Science & Nature Archive

Thursday, June 17, 2010

Book Review - The Tangled Bank

It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life and from use and disuse: a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

So ends Darwin's Origin of Species, giving the inspiration for the title of Carl Zimmer's latest book, The Tangled Bank: An Introduction to Evolution. It is described as a textbook on evolution for non-biology majors, and it is very good.

The term, 'evolution', is pretty broad. In general, when people talk of biological evolution, there are two broad categories they're referring to. The first is the concept of common descent with modification - that all life on this planet is related, and that populations of organisms change over time. The second is the theories describing how that works, with natural selection being the most famous. Pretty much every book that covers evolution will cover both areas to some extent, but often times they will focus on one area over the other. The Tangled Bank covers more of the latter subject. Of course, it uses examples, but it is more about how evolution works rather than a fossil by fossil account of the evidence for common descent (for that type of book, read Donald Prothero's Evolution: What the Fossils Say and Why It Matters - also, realize that there's much more evidence for evolution than just fossils).

Let me give an example of one of the concepts I learned about - Hardy-Weinberg Equilibrium. This term is probably familiar to biology majors, but it's not something us non-biologists generally read about in most popular books or magazine articles on evolution. The concept has to do with allele frequency. As a refresher, an allele is a variation of a gene. Think back to your high school biology class, and the genetic experiments of Gregor Mendel. For example, Mendel discovered a certain gene* that controlled pea color - one version would make them green, while the other would make them yellow. Each version is called an allele. Remember further, that us eukaryotes carry two copies of a gene (actualy, at least two - it can get a bit more complicated than this). So, individual plants in a population of all green peas might all carry two copies of the green allele - GG, and individual plants in a population of all yellow peas might all carry two copies of the yellow allele - YY. Now, if you were to bring those two populations together, the alleles woud start mixing, and you'd end up with three different combinations that the plants could have - GG, YY, and GY (GY and YG are the same thing). What Hardy-Weinberg equilibrium tells us, is that according to just random mating and chance distribution, these allele combinations should all be present in certain ratios. In this example, half of the plants would likely be GY, one quarter would be GG, and the remaining quarter would be YY. But what if you checked up on your pea population, and found that it didn't match the Hardy-Weinberg equilibrium? What if less than a quarter of the plants were GG, and more than a quarter were YY? Well, then we could conclude that something about the Y allele was advantageous to the plants, and that natural selection was pushing the population to have more plants with the Y allele.

This concept of Hardy Weingberg equilibrium can be applied to more complicated scenarios. It doesn't have to be just two alleles, and the initial distribution doesn't have to be 50/50. However, for any combination, the Hardy Weinberg equilibrium is the distribution you'd expect if there weren't any natural selection, and measuring how much the actual distribution varies from the Hardy Weingberg equilibrium is a measure of how strong the selection is.

To me, that's a pretty interesting concept, and it wasn't something I'd given much thought to before reading Zimmer's book. However, the book didn't go into much more detail than what I just gave in my summary. If you're not of a technical bent, that may be all you need. I realize that Zimmer's goal was to provide a book for non-biology majors, so maybe that's all the detail he felt was necessary. However, to someone like me, who may not be a biology major but wouldn't mind seeing a little light math, Zimmer's explanation was a little too superficial. I mean, if you follow that Wikipedia link I provided and read the explanation of Hardy Weinberg equilibrium, the math isn't all that hard. It's just a bit of algebra. Maybe as an engineer who works with equations all day long I'm a bit biased, but it's not as if you need to understand any calculus or differential equations to follow the basics of Hardy Weinberg equilibrium.

I can't discuss this book without mentioning the illustrations. Practically every page of the book has a figure or a graph. I'm sure that the printing cost associated with this contributed to the $50 price tag for the book, but it really makes it easy to understand certain concepts that would be difficult to get across with just words.

This book was published right around the same time as Richard Dawkins' The Greatest Show on Earth: The Evidence for Evolution, so there were inevitably comparisons. But the truth is that they're just not the same kinds of books. In my discussion above on the broad meanings of evolution, I said that Zimmer's book covered more the theories of evolution. Dawkins' book was more of a look at the evidence itself. Zimmer's book was a textbook with color illustrations on each page, while Dawkins' book was a popular book with few illustrations. Comparing the two is comparing apples to oranges.

