Thursday, 31 July 2008

Imindain - Black Water

Imindain is a great funeral(ish) doom metal band out of the UK. This track, Black Water, is among their best.

Just thought I'd post this to get the word out about such a great band!

Wednesday, 30 July 2008

"Dr. Dino" should be in jail for more than tax offences.

I came across a quote from Kent Hovind today, taken from a transcript of a radio interview he did. I knew that Kent Hovind was a sleezy, amoral nutjob but I never knew he was this batshit crazy:
"If you read the rules God gave to have a perfect society, they are phenomenal. [...] Whenever somebody commits the following crimes they are to be executed, publicly. And whoever is the offended party gets to throw the first stone [...] There is just the relief when you get to throw the rock at the person who offended you, or harmed you, or raped you, or stole from you, or something. I think Man is designed to need that satisfaction, that relief of taking vengeance. I think that is way God - I think that is the way human nature is. "

Allow me to paraphrase: "It's human nature to extract revenge on people who offend us. God made us this way. It's only natural for us to publically execute people who commit crimes." So much for all this "turn the other cheek" stuff that Christians are supposed to believe in.

Looking a little deeper, I found this site: "Quacky Quotes of Hovind's Ethics". That guy has said some really messed up shit. Take his stance on women having independance:
"This guy comes home from work, "Hi Honey, what's for supper?" "Whatever you're fixing." You know, she just got back from one of those meetings, those femi-nazi meetings. He said, "Honey, the house is kind of a mess, have you been busy today?" She said, "If you don't like it you clean it up." This went on for ten minutes. And finally he said, "How would you like to not see me for a week?" She said, "That would be fine with me." And sure enough on the the seventh day her left eye started to open just a little bit."

If you wife doesn't serve your every whim, then beat her? Disgusting. There are lots of other qoutes on that page, discussing his view on the Middle East ('kill them all and make sure you use bullets dipped in pig's blood so they don't go to heaven'), prison overcrowding ('excute criminals to make more room') and premarital sex ('girl's wouldnt have prematiral sex if they were threatened with death by stoning').

And they call us atheists the immoral, evil ones.

Tuesday, 29 July 2008

So that explains it!

So THIS is why the dinosaurs went extinct!
"Well theoretically (relating to doctrine) the extinction of the dinosaurs (this may be arguable) happened due to the war that raged between Lucifer (Satan) when he rebelled and the third of the angels he took with him, and God and the angels of Heaven. Since Satan was cast down to earth (and became the God of this earth) he could have easily destroyed the dinosaurs himself, to spite God or for whatever other reasons. Or it could have happened during the war. That's one way of looking at it. It makes sense."
It all makes so much sense now! < /sarcasm >

Christians: Keep your tumors for God!

I've been thinking: are Christians against the idea of having tumors removed? Your first reaction to such a question would probably be "No, why should they be?", but if you put a bit of thought into it, any Christian who is against abortion should also be against having surgery for cancer.

First of all, there are alot of similarities between a developing fetus and a malginant tumor, both morphological and physiological. An embryo at the two, four, or sixteen cell stage or even as far developed as a blastocyst is, to be general, a rapidly dividing mass of cells. Such a description can also be applied to a tumor. In a developing embryo, stem cells divide and continue to divide, much like tumor cells. Here the only difference is that in a tumor, the cellular growth and division is completely uncontrolled, while in an embryo, growth and division is carried out in line with a complex developental program. Fetal cells eventually proliferate into specific cell types with their own specific destinies and limitations on growth and division. Nevertheless, the basic cells from which more specific tissue is derived from - the stem cells - are much like tumor cells in that they divide and divide and can continue to divide without any end in sight. Tumor cells can kind of be thought as stem cells on steroids. The fetus during the first trimester (the period where the vast majority of abortions are performed), then, can be seen as akin to a tumor following a strict script.

I can already anticipate an argument against my analogy that Pro-Lifers are likely to use: "There is a difference between tumors and embryos: Embryos are alive! Life begins at conception remember!". Well, this argument is pretty darn weak. If life begins at conception, if a single fertilized ovum is alive, then why are tumor cells not alive as well? One response might be the difference lies in the potential of a fertilized ovum to produce a new being. But again, this is a weak argument. What about the tumors that are caused by uncontrolled stem cell proliferation? In theory, one can use stem cells to create new tissues of whatever type; it may even be possible to recreate a fully formed being using stem cell technology (though, admittedly, with our current technology and knowledge, this is a bit of speculative fantasy). These tumors came from cells that have that potential. Why, then, do tumors not count as being alive? The answer is, if you consider life to begin at conception, then tumors are alive as well. Removing a tumor is just as much 'murder' as having an abortion.

This leads to another argument, though. Someone could easily make the claim that tumors are different still because they are dangerous and directly threaten lives. To those who wish to make such an argument, I should point you in the direction of ectopic pregnancies. An ectopic pregnancy is one where the developing fetus becomes implanted in tissue other than that of the wall of the uterus, often in the fallopian tubes. Such cases are very dangerous and unless the fetus is aborted, can be fatal. Pregnancies, like tumors, can threaten the life of a mother. Not all pregnancies, of course, are ectopic, but neither are all tumors dangerous; some are benign rather than malignant. So if it is ok to remove a tumor because it is life threatening, then why is it not ok to abort a fetus if it is life threatening? Many pro-life groups have such a staunch anti-abortion stance that they object to such life saving procedures. They claim that it's part of "God's plan" if the mother dies during childbirth. Then why is it not part of "God's plan" when someone gets cancer? Shouldn't they be against having tumors removed for fear of messing with his divine scheme?

Maybe I'm way off the mark here with my analogy between the developing fetus and tumors. I'd like to hear a good argument against it though, so if anyone has something to say, just leave a comment.

Frankly, I'm not surprised.

By now you've all heard about the nutjob who shot and killed two people at a Unitarian Universalist church in Tennessee. It's a absolute tragedy. Of course, the religious right deny that he was one of theirs; instead I've been reading quotes similar to this:
The gunman was not affiliated with the church. I suspect he has no idea about what a Unitarian church is....but just wanted to kill "Christians." The larger lesson here is that the world is becoming increasingly hostile to the church. Our church gets death threats all the time.....

Again, espousing the persecution-complex that is so common in Christians. I don't blame them for wanting to distance themselves from a psychotic killer, but it really disgusts me that they so readily turn such a tragedy into an excuse to cry about "intolerance" towards Christians.

I wonder what they have to say now that it's been confirmed that the killer wasn't targeting Christians. He knew very well what a Unitarian church is. From the Associated Press:
A four-page letter found in Adkisson's SUV indicated he picked the church for the attack because, the Knoxville police chief said, "he hated the liberal movement" of the congregation....Adkisson "stated that he had targeted the church because of its liberal teachings and his belief that all liberals should be killed because they were ruining the country," investigator Steve Still wrote.

The only people being targeted here were "liberals". This sicko slaughtered people in front of little children simply because they differed from his own world view. And what worries me is that he isnt the only religous wingnut that thinks liberals are scum and should be killed. Fortunately, he's one of the very few that would act upon those thoughts but the point remains the same. There is no persecution of Christians in the Western world. THEY are the ones doing the persecuting, the fighting, the killing.

