Modern medicine? Pshaw!

FOXNews has a new article that reveals an absolutely apaling statistic: over half of Americans say they believe God can save patients from dying if doctors determined that medical treatments were futile. One third of those surveyed said that patients should have the right to demand such treatment - i.e. the right to demand to be prayed over rather than given medical treatment. And what's more disturbing is this quote:

"When asked to imagine their own relatives being gravely ill or injured, nearly 20 percent of doctors and other medical workers said God could reverse a hopeless outcome."

One fifth of America's medical personelle believe that God can save the lives of those with terminal illnesses.

These statistics disgust me for two main reasons.

Firstly, the belief that God can intervene when doctors cannot is the start of a slippery slope. I can understand that when a person is terminally ill, and there's nothing that doctors can do to save them, family members may be inclined to cling to whatever gives them hope that their loved one will pull through. It's human nature to want to hope such things, and it makes sense that people would look to God for that hope. However, if people really, actively believe that God can send down a miracle and save their loved one better than professional medical staff can, then what's to stop such people from not bothering to seek medical care to start with? If God is more of a powerfull healer than doctors, then why not prey for God to send down a miracle instead of seeing a doctor in the first place? Believing that divine intervention can save the lives of terminally ill patients can very well lead to a dependance on God rather than modern medicine for treatment. If such a trend were to develop, it would be quite a medical disaster. Already, we've seen cases - usually in evangelical families - were people have relied on God to heal their children rather than taking them to see doctors...with fatal results.

The second problem with this is that it greatly devalues the hard work medical personelle do to save a life. If a terminally ill lukemia patient makes a turn for the better, his cancer goes into remission, and it's chalked up to "divine intervention", then the hard working doctors that put so much effort into saving his life don't get the credit that they deserve. Even if the doctors have claimed further medical treatments to be futile, the work they did beforehand, the effort and resources they put into saving his life, becomes devalued. What worth do doctors have when God trumps their work?

I am also disturbed by the number of doctors who believe that God can intervene and save lives when they cannot. I would be very frightened if I were told by a doctor "Well there's not much I can do for you, but if you pray hard enough, God might heal you instead." I see this as going against the Hippocratic Oath. Doctors are supposed to do what they can for the good of their patients, and not to do any harm. A reliance on God to heal, whether medical treatment is futile or not, does more harm than it does good.

The Crichton Dilemma

I have a deep, dark secret to admit. I am a fan of Michael Crichton.

Now, to a lot of people, admitting such a thing is no big deal. "What's wrong with enjoying his work? I mean, Jurassic Park was great!" they might say. But to someone as science-centred as myself, it is a big deal.

I've been a fan of Micael Crichton for a long time. The first book of his that I read was The Lost World, the sequel to Jurassic Park, back when I was in 4th Grade (I remember it clearly, my 4th grade teacher asking me if my parents approved of me reading something filled with explicit language and violent, gorey scenes - the book was entirely unlike the crappy movie version). Since then, I've read about half of his most well known works (Sphere, Timeline, Prey, State of Fear, and Next). And I liked them. All of them. And I'm eagerly awaiting his next book, to be released this December. The reason I like his work is because they always include lots of science. Whether it be the science of genetics, as in Next or quantum mechanics, as in Timeline, Crichton's books have always been centered around science.

But what has caused alot of science-minded folks to dislike him is the precieved "anti-science" message his books have. Jurassic Park had genetically reconstructed dinosaurs....that went on a rampage, destroying and killing all in their path. Prey featured nanotechnology and self-reproducing nanobots...that devoured people and took over their lives. Timeline had timetravel and quantum mechanics....and people ended up going back in time, getting killed in horrific ways. Alot of people read his books and walk away with a feeling that Crichton is completely anti-science, like he's saying "Look at all the terrible things that science causes! People die and their lives are ruined because of what science does!" and this has caused alot of people to shun him and his work.

