Genome Size, Complexity, and the C-Value Paradox

Forty years ago it was thought that the amount of DNA in a genome correlated with the complexity of an organism. Back then, you often saw graphs like the one on the left. The idea was that the more complex the species the more genes it needed. Preliminary data seemed to confirm this idea.

In the late 1960's scientists started looking at the complexity of the genome itself. They soon discovered that large genomes were often composed of huge amounts of repetitive sequences. The amount of "unique sequence" DNA was only a few percent of the total DNA in these large genomes.¹ This gave rise to the concept of junk DNA and the recognition that genome size was not a reliable indicator of the number of genes. That, plus the growing collection of genome size data, soon called into question the simplistic diagrams like the one shown here from an article by John Mattick in Scientific American (Mattick, 2004). (There are many things wrong with the diagram. Can you identify all of them? See What's wrong with this figure? at Genomicron).

Today we know that there isn't a direct correlation between genome size and complexity. Recent data, such as that from Ryan Gregory's website (right) reveals that the range of DNA sizes in many groups can vary over several orders of magnitude [Animal Genome Size Database]. Mammals don't have any more DNA in their genome than most flowering plants (angiosperms). Or even gymnosperms, for that matter.

Many of us have been teaching this basic fact for twenty years. The bottom line is ....

Anyone who states or implies that there is a significant correlation between total haploid genome size and species complexity is either ignorant or lying.

It is notoriously difficult to define complexity. That's only one of the reasons why such claims are wrong. Ryan Gregory wants everyone to know that the figure showing genome sizes in different phylogenetic groups is not meant to imply a hierarchy of complexity from algae to mammals.

A recent paper by Taft et al. (2007) says complexity can be "broadly defined as the number and different types of cells, and the degree of cellular organization." We can quibble about the definition but there's nothing better that I know of. The real question is whether organism complexity is a useful scientific concept.

Here's the problem. Have some scientists already made up their minds that mammals in general, and humans in particular, are the most complex organisms? Do they construct a definition f complexity that's guaranteed to confer the title of "most complex" on humans? Or, is complexity a real scientific phenomenon that hasn't yet been defined satisfactorily?

I, for one, don't know whether humans are more complex than an owl, or an octopus, or an orchid. For all I know, humans may be less complex by many scientific measure of complexity. Plants can grow and thrive on nothing but water, some minerals, and sunlight. We humans can't even make all of our own amino acids. Does that make us less complex than plants? Certainly it does at the molecular level.

Back in the olden days, when everyone was sure that humans were at the top of the complexity tree, the lack of correlation between genome size and complexity was called the C-value paradox where "C" stands for the haploid genome size. The term was popularized by Benjamin Lewin in his molecular biology textbooks. In Genes II (1983) he wrote.

The C value paradox takes its name from our inability to account for the content of the genome in terms of known function. One puzzling feature is the existence of huge variations in C values between species whose apparent complexity does not vary correspondingly. An extraordinary range of C values is found in amphibians where the smallest genomes are just below 10⁹bp while the largest are almost 10¹¹. It is hard to believe that this could reflect a 100-fold variation in the number of genes needed to specify different amphibians.

So, the paradox arises even if we don't know how to rank flowering plants and mammals of a complexity scale. It arises because there are so many examples of very similar species that have huge differences in the size of their genome. Onions, are another example—they are the reason why Ryan Gregory made up the Onion Test.

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

Imagine the following scenario. You are absolutely convinced that humans are the most complex species but total genome size doesn't reflect your conviction. The C-value paradox is a real paradox for you. Knowing that much of our genome is possibly junk DNA still leaves room for plenty of genes. You take comfort in the fact that under all that junky genome, humans still have way more genes than simple nematodes and flowering plants. You were one of those people who wanted there to be 100,000 genes in the human genome [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome].

But when the genomes of these species are published, it turns out that even this faint hope evaporates. Humans, Arabidopsis (wall cress, right), and nematodes all have about the same number of genes.

Oops. Now we have a G-value paradox, where "G" is the number of genes (Hahn and Wray, 2002). The only way out of this box—without abandoning your assumption about humans being the most complex animals—is to make up some stories about the function of so-called junk DNA. If it turns out that there are lots of hidden genes in that junk then maybe it will rescue your assumption. This is where we get some combination of the excuses listed in The Deflated Ego Problem.

On the other hand, maybe humans really aren't all that much more complex, in terms of number of genes, than wall cress. Maybe they should have the same number of genes. Maybe the other differences in genome size really are due to variable amounts of non-functional junk DNA.

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1. Thirty years ago we had to teach undergraduates about DNA reassociation kinetics and C_ot curves—the most difficult thing I've ever had to teach. I'm sure glad we don't have to do that today.

Hahn, M.W. and Wray, G.A. (2002) The g-value paradox. Evol. Dev. 4:73-75.

Mattick, J.S. (2004) The hidden genetic program of complex organisms. Sci Am. 291:60-67.

Taft, R.J., Pheasant, M. and Mattick, J.S. (2007) The relationship between non-protein-coding DNA and eukarotic complexity. BioEssays 29:288-200.

[Photo Credits: The first figure is taken from a course webite at the University of Miami (Molecular Genetics. The second figure is from Ryan Gregory's Animal Genome Size Database (Statistics).]

We're Number 2!!!

 
There is much wailing and gnashing of teeth in Toronto today as word has just been received that the Burj Dubai, under construction in the United Arab Emirates (UAR), has surpassed 553 metres. This makes it the tallest building in the world. The record has been held by the CN Tower in Toronto for over 30 years.

The bad news is reported in The Toronto Star [CN Tower no longer world's tallest].

