Saturday, March 31, 2012

A Ticket to Hope

Even as excitement over the 640 million dollar lottery jackpot fades even faster than the money of its lucky winner surely will, the lessons it teaches us about psychology, risk, and reward remain important.

The obvious first lesson: humans are not rational. Since we all knew that already, let's move on.

The second, slightly less obvious lesson: this irrationality is a double edged sword. While anyone who acts truly without reason is a danger to themselves, and perhaps to others, the occasional, completely irrational action makes life much more interesting. Lotteries illustrate this quite well. On the surface, they are nothing but a way for the state to make money off of those who didn't pay attention in math class, an "idiot's tax." In fact, the money made from lotteries is great for states, as it appears to be the one form of revenue which isn't a matter of heated debate at the moment.

Of course, if money were to grow on trees, inflation would quickly render it worthless. This money which the government rakes in from the lottery has to come from someone, but who? Here, we see the scary, unfortunate side of human irrationality: many of those who regularly buy lottery tickets cannot afford to do so. In fact, those earning under $13,000 a year spend 9% of their income on lottery tickets. Now, sadly, I do not have access to full text article for this study, nor the inclination to pay $35 just to obtain it, so I cannot comment on the methodology of the study. In one somewhat obvious flaw in the way the numbers are reported, people with this income are going to spend a disproportionate amount of their money on anything, even if they were to spend the same amount per week as the general population. While this is indubitably a sad statistic, the factors behind it are far from surprising. When people are desperate, they'll buy hope in any form, even a worthless piece of paper.



Despite this, I don't advocate abolishing the lottery. While it may have its downsides, I believe, like many irrational things, it does more good than harm. Anyway, if adults have a right to do whatever they want with their money, why not let them donate it to the government? (This, incidentally, is why I believe that gambling should be legal. If people can waste money on scams like bottled water, which is worthless and boring, why not let them waste money on things which are worthless and exciting?) While spending over a thousand dollars per year on lottery tickets may be incredibly stupid, a ticket once a year, or even once a month, is pretty much harmless. In fact, the fun of imagining what you'll do with the money may justify the tiny cost of a ticket. Yes, you could dream without the ticket as well, but, somehow, the one-in-a-million odds make it seem much more realistic than the zero-in-a-million odds you'd have without the it. In addition to providing funds for education, the lottery even has some educational value in and of itself! It provides a familiar jumping off point for math teachers to introduce their students to probability, and, since the chance of winning anything is so low, a rather effective way for parents to teach their children about risk. (Slot machines, on the other hand, are not particularly effective in this regard. My parents had an friend who, while driving through Las Vegas, put some coins in one in order to teach his daughters not to gamble. The gods must have a sense of humor, since he won several times in a row.)

The bottom line: while excessive gambling, of any form, is destructive, a lottery ticket once in a blue moon may be worth it if you look beyond the money. Without the occasional irrational decision, life becomes rather dull.

(Okay, I think I've just convinced myself to apply to Caltech, since I'm slightly more likely to get in there than to win the lottery. The nerdy high school student's form of gambling is fun :D )

Saturday, February 25, 2012

Catholics are Not Weird(er Than Anyone Else)

For Lent, I have given up bashing my former faith.


I suppose I should explain this a bit further. No, I have not given up atheism and returned to the fold. That would require a compelling reason, and, so far as I have seen, no such reason exists. In fact, excepting priest jokes, I will not be giving up anything for these next 40 days, because I really have nothing against Catholicism. From what I have seen of Protestantism, Catholicism is one of the sanest forms of Christianity, and one of the sanest forms of religion which is widely practiced. (Of course, being among the sanest forms of Christianity does not make a belief sane. Also, I am probably biased, as I am related to quite a few very sane Catholics.) I must admit, I often get a little prickly when bloggers, both atheists and fundamentalists, single out the Vatican as the craziest, most evil institution humanity has created. Does the Pope say crazy s**t? Certainly. This one, Benedict XIV, especially. Have people committed great evil in its name? Certainly. this is true for time-tested religion which I am aware of. Do they continue to do so today? Certainly, though to a much lesser extent than in the past. But it also does much good. In fact, today, the good may even outweigh the evil. 


So, in the remainder of this post, I'll list and explain a few ways I think my past faith is misrepresented in pop culture and among internet atheists and fundamentalists.


