Field of Science

My collection

I collect these. If you can't figure out what 'these' are, the answers are located to the right of each animal. Two stand out. Which?

Banded mongoose
Genet
Snow leopard
White-faced saki
Red fox
Spotted hyena
A cichlid fish
Striped Hyena
True lemming
Western gorilla
Meerkat
American bison
Loggerhead sea turtle
Mediterranean monk seal
Chicken
Capybara
Sally Lightfoot crabs
Indri
Mungos mungo
Genetta genetta
Uncia uncia
Pithecia pithecia
Vulpes vulpes
Crocuta crocuta
Pundamilia pundamilia
Hyaena hyaena
Lemmus lemmus
Gorilla gorilla
Suricata suricatta
Bison bison
Caretta caretta
Monachus monachus
Gallus gallus
Hydrochoerus hydrochoerus
Grapsus grapsus
Indri indri

Clearance fail

Found this great offer at Toys R Us.



(For more of the same great stuff, go to Failblog.org.)

Ray Comfort demolishes atheist film festival

WorldNutDaily is a precious source of right wing inanity. In

TESTING THE FAITH
Atheists stage festival for anti-religion films
'Evolution: The Musical,' rants by George Carlin, Woody Allen

they report that
What is being billed as the first-ever Atheist Film Festival and featuring a large number of films that largely address religion will be held in San Francisco Sunday – and it lumps Jesus along with Zeno [sic! - I trust they mean Xenu], Flying Saucers, The Flying Spaghetti Monster and Eden.
Perhaps they write Zeno in a manner akin to PZ writing Jebus (i.e. to not take his name in vain, right?), but I find it more likely that they are ignoramuses.

But, to their credit, in the first half of the short article they do their best to report fairly about the film festival, focusing on the facts. Like, it will be in San Francisco this Sunday from noon to midnight (so it ended minutes ago). Then, being the bastion of religious fundieness that they are, they must of course bring in a detractor, and must list this person's credentials to elevate the pending criticism of the film festival to a level that their readers can acknowledge as sufficient to dismiss the whole thing as childish and irrelevant. So who do they bring in? None other than Ray comfort. If you don't know him, let me start by saying that he is one of the most ignorant of all creationists that I have ever heard about. He is the banana-man. He has challenged Dawkins to a debate, offered him $20,000 for all the pain and suffering, and (ta-daaa) he has written a book about how stupid atheists are, and this book, ironically, relegated Dawkins' The God Delusion from Amazon's best-seller list when it was released. So there! Take that for credentials, and take this for rebutting the atheist film festival:

Oh, there's even more about his credentials (I'm actually sort of live-blogging the article as I read it):
Comfort, who works with Living Waters ministry and has argued against atheism at Yale University, debated the issue on ABC's Nightline and has authored some 60 other books, including "God Doesn’t Believe in Atheists," "How to Know God Exists" and "Evolution: the Fairy Tale for Grownups," has told WND it's atheism, not faith, that lacks a foundation in reality. [My emphasis.]
Well, then, with sixty books, which is at least five times as many as Dawkins has written, there's just no contest is there. And, oooh, he has argued at Yale - bulwark of erudition. Can't get much more respectable than that.

Comfort's arguments against atheism are
  1. Evolution is a logical impossibility, because all sexual animals had to evolve a male and a female at the same time, otherwise the species could have kept going, and
  2. If there's no God, then we are not morally accountable.
PZ Myers have dealt with the male-female evolution issue here (it's a singularly asinine claim). As for godly morals:
"I also show that the 'God' issue is moral rather than intellectual. No one needs to prove that God exists. Creation is clear evidence for any sane person that there's a Creator. But if I can convince myself that there is no God, it means I am not morally accountable, and evolution opens the door to a whole lot of sinful delicacies such as pornography, fornication, lying, theft, and of course writing bad reviews for a book I haven't read," he continued.
Call me insane, then. See if I care. I didn't know that there is anything against pornography in the Bible. As for fornication, lying and theft (I'm surprised he didn't mention murder, since that's one of the usual suspects), the moral codes we all possess in that regard do not come from God or the Bible, but are evolved. Bottom line is that people of different religions, and people of none, are just as moral in these regards as Comfort's preferred brand of Christians. In fact more so, as studies have shown in abundance (e.g. Church goers more likely to steal newspapers).

As for the atheist film festival, I'd like to hear from someone who went. Comfort? Stein? Anyone?

Dawkins launches anti-indoctrination summer camp

Richard Dawkins is co-organizing an atheist summer camp. Reading the headline, Richard Dawkins launches children's summer camp for atheists, I at first thought that it sounds as bad as the Christian camps that are so common in the U.S. The fear is that impressionable children will come home indoctrinated, as in "All you have to remember is that Jesus died on the cross for your sins, and if you believe in him you will go to Heaven when you die," as I overheard a very young woman conclude a church class of much younger children.*

But if you read the article you'll see that the emphasis is on children learning to think for themselves - a notion anathema to everything religious.
Camp-goers will be given lessons in rational scepticism, as well as sessions in moral philosophy and evolutionary biology.
The totally mandatory objection from the Church of England sounds thus:
A spokesman for the Church of England questioned Dawkins' decision to stage a summer camp for atheists.

"We would defend the right for anyone to set up an event like this, as long as the young people are happy to attend," he said.

"But in his imitation of the type of youth events that religious groups have been running for years, Dawkins makes atheism look even more like the thing he is rallying against."
So children getting together in the summer, in a confined place, hiking and canoeing, learning something, having fun, etc. means that it looks like religion? Talk about purview. "I did it first, so don't imitate me. Go away," is children speak.


* True story, my friend Jack. True story.

Conservative anti-tolerance on t-shirts

Damn!, WorldNutDaily is one frightening place. They're selling t-shirts with some hardcore conservative slogans. And by 'hardcore conservative', I mean the worst redneck-fundie-Klan-material kind of people. Check out these three:



The general disdain and dismal tolerance for people with different views that conservatives naturally possess really shines in this abyss that WorldNutDaily is.

