Field of Science

Hawking and Benedict XVI, evolutionary biologists

Why is it that the Vatican invites Stephen Hawking to a conference on evolution? If I remember correctly, he is a cosmologist, not a biologist. From the article:
Pope Benedict XVI this morning opened the conference, organised by the Pontifical Academy of Sciences, which will last until next Tuesday. He said that like modern Popes before him, he saw no contradiction between the Christian concept of Creation and science. He cited Galileo, whom, he said "saw nature as a book whose author is God in the same way that Scripture has God as its author." He added: "To "evolve" literally means "to unroll a scroll", that is, to read a book. The imagery of nature as a book has its roots in Christianity, and has been held dear by many scientists."
Except that that old meaning of the word "evolve" is not what it means in contemporary biology. My feeling is that this is the usual way for the Vatican to interpret science: Through the centimeter thick spectacles of preconceived dogmatic conclusions.


Update:
The pontiff also managed this elaborate feat of sophistry (source):
"In order to develop and evolve, the world must first 'be,' and thus have come from nothing into being. It must be created, in other words, by the first Being who is such by essence."

(...)

Moreover, the Pontiff continued, the recognition of a spiritual being prior to the material world "points to the existence of the intellective soul of a free transcendent subject." This, he said, affirms the Christian belief that every person has a soul, which is immortal.
Snort! I wonder if the Pontifical Academy of Sciences (chortle!) has it's own scholarly work on logical reasoning. Aristotle turns in his grave.

Of course the UN and WHO would send me money

Today's email correspondence included this letter from Brazil with my reply at the bottom:

To: "Fabiano de Andrade Caxito" <fcaxito@cidadesp.edu.br>
Subject: Re: Send Your Reply To This Email:sweeptakesdept@live.com

On Fri Oct 31 15:32 , 'Fabiano de Andrade Caxito' sent:

Send Your Reply To This Email:sweeptakesdept@live.com

World Health Organization
Winning Batch No:UHM/768/847

Dear Beneficiary.
This is to notify you that The Codex Alimentarius Commission (CAC), created in 1962 by the Food and Agriculture Organization of the United Nations (FAO), World Bank and the World Health Organization (WHO), Has chosen you by the Health Assembly and Executive Board of health As one of the winner of a Trust Fund for improvement of global public health and food security, by promoting the provision of safer and more nutritious food and contributing to a reduction in foodborne disease.

To help Improve the health conditions, quality standards of nutritious food in the world and to celebrate the 60th anniversary celebration,We are giving out a yearly donation of The ATM Card Value the sum of Five
Hundred Thousand United State Dollars ($500,000.00) to 2 lucky recipients, a Monthly promotion from the W.H.O, UN, WORLD BANK and the EU in accordance with the enabling act of Parliament and supported by the Queen of England.
Fill out the below information and send it to the Payment Remitance Office Via their email contact address:


Yeah, that sounds something the UN and WHO would do. Give out money to random people. And that would of course be coming from Brazil. Why not?

Save the rain forests or feed the hungry?

Whenever I remember, I go to therainforestsite.com and click six links which generates advertisement money of which 100% are used to purchase rain forest, send food to hungry children, etc.



Mostly I click them all (total of 12 clicks), but sometimes I am too busy with something else, and I elect to click just the most important two or three. But which ones are they? How should I prioritize?

    A. Food for the hungry
    B. Free mammograms
    C. Health care for children
    D. Child literacy
    E. Saving rain forest
    F. Food for rescued animals

Please do tell.

Don't you call me an atheist, you

Campbell Brown hosts NO BIAS, NO BULL on CNN, and in this clip she gives Senator Elizabeth Dole of North Carolina the prize for the ugliest campaign ad this time around. Dole makes an accusation that's so vicious and denigrating and everything that's bad that it's just too damn much for Campbell Brown and all those of us who are sick and tired of this ugly election. We are fed up to here taking this bull from the people who are so chock full of bias.

Dole is accusing Kay Hagan of being... an atheist!!! What? How goddamn low can you stoop? Call her a socialist. Call her a vicious lesbian. You can do anything, but lay off calling her an atheist. They don't even even believe in God! I could understand if she said she didn't believe in God, but calling her an atheist is just over the top. Hagan is a freaking Presbytarian! So there, stop those vicious lies, Elizabeth Dole.

Now, with that out of the way we can resume our daily lives full of church-going, prayer, and miracles. Remember, prayer works. It really does. Especially next Tuesday, so stay home all day and pray hard, those of you who root for McCain.

The Tangled Bank

PZ Myers of Pharyngula organizes a biweekly carnival of science blogging called
The Tangled Bank. This time around it's on Neural Gourmet, featuring a lot of posts about biology, but with the impending election, also several posts on the intersection of science and politics.

Obama takes the cake with his infomercial

Everyone has got to see this.



Via ERV.

"I'll let Sarah Palin handle the economy"

My predictions for Obama's first term

I will make a prediction, and know that if it does not come true everyone will forget that I made it. If it does come true, and I predict that my prediction will indeed come true (bonus prediction), then I will be celebrated by all the nutjobs who believe in crazy shit like astrology, tarot, that uttering 'Macbeth' in a theater is bad luck, fortune cookies (wait, those actually work), miracles, prayers, albino amulets, rhinoceros horn for potency, dowsing, angels, et cetera, et cetera.

Back to the prediction...

I have seen into the future, and the future looks grim. A week from now Obama will become our next President-elect in a landslide election [English, Danish], and both houses of congress will be ruled by the Democratic Party. Shortly after taking office, Obama will initiate his secret plan to fundamentally alter the fabric of America as we know it.

As promised, the first thing he will do is raise taxes. Not just for the rich who earns more than $250,000 per year. Everyone will be paying more, regardless of income, and the tax burden will eventually match that of northern European countries [English]. Both large and small companies will be taxed so hard that many lose the incentive to do business, and as a result many companies close down, and are eventually bought up by the state [English, Danish]. This includes all insurance companies (health, home, life, auto, etc.), all banks, and all car manufacturers, which will lead to a sharp decrease in the variety of products available to consumers. Only hybrid cars will be produced.

While hospital visits are going to be free for all [English], most people who really need the attention won't get it, because now everyone is forced to seek medical attention for minor problems such as headaches and hemorrhoids. Also, health care professionals will be working less efficiently, now that there is no longer any monetary incentive to work harder, and because the resurgence of labor unions will make it practically impossible to fire anyone.

Eventually, but definitely within his first term, Obama will have changed American society to a degree where no one no longer sees any incentive to work. Bureaucrats will rule society, and they will make it next to impossible to get anything done. Dissenters will no longer be allowed to publicly convene, and the police will crack down upon anyone who publicly disagrees with the administration's policies. Most newspapers and TV stations will cease to exist, and the rest will become state run under the control and censorship of the government.

Initially Obama will make many changes to save the environment [English], including making it illegal to trespass any and all national parks, state parks, national forests, and wildlife refuges. Hunting any of the government's wildlife will be made a federal offense by August 2009. However, about half way into his first term, Obama will change policy once again, and initiate government run mining, logging, and oil extraction in every corner of America, and most endangered species will go extinct as a result of government sponsored hunting and habitat destruction.

The Obama administration will not only legalize abortion as one of his first major policy changes, but will make it mandatory except for those who have obtained permission to have a child [English, Danish].