1. All those weird traditions:






Yes, Catholics do some very strange things. Mass must be ming boggling the first time, what with all of the ritualistic responses, the times to sit, stand, and kneel, and the set structure of readings, same the world round, handed out by Rome. Just be grateful it isn't in Latin anymore, and that you only have to fast for one hour before, rather than on from midnight of the day before.


This level of ritualism is not whatsoever surprising in a 2000 year old faith. Protestants have every right to argue that this level of ritualism obscures true faith in the true God. We atheists don't really have this right, since we don't believe their is a true god. Many of us do, however, say that this ritualism is a silly way of worshipping a silly, made up god. Well, I certainly agree that this is a made-up god, and that a real God wouldn't care whether or not we get our Hail Marys right. Both sides are missing something here, however. There rituals are not to please God, they are to remind ourselves of our relationship with Him, and to help us improve ourselves. So while they may not be to everyone's personal taste—personally, I tended to hate them and daydream extensively during Mass—they are not as harmful or stupid as many make them out to be. 


2. Interpretation of the Bible:


Catholics do not interpret the Bible literally, thank the Flying Spaghetti Monster. Of course, there are quite a few individual Catholics who, against the doctrine of the Church, choose to do so, thereby making all others look bad. In fact, though the Church takes no official position on the evolution of life or of the cosmos, it leaves the possibility of "theistic evolution" open, and advises us to follow our own minds,  


"Though faith is above reason, there can never be any real discrepancy between faith and reason. Since the same God who reveals mysteries and infuses faith has bestowed the light of reason on the human mind, God cannot deny himself, nor can truth ever contradict truth" (Catechism of the Catholic Church 159). 


In practice, this means that evolution and the big bang are taught in Catholic schools. In my personal experience, my classes on evolution in Catholic school by a Catholic teacher were much more extensive than those taught in a much more advanced class at a public school. Of course, this freedom with scripture comes with a price:


3. The Infallibility of the Pope:

Yes, this is doctrine. No, no one actually believes it. Or, at very least, I have never met anyone who accepts it, and I know quite a few Catholics. Sadly, I can't find any stats on this. Hell, even Pope John Paul II himself barely believed it: "I am only infallible if I speak infallibly but I shall never do that, so I am not infallible."

More broadly, there is no tradition within Catholicism of leaving the Church the moment you disagree with something, so many people with wildly heretical beliefs stay in for reasons of family and tradition. While you can never know a person's specific position from their denomination, this is especially true for Catholicism. There's a wide range of beliefs among those who accept the Catholic mantle—deists with strong Buddhist influences and fundamentalist Christians take the same communion and say the same confession. Tradition is more important than doctrine, and, while the Vatican may not agree with this, they cannot effectively control anyone's thoughts. 


4. Everyone Else is Crazy Too:


Now, not all religions are created equal. Some have led more people to evil than others; some have more well intentioned harmful effects than others; some have beliefs which are even further than reality than others. Inevitably, this has become a personal and specific post. After all, I have only been one religion. I'm sure there are those who can write such defenses for Mormon, or even Scientology. (Okay, the latter might be a bit of a challenge. ) Religious fundamentalism and extremism are independent of sect, and one set of crazy beliefs is not much better than another. 


 My we's and they's are a little bit messed up throughout the whole post. I considered editing for consistency, but I couldn't decide how to define us and them or whether to call myself a member of neither side or of both. 

Tuesday, February 7, 2012

Tax The Rich—That's Where the Money Is

What with all this Occupy-inspired talk about "fairness" in our tax system, I can't help but think that we have forgotten the primary purpose of taxes: to pay for government services. Taxes are not to take from the rich and give to the poor, or even to 'level the playing field'—what most people mean by 'level the playing field' is to tilt it to favor whichever team they think is weaker or more deserving of their aid. The government is not Robin Hood, nor should it be. Those who work hard deserve to keep what they earn, and it's hard, bordering on impossible, to design a tax system which can effectively distinguish earned from unearned wealth. (Though raising the capital gains tax to make it equal to, if not higher than, the income tax would be a good start.) Equalization of society is not the primary purpose of government, nor should it be. Of course, a truly level playing field—one where everyone starts off with same equipment, must play by the same rules, and can keep the points they earn—is certainly something to work for, and is the basis of the free, free-market society which our government claims to work for. In other words, it is the responsibility of the government to enforce enough laws to protect everyone's rights, to have just enough of a military as is necessary for defense, and to provide services such as roads, schools, parks, and libraries to make life better for everyone and prevent poverty from becoming generational.

