Latest Challenges to the Teaching of Evolution

World-first hybrid shark found off Australia
(By Amy Coopes, Agence France Presse, January 3, 2012)

Scientists said on Tuesday that they had discovered the world's first hybrid sharks in Australian waters, a potential sign the predators were adapting to cope with climate change.

The mating of the local Australian black-tip shark with its global counterpart, the common black-tip, was an unprecedented discovery with implications for the entire shark world, said lead researcher Jess Morgan.

"It's very surprising because no one's ever seen shark hybrids before, this is not a common occurrence by any stretch of the imagination," Morgan, from the University of Queensland, told AFP.

"This is evolution in action."

Colin Simpfendorfer, a partner in Morgan's research from James Cook University, said initial studies suggested the hybrid species was relatively robust, with a number of generations discovered across 57 specimens.

The find was made during cataloguing work off Australia's east coast when Morgan said genetic testing showed certain sharks to be one species when physically they looked to be another.

The Australian black-tip is slightly smaller than its common cousin and can only live in tropical waters, but its hybrid offspring have been found 2,000 kilometres down the coast, in cooler seas.

It means the Australian black-tip could be adapting to ensure its survival as sea temperatures change because of global warming.

"If it hybridises with the common species it can effectively shift its range further south into cooler waters, so the effect of this hybridising is a range expansion," Morgan said.

"It's enabled a species restricted to the tropics to move into temperate waters."

Climate change and human fishing are some of the potential triggers being investigated by the team, with further genetic mapping also planned to examine whether it was an ancient process just discovered or a more recent phenomenon.

If the hybrid was found to be stronger than its parent species -- a literal survival of the fittest -- Simpfendorfer said it may eventually outlast its so-called pure-bred predecessors.

"We don't know whether that's the case here, but certainly we know that they are viable, they reproduce and that there are multiple generations of hybrids now that we can see from the genetic roadmap that we've generated from these animals," he said.

"Certainly it appears that they are fairly fit individuals."

The hybrids were extraordinarily abundant, accounting for up to 20 percent of black-tip populations in some areas, but Morgan said that didn't appear to be at the expense of their single-breed parents, adding to the mystery.

Simpfendorfer said the study, published late last month in Conservation Genetics, could challenge traditional ideas of how sharks had and were continuing to evolve.

"We thought we understood how species of sharks have separated, but what this is telling us is that in reality we probably don't fully understand the mechanisms that keep species of shark separate," he said.

"And in fact, this may be happening in more species than these two."

Evolutionary Lessons From Superbugs
(James A. Shapiro, HuffingtonPost.com, January 8, 2012)

Virulent drug-resistant "superbugs" are back in the news. We have a lot to learn from these small but smart creatures. To the dismay of many in the pubic health field, the FDA just dropped plans to enforce a 1977(!) decision to limit the use of antibiotics in animal feed, which facilitates the emergence of antibiotic-resistant pathogens. A December 23, 2011 article in Wired by Maryn McKenna ("FDA Won't Act Against Ag Antibiotic Use") and a December 27, 2011 New York Times blog by Mark Bittman ("Bacteria 1, F.D.A. 0") tell the story. I'll leave it to others to discuss the political ramifications of this disastrous (in)action. Here, we'll look at it as another reflection on public misunderstanding of modern evolutionary science.

How do bacteria acquire antibiotic resistance? How do they become pathogens? We currently know a great deal about the genetic basis of these critically important bacterial properties. We also know how resistance and virulence are acquired and spread to new species. The story of how we came to this knowledge is a fascinating and instructive chapter in the history of science -- it illuminates the insight that scientific "fact" consists of more than experimentally confirming hypothetical predictions.

In the early days of molecular biology, bacterial geneticists applied conventional evolutionary concepts from the pre-DNA period to explain the evolution of antibiotic resistance. The theory was that mutations could alter the structure of cell components and either block entry of the drugs into the bacteria or prevent their action on cellular targets, such as the enzymes essential to cell wall synthesis. Even if the initial mutation did not confer a high degree of resistance, accumulation of several sequential changes would result in resistance to the antibiotic levels used in clinical medicine. Indeed, a wide variety of laboratory experiments confirmed this theory, and bacterial geneticists isolated the predicted mutant strains. In virtually all cases, the resistant mutants grew less well than the parental sensitive bacteria, leading to the comforting conclusion that resistant bacteria would not significantly accumulate in nature. The degree of confidence was so great that the U.S. Surgeon General in 1967 declared that "the war against infectious diseases has been won" (Fauci 2001).

