Tuesday, August 26, 2008

Giving Yourself to the Algorithm

My mind is going in a thousand places at once at the moment, but I feel like I should put down a little of this on paper/electronic bits.

So, as I've said before, my undergrad background is in philosophy & religion and psychology. I'm in grad school now for a masters in religious studies, but am splitting my time between that and cognitive sciences, as I'm pursuing a Ph.D. in cognitive sciences, probably cognitive psychology, but I'm looking at places where most professors are in the field of neuroscience, as that's the area I'm interested in, and cognitive psychology and neuroscience are trending towards merger anyway.

The areas I'm primarily interested in are perception and memory. These are intimately linked fields, and also tend to go hand-in-hand with issues of learning. Cognitive psychologists since Hermann Ebbinghaus have studied memory (often by rigorous self experimentation), and have come to some surprising conclusions - the spacing effect being one that interests me a great deal. Basically, this is an important combination of experimental knowledge about the learning curve and forgetting curve. This tells us something very important about how best we learn. Combined with the insights of other cognitive psychologists like Elizabeth Loftus and Robert A. Bjork, we should by now have actually implemented some of what we have learned in our methods of teaching.

Have we? Oh, hell no.

You see, cognitive psychologists, historically, have lost out. We haven't been listened to all that much. Part of the problem is that while we have excellent experimental evidence of how best to learn and retain information (remember just before you forget something), it is impractical (or at least incredibly hard) to do this outside of a laboratory setting. "Just before you forget it" sounds like a very vague statement, and is indeed difficult, at first, to quantify. Ebbinghaus paved the way, and we've refined it since then. The answer to our problem, as it has been often before, is to use computers. A complex algorithm can calculate this curve for an individual relatively easily. At that point, it is merely a problem of sticking to a regimented schedule.

Now, briefly, I want to clarify what I mean by "learning" and "knowledge". Knowledge is a thorny topic, as I'm sure The Rooster can tell you. Here, I'm going to avoid the problems of the word itself and simply refer to any facts/procedures/information that you take in. Thus, in this case, knowledge need not be "true." It is simply information which you are interested in taking in, storing, and recalling. In case you're wondering, that's basically what I mean by learning here - effectively taking in information, storing it for as long as need be, and then being able to recall it at will. Now, let us think about this...

Most people have little problem with taking in information. In the absence of learning disabilities, such as dyslexia, we have hardly any problem with taking in information like addition tables, multiplication rules, grammar rules, etc. Storing information was thought for a while to be possibly a problem...however, we know are getting increasing evidence that the actual storage capacity of the brain is not something we need to be concerned about. It is not infinite, by any means, but large enough so that we needed be concerned with it. This has largely to do with the way that the brain forms connections between neurons - something that we call long-term potentiation. Increasingly, we are seeing that there is an interaction between patterns of firing and specific neurons firing. This is incredibly over-simplified, as I don't want to get into the neuroscience of memory or recognition at this moment, and would rather stay at the more abstract psychological level.

So, our problem is really recalling information (isn't it always?) It is unlikely that once something is actually committed to long-term memory (this is a psychological short hand for a lot of complicated neurobiological activities) that we lose that storage. Instead, we lose the ability to recall the information (again, psychological shorthand. This is why in the modern day, you really have to study both to speak with any kind of knowledge about the subject, and design some very interesting studies). Now, long-term potentiation depends upon the repeated simultaneous activation of communication between neurons, so, obviously, repetition helps. We know, however, that pure repetition is not enough. Constant repetition is merely keeping the information in your working memory (this usually involves a different brain region), the way you repeat a phone number to yourself before you dial it. If anything interrupts you, for even a second, you may completely lose the number. Long-term memory is different, though teasing the two apart, and how exactly something gets from short-term memory to long-term memory is quite a complicated process. Look up the history of this type of work, it's fascinating.

So...we have been almost blasted fools in our teaching methods for years. We know that cramming doesn't work. We know that with a careful schedule, we can use the spacing effect to our benefit, but it's hard. It takes dedicated and individualized effort, but it's possible. Most teachers do not do this, because it is so impractical and hard to implement. And it takes a lot of individual effort on the part of the student. Also, there is a huge movement to say that "mere memorization" is nothing. Here's where you can take an interesting tack - memorization is learning in quite a few situations, and forms the bedrock upon which more important theories and creativity can be built. For example, you have to memorize the alphabet and a certain amount of words in your vocabulary to be able to read. If you did not, you would have to look up every letter and every word to process this post. Let's be thankful for that memorization, at least. When you memorize something in this form, it becomes almost automatic in recall. It is important to differentiate between spoken and written language in this case - different neuroanatomy comes into play. Likewise, mathematics becomes an automatic skill. The further you progress in math, and the more you use it (the same with reading), the more automatic it becomes. It is the same with just about any body of knowledge. The less you use it, the more it fades into a state that is difficult to retrieve.

For instance, I know Latin, Hebrew, a little Greek, and am learning German. I find if I take a month off from reading anything in these languages, it takes quite a while to get back into any sort of fluency. If I take a summer off, then I have to go back to remind myself of some basic grammar rules before I can read them. A year, and they seem quite impenetrable without further reflection. Wouldn't it be wonderful to just be able to recall anything at will within a few months.

Well, I think that this is slowly becoming possible. Check out this site, SuperMemo, a program created by Piotr Wozniak. Wozniak has undertaken an extreme form of self-experimentation, in the form of Ebbinghaus. And does it work? If you stick to the schedule, yes...with amazing results. Check out the May 2008 (16.05) edition of Wired Magazine for a treatment of the subject.

Wozniak has made a breakthrough of sorts - the realization that the brain operates in a way similar to computer networks (vastly more complicated, and neurons are not really like semiconductors, but they do perform some complicated integration functions and can operate like complex networks of boolean gates). By breaking down the learning process to an algorithm, and using a computerized helper, you can train yourself to learn better. By giving yourself up to the algorithm, you can take use the mechanical interactions of your brain to your advantage. This sounds mildly religious (in the John Dewey sense), and in that way, it probably is. You have to give significant time and ritual to it, if you want it to work. The problem is that this will significantly destroy your chance of ever having a "normal" social life.

