How we evolve

Seed has an article about How We Evolve. It’s a fantastic read that I won’t try to break down since it’s already written in an enormously friendly manner. I do, however, want to focus on one part.

“Intelligence builds on top of intelligence,” says Lahn. “[Culture] creates a stringent selection regime for enhanced intelligence. This is a positive feedback loop, I would think.” Increasing intelligence increases the complexity of culture, which pressures intelligence levels to rise, which creates a more complex culture, and so on. Culture is not an escape from conditioning environments. It is an environment of a different kind.

There’s the pervasive notion that human evolution has stopped because we have this flat-seas type of environment where no selection pressure is applied except in the most extreme of circumstances. Indeed, this is a major subject of the article (I guess I did break it down a little). I just find it tremendously unfortunate that even biologists have it in their heads that humans face such limited evolution; the recent comments from Steve Jones are especially disheartening. It’s just something everyone needs to face: evolution happens and nothing stops it except extinction.

It still isn’t random

This is apparently some confusion over my post about why natural selection is not random. It’s a fairly elementary issue at hand, but it evidently needs to be addressed. One reader mentions,

Natural selection is a product of selective pressures. Those selective pressures are random in that they do not try to produce anything specific (ie: original appendages, limbs, organs, organ systems, body plans, etc… or the DNA that codes for them).

This user is right so far, even if the language is a bit dicey. A particular environment produces conditions to which a population then responds. A research job from a biology professor of mine will do fine here: there are two species of fish in a stream, one small, one large. This stream is divided into two sections: an upper area and a lower area. The division is due to a small waterfall. Now, the small fish in the top section of the stream tend to be vibrant in color while the lower small fish are a more gray color. The hypothesis is that the large species of fish is unable to traverse the waterfall so thus unable to eat the upper small fish, hence their vibrancy. So the research team takes some large fish and introduces them into the area with the vibrant fish. Sure enough, the fish lose their vibrancy pretty quickly. Conclusion: The hypothesis was not falsified because a correlation between color vibrancy and survival was shown upon introduction of the large fish species to the upper stream.

So now here’s where the user goes awry.

Hence, natural selection is random.

He concludes that because the selective pressures happen without regard to a particular species that the reaction of the species is thus random. Do you see the inane logic? This is like saying that because what particular rocks, gas, and space junk goes into the making of a planet can be called random that the force behind the accretion process – gravity – is random.

It’s all very simple. Natural selection is the process of differential survival of organisms based upon how they respond to a given environment. That means that natural selection happens with regard to adaptability. And maybe this is the kicker for this silly creationist. That’s really all “non random” means – with regard to adaptability. That’s why any aspect of genetic drift or mutation is considered random. It happens regardless of whether an organism will do better, worse, or the same in its survival. Were natural selection random then we should expect to see a number of vibrant fish swimming around the upper stream which is in comparable proportion to the number swimming around prior to the introduction of the large fish species. Of course we do not see anything like that. What we do see is differential survival based upon the response of the organism to a particular environment – the fish which survived were less vibrant, on average, than the fish which were quickly eaten.

It still isn't random

This is apparently some confusion over my post about why natural selection is not random. It’s a fairly elementary issue at hand, but it evidently needs to be addressed. One reader mentions,

Natural selection is a product of selective pressures. Those selective pressures are random in that they do not try to produce anything specific (ie: original appendages, limbs, organs, organ systems, body plans, etc… or the DNA that codes for them).

This user is right so far, even if the language is a bit dicey. A particular environment produces conditions to which a population then responds. A research job from a biology professor of mine will do fine here: there are two species of fish in a stream, one small, one large. This stream is divided into two sections: an upper area and a lower area. The division is due to a small waterfall. Now, the small fish in the top section of the stream tend to be vibrant in color while the lower small fish are a more gray color. The hypothesis is that the large species of fish is unable to traverse the waterfall so thus unable to eat the upper small fish, hence their vibrancy. So the research team takes some large fish and introduces them into the area with the vibrant fish. Sure enough, the fish lose their vibrancy pretty quickly. Conclusion: The hypothesis was not falsified because a correlation between color vibrancy and survival was shown upon introduction of the large fish species to the upper stream.

So now here’s where the user goes awry.

Hence, natural selection is random.

He concludes that because the selective pressures happen without regard to a particular species that the reaction of the species is thus random. Do you see the inane logic? This is like saying that because what particular rocks, gas, and space junk goes into the making of a planet can be called random that the force behind the accretion process – gravity – is random.

