Science Education and Teaching Controversy

I'm beginning to realize that there are (at least) two fundamentally different approaches to teaching science. One strategy, which I'll call the "fact-based" approach, concentrates on communicating facts about the natural world. The other approach, which I'll call the "methodological approach" concentrates on teaching students how to acquire knowledge.

In the fact-based approach to science education, the emphasis is on making sure that students have a sound knowledge of the basic principles of physics, chemistry, geology, and biology. Let's take the teaching of evolution as an example. If you follow this strategy then you will want your students to know about the main mechanisms of evolution and the known facts about the history of life. You will only teach things that are supported by scientific evidence. In order to pass the course, students must demonstrate that they have acquired, and understand, the facts.

The goal here is to send students out into the real world armed with an understanding of what science has learned. Hopefully they'll be able to use that knowledge of evolution to choose the "right" side in any controversy.

The methodological approach concentrates on teaching students how to acquire knowledge using the scientific method. This "method" is not the kindergarten version so often seen in schools but the more fundamental version that emphasizes evidence, skepticism, and rational thinking. The idea here is not only to teach facts—although that's important—but to teach why those facts should be accepted as true. Another major goal of this method is teaching critical thinking and the desired outcome is a group of graduates who will be able to apply the methodology to any problem they encounter in the future. This includes problems that don't fall into the traditional science fields of physics, chemistry, geology, and biology.

The fact-based approach tends to avoid any distractions that might confuse students about what is known and what isn't. Thus, Intelligent Design Creationism cannot be discussed in this type of curriculum because there's nothing factual about creationism. It's not part of science.

That restriction doesn't apply if you are trying to teach critical thinking because the most important part of your objective is teaching students how to argue and how to reason. In that approach, you actually want to encourage controversy and debate in the classroom because that's how you learn to distinguish between wheat and chaff, or science and pseudoscience.

I was prompted to think about these two different approaches by a recent issue of Science containing a number of articles about science education.¹ One of them is "Arguing to Learn in Science: The Role of Collaborative, Critical Discourse" by Jonathan Osborne [April 23, 2010: doi: 10.1126/science.1183944]. Here's the abstract ...

Argument and debate are common in science, yet they are virtually absent from science education. Recent research shows, however, that opportunities for students to engage in collaborative discourse and argumentation offer a means of enhancing student conceptual understanding and students’ skills and capabilities with scientific reasoning. As one of the hallmarks of the scientist is critical, rational skepticism, the lack of opportunities to develop the ability to reason and argue scientifically would appear to be a significant weakness in contemporary educational practice. In short, knowing what is wrong matters as much as knowing what is right. This paper presents a summary of the main features of this body of research and discusses its implications for the teaching and learning of science.

Clearly, this approach is consistent with bringing creationist ideas into the classroom in order to teach students why they are wrong. You will also want to bring up astrology and the ancient theory of demon possession if that helps make the point. You can't discuss every single controversy, but, at the very least, you should include the "active" ones—the ones students will encounter as soon as they step outside the classroom and watch FOX News or listen to their preacher on Sunday morning.

"Teaching the controversy" is good science if you adopt the methodological approach to science education but it's anathema if you adopt the fact-based approach.

Here's A.C. Grayling, a philosopher at Birkbeck College, University of London, and also a Fellow of St Anne's College, Oxford, giving his opinion on science education. Can you guess which approach he favors? Why isn't he aware of the "controversy" in science education? I wonder if he avoids all controversial topics in his philosophy classes?

---

1. Thanks to Bruce Alberts who, as editor-in-chief, is trying to promote more emphasis on science education.

P.S. I don't want to discuss whether the methodological approach is possible in American schools. If you think that science teachers are too stupid to adopt this approach, or if you think that many of them are secret creationists, then that's an entirely different problem. It's a defeatist attitude to conclude that the quality of science teachers is so bad that science education can't be fixed. If you have bad science teachers then the first step is to replace them with good ones. The sooner the better.

Junk RNA or Imaginary RNA?

