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.