Friday, 25 September 2009

A.C. Grayling Knows This Much

AC Grayling is perhaps one of the better known philosophers of today, and he recently wrote a piece for The Guardian entitled "This Much I Know", filled with interesting philosophical tidbits. Here are a couple that I found the most poignant.

Science is the outcome of being prepared to live without certainty and therefore a mark of maturity. It embraces doubt and loose ends.
The democracy of blogging and tweeting is absolutely terrific in one way. It is also the most effective producer of rubbish and insult and falsehood we have yet invented.

A human lifespan is less than a thousand months long. You need to make some time to think how to live it.

I'm not sure it is possible to think too much. You don't refresh your mind by partying in Ibiza.

Thursday, 30 July 2009

Fox News needs a lesson in geography...

Fox News might be the self-proclaimed "Fair and Balanced" (yeah right) news channel but it would seem they spent too much time mopping up Bill O'Riley's vile spew and not enough time reading their geography text books.

Notice anything a little off here?

I ask: how can anyone find Fox News a trustworthy source for information pretaining to issues in the Middle East when they don't even know the correct location of Egypt?

(via Media Matters)

Sunday, 26 July 2009

The Food Network caves to Big Prayer™

The Food Network is not a television station that I watch alot (mainly because it makes me very hungry whenever I do), but earlier today I was watching a show about using liquid nitrogen in the kitchen. During one of the commercial breaks, an ad caught my attention. It featured a man, on the street, lamenting about the world's economic situation (try as I might, I can't seem to find the ad on Youtube). What piqued my interest was that the man began saying how he began praying that things would get better...but it didn't seem that prayer made any difference. He went on to say how he was beginning to question if prayer actually did anything. "Alright," I said to myself, "an ad supporting critical thinking and rationality!" That's when the ad turned a different direction: the answer, the man said, was because he simply wasn't praying big enough.

The ad, it turns out, was for a book called Pray Big. There wasn't really any information about the book, but it gave a website to check out: So I did.

Pray Big, sponsored by "Crossroad Christian Communications" (the folks responsible for spewing out 100 Huntley Street) is written by Will Davis Jr., a guy who resembles a wimpy Al Bundy. He likes to point out that his official title is Dr. Will Davis Jr., despite the fact that his CV consists of a BA in History from Baylor University and a Masters in divinity and a "doctorate in ministry", whatever the hell that is, from Southwestern Baptist Theological Seminary (try getting a PhD from a real University before calling yourself a doctor next time, Davis).

The website claims:
"Will Davis Jr. offers straightforward guidance on how you can pray with focus and confidence for big things, small details, other people and, yes, even yourself. He teaches you how to pray and includes one hundred pinpoint prayers based on the Bible."
Davis supposedly teaches the idea of "big, pinpoint prayers". In other words, he thinks that prayers work better if they are specific and for big things (ignoring the fact, of course, that prayer of any kind doesn't work at all). He claims that when people pray they typically "underask" for things from God. The problem with prayer, he says, is that people should ask for MORE.

To be honest, I'm not surprised by this at all. The whole idea of prayer is inherently a selfish one. Christians believe that God put humans on the planet for the sole purpose of worshiping him, and nevertheless, they expect that their God should give them whatever they demand, just as long as they put their hands together, close their eyes and whisper some words off into the aether. Davis simply takes the egotistic concept of prayer and stretches it to the next level: don't ask for wimpy things, ask for BIG things!

But the bigger issue here is: why is the Food Network airing ads for this Christian hogwash? They are a private company, so I suppose they are allowed to air whatever ads they wish, but what do you think the chances are of airing an ad supporting a secular or humanist view? What do you suppose their excuse would be rejecting such an ad?

Friday, 17 July 2009

BBC puts 'mediums' to the test: Surprise! They're hacks!

Psychic "mediums" are con artists. Most critically thinking individuals are readily aware of this fact, but a large portion of the general public seems unaware of this. Why else would Sylvia Brown be a frequent guest of Montel Williams (despite her being wrong, wrong, wrong on so many occasions)? Why else would John Edwards have had a popular day-time TV show?

In an attempt to inform the general public and help keep people from being swindled by these snake-oil salespeople, the BBC put three mediums up to the test. The result: they're all cheaters. Big surprise there. Video below:

They took three mediums to "The Chocolate Factory", a made up factory with a fictitious history which they published on an "official" website, as well as planting tidbits of info around the building (like a portrait of the fake original owner, complete with his name on a plaque). They then took the mediums through the building and asked them to "channel" the history of the factory.

They all were able to "divine" the fictional history of the factory. Funny how they could contact the ghost of a person who never even existed.

The reasonable explanation, of course, is that they had read the information of the website before hand. Nevertheless, they all presented the information as having come from a channeled spirit.

And, as usual, once they are told that the whole thing was made up, they attempted to make excuses: "Oh, I was just testing you", "oh, I was reading your thoughts instead", "oh I wasn't wearing my glasses when I standing in front of George Bull's portrait".


Wednesday, 8 July 2009

Beer, Chemistry and Marketing, a violently exothermic reaction of the brain.

Television advertisements.

Some of them can be absolutely ingenious. Some of them can be incredibly annoying. And some of them can be unquestionably, mindbogglingly stupid. The latest marketing campaign for Miller Genuine Draft beer belongs to this last category.

You've probably seen the commercials. They portray someone in a tough situation where they are uncommonly open, and consequently resolve the situation to their benefit. This is complete with their marketing slogan: "Miller Genuine Draft is in a clear bottle because it has nothing to hide", showcasing their unique clear bottles. And it's those damn clear bottles that make this marketing campaign so stupid. It would seem that the folks at Miller forgot to hire a chemist or two for their marketing department, because beer is bottled in dark bottles for a reason.

One of the key ingredients in beer is hops. Hops contributes much to the flavour of beer, through a class of chemicals known as isohumulones. Isohumulones are in all types of beer, and are perfectly fine. They are not a problem by themselves. Problems can arise, however, because of another chemical found in beer: riboflavin.

Ribovlavin (better known as Vitamin B2) is found in all kinds of foods and beer is no exception. Unfortunately, riboflavin and isohumulones don't get along very well. Riboflavin tends to break down isohumulones, so having them both in beer can be problematic. Normally, this is not a big deal, though, because the chemical reaction whereby riboflavin degrades isohumulones requires a catalyst, and that catalyst is light. This is the reason why beer comes packaged in dark-coloured bottles. The dark colouration keeps out light, and prevents the isohumulones from breaking down.

Why is isohumulone degradation a bad thing? Well, when these chemicals are broken down by riboflavin, they form a compound called 3-methylbut-2-ene-1-thiol. This compound gives the beer a very, very bitter taste: the beer becomes spoiled (unless you happen to enjoy very bitter beer, I suppose). If this happens to beer, then it is often referred to as being "skunky". Little wonder why: 3-methylbut-2-ene-1-thiol is very similar to the compound used by skunks in their spray.

So beer that is bottled in clear bottles like Miller Genuine Draft (as well as Corona, and beers bottled in green bottles like Heineken) will end up spoiling and becoming very bitter much quicker than beers packaged in dark bottles.

So does Miller Genuine Draft really have nothing to hide? I think the fact that their beer contains skunk juice is something worthy of keeping hidden.

EDIT: It's been brought to my attention that Miller uses a strain of hops that contains a more light-stable form of isohumulone to prevent their beer from skunkifying when exposed to light. Nevertheless, the chemistry remains the same and is still interesting. Take note all you home brewmasters out there.

