Wednesday, 12 December 2007

"Health Dowsing", lacking in both logic and math.

Ah, dowsing. What knowledge and wisdom can come from a little dangling crystal or a bouncing stick? For those of you who are not familiar with it, dowsing is a pratice whereby a lunatic person attempts to locate a particular object (water source/oil patch/dead body) by dangling a crystal/watch or by holding out a long forked stick. Supposedly the tool of choice will begin to sway back and forth or bounce up and down the closer one gets to what they're looking for. Dowsing comes in all shapes and forms (all of which are fraudulent) : water dowsing, oil dowsing, dowsing to find burried corpses or lost items, and one that I just stumbled upon: "Health Dowsing"

Aparently, health dowsing is used to determine whether certain "spots" are good or bad for your health. It's usually done over a map to find out where a "healthy" spot to build a building is, but it can be done on the actual ground as well. And, as this video from James Randi's 1991 show Psychic Investigator evidences, it offers up a heaping cup of bad math along with its pseudoscience.

The basic test that Randi gives is fairly simple: if certain "spots" indeed have a "bad" or "good" impact on ones health, then each dowser should agree on the impact of a particular spot. Randi placed three blue circles on the floor of the studio, one of which has been determined to be a "bad spot" by a dowser beforehand. The test is for another dowser to determine which is the bad spot. If dowsing is real then the same spot should be picked. Note that picking the same spot does not prove that dowsing works - the test really ammounts to a 1 in 3 guess.

In the video, the dowser does manage to pick (guess) the correct spot, but he does something else. He "works in percentages", id est he tells you what percent of the spot is "good" or "bad". The math behind this should be fairly simple, shouldnt it? Well the guy gets it totally wrong. He finds that the first spot is bad; moreso, it is 30% bad. The second is a good spot which is 50% good. The final one is bad at about 70%.

Now, anyone (except maybe this guy) can tell you that a total always adds up to 100%. In the case of the "good" and "bad" spots, there's only two options: good or bad. Therefore the percent good and the percent bad should add up to 100% (if something is 10% good then what is the other 90%? It has to be 90% bad, of course). But this doesnt really match what the guy is saying. The first one he first determines to be definately bad. But then he says it is only 30% so. This would indicate that the spot is 70% good. In other words, it's almost 2.5 times as good as it is bad. Why, then, does it count as a "bad" spot?

His second attempt makes even less sense. This time he determines that the spot is 50% good, "quite good" he pronounces. Well, that would mean that the spot is also 50% bad. If 50% good is "quite good" then the spot is also "quite bad". If it's equal parts good and bad, then what does this mean? Does it do nothing?

The last one he finds 70% bad (30% good), which he thinks is very detremental to one's health. If the first one was only 30% bad and is unhealthy, then why is the one that's 30% GOOD not healthy? Then he claims that the second one was the best for your health. Yet, that spot was 50% good whereas the first one was 70% good. So shouldnt that be the best spot?

These numbers make absolutely no sense. How anyone could believe this kind of nonsense is beyond me. How people can actually hire and pay people like him to determine where their homes and offices should be constructed is even more astounding.

Sunday, 9 December 2007

Virus Prevention and Control Part II

Continuing on antiviral drugs...

While viruses have fewer targets for drugs due to their smaller number of gene products, there are still many targets for potential drugs. Processes such as viral attachment, absorption, fusion, replication, transcription, translation, assmebly, anf virion release are a few such targets.

Entry inhibitors: One particularly effective drug target is that of virus entry into the cell. If the virus cannot enter a cell, then it canont cause an infection. One example is TAK799, a drug that blocks the HIV gp120 protein from attaching to the CCR5 co-receptor on T-cells. This prevents viral fusion, effectively blocking the entry of the virus. Other examples are Heparin and dextran sulfate, which are effective against many viruses, and Amantadine, which is used against influenza (specifically, it blocks the action of the M2 ion pump, thereby preventing the pH change in the endosome, resulting in the virion being trapped).

Replication inhibitors: Inhibiting viral replication is a favoured target of antiviral drugs. Most of the replication inhibitors are analogues of nucleosides, and are also chain terminators. They can be acyclic GTP analogues, acyclic nucleoside phosphonates, dideoxynucleotides, and pyrophosphate analogues. There are some non-nucleoside inhibitors as well. A well known example is that of Lamivudine which is given for Hepatitis B and HIV. Also known as 3TC, it has a sulphur at the 3' carbon instead of a hydroxyl group. This means that the growing DNA chain cannot be extended and elongation is terminated. It is only incorporated by reverse transcriptase, and not by cellular replication machinery, giving it specificity for infected cells.

Usully the mechanism by which replication inhibitors work is complex. First the drug is activated by the viral thymidine kinase enzyme, and then is selectively use by the viral replication machinery. This means that specificity is dependand upon two factors: that cellular kinases do not recognize it as a substrate, and that the cellular replication machinery does not use it as a valid nucleoside. Strains which are resistant, then, can have mutations in two different aspects.

Non-nucleoside analogue inhibitors work by some other method. They may affect the binding of a nucleoside to the polymerase or affect protein oligmerization.

Protease inhibitors: Many viruses require proteases to cleave their gene products from polyproteins (such as HCV, or the HIV protease). By inhibiting these, the assembly of the virus is also inhibited.

Neuraminidase inhibitors: In influenza, the virion is assembled at the cellular membrane and is attached to the cell surface by sialic acid. Neuaminidase cleaves the sialic acid, freeing the virion. Drugs which inhibit this chemical thus prevent virus release.

Viral Stability Inhibitors: Viruses with lipid envelopes are sensitive to detergents. Using detergents to break up the envelope will render the virus avirulent. Nonoxynol-9 is one such reagent. It is commonly used in spermacides to prevent HIV and HSV infections. Another is ST-246 which is used against poxviruses.

Antiviral Drug Resistance
Resistance to antiviral drugs is as big of a problem as that of bacteria to antibiotics. For example, before the introduction of HAART (higly active antiretroviral therapy), the drug Foscornet was used to treat HCMV which caused retinitis in 30% of HIV patients. Unfortunately, HCMV strains quickly became resistant to the drug and it can no longer be used.