If you'd like to get more of a taste of the book, I've found two excerpts available for download online. Chapter 1, Evolution: An Introduction is availabe from Carl Zimmer's own site. Chapter 10, Radiations and Extinctions is available from the National Center for Science Education. You can also read Zimmer's announcement of the book on his blog, to hear his intentions in his own words.

All in all, The Tangled Bank was very good. It was a nice broad introduction to many of the theories and mechanisms of evolution, but without getting too technical for those of us that don't plan to go into careers in biology. Unfortunately, being a textbook, it's a bit pricey. You may try going to your library to check it out, find it used, or maybe be lucky enough to be able to borrow it from a friend. However you manage to get your hands on a copy, I definitely recommend this book.


*Mendel's insight was that there were units of heredity, now known as genes, as opposed to the prevailing concept at the time of blending inheritance, but he didn't actually know the mechanism responsible. It wasn't until later that other scientists discovered that genes were contained on chromosomes, and later yet that scientists discovered that chromosomes were made of DNA.

Friday, March 26, 2010

Book Review - Guns, Germs, and Steel

Guns, Germs, and Steel: The Fates of Human Societies is a Pulitzer Prize winning book by Jared Diamond. To quote from the book itself, it is "A short history about everyone for the last 13,000 years." Diamond has attempted to explain why world history has taken the course it has. But he's more interested in large scale trends and causes, as opposed to battle by battle or even war by war tracking of history. Or, to put it another way, he was taking a more scientific approach to history, as opposed to just stamp collecting. Wikipedia has a good overview of the book, so I'll only present a brief summary here.

To use an example, we all learned in school of the European conquest of the Americas, even though the Europeans were vastly outnumered. We've been taught many of the factors that lead to that result, most notably the superior weapons technology of the Europeans, horses, and the diseases that Europeans brought with them. Diamond noted all these proximate causes (and a few others), but then moved on to ask why the Europeans had developed those advantages, and not the other way around. Why hadn't Motecuhzoma sent ships to conquer Spain?

According to Diamond, much of the advantage of certain regions was a result of geography and the indigineous plants and animals. To help support his case, Diamond looked at native plant species around the world, how nutritious they were, and how easily they could be domesticated. Wheat, for example, is a very nutritious crop, with a fairly high protein content for a plant. It required only a single mutation in wild wheat, inhibiting the seeds from falling off the crop when ripe, to make it suitable for agriculture. Teosinte, by comparison, required many more mutations to become domestic corn (maize), which isn't as nutritious as wheat. As it turns out, Eurasia has a greater number of nutritious, easily domesticated plants than any other region.

Eurasia also had a higher number of potential livestock candidates. In many regions of the world, the Pleistocene extinction event killed off most large mammals at the end of the last ice age (there is debate over the cause of this extinction, but that's largely irrelevant to Diamond's hypothesis). If you don't have large wild mammals, you can't domesticate them into livestock. But you can't just domesticate any large animal. In this section of the book, Diamond quoted Tolstoy, "Happy families are all alike; every unhappy family is unhappy in its own way." There are many traits an animal has to have to make it suitable for domestication (diet, behavior, lack of aggression, social structure, etc.), but missing any one of them would make an animal unfit for domestication. Diamond used this reasoning to show why, for example, zebras weren't domesticated in Africa like horses were in Eurasia, or why bears or rhinos weren't suitable to domesticate for food or as draft animals.

Diamond went on to argue how differences in geography allowed agriculture and domestic animals (referred to collectively as food production) to spread more easily in some regions than others once they had been developed. Eurasia, without any great barriers such as deserts, and with an east-west axis that meant the climate was more similar along its breadth, facilitated this spread more so than other regions.

Once regions had developed food production, they could maintain higher population densities. Initially this gave them a military advantage just through shear numbers. But eventually, by providing for an artisan class that didn't have to grow its own food, it led to technological advantages, as well. The high population densities, along with domestic animals, also contributed to those regions having endemic diseases that didn't exist elsewhere.