"The accomplishment of being the world’s tallest free-standing structure is another defining moment for the multinational team of over 5,000 people who are using their collective intelligence to make this iconic structure a symbol of human achievement," said Mohamed Ali Alabbar, head of Emaar Properties, which owns the new tower. "This architectural and construction master-piece is truly an inspirational human achievement that celebrates the can-do mindset of Dubai."

CN Tower officials are playing it cool and, so far, the website still calls it "the world's tallest building." A short statement, sent out by email, said, "When the time comes and the building is complete, we will congratulate the Burj Dubai project on their unique achievement."

Okay, so we're not quite ready to officially concede just yet but the writing is clearly on the wall, so to speak.

A separate article in The Toronto Star attempts to console us by pointing out that we're #2 in a lot of things. It's nothing to be ashamed of [CN Tower topples to Number 2]. Some people wonder what all the fuss is about. An unidentified woman is prominently quoted in the print version of the story—the one that's being sold on the newsstands and delivered to suburban doors.

One woman, who didn't want to give her name, shrugged off the slight to Toronto as "such a guy thing."

"Who really cares? Trust me, length doesn't matter."

Fossil Horses and Directed Evolution

I'm teaching part of a course on Popular Scientific Misconceptions. In my section we'll be talking about the evolution/creationism controversy and part of the discussion involves analysis of the techniques used by Jonathan Wells to denigrate evolution in his book Icons of Evolution. One of the chapters is Fossil Horses and Directed Evolution.

For those of you who haven't read the book, the essential point is that scientists used to show the evolution of horses as a linear transformation from a small primitive horse-like creature to large modern horses. Over the years, this idea has been replaced by a branching representation where there are many different lineages, some of which have gone extinct. The history of this change is described in today's posting by Laelaps, which contains numerous examples of the figures and drawings that have been published over the years [The Branching Bush of Horse Evolution]. The most recent one is shown above. I'm posting the link here in part so my students will read it and it part so that everyone else will check it out. Laelaps has put a lot of work into the posting and he deserves the attention.

Jonathan Wells doesn't really object to the fact that the pattern of horse evolution has changed, although it does reinforce his point about scientific evidence being ephemeral. What upsets him is that the old version implied some direction to evolution and this, in turn, implies a director. According to Wells, the campaign by scientists to change the diagrams was only part of a larger, more sinister, goal.

The reason for their campaign, however, is more interesting than the horse icon itself. People used to regard the old icon as evidence that evolution was directed, either supernaturally or by internal vital forces. Neo-Darwinists now ridicule directed evolution as a myth, and cite new evidence that evolution is undirected.

But the doctrine of undirected evolution is philosophical, not empirical. It preceded all evidence for Darwin's theory, and it goes far beyond the evidence we now have. Like several other Darwinian claims we've seen, it is a concept masquerading as a neutral description of nature.

This is a strange line of reasoning. The original claim that horse evolution was directional surely falls into the same category that Wells criticizes. It must be philosophical, not empirical. Therefore, Wells should approve of scientists who refute the false evidence of directionality in order to remove a philosophical myth from the story of horse evolution. It seems logical that reverting to the null hyporthesis—no evidence of directionality—is preferable to promoting a mechanism that by Well's own admission might be supernatural.

That's not how Well's sees it.

Clearly, biology students are being taught materialistic philosophy in the guise of empirical science. Whatever one may think of materialistic philosophy, there is no doubt that it is being imposed on the evidence rather than inferred from it. And this is the real significance of neo-Darwinian efforts to reverse the picture of horse evolution. Although there are scientific issues involved, what really matters is the myth.

I'm looking at the tree of horse evolution. I don't see any evidence of directed evolution, do any of you? What's wrong with saying that there's no evidence of directed evolution; therefore we have to conclude that it wasn't directed?

Jake Young Wants Atheist Scientists to Keep a Low Profile

 
We've heard it all before. Those "New Atheists" like Richard Dawkins, Christopher Hitchens, and Sam Harris are doing far more harm than good. They're turning off the general American public and making it more difficult to get them interested in science. Why is that? It's because the New Atheism links science to a lack of belief in God and the public won't buy into science if they think it requires atheism.

Here's how Jake Young summarizes his position [Why Pairing Science and Atheism is High-Brow].

Listen, I am an atheist. I do not believe that religion and science are internally consistent. However, if there is one thing that I have learned about politics, it is that political discussions are not predicated on internal consistency. (Example: Prior to WW2, the American public was in favor of lend-lease, yet was not in favor of entering the war. These two propositions are mutually exclusive.) Whether or not, religion and science are internally consistent is largely beyond the point. The point is what we can reasonably expect the public to accept. The public is not going to accept both atheism and science over the short-term.

Jake isn't very clear about how he intends to proceed. I can only surmise that he will disguise his true feelings (that religion and science are internally consistent) in order to appease theists who want to learn about science.

This concept—hiding what you believe to be true for some "higher" purpose—is called framing by Jake's fellow accommodationists. Indeed, as you might expect, Jake quotes approvingly from the master framers, Nisbet and Mooney, who also want the New Atheists to go away quietly. And as quickly as possible.

I wonder how Jake Young feels about the books by Francis Collins, Ken Miller, and Simon Conway Morris that strongly advocate the compatibility of organized religions and science? Does he think that atheist scientists should refrain from making any comment about them even if they totally misrepresent science?

The next paragraph is.

Further, embracing a big-tent approach will not prevent scientific or even atheistic values from taking over. While the majority of the American public is religious, the number of atheists is growing. New atheists will be created in the same way that new atheists have always been created: by a kid waking up in class one day and saying, "You know that invisible man business doesn't make sense."

Jason Rosenhouse over at Evolutionblog demolishes the idea that keeping a low profile is the best strategy for making atheism acceptable [Young on Dewey on Being High-Brow]. It didn't work for gays. It didn't work for women either [Suffragettes].

