Saturday, July 25, 2009

Thunderf00t debates Ray Comfort

The atheists and pro-science YouTube user Thunderfoot have just posted a series of videos of a debate he recently had with Ray Comfort.

It's a great debate, and well worth watching.

It's a good debate, because it clearly demonstrates the differences between the two worldviews. One is fact-based, the other isn't.

If you have a YouTube account, and aren't subscribing to Thunderf00t's channel, go subscribe

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Wednesday, July 22, 2009

Chimpanzees get AIDS too

This is really more the area of Tara or ERV but I still thought I'd comment on this piece of news.

African primates can be infected with over 40 different simian immunodeficiency viruses (SIVs). These diseases are related to two diseases which infects our particular species of primates, Homo sapiens, human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) - indeed the two types of HIV are the result of SIVs crossing the species barrier.

HIV is considered an epidemic with more than 30 million people suffering from it worldwide (source - .pdf). As people hopefully know, HIV 1 and 2 will, if not treated by medicine, result in acquired immune deficiency syndrome (AIDS), which is fatal. 2 million people died from AIDS in 2007.

HIV and AIDS is one of the top prioritized areas of medical studies, and both the evolution of HIV from SIV and the connection between HIV and AIDS are well understood. This doesn't, however, keep some people from either claiming that HIV/AIDS is man-made, or that AIDS doesn't exist.

One of the arguments used by both groups is that SIV doesn't lead to AIDS in primates - the one group to argue that HIV couldn't have evolved from SIV, the other to argue that AIDS is not real.

Neither group makes sense. The lack of development of AIDS in SIV carrying primates is by no means evidence of there being no SIV-HIV connection, nor evidence of there being no HIV-AIDS connection.

Still, this matters even less now. Researchers have found out that some primates can get AIDS.

Nature has a new paper by Beatrice Hahn et al.

Increased mortality and AIDS-like immunopathology in wild chimpanzees infected with SIVcpz (link takes you to the abstract, the paper is behind a paywall)

African primates are naturally infected with over 40 different simian immunodeficiency viruses (SIVs), two of which have crossed the species barrier and generated human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2)1, 2. Unlike the human viruses, however, SIVs do not generally cause acquired immunodeficiency syndrome (AIDS) in their natural hosts3. Here we show that SIVcpz, the immediate precursor of HIV-1, is pathogenic in free-ranging chimpanzees. By following 94 members of two habituated chimpanzee communities in Gombe National Park, Tanzania, for over 9 years, we found a 10- to 16-fold higher age-corrected death hazard for SIVcpz-infected (n = 17) compared to uninfected (n = 77) chimpanzees. We also found that SIVcpz-infected females were less likely to give birth and had a higher infant mortality rate than uninfected females. Immunohistochemistry and in situ hybridization of post-mortem spleen and lymph node samples from three infected and two uninfected chimpanzees revealed significant CD4+ T-cell depletion in all infected individuals, with evidence of high viral replication and extensive follicular dendritic cell virus trapping in one of them. One female, who died within 3 years of acquiring SIVcpz, had histopathological findings consistent with end-stage AIDS. These results indicate that SIVcpz, like HIV-1, is associated with progressive CD4+ T-cell loss, lymphatic tissue destruction and premature death. These findings challenge the prevailing view that all natural SIV infections are non-pathogenic and suggest that SIVcpz has a substantial negative impact on the health, reproduction and lifespan of chimpanzees in the wild.

In other words, there is a non-trivial health cost in being infected with SIVcpz.

This is not a trivial finding. As Nature makes clear in it's news release on the story (Wild chimpanzees get AIDS-like illness) this will impact future research.

The results suggest that it will not be possible to find the key to HIV immunity in the chimpanzee genome, as scientists had hoped. However, the study, published in Nature, sets the stage for researchers to gain insight into how HIV and SIV cause disease in their hosts by studying the responses of different primates to the viruses. Wild monkeys that have coexisted with SIV for a long time — such as sooty mangabeys and African green monkeys — seem to have evolved the ability to control SIV, and so do not become ill when exposed to the virus. The new paper, however, shows that chimpanzees — which, like humans, were exposed to SIV more recently — are sickened by the virus.