I look at it differently though. I dont see Crichton as having a totally anti-science message. Rather, his work acts as a caution. His stories all tell of the bad things that can happen if we do not use our newfound discoveries and technologies in a responsible manner. Crichton is not saying science is bad. He's saying "Be careful. Science can give us some totally amazing things but it can be terrible if we are not responsible". And this is a message that I agree with completely. I absolutely love science (so much that I have dedicated my life to it!) but it is easy to see how science can be dangerous if used improperly - look at the atomic bomb, for instance.

This is not to say that I support Crichton and his views entirely. Crichton is known for being a climate change denier (his book State of Fear was about 'ecoterrorists' deliberitely changing the climate to convince the public of, well, climate change), and has even said that SETI is more of a religion than science (!). However, this is immaterial concerning his views on whether science is good or bad.

Nevertheless, I am a fan of Michael Crichton. Many people may think that, as a scientist, I should be ashamed of that. But I'm not. His stories are always interesting, thrilling and carry an important message of scientific responsibility (even if he does get some of the scientific details wrong). Why should one be ashamed of liking that?

Well I'm stumped.

Alright guys, we've been trumped. I guess God must exist after all:

"Any Atheist who can prove why and how the sky is staying without falling without the help of pillars???

Sky is not resting on pillars, right? So who is keeping this sky afloat on on heads in the middle of nowhere. What is the cause of "sky" hanging without any support?

Answer me and I will become an Atheist."

I hear that the atmosphere is composed of gasses but that couldn't possibly have anything to do with it, right?

Hold on a second, my Sarcasm Meter just went nuclear.

A Lesson in Logical Reasoning

One common tread I've noticed (and undoubtedly anyone with an iota of intelligence has also noticed) that runs though silly religous arguments is that for the most part, people do not know how to reason logically. Just take a quick look at Fundies Say The Darndest Things and you'll immeadetly realize that; pretty much every post is ladened with at least one type of fallacious reasoning.

However, by far the most common form of illogical reasoning is the type where someone equates two totally unrelated things as being the same, or where someone claims that two things which are similar in some superficial way as being the same thing. For example, take this gem:

"Imagine that you could listen to or talk face-to-face with satan about any subject that has to do with God.

Then bring to remembrance anything you've heard atheists say against God. (Or if you are an atheist, you know your own sentiments and thoughts).

Now, if you try, you will find that it is impossible to imagine satan expressing sentiments about God different than what atheists express. Satan certainly is not going to speak positively about God, and neither are atheists. So, what both think and verbalize is in complete harmony with one another.

Atheism is therefore a doctrine of demons, and in many, if not all cases, atheists are demon-possessed."

The reasoning behind this kind of claim goes something like this:
X is A
Y is also A
Therefore X is Y.
The problem with this kind of thinking should be pretty obvious. For example, swans are white (yes I know there are also black swans). A Boeing 747 is also white. Therefore swans are simply miniture Boeing 747s. Swans fly. Boeing 747s fly. Swans really must be Boeing 747s.

Obviously, this is not true.

This kind of reasoning only works if A, that characteristic which is shared by both subjects, X and Y is a defining characteristic of either X or Y. Let me explain.

If, for example, you said that birds were defined as "animals which have two feathery wings", then anything that has the characteristic of "having two feathery wings" would be classified as a bird. Now:
Birds have two feathery wings.
Swans have two feathery wings.
Swans are birds.
This works because of the use of a defining characteristic. Defining characteristics are such that anything with that characteristic falls into that classification; and anything that is NOT classifed as such CANNOT have that characteristic.

Confused?

"Two feathery wings" is a defining characteristic of birds. Anything with that characteristic (anything with two feathery wings) falls into that classification (is a bird). Anything that is not classified as such (anything that is not a bird, such as a gazelle, or a whale) CANNOT have that characteristic (they CANNOT have two feathery wings). This is what is meant by a defining characteristic.

Being white and flying is not a defining characteristic of Boeing 747s or swans, so this kind of reasoning fails in such a case.