The Second Amendment is removed from the constitution in the first half of 2010 [English], which is followed by a sharp increase in crime rates, as people can no longer defend themselves. Criminals will be armed with automatic weapons which formerly belonged to members of the militia. Militias will be outlawed at the same time.

President Hussein Obama, as he will be officially known, publicly announces shortly before his second term, that he is in fact a Muslim, and has been a Muslim since birth [English]. He will claim that reports of him saying that he was a Christian were taken out of context. The government orders that mosques are built in every large city in America, and that all elected officials be sworn in on the Quran [English].

As Joe Biden predicted, Obama will be tested within six months after taking office [English, Danish]. In May 2009, to be exact. After having withdrawn all forces from Iraq and Afghanistan by April, the Taleban and surviving leaders of Saddam Hussein's Bath party take control of the vacated countries, which both launch coordinated attacks on American military bases in the Middle East. American casualties top those of the Vietnam War, as all bases are demolished. Subsequently, six countries in the region, including Iraq, Egypt, and Iran strike Jerusalem and Tel Aviv with long range missiles, destroying all Christian and Jewish historical monuments. Within 3 years from now Israel is divided into a southern zone occupied by Jordan, and a northern zone occupied by Syria. Obama acknowledges the new distribution of land, and negotiates a favorable trade agreement with the newly formed alliance of Middle East Countries. The US supplies the MEC with nuclear weapons technology and raw materials.

Blogs will be outlawed in November 2009.

Christopher Hitchens speaking in Claremont

Christopher Hitchens will be speaking at Pitzer College in Claremont, CA on November 11th. It might be on "social change." Might be on democracy. I'm not quite sure. It just might be a rant about the pathetic status of society.
The purpose of Dining with Democracy is to facilitate discussion, debate, and dialogue about important contemporary political and social issues in a participatory atmosphere, and to bring the leaders of today to inspire the leaders of tomorrow.
I will - probably - be there, mainly because Hitchens is a master wordsmith. All right, really mostly because he is a well-known author and atheist. It is guaranteed to be entertaining. Just take a look at this article in Slate on Palin. Pure Gold.

God Is Not Great: How Religion Poisons Everything, Christopher Hitchens, 2007.

Development shapes evolution in silico

ResearchBlogging.orgWhy are there so few extant phyla or basic body-plans? There are only about 35 phyla, and nine of them include 96% of all living species. There used to be many more, back in the early days of the cambrian explosion, so one has to wonder why so many phyla were singled out for extinction, and just a few have gone on to do very well.

The usual way to learn about our evolutionary history is to look at fossils. Unfortunately, fossils don't tell us very much about how the organisms developed, and this is sad because development is believed to have everything to do with organismal evolution. Comparative molecular biology is useful in tracing the actual events as they unfolded in the past, but it is still very difficult to deduce what really happened, and what caused the appearance of one body-plan instead of another.

Borenstein and Krakauer attempts a third path, namely a computational model of development. This has the obvious advantage that everything that happens is knowable; whatever leads to the origin of a new body plan can be studied in detail. The caveat is then that only the elements that has been put into the model can affect what goes on. In other words, much more control and illumination, at the expense of realism. The challenge is to either make the model as realistic as possible, or make it exactly suitable to answer the question that we are interested in. Here the latter approach is taken.

Their goal is to investigate the effects of developmental bias on evolutionary trajectories, and thus to shed some light on the hypothesis that the evolutionary history of phyla can be partly explained by developmental bias without the need for natural selection. No doubt that everyone on their right mind realizes that natural selection played a huge role giving the evolutionary pathways a direction, but this paper imagines how much direction can be explained without the mechanism of natural selection.

The model they propose is a simple genotype-phenotype map where the mapping is given by a developmental matrix. This matrix describes how the binary genotype (i.e. the genetic configuration) maps onto a phenotype (the complete description of the organism, including morphology, physiology, etc.). What that means is that a genotype through this mapping becomes a certain phenotype, and further that there need not be a one-to-one correspondence between the two. This results in canalization, meaning that several distinct genotypes creates identical phenotypes. Changing between these genotypes has no phenotypic effect, so the genotype is robust to mutations.

The developmental model can be thought of as a set of regulatory genes that are either turned on or off (1 or 0), while the resulting phenotype is the subset of transcription factors that the genes can affect to be expressed or not, thus defining the organism. In between these, the developmental matrix describes how the genes interact, setting the stage for epistatic interactions between the genes.


Figure 1. Pairwise Hamming-distances between organisms within and among phyla.

The main result presented in the study is that by letting the developmental map evolve without natural selection, the disparity between diverging groups (phyla) increases, while the genotypic and phenotypic variance becomes smaller within the groups (figure 1: hamming distance is a measure of how many mutations the two genotypes are away from each other). This is nicely illustrated in figure 2, where the phylogeny has been traced first ancestor to all the varieties present after the organisms have evolved. Notice how lineages with common histories have similar or identical phenotypes.


Figure 2. Phylogenetic tree of evolved organisms.

Developmental bias has the effect of reducing the possible phenotypes to a subset of visible phenotypes. Once development has gone down a specific path, it is forever stuck with that type. The changes that can be made after that fact is much more limited than the changes that were possible given the basal body-plan way back in time. Thus, the idea goes, we have many species within each phylum, but they are all stuck with the basic body-plan of that phylum, forever destined to not to roam far in genotype-space.


Elhanan Borenstein, David C. Krakauer (2008). An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution PLoS Computational Biology, 4 (10) DOI: 10.1371/journal.pcbi.1000202

Plan to kill Obama unraveled

Federal authorities in Tennessee announced today that they have arrested two alleged white supremacists in an alleged plot to assassinate Democratic presidential candidate Barack Obama by driving their vehicle at top speed and firing high-powered rifles at him from their car windows.
They also wanted to shoot and decapitate a large number African Americans.

This is definitely good news. First because thwarting youngsters with plans to murder anyone is always good, but also because it sends a clear message to those retards who will not vote for Obama because he is black: If your problem is that Obama is black, then you're in league with those we fought against in WW2.

And yes, there are plenty of racists out there that will not vote for a black candidate. Remember Tom Bradley? (All right, so I don't remember him anymore than I remember the Beatles, but you get the drift.)

Sources: L.A. Times | Politiken

Palin against democracy now?

The New York Times reports on speaches given by McCain in Ohio, Biden in North Carolina, and Palin in Virginia. From the article:
Ms. Palin also voiced an argument that is gaining currency among Republicans who fear a Democratic landslide on Nov. 4: that the presidency and the two houses of Congress should not all be controlled by a single party.
I find that argument amusing. Is there any chance in Hell that the same argument would be made by Palin or any other republican had both the congress and the White House been controlled by the GOP?

I don't think so!

In fact, the argument is anti-democratic (as against democracy, not the Democratic party), since it suggests that there should be some higher principle determining who controls the houses that is not public opinion. Slippery slope argument.

Diamond bodyguards

I still have to write about my experience with Jared Diamond last Thursday. Keeps on slipping into the future...

But I will share this funny story about one of his two bodyguards. He was a big guy - at least 6 foot and 250 pounds. He stood there close by staring straight out through tight slits, not wavering. Pro.

Later, at the reception, I saw one of the organizers approaching him, asking a question. I imagine she offered him a drink of water or some such, and he seemed to answer in the negative, still staring straight. She came from the side, so he weren't able to see her at all when he answered.