Monday, 22 June 2009

Sex Determination and Lizards

Sex determination is a pretty hot topic in molecular biology. Trying to elucidate the underlying mechanisms that determine whether a fetus is male or female has been a productive field. Many species rely on a hemizygous1 method of sex determination, and we humans are no exception (but rather, we are the rule). Males are XY and females are XX, and this is the way it works in all mammals2 (even in monotremes like the platypus, though monotremes go to the extreme and can have as many as ten sex chromosomes; a male platypus is XYXYXYXYXY, for instance). Birds rely on a similar ZW system, but in this case, the females are heterogametic; females are ZW and males are ZZ. Some insects use an entirely different system, the XO system, where there is only one sex chromosome - X - and females have two (XX) whereas makes only have one (XO)3.

Despite the system used to determine sex, all the above examples have something in common: they all rely on genotypic sex determination (GSD). In these cases, it is the sex chromosomes (the number, presence or absence) which determines the sex of the resulting fetus. GSD, however, is not the only mode of sex determination. External environmental factors may also influence sex determination. Crocodiles, for example, have no sex chromosomes whatsoever. It is the temperature of the eggs which determines the sex; eggs laid in a warm nest become male and those in a cooler nest become female. Environmental sex determination (ESD) and GSD are not mutually exclusive, of course, and it has been known that many species of reptiles rely on both GSD and ESD. The interaction between ESD and GSD in these species was not thought to be a complex one; eggs at moderate temperatures use GSD, but the sex-chromosome method is bypassed and a temperature-dependant method is used if the eggs are at more extreme temperatures.

A new paper in Current Biology, however, shows that things might not be so simple.

Rajkumar S. Radder, David A. Pike, Alexander E. Quinn, and Richard Shine looked at sex determination in the eggs of the lizard Bassiana duperreyi4. They were examining how temperature effected the sex of the hatchlings when they noticed a correlation between the size of the eggs and the resulting sex: those eggs that were larger had female hatchlings and the smaller eggs had male offspring.

Of course, a simple correlation like this does little to prove an actual relationship and may simply be coincidence. So Shine and colleagues decided to try adding or removing yolk from the eggs during their development. What they found was pretty astounding. When they added extra yolk to the eggs, the hatchlings came out female, even if the sex chromosomes had already determined the sex to be male. And those eggs that had yolk removed switched to male even when the sex chromosomes had been set to female. This finding would suggest that sex determination in B. duperreyi is determined by a complex interaction of a minimum of three factors: sex chromosomes, temperature and egg size.

This also suggests that sex determination in any species may not be as simple as once thought.


1. Hemizygous may not be a term you learned in Genetics 101. Whereas homozygous and heterozygous refer to having one or two different alleles, respectively, hemizygous refers to having only one of a set of two chromosomes. Female humans have two X chromosomes (XX), whereas males are XY; they are hemizygous with respect to the X chromosome. You could also refer to females as homogametic and males as heterogametic.

2. To be more specific, sex determination in mammals relies on a gene called sry (Sex-determining Region Y) located on the Y-chromosome. The gene encodes for a transcription factor called TDF (testis determining factor). When TDF is expressed, it influences the undeveloped gonad to develop into testes instead of the default state of developing into ovaries. If the SRY region of the Y chromosome is deleted or mutated, then the resulting child will be phenotypically female but genotypically male. Likewise, a translocation of SRY onto an X chromosome can lead to children who are phenotypically male but genotypically female. Interestingly, TDF does not begin to work, and consequently sex is not determined, until after the nipples have developed, which is why men have nipples that are pointless (beyond giving purple nurples, of course).

3. One interesting downside of this system is that it can lead to bilateral hermaphroditism. It is possible for the X chromosome to form a "ring chromosome" where the ends of the chromosome fuse together to make a ring. This ring chromosome is easily lost during cell division. If an embryo begins as XX (female), and very early on in development (at the 4 cell stage, say) a ring chromosome is formed and lost in one cell, the embryo will become split right down the middle, one side being male and the other side being female. This is rare, but not uncommon, in Drosophlia. Such flies are called gynandromorphs.

4. Rajkumar S. Radder, David A. Pike, Alexander E. Quinn, and Richard Shine. Offspring Sex in a Lizard Depends on Egg Size. Current Biology, 2009; DOI: 10.1016/j.cub.2009.05.027

Monday, 15 June 2009

Move over Boy Scouts, make way for the O.O.T.S.S.O.E.R.A.A.A.P

That is, the Order of the Science Scouts of Exemplary Repute and Above Average Physique. If you do science, this is the organization to be part of! And just like the Boy Scouts, you earn badges (to show off on your website/blog/whatever - along with a brief explanation how/why you've earned each one) for doing awesome sciencey stuff!
Here are the one's I've earned:

The "talking science" badge: Required for all members. Assumes the recipient conducts himself/herself in such a manner as to talk science whenever he/she gets the chance. Not easily fazed by looks of disinterest from friends or the act of “zoning out” by well intentioned loved ones.

The "I Blog About Science" badge: In which the recipient maintains a blog where at least a quarter of the material is about science. Suffice to say, this does not include scientology. Don't know exactly what porportion of my blog is about science but it's definately more than 1/4.

The "I’m pretty confident around an open flame" badge: Recipients have demonstrated proficiency around open flames in laboratory settings. I regularly use a Bunsen burner without disasterous consequences.

The "Destroyer of Quackery" badge: In which the recipient never ever backs down from an argument that pits sound science over quackery.

The "Sexing Up Science" badge: In which the recipient has had experience with things such as selective breeding, crossing, mate selection, prokaryotic conjugation, fertility studies, STD related microbiology, and/or any other acceptable interpretation of the badge. I vowed never to breed Drosophlia
again but at least it got me this badge.

The "has frozen stuff just to see what happens" badge, levels 1-3: In which the recipient has frozen something in the freezer (I)/dry ice (II)/ liquid nitrogen (III) for the sake of scientific curiosity.

The "I’ve done science with no conceivable practical application" badge. Perhaps this should be known as the "basic research" badge.

The "I know what a tadpole is" badge: In which the recipient knows what a tadpole is. Basically, an easy way to get a badge that looks a little like the semen one above.

The "Cloner" badge: In which the recipient has cloned something or other. I've done more cloning than you can shake a stick at. A cloned stick, even.

The "totally digs highly exothermic reactions" badge. Because who doesn't enjoy a fanciful display of exothermic activity?

The "somewhat confused as to what scientific field I actually belong to" badge. I'm trained in genetics, but I do molecular biology in a biochemistry lab. You tell me what my field is.

The "Works With Acids" badge. Usually only HCl and acetic acid, but hey, DNA
is technically an acid too!

The "Non-explainer" badge (Level 1): Where the recipient can no longer explain what they do to their parents.

Sunday, 14 June 2009

My take on accomodationism.

Lately the science blogosphere has been abuzz with discussion about accomodationism. It all started off with a piece by Jerry Coyne for New Republic on the subject, which has since stirred the pot and prompted Chris Mooney, Jason Rosenhouse, Ken Miller and P.Z. Myers to give their two cents on the issue (a chronological list of postings and replies [as of June 12th] can be found here). There is alot to read about accomodationism but it all revolves around one question: is there room in science for religion - that is, can science and religion get along, or are they diametrically opposed?

And if you ask me, no, they can't and yes, they are.

The simple reason why is because science deals with the observable, the empirical, the testable; while religion deals with the metaphysical, the unobservable, the untestable. To be a scientist requires, then, a certain mindset - one that forsakes reliance in the intangible and deals wholly with physical reality. For one to have this scientific mindset and still hold a belief in religion requires a measure of doublethink in the true Orwellian fashion.