This is a departure from what most people thought computer-aided learning would be. The idea was that we would use machines to store all the information that was trivial to us and free up space in our brains for real learning. The problem is - what are we using that space for now? Not much, in most people's estimation. Computers have freed up our time, but we haven't progressed much in learning, unfortunately. Wozniak wants to turn this around - use the computer to boost our own natural abilities, our own brains. Once you accept that the mind and the brain are really the same thing in basically every "conscious mind" process you want to talk about, then you can learn to use this to your advantage - all the messy, mechanical brain processes that contribute to our consciousness and learning.

It takes dedication and effort, but it is possible...if you're willing to give up on other elements of your life.

Any thoughts?


Monday, August 25, 2008

Epigenetics 101

In response to The Rooster, who I am glad to hear from again, let me also suggest this adventure into Blogging Heads, a discussion between PZ Myers and Abbie Smith, two researchers and people that I deeply admire and respect. I suggest you all put these two people on your blog-rolls, and check on them often. Great posts, great ideas. This one took place a while ago, but, hey, Rooster helped me remember it. Thanks!


I mean, what happened?

So, it’s another leap year, which means it’s another election season. I’ve lived long enough to really remember a couple such seasons. Of the seasons I can really remember, one feature always stands out that defines an election process: the slander. It seems that elections have become increasingly focused on which candidate/party can throw the most mud on the opposing candidate/party.

I guess the reason I decided to write this is due to a commercial I just saw while watching the Democratic National Convention. It was an ad put out in support of John McCain stating that despite increasing food prices and shaky social security, Obama wants to increase our taxes. It ended with the now-common question, “Is he ready to lead?”

My thoughts below the fold.

Now, correct me if I’m wrong, but wouldn’t increased taxes actually help us? People gripe and complain about having to pay taxes, but do they think about where that money goes? Do they think it is any coincidence that countries with higher tax rates (such as pretty much all of Europe) have better health care and often better standards of living?

People are complaining about the cost of gas, and often cite an overbearing tax on fuel. Well, since that tax goes towards paying for roads and highways – building better roads, keeping them in good condition, paying for law enforcement, etc. – I’ll happily pay it. Then the people look at Exxon’s profits and don’t really get angry at that link between those profits and gas prices. I find that odd.

With the economy as far down the toilet as it is, I personally would be in full support of increased taxes to try and remedy these problems. Hell, take half my paycheck if it means I’ll have full healthcare when I need it. I can pass on the beach house and new car. Just don’t raise our already unsolvable national deficit by borrowing more money from foreign powers that may not be that friendly towards us. That tactic may just have something to do with our current problems. (The war in Iraq is the first war in United States history that has been fought without raising taxes, and instead riding on foreign loans. The economy has done well because of it, huh?)

With the tax rant out of the way, let me address the smear ads. First of all, I put my fullest respect behind Obama for his resistance to engage in such acts despite the relentless attacks made by McCain’s campaign. With Biden as the VP nominee, we will start seeing the Democrats lobbing some bombs towards the Republicans, which does sadden me, but I can see the need in the current situation.

Where did we go wrong with our politics? Was it when we allowed corporations and religions to weed their way into our government? Was it when he with the biggest moneyclip was best fit to lead? I really don’t know, but it is despairing. And I know there is a lot to politics such as this, and far too much to get into for a short post like this...maybe some other time.

Now, here I may slip a bit towards a political leaning, turning this blog from an attempted neutral to a more Democratic tone. But, on the question of “Is he ready to lead?” I present to you a counter question: is a 72-year-old hawk who believes a gas tax holiday will relieve the people and who can’t remember how many houses he owns fit to lead?


Metaethics 101

For people interested in moral philosophy, this is a great conversation about a view called moral realism. My only problem is that Loeb and Railton both seem to assume that if moral propositions are truth-apt (can be true or false), then they must refer to entities or properties that belong to a mind-independent world. However, there is a family of metaethical views called 'cognitive irrealism' which claims that moral propositions can be truth-apt without referring to intrinsically normative features of the world. In any case, this video is an excellent introduction to metaethics for the non-specialist.


Sunday, August 24, 2008

A Response to Another Blogger

As you may have noticed from this post, Tom Sheepandgoats and I have been engaged in an ongoing debate. I have to say the debate has been quite civil so far, which I'm very glad for. I've enjoyed it. Tom recently posted on his own blog a bit of a response to the debate as a whole, and specifically about some things that Okada said. I responded, and as the response was really long and deals with several issues that I've been meaning to cover here, I'm going to repost my response below the fold.

So, go read Tom's post, or re-read the original debate, and then come back.

Back? Good, here we go:


I, likewise feel compelled to respond to this, though probably not for the same reason that Okada has.

First off, I think it is entirely a false premise to say that we, as atheists, or even just as human beings, do not object to the types of things that parents indoctrinate or inculcate in their children. You list a large array of things that children apparently pick up from their parents. Let me also include racism, fanaticism, hatred, bigotry, zeal, jihadism, strong nationalism, etc, etc.

I indeed object to indoctrination in all of the above cases, as well as in those cases where parents teach their children to not value education and learning, or curiosity, or creativity. I am disappointed in quite a lot of things about the way that children are raised. Religious indoctrination is merely one item. Do I speak for all atheists? No, certainly not, just as I assume that you do not presume to speak for all Jehovah's Witnesses. Most of the atheists that I know, however, would like to not even have to argue about modern religion, much in the same way that we don't have to argue about unicorns, leprechauns, Thor, or Zeus (most of the time). We would like not even to have to label ourselves atheists, in the way that I imagine you do not label yourself an atheist for all the gods that you do not believe in (although, technically, you would be defined as such.)

In fact, I am horribly disappointed my a lot of other atheists, as I am disappointed by my fellow Americans, and my fellow human beings. Atheism is merely one part of my identity, and it is in no way consuming of most of my thought. Unfortunately, however, I feel the need to continually bring it up and argue from the non-religious point of view because religions, now more than in a long time, are encroaching more and more in our laws, government, and public life. Also, there is a very strong belief prevalent in at least America that atheists are somehow sub-human and not to be trusted or sometimes, even allowed to live. That is a viewpoint that I will argue against for as long as I am able. But, likewise, I argue just as strongly against alternative medicines, legal issues, especially those involving the Constitution and Bill of Rights, and scientific topics.

