Evolution 101

Saturday, February 25, 2006

Random or Nonrandom?

GordonOKC asks: Richard Dawkins is emphatic when stating evolution is "nonrandom". Can you please elaborate?

Sure, no problem. For those of you that don’t know, Richard Dawkins is a zoologist at the University of Oxford in England, serving as Professor of Public Understanding of Science. He’s best known for his books, starting with “The Selfish Gene” in 1976, which is an excellent work of popular science. I highly recommend that book and any others that he’s written, by the way. He’s also served as a vigorous critic of creationism and intelligent design, and it could be argued that he’s now one of the most prominent living critcs.

So why would Dawkins be so emphatic about evolution being nonrandom? Well, because one of the ideas about evolutionary theory that’s often promoted by creationists is that evolution is a completely random process. The creationist would say, if evolution is true, then all organisms have developed randomly. This is usually followed by some quotation of statistics, implying that it would be more likely for a 747 to assemble itself out of a junkyard than for a single protein molecule to develop with random processes. This creationist argument is not an accurate description of evolution, though- it uses what’s called a “strawman.” This means that, instead of engaging an opponents actual argument, you construct a weaker version of their argument, called a strawman, and then argue against that. The creationist argument that characterizes evolution as a completely random process is just such a strawman.

Well, if the creationist assertion that evolution is a completely random process is wrong, that explains why Dawkins would be emphatic in stating that it’s nonrandom. But that’s not the whole story. Evolution is a nonrandom process, but it’s also propelled by random mechanisms. What do I mean by this?

There are two basic forces that function within evolutionary theory. One is selection. This can be natural, as in the evolution of finch species in the Galapogos Islands, or it can be artificial, as in the evolution of animal and plant species because of human culture. Neither of these is random- the selective force of the environment is the deciding factor on whether one population will be successful or not. The other basic force is mutation. This force is random, at least to a certain extent.

Mutations are mistakes. Every organism contains DNA that is copied every time a cell divides. DNA is a strand of four different nucleotides, adenine, cytosine, thymine, and guanine. These can be written as a string of letters represented by the first letter of their name, A,C,T, and G. A strand of DNA can thus be represented by a string of those four letters, in any combination.

When a strand of DNA is copied, there can be errors. These errors can be caused by a number of factors, including radiation, certain chemicals, or viruses. Radiation, especially ultraviolet radiation, tends to affect adjacent thymine bases, so it’s not completely random, but it’s very close. But there is also a base rate of mutation that occurs randomly but at a measurable average rate, that results in one base being switched with another during copying. In humans, this rate is at about 1 mistake per 100 million base pairs every generation. This is about 175 total mutations per individual.

Now, most mutations don’t affect an organism’s ability to live and reproduce. These kinds of mutations are called silent mutations. Since they’re not selected for or against, they accumulate at a regular rate in populations. But some mutations can affect genes either positively or negatively, with the result of having a positive or negative effect on the ability of an organism to survive in its environment, what we would call an organism’s fitness.

Now here’s where the random mechanism of mutation hits the nonrandom force of selection. In any given population, individual organisms will have a wide range of mutations. A small percentage of those individuals will have mutations that decrease their fitness, and they will be selected against, with the result being that their genes are taken out of the population’s genome. Another small percentage of those individuals will have mutations that increase their fitness, and they will be selected for, with the result being that their genes are increased in the population’s genome. So over time, we see that a population will become increasingly adapted to its environment, because positive mutations are selected for and negative mutations are selected against. The random mechanism of mutation is utilized by the nonrandom force of selection to drive evolution forward.

We can see examples of this nonrandom selection in the phenomenon known as convergent evolution. Convergent evolution refers to instances where similar physical characteristics have evolved in two different organisms that do not have a close evolutionary relationship. For example, the evolution of wings in both birds and bats. The function of wings is the same in both birds and bats, but the structures of both instances of the appendage show wide differences. For example, the surface area of a bird’s wing is made up of feathers that attach to the entire length of the arm, while in a bat’s wing it is made up of membrane stretched between individual digits. In addition to these obvious structural differences, bats and birds have different ancestries. Bats are mammals, and so belong to the synapsid lineage which parted ways from the reptiles lineage, to which birds belong.