Right, but most likely for the wrong reasons. 

Why, then, do I say we should tax the rich? Because, quite simply, they have the money. To be fair, yes, we must tax the middle class as well, though to admit this is to slaughter one of the greatest sacred cows of contemporary American politics. While a flat tax, perhaps with a few deductions for educational and medical expenses, would perhaps be better than our current, easily exploitable mess, it is still far too simple to be effective—the equivalent of fixing your laptop with duct tape. Instead, I believe the best solution to our system is still a modification of our current graduated income tax. If we must take money from somewhere, we must take it from wherever it does the least damage. So those shouting that we should "tax the rich and the corporations" only have half of the story right. If we raise or corporate tax rates, we only give them more reason to pack up and move overseas. High taxes on business are not a harmless way to take money to support the government.

High taxes on very high incomes, capital gains, and inheritance are. The first, though it takes away earned wealth, does so in a relatively harmless way. While high taxes on high incomes bring in a lot of money for government programs, they do not have a very strong effect on those who pay them; surely, there's not very much worth having that one can afford on a two million salary, but not a one million. There are very many things worth having that one can afford on a hundred thousand dollars that one cannot afford on fifty thousand. Taxes on capital gains and inheritance are taxes on almost entirely unearned wealth, and, therefore can be much higher than income taxes without facing the same resistance or causing the same damage.  If we need to raise taxes to pay our bills, then we should raise them where it is relatively harmless, not where it hurts. To do otherwise is not simply unfair, it is harmful to our economy.

Disclaimer: I've never actually studied economics, aside from a little bit of reading on my own and participation in quite a few debates. Actually, you probably shouldn't listen to anything I say, but I'll say it anyway, because what are blogs but a chance for those without knowledge to voice opinions? :P

Wednesday, November 23, 2011

When people think of San Francisco and diversity, they probably think of something like this:
Often overlooked is different kind of San Francisco diversity: that of the of flora and fauna found in the city's parks. Even within an urban area, life can thrive in many forms. For as long as I can remember, I've been learning about this kind of life, at first by helping, or at least, attempting to help, my father in our backyard, then by exploring parks with my dog, and, most recently,  by learning as much biology as my brain can hold from classes and books. Needless to say, the latter is not quite as enjoyable. For that reason, I've given myself a challenge intended to combine textbook botany with real life exploration: to identify and photograph every species of native plant in the city, to do a bit research into the story of each plant, and to post both photos and stories on a new blog, http://sfbiodiversity.blogspot.com/. I'll try not to let this get in the way of my incredibly infrequent posting here. 

Monday, August 29, 2011

Tuesday, August 9, 2011

Can We Separate Knowledge and Belief?

The National Science Board, which governs the National Science Foundation (NSF) and publishes Science and Engineering Indicators, a biennial survey of national and international science literacy, is revising some of its questions in an attempt to separate students' scientific knowledge from their religiously motivated beliefs. Specifically, the two true/false questions, "The universe began with a huge explosion," and "Human beings, as we know them today, developed from earlier species of animals," have been modified to include the qualifying statements, "According to astronomers..." and "According to evolutionary theory..."

Is this a sad example of science bowing to superstition or a necessary move in our struggle to understand—and to fix—the gaps in our education system? One thing is certain: this isn't a problem we should have to deal with. What chemistry teacher has ever had to worry whether or not her students accept atomic theory? What physics teacher has had to ask his students for their personal opinions on gravity? Evolutionary theory is arguably as important to biology as atomic theory is to chemistry, so why should students be given the option to doubt it for entirely nonscientific reasons?