It’s all very simple. Natural selection is the process of differential survival of organisms based upon how they respond to a given environment. That means that natural selection happens with regard to adaptability. And maybe this is the kicker for this silly creationists. That’s really all “non random” means – with regard to adaptability. That’s why any aspect of genetic drift or mutation is considered random. It happens regardless of whether an organism will do better, worse, or the same in its survival. Were natural selection random then we should expect to see a number of vibrant fish swimming around the upper stream which is in comparable proportion to the number swimming around prior to the introduction of the large fish species. Of course we do not see anything like that. What we do see is differential survival based upon the response of the organism to a particular environment – the fish which survived were less vibrant, on average, than the fish which were quickly eaten.

Stop with the apologies

I recently visited the National Zoo in Washington D.C. It was somewhat late in the day so animal activity was down a bit, but it was still pretty interesting. The golden lion tamarin was by far the best animal in the park for me; what’s more, it was featured in quite a few exhibits (as well as the Balitmore Aquarium, for some reason). But there was one huge pitfall: Apology for exhibiting evolution.

Upon entering the Think Tank I expected to see a few apes, hopefully an Orangutan. I did see those things, but I also saw a decent sized section devoted to human evolution (with a primary focus on tool use). The problem was what amounted to an apology for a branch of science. A sign at the entry warned visitors that they may be offended by what they are about to see.

So? Who cares if people are offended? It isn’t the job of the zoo, especially a publically funded one, to apologize to people who have yet to gain a grasp on evolution. If they find it offensive, then that’s just too bad. No organization wishing to present scientific information to the public (and the zoo, other than this instance, does a fine job) should (essentially) be apologizing for that information. What a few yahoos think does not change the truth value of anything in science.

Why Natural Selection is Not Random

Update: Read this article instead.

Every once in awhile (read: all the damn time), a creationist will say evolution is random. Sometimes they say natural selection is random (the words are rather interchangeable among some creationists). But one creationist does us one better and calls both of them random (and the Big Bang, too). So here is an article I wrote quite a few months ago on the topic. The first couple grafs were mainly meant to be topical, so at this point they’re a bit out of date. Deal.

Why Evolution Is Not Random

During a CNN June debate, Republican presidential candidate Mike Huckabee raised his hand when asked whether or not he accepts the theory of evolution. More recently, the Florida Board of Education spent several months deciding if the mere word ‘evolution’ should appear in the curriculum. After many debates, a compromise was met where evolution was referred to as only a theory, not a fact (gravity is also a theory, not a fact). In the Spring 2008 Ben Stein will revive his career on the silver screen. But rather than asking if anyone has seen Bueller, he will be questioning the motives of the scientific community at large. An overwhelming majority of biologists regard the notion of intelligent design – the proposal that life is so complex there must be a creator – as unscientific. Ben Stein sees a conspiracy.

Behind all of these cases is a fundamental underpinning: the desire to bring more people to God. But what is often accepted is the erroneous means to this end. The very public war against the theory of evolution has brought many of these means to light for evolutionary biologists, the crusaders and rottweilers of Charles Darwin’s revolutionary theory.

Perhaps the most vibrant means is the argument against plausibility. To be at all likely, evolution cannot be a random process. Yet this is exactly the case made by many creationists and, indeed, is one of the more popular starting points in a stance opposing the theory of evolution.

One of the reasons creationism could be considered plausible is that it makes complex life likely. If a supreme being exists which can do as he pleases and has the means, then why not create life? This does fail to answer the nature of the origin of a being complex enough to create life (and presumably the Universe), but all things equal, evolution does not address the issue of the origins of life (nor did Charles Darwin ever intend for it to do that). So if one is to parallel the situation, it is well enough to side-step answering the origin of a supreme being for our current scope.

So it follows that if creationism, from at least a certain point, makes complexity likely, then the creationist argument that evolution is random must have a basis in opposing the likelihood of complex life forms. Dr. David Menton of the $27 million Creationist Museum in Kentucky and graduate of Brown University with a Ph.D. in cell biology, puts the creationist standpoint succinctly, saying “Evolutionists feel vulnerable to evolution being pure chance.”

But what of “pure chance”? Evolution consists of many mechanisms, but the two big driving forces are natural selection and random mutation. (To be fair, random mutations should be considered more as just a force rather than a driving force.) So why do some consider these mechanisms to be random? Dr. Menton appeals to the idea that “science is built on a statistical foundation.” Natural selection and random mutations do not result in complex life forms because such occurrences are greatly improbable. Answers in Genesis, the group which runs the Creation Museum, explains further on their website, http://www.answersingenesis.com. “The probability of the chance formation of a hypothetical functional ‘simple’ cell, given all the ingredients, is acknowledged to be worse than 1 in 1057800.” In other words, evolution is about as likely as all the atoms in the Statue of Liberty moving in one direction and then the other, making her appear as though she was waving to all who came to America. It’s possible, but so unlikely that it isn’t worth devoting much thought.

