Flu virus evolution

Earlier this week, The New York Times website posted an interesting article by Carl Zimmer in which he discusses how viruses are able to continually evolve into new varieties, and how that relates to the current "swine flu" pandemic. Here are some of the highlights:

The current outbreak shows how complex and mysterious the evolution of viruses is. That complexity and mystery are all the more remarkable because a virus is life reduced to its essentials. A human influenza virus, for example, is a protein shell measuring about five-millionths of an inch across, with 10 genes inside. (We have about 20,000.)

Some viruses use DNA, like we do, to encode their genes. Others, like the influenza virus, use single-strand RNA. But viruses all have one thing in common, said Roland Wolkowicz, a molecular virologist at San Diego State University: they all reproduce by disintegrating and then reforming. [...]

Viruses are diverse because they can mutate very fast and can mix genes. They sometimes pick up genes from their hosts, and they can swap genes with other viruses. Some viruses, including flu viruses, carry out a kind of mixing known as reassortment. If two different flu viruses infect the same cell, the new copies of their genes get jumbled up as new viruses are assembled. [...]

As new hosts have evolved, some viruses have adapted to them. Birds, for example, became the main host for influenza viruses. Many birds infected with flu viruses do not get sick. The viruses replicate in the gut and are shed with the birds’ droppings.

A quarter of birds typically carry two or more strains of flu at the same time, allowing the viruses to mix their genes into a genetic blur. “Birds are constantly mixing up the constellation of these viruses,” said David Spiro of the J. Craig Venter Institute.

From birds, flu viruses have moved to animals [sic], including pigs, horses and humans. Other viruses, like H.I.V. and SARS, have also managed to jump into our species, but many others have failed. [...]

Only a few strains of influenza have managed to become true human viruses in the past century. To make the transition, the viruses have to adapt to their new host. Their gene-building enzymes have evolved to run at top speed at human body temperature, for example, which is a few degrees cooler than a bird’s.

Influenza viruses also moved from bird guts to human airways. That shift also required flu viruses to spread in a new way: in the droplets we release in our coughs and sneezes. [...]

Up to a fifth of all Americans become infected each flu season, and 36,000 die. During that time, the flu virus continues to evolve. The surface proteins change shape, allowing the viruses to evade the immune systems and resist antiflu drugs. [...]

From time to time, a new kind of flu emerges that causes far more suffering than the typical swarm of seasonal flu viruses. In 1918, for example, the so-called Spanish flu caused an estimated 50 million deaths. In later years, some of the descendants of that strain picked up genes from bird flu viruses.

Sometimes reassortments led to new pandemics. It is possible that reassortment enables flu viruses to escape the immune system so well that they can make people sicker and spread faster to new hosts.

Reassortment also played a big role in the emergence of the current swine flu. Its genes come from several ancestors, which mainly infected pigs. [...]

In the late 1990s, American scientists discovered a triple reassortant that mixed genes from classic swine flu with genes from bird viruses and human viruses. All three viruses — the triple reassortant, and the American and European pig-bird blends — contributed genes to the latest strain.

Interesting Court Ruling

On Friday, a District Court in California ruled on a case, C.F. v. Capistrano USD (PDF), in which the central issue was whether a high school teacher violated his students' religious freedoms by making statements in class that were openly hostile to religious beliefs. While the Establishment Clause of the Constitution stipulates that the government (including public schools) cannot establish or promote a particular religious belief, the Free Exercise Clause makes it illegal to prohibit the free exercise of religion. The Courts ruling on behalf of the plaintiffs basically says that a teacher did, in fact, infringe on the religious freedom of his students when he referred to creationism as "superstitious nonsense."

This isn't the only statement made by this teacher (a Mr. Corbette) which was questioned. It was, however, the only one for which the Court opined there was no secular purpose...meaning the intent of the language served no legitimate purpose other than to show a disapproval of religion. Ed Brayton has written a nice summary and opinion here. Unfortunately, you won't be able to access that link from school since it's a (!gasp!) blog.