There were problems both with the science and the new public health policy based on it. The Surgeon General "misunderestimated" the bacteria, which followed their own evolutionary rules and did not listen to what the scientists said they should do. Although experimentally confirmed, the mutation theory of antibiotic resistance failed to account for most cases in the real world. Resistance continued to spread among bacteria isolated in clinics around the globe. Even more ominously, different strains of pathogenic bacteria increasingly displayed resistance to more than one antibiotic at a time. Research pioneered in Japan found that multiple antibiotic resistances could be transferred simultaneously from one bacterial species to another (Watanabe 1967). The DNA agents responsible for this transfer are circular molecules that are called multidrug resistance plasmids, which can move from one cell to another (Clowes 1973; Novick 1980). Moreover, the resultant multiply resistant bacteria were not altered in their cellular structures or inhibited in their growth properties. Rather, they had acquired new biochemical activities that could destroy or inactivate the antibiotics, chemically alter their targets, or remove them from the bacterial cell (Davies 1979; Levy 1998).

Multiple antibiotic resistance clearly represented genome change and evolution of a type unimagined in the pre-DNA period. DNA molecules could be transferred "horizontally" between unrelated cells rather than inherited from ancestral cells. Moreover, horizontally transferred DNA could carry complex sets of genetic information encoding multiple distinct biochemical activities. Evolutionary leaps involving several characteristics at once could occur through horizontal DNA transfer.

Over time, it became increasingly clear that bacteria and other microorganisms engage in a great deal of horizontal DNA swapping. In addition, these small cells have an ample toolbox of natural genetic engineering mechanisms to incorporate and rearrange this horizontally acquired DNA (Miller 1998; Shapiro 2011). In the early 1980s, two obscure French-Canadian microbiologists published a book called A New Bacteriology, postulating a radically different approach to thinking about bacterial evolution (Sonea and Panisset 1983). Sonea and Paniset argued that bacteria have a huge collective genome distributed throughout nature in different kinds of cells, in viruses and latent in the environment. When a new ecological niche appears, bacteria can assemble the genomic assets they need to exploit the opportunity.

Subsequent research has bolstered Sonea and Paniset's initially outlandish idea. First of all, we know that bacteria have all the abilities they need to acquire DNA from the environment, from viruses and from other cells. Secondly, detailed study of many bacterial characteristics, especially pathogenicity (the ability to cause disease) and virulence, indicate that they are encoded by plasmids or by critical segments of the DNA, so-called "genomic islands" (Hacker and Carniel 2001; Juhas, van der Meer et al. 2009). The sequences of genomic islands show that they have been acquired from unrelated organisms and integrated into the cellular genome by natural genetic engineering methods. (Future blogs will explore these methods in more detail.) Finally, the new field of "metagenomics" (viz. isolating and analyzing mass DNA samples collected directly from the environment) has demonstrated that there are vast ecological reservoirs of viral and other extracellular DNA encoding many properties useful to bacterial cells (Gilbert and Dupont 2011).

The DNA sequences that encode molecules needed for essential virulence processes in pathogenic bacteria are most often found on plasmids and in genomic islands, indicating that they are subject to frequent horizontal transfer (Tseng, Tyler et al. 2009). These virulence molecules almost invariably include several that associate to form complex structures, which span across the membranes and cell wall that comprise the bacterial envelope. These envelope-spanning structures have proven essential to the transport of large biological molecules (so-called "macromolecules") from one cell to another. The pathogens use these molecular transport systems to inject protein and RNA molecules into cells of the host organism (whether animal or plant). In so doing, they subvert host cell regulatory circuits in a way that meets the invading bacterium's needs (Bhavsar, Guttman et al. 2007). Truly, bacteria are the smartest cell biologists on the planet because they control events in cells of higher organisms in a way that mere human scientists can only dream of imitating.

The bacteria also use these or similar macromolecular transport structures to acquire DNA from the environment or transfer DNA between cells (even to cells of plants and, at least in the laboratory, to fungus and animal cells) (Chilton 1983; Sprague 1991). These structures are further used for so-called "twitching" movement across solid surfaces (Mattick 2002) and are related to other envelope-spanning structures involved in synthesis of high-energy storage molecules and rotation of bacterial flagella (literally, "whips") for swimming through fluids (Egelman 2010; Filloux 2011). Thus, there has been a wide-ranging use and reuse of these elaborate systems in the course of bacterial evolution. Since the Intelligent Design (ID) advocates point to the bacterial flagellum as an example of an "irreducibly complex" structure that could not have evolved by Darwinian evolutionary processes (Behe 1996), they need to address how such intricate and clearly related biological inventions have come to be diversified for so many different uses. Certainly, the ID argument is greatly undermined if it has to invoke supernatural intervention for the origin of each modified adaptive structure. At the same time, it is fair to recognize that the evolutionary science community is also challenged to come up with detailed explanations for the origin and diversification of a basic complex functional design.

