Thursday, 28 August 2008

These things just write themselves!

Via Ed Brayton:

Who needs to criticize Republicans? They do a pretty good job at doing it themselves (emphasis mine).

In an alley behind a non-descript row of brick buildings on North Speer Boulevard, and on the other side of a large metal gate with armed guards standing in front, Republicans have set up a "war room" in Denver... Republican National Committee Chairman Mike Duncan said the team of nearly two dozen staffers at the opposition headquarters will be "fact-checking" statements made by the Obama campaign and by speakers during the convention.

"Just consider this the Ministry of Truth," quipped Dick Wadhams, chairman of the Colorado Republican Party.

Maybe it's been a long time since Wadhams has read 1984, if he's read it at all, but anyone who is familiar with Orwell's classic knows what the Ministry of Truth is. It was the Ministry in charge of "rewriting history"; in other words, fabrication of outright lies to support the government.

A fitting title for a Republican "fact-checking" "war room".

Wednesday, 27 August 2008

Dennis Miller on Religion

Here's a clip of Dennis Miller from all the way back in 1990. Be forewarned, as is common with Miller's style, there is an abundance of NSFW language:

I've always been a fan of Miller even though he's been labelled as a conservative and supports John McCain (though he's pro-choice and supports gay marriage). It's nice to see him taking potshots at religion.

Best line: "They say they don't favour any particular denomination but I think we've all seen their eyes light up at 10s and 20s."

Monday, 25 August 2008

Jesus: Tired of toast and windows, tries sinks

Jesus has returned again, this time as a rusty sink stain.

I'm sorry guys, but that isn't Jesus. It's obviously Darth Vader. May the force be with you.

Science and religion: are they mutually exclusive?

The argument over whether or not science and religion are incompatible is almost as old as empirical science itself, and the debate rages on today. Recently, the American Association for the Advancement of Science (AAAS) released a video response to the propaganda-ridden documentary film, Expelled. The video is below:

It features a slew of scientists, like Francis Collins, talking about how their faith and their science don't compete with each other, hearkening to Stephen J Gould's non-overlapping magisteria. Now, I know that the idea that religion and science are compatible has come up alot recently concerning the subject of evolution, and I know that "theistic evolution" seems to be gaining popularity (that is, more theists are accepting evolution, rather than evolutionists accepting theism). The argument goes that God created the world and gave the spark of life, and then used evolution to guide the development of organisms.

But if you ask me, this is blatant doublethink. The Bible gives special precedence to humans. We are supposedly God's chosen organism. After all, he supposedly created the whole universe just to have a place to put us so we could worship him. Now, suppose that you could roll back time and start everything over again. God gives the spark of life and pushes the START button on evolution. What would happen? There are two possibilities. First, due to the random nature of mutations and chance effects of environmental pressures, evolution would proceed differently than it had the first time around. After 4.5 billion years, it would be very likely that humans would not be the dominant, intelligent lifeform, if humans would evolve at all. If that was the case, then how could humans be the "chosen" organism if our development was never a guarantee? The second possibility is that evolution would proceed exactly as it had the first time, the same mutations being made, the same environmental pressures arising; in a sense, evolution would be guided by God's hand, and each chance occurrence was fated to happen. In this case, the rules of evolution - namely, random mutations being directed and chosen by the environment - are violated; there is no chance or randomness if they were always fated to occur. In other words, God would have effectively created humans, albeit through a lengthy and drawn out process. Whichever of the two possibilities would occur, the conclusion is seemingly the same: there are areas of Biblical religion and evolution that are incompatible. Acceptance of one means you cannot accept 100% of the other.

But let's put theistic evolution aside for a moment. The bigger question that remains to be answered is whether or not science as a whole is incompatible with religion. As stated before, the AAAS seems to take the stance that religion and science are two separate fields that answer different kinds of questions. They are compatible because they have nothing to do with each other. I disagree with this idea completely.

If you accept the Biblical, Abrahamic God, then you accept a god who has influence on our physical world. Even if God is supernatural, and supposedly outside the reach of science, if he has an effect on our natural world, then there has to be an entirely naturalistic mechanism by which this happens. Even the creation of the universe, a material, physical thing, would require a naturalistic explanation. Such mechanisms ARE within the realm of scientific inquiry. Science and religion, therefore, do overlap, do conflict. Unless, of course, you subscribe the the belief of a God that is utterly outside physical experience, and does not interact with the material world. Then, I ask, what is the point of such a God? The existence of such a God would have no practical difference than if he did not exist at all; belief would be pointless (and a waste of time with all the praying and worshipping).

Moreover, scientific investigation has time and time again shown many things in the Bible to be blatantly false; and if some parts of the Bible are false, how can we be sure that other parts of the Bible are not also false? How can one believe that any part of the Bible is true - literally or otherwise - if science has continually shown it to be flawed?

It seems to be that science and religion are mutually exclusive. You cannot be 100% scientific and 100% religious simultaneously. Full acceptance of one requires only partial acceptance of the other; and if you are only "partly" scientific then you're a bad scientist. Likewise, if you are only "partly" religious, you're a poor Christian/Muslim/Jew etc (or at least, you're cherry picking the parts you wish to believe in, with no clear criteria for your choice). I feel that any attempt to reconcile religion with science is merely an attempt at desperately holding on to something that makes you "comfortable" with life, something that makes you "happy".

Science is not about what makes you happy. It's about finding the truth. And when it comes to truth, religion has a habit of falling short.

T-Rex - Chicken Link Looking a bit Tenuous?

