Monday, November 30, 2009

Trailblazing: The Royal Society's Interactive Timeline of Science

The Royal Society of London is celebrating the beginning of its 350th anniversary in 2010 by releasing free PDFs of some of their most fascinating and influential papers, from Issac Newton's theories on light and color in a letter written in 1672, to James Lovelock's 2008 paper on Geoengineering.  All the papers are shown in chronological order on their Trailblazer timeline, which also includes some short introductions to each work, along with other historical events for context.  

One of my personal favorites is a memoir of Barbara McClintock, a geneticist who made important discoveries regarding gene transpositions and, strangely enough, inspired and shaped a lot of my own research processes and ideas.  Take some time and check these papers out. 

Sunday, November 29, 2009

The Accomodationism Debate

There has been an ongoing debate in the atheist/science communities, about whether religion and scientific theories, most often the theory of evolution, are compatible.  One one side are atheist stalwarts, such as P.Z. Myers and Jerry Coyne, who claim that believing in evolution is incompatible with religion.  On the other side are people like Eugenie Scott, and most recently Michael Shermer.  These "accomodationists" claim that there is no conflict, and that "religion [and] evolution can live side by side" as Shermer has claimed in an editorial for CNN.  Jerry Coyne has gone on and responded to the article on his blog.

But it seems like the two sides are talking about two very different things.  Scientists like Coyne seem to be arguing that we believe the theory of evolution because it follows from the scientific method.  And because religion is based on faith and not evidence, religion is incompatible with someone who uses the scientific method, and therefore should believe evolution.  And so someone who holds a belief in evolution for the right reasons also should not hold religious beliefs.

The accomodationists, however, are arguing the reverse, that someone who holds religious beliefs can also hold a belief in evolution.  If a person who holds religious beliefs begins to believe that evolution is true, does she become more or less rational?  If you're already willing to hold beliefs based on faith, it is now possible for that person to hold other beliefs, be it evolution or fairies, and justification becomes almost irrelevant.  In that sense, I don't think its any more or less irrational for a religious person to believe in evolution than it is to hold religious beliefs in the first place.

That said, I also don't think scientists should be parading around commending religious people who happen to believe in evolution.  At best, those people are capable of scientific thinking, but are unwilling or unable to apply the scientific approach to their religious beliefs.  At worst, they are incapable of taking a rational or scientific approach and they believe in evolution for irrational reasons.

Getting everyone to believe in the theory of evolution should not be the goal.  It should be scientific literacy, and the ability to think critically.  And that is incompatible with holding religious beliefs, if you're willing to apply the same standards to all of your beliefs.

Friday, November 27, 2009

Intelligence Squared Debate: Is Atheism the new Fundamentalism?

The next Intelligence Squared debate considers the motion:  "Atheism is the new Fundamentalism" this Sunday, November 29th, at 7:00pm GMT (that's 2:00pm Eastern time).  It pits Richard Dawkins and A.C. Grayling (against the motion, obviously), against Richard Harries, the former bishop of Oxford, and Charles Moore, former editor of The Daily Telegraph, at Wellington College, Berkshire. It will be chaired by the Headmaster of Wellington Anthony Seldon.  It's also the first I2 debate that will be live-streamed, right here, starting the live feed at 6:45pm GMT (1:45pm Eastern).

There is also a twitter hash tag, #iq2atheism, where you can post questions that may be posed to the panel during the Q&A session.  

I urge everyone to tune into this one if you're not stuck in holiday traffic driving back home (Hopefully I get home in time, driving from New York back to Boston).  I greatly enjoyed the previous I2 debate I watched:  "The Catholic Church is a force for good in the world.", in which Christopher Hitchens and Stephen Fry made Ann Widdecombe and Archbishop John Onaiyekan look completely foolish.

Tuesday, November 24, 2009

Technorati Claim


This is just a post to get my blog up on Technorati. Its a bit difficult to weave the code number into the conversation. Pay no attention to the man behind the curtain :-)

Facilitated Communication Scam

So I read this article on CNN, about Rom Houben, a man who was supposedly misdiagnosed as being in a vegatative state for 23 years, but has been discovered to be conscious, and able to communicate. 

Rom Houben was 23 at the time of the near-fatal car crash in 1983 that left him paralyzed. Doctors presumed he was in a vegetative state following the accident and they believed he could feel and hear nothing.
Neurologist Dr.Steven Laureys of the University of Liege, in Belgium carried out a brain scan using state-of-the art scanning system and discovered that Houben's brain was fully functional.

Sounds like a horrible misdiagnosis, and such a shame for a man to spend 23 years unable to tell anyone that he is actually conscious.  It is horrible, but for a much different reason that is uncovered as we dig further:

In an interview with the UK's ITV news Monday, Rom communicated by typing on a special keyboard attached to his wheelchair, and aided by his carer.
But taking a look at the video, the carer seems to be doing more than just aiding him.  This is known as facilitated communication, and has been shown in most cases to be either a complete scam, or at the very least that the facilitator is unknowingly influencing the supposed communicator.

In some cases, for patients with cerebral palsy, for example, FC is effective in allowing a person with a physical handicap to communicate. However, in many others it has been shown to be the facilitator actually communicating.  One thing about the video suggests to me it's very unlikely that this is real communication from Rom:  sentences are being typed at very high speeds.  Regardless of how functional his brain actually is, his body is still only partially functional.  It's very unlikely he could signal her to type that quickly.  I can't believe that the reporter is actually falling for this without the slightest hint of skepticism. 