Another good example of convergent evolution can be seen within the mammal lineage itself. The first divergence in the mammal lineage was between monotremes, which are mammals that lay eggs, marsupials, which are mammals that carry their young in pouches, and placentals, which give birth to fully-formed live young. Throughout most of the world, placental mammals have become the dominant groups, but the only place where marsupials have remained was Australia, at least until it was colonized by man. Marsupial mammals evolved to fill the same niches that placental mammals did- including carnivores. The thylacine, or Tasmanian tiger or Tasmanian wolf, looked incredibly similar to the placental wolf, but it was more closely related to the kangaroo or the koala bear. But the same nonrandom selective forces of the environment that shaped the evolution of the placental wolf also shaped the evolution of the Tasmanian wolf, and so they developed very similar physical characteristics.

So, to review, evolution is both random and nonrandom. The instances of individual mutations are random events, and provide a population with a certain amount of variation. This variation is the basis on which the nonrandom selective force of the natural environment directs evolutionary change.

Saturday, February 18, 2006

What is Species?

Today I’m going to be killing two birds with one stone, so to speak, answering two related questions from the website. Mr. Neil and Asimov both wrote in to ask about the concept of “species.” This is an excellent question because this cuts right to the heart of what most people think about when they consider evolution- the formation of new species. And if you remember from the Darwin Day podcast, the mechanism of natural selection was what Darwin proposed as the way for new species to originate. But the title of his book, “On the Origin of the Species,” assumes the concept of species, so what exactly is it?

Although you’d think that it’d be a simple matter to distinguish between two species (for example, a cat from a dog), like most aspects of science, this is not the case. As a matter of fact, there does not yet exist a universal, objective definition for species. There do exist several imperfect methods of classification that have been used a various times, and though taken together, they are able to come very close to a truly objective standard, on their own they are lacking.

The first category is typology. This means that all members of a species conform to a set of fixed characteristics, and goes back to the classical standard of defining a new species. Once a new organism was discovered, the first example was killed, stuffed, or fixed in some manner, and then brought back to a museum and placed in a drawer. This was called the “type specimen,” and any other organisms that were thought to belong to its species would have to be compared to it. However, we know now that different physical characteristics can exist in members of a population without necessarily implying a difference in species.

The next category is Morphometry. This means that all members of a species will share certain physical characteristics. This is similar to what I just described with typology, with the subtle difference that instead of beginning with a type specimen, individual organisms are grouped by the way they look. While this seems to be common sense, the study of genetics has shown us that some organisms can look very similar without being closely related.

This next category is probably the most well-recognized- that of sexual isolation. This means that all members of a species are able, or are potentially able to interbreed. As some of you may be thinking, this completely precludes those organisms which reproduce asexually. This is true, and I’ll address that later. Sexual isolationism depends on the fact that usually there exists some kind of geographical barrier that separates two groups of one population for an extended period of time, during which both groups evolve independently of the other, and are eventually sexually incompatible for any number of reasons. The most glaring problem with this category are hybrids. Hybrids are the progeny of a sexual union between two organisms which are classified as separate species, but which are still closely related. Mules, for example, are the result of a cross between a horse and a donkey. Tigers and lions are also somewhat famously known to hybridize. In most cases, the hybrid progeny is sterile, and so the sexual isolationist could say that hybrids are no challenge to this definition of species, however, a small percentage of hybrids are able to breed back to one of the parental species, and so it would theoretically be feasible to generate a fertile, true-breeding hybrid species given enough time and resources.

The only other way to define a species is by the category of phylogeny. This means that all members of a species have a common ancestor, and that the lineage of the species is continuous. Now, taken on its own, it would be difficult to distinguish one species from another, since all organisms ultimately have a common ancestor, and so divergence between different groups are assumed based on evolutionary mechanisms. The most common way to do this now is through genomic analysis- by comparing the DNA sequences of different organisms we can determine phylogenetic relationships and thus distinguish between species.

But where does that leave asexual organisms? Well, we just do the best we can, and omit the third category I mentioned, that of sexual isolationism. This would include animals which reproduce by parthenogenesis, plants which reproduce by apomixis, as well as all bacteria, archaea, and protists. For these organisms, the concept of “species” is more like a temporary tag than anything stamped in metal. Evolutionary forces exerted on these organisms make their genomes more plastic through time, so they seem to be constantly in phenotypic flux. Sexual organisms, by comparison, have traded vertical plasticity for horizontal plasticity, and have populations with a high amount of genetic variation instead.