So if evolution is such a stupendously unlikely thing to happen, then why do we give it any credit? Why bother with such odds? If evolution is unlikely, then a mechanism which provides a path to complexity is necessary if the theory is to survive scientific scrutiny – nay, if it is to survive any scrutiny. Natural selection is the answer for most biologists. Ken Miller, a professor of biology at Brown University, perhaps best known for his testimony in the ‘Intelligent Design’ trial (Kitzmiller v. Dover Area School District) in Dover, Pennsylvania (and subsequent appearance on Comedy Central’s The Colbert Report), but also famous for his opposition to creationism, is one such biologist.

“I have no idea why someone would take a term like natural selection and say it is random”, said Miller when reached for an interview.

Miller sees natural selection as one of the essential paths to complex life forms. Such a mechanism gives species the ability to filter out what doesn’t work and leave what does. Professor Miller echoes this notion, saying “[n]atural selection is a distinctly non-random process that acts as a sieve through which genetic changes are filtered.” Just as a sieve filled with various rocks will not end up filtering out its contents randomly, natural selection does not filter organisms randomly.

But how else can it be said natural selection is non-random? In The Origin of Species, Charles Darwin compares it to artificial selection. That is, when humans breed, say, dogs, for particular traits, they are applying a form of selection pressure to a phenotype (a particular dog or particular dogs). This in turn results in the great variety we see among our beloved pets. The key difference here, however, is that this form of selection had a particular goal in mind, i.e. floppy ears, sleek body, fluffy coat, wrinkly skin, etc. Humans were able to apply their foresight and consciousness to the reasoning behind the selection. Nature does not do this.

This notion that natural selection is both a non-random process and an undirected one at the same time can lead to confusion. The concept is essentially that this mechanism lends itself to increasing complexity because it builds in cumulative steps. For a step to be cumulative, it (quite obviously) must be based on the previous step. A random process does not lend itself to cumulative steps because, by definition, it is not based on anything. So in this way natural selection is non-random. But it also does not look to end in the phenotype of a tiger or a bat. It has no conscience, merely results. For this reason, it is undirected.

But the second key ingredient in evolution is random mutation. As Jay Labov of the National Academy of Sciences points out, “[n]atural selection acts on things that are already there.” Without random mutations, there isn’t much there; certainly not enough to account for the great genetic variation seen within species today.

There is dissent, however, from the creationist side. Dr. Menton certainly agrees that natural selection can only act on what it is given (“I believe [it] occurs. I believe in it completely”), but he disagrees that the genetic variation is available for one species to become another. This is because “[r]andom mutations do not provide for the raw material for novel information. It’s like going to Midas and asking for a dozen yellow roses. They just aren’t there,” he says. Without these genetic changes, “[w]e don’t see natural selection producing novel features.” Menton goes further to add that something like a reptile does not have the raw material to produce the features, such as wings, which are seen in birds.

The first issue of whether or not random mutations can add novel information can be answered in day-to-day life. Mutated animals (including humans) are fairly common. A person with an extra finger or a snake with two heads are both examples of organisms which have mutations. These are deleterious (bad) mutations, but they aren’t the most frequent. More commonly, neutral mutations occur. These aren’t particularly acted upon by natural selection because most genes tolerate changes quite well, according to Miller. Sometimes, however, a gene will mutate and it will be beneficial. It may extremely slight, but if it offers any survival advantage at all, it is more likely to survive the sieve of natural selection. For example, a mutation which makes a bacterium immune to antibodies will quickly spread throughout the population.

A second issue is whether or not natural selection can produce novel features. Assuming random mutations do not provide for novel information (they do), natural selection can still produce novel features. Dr. Menton’s example of reptiles and birds works perfectly.

“Reptilian ancestors of birds had wherewithal to produce feathers,” says Miller. When speaking of the more than dozen dinosaur fossils which show feathers, he continues, “One (Shuvuuia deserti) has tested positive for the major protein found in bird feathers.”

What does this mean? Simply, ancestors of modern day reptiles had the information to create novel features. But it is “[e]nvironmental factors [which] may turn genes on and off,” says Labov. Whether or not the genes needed to create the particular feature of feathers show up in a phenotype is determined by need, which is governed by natural selection.

