Monday, 17 December 2007

God, Morality, and Progress

I recently finished reading Richard Dawkins's The God Delusion. Partially this has been because I admire Dawkins but have read comparatively little of his work, and partially this is because I have gotten rather annoyed with people that criticise the book without having read it (which seems to amount to most published reviews and many book-length rebuttals). Mostly, however, I read it because the Evolution Studies Group at Dalhousie chose it for their most recent reading.

Although one might think that it comprises mostly biologists, this group is actually made up mostly of people from the social sciences: philosophers, mainly, with some historians and sociologists for good measure, and I believe a stray psychologist or two as well. This makes for some interesting discussions, usually in directions that I cannot predict. In the case of Dawkins, though, I am right at home: a biologist wandering through theology, generally in agreement with the philosophers, but somewhat out of place all the same.

Much of the criticism of Dawkins is levelled at his lack of philosophical sophistication. I had heard this myself, but did not appreciate it until the philosophers explained things. Indeed, as it turns out, there are far better versions of the historical proofs for God's existence than are addressed by Dawkins. They are just as flawed, only in a more sophisticated fashion, and take far more verbiage to refute. I would argue that a proper refutation would require the book to be twice as long as it is, and probably nowhere near as witty. More than that, Dawkins's intent is not to provide the final word in the question of God's existence (something that talented philosophers and theologians have attempted for millennia) but to demonstrate that his dismissal of said entity's existence is not without consideration of the more famous arguments. Still, I would be a little less embarrassed by proxy if Dawkins had at least acknowledged that he was not dealing with the best versions of the arguments, that he had considered them but found them to be just as lacking. Instead he seems to think that any one version is as good as any other, and tackles at best mediocre and at worst laughable takes on the matter.

His argument against the existence of God is oddly one-dimensional: he merely refutes the argument from design (which as a biologist I know to be complete poppycock, although an understanding of that may take some considerable education to acquire fully). He does so very well, but I am not certain that he has made his case merely through the inversion of a popular (if fallacious) argument. He does take it to be illustrative of a far more powerful concept, though, one which I feel is the most important aspect of the matter: there is really no reason to support the notion of God in the first place. The argument from design purports not only the existence of God but that God created, designed, or guided the development of the material universe. As Dawkins succinctly puts it, a universe with such a God is demonstrably different from a universe without one, and every prediction made by the creator/designer/intervener-God hypothesis can be shown to be contradicted. There is thus no evidence for God, and Occam's Razor suggests strongly that such a fantastic entity must therefore be very unlikely. As Carl Sagan put it, extraordinary claims require extraordinary evidence, and here we have one of the most extraordinary claims ever put forth, with no evidence whatsoever. Still, this is not a demonstration of non-existence, and it leaves the reader somewhat unfulfilled.

It is a tremendous stretch from the purely philosophical discussion of the existence of a creator God to assertions of God's nature and desires, and of God's past actions, as are made in the Bible. The number of a priori assumptions that must be made to require that God fit the character of the Bible is stupendous: one must specify God's positions on a vast number of completely arbitrary issues (positions that are themselves often impossible to justify without a holy text to dictate them). However, it is exactly this version of a God that is used by the faithful to argue for a religious foundation of morality. This is implied in every offhanded assertion that atheists are immoral, or less moral than the religious: God dictates morality, and without God, one's morality is arbitrary.

This is an assertion that has repulsed me for as long as I have been aware of it. It is demonstrably false, both from a philosophical perspective and from empirical evidence. I would argue that the opposite is in fact true: I (as an atheist) try to do good because it is good, not out of fear of punishment or hope for reward. I identify what is good through reflection and compassion, and while my complete set of "good acts" may differ in small ways from that of another, I have enough confidence in the goodness of human nature to expect that it will not differ substantially. We each have our own moral compass, and each points in more or less the same direction. (I make exceptions, of course, for psychopathic individuals such as Hitler, Stalin, and more recently, Saddam Hussein. Of course, while the religious like to attribute their evils to atheism -- a demonstrable falsehood in Hitler's case, at least: he outlawed atheist groups, and ranted against the evils of atheism -- the fact of the matter is that these were twisted, evil people, and fortunately such are very rare in society.) Dawkins makes a compelling point on the matter: the Bible is full of contradictions on what is ethically correct, and so one must choose which one agrees with. What one agrees with is guided, either by one's own moral compass or by edicts from one's church, but ultimately, it is and must be guided.

