs to Sir Fred Hoyle and Chandra Wickramasinghe, and is referred to as panspermia. This hypothesis predicts that the origin of life is exceedingly rare, but several forms of that life (unicellular) will be extremely hardy and able to survive interstellar travel (provided it is suitably sheltered) in astroids or comets. These bacteria like organisms find themselves blasted out into space during extreme volcanic eruptions, or impact events and then go on to seed other worlds with life. If this is the case the DNA/RNA mechanism might also be somewhat common in our galaxy as these unicellular space travelers would make planet fall and seed evolutionary processes on different worlds. If you think this is far fetched, there are chunks of Mars that have landed on Earth after being ejected by some phenomena. There is even some evidence that at least one of those Martian bits experienced ancient Martian life. So the mechanism isn't implausible. However there is little evidence for it.

As for the great biological mystery (I will not spoil) at the heart of Pandora, I have no explanation. Is it plausible? I don't know. Possible, but contingency would predict the Pandoran system to be rare I think. But I am not bothered. I will remember Orgel's Second Rule (remember to place tongue in cheek) when thinking about it...."Evolution is cleverer than you are."

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07 March 2009

Oklahoma House of Representives oppose Richard Dawkins as speaker at OSU

The Oklahoma House of Representives has issued a Resolution opposing the invitiation to speak, by Oklahoma State University, of Richard Dawkins. A state sponsored, bona fide, Resolution (State of Oklahoma 1st session of the 52nd Legislature, 2009, House Resolution 1015)! In so doing they have demonstrated a complete disregard for concepts like irony, hypocrisy, and unintentional comedy. The Onion could scarcely do a better job of ridiculing the Oklahoma House, or satirizing parochial politics better than the god-squad in Oklahoma.

It is a
A Resolution opposing the invitation to Richard Dawkins to speak on campus; encouraging the University of Oklahoma to engage in a certain discussion of certain scientific theories; and directing distribution.


The state legislature is encouraging a "certain discussion of certain scientific theories?" On what grounds ought they do this? What scientific qualifications do the honorable members of the House possess that they should be offering ideas about what is good or bad science? How certain a discussion I wonder? What certain theories you may ask? Of course you needn't ask because you already know. Besides they inform us very early in their Resolution.

Under the guise of academic freedom, members of the Oklahoma House are trying to force OSU, indeed any university I would guess, that gets public funding to teach either intelligent design (hereafter ID) or straight creationism (hereafter tucked into my ID abreviation because they are one and the same thing). The wording of the Resolution pretends to want to foster a university which is "open to all ideas, and should train students in all disciplines of study and research, and to use independent thinking and free inquiry." This is an assortment of meaningless nonsense. There are obvious objections. What would it mean to be "open to all ideas?" If a professor wanted to teach a course on the therapuetic benefits of bondage gangbangs would Todd Thomsen (the representative who appears to be pushing Resolution 1015) and his gang be open to the possiblities? Would they embrace this fresh, counter-intuitive idea, that would presumbly be short on data, and even shorter on sound methodology? The hypothetical professor's idea is certianly ripe with independent thinking, and encourages free inquiry. Would they support a field course on cryptozoology, that taught the wildlife biology of unicorns, bigfoots, Lochness monsters? Just what is it they want OSU to allow? R1015 is actually short on such specifics but we can infer a great deal of their specific aims by examining that which they aim their extreme antipathy.

All disciplines? What does that even mean? What more can reasonably be added to college curriculae? Clearly our minds must be open to new possiblities, but they should be so open that our brains fall out. That Resolution 1015 singles out Dawkins is something of a surprise, but that it would then attack the science of evolutionary theory, Charles Darwin was not.

You are probably wondering just what R1015 has to say...

WHEREAS, the University of Oklahoma has planned a year-long celebration of the 200th birthday of Charles Darwin and the 150th anniversary of Darwin’s theory of evolution, called the “Darwin 2009 Project”, which includes a series of lectures, public speakers, and a course on the history of evolution; and

WHEREAS, the University of Oklahoma, as a part of the Darwin 2009 Project, has invited as a public speaker on campus, Richard Dawkins of Oxford University, whose published opinions, as represented in his 2006 book “The God Delusion”, and public statements on the theory of evolution demonstrate an intolerance for cultural diversity and diversity of thinking and are views that are not shared and are not representative of the thinking of a majority of the citizens of Oklahoma; and


I must confess that I doubt Todd Thomsen, or the other authors of R1015 have even cracked the cover of The God Delusion or read any thing but quotes of Dawkins "public opionions", nor ever listened to him discuss evolutionary theory. A harsh accusation I grant you, but one born of some unpleasant experiance. Dawkins is in no way obligated to hold an opionion commensurate with that of "the thinking of a majority of the citizens of Oklahoma." Nor is OSU's biology department or its College of Arts and Sciences in any way similarly obligated to parrot the purported sentiments of most of the thinking citizens of Oklahoma. Charges like cultural intolerance, and intellectual intolerance are, when left vague, ultimately pointless. What does it mean specifically to call Dawkins intolerant? The authors of R1015 are not concerned with specifics, just making the charge, and the careless implication.