NY Times also writes about this study: Chimpanzees Do Die From Simian AIDS, Study Finds

Update: Carl Zimmer has written a great blog post about this.

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Thursday, July 09, 2009

Klinghoffer spews nonsense again

One of the token non-Christian of the Discovery Institute, David Klinghoffer, has once again open his mouth to talk about stuff he knows nothing about. This time in the Jerusalem Post.

The alphabet of life

DNA are three letters full of paradox. What they represent remains little understood by the public, yet they are on everyone's tongue. Amid the chatter of popular culture, the truth gets lost that DNA is one of the most powerful clues we have of the existence of a spiritual reality, maybe to the existence of God.

One has to be in awe of Klinghoffer's ability to start up an article with something as mindbogglingly stupid as this paragraph.

Yes, DNA is widely talked about by people who has little understanding of what it is. Klinghoffer is a good example of this. DNA is not in any way or sense a clue for "a spiritual reality, maybe to the existence of God".

An acronym for deoxyribonucleic acid, DNA refers to the form taken by the biological information that directs the production of proteins and other cell components. In 1953, James Watson and Francis Crick famously described its double-helix shape. The information thus encoded, the genome, influences how a living organism's body gets constructed, though how far this goes, and how it works, are questions that remain obscure.

The questions are not as obscure as they used to be, and through continuous research they will become less obscure over time.

We talk about DNA as familiarly as we do the USA. The idea that your genes determine your susceptibility to diseases and addictions is a stock theme of popular health discussions. On TV cop shows, law-enforcement officials are constantly using DNA to solve cases, whether new or "cold" - as real police do.

DNA evidence is in itself not enough to solve a case, and the type of TV shows where they indicate this, are not worth watching. DNA can be used as part of the evidence against someone, but it cannot stand alone. On the other hand, it can, by itself, be used for proving the innocence of someone - yet this much more common usage is never part of the TV series plots, is it?

For a fee, DNA testing can shed light on anyone's genetic ancestry, including whether you have "Jewish genes." There is supposed to be a "God gene" for religious belief in general. And a "gay gene." And so on.

Given the fact that it's only in reasonable recent times, say the last couple of hundred years, that ethnic Jews were allowed marry anyone outside their ethnic group (due to bigoted laws), it would seem reasonable to assume that they share a lot of ancestry. "Jewish genes" would be genes common to people with Jewish ancestors.

The concept of a "God gene" and a "gay gene" are a bit simplistic. It's well established that being homosexual is genetic in nature (people don't "choose" to be homosexual), and it's suspected that there might be a biological (read: genetic) explanation of why some people are more likely to be religious/spiritual than others.

But all this is trivial compared to the largely unheralded insight gained from the Human Genome Project, completed in 2003. The insight is disturbing. It is that while DNA codes for the cell's building blocks, the information needed to build the rest of the creature is seemingly, in large measure, absent.

Given the amount of junk DNA (which isn't junk) in each individual (more than 90% of all DNA), I find it interesting that someone can claim that information is absent.

Also, Klinghoffer obviously doesn't know what he's talking about. We know a lot about what information is used to "build the rest of the creature". E.g. we know that Stat5 is used to determine the growth (.pdf)

CONSIDER THE HOX "master" genes that supposedly determine the spatial configuration of the front and back ends of creatures as diverse as frogs, mice and humans. As British physician James Le Fanu writes in a fascinating new book, Why Us? How Science Rediscovered the Mystery of Ourselves (Pantheon), Swiss biologist Walter Gehring showed that "the same 'master' genes mastermind the three-dimensional structures of all living things... The same master genes that cause a fly to have the form of a fly cause a mouse to have the form of a mouse." The physically encoded information to form that mouse, as opposed to that fly, isn't there. Instead, "It is as if the 'idea' of the fly (or any other organism) must somehow permeate the genome that gives rise to it."