My view of atheist ethics goes further than this. I pity the religious people who do what they identify as good exclusively through hope for reward or fear of punishment. Such a view of morality must result in little short of paranoia. Life is far more than what one understands as a toddler, when every interaction with the wider world revolves around pleasing one's parents. I suspect (and others in the group agreed) that in fact the deeply religious operate more by their own moral compasses than by constant comparison against some Biblical standard of behaviour. They may calibrate their compasses by Biblical standards, but ultimately they operate, to all intents and purposes, autonomously. The religious fear that atheism leads to chaos overlooks the fact that they themselves operate using the same equipment as the atheists, with more or less the same effects. Many aspects of our morality are, I am fairly certain, so deeply ingrained as to be universal: the edict that one must do unto others as one would have them do unto you is one such aspect. Other things, such as conservative sexual standards, are functions of culture: how one calibrates one's moral compass is not ingrained. The only difference is that the religious have an external and absolute set of standards, while atheists must come to their own conclusions.

This leads to the real argument behind religiously-guided morality: that without that external set of standards, people will have differing moral compasses. The religious do not trust that moral compasses will all point in more or less the same direction (aside from the psychopaths, who will not be improved through religious influence). One might say that atheists such as I have faith in humanity, but I would not go so far. Humans are social animals, and all social animals have internal mechanisms to help them to get along with others of their kind. Our moral compass is a manifestation of those mechanisms, and all the more wondrous for it. That it varies, and that it is influenced by others, allows it to evolve.

This brings up another point made by Dawkins: that morality evolves. Darwin was, by the standards of his day, liberal and progressive, and yet he held attitudes toward race that would make modern-day conservatives cringe. As Dawkins put it, the moral Zeitgeist has changed. We see this as a good thing: racial bias (to take just the one example) has proven to be founded in error and has been perpetuated to the detriment of all. The fact that European culture and those derived from it is more liberal than it was a hundred years ago can be argued to be a good thing from any number of perspectives. I would certainly make those arguments myself, but I would also point out that, having been brought up in a liberal environment, I would see any change in the moral Zeitgeist towards the direction of the values that I hold myself as a good one, regardless of the direction of that change. If I were taught from an early age that (say) people of Asian descent were constitutionally untrustworthy, and this was a common belief in the culture in which I grew up, a history of cultural change towards distrust of Asians would be seen as a good thing. The fact that I can attribute such differences to differences and misunderstandings between cultures leads me to believe that, by objective standards (if they can be said to exist at all), modern European morality has improved from its past state, but I must still be cautious of the very real possibility that a perception of positive progress in other values is merely a reflection of them having become more like my own, which may in turn be entirely arbitrary from an objective standpoint.

So, is the prospect of objective morality actually viable? I would like to think that it is, at least for the major issues: respect for the persons and property of others. The Golden Rule ("do unto others as you would have them do unto you") is key here, applied to all humanity. There are many less critical issues, in which I may disagree with others, but my (and most liberals') compass is calibrated by another, relativistic, edict: "live and let live." In other words, I allow others to decide what is right and wrong for them, so long as it does not affect me. I believe that the core of objective morality follows from these two edicts (although I will grant the possibility that I have not -- yet -- identified some further guideline for morality that further refines matters). There are of course situations in which my application of these guidelines differs from another's; further refinement of each compass may be necessary, but I do not believe that objective morality need cover all possible situations. Personal moralities are, I am fairly certain, tied up with personalities, and so cannot be the same for all people; at this point, they are perhaps not properly called "moralities" in the first place. But the fundamentals are the same, for the religious and the atheist alike: we all want to live in a safe place, where we will not be assaulted or robbed or otherwise abused, and that has nothing at all to do with religion. Making the world a safe and secure place is not a mandate of religion: it is a mandate of humanitarianism, something that we all share.

Saturday, 10 November 2007

More Thoughts on Immigration

This is another publication that my father e-mailed me. I have found it online here, and it is another, more direct, screed against immigration across the southern US border. Again, because it is not my work, I will only link to it, but again, I recommend reading it before reading my response.

To begin with, I certainly sympathise with the wish that these people change their own country for the better; I would in fact dearly love to see that happen. However, their situation is far removed from that of the Revolutionary War era colonists. In many ways, ours is the heel from under which these people are trying to escape. America is the idyllic land of plenty, after all, and our patriotic posturing does nothing to diminish that image. We project exactly the image that draws them to us, and we do little to ease their misery where they come from.

I have had my own Mexican border experience. I drove through Tijuana to get to my partner's sister's wedding, and saw from a distance but nevertheless firsthand the abject poverty and desperation that has unfortunately come to characterise that city. That people would want to get away from it is more than understandable; it would be surprising to find anyone wanting otherwise. There is most certainly a problem here, and elsewhere along the border, but the solution to the problem is not merely to make it harder for desperate people to escape their predicament. (I would emphasise as well that I acknowledge that even legal immigration will not necessarily allow them to escape their predicament. This is a deeper and more complex
issue than the right wing is usually willing to acknowledge, one which requires a concerted effort on many fronts to resolve.)