The key part of the ruling is this:

The Court turns first to Corbett’s statement regarding John Peloza (“Peloza”). This statement presents the closest question for the Court in assessing secular purpose. Peloza apparently brought suit against Corbett because Corbett was the advisor to a student newspaper which ran an article suggesting that Peloza was teaching religion rather than science in his classroom. Corbett explained to his class that Peloza, a teacher, “was not telling the kids [Peloza’s students] the scientific truth about evolution.” Corbett also told his students that, in response to a request to give Peloza space in the newspaper to present his point of view, Corbett stated, “I will not leave John Peloza alone to propagandize kids with this religious, superstitious nonsense.” One could argue that Corbett meant that Peloza should not be presenting his religious ideas to students or that Peloza was presenting faulty science to the students. But there is more to the statement: Corbett states an unequivocal belief that creationism is “superstitious nonsense.” The Court cannot discern a legitimate secular purpose in this statement, even when considered in context. The statement therefore constitutes improper disapproval of religion in violation of the Establishment Clause.

As a science teacher, my first impulse here is to applaud this ruling. I understand that Mr. Corbett did not want to give another teacher a platform to try to pass of supernatural beliefs (which are, by definition, not scientific) as legitimate science. This is a stance taken by many in the scientific and educational communities. Mr. Corbett crossed the line, however, when he used emotionally charged language to denigrate the beliefs of that teacher as part of his classroom instruction.

Public school teachers have the responsibility, as professionals, to provide the best education possible to their students. I will continue to stand firmly behind my assertion that this is ONLY accomplished in science when we teach SCIENTIFIC principles, including the robust and well established theory of biological evolution. I will stand firmly behind my assertion that trying to force public schools to teach religious views such as creationism, creation science, or intelligent design in science classes is absolutely unconstitutional. And I will stand firmly behind my assertion that to profess a religious belief which involves special creation in any form means that you have to be able to explain away mountains of hard, well-established scientific evidence...or simply be willing to accept that your beliefs are not in line with current scientific thinking.

HOWEVER...I also will stand firmly behind the idea that a student's religious belief (or lack thereof) is their belief which they are entitled to. How a student sees themselves in relation to a higher power is at the core of their understanding of the world and themselves. When a teacher, acting as a professional public educator, intentionally bashes a particular religious belief for no other purpose than to advance their own atheistic worldview is nothing short of educational malpractice. And it makes it that much more difficult for those of us who are trying to have real, open, and honest conversations about the relationship between science and religion.

As Brayton puts it so well:

There will inevitably be conflicts between things taught in school and the religious beliefs of some students. When those conflicts occur, a teacher has to handle those situations with some degree of sensitivity. It is one thing to tell a student that they are teaching something because it is the position best supported by the evidence; it is quite another to tell them that their religion makes them incapable of seeing the truth and that their religion is a fraud believed in by fools. I think this teacher clearly crossed over the line here, and not just in the one statement the court found to be a problem.

I couldn't agree with him more.

Missing links

There's a good reason why you don't hear knowledgeable people talking about "gaps" or "missing links" in the fossil record. It's because, while the fossil record will never be complete, scientists are continually discovering new fossilized species. And these new species continue to show transition of life from one form to another throughout evolutionary history. As ScienceNOW reported last week, scientists have recently discovered the fossilized remains of a land dwelling mammal that appears to be an ancient relative of modern seals, sea lions, and walruses.

The 20-million- to 24-million-year-old Arctic fossil sports webbed feet instead of flippers, providing a long-sought glimpse of what such animals looked like before they dove into the sea.

Before marine mammals swam through the world's oceans, their ancestors meandered on land. Researchers have founds several intermediate fossils that trace the transition from land to water in whales and manatees, but they have no such record for pinnipeds--seals, sea lions, and walruses. Much to scientists' dismay, the most primitive pinniped fossils, which date to between 20 million and 28 million years ago, had full flippers, making it hard to pinpoint how the animals evolved to live in an aquatic environment. [...]

The 110-cm-long animal, Puijila darwini, resembled an otter, with a long tail, doglike teeth, and webbed feet. Like an otter, its body was adapted for swimming but spent most of its time on land. Rybczynski says that although the creature wasn't the direct ancestor of modern pinnipeds, it reveals what these ancestors might have looked like before they became fully flippered. She also says that finding this primitive fossil in the Arctic suggests that this area could be the center of pinniped evolution, contradicting the prevailing idea that the mammals evolved along the western coast of North America.

