7.29.2008

wordiology

I know its not a word, really. But seriously, people get completely bent out of shape about "inventing" words. Really? All words are invented. In my view, I would rather a word be invented instead of co opting another word and re-tasking it. So, wordiology. Word study, or word philosophy. (Which to the Greeks, who had -logy first, was study/science/philosophy--there wasn't a real distinction then...)
I spend a lot of time getting annoyed by people who use different words to mean the same thing. I was listening to Talk of the Nation this morning, they were talking about business world slang. Some of it was very interesting. Personally, I think its businesspeople wanting to have their own jargon (spake the bio major...), but this is beside the point. There are so many ways of describing things and everyone has their own context for a word. In business, a contractor is someone who works on a by-contract basis. In construction, a contractor is something much more specific.
You see this a lot if you're in a specialized field. Laymen will use your jargon and take it literally, or worse, misunderstand something that doesn't appear in the common use lexicon. I mean, if I started talking about ecosystem relations, niche predators, and tertiary consumers, most people would have half a clue as to what those are, but wouldn't necessarily understand the intricacies. There is nothing wrong with this, but its the fact that many people think they get it since they have an inkling of understanding. It is the unwillingness to admit to ignorance of a complex subject that is frustrating.
This comes to the forefront with subjects like evolution. Scientists don't use the word "theory" like laymen do. To a layman, a "theory" is your idea of how something works, with maybe a little evidence thrown in. To a scientist, a "theory" is how something works in all observed cases, but since all cases haven't been observed, there may be an exception or aberration. So when someone says, oh, evolution is just a theory---well, yeah. So is gravity. But no one has ever seen gravity not work unless there was another force involved (such as lift). Same case with evolution. There are very few species where a family tree cannot be drawn back into other species, and those that can't are researched intensely by those in evolutionary science. The other issue is that often things can get personified: 'X' changed in this way because it was better suited to this environment. Not how it works. For those who would like to know, here's the short version:
In any population, there is a range of genetic diversity. This occurs from random genetic mutation, which is a side effect of imperfect gene copying. If the mutation is not harmful the individual, (in that, kill it before it can breed sort of way) it will be passed on to that individuals offspring and take a place in the gene pool. These mutations can be anything, from things you can't see externally, like sickle cell anemia, to very obvious things, like albinism. Some of them are completely arbitrary, like a widows peak, a cleft chin, or tongue curling. These are all monogenic (dominant/recessive) traits in humans, and don't really have an effect on our "fitness".
But lets look at albinism. In most cases, around the world, being pure white is not so good. Its really hard to blend in to the forest, grasslands, swamp, etc, when one is white. It can also leave the individual more susceptible to skin damage from the sun (polar bears have black skin under all that fur for this reason). So when a genetic mutation for albinism appears, it is unlikely that it is going to be very common, since that individual is not liable to live long enough to reproduce, being easy to spot by predators and by prey. But suppose our white friend is an arctic creature. A white animal would blend in much better with snow and ice. In this case, the individual would be ideally suited to the environment, and would likely be healthy and live a long life, and hence produce more offspring. Since it passes its genes on to the next generation, a portion of these offspring will also be white. These offspring will be able to out-compete their darker colored siblings, and will be more likely to breed as well. Over time, the albinism gene would spread throughout the population, until the whole species had the albinism gene--and, ta-da: evolution.
This is a simple good/not good scenario for mutation. A more complex one would be sickle cell anemia, which is a monogenetic syndrome which effects the structure of hemoglobin in the blood. If one has both of the recessive sickle cell genes, one has sickle cell. If, other other hand, one has only one or none of the sickle cell genes, then one is normal.

S = normal gene       s = sickle cell gene

SS = normal individual
Ss = unlikely to show symptoms of sickle cell
ss = sickle cell patient

Sickle cell can kill, but it is extremely prevalent in tropical populations. Why would a potentially deadly gene be so widespread? It is because the heterozygous individual (Ss) is resistant to malaria, which is abundant in the tropics. The heterozygous expresses both genes, but in most cases, the "good" gene can make up for the "defective" one. If one looks at Mendelian genetics, it shows that of all of the children a heterozygous couple can have (both Ss):

    S   s
S SS Ss
s Ss ss

one will be sickle cell, one won't have the gene but will be susceptible to malaria, and two will be sickle cell carriers and resistant to malaria. To mother nature, two out of four ain't bad, and so that is what gets passed on.
This stuff can take some thought, but its not really difficult to understand. The easiest examples are bacteria, or populations decimated by disease. Wipe out a major portion of the population, and whatever could survive that destructive force will reproduce and create a new population resistant to whatever that force was, be it antibiotics or the bubonic plague.
I think this is all fascinating, but alot of people don't understand it, and don't want to.

to be continued?