If this communication is part of the evidence used to determine this man's consciousness**, than it needs to be properly tested.  James Randi has done test before, and its not complicated:

I went there and I told her, 'If you satisfy me that facilitated communication actually does work, then we'll talk about the possibility of telepathy.' 'You know, there's no need for that Mr Randi, it works, we know that it works.' I made up before I went a bunch of cards with random words on them: 'basket', 'car', 'ball', 'cup', and then with the facilitator sitting there and with the child sitting there, I reached in and took one at random, turned it over; if it said on it, 'car', and I would say to the child, 'The word is car, c-a-r, car' and show the child the card. I would say, 'Now I want you with Florence's help, would you type out the word 'car'. And Florence would take the hand and 'c-a-r' would come out on the tape. We did this eight or ten times. And I would say, 'Now we're going to continue the experiment with one change only. I want Florence to leave the room for a count of 15, and then come back into the room.' So she'd leave the room, and while she was out of the room, I would select a card at random, say to the child, 'The word is 'basket', b-a-s-k-e-t, basket.' Florence would come back into the room, and guess what the child typed? 'Boy', 'man', 'woman', 'brother', 'sister', and when I said, 'No, I'm sorry, all of those are wrong. The facilitator looked down at the keyboard with a determined look on her face and using the child's hand, typed out a message which read approximately, 'I don't like this man from Florida Florence, he's trying to take you away from me. You are my only connection with the world. Florence, please send him away; he's a very bad man.' Now I don't think that Florence thinks that she is doing the typing. I honestly think that Florence believes that the child is doing the typing.

Note that I'm not necessarily suggesting the facilitator is knowingly trying to deceive anyone.  As Randi suggested, in many cases the facilitator is honestly surprised to find out that they are influencing the responses.  It's similar to the ideomotor, or Oujia board, effect, where very tiny movements you don't realize you're making, along with some reason to believe the movements are coming from somewhere else (whether it be a ghost or a partially paralyzed man), can cause you to believe that an object is moving, and you have no influence over that movement. 

Whether this is trickery or an honest attempt to help a paralyzed man, it's a horrible tragedy for a family to be given false hope of the ability to communicate with their loved one, when it's most likely not really him their communicating with.  I would imagine that eventually this FC claim will be tested, and the family's disappointment is going to be very tragic indeed.

If it turns out that this is, in fact, charlatanism, than it is a most disgusting and vile act.  Praying on people's despair and hope of being reunited, in a sense, with a loved one is a gross power play, no different from cold readers like John Edward (a.k.a. The Biggest Douche in the Universe) taking advantage of those mourning their deceased family and friends.  I sincerely hope that isn't the case here.  But more importantly, I sincerely hope the family will be able to emotionally handle learning that this communication is not real, because the evidence suggests it is not.

**The article says that the doctor used "state-of-the-art scanning equipment" to determine that his brain is functional, but consciousness is generally assessed by using standardized behavior tests, such as the JFK Coma Recovery Scale (CRS-R), which tests various abilities such as responding to visual and auditory stimuli, arousal, and ability to communicate.  The article mentions the CRS-R, but is not clear on whether it was used in this case.  The brain scans were only mentioned, and not described in enough detail to consider the validity of the doctor's methods.

Saturday, November 21, 2009

Love This

I love watching someone getting caught up in their own nonsense.  Especially Deepak Chopra:

It's a microcosm of Deepak's entire belief system:  completely inconsistent with reality, and with itself.

Way to entirely miss the point

Billboards and bus ads for atheist and humanism organizations have been around for a while now, both throughout the U.S., and in other countries.  The latest ads by the British Humanist Association touch on a subject that Richard Dawkins talks about in his book, The God Delusion:  that labelling children with their parents' religious beliefs is wrong.**

The message is that calling a child a "Christian child" or "Muslim child", for example, is incorrect.  Children don't have the ability to understand what this label means.  Just as we would never call a child a Democrat or Republican, socialist or capitalist, deontologist or utilitarian, we should not give children religious labels.

I think the message is fairly clear.  It says nothing about atheist children, because that would be equally ridiculous.  Unfortunately, not everyone seems to get the point, including Ruth Gledhill, who wrote an article about the ads on Times Online.  Let's start with the headline:

Children who front Richard Dawkins' atheist ads are evangelicals.

Really?  WTF?

First, the obvious.  THEY ARE NOT FUCKING EVANGELICALS!  It's as if she can't read.  Second, these aren't Dawkins' ads, he is not affiliated with the British Humanist Association.  Nor are they pro-atheist ads, its equally silly to label children as atheists as it is to give them a religious label.

At least she correctly identified them as children. 

The kids in the ad are children of Brad Mason, a Christian pastor.  He says:

“It is quite funny, because obviously they were searching for images of children that looked happy and free. They happened to choose children who are Christian. It is ironic. The humanists obviously did not know the background of these children.”

They happen to choose children who are Christian children of Christian parents, because the majority of people in the UK are Christians.  But again, it doesn't matter, because the kids are not Christians.  Their parents are Christians, and in all likelihood, they will end up being Christians due to that influence, but they don't yet have the capability to make those decisions themselves.

In fact, the BHA said as much, later in the article:

The British Humanist Association said that it did not matter whether the children were Christians. “That’s one of the points of our campaign,” said Andrew Copson, the association’s education director. “People who criticise us for saying that children raised in religious families won’t be happy, or that no child should have any contact with religion, should take the time to read the adverts.
“The message is that the labelling of children by their parents’ religion fails to respect the rights of the child and their autonomy. We are saying that religions and philosophies — and ‘humanist’ is one of the labels we use on our poster — should not be foisted on or assumed of young children.”

If I haven't mentioned it before, I enjoy a well-designed figure: a simple, graphical representation of some complex data.  I'm a big fan of Edward Tufte's books. Jen over at Blag Hag gets a nod from me for representing the complexities of this article in a great graphic:

Well done.