Much of the accomidationism discussion has talked about Gould's Non-Overlapping Magisteria (NOMA). In his 1999 book, The Rock of Ages, Gould proposed that science and religion attempt to explain different aspects of life: science attempting to explain how the world works and religion attempting to explain how we should act. If kept separate, then, the two magisteria should never conflict with one another. Accomidationists tend to use NOMA to suggest how science and religion can co-exist: if people keep them separate then there should be no problem with believing in both. Unfortunately, there is a big problem with using NOMA to justify accomodationism: the two magisteria DO NOT stay separate. Religion constantly makes an attempt to explain how the world works - take creationism for an example. Religion makes many claims about the physical world, which is supposedly science's realm. And many times, what religion claims and what science posits conflicts. To believe BOTH means you have to twist one to fit the other - usually twisting religion to fit science. The usual way is to claim that certain Biblical statements are just "symbolism". This poses a question: how do you decide which aspects to take "for real", and which are just "symbolism" (the answer is, of course, there is no criteria for deciding this). And if ANY of the Bible is symbolic, then what reason do you have to believe that any of it is real?

But there lies a bigger problem with accepting NOMA as a basis for accomodationism. If one is able to keep the magisteria separate, the very fact that one accepts the religious magisterium means that one accepts the idea that there are intangible, untestable entities and processes in existence. As a scientist, how could you ever divorce that idea from explaining the observable world? What keeps you from invoking the metaphysical to explain the physical? Again, there is no defined criteria for this judgement. One is resigned to proposing that there might be some unknown, intangible - in other words, unscientific - entity/process behind the physical world. And at that point, one ceases to be a proper scientist.

Now, I want feel I should say that this does not mean you cannot be a good scientist and be religious, or that being religious necessarily makes one a bad scientist. What matters is whether or not you incorporate your religious beliefs into your scientific activities. Once you try mixing the two, you cross the line from "good scientist" to "poor scientist". This is what separates the Ken Millers from the Michael Behes; Miller, while openly Christian, leaves his religion out of his science, and Behe, also openly Christian, insists on mixing the two. The problem lies, as I said above, in that to do this requires a measure of doublethink. You have to ignore (or attempt to explain away) the areas where science and religion are in disagreement, and you have to use the metaphysical for religious purposes and the physical for the scientific despite having no clear reason why they should be kept separate in the first place.

No doubt the accomodationism debate will continue. One wonders if it will ever be settled.

Why Biorad is one of my favourite companies.

If their first video wasn't awesome enough, this one is:

I also think it's funny how they made a 70's-esque video about a technique that was not developed until the mid-80's (unless you coun't Kleppe's paper as describing PCR1).

1. Kleppe K, Ohtsuka E, Kleppe R, Molineux I, Khorana HG "Studies on polynucleotides. XCVI. Repair replications of short synthetic DNA's as catalyzed by DNA polymerases." J. Molec. Biol. vol. 56, pp. 341-61 (1971)

Sunday, 7 June 2009

Creepy-Crawlies and Conservatives

A new study has purported to find correlations between political alignment and the degree to which things disgust you.

The study, conducted by David A. Pizarro, Yoel Inbar and Paul Bloom, and published in Cognition and Emotion, surveyed 181 American adults by subjecting them to a "Disgust Sensitivity Scale" (DSS), to assess their level of disgust in various situations. The subjects were then assessed on a political ideology scale. They found that those who tended to be easily disgusted also tended to be political conservatives.

Pizarro and colleagues followed this up by surveying 91 undergrads by giving them the DSS and then asking them their opinions on issues like abortion, same-sex marriage and gun control. Again, they found a correlation between conservative views and being easily disgusted.

This is a pretty interesting find, but it raises a major question: if conservatives are easily disgusted by creepy, slimy things, then why do so many conservative politicians turn out to be complete slimeballs?


Yoel Inbar; David A. Pizarro; Paul Bloom. Conservatives are more easily disgusted than liberals. Cognition & Emotion, 2008; 23 (4): 714 DOI: 10.1080/02699930802110007

A more in-depth article about this study and a related one can be found at ScienceDaily:

Saturday, 6 June 2009

Bill O'Reilly caught lying once again.

If there is anything that annoys me more than fanatical right-wingers who inanely babble on about topics they know nothing about, it's fanatical right-wingers who inanely babble on about topics they know nothing about and then lie about it. Bill O'Reilly fits nicely into that latter category.

By now, everyone has heard about the absolutely tragic murder of Dr. George Tiller, who ran a women's health clinic in Kansas that provided late-term abortions for women who needed them due to dire medical complications. Dr. Tiller has been a target of radical pro-lifers for years, having been shot once before, and had received a constant barrage of death threats and pointless lawsuits.

The man who shot and killed Dr. Tiller acted alone, and one should not judge the entire pro-life movement on the actions of one deranged individual, though I can't help but feel that his malicious deed was in part due to the movers and shakers in the pro-life camp; had they not spilled their hate-fueled campaign against Tiller, then he would likely be alive today. And one such person who specifically targeted Tiller was Bill O'Reilly.

In fact, O'Reilly held such disdain for Dr. Tiller that he commonly referred to him as "Tiller the Baby Killer". And after Tiller's death, do you think that O'Reilly felt any remorse about making him a constant target for the right-wing media? Of course not! He just lied about ever calling Tiller a "baby killer" in the first place:
"It took just minutes after the report of Tiller's murder for the far-left loons to hit the websites. Postings on the Daily Kos and The Huffington Post immediately blamed me and Fox News for inciting Tiller's killer. Even though I reported on the doctor honestly, the loons asserted that my analysis of him was "hateful."

Chief of among the complaints was the doctor's nickname, "Tiller the baby killer." Some pro-lifers branded him with that, and I reported it. So did hundreds of other news sources. But the bigger picture here is the glorification of Tiller."

"Oh, I didn't call him "Tiller the baby killer," O'Reilly claims, "I just reported that other pro-lifers called him that." Well, not according to Media Matters:

"However, O'Reilly has not only "reported" on the term's usage by "pro-lifers," but he has adopted it himself, repeatedly referring to Tiller as "the baby killer" on his Fox News show:

  • On the May 15 edition of The O'Reilly Factor, O'Reilly stated that Kathleen Sebelius, who was then the governor of Kansas and is now secretary of health and human services, "is the most pro-abortion governor in the United States. Based upon Dr. Tiller, the baby killer in her state, and all of that. All right? So there's no doubt."
  • On the May 11 edition of The O'Reilly Factor, O'Reilly said Sebelius "is pro-abortion. She wants the babies done for. This is -- she supported Tiller the baby killer out there."
  • On the April 27 edition of The O'Reilly Factor, O'Reilly said that Sebelius "recently vetoed a bill that placed restrictions on late-term abortions in Kansas. The bill was introduced because of the notorious Tiller the baby killer case, where Dr. George Tiller destroys fetuses for just about any reason right up until the birth date for $5,000."
  • On the April 3 edition of The O'Reilly Factor, O'Reilly said, "Tiller got acquitted in Kansas, Tiller the baby killer."
  • On the March 27 edition of The O'Reilly Factor, O'Reilly stated: "Now, we have bad news to report, that Tiller the baby killer out in Kansas -- acquitted. Acquitted today of murdering babies. I wasn't in the courtroom. I didn't sit on the jury. But there's got to be a special place in hell for this guy.""
How does it feel to have your own words come back and bite you in the ass, O'Reilly?
Bill O'Reilly is a vile, little man - vile for his moronic, loud-mouthed attitude, vile for his asinine ideology and vile for constantly lying through his teeth.

Thursday, 14 May 2009

On Assumptions and Conclusions

One of the things that creationists often say that really annoys me is that evolution and creationism are not all that different in that they both rely on the same facts and observations, but come to different conclusions because they use different starting assumptions. Biologists, they claim, begin with the assumption that natural selection, common descent and descent with modification are all real phenomena, while creationists begin with the assumption that the Bible is the inerrant word of God. They posit that, because the two groups use different starting assumptions, they interpret the data differently, in a way which confirms their preconceived views; when a biologist looks at a giraffe, she sees the byproduct of billions of years of evolution, whereas a creationist sees obvious design.

This claim is absolute rubbish. Anyone who makes such a claim is exposing their incredible ignorance of the scientific method. In fact, such statements run completely contrary to the way the scientific method is supposed to work!

