Tuesday, 15 July 2008
Because killing your child is obviously way better than autism.
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.
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
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
"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.
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."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?"
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
Breakthrough!
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!
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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!
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.
-CodeforSyn
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.
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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).
Scooped!
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
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.
Friday, 27 June 2008
Painfully Dumb
"Evolution is nothing but a denial of God. Let me pose a question to the godless! On a clear crisp night, when the moon is full, what do you see? Do you see a formless terrain on the moon? If you do, it is because God has placed a veil over your eyes. The entire moon is the face of a man, formed by the shadows of the moons features. It is a beautiful face but mysterious. It's eyes are those of an old man, while it's nose and mouth are those of a child. It's expression is a look of awe. How could there be a face sculpted on a body that circles a body with creatures having a similar face? The odds of this occuring by accident are astronomical, leaving only one answer: IT WAS SCULPTED BY GOD." - Jerome Shaunnessey
Ouch.
Have you recovered from your migrane yet? Ok, good. Let us critique this statement, shall we? Mr. Shaunnessey here is basically claiming that the moon resembles a man, and this is absolutley improbable to have occured by chance, so it had to have been made by God. The idea of a "man in the moon" is far from an original idea. Im sure you've heard of it before and spent time as a child trying to pick out the vaguely humanoid features on the moon's surface. Personaly, I've never been able to see a man's face but maybe I'm simply not imaginative enough. And THAT is the key word here - imagination. The "man in the moon" is nothing but imaginative. There is no "face". This is supported by countless high-resolution images of the moon taken over the last few decades. Take a look at this picture and try to point out what resembles a face. Not only that, but we have actually been on the moon (despite claims otherwise) and we know with certainty that the terain is pretty formless (at least in respects to resembling a face).
But lets ignore that for just a moment. If the moon really did resemble a face, then all cultures around the world should have made such a moon-to-face association, shouldnt they? All cultures have faces, do they not? If a face in the moon - designed by God, no less - really existed, then all cultures should see a face in the moon. But, this is not the case. The Chinese and mesoamerican cultures believed the moon displayed a rabbit; whereas Shia Muslims believe that the name of Muhammad's son-in-law, Mauli Ali, is written across the moon. There are many other shapes that can easily be seen in the dark and light spots displayed across the moon. Try and come up with your own; if you look hard enough, and have a good imagination, you can see pretty much anything up there.
What's more, Shaunnessey claims that the face has "eyes...of an old man, while it's nose and mouth are those of a child". He then says that the Earth has creatures with "similar faces". I cannot think of a single person with the eyes of an old man and the mouth of a child. That sort of sounds like a debilitating genetic condition to me. Perhaps Shaunnessey grew up next to Chernobyl, but claiming the man in the moon resembles people on Earth is a stretch.
And then comes the kicker: "The odds of this occuring by accident are astronomical". Astronomical? Really? I guess the odds of Jesus appearing on a grilled cheese sandwich is also astronomical, or the Virgin Mary appearing in a stain on the highway or the Pope on a pop-tart (thanks, Skeptical Enquirer!) is also astronomical, but it happens. Alot. The man on the moon is a simple case of pareidolia and nothing more.
And, being a typical creationist, Shaunnessey includes a clause that makes his statements unfalsifible: "Do you see a formless terrain on the moon? If you do, it is because God has placed a veil over your eyes." In other words, if you dont see his proof as being selfevident, its because God is making you not see it, not because he's wrong. How typical.
I've read some really wacky claims for "proof" of God's existence, but this ranks up there as one of the craziest. In actuality, the only thing that this proves is Poe's Law.
Saturday, 10 May 2008
Ignorance at Work
I kinda get the feeling that alot of the protestors, however, dont really know much about what they are protesting. Yes, China has had a deplorable record of human rights violations and is infamous for the amout of stifling they do on personal freedoms and censorship of the press. Tibet (the Dalai Lama in particular) also has not been so kind in the past. Who's right and wrong is a bit of a tricky issue.
Nonetheless, I get the feeling that many of the pro-Tibet side dont know all there is to know about the issue. They are, i n a word, ignorant. And the following picture is proof of this:
The answer is Yes. Yes, we did, in 1936. Please learn your history before you protest kthnx.