Saturday, 26 July 2008

Biotech gets in on the viral marketing goodness.

Viral marketing has been a big trend in marketing in the last few years. It seems every company has made a viral video of some sort to attract potential customers. Often, these videos dont give any selling points or information about what products are being sold; rather they kinda make you go "WTF?". I guess the point is simply to bring attention to the company and the product.

It would seem that biotechnology companies are getting in on the trend as well. Below are some such videos from some well known biotech companies.

The first is "The PCR Song" by "Scientists for Better PCR", a group made up by Biorad to parody those 1980's songs like "We are the World", sung by a whole slew of celebreties/artists. This is probably the best known biotech viral video, and for a good reason: it's pretty darn catchy.

Eppendorf recently tried their hand at viral marketing and came out with a boy-band parody called "It's called EpMotion", for their EpMotion automated pipetting system.

Next comes one from Applied Biosystems. This one is kinda strange in that it starts off as a pretty regular, boring commercial for their thermal cyclers, but then breaks down and busts a move:

Invitrogen has really gotten into viral marketing, with a whole series of ads featuring Scotts Angus and Dougal:

Heres one aimed at the chemists and pharmaceutical companies for Agilent's mass specs:

I'm on the look out for more!

Thursday, 24 July 2008

God: Not a fan of that thermodynamics stuff.

Phil Plait over at Bad Astronomy has a nice post about how plate tectonics proves to be a major problem for creationists. I suggest you go read it since he can explain it alot better than I can. Here's the rundown, though, for those of you who like clicking as few links as possible:

Plate techtonics is a well known process (although, to be honest, it's really only been widely accepted since the 1960s). We know about it because we can directly observe it happening. We can also determine the actual rate of continental drift: it's a very very slow one (an inch or so a year). Based on geologic data that suggests the orientation of the plates in the past, we know that it has taken the plates millions of years to get where they are today. The problem for creationists lies with heat. As with most (all?) geologic processes, the movement of tectonic plates around the Earth releases heat. Since the plates move slowly, not alot of heat is given off by this process. However, Creationists claim that the Earth is a mere 6000 years old; what's more is that they explain away plate tectonics by claiming God made the plates move really really fast after the flood to get to their current positions. However, such an incredibly rapid motion would, accoring to the National Centre for Science Education, release enough heat to boil away the oceans and completely melt the Earth's crust!

Of course, I can already anticipate some wacky creationist counters to this. They would probably point out that God would just raise the boiling/melting points of the Earth and its oceans. The heat, then, wouldnt cause a problem. Well, except that raising the boiling/melting point means raising the environmental pressure (Pressue and temperature are both intimately entwined. 'Boiling point', for instance, is defined as the "temperature at which the vapor pressure of the liquid equals the environmental pressure surrounding the liquid"). In order to prevent catostrophic environmental changes from happening from the release of that much heat, the environmental pressure would have to such incredible levels that living creatures would find it very difficult to continue living. The only way to get around this would be for God to change the very laws of thermodynamics. And all for only a period of 40 days so the world could appear to be older than it actually is. That God guy - not a fan of thermodynamics.

Wednesday, 23 July 2008

Bluebirds of the Mesozoic

One of the most enigmatic aspects of dinosaurs are their colour. Aside from what we've gathered from only a handfull of fragments of fossilized skin, anything about the colouration or patterning of dinosaurs and ancient birds is really unknown. Artists go to great lengths to illustrate "realistic" pictures of ancient creatures, but they simply are just an artist's rendition, something pulled from the imagination. However, it's possible that taking an "educated guess" about the plumage of ancient birds might become as extinct as the creatures themselves.

An article published in the most recent issue of Biology Letters by Vinther et. al details a new discovery regarding the colouration of fosilized feathers (Vinther et al. Biology Letters 10.1098/rsbl.2008.0302). The article discusses a known fossil of a feather from the Crato
Formation in Brazil (Figure 1a in the article). The reason the fossil is impressive is twofold: firstly, it is very well perserved and shows amazing detail, including the barbs and barbules. Secondly, and more importently, it shows a striking banding pattern. Previous studies on the fossil showed the black bands to be made mainly of tiny carbon structures (Davis and Briggs, 1995). This is hardly a surprise, because fossil feathers are usually composed mainly of carbon. Use of scanning electron microscopes (SEM) showed the structues to be oblong bodies about 2 microns across. These were thought to simply be fossilized feather-degrading bactera from our very distant past.

Vinther et. al. took another look at this fossil. They took a wing from a Red-winged Blackbird , ground it up, froze it and then compared SEM images of the feather to the fossilized bacteria. What they discovered was that the bacteria weren't bacteria at all! Instead, they showed an incredible similarity to eumelanosomes, the structures in feathers that give them dark pigmentation. The authors concluded that this was no mere similarity; the structures are ancient eumelanosomes! This would mean that the dark bands on the feathers were actually dark-pigmented bands on the living specimen. The lighter parts of the feathers showed none of these structures, and would then mean that they were lighter (if not white) bands on the original feather. This makes much more sense than the original bacteria hypothesis; after all, why would bacteria only perserve in the dark areas of the fossil and not the light ones? It is more likely that, since eumelanin (the pigment-prodicing chemical in melanosomes) is resistant to degredation to chemicals, the black feathers themselves are more resistant to bacterial decay than white feathers. All this means that, by examining fossilized feathers for eumelanosomes, we can determine what the patterning of ancient birds looked like!

But it gets even better. Melanosomes don't just give a dark, black pigmentation. Melanosomes of different shapes, arrangements and distributions confer different colours like red, black, or brown. Other types of melanosomes, like Phaeomelanosomes, can give other colours like yellow, though the authors caution that it is unknown if these melanosomes preserve the same as eumelanosomes. But, if they do, this would suggest that not only can we determine the patterning of ancient birds but also their colouration! This could potentially extend to determining the colouration of feathered dinosaurs as well. Also, it has implications in understaning the behaviour and ecology of these ancient creatures. As the authors state, birds have the ability to see a broad range of colours; this is one good reason why birds have evolved elabourate and colourful plumages. Thus, knowing the plumages of ancient birds and dinosaurs could give us some insight into the way they lived (assuming, of course, that colour vision didn't evolve after birds had sufficently diverged into their modern-day descendants). Perhaps the illustrations we see in books, magazines and on TV will soon be alot more accurate!

Tuesday, 22 July 2008

Sleezy tactics by Alberta Right To Life

Two weekends ago, Jessica and I took a trip to Red Rock Coulee, a "natural area" (note: not national/provincial park, though there was a park attached to the "natural area") in southern Alberta, about 30 minutes southwest of Medicine Hat. Our reason for travelling was twofold; we wanted to take a mini-vacation for the weekend and she wanted to get some insects for her collection from an ecosystem unlike that of Edmonton. Red Rock Coulee was situtated near some badlands so it seemed like an ideal place to go.

