Science & Nature Archive

Friday, August 6, 2010

Genetic Determinism

DNAI got into a discussion with a few co-workers last week on a topic that I'd thought most educated people agreed upon to a large extent - the limits of genetic determinism. In the old argument of nature vs. nurture, I thought most people realized that who we are is a combination of both influences. However, in that conversation, I was the only one who thought environment played a big role, while the other two thought it was mostly down to genetics. Anyway, a few days after our conversation, I sent them an e-mail explaining how environment can contribute to our traits, and decided that it might be worth posting a modified version of it here on the blog. So, to anyone who puts too much stock in genetic determinism, here's some information on how environment also plays a strong role in our development.

First, there's an example that's so obvious that we almost forget about it - muscle size. Genetics gives us a potential muscle size & strength, but our actual muscle size can be greatly affected by diet and lifestyle, particularly by being active or working out. This is a clear example of genetics and environment interacting to produce a trait.

Here's an article on height (since that was one of the traits my coworkers and I discussed specifically). Based on studies between twins and other relatives, it looks like genetics is 60 to 80% responsible for height, and environmental factors, particularly nutrition, are responsible for the remaining 20 to 40%.

Here are a couple more links on height.

One important caveat on twins that doesn't get mentioned in many of these articles - identical twins don't look so similar solely because of their shared genetics (although that is the biggest reason). It is also due to the shared environment in the womb. That's why fraternal twins look more similar that siblings that didn't develop together. So, it's not enough to look at identical twins in these studies - you have to use fraternal twins as a control for early developmental factors.

Here's a really good site on the 'nature vs. nurture' debate that focuses on intelligence. I'm giving the link to the conclusion, but if you follow the links on the site, you can find the evidence they list. To quote part of that site:

Through the research we have done, it seems that heredity, as well as environment plays an important role in humans’ mentality; but these are not exactly equal in influence. A person’s entire environment seems to be more effectual in determining his mental ability than heredity is. The most fundamental way to explain our opinion is quite comprehensible. It is that heredity determines one’s potential, but environment determines how far one will reach that potential during his lifetime. In other words, every individual has a destined mental potential, but how much of that potential the individual will be able to gain solely depends on the environment that the individual grows in.

Here's another article that touches briefly on genetic determinism, mentioning an experiment where cloned plants (i.e. genetically identical) were grown in different environments, and the plants grew differently depending on the environment they were in.

Another point against genetic determinism is the fact that our cells aren't perfect machines, where given inputs give precise outputs. Cells are a cluttered stew of molecules inside a membrane. Depending on how molecules are dispersed throughout the cell, two genetically identical cells may have different reactions to the same conditions. Carl Zimmer's book, Microcosm, has a good explanation of this, if you ever get a chance to read it. A good example, one which made headlines, is the first cloned cat. Although it has identical nuclear DNA to its mother, it has a different color pattern, because the activation and inactivation of the responsible genes is more or less random.

Here are two more links, dealing with related themes that we discussed. The first link is to an article on the Flynn Effect (the fact that IQ scores have been increasing). We also discussed abstract thinking, and whether or not it's a learned skill. The second link below includes a discussion of a study done in Uzbekistan which seems to confirm that abstract thinking is learned (though the article also mentions potential problems with the study).

Okay, so what's my point in all this? Genetics plays a significant role in who we are, but so do environmental factors, and even random chance has a part. So, given the long complicated history that has led to the current conditions in the world, unless two people have had very similar upbringings, it would be nearly impossible to tell how much of the difference between them was due to genetics.

Friday, July 9, 2010

New Comments

Well, I don't have anything really substantive for this week. I did leave two decent comments, though, in response to visitors. First is a discussion of why humans should be considered apes. Second is a bit of politics in response to a guy who didn't like my response to Gary Hubbell's anti-liberal article.

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.


Selling Out