Freedom in the Classroom (2007): Persistent Irrelevance

 
I'm discussing the Freedom in the Classroom (2007) report from the American Association of University Professors [Freedom in the Classroom (2007].

The first posting covered the issue of indoctrination and made the point that Professors have to allow for debate in the classroom [Freedom in the Classroom (2007): Indoctrination]. The second posting discussed the report's comments on balance in the classroom—the proposition that Professors are obliged to present both sides of a controversy Freedom in the Classroom (2007): Balance. In the third posting, I present the discussion about intolerance and a hostile learning environment [Freedom in the Classroom (2007): Intolerance].

This posting addresses the criticism that "instructors persistently interject material, especially of a political or ideological character, irrelevant to the subject of instruction."

Persistent Irrelevance

The 1940 Statement of Principles provides that teachers "should be careful not to introduce into their teaching controversial matter which has no relation to their subject." The origin of this admonition lies in the concern of the authors of the 1925 Conference Statement on Academic Freedom and Tenure for immature youth or, more accurately, a concern by the administrators of small and often denominational colleges for potential adverse parental reaction to their children's exposure to thought contrary to the conventional pieties of small-town America.14 The admonition was reconsidered and addressed in an interpretive comment to the 1940 Statement, appended by the joint drafting organizations in 1970:

The intent of this statement is not to discourage what is "controversial." Controversy is at the heart of the free academic inquiry which the entire statement is designed to foster. The passage serves to underscore the need for teachers to avoid persistently intruding material which has no relation to their subject.

The 1940 Statement should not be interpreted as excluding controversial matter from the classroom; any such exclusion would be contrary to the essence of higher education. The statement should be interpreted as excluding "irrelevant" matter, whether controversial or not.

The question, therefore, is how to determine whether material is "irrelevant" to classroom discussion. In some contexts, the meaning of "irrelevance" is clear. Students would have every right to complain if an instructor in ancient history dwelled on internecine conflict in her department or if an instructor in American literature engaged in lengthy digressions on his personal life. But such irrelevance is not the gravamen of the contemporary complaint.

The question is not so much about trivial irrelevance, it's about serious deviations from the advertised course content. But how do we define those serious kinds of irrelevance? Are all irrelevant comments out-of-bounds? Should the university set up some sort of "irrelevance police" to check out every classroom?

Clearly not. But students and members of the general public don't seem to have a problem with this sort of tactic. The greatest danger these days comes from threats that are outside of the academic community. This report should be required reading for students at university.

The group calling itself Students for Academic Freedom (SAF), for example, has advised students that "your professor should not be making statements . . . about George Bush, if the class is not on contemporary American presidents, presidential administrations or some similar subject." This advice presupposes that the distinction between "relevant" and "irrelevant" material is to be determined strictly by reference to the wording of a course description. Under this view, current events or personages are beyond the pale unless a course is specifically about them. But this interpretation of "relevance" is inconsistent with the nature of higher education, in which "all knowledge can be connected to all other knowledge." Whether material is relevant to a better understanding of a subject cannot be determined merely by looking at a course description.

Excellent point. Surely we don't want classrooms where the Professor is forbidden to make comments about real world events and how they might relate to the material in the course or to the ideas that are being discussed?

Might not a teacher of nineteenth-century American literature, taking up Moby Dick, a subject having nothing to do with the presidency, ask the class to consider whether any parallel between President George W. Bush and Captain Ahab could be pursued for insight into Melville's novel? Might not an instructor of classical philosophy, teaching Aristotle's views of moral virtue, present President Bill Clinton's conduct as a case study for student discussion? Might not a teacher of ancient history ask the class to consider the possibility of parallels between the Roman occupation of western Mesopotamia and the United States' experience in that part of the world two millennia later? SAF would presumably sanction instructors for asking these types of questions, on the grounds that such questions are outside the purview of an official course description. But if an instructor cannot stimulate discussion and encourage critical thought by drawing analogies or parallels, the vigor and vibrancy of classroom discussion will be stultified.

This committee of the American Association of University Professors had some smart people. They were able to summarize the problem succinctly. Here are their names.

• MATTHEW W. FINKIN (Law), University of Illinois at Urbana-Champaign, chair
• ROBERT C. POST (Law), Yale University
• CARY NELSON (English), University of Illinois at Urbana-Champaign
• ERNST BENJAMIN (Political Science), Washington, D.C.
• ERIC COMBEST, staff

The committee deals with a number of specific examples, including that of Prof. Turner who was dismissed from the University of Pittsburgh in 1934 for comparing contemporary political figures to historical figures in his history course. The committee concludes with,

How an instructor approaches the material in classroom exposition is, absent breach of professional ethics, a matter of personal style, influenced, as it must be, by the pedagogical goals and classroom dynamics of a particular course, as well as by the larger educational objective of instilling in students the capacity for critical and independent thought. The instructor in Melville or classical philosophy or Roman history must be free to draw upon current persons and events just as Professor Turner did seventy years ago. Instructors must be free to employ a wide variety of examples in order to stimulate classroom discussion and thought. If allusions perform this function, they are not "irrelevant." They are pedagogically justified.

At root, complaints about the persistent interjection of "irrelevant" material concern the interjection of "controversial" material. The complaints are thus a variant of the charge that instructors have created a "hostile learning environment" and must be rejected for the reasons we have already discussed. So long as an instructor's allusions provoke genuine debate and learning that is germane to the subject matter of a course, they are protected by "freedom in the classroom."

Freedom in the Classroom (2007): Intolerance

 
I'm discussing the Freedom in the Classroom (2007) report from the American Association of University Professors [Freedom in the Classroom (2007].

The first posting covered the issue of indoctrination and made the point that Professors have to allow for debate in the classroom [Freedom in the Classroom (2007): Indoctrination]. The second posting discussed the report's comments on balance in the classroom—the proposition that Professors are obliged to present both sides of a controversy [Freedom in the Classroom (2007): Balance].

