Monday, 23 February 2009
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
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 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
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
"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.
Friday, 13 February 2009
"Re: “Evolution, creationism debate still simmers; Iconic naturalist would be amazed at the controversy over his ideas,” The Journal, Feb. 7.
Religious beliefs aside, one would be hard pressed to believe in evolution. The fossil record does not support it and the mathematical improbabilities of us evolving out of nothing are staggering.
Chris Eckert, an evolutionary biologist at Queen's University, is correct in saying that there are numerous species, but that in itself does not point to evolution. That’s happened thanks to the marvellous DNA in all living things, which allows for numerous variations, as any dog breeder can testify. This can be called microevolution. However, a dog will still only produce a dog, no matter how you tweak it. If you really stop to think about it, if for example birds evolved from dinosaurs, how did the intermediate creature survive for several million years with legs that are now useless but which are not quite wings yet either? He’d be a sitting duck for predators.
Apes can mimic a few words taught by trainers in response to rewards, but lack the throat and brain structure necessary for speech, vocabulary and grammar. One can go on and on why macroevolution is impossible, but evolutionists keep insisting on reviving a dead horse.
Peggy Heather, Edmonton"
While not nearly as long as Hendrickson's nigh-on-incoherent babbling, Peggy no less piles on the stupid.
First of all, the fossil record DOES support evolution. In every way, shape, and form does the fossil record support evolution. To doubt this shows you know nothing of evolution nor the fossil record. What does the fossil record show? It shows us the gradual progression of life from simple organisms to more complex organisms over the period of millions upon millions upon millions of years. It shows us early forms of body patterns familiar to us and it shows these patterns changing over time to become what we see today. It shows the beginning of different families of organisms and the ends of other families. All of these things are predicted by evolution. There is not a single aspect of the fossil record that does not support evolution, and if you claim otherwise, then you are either ignorant or lying.
Secondly, the mathematical improbabilities of us evolving "out of nothing" matter very little. The improbability of winning the lottery is staggering, yet someone always wins. Improbable does not imply impossible. Even if the chances of life evolving were one in one hundred billion trillion, the fact is, it happened. A lot of these arguments about the probability of life evolving are terribly fallacious: they scrape together large numbers they assign arbitrarily and output a large number that generally means nothing. People look at the large number and think "wow, that number is too large for me to grasp. I cannot argue against such a big number. I guess the conclusions drawn from this big number must be right." Dangle a few dozen zeros after the 1 in front of people and you're bound to get someone who believes you, no matter how asinine your argument.
Peggy follows this up by outright accepting microevolution. But what keeps her from accepting macroevolution? What is the barrier that prevent macroevolution while allowing microevolution? She doesn't say! Perhaps this is because there simply ISN'T one. Macroevolution is what happens when microevolution continues for long periods of time. Sure, a dog still produces a dog over the course of a few centuries, but give it a few million years of microevolution and what you're left is not going to be anything like a dog. She asks regarding the dinosaur-to-bird transition: "how did the intermediate creature survive for several million years with legs that are now useless but which are not quite wings yet either?" What makes her think that legs became useless once wings began to evolve? I wonder how she explains the birds perching on the branch outside her window if she thinks having wings means legs are now useless. She obviously does not understand how evolution works in the least.
She then talks about apes lacking the necessary anatomy and brain functions for proper speech, yet can mimic words taught by trainers in response for rewards. What better evidence is there for evolution? Other primates cannot speak like us, yet still have the capacity to learn speech. How else could one explain this except in light of evolution?
I think that someone should tell Peggy that "macroevolution" is not a dead hose by any means. Evolution is stronger than ever before. Every day that goes by, we find more and more evidence for evolution. There is no single scientific principal that is more strongly supported than evolution.
Hopefully tomorrow's edition of the Journal will contain some pro-Darwin rebuttals to today's display of idiocy, but I wouldn't hold my breath.
Thursday, 12 February 2009
First to share their nonsense was D.M. Hendrickson, of Bittern Lake:
"Re: “Happy birthday, Mr. Darwin; Evolution's bold insights, so well explained 150 years ago, resonate daily in a land dependent on fossil fuels,” by Paula Simons, Feb. 7.
Surveys show that about 40 per cent of Canadians reject Darwinism today, whereas Paula Simons claims Alberta “owes its prosperity, its very identity, to the reality of evolution.” Nonsense. Prehistoric plants that turned into fossil fuels do not require any theory of evolution to superimpose upon their existence some more certain reality or better understanding; it is the industrial capabilities of being able to extract the oil that give us the oil, not some spurious suppositions about how all life was not a direct creation of God."