The article implies that all illegal immigrants are drug smugglers, burglars, and vandals. Many may be, but I would be surprised if all or even most were. Mostly, they just want a better life for themselves and their families, and I would not deny them that. These people, as the article freely admits, are desperate. Fencing them out will not alleviate that. Treating them like human beings will. In fact, I am amazed at the lack of empathy expressed in this piece. The allusion to the Boston Tea Party in the last paragraph reminds me more of Marie Antoinette's "let them eat cake": the Americans here simply have no comprehension of what life is like for the Mexicans. Honestly, I may not have a clue as to what life is like for Americans
on the border, and I certainly wouldn't want to live there. But I can tell pretty clearly that the Americans on the border do not know or care what life is like for the Mexicans on the border. I can say with certainly that, however desperate the Americans may think their lot is, that of the Mexicans is considerably worse.

Actually, rereading this article, I find myself appalled at the writer's lack of empathy. "The first time Kennedy saw 30 illegals
dashing across his property, he'd trip over his Guatemalan lawn guy rushing to the Senate floor to demand enforcement"? I would hope not. I would not. I am not "confused", or without logic, or "all emotion." I want for these immigrants no more than they want for themselves: a reasonable chance at making an honest, sustainable living. You want emotion? My emotional reaction to this is that Americans tend to act as though they are a different and superior species from all other
humans on the planet, and this article does nothing to persuade me otherwise. These are *people* that we're talking about here, human beings, not "just Mexicans". I find that this attitude puts the lie to the supposedly superior moral sense that the Christian right likes to pat itself on the back for.

So, how should we fix things? Honestly, this is not a matter to which I have given enough thought to feel competent to suggest solutions. I am not familiar with the legislation in question, and as such will not speculate on its effectiveness. Amnesty and guest-worker programmes are one step, perhaps in the right direction; I am not sure. I would emphasise that I deplore the Gastarbeiter situation in Germany as you have described it to me. Ultimately, the solution there is to make
things in the Middle East better for the Gastarbeiter, and here to improve the lot of Mexico. More than that, we need to recognise the worth of each of these places, to help their natives acknowledge that they need not leave to improve their lots in life. That cannot happen, of course, unless they genuinely can improve their lots in life in their own countries, and we must acknowledge that, to some extent at least, their inability to do so is our own fault. I think that unrestrained capitalism, combined with an almost religious patriotism, is ultimately at the root of the problem. I do not advocate abandoning capitalism (at least not as regards international competition) but it must be regulated far more, with an eye to the living condition that it fosters amongst other countries, if it is to be fair.

The article's bias is likewise apparent in its disparagement of the ACLU and its approval of the Minutemen. I do not doubt that the latter organisation has many good people with genuine concern for their country amongst it, but the fact remains that it is at its heart a vigilante organisation. Yes, we need to patrol our borders more effectively, but we need to do so with accountability, a principle inherently lacking in vigilante organisations. As for the ACLU, I am not sure what that particular organisation's role in this affair is, and this article does not give the impression that its author attempted to find out. I doubt that the ACLU is "confused": human rights are human rights, and are not limited by nationality or legal status, and with the high emotions, low opinion of immigrants, and lack of accountability here, I would be suspicious as well of how people were treated.

To summarise, I think this article is a prime example of how conservativism is anything but compassionate.

Saturday, 6 October 2007

The Next Big Question

Last week I attended the Canadian Institute for Advanced Research's Next Big Question event. It was an interesting idea, one which has fallen more out of fashion than I would have liked: a public lecture on scientific topics. Importantly, attendance was free, and although I recognised a substantial fraction of people in the audience (CIfAR is a funding body, from which many of my colleagues, including both my former and current graduate supervisors, have benefitted), there were a number of people from the community at large, and that was good to see. It was also interesting to hear their questions, which were good but which belied a general lack of understanding about the subjects at hand. This is a problem, of course, but it is exactly this sort of problem that public science lectures are meant to address.

The idea behind the event was to have representatives from different CIfAR programmes answer a (presumably CIfAR-chosen) "Big Question" pertinent to their research. Although there are around a dozen such "Big Questions", only three are posed at each event; the event "tours" major Canadian cities, with a different subset of "Big Questions" asked at each. All are available at the site, and there is much good food for thought there. The three "Big Questions" asked at this event (the first of the series -- so if you have the opportunity, you can still go to future events, and I would recommend it) were: "How do we build a quantum computer?", "What makes societies succeed?", and "How to microbes change the oceans?"

That the questions were chosen my CIfAR and not the speakers was obvious from the first talk, which was not so much about how to build a quantum computer (although that was covered) but why. It is an interesting topic, one about which I am now motivated to learn more, but still one very much in its infancy. A number of strategies proposed for building such computers was presented; the unit of measurement for quantum-computer memory is the quantum bit (or "qubit"), of which the most advanced design has twelve. The most promising technology currently has only managed to produce four. Considering that eight regular bits corresponds to one letter, that is not much, especially considering the scale of problems that these machines are hoped to tackle. Those problems are, of course, the (partial!) answer to the presenter's preferred question: why to build a quantum computer. These included applications in quantum mechanical models and in large-scale simulations, but perhaps the most compelling case was made for cryptography. A quantum computer can crack pretty much any code set up by a regular electronic computer, and it can set up codes that are completely uncrackable by the same technology (I do not recall whether they might be crackable by other quantum computers, though). Impressive stuff, indeed!