Remember that paper published in Science last year? The one that described how researchers at North Carolina State University had extracted collagen fibres from a Tyrannosaurus Rex bone? The one that showed how the T-Rex collagen was similar to collagen taken from chicken bones, and gave us all hopes for extracting biological material - maybe even DNA - from ancient bones?
Yeah. Turns out that the evidence for the T-Rex/Chicken link might be a bit tenuous.

Last month, Tom Kaye at the Burke Museum of Natural History and Culture published a paper in PLoS ONE showing that the collagen that was extracted might not be collagen at all! His paper showed that, instead, it is possible that the "collagen" was a biofilm, a layer of bacterial growth. He explained that "[when] biofilms coat a substrate, and that substrate is subsequently removed, the biofilm will retain much of the original morphology. This can explain the quantity and similarity of structures found in fossil bone and indicates that these structures are unlikely to be preserved dinosaurian tissues but the product of common bacterial activities."

Of course, this doesn't disprove that the sample was collagen. Rather, it provides an alternative interpretation of the data. You can read both papers and weigh the evidence and decide for yourself. However, it does not end there.

Pavel Pevzner et al. at the University of California, San Diego, have written a rather scathing critique of the dinosaur collagen claim (here and here). Calling the original paper "computationally illiterate". He claims that the protein spectra data that has been released so far is insufficient to show the data is statistically significant and cannot rule out false positives. Mary Schweitzer and colleagues, the original paper's authors, have so far kept most of the 48,000 pieces of mass spectrum data under wraps. This comes after they already retracted three of the proteins for not being statistically significant.

Now, I'm not saying that their claim was falsified. But to keep all of their data that should show that their conclusions were relevant hidden is kinda...suspicious. When someone publishes an article claiming that you were looking at slime and not collagen, then wouldn't you want to release the rest of the data to back up your claim? I don't understand how the original paper was published sans data in the first place. Science does not make the matter any better by only publishing the critique online as a "technical comment". Could they be down playing the controversy to keep the sensationalism of the original paper?

Hopefully the creationists don't get their dirty paws all over this. Undoubtedly, they'd use this as fodder for a "evolutionists are faking evidence again. Dinosaurs and birds aren't related" argument. You know how they keep bringing up Piltdown Man...

Saturday, 23 August 2008

Yndi Halda

Yndi Halda is a post-rock band out of the UK. They play some of the most stunningly beautiful music I've ever heard. It's incredibly atmospheric and even feels optimistic, something that differs them from alot of post-rock bands. The video above is a clip from one of their songs (their best, in my opinion), "We Flood Empty Lakes" - the full track is 14 minutes long. The song really reaches a climax at about 4 minutes into the clip. One of the greatest pieces of music. Ever.

Friday, 22 August 2008

And so it begins.

I've posted before about how dangerous the "Green Vaccine" movement is. I've pointed out how Japan shows a perfect example of what happens when fears over vaccines keep parents from vaccinating their children. And I predicted a similar trend would start in North America if the "antivaxxers" weren't stopped.

And it's already begun.

"Measles cases in the U.S. are at the highest level in more than a decade, with nearly half of those involving children whose parents rejected vaccination, health officials reported Thursday. Worried doctors say they are troubled by the trend fueled by unfounded fears that vaccines may cause autism. The number of cases is still small, just 131, but that's only for the first seven months of the year. There were only 42 cases for all of last year[...]In a typical year, only one outbreak occurs in the United States, infecting perhaps 10 to 20 people. This year through July 30, the country has seen seven outbreaks, including one in Illinois with 30 cases, said Seward, of the CDC's Division of Viral Diseases."
Measles was a big problem in America prior to the introduction of vaccination in the 1960s, after which, cases and outbreaks plummited. Parents have began to reject vaccinations, and now measles are becoming a big concern again. Why don't people realize this? Why must people insist that vaccines are harmful despite the plethora of scientific evidence showing otherwise?

Scientists and doctors need to speak out about this. Facts and evidence have to be given to the general public to counter the complete ignorance of the Green Vaccine. This literally can be a matter of life or death.

Ooh Fancy

I just got me one of those FeedBurner things. I don't really know what it does other than keep track of the hits my blog gets and who (if anyone) subscribes to it.

All I know is that I have now developed a compulsive habit of clicking refresh on my "Live Hits" page over and over....


...One hit! Another Google Bot! Score!

EDIT: I ust realized that I dont have any way of knowing whether or not messing around with FeedBurner has screwed up my original blog feed. So, if you're reading this post via a feed and not through my actual blog site, It'd be appreciated if you left a comment telling me everything's a-Ok.

Thursday, 21 August 2008

Scientists are so ignorant!

EDIT: For some reason this entire post disappeared. I cant embed the video at work because the computers in the lab hate Youtube...I'll fix it when I get home

EDIT AGAIN: Alright, fixed :)

If I didn't know for a fact that Edward Current's videos were satire, then I would be compelled to think that this video was entirely serious. That's the sad reality of the anti-science being pushed by Evangelical Christians.

Check out Current's other videos if you like satire done well.