Gay Pride sponsors

Pepsico sponsors the LGBT Gay Pride in Phoenix, AZ. If you go to Phoenix Pride, wait for the Flash app to load, click on sponsors, and then choose 'Festival Sponsors', you'll get this page:


Pepsico is near the top right.

The AFA has been ranting incessantly against Pepsico for "not remaining neutral in the culture wars," and while I vehemently disagree with the AFA that that is a problem (I also disagree that homosexuality is a problem, btw), the list of sponsors of Phoenix Pride make me wonder why the AFA rails only against Pepsico. Wells Fargo, Jose Cuervo, Bud Light, Orbitz, Smirnoff, Comfort Inn, and Radisson are some of the more well known sponsors. I simply can't wait for the AFA to ask all of these to remain neutral in the culture war that the AFA is so anxious to stir up.

Texas Freedom Parade, Atlanta Pride, and Cleveland Pride are also sponsored by Pepsico. And by Heineken, American Airlines, Audi, Delta, Whole Foods, Time Warner Cable, Petco, Walgreens, Enterprise rent-a-car, and... (wait for it) Coca-Cola. And that's just to name a few.

But the emails I get from the AFA pits Pepsico as the only sinner. What's up with that?

The AFA email says
PepsiCo refuses to give any money, or to show any compassion, to help its employees who are caught in this destructive and aberrant lifestyle. But they give massive amounts of money to help promote the lifestyle.
Well, that would be because only homophobes think this "lifestyle" is destructive and aberrant (how rude can you get?). Pepsico seems to want to promote tolerance towards this minority which is being treated badly by the majority. If Pepsico employees are gay, then I suppose the AFA would want Pepsico to give money to prayer groups to change their sexual orientation?

NCSE reviews ID literature

On the National Center for Science Education's website is a review of Thomas Woodward's Darwin Strikes Back from 2006. Woodward sent me this book as a gift in 2007, but I have never gotten through all of it. It's tiring to read something that distorting. My copy is filled with notes in the margin where I felt Woodward was clearly ignorant of the science. Jason Rosenhouse (of EVOLUTIONBLOG) lists three difficulties with Woodward's book:
  • He presents an inaccurate and caricatured version of evolutionists’ arguments.
  • He does not reference the most scholarly refutations of ID arguments, but focuses instead on short book reviews and popular- level articles.
  • When he discusses the scientific details, he routinely gets important things wrong.
I especially agree with the third of these points; getting the science wrong really is almost expected when the author has no proficiency in the subject (Woodward has a B.A. in History and a Th. M. in Systematic Theology). Honestly, having to refute scientific arguments from someone not well versed in the field is really annoying. Rosenhouse spells it out in his review:
[The representation of taxonomy] is merely a taste of all that is wrong with this book. Woodward makes much of the fact that scientists use strong rhetoric in denouncing the arguments of ID folks. Of course they do. Woodward and his ilk run around the country accusing scientists of the crassest sort of ignorance and incompetence. The ID literature asserts that the common wisdom in every branch of the life sciences, whether in genetics, evolution, paleontology, anatomy, biochemistry and so on, is simply wrong. People study for years to become experts in any one of these disciplines, and then they have to put up with people bearing obvious religious and political agendas completely distorting everything about their subject. Is it surprising that they respond with anger? [My emphasis.]
Seriously!

Currently in transition

This article in the Examiner is a beautiful piece about transitional forms in evolution. Jonathan Montgomery edited a very long tract from TalkOrigins: 29+ Evidences for Macroevolution, and has made it an quick and enjoyable read.

He gives an example of a species currently in transition: the penguins. We know they used to be able to fly, but they are now clearly better adapted for life in the sea.

Whenever I see sea otters in zoos or aquariums I can't help seeing organisms representing a species in transition. Most clearly in my mind is the image of this one otter I saw in New York Aquarium. When moving on solid ground, it just dragged its hind legs over the wet rocks. It was just as efficient, or more, as using them for walking. And in water, it used those hind legs together with its powerful tail for very adroit maneuvers. Give it a while and those otters could end up looking more like seals or sea lions, or something else as well adapted to the niche of the sea.


Click image for source and more otters.

But, as Jonathan Montgomery writes, in fact all species are in transition. Humans too.
The fact is, all living things are transitional. We just don't know what they'll be in the future. All modern animals are only another snapshot. It's just that we happen to be around right now, and we think that because we're here to see it, we must somehow be special.

We're only another link in the chain of life, but what an epic journey that is. This is a strange and wonderful world, and it's astounding to consider that we're a product of it. Embracing our heritage does not rob us of anything. It gives us knowledge, insight, and the power to take control of our future.
How true.

God seeks gap

The John Templeton Foundation has been buzzing in the blogosphere recently. Blogged by Jerry Coyne, PZ Myers, and Richard Dawkins.

The newest Jesus and Mo comic chimes in:


Via Pharyngula.


Disclaimer: The Ph.D. stipend, tuition and fees of yours truly was for the first two years or so paid by a Templeton grant to my advisor, Chris Adami. No further ties exist (but I wish they did).

Featured

It's flattering when people blog about my blog-posts. Doesn't happen often. Makes me suspicious when the blogger also fancies posting half-naked pictures of himself, though. But, at least no outright acrimony this time.

Encore creationism

Suppose the two accounts of creation in Genesis 1 and 2 don't refer to the same event. Suppose they refer to a first one where the Universe, Earth, and animals, including a homo species, were created, and the second was the event where man was imbued with divine genes. Would this 'encore creationism' "resolve the debate [between the "academic Left and the Fundamentalist Right"] with minimal damage and still maintain the integrity of both sides as well as the sanctity of the Bible"?

In an interesting article in the Christian Post, Allan J. Epling proposes that the Bible is indeed a divine text, but that a different interpretation will remove the conflict between the religious right and the scientific community.

Eplings proposes three assumptions to resolve the debate:
Assumption number one: There is a God

Assumption number two: The first two books of Genesis describe two different events that we interpreted in the past as one event that we call "The Creation".