So here we have a fossil that shows characteristics of both land mammals and marine dwelling pinnipeds. That, my friends, is by definition a transitional fossil, which fits neatly into a "gap" in the fossil record. And as interesting as the fossil itself is, the story of its discovery is the stuff of science folklore:

In 2007, vertebrate paleontologist Natalia Rybczynski of the Canadian Museum of Nature in Ottawa and her colleagues were returning to their camp from a long day of fieldwork in the Canadian Arctic when they ran out of fuel. While Rybczynski left to get more gas, her graduate student, who was supposed to make sure that the vehicle was refueled, scuffed the ground in irritation and uncovered part of a shin bone. By the time Rybczynski returned, her colleagues' hands were filled with little black bones, and they were doing what Rybczynski refers to as "the fossil dance." Within a few days, the team had recovered most of the skeleton.

At first, they thought they had uncovered some sort of strange otter, but when they examined the fossils back in the lab, the teeth and parts of the skull hinted that the animal was a flipper-less, primitive pinniped. They couldn't be sure, because they lacked the diagnostic portion of the skull. Within minutes of returning to the field in 2008, they found what they were looking for and celebrated with another round of fossil dances. The skeleton represents the most primitive pinniped to date, the team reports...

You see how that works? You make an observation, collect data, learn as much as you can from that data, and then use that data to make predictions that drive further testing.

Science. It's good stuff.

(Image credit: Mark A. Klingler via Origins)

More on Texas

The National Center for Science Education (NCSE) is a non-profit organization dedicated to protecting the teaching of evolution in public school science classrooms. The organization's executive director is Dr. Eugenie Scott, who holds a PhD in physical anthropology from the University of Missouri.

Dr. Scott appeared last week on NPR's Science Friday program, where she discussed the recent adoption of new (creationist friendly) science education standards in Texas. In her interview with host Ira Flatow, she discusses the new standards, why wording and language are important, and what exactly is at stake with the passage of the new standards. You can access the interview and listen to it by following the above links, or you can download an mp3 of it here.

Here is video of Dr. Scott's testimony before the Texas State Board of Education last month:

Easter Bunny biology

I pulled this essay by Darksyde off of DailyKos yesterday (thanks to the Panda's Thumb for pointing pointing it out).

Rabbits are mammals of course and at first glance they appear to fall in with squirrels, mice, chipmunks and a bunch of other adorable little critters that make up the most successful order of mammals on earth today: rodents. [...]

More recent anatomical comparison (however) suggests rabbits may not be rodents at all. In fact, they might be an offshoot or close relative of early Artiodactyls like the indohyus on the left. Modern artiodactyls include the largest, most unrabbit-like animals on earth today. But back in the Paleocene they were tiny and some, like mouse deer, still are. With tens of millions of years to work with, it's entirely possible an early artiodactyl or forerunner of same evolved into an order of their own, called Lagomorphs, now represented by rabbits, pikas, and hares. If so, one of the closer extant relatives of petite bunny rabbits would be the great Blue Whale!

So if you noticed that the bunny delivering your Easter-goodies yesterday morning seemed to be a little pre-occupied, it's probably because he was in the middle of a major identity crisis. But while this may be unnerving for the poor rabbits who now may find themselves classified more closely to giraffes and whales, it is a great illustration of how scientific models are constantly changing as new information and ideas become available.

Darksyde does end his essay on a somber note:

Alas...I must report that at present there is no evidence in the fossil record of a mansized, bipedal rabbit creeping around in the wee hours delivering candied eggs or self portraits rendered in sweet chocolate. But...it wasn’t all that long ago, in geologic time, when ancestors of the mammals celebrating Christ's resurrection today sat in the crook of a tree, munching leaves, pondering the primeval world before them with hare-sized brains. Evolution moves in mysterious ways.

