Stephen Fry blows it by assuming he knows the mind of god

This video is making the rounds and a lot of atheists are wetting their pants over Stephen Fry's response to the question of what he would would say to "he, she, or it" if he encountered god when he dies.

My questions would be "Who are you? Which groups of humans (if any) got it right when making up a religion? Tell me about yourself and why you didn't reveal yourself to me."

That's not what Stephen Fry would do. He makes the assumption that he knows the mind of god and attacks the god for not being nice to humans. In other words, he accepts the problem of evil and assumes that the god he is facing gives a damn about some obscure species on a minor planet in one of billions of galaxies. Later on Stephen Fry concedes that he could be talking to the Greek gods or some other gods but by then it's too late.

The god he is addressing may or may not have done any of the things in the Bible. If he isn't that god then he will know that Stephen Fry is attacking a strawman. If he is the god of the Bible then presumably he/she/it had his/her/its reasons for doing apparently evil things and Stephen Fry is about to get educated about the real mind of god. That may turn out badly for Stephen Fry.

If you ever run into any real gods I'd advise you not to mess with them.


Many of my atheist friends think that Fry's response is fantastic because he really shocks the interviewer, Gay Byrne [Stephen Fry on God]. That's naive. Most intelligent Christians have developed some very good rationalizations concerning the problem of evil. They've heard it all before and they know how to respond. One of the classic responses is that cannot they know the mind of god. But Stephen Fry knows the mind of god and this is puzzling because Fry is an atheist.

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American scientists think science education is a problem

The results of the latest PEW/AAAS survey are getting a lot of attention [Public and Scientists’ Views on Science and Society]. Most people focus on the fact that the American public doesn't accept evolution and anthropogenic climate change. That's not news.

The real issue is what can we¹ do about it. Alan Leshner, Chief Executive Officer of AAAS and Executive Publisher of Science, thinks he has the answer. Here's what he writes in an editorial "Bridging the opinion gap" ...

Speaking up for the importance of science to society is our only hope [my emphasis, LAM], and scientists must not shy away from engaging with the public, even on the most polarizing science-based topics. Scientists need to speak clearly with journalists, who provide a great vehicle for translating the nature and implications of their work. Scientists should also meet with members of the public and discuss what makes each side uncomfortable. In these situations, scientists must respond forthrightly to public concerns. In other words, there needs to be a conversation, not a lecture.

Isn't that insightful? Here we are in 2015 and nobody ever thought of that before now! Can you imagine how much better off we'd be if scientists have only started speaking up 40 years ago, or even 10 years ago?

Scientists have been engaging with the American public about evolution for half a century and it has not worked. They've also been speaking to journalists.²

Fortunately, there are some people who have gone way past these naive views and actually thought seriously about the problem. Here's are the results of two questions from the survey.

• Only 16% of AAAS scientists and 29% of the general public rank U.S. STEM education for grades K-12 as above average or the best in the world. Fully 46% of AAAS scientists and 29% of the public rank K-12 STEM as “below average.”
• 75% of AAAS scientists say too little STEM education for grades K-12 is a major factor in the public’s limited knowledge about science. An overwhelming majority of scientists see the public’s limited scientific knowledge as a problem for science.

I agree with those scientists. We are part of the problem because we are not doing a very good job of educating students in the ways of science. The long term solution is to do a far better job of teaching about science. We should not be graduating students from university who reject evolution and climate change. We should not be giving out degrees to students who fall for pseudoscience gobbledegook like homeopathy and astrology. If we do that then we are not doing our job as educators and survey results like these are not going to change in the forseeable future.

Now, to be fair, Alan Leshner recognizes the problem even if he's wrong about the solution.

The public's perceptions of scientists' expertise and trustworthiness are very important, but they are not enough. Acceptance of scientific facts is not based solely on comprehension levels. It can be compromised whenever information confronts people's personal, religious, or political views, and whenever scientific facts provoke fear or make people feel that they have no control over a situation. The only recourse is to have genuine, respectful dialogues with people. Good venues are community clubs, science museums, science fairs, and religious institutions. Working with small groups is more effective than working with large groups.