Another important distinction to make about religious indoctrination is that the consequences for disagreeing with your parents is much greater than for other things. My father was very much a Ford man for most of his life. I like Jeeps, and now whatever gets better mileage and will get me where I need to go. Dad has in fact changed his mind as the years passed, and he hardly gave me any problems for not agreeing that Ford made the best cars in the world. I am not as conservative as my parents, as we do debate certain issues, but I have not been disowned for not agreeing with them. However, religion is another matter entirely. There tend to be much more significant consequences, both in the family and in the larger community, for leaving a religion or disagreeing with it. This can range anywhere from constant shame and guilt, to disfellowshiping, to a death penalty. If there are any other groups out there that are willing to kill or completely disown their children just for forgiving them, then I am equally against them. I do not think that any child should have to live with the fear of losing their parents' love, or losing their life, because they disagree with their parents, either on religious topics or otherwise. That is my stance, and hence, one reason that I argue against the religious indoctrination of children.

Likewise, sometimes it in fact is the case that people other than the child's natural parents have their best interest at heart. This is why we have social services, to take children out of homes where they will be abused or neglected. Natural parents do not, always, mean the best parents.

Also, as to:

"With religious yearnings nearly universal throughout human experience, it really is a fantastic idea to suggest that failure to break that pattern amounts to child abuse!"

Racism, for most of human history, has been nearly universal. Should we have, likewise, thought it ignorant, arrogant, or terribly wrong to try to teach children differently? You yourself have often said on your own blog that religions throughout the world have promoted divisions and hatred. I would find it odd that you call yourself an evangelical and yet would not say that you want the very same thing that we do? To "break the cycle" of most of this indoctrination? You want converts to your religion, we want converts out of religion. Whether that means atheism, agnosticism, or just a strong appreciation for humanity, it doesn't really matter to me. I am not horribly tied to my atheism, and if someone could actually convince me of the existence of a god, I would certainly change my mind.

And yes, let me use some buzz words: critical thinking and scientific evaluation. Presumably you want those you are evangelizing to think critically about their own faith. We want people to think critically about everything - not just their religion, but their political leanings, their ideas about medicine, and every scientific study that comes out. No one should get a free lunch.

I completely disagree with the statement that you are not "invited to consider" the fantastic improbability of evolution. In fact, evolutionary biologists, including Stephen Jay Gould and Richard Dawkins, have written entire books on this topic, and mention it quite frequently in their books. However, there is another important fact to consider. Let us consider a crystal - any crystal is an incredibly highly ordered arrangement of atoms. Statistically, that any crystal at all should exist by chance in the state it exists is vanishingly improbable - impossible by any stretch of the imagination, you might say. But, the crystal exists. And it has to exist in some state. Therefore, no matter how unlikely any one state is (and they are all equally implausible), one of them has to be correct. There is an entire field of chemistry and mathematics dedicated to this: statistical thermodynamics. I encourage you to read some non-technical treatments of it, as it is quite fascinating. There is another important point, however - crystals, as well as organic compounds like DNA, and evolution, is not governed entirely by chance. Crystals, molecules, and evolution are all guided by physical laws - the laws of physics and chemistry, and by natural selection. Mutation only allows for new variation, as does sexual recombination (otherwise, your children would be nearly perfect clones of you. I assume that you are willingly to admit that your children vary to some degree from you and your wife, and it is that range of variation upon which natural selection acts - as well as numerous other factors. Genes are one level of abstraction back from what selection typically operates on - it is the ultimate cause of evolution, but most often we do not directly see selection happening on the genome itself.)

Are mutations rare? Certainly. I take issue with the rest of this paragraph, however - "Gene replication seems accurate almost to perfection. "Typically, mistakes are made at a rate of only 1 in every ten billion bases incorporated," states the textbook Microbiology. (Tortora, Funke, Case, 2004, pg 217)"

I do not know of any case where only a single gene is replicated. I am forced to guess among several options of what you mean - translation from a gene to mRNA? There are errors that can occur here, certainly. Replication of all the chromosomes when a cell divides in mitosis? There are errors that can creep in here as well. However, the most important one, for the sake of evolution, is the process called meiosis, where germ cells split into gametes, and yes, mutations, as well as recombination, happens here as well, producing a large amount of variability. As for your quote that mutations occur only in 1 for every ten billion base pairs incorporated, this possibly a true but misleading statement, in the same way that moon hoaxers say that Hubble has never imaged the moon to search for the landers or rovers (completely true, but misleading, as Hubble cannot resolve that small of a detail, purely do to the laws of optics). The human genome has about 3.5 billion base pairs. Imagine, for a moment, all the eggs and sperm that are created over a lifetime - each one with another splitting of the genome. At least one mutation, statistically, would have to occur for everything three eggs or sperm. I don't think I need to remind you of the vast number of gametes that are in a typical man's ejaculation. Thus, it is statistically likely that every child (or every other child) will have at least one mutation. However, in fairness, I would like to see the entire context of the quote that you pulled this from, as it seems like a very isolated fact. Is this on average? An average rate for humans? In what kind of cells? Without this kind of information, this fact, in isolation, cannot be evaluated accurately or fairly.

Indeed, a fair amount (perhaps a great amount) of mutations are at least slightly deleterious. The majority of sexual acts do not lead to viable children, and the female body aborts a great number of fertilized embryos before they attach to the uterine wall, after they have attached, or at some time during the progression of the pregnancy. Miscarriages are the most spectacular example of this, but the rate of successful reproduction is statistically quite low. Nevertheless, if you have children, I feel that you will agree that children are born because people keep trying, and those mutations that are only slightly deleterious, or only cause harm later in life, or are completely neutral, or are slightly beneficial, or are very beneficial all get through. Slightly deleterious does not equal inviable, and sometimes, these can lead to beneficial traits depending on the environment. What's the evidence for this, you might ask? Sickle-cell is the most well known. A single mutation that causes anemia, but protects the body against malaria. All those children who did not die of malaria lived long enough to reproduce, and now in areas of the world that are heavily infested with malaria-carrying mosquitoes there are populations where sickle-cell anemia is ubiquitous, despite the costs of anemia.