This posting addresses the third item in the report; namely the charge that "instructors are intolerant of students' religious, political, or socioeconomic views, thereby creating a hostile atmosphere inimical to learning."

Hostile Learning Environment

Contemporary critics of the academy have begun to deploy the concept of a "hostile learning environment," which was first developed in the context of antidiscrimination law. The concept has been used in universities to support speech codes that suppress expression deemed offensive to racial, ethnic, or other minorities. The concept is now being used in an attempt to suppress expression deemed offensive on religious or political grounds.

The statement On Freedom of Expression and Campus Speech Codes, adopted as Association policy in1994, acknowledges the need to "foster an atmosphere respectful of and welcoming to all persons." An instructor may not harass a student nor act on an invidiously discriminatory ground toward a student, in class or elsewhere. It is a breach of professional ethics for an instructor to hold a student up to obloquy or ridicule in class for advancing an idea grounded in religion, whether it is creationism or the geocentric theory of the solar system. It would be equally improper for an instructor to hold a student up to obloquy or ridicule for an idea grounded in politics, or anything else.

Hmmm ... while I agree with the sentiment here I'm not sure I agree entirely with the words. If a student in an astronomy class started arguing with their Professor by claiming the sun goes around the Earth, it would be almost impossible for that Professor to respond to the attack without making fun of the student's beliefs. There really are some ideas that are so far removed from reality that they can be mocked in public.

Similarly, a student who claimed that women are inferior beings who deserve to be stoned to death for adultery does not have to be treated with undue reverence in the classroom just because their views are based on religion. And students who advocate the position that scientists are frauds and liars because evolution conflicts with the Bible do not necessarily deserve to be treated with kid gloves. I agree that obloquy is almost always inappropriate. I certainly agree that harassment and discrimination are wrong. But a little bit of ridicule may be okay.

But the current application of the idea of a "hostile learning environment" to the pedagogical context of higher education presupposes much more than blatant disrespect or harassment. It assumes that students have a right not to have their most cherished beliefs challenged. This assumption contradicts the central purpose of higher education, which is to challenge students to think hard about their own perspectives, whatever those might be. It is neither harassment nor discriminatory treatment of a student to hold up to close criticism an idea or viewpoint the student has posited or advanced. Ideas that are germane to a subject under discussion in a classroom cannot be censored because a student with particular religious or political beliefs might be offended. Instruction cannot proceed in the atmosphere of fear that would be produced were a teacher to become subject to administrative sanction based upon the idiosyncratic reaction of one or more students. This would create a classroom environment inimical to the free and vigorous exchange of ideas necessary for teaching and learning in higher education.

Right on! Once again, the authors of this report have hit the nail on the head. Students should be encouraged to speak out but they can't hide behind charges of intolerance or "hostile learning environment" when their opinions are criticized.

Freedom in the Classroom (2007): Balance

 
I'm discussing the Freedom in the Classroom (2007) report from the American Association of University Professors [Freedom in the Classroom (2007].

The first posting covered the issue of indoctrination and made the point that Professors have to allow for debate in the classroom [Freedom in the Classroom (2007): Indoctrination].

But allowing for classroom debate is not sufficient. I'd go one step further, I would insist that Professors actually address the contrary opinions in the classroom and provide references to the writings of other academics who present the other side of the controversy.

The reason for advocating this is to avoid indoctrination by default. If the students are unaware of the controversy—which they often are—then the Professor is guilty of bias by not alerting students to the possibility that they can hold a valid, but different, opinion.

I was recently alerted to this problem when I learned that our second year students had never heard of random genetic drift or punctuated equilibria in their first year biology class Organisms in Their Environment. This course is taught by members of the Dept. of Ecology and Evolutionary Biology and the course description is,

Evolutionary, ecological, and behavioural responses of organisms to their environment at the level of individuals, populations, communities, and ecosystems.

I think my colleagues may be guilty of indoctrination if they're only presenting an adaptationist view of evolution and not alerting our students to other mechanisms of evolution.

The AAUP report covers this issue as well.

Balance

Current charges of pedagogical abuse allege that instruction in institutions of higher education fails to exhibit a proper balance. It is said that instructors introduce political or ideological bias in their courses by neglecting to expose their students to contrary views or by failing to give students a full and fair accounting of competing points of view.

I completely agree with this charge. I think it's criminal if Professors don't bring up contrary views in the classroom. How do universities ensure that Professors present both sides of a controversy?

We note at the outset that in many institutions the contents of courses are subject to collegial and institutional oversight and control; even the text of course descriptions may be subject to approval. Curriculum committees typically supervise course offerings to ensure their fit with programmatic goals and their compatibility with larger educational ends (like course sequencing). Although instructors are ethically obligated to follow approved curricular guidelines, "freedom in the classroom" affords instructors wide latitude to decide how to approach a subject, how best to present and explore the material, and so forth. An instructor in a course in English Romantic poetry is free to assign the poetry of the Harlem Renaissance so long as the course remains focused more on John Keats than on Langston Hughes.

This is how universities and departments are supposed to work. Collectively, they draw up guidelines for courses in order to make sure that all the essential topics are covered. Once the course is under way, there should be some feedback between what's supposed to be taught and what is actually taught in the classroom. Unfortunately, this doesn't always occur. Even more unfortunately, it's not always true that the department as a whole is aware of some controversies.

In the case that I alluded to above, I'm not certain that the Dept. of Ecology and Evolutionary Biology thinks there's a problem with the way our first year course is being taught. Does that absolve them of the charge of indoctrination?