Perhaps he and some other scientists can sit down in small groups with Republican members of Congress and change their minds. Maybe you could do it in their churches. (Remember to be respectful when dialoguing with John Boehner.) Meanwhile, I believe that's not the "only hope." I think educating our young people is a better investment in time and effort even though it won't pay off for a generation.

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1. I say "we" because the same problems exist in Canada.

2. Maybe Alan Leshner should have a little chat with Elizabeth Pennisi.

My community is outraged over trash

My community (Peel Region, west of Toronto, Ontario, Canada) is changing the way it collects trash so it put out a pamphlet to advise citizens of the upcoming changes. Here's the cover.

It's a little chilly right now to be putting out the garbage with no clothes on but even in the summer I'll probably throw on a shirt. I might consider the naked method but only if it were very late at night or if I were as good-looking as the guy in the picture.

At least two members of the community are outraged. Can you guess why?

Peel’s ‘naked man' trash pamphlet sparks outrage

Check out My Secret Atheist Blog for more pictures of naked men.

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Vision and Change

A few years ago the AAAS (American Association for the Advancement of Science) sponsored a study of undergraduate education in the biological sciences. The study groups published a report in 2011 called Vision and Change in Undergraduate Biology Education: A Call to Action. Since then a number of disciplines, including biochemistry and molecular biology, have been trying to encourage university teachers to implement these proposals. So far, the "call to action" has pretty much fallen on deaf ears. Most professors are reluctant to admit that their teaching needs improvement and they are reluctant to read this report or any other part of the pedagogical literature.

“Scientists should be no more willing to fly blind in their teaching than they are in scientific research, where no new investigation is begun without an extensive examination of what is already known.”

Bruce Alberts, NRC, 1997What could be wrong with this?

The time has come for all biology faculty, particularly those who teach undergraduates, to develop a coordinated and sustainable plan for implementing sound principles of teaching and learning to improve the quality of undergraduate biology education nationwide. The stakes are too high for all biologists not to get involved with this national call for change.

The main recommendations are that we should concentrate on teaching fundamental concepts and principles and not facts and that we should adopt a student-centered form of learning.

The recommendations discussed in this report include the following action items aimed at ensuring that the vision of the conference becomes an agenda for change:

1. integrate Core Concepts and Competencies throughout the Curriculum

• Introduce the scientific process to students early, and integrate it into all undergraduate biology courses.
• Define learning goals so that they focus on teaching students the core concepts, and align assessments so that they assess the students’ understanding of these concepts.
• Relate abstract concepts in biology to real-world examples on a regular basis, and make biology content relevant by presenting problems in a real-life context.
• Develop lifelong science-learning competencies.
• Introduce fewer concepts, but present them in greater depth. Less really is more.
• Stimulate the curiosity students have for learning about the natural world.
• Demonstrate both the passion scientists have for their discipline and their delight in sharing their understanding of the world with students.

2. Focus on student-Centered Learning

• Engage students as active participants, not passive recipients, in all undergraduate biology
  courses.
• Use multiple modes of instruction in addition to the traditional lecture.
• Ensure that undergraduate biology courses are active, outcome oriented, inquiry driven, and relevant.
• Facilitate student learning within a cooperative context.
• Introduce research experiences as an integral component of biology education for all students, regardless of their major.
• Integrate multiple forms of assessment to track student learning.
• Give students ongoing, frequent, and multiple forms of feedback on their progress.
• View the assessment of course success as similar to scientific research, centered on the students involved, and apply the assessment data to improve and enhance the learning environment.

"Appreciating the scientific process can be even more important than knowing scientific facts. People often encounter claims that something is scientifically known. If they understand how science generates and assesses evidence bearing on these claims, they possess analytical methods and critical thinking skills that are relevant to a wide variety of facts and concepts and can be used in a wide variety of contexts.”

National Science Foundation, Science and Technology Indicators, 2008The evidence is in. Whether or not we should change is a no-brainer.

The other two recommendations have to do with implementation .... this is the tough part.