Lagomorphs are highly social and quick on their feet. They breed fast, they evolve fast, and they can live patiently underground in sand, soil, or snow nibbling at dead roots and fallen leaves, while the world above convulses in nuclear holocaust or climatic catastrophe. Given time, who can say what the distant future holds for our lovable long-eared friends? So let’s not count out Peter Cottontail, or something a heck of a lot scarier, just yet.

Texas BoE Chairman

I don't know where to begin with this one...it's like a school lunch, you've just got to digest it for awhile:

I do like the part about "somebody needs to stand up to these experts." I agree. Who do they think they are being all..."experty" and stuff. That's the last thing we need in education is experts.

It's good of him to bring up Stephen Jay Gould, and he's right that Gould had issues with both the stasis of species and the Cambrian Explosion...so you know what Gould did about that? He proposed a new theory...a new model...a new idea of how evolution works. It's call punctuated equilibrium, and you can read all about it in almost any biology textbooks. Gould's work strengthened the theory of evolution, because it's an example of GOOD, SOLID SCIENCE.

Oh, and the Cambrian explosion took place over about 30 million years. And while that's still a relatively short period of time in the Earth's 4.6 billion year history, it's not really as sudden as creationists would lead you to believe.

Natural selection is not an unguided process. Beneficial traits are passed on in greater frequency than harmful ones because organisms with beneficial traits in a particular environment are more likely to pass on their genes to the next generation. That is a guided, selective process...there's nothing random about it.

Stasis (groups of organisms that stay the same for long periods of time) absolutely supports the theory of evolution by natural selection. If we understand that organisms that are better adapted to their environment are more likely to pass on their traits, then it follows that a type of organism that is well adapted to its environment probably isn't going to change much unless there is a significant change to the environmental niche that they occupy.

Texas, Continued

Last week, I wrote a post here about the fight over science standards that was happening within the Texas state board of education. The news, at that time, was good. Creationists had failed to get the needed votes to re-insert a clause into the standards requiring the teaching of "strengths and weaknesses" of the theory of evolution. Unfortunately, I jumped the gun a little, as Phil Plait at Bad Astronomy points out:

After that, the news sinks rapidly. The far-right Republicans on the Board were not finished. They put in language to weaken the Big Bang theory, saying that there are different estimates for the age of the Universe. You can try to be coy and say this is also strictly true, but again that’s a cheat and a lie. The woman who proposed this is obviously a young-Earth creationist, and when she says "different ages", she means 6000 years. This belief in a young Earth, is, simply, dead wrong. We know the Universe is 13.7 billion years old, and the Earth, while younger than that, is still 4.55 or so billion years old itself. This is not some random guess, this is rock-solid (literally) science, confirmed independently from such diverse scientific fields as astronomy, physics, chemistry, anthropology, archaeology… and even the study of how languages change over time shows the humanity is older than 6000 years.

These same people on the Board added language to the standards to weaken teaching about global warming. Don McLeroy, who is a creationist and also the Chairman of the BoE, said that climate change is "hooey". They also attack the science on the complexity of the cell, and the initial genesis of life (called abiogeneisis; life from non-life). These are all standard creationist tactics.

I guess the bright side of this is that maybe Texas will replace Kansas as the international laughingstock when science standards are discussed. But the damage that this could potentially do to science education in one of our largest states, especially in a time when society is so worried about our children falling behind the rest of the world in science, is extremely scary. You can believe what you want...that's your right. But to force those beliefs on the rest of society by manipulating the political system is not only illegal, but is a gross bastardization of religion.

Evolution in Texas

In January, the Texas State Board of Education took a preliminary vote on a new set of science standards that will govern how science is taught for the next 10 years in the Lone Star State. I wrote about it here. As with most science-standards debates, most of the discussion centered around evolution. For the past 20 years, the Texas standards have included this language:

The student is expected to analyze, review, and critique scientific explanations, including hypotheses and theories, as to their strengths and weaknesses using scientific evidence and information.

The new standards will take out this "strengths and weaknesses" language and replace it with:

The student is expected to analyze and evaluate scientific explanations using empirical evidence, logical reasoning, and experimental and observational testing.