7.25.2008

Holy Sequel, Batman!

I saw Dark Knight last night. For those of you who haven't seen it, I will do my best not to reveal any spoilers, but if you don't know who Harvey Dent is, and who Two Face is, I would suggest you don't read any further.


ok, they gone now?

Alright, here's the thing. We all know that originally Harvey Dent is a good guy, and a friend--or at least acquaintance--of Bruce Wayne. He has some terrible accident that affects half of him, and ergo becomes Two Face. As villains, pairing Two Face and Joker is practically kismet: both are obviously psychotic, bent on destruction, and motivated by reasons we aren't always clear on. (And, in case you hadn't heard, Heath Ledger's Joker is truly frightening and brilliantly portrayed. He really is not firing on all cylinders here, and the effect is so creepy it makes your skin crawl.)
Admittedly, and like all superhero movies, they have some issues with physics and technological probability; this is almost unavoidable, but, like the first entry in this saga, they do try to off-set a good deal of it, which I personally appreciate. The acting is impeccable from all, the plot takes several unexpected twists, and some of the psychology involved is rather advanced for an action flick.
Here's my only real complaint.
Harvey Dent's transformation into Two Face is, in this interpretation, realized through a terrible burn. Burns, especially those chemically accelerated, can be truly horrific. Beyond just the sheer physical damage, the destruction of skin, nerves, etc., they are agonizingly painful, and once the skin barrier is gone, leave the victim extremely vulnerable to infection. The scarring, even with skin grafts, is awful, and can often lead to restricted motion, depending on where the burn is located. As a way to make an otherwise good man lose his final grasp on sanity, it does its job well, but...well, here's the thing. Dent's injuries are bad: really, really bad. As in, no more cheek or lips on the left side of his face. No eyelid, and from what I could tell, no tear duct either. Chin bone showing through skin, jaw bone visible as well. There are a few muscles left so he can move his jaw, but not really.
Seriously? I don't want to be too picky, but burns being what they are, wouldn't you think that the real thing would be more horrific that taking it so completely over the top? There is mention of his refusing painkillers (which would have left him in shrieking agony) and skin grafts (which with those injuries, I think the doctors would have overruled him on that)--and then gets up, starts running around and killing people.
And I swear to god, the only thing I can think is, "Huh. Well, aside from being blind in that left eye since its getting no moisture at all, he's gonna be dead from infection in about 12 hours at this rate."
This didn't ruin the movie, but it did annoy me.