3. Promote a Campuswide Commitment to Change

4. Engage the Biology Community in the implementation of Change

Notice that MOOCs and online learning are not prominent objectives in Visions and Change. You have to wonder why AAAS isn't inviting the members of these study groups to give plenary lectures at their 2015 meeting instead of the President of Coursera [see President of Coursera to give plenary lecture at AAAS meeting]. Maybe they've changed their minds since 2011?

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Evidence-based teaching

A lot of people have spent a lot of time and effort studying undergraduate education. Why not pay attention to what these experts have to say? There's a good book on the subject published by the National Academies (USA). It's called Reaching Students: What Research Says About Effective Instruction in Undergraduate Science and Engineering (2015).¹

Here's are some excerpts from the Preface.

This book is based on the 2012 NRC report on DBER [discipline-based education research], as well as on interviews with expert practitioners who have successfully applied findings from DBER and related research in their classrooms, departments, or institutions. The goal is to summarize the most salient findings of the NRC committee and the experience of expert practitioners about how students learn undergraduate science and engineering and what this means for instruction. This book presents new ways of thinking about what to teach, how to teach it, and how to assess what students are learning. To encourage instructors and others to apply this information in their institutions, it also includes short examples and longer case studies of experienced practitioners who are implementing research-based strategies in undergraduate science and engineering courses or across departments or institutions. Although these findings could apply to a variety of disciplines, this book focuses on the disciplines addressed in the NRC study-physics, astronomy, biology, chemistry, geosciences, and engineering.

This book is intended for anyone who teaches or plans to teach undergraduate courses in science and engineering at any type of higher education institution or who is in a position to influence instruction at this level. Throughout the book, the term “instructor” is used broadly to refer to the full range of teaching staff—tenured, non-tenured, or adjunct faculty; lecturers and similar teaching positions; and postdoctoral scholars or graduate students with teaching responsibilities. Although many of the strategies and ideas in these pages are geared to instructors, others with an interest in science and engineering education will find suggestions for encouraging or supporting research-based instruction. These other audiences might include department heads; faculty development providers; provosts, deans, and other higher education administrators; leaders of professional societies and associations for science and engineering; and those with policy roles in higher education or science education.

There's lots of interesting stuff in this little book but the main emphasis is on teaching fundamental concepts rather than facts and on student-centered learing (active learning).

The report recognizes that university lecturers need to change the way they are teaching and it won't be easy.

Throughout the chapters you will find concrete examples and case studies that illustrate how skilled instructors and leaders from various disciplines and types of institutions have used findings from DBER and related research on learning to design and support instruction in their classrooms, departments, or institutions. These examples may inspire, intrigue, challenge, or provoke you. Whatever your reaction, the examples are intended to encourage reflection and discussion about effective ways to help students learn science and engineering.

This type of reflection is not always easy. Instructors may be unaware of this body of research. Even if they aware, they may be disinclined to change teaching methods that are familiar or ubiquitous in their departments and seem to be working, at least for some students. Departmental and institutional cultures may also present obstacles to changing practice, as discussed in later chapters.

On a positive note, however, as a scientist or an engineer you already have the intellectual tools and experience needed to examine students’ learning and your own teaching from a research perspective. Every day, you tackle research problems in your discipline, consider various strategies to solve those problems, try out a strategy, and revise that strategy based on the results. Why not apply this same mindset to your teaching? The research is there, and so are a variety of curriculum materials, professional development opportunities, and other resources. With some effort, the rewards will be there, too—better educated students, greater professional satisfaction, and a brighter outlook for society.

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1. You can download the book for free. All you have to do is sign in.

President of Coursera to give plenary lecture at AAAS meeting

The American Association for the Advancement of Science holds a meeting every February. This year the meeting is in San Jose, California. There are four plenary lectures [Plenary Lectures 2015]. Three of them will be given by prominent researchers who will be talking about science. The fourth is by Daphne Koller, President and co-founder of Coursera.

Coursera is a for-profit company offering "universal access to the world’s best education." What they mean by "best education" is MOOCs offered by professors at the "top" universities. There's no evidence to support the claim that the best undergraduate courses for the general audience are those given by professors at Stanford, MIT, Princeton, and Harvard. Indeed, there's quite a bit of evidence that this isn't true.