Also note that this kind of reasoning only works when describing categories, such as "birds". This reasoning allows one to classify subjects but not to make assertions that one thing IS another thing. For example:
Swans have two feathery wings.
Geese have two feathery wings.
Therefore swans are geese.
This does not work; "geese" applies to a specific bird (or a handful of species) rather than to a broad "class" of birds.

When we look back at the reasoning given in the original fundie argument, we see it violates both of these rules. It does not pretain to defining characterists (anti-God sentiments surely are part of being an atheist, but are not a defining characteristic; it is entirely plausible that one can be "anti-God" but not be an atheist), and it does not apply to categories (neither "Satan" nor "atheist" are categories).

Alas, this kind of reasoning is rampant amongst fundies. A vast number of arguments can be countered based on the fallacy outlined above alone. Its a shame (and kinda funny) that so many people keep coming up with this kind of argument and expect it to stand up to scrutiny.

Techniques in Molecular Biology: Western Blotting

Today I thought I'd go into a little detail on one of the most common experimental techniques used in molecular biology - one that I've done far too many times this summer - the western blot.

In general, western blots are a technique that is used to determine the presence of a particular protein from a biological sample. For example, let's say that you've introduced a plasmid carrying the gene for alcohol dehydrogenase into E.coli and you want to check to see if the bacteria are actively transcribing and translating the gene. An easy way to check this is with a western blot. Westerns are also a useful diagnostic tecnhique in medical labs: westerns can tell you whether a protein is the wrong size, or if a particular protein from a virus or bacterium is present in a sample from a patient.

The theory behind Western Blotting is rather simple. First, you need a sample of proteins. These can be obtained in a variety of ways but they way that I'm most familiar with is through the use of sonication. A culture of cells is grown which (supposedly) express the protein you're interested in. By subjecting these cells to very high frequency sound, the cells rupture and spill all of their contents. One can then put the sonicated sample into a centrifuge, so all of the cellular debris clumps together at the bottom of the test tube, and the proteins in the cell are left floating around in the supernatant.

Now that all the proteins have been isolated, you need to seperate all of them. This is done by using electrophoresis on a polyacrylamide gel. Polyacrylamide forms a mesh through which the proteins travel through when an electric current is applied. Bigger proteins travel though the gel slower than smaller proteins; this, then, allows us to seperate all of the proteins based on their size. At this stage, it is possible to use a protein stain to stain the gel. This will allow us to easily visualize the proteins on the gel. Unfortunately, unless you were working with a pure sample of your protein of interest, you'd see a large smear since the gell contains ALL the proteins from the sonicated cells. To determine the presence of your protein of interest, you'd need a way to specifically visualize your protein and not the rest. Western blotting allows us to do this with ease.

We can speficically visualize whichever protein we want, but polyacrylamide gels do not allow us to do this. Thus, the next step is to transfer the protins to a medium which we can use to probe for a specific protein. One commonly used material for this is nitrocellulose membrane. Nitrocellulose has a very useful property - pretty much any protein sticks to it like glue (this also makes it a little tricky to handle, because you dont want proteins from your hands sticking to it and messing up your results. By making a nitrocellulose-polyacrylamide gel sandwich, and applying an electric current, you can force the proteins in the gel to transfer to the nitrocellulose. The membrane should then contain the proteins seperated as they were on the gel.

Now you're ready to detect specific proteins. This can be accomplished by using antibodies against whichever protein you're interested in. Alot of companies sell antibodies for commonly used proteins. Alternatively, you can design your protein so that it contains a "tag" - a short sequence of amino acids - at one end of the protein which is absent in proteins naturally produced in cells. You can buy antibodies which recognize different tags, and thereby bind only to your protein of interest. These antibodies will bind directly to the proteins on the membrane. Next, secondary antibodies are applied. These will bind specifically to the first antibodies.