The next talk, on successful societies, was unusual even for this event. Not only was the question posed by CIfAR, but the group tasked to answer it was itself the result of CIfAR's own initiative, rather than (as is the more common case) some independent researcher putting together a proposal for the group. This group is impressively heterogeneous, comprising historians, psychologists, sociologists, economists, and even a biologist or two, and its focus is the same as the Big Question that its representative addressed: "What makes societies succeed?" Of course, such a question is impossible to answer without a definition of "success", and so far the group has spent much of its four years addressing just that, and how to identify it in any given society. I was pleased that the definition was not simply GDP or per-capita income: it had to do with education levels, access to health care, lifespan, and so on. Contrasts were drawn between different countries with similar historical and geographical circumstances but which have had different levels of success, and the reasons for the differences are the focus of this group. The talk brought strongly to mind the work of Jared Diamond and Ronald Wright (the latter's book, A Short History of Progress, I cannot recommend highly enough), as well as more quantitative work by Dalhousie's own Hal Whitehead, all of which carries with it the cautionary message that we must change much about our own society if we do not want it to fail spectacularly.

The final talk, by a professor that I had met but had not gotten to know well at UBC, was about microbial biodiversity. The emphasis here was on the sheer volume of unknown species in existence on Earth, a topic very close to my own heart. Furthermore, although we can characterise the processes that occur on our planet on a global scale, much of the details (such as which organisms do what, how effectively, and what happens when they are perturbed) are a complete mystery. Changes in the oceans' microbial life could have drastic impacts on the world's climate, which we cannot now predict because we have only an inkling of how diverse that life is. At the same time, I did not find the talk very well executed; the speaker was very good, but his understanding of some topics was a little light (he is a virologist, and the sorts of errors that he made about eukaryotes were things that only specialists would catch), and some of his more sweeping statements I thought more dramatic than necessary.

At the end of the three presentations, the audience was asked to vote for what they thought was the "Next Big Question". Given my field of inquiry, I was not at all surprised to be in the midst of a show of hands for the microbe talk; I was surprised, however, at how obvious was the majority of hands from the rest of the auditorium for the same topic. The speaker evidently had impressed his audience, and I did feel some pride in a topic so close to my own being appreciated. I felt a bit of a traitor for it, but I did not vote for that myself. Make no mistake: I am in the right field for me. What I study is more interesting to me than anything else in the world, and I enjoy my labwork immensely. However, my vote went to the societal research, because whatever I might discover or establish will not count for anything if there is not a society around to appreciate it in the future. We as a culture are rapidly approaching the point at which we must change drastically or collapse, and how we must change is a compelling question. What probably clinched the matter for me was that the UN has come to this research group, to ask for recommendations to give to some of those less-successful nations that ask why their neighbours do so much better than they. If there is any chance of this group having any influence, it will be inestimably more important than my own field of study.

That having been said, the vote was all in fun: no decisions were made on its basis, and the funding was guaranteed for each group long before these events were even planned. My personal suspicion was that it was a ploy to keep the audience's attention, although I would prefer to think something less cynical. In any event, it was a good experience, and a nice exposure to a generally good idea -- that of making science more accessible, and more compelling, to the general public.

Sunday, 9 September 2007

The Commandments of Science

I have been reading blogs more than is good for me (and I must admit that writing one is not something that I have time for, either), but every so often I come across something that reminds me that, however much time I may spend on them, I am not (entirely) wasting my time by reading blogs. This example was not a post on a blog: it was a comment. The comments section of a blog post is often more enlightening than the post itself, something not realised by people who only read what shows up on their RSS reader. This particular example was on a post on EvolutionBlog on an interview on Fox News discussing Ken Ham's new Creation Museum. The interview itself was somewhat predictable, and not very noteworthy; the post was mainly there to allow those of us unable or unwilling to watch Fox News see how each side presented itself (a service which is in itself much appreciated!). A commenter called Hoary Puccoon, however, wrote a truly remarkable piece. Since I suspect that this is a pseudonym, and since no Web site or blog was given, I fear that this will fall into undeserved obscurity. (I recognise that my own blog is not likely even more obscure than the comments section of a far better established blog, but at the very least this renders it more prominent to me, and any further dissemination that it can achieve is good.) This is the complete comment, with nothing changed except the formatting.

The whole is-there-a-god thing bores me. But why doesn't anyone emphasize how ethical science is-- and how unethical the creationists look to scientists?