On the way from our hotel in Medicine Hat to Red Rock Coulee, we passed by a trailer displaying a big advertisment by the Alberta Right To Life Group, seen below:

If you can't read it, it says "Abortion kills BABIES and hurts women!!", underneath which is a phone number (1-800-665-0570). The opposite side of the trailer declared "1 in 3 babies is killed by abortion!!", complete with a really crappy cartoon of two babies and one 'ghost' baby.

Wondering where they got their statistics, and to contest how abortion hurts women and "kills babies", Jessica called the phone number, expecting to get a small-town Pro-Life group. She didn't.

The lady who answered was an operator for the Canadian Crisis Pregnancy Hotline, out of Winnipeg. After talking things over with her, we found out that the Crisis Pregnancy Hotline has nothing to do Alberta Right To Life (or any anti-abortion groups), and had no idea that the group was using their phone number on anti-abortion propaganda. The hotline takes a neutral stand on the issue, being neither Pro-Life nor Pro-Choice (although, if you think about it, taking no stance on the issue is basically akin to letting people make their own decisions on abortion, which is what being Pro-Choice is all about).

This makes me wonder why Alberta Right To Life would put the number on their advertisment. One reason, which I think is likely, is that the sign is there to stir up an anti-abortion fever in small town Alberta. Residents would call the number thinking they will have a chance to vent their disgust to like-minded people at Alberta Right To Life, only to get connected to the Pregnancy Crisis Hotline and proceed to give them a tongue lashing about how they are evil, sinful baby killers for giving out information and help to women considering abortions.

Of course, this is just speculation on my part. There's no way to know for sure short of contacting the group themselves. I took a look on their website for contact info but couldn't find one for the Medicine Hat branch (the ones most likely to be behind the sign). I also found that the group has another website,, that claims abortion is the major cause of breast cancer in women, and that there is a big cover-up conspiracy by doctors to supress this info (more on this bullshit in a later blog post...)

But the sign leads me to think that the group is sleezy for three reasons. First, they dont say where they got any of their statistics. The statistics we found on abortion rates didn't match theirs at all. Without any reference to where the stats came from, how are people going to determine whether or not the group is truthful or lying through their teeth? Most people will take the numbers as truth without even thinking to look them up, but they wouldnt be able to do it even if they wanted to. Secondly, the use of the Pregnancy Crisis Hotline's number (and without stating what the number is for) is sleezy. I doubt doing so is illegal, since the number is freely available to the public, but who knows how many people have called it thinking they are going to get Alberta Right To Life and end up yelling at some poor soul in Winnepeg? And third, the sign spreads blatent lies about abortion (how is it "killing babies" or "hurting women"? Again, no references). I don't know how a group goes about putting up signs like that. I dont think it's legal if it's on public ground (because the group has an obvious religous impetus). Perhaps it's private land? I'm not familiar enough with the Medicine Hat area to know. I'll keep searching for a contact for the Medicine Hat branch so I an question them about it...

Monday, 21 July 2008

Answers in Genesis tries to play with the big boys, fails epically.

One of the things that is often used to laugh at how silly Creationists and, more specifically, Intelligent Design, is, is that it makes no predictions, no testable hypotheses, and porponents lack published papers in scientific journals. Some time ago, Answers in Genesis tried to address these criticisms by starting their own journal (Sorry, AiG, but it doesnt count when you need to start your own journal to publish your own papers, and the peer-review process only works when people outside of your own little group review your science). Nevertheless, we all still chuckled because their papers were non-technical drivel with faulty reasoning and laughable conclusions. Now, the folks over at AiG have tried to remedy this by attempting real 'semi-technial' research. In their article, they compare the fitness of an antibiotic resistant strain of Serratia marcescens to a suseptible strain, in an attempt to discredit evolution of antibiotic resistance (and thus, micro- and macroevolution). But, as the folks over at The Panda's Thumb point out, they fail majorly.

The first problem with their research is breaking one of the golden rules of research: if you are examining a particular variable, everything else needs to remain constant. For example, if you are trying to determine if regular or supreme gasoline gives you a better fuel mileage, you have to compare the two types in the same car, or at least the same model of car. You cant put regular in a Civic, put supreme in a Prius and then declare that supreme is better because the Prius goes further. There is no way to determine if the difference was caused by the gasoline itself of if other factors that differ between the two cars were the cause. You'd have to do the experiment in the same (type of) car. Everything except the variable you are testing needs to remain the same. The same thing goes with working with bacteria. If you are going to compare two strains - one resistant to Ampicilin, the other not - then both strains need to be genetically identical sans the resistance gene. This is one of the most basic, common sense rules about research. Its also the first rule that Answers in Genesis breaks in their 'research'. They compared an S. marcescens Amp resistant strain (it's never explicitly stated where they obtained it, but they allude to Dr. Robert Williams at the Texas Medical Center who has aparently kept the strain going) to a "wild type" that they, get this, isolated from a random sample of pond water. They have no way (short of sequencing the entire genome of each strain) if both strains are genetically identical. One is resistant to ampicilin, the other isnt. But is that the only difference? Most likely not. How can they conclude with any certainty that any fitness difference between the two were because of the resistance gene? They can't. It's as simple as that. They cannot make such a conclusion because they used grossly improper research technique; their findings are absolutely worthless.

The second big problem with their research is that they dont understand what the heck "fitness" means. They define fitness as as ‘growth rate and colony “robustness” in minimal media’ (What the heck is a "robust" colony? That's a pretty subjective qualifier). Unfirtunatley, because of their lousy techniques mentioned above, they can't tell if a smaller colony is less fit (by their definition) because of the resistance gene or some other factor they did not controll. Not only that but the figure they use to describe the growth curves has no error bars, so you cannot tell how accurate their numbers are and whether or not the difference between the two strains is statistically significant (it likely isn't). They then go on to conclude that the resistant strain is "less fit" than the wild type. This makes little sense, considering 92% of Serratia marcescens infections in hospitals are antibiotic restistant (which they state in their own paper). If such strains were less fit then why are they more common than the wild type strain? Because hospitals use antibiotics and the resistance provides a reproductive (fitness) advantage. But because they use a lousy definitation of fitness, they conclude that resistant strains are less fit.

The third big problem is that they dont seem to know the difference between "compete" and "compare". What they did in their paper was compare the two strains. They plated one on minimal media and counted the colonies. Then they plated the second on minimal media and counted the colonies. They compared the numbers, etc. Nevertheless, they constantly refer to the bacteria "competing". There is a big difference. Let's imagine we have two cages, each with a mouse. You feed Mouse A ten pieces of cheese, and it eats all of them. You feed Mouse B ten pieces of cheese, and it eats all of them. Comparitively, both mouse seem the same. But put both mice together and feed them some cheese, and mouse A eats 90% of it, while mouse B only gets 10% of it. This is because Mouse A outcompetes Mouse B. This is not what AiG did. They compared the two strains. They didn't make them compete. So how could they conclude that the non-resistant strain of Serratia marcescens outcompetes the resistant strain? They can't.

And even if all this was forgiven, if they had used proper technique, they had made the strains compete, used a proper definition of fitness....their conclusions are still wrong. If they had bothered to look, this exact experiment had been done before (properly), and the authors concluded the exact opposite of what AiG found.