How can viruses become resistant to drugs?
Polymerase fidelity: DNA Polymerase has a proofreading ability which allows it to remove incorrect nucleotides and nucleoside analogues. This means that viruses that use DNA Polymerase may be albe to avoid incorporating the drug into its growing DNA chain. RNA polymerase, however, lacks proofreading ability, meaning RNA viruses have a much higer error rate, and consequently, mutation rate, than DNA viruses. This could be the cause behind the aparent restriction in genome size of RNA viruses.

Also, no polymerase is 100% efficent at proofreading; if a mistake is made, it could potentially lead to a mutation that confers resistance to a drug.

Quasispecies: Viruses do not reproduce clonally, so each virus may be different. They are subject to evolutionary selection pressures so many different forms of a virus are produced; a drug is then not effective against all of them. An example is the resistance of Cidofovir in orthopoxvirus.

How can we determine if resistance will be a problem?
1) Pass the virus through a cell culture, increasing the concentration of a drug
2) Select the strains which gain resistance
3) Sequence the polymerase gene (or other gene target, depending on the drug) and determine where the mutations lie
4) make recombinate strains that contain the mutations
5) check for resistace in cell cultures and in mice
The last three steps are known as "marker rescue".

How can resistance be prevented?
Use drugs more cleverly! Using two or more antiviral drugs which have independent mechanisms will reduce the chances of a strain becoming resistant. A "drug vacation" may also work by reducing the selective pressure on strains to become resistant (though this has the added risk of allowing virus titres to increase).

Virus Prevention and Control Part I

As part of preperation for my immunology final, I'm going to write a bit about controlling and preventing virus outbreaks.

When people think of controling and preventing viruses, the first thought that comes to mind is, of cource, vaccines. But vaccines are only part of the picture. There are also "low tech" methods of virus control that can prove to be effective. First of all, by controling the quality of food and water, many viruses, like noravirus, can be prevented from spreading. Poor food and water quality is a major vector for virus spread. Likewise, insects can be a vector for viruses; controling insect populations thus controls these viruses. An example of this is the recent attempts at controling the mosquito populations in North America to stem the spread of West Nile Virus. Other animal populations also need to be controled - wild mammals, for instance, to keep rabies from being spread. A very important factor which also needs to be controlled is the use and sharing of needles to stop HIV and Hepatitis C infections. A few cities have taken the controversial option of providing "safe injection sites" to prevent drug users from using unsafe needles. Education about the dangers of sharing needles has also been used as a way of preventing these diseases. Quarintine is another method of keeping virus infections from spreading, as can be seen in the SARS outbreaks in Toronto a few years ago. These "low tech" solutions often prove to be as effective as vaccines.

When it comes to vaccines, however, two strageties are used. The first is to use a live, attenuated, vaccine and the other is to use a killed, subunit, or recombinant vaccine. Each has its benefits and hazards.

Attenuated vaccines: These vaccines are made up of living virus particles which have been "attenuated", or mutated, so that they are no longer a health risk. This provides a long lasting immunity that is both humoral (invokes antibodies) and cell-mediated. There is a risk, however, that the live virus can mutate back into the fully hazardous form. This risk is minimized by using multiple non-revertable mutations to make the attenuated form. Nonetheless, this is still a risky method to use in people who are immunocompromised.

A good example of an attenuated vaccine in action is the Sabin polio vaccine. Using three different strains of the polio virus, the strains were serially passed (ie, passed from one host to another) through multiple cell tissue types. The resulting virus had accumulated non-revertable mutations in the 5' UTR and in the viral VP3 capsid protein. This resulted in a avirulant strain which was used very effectively as a vaccine.

Killed/Subunit/Recombinant Vaccines: These viruses are not living, mutated forms. They are whole or partial subunits of viruses that have been killed by heat or chemicals. They are not as effective as attenuated viruses because the immunity they provide is not as long lived and often only provokes a humoral response. Nevertheless, they are safer to use.

An example of this is the HPV vaccine. The vaccine is a mix of VLPs (virus-like particles) which consist of the viral L1 capsid protein. It gives immunity to HPV types 6, 11, 16 and 16. Interestingly, this vaccine has created some ethical questions surrounding vaccinations. HPV poses a health hazard to women but not to men. However, men can act as carriers. Should men get vaccinated even though it gives no personal benefit to them?

Antiviral Drugs: If vaccines arent a feasible option, though, then there's the option of antiviral drugs. Antiviral drugs are not as easy to come by as antibiotics. Viruses dont have nearly as many genes as bacteria, so there are not as many targets for the drugs to work against. Also, many potential antiviral drugs have toxic effects on human cells. Only a handful of antiviral drugs are known, most of which have been discovered in the last 25 years, but the rate of discovery is increasing.

How are these drugs found? There are multiple ways:
Plaque reduction assays: The virus is plated onto a lawn on tissue, forming viral plaques. An increasing amount of the potential drug is added to the plates and the effect on the plaque number is observed. The higher the decrease in plaques, the better the drug works. To determine how effective the drug is to use practically, however, the Selectivity Index (SI) of the drug must be calculated: SI=CC50/EC50 where
CC50= the concentration of the drug that kills 50% of the host cells (Cytotoxic concentration)
EC50 = the concentration that kills 50% of the virus (Effective concentration)
The higher the SI, the more effective the drug is.
Viral growth inhibition assays: The growth of a virus versus the concentration of a drug can also be visualized and used to determine the drugs effectiveness. One method is to use 3H-Thymine (radioactive thymine) to measure the amount of viral DNA replication that occurs when different concentrations of drug are applied. Another method is to use a fluorescant protein like GFP or another visual marker like the lux operon or Lac Z operon to visualize the actual viral particles in stitu or in animal tissues. The effect of differeing concentrations can then be visualized.
Enzyme inhibition assays: These assays determine how effective a drug is on a certain virus enzyme. The test require a certain amount of knowledge concerning the pharmacology of the drugs to be tested because they have to use the form of the drug that is metabolically active within cells. One technique commonly used is FRET (fluorescene resonance energy transfer). This involves measuring the amout of light emitted by a fluorecant dye versus the drug concentration. For example, if the drug target being tested was an HIV protease, then a molecule would be constricted consisting of a protein (that the protease cleaves) with a dye on one end and a quench molecule on the other. Under normal circumstances, the fluorescant dye would not emit light because the quench molecule would quench it. With an active HIV protease however, the protein would be cleaved and the flourescant dye would be free to emit light. If the drug is applied, however, then the protease would not work and there would be no light emitted. By determining the amout of light given off (or lack thereof) one can determine how effective the drug is against that HIV protease.