To make a valid charge that instruction lacks balance is essentially to charge that the instructor fails to cover material that, under the pertinent standards of a discipline, is essential. There may be facts, theories, and models, particularly in the sciences, that are so intrinsically intertwined with the current state of a discipline that it would be unprofessional to slight or ignore them. One cannot now teach biology without reference to evolution; one cannot teach physical geology without reference to plate tectonics; one cannot teach particle physics without reference to quantum theory. There is, however, a large universe of facts, theories, and models that are arguably relevant to a subject of instruction but that need not be taught. Assessments of George Eliot's novel Daniel Deronda might be relevant to a course on her Middlemarch, but it is not a dereliction of professional standards to fail to discuss Daniel Deronda in class. What facts, theories, and models an instructor chooses to bring into the classroom depends upon the instructor's sense of pedagogical dynamics and purpose.

Fair enough. One could perhaps argue that random genetic drift and punctuated equilibria, for example, are not essential topics in a first year course on evolution. But you'd have to be a damn fool to make such an argument. I think these are "theories, and models ... that are so intrinsically intertwined with the current state of a discipline that it would be unprofessional to slight or ignore them."

To urge that instruction be "balanced" is to urge that an instructor's discretion about what to teach be restricted. But the nature of this proposed restriction, when carefully considered, is fatally ambiguous. Stated most abstractly, the charge of lack of balance evokes a seeming ideal of neutrality. The notion appears to be that an instructor should impartially engage all potentially relevant points of view. But this ideal is chimerical. No coherent principle of neutrality would require an instructor in a class on constitutional democracy to offer equal time to "competing" visions of communist totalitarianism or Nazi fascism. There is always a potentially infinite number of competing perspectives that can arguably be deemed relevant to an instructor's subject or perspective, whatever that subject or perspective might be. It follows that the very idea of balance and neutrality, stated in the abstract, is close to incoherent.

We concede this point. Nobody is asking an adaptationist Professor, for example, to give equal time to punctuated equilibria and Gould's hierarchical theory of evolution. That would be absurd and it would go against one of the most important principles of good education, namely the idea that students should be exposed to the passionate opinions of experts in the field. I don't like the mamby-pamby, politically correct view that we have to be dispassionate reporters of facts in the classroom.

The ideal of balance makes sense only in light of an instructor's obligation to present all aspects of a subject matter that professional standards would require to be presented. If a professor of molecular biology has an idiosyncratic theory that AIDS is not caused by a retrovirus, professional standards may require that the dominant contrary perspective be presented. Understood in this way, the ideal of balance does not depend on a generic notion of neutrality, but instead on how particular ideas are embedded in specific disciplines. This is a coherent idea of balance, and it suggests that balance is not a principle that can be invoked in the abstract but is instead a standard whose content must be determined within a specific field of relevant disciplinary knowledge.

The authors of this report have clearly thought about these criticisms a great deal. They are to be congratulated on crafting an excellent summary of the important issues in university education. The point here is well-taken. The point about "balance" in the classroom is not to enforce strict bland neutrality. It's to make sure that the opinions of Professors are placed in the appropriate context of the discipline.

There might be a controversy about "appropriate context." Maybe there are many evolutionary biologists who believe that "balancing" adaptationism with silly ideas about pluralism is not required in order to maintain professional standards? How do we resolve that?

This part of the report closes with a succinct statement of a principle that most people don't appreciate.

If scholars must be free to examine and test, they must also be free to explain and defend their results, and they must be free to do so as much before their students as before their colleagues or the public at large. That is the meaning of "freedom in the classroom." To charge that university and college instruction lacks balance when it does more than merely summarize contemporary debates is fundamentally to misconstrue the nature of higher learning, which expects students to engage with the ideas of their professors. Instructors should not dogmatically teach their ideas as truth; they should not indoctrinate. But they can expect their students to respond to their ideas and their research. As students complete different courses taught by different professors, it is to be hoped that they will acquire the desire and capacity for independent thinking.

This puts some of the onus on the students. They have an obligation to engage in their own education and not to just sit there and soak up facts. This is not the normal politically correct view of university education. In that view, students can never be blamed for the problems in the universities.

(BTW, just for the record. There are lots of problems in universities and I think that Professors are to blame for most of them.)

Freedom in the Classroom (2007): Indoctrination

 
The American Association of University Professors has just published a document called Freedom in the Classroom (2007) [Freedom in the Classroom (2007]. The report was written by a subcommittee on Academic Freedom and Tenure.

This report addresses some very important issues that relate to the role of university Professors in general but it is especially relevant in the context of the evolution/creationism controversy. Michael Bérubé has written a very nice article about freedom in the classroom for the latest issue of Inside Higher Education [Freedom to Teach]. It's worth reading. One of my favorite philosophers, Janet Stemwedel has posted a really comprehensive and thoughtful article on her blog Adventures in Ethics and Science [Freedom in the classroom]. This is such an important issue that I'd like to add my two cents. It's an issue that comes up frequently in my own classes and in lunchtime discussions with colleagues.

The report covers four "charges" against Professors.

Critics charge that the professoriate is abusing the classroom in four particular ways: (1) instructors "indoctrinate" rather than educate; (2) instructors fail fairly to present conflicting views on contentious subjects, thereby depriving students of educationally essential "diversity" or "balance"; (3) instructors are intolerant of students' religious, political, or socioeconomic views, thereby creating a hostile atmosphere inimical to learning; and (4) instructors persistently interject material, especially of a political or ideological character, irrelevant to the subject of instruction. We address each of these charges in turn.

I'll discuss each of these charges in separate postings.

Indoctrination

Professors are often accused of indoctrinating students rather than educating them. This charge arises when a particular group, such as religious fundamentalists, perceive that their views on the literal truth of the Bible are not getting proper attention in the university.