More sillyness from the crazies at WorldNetDaily

The crazies over at WorldNetDaily have sent their monkeys to their typewriters again and have produced an article not entirely unlike what you would expect from simians banging away at a keyboard. Columnist Dennis Prager has written up a list of the "deleterious consequences of secularism". Alot of them are simple rehashes of the same, tired, religious arguments we've all heard a million times over. Nevertheless, let's dissect them one by one, shall we?
1. Without God, there is no good and evil; there are only subjective opinions that we then label "good" and "evil." This does not mean that an atheist cannot be a good person. Nor does it mean that all those who believe in God are good; there are good atheists and there are bad believers in God. It simply means that unless there is a moral authority that transcends humans from which emanates an objective right and wrong, "right" and "wrong" no more objectively exist than do "beautiful" and "ugly."
Prager here has made one large, fatal, assumption: he assumes that "good" and "evil" can only be defined by God. In actuality, "good" and "evil" have been determined almost entirely by our societies and by simple facts of human nature. Stealing is "evil" because it puts innocent people at a disadvantage. Buying a homeless guy a sandwich is "good" because it helps someone live their life easier. These are not metaphysical concepts handed down by some sky God; rather they can simply be explained as artifacts of our human evolution. Humans everywhere, regardless of whether or not they live in a secular society, have morals because morals were necessary for our distant ancestors to survive. Living in a society conferred a distinct survival advantage, and those acts which helped such societies flourish are those which we deem "good". Likewise, acts which were detrimental to the functioning of society are those we deem "bad". Our morals are not inscribed on slabs of stone, handed down from the Mount. They are inscribed on us through the course of our evolution.

Furthermore, if our moral compass were given to us via God, then one would expect that there would be some sort of moral absolute. This is indeed not the case. While, for the most part, societies have the same morals - no killing, stealing, lying - many societies have slight variations. Why did the Vikings think it was morally acceptable to pillage helpless monks along the coasts of England, while at the same time, they had very harsh punishments for murder? If there was moral absolutism, then their actions should have been morally abhorrent to them. Pillaging was something that helped their society survive, and it is likely that this is a large contributing factor to the moral acceptance of their pillaging actions.

Not only this, but God is possibly one of the worst candidates for determining "good" and "evil". If he were the authority on such matters, then I suppose slaughtering children for laughing at baldness is "good", and wearing polyester is "evil". I'd trust the moral relativism of human societies over the moral absolutism of God anyday.

2. Without God, there is no objective meaning to life. We are all merely random creations of natural selection whose existence has no more intrinsic purpose or meaning than that of a pebble equally randomly produced.

Again, Prager is making an unwarranted assumption: who says there needs to be a "higher" purpose to life? What intrinsic purpose is there to the life of an ant or a gazelle? Humans have no more of a purpose than any other animal, and assuming that humans should have a higher purpose is unjustifiably anthropocentric. Is this to say humans have no purpose beyond passing on our genes? Hardly. Humans can have a higher purpose - but that purpose is not given by any God. You give yourself a purpose in life. My purpose in life is to do scientific research, to learn, explain, and help make the world a better place. Living in a secular society, or denying God does not subtract from having a "purpose". Quite to the contrary, it gives you the freedom to choose your own purpose in life.

3. Life is ultimately a tragic fare if there is no God. We live, we suffer, we die – some horrifically, many prematurely – and there is only oblivion afterward.

I fail to see how this is a detrimental effect from a secular society. Sure, it's depressing, but that's the nature of reality. Life is not always sugar coated fun and games. Believing in something simply because it makes you happy is a pretty lousy reason for believing. If I were to go to the doctor, and he were to tell me that I was diagnosed with cancer, what good would it do to say "No, I prefer to believe that I'm healthy. Having cancer would be such a tragic fare"? One cannot forsake truth simply for comfort. All other creatures on the planet face the same tragic fare of life, suffering and death, and they seem to accept that fate. What we as humans can do is strive to reduce the suffering in the interim.

4. Human beings need instruction manuals. This is as true for acting morally and wisely as it is for properly flying an airplane. One's heart is often no better a guide to what is right and wrong than it is to the right and wrong way to fly an airplane. The post-religious secular world claims to need no manual; the heart and reason are sufficient guides to leading a good life and to making a good world.

We do have instruction manuals. We call call these instruction manuals "laws". To say that secular society claims that no manual is needed to keep our behaviour on the right track is tantamount to claiming secularists crave for anarchy. This is entirely untrue. As outlined in Point 1 above, we need rules for a functioning society, regardless of where those rules are derived from.

5. If there is no God, the kindest and most innocent victims of torture and murder have no better a fate after death than do the most cruel torturers and mass murderers. Only if there is a good God do Mother Teresa and Adolf Hitler have different fates.

Again, this is simply the cruel nature of life. It might be comforting to think that good people will suffer a fate better than those who are evil, but it isn't reality. In fact, belief that doing good will get you into heaven when you die only cheapens acts of kindness; shouldn't one be kind out of the goodness of your heart and not because you want to belong to some kind of exclusive club when you die?

6. With the death of Judeo-Christian values in the West, many Westerners believe in little. That is why secular Western Europe has been unwilling and therefore unable to confront evil, whether it was Communism during the Cold War or Islamic totalitarians in its midst today.

This is one giant non sequiter. What does "believing in little" have to do with "confronting evil"? Western Europe has not confronted the "evils" of Islamic totalitarians today or communism during the Cold War not because they didn't believe in anything, but because they did believe in something: acceptance and tolerance of people who's views may disagree with ours. If "believing in something" is simply rightwing speak for "intolerance and discrimination", then Western Europe is better off "not believing".