When she withdrew whence she came, he just couldn't help himself taking a peek at her. But I saw him. Just a quick glance to see who he had been talking with. What was the face that went with that voice? For a moment he wavered, taking a break from scanning the bushes for snipers.

How unprofessional!

How endearing.

Albinos hunted for body parts in Tanzania

There are 150,000 albinos in Tanzania, and 27 of them have been killed so far this year because witch doctors need parts of their bodies to fashion into lucky charms (Politiken).

The issue is apparently very big in Tanzania, judging by the number of news articles covering albino killings: news.google.com

That superstition hurts is of course nothing new.
  • In China they believe that consuming rhinoceros horn enhances virility.
  • In Catholicism they believe that eating human flesh and blood strengthens faith.
It's all dumb as heck, and the root cause of these problems is lack of education. There is no more efficient way to lead us all out of the darkness that superstition is than good education for all. Granted, that's easier said than done. So I'll just go ahead and say it, and leave it up to someone else to do something about it.

Danish priests believe in witchcraft

Aalborg Zoo has hired a real witch to entertain children and adults this Halloween weekend.

Denmark doesn't traditionally celebrate Halloween, but I guess it spills over from the US, as does so many other things, like Intelligent Design, the B.S. degree, sitcoms, and the Big Mac.

Anyhow, some Danish priests were serious when they warned parents not to subject their children to a "declared" witch's brew and amulets. They informed that the witch, Dannie Druehyld, has been practicing for years and takes her vocation quite seriously.

Aalborg Zoo responded by saying it is all 100% fun and zero percent religion. [Politiken]

Denmark is very secular society, but let there be no doubt that we have our fair share of crazy people who believes in the occult: Priests. They are about the only ones, though. When I was a teenager and Dungeons & Dragons was a popular role-playing game, some adult christians made an appreciable ruckus about D&D. Children were being led into satanism and away from God by fooling around with what the adults saw as real, while the kids of course knew and proclaimed to be just for fun.

Azusa Pacific University and sex

Azusa Pacific University is an evangelical christian college in SoCal. In their statements about their belief we learn that their motto is "God First," and that they "believe the Bible to be the inspired, the only infallible, authoritative word of God."

How they deal with the glaring contradictions in the Bible is not explained, but not to worry, because we get to read about something much better, namely their views on sex, and it comes with a great surprise in the end:
8. In Scripture, several sexual behaviors are expressly forbidden, which include but are not limited to: fornication, adultery, incest, unnatural sexual intercourse, and homosexual acts (Exodus 20:14; Leviticus 18:7-23, 20:10-21; Matthew 5:27-28; Romans 1:20-27; 1 Corinthians 6:9; Galatians 5:19; Ephesians 4:17-19; Colossians 3:5).

Azusa Pacific University pledges to guide the university community toward understanding and embracing their God-given sexuality as reflected in this statement. Any deviation from a biblical standard of sexual behavior is sin and therefore is an opportunity for repentance, grace, and redemption, so that as a community we might honor one another and glorify God.
In other words, it makes sense to explore fornication, incest, homosexuality, etc. because it leads to God. That would be quite an incentive for prospective students who weren't admitted to UCSB.

Sarah Palin is more incompetent than inexperienced

Sarah Palin has been accused of being inexperienced, and that would arguably be somewhat of a disadvantage as a vice-president. However, recently she has made such a mess on a number of occasions that I would venture that the real problem is not that she is inexperienced, but that she is massively incompetent and scathingly ignorant.

Here are a few quotes in support of this assertion:

Calling Chavez a dictator and fumbling foreign relations
Palin: "through negotiations or sanctions, if necessary, we can pressure dictators like Hugo Chavez to make it clear that they cannot mess with the United States whenever they feel like it."
Chavez: "The poor thing, you have to feel sorry for her," he said with a dismissive wave of his hand. Palin, he said, is "a beauty queen that they've put in the role of a figurine." Associated Press | Politiken

Campaign staff in a rut over her ignorance
"Her lack of fundamental understanding of some key issues was dramatic," said another McCain source with direct knowledge of the process to prepare Palin after she was picked. The source said it was probably the "hardest" to get her "up to speed than any candidate in history." CNN

Inflating foreign policy credentials
Couric: Explain to me why that enhances your foreign policy credentials.
Palin: Well, it certainly does because our-- our next door neighbors are foreign countries. They're in the state that I am the executive of. And there in Russia-- Huffington Post

Ignorance of VP role
But this week, she said one of the vice president's roles is to be "in charge of the United States Senate," which she said would enable her to "really get in there with the senators and make a lot of good policy change." Boston.com

Dumb on domestic issues
Speaking before voters in Colorado Springs, the Republican vice presidential nominee claimed that lending giants Fannie Mae and Freddie Mac had "gotten too big and too expensive to the taxpayers." The companies, as McClatchy reported, "aren't taxpayer funded but operate as private companies. The takeover may result in a taxpayer bailout during reorganization." Huffington Post

New book from professor Ayers

Bill Ayers, professor of education at University of Illinois, Chicago, is set to release a sequel to his memoirs Fugitive Days from 2001. His publisher has announced that Ayers wished it to not be released before the election, and the date has thus been set to November 12th.

You wonder why, right? Why not release it before the 4th, and cash in?

"Obama and I planned the bombing of the Pentagon together. He was very much in on it, and as a radical lefty like myself didn't think twice about being part of it, as long as nobody would get hurt."

Nah, that doesn't sound likely to be in the new book, does it? Obama was 10 or 11 at the time!

My guess is that there isn't anything incriminating about Obama in the book whatsoever, but that Ayers has foreseen that an early release would shift focus from the present issues, which is winning the election for Obama, and allow even more easy shots from the McCain campaign.

Obama is beautiful world

Small coastal town of Obama, Japan has thrown in its support for Barack Obama with this song:

Via Weekend America, where you'll also learn that McCain Correctional Hospital, NC will not be supporting John McCain.

Of course the Vatican knows the stories are ridiculous

Salon also interviewed Bill Maher about Religulous, his new comedy/documentary that came out recently. It is apparently doing much better than Expelled: No Intelligence Allowed did. That one was about the expulsion from academia of those who believe in Intelligent Design, and it flopped big time (hint: it is a big bunch of lies).

Anyway, I haven't seen Religulous yet, but there is a revealing scene described in the interview:
Salon: Well, you've got these two Vatican priests in the film, and one of them, Reginald Foster, is this very funny guy who is totally not defending the most ridiculous aspects of Christianity.

Bill Maher: He's actually debunking them! Here's a guy who lives down the hall from the pope. We saw where the pope lives. And he's just saying, "Ah, they're all just stories." It gave us a real insight that perhaps some of these people who are in the hierarchies of the religions -- they don't really believe it. But they understand that you can't tear it all down for the common man, that people need their stories. It's just amazing that he would say it to me publicly, and on camera.

Society without god

My friend Phil Zuckerman, Professor of sociology at Pitzer College, has a new book out about the godlessness of Scandinavia: Society Without God. The take-home message is that some of the most prosperous nations by any measure are also the most godless. Belief in gods is no necessity for a society to have happy, wealthy, caring, etc. citizens.