**Dawkins argues that this is actually a form of child abuse.  You may disagree with this particular argument, but its not that important for the ad.  It's enough to realize that labelling a child is incorrect, because they don't have the capability of understanding and really accepting freely the label.

Formal Act of Defection from the RCC

About 6 months ago, I read a blog entry by Jim Gardner on his blog, How good is that?.  I knew prior to reading this that because I was baptized as a Catholic, the church still considers me a member.  The statistic of 1.131 billion Catholics that's most often used includes me, and anyone else who has been baptized, regardless of current practices or beliefs.  That number even includes those who are gay, divorced, have had an abortion, etc.; as long as you were baptized, you're still counted.  What I was unaware of is that according to Roman Catholic canon law, I can request a "formal act of defection" from the faith, which results in a note on my baptismal record stating that I have left the church.  Jim followed up with the letter he has written to his archdiocese requesting this act.

I wasn't a regular reader of Jim's blog (I am now, he's in my Google Reader account), but I found the article because I had been very angry, as was Jim, about hearing that the pope was telling blatant lies about condom use being the cause of the AIDS epidemic in Africa, and about the news coming out about the sexual abuse going on in church.  I had always had a bit more virulence towards the Catholic Church than others, since I had the more experience there than with any other church.  That said, I was never that concerned with my former religion, as opposed to others.  It seemed more benign, since it was so much more about strange ritual and tradition, and not so much about preaching eternal damnation, at least in my experience.  However, hearing this pronouncement pissed me off to no end, and made me realize that while my parish, and the church my family went to was fairly boring and uncontroversial, the Catholic Church has enormous amounts of influence across the globe, and is generally using it to spread misinformation and nonsense.**  I was reading a lot of atheist blogs that talked about it to blow off some steam, and read about what others were thinking and feeling about the situation.

When I read Jim's post, I felt this was something all of us who are no longer Catholic should do.  I know a lot of people are content with just no longer going to church and getting on with it.  They may feel that taking time out to write a letter getting formal recognition for no longer being a Catholic from the RCC is like writing a letter to Santa Claus to tell him how ridiculous the idea of flying reindeer are.  The main concerns I'm addressing in my letter, however, are not necessarily my atheism in terms of theological beliefs, but about kindness, thoughtfulness and morality, and the lack of it in the Catholic Church.  I think it's important to call them out not because I think they're wrong, but because the are becoming a real hindrance to progress in the world.  If many more former Catholics do this, the RCC might even begin to reconsider some of their positions (I know its unlikely, but its more likely than if no one says anything.)  Even if the church itself doesn't change, a large number of Catholics officially renouncing their religion will certainly be made known, and will affect many others. 

I'm rather embarrassed to say, however, that halfway through writing a letter to my own archdiocese, it got stored away in a directory on my computer, and I forgot about it until now.  Luckily, while thinking about ideas for posts here, I stumbled back upon my letter, and decided that I should finish it and send it along.

I'm posting here before I finish because I think some other Catholics might be interested in knowing about this.  I suspect few Catholics are aware of this. I'd love to see many more people writing their archdiocese to be officially recognized as no longer Catholic.  The letter so far includes some background about my involvement with the church, and a short outline on the reasons I am requesting this defection. It is fairly similar to Jim's letter, not because I'm too lazy to come up with something more creative, but because 1) I think Jim's letter is excellent, and 2) I want to make sure I include the necessary information, and since Jim had already spoken to a clergyman, I assume he has included what is needed.

I'll post my final letter once it's finished, as well as any news afterward.  Wish me luck!

** I know that the RCC also does a lot of charity and good in developing countries, but I contend that the bad far outweighs the good.  I would watch the recent Intelligence Squared Debate, considering the motion "The Catholic Church is a force for good in the world" if you disagree (or if you'd enjoy watching Stephen Fry and Christopher Hitchens wittily and completely obliterating their opponents, Archbishop John Onaiyekan and Anne Widdecombe)

Tuesday, November 17, 2009

Great resource for countering Anti-Vaccination rhetoric

Brian Dunning at the Skeptoid podcast just did an episode on ingredients in vaccines, which are often claimed to be harmful by anti-vaxxers (the link also contains a text transcript of the audio).  These claims are baseless, and the podcast addresses the most commonly cited ingredients.  Some are just plain lies (aspartame, anti-freeze, aborted fetal tissue), others are just scary sounding, without any real negative effects (formaldehyde, aluminium), and some are much more complicated than any anti-vaxxer is willing to think about (mercury, live viruses).  If you ever have to deal with intellectual lightweights and their anti-vaccination arguments, this is a really nice, compact resource.

And if you're not subscribed to the Skeptoid podcast, do it now!  It's a great listen, and each episode is only about 10-15 minutes long, so he gets the pertinent information to you without a lot of filler.


Well no sooner did I post this than I read all over the blogosphere that the king anti-vaxxer himself, Bill Maher, published a post on the Huffington Post, a bastion for pseudo-scientific nonsense, titled Vaccination: A Conversation Worth Having.  Its complete rubbish; basically trying to argue that he's the open-minded one, because he's willing to believe any woo-based conspiracy that invokes the fear of "Big Pharma."  Opac at Respectful Insolence already posted a devastating rebuttal here, check it out.

Sunday, November 15, 2009

Catholic Church in D.C. Will Pull Services over Gay Marriage

The Catholic Church isn't happy about D.C.'s same-sex marriage bill.  Ho-hum, no surprise, of course.  They've now resorted to the "I'm taking my toys and going home..." tactic:

The Catholic Archdiocese of Washington said Wednesday that it will be unable to continue the social service programs it runs for the District if the city doesn't change a proposed same-sex marriage law, a threat that could affect tens of thousands of people the church helps with adoption, homelessness and health care.