As an example of how Diamond was attempting to explain the grand patterns in history over tens of thousands of years, he pointed out that someone could ask why, out of all the areas of Eurasia, Western Europe currently dominates the world stage, and not Eastern Asia. He stated that this simply might be a short term 'blip', and not part of the long term trend (just look at the resurgence of modern China).

As I said, this is only a brief summary of the book. Diamond had many more reasons and examples that he used to support his hypothesis.

Some parts were more convincing than others. It also didn't help that in a few examples he brought up that I already knew a bit about, I saw some mistakes. For example, when discussing ancient human history, he compared the Out of Africa hypothesis to the multiregional hypothesis. The weight of evidence strongly favors the 'Out of Africa' hypothesis, but Diamond seemed a little more ambiguous in the book. In another section, discussing why cultures might be resistant to adopting certain technologies, he brought up the old QWERTY/DVORAK controversy, claiming that DVORAK is clearly superior to QWERTY, but market forces have kept it from being adopted. This is an old urban myth that isn't true. There haven't been many actual studies comparing the two keyboard layouts, and the studies that have been done don't show a very big advantage of one design over the other (certain advantages of each layout are offset by different advantages of the other layout).

Overall, I thought the book was very interesting, and that Diamond did a good job of presenting his case. I'd definitely recommend it.

Update 2010-03-29 - Slightly revised wording in 4th from last paragraph.

Friday, February 19, 2010

Confidence in Scientific Knowledge

Test Tubes & BeakersAs evidenced by one of my recent blog entries, I tend to place a lot of value in science. I think it's the best method we have for answering questions with objectively true answers, and I think we can have a pretty high confidence in the answers it gives us. But, as a few people have recently asked me, where does that confidence come from? Throughout the past, people have had explanations for aspects of the universe that they believed were correct, but have since turned out to be wrong (e.g. the Sun orbiting the Earth). Given humanity's history of failed explanations, shouldn't we expect that many of our current explanations are also wrong, and be a little more cautious in our certainty?

The simplest reason to be confident in science is a pragmatic one - just look at the results. Science as the formalized discipline that we're used to is a fairly recent development. It's only been around a few hundred years, getting started in the Renaissance, but not really coming into its own until after the Enlightenment. But look at how fast our technology has progressed in that short time compared to the previous millenia of human existence. We've invented telescopes, steam engines, automobiles, semiconductors, airplanes, computers, TVs, radio, lasers, vaccines, antibiotics, cures for some cancers. We've sent people to the moon. These accomplishments are all based on knowledge that we've learned through science. It seems very unlikely that we would have been able to accomplish all of that if we didn't have a pretty accurate understanding of reality. Granted, there are other fields of science that haven't yielded practical applications, and possibly never will. For example, understanding the Big Bang may not ever give us any new technologies. However, given the technologies we have developed from other fields, we know that the methods produce reliable results.

Moving away from pragmatism, let's look at how science works. Richard Feynman once said, "Science is a way of trying not to fool yourself. The first principle is that you must not fool yourself, and you are the easiest person to fool." There are all types of ways that we can make mistakes in our reasoning. There's a great article I've linked to before from this site, which does a fantastic job of discussing this: The double-blind gaze: how the double-blind experimental protocol changed science. The article is focused on medicine, but it's applicable to science in general. The article mentions a few of the confounding factors that can affect our reasoning, including the placebo effect, the re-interpretation effect, and observer bias. Wikipedia has a whole list of cognitive biases. A big part of science is recognizing and accounting for all these potential mistakes. Along similar lines, science is not just a search for evidence that confirms your ideas. It's a search for evidence that would disprove your ideas. A big part of science is recognizing when you're wrong.