There is a review of it on Salon, which is largely favorable, but does reprimand it for basing it's conclusions on perhaps too few data, and for not bringing up the "dark undercurents of Scandinavian life: dismal weather, a heavy tax burden, low fertility, high alcoholism, a suicide rate twice that of America. (Maybe godlessness has its downsides?)"
  • Dismal weather? That's a critique that has anything to do with the topic at hand? Come on!
  • High taxes is of course what keeps a good society running - something that Americans have yet to realize. Scandinavians do complain about the tax burden, but those who are serious are free to move (and some do). The rest stays, and apparently prefer to reap the innumerable benefits that the taxes afford everyone.
  • Low fertility. Is. A. Good. Thing.
  • High alcoholism... I don't know that it is worse than so many other places, but I could believe it. That's a bad thing. But not very bad. Alcoholics don't hate people who don't believe in drinking.
  • The suicide rate is high, that is true. No studies have suggested that it has anything to do with godlessness. It is rather an effect of the long hours of darkness during the winter (I didn't make that up, but I do admit that I am just throwing it out there).
The review ends on this note about imagining living in a society where most people don't believe the story of Noah's Ark is history:
Well, we'll have to imagine it because America will never be that country. And Zuckerman has come up with some good reasons why: our Puritan ancestry; the increased religiosity associated with immigrants and the poor; the mad proliferation of faiths that forces churches to compete for worshippers. In my mind, there's a larger reason. Despite the religious skepticism of our Founding Fathers, the exceptionalism that has marked America's character from the start has always demanded divine corroboration. Take away God, and our destiny doesn't look quite so manifest. The shining city on a hill becomes just another city, just another hill.
Take away God, and your destiny isn't certain. That's an argument that America will never be godless? Convincing who?


Update 10/24:
Phil Zuckerman directed my attention to a list of suicide rates on NationMaster.com.
It is clearly completely bogus that Denmark has a suicide rate twice that of the US:



Update 10/24 a little later:
Louis Bayard wrote me back that he had gotten the information from an article in Time about a book The Scandinavians by Donald S. Connery. Mr. Bayard had "no intent to mislead or offend," he wrote me.


Update 10/27:
Louis Bayard wrote me another email pointing out that the statistics above are for males only. For females the numbers are 11.3 and 4.4 for Denmark and the US, respectively. So, for females the suicide rate is more than twice as high in Denmark.

Obama can't lose

Charlie Cook, political journalist, offers six factors indicating that Obama will win in two weeks:
  1. No candidate this far back two weeks out has ever won.
  2. Early voting is going strong and even if something big happens, those votes are already cast.
  3. The Democrats have a 10% advantage in party registration; in 2004 it was even.
  4. Obama is outspending McCain 4 to 1 in many states.
  5. There is no evidence for the so-called Bradley effect in the past 15 years.
  6. Obama is safe in all the Kerry states and ahead in half a dozen states Bush won.

While I despise the system where the money matters to such an extreme extent in the election, I now realize that many people giving smaller amounts can actually outcontribute the rich donors. As a result Obama raised more money in September than the monthly domestic product of 46 countries ($150 million). So, the lesson is that this voting with your money does not necessarily always favor the GOP.

Give me your questions for Jared Diamond

On Thursday I am invited to a question session before Jared Diamond gives his talk at Harvey Mudd College, and I would like to solicit questions for him from you.

Please go ahead and post a question or two in the comments that you would like me to ask Jared Diamond, and I shall do my best to do so. Or you can email me at bjorn@bjornostman.com.

I will attempt to take some notes and then report back here about the event.

Jared Diamond is of course an American evolutionary biologist, ornithologist, biographer, physiologist, and non-fiction author. Most famous are his books Guns, Germs, and Steel and Collapse (the latter on which he will be speaking Thursday evening), but also The Third Chimpanzee and Why Sex Is Fun, as well as a number of less famous books on diverse scientific topics. He speaks twelve languages. I will present the questions in English only.

My own pet creationist

Alternative blog-post titles:
  • Babu strikes again
  • Cretinist science writer
  • The truth about science in Russia
As an evolutionary biologist with a side-interest in the debate between evolutionists and creationists, I have my own little pet creationist whom I have read a bunch of articles by, and whom I have corresponded with on several occasions.

Babu Ranganathan. Pronounced Ranga-nathan. He is a conservative Christian and a reformed Baptist. At the age of fourteen, Jesus himself entered Babu's heart and converted him from the heathen hindu that he was. He has a B.A. in Bible and Biology (sic) from that über-christian college (can you guess it?) Bob Jones University. You can read his bio here if you scroll to the bottom.

Today he has yet another of his amazingly asinine pieces of pseudo-science mumbo jumbo in Pravda, of all places (Pravda means 'truth' in Russian, lest you forget).

In it, he argues that there really are no transitional fossils. Instead there are fully formed species that scientists interpret as evidence of common ancestry, whereas creationists see them as evidence of common functions used to solve similar problems of design, and neither position can be scientifically proved. It's a familiar outline to those who have read anything by young-earth creationists before.

He starts be defining a true transitional form as a fossil that has two structures that have a similar function, but of which neither is complete nor functional. This is of course hilariously wrong already: No sane person would require a transitional form to lose the use of one function while evolving the other, which would then only be working once the second is fully formed. We are asked to imagine a fish with part fins and part legs, neither of them being of any benefit to the fish, just sitting there ready to be snapped up by a predator until its offspring's offspring's offspring finally evolved proper legs and the ability to walk. I trust it is clear to anyone with half a brain how preposterous this definition is. Additionally, since fully formed isn't defined, this whole definition doesn't work in any way whatsoever.

Babu should be forgiven for not knowing much about science. Bible is his major, and biology is his minor. But he really should not be forgiven for spreading his cretin gibberish when he makes no effort to learn about evolution. I once emailed him in regard to one of his articles about mutation and natural selection (the gist of it being that mutations just aren't the source of variation that natural selection acts on, because... well they just aren't). This was his reply:
Dear Bjorn,

Please review below some prominent quotations from scientists. These quotations are found in Dr. Walt Brown's site: www.creationscience.com . I urge you to look through that website's table of contents. There's much interesting information.

Sincerely,
Babu
The quotes were appended for my perusal, and I looked at a few and wrote back.
They may be prominent quotations from scientists, but not many of them are quotations from prominent scientists. Arthur Koestler, for instance. I mean, why the hell are you quoting him at all? He knew nothing of biology! Also, many of your quotes are from long, long time ago. We did learn a whole lot since then, and you can hardly blame Crow and Nilsson for their views considering they were expressed 50 years ago.

However, your list is long, and I have only been able to look into a few. I do have real science research to do also, you know. I'd like to tell you more about it, but instead I promise to let you know as soon as something is published about it.

I wonder if you know about gene duplication? One idea here, among others, is that when a gene is duplicated, there are two copies of the same gene, and one of them is then free to mutate all it can, while the other one is constrained by selection to keep producing the essential protein. Did you hear about this at all?

Lastly, I must apologize for my tone of voice in some of these emails to you. I am normally a very forgiving and easygoing person, but the truth is I accuse you of either purposefully flat out distorting the truth in the media, or really not being very intelligent while pretending to know something about science. So call me arrogant if you will, but I do in fact look down on people being guilty of either of these two sins.

Until next time,
Bjorn
He was gracious enough to respond with much more calm than I was able to muster:
I have remotely heard of what you are saying. I have not done enough research on it. But, considering that DNA and genetic information cannot come into existence by chance such gene duplication was most probably designed by the Maker as a back-up precisely because mutations over time may destroy one of the sets of genes.In any case, this is no help for your argument, because how did evolution come about when such a complex mechanism as gene duplication was still supposedly evolving. DNA has mechanisms for repairing mutations. If these mechanisms were still evolving, and by chance at that, how could DNA have come into being.