Daphne Koller is going to talk about The Online Revolution: Learning Without Limits. Keep in mind that at the end of every article published in Science (AAAS publication) there's a small notice stating that, "The authors declare no financial conflict of interest" or statements that clearly spell out the conflicts.

Why is AAAS asking someone to give a plenary lecture about selling online courses from someone with a clear financial interest in promoting her company?

Science education is important and there's plenty of evidence that universities are graduating students who don't understand science and aren't capable of critical thinking. There are hundreds of people whose main research interest is pedagogy and especially science education. They have proposed solutions to the problem and suggestions on how we should change the way we teach. Very few of them think that MOOCs are the answer and very few of them are trying to market their ideas for profit [ Reaching Students: What Research Says About Effective Instruction in Undergraduate Science and Engineering (2015)].

Why not ask some of those experts to address the AAAS meeting and possibly explain what's wrong with canned videotaped lectures? MOOCs are just ways of transferring the way we teach now to the mass market. But what if the traditional way we now teach (lectures) is wrong? Isn't that a question that the delegates at San Jose ought to think about?

Here's Daphne Koller giving a TED talk. Near the end she talks about the importance of "active learning" (student-centered learning). I'm a big fan of student-centered learning. She implies that having students take online courses from "top" educators is consistent with active learning but she's wrong. It's the exact opposite. In my opinion, it's a step backwards and by promoting MOOCs we are going to make it more difficult to convince professors to change the way they teach. Instead, the ones who are good at delivering traditional lectures will bring in money for themselves and their universities.¹ They will be getting the kudos and the teaching awards instead of those who are paying attention to evidence-based methods and trying to improve undergraduate education.


Here's another video. It's an interview with Daphne Koller from June 2013. Listen to the first few minutes and you'll hear a different view of active learning. Here, she explains the concept of the "flipped classroom" where students watch online videos and then come to class to participate in "something that's much more engaging and stimulating, active learning" (4 mins). There's nothing wrong with that except that students could read a textbook instead of watching a video. The important part of the learning is what happens in the classroom and not what happens in the textbook or the taped lecture.

She also explains how they are going to make money (5-6 mins).

Daphne Koller is very fond of repeating the myth that the best courses are the ones taught at the top research universities. (She happens to be a teacher at one of these universities.) I bet she can't prove it unless she's talking about very specialized upper level courses.

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1. For-profit companies like Coursera offer kick-backs to the professors and schools that contribute courses.

Learn biology with Eric Hovind

If you want to learn biology, I suggest you take this course taught by Eric Hovind. It's a good illustration of the importance of MOOCs and how they are eventually going to replace professors at universities.

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About half of all cancers are just bad luck. It's not your fault.

There's been a lot of talk recently about a paper claiming that two thirds of all cancers are due to bad luck [Bad Luck of Random Mutations Plays Predominant Role in Cancer, Study Shows]. The take-home message was that you could get cancer even if you ate "healthy," took lots of vitamins, didn't smoke, and went to the gym every day. That's not what people wanted to hear.

But scientists have known for decades that many cancers are due to random mutations that just happen. These cancers are not hereditary and are not caused by the environment. There's nothing new here.

That didn't stop a number of people from criticizing the article and some of the criticisms were justified. Nevertheless, what the article showed was that cancers tended to occur more often in tissues with lots of cell divisions (and DNA replications). That's exactly what you expect if random mutations due to replication errors are the cause of the cancer mutations.

David Gorski of Science-Based Medicine sorts it all out for us [Is cancer due mostly to “bad luck”?]. Please read his lengthy article if you want to understand the issues. David Gorski concludes ...

It’s understandable that humans crave explanation, particularly when it comes to causes of a group of diseases as frightening, deadly, and devastating as cancer. In fact, both PZ Myers and David Colquhoun have expressed puzzlement over why there is so much resistance is to the concept that random chance plays a major role in cancer development, with Colquhoun going so far as to liken it to ” the attitude of creationists to evolution.” Their puzzlement most likely derives from the fact that they are not clinicians and don’t have to deal with patients, particularly given that, presumably, they do have a pretty good idea why creationists object to attributing evolution to random chance acted on by natural selection and other forces.