RNA is very popular these days. It seems as though new varieties of RNA are being discovered just about every month. There have been breathless reports claiming that almost all of our genome is transcribed and most of the this RNA has to be functional even though we don't yet know what the function is. The fervor with which some people advocate a paradigm shift in thinking about RNA approaches that of a cult follower [see Greg Laden Gets Suckered by John Mattick].

We've known for decades that there are many types of RNA besides messenger RNA (mRNA encodes proteins). Besides the standard ribosomal RNAs and transfer RNAs (tRNAs), there are a variety of small RNAs required for splicing and many other functions. There's no doubt that some of the new discoveries are important as well. This is especially true of small regulatory RNAs.

However, the idea that a huge proportion of our genome could be devoted to synthesizing functional RNAs does not fit with the data showing that most of our genome is junk [see Shoddy But Not "Junk"?]. That hasn't stopped RNA cultists from promoting experiments leading to the conclusion that almost all of our genome is transcribed.

Late to the Party

Several people have already written about this paper including Carl Zimmer and PZ Myers. There are also summaries in Nature News and PLoS Biology.That may change. A paper just published in PLoS Biology shows that the earlier work was prone to artifacts. Some of those RNAs may not even be there and others are present in tiny amounts.

The work was done by Harm van Bakel in Tim Hughes' lab, right here in Toronto. It's only a few floors, and a bridge, from where I'm sitting right now. The title of their paper tries to put a positive spin on the results: "Most 'Dark Matter' Transcripts Are Associated With Known Genes" [van Bakel et. al. (2010)]. Nobody's buying that spin. They all recognize that the important result is not that non-coding RNAs are mostly associated with genes but the fact that they are not found in the rest of the genome. In other words, most of our genome is not transcribed in spite of what was said in earlier papers.

Van Bekal compared two different types of analysis. The first, called "tiling arrays," is a technique where bulk RNA (cDNA, actually) is hybridized to a series of probes on a microchip. The probes are short pieces of DNA corresponding to genomic sequences spaced every few thousand base pairs along each chromosome. When some RNA fragment hybridizes to one of these probes you score that as a "hit." The earlier experiments used this technique and the results indicated that almost every probe could hybridize an RNA fragment. Thus, as you scanned the chip you saw that almost every spot recorded a "hit." The conclusion is that almost all of the genome is transcribed even though only 2% corresponds to known genes.

The second type of analysis is called RNA-Seq and it relies on direct sequencing of RNA fragments. Basically, you copy the RNA into DNA, selecting for small 200 bp fragments. Using new sequencing technology, you then determine the sequence of one (single end) or both ends (paired end) of this cDNA. You may only get 30 bp of good sequence information but that's sufficient to place the transcript on the known genome sequence. By collecting millions of sequence reads, you can determine what parts of the genome are transcribed and you can also determine the frequency of transcription. The technique is much more quantitative than tiling experiments.

Van Bekel et al. show that using RNA-Seq they detect very little transcription from the regions between genes. On the other hand, using tiling arrays they detect much more transcription from these regions. They conclude that the tiling arrays are producing spurious results—possibly due to cross-hybridization or possibly due to detection of very low abundance transcripts. In other words, the conclusion that most of our genome is transcribed may be an artifact of the method.

The parts of the genome that are presumed to be transcribed but for which there is no function is called "dark matter." Here's the important finding in the author's own words.

To investigate the extent and nature of transcriptional dark matter, we have analyzed a diverse set of human and mouse tissues and cell lines using tiling microarrays and RNA-Seq. A meta-analysis of single- and paired-end read RNA-Seq data reveals that the proportion of transcripts originating from intergenic and intronic regions is much lower than identified by whole-genome tiling arrays, which appear to suffer from high false-positive rates for transcripts expressed at low levels.