Science also trains us to think less in terms of absolute certainty, and more in terms of degrees of certainty. If you're being honest with yourself, there's no way to be absolutely certain of anything. It's possible that we're living in The Matrix, or hallucinating, and nothing is as it seems (if this sounds familiar, I've discussed it before). In normal everday conversation however, we tend to ignore those types of outlandish possibilities, and say that we're positive of something, even if technically we mean nearly positive. There are many things we've learned through science that we can say that we're positive are true. The roughly spherical shape of the Earth, the Earth orbiting the Sun, common descent (if not all the exact lineages and mechanisms), are examples of a few of those facts. We should no sooner expect those facts to be overturned than we should expect to wake up on the Nebuchadnezzar fighting alongside Neo. Other things we've learned through science don't have quite as much evidence. Antrhopogenic global warming is an example of this. We can say that we're really darned sure that climate change is happening and that we're responsible, but it's not quite so certain. It would still be really surprising to see AGW turn out to be false, but not earth shattering. You can keep moving down through levels of certainty through things like String Theory, which doesn't really have any evidence confirming it specificaly over other theories, but which is at least consistent with known evidence. If string theory turned out to be false, I wouldn't be all that surprised. You can go even further, and find theories inconsistent with known evidence, such as the supposed link between vaccines and autism, or the aether theory of light. We can be pretty sure that those ideas are false.

In addition to making us think in terms of degree of certainty, science also makes us think in terms of degree of accuracy. Isaac Asimov wrote a good essay titled, The Relativity of Wrong. You should read the whole thing, but here's a great quote from that essay, "When people thought the earth was flat, they were wrong. When people thought the earth was spherical, they were wrong. But if you think that thinking the earth is spherical is just as wrong as thinking the earth is flat, then your view is wronger than both of them put together." An example I've used before is the atom. The current model is the valence shell model, where electrons have a probability of being in particular positions relative to the nucleus. This is an improvement over the Bohr model, where electrons travel in circular orbits around the nucleus and where the orbit radii are defined by quantum mechanics. The Bohr model was an improvement over the Rutherford model (or Solar System model), where the electrons orbited the nucleus, but quantum mechanics wasn't incorporated to predict the orbit radii. The Rutherford model was an improvement over the plum pudding model. And the plum pudding model was at least more accurate than not knowing of the existence of electrons. So, you can see how our explanations have gotten more and more accurate concerning the structure of an atom. Our current model may also be supplanted, but at least we're zeroing in on the truth.

Those are the reasons why we can have confidence in what we learn through science. It's produced results that just wouldn't be possible if the methods didn't work. But it's not simply a matter of thinking that everything science reveals is absolutely right - it's recognizing how science works, what explanations are most likely to be true, and how close we should expect those explanations to be to the actual truth.

Friday, January 29, 2010

'Scientific' Facts

MicroscopeSometimes, a term that you've heard your whole life suddenly seems strange, That's how it is for me and 'scientific facts'. When you think about it, that phrase seems a bit redundant. If something is true, it's a fact. It's that simple. It doesn't matter how you came to know it. If a statement lines up with objective reality, it's a fact.

What does it add to describe a fact as 'scientific'? I guess the first thing is to understand is what's meant by science. Generally, there are two related meanings to the word. The first is that it's a method. We should all know this method from grade school - come up with an explanation, gather evidence to test the explanation, refine your explanation, and repeat. The second is the body of knowledge we've learned through that method. But the thing is, everything that has an objective answer can be examined through science.

Consider an example. Some would consider the Earth orbiting the sun a 'scientific' fact. We as humanity may have learned about it through science, and we as individuals may have learned it in science class, but it doesn't change the fact that it's true. It's not as if the Sun used to orbit the Earth until Galileo came along. Can't we just call it a plain old fact?

There are a couple reasons I bring this up. One is for the people who like to point out that science can't tell us anything with absolute certainty, and therefore science doesn't deal in facts (like this exchange I had). When you consider things like solipsism and Last Thursdayism, you have to grant that for fact to have any meaning, it must mean very high level of certainty, and not 100% absolute certainty. Going by that definition, science certainly does deal in facts.

The other is for the people who think of science as something separate, as not really describing things as part of their world. To them, it may be a 'scientific' fact that evolution occurs, but but in their world, science is wrong, so describing evolution as 'scientific' means it may not have actually occurred.