Assumption number three: The Flood of Noah was a catastrophic regional flood, not a global one.
Assumption two implies that after the creation of a primitive man, much later on Adam received the 'the breath of life' from God:
Now imagine another timeline that began about 6000 years ago in the area around the present Black Sea, somewhere in modern Turkey. God came back to Earth and began creating some new creatures in a place the Bible calls "The Garden of Eden". One of these was a genetically superior form of man, named Adam in the Bible, that lived 930 years, was immune to all disease, didn't bear children until past 100 years of age, communicated with God daily, and, according to ancient legends outside the Bible, his body didn't decay at death like present man's does. This was a genetically different man to modern man, separate in species to the "primitive man" that had "evolved" outside the Garden. Both co-existed on the earth in separate locations.
Apparently the idea that the flood was global stems from a mistranslation from the Hebrew bible:
The ancient Hebrew word used for world was "erets" which also means "land", "country", and "ground". Because the ancient Hebrew scribes in the first millennium BC didn't understand the meaning of the statement "All that God created..." they asssumed the word meant world. The word "erets" is used elsewhere throughout the Bible to refer only to land or country, and is only used to mean world in the flood description. Because they didn't know of the two separate creations, they could only assume it meant the original creation and not just the things created in the Garden of Eden. It would be more accurate to substitute the words "land" or "ground" in every case where the word "world" is used in modern translations. This was the "world", the land of Eden, that was destroyed in the flood and now is probably under 600 feet of water in the present Black Sea.
Then, in Epling's scenario, Noah's "divine" line and those primitive humans from outside the 'land of eden' that survived the flood interbred and we are the result of that.

I doubt many are going to be happy with this new interpretation. The Christian fundamentalists won't like this last part, because it implies we are somewhat less than what God intended in the second creation:
It would mean that genetically we all have the DNA of both the man that came out of Evolution, with God's help, and the man Adam that was created in the Garden of Eden.
On the other side of the fence, the atheists will of course never agree to Epling's first assumption, and will continue to interpret everything in the Bible as words of men about God, and not the other way around.

But I do think 'Encore creationism' deserves its own mention among the other types of Christian creationisms. It sounds somewhat like Progressive creationism, but is distinct in the thinking of Genesis 1 and 2 as different events.

A nagging suspicion of evophobia

Every week I get emails with the table of contents from both Nature and Science1, those high impact journals that careers are built on. What I always do, being waaay too busy to read all of it (i.e. the tocs), is to search through them with the term 'evol', and check out the papers and other articles that are about evolution (avoiding stellar and galactic evolution, as well as all things revolutionary). What I have now observed week after week for years is that Nature consistently has many more matches, and thereby articles on evolution, than Science does. Most often Science have none (like this week), whereas I don't recall Nature ever having none. Only once have I seen Science having more matches than Nature.

So what does that mean?

Does it it mean that Science, being an American journal, is more evophobic2 than the British Nature? Just like Americans are (still) more evophobic than the Brits?

I just really, really hope not, but the numbers I have given you showing significantly fewer evolution papers in Science than Nature counted per number of articles in each journal over the last 100 weeks are hard to ignore. Oh! Make that "the numbers that I have not given you."


1 I'm subscribed to several others, but you can go crazy with Bonferroni dealing with that, if you so please.

2 Don't forget where you saw that term first!
Update: Of course the term already exists. I had a (nother) nagging suspicion as I was authoring the above. A quick search turned up more than 300 hits.

Change must come from within

Do watch this video.



"In reality, people are rising up togethe across Iran against the cracdown, in a display unseen since the 1979 Islamic Revolution.

"They are calling for a reformation of the country into a truly democratic state.

"This would change the politics of the Middle East completely."
The Iranian people may turn out to be the force that changes Iran, the Middle East, and thus the World.

More on Diamond, Wemp, and Shearer

In the continued saga of Jared Diamond's story about Daniel Wemp in The New Yorker, here's a nice review of the situation (though it leaves out Biber's linguistic analysis). The author, Craig Silverman, is a friend of Rhonda Shearer, and yet gets away with being impartial:
Let me be clear: I’m not saying that Diamond forged his notes. I don’t think that’s the case in any way, shape or form. My guess, and that’s all it is at this point, is that Wemp spun some tall tales without realizing they could come back to haunt him. One expert quoted in the Science article suggests this was the case:
Anthropologist Pauline Wiessner of the University of Utah in Salt Lake City, a leading expert on tribal warfare in PNG, thinks Diamond was naïve if he accepted Wemp’s stories at face value, because young men in PNG often exaggerate their tribal warfare exploits or make them up entirely. “I could have told him immediately that it was a tall tale, an embellished story. I hear lots of them but don’t publish them because they are not true.”
The part emphasized here is also my best guess of what went on, but it is emphatically not something that Rhonda Shearer agrees with. She is of the persuasion that Diamond fabricated the whole thing for monetary gain (see my discussion with Shearer here).

Orangutans to replace chimpanzees as our closest relative?

ResearchBlogging.orgA quick heads up for those interested in human evolutionary history: In Journal of Biogeography Grehan and Schwartz presents evidence for the hypothesis that the closest living relative of humans is the orangutan, and not the chimpanzee.

The phylogenetic tree of the relationship of these four apes would then look like figure B, rather than the usual one in figure A:


My own beautiful cladograms.

Their conclusion is based on morphological data, rather than molecular data (DNA), and they counter that the well-known percentages of DNA that humans share with other apes are "primitive retentions" (older traits with a deeper evolutionary past shared by a larger group of species). Humans share 98.4% with chimpanzees, 97.5% with gorillas, and 96.5% with orangutans.

The morphological data on which their study is based include features of anatomy, reproductive biology, and behavior. For example, among the great apes only humans and orangutans have thick tooth enamel, long hair, male facial hair, concealed ovulation, a preference for private, face-to-face mating, and an ability to construct shelters and beds.

No doubt this is going to cause a fair amount of debate in the scientific community. Which is great. Stay tuned.