This type of assay can be easily done by automated machines in multi-well titre plates, resulting in high throughput screening of potential drugs against particular drug targets.

Tuesday, 4 December 2007

And another legend lost...

This Friday, Seymour Benzer passed away. Benzer was a very important person in the history of molecular biology - among his other accomplishments he probed the fine structure of a gene and mapped the rII locus of bacteriophage (I think it was phage Lambda). Every student in genetics learns about his work but most dont know of him by name. It's a shame. The work he did as part of the famous "phage group", along with Luria and Delbruck, eventually lead to Crick and Sydney Brenner to establish the triplet code for DNA translation.

This comes not long after the loss of Arthur Kornberg. Its been a bad winter for molecular biology.

The Republican Youtube Debate Translated

Last week, the Republican party had a little debate on Youtube, and people from the public got to pose questions to all of the candidates. Of course, the susbject of the Bible was brought up:

"I am Joseph. I am from Dallas, Texas, and how you answer this question will tell us everything we need to know about you. Do you believe every word of this book? Specifically, this book that I am holding in my hand, do you believe this book? "

The candidates' replies were rife with sucking up to the religious right and attempts at making themselves look like "good moral, religious people" (the thought of which is humorous; "moral" and "politician" are mutually exclusive) and for those of us not fluent in bullshit, I have taken the liberty of translating their responses into rational English.

Giuliani: "OK. The reality is, I believe it, but I don't believe it's necessarily literally true in every single respect. I think there are parts of the Bible that are interpretive. I think there are parts of the Bible that are allegorical. I think there are parts of the Bible that are meant to be interpreted in a modern context.
So, yes, I believe it. I think it's the great book ever written. I read it frequently. I read it very frequently when I've gone through the bigger crises in my life, and I find great wisdom in it, and it does define to a very large extent my faith. But I don't believe every single thing in the literal sense of Jonah being in the belly of the whale, or, you know, there are some things in it that I think were put there as allegorical."

TRANSLATION: "Just like any other Christian, I like to pick and choose which parts of the Bible I take literally and which parts I think are just symbolism, even though there really is no rational way of determining which parts are the symbolic parts. This way, I can cherry-pick to avoid the inconvience of having draconian beliefs along with the ones that make me a good, moral person! Also, I never read it, but I have a copy on my bookshelf somewhere."

Romney: "I believe the Bible is the word of God, absolutely. And I try I try to live by it as well as I can, but I miss in a lot of ways. But it's a guide for my life and for hundreds of millions, billions of people around the world. I believe in the Bible....I believe it's the word of God, the Bible is the word of God. The Bible is the word of God. I mean, I might interpret the word differently than you interpret the word, but I read the Bible and I believe the Bible is the word of God. I don't disagree with the Bible. I try to live by it."

TRANSLATION: "Lots of people around the world belive in the Bible, so why wouldnt I? I dont always live my life by the Bible, but I am a good moral person nontheless. This is totally completely 100% different from atheists being moral people and not living accoding to the Bible because we all know atheists are souless heathens who will burn in hell. Also, the Bible is open to subjective interpretation, yet it gives us absolute morals we must live by. Please ignore this aparent contradiction. Did I mention that the Bible is the word of God? The Bible is the word of God."

Huckabee: "Sure. I believe the Bible is exactly what it is. It's the word of revelation to us from God himself. And the fact is that when people ask do we believe all of it, you either believe it or you don't believe it. But in the greater sense, I think what the question tried to make us feel like was that, well, if you believe the part that says “Go and pluck out your eye,” well, none of us believe that we ought to go pluck out our eye. That obviously is allegorical. But the Bible has some messages that nobody really can confuse and really not left up to interpretation. “Love your neighbor as yourself.” And as much as you've done it to the least of these brethren, you've done it unto me. Until we get those simple, real easy things right, I'm not sure we ought to spend a whole lot of time fighting over the other parts that are a little bit complicated. And as the only person here on the stage with a theology degree, there are parts of it I don't fully comprehend and understand, because the Bible is a revelation of an infinite god, and no finite person is ever going to fully understand it. If they do, their god is too small."

TRANSLATION: "I believe that it is 100% fact that you either believe in all of the Bible or none of the Bible. But some of it is allegory. And some of it no one understands. But, even if we dont understand it, we should belive it anyway! Beliving in something you dont understand and not questioning it is the key to being a good Christian. All that confusing stuff we can ignore for now anyway, because we should focus on The Golden Rule. What was that? Atheists have been saying that The Golden Rule is all that matters for years? And you can be a good moral person without the Bible? Poppycock! My life partner campaign supporter, Chuck Norris, and I are the only ones who can talk about the Bible because I have a theology degree! Your god is puny!"

I think no further comments are necessary.

Thursday, 29 November 2007

Dover part 2: Polk County, Florida

Hot off the heels of the NOVA doccumentary on the Dover trials comes something that will probably give you that eerie feeling of deja vu: the school board in Polk County, Florida has had a majority vote to include intelligent design as part of the school science cirriculum. The board has voted 4 to 2 on teaching intelligent design along with evolution. The currently proposed standard for Polk county schools lists evolution and biological diversity as one of the "big ideas" that students should know to have a well grounded science education, and 4 of the board members are in direct opposition to this.

Quote board member Margret Lofton (emphasis mine):

"If it ever comes to the board for a vote, I will vote against the teaching of evolution as part of the science curriculum," Lofton said. "If (evolution) is taught, I would want to balance it with the fact that we may live in a universe created by a supreme being as well."

""It crosses the line with people who are Christians," according to her. "Evolution is offensive to a lot of people." Let me paraphrase this for you: "It doesnt matter if something is true, some people find it offensive so we shouldnt teach it." What complete idiocy.

Thankfully, the scientific community in Florida is up in arms about this decision and strongly supports the current scientific standards proposal.

I dont know if these people are ignorant of the whole Dover case or what. This all seems like the same situtation all over again. Im just waiting for the Discovery Institute to get involved.

Wednesday, 28 November 2007

Mysterious protein of mystery

I'm writing this from the computer lab in the botany wing of biosci waiting for my lab to start. We're going to be down here trying to determine what gene our original cDNA came from and what organism it belongs to. I thought Id go ahead and try it out myself before the lab begins but Im running into some problems.