7.21.2008

Welcome to The Jungle

I like the FDA. Its one of my favorite institutions. One has a distinct peace of mind when there is an organization that makes sure my medications are safe and effective, and that the food I eat is fit for human consumption.
In theory, at least.
Given the recent happy fun time with salmonella poisoning, as well as numerous articles (see Discover Magazine, New Scientist) about the utter inadequacy of drug testing, one does have to wonder what is going on. In recent years, the approval procedure performed by the FDA has been paid for by the companies themselves (somehow this seems like a bad idea). Eighteen years ago, if the FDA made a mistake, approved and unsafe or ineffective drug, or did not perform rigorous inspections of food prep factories, there would be a congressional hearing to explain what happened. There have been two oversight hearings since then. The relationship between the FDA and the prescription drug industry is very friendly. The drug companies even gave the FDA commissioner an award for doing a good job.
Wait a tick there...
As a monitoring agency, I would hope that the relationship between the FDA and the drug companies would be an adversarial one, with the drug companies constantly complaining about the stringent requirements enforced by the FDA. This used to be true. It isn't now. There are some rather obvious reasons for this, not the least of which is the drug companies funding of congressional campaigns.
Recently studies have shown that bladder control drugs are strongly connected to the onset of Alzheimer's, to the point that if a patient is taken off of the drug, they lose all symptoms of dementia. This is just one sign of the fact that the monitoring and research of these drugs is insufficient. This isn't just the FDA's fault. If there is no money, no vigilance on the part of either the congress or the citizens, and a strong motivation to keep things the way they are, who the hell is surprised that things slip through? There are reasons that we have these regulations, and those are to prevent the spread of disease and to prevent drug companies from selling snake oil (potentially harmful snake oil) to unwitting consumers. As a student of biology, I know the high likelihood of things not going quite to plan, and the temptation to alter results even a little bit to make it fit your hypothesis.
This is not how science is done. It is certainly not the goal of science, which is to test the hypothesis, and take that data, be it positive, negative, or completely random, and form another hypothesis based on that data. There is no wrong answer. When money gets involved, the answer is always "does this result cost us more money or get us more earnings?" The drug companies often complain about the expense of developing a new drug. If this is so, why is it that they are paying such enormous amounts of money to campaigns? Why is it that the executives are multimillionaires? In other words, where is the corporate focus? It should be in providing the best, safest drug possible, which will be used widely because it IS in fact the safest and most effective drug on the market. If your goal is merely to make your executives and stockholders rich, I would suggest that you invest in alternative energy sources right now, since they are going to be getting popular Real Soon Now.
I find this all extremely frustrating, because of all of the Federal Institutions I would want to participate in in my career, the FDA and the CDC are it. If the first goal is to please the drug companies and the second to keep people safe--maybe I want to become a Congresswoman before anything else.
They need money, oversight, educated employees, and a distinct line between their goals and those of the drug companies. Until those things happen, I think I'll be getting my tomatoes from the local farm stand.

7.15.2008

Crash and Burn

I've been watching this housing crisis unfold, listening to Public Radio and the BBC. It breaks my brain that these kinds of shenanigans have been able (and allowed!) to go on for as long as they have. It used to be that a perspective home buyer put 20% down--they were required too. These days, 5% down is not only possible, but common, and it was even feasible to put no money down.
Let me repeat that.
It has been possible for a person to put no money down on a home loan for a $270,000 home purchase.
Lets do some math, ok? Assuming this is a standard 30 year mortgage, at 6.75% interest, this individual will pay 18,500 dollars in interest, if they keep to the payment schedule. The median household income in the US is about $48,000 a year. This means that this person's home is worth 6 times as much as they make in a year. In 1967, the median income was $37,000. The average home price was $20,100 (sources here, and here). Adjusted for inflation, those come to $227,500 and $123,000, respectively. The price of the home was 54% of the yearly income.
So, lets go over this again. The price of the house has skyrocketed 45% in adjusted value, and the average pay a person gets have plunged by 474%.

What?

Am I the only one who sees a problem here? Never mind the fact that people are woefully underpaid anymore, but when buying a home is 600% of your combined salary--thats two earners, most times--its nearly impossible to buy a home with a 20% down payment (that would be $54,000, for those keeping track). Now, in a normal market, with responsible lenders, this would lead to a decrease in the number of loans being granted, which would cause one or both of two things: a drop in the prices of houses to match what people can actually and responsibly spend, or a jump in salaries as employees got more and more annoyed at their inability to purchase a home.
As we can see, this hasn't happened. Instead, there has been a steady decrease in the amount required to make a downpayment, as well as a decrease in due diligence on the part of lenders, in checking the income of the buyer and only providing a loan they have a good chance of repaying. I have heard of single mothers making $27,000 a year being given loans for $400,000 houses. That is fifteen times what she makes in a year. Who on earth thought that this woman would be able to pay this loan?
Whats worse is that the ability to get these loans disguises just how much the average household income has declined, even since 1968. Talk about not getting by in America. You aren't doing nearly as well as your parents or even grandparents were, and are likely doing alot more work for it--and while your pay hasn't gone up, costs have. The artificially low prices of Asian goods leads to a false sense of cost--and that isn't going to last forever, especially as the Chinese economy becomes a real force in the world.
What's the bottom line? Alot of people who want to make money have made it easy for Americans to get deeply in debt buying houses they cannot afford but assuaging the feeling of money-tightness by providing underpriced consumer products which they can afford--and if they can't they can buy it with more credit.
I can't wait for the credit card crash.

Dammit Universe.