Many of us dismissed the earlier results as transcriptional noise or "junk RNA." We thought that much of the genome could be transcribed at a very low level but this was mostly due to accidental transcription from spurious promoters. This low level of "accidental" transcription is perfectly consistent with what we know about RNA polymerase and DNA binding proteins [What is a gene, post-ENCODE?, How RNA Polymerase Binds to DNA]. Although we might have suspected that some of the "transcription" was a true artifact, it was difficult to see how the papers could have failed to consider such a possibility. They had been through peer review and the reviewers seemed to be satisfied with the data and the interpretation.

That's gonna change. I suspect that from now on everybody is going to ignore the tiling array experiments and pretend they don't exist. Not only that, but in light of recent results, I suspect more and more scientists will announce that they never believed the earlier results in the first place. Too bad they never said that in print.

---

van Bakel, H., Nislow, C., Blencowe, B. and Hughes, T. (2010) Most "Dark Matter" Transcripts Are Associated With Known Genes. PLoS Biology 8: e1000371 [doi:10.1371/journal.pbio.1000371]

Is God Dead?

 
I stumbled upon this while looking for something else. It's the cover from April 8, 1966. I remember it well. It didn't seem like such a big deal at the time. We all assumed the answer was "yes." Not a big deal in the '60s.

If I recall correctly, the inside article was about some dude named Friedrich Nietzsche. Weird name. Nobody cared. The cover said it all.

---

The Essence of Christianity

Right now there's a conference going on in Oxford, United Kingdom—that hotbed of Christian apologetics (and Richard Dawkins). John Wilkins is there. One of the topics is defining religion [Ruminations in Oxford].

John's "ruminations" remind me of the ongoing debate over the conflict between science and religion. Everyone knows that the conflict exists but everyone has their own idea about how far it penetrates into religion. As you all know, various accommodationists are trying hard to wall off a protected area of religion that science cannot enter. That allows science and religion to co-exist peacefully.

In order to do this, the accommodationists have to define the essence of a religion. They agree that belief in a six thousand year old Earth conflicts with science but, according to them, that's not an essential belief in Christianity. The people who believe that sort of nonsense don't represent the serious "sophisticated" Christians (like the ones in theology at Oxford). So, what are the essential beliefs that don't conflict with the scientific way of acquiring knowledge?

Here's how Michael Ruse describes them in his latest book, Science and Spirituality: Making Room for Faith in the Age of Science (p. 182). I wonder how many of the people at the conference will agree with Ruse about the four items that are essential for Christians? I wonder how many of them agree with Ruse that none of these four conflict with the scientific way of thinking?

With an eye to the discussion of the previous chapters, I want to pick out four items or claims that are central to Christian belief—four items that the Christian takes on faith. If you do not believe in these, then you should not call yourself a Christian. First, that there is a God who is creator, "maker of heaven and earth." Second, we humans have duties, moral tasks here on earth, in the execution of which we are going to be judged. Hence, God stands behind morality. Third, Jesus Christ came to earth and suffered because we humans are special, we are worth the effort by God. The usual way of expressing this is to say that we are "made in the image of God." We have "souls." Fourth and finally, there is the promise of "life everlasting." We can go to heaven, what ever that means.

Let me spell out carefully what I see as the task in this and the next chapter. It is not to defend Christianity as a true or compelling belief system. I take it that you can enter these chapters as an agnostic or an atheist and depart in the same frame of mind. I do not want to dissuade people from Christianity, nor do I want to convince them of it. I want to explain in a fair manner what is meant by Christianity in terms of the four points introduced in the last paragraph. I also want to show that you could hold these, if you so wish, in the light of modern science—if you prefer, in the face of modern science. In other words, the Christian's claims are not refuted by modern science—or indeed threatened or made less probable by modern science.

Here's my quick take on the four items.

1. God the creator: It's possible to imagine a Deist God who starts off the known universe then goes off somewhere to watch perpetual reruns of The Lawrence Welk Show. (Where does he go?) This sort of God does not conflict directly with science, even if you define science as a way of knowing that requires evidence, skepticism, and rationality. It's an unnecessary God but a relatively harmless one compared to some others. Nobody I know believes in such a God, including Keith Ward, Ken Miller and Francis Collins.