The genetics and genomics of bacterial antibiotic resistance and virulence teach us some fundamentally important lessons about evolution. They also pose some significant challenges to scientific explanation. The main evolutionary lessons are:

(1) Living cells are not solely dependent upon vertical inheritance for acquiring DNA encoding new traits; they can definitely acquire DNA by horizontal transfer from other cells, often of different species or even different kingdoms.

(2) Multiple genomically encoded functions can be acquired at once in a single DNA transfer event; in other words, evolutionary change can be sudden and does not have to proceed one trait or one small change at a time.

(3) Once a complex invention has arisen in evolution, it is subject to modification and adaptation to a variety of different uses, sometimes related functionally (as in macromolecular transport) but sometimes of quite different function (as in twitching and flagellar motility).

In addition to these three important lessons, the bacteria pose at least two great challenges to evolutionary science:

(I) How did the first functional envelope-spanning complex originally arise in evolution? Although we can easily reject the supernatural solution ID advocates propose in response to this question, we also have to acknowledge that we still have no clear scientific answer to it.

(II) How did the bacteria come to be such sophisticated cell biologists and evolve the capacity to produce molecules that subvert the cell control regimes of higher organisms to their own (i.e. the bacteria's) benefit? To my mind, this is a far deeper and, ultimately, far more rewarding question to pose.

Let us conclude this blog in the head-scratching mode, which is the right place for scientists to be. I am in the habit of telling students, "If you're not confused, you're not doing science" -- by which I mean: if we already know the answer, there is nothing new to learn from asking the question. Even when we think we know the answer, as in the case of bacteria evolving antibiotic resistance, nature may well have another solution we never considered. It is salutary to remember that this last point proves more often to be the rule than the exception.

Virulent drug-resistant "superbugs" are back in the news.

Here, we'll look at it as another reflection on public misunderstanding of modern evolutionary science.

Let us conclude this blog in the head-scratching mode, which is the right place for scientists to be.

Government changes Free School model funding agreement to ban creationist schools
(British Humanist Association Press Release, January 10, 2011)

The British Humanist Association (BHA) has welcomed a new revision of the model funding agreement for Free Schools by the Government in order to preclude ‘the teaching, as an evidence-based view or theory, of any view or theory that is contrary to established scientific and/or historical evidence and explanations.’ This highly significant change has been made in order to ban creationism from being taught in Free Schools, and prevent creationist groups from opening schools. The change follows the BHA coordinating the ‘Teach evolution, not creationism!’ campaign, which called for this precise change.

In September, the BHA came together with thirty leading scientists and science educators including Sir David Attenborough, Professor Richard Dawkins and Professor Michael Reiss, and five national organisations to launch ‘Teach evolution, not creationism!’, which called on the government to introduce statutory guidance against the teaching of creationism and garnered significant press coverage. The BHA also launched a government e-petition making the same call, which has now garnered over 20,000 signatures.

In subsequent written correspondence with civil servants, the BHA stated that ‘Our concern is for the government to make absolutely clear that there is no chance it will ever accept [creationist Free School] bids, or allow any state-funded school to teach creationism as science, anywhere in the curriculum, and this is only possible through a change in the law… we would support any adjustment to the model funding agreement to add a statement [to this effect]… Could we request that the next time the [Free School] model funding agreement is reviewed, our desire for this point’s inclusion is considered?’

BHA Chief Executive Andrew Copson commented, ‘We congratulate the government for taking this significant step to prevent creationist Free Schools. There is still further work to be done to ensure that all schools, not just Free Schools, are prevented from teaching creationism, to include evolution in the primary National Curriculum, and to ensure evolution’s teaching in all schools. We look forward to working with the government and all those who care about rational and evidence based education to achieve these additional changes.

There is still further work to be done to ensure that all schools, not just Free Schools, are prevented from teaching creationism, to include evolution in the primary National Curriculum, and to ensure evolution’s teaching in all schools.

Missouri, The 'Stupefy Me' State?
(Shawn Lawrence Otto, HuffingtonPost.com, January 13, 2011)

Six Missouri republicans -- "the stupefy me six," let's call them -- are hard at work trying to make Missouri kids stupid. House Bill 1227, introduced in the Missouri House of Representatives on January 10, will, if enacted, require "the equal treatment of science instruction regarding evolution and intelligent design," according to the bill's language.

In other words, the bill will require the equal treatment of religious opinion and science, depriving Missouri kids of the knowledge they need to compete in the knowledge economy, and robbing them of a clear understanding of how to tell the difference between real knowledge and someone's truthy opinion.