I aligned my sequences last week but I was a little wary of the results because my sequencing reactions didnt work out all that well. The chromatograms showed a really weak signal all around so it was tough, if not impossible, to determine the correct bases where I got a string of N's. This meant that alot of spots in my sequence were really unknown. The resulting consesus sequence was a little suspect because of this.

I saved the consensus sequence anyway and used it to run a Blast search on NCBI. I should have been able to figure out what the gene was (I know its a form of actin but what form of actin?) and the organism it came from. Except, this didnt happen. I have a whole schwack of results, and about 10 of them all have the same Query coverage, total score, max score, E-value and max identity. Unfoturnately, theyre all from different organisms so I dont know which one is the "right" one. The query coverage and max identity are 83%, which means that my sequence is about 83% identical to these sequences...which isnt all that great. If my sequence was the same as a sequence in the database, then the values should be like 95% or more. This means one of two possible things: either the sequence isnt in the database and the closest thing to it is only 83% identical or my sequence is wrong. I think the latter is more likely. They all are beta-actin genes, though, so at least this tells me my gene is probably a beta actin.

Thursday, 22 November 2007


You know how Dr. Bruce Banner turns into The Hulk when he gets angry? And how The Hulk's massive green body is like twice the size of Dr. Banner? Isn't that a violation of the first law of thermodynamics?

Tuesday, 20 November 2007

Just how big is the universe?

This big. And that's just the VISIBLE universe. These maps only show the distances to galaxies, clusters, nebulas and the sort that are relatively close to the Earth. Most galaxies are so far away that their distances cannot be accurately calculated and aren't included. Use the zoom-in buttons to see how the Solar System compares to the immense vastness of the universe. Just consider the Earth's place in all of this: a infinitesimal speck amonst a plethora of other infinitesimal specks. The sun is one star in an estimated 30 billion trillion (3x10²², or 30000000000000000000000). I challenge you to find a thought more humbling than that.

And yet another reason to hate Chuck Norris

As if those asanine "Chuck Norris Jokes" that are all the rage with mush-minded frat boys and his vapid, plotless, doldrum-inducing action movies weren't enough for you to despise Chuck Norris, I've uncovered some facts that might make you hate him even more.
Last night, on G4TV's Attack fo the Show I saw the clip below:

Yes, that is Chuck Norris, and yes, he is endorsing a presidential candidate. If any of you dont remember who Mike Huckabee is, he was the governer of Arkansas who was featured on Talking To Americans - the one that congratulated Canada on our "national igloo".

It seems that Mr. Norris is a staunch supporter of Mike Huckabee. That alone might not arouse your ire for Chuck Norris, but get this: Huckabee is (not surprising for a politician from Arkansas) a rightwing fundie. He has been quoted (I'll find the exact quoute later) with saying that, if science and religion were at odds with one another, he would pick religion because "science changes constantly with new facts, and religion never changes". He obviously have little understanding of the scientific method and how the constant revision of facts upon being presented with new evidence is what makes it so powerful. Anyway, after realizing that Norris is endorsing someone who would likely turn America into some draconian theocracy, I began to do a little research on him. What I found was disturbing.

Firstly, he is an outspoken critic of evolution, and supports creationism. If that were not bad enough, he holds the theory of evolution responsible for school shootings, commenting:
"We teach our children they are nothing more than glorified apes, yet we don't
expect them to act like monkeys
Basically, he thinks that evolution tells us that humans are nothing more than "glorified apes", and kids are going to act like wild animals, shooting and stabbing each other in the schoolyards. No doubt, Huckabee also shares this view and would try to get evolution thrown out of schools were he to become president.

Aparently, Norris also belives that there is an "atheist conspiracy" in the United States that is working to make Christianity illegal. Not only is he ignorant but he's delusional as well! Futhermore, to stop the growing "threat of secularization", he said that,were he to become president, he would tattoo "In God We Trust" on the forehead of all atheists, and even deport all liberals from the country (and "force them to listen to Bill O' Reilly every day for five years", but this must be a misquote, because the US doesn't torture, right?)

Mr. Norris is a contributing writer to the site WorldNetDaily (aka WorldNUTDaily for the outrageous conservative drivel the site publishes) and I took a look at a few of his articles. In one, he complains about abortion and how evolution has lead to "human degredation" and "fetal devaluation". He claims that "life begins at conception" - his evidence for this, you ask?
"Before our embryonic twins were surgically placed into my wife Gena, the nurse
told her, ''I want to show you something.'' She wheeled Gena to the incubator
where they were kept and gently opened the door. The incubator was bathed in
warm light and soft classical music. Gena later told me it was the most incredible sight she had ever seen. ''It was like looking at something from heaven,'' she explained.
That was only 2 days after conception! Whether or not Gena had become pregnant,
we were fully convinced at that moment that life begins at conception.
Thirty-two weeks later our twins were born."

He looked in an incubator at two embryos which had been fertilized only days before and, because it was "beautiful" it MUST constitute a human life. Real convincing, there, Chuck.

Other articles he's written go on and on about how terrible it is not to teach the Bible in schools (as if it were literal truth) and how the media is so liberally biased.

After finding all of this, I am convinced that Chuck Norris has the intelligence of a sponge cake. I couldn't stand him when he was only making crappy movies, I REALLY couldnt stand him with morons began telling those lame "jokes" about him and now I utterly detest the man. It's a shame that he's so popular, and it's disgusting that he has been using his fame to promote his backwards conservative beliefs.

Sunday, 18 November 2007

Responses to PBS "Judgement Day" program

Last Tuesday, PBS ran a two hour special on NOVA about the infamous Dover School District "Evolution vs Intelligent Design" trials. Jessica and I watched it and we found it to be a very well put together program, which explained in a very easily comprehensible way what science is, why intelligent design IS NOT science, and how the members of the Dover school district were religiously motivated when trying to teach students intelligent design as an "alternative to Darwinian theory". It was one of the better episodes of NOVA I've seen and was greatly pleased that PBS stood up for science cand didnt play the "Christian apologetic" card. Many other people, it seems, were not so pleased. The PBS ombudsman has released an article publishing some of the emails and letters they recieved from viewers; many of which were complaints about the "one sidedness" of the show.

Here's a few choice excerpts from some of the letters (emphasis mine):

"I realize that PBS has always treated the neo-Darwinian theory
of Evolution as sacred and beyond question but last night's dose of
Darwin-worship was so strong and so contrary to any genuine search for truth
that I can
no longer consider support of public television a
morally defensible practice

So, basically, because PBS, on a show dedicated to science, chose to support the science and not the religious rhetoric, supporting public television is now immoral? You've got to be kidding me.