Because outdated dogma is more important to Catholics than compassion and helping their fellow man.  The Washington Post article continues:

Under the bill, headed for a D.C. Council vote next month, religious organizations would not be required to perform or make space available for same-sex weddings. But they would have to obey city laws prohibiting discrimination against gay men and lesbians.
Fearful that they could be forced, among other things, to extend employee benefits to same-sex married couples, church officials said they would have no choice but to abandon their contracts with the city.

This is nonsense.  The Church can't discriminate against many other marriages it does not recognize:  people who have been divorced, Jews, Muslims, Protestants, etc.  Why has there been no outcry over any of these?  This is obviously just bully tactics from a group of religious thugs with no compassion for their fellow human beings. 

From the archdiocese's spokeswoman:

"If the city requires this, we can't do it," Susan Gibbs, spokeswoman for the archdiocese, said Wednesday. "The city is saying in order to provide social services, you need to be secular. For us, that's really a problem."

No, the city says that if we give you money for services, then you have to play by the same rules as everyone else.  The government can't give you special dispensation; there's this pesky separation of church and state stuff.

There are grumblings on the TALK section of the WP article about the passage of the bill itself being an infringement on religious freedom, according to the First Amendment.  Patrick Deneen is an associate professor of government at Georgetown, and says:

There is a basic conflict here between the claims of those seeking the legalization of gay marriage and the claims of religious liberty - not only for religious institutions per se, but individuals (such as individuals who might offer privately contracted services, such as wedding photographers, whose faith beliefs could be compromised by providing their service to a gay couple, and who would be subject to anti-discrimination lawsuits). Another area where there is a conflict is the right of religious organizations not to provide certain services or benefits, such as certain spousal employment benefits or adoption services. More broadly (going beyond the gay marriage issue), without exemptions, religious organizations can be forced to act in ways that go against their tenets, for instance, in being forced to provide contraceptive benefits in health care policies. Here the various claims run against the free exercise clause of the First Amendment. In these sorts of instances, there is a demand that religious organizations essentially act as secular organizations.

To the best of my understanding, the First Amendment does not require the government to check with every religious organization before passing any single law.  The Catholic Church is free to do as it pleases, UNLESS it wants tax money, in which case, it DOES have to act as a secular organization (see: Separation of Church and State).  As long as everyone has to follow the same set of rules, no religious group gets any advantage.  

I'm curious if there are secular or more tolerant religious groups that would be willing and able to take over the charity work that the Catholic Church.   If they can find alternatives, this could be a good thing in the long run.  I hope there are groups in the D.C. area letting their government know that there are people out there willing to pick up the slack, and will gladly extend the same benefits to same-sex couples as all others.  And the D.C. Catholic Church could be the one who loses big.

One can hope, right?

Wednesday, November 11, 2009

Murder and Religion

In the wake of the killings at Fort Hood by Army Maj. Nidal Malik Hasan, a Muslim, Arsaian Iftikhar has written a piece arguing that these murders were not a religious act.  I can't say either way whether Maj. Hasan was motivated by his religion to do what he did, because I haven't seen enough evidence for his particular case.  But Iftikhar tries to argue that all cases murder have no religion.  His main point is this:

Simply put; murder is murder and has no religion whatsoever.

If murder cannot be a religious act, then religion could not have been a significant motivation for the act.  Iftikhar completely fails to show that religion cannot be a motivator of murder, or even that it wasn't a motivator in Maj. Hasan's single case.

He starts off suggesting that the Quran forbids the taking of human life:

Most of the world's 1.57 billion Muslims know that the Holy Quran states quite clearly that, "Anyone who kills a human being ... it shall be as though he has killed all of mankind. ... If anyone saves a life, it shall be as though he has saved the lives of all of mankind."

Cherry-picking verses from a holy book is something Christians are notorious for, but its equally useless for the Quran.  There are plenty of verses I could choose to paint a completely different picture.  In fact, the verse he cites (Sura 5:32), with the context he conveniently omitted, has a different interpretation:

Because of this, we decreed for the Children of Israel that anyone who murders any person who had not committed murder or horrendous crimes, it shall be as if he murdered all the people. And anyone who spares a life, it shall be as if he spared the lives of all the people. Our messengers went to them with clear proofs and revelations, but most of them, after all this, are still transgressing.

And considering what counts as a "horrendous crime" (just take a look at the examples from the Skeptic's Annotated Quran for an idea), this does not prevent fundamentalist Muslims from killing most non-Muslims. 

But it doesn't even matter what the Quran actually says.  There are a significant number of Muslims who admittedly commit murder because they believe they will be rewarded in heaven, specifically because of their religion.  Most Muslims, however, believe that their religion forbids it.  Regardless of what the Quran actually says, you cannot claim that either group's motivations are something other than their religious beliefs.  Their beliefs are mutually incompatible, and yet both are motivated by primarily by them.   

Iftikhar is committing a No True Scotsman fallacy here.  Because his and many others' view of Islam is as a religion of peace, No TRUE Muslim could be motivated by their religion to commit murder. But of course, this making the definition of a Muslim include someone who holds this belief.  Iftikhar is assuming his conclusion in his argument, rather than proving it.

Iftikhar continues by criticizing the conservative media for playing up the fact that Maj. Hasan was a Muslim:

True to form, many conservative media pundits wasted little time in pointing to reports that Hasan had said "Allahu Akbar" (Arabic for "God is great") at the start of his murderous rampage. News coverage continuously showed the looping convenience store black-and-white videotape footage of Hasan wearing traditional white Islamic garb.