However, sometimes this potential for genetic variation can lead to situations where even sexual isolationism isn’t truly a cut-and-dry distinction. The evolution of new species often involves geographic variables, such as altitude, latitude, or bodies of water. Remember, the selective force that drives evolution is the ability of a population to adapt to a particular environment- if confronted with a different environment, a population has to adapt different characteristics. If those geographic variables exist linearly- that is, in a straight line- then we would expect to see a linear range of different species. We would also expect that similar species existing close to each other along that line would be able to interbreed or hybridize to a certain extent. What would happen, though, if instead of using a straight line, a population evolved along a circle? Let’s say, around a mountain range, or around a lake? This would then be called a “ring species.” What makes a ring species troublesome is that, if you start at the beginning of the ring and follow the different species in one direction, you find that each neighboring species can interbreed, until you come “full circle” and are back at the original species, which can not interbreed with the final species. There are several good examples of this, including the Ensatina salamanders of the California Simi valley, the Greenish warbler of Eurasia, and the Larus gulls which circle the Arctic.

I realize this is hard to visualize through a podcast, but try to imagine a circle drawn with the letters A through E written clockwise along the circle. If each of these letters represents a different subspecies, then A can interbreed with B, B can interbreed with C, C can interbreed with D, and D can interbreed with E. So far, this group of subspecies would be considered one big species, since in totality they can interbreed. But if you pair A and E, they cannot interbreed. So this poses a problem for those who would argue that sexual isolationism is the best objective criterion for defining a species: Clearly A and E are separate species by that definition, but there exists a continuous range of other populations that can interbreed between the two extremes. In this situation, the entire group of subspecies is considered a ring species. If, in the future, the intermediate subspecies B, C, and D go extinct for any number of reasons, then we’d be left with only subspecies A and E, in which case there’d be no problem calling them separate species.

Now, the concept of a species, and the various criteria that go into forming that concept, contain within them the idea of species organization. Because after all, what good is it dividing different organisms into species if you can’t arrange them in groups? And in fact, it was a man named Carl Von Linne (or Linneus) who first began to systematically divide organisms into species as part of his classification of all living creatures. It because of him that the scientific name of all organisms involved two names- the genus followed by the species name, usually in Latin or Greek. This organization, called taxonomy, is based on the principle of hierarchical organization. As you go up the hierarchy, you encompass more individual organisms. So, a species includes all populations of one organism, a genus includes all related species, a family includes all related genuses, all the way up to Kingdom, which Linneus considered the highest classification possible.

The problem with Linnean taxonomy is that it only organizes according to shared characteristics. While shared characteristics often accompany common descent, this is not always the case. A more meaningful method of taxonomic organization is called cladistics, in which taxonomic relationships are defined based on shared characteristics derived from ancestral population. A written example of this organization is called a cladogram, and looks something like a family tree, which is essentially the same kind of relationship that is implied. In a cladogram, however, each branch point only contains two branches, so that the organisms which are descendent from that stem can be divided into two groups based on one characteristic that one group of organisms share that the other group does not. In this way, evolutionary relationships can be inferred- two species that are separated by only two branch points on a cladogram are more closely related than two species that are seaparated by five branch points. In molecular biology, these branch points are determined by nucleotide or amino acid sequence similarity, and one can predict evolutionary relationships based on the cladistic hierarchy of a species’ genome.

So, just to review everything I’ve talked about- the concept of species is not a clear-cut as most people assume- in fact in some instances, like that of a ring species, it can be downright paradoxical. But regardless, there still exist many ways, through morphology and genetics, that we can distinguish between different types of organisms and even confirm evolutionary relationships between them.

That’s it for this episode of the Evolution 101 podcast. I hope you’ve noticed the new logo that was designed by our listener Sasha Richey.