Generally, the scientific method works like this: you gather observations and empirical data, and from analysing the observations and data, you draw out general conclusions which explain all of the data. In other words, science does not start with any unfounded assumptions; it begins with the data, and from the data determines general principals on how the world works. Scientists do not begin by assuming the nonexistance of God - God doesn't even factor into the equation for the most part. In the case of evolution, biologists do not begin with assuming God does not exist and then interpret the data in a secular manner; instead, biologists determine from the data that species arise from a purely naturalistic process, and God's non-involvement follows as a natural conclusion.

Creationists, on the other hand, follow such counter-scientific principals to the tee. They start with their supposed conclusions - goddidit - and then ask "What facts can we find that support our conclusion?" To creationists, facts follow conclusions and not the other way around. They begin by assuming that the Bible is the inerrant word of a supernatural entity, and then stretch, skew and distort any facts they find to try and make them fit into their biblical beliefs.

The idea that science and religion simply begin by making different starting assumptions is antithetical to science. This is a big part of the reason why "creation science" is such a huge joke.

Tuesday, 14 April 2009

New Answers in Genesis Ad: Godless Heathens will Kill You / We Kill Godless Heathens

Answers In Genesis, the very same group of know-nothings that brought you The Creation Museum and the pitiful attempt at "real science" known as the Answers Research Journal, are starting to branch out with new advertising. Check out their new ad below:

Their little slogan makes me wonder: "If you don't matter to God, you don't matter to anyone", said while a wife-beater clad youth points and cocks a gun at the camera.

This can be taken in two different ways:

1) "If you think that God does not exist - that you don't matter to Him - then you don't think life has any meaning. To atheists, your life and the lives of others don't matter. Godless atheists will have no moral qualms about killing you (and probably will)."


2) "If you think that God doesn't exist, then you don't matter to anyone. Especially not us Christians. So don't be surprised when we start shooting you atheists, because you just don't matter."

I wonder which message they were trying to send. Either way, it's absolutely appalling, not to mention completely untrue. Just because one does not believe in a bearded man in the clouds does not mean one cannot be a compassionate individual who cares for the lives of others. To suggest otherwise is a complete non sequiter. There is no link between belief in a deity and compassion for your fellow man. Once again, Answers in Genesis glows like a big, shiny beacon of ignorance.

Friday, 3 April 2009

Everything you wanted to know about Chromosome 2 and evolution but were afraid to ask.

I recently joined Yahoo! Answers to give me something to do on my lunch breaks at work by answering peoples' questions about molecular biology and genetics (a niche that needed filling because it only took me a week to become a "Top Contributor" in biology). Yesterday, there was a challenge put towards "evolutionists" (ugh, how I hate that term): give the one (1) piece of evidence you would put forth to a creationist to try and sway his/her opinion on whether humans descended from earlier primates. There is literally a whole boatload of evidence to support man's descent from earlier primates, but picking the single piece of evidence to sway a creationist's opinion was tough. I thought about it for a minute and decided to present the case from Chromosome 2. I thought I'd reproduce my answer here:

You want one convincing proof? Consider this:

I'm sure you've heard that humans and chimpanzees have the vast majority of our DNA in common. You're also probably not convinced by this argument ("I don't what if two organisms share the same genes? How does this prove that they came from the same lineage?"). But for now, forget about how very similar we are in our genetic sequence and let's focus on our chromosomes.

If you need a refresher, remember that the number of chromosomes a species has tends to stay the same from generation to generation. A fruit fly has four autosomal chromosomes and one pair of sex chromosomes; it's offspring will all have the same number. What about us humans? We have 23 pairs of chromosomes; 46 chromosomes in total. If you took a karyotype - that's a display of all the chromosomes in a cell - of an ape (I know you're skeptical of humans being primates, but lets call 'em primates for now) you'll notice something different from human chromosomes: there's two extra! Apes have 48 chromosomes.

You might wonder how this proves we evolved from an ancestral primate. You might even suspect that it is evidence against such a claim, since an ancestral primate would have had 48 chromosomes, and that number would have likely stayed constant down the generations, while in us, it's different. Well, this information alone does not prove much. But let's take a look at what the genome sequence shows us.

The sequence of the human genome showed an interesting fact about our Chromosome 2. The area around the very centre of chromosome 2 (known as a centromere) looked an awful lot like telomeric DNA. Telomeres are the regions at the very ends of chromosomes; what were they doing in the centre of chromosome 2? Furthermore, each arm of Chromosome 2 had what appeared to be their own centromeres. Chromosome 2 was looking to be quite an oddity. No other human chromosome displayed these characteristics.

Once the chimpanzee genome was sequenced, things got even more interesting. One of the chimpanzee's chromosomes was pretty much identical to the top half of the human Chromosome 2. Another chimpanzee chromosome was nearly identical to the bottom half of Chromosome 2. On top of this, the banding pattern of these two chromosomes (as well as the same chromosomes in many other species of primates) was a complete match to the banding pattern of Chromosome 2.

Coincidence? Not likely. What this is, is evidence of a chromosomal fusion. An ancestral primate, ancestor to humans, chimpanzees and apes, had 24 pairs of chromosomes. Eventually, this lineage diverged: apes and chimps went one way and we humans evolved along a separate path. But something interesting happened in the lineage that was to become humans: the two extra chromosomes from that ancestor fused together end to end to become human Chromosome 2. This is why our Chromosome 2 has what appears to be telomeres in its centre, and what appears to be two extra centromeres, one on each arm.

The only way to explain Chromosome 2's odd characteristics and similarity to other primates is with a chromosomal fusion. And the only way this could be possible is if we were descended from a common primate ancestor.

So, I put the question to you: if you could give only one single line of evidence for man's primate ancestry to change a creationist's mind, what would it be?

Wednesday, 25 March 2009

Perhaps the Virgin Mary made her do it?

The small French town of Lourdes is perhaps best known for its masses of pilgrims who go there to seek the supposedly holy waters of a small grotto in search of miraculous healing. Of course, of the hundreds of millions of people who have visited Lourdes (9 million last year alone), there have only been a handful of "confirmed miracles", meaning if Lourdes' history were thought of as a drug trial, the FDA would have condemned miracles long ago.

But now, Lourdes is beginning to get a new reputation. One for a completely different kind of crazy than the usual delusional flocks of faithful: a woman in Lourdes, who thought she was possessed by the devil, stabbed her mother to death using a crucifix (the crucifix scene from The Exorcist comes to mind...).

She apparently told police "I had visions in a dream. I saw that I was the devil, that I was evil," and proceeded to beat her mother senseless with anything within reach before murdering her with a crucifix. She was promptly carted away to the loony bin.

This is what I don't get. Lourdes is filled to the brim with Catholic pilgrims every year. Ask any random assortment of pilgrims, and at least some are sure to tell you that "God has spoken to them" or that their faith is strong because "God had revealed himself" to them. Lourdes itself is a place that became famous after a teenage girl claimed to have seen the Virgin Mary herself. Yet, none of these people are put though psychiatric assessment.

Why is it that when someone claims to see or hear God or Jesus, it's taken as a divine event. Yet when someone claims to hear or see the devil, they're labelled as crazy and institutionalized? It's a complete double standard. Both are controlled by the same psychological phenomena: they're both simply delusions of an imaginary being.

One might make the claim that, as in the case above, those who think themselves under the control of the devil commit violent acts, but that would be ignoring the multitude of times throughout history that masses of people were murdered after some leader believed he had been told by God himself that it was a good idea. (George Bush and Iraq, anyone?)

It's time to stop treating Godly visitations as being sane.

Monday, 16 March 2009

The Kunkel Method, or How You - Yes, You! - Can Intorduce Any Mutation you Please into any Gene you Want!