I agree with him here; the media's overplaying of Hasan's religion sends the message that being a Muslim is a warning sign, that we should be wary of anyone who practices Islam.  Its prejudicial, and the media should stick to the facts at hand, rather than focus on a specific character trait which may or may not have been a factor in the crime.  However, he goes on to say something that I can't imagine anyone would actually believe:

First of all, someone simply saying "Allahu Akbar" while committing an act of mass murder no more makes their criminal act "Islamic" than a Christian uttering the "Hail Mary" while murdering an abortion medical provider, or someone chanting "Onward, Christian Soldiers" while bombing a gay nightclub, would make their act "Christian" in nature.

This is bordering on absurd.  Is he really suggesting that bombing an abortion clinic or a gay nightclub isn't religiously motivated?  What other motivations for these actions are there?   Many Christians have made it very clear that their faith is the overwhelming reason behind their position against abortion and homosexuality.  Similarly, there is a venerable history of Muslims who have made it clear that it is a duty to kill infidels, and its quite possible that Maj. Hasan holds similar beliefs. 

I understand that a Muslim saying "Allahu Akbar" or a Christian saying "Hail Mary" is not necessarily proof that their crime was religiously motivated.  There are other explanations.  For example, perhaps a religious person would pray before committing a crime in order to ask forgiveness in advance, knowing his actions are wrong and not condoned by their faith.  But without other evidence, the most likely explanation is that faith motivated the actions.

Iftikhar then quotes Professor Juan Cole of the University of Michigan:

"One most certainly does insult Muslims by tying their religion to movements such as terrorism or fascism. Muslims perceive a double standard in this regard: Timothy McVeigh and Terry Nichols would never be called 'Christian terrorists' even though they were in close contact with the Christian Identity Movement. No one would speak of Christo-fascism or Judeo-fascism as the Republican[s] ... speak of Islam-o-fascism. ... [Many people also] point out that [it was] persons of Christian heritage [who] invented fascism, not Muslims."

I absolutely agree that there is double-standard in this country.  We are willing to call Muslim extremists "terrorists", while we shy away from the word when it appears that a Christian's religious ideals motivated their crime.   There absolutely are Christo-fascist groups of people in the U.S., and more should be done to point out the fact that their beliefs are chiefly motivated by their religion.

But the point is not that either all terrorists are motivated by religion or none of them are.  The fact is there are a variety of reasons why people commit heinous crimes.  That does not mean we should shy away from the fact that some use religion as a justification for them.  It doesn't matter who invented fascism and what religion they were.  Each fascist group has their own motivations, some religious, some not.  Our euphemistic language designed to shy away from blaming religion is harmful, because it makes us less able to combat extremism effectively.

Iftikhar goes on to make a suggestion to the U.S. military:

Thus, with thousands of patriotic American Muslim women and men proudly serving in our United States Army in places like Iraq and Afghanistan, perhaps it would behoove our army leaders to consider sending a strong message of American unity by appointing an American Muslim to be a part of the prosecution team against Hasan.
This would help show that the mass murders allegedly committed by Hasan have nothing to do with the teachings of our religion.

It would show nothing of the sort.  It would show that, just as in every other religion, there are good and bad.  There are those who have religious faith and act morally and justly, and others who use it to justify atrocities.  In Islam, and other religions, the majority of believers fall into the first category.  But we must not deny that the second does exist, and is significant.  Pretending that religion does not motivate these people is denying the real problem, and will hurt everyone, believers and nonbelievers alike.

Monday, November 9, 2009

Dealing with Death

XKCD is one of my favorite webcomics, and the comic up on Friday stirred up a lot of thoughts and feelings for me this weekend.  Here's the comic:

Hemant at Friendly Atheist already wrote about the virtues of being an organ donor, and I won't repeat them here. Hemant did say something that resonated with me, and something I thought about when I first saw the comic as well:

The latest XKCD offers a beautiful explanation of why most atheists don’t fear death — we know that it’s possible for us to make a difference even after we die.

While I feel good about my decision to be an organ donor, it still didn't help me feel better about the fact that I will die someday.  Being an atheist and a scientist is humbling, considering the vastness of our universe, and how insignificant a part each of us plays in it, but I haven't completely lost my ego.  Considering the idea of not existing anymore was difficult to deal with.   

The idea presented at the beginning of the comic, that the essence of something is not the things it is made of, but the arrangement, the pattern, of those things, brought me back to what originally strengthened my convictions about being an atheist.  I was fortunate enough to be free enough to consider atheism at a young age.  When most atheists I know were questioning their religious beliefs, I was questioning whether my atheistic views were based on a solid foundation.  One of the last problems I had with my position was that I couldn't explain where my consciousness is, and where it came from.  It seemed so magical, so unexplainable, that there was part of me that couldn't accept that a materialistic world-view was justifiable given it.

Luckily, I found Douglas Hofstadter's books: del, Escher, Bach: An Eternal Golden Braid, The Mind's I (co-edited by Daniel Dennett), and I Am A Strange Loop, which introduced me to this idea that the patterns of activity in our brain is what's fundamental to us.  When these patterns became complex enough, they became able to represent self-referential thought (thinking about myself), in what Hofstadter calls "strange loops."  He argues that these strange loops are where consciousness comes from.  This may not have answered all my questions**, but it did convince me that materialism was a better foundation for consciousness than another theory.

So what does this have to do with dealing with the fear of dying?  While reading I Am A Strange Loop on my commute home one afternoon, the book took a turn that surprised and shook me, when Hofstadter discusses his wife's untimely illness and death.  It was a very moving account.  I had trouble fighting back tears while reading it, which doesn't usually happen to me while reading.  It did make it somewhat awkward sitting next to total strangers on a commuter rail train.    During this time, he talks about what it means to be close to someone, to love someone:

...the idea I am proposing here is that since a normal adult human brain is a representationally universal "machine", and since humans are social beings, an adult brain is the locus not only of one strange loop constituting the identity of the primary person associated with that brain, but of many strange-loop patterns that are coarse-grained copies of the primary strange loops housed in other brains.  Thus, brain 1 contains strange loops 1, 2, 3, and so forth, each with its own level of detail.  But since this notion is true of any brain, not just of brain 1, it entails the following flip side:  Every normal human soul is housed in many brains at varying degrees of fidelity, and therefore every human consciousness or "I" lives at once in a collection of different brains, to different extents.

Hofstadter defends his view throughout most of the book, and I definitely couldn't do him justice in a short blog post, so I must highly recommend the book if this is intriguing to you, rather than try to explain it all here.  The point is, although the main pattern may disappear when someone dies, part of that person's consciousness lives on.  It lives on in their family, friends and loved ones.  I'm under no illusions that I will live on forever in the standard sense of being fully aware of myself, my "I", in my own brain, or some surrogate.  But knowing that I am a part of the people I love, and I can have an effect on this world even after I'm gone, not just my physical pieces, but my self, my "I", has given me a sense of peace about my mortality. 

Hofstadter concludes one of the chapters in I Am A Strange Loop with his insights on what happens to these distributed versions of a consciousness over time, and what funerals accomplish in terms of these strange loops.  This passage has given me comfort in the past; it's something that I'd like read at my funeral when the time comes:

Halos, Afterglows, Coronas
In the wake of a human being's death, what survives is a set of afterglows, some brighter and some dimmer, in the collective brains of all those who were dearest to them. And then those people in turn pass on, the afterglow become extremely faint. And when that outer layer in turn passes into oblivion, then the afterglow is feebler still, and after a while there is nothing left.
The slow process of extinction I've just described, though gloomy, is a little less gloomy than the standard view. Because bodily death is so clear, so sharp, and so dramatic, and because we tend to cling to the caged-bird view, death strikes us as instantaneous and absolute, as sharp as a guillotine blade. Our instinct is to believe that the light has once and for all gone out altogether. I suggest that this is not the case for human souls, because the essence of a human being--truly unlike the essence of a mosquito or a snake or a bird or a pig--is distributed over many a brain. It takes a couple of generations for a soul to subside, for the flickering to cease, for all the embers to burn out. Although "ashes to ashes, dust to dust" may in the end be true, the transition it describes is not so sharp as we tend to think.
It seems to me, therefore, that the instinctive although seldom articulated purpose of holding a funeral or memorial service is to reunite the people most intimate with the deceased, and to collectively rekindle in them all, for one last time, the special living flame that represents the essence of that beloved person, profiting directly or indirectly from the presence of one another, feeling the shared presence of that person in the brains that remain, and this solidifying to the maximal extent possible those secondary personal gemmae that remain aflicker in all these different brains. Though the primary brain has been eclipsed, there is, in those who remain and who are gathered to remember and reactivate the spirit of the departed, a collective corona that still glows. This is what human love means. The word "love" cannot, thus, be separated from the word "I"; the more deeply rooted the symbol for someone inside you, the greater the love, the brighter the light that remains behind.

In fact in some ways, I think my views are more optimistic than Hofstadter's.  I think he's wrong that those afterglows eventually have to go out.  Even though, as generations go by, less and less people will know me by name, those who they do know may have been affected by me.  I know that I would be a much different person if it wasn't for my family members and friends, who have also been affected by their parents and friends.  And I will in turn affect the next generation, who have the potential to affect future generations, which can go on to infinity.

I know that some may not feel much better about the fact that they will eventually pass on after hearing this, but I hope that some can find solace as I have.  And if not, keep learning, reading and absorbing.  You never know when some new way of thinking will hit you, and change your outlook for the better.

**As an example, I still think there is a boot-strapping problem with Hofstadter's explanation, although I can't figure out exactly where it comes from. This suggests to me that it has more to do with my conscious-thinker-centric ego, and this entrenched idea that consciousness should be more complicated, than it being a real problem.

Friday, November 6, 2009

Guess who's complaining about sex toys...

If you said the Catholics, you'd be right...

Researchers at Duke University advertised for female participants in a study on sex toys:

The ads, which were posted around campus and on a research study Web site, sought female students at least 18 years old to "view sex toys and engage in sexually explicit conversation with other female Duke students."

Participants will be asked to complete online questionnaires about their sexual attitudes and behaviors and visit the lab for a "one-hour party" with seven or eight women. Not only will the students be asked to complete a second questionnaire a couple of months later, they will receive a gift bag and be given the opportunity to purchase items at a significantly reduced rate, according to the ad.

But of course the thought of someone enjoying their sexuality without the goal of having children concerns Catholics, including Father Joe Vetter, director of the Duke Catholic Center:

"My understanding is there is a concern on campus about promiscuity," Vetter said.
In recent years, some university health centers have touted sex toys as alternatives to risky sexual behavior and serial promiscuity. The study, Vetter said, was designed by health care workers to see whether such approaches work.
"I'm concerned about promiscuity also," Vetter said. "And to be honest, I don't have the solution. ... My concern is these students are in this developmental phase, and I don't think it's a good developmental practice to just tell somebody to just sit around and masturbate. I don't think that promotes relationships."

Because a celibate priest is the person we should be consulting about healthy, sexual relationships.  He provides no evidence that sex toys hurt relationships, which is potentially what studies like this COULD find out.  (I know that this particular study may not be looking into how it affects relationships, but if it was, I doubt that would change the attitude of most Catholics.)   Nor does owning a sex toy imply that you'll just sit around masturbating constantly.

The fact is, we have sexual desires.  What is the problem with dealing with those desires in a safe way, without the risks of STDs or unwanted pregnancy?  The Catholic Church's position on this is pretty much in line with the rest of their opinions, completely inconsistent with facts and logic.

Derren Brown's New Website: Science Of Scams

Just found a great website run by Derren Brown and Kat Akingbade, called  They have posted a number of videos on YouTube, apparently showing some psychic or paranormal activity.  They then explain how they performed the stunt through science.  Here's an example

Head to the site for the rest of the videos.  They also have a number of older videos, including some of James Randi and Penn & Teller debunking various paranormal claims (see the Factoid tab for these). 

For anyone not familiar, Derren Brown is a brilliant magician, mentalist, and skeptic from the UK.  (Yes, it's a bit of a man-crush).  Go check out the site, especially if you believe in psychics, ghosts, or chi energy.  You need a good dose of skepticism, and Derren Brown is the guy to do it.

Frank Schaffer takes on the "New Atheists"

Frank Schaffer's article tries to claim that the New Atheists (Dawkins, Hitchens) are just as fundamentalist as Religious Right Christians.  Its a ridiculous argument that has been made many times before, but his is especially specious.  Its full of ad hominem nonsense that has nothing to do with their belief systems, as well as a bizarre love-fest for Dan Dennett.

A fundamentalist holds her beliefs regardless of evidence, and there is no criteria which would cause her to even question, let alone change those beliefs.  Schaffer even describes Dawkins' explanation of this from The God Delusion (TGD):

In the preface to the paperback edition, Dawkins responds to the criticism that he is just as much of a proselytizing fundamentalist as those he criticizes. Dawkins answers, “No, please, it is all too easy to mistake passion that can change its mind for fundamentalism, which never will . . . it is impossible to overstress the difference between such a passionate commitment to biblical fundamentals and the true scientist’s equally passionate commitment to evidence.”

But notice how he responds:

As a scientist Dawkins claims that by definition his passion can’t be like other, lesser people’s passions, because as a scientist he is above such things.

This is nonsense.  Dawkins says no such thing about "lesser people".  He gives examples in the rest of the book of how his beliefs about God, evolution, etc. could be changed.  It has nothing to do with some natural superiority of scientists, it has to do with the scientific method, which values evidence over personal conviction.  This is one of many examples of Schaffer trying to make Dawkins seem like the token smug asshole atheist.

Even if Dawkins did feel this way, it doesn't change the fact that he is capable of changing his belief system given evidence, and lays out how that might be done.  No reason is given to suggest that Dawkins is lying/mistaken about this, and I can't think of one.  Even if he is a smug atheist with a vast superiority complex, this ad hominem still has no bearing.

The other way Schaffer tries to bolster his position is to act as if because he has nice things to say about some atheists, like Dan Dennett, his criticism of other atheists is somehow more balanced.  Unfortunately, the only difference he claims between Dennett and Dawkins is about presentation and personality:

One reason I find Dennett so appealing is his decency. His humility, wit, and empathy speak volumes to me and lends a solid gravity to his wisdom.
Being humble, witty, and empathic has no bearing on whether one's arguments are good or bad.  Not to mention that nothing he presents about Dennett is vastly different from Dawkins' and Hitchens' positions on religion:

[Dennett] seems fair and knowledgeable about religion, acknowledging that all religions have a toxic component and yet that they also have a good side.

Dawkins has clearly stated positive elements of religion, including feelings of consolation and inspiration in chapter 10 of TGD.  He discusses whether its possible to derive these from sources other than religion, but he acknowledges that these positive effects of religion are real and useful to many people.

He brings up an instance where Dennett apparently publicly disagrees with Dawkins:

Dennett also wrote a review of Dawkins’s The God Delusion for Free Inquiry, saying that he and Dawkins agree about many ideas, “but on one central issue we are not (yet) of one mind: Dawkins is quite sure that the world would be a better place if religion were hastened to extinction and I am still agnostic about that.”

Whoa.  Dennett really gave it to Dawkins there.  Notice that Dennett doesn't even disagree.  His claim is essentially that he does not have enough evidence to make a decision.

The rest of his article presents two more tactics for labelling Dawkins as fundamentalist.  First, Dawkins' website has a store were people can buy atheist pins and t-shirts.  Anyone who would wear an atheist pin/shirt must be a fundamentalist preacher of atheism, therefore Dawkins is a fundamentalist.  I don't think I have to explain why this is ridiculous. 

Second, he blantantly misrepresents Dawkins arguments from TGD (or perhaps he's too stupid to understand them).  For example, take a look at what he has to say about Dawkins' discussion about the anthropic principle:

Instead of God, Dawkins says he’s discovered “the anthropic principle.” So Dawkins has invented a theology with a scientific-sounding name. He even has doctrines, what he calls the “six fundamental constants of nature,” which for him fill in the “gaps.” Believers could say that God chose these six “laws” to encourage the evolution of life, but Dawkins won’t buy this, because God can’t be explained by Dawkins. Apparently the origin of life, however, can be explained by Dawkins. Dawkins says that the chance that a God exists who was able to figure Dawkins’s six rules out, and thus create the “just right” conditions for life, is as improbable as these rules being “created” by chance.

He couldn't have even read this section of the book.  Dawkins didn't make up these six "laws", they come from Martin Rees' Just Six Numbers, which Dawkins states (directly in the text, no less, not even in a footnote).  This was also clearly just an example, that there might be more or less numbers that define fundamental constants of the universe.  Schaffer is either claiming that physicists are fundamentalist because based on all evidence, certain forces (e.g., the strong force) are the same throughout the universe, or this concept was too complicated for him to even begin to understand.

Dawkins also didn't discover the anthropic principle.  Its a standard principle used to explain why it appears that a place seems well suited for whatever exists there.  For example, its clear that if the Earth wasn't well suited for human life, then we wouldn't have arose here.  Dawkins also never claims the explain the origin of life, but he does explain why its much more probable that God was not involved than if he was.  Schaffer tosses in some more ad hominem, to make it sound as if Dawkins is just making stuff up without any explanation.  The rest of his discussions of TGD are equally obtuse.

Schaffer never addresses any of the actual arguments made in TGD, he just flaunts his blatant ignorance of the arguments made.  He would prefer to cater to those who are proud of their ignorance, and know, without even reading Dawkins' book, that its much too complicated for common folk to understand.  I can't claim that all the arguments made in TGD are simple enough for anyone to understand, but if Schaffer wants to write about this stuff, he should at least make an effort.

I could go on to the section on Hitchens, but I can't bring myself to read any more of this drivel.  Wake me up if he says something interesting or even partially accurate.

Tuesday, November 3, 2009

The future LHC is preventing the present LHC from working?

So this is a pretty old story from the New York Times about two physicists, Holger B. Neilsen and Masao Ninomiya, who believe that the Large Hadron Collider (LHC) at CERN in Switzerland is causing itself to malfunction from the future (cue The Twilight Zone theme).  I read it a few weeks ago when a friend posted it on facebook, and a number of people blogged about it, including PZ.  

I know how bad scientific reporting is today.  I thought that perhaps the story was misrepresenting the hypotheses in their papers, so I decided to read one of them myself (found here from  I'm not a physicist;  I haven't even taken a course since AP Physics in high school, so I didn't expect to understand all of it.  But I could get a general idea of what they thought was going on.  And after reading their paper, it seems the the NY Times article doesn't being to explain how crazy this theory actually is.

I initially expected their theory to suggest that sub-atomic particles affect each other in some complex way that amounts to backwards causation.   But their not just talking about backwards causation at the sub-atomic level.  They're suggesting that the Higgs is actually causing macroscopic changes, such as the malfunction of the LHC, or even the decision by Congress to stop funding the SSC (Superconducting Super Collider), which was another particle accelerator that potentially could have detected the Higgs boson, if completed:

... the great Higgs-particle-producing accelerator SSC, in spite of the tunnel being a quarter built, was canceled by Congress! Such a cancellation after a huge investment is already in itself an unusual event that should not happen too often. We might take this event as experimental evidence for our model in which an accelerator with the luminosity and beam energy of the SSC will not be built.
Since the LHC has a performance approaching the SSC, it suggests that also the LHC may be in danger of being closed under mysterious circumstances.

I'm not familiar with any current theories of physics suggesting that fundamental particles directly affect the decisions of a governing body.  Noe that they aren't just suggesting that the outcome (closing the SSC) is consistent with their theory, they're actually presenting this as evidence of the theory!  And why exactly does the closing of the LHC have to be mysterious?  Is that really a concern of the Higgs boson?  They continue:

Even though some unusual political or natural catastrophe causing the closure of the LHC would be strong evidence for the validity of a model of our type with an effect from the future, it would still be debatable whether the closure was not due to some other cause other than our SI -effects.

No, it wouldn't be debatable, it would be almost a sure thing that it was due to something other than your crazy theory.  Anyone debating that an infinitesimally small particle from the future is the most likely cause of a political decision to close the LHC would be considered delusional, unless they hold a degree is physics.

They go on to suggest a way to avert the catastophe they've postulated:

If a card drawing game or a quantum random number generator causes the closure of the LHC in spite of the fact that it was assigned a small probability of the order of, say 10−7, then the closure would appear to very clear evidence for our model. In other words, if our model was true we would obtain a very clear evidence using such a card-drawing game or random number generator.

A drawn card or a random number causing a restriction on the LHC could be much milder than a closure caused by other means due to the effect of our model. The latter could, in addition, result in the LHC machine being badly used, or cause other effects such as the total closure of CERN, a political crisis, or the loss of many human lives in the case of a natural catastrophe.
Thus, the cheapest way of closing the main part of the LHC may be to demonstrate the effect via the card-drawing game.

Why would the Higgs boson make sure to close the LHC in the way we want it to, by playing a card game with you?  Add in an alarmist rant about the loss of human life without any real evidence or rationale, and we have a pretty standard physics paper*.

The rest of the paper concerns how to set-up the card-drawing or random number game, including how to determine the probability distribution of the cards used.  It seems to me that if the Higgs boson will really stop the LHC from detecting the particle, it shouldn't matter how low the probability is; it will be shut down no matter what.  But they've determined a probability based on the power of the collider.

Being a layman when it comes to modern particle physics, it's perfectly possible that I'm greatly mistaken, and their theory is a respectable, if not a likely, one.  But nothing I've read in their paper suggests to me that this is nothing but wild conjecture.  If any physicists out there can enlighten me about why I should take this seriously, please do!

* I'm being facetious of course, most physicists are doing and publishing real science.  However, I do notice that physics tends to produce more papers that seem like total BS.  I'm not sure if it's because there are more physicists who prefer idle speculation over science, or if it's due to my own ignorance.

Thanks to Justin for the New York Times article.

Sunday, November 1, 2009

It's Alive! Again... Sort of...

I've been trying to resurrect my computer after the latest Kubuntu upgrade completely torched it, so I have nothing to post tonight.  I can finally access my Windows XP partition, so that's a start.  Hopefully I'll be back up and running (and posting) tomorrow.

As for some good news, I'm officially published!  Got a paper accepted to a Bioinformatics conference, about a new NLP system we're currently working on in the lab.  First of many, hopefully...