Sunday, February 12, 2006

Darwin Day

I realize that I said this would be a weekly podcast, and it will, but I thought that this would be a good time to have a special episode since today is Charles Darwin’s birthday. Over the past couple years, more and more science enthusiasts have been celebrating today as “Darwin Day,” mostly just as a way to bring more attention to evolutionary theory in the context of the creation/evolution controversy in popular culture. This isn’t the only holiday of its kind- science enthusiasts have celebrated Isaac Newton’s birthday as Newtonmas, since his birthday is December 25th on the Julian calendar. When I was in high school, my chemistry teacher celebrated “Mole Day,” which honors the number of atoms in one mole of any substance, and I’ve heard that mathemtatics teachers celebrate Pi Day, which honors the number of the ratio between the circumference and radius of a circle. Creationists may use this day to accuse scientists of having a religious reverence for Darwin in the same way that Christians do for Jesus, Muslims do for Mohammed, and Buddhists do for the Buddha. To contradict this, I would like to point out one major difference- no scientist I have ever known has ever prayed to Darwin for a favorable result to an experiment.

But certainly Darwin has made an impact in popular culture, even in his own time. But a question posted to the messageboard by thoughtsurfer from Chicago seemed interesting to me. He says,

“A couple of years ago, my friend's wife looked at my Darwin fish on my car and said, "By the way, who's this Darwin guy?" I was pretty shocked by the question. I realize that most people won't know the fine details of most scientific theories, but to have never heard the name. I told her that was like not knowing who George Washington was.
Have there been any recent polls about how many Americans actually know what Darwinian theory is?”

That also seems shocking to me. But I went to religioustolerance.org, a great reference for religious statistics, and I was able to find a citation of a Gallup poll of Americans from 1991. Although this poll didn’t directly ask people if they knew who Charles Darwin was, it did as what beliefs they held in respect to creation and evolution. People were given three options: 1) strict creationism, 2) theistic evolution, which means that God directed the evolutionary process after creating basic organisms, and 3) naturalistic evolution, which omits any mention of the supernatural at all. The results showed that nearly half of all Americans believe in strict creationism, and less than ten percent believe in evolutionary theory as a naturalistic process. When the demographics were broken down, it showed that men were more likely to reject creationism than women, people with college educations were much more likely to reject creationism than people with only high school diplomas, and rejection of creationism increased directly with salary. Blacks were also more likely to accept creationism than whites. A similar poll in 1997 showed little change in these trends, but also compared laypeople to those with a science background. The results were pretty clear- 90% of people who’ve had some kind of science training rejected creationism outright, and over half accepted evolutionary theory as completely naturalistic.

This data helps motivate me to continue to engage in scientific outreach, such as this podcast. Although thoughtsurfer’s friend’s wife may have been less likely to accept evolution and, presumably, know about Charles Darwin as a woman, but she’d be even more likely to do so without any idea of the scientific principles and facts underlying it.

So who was Charles Darwin, anyway? Was he just some guy who thought up a crazy idea that just happened to be accepted as science and is advanced for the sole purpose of contradicting established religious beliefs? Hardly. Darwin was born on this day in 1809 in England to a wealthy doctor and member of the Unitarian church. (Incidentally, he shared his birthday with Abraham Lincoln, if that helps you place him in history) His paternal grandfather was Erasmus Darwin, who was a physician, inventor, and naturalist who theorized about evolution before his grandson was even born. Although his father wanted him to continue in the family tradition of medicine, Darwin was fascinated with science and biology at a very young age. Rejecting medicine, Darwin was enrolled in school to become an Anglican pastor and did very well as a theology student, but interrupted his education to continue his study of nature when he got the opportunity to travel on board a ship that was traveling to South America, called the Beagle. This journey took five years, and during this time Darwin spent most of his time observing different species and collecting fossils and specimens, as well as writing volumes of notes. He also spent time reading the work of geologist Charles Lyell, who had clearly shown that geological features such as rivers and canyons were the result of gradual changes caused by natural forces working slowly over time. It was particularly while visiting the Galapogos islands, which are a long chain of islands each separated from the other, and very far removed from the South American mainland, that Darwin made the observation that each island contained a slightly different species of finch. He wondered if each species could have derived originally from a single ancestor, which led to the idea of new species forming from existing populations. But this was not an idea that was unique to him- remember, his grandfather Erasmus Darwin had written about a very similar process, and Jean-Baptiste Lamarck, who I mentioned in the previous episode, had also theorized that species could change over time. What made Darwin’s idea unique was the mechanism that was proposed. In science, simply making an observation is not enough to warrant attention, nor is discussing the implications of those observations. For the scientific community to take notice, you have to provide a way to explain how those observations are taking place- you need a mechanism.