Reference:
John R. Grehan and Jeffrey H. Schwartz (2009). Evolution of the second orangutan: phylogeny and biogeography of hominid origins Journal of Biogeography, in press.

Homosexuality is not a choice

ResearchBlogging.orgWhat are the causes of homosexual behavior in animals? Contrary to what most people probably think, homosexual behavior is not just common in animals, it is catholic.

A new paper in TREE has gotten a lot of press (most papers on sex do, I suspect): Same-sex sexual behavior and evolution, by Bailey and Zuk at UC Riverside.

In their table 2 (email me for copy of PDF) they list a wealth of hypotheses about the nature of homosexual behavior, but I find it very incomplete:

Adaptive explanations: Social glue, Intrasexual conflict, Practice, Kin selection, Indirect insemination, Overdominance, Sexually antagonistic selection
Non-adaptive explanations: Mistaken identity, Prison effect, Evolutionary byproduct, Maladaptation, Infection

I do very much appreciate this list, because so many people insist - consciously or not - that there must be an adaptive reason for homosexuality. There need not be. My own personal, unfounded, suspicion is that homosexuality in humans can best be described as a by-product; hormonal balances in utero that sometimes (say, about 10 percent of the time) shift slightly, changing the preference for sexual partners. But notice that whether an adaptive or non-adaptive hypothesis is supported, they all imply that the animal does not choose to be sexually attracted to one sex or the other. It would be rather hard to argue that fruit flies and penguins choose it (I dare you to try), and if so, it makes me wonder what basis there is left to suppose that humans do.

I said I find the list incomplete, so what missing? This:

The Christian explanation: Choice

It's more than a common idea among American Christian homophobes that homosexual people choose their own sexual desires. For example, one person commented on my post about Safeway posters that "Homosexuals choose a lifestyle, they are not born that way." Which is completely unfounded. There are many Christian prayer groups that try to help homosexuals change their ways (e.g. Exodus International). Their stupid prayer groups does nothing but suppress the nature of homosexuals. Why do I believe that? Because that's what the evidence tells us. The evidence from animals, and the fact that no heterosexual would ever admit that they chose to be heterosexuals, which leaves no argument left that anyone ever chose to be homosexual either.

Reference:
Nathan W. Bailey, Marlene Zuk (2009). Same-sex sexual behavior and evolution Trends in Ecology & Evolution

As they say

Few things make me laugh out loud for real on the interwebs. This comment on Facebook is the first in ages:

Creation science 101, soon it will have begun, the truth for you and me, down in Tennessee

Tennessee has got the crazies. We aren't surprised. Bible belt blockheads.

Jason Groppel, a local teacher is organizing a weekly Creation 101 series at a local church aimed a high schoolers and first year colelge students. Why?
"Studies show that 75 percent of kids raised in Christian homes lose their faith their first year of college. That is why we are gearing the class toward high school and college-age students," he said. "But it is open to anyone truly interested in the topic.
Open to anyone is the good news. Anyone in Clarksville, TN who could make it to First Assembly of God on Fort Campbell Boulevard this Wednesday and ask some good questions. If needed I'd be happy to help with a bunch of questions to raise, even though
Groppel insists the series is not "dogmatic or doctrine-specific, and the classes most definitely are not designed to be debates."
The hell? He makes it sound like avoiding debate is a good thing? But I can see why:
"We just hope to give kids the tools they need to think for themselves and not just accept what they are taught as factual in school science classrooms," Groppel said.
Because they will given tools to enable them to think for themselves. No talking back necessary.

What can the high schoolers expect to learn, then?
"Evolution and creation are both religions — you have to have faith to believe either one of them," said Jason Groppel, a local teacher and member at First Assembly.
The old canard, evolution is a religion, again. From a teacher. Who clearly knows nothing about evolutionary theory. That is pathetic. This is funny:

Linguistic analysis of Jared Diamond quotations

Jared Diamond is being sued for defamation for $10 million, as I mentioned earlier, and now the plaintiffs have upped the ante by bringing in a professor of linguistics who, by the use of corpus linguistics, maintains that Diamond's quotations of Daniel Wemp, on which the story on revenge warfare is based, are highly unlikely to have been uttered in speech, but much more likely to originate from written english. Breathe.

The original story by Diamond is no longer freely accessible at The New Yorker; one now has to be a subscriber, which I'm not. If you are in possession of the full article, please let me know.

Here's the the report by the linguist, Douglas Biber.

Here's an article on StinkyJournalism.org also by Biber, in which he explains corpus linguistics and touches upon Diamond's quotes.

Here's an example from Biber's report of a quote atributed to Wemp:

“ ‘Soll did have a son, but he was only six years old at the time of his father’s death, much too young to organize the revenge,’ Daniel said. ‘On the other hand, my father was felt to be too old and weak by then; the avenger should be a strong young man in his prime. So I was the one who became expected to avenge Soll.’ ”

My comments: First, this particular quote doesn't seem so unlike to have been spoken. That doesn't make up for formal analysis, but I'm just saying... not convincing. Then, because I have not read the original article, I do not know if Daniel Wemp and Jared Diamond conversed in English. If they did, did Diamond say that these are the exact quotes? If not, Biber's argument falls apart. It is easily imagined (but I don't know) that Diamond edited the spoken words for the article to improve readability. On the other hand, it is well known that Diamond speaks 12 languages, and among those Fore - a New Guinea language that could have been the language they spoke together. I don't know. None of this is addressed in Biber's article.

It's going to be interesting if this corpus linguistic analysis will be refuted, and if not if it's even admissible in court, given that the case doesn't get thrown out long before that would take place (as it should be).

Taking Intelligent Design seriously

One Intelligent Design advocate commented on a previous post, asking me to show him/her how I would argue for Intelligent Design, because, in this person's view, that's the only way to understand something, trying to argue for it, as opposed to trying to disprove it. I wholeheartedly disagree with that view, but I don't think there is any danger in giving a theory (scientific or not) one's best shot, so to speak. So here goes my attempt at arguing for ID, in the most honest way that I am able, with a ending explaining why I am not an adherent (but add to that that ID obviously is not a scientific theory, because science is about invoking natural causes, not supernatural ones).