In molecular biology, there are often occasions where you might want to introduce a specific mutation into a particular gene. Let's say you are examining a particular protein, and you want to find out how crucial a certain cystine residue is. You might want to change that cystine residue into, perhaps, a tyrosine residue, and observe how the protein behaves. You could do this by random mutagenesis and sifting through thousands of mutants until you find the one that you need, or you could do it a much quicker way.

The Kunkel method is one such way, and it is actually quite simple, both practically and theoretically. The first step is to clone the gene you want to mutate into whatever plasmid you choose to use. You can use whatever cloning procedure you wish. It doesn't really matter how you clone, just as long as you have a plasmid with your gene in it.

Next, the plasmid must be transformed into an E.coli strain that is ung- dut-. The dut gene encodes for dUTPase, an enzyme that prevents the bacteria from incorporating uracil during DNA replication (remember that uracil pairs with adenine but only in RNA. It is dUTPase that prevents uracil from being used in DNA by destroying all the cell's reserves of uracil during replication). A strain that lacks ung (dut-) will then randomly add uracil to your plasmid when it replicates. E.coli, however, have a backup mechanism in case dUTPase fails. This is uracil deglycosidase, encoded by the ung gene. Uracil deglycosidase cleaves out any uracil that has been added to DNA if dUTPase has been slacking on the job. Transforming into a strain that is also dut- will make sure the uracil in your plasmid stays there.

The next step is to design a primer that contains the region of the gene which you wish to mutate, along with the mutation you want to introduce. If you wanted to change a cystine to a tyrosine, then your primer would span the codon for cystine, but contain the necessary base pair changes to turn that cystine into a tyrosine. This primer will anneal to your plasmid when it denatures, even if the primer does not match it's target 100%. Once you isolate your uracil-containing plasmid, you can do PCR using your mutated primers to create hybrid plasmids: each plasmid will now contain one strand without the mutation and uracil bases, and another strand with the mutation and lacking uracil.

The final step is to isolate this hybrid plasmid and transform it into a different strain that does contain the ung gene. The uracil deglycosidase will destroy the strands that contain uracil, leaving only the strands with your mutation. When the bacteria replicate, the resulting plasmids will contain your mutation on both strands. In essence, you have completely replaced the original gene with your mutated version! You are then free to do as you wish with your new mutated gene.

The Kunkel method, however, is a bit outdated. Many bioscience companies offer kits that allow you to do site-directed mutagenesis even easier. Stratagene, for example, provides a kit that works as follows:

1) Transform your plasmid with gene of interest into any regular laboratory strain. Most strains will be dam+. The dam gene allows the bacteria to methylate the DNA in the plasmid (that is, they will add methyl groups to spots on the DNA. This is a mechanism that the bacteria has to allow it to determine what DNA is its own, and what DNA might be from an invading virus, since viral DNA will not be methylated).

2) Isolate the methylated plasmid, and do PCR with primers containing the mutation you wish to introduce. This will create hemimethylated plasmids: one strand (the one with the original gene) will be methylated and one (the one with your mutated gene) will not be methylated.

3) Add a small amount of the enzyme DpnI to the reaction mix. DpnI actively cleaves up methylated DNA. This will destroy the strands from the original plasmid and leave only your mutated strands.

4) PCR the remaining fragments to produce complete plasmids that contain your mutated gene.

And there you have it. Now you can mutate any gene you want in any manner you wish, and only take a day to do it. No more screening thousands of mutants! Huzzah!

Wednesday, 4 March 2009

Canadian Government Continues to Dig its own Scientific Grave

Our government continues to inch its way closer to being scientifically six feet under. The latest anti-science nonsense from Harper's regime: rejecting a motion to recognize Charles Darwin on his birthday and the marvelous theory he formulated.

According to the official records, MP Pierre Paquette rose to make the following request:
Mr. Speaker, I seek the unanimous consent of the House to adopt the following motion: That the House acknowledge the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication On the Origin of Species by Natural Selection or the Preservation of Favoured Races in the Struggle for Life, which launched the theory of evolution, the only proven and recognized scientific explanation for the origin of man. I believe you will find unanimous consent for adoption of this motion.
It was promptly rejected.

According to The Canadian Press, most of the "nays" came from the Conservative MPs (big surprise there), whereas the majority of votes were "yays" from the other parties. Unfortunately, Paquette was looking for a unanimous decision, so "mostly yes" wasn't good enough.

In other words, our government has officially rejected evolution.

Now, perhaps the wording has something to do with this. Including "unanimous" was probably a big mistake, but the bigger problem lies in calling evolution "the only proven and recognized scientific explanation for the origin of man." While this is technically correct - evolution IS the only scientifically accepted theory of man's origins and has been observed, tested and pretty much proved over and over again - politicians are not scientists. They are laypeople who have a cursory understanding of evolution at best and a complete ignorance at worst. Asking them to pass a motion firmly stating that evolution has been proven and is the only accepted theory in the scientific community, when they don't really understand the nature of the theory and its proofs, is a dumb idea. Even if the nay-sayers DID accept evolutionary theory, their lack of understanding of evolution would probably have prevented them from voting for the motion.

This article from Maclean's argues that the reason it was rejected was because the conservatives have decided that they are going to vote no on any motion presented by the other parties, which, if true, is incredibly petty.

Either way, our government just gave another "Eff You" to science.

A nod to Larry Moran for bringing this to my attention.

Monday, 23 February 2009

Work, work, work.

So I gots me a job.

I am the new lab tech in Kevin Wilson's lab over at the U of A's biochemistry department. I'm pretty excited about it, but a little nervous at the same time. Biochemistry really isn't my background, though most of the work I'll be doing is on the molecular biology side, stuff that I am comfortable with. For the fist month or so, I'll just be doing some odd jobs; the lab needs some organization and such.

The work Dr. Wilson does is pretty interesting. He works on ribosomes. More specifically, he's interested in ribosomal translocation: the process whereby the ribosome moves along the mRNA after an amino acid has been added to the growing peptide chain. Even more specifically, he's interested in a translation factor called EF-G (elongation factor G). Once an aminoacyl-tRNA with it's attached amino acid has bound and the peptide bond formed, EF-G helps the ribosome to translocate over to the next codon after the aminoacyl-tRNA has been ejected. How EF-G helps this process is what he's trying to understand.

There's a possibility that, once I get more familiar with the techniques and experiments he is carrying out, I could get to actually help out with his research, instead of doing generic tech stuff like preparing reagents, and I might get my name on a few papers if this is the case. Definitely something to be excited about.

I'm also excited about learning some new techniques. I've done lots of DNA extraction and a little with mRNA, but I'm going to need to learn how to isolate ribosomes. It should be somewhat similar to isolating mRNA, since ribosomes are composed of RNA as well (rRNA), but they have many associated proteins (r-proteins) as well. It'll be interesting. There are other things I might need to learn like FPLC (fast protein liquid chromatography), and how to use a fluorescent microscope.

I have to meet him and the biochemistry department manager today to go over the terms of my employment and sign some contracts, etc. My start date is likely to be March 1st (or 2nd, since the 1st is a Sunday), though I wouldn't mind beginning sooner.

I'm glad to be employed though. I was getting agitated from being out of a lab for so long. Ah, the smell of β-mercaptoethanol* in the morning....

*Note: Don't purposefully smell β-ME. It really stinks, and can cause respiratory and nasal irritation if inhaled. It smells strongly of fish, if you really must know.

Wednesday, 18 February 2009

I Think We're Going to Need a Bigger Barbeque.

Myostatin is an interesting protein. It plays a crucial role in muscle development; namely, it limits the growth of muscles past a certain point. Thus, if one blocks myostatin, then muscles continue to grow bigger and larger than they're supposed to. Certain breeds of dogs have been bred for mutations in the myostatin gene, and recently, drug companies have begun to manufacture myostatin inhibitors for lazy bodybuilders, but also as a potential treatment for muscular dystrophy.