7. Without God, people in the West often become less, not more, rational. It was largely the secular, not the religious, who believed in the utterly irrational doctrine of Marxism. It was largely the secular, not the religious, who believed that men's and women's natures are basically the same, that perceived differences between the sexes are all socially induced. Religious people in Judeo-Christian countries largely confine their irrational beliefs to religious beliefs (theology), while the secular, without religion to enable the non-rational to express itself, end up applying their irrational beliefs to society, where such irrationalities do immense harm.
And it was largely the religious, not the secular, that burned "witches" at the stake in Salem, that believed a woman could turn into a pillar of salt, that believed in slavery was entitled to them by God. If you want to compare the irrational beliefs of secular people to those of religious people, you'll find the scale dips mightily on the religious side. It is absurd to say a secular society would breed irrationality because we have ample evidence both historical and modern that shows religious belief to spawn irrational thoughts that extend beyond the realm of theology (one only needs to take a look at the 2012 doomsayers/Nefilim conspiracy theorists to see this!). A secular society would teach people critical thinking, how to be rational, so irrational thoughts wouldn't need a place to be expressed. It is in a religious society, where every aspect of life is guided by an irrational belief based on an irrational book about an irrational god that does immense harm.
8. If there is no God, the human being has no free will. He is a robot whose every action is dictated by genes and environment. Only if one posits human creation by a Creator that transcends genes and environment who implanted the ability to transcend genes and environment can humans have free will.
The topic of free will is one of deep, interesting philosophical discussions, the details of which are not of the essence in this post. But to say that free will is only possible if humans were created by a Creator is setting up a false dichotomy. It is entirely possible that free will (or the illusion of it) came about during our evolution. I am by no means an expert on this subject, so I will direct interested parties to the Stanford Encyclopedia of Philosophy page on Free Will.
9.If there is no God, humans and "other" animals are of equal value. Only if one posits that humans, not animals, are created in the image of God do humans have any greater intrinsic sanctity than baboons. This explains the movement among the secularized elite to equate humans and animals.
Again, who says that humans need to have "greater intrinsic sanctity" than baboons, or lions, or goats? I have yet to hear a rational argument (or even an irrational one) regarding why humans need to be "better" than mice or deer or cattle. And if we really must have a greater intrinsic value, might it not be our sentience, our higher cognitive functions, our ability to think and reason (at least for some of us) that gives us that value? Why look to God to give us a special place on Earth when it can be found in our very own humanity?
The reason the "secularized elite" wish to equate humans and animals is because humans ARE animals. Animals can be defined as "A multicellular organism of the kingdom Animalia, differing from plants in certain typical characteristics such as capacity for locomotion, nonphotosynthetic metabolism, pronounced response to stimuli, restricted growth, and fixed bodily structure." Do we not fit such a description perfectly?
10. Without God, there is little to inspire people to create inspiring art. That is why contemporary art galleries and museums are filled with "art" that celebrates the scatological, the ugly and the shocking. Compare this art to Michelangelo's art in the Sistine Chapel. The latter elevates the viewer – because Michelangelo believed in something higher than himself and higher than all men.
This is probably one of the most absurd claims Ive heard. Admittedly, the works of many of the greatest artists have been inspired by religion, but to say that without God, there would be no inspiration for great art is ridiculous. The contrary is evident when you consider the likes of Pablo Picasso. Unarguably one of the most influential artists of modern times, Picasso was an atheist. God inspired none of his works, yet his works were great. Frank Lloyd Wright, an architect who designed some of the most famous modern buildings, was also an atheist. It should be obvious that God is not a requirement for great art.
11. Without God, nothing is holy. This is definitional. Holiness emanates from a belief in the holy. This explains, for example, the far more widespread acceptance of public cursing in secular society than in religious society. To the religious, there is holy speech and profane speech. In much of secular society, the very notion of profane speech is mocked.
Yet again, who says there needs to be "holiness"? Prager seems to have a habit of saying a secular society would be without something, yet not showing how that something is needed to a proper, functioning society. Of course there would be nothing holy in a secular society! Its a secular society! Unless someone can show me how holiness is necessary, then I fail to see how this is a detrimental effect of secularization.
12. Without God, humanist hubris is almost inevitable. If there is nothing higher than man, no Supreme Being, man becomes the supreme being.
See above.
13. Without God, there are no inalienable human rights. Evolution confers no rights. Molecules confer no rights. Energy has no moral concerns. That is why America's founders wrote in the Declaration of Independence that we are endowed "by our Creator" with certain inalienable rights. Rights depend upon a moral source, a rights giver.
Another "moral" argument. Humans have human rights but they were not given to us by God. We have decided on our own inalienable human rights based on our own humanity, based on helping other humans, in the name of fairness and equality. Why does the United Nations, a secular organization which represents countries of all cultures and faiths spend so much time on human rights if such rights do not exist in the absence of God? It's because they are right we have decided amongst ourselves to ensure everyone on the planet gets treated fairly and equally. In a religious society, the situation would be quite to the contrary. In a religious society, not everyone is equal, and not everyone is fair. "Human rights" would only apply to a select few - those that subscribe to the religion of choice. One only has to look as far as gay marriage to see that religious society denies rights rather than bestows them.

14. "Without God," Dostoevsky famously wrote, "all is permitted." There has been plenty of evil committed by believers in God, but the widespread cruelties and the sheer number of innocents murdered by secular regimes – specifically Nazi, Fascist and Communist regimes – dwarfs the evil done in the name of religion.

Ah, it was only a matter of time until Prager whipped out a reductio ad hitlerum argument tied into a strawman argument. First of all, the Nazi regime was not a secular regime in the least. Gott Mit Uns was the national motto for crying out loud! Hitler was explicitly Christian, and anger over the idea that the Jews killed Jesus was one of the contributing factors to his plan of wiping out the Jews. There is a literal wealth of information identifying Hitler and the Nazi regime as religious that I wont bother to go into all the detail. Not to mention that fascist Italy had direct ties with the Vatican, and Mussolini was endorsed by the Pope himself.
Secondly, there has never - NEVER - been a case where innocents have been murdered in the name of secularism. I cannot deny that there have been atrocities committed in secular societies but the question is whether or not it was the secularism that lead to such atrocities; the answer is no. It was not secularism that caused the murder of innocents, but twisted political ideologies irrespective of secular beliefs. Did Stalin kill innocents because he was an atheist? No. He killed innocents because he was a power-crazy dictator. When it comes to atrocities and the murder of innocents, the Bible trumps all on nearly astronomical scales.