The Six (and counting) Commandments of Science

  1. Thou shalt not lie. Fudging data is a mortal sin, enough to terminate one's career.
  2. Honor thy fathers. You must give credit to the previously-published work of other scientists.
  3. Thou shalt not bear false witness against thy neighbor. Misrepresenting another scientist's work merits public exposure and condemnation. (The creationists never understand just how immoral their quote-mining seems to scientists.)
  4. Love thy neighbor. Ad hominem arguments are not acceptable in scientific discourse.
  5. By their works ye shall know them. If Linus Pauling is a legend and Watson and Crick are complete unknowns, whose model of DNA is accepted? W&C's-- because theirs is right and Pauling's was wrong.
  6. Let your yeas be yeas, and your nays, nays. Scientists must define their variables explicitly, and not fudge and say, 'oh, I really meant something else' if their hypothesis is disproven. (This is actually why theism versus atheism doesn't much matter in practicing science. God, whether he/she/it exists or not, is too fuzzy a variable to produce clear results.)

This could probably be worked up to ten commandments, but the point is, scientists, whether theists or atheists, do have strict rules of ethics-- which the creationists constantly violate. This point needs to be hammered into the public discourse. The creationists aren't just getting a few dry facts wrong-- they are undermining the entire ethical basis of science. Letting the fundies get away with claiming they represent morality is, in my opinion, morally wrong.

While obviously aimed towards the creation/evolution controversy rampant in the USA, and something that the creationists would do very well to read and understand, it is also absolutely right about how science works. The only change that I would make is one of ordering; some of the more important issues in discussing creationism are almost trivial (or taken for granted) in discussions of science. Each of these points deserves further elaboration, here in an order that makes more sense outside of the creation/evolution discussion.

  1. "Thou shalt not lie." This is absolutely binding in science. There is in science, as anywhere, room for cynicism, but never when one reports data. This is one of the reasons -- the main reason -- why most papers have separate "results" and "discussion" sections. The "discussion" section is interpretation, and there the scientist may be dead wrong (although s/he must support every significant assertion with data, either hir own or someone else's through citation), but the "results" section is pure fact. It is for this reason that scientific data are never published without an accounting of how the data were acquired. Should the data in fact be wrong, repeating the experiments or observations that produced those data will show that. Scientists demand transparency and accountability. Anything worthy of inclusion in the scientific canon must pass through editorial and peer review before publication, the latter process being undertaken by specialists, often the reporting scientists' competitors. Because of this, it is very hard to get away with a deliberate tampering of data (although it does -- very occasionally -- happen). Incorrect data resulting from a misreading of experimental results, or from the application of an incorrect analysis to such results, are generally dealt with graciously by both the discoverer and the scientists reporting those incorrect data. Should something -- anything -- in the "results" section prove to be a conscious fabrication, however, sooner or later, someone will find out, and their perpetrators' careers are over: nobody will take them seriously again. Scientists are unforgiving of frauds.

    It is worth noting here that faked-data scandals (including the creationists' favourite, "Piltdown Man") are invariably brought to light by scientists. It is for this reason that science is called "self-correcting".

  2. "By their works ye shall know them." There is a status system in science. This is based, among other things, on credentials, networking, position, seniority, and awards. Status in science is never inherited or bought or bestowed. Everyone in science must work for their status, producing and interpreting data and hypotheses that withstand the most exacting scrutiny. Status ultimately comes from one's ability to do that work. Since anybody -- even a high-school dropout -- can challenge any piece of work (assuming that they have novel interpretations or data, that these make sense, and that they are articulated intelligibly), science is in a sense the ultimate classless society. In other words, one must prove oneself, but anyone and everyone is given the opportunity to do so. If proving oneself means showing that a highly-regarded scientist is wrong, so be it. Science values truth* more than status.
  3. "Thou shalt not bear false witness against thy neighbor." This actually follows from the first two points. One must be honest, and one must acknowledge one's sources honestly. Scientists take a dim view to having words put in their mouths. Intentionally misrepresenting others' work is not as bad as making up one's own, but it is still a grievous breach of ethics. For the most part, it does not happen in science, but when it does, it is quickly established as such, and is thereafter ignored.

    Unfortunately, this is not how mass media operates. Non-scientifically-trained writers and editors tend to take things out of context, or to reword things in manners that they may think are paraphases but actually have significantly different meanings scientifically. Corrections in the popular literature often go unregarded, so that a single misinterpretation may plague a scientist for the rest of their career. (The classic example of this is the tendency for creationists to use quotes by the prominent evolutionary biologist Stephen Jay Gould out of context to suggest that he did not believe that evolution was a real thing.) Given the complex and often-conditional nature of their work, many scientists simply refuse to discuss their work with the media. The irony of this is that scientists in general value communication -- which is why they tend to be eager to publish and to teach.

  4. "Let your yeas be yeas, and your nays, nays." Although it may not seem that way to the uninitiated, science demands clarity and simplicity. Much of scientific jargon is essential because it is unambiguous; new terms are always carefully defined before they are used. Of course, words do get redefined, or used in different ways by different scientists; but in such cases, the scientists are always careful to indicate the meanings that they employ.