"After tonight's program on Intelligent Design it proves that
PBS has a "design" of its own — it's one that is driving the country to
destruction — your bias is completely counter to history, to the very foundation
of our nation and history of nations. Every part from beginning to end
had its own objective; completely counter to the Truth which is proven in the
rise and fall of nations

Aparently, countering "the Truth" (id est the Bible) has been the cause of the collapse of nations throughout history. I'd bet good money that this guy slept through history class. This letter also displays the sickening misconception that the United States was founded as a Christian nation. Perhaps the study of the founding fathers and reading the Decleration of Indepenance should become mandatory in American schools. Maybe then the myth that the US is a "Christian nation" would be dispelled.

"It doesn't take a "Rocket Scientist" to figure out that if we,
as humans, evolved from monkeys . . . THEN WHY? . . . Are there STILL Monkeys???
We were "Created" by God!!! Pull up AOL now and you'll notice the Gov. of
Georgia praying for rain, (No Doubt to GOD). When 9/11 happened what did every
good neighbor do? PRAY. Not to monkeys . . . To our "Creator"!!! It shouldn't
take tragic and desperate circumstances for people to realize this fact!!! GOD
BLESS AMERICA!!! In GOD We Trust!!!"

Yet another example of the painful ignorance people have of evolution. It gives me a headache trying to figure out why some people cannot grasp what it is that evolution teaches. Nowhere does it say that we evolved FROM monkeys. Humans and monkeys both evolved from some other common ancestor. Apes are not our ancestors but theyre more like our cousins. Also, because people prayed to God after 9/11 doesnt prove his existance. That's a complete non sequitur. I also find it amusing that people are still using AOL (there's something to be said about the intelligence of fundies and AOL users but I'll let you draw your own conclusions).

"I measured the time from the beginning of the program to the first
time an idea from ID theory was even presented (25). If I had time I could make
a chart of how many times a positive statement was made pro evolution
(uncontested) vs. pro ID statement (each contested or refuted). "

Hmm perhaps this is because Intelligent Design is false and evolution is our current best understanding of the natural process of speciation? The one major point of the Dover trial was to show that ID was not science, so why would the doccumentary give a "pro-ID" stance at all? Of course it was "pro-evolution" - that was the outcome of the trial! If the outcome had been reversed and evolution pronounced baseless mumbo-jumbo while ID was the Gospel truth (pardon the pun) then things would have been different. But that is not the case. ID was presented as a refuted non-scienctific religious idea BECAUSE IT IS A REFUTED NON-SCIENTIFIC RELIGIOUS IDEA.

"I am glad I have not donated any $ to KQED for many years since I would not want to contribute to the propagation of the false, erroneous, illogical theory of macro-evolution. If evolution were true and man "evolved" from apes, why do we have apes and monkeys co-existing with man? Why have the apes not all turned into humans? Then, there's the immoral implication of evolution. "Survival of the fittest" follows from evolutionary theory. Evolutionists, to be logical and true to their faith (it takes faith to believe in it since there is no clear, unimpeachable physical evidence for macro-evolution) should see nothing wrong with what Hitler, Stalin, Pol Pot, etc., did in the genocides of millions of people."

This one has three pathetic points. First, this guy also says that macroevolution is "illogical". I'd like to know his reasoning for this. Macroevolution is possibly one of the most logical ideas I can think of. Animals with genes that make them more fit have more offspring. More offspring with this gene means a change in allelic frequencies. Over time, the more fit gene is kept and the less fit gene dies out. What's so illogical about that?
Secondly, this guy also displays the ever-so-present lack of understanding of how evolution works. Again, we didnt evolve "from monkeys", we evolved along side of them. Apes have not "turned into humans" because that's not how evolution works! Why can't people undersand this!? The third thing he says is the often used "Evolution = survival of the fittest = killing off weak people = OMG HITLER MASSMURDER" argument. He combines this with the claim that there is no physical evidence for macro-evolution (there is. Tons of it.). Hitler (and Pol Pot, and Stalin) did commit genocide, there is no denying that. But what people have to understand is that "fit" and "weak" do not mean the same thing. Survival of the fittest DOES NOT MEAN survival of the strongest or fastest, biologically or socially. Fittest = better chance at producing offspring. From what I know, Hitler didnt exactly send the Jews to Auschwitz because they were having more kids. This disgusting misconception that "survial of the fittest" ammounts to killing off socially weak people is rampant in creationist thinking and ammounts to little more than extreme Social Darwinism, a concept that has long been abandoned.

"Surely you could have interviewed prominent scientists,
philosophers and theologians who could explain how the two theories are actually
one and the same. Typical humanistic, lefty propaganda staged to move the feeble
mind to a certain point of view. Garbage, really. You should fire the writers
and producers.

The two theories are NOT one and the same. Evolution is a naturalistic process that occurs over immense periods of time. Intelligent Design is when a magical entity sneezes and POOF you've got another living thing. The two ideas are almost antithetical. Once again, the point of the program was not to compare and contrast Evolution and ID; the point was to tell the story of the Dover trial, during which ID was shown to be a flimsy psuedoscientific religious argument. Why are people surprised that this is the idea expressed in the show?

"It was fascinating to see those dipstick high school teachers,
bolstered by the heir to the Darwin fortune explain the impossible and to the
great lengths that these . . . will go to deny that there is a greater power
than some . . . that passed teacher's college in some backwater . . .

Yeah, because Darwin totally made it rich off of his ideas. I'm pretty sure I saw him on the 1888 Forbes 500.

There are a ton of other letters but it would take a century to write a full response to all of them. Read them if you like but I take no responsibility if your blood pressure skyrockets due to the sheer ignorance that most of the letters wallow in. There are a few letters commending PBS on what was truely an accurate and well presented program, but the vast majority of them are drivel from fundies. Be warned.

Saturday, 10 November 2007


While just browsing the internet I came across a couple of facts that I found rather interesting:

The first is about the infamous fugu pufferfish (Takifugu spp.) It's a well known fact that a great majority of the human genome is comprised of so called "junk DNA" (regions of DNA that has no aparent function, for those of you who dont know). What's interesting about Fugu is that it has pretty much no junk DNA whatsoever.