Thus, "So such errors are not only extraordinarily unusual, but also only a similar infinitesimally tiny proportion of such errors are beneficial....that is, useful for evolution. And any winning mutation has to be beneficial enough to confer upon its recipient a significant trump in the "struggle for survival."" is completely inaccurate. A mutation need not be obviously beneficial to be useful for evolution. We recognize now more than ever the influence of genetic drift - that is, the random drift of genetic differences in a population that can lead to speciation. Likewise, "significant" is a misleading word. Any population model will show you that even a marginal benefit can exponentially spread through a population because reproduction, and things like the weather, are iterative functions, and small differences add up over the long run (this, by the way, is why predicting the weather more than a few days in advance is mostly a futile effort. Initial factors are hard to assess, and any small change can very rapidly spread through the whole system.)

If you need some more evidence for this, I suggest looking up Richard Lenski's most recent paper on his 20 year experiment with E. coli bacteria. He evolved one population to feed on citrate, a trait which no E. coli ever has done before. The process took about 20 years and 44,000 generations, and it only happened in one of his twelve populations. It came about through three mutations - one that was slightly deleterious and decreased the overall fitness of the bacteria, another that was entirely neutral, but set the stage for a third mutation, which in combination with the previous two, allowed the bacteria to create an enzyme to digest citrate, leading to the run-away reproduction of that population of bacteria. And yes, he has documented and copies of every generation of each population for the entire twenty years. He's even willingly to loan out populations, if you would like to run the experiment yourself.

I am not calling you, or anyone else, a "superstitious ignoramus." I think you are probably ignorant of advances in the field of evolutionary biology, but I am likewise. As I've stated on my own blog, ignorance is forgivable. Refusing to educate yourself (and I'm not saying that this applies to you), and then arguing against a position, is entirely unforgivable.

"These “probability” arguments, however (and there are many of them) are entirely inadmissible to science! Not because they are not weighty, but because science has no way to weigh them. They don’t adapt themselves to the scientific method, with its insistence on repeatable experiments." Again, wrong. Science is entirely a probability argument. We are sure that our standard models of physics are probably right, at least mostly. We are sure that our understanding of gravity is probably right, as we as we have been able to study it. We are sure that our understanding of evolution by natural selection is probably correct, due to the evidence that we have thus far, and its strong predictive value. All of these things, as all scientific theories are, are probability assessments of the likelihood of the theory being correct. Every experiment that is conducted, every prediction that turns out to be right (and in the case of evolution, I highly recommend that you look up Neil Shubin's finding of Tiktaalik for such a case), every time we make a prediction into a new area on which we have no previous evidence and it turns out to be right, every time we find new evidence that we previously had no idea about and it falls in line with our theory...these are all cases in which we are made more confident that our theories are correct. But they are always falsifiable, and we are always willingly to give them up (and yes, indeed, sometimes grudgingly) when new evidence comes around that contradicts our theories. Do not take this to mean that a single experiment with a negative outcome will completely overturn a scientific theory. There are a thousand reasons why an experiment could come up with a negative result, and most of them are due to experimenter or methodological errors. If you want to overturn a scientific theory, you have to do it the hard way, the scientific way, and establish a literature as strong (indeed, stronger) than the literature that precedes it. Einstein was not immediately accepted - he had to prove his case. What he had an advantage in was that relativity resolved several problems with observed celestial phenomena, such as the erratic orbit of Mercury. Likewise, Darwin was not immediately accepted - but he had the weight of evidence, a plausible mechanism, and strong predictive value on his side. This is not to say that evolutionary theory has not changed - in fact, Darwin may recognize only a little of it by now, especially since he had no understanding of genetics. The point is that every time we test evolutionary theory (and we do, daily), we find more supporting evidence for it.

Does this mean it is dogma? No. It is always possible to overturn. This is a problem that I often have when arguing with people who are not in the sciences - they think that scientists are all dogmatic thinkers and just toeing the party line. I think this shows that the person has not met too many scientists, been to any scientific conventions, or watched debates. We're contentious people. We love arguing. We love proving other people wrong. If nothing else, you could appeal to human greed - we'd all love to win that Nobel Prize. And how do you do that? Mostly by proving older scientists wrong. Science advances in this way. When you're constantly getting more evidence that you're correct, it gets boring. Every time we confirm Einstein, we're glad to have that confirmation, but we're all a little sad too - they're nothing new to learn. We don't appreciate "Eurekas!" or "Just as I expected" anywhere near as much as we love to hear a "Huh, that's interesting..." or "Man, I don't get this at all!" There's something new for us there, something else to figure out. Plus, it keeps us employed. Trust me, if anyone out there could actually disprove evolution, they would be jumping at the bit - a Nobel Prize, a new field of biology, and all the fame they could ever want. You say most people are guided by their lower emotions and desires, but you don't think that scientists, some of the most contentious people out there, don't want to be right about what they're studying, or to prove someone else wrong? I'm sorry, but it seems that you're arguing for a conspiracy theory involving every scientists who lives. That, I find highly implausible. But, if you have evidence, please show me. That's all I'm asking.

This is also not to say that there are not some major problems with evolutionary theory, but it is incredible to say that the people working in the field do not know of these. In fact, it is the scientists working in evolution who are the most vocal about these problems. Find any debate by scientists in evolutionary theory - read any book about it - read any paper published in the field. They are all quite aware of problems, and are all willing to work on them, or are already busy with it.

As to your example of Thomas Huxley - please. First, will you please find the actual reference of that quote? It is possible that he said it at some point, but most people credit it to him during an 1860 debate. The first commercial typewriter did not come on the market until years after. This is a pedantic point, and really is not the main point of my argument against this. The idea actually goes back as far as Aristotle, and has been very popular throughout the years.

My main point of argument against this point is thus: the example is intended as a thought experiment of an infinitely running random string generator. It is almost tautological that eventually, some string of Shakespeare will emerge from it. Indeed, computer models have already done just that. In mathematical terms, we call this "almost certain." Given an infinite amount of time, a random string generator will almost certainly come across a given string (e.g. "To be or not to be, that is the question.") If you increase the number of random string generators, the statistical time required goes down in relation to a very simple mathematical formula.

But, as I've said before, evolution is not a matter of pure chance. When you take out the purely "random" factor, the time required to match any string drops to quite a low amount.