    Scientists are expected to stand by, and to defend, what they present to the scientific community. They may, and often do, change their minds, but they lose respect if they say that they really meant something that they did not say. To use a metaphor often mentioned in the creation/evolution debate, the goalposts may not be moved. Once terms are agreed upon, they may not be changed, and if an explanation fails to account for any given phenomenon under those terms, it must be discarded. The only exception to this is when additional data can be produced to account for the phenomenon under question.

  5. "Honor thy fathers." Citing others' work goes beyond courtesy. If one did not acquire a given datum, one should acknowledge its source. This allows for the data supporting original ideas to be investigated, to determine whether or not they actually apply to the new idea. If one is arguing for or against an idea already articulated in the scientific literature, one should indicate whose idea it is, which allows for arguments both for and against older ideas to be interpreted in the context of the ideas' original construction. It also allows for those whose ideas have been misunderstood or misinterpreted to present their arguments explaining that.

    All of this pertains to an aspect of science not commonly appreciated amongst the lay: it is a social enterprise. Many scientists are intensely competitive, but all acknowledge that, ultimately, science is a collaborative process. Everybody has access to, and can use and interpret, everybody else's published data. Progress cannot be made otherwise.

  6. "Love thy neighbor." This is actually not that important in science itself; it is more a question of style than anything else. The expectation actually goes further than this, though. In the scientific literature, one never refers to others except through their publications. All that matters in science is science; the personal lives of individual scientists are irrelevant. Scientists have friends, but friendships are acknowledged at most in the (invariably brief) "acknowledgements" section of scientific papers. Everything else in a scientific publication is regarded as timeless, outside the scope of personal activities and allegiances, and anything that does not directly affect the work being published is omitted. Such matters impede papers' being relevant and understandable indefinitely, which is as close to immortal as any scientist can hope their work to be.

I am fairly certain that I will want to re-order these, probably soon after I hit the "post" button. (Arguments about this order will be gratefully accepted!) I make exceptions for the first and last points, which will always be first and last. But overall, it is a good list (and much tidier than mine in its original presentation). I will be happy to see it get more widespread dissemination.

* "Truth" is a somewhat dangerous word to use in descriptions of science for the layperson. In science, "truth" is always provisional, "proof" always conditional. This is not to say that scientists are necessarily postmodernists; indeed, I would argue that science is inherently opposed to postmodernism. Rather, scientists accept that the world around them is a real place, and that it operates in a consistent fashion. What scientists regard as "true" is their best understanding of how independently verifiable observations and/or experimental results fit with one another. New observations or experiments may require the re-evaluation, and sometimes indeed the replacement, of established understandings, but such understandings did not become established without having already proven themselves consistent many times over.

Saturday, 1 September 2007

Some Thoughts on Immigration

A while ago, my father and I started to send each other links to political opinion pieces. My responses to his posts quickly grew in length, and I flatter myself to believe that others might find them of interest as well. So, given that I plan on discussing politics on this blog as well as science, I will repost my responses to my father's findings here.

This first article is one about immigration into the USA. This has been a popular rallying point for American conservatives of late; both sides of the issue are certainly prone to agree that there is in fact an issue, that illegal immigration is a problem. The article sent to me by my father, though, presents another angle. Since it is not my work, I will only link to it here; should that link not work, a quick search is likely to turn the article up. It regards the "immigration crisis" in the USA, and compares it to the situation in South Africa. The author, however, seems to think that SA was better off under apartheid, and has a surprisingly negative view of Nelson Mandela. I encourage my readers to read the whole thing first. My response to it follows.

I find this article interesting, in many less-than-complimentary senses of the term. Certainly, there is a germ of truth, but come on: Nelson Mandela is about as evil a man as Ghandi or MLK. Granted, neither of those men resorted to armed conflict, but Mandela has been a paragon of civility, thoughtfulness, and humility after he was released from prison. He has gone so far as to stop his own ANC from censoring references to their violent history. His days of inciting "revolution in the streets, strikes, civil unrest and... sheer terror and murder" are long over, copiously apologised for, and in all likelihood necessary. In the years since apartheid fell, South Africa has continued to be one of the saner places in Africa. Granted, it still has a long way to go, but if I were to settle in Africa, SA springs right to the top of the list of places to check out.

There is a substanatial difference between the USA's "immigration crisis" and SA's apartheid. Most prominently, apartheid was an appalling oppression of native peoples by a colonially-derived minority. The USA, on the other hand, is a nation of immigrants (save for a tiny few natives, hanging on to what shreds of land, culture, and respect have been left them by our colonially-derived majority), and the discrimination of immigrants from anywhere but the places from which the original colonists came has gone on for as long as those original colonists (and their descendants) have been on this continent. We no longer denigrate the Irish, Italians, or Jews, for instance, while Latin Americans were not an issue until recently. The
discrimination has persisted, although its targets have changed. The USA, and its particular flavour of Western culture, did not collapse as a result of a lessening of vigilance against cultural encroachment by any of those groups, and has arguably been strengthened by it.