First, contrary to what many anti-ID debaters have argued, it doesn’t matter what the motivations for the origination and adherence to intelligent design are. Many other scientists have begun fruitful research motivated by a desire to elucidate God’s work, and yet no one disagrees that this doesn’t matter, as long as the results are testable and reproducible. I therefore do not think that ID can be dismissed simply because it is religiously motivated.

Second, in anthropology, criminology, and possibly other areas of science, detecting design is a valid and important undertaking. It is valid to ask the question whether a stone of a particular shape was designed (with the intent of function coming before the form of the object), as opposed to appearance by natural causes (fashioned by geological processes, or in the case of living organisms, evolved). Similarly, despite any preconceptions (and lots of evidence that organisms evolve), we can ask whether there is any evidence for prescient design in living organisms. Did some conscious designer (who need not be specified anymore than a crime lab investigator need suggest who the murderer is, when he concludes that death was not an accident) have a hand (and mind) in the origin of any part of what makes up living organisms?

Without initially considering how to detect intelligent design, I think it beneficial to ponder how such evidence would be dealt with statistically. Imagine that some hitherto unexamined system turns out to show evidence of design. This would be breaking news, of course, and suddenly there would be researchers trying to back up as well as demolish the claim of design. If it is found on second look that there is indeed a way that this system could have evolved by natural causes (a claim that would have to be independently tested for good measure), then the hypothesis that a designer was involved would have to be dropped. The two models (design vs. nature) aren’t equal in the sense that so far many biological systems have been shown to be caused by natural processes, whereas none have been shown to be designed, and the burden of proof is therefore on the hypothesis of design. Evidence that the system evolved therefore rules out the hypothesis of design, and best scientific practice is then to abandon the idea of design in this case. On the other hand, if continued research fails to explain the data by natural causes, then the hypothesis grows in strength, as it becomes more and more unlikely that it will ever be falsified. This is not special to claims of intelligent design. Rather, this is the general rule for all research. As is often stated, nothing in the natural sciences can be proven beyond any doubt, but only, as they say in the courtrooms, beyond any reasonable doubt. This doesn't mean, though, that by disproving evolutionary theory we have proved that a designer designed stuff. However, if evolutionary theory were to fall with all at once (that would take a whole lot of odd results from all over the field of biology, and possibly physics, geology, and astronomy as well), then no other scientific theory would be present to take over, and it would thus lend some credibility to Intelligent Design. However, this setback would emphatically not stop scientists from looking for new scientific explanations for the evidence.

So how about it, then? Do we see design in nature? The short, confounding, answer is yes, we see much design in living organisms. Wings really are designed for flying, the immune system is designed to thwart intruders, and Toxoplasma gondii really is designed to infect mammal eyes, hearts, brains, and livers. Further, the teleological inference is that since they appear designed, then they are designed with those functions in mind. It would appear true that the design is prescient, but that is something that would have to be established. The design that can be inferred so far is not that of preconceived plan, but of exceptional fit to function. Again, in order to make the leap from the latter to the former, it has to be shown more probable that it was consciously designed than designed by nature (evolved).

Then how would someone go about proving teleological design? William Dembski and Michael Behe are the only two people who have proposed any such tests. Dembski proposed specified complexity (basically, it’s too improbable to have evolved so it must be designed), and Behe proposed irreducible complexity (this could not have evolved because taking away any component of the system ruins its function). Specified complexity is widely refuted (as I recall, he even himself admitted something to the effect of it not working, but please look that up yourself), but irreducible complexity far less so (but see this post for a rebuttal). The appeal of irreducible complexity is that it is actually (wait for it…) testable. Data can be gathered, and it can be falsified. This is the signifying strength of scientific hypotheses. You can gather data, and that data can serve as evidence for or against the hypothesis. If I hypothesize that flagella could not have evolved, because taking away any of its components would destroy its function, then that’s directly testable. If trying this out molecularly, and it is found that it never works without all components, and that no other components have homologues elsewhere, and that no components have other functions, and if theory and experiments didn't predict that more than one change can in fact occur at the same time, then we can start taking the hypothesis seriously. That would be a problem for evolutionary theory. But as it turns out, flagella (and all other systems looked at) can be split into smaller components that do serve different purposes, and it is possible (even probable) that two changes could occur at the same time, so that alone shoots big holes in irreducible complexity. The same goes for other systems: blood-clotting cascade, eyes, immune system… Anything looked at so far.

And this is the problem for Intelligent Design at the moment (I’m still trying to argue for it here). Some major setbacks have occurred, but who knows, it might be that some clever(er) person comes around one day to show us that all those things in nature that look so designed by some unnamed very intelligent designer are indeed fashioned with those functions in mind, and not in nature. Until then, Intelligent Design, R.I.P.

Related posts:
10 minutes on Intelligent Design
Why teach Intelligent Design?
The red swan hypothesis
Intelligent Design is a failed scientific theory
The big Judge John E. Jones III interview
Khmer Rouge chemistry

Safeway gay pride

The noxious AFA sent me an email encouraging me to send Safeway an email telling them to remain "neutral in the culture war." I just love (to hate) that phrase. They said the exact same thing about Pepsico. Funny, encouraging private companies to be neutral on a topic that they themselves feel very strongly about. Silence the opposition! Whatever.
Safeway wants you to know how proud they are to support homosexuality. In fact, they want you to support it too! [Because, you know, advertising bigotry doesn't really work anymore.]

In Safeway branded stores across America, Safeway is placing large posters encouraging you to celebrate the gay lifestyle with them during the entire month of June. [And by "celebrate", the AFA would like you to think that you'll be up on that bus, half-nude, dancing to techno-music.]