Another point, though, to what are you comparing the improbability? To the probability of humans arising? Well, it's true that if you run back the evolutionary clock that humans may not ever emerge. No evolutionary biologist argues that humans have to arise from evolutionary principles. It is indeed an incredibly "lucky" happenstance that we are sitting here to argue today. That SOMETHING would evolve out of the chemistry of life is much more probable, and that, at heart, is all that evolutionists argue.

I also find it highly ironic that you take the "infinite monkey theorem" so literally when in the very next paragraph you chastise others for the same error. First off, the "experiment" when you cite was more of a performance art piece, and in no way replicated any of the conditions of the thought experiment. Likewise, it is a thought experiment, and one that can be confirmed mathematically. It also helps that we actually have evidence for evolution and speciation. I suggest you check out the literature, a lot has changed in the past 50 years, and a lot of really exciting stuff has happened in the past decade or less. If, on the other hand, you have some firm evidence that evolution is wrong, please present it. If, however, you merely find it highly implausible, well, I'm sorry, but that is never an acceptable answer. That the speed of light is a universal constant, no matter the frame of reference from which you measure it, seems equally implausible to many people. Unfortunately for them, every bit of evidence we have confirms it.

@ Vargas:

I feel like I've already dealt with most of your argument in what I've said to Tom. I would like to say, however, that biologists and chemists are indeed working on the issues of abiogenesis, and recently there have been many advances here. Please, again, as I would tell anyone, check the literature. Lastly, no scientist claims that life appeared "BLAM", just like that from nothing. That, in fact, is the creationist stance. Scientists are working out all the numerous complex pathways through which life comes about. Creationists are quite happy to say "There was nothing, then God did it, then life!"

@ Showme:

It's funny that you do bring up the fossil record, which is far and away one of the most constant proofs of evolutionary theory. Please, explain to me why you feel it is not. Likewise, Peking Man, and several others, were indeed hoaxes. But, it was other scientists who figured it out when they finally got to look at the actual bones (everyone was given only plaster casts originally, which significantly limits the amount of evidence that you have). Scientists figured out that Peking Man and other hoaxes were completely unbelievable, due to overwhelming evidence of the actual evolutionary pathways of humans. Another major disadvantage to early researchers was they they did not have the use of molecular biology - that is, DNA. If someone tried to hoax us again with bones, it is a relatively simple matter to sequence the DNA and judge just how related the bones actually are. Again, I will ask you as well to check the literature, and tell me what you have problems with.

@ Tom, again,

Again, please, tell me why you feel it is so uncompelling, and we can argue that. Personal incredulity does not mean much to me, one way or the other.

Likewise, I would agree that Jehovah's Witnesses probably have an internally consistent position. But, I would argue, so do most religions, and so do conspiracy theories. Once you allow the premise of a conspiracy or a supernatural entity, ~anything~ can be brought in as internally consistent with a little thought. This is why science is committed to methodological naturalism - if you accept the supernatural position, there is no way to distinguish between various hypotheses for their likelihood of being correct. Consider medicine: it is entirely possible that God or demons are the root cause of AIDS, diabetes, or any number of diseases. However, we have no way to prove this or distinguish between God, a demon, or pixies causing illness. Instead, we search for natural mechanisms and effective treatments (often, effective-enough or what we can do presently to alleviate suffering while we continue to do research). This is the only way science can progress, and I hope you will at least recognize this point. Once science allows for a supernatural explanation, any supernatural explanation, all bets are off for any progress. And this is not an argument against Jehovah. It is equally an argument against Hindu gods, homeopathy, therapeutic touch, chi, etc. I hope we're at least somewhat in agreement on this point.

Lastly, I severely disagree with this: "I think there is strong evidence for God. This post presents some of the probability sort….by smashing one position, it leaves the other one to stand." I think this is a false dichotomy. Even if you could completely disprove evolution (which, again, I'm willing to hear what evidence you want to bring), this does not leave God as the only other hypothesis, much less Jehovah of the Jehovah's Witnesses. It is merely one other possible answer. I think this is a major distinction between scientists and religious people. The scientists job is to come up with as many possible explanations as possible and test each one for plausibility. God is a possible explanation, but only if absolutely nothing else could possibly account for the data. Thus far, we have not run into that point. The religious person typically jumps directly to God as the explanation, without considering all the other innumerate possibilities in between.

Finally, I want to tell you that I'm also posting this reply on my own blog, because it deals with several issues I've been meaning to get around to writing a post for. I also realize this comment is ridiculously long, but I want to be thorough, and I'm certainly willing to continue this conversation here, or on my blog.

As always, I am eager to hear back from you.



Saturday, August 23, 2008

How big is Big?

So, Okada and I were having a discussion recently on the likelihood of evolution, and it started making me think of the size of the universe, how long it's been in existence, and the inability of humans to really comprehend such things. I consulted NOVA's website (one of the COOLEST places online) and got a few basic numbers, which I'll do my best to break down for everybody and give you some rough idea of just how significant we really are in the universe.

A warning: there are big numbers below the fold...

Okay, let's start off with the concept known as a "light-year." It's a term lots of us are familiar with thanks to Star Trek and the like, but just what is it? Well, light travels at roughly 300,000 kilometers per second (186,411.36 miles/sec). So, with a quick bit of number crunching later, we know that light travels at 9,467,280,000,000 kilometers per year (300,000 x 60 x 60 x 24 x 365.25), which gives us the distance of a light-year: over 9 trillion kilometers.

So, now that we have that number down, let's go with figuring out how big the universe really is. The closest galaxy to our own Milky Way of any real size is Andromeda, which is 2 million light-years away. That translates as 18,934,560,000,000,000,000 kilometers away. The farthest point in the universe that we can see is about 12 billion light-years away, which is a whopping 113,607,360,000,000,000,000,000 kilometers away. Now, keep in mind that's a radius, not an area or anything like that. That is the distance from us, the center of our visual sphere of the universe. There is another 12 billion light years in every other direction. Our visual sphere's volume is a number that is just astronomical...6.141974554241230393692905613093x10^69 cubic kilometers.

I've started throwing around the term "visual sphere," and I think I should elaborate on that a bit. Since we rely on light to see these distances, we can only see something that's as far away as light has had time to travel. So, if it's the 12-14 billion light years or so away from us and sheds light, we can see it here now. That forms our visual sphere of the universe. That means the universe is possibly much, much larger than what we can see.