Nice try, Answers in Genesis, but you're not cut out for this kind of thing. Leave the research to the people who know how to do it. Leave the science to the scientists.

Saturday, 19 July 2008

The big myth

I copied this from a forum post which was, in turn, copied from a [unnamed] website, so it's hard for me to give credit to whoever originally wrote this. But whoever you are, I salute you! I present: Jesus - the Myth behind the Man.

"We'll start thinking about Christian borrowing by asking a simple question:

By what criteria can we decide what ancient godman stories were new and original, and what ancient godman stories were myths built up from the religious ideas of their day?

Here's what I mean..

When Osiris is said to bring his believers eternal life in Egyptian Heaven, contemplating the unutterable, indescribable glory of God, we understand that as a myth.

When the sacred rites of Demeter at Eleusis are described as bringing believers happiness in their eternal life, we understand that as a myth.

In fact, when ancient writers tell us that in general ancient people believed in eternal life, with the good going to the Elysian Fields and the not so good going to Hades, we understand that as a myth.

When Vespatian's spittle healed a blind man, we understand that as a myth.

When Apollonius of Tyana raised a girl from death, we understand that as a myth.

When the Pythia , the priestess at the Oracle at Delphi, in Greece, prophesied, and over and over again for a thousand years, the prophecies came true, we understand that as a myth.

When Dionysus turned water into wine, we understand that as a myth. When Dionysus believers are filled with atay, the Spirit of God, we understand that as a myth.

When Romulus is described as the Son of God, born of a virgin, we understand that as a myth.

When Alexander the Great is described as the Son of God, born of a mortal woman, we understand that as a myth.

When Augustus is described as the Son of God, born of a mortal woman , we understand that as a myth.

When Dionysus is described as the Son of God, born of a mortal woman, we understand that as a myth.

When Scipio Africanus (Scipio Africanus, for Christ's sake) is described as the Son of God, born of a mortal woman, we understand that as a myth.

So how come when Jesus is described as the Son of God, born of a mortal woman, according to prophecy, turning water into wine, raising girls from the dead, and healing blind men with his spittle, and setting it up so His believers got eternal life in Heaven contemplating the unutterable, indescribable glory of God, and off to Hades—er, I mean Hell—for the bad folks...
how come that's not a myth?"
The answer is, of course, it is a myth. Just like every other godman, every other miracle worker, every other prophecy fullfiller, Jesus' life is a myth. Christians need to realize theyre worshiping the same myth as the ancient "heathens" they look down upon.

Friday, 18 July 2008

And I thought things couldnt get any more ridiculous.

It's official. Now I've heard everything.

These people want Jesus as president. Seriously. When election day comes, they want to write in Jesus for president.

You hear that noise? That's the sound of America going down the drain.

Will people please use their brains for a second?

So today Stats Canada released some statistics on crime rates across the country. I read about it on Yahoo Canada News, which you can read for yourself here. The jist of it, though, is that, overall, the crime rate for Canada as a nation has decreased for the third year in a row. Go us! Moreover, the stats show:
"Crime rates were down in all provinces and territories, except Newfoundland and Labrador, the Northwest Territories and the Yukon. Overall crime rates remained highest in the western provinces.

Saskatchewan's crime rate fell 3.5 per cent but still was the highest in the country, including the highest rate of violent crime. Manitoba's 62 homicides last year were up 23 from 2006, giving it the highest provincial homicide rate and Manitoba's highest murder rate since recording began in 1961.

"For the fourth year in a row, the lowest provincial (crime) rate occurred in Ontario and Quebec," said the agency."

Alow me to recap. The areas with the highest crime rates are the western provinces, with Saskatchewan at the top. The only areas with increasing crime rates are Newfoundland, the Northwest Territories and the Yukon. Ontairo and Quebec have the lowest crime rates.

Now read the comments people left about the article. Many people have said things along the lines of "Gee Im glad I dont live in Newfoundland! I'll stay here in BC". One guy commented that Newfoundland seems like "a suburb of Iraq". Waaaait a second here. Does anyone know the difference in highest crime rate and an increasing crime rate?

Newfoundland has an increasing crime rate. That does not mean it has a HIGH crime rate. If the crime rate in Newfoundland went from 1% in 2007 to 3% in 2008, that means it has an increasing crime rate. If Alberta had a crime rate in 2007 of 40% and that dropped to 38% this year, then the crime rate decreased. But which one is HIGHER? Of course these numbers are made up for illustrative purporses but the point remains. The article said Newfoundland had an increasing crime rate, not that it had a high crime rate. It explicitly stated that the highest crime rates were in western Canada!

Another point that seems to have passed people by is that these statistics are based on a per capita level. A province that had one person and one crime would have a crime rate of 100%. Nevertheless, there was only a single crime committed in that province that year. A province of 10,000,000 people with 5,000,000 crimes would have a crime rate of 50%. Which would you think is the safer place to live? If the number of crimes were kept constant (i.e. if the same number of banks were robbed in each province, the same number of people were killed, etc.) then the provinces with the smaller populations would come out with the higher crime rates.

This is really simple stuff. Why can't people get their heads around it? An increading crime rate doesnt mean a high crime rate. Newfoundland isnt a "suburb of Iraq". If anything, western Canada is Bagdad's backyard. Take a look at the picture below: (click it for a better look, it comes out like crap on my blog)

The National crime rate is about 7%. The provinces with the lowest crime rates are at about 5.5%. Newfoundland is a tad over 6%, making it one of the provinces with the lowest crime rate (pretty much smack dab in the middle actually). Compare that to the rates for the provinces out west: they are much greater than the national average.

So why the hate on Newfoundland? Yes, the province has an increasing crime rate, but its still a LOW crime rate. Its pretty ironic and kinda sad when commenters from western Canada call Newfoundland a "suburb of Iraq" when they live in the part of Canada with the highest crime rates. Maybe I'm just irate because I'm a Newfoundlander and people are "trashing" my home province, but seriously, people need to learn how to understand statistics.

God isn't a scientist, he's a fine arts professor.

Once again, the good folks at Fundies Say the Darndest Things have provided me with some creationist fodder to debunk. Today's post comes from Gideon over at Here it is in full:

The sun has gives off ultraviolet rays doesn't it? And it has been proven that humans in fact, need the nutrients of these rays in order have healthy skin, and so on. But when a human has too much UV, the effects have proved harmful. Knowing this however, He decided to create the ozone layer and a magnetic field to shield us from such radiation. Also, while the earth rotates it is slightly tilted as it hangs, and with good reason: If that tilt was even 1 degree higher or lower than it is now earth would suffer through unstable seasonal change, orbital change, and much more... also making it impossible for us to live on it. As we know, scientists do not just analyze they also have the ability to create; a scientist does not only make observations. So God therefore that would make God a perfect scientist because he knows everything and can create anything (like the examples shown above) perfectly, unlike us human scientists. And so you see, God uses logic even for these basic things. Did that make sense?