2. God stands behind morality and He will judge us: There's no scientific evidence to support the notion that morality has anything to do with supernatural beings and plenty of evidence against it. There's no scientific evidence that you will be judged by anyone except other humans. This belief conflicts with science.

3. Jesus Christ is/was God: The idea that a supernatural being appeared on Earth in the form of a real human and lived among a group of primitive farmers in some obscure part of the world is not consistent with anything we know by applying scientific reasoning. It conflicts with science big time. So does the idea that we have something called a "soul" that no other animal possesses.

4. When you die you go to heaven: Totally inconsistent with a scientific way of thinking. In spite of several thousand years of tying, no evidence of heaven has ever been produced. Or hell, for that matter. There is nothing about this silly belief that's even remotely consistent with science.

---

Visitors

 

---

Clarity vs Obscurity

 
Richard Dawkins says, "There are people who are so in love with obscurity—a nice warm fuzzy feeling of obscurity and obscurantism—that, if you say something clearly, they feel threatened." See the video below.

For some reason this reminds me of a book I just read by Keith Ward called "The Big Questions in Science and Religion." Perhaps it's because of the blurb on the back cover that says,

Ward effortlessly flows from one fascinating insight to another about the often contentious relationship between diverse religious views and the new scientific knowledge. Writing with both passion and clarity, he masterfully converys the depth, the difficulty, and the importance of the greatest intellectual and existential questions of the modern age.

"Clarity"? Don't make me laugh. Keith Ward has never met an example of obscurantism that he doesn't embrace.

Ward is a colleague of Dawkins at Oxford. I wonder if Dawkins was thinking of him when he made his statement? Or, he may have been thinking of another colleague, Alister McGrath.

---

[Hat Tip: Clarity - A very nice statement by Dawkins, at RichardDawkins.net.]

Correlations

 
It's fascinating how opposition to science correlates with other positions on various issues. There's a reason why we call them IDiots.

Canada is in the midst of a debate on abortion. Right now there are no laws in Canada that prohibit abortion. We are a pro-choice country.

The current Conservative government under King Harper wants to change that but they're going about it in a very underhanded way. The first step is to refuse funding to foreign aid programs that permit abortion. The second step seems to be to refuse federal funding to a number of women's groups that are pro-choice.

What has this got to do with correlations? Denyse O'Leary, that's what. Denyse is a well-known anti-science writer who support just about any cockamainy idea from Intelligent Design Creationists. Now she's weighed in on the abortion issue. Here's her open letter to the Prime Minister [Off topic: Advice to the government re abortion funding]. Judge for yourself whether her views on this issue are any more coherent than her anti-science views.

Mr. Prime Minister and excellent minister Bev Oda:

Please stand firm against the people who will get money from aborting babies in other countries, if you cave in.

This is for a number of non-religious reasons:

1. There is NO reason to believe abortion will even be voluntary. And what can we do if it isn't? It is better if we Canadians just do not fund it. (If people in other countries want to force women to be aborted, to meet grant-based population reduction quotas, we cannot stop them. But at least we had nothing to do with it, right? It's not like the cheque is stamped 'From a grateful CANADA'. Surely, there are some shames we cannot stoop to.)

2. Contrary to population whackos, most of the world is in steep demographic decline. This is bad news for business, pension plans, etc. Why add to the problem? Right now, YOUR government is advertising for healthy young workers from abroad. So we should kill their successors?

3. Abortion clinics are run by people who do not mind killing babies for a living. Even if you didn't agree that that is a problem, a number of other evils result, including: Teachers molest underage girls and ship them to clinics for discreet abortions, unbeknown to their parents. Abortion clinics may also function on the adoption black market. = Would you keep it for a while instead of killing it, if we get you some money?

4. No one should believe anything an abortion clinic operator says about not killing viable babies. If he really cared about stuff like that, he would not likely do what he does now. So you can assume, for practical purposes, it is unreliable.

5. Some babies may be sold for research that should never be done on a human being, but remember that they do not technically exist.