Clinicians could easily have predicted that a finding consistent with the conclusion that, as a whole, probably significantly less than half of human cancers are due to environmental causes that can be altered in order to prevent them would not be a popular message. Human beings don’t want to hear that cancer is an unfortunately unavoidable consequence of being made of cells that replicate their DNA imperfectly over the course of our entire lives. There’s an inherent hostility to any results that conclude anything other than that we can prevent most, if not all, cancers if only we understood enough about cancer and tried hard enough. Worse, in the alternative medicine world there’s a concept that we can basically prevent or cure anything through various means (particularly cancer), most recently through the manipulation of epigenetics. Unfortunately, although risk can be reduced for many cancers in which environmental influences can increase the error rate in DNA replication significantly, the risk of cancer can never be completely eliminated. Fortunately, we have actually been making progress against cancer, with cancer death rates having fallen 22% since 1991, due to combined efforts involving smoking cessation (prevention), better detection, and better treatment. Better understanding the contribution of stochastic processes and stem cell biology to carcinogenesis could potentially help us do even better.

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Is Intelligent Design Creationism winning the debate in the scientific community?

Back in 1998 the Intellignet Design Creationists published the Wedge Strategy. They set themselves several goals including some twenty year goals that they hoped to achieve by 2018 (three years from now). They are ...

• to see intelligent design theory as the dominant perspective in science
• to see design theory applications in specific fields, including molecular biology, biochemistry, paleontology, physics and cosmology in the natural sciences, psychology, ethics, politics, theology, and philosophy in the humanities, to see its influence in the fine arts
• to see design theory permeate our religious, cultural, moral, and political, life

They aren't even close to achieving the first two goals but I think it's fair to say that they are well on their way to achieving the third goal in the United States. I don't think they've had much success in other countries. Perhaps readers in Europe, India, Africa, and China could let me know if design theory has permeated their culture and their politics?

Casey Luskin has recently posted a progress report in Evolution News & Views (sic) [In the Darwin Debate, How Long Before the Tide Turns in Favor of Intelligent Design?]. He's very optimistic. He lists thirteen (13) recent victories for Intelligent Design Creationism and concludes ...

Don't expect a revolution overnight. We are in this for the long haul, recognizing that it can take time for the truth to slip past the checkpoints that the Darwin lobby sets up to keep the public uninformed. In the end, though, I'm optimistic because the fundamentals of ID -- the science underlying the inference to design in nature -- are sound. The truth will win out, though it may tarry in doing so. Or to put it another way, the tide of ID is already well on its way in. We need to focus on telling people about it.

They'd better hurry. There's only three years left.

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On the credulity of those posing as the champions of science

Barry Arrington, the chief IDiot on Uncommon Descent, has just published a post on The Credulity of those Posing as the Champions of Science.

Turn off your irony meters. You were warned.

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80% of Americans support mandatory labels on food containing DNA

A recent survey reports that 80.44% of Americans believe that there should be mandatory labels on food containing DNA [Food Demand Syrvay]. Slightly more (82.28%) think there should be mandatory labels of food produced with genetic engineering.

It's easy to mock the respondents for being scientifically illiterate but that's not fair. The real idiots are the people who asked the question.

Ilya Somin has been thinking about what should be said in this mandatory label [Over 80 percent of Americans support “mandatory labels on foods containing DNA”]. Here's one possibility ...

WARNING: This product contains deoxyribonucleic acid (DNA). The Surgeon General has determined that DNA is linked to a variety of diseases in both animals and humans. In some configurations, it is a risk factor for cancer and heart disease. Pregnant women are at very high risk of passing on DNA to their children.

Can anyone think of foods that would not carry this warning? What do you eat if you want to avoid DNA?

Did you notice that 87% of Americans want labels on meat to identify the country of origin? Is that because they don't know where New Zealand lamb comes from? Or is it because they want to make sure they're getting genuine Canadian bacon?

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Francis Collins rejects junk DNA

Francis Collins is the Director of the National Institutes of Health (NIH) in the USA. He spoke recently at the 33rd Annual J.P. Morgan Healthcare Conference in San Francisco (Jan. 12-15, 2015). His talk was late in the afternoon on Tuesday, January 13, 2015. You can listen to the podcast on the conference website [J.P. Morgan Healthcare Conference].