Again, there is a very large part of the DNA we still doesn't know what's used for, so for anyone to make any claims is premature at best.

I had not heard about James Le Fanu and his book, but the briefest google search turns up some less than flattering reviews, see e.g this review in the Telegraph. He is of course a creationist, using tired old creationist arguments (the complexity of the eye), so it's hardly like he is a credible source. Of course, it's ironic that he quotes Walter Gehring, who is one of the discovers of PAX6 which is a master control gene for eye development.

Of course, given the creationists' habit of quote-mining, I tried to search for the quotes from Walter Gehring, but I haven't been able to find them anywhere else than in this article and on the Discovery Institute's website. Not a good sign.

Such an understanding, of nature driven by a force outside nature, was dominant in biology before Darwin. Baron Georges Cuvier (1769-1832), director of Paris's Musee d'Histoire Naturelle, held that there was an unknown biological "formative impulse," an organizational principle of some kind that directed the formation of diverse kinds of life.

And Lamack believed that the environment helped shape the animals (giraffes got longer necks because they reached for the top leaves). So what? We now know, and understand, more about how things works - not only because of Darwin's discoveries, but because of all the supporting discoveries done since then (or in the case of Mendel's discovery of inheritance, before then).

The concept goes still further back. Much further. What Cuvier called the "formative impulse," was called God's "wisdom" by the rabbis. The Bible teaches, "The Lord founded the earth with wisdom" (Proverbs 3:19).

The Bible also teaches that everything was created in six days, that light was created before sources of light, that there was a global flood, that some people lived far beyond human lifespans, that the Jews were hold as slaves by the Egyptians. Let's just say that the Bible is not the most reliable source of knowledge.

WITH DNA, there is, in one sense, less there than meets the eye. But in another sense, there is much more. For if DNA can't entirely account for the way bodies are put together, there remains something deeply suggestive about the fact that curled at the heart of every cell there lies a code. How did it get there?

This is the argument from ignorance when it's absolutely worst. DNA can account for the way the bodies are put together, but we don't know the exact mechanisms.

If we didn't know how atoms bind together to form molecules, we could use the same kind of stupid arguments. How does H2O form? How do the atoms know how to bind? Of course, we do understand the mechanisms behind this, so no one claims that some sort of outside guidance must put them together.

DNA is not a code in the sense that people normally use the word, any more than atoms are codes. Yes, DNA can form things, according to some yet to be discovered mechanisms, as can atoms according to well known mechanisms.

A staple of media coverage of DNA is the story, repeated endlessly, about some scientist or other who's the latest to synthesize molecular precursors of DNA (or its genetic partner, RNA), thus purportedly showing how biological information could have arisen on Earth unaided. The problem with these demonstrations is that they always depend on intelligent guidance, that of the scientist in his lab, thus suggesting the very opposite lesson of the one intended.

Seems like we're suddenly changing the subject. We're gone from talking about how we don't know how DNA (or rather cells) form organisms, to talking about not knowing about how life started.

Anyway, Klinghoffer has of course completely misrepresented what the experiments were about. Yes, the experiments are "guided", but they replicate conditions well known to have existed when the building blocks of life first appeared. Given the fact that they set out to demonstrated that there were sufficient conditions at the time for life to start spontaneously, they were quite successful.

In another new book, Signature in the Cell: DNA and the Evidence for Intelligent Design (HarperOne), my colleague Stephen Meyer, a Cambridge University-trained philosopher of science, reminds us of the failure of every avenue by which science has tried to explain the origin of the genetic information required for the first life. Explanations depending on unguided material processes alone usually founder on a chicken-or-the-egg paradox: notably, that "specified information in DNA codes for proteins, but specific proteins are necessary to transcribe and translate the information on the DNA molecule."