It is not indoctrination for professors to expect students to comprehend ideas and apply knowledge that is accepted as true within a relevant discipline. For example, it is not indoctrination for professors of biology to require students to understand principles of evolution; indeed, it would be a dereliction of professional responsibility to fail to do so. Students must remain free to question generally accepted beliefs if they can do so, in the words of the 1915 Declaration of Principles on Academic Freedom and Academic Tenure, using "a scholar's method and . . . in a scholar's spirit." But professors of logic may insist that students accept the logical validity of the syllogism, and professors of astronomy may insist that students accept the proposition that the earth orbits around the sun, unless in either case students have good logical or astronomical grounds to differ.

This is an important point. Professors are not obliged to present ideas that are in conflict with the established "truth" in a discipline. They are, however, obligated to permit dissent from this established truth provided students can present a scholarly argument. However, students need to understand that although they have the freedom to challenge the "accepted beliefs" they must be prepared to defend their challenge. Professors are under no obligation to simply permit speeches in the classroom without making any comment.

We all understand that some positions are so overwhelmingly correct that it makes no sense to try accommodate an opposing view. But not all positions fall into this category. Sometimes a Professor will argue a certain point of view that may not be universally accepted within the discipline. Is this indoctrination?

It is not indoctrination when, as a result of their research and study, instructors assert to their students that in their view particular propositions are true, even if these propositions are controversial within a discipline. It is not indoctrination for an economist to say to his students that in his view the creation of markets is the most effective means for promoting growth in underdeveloped nations, or for a biologist to assert her belief that evolution occurs through punctuated equilibriums rather than through continuous processes.

Indoctrination occurs only when instructors dogmatically insist on the truth of such propositions by refusing to accord their students the opportunity to contest them. Vigorously to assert a proposition or a viewpoint, however controversial, is to engage in argumentation and discussion-an engagement that lies at the core of academic freedom. Such engagement is essential if students are to acquire skills of critical independence. The essence of higher education does not lie in the passive transmission of knowledge but in the inculcation of a mature independence of mind.

What this means is that Professors cannot refuse to allow debate in the classroom. In my experience this rarely happens. If there's a lack of debate and argumentation it stems more from self-censorship among the students than from censorship by the teacher. Most of us would dearly love to hear more from our students—especially if they disagree with us. It seems that no matter how provocatively I present an opinion I can never get a rise out of my students.

Nobel Laureates Max Delbrück, Alfred D. Hershey, Salvador E. Luria

 

The Nobel Prize in Physiology or Medicine 1969.

"for their discoveries concerning the replication mechanism and the genetic structure of viruses"

Max Delbrück (1906-1981), Alfred D. Hershey (1908-1997), and Salvador E. Luria (1912-1991) received the Nobel Prize in Physiology or Medicine for founding the phage group and stimulating hundreds of scientists to study molecular biology. That's not exactly what the citation says but nobody is fooled. This is an unusual Nobel Prize. While the work that these three men did is impressive there's no real breakthrough or discovery that links all three. In a sense, they are getting the Nobel Prize for being teachers and mentors. That is entirely fitting and proper.

Their influence was enormous. Delbrück especially was the man behind the curtain throughout most of the 50's and 60's. His name comes up repeatedly in biographies and memoirs. Recall that the book Phage and the Origins of Molecular Biology was dedicated to him [Waiting for the Paradox].

The photograph on Monday's Molecule #42 shows a bacteriophage particle that has burst and spilled its DNA onto the electron microscope grid. It's a fitting symbol of the phage group that Delbrück, Luria, and Hershey founded.

The Presentation Speech was given by Professor Sven Gad of the Royal Caroline Institute.

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

Man, animals, plants, microorganisms, they are all preyed upon by viruses. Even bacteria have their own viruses, somewhat misleadingly called bacteriophages - "bacteria eaters". These were discovered at the time of the first world war but the subsequent 25 years of research did not contribute much to our knowledge of their true nature. However, about 1940 Max Delbrück became interested in bacteriophages and soon thereafter so did Salvador Luria and Alfred Hershey. Their aim was to study the most fundamental of all vital processes - replication. They expected to find in the bacteriophages a model, sufficiently primitive to permit an attack on this problem with hopes for success.

The constellation was promising: one physicist, Delbrück, one physician, Luria, and one biochemist, Hershey. With their different backgrounds and approaches they were able to launch truly concentric attacks on the fundamental problems. They worked independently but in close contact. Early on they formed their own school and the stimulating intellectual climate they created attracted talented scientists from many different fields and with many different attitudes. Under their direction the development proceeded with explosive speed.

The honour in the first place goes to Delbrück who transformed bacteriophage research from vague empiricism to an exact science. He analyzed and defined the conditions for precise measurement of the biological effects. Together with Luria he elaborated the quantitative methods and established the statistical criteria for evaluation which made the subsequent penetrating studies possible. Delbrück's and Luria's forte is perhaps mainly theoretical analysis, whereas Hershey above all is an eminently skillful experimenter. The three of them supplement each other well also in these respects.

The research proceeded along the lines Delbrück had set for a little more than ten years. During this period the bacteriophage life cycle was mapped out in detail. The various phases of the replication process were dissected and studied separately. The final picture of the sequence of events was briefly as follows.

A bacteriophage particle consists of a core containing nucleic acid, enveloped in a protein shell. The shell contains an enzyme that reacts specifically with a substance in the cell wall and which produces an erosion in the cell surface through which the bacteriophage core enters. The protein shell remains outside and does not further participate in the process of infection. With the entrance of the bacteriophage core the activity of the cell is radically changed. Its chemical tools remain intact but its regulating center is switched off. Instead the bacteriophage core takes command and directs the chemical activity exclusively towards production of new bacteriophage particles. The various components of the virus, nucleic acid and several proteins, are produced separately and only in the terminal phase are they put together to form "mature" particles. When this stage is reached the cell wall is dissolved and the newly formed virus is released. This process proceeds with almost inconceivable speed. One virus particle may in 10 to 15 minutes give rise to more than a thousand new particles.