That having been said, there is a substantial difference between the current and previous "immigration crises", in that Latin Americans come from the same continent, and so are able to arrive under their own power, often illegally. I do not question that this is a problem. However, I also do not see that allowing Latin Americans to immigrate legally will hurt things. We have been very bullish on free trade, generally without consideration of its consequences in other countries. Free trade has resulted in a widening of the gulf between the developed and developing countries, and an inevitable consequence of that is that people in the developing countries will want to move to the developed ones. The only way that free trade can also be made fair for all is if people are also allowed to move freely over borders; until we allow that, we are asking for those whose livelihoods we have rendered harder and harder to want to come here all the more desperately. If we are not to change our trade policies, we will have to deal with these unwanted immigrants one way or another. Like distributing condoms to teenagers or clean needles to drug addicts, I believe that it is better to deal with our problems in a conciliatory but humane and (most importantly) effective manner, rather than repress or deny them.

Do I worry about them changing our culture? Not terribly. One of the things that I have grown to appreciate from living in Canada is the extent to which the USA is truly a "melting pot", in which cultural differences do not persist beyond a generation. Maybe the average skin tone will become a little darker in the USA, maybe Spanish will be a more common language, maybe the percentage of Catholics will rise, but not so much as to overwhelm the current culture. I would go
so far as to say that America's cultural strength comes in large part from its assimilation of other cultures. There will always be those that resist the most prominent group being assimilated at any one time, but what they regard as "normal" contains a good deal of what their parents were resisting before them.

Meanwhile, I found much in this article to reveal more than was perhaps intended. Its author is obviously a social conservative (she puts gay rights in the same basket as pornography, for instance, two "problems" of very different nature). She has a shockingly dim view of non-Whites, implying that they do not share with us a desire to live peacefully and safely. Yes, there are many "primitive" aspects of indigenous African cultures, many of which really should be abolished (female genital mutilation, for instance, or some of the superstitions about health). There are also positive aspects of those cultures; the fact that I may not be able to name them does not mean that they do not exist (I am not an anthropologist, after all!), but I would be very surprised if they were not there. South Africa has many problems, but it is not as "broken" as this author implies, unless one is a white supremacist, as she appears to be.

I did a little bit of Internet research on "Gemma Meyer". This is the only piece of writing available attributed to her, and what is included here is the only bit of biography. She has no entry on Wikipedia. I suspect that "Gemma" is in fact an invention to lend credibility to this piece's reactionary stance. (The reactionary nature is emphasised by its being republished on a neo-Nazi site as well.) The only thing that implies otherwise is the article's lack of American optimism, but I am sufficiently cynical as to suspect this to be an attempt both to give the piece added realism and to spur American conservatives to more concerted action. I may well be wrong, but in any event I do not believe that this author is a reliable source.

Comments are welcomed!

Sunday, 26 August 2007

The Meaning of the Word "Opisthokont"

The name that I have chosen for this blog is bound to be an unfamiliar term for most people. It probably represents an unfamiliar concept as well, so I will start gently. It is a term that denotes a specific, large, and (to humans) very important group of organisms. The importance of the group is probably understandable once one understands that humans are opisthokonts. So, however, are all other animals. So are all fungi! Rounding out the group are a number of single-celled organisms known to be related to either animals or fungi or both. Notably absent from this group are plants, algae, and quite a few other organisms, including all bacteria.

What can animals and fungi have in common that plants do not? Well, think of a sperm cell. This is a tadpole-like thing, with a roughly spherical cell body and a single, tail-like flagellum trailing behind. The cell swims by wiggling its flagellum, again much like a tadpole swims by wiggling its tail. As it happens, this is a very unusual cell type. Most other flagellated organisms swim with their flagella in front, pulling themselves through the surroinding medium. Only the flagellated cells found in animals, fungi, and related microbes swim with their flagella behind. This gives rise to the name: "opistho-" means "behind", and "-kont" refers to the flagellum.

One could easily be forgiven for finding this a minor difference, given everyday experience. To most of us, animals are things that move around and eat things, and plants and fungi are rooted in the ground. However, there are animals that are rooted to the ground as well (including sponges, corals, and sea squirts), and animals that do not eat (such as some of the worms living near deep sea hydrothermal vents). There are fungi that do not grow in the ground (yeasts are fungi, for instance, and do not root themselves in anything). Everyday experience, it turns out, is insufficient to categorise life; science has moved well beyond that.