The secondary antibodies are the key to detection of your protein. Attached to the secondary antibodies is an enzyme. Which enzyme is attached is a matter of the method of detection used. There are multiple ways of detection, but the most commonly used methods are chemiluminescent detection and pigment production. Both methods work in a similar way; attached to the antibody is an enzyme which will convert a substrate into a product when applied to the membrane. In the case of pigment production, the product is a pigment which can be direcly visualized on the membrane. In the case of chemiluminescent detection, the conversion from substrate to product produces light, which can be detected on a piece of X-ray film. In both cases, the result is a dark band representing your protein of interest. Where there is a dark band, there is the secondary antibody/enzyme; where there is secondary antibody, there is primary antibody; and where there is primary antibody, there is your protein of interest.

The image to the right shows what this end result looks like. You can also run a protein ladder along side your sample, which will show the size of known proteins, so you can determine the size of your protein.The whole process of western blotting can take a few hours to complete (or all day if you're bad at it like me). There is, of course, alot more to western blotting than this; what I've presented is a very generalized idea of how western blotting works. Nevertheless, it is a reliable way to detect the presence of any protein you want in a sample, and has become a staple technique of molecular biology.

Couldn't Have Said it Better Myself

Here's a clip from Henry Rollins' show, where he discusses the evolution vs Intelligent Design 'debate'. Rollins has such a way with words.

I couldn't have said it any better myself.

Stockwell Day gets it; Winnipeg MP almost gets it.

Well it seems that the Phelps clan probably won't be making any appearances in our country any time soon. They've been barred from our country. CBC News reports:

"Public Safety Minister Stockwell Day's office sent an alert to border patrol to "look out" for people with signs and pamphlets consistent with the messages that the church promotes and to keep them out of the country, Winnipeg MP Pat Martin told CBC News on Friday"

At least Stockwell Day gets it. These people are vile, disrespectful excuses for humans and shouldn't be let into our country. This is great news. However, I have a bit of a bone to pick with Winnipeg MP Pat Martin...

""Entering Canada by a U.S. citizen isn't an absolute right, and if you're coming here only to disrupt the social order and to promote what we consider to be bordering on hate crimes or hate language, they shouldn't come into Canada," Martin said."

He's absolutely right that entering our country is not an absolute right, but whats this about 'bordering' on hate crime or hate language? How can someone in our country publicly exclaim "Jesus Sucks" and be charged with hate crimes, yet a known hate group can come into our country, spew thier vile, hateful filth and that only boarders on hate crimes? It IS a hate crime. It IS hate language.

The reason why the Westborro Baptist Chruch's members havent been locked up or at least fined for what should be obvious reasons is beyond me. Oh, wait, nevermind. It's probably because they hide behind that impervious shield of religion. They get away with saying what they please because it's their "religion". They get to spew their intolerance because disagreing with them means you are intolerant.

So far they've only been barred from entering our country - the boarder guards have been instructed to turn them away. They haven't explicitly been BANNED from Canada and they may make their way in elsewhere. Hopefully the government realizes the need to have these lunatics outright banned and follow Massachusetts and keep them out for good.

A Busy Week for the Phelps Clan

It's been a busy week for those fear-mongering, inhuman folks in the Phelps clan. Only a few days ago, the Westboro Baptist Church were hit by a fire that destroyed their church (whether it was arson or not it was arson has yet to be determined). This weekend, they are going to be in Red Deer, picketing the Laramie Project, and now this:

"A church group described in a British documentary as "the most hated family in America" says it will head to Canada this weekend to protest Tim McLean's funeral.

The daughter of the founder of the Westboro Baptist Church, based in Topeka, Ka., told CTV.ca she and several other church members will go to Winnipeg on Saturday to demonstrate against what she described as McLean's "filthy way of life." Shirley Phelps-Roper said his life was emblematic of Canada's moral decay."

The WBC are claiming that Tim McLean's death was a gift from God. They are claiming that he lead a "filthy" way of life (who knew that the WBC was against carnies?!). They are claiming that he came from a "rebel country" ( a "fag nation' as Phelps has previously refered to Canada). And they are heading to Winnepeg to picket his funeral.