He got the inspiration for that mechanism from another man, Thomas Malthus. Malthus was a British political scientist and demographer who wrote wrote an essay demonstrating that, even by our best efforts, the human population would increase exponentially while the food supply would increase linearly. That is to say, the number of people would soon outnumber the availablility of food, and chaos would result. Darwin applied this principle to his idea of speciation- if a certain number of individuals in a population were competing for a limited food source, only those individuals who were best adapted to secure that food and reproduce would contribute offspring to the next generation. Eventually, those individuals that were poorly adapted to their environment would be bred out of existence, and only the best-adapted individuals would remain. Now, admittedly, this seems to be common sense to us now, but it was a revolutionary idea at the time. Darwin published his theory in 1859, calling it, ON the Origin of the Species by means of Natural Selection. Many people don’t know that Darwin wasn’t the only person to come up with this theory- a man named Alfred Russel Wallace, another naturalist working in Borneo had come up with the same idea independently.

Darwin published his theory reluctantly, because he knew that many people, especially those in religious circles, would object to it. But when he knew that Wallace had come to the same conclusions independently, he knew it was necessary to do so. If you get the chance to read Darwin directly, and I highly recommend that you try- you’ll find that Darwin is probably his own worst critic. I find this very commendable as a scientist- it’s a mark of scientific integrity to note the weaknesses of one’s explanation and the alternative explanations for one’s observations. Certainly Darwin’s theory was not complete- it was based on evidence, but he didn’t have nearly as much as he would have like. Fortunately, the discovery of countless fossils since his death and the burgeoning field of paleontology have provided and incredible amount of evidence in support of his theory. Another weakness of Darwin’s theory was that there was no proposed mechanism for the inheritance of traits. The work of Gregeor Mendel, which was carried out during Darwin’s lifetime but laid undiscovered until the early 20th century, showed that traits were inherited in discrete units, called genes. Further work showed that these genes were carried within cells’ deoxyribonucleic acid, or DNA, and Watson and Crick demonstrated the structure of DNA, leading to the modern field of molecular biology.

So, although Darwin’s work was important to the progress of science, I want to make it clear that there was nothing special about the man himself that led to his theory- he was doing nothing more than synthesizing existing science with new theories. If he hadn’t been born, we’d likely be discussing Wallace’s theory of natural selection instead. I also want to make it clear that evolutionary theory does not begin and end with Darwin. As I hope I’ve shown, the work of countless other scientists led up to his work, as well as have developed his work in the years past his death.

But regardless, happy 197th birthday, Charles, and thanks for all your hard work.

Thursday, February 09, 2006

What is NOT Evolution?

Last week I attempted to answer the question, “What is Evolution?” and I hope I was able to do so sufficiently. At the very least, I haven’t received any emails complaining about it. This, week, I’d like to look at the flip side of this question, “What is NOT Evolution?” In my experience, the main reason why people have a mistaken view of evolutionary theory is because someone has taught them something as evolution that is decidedly not. Most often, this teaching comes from creationists, who have it in their best interests to promote a strawman idea of evolutionary theory, the better for them to tear down. I’m going to focus now on one of Creationism’s prime offenders, Dr. Kent Hovind, or as some people may know him, Dr. Dino, from his website of the same name. Dr. Hovind is infamous for portraying evolutionary theory incorrectly, and I could probably devote a year of podcasts to his gaffs, but I’ll just start with one. In 2000, Dr. Hovind worked with Jack Chick publications to revise one of their most blatant anti-evolutionary tracts, which is called “Big Daddy.” This tract can be found at Jack Chick’s website, www.chick.com. During the course of the tract, the assertion is made that there are, in fact, Six basic concepts of evolution.

1) Cosmic Evolution: big bang makes hydrogen
2) Chemical Evolution: higher elements evolve
3) Planetary Evolution: evolution of stars and planets from gas
4) Organic Evolution: life from rocks
5) Macroevolution: changes between kinds of plants and animals
6) Microevolution: changes within kinds

This is patently false. Dr. Hovind was a biology teacher at one point, he should know as well as I do that there’s nothing about the Big Bang that relates to evolutionary theory. The first three “concepts” that are listed don’t even refer to biological principles- it’s astrophysics. The fourth concept refers indirectly to the concept of abiogenesis, the process by which life formed from non-life. This concept is biochemical in nature, and while it is of tangential interest to evolutionary theory, it has nothing directly to do with biology per se. Biology is the study of things that are alive- not the study of things that become alive. Although evolutionary theory assumes that life arose at some point in time, it is unnecessary to the theory to posit an mechanism for how that life came into being.