R1015 demonstrates a decided annoyance with evolutionary theory, Charles Darwin, and any celebration of either or both. It accuses the scientific establishment at OSU of presenting "a biased philosophy on the theory of evolution to the exclusion of all other divergent considerations rather than teaching a scientific concept" not only by inviting Dawkins, but by its focus on Darwin this year. What other divergent considerations? Again the authors glide by it. But we can bet they are not upset by the fact that hypotheses utilizing group selection are not more widely examined, or the novel and engaging ideas of Lynn Marguilis concerning the role of cooperation as a driver of evolutionary trends are not being widely accepted among evolutionary biologists. The reason for this is that those minor scientific arguments (which will be settled by experiental results that are subsequently duplicated in various independent labs) do not claim to be doing anything other than expanding the mechanisms by which evolutionary change happens. ID is exactly the thing with which the authors of R1015, and presumbly most of thinking Oklahoma want to see in the class rooms of OSU. The problem is that pesky scientific method, that ignores ideas, no matter how novel, free wheeling, or paradigm shifting if they come with no data, no experiment, er...well, with absolutely nothing but the earnestness of the their claimants. While the authors don't want to bring up ID, it is the only thing about which they can be talking.

But what has been resolved? (The caps are theirs not mine)

NOW, THEREFORE, BE IT RESOLVED BY THE HOUSE OF REPRESENTATIVES OF THE 1ST SESSION OF THE 52ND OKLAHOMA LEGISLATURE:

THAT the Oklahoma House of Representative strongly opposes the invitation to speak on the campus of the University of Oklahoma to Richard Dawkins of Oxford University, whose published statements on the theory of evolution and opinion about those who do not believe in the theory are contrary and offensive to the views and opinions of most citizens of Oklahoma.

Dawkins has said that most people who think there is an alternative explanation for the diversity of life on are simply ignorant of the facts. His views about evolution are as it happens not opinions per se in the same way that my thoughts on the sun being the center of our solar system are not opinions. It is demonstrable, verifiable fact. Evolution is as demonstrable as heliocentricy. In fact it stands as one of the three great pillars of scientific success in the past 200 years. The other two relativity, and quantum mechanics being found in physics. When more ID nitwits understand those two theories better they will have no choice but oppose them as well. Being offended by facts can happen I suppose, but it won't stop their being true.

1015 further "resolves" that
THAT the Oklahoma House of Representatives encourages the University of Oklahoma to engage in an open, dignified, and fair discussion of the Darwinian theory of evolution and all other scientific theories which is the approach that a public institution should be engaged in and which represents the desire and interest of the citizens of Oklahoma.


OSU's biology department is already engaged in an open, dignified discussion of evolutionary theory and has been for several decades. I do wish they would spell out what they think is unfair about the current approach. Evolutionary biology is a lively field, full of intense inquiry, disaggreement and research. What can we add that isn't already being discussed? If the authors of R1015 would like professor's of biology to teach something they call "the controversy" (IDers prefer to think in terms of a false dichotomy. In their mind there is Darwinian evolution and ID. Here they are utterly wrong. There is currently only evolutionary biology because IDers have produced no science at all). There is no scientific controversy to teach. It seems that simply because some, perhaps sizable, percentage of Oklahomans prefer a literal interpretation of their scripture, the authors of R1015 think science classrooms should waste valuble time on mythology. Sadly for the proponents of R1015 scientific truth is not adjudicated by democratice means.

Opposing Dawkins as a speaker, while at the same time crying over academic freedom, fair and dignified discussions, and asking for free inquiry all seem like counter-productive moves. It would be hard to ignore the fact it also seems utterly inconsistent with the stated goals of the distinguished representatives in question. "Please, we want free inquiry, we want a fair and balanced appraisal of the issues, but...uh...this guy shouldn't be allowed to speak."
Did the authors of R1015 not see this? Apparently not.

Finally R1015 resolves:
THAT a copy of this resolution be transmitted to the President of the University of Oklahoma, the Dean of the College of Arts and Science at the University of Oklahoma, and the Chair of the Department of Zoology at the University of Oklahoma.


This is easily the only intelligent thing accomplished by R1015. They decided to send a copy to the people that offended them. Well done.

Post Script:
Clearly the authors of R1015 are creationists who hold a more or less fundamentalist, literalist position of the bible. As such they are likely completely in the dark about how science works. Only in this way can they think that all that is needed for creationism to be more widely believed among biologists is for more "discussion." The simple fact is that there is just nothing to discuss. The past one hundred and fifty years of research have established evolution as scientific fact. Discussion won't shift that paradigm. The only thing that possibly could cause a change in the scientific view would be actual research that falsified the evolutionary hypothesis. No one is opposeing such research, and I invite the proponents of ID to get well on with it.

If you don't hold a literalist view of your scripture I suppose science is not a threat to your religious views. If you take the position of metaphor, and allegory then what bother is it that we are kin with the rest of the biosphere? There are probably ways to make even greater, more beautiful religious metaphors awaiting you in the sciences. No doubt such a view is more work and all yours to do, but why set your belief system on the tracks of the scientific endeavor? The literalist of the cosmos has already been run down.
Move along, nothing to see here.

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