Let's dismantle this piece by piece, shall we?
"The sun has gives off ultraviolet rays doesn't it? And it has been proven that humans in fact, need the nutrients of these rays in order have healthy skin, and so on. But when a human has too much UV, the effects have proved harmful. Knowing this however, He decided to create the ozone layer and a magnetic field to shield us from such radiation."
Yes, the sun does give off ultraviolet rays, in three forms: UVA, UVB and UVC. This might be the only thing in Gideon's entire post that he actually gets right. But it has not been proven that humans "need the nutrients of these rays in order to have healthy skin and so on". This is because the rays dont have any nutrients! Ultraviolet rays are composed of photons with a wavelength shorter than that of visible light (but longer than X-rays). In the mid-1800's James Clerk Maxwell showed that light - photons - are a form of electromagnetic radiation. In other words, ultraviolet rays are a form of electromagnetic radiation. UV is energy. As such, it is absolutely impossible for UV light to have any nutrients. "Nutrients" are chemicals necessary for the metabolism of an organism which must be taken in from the environment. They are physical, material substances. UV, energy, cannot "carry" nutrients.

Nevertheless, ultraviolet light is necessary for our health. The biosynthesis of Vitamin D requires UVB light as a catalyst; people who do not get adequate exposure to natural UVB light end up becoming deficent, a condition known as rickets. This might be what Gideon was alluding to but was too ignorant to get the facts right. Too much of it is also dangerous. UV light causes pyrimidine dimers in your DNA: pyrimidine bases, like thyamine will pair with each other in the same strand. This causes the DNA to bulge, preventing replication enzymes from working and causing mutations. This is why you get a sunburn that often peels; your cells get enough mutations that they kill themselves off to prevent themselves from becoming cancerous.

However, while the ozone layer does work to keep out harmful UVB and UVC rays (UVA is not as harmful - it's what's emitted by blacklights), the earth's magnetic fields does pretty much nothing to protect us from ultraviolet light (and it would be pretty crappy if it did protect us. Since the magnetic field has varried in intensity and direction over time, so would our exposure to UV). Chemicals like CFCs destroy ozone molecules, putting us at higher and higher risks of overexposure to UV light. Gideon seems to think that the protection against UV is a gift from His Almighty. This kinda makes me wonder though. Does Gideon think his God is stupid? Why would God design us so that we require something that could easily kill us as an essential factor for life? Wouldn't it be smarter to make sure that everything we require for our metabolism isn't harmful? Was this an oversight on God's part? For someone who's supposedly infinite in his foresight, it seems a bit odd that he would do this.
"Also, while the earth rotates it is slightly tilted as it hangs, and with good reason: If that tilt was even 1 degree higher or lower than it is now earth would suffer through unstable seasonal change, orbital change, and much more... also making it impossible for us to live on it."
Wrong, wrong and more wrong. The Earth's tilt is caused (most likely, the debate is still open on the cause) by the shape of the Earth itself. The Earth is not a perfect sphere; and because of this it rotates with a bit of a wobble. This wobble gives the Earth it's tilt. It is also the reason why the rest of Gideon's claim about the Earth's axis is bunk. The Earth is not tilted because an axis of plus or minus one degree would spell disaster. In fact, the angle of the Earth's axis has changed over time: it changes from 21 degrees to 25 degrees and back again once every 41,000 years (much more of a deviation from the current tilt of 23.5 degrees than the "deadly" 1 degree difference claimed by Gideon). The tidal forces on the Earth due to the gravity of the moon also have an effect on the tilt of the Earth; this is called nutation, and occurs in a cycle of 18.6 years. This means that the axis of the Earth changes (assuming that the rate of change of the Earth's tilt is constant) at least one degree every 5100 years1. If such a change in the axis would cause "unstable seasonal change, orbital change, and much more... also making it impossible for us to live on [Earth]", then humanity would have been wiped out within recorded history. Even if you believed in Young Earth Creationist claims that the earth is only 6000 to 10,000 years old, if Gideon's claim were true then humanity would have been wiped out at least once. Obviously, this is ridiculous. The truth is that the Earth's tilt is due to the shape of the Earth and the exact angle of the tilt varries at a known rate. There is nothing special about the Earth in this respect - even the moon has axial tilt - and there certainly isn't any "design" aparent in this regard.
"As we know, scientists do not just analyze they also have the ability to create; a scientist does not only make observations. So God therefore that would make God a perfect scientist because he knows everything and can create anything (like the examples shown above) perfectly, unlike us human scientists. And so you see, God uses logic even for these basic things. Did that make sense?"
Gideon is right that scientists do not only make observations, but they also make interpretations of those observations to try and elucidate the way Nature works. What scientists create are working models of Nature. We use experimentation to ask Nature a question and we evaluate her reply. God would not make a perfect scientist at all. Scientists seek answers; God, in all his infinite knowledge, supposeldly already knows the answers (just like a Creationist, eh?). This would make him a terrible scientist: the whole purpose of science is to find the answers to how the world works. If all the answers were known then science would be futile (thankfully, this isnt the case). And if God knows all the answers, then he has no working models to create. God would be just about the worst scientist you could imagine, and not just because he's only had one publication in the 6,000 year's he's supposedly been working. So, no, Gideon. That doesn't make sense.
1. An entire cycle takes 41000 years, so it takes 20500 years to go from 21 degrees to 25 degrees, a difference of 4 degrees. If the rate of change is constant, then the tilt changes once every 20500/4=5125 years.

Thursday, 17 July 2008

A Vaccine For the Mind

Vaccines work by prompting your immune system to recognize, and learn how to properly deal with, a virus or bacteria of a certain type. In this manner, vaccines provide protection against an antagonist, a shield to keep your body safe from the damages of pathogens.

After so many years of dealing with creationists and their ilk, I've come to notice that the way they act is similar to the way vaccines work. Religion seems to put up an impregnable barrier around their minds that keeps out science, facts, and rational thoughts. Religion acts just like a vaccine, except it works on the mind to keep out facts rather than on the body to keep out pathogens. This has lead me to coin a new term: Religion acts as a factcine on the mind. Creationists have been factcinated against critical thinking.

This applies to other groups too: astrologers, new age practitioners, 9/11 truthers, the entire Green Vaccine movement, psychics and their supporters - they all have been factcinated in one form or another to ignore the facts. And, just like a vaccine teaches your body how to fight off a pathogen, so does factcination teach these people to actively fight away facts. Factcination is dangerous: not because factcines contain dangerous chemicals like vaccines supposedly do (they don't) but because they contain even more dangerous stuff: vile lies and ignorance.

Wednesday, 16 July 2008

Location, Location, Location

When election time comes around, there is endless debate over voter statistics: who's voting for who, voting trends within different social groups, etc. Undoubtedly, candidates are always looking for a way to swing the vote in their favour, and they will try a multitide of tricks to change the way people vote. But one aspect of voting patters has so far gone ignored: the location of polling stations. If the location of polling stations could affect the outcome of a vote, it could end up being a powerful way of affecting voting patterns. As it just so happens, new research has shown that it might just be the case.