DNA is language. You would not argue that errors in a printing press won't bring about a book written by Skaespeare, but you have no problem with DNA coming into existence by chance. Duplicate genes just add to your problem. There are just more mechanisms for you to explain by chance origin.

One of Skaespeare's books is enough a problem to explain by errors in a printing press, much less two of them! Two sets or duplicates of the same book and you're saying one of the books alone can be subject to unlimited mutations (random changes) and will in time evolve into a totally different book. Not rational. When will this other book express itself? If it does it won't have much to say!

At this point I gave up because I realized which of the two accusations that I made to his face was the correct one. See if you can figure it out for yourself, too.


In Russia they get Babu, while in Pakistan they get Tiktaalik, a fish with legs.

We may be evolving, but I don't give a shit

Paul Ehrlich, professor of population studies at Stanford, puts words on something that I often have thought (Seed, Oct. 7th, 2008). While I study evolutionary biology, and am interested in our evolutionary past, I don't really have a great interest in speculating about our evolutionary future. Partly because there are too many (known) unknowns, and, as Ehrlich says it,
"The fate of our civilization, and maybe our species may be determined by the next five generations. So I don't really give a shit what's happening to our genetic evolution."
He explains that the environment is changing too fast for evolution to be able to save us. Basically, if humans can't cope with the rapid climate change, and other human induced changes to our environment, then evolution won't be able to save us either.
The global climate is changing too violently for DNA to respond by fiddling around with heat regulation and hair thickness; forests everywhere are being clear-cut too quickly for their inhabitants to adjust, and so food chains are coming undone; the collapse of global fisheries has been identified as an imminent calamity; and a nuclear disaster would constitute a catastrophe many orders of magnitude larger than what nature could readily absorb. If any of these nightmare scenarios comes to pass, Ehrlich fears, evolution will be unable to help us. It may be operating faster than we thought, but it's not that fast. Problems like smog and acid rain seem almost quaint, and even to be longed for.
In my opinion, the main lesson from evolutionary biology about our future is that changes in the environment kills. Species go extinct all the time as they buckle under habitat destruction. It's a cruel fact of life, and we can only hope that we are smart enough to take care of the calamity that we have caused by multiplying ourselves, as we were commanded.


In that vein, please click to save our rainforests. You are helping to protect 11.4 square feet of rainforest.

Early retirement

 - I want to strike it rich and retire early.

Who said that? Well, many people do. And even more people have the desire. But suppose they really did it. Consider this true story from our human past, at a key turning point in human evolution four million years ago. The scene is the well known leader ape-man defeats rival clan's leader with a bone in 2001: a space odyssey:

Our hero of the tribe is about to fight the leader of the rival clan as in a flash of genius he picks up a femur lying around and uses it as a weapon to blow his opponent to smithereens. The bone is thrown, and you know the rest of the story.

But back on Earth, still four million years ago, our hero is celebrated as the clan quickly dominates all others perfecting the use of their new found weapon. He now no longer has to do much else that remind people that he invented the club, and they gladly provide him with everything his heart desires. He gets all the best mates, all the best food, and all of it without lifting a finger, because his invention has made his now fast growing clan the richest and mightiest in the Serengeti. He has, in words unfamiliar to him, retired early.

Now consider whether this likely went down this way. Would the rest of the clan really treat him like a king who needn't ever provide for himself ever again as long as he lived? It is arguable that his contribution to the clan was worth so much that the clan should now treat him for the rest of his life. However, nothing actually works like that anywhere in the animal kingdom. Nowhere would apes, or monkeys, or dolphins, or little white mice accept that one of their own could retire early because of what they did in the past. Everywhere but among humans, that is. 

In fact, the individual who invents something which increases the wealth and improves the lives of its conspecifics is exactly that last individual that should retire. If he does, society is now left without one of its smartest individuals, one of their very best inventors. Instead of retiring, our leader should continue to create new inventions, doing what he does best for the betterment of society. In short, retiring is a waste! A waste of ape resources, if you will.

Luckily, it doesn't seem to be case that very many great contributors to society elects to spend the last 50 years of their life in an armchair or snorkeling at the Great Barrier Reef.  I recall that some people did retire early in their life after becoming millionaires in the dot-com bubble, but I wonder how much people like them really could have contributed in any way if they hadn't retired. I can think of many others who chose to continue working even after striking it rich at a young age, and even more who aren't financially able to do so, but who never would either way. Scientists, for example, are not driven by money, but by a desire to learn. At least that is what I have heard, and I could be wrong. If I am, perhaps that's why scientists get such pathetic salaries?

Stolen beach

Good name for a rock band, but an implausible real life scenario, I would think. However, Jamaica is missing 400 meters of beach. The sand has been lifted. I'm so confused. Who would want it? How would they move it? What's left on the beach? What is under sand? Dr. No's bunker? I thought it was just more sand.

The Votemaster

The Votemaster, aka Andrew S. Tanenbaum, runs a site dedicated to providing the most accurate poll on the internet, or something to that effect. He is an American expatriate, professor of computer science in the Netherlands, and runs a website called electoral-vote.com

The updated electoral map from today looks like this:


I'll be looking forward to seeing how that will change following Colin Powell's endorsement of Obama today. 

Right now it looks like Ohio will go to Obama, and while I'd like Obama to just win, I'd also like to see a president win the election losing Ohio. Because that, apparently, has never been done.

Sammy the Whale shark

Speaking of seafood, the multibillion dollar Atlantis hotel in Dubai has somehow acquired a whale shark in their gigantic aquarium. It's a girl named Sammy (!?). The hotel claims that a local fisher who caught it in the wild thought it was sick and proceeded to release it in the hotel's fish tank. Former employees, on the other hand, claim the hotel management always wanted a whale shark as an attraction. The whale shark is listed as vulnerable (that's not good), so it is against international law to keep them in captivity. Atlantis hotel says they were planning the release it as soon as possible.

Seriously, which story sounds more plausible?

There's loads more information about Sammy here:
Hvalhaj fanget på luksushotel
Free Sammy the Shark

Naked kid in a restaurant

My youngest son is nearly two, and, like his older brother, is a total fan of Ultraman (they are half japanese, after all). Every day they go nuts in at home playing Taro and Seven, running, jumping, and punching and kicking stuff and each other. Luckily, no one was hurt™.

This evening we found ourselves with company in a huge Chinese restaurant in Alhambra, Blue Ocean Seafood Restaurant. Always a good sign when a Chinese restaurant is chock full of Chinese people. But the really good thing about it was that it was big and noisy, because that made it possible for all the children to make a lot of noise, and for my youngest to pull off a trick he recently invented: He spills a little bit of water on his shirt, and then starts taking it off, not wanting to wear wet clothes, of course. Then, he takes his little Ultraman figure and runs around between the tables, air-punching and kicking while going "swatch!" without his shirt on, and no one seems to really mind, the waiters least of all.

The food was good, too.

The larger view

My wife is funny. A while ago she was invited to get a free facial treatment, but she really didn't feel like it, because she would have to do before and after photos. Instead she proclaimed "I want to be a model for reflexology." I nearly wrecked the car.

Then, today she was talking to a newcomer who asked her about her education. She answered that she has a Ph.D. in astrophysics, and this person then went on to ask "Then, what do you think about global warming?" As if that was funny enough, she answered "well, the Universe is cooling down."