The revised standards eliminate the "back door" approach to creationism that is the intent of "strengths and weaknesses" language, and have been endorsed by dozens of scientific and professional organizations. On January 23, the Texas board of education gave preliminary approval to the revised standards after an amendment to re-insert the "strengths and weaknesses" language failed on a split 7-7 vote.

Final action on these standards was scheduled for today and tomorrow, following a public hearing date on Wednesday. Earlier today, evolution opponents again failed to pass an amendment restoring the "strengths and weaknesses" language on a split 7-7 vote.

A last-ditch effort by social conservatives to require that Texas teachers cover the "weaknesses" in the theory of evolution in science classes was rejected by the State Board of Education Thursday in a split vote.

Board members deadlocked 7-7 on a motion to restore a long-time curriculum rule that "strengths and weaknesses" of all scientific theories – notably Charles Darwin's theory of evolution – be taught in science classes and covered in textbooks for those subjects.
[...]
The tie vote upheld a tentative decision by the board in January to delete the strengths-and-weaknesses rule in the new curriculum standards for science classes that will be in force for the next decade.

Those standards spell out not only how evolution is to be covered, but also what is supposed to be taught in all science classes in elementary and secondary schools, as well as providing the material for state tests and textbooks.

A final vote is scheduled for tomorrow, but the results are expected to be the same. Proponents of science education claim this as a major victory in their struggle to keep creationism out of science classes, since the Texas standards typically have a large influence on what textbook publishers include in their books.

Jurassic Lark

Scientists in China recently published a report in Nature that details their study of a newly discovered fossilized dinosaur species. What makes this new species (which they plan to name Tianyulong confuciusi) interesting is that it appears to have had structures on its skin that resemble feathers. From The Economist:

That birds are the descendants of dinosaurs is now accepted by almost all evolutionary biologists. The clinching discovery was of animals that were clearly dinosaurs, and clearly could not fly, but which had feathers. That did raise the question, though, of why one twig of the great dinosaur tree had developed such strange outer vestments, even before it developed wings.

This isn't the first time that a feathered dinosaur fossil was discovered. What's noteworthy about this particular fossil, though, is that it's from a group of dinosaurs that aren't "supposed" to have feathers based on our current understanding of dinosaur evolution.

The new species belongs to a group of dinosaurs called the Ornithischia. This group, which includes such famous names as Stegosaurus and Triceratops, is one of the two clades into which the dinosaurs are divided. The other is the Saurischia, whose famous members include Diplodocus and Tyrannosaurus. The Saurischia also include all the immediate ancestors of birds.
[...]
Such “protofeathers” have been found on other dinosaurs, but until now those species have, like those that sport true feathers, all belonged to a part of the Saurischia that includes the birds. Yet the split between Ornithischia and Saurischia goes back to the very beginning of the dinosaurs, 80m years before the first birds and about 100m years before T. confuciusi. So if the feather-like structures of T. confuciusi really have the same origin as feathers, then such structures must have been there from the outset, and be characteristic of dinosaurs as a whole.

To illustrate this, draw a capital "Y". The stem of the "Y" represents an ancestor common to all dinosaurs. The arms of the "Y" represent the two groups of dinosaurs that evolved from that common ancestor. Until now, all known feathered dinosaurs have belonged to the group on one arm of the Y. This has led scientists to the conclusion that birds evolved from this group of dinosaurs (the Saurichia). This new fossil (T. confuciusi), however, belongs to the group of dinosaurs on the OTHER arm (the Ornithischia). This leaves us with a few possibilities:
1. Feathers evolved independently in both groups of dinosaurs, or
2. Feathers were a characteristic of the ancestral species, or
3. The current model for dinosaur evolution and classification is completely wrong.

The simplest of the explanations is that early feathers were present in the ancestral group, and these early feathers were passed on, through evolution, to both the Saurichia and the Ornithischia. Most dinosaur species in each group evolved to be featherless, but one or a few species in each group also apparently retained the early feathers. The trait of feathers eventually died out on one arm of the "Y" (the Ornithischia). On the other arm (the Saurischia), the feathered species of dinosaurs were the earliest ancestors of modern birds.