A study recently published in PNAS1 has shown that the location of a polling station can have a bias on the outcome of the poll. The authors predicted that a voting station in a school would have a higher proportion of voters supporting a raise in taxes to increase spending on education than polling stations set up in other areas. They then analyized data from one such poll, done in Arizona in 2000. The data showed that stations set up in schools had a higher ratio of voters in support of the tax increase than did other stations. They also performed a second study, using an online poll. Participants were given the same online poll, but the background images were changed between participants; some were shown images of schools and others were shown control images (offices, etc). The results echoed the analysis of the 2000 Arizona poll data: the polls done in a school enviornment were more likely to vote in favour of raising taxes to increase spending on education.

This means that the polling stations can be used to manipulate the outcome of any poll. Stations set up in churches will be more likely to vote against gay marriage. Set up a polling station in a laboratory to swing a vote in favour of stem-cell research. Since churches are often used as a polling station in rural comminuties, this could mean that liberal/democratic candidates are facing an unfair disadvantage.

There are obvious ethical implications of this. Polls are supposed to be fair and unbiased: using the polling location to your advantage - "contexual priming of polling locations", as the study authors call it - should be against the rules. The findings of this study beg for an unbiased, fair location for polling stations. In a time where voter support on hot-issue topics can be changed by as little as where candidates ate breakfast this morning, however, achieving a state of total non-bias is going to be a bit easier said than done.

1. J.Berger et al. Proc. Natl. Acad. Sci. USA doi:10.1073/pnas.0711988105;2008

Tuesday, 15 July 2008

Because killing your child is obviously way better than autism.

The climate in North America concerning vaccines is quickly becoming a rather hostile one due to the masses of "Green Vaccine" supporters out there using pseudoscience, and often, blatent lies, to have vaccines banned. They believe that vaccines contain things like mercury and - yes, Ive actually heard this one - pieces of aborted babies, and claim that this is the cause of a slew of childhood ailments; in particular, they claim that vaccines are directly causing rising rates of autism. Anyone with a rational, critical thinking mind will realize that the "Green Vaccine" movement is a bunch of nonsense....but things may have just got a bit worse.

The leading funder of autism research in the US has just approved a proposal to run a tiral on the use of chelating agents to treat children with autism. Chelating agents are chemicals which are able to sequester metal ions, like magnesium, copper or zinc: they bind to metal and make them easier to excrete. They are used as a treatment for heavy-metal poisoning and often as a component in New Age "detoxifying" schemes. Unfortunately, they can be incredibly dangerous to ingest. Your body needs metal ions for alot of critical enzymes to work. DNA polymerases, the class of enzymes responsible for replicating your DNA, require magnesium to work. It is for this reason we use such agents in molecular biolgy: when we want a reaction to stop, we add a chelating agent like EDTA to keep the enzymes from working any further. Ingesting chelating agents runs the risk of preventing such enzymes from working and can be deadly.

The logic behind the idea is this: mercury in vaccines causes autism in children, so we give them chelating agents to bind up all the mercury and they should get better. Besides the fact that mercury in vaccines causing autism has been repeatedly scientifically discredited, this is a really bad idea. Chelatig agents have been shown before to have little medical benefit outside of heavy-metal poising. One study with rats has shown that chelating agents can lead to cognitive problems. If that weren't bad enough, three years ago, a 5 year old autistic child in Pennsylvania died after having been given a chelating agent injection. And even if autism was caused by high levels of mercury (it isn't, and has never been documented), using chelating agents would be a poor treatment since the cellular damage caused by mercury is permanent, unrepairable damage.

Funding this is a waste of tax-payer money since it's testing a treatment for something that has never been shown to be an actual symptom of mercury toxicity. Such a clinical trial is only pandering to the Green Vaccine people. Of course the director of NIMH, the institution carrying out the trial, denies this, saying the study "came up in the first place because we were getting reports that this was a therapy in broad use and there were very substantial questions about both its efficacy and its safety”.

The trial still has to be approved by an ethics board since it involves children and poses a greater than minimal risk to their health. Hopefully the trial will be denied, but the fact that it was approved for funding speaks volumes about the political clout the Green Vaccine movement has. They need to be hit with some science, and hit hard. Too bad the inpact would be softened by their willful ignorance of the facts.

Thursday, 10 July 2008

It's Called the Road, It's Called the Rainbow Road.

Ive been singing this song over and over ever since I heard it.
The Rainbow Road tracks are always the toughest tracks of any Mario Kart game.
And they always have a very distinct soundtrack to them. That music has now been made even more awesome:

It's Rainbow Road, Its where you go when you die, It's Rainbow Roaaaaaaad...I'll miss you again Uncle!

Wednesday, 9 July 2008

Note to self: Bring MP3 player to work

Because I'm really beginng to get annoyed by the radio.
For the last month and a half, we have been listening to the radio in the lab to have some background music to keep things from getting too dull. For reasons that were never explained to me, the station we picked was Sonic. They play lots of "modern rock" (read: overproduced "megahit" tripe you can hear on any "rock" show). One thing that slowly became apparent to me, though, is that they play the same handful of songs over and over and over. After hearing the latest single from The Offspring 3 times in one hour my brain began to liquify. Thier playlist rotation consists of probably 10 songs, interspersed with an few different songs from the same artists. That station is so incredibly repetitive that it really reaches the limits of my patience.

Today, we picked a new station since we all got sick of listening to the same few songs over and over and over. So we picked Bounce, or whatever it's called. And guess what?
SAME PROBLEM, DIFFERENT SONGS. Instead of listening to the same latest rock tunes a million times a day, we now hear the same pop/hip hop songs a million times a day. I began keeping a mental tally: In the last 6 hours, I've heard the same Miley Cyrus song 4 times, some retarded R&B song called "Busted Baby" 5 times, and a handful of other songs, the names of which I dont remember (I dont even like this kind of music so what do I care about the song names?) , 3 times. That's a playrate of almost once an hour for the more common songs.

This makes me wonder if the stations are being paid by the artists/recording companies to play these songs so often. "We'll give you $20,000 but you have to play Miley Cyrus at least once every 20 minutes!" I have enough music on my computer that if I were to listen to it on random, I would hear the same song maybe once every FEW DAYS. Am I supposed to believe that a professioal radio music station has a more limited selection of music than I do? Maybe I could understand it if one station were like this, but so far we're two for two. I wouldnt be surprised if we tried a new station and were faced with the same bullshit repetitiveness.

Maybe I should switch the station to CBC Radio 1. Yeah, the music on it might suck but at least there are interesting and informative shows, as well as the news, that they play. The station doesn't suffer the same repetitiveness that the others do; but I doubt that changing the station to CBC would be one that would go over well with my lab mates. After all, they were the ones that picked out the stations that play constant tripe to begin with. Is it too much to ask for a station that caters to those of us whose attention spans last longer than a few minutes?

There goes that damn Busted Baby song again...

Monday, 7 July 2008

More creationist dumbosity

Here is yet another quote from my favourite website, Fundies Say The Darndest Things. It's a pretty long quote where the fool asks a list of questions, so I'll answer them in order.

"1. If evolution is unguided and is a completely natural process, how does nature "KNOW" which traits are beneficial and which traits are not? For example, how did nature know to make a digestive system and a sewage system for the removal of our bodily wastes? Did these systems just "pop up" out of nowhere in organisms? Or did organisms start out with half-systems and couldn't remove waste and digest food? If the latter is the case, how did organisms ever survive
long enough to reproduce?"