So really, none of Prager's 14 arguments holds up to any scrutiny. Many of them do not even explain how the effects Prager posits secularism leads to are detrimental to society. And many more are age old misconceptions on morality.

Then again, what else does one expect from WorldNetDaily?

Wednesday, 20 August 2008

Modern medicine? Pshaw!

FOXNews has a new article that reveals an absolutely apaling statistic: over half of Americans say they believe God can save patients from dying if doctors determined that medical treatments were futile. One third of those surveyed said that patients should have the right to demand such treatment - i.e. the right to demand to be prayed over rather than given medical treatment. And what's more disturbing is this quote:
"When asked to imagine their own relatives being gravely ill or injured, nearly 20 percent of doctors and other medical workers said God could reverse a hopeless outcome."

One fifth of America's medical personelle believe that God can save the lives of those with terminal illnesses.

These statistics disgust me for two main reasons.

Firstly, the belief that God can intervene when doctors cannot is the start of a slippery slope. I can understand that when a person is terminally ill, and there's nothing that doctors can do to save them, family members may be inclined to cling to whatever gives them hope that their loved one will pull through. It's human nature to want to hope such things, and it makes sense that people would look to God for that hope. However, if people really, actively believe that God can send down a miracle and save their loved one better than professional medical staff can, then what's to stop such people from not bothering to seek medical care to start with? If God is more of a powerfull healer than doctors, then why not prey for God to send down a miracle instead of seeing a doctor in the first place? Believing that divine intervention can save the lives of terminally ill patients can very well lead to a dependance on God rather than modern medicine for treatment. If such a trend were to develop, it would be quite a medical disaster. Already, we've seen cases - usually in evangelical families - were people have relied on God to heal their children rather than taking them to see doctors...with fatal results.

The second problem with this is that it greatly devalues the hard work medical personelle do to save a life. If a terminally ill lukemia patient makes a turn for the better, his cancer goes into remission, and it's chalked up to "divine intervention", then the hard working doctors that put so much effort into saving his life don't get the credit that they deserve. Even if the doctors have claimed further medical treatments to be futile, the work they did beforehand, the effort and resources they put into saving his life, becomes devalued. What worth do doctors have when God trumps their work?

I am also disturbed by the number of doctors who believe that God can intervene and save lives when they cannot. I would be very frightened if I were told by a doctor "Well there's not much I can do for you, but if you pray hard enough, God might heal you instead." I see this as going against the Hippocratic Oath. Doctors are supposed to do what they can for the good of their patients, and not to do any harm. A reliance on God to heal, whether medical treatment is futile or not, does more harm than it does good.

Monday, 18 August 2008

The Crichton Dilemma

I have a deep, dark secret to admit. I am a fan of Michael Crichton.

Now, to a lot of people, admitting such a thing is no big deal. "What's wrong with enjoying his work? I mean, Jurassic Park was great!" they might say. But to someone as science-centred as myself, it is a big deal.

I've been a fan of Micael Crichton for a long time. The first book of his that I read was The Lost World, the sequel to Jurassic Park, back when I was in 4th Grade (I remember it clearly, my 4th grade teacher asking me if my parents approved of me reading something filled with explicit language and violent, gorey scenes - the book was entirely unlike the crappy movie version). Since then, I've read about half of his most well known works (Sphere, Timeline, Prey, State of Fear, and Next). And I liked them. All of them. And I'm eagerly awaiting his next book, to be released this December. The reason I like his work is because they always include lots of science. Whether it be the science of genetics, as in Next or quantum mechanics, as in Timeline, Crichton's books have always been centered around science.

But what has caused alot of science-minded folks to dislike him is the precieved "anti-science" message his books have. Jurassic Park had genetically reconstructed dinosaurs....that went on a rampage, destroying and killing all in their path. Prey featured nanotechnology and self-reproducing nanobots...that devoured people and took over their lives. Timeline had timetravel and quantum mechanics....and people ended up going back in time, getting killed in horrific ways. Alot of people read his books and walk away with a feeling that Crichton is completely anti-science, like he's saying "Look at all the terrible things that science causes! People die and their lives are ruined because of what science does!" and this has caused alot of people to shun him and his work.

I look at it differently though. I dont see Crichton as having a totally anti-science message. Rather, his work acts as a caution. His stories all tell of the bad things that can happen if we do not use our newfound discoveries and technologies in a responsible manner. Crichton is not saying science is bad. He's saying "Be careful. Science can give us some totally amazing things but it can be terrible if we are not responsible". And this is a message that I agree with completely. I absolutely love science (so much that I have dedicated my life to it!) but it is easy to see how science can be dangerous if used improperly - look at the atomic bomb, for instance.

This is not to say that I support Crichton and his views entirely. Crichton is known for being a climate change denier (his book State of Fear was about 'ecoterrorists' deliberitely changing the climate to convince the public of, well, climate change), and has even said that SETI is more of a religion than science (!). However, this is immaterial concerning his views on whether science is good or bad.

Nevertheless, I am a fan of Michael Crichton. Many people may think that, as a scientist, I should be ashamed of that. But I'm not. His stories are always interesting, thrilling and carry an important message of scientific responsibility (even if he does get some of the scientific details wrong). Why should one be ashamed of liking that?