So, let's say you want to make the ultimate road trip and drive over to Andromeda for the weekend. We've all been in a car going at 60 miles per hour, which translates as 96 kilometers per hour. To drive from Earth's surface to the edge of Andromeda, it would take our interstellar Prius approximately 23,478,260,869,565 years. You can do the gas math for that one if you really want to.

Now, you can look at these numbers and think about how big the universe is. Really think about it for a second...something you may notice is that our minds are incapable of wrapping around ideas like 2 billion light-years. Hell, we can barely comprehend what 10,000 is. Don't believe me? Try this game...imagine a penny. One tiny little piece of copper-plated zinc with the face of Lincoln stamped on it. Not hard to do, right?

Try ten pennies. Ten Lincolns in a row. Not even breaking a sweat, are you? Now do one hundred; ten rows of ten. You've probably seen this before in your lifetime, so no big deal. What about a thousand pennies? That square of 100 pennies stacked ten high. Okay, sure. Ten-thousand? One-hundred-thousand? A million? How high can you go before you can no longer picture the size of that number of pennies? It doesn't take too many zeros before it becomes impossible. (Fun fact: according to various sources, there are somewhere between 140- and 200-billion pennies in circulation today) Do this exercise with seconds (Okada's favorite method) and you'll get the same idea about time.

So, with your newfound knowledge of just how big the universe is, and just how old it has to be in order for us to have seen the horizon of our visual sphere, how is it hard to believe that evolution can and did occur? And is it that much more of a stretch to say that something as advanced as humanity could spring up from the innumerable cellular developments that occurred over the 14 billion-or-so year span? Is it hard to believe that it could *gasp* happen again, somewhere else?


Thursday, August 14, 2008

Hard-Hitting Movie Commentary, tonight at 9!

An up-and-coming movie has stirred up a lot of controversy over its content. In case you've been keeping clear of all news entertainment-related (which is certainly understandable), I'm talking about Tropic Thunder.

Why has this engendered so much controversy? Well, the majority of it stems from the fact that some people or groups feel that the moving is making fun of minority groups, people with disabilities, obese people, etc. There's a wide range of offended people, apparently, who all feel that this movie is portraying negative stereotypes of those they identify with.

For a rather typical example of such protests, check here, a commentary by Timothy Shriver, Chairman of the Special Olympics. Go and read it, and I'll offer my commentary below the fold.

Well, let's think about this. His point is that Tropic Thunder portrays people with cognitive disabilities in a humiliating manner. I think the problem here (and the problem with every other similar response to the movie that I've heard) is that people refuse to see beyond the surface portrayal, i.e., they see a white man in blackface in the film and say "Ohmigoodness! Blackface is totally disrespectful!"

Well...yes...Blackface does have a rather bad history, to put it lightly. So did English landowners in Ireland. We'll get back to that point in a moment. Right now, I want to make a rather strong statement. These filmmakers are free to use whatever prop, makeup, plot point, etc in their film, so long as it is not specifically targeted to incite some sort of mob violence against a specific group or person. This is a basic issue of freedom of speech. Even if the entire message of the film was simply an attempt to mock minority groups, they would and should still be able to make the film. A simple example on this would be to say that if the whole matter was that we should not be allowed to mock groups, a heckuva lot of documentaries (say, Michael Moore) would never be allowed. This is the "danger" of living in a free society - you butt up against some quite offensive and inflammatory ideas (or just plain controversial).

Note, however, that no one demands that you have to see these films, read these books, be tolerant of these ideas, or agree with them. That is, in fact, an incredibly important point. You have every right to be offended. Be offended! Please! It keeps things interested. What you don't have the right for is to NOT be offended. By that, I mean that you have no right to demand to never be offended by anything. Free societies, democracies, do not work that way.

In fact, this is the entire underpinning of democratic societies (and republics), and science as well - the necessity of coming up against controversial arguments, of meeting people who don't agree with you whatsoever, and debating the issue. This doesn't mean that it can't get heated (go to any scientific conference) or that issues can't be contentious (torture, imprisonment, death penalty, abortion, all come to mind) - if things are working right, those are exactly the kinds of things that should happen. If everyone just said "oh, this is too controversial," or "this has a negative history," democracy and science would fail. Which is exactly part of the creationist tactics - try to claim that evolution is too controversial, or leads to negative outcomes, just plain too dangerous for our fragile youngsters' minds. (Of course, they then try to subvert democratic principles with the whole "Let the kids decide" line. Well, I'm sorry. Science, as much as it shares with democracy, is not a simple majority rule (in fact, I don't think democracy is so simplistic either). It must be backed up by evidence. "Let the kids decide" is an idiotic line. Do we "let the kids decide" about mathematical laws? Laws of physics? How we should treat mental patients? No, because they don't have enough experience. If they want to conduct the experiments, and get involved in the process - more power to them, but most of them are not involved in the scientific process and do not have the background, experience, or evidence to back up what they may "decide".)

Anyway, my first main point on this is that you have the right to be offended about whatever you choose. You have the right to argue about how offended you are. You have the right to talk to other people and try to get them to agree with you and be offended as well. You don't have the right to demand that whatever it is that offends you doesn't exist, or must be changed to fit your sensibilities. This reminds me of recent cracker controversy over at PZ's blog. I also agree with Sastra's commentary on the whole matter. PZ should not have to receive death threats for what he did. He was within the realm of free speech, and if you really want to show how offended you are by it, then you should do it in debate. Likewise, if a Christian were so upset by homosexuals in his community, it would be within the realm of free speech for him to make a video of himself ripping up homosexual symbols while reading from the Bible. Obviously, I find one of these more offensive than the other, but it's within the realm of free speech, and the proper response is a better argument.

In fact, that's always the point - in a free society, the way to beat a bad argument is not to ban the offensive argument; it's a better argument. A better argument, better evidence, better science, is always the answer in these situations. Like when Watson came out with his inflammatory statements about race - the best response is neither "That's offensive, he shouldn't be allowed to say such things," or "He's an idiot." The best response is "Here's the evidence why he's wrong, and why that statement was idiotic." Just like in arguing politics, "I don't like it" is a horribly weak argument - you have to have some sort of evidence if you want to bring legal action.