This seems to be a common question among creationists. Given the idea that organisms can evolve new traits over time, they ponder how Nature can "know" when and what kind of adaptations to evolve. The answer, of course, is that Nature doesn't "know" either of these things. Nature is, to borrow a metaphor, a blind watchmaker. There is no "when" simply because the processes that drive evolution - natural selection - are at work all the time. Organisms are constantly evolving, whether it be on the micro or on the macro scale. As long as there is a selective pressure, organisms will continue to evolve. That is part of the key to the "what" question as well. Nature doesn't "know" which traits should be evolved. The traits that occur are a consequence of the environment. To answer the example in the question above, organisms that had a method of removing bodily wastes - even a very primitive one unlike our own - were more fit (that is, more likely to live to reproduce) than those without. Eventually, the number of organisms posessing digestive systems would outnumber those without. Of course, such systems would not just "pop into existance". Rather, they would be the result of a gradual building up of more primitive traits. Over time, the system would become more and more complex, since a "better" system would provide a fitness advantage over those with the previous version. At no point in this process did Nature say "Hmmm I think that organism needs a better digestive system, so I'll make them evolve one." It was the environment, selecting for organisms which gain reproductive advantages, that allowed complex systems to come into existance.

I think part of the reason why so many creationists ask this question is that they cannot get their minds around the possibility that there isnt an intelligent force behind the existance of life. They are so ingrained with the idea that an intelligent being - God - runs the universe that, when presented with the idea of evolution, they figure that there still must be an intelligence behind it, that Nature is a conscious, thinking entity (and seeing, rightly, that Nature doesnt posess such a property, they claim that God must be the Creator). For them, an intelligent designer is not a simple assumption but rather an axiom.

"2. It is often said by evolutionists that we have certain traits because they make us survive better. For example, we have eyebrows because it keeps things out of our eyes. (This is said as if nature actually KNOWS it's keeping stuff out of our eyes and decided to stick with eyebrows.) But, if we really do have certain traits because it makes us survive better, why didn't we evolve immunity to fire? Surely if we had the ability to not be harmed by fire, it would be a HUGE survival advantage to our species. But, we do not see this despite the fact that evolutionists say that evolution works to give us traits to survive better. We are immune to other certain types of things. Immunity to fire would've been a huge survival advantage, don't you think?"

Saying that evolution "works to give us traits to survive better" is a bit of an understatement. Evolution works in such a way that traits that allow us to be more fit - to have a greater chance of reproducing - are selected for. Survival post-reproduction doesn't really matter from the point of view of evolution. As long as an organism reproduces, its genes gets passed on, and the better the organism can ensure that it lives long enough to do this the better. So it's not really survival that natural selection favours: rather, it's reproductive success. Evolving an immuminity to fire would not really fit this description. Surely, an organism which evolved immunity to fire would survive over one which is not immune in an environment that is constantly bombarded with fire, but such environments do not exist. Perhaps if you moved a population of squirrels to the bowels of Hell itself for a couple million years you'd get fire resistant rodents, but such a situtation is highly improbable in reality. In the real world, organisms are rarely exposed to fire on a regular basis. An immunity to fire would not probive a distinct reproductive advantage. Quite to the contrary, if any organism did somehow evolve and immunity to fire, it would be likely to be at a reproductive disadvantage, since it would be expending energy and resources to support an immunity that the others in the population would not have to.

This is, of course, ignoring the fact that being immune to fire is a physical impossibility. The reason fire is harmful is because it's high temperatures cause physical damage to matter; it results in irreversal changes to matter it comes into contact with. Our flesh burns, our enzymes denature, our proteins break apart. The reasons these things happen is purely a chemical one. Developing an immunity to fire would mean developing chemistry totally alien to our universe. And while evolution can produce some amazing things, THAT would be a feat even Mother Nature can't do.

"3. if nature doesn't "know" anything and is unguided, how does our body know when something bad is being put into it to cause us to cough? If nature was unguided, there should be no reason why our body "knows" we have to cough. How does nature know what is good and bad? "

This is because we have a complex and effecient immune system. Foreign particles have traces on them that tell our bodies which are "bad" and which are "good. These are called antigens. We have special cells that recognize antigens and can determine which particles are harmful and which are not. This is what helps us fight off bacteria and viruses: they all express antigens which our immune cells can recognize; when such a pathogen is detected by these cells, they are eliminated (through a variety of complex ways, the scope of which is beyond the material of this article).

Similarily, when cells in the lining of the throat recognize that there are foreign particles present that should not be there, they excite a coughing reaction which works to move those particles up and out of our bodies. This is how our body "knows" when to cough. How could such a process have evolved "if nature was unguided"? It couldn't. But nature ISN'T unguided. Nature's hand is guided by natural selection. An organism with a rudimentary immune system would obviously have a reproductive advantage over one without such a system; likewise one that could remove foreign particles from its throat by coughing would be less prone to infection and the like than one who could not. Coughing provides a bonus to fitness and is easily selected for.

"4. If surviving more efficiently is one of the main purposes of evolution, why do so many people get heart disease? Shouldn't we have evolved to a point by now where fatty foods don't harm us because it would make us survive longer and better? Right now, fatty foods can kill you and give you a heart attack if you eat it too much. Some survival advantage that is for us, huh? If we all had the ability to eat any type of food we wanted without getting heart disease, that would be an even GREATER survival advantage, don't you think? "

This is kind of a rehash of the fire-immunity question above. I wont go into detail explaining why we havent become able to eat whatever we want without consequence, so I'll summarise in a few lines:

The particular effects fatty acids have on our bodies are limited by our biochemistry. That is, the reason we have adverse effects from eating too much fatty acids are biochemical ones and, thus, are governed by the laws of biochemistry. Evolving an "immunity" to these effects would mean evolving chemistry that is counter to the chemical laws which govern our (known) universe. Given enough time, we may evolve in such a way that the effects of greater fatty acid intake are less and less adverse but developing an "immunity" is highly improbable, if not impossible.

"Yet, in spite of all these objections, evolutionists will INSIST that evolution gives us traits to be able to survive better. I guess evolution doesn't see a need for us to REALLY be able to survive better considering we can burn in fire and die from too much eating. "
So basically this guy's views on evolution can be summed up as "Why haven't we evolved to be invincible? The fact that things can hurt us shows that evolution is false. Besides, organisms can't "know" when to evolve, anyway." As usual, these questions can be answered with a simple undertandsing of evolutionary principles and not taking the idea of an intelligence ruling the universe as a given. Such questions highlight the need for a better teaching of evolution in highschools, and a set curriculum for homeschooled kids (since the only exposure to evolution most of them get are lies from their parents, who are not qualified to teach anything, that evolution is an evil conspiracy lead by scientists). With the trend of school boards in the States trying to pass misnomered "Academic Freedom Bills", it's likely that education on the subject is going to worsen. These questions, as absurd as they are, might become the norm for even the most "enlightened" (and I use the term very lightly) of creationists.

Friday, 4 July 2008


I'm pretty excited right now because I had a sort of a mini-breakthrough. I didn't discover anything amazing or get interesting results or anything, but I solved a problem that had been bugging me for a while now.