According to Daniel Rokhsar, "within each taxonomic grouping, there can be wide variations in genome size that are not necessarily related to the complexity of the organism. These variations appear to be due to differing amounts of 'junk' or 'selfish' DNA, often dominated by the remains of ancient viral-like genomic infections that left hundreds of thousands of repetitive elements littered throughout the genome. The Fugu genome seems to have avoided these events and sequencing it will therefore allow us to obtain a complete vertebrate genome extremely rapidly."

It may be that Fugu represents a pristiene "primitive" verterbrate genome, since it's been untained with retrotransposons or pseudogenes. It would be interesting to find out how the species has been able to avoid this. Maybe it's genome will shed some light on the divergance of verterbrates from inverterbrates some 530 million years ago.

The second interesting thing I came across was a paper on an experiment done in 1989 by Diane Dodd (Reproductive Isolation as a consequence of adaptive divergence in Drosophila pseudoobscura 1989 Evolution 43(6) pp. 1308-1311). This experiment is awesome because it shows speciation in action. What she did was raise one strain of D. pseudoobscura which, obviously, could breed with each other. She then seperated the population in two groups. One group was raised using a starch-based food, and the other was raised on a maltose-based food. These groups were reared for several generations (I think it was 8), and after were combined into one larger group again. What resulted was the maltose group only mated with the other maltose group flies; the starch flies only mated with other starch flies. There was reproductive isolation - in other words, speciation - between the two groups that started off as one interbreeding population.

This is evolution in action, folks! If anyone ever doubts that evolution is true because "no one has ever observed it", kick 'em in the shins and point them to this paper. Not only can we see the beginnings of evolution, but we can see it in as few as 8 generations.

Tuesday, 6 November 2007

Painful Ignorance

I dont know how familiar people may be with Joseph Farah, but he's one of the bigwigs over at WorldNetDaily, a megasite for rightwing conservative nonsense. Alot of the articles wirtten there are rife with religious propaganda and unscientific garbage, but one article written by Mr. Farah has sent my bullshit meter off the charts.

In this column, he writes about the problem of global warming, or the lack thereof. Now, I do not agree with alot of the "conventional wisdom" surrounding global warming (Al Gore and his Inconvienent Truth is bunk if you ask me) but I will not deny that the Earth's climate is changing and rather quickly (whether this is caused by us people or is more of a natural occurance I'm not quite convinced). Joseph Farah has taken an alltogether different stance. He says that global warming, or more specifically, "global cataclysmic flooding" caused by global warming will never happen. Why? Because "God said so".

"First of all, in Genesis 8:22, we're told of a promise by God never to use global floodwaters again as a means of destroying life on Earth. In that promise, the Bible explicitly states: "While the earth remaineth, seedtime and harvest, and cold and heat, and summer and winter, and day and night shall not cease."
In other words, no more cataclysmic floods – the result Al Gore promises in the near future as a consequence of global warming

Basically, he thinks that because "God told us that he wouldnt flood the world again", rising sea levels cannot possibly occur due to global warming. He goes on to support his argument by saying that it's pointless to even bother worrying about the climate because God is the one that controlls it, and not man:

"It is so presumptuous and haughty of believers and non-believers alike to think man is in control of the destiny of the planet God created for us.
If it were so, would he not have warned us? With all of the prophecies in the Bible, should we not expect to be told that such matters are actually in our hands? Why would we be told exactly the opposite throughout scripture?"

Of course, the only "support" he uses for his absolutely ludicrious view is taken straight from the Bible. "This verse or that chapter says this or that" should never be used as support for an argument. It's all based on one very flawed assumption - that the words in the Bible are true. The veracity of the bible is incredibly dubious and all scientific evidence points that it's nothing more than ancient fairytales - so any argument solely based on "the word of God" is void.

In fact, as has been pointed out by Ed Brayton, Farah's claims disprove themselves. As of writing this, there is extensive flooding in Mexico, with 80% of the state of Tabasco being covered in water making an estimated 800,000 people homeless. It is in every sense of the word catastrophic. If Farah is correct in saying that the Bible "promises no more catastrophic flooding" then he's proven the bible false. I guess that means the rest of his arguments fall apart since theyre based on the same book he's just shown to be rubbish.

Farah also writes one thing that points to his lack of congnitive abilities:

"It's not that the Bible tells us there are no consequences for our actions on the planet. In fact, it quite explicitly does. But it is not the production of carbon dioxide that God finds offensive. It is the commission of sin. Nowhere in the Bible does God ever suggest that producing CO2 is sinful. "

Allow me to paraphrase: "The bible doesnt say that making lots of CO2 is a sin, so we dont need to worry about how much we produce. Nothing bad could come of it!" What a load of crap. Like Brayton put it, "The Bible doesn't say that dumping toxic waste into your drinking water supplies is a sin either, but it's still a bad idea."

This idea that global warming is not a problem simply because God didnt say it would happen is absolutely insane. It's this kind of thinking that leads people to think that global warming is nothing to worry about because "Jesus is going to return in the next 50 years anyway" (Astonishingly, 25% of Americans seem to think he's going to return this year!) How anyone could ignore scientific evidence, or even direct observation, for the word of a two thousand year old book is beyond me.

Tuesday, 30 October 2007

What I learned in school today Oct 30

Today's lecture was a guest lecture concerning viruses and their role in cancer, particularly how they can cause cancer and can be used to treat cancer.

What is cancer?

Cancer, in short, is an uncontrolled proliferation of cells. It is the 2nd leading cause of death in developed nations - 6 million people worldwide die from cancer every year. Three main therapies are used to treat it: radiation, chemotherapy and surgery. The first two are specific in that they target cells that are rapidly dividing. This may be problematic in that tumor cells are not the only cells that divide rapidly; certain bone cells, for example, quickly divide and may be targeted by these treatments.

The process whereby a normal cell becomes cancerous is called transformation. A transformation may be a change in the morphological, biochemical or growth patterns of a cell. Cells which are transformed become immortal, that is, they can grow and divide indefinately. Normal cells are subject to what is called the Hayflick Limit, at which a cell will stop dividing (this occurs when the telomeres are shortened to a length below which becomes deleterious to the cell). Cells which are transformed may have one or more altered phenotypes, such as a loss of anchorage dependance (normal cells will not grow unless attached to the extracellular matrix), loss of contact inhibition (normal cells will stop growing when they fill the available space and contact one another), a decreased requirement for growth factors (i.e. they will continue to grow even when not supplied with the signal to grow), or gross morphological changes.