This is absolutely deplorable. Do they really believe that it is God's will to have people they dislike brutally decapitated on a public bus? The Phelps clan literally makes me sick to my stomach.

With any hope, they will be denied entry into Canada. Why they would be allowed to pass when they are entirely likely to be a threat to public order and intice hate crimes.

Dead or Alive: The Debate on Viruses is Renewed

One of the biggest debates in biology today is over whether or not viruses count as life. Most scientists would contend that viruses are not alive and for good reasons: they cannot replicate on their own and require hijacking of their host's replication machinery in order to reproduce, they do not have any metabolism, they have no cellular structure and their replication is driven by spontaneous assembly or virus particles rather than by cellular division. Classifying viruses as "alive" would mean that cellular organization would not be included as a requirement for life (and opening the category up to things like prions). But according to a new article published in Nature, new findings are beginning to challenge the notion that viruses are not alive.

In 2003, a new family of viruses was discovered by researchers in France. From a sample taken from a cooling tower in the UK, researchers found a new type of virus that was infecting ameobae in the sample.¹ This virus was way bigger than any other viruses known at the time, both in physical size and genome size. Having about 900 protein-coding genes - 3 times that of the next biggest virus and larger than some bacterial species - the virus is a behemoth. It was called mimivrus, for "mimicing microbe".

But that isnt the interesting part.

The same research team recently isolated a new strain of this giant virus, again from a cooling tower - this time in Paris. Electron micrographs of the virus showed that this strain, called mamavirus, had a friend. They discovered another, tiny virus that was closely associated with the mamavirus. They nicknamed this one Sputnik because it seemed to be a satellite of its larger companion. The team noticed that the mamavirus infected ameobae, just like its mimivirus cousin, and turned the cells into a virus assembly line to pump out more mamaviruses. However, if the amoebae were coinfected with Sputnik, the little satellite virus would hijack - not the amoeba's machinery - but the viral factory set up by the mamavirus! The mamavirus particles would turn out all screwed up and less infectious. It would seem that Sputkik is a viral virus! The researchers had found the first known virophage.²

Just like bacteriophages prey on bacteria, virophages prey on bacteria. They hijack the virus' machinery (that the virus itself has hijacked from the host cell), and this causes the virus to become ill. And that is what has rekindled the debate over viral "life". How can a virus - something that supposedly isnt alive - become sick?

I dont belive that this really throws a monkey wrench in the current classification of viruses as "nonlife". What the virophage is doing is interfering with the mamavirus' "virus factory" for its own use, and the mamavirus progeny turn out sickly. This is not a whole lot different from mutating a step in the assembly line so the virus churns out avirulant progeny. Mutate gene A so that protein B isn't incorpreted into the viral capsid, and you get viruses that are less infectous. Does that mean that the virus is alive? Not really. In both cases, the same sort of assembly line is being interrupted. A virus falling prey to another virus makes neither of them any more "alive" than viruses that have been mutated in a lab. The only difference here is that the changes to the viral factory are being carried out by another virus instead of a mutagen. Does that mean that the virophages are "alive"? No more than bacteriophage are alive. The new findings, I feel, do not suggest that viruses are alive. They suggest that viruses can fall prey to their own devious schemes.

But, draw your own conclusions. The debate on whether or not viruses are alive will not end with these new findings, and is likely to only become more intense. But, regardless of whether you think viruses are alive or not, you have to admit: mimi/mamaviruses and virophages are pretty frickin' cool.

============================================
1. La Scola, B. et al. Science 299, 2033 (2003)
2. La Scola, B. et al. Nature doi:10.1038/nature07218 (2008)

And the Award for Worst (or Best?) Paper Title Goes To...

...Tracey Chapman (no, not Tracy Chapman) for her article The Soup in My Fly: Evolution, Form and Function of Seminal Fluid Proteins published last week in PLoS Biology.

Yech.