So far in our iGEM project, I've done a half dozen western blots - none of which actually worked. I would get nice thick bands on the gels after I stained them but when I did the chemiluminescent detection, the x-ray film would come out blank without fail. I'm no stranger to this occuring because the exact same thing occured to me when I did my western for Genetics 420. I only just figured out what I've been doing wrong.

To do a western, you take a sample of your protein (either crude from freshly lysed cells or stuff you've purified) and run it through a polyacrylamide gel. This seperates out the proteins on basis of their size. From here you can do two things: you can stain the gel to visualize the bands directly on the gel or you can transfer the proteins from the gel to a nitrocellulose membrane, which can then be probed with antibodies targeted specifically against the protein that you're interested in, which have a particular enzyme attached that emits light when a certain chemical substrate is added (in short, when you expose the membrane to x-ray film, you get a dark band where your protein of interest is, keeping the background bands to zero). What I've been doing is staining the gel to get a visual idea whether or not there is actually any protein on the gel, then transfering to a membrane, probing and exposing to the x-ray film. And it has yet to work.

It seems the problem is with the order in which I've been doing this. I always stain first, then transfer. Unfortunately, this is bound to fail. The stain that we use is called Coomassie Brilliant Blue. Its a stain that stains proteins by binding to specific amino acids. One amino acid that it has a particular liking for is histidine. Therein lies the problem: all of our proteins have six histidine residues at the end - a 6xHis tag it's called. It's this tag that we use to make sure our antibodies bind to only our proteins of interest. The antibodies have been created so that they bind specifically to 6xHis tags, which do not occur naturally in E.coli1. Since I was staining first, the His tags were bound with Coomassie stain. This blocked the antibodies from binding; preventing any reaction and no bands on the x-ray film. What I should have done was transfer to the membrane first, and stained the gel after (since transfer is never 100% and some proteins remain on the gel).

I'm redoing two westerns today that didn't work before. Hopefully I will actually get results this time!
1. I have heard talk of one "mysterious" E.coli protein that seems to come up over and over when using 6xHis tags in westerns, but no one knows what it is. I dont know how true this is, but it doesnt seem to be much of a problem for researchers since His tags are probably one of the most common protein tags used in molecular biology.

Thursday, 3 July 2008

Religious nescience strikes again!

Here's another aneurism-inducing quotation from a creationist:

The bible does not contradict anything in reality. And most scholars believe the bible to be the most accurate history book ever written. It also talks about many things that took up until less then 100 years ago for science to discovery such as "the life is in the blood" which turns out that life comes from the DNA in our blood.


Where do I begin with this one?

1) "The bible does not contradict anything in reality." This is blatently false. The Bible is filled to the brim with passages that contradict reality. How about the Bible giving impossible dimensions for Solomon's temple1 (resulting in the wrong number for Pi)? How about claiming that birds crawl around four legs2? How about claiming that rabbits chew cud3? There are many examples of things that are completely errorneous in the Bible.

2) "And most scholars believe the bible to be the most accurate history book ever written." Except that most scholars dont believe that at all. Perhaps most theologians, but definately not most scholars. There is actually very little in the Bible that has been supported with historical evidence. And even those few occurances that it mentions which did occur, the Bible does a very inaccurate job of describing them. Take, for example, the fact that the New Testament makes the claim that King Herrod wanted all young boys killed after Jesus was born. Its pretty certain that Herrod did exist; unfortunatley for those that claim the Bible is "historically accurate", though, Herrod is thought to have died five to ten years before Jesus was supposedly born. Another good example is the Exodus. When Moses attempted to liberate his people from the Egyptian, it was a pretty major event. Even if the leaving of so many slaves went unnoticed, it would be silly to think that no one would notice the repeated plagues - the frogs falling from the sky, the crop-devouring locusts, or the bloody water. At the very least, someone would have noticed the "angel of death", killing the first born sons. Yet, despite all of the devestating happenings, absolutely none of them were recorded by the Egyptians. Odd, for something that claims to be historically accurate. If you claim that the Bible is historically accurate, then you need to have evidence from other historical records that corroborate those claims. For most (if not all) the major 'events' in the Bible, this evidence is lacking.

3)"It also talks about many things that took up until less then 100 years ago for science to discovery such as "the life is in the blood" which turns out that life comes from the DNA in our blood" Except not. Ignoring his pittiful example, there has really been no "scientific discoveries" that have been made in the last 100 years which were explicitly stated in the Bible. Any examples to the contrary are examples of confirmation bias: creationists read a passage in the Bible, and equate it to a new discovery since they went in assuming that such discoveries were already in the Bible. The example that is provided is pretty poor, too. The idea that "life is in the blood" extends back at least as far as the ancient Greeks. And besides, DNA isnt just in our blood. Its in ALL our cells4.

Once again, a creationist speaks his mind on a topic which he is absolutely ignorant about. Such is the norm it seems.
1. 1 Kings 7:23 "He made a molten sea, ten cubits from the one brim to the other: it was round all about, and his height was five cubits: and a line of thirty cubits did compass it round about."

2. Lev 11:20-21: "All fowls that creep, going upon all four, shall be an abomination unto you."

3. Lev 11:6: "And the hare, because he cheweth the cud..."

4. Except red blood cells, which have no nucleus (or any other organelles).


As I talked about yesterday, waiting is one of the worst parts of research.
Today, I discovered another part of research that really sucks: getting scooped.
Turns out that Penn State's iGEM team is working on a project pretty much exactly like ours - making an E.Coli biosensor for bisphenol A in environmental samples. I'm not going to point fingers and cry "Thieves!" since there's no evidence they are directly copying our project, but we all thought our project was pretty novel up until 5 minutes ago. True, we havent really been scooped - their project isn't finished or been published - but Penn State has more resources at their finger tips and has the potential to blow our project out of the water. Our project has alot more aspects to it, though: we are developing a cell-free system, a degradation pathway in addition to the biosensor and tools to move the system into plants. So if we work hard, we can kick their butts. Nonetheless, we now have direct competiton. It'll be pretty embarassing in November if we lose to a team with a nearly identical (yet less intricate) project; the very idea for which was originally ours.

Wednesday, 2 July 2008

...In Which We Play The Waiting Game

Science is exciting. Being on the cutting edge of novel research is exciting. What alot of people don't realize, though, is that there are parts of science which can be downright boring. Those parts are the waiting parts.

Molecular biology is probably the most notorious for its waiting periods. The techniques used in my field can be pretty technical and can be tough to understand and do, but there is alot of waiting around. Want to do PCR? Put your PCR mix in the thermocycler, press 'start' and sit back and wait for 2.5 hours while the machine does the work for you. Want to transform bacteria? Take your competent cells, give 'em your plasmid, and put them in the incubator for 2 hours and go for coffee. The worst waiting comes when you have to order supplies. We put an order in for a site-directed mutagenesis kit and an order for the synthesis of a few genes last week; they have yet to arrive (and the kit is on backorder until next week). Until then, there's really nothing we can do in the lab. So we sit. And wait.

Research is awesome. It's just the waiting that sucks.