But myostatin mutations are also found elsewhere. Meet the Belgian Blue.

The Belgian Blue is a breed of cattle that has been selected for a naturally occurring myostatin mutation. The result is, quite obviously, a rather beefy (pardon the pun) cow that produces lean meat (since the mutation also interferes with fat deposition) and lots of it.

Perhaps it's the carnivore in me speaking, but I think that might be the most awesome breed of cattle. Ever.

Now I have a craving for a big, juicy steak...

A nod to Sentient Developments for bringing this massively delicious specimen to my attention.

Arkansas and 5 Other States Still in the Dark Ages.

I think it's really funny when Christians cry out that they're being persecuted. Christians can hold public office in any state in America. There are no laws against god-believers in the public service. Too bad the same cannot be said for atheists in Arkansas and a handful of other states:
"Arkansas is one of half a dozen states that still exclude non-believers from public office. Article 19 Section 1 of the 1874 Arkansas Constitution states that "No person who denies the being of a God shall hold any office in the civil departments of this State, nor be competent to testify as a witness in any court."
If you don't believe in God, you are legally barred from public office, and you're not even legally allowed to testify in court. I'm literally appalled that such a law exists, despite the fact that such laws were deemed unconstitutional by the American Supreme Court in the 1960s.

So next time you hear a Christian spouting their persecution complex, remind them that at least they're not legally second-class citizens in half a dozen states.

EDIT: Seems this has also been covered by P.Z; might want to head over there for a more comprehensice writeup.

Tuesday, 17 February 2009

Move over Banana, the Chicken is Ray Comfort's New "Atheist's Nightmare"

...except that it's every bit as bird brained as his first argument.
Ray thinks that the classic conundrum of the chicken and the egg is a stumper to evolutionists, but is cut and dry to those who take Genesis as fact:
"So which came first, the chicken or the egg? For those who believe the Bible, it was the chicken, and the first egg came some time later. However, it’s not so simple among the Genesis-less generation. Did the first chicken come from the first egg, or was it the chicken that first laid the first egg?"
He quotes Aristotle as posing this question himself, dumbfounded by the dilemma:
"Long ago, even Aristotle (384-322 BC) spoke of the egg dilemma. He philosophized: "For there could not have been a first egg to give a beginning to birds, or there should have been a first bird which gave a beginning to eggs; for a bird comes from an egg.""
Too bad for Ray that Aristotle lived some 2100 years before Darwin, and the idea of evolution had never even crossed his mind. (I also find it funny that he quotes Aristotle, when most classic theologians decried Aristotle's writings [and those of Plato and others] as being the works of heathens). Aristotle was a smart guy. If he had been chatting with Darwin, he would have easily seen an answer to his question.

Evolution is not stumped by this question. Quite to the contrary, evolution provides a very satisfying answer to it: the egg, of course, came first. Evolution would predict that, before there was a chicken, there was an ancestor to the chicken (let's call this ancestor a "protochicken"). The protochicken would have been very much like the chicken indeed, perhaps even phenotypically identical but genotypically distinct from the modern chicken. (This is a vast simplification of course, since there is no one type of chicken that can be called a "modern chicken"; all chickens are genotypically different at some level). A population of protochickens were subject to evolutionary pressure of some sort, certain aberrant traits were selected for, and one day, a protochicken or two (or likely, many) laid an egg, and out hatched a chicken. Evolution posits a firm solution to the chicken-or-the-egg question.

But Ray doesn't seem to get this very simple explanation:
"Let’s say evolution was responsible for the beginning, and let’s say the egg was the first to evolve (before the chicken). Why did it do that? Why would there be nothing, and over millions of years, nothing became simple organisms, then these organisms became an egg? I can understand that a fish evolved legs and lungs over millions of years--because he (and his necessary female help mate) wanted to breathe, and to walk on dry land. But why would a thoughtless egg appear first and then want to become a chicken?"
Ray shows here something that I see in creationist arguments somewhat often - the idea that organisms want to evolve. They seem to think that, for evolution to work, organisms have to want to evolve some particular trait. They suppose that evolutionary theory dictates that a giraffe evolved a long neck because it wanted to reach the leaves high up in the trees, or, as in Ray's example above, fish evolved legs and lungs because they wanted to breathe and walk on dry land. In other words, Ray is stuck behind the idea of Lamarckian evolution - that "needed" or "wanted" traits were acquired and passed on to progeny. Perhaps Ray did not get the memo, but Lamarck's ideas on evolution have been discredited for pretty much the last century or more.

There is no want in evolution. There is no thought out goal. What evolves is not product of an organism's needs or wants, but rather a product of the organism's environment. Eggs evolved shells, for instance, because those few with shells survived the rigors of the environment better than those without. It's really that simple.

Ray continues with more questions:
"If the egg was shaped with a rounded point at each end for ease-of-laying (a square egg would be painful), how did evolution know to make it that shape if there were never any chickens in the first place to know that an egg is made to be laid? Another small dilemma. How did the first egg get fertilized to become the first chicken? What or who fertilized it, and why did he fertilize it and sit on it until it hatched? How did the fertilizing creature evolve and have the ability to fertilize an egg that he found. How did he get the seed into the egg to fertilize it? And why did the (rooster) evolve as a bird? Unless he was an egg first, and if so, we have the above questions to deal with, because his egg would also need to be fertilized. Who did the fertilizing?"
Again, evolution did not "know" anything. Evolution is a blind process. It tries out many different things, and those that work best get passed on. How did the first egg get fertilized to become the first chicken? It was fertilized by a protochicken before it. Evolution is a slow, incremental process. The process to create an egg did not just come together all at once; it was the result of millions of years of tiny steps, one step an improvement on the step before it. All of the questions he asks can be explained through a basic understanding of evolutionary principals; asking such questions, then, shows Ray Comfort lacks such an understanding. (He also asked how the seed got into the egg to fertilize it. Perhaps he should Google "how a chicken egg is formed", and learn that the shell is not formed until after the egg has been fertilized. This is grade school stuff).

As with most creationist arguments against evolution, Ray displays a lack of understanding of how evolution is supposed to work. It makes me wonder if he's ever actually tried to learn about evolution aside from trying to find faults with it. I'd love to challenge him to take an exam on basic principals of evolution to see how he'd do, because from what I can tell, he doesn't have a clue.

Saturday, 14 February 2009

They'll believe just about anything...

Taken from Yahoo! Answers, a seemingly popular, vacuous intellectual void loved by Creationists:
my sister told me that my brother [hes christian ] told her that somewhere outer space they found like city but gravity didn't let the camera get closer and that the city was really Bright and they could see a figure like a castle so does any one know this story or have any footage of this ?"

They'll believe this crap, yet somehow find evolution to be unbelievable beyond comprehension. Sigh.

Friday, 13 February 2009

It's Darwin's Birthday: Edmontonians Show their Ignorance (Part II)

Continuing from my last post, we have a letter from one Peggy Heather of Edmonton:

"Re: “Evolution, creationism debate still simmers; Iconic naturalist would be amazed at the controversy over his ideas,” The Journal, Feb. 7.

Religious beliefs aside, one would be hard pressed to believe in evolution. The fossil record does not support it and the mathematical improbabilities of us evolving out of nothing are staggering.

Chris Eckert, an evolutionary biologist at Queen's University, is correct in saying that there are numerous species, but that in itself does not point to evolution. That’s happened thanks to the marvellous DNA in all living things, which allows for numerous variations, as any dog breeder can testify. This can be called microevolution. However, a dog will still only produce a dog, no matter how you tweak it. If you really stop to think about it, if for example birds evolved from dinosaurs, how did the intermediate creature survive for several million years with legs that are now useless but which are not quite wings yet either? He’d be a sitting duck for predators.