Perhaps we should all take the larger view, that while the Earth is heating up, the much bigger problem is that the temperature of the Universe is approaching absolute zero?

Talk to your parents about McCain

From Partnership for a McCain-Free White House.


"I'm calling you because I'm considering voting for McCain so that I could take you up on your offer to call you if I'm considering voting for McCain."

Survey for non-theists

Jon Lanman from Oxford University studies atheism and humanism. He is doing a survey on non-theists that's very interesting. Take the survey On Non-theism. (Via Pro-science.)

Philosophy is down the hall, dude

I have a couple of times heard people question the philosophical foundation of science. The argument goes that scientist, naturalists, secularists - people who believe science have real answers about this world we live in - have blind faith that their way of knowing is the right one. This faith is comparable, the argument goes, to religious faith, meaning that it is not based on any logical reasoning or on any sort of evidence. The trust in the scientific method is just as blind as religious faith, and therefore no more valid. The two ways of knowing are thus equal. So they say.

My answer is (and I am aware this is trivial) that knowing based on evidence that the next person can verify is better because it works. Not because of some philosophical reasoning about science and cognition, but because of the results. I trust in the scientific method first because of it's predictive power. It is so clear to anyone that the scientific theories describe what we can observe in great detail, and the progress (for lack of a neutral word) human society has seen is caused by increases in our scientific knowledge. We did go to the moon (no, really!), we can cure infections (if only there was no evolution), the bombs did explode (blame Oppenheimer), and the LHC does work (when it does). The list goes on, of course.

My point here is that all of the scientific results are not, and was not, in need of any philosophical discussion. They would have barged in on our cozy evening with or without philosophical assistance. I don't actually send people away if they do initiate a discussion about the philosophy of science, but I do feel a strong urge to cut them short with a "philosophy is down the hall, dude." I just finished reading Finding Darwin's God by Kenneth Miller. I wanted to read it before the conference I attended a little over a week ago, because Miller was speaking there. I read the first half of it quickly, because it is a beautiful defense of evolution, and an enjoyable read indeed. However, the second half is all Miller's private theology, and I got severely stuck in the middle of it. Miller is a strong defender of evolution - one of the prime witnesses on the Dover trial. I respect him a lot for that. I also respect that he has his own private belief, and would have left it at that if he hadn't gone on in his book to tell everyone how it can unite the scientific and religious ways of knowing.

Miller's argument is that his religion is totally consistent with our scientific knowledge. He is a Roman Catholic, but in his book he never defends the God and myths of Catholicism that I know of. He never even mentions the dogmatic belief in miracles, sainthood, the Papal infallibility, et cetera, et cetera. Instead he yarns about this way in which his religion and science are not opposed, but rather strengthens each other. For complete knowledge, both ways must be followed, he urges. God used evolution to create us, and therefore knowledge of God comes through knowledge of evolution, for example.

But... the problem I have with religion is that I find it all ever so implausible. Even if I were to concede that there might be some god, I certainly wouldn't think that he would be such a jealous, vain, nasty (let's cut this list short, already) being as is so carefully described in the Judeo-Christian scriptures. My reply to Miller is therefore "philosophy is down the hall, dude," because it may be all good and fine as he tells it, but it just doesn't change the fact that religious people believe in crazy stuff every day, and these people are the ones who dictate what religion means in society, not Miller.

Get inflammation here

Thanks, but I think I'll pass.


But you can click here to get it. (Via Nature e-alert.)

Fuck the south

Looking at this election map from 2004, I am reminded of a website I found that gave some voice to the consternation that I felt on seeing Bush reelected, with the apt title of Fuck the South.



It's prose is rather... direct:


"Well this gravy train is fucking over. Take your liberal-bashing, federal-tax-leaching, confederate-flag-waving, holier-than-thou, hypocritical bullshit and shove it up your ass."

Bunkum and balderdash

FactCheck.org of some renown has an early list of the election campaign whoppers of 2008. That is to say, the campaigns have had an especially difficult time with the truth this time around, because there is apparently more than enough material for FactCheck to post more than once before election day, while they usually post it just once a week before. For example:

McCain on Obama:
Sen. Barack Obama has voted to raise taxes on families earning as little as $32,000 per year, that Obama wants to tax your electricity and your heating oil, that he has voted for "higher" taxes 94 times, and that he will raise taxes for 23 million small-business owners. Each of these claims is false.
Obama on McCain:
if McCain had his way, "millions" who rely on Social Security would have seen their investments disappearing in the recent stock market turmoil. He referred to "elderly women" at risk of poverty and said families would be scrambling to support "grandmothers and grandfathers." Balderdash.
It's pronounced 'egregious', and it's a sad state of affairs that it is impossible to campaign for presidency without lying. I come from a small country (Denmark) where tactics like that usually will not go without a rebuttal. So why in the US? I'm all ears.

Visits

As of right now, this blog has had 173 visits from 16 countries. That's 81 unique visitors. 'Sawride.


Click for larger image.

No advice is the best advice


Go here for the rest: PartiallyClips - a Webcomic for Grownups.

Paris for fake prez

You gotta love her kitchen-talk at the pre-party for the after-party with fake prez Martin Sheen.


See more Paris Hilton videos at Funny or Die.

Monkey-marriage

Why not? Why not marry an ape? They're great! 

With marriage comes rights, and with rights comes responsibilities, as Steve Jones, geneticist at University College in London, has argued. He is opposed to the movement that would grant Great Apes status as persons, including the rights that comes with that. The Balearic Islands, an autonomous province of Spain, granted legal rights to all Great Apes in February 2008.

While I disagree with Dr. Jones about human evolution, I do agree that with rights comes responsibilities (e.g. that other people have rights too, and that you need to respect them), and if you aren't able to understand those, then it really doesn't make much sense. However, many humans of course don't understand their rights either. Children, for instance. Yet they have them. Ho hum.

Woman marries gorilla in a conservation effort. Not really funny, but a good idea. By WulffMorgenthaler.

At least she is marrying a silverback, and not a female, so presumably that wouldn't be a problem for right-wing bigots™.

New argument against same-sex marriage: We're not bigots

We are used to the idea that in American Christians are against gay marriage. The Bible says that homosexuality is an abomination, so they cannot allow the states to make marriage legal between two people of the same sex. (Even if they promise not to have sex?) Fair enough, that's their argument. Even if the passage condemning homosexuality (and sex with animals, which makes me wonder why Christians aren't against men being alone with calves) is right next to passages that command we publicly stone our children when they don't behave.

This argument at least is easy to dismiss for an atheist, and other non-Christians.