Now, on the other hand...every review of Tropic Thunder that I've read has talked about all these horribly "offensive" portrayals are actually satire of Hollywood types - those who would go to any length to garner a little Oscar attention, method actors, etc. On that case, the people who are being mocked are actually actors and producers...not the minority groups. That's because it's satire. And from what I've heard, anyone with a brain recognizes it as satire.

Ah yes...satire. Note, "ridicule" and "derision" are both in that description.

Now, here's the point. I imagine if you take things only at their surface meaning, a film like Tropic Thunder seems incredibly offensive. Likewise, A Modest Proposal and Huckleberry Finn are horribly offensive if taken only at a surface level. It's only when you realize that it is satire that it begins to turn around, and you realize that those who are held up as worthy of respect or stereotypes are those who are actually being mocked and held up to the light, to show just how ridiculous they actually are. It's the same with Tropic Thunder, from what I've heard.

So, I have to ask - do these people who protest this movie feel that there is no responsible way to deal with these controversial issues? That they should never be put in the public spotlight unless they are simplistically and positively portrayed? To that, I would say, I am sorry, but that's not how freedom of speech works. If you disagree - argue it. Don't ban it.

The sad thing is, reading commentary about this movie, I can see some of these people also saying things like "You know, let's march into our high schools, into every English class in the nation, open up those reader books, and tear out everything by Jonathan Swift, Mark Twain, and Benjamin Franklin! No one should be allowed to read Aristophanes either! It's too dangerous for our children! They may get the wrong ideas!"

Well, this film is rated R. That should tell you something - it's meant for adults. We expect our kids in high schools to be mature enough to deal with satire, and I think we aren't often disappointed. Kids get it. They're smarter than most give them credit for. Most of the time. I think this movie is the same way - it's only dangerous if you don't recognize it for what it is, or if you choose to make it offensive to yourself.

So, the advice of someone who may or may not even see the movie (tickets are expensive downtown), is simply this: First off, lighten up. It's satire. Learn to appreciate a sometimes more subtle form of comedy. Secondly, if it's still offensive to you, then debate it and bring in some evidence. Don't just argue it's offensive and try to get it banned.

So, there you have it, my movie commentary.

Other blog-authors, what are your feelings? Also, you guys need to post more often!


Tuesday, August 12, 2008

I'm Not Sure What You're Trying to Convince Me Of...

I was reading this...interesting...appendix on Twenty Reasons Why Genesis and Evolution Do Not Mix, by the one and only Ken Ham.

I was struck by the fact that many of his paragraphs could be taken almost word for word from the atheist's side as an argument against creationism and theism. In fact, when I first started reading, I really wasn't sure what he was trying to convince me of - the utter indefensibility of creationist and theist positions? Does ole Kenny-boy even realize this? I'm doubtful of it, but it gave me the opportunity for a good, long chuckle.

Amazingly, if we take out his several outright lies, clean it up a bit, and edit a few things, we have a good, short list of irreconcilable differences between atheists and literalist religious folks (and, conveniently, why they are wrong). Or, if we leave it as is, we have an excellent record and example of a great number of logical (and scholarly...and factual) errors, and down-right underhanded and sneaky behavior.

So, much as I may personally despise or detest the man...I guess I have to say it. Thanks, Ken Ham, for continuing to be the paragon of everything a right-minded person wants to avoid.


Thursday, August 7, 2008

Two Quick Notes about Arguing Medicine

I just want to make a quick note.

Before you mention any medical issues of dubious nature...like...say, oh, I don't know...vaccines cause autism; or Gardasil is full of toxins and harmful; or any such nonsense...

Go read Orac. Start here. And then maybe check out here; and here. Actually, just go read all of Orac. And then go read all of Science-Based Medicine. Please. Hell, even the Bad Astronomer is forced to write about this. As a last shout-out, go and read Denialism Blog. And note that name. It's quite appropriate.

The quick note is, and not that this has come up on this blog yet, but I want to go ahead and say it...if you persist in this type of nonsense, you will be considered a crank, a denier, and perhaps deluded. Not stupid, unless you persist in this ignorance.

Also...meta-analysis. Don't trust them on their faces! Meta-analysis can be a great tool...if it's used appropriately. Often it is not. There are many factors that can throw off a meta-analysis and lead to false results. Meta-analyses which show the existence of psychic powers come to mind...Go listen to Steven Novella on SGU. He talks about this a lot towards the beginning of the archive. That's if you need someone to tell you about it and don't have access to an actual researcher who can help you out with this. So, second quick note is...don't rely on a meta-analysis to support your point, unless it is an excellent...excellent study. Read it from every angle for every possible weakness, because, trust me, that is what we will do. Because that's how science works.

And no, I don't claim to be an expert on many of these topics. But a lot of the research is quite easy to find, and not too hard to understand if you put some effort towards it.

More on this later. Just wanted a quick update.


Audio-visual synesthetes

Do you hear sound corresponding to movement, even when you know that it must be just in your head (i.e., watching a television with the sound muted)? You may have a rather interesting form of synesthesia.

Check out this video for an interesting demonstration.

Synesthesia is a very strange but fascinating condition, one that I would like to spend time studying as part of a cognitive psych/neuroscience degree. Crossed sensory pathways...a very provocative idea.


Tuesday, August 5, 2008

Okada arrives

Hello everyone

I already know two of the people on this blog so this is more for anyone else that reads this. I guess I am the black sheep here not being a graduate student, although I am hoping for that to change in a year or so. Well I guess a little about me, I was a computer information systems major and now I am in the field of Biology. From there I hope to obtain either a PhD or a PharmD degree in the pharmacy field. Since I am out of school at the moment most of my time is taken up by going through the process of getting back into my school and my hobbies. I am trying to be a better skeptic everyday, listening to the Skeptics Guide to the Universe almost daily, at least until I get caught up to the most up to date podcast. Other than that I love video games, currently my poison is either Dota if anyone knows that one or I play a lot of the orange box(Portal, Team Fortress 2). I am a recovering WoWaholic and I hope this is the last time I quit!

As far as music goes, I try to have it playing whenever possible. Genres as cliche as it sounds I like pretty much anything except for country music. I browse Science Daily and other science news sites and blogs depending on how much extra time I have in my day but other than that there isn't much to do in the little town I am in, at least until I move back to college. Well I hope to contribute at least something meaningful in this blog in the future looking forward to writing and reading posts.