Apes can mimic a few words taught by trainers in response to rewards, but lack the throat and brain structure necessary for speech, vocabulary and grammar. One can go on and on why macroevolution is impossible, but evolutionists keep insisting on reviving a dead horse.

Peggy Heather, Edmonton"

While not nearly as long as Hendrickson's nigh-on-incoherent babbling, Peggy no less piles on the stupid.

First of all, the fossil record DOES support evolution. In every way, shape, and form does the fossil record support evolution. To doubt this shows you know nothing of evolution nor the fossil record. What does the fossil record show? It shows us the gradual progression of life from simple organisms to more complex organisms over the period of millions upon millions upon millions of years. It shows us early forms of body patterns familiar to us and it shows these patterns changing over time to become what we see today. It shows the beginning of different families of organisms and the ends of other families. All of these things are predicted by evolution. There is not a single aspect of the fossil record that does not support evolution, and if you claim otherwise, then you are either ignorant or lying.

Secondly, the mathematical improbabilities of us evolving "out of nothing" matter very little. The improbability of winning the lottery is staggering, yet someone always wins. Improbable does not imply impossible. Even if the chances of life evolving were one in one hundred billion trillion, the fact is, it happened. A lot of these arguments about the probability of life evolving are terribly fallacious: they scrape together large numbers they assign arbitrarily and output a large number that generally means nothing. People look at the large number and think "wow, that number is too large for me to grasp. I cannot argue against such a big number. I guess the conclusions drawn from this big number must be right." Dangle a few dozen zeros after the 1 in front of people and you're bound to get someone who believes you, no matter how asinine your argument.

Peggy follows this up by outright accepting microevolution. But what keeps her from accepting macroevolution? What is the barrier that prevent macroevolution while allowing microevolution? She doesn't say! Perhaps this is because there simply ISN'T one. Macroevolution is what happens when microevolution continues for long periods of time. Sure, a dog still produces a dog over the course of a few centuries, but give it a few million years of microevolution and what you're left is not going to be anything like a dog. She asks regarding the dinosaur-to-bird transition: "how did the intermediate creature survive for several million years with legs that are now useless but which are not quite wings yet either?" What makes her think that legs became useless once wings began to evolve? I wonder how she explains the birds perching on the branch outside her window if she thinks having wings means legs are now useless. She obviously does not understand how evolution works in the least.

She then talks about apes lacking the necessary anatomy and brain functions for proper speech, yet can mimic words taught by trainers in response for rewards. What better evidence is there for evolution? Other primates cannot speak like us, yet still have the capacity to learn speech. How else could one explain this except in light of evolution?

I think that someone should tell Peggy that "macroevolution" is not a dead hose by any means. Evolution is stronger than ever before. Every day that goes by, we find more and more evidence for evolution. There is no single scientific principal that is more strongly supported than evolution.

Hopefully tomorrow's edition of the Journal will contain some pro-Darwin rebuttals to today's display of idiocy, but I wouldn't hold my breath.

Thursday, 12 February 2009

It's Darwin's Birthday: Edmontonians Show their Ignorance (Part I)

In the wind up to Darwin Day, the Edmonton Journal ran a few articles that had to do with Ol' Chuck D and his groundbreaking work ("Happy birthday, Mr. Darwin; Evolution's bold insights, so well explained 150 years ago, resonate daily in a land dependent on fossil fuels" by Paula Simons, Feb. 7 and "Evolution, creationism debate still simmers; Iconic naturalist would be amazed at the controversy over his ideas", also on Feb 7th). As, sadly, expected for this province, those of us less evidence-oriented and more factcinated felt compelled to respond. Beware: the amount of ignorance packed into the small space of the proceeding paragraphs is likely to result in a singularity.

First to share their nonsense was D.M. Hendrickson, of Bittern Lake:

"Re: “Happy birthday, Mr. Darwin; Evolution's bold insights, so well explained 150 years ago, resonate daily in a land dependent on fossil fuels,” by Paula Simons, Feb. 7.

Surveys show that about 40 per cent of Canadians reject Darwinism today, whereas Paula Simons claims Alberta “owes its prosperity, its very identity, to the reality of evolution.” Nonsense. Prehistoric plants that turned into fossil fuels do not require any theory of evolution to superimpose upon their existence some more certain reality or better understanding; it is the industrial capabilities of being able to extract the oil that give us the oil, not some spurious suppositions about how all life was not a direct creation of God."

Hendrickson's letter fails right off the bat, starting with a complete non sequiter. Whether or not Alberta "owes its prosperity, its very identity, to the reality of evolution" has absolutely nothing to do with how many Canadians reject "Darwinism". The want of the majority does not do well when determining fact. He (she? I'll assume it's a man writing this) then continues to claim that what Alberta owes its existence to is the fact that we have the industrial capabilities to extract oil ("the oil that gives us the oil", whatever that means), and not some theory about how God didn't make the oil. This claim is absurd, of course, since, if the oil was not present, Alberta would not exist as we know it today. In other words, Alberta owes its identity to whatever process got that oil there in the first place. Now, to say that the oil was the direct result of evolution would be a stretch, but let us consider the alternative: if God had created all life on Earth within the last 6000 years, the oil simply would not be there. If not for the thousands upon thousands of generations of flora and fauna - our ancestors from eons passed, from which we evolved - dying, then there would be no oil. An ancient world, supported in part by evolution, gives Alberta the oil that is its claim to fame.

He continues:

"Simons claims “the evidence of our province’s evolutionary prehistory is all around us, for anyone willing to look.” What, pray tell, do dinosaur finds have to do with evolution? They went nowhere, precisely what evolution is not about. Does she really suppose adding “evolutionary” to the term “prehistory” adds anything to it except occasions for speculation?"

Dinosaur finds have lots to do with evolution! The entire field of paleontology has given us vast insights to our evolutionary past. The discovery of Archaeopteryx, for example, has made the idea of birds evolving from reptiles concrete. Every single fossil that is unearthed is another check in the tally of evolution's evidence. To think that dinosaur finds have nothing to do with evolution is complete ignorance.

"She would be censor, mocking those who dare be critical of the science accepted unthinkingly by the most secular elements of our society. No one would deny that organisms suffer genetic modifications and those thereby best adapted to the conditions they find themselves in are by definition most likely to survive."

I don't really understand what Hendrickson is getting at here. He gives is the tired "evolutionists are trying to silence any dissent from their dogma!" crap, and then, in the very next sentence, says that descent with modification is undeniable. More and more I'm getting the feeling that Hendrickson has no idea what he's talking about (as if his atrocious grammar and sentence structure didn't give that away already).

A little further on:

"She calls it “the harsh realities of evolution” when there are antibiotic-resistant superbugs, and wonders how we could possibly fight them without Darwin. All we need notice are demonstrable facts: that such bugs exist and that they develop in certain ways, have certain characteristics, and we must look for how we can influence those characteristics. To think we wouldn’t be doing that without Darwin or someone with similar theories is ridiculous."

Here, Hendrickson claims that we can deal with antibiotic resistant superbugs without ever taking into account any aspects of evolution. How can we do this? By noticing (1) that such bugs exist and have particular characteristics, (2) they develop in certain ways, and (3) how we can influence those characteristics. I would like to know how, exactly, Hendrickson expects us to do this in the absence of evolution. The characteristics of these "superbugs" being influenced by their environment IS evolution. We have to apply our knowledge of evolution to figure out HOW their characteristics are being influenced, and how we can counteract this. The very reason superbugs exist is because of evolution. If it weren't for Darwin, we would still be wondering why such superbugs even exist, let alone finding ways to combat them.

"So too with managing grizzly bear populations; it is not evolutionary pressure we need to note, it is environmental pressures, how the habitat and its endangerment bears upon their future prospects."