Hendrickson's letter fails right off the bat, starting with a complete non sequiter. Whether or not Alberta "owes its prosperity, its very identity, to the reality of evolution" has absolutely nothing to do with how many Canadians reject "Darwinism". The want of the majority does not do well when determining fact. He (she? I'll assume it's a man writing this) then continues to claim that what Alberta owes its existence to is the fact that we have the industrial capabilities to extract oil ("the oil that gives us the oil", whatever that means), and not some theory about how God didn't make the oil. This claim is absurd, of course, since, if the oil was not present, Alberta would not exist as we know it today. In other words, Alberta owes its identity to whatever process got that oil there in the first place. Now, to say that the oil was the direct result of evolution would be a stretch, but let us consider the alternative: if God had created all life on Earth within the last 6000 years, the oil simply would not be there. If not for the thousands upon thousands of generations of flora and fauna - our ancestors from eons passed, from which we evolved - dying, then there would be no oil. An ancient world, supported in part by evolution, gives Alberta the oil that is its claim to fame.
"Simons claims “the evidence of our province’s evolutionary prehistory is all around us, for anyone willing to look.” What, pray tell, do dinosaur finds have to do with evolution? They went nowhere, precisely what evolution is not about. Does she really suppose adding “evolutionary” to the term “prehistory” adds anything to it except occasions for speculation?"
Dinosaur finds have lots to do with evolution! The entire field of paleontology has given us vast insights to our evolutionary past. The discovery of Archaeopteryx, for example, has made the idea of birds evolving from reptiles concrete. Every single fossil that is unearthed is another check in the tally of evolution's evidence. To think that dinosaur finds have nothing to do with evolution is complete ignorance.
"She would be censor, mocking those who dare be critical of the science accepted unthinkingly by the most secular elements of our society. No one would deny that organisms suffer genetic modifications and those thereby best adapted to the conditions they find themselves in are by definition most likely to survive."
I don't really understand what Hendrickson is getting at here. He gives is the tired "evolutionists are trying to silence any dissent from their dogma!" crap, and then, in the very next sentence, says that descent with modification is undeniable. More and more I'm getting the feeling that Hendrickson has no idea what he's talking about (as if his atrocious grammar and sentence structure didn't give that away already).
A little further on:
"She calls it “the harsh realities of evolution” when there are antibiotic-resistant superbugs, and wonders how we could possibly fight them without Darwin. All we need notice are demonstrable facts: that such bugs exist and that they develop in certain ways, have certain characteristics, and we must look for how we can influence those characteristics. To think we wouldn’t be doing that without Darwin or someone with similar theories is ridiculous."
Here, Hendrickson claims that we can deal with antibiotic resistant superbugs without ever taking into account any aspects of evolution. How can we do this? By noticing (1) that such bugs exist and have particular characteristics, (2) they develop in certain ways, and (3) how we can influence those characteristics. I would like to know how, exactly, Hendrickson expects us to do this in the absence of evolution. The characteristics of these "superbugs" being influenced by their environment IS evolution. We have to apply our knowledge of evolution to figure out HOW their characteristics are being influenced, and how we can counteract this. The very reason superbugs exist is because of evolution. If it weren't for Darwin, we would still be wondering why such superbugs even exist, let alone finding ways to combat them.
"So too with managing grizzly bear populations; it is not evolutionary pressure we need to note, it is environmental pressures, how the habitat and its endangerment bears upon their future prospects."
Environmental pressures ARE evolutionary pressures. Changes in the environment put pressure on organisms; those best adapted to meet those pressures survive, reproduce, pass on their genes; the population evolves. A loss in habitat for grizzly bears is an evolutionary pressure. Unfortunately for the bears, this pressure is caused by humans, and is worsening at a faster rate than the bears can adapt.
He closes his letter with this:
The claim that those rejecting "Darwinism" are the ones fighting for rationalism and science is outright laughable. To reject Darwinism is to ignore the evidence; ignoring the evidence is the antithesis of science and rationality. Furthermore, if believing in evolution makes me "pretentious" and an "elitist", then so be it. But to claim that proponents of evolution think that they are somehow better than you shows a disturbing inferiority complex.
"Those who do not quickly sign on to Darwinism are not “fighting a rear guard action to turn back the clock 150 years and more, to return us to a medieval world view.” That is her aspersion; it is rather that arguments like those of Simons don’t make much sense unless one buys into a world view that “evolution” is the explanation for everything. It is irrational to pander to atheism at every possible turn, to think that adding the term “evolutionary” to every explication of nature somehow increases its validity. Many of the references in biology textbooks, for instance, are precisely that and no more.
She can’t abide politicians who “pander or defer to a small religious element;” she is so close-minded she cannot see that those rejecting Darwinism are the ones fighting for science and rationalism which requires in the search for truth criticisms by those who do not buy into pretentious theories of elites. Those who are not such elitists are the majority and may well have understandings closer to her castigated “religious element,” and thus it is indeed in order for decisions makers to acknowledge them."
I'm a bit astounded that the Journal would let this appear as a letter to the editor, if not for its inane content, then for its grammatical massacre. Hendrickson shows not only a complete ignorance of evolutionary theory and its consequences, but also a deep-seeded contempt for both science and scientists. It is a sickening, sobering thought that people like this exist in an age where information is literally available at your fingertips.
Monday, 9 February 2009
The brainbow is a technique which allows individual neurons in the brain, or sections of the brain, to be mapped by giving them their own special fluorescent colour1 (see image to the right). It looks pretty, and the technique itself is deceivingly simple.