Both RNA viruses and DNA viruses may transform cells into cancer cells. There are three ways in which viruses can do this: by expressing a modified version of a cellular proto-oncogene, by cis-activation of proto-oncogenes or trans-activation of proto-oncogenes.

[Proto-oncogenes are genes that, when mutated, result in the formation of tumors]

Expression of Modified Proto-oncogenes

An example of this method of cancer induction comes from the Rous Sarcoma Virus, the first oncogenic virus studied. This virus contains a gene called v-src. It is very homologous to a cellular gene called c-src (v=viral, c=cellular). The c-src gene product normally encodes for a tyrosine kinase. It contains two domains at one end of the protein (in the kinase domain), the SH3 and SH2 domains. The SH2 domain is of particular importance; it binds to phosphotyrosine residues. At the opposite end of the c-src protein lies a regulatory domain. The 527th amino acid in the protein lies in this region, and is a tyrosine. This tyrosine gets phosphorylated, and the SH2 region of the kinase domain binds to it. This results in an inactive protein. The usual fuction of c-src is to work in a signaling cascade to turn on transcription factors that will express certain genes involved in the cell cycle; when it is on, cells grow and divide. When inactive, these genes do not get expressed, and no cell growth.

The v-src gene, however, encodes for a truncated protein. It is cut off at the 526th amino acid residue. That is, it does not contain the Tyrosine residue required to keep the enzyme inactive. When expressed in a host cell, it is always turned on, resulting in contant expression of the downstream genes, and uncontrolled cellular growth and division - in other words, tumor formation.

Cis-activation of proto-oncogenes

This method involves the integration of a viral genome in to the host genome. Eukaryotic cells are often tightly regulated, with promotor sequences, and regulatory or enhancer elements controlling the expression of the gene. Insertion of the viral genome is often a random process, and in the event that the genome were to insert into the repressor element of a gene, then the repressor would become nonfunctional. This would lead to an inability to turn the downstream gene off when it is not needed. The gene would be constitutively expressed. If this gene is a proto-oncogene, then the result is likely to be the formation of a tumor.
[This is called CIS-activation because the viral agent that is causing the activation is in cis, that is, is on the same chromosome, as the gene it is infecting. "Cis" comes from "cistron", the old name for genes.]

Trans-activation of proto-oncogenes

This method involves a viral protein directly acting on a transcription factor, which causes proto-oncogenes to be upregulated. The resulting upregulation can lead to increased or unconrtolable cellular growth.


An example of how viruses can cause cancer can be seen in the Papillomavirus family of DNA viruses. There are over 106 types of Papillomavirus, and over 40 of these are able to infect the mucosal surfaces of the the genetail and aero-digestive tracts. HPV (Human Papillomavirus ) has been detected in some 99.7% of cervical cancers.

HPV has two primary viral oncoproteins: E6 and E7. They are involved in disregulating the cell cycle. During the cell cycle, cells go through a phase of DNA replication, known as S-phase. If there is damage to the DNA, or errors with improper cell division, replicating the DNA during S-phase can result in dire problems for the cell. Tumor supressor genes will stop the cell from completing S-phase if this is the case. The HPV E6 and E7 proteins block the action of these tumor supressor genes, allowing cells to go through S-phase, and thus DNA replication, growth and division, unregulated.

One tumor supressor that is affected by HPV is the Retinoblastoma protein (Rb). Rb binds a transcription factor called E2F, and keeps it from fuctioning. When E2F is needed, Rb is phosphorylated and E2F dissociates and is allowed to activate the transcription of genes involved in DNA synthesis, and consequently, progression through the cell cycle. The HPV E7 protein interferes with the E2F:Rb complex - E2F is constantly active, leading to unscheduled cellular DNA synthesis as well as viral DNA synthesis. Also, there is a "High Risk" form of E7 where Rb is not only bound but is targeted for proteosome-mediated degredation.

The cell has a safeguard against this, however. The p53 protein is translated under cellular stress or DNA damage, and it halts the proliferation of cells, and plays a role in apoptosis. This ensures that defective cells do not run the risk of becoming cancerous. This is where the viral E6 protein comes into play - it binds p53 and blocks it from fuctioning. Much like E7, E6 has a 'high risk' variant. This form of E6 recruits an E2 ubiquitin ligase which polyubiquinates the p53, marking it for degradation via the proteosome.

From the above, it can be seen that DNA and RNA viruses have deifferent roles in cancer. RNA viruses encode for viral concogenes, while DNA viruses have mechanisms evolved to counter cellular tumor-supressor genes.

Oncolytic viruses

Another area of cancer that viruses play a role is in cancer therapy. Oncolytic viruses are viruses that are used as a form of cancer therapy. In this method, live viruses are used to selectively lyse cancerous cells, while normal cells are left unaffected. The viruses infect tumor cells, replicate, lyse the cells and then spread to other uninfected tumor cells. For some viruses, this selectivity is not perfect and normal cells can be infected; however, the viruses will grow better in tumor cells than in normal cells and (hopefully) will pick tumor cells over normal ones. The ideal features of such a virus are that they cause only mild human diseases that are well characterized, have secondary inactivation mechanisms, do not damage normal cells, have low mutation and recombination frequencies, do not spread from host to host and cannot integrate into the host genome.

Once such oncolytic virus is Onyx 015, a modified version of Adenovirus. This variant lacks the adenovirus E1b55K and E1b19K proteins which block p53 and apoptosis. It is hypothesized that its E1a protein binds Rb and E2F leading to increased DNA replication of the viral genome, and lysis of the tumor cells. What keeps it from destroying normal cells is that this also activates p53, and p53 keeps the infected normal cells from spreading the virus. The infected tumor cells do not have p53 and thus are unable to stop lysis and spread of the virus to other tumor cells.

Another such virus is myxoma virus. This virus usually infects European rabbits and not humans. However, it has the ability to infect human tumor cells instead. The benefit of this virus over the Onyx 015 is that it is natural rather than engineered.

Monday, 29 October 2007

What I learned in class today...

Biology 390

My professor was gone on a conference today, so this week's Biology 390 seminar was given by our TAs. We went over three concepts which I was already familiar with, but this did present some new facts that I did not previously know. These three concepts were DNA sequencing, Ampicilin resistance, and cDNA libraries.