Safeway is dedicating itself to promoting homosexuality. An AFA supporter in New Mexico reported to us that her local store also included a "WE SUPPORT GAY MARRIAGE" poster. When she returned a day later to take a photograph of it, it had been removed because of the huge number of complaints by local customers. [Huh? Linking the charge of Safeway's dedication with the story of Safeway giving in to pressure from homophobes doesn't really make much sense. I suppose the idea is that those repugnant posters will be removed if enough shoppers complain. Sort of like when the ACLU wants biblical references removed from public buildings, except nothing in the consitution prevents private corporations from supporting sexual diversity.]

Safeway owns and operates 1,516 stores in the U.S. Safeway operates under these names: Safeway, Dominick's, Vons, Genuardi's, Randall's, and Tom Thumb. [I'll be shopping at Vons with (gay) pride.]

10 minutes on Intelligent Design

I have just watched this great recording of Ken Miller giving a lecture in front of a room full of students at the Howard Hughes Medical Institute in 2006. The first half is an introduction to evolution, and the second half is about Intelligent Design and the 2005 trial in Dover, PA. Miller is a wonderful lecturer, and it's really worth watching.

As you might recall, I asked Eugenie Scott of the National Center for Science Education, with Miller sitting right next to her, if the NCSE would object to a university professor teaching Intelligent Design in a course on biology. Her answer was that that would be okay at the university level, but not in high school. But that it should not be done in as little as 10 minutes. A lot more time is needed. Doing it in 10 minutes would be a "disservice to science."

Now I have, ironically (for an understatement), just watched Ken Miller do exactly that. In the lecture on my DVD Miller spends 12 minutes and 42 seconds talking about ID (chapters 21-24). He talks about issues related to ID also (trial, religion), but the core aspects of ID are covered elegantly in less than 10 minutes. And here's the real kicker: the students are high schoolers!

So, I don't really know what to think of this, to be honest. The bottom line is that Scott thinks talking about ID for only 10 minutes is not a good idea. At least if it is with the aim of teaching what science is and isn't, even though I did start phrase the question to be about a course in biology, not philosophy. Oh well, I kick myself for not having a better answer on hand.

Light - the vehicle of divinity

Doug Dobney posted this on his blog, and the comment form there doesn't work for me, so I'll post a reply here. His post goes like this:
"If light can diffuse and endure undiminished for half-a-billion years, it can surely do so for ever. This means that all light, from a candle or from a super-sun, sooner or later fills the entire universe. Light is undiminishable, eternal and omnipresent. In every religion that existed these qualities have been recognized as divine. So that we are forced to the conclusion that light - actual sensible light - is indeed the direct vehicle of divinity: it is the consciousness of God." - p. 72-73 The Theory of Celestial Influence (Rodney Collin)
My comment:

Sorry, but this post is inane.

Light is diminishable, not eternal, and not at all omnipresent. Physicists really know a lot now about the nature of light, and I recommend referencing that instead of this hokus pokus. For example, light is absorbed and destroyed when it hits your retina. Also, "super-sun"?!

Besides from that, the syllogism above is clearly invalid:
  • Light is A.
  • Every religion says light is A.
  • Therefore, light is the consciousness of God.
  • Men are idiots.
  • Women say men are idiots.
  • Therefore, idiocy is the direct vehicle of women.
Please.

On top of that, which of all the religions do you choose your 'God' from? Are you going to say that they are all monotheistic, and all really worship the same god?



This idea of using science to validate belief in the supernatural has got to stop. It clearly does not work: many, many scientific findings go directly against any and all religious doctrines. The moment you use science in this way, you have to go all the way. You can't pick and choose. You can do science, and you're free to scientifically test any hypothesis you put forth, however credulous it may appear to everyone else. But you cannot look for scientific facts that you construe to confirm your belief in the divine, and then ignore the rest. This is a very, very common fallacy these days. However, rarely have I seen it done as pathetically as the argument above. It's just wrong on so many levels (but at least wrong).

Invalid name

Trying to register at mylife didn't go so well.



I know it's silly of me, but I'm a tiny bit insulted at the notion that my name is invalid. It's also embarrassing for mylife that they can't handle silly Danish characters. That's not a problem on facebook, for example.

Why teach Intelligent Design?

At the 74th symposium at Cold Spring Harbor Laboratory Eugenie Scott, Barbara Forrest, and Ken Miller each gave talks about Intelligent Design:
  • The evolution of intelligent design
  • The religious essence of intelligent design
  • Deconstructing design—A strategy for defending science
Eugenie Scott at CSHL

During the question session, I had a question:
Me: When I graduate next year and begin as a professor at Harvard I'm planning to teach Intelligent Design in bio class. Is that going to be a problem for the NCSE?
Scott: Why would you teach ID in biology class?
Me: (Hesitating) Because it's a good way of teaching what science is and what it isn't, for instance, and because...
Scott: Yes, you can do that at the university level. You should not be doing that at the high school level. (...) But be aware that you if you do that, you're going to need to spend a hell of a lot of time on it.
Me: I'm gonna spend 10 minutes on it, because that's what it deserves.
Scott: No. Sir, if you do that, you'll be doing a disservice to science, quite honestly.
Miller: And incidentally, congratulations on your appointment.
Scott: But you seriously need to spend a lot of time on nature of science. You cannot just say "here is what it is," and expect the students to absorb that.
I was quite surprised by Scott answering me with question. The answer I gave was not so well thought out. What I should have said, and would have said if she had not interrupted me, is that I'd like to teach intelligent design also because it is something that students might have heard about, but might not be totally clear on. Where should the students learn about it otherwise? From their pastor? By reading Behe, Dembski, and Wells? No, from their biology professor. The professor can ignore it, dismissing it as unscientific, but that will leave more questions unanswered for the students. Unlike what I led Scott to believe by my answer, I do not intend to teach philosophy of science. I do think, despite her warnings, that it can be explained in a very short time why Intelligent Design is not science (though, as I have argued before, I do think the hypothesis that some systems are irreducibly complex is scientific). In fact, relying on the students having the tiniest rudiment of understanding of what science is and isn't (and I did mentioned that I would do it at Harvard), I think Intelligent Design can be shown not to be science within a couple of minutes. The rest of the 10 minutes can then be used to show how proposed irreducibly complex systems could have evolved.