But now, as reported today in the New York Times, some random couple have come forth with a different argument against same-sex marriage: It's not natural. (Yeah, I know it's not really a new argument.)
"It takes a man and a woman to create children and thus create a family," Mrs. Galloway, 60, told a legislative panel in Connecticut last year as it was considering a bill to legalize same-sex marriage.
"If you can't have children, you may not marry," seems to be the argument. However, to much amusement of mine, the couple explains how they tried to have children, but were unable. (All right, they don't exactly explain how.)
By protecting heterosexual marriage, what "we're trying to do is protect the foundation of society," Mrs. Galloway, a volunteer worker from Trumbull, Conn., said in a telephone interview on Saturday.
The "foundation of society" hinging on the institution of marriage, I gather. The question then is how same-sex marriages would undermine this foundation.
The notion that gender roles are unimportant in raising children is "bunk", added Mrs. Galloway. "It is not an accident that it takes a man and a woman coming together to create a child," she said.
To create a child, no. But to raise it? In some societies children are raised exclusively by women, in others they are raised solely by men once they reach a certain age. In other words, if a gay couple somehow manages to have a child, raising it should not be an issue?
Both sides are armed with sociological studies: one set showing that children prosper better with a mother and father; the other showing that children of same-sex parents are just as healthy and well-adjusted. Connecticut began allowing gay couples to adopt eight years ago.
In other words, no conclusive evidence either way. And yet,
Mr. Galloway, whose father died when he was 3, said being raised solely by women - his mother and his aunts - hindered his development and altered his sense of self-worth.
How does he know how he was raised hindered his development? Or that it altered anything? How does he know how he would have turned out if his father (or another man) had been around? That he's mildly socially retarded could have any number of causes. Perhaps because he was raised as a Christian? Or because of the trauma of losing a loving parent at a young age?

Mr. Galloway adds:
How can you be a bigot when you're looking out for society as a whole?
Because being a bigot means that you are stubbornly convinced of the correctness of your point of view, and prejudiced against those who oppose you. The NYT article does not tell me enough about him to decide whether he's a bigot or not, but I would suggest he is at least deluding himself if he thinks he is looking out for society as a whole. He has no solid evidence that what he supports will make society better, and there is plenty of reason to believe that he is really just a homophobe. If it wasn't because the couple say they aren't:
While they are Christians, the Galloways say they refuse to use religion to defend their view of marriage because it just muddies things. And they insist they are accepting of everyone, regardless of sexual orientation.
Accepting how? To have sex any way they want, but just not to have papers on each other? If two guys are married, precisely how will that undermine the "foundation of society?" To me, the law is the foundation of society, and that law is not written in stone, but can change when society feels it is time. Many people feel now is time to allow two men or two women to marry, so that they may enjoy the same benefits as married heterosexuals, and show the rest of society that they love each other. Three cheers for the Connecticut Supreme Court for ruling that same-sex couples have a constitutional right to marry.

P.S. While married, I personally don't have the urge to proclaim to anyone else that this is my woman, or whatever. I feel that we are married because we have made an agreement between the two of us to stay together and take care of each other. That's enough for me. But we needed the papers for the benefits, so we married.

Templeton, give me the fucking money

I'd like to make it officially known that I would accept a grant from the Templeton Foundation, should they see fit to offer me one. Just in case they stumble on to my blog:
Dear Templeton, please give me your money. If you would do your job and fund my research, then I promise I shall do mine and continue to do the research that I already have in mind. Additionally, I would be willing to muse about science eroding all things superstitious, should you care to print it.

Yours truly, etc...
I say this because of a discussion going on over on Pharyngula about Michael Shermer accepting money from TF for the Origins conference, which I liveblogged earlier. Many people apparently shudder at the thought of being tainted by the Touch of Templeton©, but I personally don't have any such reservations, even after reading John Horgan's account of his own experiences being one of their fellows. It's a great read, and I highly recommend it.

Shermer states his case in a letter posted on Richard Dawkins' site, in case you'd be interested in knowing what went down.

The mission of the John Templeton Foundation is to serve as a philanthropic catalyst for discovery in areas engaging life’s biggest questions. These questions range from explorations into the laws of nature and the universe to questions on the nature of love, gratitude, forgiveness, and creativity. (source)

P.S. I will award a special prize to the first who can tell me where I took the title from.

Non-functional DNA conserved in evolution

ResearchBlogging.orgWhen a stretch of DNA is really important for an organism, natural selection will make sure that it is not changed much from generation to generation. This is termed purifying selection, and whenever it is observed, the conserved DNA is responsible for some function that the organism can't do without.

Conversely, when a stretch of DNA is observed to code for an important function in the organism, it is a pretty solid guess that it is highly conserved by purifying selection. Survival and/or reproduction is difficult* without the function, so any changes to that DNA is not tolerated by natural selection.

There are many examples of this, so there is not a lot of contention over this issue. I mean, there isn't any, at all.

But now two guys at Stanford University has come along and destroyed this pretty picture. McLean and Bejerano have in mice discovered ultraconserved non-exonic elements (stretches of DNA that do not code for a protein), which do not cause a phenotype when deleted (source). In other words, while this DNA is highly conserved, showing strong purifying selection during the evolutionary history of mice, the mice seem to do fine without it. It doesn't seem to serve any function that the mouse can't do without. Astonishing!

What is going on? Surely this DNA must be doing something? McLean and Bejerano will now make a thorough investigation into the matter, and hopefully unravel this mystery.

One suggestion is that the ultraconserved DNA plays a role under some circumstance that the mice are not subject to in the laboratory. After all, the sheltered life of a lab mouse is quite different from that of wild mice. Any number of environmental conditions that are in effect outside the lab and not inside could explain the necessity. Pathogens, perhaps? It turns on expression of genes that produce a venom when the mice are eaten, maybe? Could it be that it is involved in some higher cognitive function that only Douglas Adams knew about?

McLean, Bejerano (2008). Dispensability of mammalian DNA Genome Research

* I know, I know. This is Mission Impossible. Difficult should be a walk in the park.

China dance

The Danish Prime Minister, Anders Fogh Rasmussen, is going on an official visit to China October 20-25. He will be meeting with President Hu Jintao and Wen Jiabao, Premier of the State Council.

Fogh Rasmussen's wife, Anne-Mette Rasmussen, will not be joining him on this trip. This unique opportunity to see China at a level that is permitted only a select few, to meet with world leaders, and to be pampered to the core, she misses because she
  1. is terminally ill,
  2. have to take care of the couple's 9 children who aren't invited,
  3. is politically against her husband going, or
  4. is dancing in the popular TV-show "Vild med dans" ('Crazy about dance').
Could be any one of them, except... that last one is too far out. It is the last one, of course: she will not be going because she has used up too many vacation days at her job, that she now has none left to follow her husband - the Danish Prime Minister - on this official state visit to the most populous nation in the world.

Here she is on the dance floor:

Camelpuncture

There is a great article today in the online version of the Skeptic Magazine, Puncturing the Acupuncture Myth. Harriet Hall, M.D. dismisses that acupuncture has any effect but placebo. If you believe it, then it might work, but only for alleviating symptoms - not for curing anything whatsoever. But it's a great placebo:
Psychologists can list plenty of other things that could explain the apparent response to acupuncture. Diverting attention from original symptoms to the sensation of needling, expectation, suggestion, mutual consensus and compliance demand, causality error, classic conditioning, reciprocal conditioning, operant conditioning, operator conditioning, reinforcement, group consensus, economic and emotional investment, social and political disaffection, social rewards for believing, variable course of disease, regression to the mean.
But more than that - much, much more - is the revelation-like fact that there is such a thing as camelpuncture. Yes, you got that right. Same for cats, and cows, and I guess any pet you like. The question then is whether the camel believes in it. Otherwise the placebo doesn't work!

Shinkansen Obama to choo choo Palin

I know this is a cheap one, but I simply must reiterate what is being said with this excellent picture (via Pharyngula).

As for the presidential debate yesterday, I only heard the last half on radio (don't have TV - and yes, I know I can get a few channels cheap... It's a choice!).