Wednesday, 13 August 2008

Well I'm stumped.

Alright guys, we've been trumped. I guess God must exist after all:

"Any Atheist who can prove why and how the sky is staying without falling without the help of pillars???

Sky is not resting on pillars, right? So who is keeping this sky afloat on on heads in the middle of nowhere. What is the cause of "sky" hanging without any support?

Answer me and I will become an Atheist

I hear that the atmosphere is composed of gasses but that couldn't possibly have anything to do with it, right?

Hold on a second, my Sarcasm Meter just went nuclear.

A Lesson in Logical Reasoning

One common tread I've noticed (and undoubtedly anyone with an iota of intelligence has also noticed) that runs though silly religous arguments is that for the most part, people do not know how to reason logically. Just take a quick look at Fundies Say The Darndest Things and you'll immeadetly realize that; pretty much every post is ladened with at least one type of fallacious reasoning.

However, by far the most common form of illogical reasoning is the type where someone equates two totally unrelated things as being the same, or where someone claims that two things which are similar in some superficial way as being the same thing. For example, take this gem:

"Imagine that you could listen to or talk face-to-face with satan about any subject that has to do with God.

Then bring to remembrance anything you've heard atheists say against God. (Or if you are an atheist, you know your own sentiments and thoughts).

Now, if you try, you will find that it is impossible to imagine satan expressing sentiments about God different than what atheists express. Satan certainly is not going to speak positively about God, and neither are atheists. So, what both think and verbalize is in complete harmony with one another.

Atheism is therefore a doctrine of demons, and in many, if not all cases, atheists are demon-possessed

The reasoning behind this kind of claim goes something like this:
X is A
Y is also A
Therefore X is Y.
The problem with this kind of thinking should be pretty obvious. For example, swans are white (yes I know there are also black swans). A Boeing 747 is also white. Therefore swans are simply miniture Boeing 747s. Swans fly. Boeing 747s fly. Swans really must be Boeing 747s.

Obviously, this is not true.

This kind of reasoning only works if A, that characteristic which is shared by both subjects, X and Y is a defining characteristic of either X or Y. Let me explain.

If, for example, you said that birds were defined as "animals which have two feathery wings", then anything that has the characteristic of "having two feathery wings" would be classified as a bird. Now:
Birds have two feathery wings.
Swans have two feathery wings.
Swans are birds.
This works because of the use of a defining characteristic. Defining characteristics are such that anything with that characteristic falls into that classification; and anything that is NOT classifed as such CANNOT have that characteristic.


"Two feathery wings" is a defining characteristic of birds. Anything with that characteristic (anything with two feathery wings) falls into that classification (is a bird). Anything that is not classified as such (anything that is not a bird, such as a gazelle, or a whale) CANNOT have that characteristic (they CANNOT have two feathery wings). This is what is meant by a defining characteristic.

Being white and flying is not a defining characteristic of Boeing 747s or swans, so this kind of reasoning fails in such a case.

Also note that this kind of reasoning only works when describing categories, such as "birds". This reasoning allows one to classify subjects but not to make assertions that one thing IS another thing. For example:
Swans have two feathery wings.
Geese have two feathery wings.
Therefore swans are geese.
This does not work; "geese" applies to a specific bird (or a handful of species) rather than to a broad "class" of birds.

When we look back at the reasoning given in the original fundie argument, we see it violates both of these rules. It does not pretain to defining characterists (anti-God sentiments surely are part of being an atheist, but are not a defining characteristic; it is entirely plausible that one can be "anti-God" but not be an atheist), and it does not apply to categories (neither "Satan" nor "atheist" are categories).

Alas, this kind of reasoning is rampant amongst fundies. A vast number of arguments can be countered based on the fallacy outlined above alone. Its a shame (and kinda funny) that so many people keep coming up with this kind of argument and expect it to stand up to scrutiny.

Monday, 11 August 2008

Techniques in Molecular Biology: Western Blotting

Today I thought I'd go into a little detail on one of the most common experimental techniques used in molecular biology - one that I've done far too many times this summer - the western blot.

In general, western blots are a technique that is used to determine the presence of a particular protein from a biological sample. For example, let's say that you've introduced a plasmid carrying the gene for alcohol dehydrogenase into E.coli and you want to check to see if the bacteria are actively transcribing and translating the gene. An easy way to check this is with a western blot. Westerns are also a useful diagnostic tecnhique in medical labs: westerns can tell you whether a protein is the wrong size, or if a particular protein from a virus or bacterium is present in a sample from a patient.

The theory behind Western Blotting is rather simple. First, you need a sample of proteins. These can be obtained in a variety of ways but they way that I'm most familiar with is through the use of sonication. A culture of cells is grown which (supposedly) express the protein you're interested in. By subjecting these cells to very high frequency sound, the cells rupture and spill all of their contents. One can then put the sonicated sample into a centrifuge, so all of the cellular debris clumps together at the bottom of the test tube, and the proteins in the cell are left floating around in the supernatant.

Now that all the proteins have been isolated, you need to seperate all of them. This is done by using electrophoresis on a polyacrylamide gel. Polyacrylamide forms a mesh through which the proteins travel through when an electric current is applied. Bigger proteins travel though the gel slower than smaller proteins; this, then, allows us to seperate all of the proteins based on their size. At this stage, it is possible to use a protein stain to stain the gel. This will allow us to easily visualize the proteins on the gel. Unfortunately, unless you were working with a pure sample of your protein of interest, you'd see a large smear since the gell contains ALL the proteins from the sonicated cells. To determine the presence of your protein of interest, you'd need a way to specifically visualize your protein and not the rest. Western blotting allows us to do this with ease.