Lastly, let me note that while the hypothesis of irreducible complexity can be tested, I am not implying that if that test fails evolution would have been shown not to work. The reason I say that is that Lenski, Ofria, Pennock, and Adami published a paper in Nature in 2003 showing that what is by definition an irreducibly complex system can evolve. It was done in digital organisms, so the full fossil record was available, providing proof that such systems can evolve by random mutations.
The evolutionary origin of complex features, Lenski, Ofria, Pennock, Adami, Nature (2003), 423, 139-144.

No foregone conclusions, if you please

The British government has made a move to "fund more commercial-orientated research and research in pre-specified areas," which does not bode well for areas such as evolutionary biology, and other core research fields.

If you are a citizen or ex-pat living in the UK, consider signing this petition:
We request the reversal of a policy now being applied by the UK Research Councils. This policy directs funds to projects whose outcomes are specified in advance.
Eck! Go to the site to read the whole text.

Why teach evolution?

Science (June 5, 2009) has a short interview with Eugenie Scott (subscription required), executive director of the NCSE. One question irks me:
Q: Why is it important to teach evolution? Can't doctors and most life scientists do their jobs without accepting evolution?

E.S.: You can be a mechanic without understanding the niceties of the internal combustion engine. [But] wouldn't you rather go to a mechanic who has the big picture?
Why is it important to teach evolution? Because evolution is true. Because it explains why we are the way we are, why we develop from fertilized egg to adulthood and old age the way we do. Because without it we cannot properly understand our own place in nature, and that is one of the most effective incentives for caring about the environment. Because many advances in medical research rely on an understanding of evolutionary mechanisms. Because pests, parasites, and infectious disease cannot be controlled without taking evolutionary dynamics into consideration.

When my car is broken, I trust my mechanic knows what he is doing. How can you trust that if he doesn't understand at least the basics of how the engine works? Perhaps this is not required of everyone who ever works on your motor, but at least some supervisor at the shop should. When I am sick and go to the hospital, I might be treated by people who do not believe in evolution, but I have trust that there is an M.D. around who knows the details of how antibiotics function, and how genetic diversity affects treatments. Both of those require some understanding of evolutionary theory, if not outright belief in it. Medical doctors can believe any crazy things on their day off, but without accepting it in their professional lives they are putting patients at risk.

Brains, muscles, promoters, and selection

A number of interesting evolution papers have come out recently, but I don't have time to write any proper science blog posts. Instead, here's an easy-to-write summary of what I found most intriguing.

Larger brains are not needed for social organization in animals
Based on data from carnivores (cats, dogs, bears, weasels, etc.) and fossils, Finarelli and Flynn (PNAS, May 27, 2009) conclude that no association exists between sociality and encephalization (larger brain volume/body mass ratio) across Carnivora and that support for sociality as a causal agent of encephalization increase disappears for this clade.

Those sexy muscles are bad for the immune system
Lassek and Gaulin (Evolution and Human Behavior, May 22, 2009) reports that testosterone not only leads to bigger muscles in men, but that, it also decreases the number of white blood cells, which are important for immune function. The more muscular men have more sex than weaker men, they found, but they also have worse immune systems than the slimmer ones. Since there is selection for both having lots of sex (sexual selection) and having a good immune response (viability selection), I conclude that women are not good enough at assessing male immune systems. Disappointing.

Duplication of DNA drives rapid evolution of gene expression
The promoter regions of yeast is enriched with tandem repeats, and genes whose expression is controlled by these promoters have increased rates of transcriptional divergence. Preliminary evidence suggests that it affects human evolution in a similar way. Vinces et al. (Science, May 29, 2009).

Group selection not necessary to explain lower parasite virulence
Wild, Gardner, and West (Nature, May 27, 2009) theoretically show that group selection is not needed to explain the reduced virulence of parasites, but that inclusive fitness theory suffices (i.e. selection at the level of the (parasite) organism does explain decreasing growth rates of the parasites).

Wall Street tabloid

I am aware that The Wall Street Journal is a conservative leaning newspaper, but golly! this quote from an article today about Obama's speech in Egypt is just a little too blind when it comes to the Bush administration. Under the headline 'Barack Hussein Bush' they write
He also couldn't resist his by now familiar moral self-indulgence by asserting that he has "unequivocally prohibited the use of torture" and ordered Guantanamo closed. Aside from the fact that the U.S. wasn't torturing anyone before Mr. Obama came into office, his Arab hosts can see through his claims.
The U.S. didn't torture anyone during Cheney's Bush's reign? What the hell was Abu Ghraib all about then? I have read that sentence seven times, thinking that I must be misunderstanding it. Please tell me how to fathom what the real meaning is.

Exotic evolution meetings

Here's a couple more conferences that I would really like to go to. Mostly for the venue, though. They are about evolution, but Greece and Uruguay exert an immense pull on their own.

11th International Congress on the Zoogeography, Ecology and Evolution of Eastern Mediterranean
Irakleio, Crete on September 21 to 25, 2009
Website

150 years of Darwin's Evolutionary Theory: a South American celebration
Punta del Este, Uruguay, on September 2-6, 2009.
Website
Confirmed keynote speakers: Giorgio Bernardi, Daniel Dennett, Douglas Futuyma, Takashi Gojobori, Eviatar Nevo, Francisco Salzano, Emile Zuckerkandl

So, if anyone knows of a good place to apply for money to travel to Uruguay (my first choice), then I shall be waiting to hear from you...