Science has taken its time to get to where it is today, though. Decades ago, fungi were classed amongst the "lower plants" because their cells are surrounded by rigid cell walls, a characteristic then thought to define a "plant". However, it has since been shown that the materials that make up those cell walls are completely unrelated (they are derived from sugars in plants and from proteins in fungi, for instance). More importantly, the organisms indisputably most closely related to each, which look like single-celled versions of their better-known counterparts, lack any vestige of the cell wall. In other words, the common ancestor of plants and fungi did not have a cell wall; this character is a homoplasy, something that evolved more than once in the history of life.

Genetic analysis confirms this. Most hypotheses of evolutionary history (of extant organisms, anyway) are now made by having computers analyse the DNA of comparable genes from different organisms, and these tend to connect animals to fungi, to the exclusion of plants. (There are exceptions -- there are always exceptions -- but those are from genes with a lot of evolutionary "noise". In other words, such genes are either not large enough or evolve too quickly to retain enough information to resolve the animal/plant/fungus relationship with any reliability. There are statistical tests that indicate the trustworthiness of these computer analyses, and those which are judged acceptable almost always support the close relationship between animals and fungi.)

Analysis of genes goes beyond using them to reconstruct evolutionary history directly. For instance, there is an insertion into one of the genes used in the replication of DNA, an extra stretch of about fifty nucleotides (the "letters" of DNA's "alphabet"), which is found in animals, fungi, and their close relatives, and nothing else. This might not seem particularly important, but the gene in question is important enough that it is not prone to change easily (in scientific parlance, it is "evolutionarily conserved"), and perhaps more importantly, the insertion is itself conserved. In other words, the same nucleotides (or some obvious derivation of them) are present in the same place in all opisthokonts.

Non-genetic data helps link the two groups as well. The architecture of individual cells in the single-celled relatives of animals and fungi is strikingly similar, both inside and out. This was not apparent until the advent of electron microscopy; many of the features that link the two groups are either too small to be seen with a light microscope (the "regular" kind) or are easily overlooked in favour of other, more striking features, many of which (like the cell walls already mentioned) can be taken to imply connections that do not hold up when investigated through other techniques.

These features include the arrangements of the components of the cytoskeleton, a set of protein-based rods and tubes that gives a cell its shape. The arrangement and replication of the flagella is also thought to be a conserved trait. A substantial part of my graduate work is investigating these things; while the coherence of the opisthokonts as a group is nowadays almost beyond question, the uniqueness of some of its defining characteristics is simply not known. Electron microscopy has not been around long enough for much data to have been generated, and most of what has been observed focuses on a few well-known organisms. Those organisms that can tell us the most about the relationships of living things are often obscure and poorly studied, a situation that holds perhaps nowhere more strongly than in this case.

But there is one feature that is readily observed and consistent, and that is the number and position of flagella. Like I mentioned, most organisms have flagella at the front ends of their cells, and pull themselves through their surroundings with them; opisthokonts are unusual in pushing their cells through their surroundings. Furthermore, most non-opisthokont cells have flagella that appear in twos, or are obviously derived from ancestors that had flagella in twos, while all opisthokonts' flagella appear without any others associated with them. These may not seem like significant things, but one must bear in mind that, when discussing the divergence of animals and plants and fungi, we are discussing the evolution of single-celled organisms. In that context, seemingly unimportant things like the position and number of flagella can be highly significant.

So, classifying something as an opisthokont is not a natural thing for most people. It may seem like an obscure and unimportant distinction. Classifying animals and fungi as each others' closest multicellular relatives has (so far) no known consequences to medicine or agriculture or anything else that most people would notice. But the opisthokont hypothesis is, as far as we can tell, an accurate description of the relationships of living things: it is our best understanding of the relevant facts, and the closest that science can come to the truth.

Sunday, 24 June 2007

Who I Am

There is a tradition amongst computer programmers that the first program written in a new language simply displays, "Hello world!" Unsurprisingly, it is referred to as a "hello world" program. In the spirit of pioneering computer geekiness, then, this is my "hello world!"

At the same time, this is not quite my introduction to the blogosphere. I am a long-time lurker at Pharyngula, and I have a LiveJournal account as well, but this is my first foray into the realm of serious blogging. As such, I should introduce myself to the blogosphere as well.

I am an American atheist living in Canada. My political leanings are so far to the left that they do not fit on the American spectrum (in other words, roughly in the middle of the European spectrum). As such, I expect to comment a fair bit on the inanities of the American right wing. Presently I am studying for my Ph.D. in biology, investigating the evolutionary relationships of microbes (for more details, see my posts). I get to play with electron microscopes and sequence genes. It is as much fun as one might imagine!

In fact, I may have quite a lot to comment on very soon. Today is the first day of the big annual conference of the Society for Molecular Biology and Evolution, followed by another two conferences, which will keep me interested and involved for the whole week. I have already attended a fascinating talk on human migration, and chatted with some of the luminaries of my field about my thesis project, and expect much more excitement to come. Stay tuned!