Alas, we are stuck with the country we are stuck with. Indicators serves as a test of science education, and teachers can—and should—only go so far to change students' beliefs. Perhaps we must sacrifice our ideals in order to get a more accurate view of what Americans actually know, in order to improve teaching (or at least to gasp in horror—and feel smug about our superior knowledge—as we see the shockingly low scores.) As, in my opinion, slightly biased as I have never believed in any form of creationism, it is very nearly impossible to fully understand evolution and still reject it, perhaps NSF members should perhaps focus on crafting a survey which tests for an understanding of evolutionary theory deeper than, "Oh, yeah, humans come from monkeys, right?" (No, we don't!) Adding an, "according to evolutionary theory," to more advanced questions which truly test Americans' understanding of evolution is a necessary evil if we want to see how much people really know rather than what they arbitrarily choose to believe. That said, after each sugarcoated, "according to scientists," type question, survey participants should be asked whether or not they personally agree with the statements, as is planned for the 2012 issue of Indicators, due out next January. It would certainly be interesting to see how much people can learn about evolution while still refusing to believe it.

When asking questions about the big bang, perhaps adding an, "according to astronomers," is entirely appropriate, given that your average nonscientist does not have the mathematical or physical knowledge to independently evaluate the theory, and really does have to trust the astronomers.* Considering most layman's discussions of astrophysics denigrate into philosophical debate without the slightest regard to science, it would be interesting to see a study testing whether those who believe in the big bang actually know anything about its scientific merits. Again, more difficult questions are needed to test our actual knowledge of astrophysics rather than what we believe either for philosophical reasons or because we "trust the scientists," and if a qualifier such as, "according to astronomers," is necessary to accomplish that, then it is better to sacrifice a few of our rigid ideals rather than to sacrifice science itself.



*Myself regrettably included, though that should change this school year. But, despite having Algebra II as my highest math and not a single physics class, I have *technically* finished my state's graduation requirements for math and science in my first two years of high school. The California education system isn't at all biased towards the humanities at all, is it?

Tuesday, August 2, 2011

Lamarck Vindicated

While the very mention of inheritance of acquired characteristics, commonly termed Lamarkism, after Jean-Baptiste Lamarck, is considered heresy by many orthodox neo-Darwinists, the fact is, inheritance does not depend upon genes alone, and, in some cases, traits acquired during an organism's lifetime may be passed onto its offspring through various genetic and nongenetic mechanisms, providing a new source of variation for natural selection to act upon. This is not to say that amputee mice will have tailless descendants, or that those famous giraffes which appear whenever Lamark is given his two seconds of fame in a biology class will get anywhere with their neck stretching.



No, I'm not saying this works. 



I do not support "Lamarck's Lamarckism" any more than any modern biologist supports "Darwin's Darwinism;" science has come to far in the past 200+ years for us to accurately name theories after 19th century biologists, however, we are stuck with the terms we are stuck with. First, then, let's do away with the historical reasons for the divide between "Darwinian" and "Lamarckian" evolution by mentioning the generally forgotten fact that that Darwin would be considered a Lamarckist by modern standards, in that he makes many references to evolution by use and disuse, and believed inheritance to occur by a complex and utterly unevidenced process somewhat akin to photocopying parents, acquired characteristics and all, to create offspring.  Darwin (and Wallace!) were only original in that he believed natural selection to be the primary means through which evolution occurs. 

Now, onto the real science. While the mantra "ontogeny reflects phylogeny" usually refers to the study of comparative embryology, it could perhaps just as easily describe the relationship of epigenetics, or the study of regulation, activation, and deactivation of genes, both during development and across generations, to evolutionary biology. While epigenetic mechanisms are better known for their role in development, epigenetic changes (epimutations) provide yet another source of variation for natural selection to act on, and this variation can be produced within an individuals lifetime, as well as as a directed response to stressful or changed conditions. This occurs through various means which I will discuss shortly, some of which may not count as orthodox epigenetics, but nevertheless illustrate my point that variations acquired during an organism's lifetime can be inherited and selected among. 

Inheritance of Self-Sustaining Feedback Loops

A parent cell will pass on patterns of gene activity daughter cells when said patterns are controlled by self-sustaining feedback loops. In a simple a self-sustaining feedback loop, once a gene is turned on, the presence of the gene's products sustain the gene's activity. 

Figure 9-61. Schematic diagram showing how a positive feedback loop can create cell memory.