DNA Sequencing

The method of DNA squencing we will be using in our lab was the method devised by Fred Sanger (which ultimately won him the nobel prize). It utilizes the principal of dideoxynucleotide chain termination. Dideoxynucleotides (ddNTPs) are much like regular dNTPs except for the fact that the are missing the 3' OH (thus making them DIdeoxynucleotides, see picture to the right). Since the 3' OH is necessary for the addition of the following nucleotide during DNA synthesis, if a ddNTP gets incorperated into a growing strand, the synthesis comes to a halt. These are added to a reaction along with template DNA (the DNA that you wish to find the sequence of), regular dNTPs, primers (specific to the regions flanking your template in whatever vector you chose) and DNA Polymerase.

The DNA polymerase used for this method is one that has no ddNTP discrimination, such as AmpliTaq FS - that is to say, it does not incorperate the ddNTPs with any preference. They are added to the growing strand at random. Thus, as one would expect, any reaction would contain multiple strands of varrying lengths - the ddNTPs are added at random, and the strand synthesis halts at random positions. If the reaction is left to run a sufficent amount of time, strands of every possible length are formed. For example, if your template read ACCTG, you would end up with strands that were:


The letters in bold are the incorperated ddNTPs.

Each ddNTP has attached to it two dyes, a donor dye and an acceptor dye. The donor dye, usually fluorescein, when excited by a laser, emits energy which then excites the accetor dye. The acceptor dye, usually rodamine, then fluoresces light of a particular wavelength. The acceptor dye on each specific ddNTP is different and fluoresces at a different wavelenghth - ddATP may have a dye which fluoresces at 565nm, while the dye attached to ddCTP may fluoresce at 615nm. Based on the wavelength emited, one can determine which ddNTP ended a specific fragment.

All the fragments produced by the sequencing reaction are passed through a capiliary in a sequencing machine. As in gel electrophoresis, the larger fragments run through faster than the smaller ones. The capiliary matrix must have a resolution that can discern between fragments differing by as little as one base pair. As the fragments pass through the capiliary, they pass by a laser, which excites the dyes attached to the ddNTPs. The largest fragment passes through first, and the wavelength it emits tells us what the last letter in the sequence is. The next largest is the second to pass through, and from it, we learn what the penultimate letter in the sequence is. This continues until the smallest fragment, representing the first letter in the sequence, is passed through the matrix.

A computer records the wavelengths that are emitted as they pass through, matches them up to their corresponding nucleotide, and arranges the results in the form of a chromatogram (aka electropherogram).

This is a readout of your exact sequence. Sometimes the computer is unable to determine what a particular base might be, and replaces it with an N on the readout. In this case it may be possible to look at the wavelength recorded and determine the identity of that particular base yourself.

This method of sequencing often works for fragments up to 800 bp in size. For fragments longer than this, sequencing in both directions from opposite ends of your fragment is best. For fragments less than 1.6kb, this may give overlapping fragments which can then be aligned to determine the complete sequence. For example, the pBluescript II SK+ plasmid which we are using in our lab contains two promoter sites, a T7 Promoter and a T3 Promoter. These face in opposite directions and flank the region where the template fragment has been inserted. Using these promotors, one can do two sequencing reactions, giving two sequences that can be overlapped at their ends to determine the complete sequence.

Ampicilin resistance

The topic of ampicilin resistance was brought up because it is used to select for bacterial colonies which contain a pBS II SK+ plasmid (since the plasmid confers Amp resistance to the bacteria). The gene that does this is refered to as the bla gene, which encodes the enzyme ß-lactamase. This enzyme breaks down the ß-lactam ring found in the structure of Ampicilin and other members of the Penicilin antibiotic family.

Ampicilin itself binds to a class of proteins known as Penicillin Binding Proteins (PBPs) which help in the biosynthesis of peptidoglycan, a component of the bacterial cell wall. By inhibiting the cell wall biosynthesis, the bacteria die. ß-lactamase thus ensures that the cell wall production is not inhibited by Ampicilin.

Unfortunately for molecular biologists, Ampicilin is broken down over time, so plates containing Ampicilin that have been unused for a long time cannot be used to select for Amp resistant strains.

Using Amp resistance is not without its problems. The ß-lactamase enzyme is secreted into the media surrounding resistant colonies. This means that the media immeadetly surrounding the restiant colonies is Amp free. Other non-resistant colonies can grow here. These are known as satellite colonies and will not contain any plasmids, and possibly messing up your experimental results. Another problem is the possible loss of plasmids. Since the media becomes Amp free, there is no selection for colonies that have a plasmid to grow there. Replicating the plasmid before cell division requires energy, and for cells gowing in the Amp free area, it is better for them to not have a plasmid at all. Without selection for keeping the plasmid, it is possible that it could be lost from the population alltogether.

cNDA Libraries

The final topic was that of the creation of cDNA, or Copy DNA, libraries. cDNA libraries are collections of DNA fragments that represent all of the actively transcribed genes in an organism. In other words, for every mRNA in an organism, there is made a DNA "copy" of that mRNA.

First, all the mRNA in a sample is collected. The mature mRNAs in eukaryotes have a poly(A) tail at the end of them after processing. This poly(A) tail acts as a binding site for a poly(T) primer. This primer has three sections: the poly(T) site, a XhoI restriction enzyme site and a run of "GA"s called the "GAGA" site:


The bold portion is the XhoI cutting site.

Next, the enzyme reverse transcriptase is used to transcribe backwards from the poly(T) primer to the 3' end of the mRNA template. This creates a double stranded duplex consisting of one strans mRNA and one strand DNA. This reaction uses a special form of cytosine, 5-methyl-dCTP. When added to the growing duplex, it prevents the cDNA from being chopped up by restriction enzymes.

Next, the RNA template is degraded by RNAse H, and the little pieces of RNA remaining are used as primers for DNA Polymerase I and PFU to replace the RNA strand with a DNA strand. This results in a double strand DNA duplex copied from the original mRNA template.

This cDNA needs to be able to be ligated into a vector, and an additional step is to transform the ends of the cDNA into different sticky ends. Adapters are added to each end which contain an EcoRI cut site. Next, XhoI is added, which cleaves at the XhoI site in the original primer (this is the reason for the 5-methyl-dCTP; the cDNA wont be cut up when XhoI is added). The end result is a cDNA fragment, with a EcoRI sticky end upstream and a XhoI sticky end downstream, allowing for it to be directionally cloned into a vector that has been cut with these enzymes.