Stand firm! Most of the criticism I hear about your government comes from NOT standing up for traditional Canadian values. Most of the praise I hear is for doing so.

And REPEAL Section 13 and FIRE Jennifer Lynch. Quit fooling around about that too. People are really angry.

Traditional values and civil rights are important to the people who would re-elect you.

Did I mention that Denyse is a Roman Catholic? Do you think it's relevant?

I'm sure Stephen Harper will be so proud to have the support of an intellectual like Denyse O'Leary.

---

Who Asked Katarin MacLeod to Review this Book

 
Katarin MacLeod reviews a new book on evolution—one that's intended to educate children who lack an understanding of science [Evolution (Biology)-Juvenile literature].

According to the short bio at the end of her review ...

Katarin MacLeod is an Assistant Professor in Science Education at St. Francis Xavier University in Antigonish, NS. Her areas of interest include physics educational research (PER), and the incorporation of science, technology, society and environment (STSE) outcomes into science courses at all levels to help students understand the relevancy of science, increase scientific literacy, and to promote citizenship.

Here's part of her review. You can judge for yourself whether she is competent to teach science education at St. Francis Xavier University.

Although the text is very good in describing the theory of Evolution, there are points in the book where the author makes comments that could imply that Evolution is more than a theory. For example, “…Charles Darwin revealed the solution to the mystery of evolution” (p. 7). He also makes the comment that Evolution is the most important idea in all of biology (p. 7). Such phrases may lead the reader into thinking that scientists completely understand the theory of Evolution which would be incorrect, else Evolution would be a principle or a law and not a theory. As well, it is a bit bold to claim that evolution is the most important idea in all of biology – biology is a huge field of study with other key discoveries.

Hint to Professor MacLeod. Before you review your next book on evolution you'd better brush up on the difference between a fact and a theory and learn that a theory can never become a law.

---

[Hat Tip: Richard B. Hoppe at Panda's Thumb]

Shame on the Royal Ontario Museum

 
The Royal Ontario Museum (ROM) is sponsoring a lecture by Deepak Chopra. You can see for yourself on the ROM website: An Evening with Deepak Chopra.

Here's the blurb ...

An Evening with Deepak Chopra
Wednesday, June 23, 7:00 - 8:00 pm (Doors Open 6:00 pm)

Status: Registration Starts May 14!

Director's Signature Series
The Warrior Emperor and China's Terracotta Army

World renowned teacher, author and philosopher Deepak Chopra presents his latest concepts in the field of mind-body medicine bridging the technological miracles of the West with the wisdom of the East. He will show you how your highest vision of yourself can be turned into physical reality and discuss how you can become a living cell within the body of a living universe. You don't join the cosmic dance - you become the dance. Deepak will address the deeper meaning of our existence including: What is our true nature? What is the meaning and purpose of our existence? How can I transform myself? How can I make a better world? Deepak explains how the greatest spiritual secrets are tied up in this simple answer: You can't change the body without changing the self, and you can't change the self without bringing in the soul. He explains, "It's all one process, and it begins with knowing that your body exists to mirror who you are and who you want to be."

Deepak Chopra is the author of more than 56 books translated into over 35 languages, including numerous New York Times bestsellers in both the fiction and non-fiction categories. He is a fellow of the American College of Physicians, a member of the American Association of Clinical Endocrinologists, Adjunct Professor at Kellogg School of Management and Senior Scientist with The Gallup Organization. Time magazine heralds Deepak Chopra as one of the top 100 heroes and icons of the century and credits him as "the poet-prophet of alternative medicine." For more information visit: www.deepakchopra.com

Location: Convocation Hall, 31 King’s College Circle, University of Toronto

Cost: Price: Ground VIP: $175, Rise Area: $89, 1st Balcony: $69, 2nd Balcony: $49, Behind Stage: $25

Tickets are non-refundable.

---

I Don't Have Time for This!

 

The banner headline on the front page of The Toronto Star says, "U of T cracks the code." You can read the newspaper article on their website: U of T team decodes secret messages of our genes. ("U of T" refers to the University of Toronto - our newspaper thinks we're the only "T" university in the entire world.)

The hyperbole is beyond disgusting.

The work comes from labs run by Brendan Frey and Ben Blencowe and it claims to have discovered the "splicing code" mediating alternative splicing (Barash et al., 2010). You'll have to read the paper yourself to see it the headlines are justified. It's clear that Nature thought it was important 'cause they hyped it on the front cover of this week's issue.

The frequency of alternative splicing is a genuine scientific controversy. We've known for 30 years that some genes are alternatively spliced to produce different protein products. The controversy is over what percentage of genes have genuine biologically relevant alternative splice variants and what percentage simply exhibit low levels of inappropriate splicing errors.

Personally, I think most of the predicted splice variants are impossible. The data must be detecting splicing errors [Two Examples of "Alternative Splicing"]. I'd be surprised if more than 5% of human genes are alternatively spliced in a biologically relevant manner.

Barash et al. (2010) disagree. They begin their paper with the common mantra of the true believers.

Transcripts from approximately 95% of multi-exon human genes are spliced in more than one way, and in most cases the resulting transcripts are variably expressed between different cell and tissue types. This process of alternative splicing shapes how genetic information controls numerous critical cellular processes, and it is estimated that 15% to 50% of human disease mutations affect splice site selection.

I don't object to scientists who hold points of view that are different than mine—even if they're wrong! What I object to is those scientists who promote their personal opinions in scientific papers without even acknowledging that there's a genuine scientific controversy. You have to look very carefully in this paper for any mention of the idea that a lot of alternative splicing could simply be due to mistakes in the splicing machinery. And if that's true, then the "splicing code" that they've "deciphered" is just a way of detecting when the machinery will make a mistake.

We've come to expect that science writers can be taken in by scientists who exaggerate the importance of their own work, so I'm not blaming the journalists at The Toronto Star and I'm not even blaming the person who wrote the University of Toronto press release [U of T researchers crack 'splicing code']. I'll even forgive the writers at Nature for failing to be skeptical [The code within the code] [Gene regulation: Breaking the second genetic code].

It's scientists who have to accept the blame for the way science is presented to the general public.

Frey compared his computer decoder to the German Enigma encryption device, which helped the Allies defeat the Nazis after it fell into their hands.

“Just like in the old cryptographic systems in World War II, you’d have the Enigma machine…which would take an instruction and encode it in a complicated set of symbols,” he said.

“Well, biology works the same way. It turns out to control genetic messaging it makes use of a complicated set of symbols that are hidden in DNA.”

Given the number of biological activities needed to grow and govern our bodies, scientists had believed humans must have 100,000 genes or more to direct those myriad functions.

But that genomic search of the 3 billion base pairs that make up the rungs of our twisting DNA ladders revealed a meagre 20,000 genes, about the same number as the lowly nematode worm boasts.

“The nematode has about 1,000 cells, and we have at least 1,000 different neuron (cells) in our brains alone,” said Benjamin Blencowe, a U of T biochemist and the study’s co-senior author.

To achieve this huge complexity, our genes must be monumental multi-taskers, with each one having the potential to do dozens or even hundreds of different things in different parts of the body.

And to be such adroit role switchers, each gene must have an immensely complex set of instructions – or a code – to tell them what to do in any of the different tissues they need to perform in.

I wish I had time to present a good review of the paper but I don't. Sorry.

---

Barash, Y., Calarco, J.A., Gao, W., Qun Pan, Q., Wang, X., Shai, O., Benjamin J. Blencowe, and Frey, B.J. (2010) Deciphering the splicing code. Nature 465: 53–59. [doi:10.1038/nature09000] [Supplementary Information]

Blogging Ethics

 

As Canadian Cynic notes, this applies to bloggers as well. It would be unethical for me to mention on my blog that I'd like Apple to send me a free iPhone 3Gs and a free iPad.

---

Richard Dawkins on the Nature of Scientific (and Religious) Controversy

 

---

[Hat Tip: Friendly Atheist]