This conclusion does lead to a problem with classification: instead of thinking of birds as dinosaurs, it may become necessary to start thinking of dinosaurs as specialized birds:

Taxonomically, the very definition of a bird was until recently an animal that has feathers. Now, taxonomists argue that since birds are descended from dinosaurs they should be classified merely as a subgroup of the Dinosauria. But if feathers truly are the diagnostic criterion, then perhaps things should be the other way round, and Stegosaurus, Triceratops, Diplodocus, Tyrannosaurus and their kin should no longer be thought of as terrible lizards, but as overweight, flightless birds.

Darwin meets Eminem

Maybe this is over-the-line geeky, but I'm sort of an over-the-line geeky kind of guy. So let me introduce you to Baba Brinkman, a Canadian hip-hop artist who gained a small amount of notoriety for rapping Chaucer's Canterbury Tales. His new subject is Darwin and evolution:

Science has a review of one of Baba's live performances on their website. It includes lyrics and several other videos of his work. If you're reading this from home, you can also checkout his MySpace page to hear the "Natural Selection" rap with music and a back beat.

Fossilized Footprints

While we're on the topic of fossils, check out this story:

Freshly discovered trails of ancient footprints, left on what was once the muddy shores of a river near Ileret, Kenya, indicate that some 1.5 million years ago human ancestors walked in a manner similar to that of people today. The international team of researchers who analyzed the prints say that those who left them had feet that looked a lot like ours.

The prints were probably left by Homo ergaster, an earlier, larger version of the widespread Homo erectus, says David Braun, a lecturer in archeology at the University of Cape Town in South Africa and co-author of the study set to be published tomorrow in Science. This discovery "lets us know that they were probably just as efficient at walking upright as we are," he says.

Vestigial Organs

One of the difficulties with studying evolution is that nobody was around to see it happen from start to finish. The best we can do is look at what we can see and try to use that evidence to draw conclusions about the history of life on Earth. Fortunately, the natural world is full of physical clues that show us not only how evolution occurred (and continues to occur), but also how species of organisms alive today are "related" to each other in an evolutionary sense.

Today in biology class we will be discussing some of these clues, including the presence of vestigial organs. These are structures that modern species possess but really don't serve much of a purpose. (The human appendix and tailbone are classic examples.) But while these structures might not be useful to the organisms that possess them, they can help us to draw evolutionary relationships.*
*The appendix is what's left of our cecum, which is an organ that many mammals use to digest the tough fibers in grass and other plants...the tailbone also supports the idea that humans are descended from an ancestor common to all mammals.

Here's a link to an interesting website that details some of the vestigial organs found in different species. (Hat tip to Mrs. Gingrich for sharing this link.)

Are Humans Evolving?

Monday afternoon: There's a short break in the action today at our inservices, so I think I'll try to address one of the last two Darwin Day questions from last week. As was the case with the rest of them, this is a true/false statement: Humans are still evolving.

This statement, like the rest of them, is false. While we probably won't expect humans to grow tails or gills, the collective human genome has changed considerably since our species first walked on Earth, and it continues to change as successive generations inherit our humanity.
*** *** *** *** ***
Tuesday Morning: I got interrupted yesterday, so let me try to finish my thoughts here. One of my favorite examples of human evolution is the enzyme lactase. Humans, like other mammals, produce milk to nurse their offspring. This is possible because young mammals make a enzyme called lactase, which allows them to digest lactose, the sugar found in milk. Most mammals, however, stop producing lactase as they mature and are able to provide food for themselves. This happens because the gene that codes for lactase turns off.

In some humans, this gene never turns off...with the result being that these people produce lactase throughout their lives. This is a genetic mutation that spread quickly through the human species in regions where livestock were domesticated. The advantage of this mutation is obvious: people who produced lactase could drink milk, and therefor had one more source of nutrition in their diets.

Today, we tend to see this mutation in populations that have become dependent on domestic cattle (i.e. about 90% of Americans produce lactase throughout their lives). The other 10%, who actual have the "normal" gene, quit producing lactase early in their lives and are "lactose intolerant" as adults. The rate of lactose intolerance is high (as we would expect it to be) in countries such as China that have not traditionally been dependent on domesticated cattle.