Matt Ridley on ideas having sex

As mentioned a few times already, I have just been to the 74 Symposium at Cold Spring Harbor Laboratory. The many experiences I had there will continue to fill the pages here for quite some time. Now, I'd like to summarize an interesting talk given by Matt Ridley: "When Ideas Have Sex: The Role of Exchange in Cultural Evolution"

Ridley started by comparing two objects that both are made to fit neatly in the palm of a human hand, a stone chipped for throwing, and a computer mouse. The difference is that the stone is made by one brain, while the mouse is made by many brains. Most likely there isn't a single person who could make a mouse. He then gave the example of the steam machine. Six of them, with Watts' the fourth in a line of machines each built on principles of the former. James Watts is often given the credit, but he didn't invent the steam engine any more than Fender invented string instruments. Ridley quoted a Francois (last name?): "To create is to recombine," driving home the point familiar to evolutionary biologists that recombination (a genetics term) generates variation on which novelty is built, and that this is true in cultural evolution as well. He argued that the invention (of appearance) of bipedalism, use of tools, use of fire, and language is not enough to increase cranial capacity to the point where it is today. Instead, he contends, what really required such an astounding, and otherwise disadvantageous increase in cranial volume, was the emergence of exchanges, or trade (yes, several disadvantages to having such a large brain must be overcome: high energetic cost, large skulls leading to high rates of death during birth, high costs of caring for what is basically premature infants). As evidence for this he notes that no animals exchange food. Tests have been made with monkeys, but no matter how hard they try to induce them to trade with each other, they never do. This lead him to the formula that the difference between us and them is one of kind, rather than degree. In humans this in turn led to the sexual division of labor, which is also not observed among other animals. There is not even evidence to suggest that Neandertals divided tasks differently between male and female, while there is evidence that they had language, tools, fire, and walked on two feet. Of course, one could object that Ridley's hypothesis doesn't square so well with the fact that Neandertals had larger brains that humans, though it could be hypothesized (but not tested) that the human brain is different in kind, while not larger than that of Neandertals.

What can be invented and produced further depends on the size of society. The more people can exchange ideas and items, the more technology (i.e. novel products) is created. People who have been isolated from contacts with foreigners, for example on the island of Tasmania with only 4,000 individuals, never developed new tools, but in fact their technology simplified over time. It is the differentiation of professions within society that enables large-scale constructs, like airplanes and electric guitars, none of which could ever be produced if everyone carried out all the same tasks.

Technologies evolve building on top of previous ones, but on top of that similarity to evolutionary biology, technologies may also speciate, as when a subpopulation of E. coli evolves the ability to metabolize citrate, or when dog breeds become so different that they cannot interbreed anymore, as with chihuahuas and great danes (this is at least true if all other dog breeds of intermediate size went extinct). As an example of that Ridley mentioned the internet, which he proposed is about to split into two different things: "What my daughter do [on the internet] is vastly different from what I do." If that's the only example, then I would say that this speciation hypothesis was contentious at best, but if I think about it, computers are so diverse in forms now as to compare with dog breeds, so perhaps I cannot reject the comparison.

Matt Ridley is the author of four books on human nature, and one biography of Francis Crick. His newest book will be on evolutionary economics.

Previous posts on the 74th Symposium at CSHL:
Second day at CSHL
First day at CSHL
74th Symposium at CSHL

The Darwin Myth myth

Another fucked-up book by a crazy, Christian, conservative, creationist: The Darwin Myth: The Life and Lies of Charles Darwin, by Benjamin Wiker, Ph.D. (There's always that Ph.D., but does he have a relevant Ph.D.? Let me look that up... Aha! First google-hit reveals that he is a senior fellow at the Discotute, and that his Ph.D. is in Theological Ethics, of all things odious).
Why Aren't Scientists Allowed to Believe in God? [Huh? Allowed?]

There was a time when most scientists were also deeply religious men. When scientists were not forced to choose between belief in God and the rigorous pursuit of scientific knowledge. [Ask Ken Miller if scientists today are "forced" to be atheist.] But that all ended with Charles Darwin.

(...)

Taking a "warts and all" approach, Wiker not only offers a critical, scientific analysis of Darwin's life and his history-changing theory, but exposes Darwin's ultimate goal: the elimination of God from all science—not just evolution. [A "scientific" analysis of Darwin's writings that resulted in...]

Casting aside Darwinism's politically correct veneer, The Darwin Myth reveals:

The Darwin Myth: Darwin insisted that evolution must be godless to be scientific [Straw-man!!! Who ever said that Darwin insisted this? I'm at an evolution meeting right now, everyone mentioning Darwin's contribution all over the place, and no one ever mentioned anything about a godlessness-requirement.]
Charles Darwin didn't "discover" evolution—he just put his name on it. (It was explored in the 17th Century, long before his time.) [He didn't discover evolution, no. He postulated (and described evidence to support) common descent and natural selection. What of it?]
Although not Darwin's intention, Darwinism provides an open rationale for eugenics, genocide and racism [So does the Bible. So does agriculture. And genocide and racism existed long before Darwin. (But true, it lead to eugenics, which is a disgrace, and which no respectable scientist supports today.)]
Darwin's own theory supported natural slavery—an institution he detested [Evolution does not "support" slavery. It's a scientific theory, not a treatise on ethics (but I fear that someone with a Ph.D. in Theological Ethics sees everything in the light of values).]
Many of his best friends and allies criticized Darwin's theory, and he never definitively refuted their objections [But on the points where Darwin was correct, the criticism have been refuted since, and that's all that matters.]
From Darwin's obsession with making evolution his own to his belief that progress meant the advance of secularized science against religion ["secularized" science equals science - anything that isn't secular is biased by dogma. "Secular science" is a pleonasm], Wiker shows how Darwin's legacy set atheism as the default position of the scientific community and irrevocably divorced God from science. [But atheism wasn't Darwin's concern. That so many scientists, and notably evolutionary biologists, are atheist is not out of a requirement, but because biology can now explain everything the Bible says on the matter in a plausible and testable way. And because those stories in the Bible are insane.]

Current on Darwinius

I'm still at the Cold Spring harbor symposium. Tim White spoke today in part about the Darwinius fossil, and is of the opinion that that wasn't handled too well. Edward Current of course must comment as well.



"Faith is about seeing only the evidence that you wanna see." Priceless. Edward Current always is.

And so is the appearance of Christ on a dogs ass: