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.

---

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]

Quick, Get the Popcorn

 
Yesterday Jeffrey Shallit dissected the arguments of one, Tom Bethell, who tried to argue that Intelligent Design Creationism and Creationism were different things. It was fun to read even though we've heard the same nonsense from the IDiots several dozen times. (Bethall even used the Colin Patterson quote, for God's sake!)

I thought that would be the end of it but, oh no, the IDiots have come back for more. Michael Egnor has posted a challenge to Jeffrey Shallit on the Discovery Institute blog Evolution News & Views [Jeff Shallit, Blueprints, and the Genetic Code]. After whining about how mean Jeffrey was to poor old Tom, Ednor gets to the heart of the issue. Apparently the IDiots are really taken with the fictional movie Contact. They think that because Jodie Foster can detect intelligent aliens by deciphering a signal from Vega, this means that Intelligent Design Creationism is real science.

Egnor demands that Jeffrey answer the following question ...

If the scientific discovery of a ‘blueprint’ would justify the design inference, then why is it unreasonable to infer that the genetic code was designed?

Pull up your chairs and get out the popcorn. This is going to be fun.

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[Photo Credit: The photograph is from the official website of the movie Contact]

Learning to Love Bacteria

 
We live now in the "Age of Bacteria." Our planet has always been in the "Age of Bacteria," ever since the first fossils—bacteria, of course—were entombed in rocks more than 3 billion years ago.

On any possible, reasonable or fair criterion, bacteria are—and always have been—the dominant forms of life on Earth.
Stephen J. Gould (1996)Bacteria don't get much respect in spite of the fact that many scientists have written about their importance [see Planet of the Bacteria by Stephen Jay Gould (1996)]. Over at Deep Sea News they're trying, once again, to rectify this unfortunate situation. This will be an entire week devoted to microbes [Intro to Microbial Week by Christina Kellogg].

Here are some important facts from the first posting to keep in mind whenever you're inclined to dismiss bacteria.

"The number of prokaryotes [i.e., bacteria + archaea] and the total amount of their cellular carbon on earth are estimated to be 4-6 ×: 10³⁰ cells and 350-550 Pg of C (1 Pg = 10¹⁵ g), respectively. Thus the total amount of prokaryotic carbon is 60-100% of the estimated total carbon in plants, and inclusion of prokaryotic carbon in global models will almost double estimates of the amount of carbon stored in living organisms." (Whitman et al. 1998)

and

Numerically dominant--there are approximately 1 million bacteria and 10 million viruses in a milliliter of seawater. There are approximately 0.00000000000000000002 sperm whales per milliliter of seawater.

The point about learning to love bacteria is that it's crucial to a full understanding of our place in the world of living things. This is going to come up discussions about complexity. We need to understand that our perspective is heavily biased. As Gould (1996) writes,

Our failure to grasp this most evident of biological facts arises in part from the blindness of our arrogance but also, in large measure, as an effect of scale. We are so accustomed to viewing phenomena of our scale—sizes measured in feet and ages in decades—as typical of nature.

Individual bacteria lie beneath our vision and may live no longer than the time I take to eat lunch or my grandfather spent with his evening cigar. But then, who knows? To a bacterium, human bodies might appear as widely dispersed, effectively eternal (or at least geological), massive mountains, fit for all forms of exploitation and fraught with little danger unless a bolus of imported penicillin strikes at some of the nasty brethren.

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[Hat Tip: Christopher Taylor at Catalogue of Organisms]

Gould, S.J. (1996) Planet of the Bacteria. Washington Post Horizon 119:(344). An essay adapted from Full House New York: Harmony Books, 1996, pp. 175-192.

Stupidist Blogging Tory of the week

 
Canadian Cynic has started a new award called the "Blogging Tory inanity of the week" [ Blogging Tory inanity of the week: Sep 2-8, 2007]. Now you may think that this would be a hard choice since there are so many examples to choose from. Not so. There's one hands-down winner this week and it's a Blogging Tory who tells us that "supernatural phenomena are tangible and observable." Normally I would quote the winning post but it's far better to read it on Canadian Cynic.

Mendel's Garden #18

 

The 18th version of Mendel's Garden has just been posted on Balancing Life [Mendel’s Garden at Balancing Life]. Can you guess which one of my recent postings is included?

Monday's Molecule #42

 
Today's molecule is a very big molecule. You have to describe what you are seeing in the photograph and then relate it to this Wednesday's Nobel Laureate(s). Extra points if you can relate it to a recent posting. [Hint: The Nobel Prize is the most innovative, creative, and daring prize that the Nobel Committee has ever awarded.]

There will be no free lunch this week because the contest is too easy. You can win bragging rights by sending your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the photo and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right.

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Parole Officer Can't Make You Attend Alcoholics Anonymous (because It's Religious)

 
A few months ago I posted a message about Alcoholics Anonymous. It was news to me that the program was very religious and required belief in God.

Friendly Atheist reports on a recent court decision in the United States [Forced Attendance at Alcoholics Anonymous is Unconstitutional, Says Court]. You should read the entire story as he reports it. A Buddhist was released on parole on condition that he attend a Salvation Army treatment program that included Narcotics Anonymous. The Buddhist went to some meetings but refused to participate and was sent back to jail.

The court ruled that,

… requiring a parolee to attend religion-based treatment programs violates the First Amendment… While we in no way denigrate the fine work of (Alcoholics Anonymous and Narcotics Anonymous), attendance in their programs may not be coerced by the state.

The Centre for Inquiry (Toronto) sponsors the Secular Organizations for Sobriety Group of Toronto (SOSGT), a non-religious organization for alcoholics [SOSGT].

SOSGT credits the individual for achieving and
maintaining his or her own sobriety and is ideal for those
uncomfortable with the spiritual content of 12-step programs.
The group is secular and religiously neutral.