Freshman representative Rick Brattin (R-District 124) is the sponsor of the bill; its cosponsors are John McCaherty (R-District 90), Charlie Davis (R-District 128), Andrew Koenig (R-District 88), Sue Allen (R-District 92), and Darrell Pollock (R-District 146). It is the fourth antievolution bill of 2012, joining Indiana's Senate Bill 89 and New Hampshire's House Bills 1148 and 1157.

There is so much that is wrong with -- and uncaring about -- this antiscience legislation that it's hard to know where to begin.

First, let's call a spade a spade. It's unAmerican. America was founded, in no small part, on the principles of freedom of and from religion. Our puritan predecessors fled to America to escape a religiously dominated government that was imposing its religious views on them. Now, these Missouri republicans are trying to impose their religious beliefs on all Missouri kids, by teaching intelligent design -- proven to be religion in the famous Kitzmiller v. Dover case -- in science class. Hey, Missouri Republicans: if you want to teach your kids that God created man six thousand years ago just like it says in the Bible, go right ahead. But let's do it in church. That's what we have churches for. We don't require scientists to teach evolution in church, so let's not force science teachers to teach religion in science class.

Second, it's communist-style freedom killing. Our kids deserve intellectual freedom, but the "equal treatment" provision would force public schools and "any introductory science course taught at any public institution of higher education" throughout Missouri to use put ideology ahead of knowledge. "If scientific theory concerning biological origin is taught in a course of study, biological evolution and biological intelligent design shall be taught," the bill mandates. That is mandating ideological indoctrination, just what communist governments used to do.

Third, it's economically stupefying. The United States is now in a knowledge-driven global economy. Science is everywhere. American kids have to compete. We can't afford to dumb down our science for ideological reasons. Anything that has to do with biotech, genetics, medicine, healthcare, pharmaceuticals, biology, vaccines, ecology, environmental science, public health, biosecurity, agricultural science, pesticide development, even economics and airport computer software, are based on the theory of evolution, which, by the way, has been confirmed by hundreds of thousands of observations over a hundred and fifty years. If you want your kids to make money beyond working for a fast food joint or in hotel services waiting on wealthy foreigners, don't deprive them of the knowledge tools that millions of hungrier kids are learning elsewhere.

Fourth, it's morally stupefying. "If scientific theory concerning biological origin is taught in a textbook," the bill says, "the textbook shall give equal treatment to biological evolution and biological intelligent design." Who are we to force our value systems on every student in the state, no matter their faith or age, to the extent of making sure ideologically motivated propaganda is inescapable, in every textbook, at the expense of students learning the truth? If we love and care for our children, shouldn't we give them every possible advantage we can? Shouldn't we give them every possible freedom? What are we afraid of? Is our faith so weak that it has to be mandated by law?

Fifth, it's thought stupefying. There's a guy that conservatives have been talking about lately named John Locke. But Locke is most famous for developing a system of knowledge that underlies modern science, called empiricism. Locke saw how various religions argued incessantly over who was closer to God, which beliefs were the real faith, and so on. He reasoned that this sort of argument could go on forever. There had to be some way of figuring out who was right. And so he defined what knowledge is, and showed how it is different from - and superior to -- "but faith or opinion." Evolution is knowledge. Intelligent design is "but faith, or opinion, but not knowledge" according to Locke's definitions. Science creates knowledge of the real world that is independent of our opinions and beliefs by making observations, using them to make predictions, testing the predictions, and submitting the results for peer review. The theory of evolution stands up to this test. Intelligent design does not. It is not knowledge. It is "but faith, or opinion." As Isaac Newton said, "A man may imagine things that are false, but he can only understand things that are true." In science class, we should teach our kids how to understand the way things work, not confuse them by teaching faith and calling it science.

Finally, its problem-solving stupefying. This is critically important. The United States has gotten as far as it has in terms of technology and dominance because of science. Because of our understanding that even if you haven't figured something out, you can just keep plugging away, looking for those natural causes and sooner or later you'll find them. Teaching intelligent design in school science classes is teaching a habit of mind that is toxic to that problem-solving method. It teaches you to just throw up your hands and declare that the problem is unsolvable, particularly if that problem is tough or might have consequences for a particular religious belief. It teaches you to value not diversity of ideas, but conformity. If you do that, you're basically giving up on science and on the probability of finding those answers. That is not going to take America where we need to go.

Missouri, your proud heritage and your bright children deserve better than to be forcibly dumbed down. Let's not give up on the future. Let's show them the way things work instead of stupefying them with conformist ideology.