Stephen Meyer is of course a well-known scientific ignoramus who continuously lies about science. I suggest reading the Wikipedia article on abiogenisis for a little more background, and then head over to TalkOrigins to read their articles on the subject.

DNA acts like a computer code, or like a language consisting of letters and words, arranged in specific sequences to accomplish a specific task or convey a specific meaning. As Dr. Meyer observes, the only kind of source we know of that can produce a "functionally integrated information-processing system" like that in the cell is an intelligent source.

No. DNA is nothing like computer code or languages except at the most superficial level (components which added together forms something). Computer code needs a interpreter (often a compiler) which translates the code into something which the machine in question can understand, while languages relies on common definitions (to see how even trivial differences can make huge problems, see the usage of "theory" inside and outside science). DNA on the other hand are self-replicating building blocks which gives the recipe for how organisms form. These are not trivial differences.

As a Jew, I find it intriguing, at the very least, that Jewish tradition anticipated precisely the kind of evidence that Meyer deals with in his book. DNA refers to the letters of a genetic "alphabet" that in the correct combinations encode the diversity of all life forms. Kabbala too speaks of such an alphabet, comprised of the letters of the Hebrew alphabet, with which God continually speaks the world into existence.

What is Klinghoffer trying to say here? That because we use the mental image of letters when describing DNA, it's the same as saying that a god used a specific language to create the world?

Let me give Klinghoffer a hint: There are no real letters in DNA - it's just a way we describe them, so we can understand it. Much like atoms are not really miniature solar systems - they are just described that way so people can visualize them.

Different combinations of letters produce different creatures. A century and a half before Watson and Crick, Rabbi Schneur Zalman of Liadi sought to make Kabbala accessible to ordinary readers. In the Tanya (1796), he writes of how "the creatures are divided into categories [both] general and particular by changes in the combinations, substitutions and transpositions [of the letters]."

Huh? Mysticism presented as incoherent babble.

Something is out there beyond nature, guiding the destinies of living creatures. Whether we think of it as God or some other unknown agent makes a big difference. But the progress of science from imagining existence as a purely material affair, without purpose, as Darwinian evolution still portrays the matter, to the more advanced description toward which biology increasingly points, is a major step in the right direction.

There is absolute no evidence for anything "beyond nature, guiding the destinies of living creatures", so this is a claim without merit.

And can you point to any meaningful meaning of existence as a non-material affair? I guess one could suggest that the memory of someone is non-material (ignoring the fact that memories are storied in brains), but I don't think that's what Klinghoffer is aiming at here.

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Sunday, July 05, 2009

There is something rotten in Denmark

Since my readership is generally non-Danish, I tend to write little about Danish issues, but I feel that I've been too silent on the issue of Danish politics.

Denmark is lead by a two-party (Venstre and Konservative) right-of-center government which is dependent on the support by the populist, anti-immigrant Dansk Folkeparti.

Politically, I am not far from Venstre, but ever since Anders Fogh Rasmussen became the leader of the party, I've not voted for them, for the simple reason that I'm an anti-racist, and cannot support any party which works together with racist ideologues like the people in Dansk Folkeparti.

Unsurprisingly the support from Dansk Folkeparti comes with a price, and given their anti-humanitarian views, this price is paid by immigrants. Not only in the form of more and more draconian laws, but also in the form of widespread anti-immigrant rhetoric in the Danish society. Every time there is an issue involving immigrants (or descendants of immigrants) in one form or another, Dansk Folkeparti gets in front of the camera to demonize immigrants.

This has of course lead to a stigmatization of the immigrants in Denmark. In Denmark, children of immigrants are routinely referred to as "second generation immigrants" by politicians, the press, and the public, ignoring the fact that these people have lived their entire life in Denmark.

Of course, this doesn't happen to all immigrants. Even though my mother's not Danish, I don't get referred to as a second generation immigrant - as my picture shows, I look part of the homogeneous Danish population. Instead, it's people who comes from, or descents from people coming from, countries like Turkey, the former Yugoslavia, Iraq, Somalia, Libya, etc.

These people are also referred to as Muslim. When a Dane talks about someone being a Muslim, the Dane is not talking about someone belonging to a belief system, but instead uses it as an ethnic designation. It doesn't matter if the person in question is a Christian Lebanese, an atheist Dane, or something completely different - in the eyes of the Danish society, he or she is a Muslim.

This is perhaps related to the Danish perception of themselves being culturally Christian, no matter what their actual religions beliefs are.

All of this stigmatization has led to immigrants, and children of immigrants, becoming socially marginalized at a higher rate than others. Add to this the fact that people with a "Muslim" name have a harder time getting jobs, and you'll find people with a immigrant background are overrepresented in the criminal system, though nowhere as much as Geert Wilders claims. When he visited Denmark recently, he claimed that 70% of all prisoners in Denmark were Muslims; the true number is 20%, and in real numbers it's 800 people (out of 4000 prison inmates).

Currently there is a gang war going on between the biker gang Hells Angels and immigrant street gangs. This fight is about control of the illegal narcotic trade in Copenhagen, and has claimed lives of people in both camps as well as lives of innocent bystanders. Hells Angels are of course no strangers to such gang wars, having fought with Bullshit in the eighties and Bandidos in the nineties - the later gang war made headlines around the world when they started using rocket launchers.

Even though there are two sides to this conflict, and that one of the parts have been involved in several such conflicts in the past, the general public in Denmark apparently seems to think that the Hells Angels is the good part, fighting against the evil immigrants. Something which Hells Angels spokesman, and convicted murdered, Jønke has milked for everything it is worth.

Recently, Hells Angels published an manifest in which they talked about a group of people, called Jackals, that were dangerous to society, and which they fought against. These Jackals were of course a description of the stereotypical "Muslim" gang member. Most people could see through this obviously self-serving piece of propaganda, but some took it seriously. Among these, a member of Parliament for Venstre, Søren Pind, who wrote a blog post Hvad nu hvis Jønke har ret? ("What if Jønke is right?") where he looks at the manifest, ignoring the sender, and decides that the main message is correct, thus legitimizing further the public view of Hells Angels as the righteous side.

This is the current political state of Denmark.

At the same time, Denmark has recently elected a convicted racist, Morten Messerschmidt, to the EU parliament. Giving him the 2nd highest number of personal votes ever given to a candidate for the EU parliament. He is a member of Dansk Folkeparti.

Some times I despair.

What does it take for people to wake up, and see that Denmark is heading down the drain? Not because of the Islamification of the country, as the right-winged racists claim, but because of the continuous stigmatization of entire parts of the population. That the tolerance that Danes think Denmark represents, is not there anymore (if it ever was there)?

Denmark closed the borders for immigrants in 1972, and while people from the EU can move to Denmark if they want, all other immigrants either have to be refugees or have to have close family already living in Denmark. As per April 2009, there were 405,861 immigrants and 125,232 decedents of immigrants in Denmark, which makes them approximate 10% of the population. Of these, 247,672 and 108,651 were from "non-Western countries" (which includes Bosnia-Herzegovina). The source for the numbers can be found here (.pdf and in Danish)

Given the Danish population were 5,515,287 at the end of the first quarter 2009 (source), we're talking about approximately 6.5% of the Danish population who are "Muslim". Listening to the media and the right-winged, racist propagandists, you'd thought the number was at least 3 times as high.

There is obviously always challenges to integrating people in a new country, especially if they comes from a conflict-ridden area, but as many countries demonstrates, this can be done in much larger numbers than we are talking about here. It is, however, not done by stigmatization.

Denmark should do better - most of us are better than this.

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Friday, July 03, 2009

The stupidity ... it burns!

It's been a long time since I last fisked anything on this blog, but today, I came across something which just begged to be fisked.

It's posted in something called the Christian Post so you just know it gotta be bad.

Is atheism ever morally justified?
By Randal Rauser

The title starts out burning brightly with stupidity. Atheist is simply the lack of belief in a deity, so talking about it being "morally justified" is just nonsense. You could ask if it's justified by the evidence (I think so), or if it's possible for an atheist to be moral (an old discussion, to which the answer is "of course it is"), but the whole idea of justifying lack of belief morally is just plain stupid.

"Tell me about the god you don't believe in because I probably don't believe in him either,"

There is a lot of truth in this old quip. Whenever someone identifies him or herself as an atheist we should always take the time to ask for a definition of the god this person does not believe in. It may just be that we don't believe in this god either.

Someone obviously fail to understand the whole concept of being an atheist. It's not one specific god that atheists don't believe in - it's all gods. No matter what personality your god has, the atheist doesn't see any evidence for his or her existence, and thus doesn't believe in him or her.

I think here of a well known academic who avowed disbelief in the Christian God because he was told -- with a notable absence of pastoral sensitivity -- that a childhood Jewish friend who died in a car accident was burning in hell. As a result this academic came to believe that the Christian God is arbitrary, capricious, and unjust. So when he says that he disbelieves in God, he is saying he disbelieves in a god who is arbitrary, capricious and unjust. But I don't believe in such a god either.

I understand that it might be hard to understand for a person like Rauser, but people usually becomes atheists gradually (unless of course they've always been one). What did incident did, was to lead the future academic in question down the path towards atheism. What happened, was that he started evaluating his belief in the god he was raised believing in, and found out that he didn't believe in him. That process lead on to him realizing that he didn't belief in any god.

Rauser doesn't believe that his god is arbitrary, capricious and unjust (something which he clearly is, if one is to trust his holy book), but this hasn't lead him to question the whole concept of a god.

This does not mean that the atheist friend is exonerated, that his disbelief is wholly without fault. Maybe his disbelief is in part a rationalization for a rebellious human will that refuses to submit to the divine will. (How could I know?) But is it possible that at least in part his disbelief might arise from a refusal to recognize a conception of God which is rightly rejected?

Being religious requires faith, which means belief in something in spite of lack of reliable evidence (otherwise, no faith is required). One cannot be at fault for not believing in something without evidence, so yes, the atheist friend is indeed exonerated.

Here's another example. I was raised on Jack Chick tracts (little cartoon books that convey a hyper-fundamentalist Christian faith). In one of these tracts titled "Somebody Goofed", a young man is tricked into hell. (Read the tract here: )

I find this to be a complete distortion of the doctrine of hell, and one which paints God as cruel and capricious. If this is what atheists think of the doctrine of hell then I can understand why they reject the Christian faith.

While Chick tracks are quite extreme, their general message is well supported by the Bible, which is the firmament of the Christian faith. Still, many people, including Rauser apparently reject this particular aspect of the Christian faith. That doesn't mean they are atheists.

Atheists reject the core concept of the Christian faith (and the Muslim faith, the Jewish faith, the Hindu faith etc.) - the existence of a divine being. They don't reject it out of spite, or in the face of overwhelming evidence, rather they reject it, as they find no evidence supporting the existence of such divine beings.

The discussion boils down to this. Perhaps before we judge the disbelief of the atheist, we should judge our own household. To put it bluntly, how often does our witness in the world offer moral justification for atheism?

I find the message interesting. The whole concept seems to be that atheists simply reject religion as a whole because of the mean content of some religions. This is of course nonsense - many atheists are actually fairly well versed in different religions, and understand the different nuances. What they reject is not the different messages in different religions, but instead the very core that those religions are built upon.

Still, I guess that it's likely that fewer people start on the path to atheism, if the are not confronted with the most ugly, base aspects of their religions. This allows them to safely ignore their doubts, and just continue being part of the flock (their word, not mine).

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