Anne Holden, staff member at the National Center for Science Education, further supports the point of natural selection having great genetic variation with which to work by pointing out that our “DNA can recombine and does recombine during fertilization.” The genome of an offspring is a combination of its parents’ genes, but the way in which recombination can occur is impossible to number.

Holden further cites the adaptive radiation of Darwin’s finches on the Galapagos Islands. As a result of the variation within every organism which is born, the famous finches which where pivotal in Darwin’s formulation of the mechanism of natural selection, had the ability to become distinctly varied throughout the Pacific islands they inhabited. Not only were these finches much different from the familiar European ones Darwin knew, but they were different from island to island. Depending upon the size of the food supply (nuts, primarily), the finches’ beak sizes changed accordingly. A random happenstance of small, medium, and large beaks were not the case on an island where small, hard to get shells persisted. Instead, natural selection non-randomly ‘selected’ for the birds which were best adapted to the task at hand.

It is important to restate the point of this article. Evolution has a strong random element, but natural selection is not a random process. It is this mechanism which gives rise to the great complexity seen in all living organisms today. It does not indicate what the result will be, but it does explain that complexity can be. It builds, in cumulative steps, toward greater adaptability. As a great man once said, there is a grandeur in all this.

Eyespots

History recently aired a series called “Evolve” which focused upon various aspects of evolution: wings, sex, guts, etc. But the most interesting episode was probably the one on eyes. It’s pretty clear they started out with eyes because of all the hub-bub made by creationists who find this organ to be too complex to have evolved by blind chance (what about the brain?). Natural selection is not chance (though it is blind – half credit), but such a misconception is one of the reasons eyes needed to be a starting point.

What History didn’t do, however, was get down to the cellular level of eye evolution. They may have touched upon photoreceptive cells, and that’s technically the cellular level, I suppose, but it overlooks an important aspect of evolution: everything which evolved today began its evolution (eventually) at the cellular level. So it is to my delight that I came across a Wikipedia article on eyespots.

Eyespot apparatus of euglena

Eyespots are a lot like they sound they are. They’re photoreceptive areas found in some plants cells (algae) and even in single celled organisms such as the euglena featured above. These are simply areas which cause a reaction to light – it becomes too bright, you may be too close to the surface. Swim away.

The advantage should be quite clear. The ability to detect light – not shape, size, dimension, or detail – gives an organism a lot of information about its environment. Specifically, History did address the eyespots of certain squids. These squids, only having nervous systems (no brains), would simply go into a sort of lull when coming near a certain wave length of light. As it not-so-coincidentally happens, that wave length corresponds with the wave length common near the food source of these squids.

Here’s the interesting kicker for which I think everyone should perk up: the origin of these eyespots works upon signal transduction, which is initiated by enzymes. This is what happens in every cell everywhere. Enzymes catalyze various things within cells. Lactase, for example, catalyzes lactose into galactose and glucose monomers – you drink milk, proteins (lactase) in your body will break it down into its constituents. It’s basic biology.

So how do new enzymes arise that can cause the formation of eyespots? This is a matter of a mutation within the DNA of a cell. Some “letter” of DNA is changed through some sort of error in copying. It happens all the time. You have 50-100 mutations in you right now (most, if not all, are probably neutral). DNA replication isn’t perfect. So a simply mutation can quite easily code for a new enzyme, which can cause the formation of an eyespot – the beginning of the eye. A slow, cumulative building through, perhaps, further mutation combined with the non-random action of natural selection can (and has separately over 40 times) evolve a complex eye worthy of fighting on the evolutionary stage of life.

What is a Theory and What is Not a Theory

Ever since the media (apparently not McCain) decided it would be a good idea to finally vet Sarah Palin, much has come to light. I’ll leave discussion of tax plans and foreign policy to the political boards, but there is one thing which really needs to be noted. Palin has said in the past that she thinks both evolution and creationism should be taught, referring to them as theories. She later backed off that statement. In the past couple of months, she further clarified her position:

Couric: Should creationism be allowed to be taught anywhere in public schools?

Palin: Don’t have a problem at all with kids debating all sides of theories, all sides of ideas that they ever – kids do it today whether … it’s on paper, in a curriculum or not. Curriculums also are best left to the local school districts. Instead of Big Brother, federal government telling a district what they can and can’t teach, I would like to see more control taken over by our school boards, by our local schools, and then state government at the most. But federal government, you know, kind of get out of some of this curriculum and let the locals decide what is best for their students.