Maddow on Darwin Day

Last night, the Rachel Maddow Show on MSNBC featured a piece about Darwin Day and the creation/evolution controversy that continues to play itself out in the US. As usual, Kansas was featured as a good example of "what not to do". This piece also featured one of my favorite authors, Edward Larson. Enjoy:

Visit msnbc.com for Breaking News, World News, and News about the Economy

Quick Evolution?

True or false:

Evolution occurs so slowly that scientists are unable to witness it happening

Before we talk about the answer, lets get a little context for why I would ask this. One of the common misunderstanding about evolution is that it can't be proven because it occurs over very long periods of time and therefor can't be directly witnessed. While it's true that the ENTIRETY of evolution which has led to the present diversity of life on Earth took billions of years to happen, and species in nature often change very slowly, there are also well documented cases of organisms evolving, in the wild, in a relatively short period of time.

My current favorite example of relatively quick evolution can be seen in a certain strain of bacteria that has actually developed the ability to produce enzymes called "nylonases", which are able to break down and essentially feed on the waste products from the production of nylon. Nylon is a man-made fiber that was first produced in 1935, and the bacteria was discovered in a waste pond that where a nylon-producing factory was dumping its waste water.

By studying these bacteria, biologists were able to conclude that the nylonases were completely different than any other enzyme produced by these types of bacteria. Further testing also showed that these enzymes were specific to nylon, meaning they didn't work on any other material or chemical, and therefor probably arose after nylon began being mass produced.

By studying the genome of these bacteria, scientists eventually were able to pinpoint the exact spot on the organisms' DNA where the mutation occurred that caused the bacteria to stop producing a normal enzyme and begin producing the nylonase. In most instances, a mutation affecting a major digestive enzyme would be extremely harmful for an organism. In this case, however, it allowed these bacteria to flourish in a nylon-rich environment.

This is a perfect example of evolution in nature. Random DNA mutations cause some organisms to develop traits that make them better adapted to their environment. These organisms are more likely to reproduce and pass on the genes containing those beneficial mutations. Over time (in some cases long period of time, but in this case only a few decades) the population of organisms becomes significantly different than its biological ancestors.

Evolution of Homer

As part of Darwin week, I am looking for evolution clips in popular media. I begin with The Simpsons:

Is Evolution Legal?

Today's question asked if the following statement is true or false: "In Kansas, it is illegal to teach evolution without also teaching creationism", and students were pretty evenly divided on how they felt about it.

The statement, for the record, is completely false for reasons that I'll go into in a moment. But let me begin by saying I was surprised by the number of students who thought it was illegal to teach evolution PERIOD.

In 1968, the Supreme Court ruled in Epperson v. Arkansas that state laws prohibiting the teaching of evolution in public schools to be unconstitutional as a violation of the establishment (what is commonly, but perhaps incorrectly referred to as the "separation of church and state").

In response to this ruling, states begin issuing "equal time" laws which stipulated that evolution would be taught, but equal instructional time must be given to teaching creationism. In 1982, these laws were declared unconstitutional by a federal court's ruling in McLean v. Arkansas. In 1987, the Supreme Court issued a similar ruling in Edwards v. Aguillard. With this ruling, the court not only declared it unconstitutional to require "Creation Science" to be taught alongside evolution, but also declared that teaching "creation science" undermined the provisions of a comprehensive science education.

In response to the Edwards decision, creationist groups began removing all references to God or the Bible from their materials. This movement culminated in "Intelligent Design", which was declared unconstitutional by a federal court judge in the 2005 Kitzmiller v. Dover ruling.

I guess the take home message from all of this is that:
1. It is unconstitutional to prohibit the teaching of evolution in public school science classes.
2. It is unconstitutional to require the teaching of creationism (in any form) in public school science classes.
3. This is true in Kansas, along with the rest of the United States.

It is important to keep in mind that these court cases are not made in judgement of any particular religious belief. They do not, or cannot, speak to the validity or truth on any one particular belief system over another. All they do is define, legally, what the bounds of science are, and therefor what can and can't be taught about the origins and diversity of life (including humans) in public school science classes.

