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)."

or

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 understand...so 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:
"THE CITY OF GOD ? IS IT TRUE THEY FOUND IT?
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.