New nucleic acid is formed in principle through repeated duplications. On rare occasions a synthetic error may occur, resulting in the appearance of a unit with a structure that at some point differs from that of the others. If the error is not sufficiently serious to make the new unit non-functional, it will be repeated at subsequent duplications and the final harvest of bacteriophages will contain a number of particles with properties that differ from those of the parental type. Through a "mutation" a new variant has appeared.

One and the same cell can be simultaneously infected by two or more related virus particles. If so, an exchange of parts may take place between two units in a so-called recombination process. In this fashion new variants are formed with the characteristics of the original types in various combinations. An analysis of the properties of the recombinants may give information on the genetic structure of the virus. The rapid multiplication of the bacteriophages has made it possible in a short time to collect numerous mutants and to perform systematic crossing experiments. By this means their genetic structure has been established in ever finer detail.

Such was the situation at the beginning of the 1950's. The biological phenomena had been sorted out and placed in correct relations. The picture of the nature and mode of action of the virus which was thus obtained differed essentially from previous concepts. Most important perhaps are the evidence of an interaction between the virus and the host cell and the fact that the regulation of the cellular activity can be affected by the introduction of foreign, genetically active structures.

These discoveries have decisively influenced the development within many fields of biological research. The charting of the fundamental processes in the life cycle of the bacteriophages was a necessary condition for attempts to define them in chemical terms, on the molecular level. At first the scientific community in general had struck a reserved attitude to bacteriophage research. It was considered to be of interest as a curiosity but of little importance to biology in general. Gradually this attitude has changed. It is now clearly evident that in principle the same mechanisms regulate the activities of bacteriophages, micro-organisms and more complex cellular systems. Therefore, Delbrück, Hershey and Luria must in fact be regarded as the original founders of the modern science of molecular biology.

Their discoveries have also had great importance for the geneticists. It is mainly through studies of bacteriophages that the mechanisms of the genetic regulation of the vital processes have been revealed.

Last but not least, bacteriophage research has given us the better insight in the nature of viruses which is necessary for the understanding and combat of virus diseases of higher beings. A long time has passed since the discoveries were made. However, their general biological and medical importance was only gradually recognized and only in later years has the wide range of their applicability become fully evident.

Max Delbrück, Alfred Hershey, Salvador Luria.

Thirty years ago you embarked upon a research project which to most members of the scientific community must have appeared as overambitious. You set out to solve the most fundamental of all biological problems, that of self-replication. By making the lowly bacteriophage your subject you probably also raised many eyebrows. However, by your sense for the importance of strict scientific methodology, your brilliant experimental skill and above all your imaginative approach you succeeded in making the impossible feasible. The realization that bacteriophage after all is a respectable representative of all living matter was slow in coming. Today, however, the general applicability of the principles you established is beyond doubt and the full impact of your achievements is finally felt. You have been awarded this year's Nobel prize in physiology and medicine for your discoveries concerning virus replication and genetics and we hereby acknowledge the importance of your contributions to the biological and medical sciences. On behalf of Karolinska Institutet I beg you to accept our heartfelt felicitations.

I now ask you to receive your prize from the hands of His Majesty the King.

Tangled Bank #88

 

The latest version of the Tangled Bank has been posted on Behaviorial Eology Blog [Tangled Bank #88].

The Good People of Halifax

 
On this sixth anniversary of Sept. 11, 2001 Mike Dunford has posted excerpts from a Stephen Jay Gould essay Apple Brown Betty [9-11].

I hope you'll forgive my Canadian chauvinism on this occasion as I post parts of another Stephen Jay Gould essay [The Good People of Halifax].

My latest visit among you, however, was entirely involuntary and maximally stressful. I live in lower Manhattan, just one mile from the burial ground of the Twin Towers. As they fell victim to evil and insanity on Tuesday, September 11, during the morning after my 60th birthday, my wife and I, en route from Milan to New York, flew over the Titanic’s resting place and then followed the route of her recovered dead to Halifax. We sat on the tarmac for 8 hours, and eventually proceeded to the cots of Dartmouth’s sports complex, then upgraded to the adjacent Holiday Inn. On Friday, at 3 o’clock in the morning, Alitalia brought us back to the airport, only to inform us that their plane would return to Milan. We rented one of the last two cars available and drove, with an intense mixture of grief and relief, back home.

.......

I know that the people of Halifax have, by long tradition and practice, shown heroism and self-sacrifice at moments of disaster -- occasional situations that all people of seafaring ancestry must face. I know that you received and buried the drowned victims of the Titanic in 1912, lost one in ten of your own people in the Halifax Explosion of 1917, and gathered in the remains of the recent Swissair disaster.

But, in a sense that may seem paradoxical at first, you outdid yourselves this time because you responded immediately, unanimously, unstintingly, and with all conceivable goodness, when no real danger, but merely fear and substantial inconvenience, dogged your refugees for a few days. Our lives did not depend upon you, but you gave us everything nonetheless. We, 9000 strong, are forever in your debt, and all humanity glows in the light of your unselfish goodness.

And so my wife and I drove back home, past the Magnetic Hill of Moncton (now a theme park in this different age), past the reversing rapids of Saint John, visible from the highway, through the border crossing at Calais (yes, I know, as in Alice, not as in ballet), and down to a cloud of dust and smoke enveloping a mountain of rubble, once a building and now a tomb for 5000 people. But you have given me hope that the ties of our common humanity will bind even these wounds. And so Canada, although you are not my home or native land, we will always share this bond of your unstinting hospitality to people who descended upon you as frightened strangers from the skies, and received nothing but solace and solidarity in your embrace of goodness. So Canada, because we beat as one heart, from Evangeline in Louisiana to the intrepid Mr. Sukanen of Moose Jaw, I will stand on guard for thee.