McCain said more than a couple of times that Obama plans to raise taxes, and I didn't hear Obama deny that. I think this is the biggest hurdle for the Obama campaign: explaining why it is important to raise taxes, and how it will benefit everyone. Because it will. However, Americans of course just want more for themselves right here and now, missing the bigger picture as usual.

Best caller ever

This is the best caller ever on THE ATHEIST EXPERIENCE. He asks these stupid questions, and then answers them all by himself. I bow to you, best caller ever.

Evolution and pleiotropy

ResearchBlogging.orgPleiotropy is the effect of one gene affecting multiple traits, as when Drosophila genes are expressed in more than one place during embryogenesis. For a bunch of examples of that, see
Repression and loss of gene expression outpaces activation and gain in recently duplicated fly genes, Oakley, Østman, and Wilson, 2006, PNAS, 103, 11637.

In my own work on computer simulations of epistatic interactions, it is clear that pleiotropy has the effect of changing the phenotype more per mutation than withoput pleiotropy. With pleiotropy, more than one trait gets affected by each mutation. And each trait can potentially be affected by the same amount (i.e. numerical value), so if a mutation affects five instead of one trait, it can change the fitness five times as much. Admittedly, this is a result from simulating a very simple model, but that it has biological relevance is suggested (among other considerations) in a recent Nature paper by Günter Wagner et al. where they measure pleiotropy in mice. They show that a substitution at a QTL has an effect on each trait that increases with the total number of traits affected. While mutations in many genes produces only a small effect on a few traits, those that affect many traits does so with higher effect.
Pleiotropic scaling of gene effects and the ‘cost of complexity’, Wagner, Kenney-Hunt, Pavlicev, Peck, Waxman, Cheverud, 2008, Nature, 452, 27.

The significance of this observation is that once the environment changes, and the population is forced to adapt, those organisms that exhibit much pleiotropy in the genomes can adapt really fast. And that organisms can adapt way faster than we normally imagine became increasingly clear when a paper came out this year about a lizard, Podarcis sicula. This lizard evolved differences in head morphology, bite strength, and digestive tract structure in a very, very short period of time. How short? Ten thousand years? That would be short by evolutionary standards. But no, it took just 36 years! In about 30 generations the lizards evolved larger heads, stronger bites, and cecal valves - a structure in the gut that can constrict, slowing down the passage of food, giving more time for digestion. Behaviorally the lizards changed their diet to include much more plant material, and the morphological changes were adaptations to this new lifestyle. Clearly the lizards became a new species, as they moved into a new niche. You can read more about that all over the web - it deservedly got a ton of coverage - but I recommend Science Daily for this one.
Herrel, Huyghe, Vanhooydonck, Backeljau, Breugelmans, Grbac, Van Damme, and Irschick (2008). Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource PNAS, 105 (12)

In which a leading geneticist makes a fool of himself

Geneticist Steve Jones claims that human evolution has grind to a halt, and that our descendants a million years hence will look just like us. John Wilkins has a nice rebuttal of this ridiculous notion, but I'd like to add that another reason why Jones is off track.

Whether a species evolves or not - change vs. stasis - depends on the environment. For a very short time in evolutionary terms the environment has been relatively stable, but once that changes - and it always does - species change with it.

There are two ways in which humans could slow down their own evolution in such an event: i) keep the effective population size large, or ii) use technology and medicine to minimize the impact of the environment. The former implies the upkeep of a global, sexually mixed society, and the latter the constant use of said technologies. Suggesting that either is certain for a million years is naïve in the extreme.

Natural Selection Fails to Optimize Mutation Rates

ResearchBlogging.orgRich Lenski's group published this paper in PLoS Computational Biology less than two weeks ago:
Clune J, Misevic D, Ofria C, Lenski RE, Elena SF, Sanjuán, R. (2008). Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes. PLoS Comput Biol 4(9). PLoS Computational Biology, 4 (9).

In the Ph.D. program I'm in we are required to give a journal club talk once per semester (the result of which is that that's exactly how many we give), and I chose to do this one for last Wednesday because it is something I worked on briefly in the NK-landscape a while back*.

Clune et al. used AVIDA to investigate if natural selection is sufficient to evolve mutation rates that are close to the static mutation rates that optimize fitness. First they do a bunch of runs with different mutation rates to find which one optimizes fitness, and find a genomic mutation rate of Uopt=4.641 (figure 1). Then they allow the value of the mutation rate to change by mutation, and compare the evolved mutation rates and resulting fitness to that of the static ones. They find that the evolved mutation rate is much lower than Uopt, and that the average population fitness is also much lower than that obtained for Uopt. In other words, a population left to evolve by natural selection does not evolve a mutation rate that benefits the population the most.


Figure 1: Population average fitness of with static mutation rates (solid black line) compared to evolving mutation rates (red and blue dots). Initial conditions were U=1 (red) and U=10-3 (blue).

Their hypothesis to explain this puzzling observation is that selection against the mutational load wins over the adaptive benefit of a high mutation rate. When a population sits on top of a local peak in the fitness landscape, it has two choices: Either evolve a low mutation rate, so that it avoids deleterious mutations, which lowers the average population fitness, or it evolves a high mutation rate, so that it can locate another higher peak somewhere not so far away in genotype space. Their result suggest that the former strategy wins. The short-term effect of minimizing the mutational load wins over the long-term benefit of adaptation.

They then went on to hypothesize that it is the topology of the fitness landscape the decides which of these alternatives wins. In AVIDA the fitness landscape is very rugged, meaning it has many fitness peaks and valleys. They therefore constructed an explicit landscape in which they could manually adjust the size of a valley that the population would need to cross in order to adapt. Since adaptation is fast, they also switched the landscape every 300 generations between two "seasons" (figure 2). This has the effect of needing more beneficial mutations to optimize fitness, resulting in a longer time of adaptation (which leads to better statistics). As can be seen in this figure, when there is no valley, the population does indeed evolve a mutation rate identical to the static optimal mutation rate. But with a valley size of 2 or 3, both the mutation rate and the resulting fitness is lower than that of a population with the optimal static mutation rate.


Figure 2: Explicit fitness landscapes. First and second column show how the fitness landscape alternate between the two "seasons". The third column is the reulting fitness as a function of the mutations rate. Solid line are static mutation rates, and red and blue points are for simulations with evolving mutation rates. The greater the valley is, the harder is is for natural selection to evolve the optimal mutation rate, and it thus fails to optimize fitness when the landscape is rugged.

What does that mean for us? For one thing is means that when using evolutionary algorithms to find solutions to human problems we need to be careful setting the mutation rate so that optimal solutions are found.

It also suggest there is a barrier preventing real populations of living organisms to optimize their reproductive output when their mutation rates can evolve. Mutation rates do vary between species and individuals. When errors are made by the DNA copying machinery during meiosis and mitosis, there are ways to correct for it. How well that is done depends on proteins that are products of genes, that themselves are prone to copying-errors. It is practically impossible to attain a 100% fidelity (i.e. zero mutation rate), but it is in principle straightforward to select for a machinery that allows more mutations to slip through uncorrected. But alas, the landscape dictates the dynamics and prevents high mutation rates.


* In the NK-landscape I found that I could only avoid fixation of a mutator-lcous with zero mutation rate by updating the environment every ten generations. This has the effect of requiring the population to continuously adapt. This was for K=3, which means there is a fair amount of epistasis - the landscape has many local peaks.