The last two concepts are really just one concept, separated by differences in scale. It is primarily creationists that talk about macro versus micro evolution, and when they do so, they do so to imply that different mechanisms are needed for each. This is also patently false. As I just said, both are evolution, but vary in terms of scale. Just as macro and micro economics are based on the same mechanisms, so are macro and micro evolution.

You also want to notice the word “kinds” in the tract. Dr. Hovind talks about changes between kinds and within kinds of animals. The word, “Kinds” is a Biblical term, and not a scientific term. Many creationists like to use the word kinds because scientists can point to examples of one species evolving into another species, at which point they retort with, “yes, but they’re both still the same kind.” This would presumably make “kinds’ synonymous with the classification genus, but I’ve run across creationists that will even backpedal on that, and say that “Kind” is synonymous with “order” Which, of course, means that they’d have no problem with the idea of pigs and cows evolving from a common ancestor. Doesn’t seem like that far of a stretch, right? Well, all primates belong to the same order also, so if Kinds is synonymous with order, then they’re admitting that chimpanzees and humans evolved from a common ancestor also.

Moving on, I want to talk about another creationist trick. Instead of mucking about with pseudoscience, this involves the Really Bad Analogy. A good example of this comes from evangelist Ray Comfort, who hosts the show Way of the Master with Kirk Cameron. I’m going to read a transcript from the show where Comfort gives an analogy of evolutionary theory. Quote:

It's my theory of where the soda can comes from. Billions of years ago, there was a big bang in space- nobody knows what caused the big bang, it just happened. And from this bang issued a huge rock, on top of the rock was found a sweet brown bubbly substance. And over millions of years, aluminum crept up the side and formed itself in a can, then a lid, and then a tab. And then millions of years later red pain, blue paint, white paint, fell down from the sky and formed itself into the words, "Twelve Fluid Ounces. Do Not Litter.” You say, what you’re doing is insulting my intellect, and so I am. As we know, if the can is made, there must be a maker. If it’s designed, there must be a designer. To believe the soda can happened by chance is to move into an intellectual free zone, is to have an echo when you think, is to have brain liposuction. End quote.

Comfort insults all our intellects with this. Of course his analogy sounds ridiculous, because it involves the evolution of a non-living thing. Evolutionary theory is a theory of biology- it’s going to sound ridiculous if you frame it out of context. This is nothing more than Paley’s watchmaker argument, dressed up for a teenaged audience, because let’s face it, who else is going to be impressed by a soda can?

And finally, I want to look at an evolutionary misconception that doesn’t come from creationists- it actually comes from a biologist that Charles Darwin held in high esteem. His name was Jean-Baptiste Lamarck, and he formulated a theory of evolution before Darwin put pen to paper. Unfortunately, although he was well-intentioned, he was wrong. But we was wrong for a pretty good reason- the mechanism that he proposed makes a little more intuitive sense than Darwin’s mechanism of natural selection. According to Lamarck’s theory, individual organisms acquired traits throughout their lifetime and then passed them on to their offspring. The classic example of this is the giraffe, which he believed gained a long neck by successive generations of individuals straining to reach high leaves, stretching their necks out bit by bit over the generations. Another, more blatant example of this would be someone who exercises their whole life, building huge bicep muscles, and then has a child with larger than normal muscles. This just doesn’t happen. Another aspect of Lamarckianism that still hangs around is the idea that evolution has a goal. It does not. Organisms evolve because of pressure to adapt, nothing more. Bugs, plants, and bacteria are all as well-adapted as humans are, and we are all at the same level of evolution. In fact, you might even say that bacteria are more highly evolved since they are able to adapt to environments that humans couldn’t even venture into with specialized equipment. Bacteria may even be able to withstand the rigors of space travel.

So, I hope I’ve been able to dissuade you from these false conceptions of evolutionary theory, and I hope that you’re able to recognize these as false when they’re put forth by creationsist or others ignornant of evolution.