To any person remotely familiar with science, there should be a glaring initial error in that statement. It doesn’t have to do with the merits of debating evolution, but with this notion that there are alternative theories to evolution. Given the context of what Palin has said in the past in addition to her beliefs, it’s overwhelmingly clear she has it in her head that creationism is somehow a theory. Insofar as my theory that ice cream is great can be considered a theory, yes, creationism is a theory. But it is not in any way a scientific theory. The requirements to reach this high level are rigorous. For starters, what predictions does creationism make? What experiments can be carried out to falsify the hypothesis? Can others repeat these experiments? Are there other plausible explanations? Are there better explanations?

In the case of evolution, we see predictions a-plenty being made. We could easily falsify the hypothesis by finding a rabbit in the pre-Cambrian. And we can culture any number of species and see how they adapt to their environments. In truth, the evidence is far more overwhelming, far more testable, far more falsifiable, and far more concrete than I’ve just touched on here. But that’s a question for later. The question here is, why doesn’t the daughter of a science teacher know the difference between a layman theory and a scientific theory? Hell, why doesn’t an educated adult know this?

The truth is evolution is the backbone to every field of biology. It is what creates a coherent picture. From nucleic acids to substrates fitting active sites to differential survival of members of a population, evolution provides the only sensical view of life from its beginnings – and it has yet to be falsified to any point that isn’t merely a shaping and strengthening of the theory. Sarah Palin should know better.

Beware What You Read

It’s quite common for the media to exaggerate claims or to use the tactic of fear to get readers or viewers. At the risk of contradicting my last post on anecdotal evidence, just watch an episode of Dateline. Your mattress may be ridden with bed bugs!

So it comes as little surprise that Yahoo! has an article up noting that triclosan (a pesticide) may do more harm than good.

There are concerns that triclosan may contribute to the rise of antibiotic-resistant bacteria. It’s also present in human bodies and breast milk, as well as in streams. The Environmental Working Group says triclosan has been linked to developmental defects, liver toxicity, and cancer in lab studies. It also may affect thyroid and other hormones that are crucial to normal development.

These “concerns” are rather fabricated. It may very well be true that triclosan has horrible, apocalyptic effects that will stunt your growth and give you cancer. But it’s pretty unlikely. And the honest results of the study bear this out.

Further research is clearly needed to assess whether the emergence of antibiotic resistance in the community setting is associated with the growing use of soaps containing triclosan.

The reason for this is that the study had so many variables in it, it’s basically pretty tough make a definitive determination one way or the other. For starters, there is no known baseline resistance for triclosan. That is, no one knows how much triclosan resistance is naturally in bacteria populations and how much is there due to the increased use of triclosan. Then there’s the fact that the studies didn’t bear out higher rates of resistance in these ‘natural’ settings. If you control the environment and allow little to no contaminantion, yes, facing specific bacteria against a pesticide may very well result in an increased resistance. There are no guarantees in evolution, but the effects of natural selection can be a bit exaggerated in the lab. One possible reason no resistance was found in the uncontrolled environments is that any added genetic mutations are too specific and costly to do well.

So essentially, it is inconclusive whether there is any added danger to using soaps with triclosan in them. Bacteria is unlikely to become resistant outside a lab, especially when there is more than one species at a time vying for survival against this pesticide. Again, there are no guarantees in evolution, but I’m betting your livers and thyroids are safe.

But to be fair, the Yahoo! article is initially focused on pointing out that anti-bacterial soaps are no more effective at hand hygiene than traditional soap and water. This is an accurate description of the findings of this study. I just hope Yahoo! is more careful next time when they want to elicit fear from readers. I won’t hold my breath.

Great New Tiktaalik Research

Details of Evolutionary Transition From Fish to Land Animals Revealed

So the jist of this new research is that Tiktaalik roseae has been vetted a bit better. Researchers viewed several Tiktaalik fossils and discovered some interesting new information on its internal anatomy. Of specific interest is the hyomandibula. Its function has changed significantly from its early arrival in fish to its current use in mammals. As it stands, this bone functions as part of the ear for mammals. It also functions as part of cranial motions for fish, namely it is very important to gill respiration. In Tiktaalik, it had a transitional function. That isn’t to say it acted as a sort of ear-gill. It didn’t. It had a function that resulted in better cranial movement, inherently giving it less importance toward gill respiration.

What’s really important here is to realize that this is the exact same bone in mammals as it is in fish. If Tiktaalik lies somewhere between fish and most land animals, we should see quite a few features lying in between. That’s precisely what we see. What’s further, this should help to demonstrate that when scientists speak of transitional features, they do not mean hybrid phenotypes like ear-gills or the silly crocoduck