Environmental pressures ARE evolutionary pressures. Changes in the environment put pressure on organisms; those best adapted to meet those pressures survive, reproduce, pass on their genes; the population evolves. A loss in habitat for grizzly bears is an evolutionary pressure. Unfortunately for the bears, this pressure is caused by humans, and is worsening at a faster rate than the bears can adapt.

He closes his letter with this:

"Those who do not quickly sign on to Darwinism are not “fighting a rear guard action to turn back the clock 150 years and more, to return us to a medieval world view.” That is her aspersion; it is rather that arguments like those of Simons don’t make much sense unless one buys into a world view that “evolution” is the explanation for everything. It is irrational to pander to atheism at every possible turn, to think that adding the term “evolutionary” to every explication of nature somehow increases its validity. Many of the references in biology textbooks, for instance, are precisely that and no more.

She can’t abide politicians who “pander or defer to a small religious element;” she is so close-minded she cannot see that those rejecting Darwinism are the ones fighting for science and rationalism which requires in the search for truth criticisms by those who do not buy into pretentious theories of elites. Those who are not such elitists are the majority and may well have understandings closer to her castigated “religious element,” and thus it is indeed in order for decisions makers to acknowledge them."

The claim that those rejecting "Darwinism" are the ones fighting for rationalism and science is outright laughable. To reject Darwinism is to ignore the evidence; ignoring the evidence is the antithesis of science and rationality. Furthermore, if believing in evolution makes me "pretentious" and an "elitist", then so be it. But to claim that proponents of evolution think that they are somehow better than you shows a disturbing inferiority complex.

I'm a bit astounded that the Journal would let this appear as a letter to the editor, if not for its inane content, then for its grammatical massacre. Hendrickson shows not only a complete ignorance of evolutionary theory and its consequences, but also a deep-seeded contempt for both science and scientists. It is a sickening, sobering thought that people like this exist in an age where information is literally available at your fingertips.

Happy Darwin Day Everyone!

Happy 200th Birthday, Chuck!

Monday, 9 February 2009

There's a Pot of Gold at the End of the Brainbow

In the last two years, a new technique has taken the neurobiology world by storm: the Brainbow.
The brainbow is a technique which allows individual neurons in the brain, or sections of the brain, to be mapped by giving them their own special fluorescent colour1 (see image to the right). It looks pretty, and the technique itself is deceivingly simple.

It takes advantage of something called the Cre/lox system. Cre is an enzyme (a recombinase, to be precise) which will cleave out any DNA that is flanked by sites in DNA with a particular sequence, "lox sites". So if you have Your Favourite Gene (YFG) sandwiched between two lox sites, then Cre will splice YFG out of the DNA. But what if you used two pairs of lox sites? For example, what if you constructed your DNA to look like this:
If the loxA pair is cleaved, then Gene 1 is cut out; if the loxB pair is cleaved, then Gene 2 is cut out.
The scientists who developed the Brainbow realized that they could use this to make the neurons express one of many different fluorescent proteins. (See image to the left, taken from Nature2, click to embiggen) They used nestled lox sites as described above, using multiple fluorescent proteins. The Cre protein is able to cleave a single lox pair, multiple pairs, or no pairs at all. The decision on which pair(s), if any, to cleave is made at random in each cell. What results is a cell that expresses a random colour. If enough colours or colour combinations are Incorporated into the construct, every neuron, in theory, will have its own randomly chosen fluorescent glow. This makes mapping the connections in the brain much easier than ever.

And it makes for pretty artwork too.

1. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system, Nature, November 1, 2007.

2. Neuroscience: Making Connections, Nature, 457, 524-527 (2009)

Sunday, 8 February 2009

Darwin is correct.

Found this on Digg:I think this says alot about the state of science education in the Western world. Namely, that it isn't good enough.

Saturday, 7 February 2009

New Atheist Bus Campaign Coming to Edmonton

I wish.
Or how about...

Ph’nglui mglw’nfah Cthulhu R’lyeh wgah’nagl fhtagn!

Make your own lovely bus campaign slogans here!

More Recognition for U of Alberta iGEM

Our 2008 iGEM project was featured in the latest issue of The Scientist magazine.
To be more precise, the article is about iGEM in general, but contains an online supplement, with videos of 5 teams explaining their projects. Our project is the fist one listed.
Yay for publicity!
Take a look and listen to Jason explain all about Bisphenol Eh!

Monday, 2 February 2009

Harper Government Continues Anti-Science Streak

Apologies if I may be a bit late on the issue here; I haven't really been paying attention to Canadian politics much lately. The Harper government recently released the federal budget, and things are not looking up for science in Canada:
The Canadian Institutes of Health Research, the Natural Sciences and Engineering Research Council of Canada and the Social Sciences and Humanities Research Council of Canada are streamlining operations and aligning programs with the objectives of the Government’s Science and Technology Strategy and national research priorities. Through closer coordination, these agencies are improving the effectiveness of existing programs, aligning their programs with their core roles and fostering the development of innovative new programs.

These savings will be used in this budget to support repairs at post-secondary institutions, to upgrade key Arctic research facilities, to expand the Canada Graduate Scholarships program and graduate internships, and to support new world-class research facilities. This budget also sets aside $750 million to support the current and future activities of the Canada Foundation for Innovation.

In other words, Harper and his cronies have decided to reduce research grants and funding for basic research, while at the same time, trying to increase the number of graduate students in the country. That's almost paradoxical. It's kinda hard for grad students to find a supervisor, if potential supervisors can't get new funding to support them!

On top of this, the Conservatives seem to be playing favourites with Canadian research institutions. Genome Canada got absolutely no new funding this year, while the Institute for Quantum Computing got a grant for $50 million that wasn't even peer-reviewed.

And thus science in Canada continues sliding downwards. As someone who's trying to find a job in the scientific community right now, this is very disheartening. I very much want to be involved in Canada's scientific community, but the Harper government seems like it's doing whatever it can to force me, and many other young, aspiring scientists, to take our talents abroad.

Sunday, 1 February 2009

In God We Don't Trust

The folks over at NBC have a poll up asking whether or not "In God We Trust" should be removed from U.S. currency. The "No" side is winning, unsurprisingly, 84% to 14%.

The issue of removing the official American federal motto - which, by the way, has only been official since 1956 - is one I hear popping up in the news every so often. Of course, the idea is constantly scoffed at in the media, but it is one that I support. Separation of church and state is, by constitution, mandatory in America and the motto does nothing to achieve this.

But that is not the main reason why I think "In God We Trust" should be removed from coinage, or anything that has to do with politics. The main reason I think is because it is quite simply wrong.

I don't trust in God (but then again, I'm Canadian, so I don't count). Any reasonable American doesn't trust in God. I mean, that God fellow is notoriously untrustworthy. Think of all the poor cancer patients who have been prayed for, only to die a few short months or even weeks later. Think of the residents of New Orleans who, when hurricane Katrina hit, prayed for their situation to get better, only to find their city spiral into wreck and ruin. For someone who is supposed to hear all those prayers, and give aid to those who really need it, you really can't trust him to deliver on that.

He's also a deceitful God. Consider the story of Isaac and Abraham. God tells Abraham "You must take your son Isaac, and sacrifice him to me, to prove your faith!" Now, when a voice booms down from the sky, commanding you to kill your kid, you have to be very very sure that's what the disembodied voice told you to do. You don't want to be mistaken about that sort of thing. God must have reassured Abraham that, yes, honestly, he had to kill his son. Abraham trusted God. But right at the very last second, God sends an angel down to stop Abraham and is all "Haha, just kidding man, I can't believe you fell for that shit! Go sacrifice that ram instead." Now, does that sound like someone you can trust? Someone that makes you almost murder your child just for a laugh? I don't think so.

And what about the second coming of Jesus he promised? It's been two thousand years and he hasn't shown up yet. I don't think he's coming. We've been duped. Mislead.

So no, in God we don't trust. God's a lying bastard.