We can speficically visualize whichever protein we want, but polyacrylamide gels do not allow us to do this. Thus, the next step is to transfer the protins to a medium which we can use to probe for a specific protein. One commonly used material for this is nitrocellulose membrane. Nitrocellulose has a very useful property - pretty much any protein sticks to it like glue (this also makes it a little tricky to handle, because you dont want proteins from your hands sticking to it and messing up your results. By making a nitrocellulose-polyacrylamide gel sandwich, and applying an electric current, you can force the proteins in the gel to transfer to the nitrocellulose. The membrane should then contain the proteins seperated as they were on the gel.

Now you're ready to detect specific proteins. This can be accomplished by using antibodies against whichever protein you're interested in. Alot of companies sell antibodies for commonly used proteins. Alternatively, you can design your protein so that it contains a "tag" - a short sequence of amino acids - at one end of the protein which is absent in proteins naturally produced in cells. You can buy antibodies which recognize different tags, and thereby bind only to your protein of interest. These antibodies will bind directly to the proteins on the membrane. Next, secondary antibodies are applied. These will bind specifically to the first antibodies.

The secondary antibodies are the key to detection of your protein. Attached to the secondary antibodies is an enzyme. Which enzyme is attached is a matter of the method of detection used. There are multiple ways of detection, but the most commonly used methods are chemiluminescent detection and pigment production. Both methods work in a similar way; attached to the antibody is an enzyme which will convert a substrate into a product when applied to the membrane. In the case of pigment production, the product is a pigment which can be direcly visualized on the membrane. In the case of chemiluminescent detection, the conversion from substrate to product produces light, which can be detected on a piece of X-ray film. In both cases, the result is a dark band representing your protein of interest. Where there is a dark band, there is the secondary antibody/enzyme; where there is secondary antibody, there is primary antibody; and where there is primary antibody, there is your protein of interest.

The image to the right shows what this end result looks like. You can also run a protein ladder along side your sample, which will show the size of known proteins, so you can determine the size of your protein.The whole process of western blotting can take a few hours to complete (or all day if you're bad at it like me). There is, of course, alot more to western blotting than this; what I've presented is a very generalized idea of how western blotting works. Nevertheless, it is a reliable way to detect the presence of any protein you want in a sample, and has become a staple technique of molecular biology.

Friday, 8 August 2008

Couldn't Have Said it Better Myself

Here's a clip from Henry Rollins' show, where he discusses the evolution vs Intelligent Design 'debate'. Rollins has such a way with words.

I couldn't have said it any better myself.

Stockwell Day gets it; Winnipeg MP almost gets it.

Well it seems that the Phelps clan probably won't be making any appearances in our country any time soon. They've been barred from our country. CBC News reports:

"Public Safety Minister Stockwell Day's office sent an alert to border patrol to "look out" for people with signs and pamphlets consistent with the messages that the church promotes and to keep them out of the country, Winnipeg MP Pat Martin told CBC News on Friday"

At least Stockwell Day gets it. These people are vile, disrespectful excuses for humans and shouldn't be let into our country. This is great news. However, I have a bit of a bone to pick with Winnipeg MP Pat Martin...

""Entering Canada by a U.S. citizen isn't an absolute right, and if you're coming here only to disrupt the social order and to promote what we consider to be bordering on hate crimes or hate language, they shouldn't come into Canada," Martin said."

He's absolutely right that entering our country is not an absolute right, but whats this about 'bordering' on hate crime or hate language? How can someone in our country publicly exclaim "Jesus Sucks" and be charged with hate crimes, yet a known hate group can come into our country, spew thier vile, hateful filth and that only boarders on hate crimes? It IS a hate crime. It IS hate language.

The reason why the Westborro Baptist Chruch's members havent been locked up or at least fined for what should be obvious reasons is beyond me. Oh, wait, nevermind. It's probably because they hide behind that impervious shield of religion. They get away with saying what they please because it's their "religion". They get to spew their intolerance because disagreing with them means you are intolerant.

So far they've only been barred from entering our country - the boarder guards have been instructed to turn them away. They haven't explicitly been BANNED from Canada and they may make their way in elsewhere. Hopefully the government realizes the need to have these lunatics outright banned and follow Massachusetts and keep them out for good.

Thursday, 7 August 2008

A Busy Week for the Phelps Clan

It's been a busy week for those fear-mongering, inhuman folks in the Phelps clan. Only a few days ago, the Westboro Baptist Church were hit by a fire that destroyed their church (whether it was arson or not it was arson has yet to be determined). This weekend, they are going to be in Red Deer, picketing the Laramie Project, and now this:

"A church group described in a British documentary as "the most hated family in America" says it will head to Canada this weekend to protest Tim McLean's funeral.

The daughter of the founder of the Westboro Baptist Church, based in Topeka, Ka., told she and several other church members will go to Winnipeg on Saturday to demonstrate against what she described as McLean's "filthy way of life." Shirley Phelps-Roper said his life was emblematic of Canada's moral decay."

The WBC are claiming that Tim McLean's death was a gift from God. They are claiming that he lead a "filthy" way of life (who knew that the WBC was against carnies?!). They are claiming that he came from a "rebel country" ( a "fag nation' as Phelps has previously refered to Canada). And they are heading to Winnepeg to picket his funeral.

This is absolutely deplorable. Do they really believe that it is God's will to have people they dislike brutally decapitated on a public bus? The Phelps clan literally makes me sick to my stomach.