Harper Says Canada Should Stay in Afghanistan

 
I'm really annoyed at all you Australians. We sent you our Prime Minister on the understanding that you would keep a muzzle on him and give us a bit of a break. Instead, you allowed him to hob-nob with John Howard. Now look what you've done. Our Prime Minister, Stephen Harper, has caught the war bug from yours. According to Reuters Canada this is what Harper said in your parliament [Harper vows continued support for Afghanistan].

CANBERRA (Reuters) - Prime Minister Stephen Harper, under fire at home for a troop commitment to Afghanistan that has cost 70 lives, said on Tuesday he would not abandon the country.

"This cause is global and necessary," Harper said in a speech to Australia's parliament on the anniversary of the September 11, 2001, attacks on the United States.

"Because as 9-11 showed, if we abandon our fellow human beings to lives of poverty, brutality and ignorance, in today's global village, their misery will eventually and inevitably become our own," said Harper.

9-11 showed no such thing. Don't you remember? They didn't attack America because they were poor, miserable, and stupid, they attacked because they hate freedom and democracy. If we stay in Afghanistan and force them to be free and democratic then they'll hate us even more,

Hmmm ... there seems to be something wrong with that argument ....

Okay, let's try this. If we stay in Afghanistan we'll have just as much success as the British did before World War II and the Russians did in the 1980's.

Nope .... that one doesn't work either.

The heck with it. Let's just get out as fast as we can and allow the people of Afghanistan to deal with their own problems.

By the way, you Australians can keep him. We don't want him back.

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[Photo Credit: REUTERS/Tim Wimborne]

Are You as Smart as a Third Year University Student? Q3

Question 1
Question 2PDB's (Protein Data Bank) molecule of the month for September is citrate synthase, one of the enzymes of the citric acid cycle. Read the PDB website to find out more about this interesting enzyme. [Hat Tip: Philip J at Biocurious]

Citrate synthase catalyzes the following reaction,


One of the most interesting things about this reaction is that the standard Gibbs free energy change of the reaction (ΔG^°′) is −31.5 kJ mol^-1. Here's a question that I ask of my second year students.

---

Like most reactions in vivo, the actual Gibbs free energy change for this reaction is zero. Normally you might expect that such a large negative standard Gibbs free energy change would indicate that the forward reaction is coupled to the synthesis of ATP. Indeed, the hydrolysis of the similar thioester bond in succinyl CoA (Step 5 of the citric acid cycle) is coupled to the synthesis of GTP (or ATP). However, in the case of the citrate synthase reaction, the available energy is used for a different purpose. What is this purpose?

Are You as Smart as a Third Year University Student? Q2

 
Question 1
I thought it might be fun to post some multiple choice questions from old exams to see if Sandwalk readers are as smart as my old third year molecular biology students. Here's a question from 1998.

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The sequence of the coding region of an E. coli ribosomal protein mRNA consists of 21% G's and 23% C's. What do you predict would be the composition of the part of the gene (double-stranded DNA) from which this mRNA coding region is derived?

            a) 56% T's
            b) 44% T's
            c) 28% T's
            d) 23% T's
            e) impossible to answer correctly

Framing a Press Release

 
There's been an ongoing debate about framing in the blogosphere. You can see the latest manifestation on Pharngula [When did ‘framing’ become a synonym for religiosity?]. The idea behind framing is to present your science in a way that appeals to and engages the public. The opposition to framing comes from those—I am one—who fear that framing is another word for spin and that in attempting to appeal to the public you often distort or misrepresent the science.

Let's look at how press release writers use framing. This press release is from Ohio State Medical Center. It reports on a paper by Calin et al. (2007) that has just been published in Cancer Cell. The paper looks at the expression of RNA's from highly conserved sequences that do not encode proteins. These are similar to the conserved noncoding elements that we discussed before [Adaptive Evolution of Conserved Noncoding Elements in Mammals] except that they are transcribed.

The first two lines of the press release say,

COLUMBUS, Ohio – Research here shows that an obscure form of RNA, part of the protein-making machinery in all cells, might play an important role in human cancer.

These ultraconserved non-coding RNAs (UCRs) have been considered “junk” by some researchers, but a new report in the September issue of the journal Cancer Cell indicates that this may not be the case.

This is quite ridiculous. I don't know of any researcher who would declare that ultraconserved sequences are junk. This just seems like a distortion of the paper in order to frame the work in a way that's more appealing to the public. The idea is to make it look like this paper overturns the current dogma about junk DNA.

But maybe that's unfair. Maybe the authors themselves make such a claim in their paper and the press release isn't engaging in spin.

Here's part of a paragraph from the introduction to the paper.

A large portion of transcription products of the noncoding functional genomic regions have significant RNA secondary structures and are components of clusters containing other sequences with functional noncoding significance (Bejerano et al., 2004a). The UCRs represent a small fraction of the human genome that are likely to be functional but not encoding proteins and have been called the “dark matter” of the human genome (Bejerano et al., 2004a). Because of the high degree of conservation, the UCRs may have fundamental functional importance for the ontogeny and phylogeny of mammals and other vertebrates.

Oops! The authors themselves admit that these sequences are thought to be functional. There's nothing in the paper about junk DNA and there's certainly nothing about researchers who think these sequences might be junk.

The more I see examples of framing the more I dislike it. It's bad enough that the practice exists but the attempts by Mooney and Nisbet [Framing Framing] to justify it are not going to help us clean up science writing. If Mooney and Nisbet would take on the worst abusers of framing then I would have a lot more respect for their position.

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Calin, G.A. et al. (2007) Ultraconserved Regions Encoding ncRNAs Are Altered in Human Leukemias and Carcinomas. Cancer Cell 12:215-229. [Summary][PDF]