Oh well, I'm not be expressing myself as clearly as I'd like, but it's late on a Friday, and I'm about ready for some supper and a beer. I guess the main point I'm trying to get across is something I already said in the first paragraph. Calling something a 'scientific' fact is redundant. Statements are either true or not, and if they're true, then they're facts. Since we can study everything with an objective answer through science, it really doesn't add anything to describe any facts as scientific. If they're not scientific, they're not really facts to begin with.


Added 2010-02-01 I thought about this a bit over the weekend, and realized that that last sentence might come off as a bit smug. So, I thought that maybe I should list a couple examples.

As the first example, consider the claim that Hawaii is the 50th state of the U.S. To look at this scientifically, we need to gather evidence to support that claim. We could start off by looking at current legal documents, which show that Hawaii is definitely a state. We could move on to archived documents, and find the Hawaii Admission Act, which shows when Hawaii became a state. We could move on to find documents of when each of the previous 49 states became states. We could study newspaper articles from each of those periods for additional confirmation. After studying all that evidence, then we could say that it is a 'scientific' fact that Hawaii is the 50th state of the U.S.

Next, let's move on to something that some would think was a bit more subjective. Consider the claim that I love my wife and daughter. To test this, people could observe my behavior around my family, and the actions I commit in relation to my wife and daughter. They could study my involuntary facial expressions, to see how I react around them. They could observe my behavior when they're not around, looking for signs of loneliness, or observing how I talk about them. So, even the claim that I love my wife and daughter can be considered to be a 'scientific' fact, since we can use the scientific method to investigate it.

That's what I mean when I say that all facts worth talking about are scientific. Sometimes, we only practice rudimentary forms of the scientific method to determine their veracity, but, at least in principle, the scientific method can be applied to them.

Thursday, November 5, 2009

Ray Comfort - Still Ignorant on Evolution

On the Origin of Species - The Ray Comfort EditionWow. Just, wow. I know I've talked about Ray Comfort more times on this blog than is healthy (for example - here, here, here, here, here, and here), but now, not just is he publishing his drivel on his own, making scam websites, or getting followers to put the equivalent of junk mail into books at the book store. Now, he's been published in a blog on the U.S. News and World Report website, and boy is it ignorant.

The background of this article is this. Ray Comfort is publishing two versions of a reprint of Darwin's Origin of Species, along with an introduction in each version. The first version was abridged, and the introduction was made publicly available on the web. After the negative publicity it received, Comfort made his second version unabridged, and supposedly with a modified introduction. To give an idea of the introduction, here's how Comfort himself described it (be forewarned - there are many falsehoods and examples of bad logic in just these two paragraphs*).

This introduction gives the history of evolution, a timeline of Darwin's life, Hitler's undeniable connections to the theory, Darwin's racism, his disdain for women, and his thoughts on the existence of God. It lists the theory's many hoaxes, exposes the unscientific belief that nothing created everything, points to the incredible structure of DNA, and the absence of any species-to-species transitional forms.

It presents a balanced view of Creationism with information on scientists who believed that God created the universe—scientists such as Albert Einstein, Isaac Newton, Nicholas Copernicus, Francis Bacon, Michael Faraday, Louis Pasteur and Johannes Kepler. It uses many original graphics and "is for use in schools, colleges, and prestigious learning institutions." The introduction also contains the entire contents of the popular booklet, "Why Christianity?"

Towards the end of September, Dan Gilgoff posted an entry in his God & Country blog on U.S. News & World Report describing Comfort's book (the first version). After all the feedback Gilgoff got for that entry, he decided to revisit the issue. He set up an online debate between Ray Comfort and Eugenie Scott, the executive director of the National Center for Science Education. The debate consisted of four posts in total - Comfort's original argument, Scott's original argument, Comfort's response to Scott, and finally, Scott's response to Comfort.

I guess there are several ways I could have addressed this in a blog post, but I've decided to focus on Comfort's second post. That one struck me as so out and out ignorant, that it seemed a ripe target. I encourage you to read Scott's response first, but I thought I could supplement what she already wrote.

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