Monday, August 4, 2008

New President for the JREF

Exciting news! And a huge congratulations to Phil Plait over at the Bad Astronomy Blog! Phil has accepted the invitation to become the new President of the James Randi Educational Foundation. Randi's still going to be around, don't worry! He's just moving on to a Chairman position to spend more time working on his books. Phil says he's definitely going to be focusing on the Educational part of the Foundation, and I'm certainly proud to hear it! I know Randi has been a huge influence on me (along with Sagan, and yes, Phil [and PZ too!]) in my skeptical education, so this is just great news.

Go read about it on Phil's blog, or check out Rebecca's summary over at Skepchick, where I heard it first.

I am reposting the press release below the fold, for those of you who want to read it here:

James Randi Educational Foundation Press Release August 4, 2008

For immediate release

The JREF Welcomes New Foundation President Dr. Philip Plait

The James Randi Educational Foundation (JREF) is pleased to announce that Dr. Philip
Plait – renowned astronomer, author, and skeptic – will be taking on the role of President of the JREF effective immediately.

The goals of the JREF are to bring critical thinking to the public, expose pseudoscientific frauds, and promote real science and rationality.

“Phil is a skeptic, a scientist, and a colleague, and his ideas and vigor will take the JREF very far indeed. We’re pleased and proud to have him take the reins,” said James Randi, internationally known magician and critical thinker, who is the founder and outgoing president of the JREF. “I will now be dedicating much of my time to completing my next two books, Wrong!, and A Magician in the Laboratory.”

Dr. Plait has a long affiliation with the JREF. He has been a speaker at all of The
Amaz!ng Meetings – a JREF-sponsored annual conference series and the largest gathering of critical thinkers in the world – and over the years has provided valuable advice and support for the JREF in scientific and other matters. During that time he has grown to be a strong part of the Foundation.

Before joining the JREF, Dr. Plait spent ten years performing scientific research using the Hubble Space Telescope, much of it as a contractor at NASA’s Goddard Space Flight Center. It was at this time that he created the Bad Astronomy website, where he critically (and humorously) analyzes various astronomical myths and misconceptions. His debunking of the Moon Hoax (people who think NASA faked the Apollo Moon landings) became an Internet favorite, bringing in tens of millions of views.

His award-winning Bad Astronomy Blog is one of the largest and most popular scientific blogs in the world. In July 2008 it was acquired by Discover Magazine, where his audience continues to grow. Plait is an internationally sought-after lecturer and has given numerous interviews on national TV, radio, and podcasts. He has written two popular level science books: Bad Astronomy (Wiley and Sons, 2002), and the upcoming Death from the Skies! (Viking 2008), which deals with cosmic catastrophes. It was his first book that brought him to the attention of Mr. Randi, who asked him to speak at the JREF’s 2003 conference.

In fact, Plait attributes his current stature in the skeptical community to James Randi. “When I was young, I believed in all sorts of antiscientific silliness like the Bermuda Triangle, astral projection, and the like. But then I saw Mr. Randi on television masterfully and literally dissecting psychic surgery [con artists who fake using psychic powers to do phony surgery on desperately ill victims], and he opened my eyes – and my brain – to the idea that reality is a better place to live in than fantasy. I owe it all to Mr. Randi, so I am very excited and deeply honored to continue his vision with the JREF.”

Outgoing President James Randi has pursued “psychic” spoonbenders, exposed the dirty tricks of faith healers, investigated homeopathic water “with a memory,” and generally been a thorn in the sides of those who try to pull the wool over the public's eyes in the name of the supernatural. He is the author of numerous books, including The Truth About Uri Geller, The Faith Healers, Flim-Flam!, and An Encyclopedia of Claims, Frauds, and Hoaxes of the Occult and Supernatural. Mr. Randi's long-standing challenge for proof of claims of the paranormal now stands as a $1,000,000 prize administered by the Foundation. It remains unclaimed. Mr. Randi will become the Chairman of the JREF Board of Directors, where he will continue to guide the JREF and be a driving force for its endeavors.

With Dr. Plait at the helm, the JREF will be expanding its efforts, including educating children. “I want to teach kids about the wonders of the real Universe. We can do this by partnering with the educational community and developing fun, hands-on materials that schoolchildren can use in the classroom to teach them about critical thinking and the scientific method. Science is sometimes taught as being cold and dull, but nothing could be more wrong! It’s exciting, it’s fun, and it’s cool. Kids are natural scientists, and we need to encourage that, foster it, and let it grow.”

The JREF was established in 1996 as a registered 501(c)3 organization under the IRS code, and as such, all donations to the Foundation are tax-exempt to the full extent under the law.

For further information and media inquiries, contact the JREF:
Via phone: +1-954-467-1112
Via email: jref@randi.org

More information on the James Randi Educational Foundation can be found online at

Print-quality photographs of Dr. Plait are available on his website at
http://www.badastronomy.com/pr/images.html. Pictures of James Randi are available at

So...congrats Phil! Come over to Chicago sometime, and I'll take you out for drinks!


Friday, August 1, 2008

Vacation, and some good links

I'm going to be on vacation, starting tomorrow. I'll try to post some while I'm at home, but honestly, I think I'll probably just sleep most of the time.

In the meantime, I'm sure The Rooster and DirtyGaijin will keep you entertained. If not, however, then just navigate yourself over to Thunderf00t. Always interesting, and hours of videos to watch. Likewise, he has a great number of links to follow for your better education and enjoyment.

Also, I want to direct you towards this reply letter from a librarian. Absolutely brilliant, and what we should all aspire towards. This, to me, is actually a really good understanding of what was intended by the Founding Fathers. Note, this is quite different from what those on the Right (and often those on the Left these days) will say about that topic. Tip o' the electronic card catalog to Skepchick.

Also wik, please welcome our Robot Overlords. This is actually an example of real progress in robotics. I'm most impressed by the thing's resistance to being kicked and moving over the ice. The recovery seems almost...natural...which is so...unnatural. Ah! Uncanny valley! Tip o' the articulating leg to Phil Plait over at Bad Astronomy.

Also also wik, go and read about Sonic Hedgehog, or shh, over at Pharyngula. Good discussion. Take some time and read up on evo-devo. I highly recommend it. Just put down plastic tarp for when your head explodes (and oh...it will...).

Anyway, hope you kids have fun while I'm gone. Keep the place clean.