The general form of an inherited positive feedback loop
(source: http://www.ncbi.nlm.nih.gov/books/NBK28289/)

The fungus Candida albicans, a human pathogen, has two genetically forms, white and opaque. Cells in the white form are nearly spherical, form white, dome shaped colonies when grown on agar, and are suited to bloodstream infections, whereas cells in the opaque form are larger, more elongated, form darker, flatter, colonies, and are suited to skin infections. White cells generally remain in the white form and produce white offspring, however, approximately one every 10,000 generations, a white cell will spontaneously switch to the opaque form, and will produce opaque offspring for many generations before switching back. Switching between forms is regulated by the gene WOR1, whose product, the protein Wor1, is present in very low levels in white cells. In opaque cells, Wor1 is present in large quantities, and binds to its own promoter, leading to the production or more Wor1. In other words, little or no Wor1 leads to more little or no Wor1, and white cells, while high levels of Wor1 leads to sustained high levels of Wor1, and opaque cells. (Zordan et. al., 2006) Stressful conditions which restrict cell growth lead to increased switching to the opaque form, which is better able to reproduce. (Alby and Bennet, 2008)  

Now, what does any of this have to do with evolution? Aside from the fact that C. albicans most likely evolved such a system to quickly adapt to changing conditions, quite a lot. First of all, it shows that a trait, acquired during an organism's lifetime as an adaptation to environmental characteristics can be passed on to its descendants. While this feedback loop has only two states, and so does not have the potential for much evolutionary change, all cells have many self-sustaining feedback loops, and the millions combinations of these loops present a source of variation which natural selection can act upon. 

Chromatin Marking Systems

Transcriptional regulation, that is, the processes by which cells "choose" which sequences to transcribe, is the best known epigenetic process. While it occurs through various means, understanding any kind of transcriptional regulation requires understanding the way in which DNA is packed into chromosomes. A human cell contains about two meters of DNA, without a very tight packing system, such a long molecule would obviously not fit inside such a small space. This system is better illustrated than described: 
Figure 4-37. A model for the structure of a lampbrush chromosome.
DNA packing

In DNA methylation, the best understood form of chromatin marking, a methyl (CH3) group is added onto the base cytosine, which does not change the meaning of the DNA sequence, but makes it much less likely to be transcribed. Patterns of methylation are copied as DNA is copied and always transmitted from mother to daughter cells. Patterns of methylation can be changed during a cell's lifetime, and changes in methylation are absolutely necessary for the normal development of a eukaryotic organism. 

Inheritance of methylation patterns.

It is easy to see how methylation can affect evolution in unicellular, asexual organisms, since offspring are clones of their parents, methylation and all. Natural selection can act on changes in DNA methylation just as it acts on changes in DNA, and, since changes in methylation are produced faster and more often in relation to chances in the environment than changes in DNA, this allows unicellular organisms to evolve faster through epigenetic mutation than they could through genetic mutation alone, which may have medically significant consequences when we consider the evolution of antibiotic resistance in bacteria, etc.  

While there are several other mechanisms of epigenetic inheritance which may play an important role in evolution, this post is getting way too long. For anyone interested, RNA interferenceother sorts of chromatin marking, and prions provide some more examples of non-genetic inheritance systems, and yellow mice (sorry, I can't find anything beyond the abstract+references)local hypermutation, and the effect of environmental conditions on recombination in the oh-so-well studied fruit fly, provide examples of semi-Lamacrkian evolution in real life. (Yes, my sources range from wikipedia to fairly technical journal articles. Either I was being lazy or striving to include something for everyone; you choose which to believe.)

None of this is to say that we should throw out the modern synthesis of evolutionary biology, or to say that natural selection is not the main driving force of evolution, only that we need to keep in mind that genetic mutation is not the sole source of variation which plays a role in evolution. Many of the sources of variation described here are only applicable to unicellular, asexual organisms, and a major criticism of the ideas presented here lies in the Weismann barier, which prevents genetic information from flowing from the soma (body) cells to the germ line (reproductive) cells, but which may not be utterly impermeable. As we learn more about genetics, epigenetics, and evolutionary theory, the interactions between these factors will become clearer. 

Finally, I can't help but recommend the book Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life, by Eva Jablonka and Marion J. Lamb, from which many of the ideas and examples in this post were taken, for anyone with even a small amount of biological knowledge and interest. It contains the best history of evolutionary biology I have found, combined with groundbreaking research, and is for the most part written at a popular level, which is to say that with a recent college-level introductory biology course, I was wishing the authors would hurry up a bit during the technical chapters, but enjoyed them nonetheless.