It takes advantage of something called the Cre/lox system. Cre is an enzyme (a recombinase, to be precise) which will cleave out any DNA that is flanked by sites in DNA with a particular sequence, "lox sites". So if you have Your Favourite Gene (YFG) sandwiched between two lox sites, then Cre will splice YFG out of the DNA. But what if you used two pairs of lox sites? For example, what if you constructed your DNA to look like this:
---loxA-loxB--Gene1--loxA--Gene2--loxB---If the loxA pair is cleaved, then Gene 1 is cut out; if the loxB pair is cleaved, then Gene 2 is cut out.
The scientists who developed the Brainbow realized that they could use this to make the neurons express one of many different fluorescent proteins. (See image to the left, taken from Nature2, click to embiggen) They used nestled lox sites as described above, using multiple fluorescent proteins. The Cre protein is able to cleave a single lox pair, multiple pairs, or no pairs at all. The decision on which pair(s), if any, to cleave is made at random in each cell. What results is a cell that expresses a random colour. If enough colours or colour combinations are Incorporated into the construct, every neuron, in theory, will have its own randomly chosen fluorescent glow. This makes mapping the connections in the brain much easier than ever.
And it makes for pretty artwork too.
1. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system, Nature, November 1, 2007.
2. Neuroscience: Making Connections, Nature, 457, 524-527 (2009)
Sunday, 8 February 2009
Saturday, 7 February 2009
Our 2008 iGEM project was featured in the latest issue of The Scientist magazine.
To be more precise, the article is about iGEM in general, but contains an online supplement, with videos of 5 teams explaining their projects. Our project is the fist one listed.
Yay for publicity!
Take a look and listen to Jason explain all about Bisphenol Eh!
Monday, 2 February 2009
The Canadian Institutes of Health Research, the Natural Sciences and Engineering Research Council of Canada and the Social Sciences and Humanities Research Council of Canada are streamlining operations and aligning programs with the objectives of the Government’s Science and Technology Strategy and national research priorities. Through closer coordination, these agencies are improving the effectiveness of existing programs, aligning their programs with their core roles and fostering the development of innovative new programs.
These savings will be used in this budget to support repairs at post-secondary institutions, to upgrade key Arctic research facilities, to expand the Canada Graduate Scholarships program and graduate internships, and to support new world-class research facilities. This budget also sets aside $750 million to support the current and future activities of the Canada Foundation for Innovation.
In other words, Harper and his cronies have decided to reduce research grants and funding for basic research, while at the same time, trying to increase the number of graduate students in the country. That's almost paradoxical. It's kinda hard for grad students to find a supervisor, if potential supervisors can't get new funding to support them!
On top of this, the Conservatives seem to be playing favourites with Canadian research institutions. Genome Canada got absolutely no new funding this year, while the Institute for Quantum Computing got a grant for $50 million that wasn't even peer-reviewed.
And thus science in Canada continues sliding downwards. As someone who's trying to find a job in the scientific community right now, this is very disheartening. I very much want to be involved in Canada's scientific community, but the Harper government seems like it's doing whatever it can to force me, and many other young, aspiring scientists, to take our talents abroad.
Sunday, 1 February 2009
The issue of removing the official American federal motto - which, by the way, has only been official since 1956 - is one I hear popping up in the news every so often. Of course, the idea is constantly scoffed at in the media, but it is one that I support. Separation of church and state is, by constitution, mandatory in America and the motto does nothing to achieve this.
But that is not the main reason why I think "In God We Trust" should be removed from coinage, or anything that has to do with politics. The main reason I think is because it is quite simply wrong.
I don't trust in God (but then again, I'm Canadian, so I don't count). Any reasonable American doesn't trust in God. I mean, that God fellow is notoriously untrustworthy. Think of all the poor cancer patients who have been prayed for, only to die a few short months or even weeks later. Think of the residents of New Orleans who, when hurricane Katrina hit, prayed for their situation to get better, only to find their city spiral into wreck and ruin. For someone who is supposed to hear all those prayers, and give aid to those who really need it, you really can't trust him to deliver on that.
He's also a deceitful God. Consider the story of Isaac and Abraham. God tells Abraham "You must take your son Isaac, and sacrifice him to me, to prove your faith!" Now, when a voice booms down from the sky, commanding you to kill your kid, you have to be very very sure that's what the disembodied voice told you to do. You don't want to be mistaken about that sort of thing. God must have reassured Abraham that, yes, honestly, he had to kill his son. Abraham trusted God. But right at the very last second, God sends an angel down to stop Abraham and is all "Haha, just kidding man, I can't believe you fell for that shit! Go sacrifice that ram instead." Now, does that sound like someone you can trust? Someone that makes you almost murder your child just for a laugh? I don't think so.
And what about the second coming of Jesus he promised? It's been two thousand years and he hasn't shown up yet. I don't think he's coming. We've been duped. Mislead.
So no, in God we don't trust. God's a lying bastard.