Science and Religion

I just read a great article about science (specifically evolution) and its relation to religious faith.

One of the things that mars our culture is the fracture between faith and science. It impoverishes our inquiry into the realities that make up our life and world. This is a false opposition.
[...]
It is a mistake to treat the theology of creation in the Book of Genesis as a scientific textbook. It does unfold a profound and valid truth about the world in which we live, its order and purpose. The Book of Genesis speaks about the relationship between God and creation and especially about the place of humanity in that relationship. That wonderful narrative of creation offers us a first vision of an “ecology of holiness” in which every material and living thing has a place and its creativity is consecrated in goodness by God. The account of creation in Genesis is pointing us beyond the question “how?” to the question “why?”
[...]
The anniversary of Darwin's birth is an invitation to renew the conversation between science and faith. Christianity can contribute to the progress of science, not only by encouraging scientists in the search for truth, but by inviting them to consider these wider questions that go to the heart of our common and necessary search for understanding.
[...]
This alerts us to the question that lies within all our other questions: the choice that humans alone have to make between good and evil. It is a question planted at the heart of Genesis's account of creation. It is as much a question for the scientist as for the believer. It, too, is about our freedom. Darwin's theory does not take away the reality of that freedom and the moral responsibility it gives us.

True knowledge comes not from scientific or religious dogma. True knowledge is found in the continual search for truth...both physical and spiritual.

Man and Monkeys

Common responses to evolution questions:

Teacher: What do you know about evolution?
Student: It says that man came from chimps/monkeys.
Teacher: So what questions do you have?
Student: If man came from chimps/monkeys, then why are there still chimps/monkeys alive today?

One of the biggest obstacles to teaching the theory of evolution in biology class is getting students over the false preconceptions of what the theory really says. In order to kick off our "Darwin Day" activities, I had each of my classes reflect on these statements, and describe whether they thought the following statement was true or false: "The theory of evolution states that man evolved from monkies/chimps."

This statement is false. Evolution (descent, with modifications, from common ancestors) gives us a picture of the history of life on earth that looks much like a family tree. If we use this analogy, then humans occupy a distinct branch of that tree. Chimps, being our closest living "relatives" would occupy a second branch that is near but distinct from ours. If we go back down that family tree a ways (back in time) there is a "common" ancestor that both chimps and humans evolved from. If we continue traveling backwards, we would come to an earlier ancestor that all primates evolved from. In this way, as we travel backwards, we would continually come to points where we share a common ancestor with all mammals, all vertebrates, all animals, all multicellular lifeforms, and eventually we would reach the trunk of the tree that represents the common ancestor to all life.

To use the vocabulary of this analogy, then, chimps would represent our "cousins" rather than our "grandparents". But, in reality, all organisms would represent differing degrees of cousins. The ancestral species--the true "grandparent" on our family tree--would be represented by a species that shares similarities with both chimps and humans, but is probably distinct from anything living on Earth today. So humans DID NOT "come" from chimps/monkeys. Humans and other primate species DID evolve from a common ancestor. But the same can be said for any two organisms or any variety, human, chimp, monkey, or otherwise.

New Mexico Anti-evolution Bill

Another anti-evolution bill has popped up. This time in the New Mexico state Senate. As reported by the National Center for Science Education:

If enacted, the bill would require schools to allow teachers to inform students "about relevant scientific information regarding either the scientific strengths or scientific weaknesses pertaining to biological evolution or chemical evolution," protecting teachers who choose to do so from "reassignment, termination, discipline or other discrimation [sic] for doing so."

This is another "back door" argument. Proponents of creationism have consistently re-labeled their tactics (equal time, scientific creationism, intelligent design, academic freedom, etc.) and have consistently had their tactics declared unconstitutional in the courts. So if they aren't able to legally introduce creationism, the next best thing is to make evolution look like a week theory, or a theory in jeopardy (neither of which, by the way, is accurate). The logic behind this goes something like this: 1) evolution and creationism are competing ideas used to explain the diversity of life of Earth, and 2) creationism can't be legally taught in science classes but if 3) people can be convinced that evolution is "weak" then 4) by default they will accept the creationists perspective as true.