The important bit is at the 30 minute mark where he comments on a question about junk DNA. This is what Francis Collins said last week ...

I would say, in terms of junk DNA, we don't use that term any more 'cause I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn't functional. There will be parts of the genome that are just, you know, random collections of repeats, like Alu's, but most of the genome that we used to think was there for spacer turns out to be doing stuff and most of that stuff is about regulation and that's where the epigenome gets involved, and is teaching us a lot.

What seems like "hubris" to Francis Collins looks a lot like scientific evidence to me. We know enough to say, with a high degree of confidence, that most (~90%) of our genome is junk. And we know a great deal about the data that Collins is probably referring to (ENCODE)—enough to conclude that it is NOT saying what he thinks it says.

It would be bad enough if this were just another confused scientist who doesn't understand the data [see Five Things You Should Know if You Want to Participate in the Junk DNA Debate] but he's not just any scientist. He's a powerful man who talks to politicians all the time and deals with the leaders of large corporations (e.g. the J.P. Morgan Conference). If Francis Collins doesn't understand the fundamentals of genome science then he could mislead a lot of people.

Collins has many colleagues surrounding him at NIH and other agencies in Washington. These scientists also make important decisions about American science. I'm assuming that he reflects their opinion as well. If not, then why aren't they educating Francis Collins?

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Hat Tip: Ryan Gregory

Functional RNAs?

One of the most important problems in biochemistry & molecular biology is the role (if any) of pervasive transcription. We've known for decades that most of the genome is transcribed at some time or other. In the case of organisms with large genomes, this means that tens of thousand of RNA molecules are produced from regions of the genome that are not (yet?) recognized as functional genes.

Do these RNAs have a function?

Most knowledgeable biochemists are aware of the fact that transcription factors and RNA polymerase can bind at many sites in the genome that have nothing to do with transcription of a normal gene. This simply has to be the case based on our knowledge of DNA binding proteins [see The "duon" delusion and why transcription factors MUST bind non-functionally to exon sequences and How RNA Polymerase Binds to DNA].

If you have a genome containing large amounts of junk DNA then it follows, as night follows day, that there will be a great deal of spurious transcription. The RNAs produced by these accidental events will not have a biological function.

Richard Lewontin and Tomoko Ohta win the Crafoord Prize in Biosciences

"for their pioneering analyses and fundamental contributions to the understanding of genetic polymorphism"

It is the great irony of modern evolutionary genetics that the spirit of explanation has moved more and more towards optimal adaptation, while the technical developments of population genetics of the past 30 years have been increasingly to show the efficacy of non adaptive forces in evolution.

Richard Lewontin
"A natural selection" Nature May 11,1989 p.107

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The ‘neutral theory’ proposed that most evolutionary changes at the molecular level were caused by random genetic drift rather than by natural selection. Note that the neutral theory classifies new mutations as deleterious, neutral, and advantageous. Under this classification, the rate of mutant substitutions in evolution can be formulated by the stochastic theory of population genetics. Kimura's theory was simple and elegant, yet I was not quite satisfied with it, because I thought that natural selection was not as simple as the mutant classification the neutral theory indicated, and that there would be border-line mutations with very small effects between the classes. I thus went ahead and proposed the nearly neutral theory of molecular evolution in 1973. The theory was not simple, and much more complicated, but to me, more realistic, and I have been working on this problem ever since.

Tomoko Ohta
Current Biology, August 21, 2012

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HatTip: Jerry Coyne (student of Lewontin): Dick Lewontin and Tomoko Ohta nab the Crafoord Prize

The Nature of Science (NOS)

There is a growing recognition among teachers that we need to teach the "Nature of Science" (NOS). Ideally, this should begin in the primary grades and extend all the way through university. Teaching about the nature of science should not be restricted to students who major in science. Every student should learn about the nature of science.

This is not controversial. I'm not aware of anything in the recent pedagogical literature that argues against teaching the nature of science. What's controversial is how to describe what science is all about.