With any hope, they will be denied entry into Canada. Why they would be allowed to pass when they are entirely likely to be a threat to public order and intice hate crimes.

Wednesday, 6 August 2008

Dead or Alive: The Debate on Viruses is Renewed

One of the biggest debates in biology today is over whether or not viruses count as life. Most scientists would contend that viruses are not alive and for good reasons: they cannot replicate on their own and require hijacking of their host's replication machinery in order to reproduce, they do not have any metabolism, they have no cellular structure and their replication is driven by spontaneous assembly or virus particles rather than by cellular division. Classifying viruses as "alive" would mean that cellular organization would not be included as a requirement for life (and opening the category up to things like prions). But according to a new article published in Nature, new findings are beginning to challenge the notion that viruses are not alive.

In 2003, a new family of viruses was discovered by researchers in France. From a sample taken from a cooling tower in the UK, researchers found a new type of virus that was infecting ameobae in the sample.1 This virus was way bigger than any other viruses known at the time, both in physical size and genome size. Having about 900 protein-coding genes - 3 times that of the next biggest virus and larger than some bacterial species - the virus is a behemoth. It was called mimivrus, for "mimicing microbe".

But that isnt the interesting part.

The same research team recently isolated a new strain of this giant virus, again from a cooling tower - this time in Paris. Electron micrographs of the virus showed that this strain, called mamavirus, had a friend. They discovered another, tiny virus that was closely associated with the mamavirus. They nicknamed this one Sputnik because it seemed to be a satellite of its larger companion. The team noticed that the mamavirus infected ameobae, just like its mimivirus cousin, and turned the cells into a virus assembly line to pump out more mamaviruses. However, if the amoebae were coinfected with Sputnik, the little satellite virus would hijack - not the amoeba's machinery - but the viral factory set up by the mamavirus! The mamavirus particles would turn out all screwed up and less infectious. It would seem that Sputkik is a viral virus! The researchers had found the first known virophage.2

Just like bacteriophages prey on bacteria, virophages prey on bacteria. They hijack the virus' machinery (that the virus itself has hijacked from the host cell), and this causes the virus to become ill. And that is what has rekindled the debate over viral "life". How can a virus - something that supposedly isnt alive - become sick?

I dont belive that this really throws a monkey wrench in the current classification of viruses as "nonlife". What the virophage is doing is interfering with the mamavirus' "virus factory" for its own use, and the mamavirus progeny turn out sickly. This is not a whole lot different from mutating a step in the assembly line so the virus churns out avirulant progeny. Mutate gene A so that protein B isn't incorpreted into the viral capsid, and you get viruses that are less infectous. Does that mean that the virus is alive? Not really. In both cases, the same sort of assembly line is being interrupted. A virus falling prey to another virus makes neither of them any more "alive" than viruses that have been mutated in a lab. The only difference here is that the changes to the viral factory are being carried out by another virus instead of a mutagen. Does that mean that the virophages are "alive"? No more than bacteriophage are alive. The new findings, I feel, do not suggest that viruses are alive. They suggest that viruses can fall prey to their own devious schemes.

But, draw your own conclusions. The debate on whether or not viruses are alive will not end with these new findings, and is likely to only become more intense. But, regardless of whether you think viruses are alive or not, you have to admit: mimi/mamaviruses and virophages are pretty frickin' cool.

1. La Scola, B. et al. Science 299, 2033 (2003)
2. La Scola, B. et al. Nature doi:10.1038/nature07218 (2008)

Tuesday, 5 August 2008

And the Award for Worst (or Best?) Paper Title Goes To...

...Tracey Chapman (no, not Tracy Chapman) for her article The Soup in My Fly: Evolution, Form and Function of Seminal Fluid Proteins published last week in PLoS Biology.


Move over Godwin, here comes Gore

We skeptics are very familiar with Godwin's law. This law refers to the pratice of reductio ad hitlerum, or arguing that something is bad or wrong because Hitler/the Nazis did it/used it/approved of it. More specifically, it was coined in the 90's by lawyer Mike Godwin and states:

"As a Usenet discussion grows longer, the probability of a comparison involving Nazis or Hitler approaches one."

In other words, argue online long enough, and someone will pull a reductio ad hitlerum. But now that climate change has become a major issue and climate change deniers are on the rise, a new law has been coined. This law is Gore's Law:

"As an online climate change debate grows longer, the probability that denier arguments will descend into attacks on Al Gore approaches one."

If this kind of thing becomes more common, will arguing reductio ad goreum become the trend?

Friday, 1 August 2008

So what was Darwin, a Priest of Ra?

Wouldn't you know it? Evolution is aparently a form of sun worship:
The Second Law of Thermodynamics was set in motion in Genesis 3 - after the Fall. Evolution, which is a form of sun worship, says that the sun provides the energy needed to keep life going on this planet. Yet, for some inexplicable reason, this supposedly life-sustaining aten cannot prevent death from occurring, nor can it bring the dead back alive.

No, the Second Law cannot prevent microevolution from occurring, but, sans divine intervention, will shut down the primary god that evolution worships.

Has it occurred to you that in Eternity Future there will be no need of the sun?
Evolution doesnt say that the sun is needed to sustain life on Earth. Basic freaking biology says that the sun is needed to sustain life on earth. And what does the sun not preventing death or reversing death have to do with anything? Those issues are entirely external to evolution.

Not to mention that this is another bastardization of the second law of thermodynamics. Entropy really isnt that hard to understand. Though, if most creationists can't seem to get their heads around a little basic biology, it shouldn't be surprising that they're totally lost when it comes to thermodynamics.