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.

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.

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.

Why can't we teach properly?

The popular press usually screws up whenever it writes about universities and education. This time they got it right. Richard Pérez-Peña published an article in The New York Times a few weeks ago about new ways of teaching science [Colleges Reinvent Classes to Keep More Students in Science]. It was reprinted in The New York Times supplement that arrives with my Sunday copy of the The Toronto Star. The new title is Colleges Try to Enliven Science Teaching. (I don't have a link.)

The opening paragraphs set the tone ...

Hundreds of students fill the seats, but the lecture hall stays quiet enough for everyone to hear each cough and crumpling piece of paper. The instructor speaks from a podium for nearly the entire 80 minutes. Most students take notes. Some scan the Internet. A few doze.

In a nearby hall, an instructor, Catherine Uvarov, peppers students with questions and presses them to explain and expand on their answers. Every few minutes, she has them solve problems in small groups. Running up and down the aisles, she sticks a microphone in front of a startled face, looking for an answer. Students dare not nod off or show up without doing the reading.

Both are introductory chemistry classes at the University of California campus here in Davis, but they present a sharp contrast — the traditional and orderly but dull versus the experimental and engaging but noisy. Breaking from practices that many educators say have proved ineffectual, Dr. Uvarov’s class is part of an effort at a small but growing number of colleges to transform the way science is taught.

Should politicians and lawyers ban the teaching of some subjects in public schools?

The Scottish Secular Society (SSS) was upset that creationism might be slipping into some schools in Scotland. They petitioned the Scottish government requesting that teaching creationism be banned in public schools in Scotland.¹ Government officials refused on the grounds that there were already mechanisms in place to ensure that students received a proper science education [Schools creationism ban rejected by Scottish Government].

The official said,

Safeguards include; school managers having oversight of curriculum planning and resources; local authorities with robust complaints procedures, independent school inspections and the development of curriculum materials through a collegiate approach that provides for early identification of any inappropriate material.

This seems like the proper approach to me. Governments can set up mechanisms to create standardized curricula and that should include descriptions of what should be taught in each grade. They can even pass a law saying that all schools have to adhere to the guidelines.

I don't think they should be responding to pressure groups that want to ban the teaching of certain subjects. Most of us would react strongly to any government that banned teaching of sex education, evolution, communism, Islamic culture, feminism, gun control, or post-modernism.² We should also be wary of banning other subjects even though we are certain that they are wrong—subjects such as Young Earth Creationism. If you give politicians the right to ban teaching of certain subjects then don't be surprised if it backfires.

It's best not to give them that power in the first place but to rely instead on curricula and standards that are developed by educators and enforced by educators. Mistakes will be made but it's better in the long run to do it that way than to have education influenced by the power of lobbyists and pressure groups and petitions.

Jerry Coyne disagrees. He thinks that the Scottish government should have banned the teaching of creationism [Scotland refuses to ban teaching of creationism]. This is one of those issues where Jerry and I strongly disagree. He wants to fire teachers who teach creationism and he wants government to pass and enforce laws that prohibit the teaching of certain subjects.

Here's the letter he wrote to Fiona Robertson, the director of Scotland’s Learning Directorate.

Dear Ms. Robertson,

As an American professor who teaches evolutionary biology, I was deeply disappointed to read in The Herald of Scotland that your country’s education directors refuse to ban the teaching of creationism to schoolchildren....

As the author of a popular book on the evidence for evolution (Why Evolution is True), I am fully aware of the massive evidence for evolution and the complete absence of evidence for any creationist views, which invariably stem from Biblical literalism. Creationism is thus a purely nonscientific view based on religion, and I’m saddened that Scotland won’t take even a minimal stand to ensure that its children are not indoctrinated with such bogus "science". The truth of evolution, I’ve found, is not only fascinating, based as it is on mountains of diverse but congruent evidence, but also deeply enlightening, showing us how our own species, and other species as well, came to be. It is the true story of our origins.

I hope that Scotland, like England and Wales, will have the resolve to explicitly establish some guidelines about what Tim Simmons, head of the Curriculum Unit, called "well-established science." Without an explicit statement that creationism is not well-established science, schools are at the mercy of whatever their teachers want to impart about the origins and diversity of organisms.

Thank you for your consideration.
Cordially,
Jerry Coyne
Professor
Department of Ecology and Evolution
The University of Chicago
Chicago, IL 60637 USA

I don't agree with Jerry Coyne. I'm all in favor of teaching evolution and proper science but I'm also in favor of teaching students why things like creationism, astrology, and homeopathy are wrong and why the Loch Ness monster doesn't exist.

It's a bit ridiculous to pass laws banning the teaching of every single thing that "is not well-established science."

It's true that "schools are at the mercy of whatever their teachers want to impart" but the way to fix that problem is to change the views of society, and teachers, about evolution and creationism. There isn't much evidence that simply banning certain subjects will actually change whether students believe them or not. If that were true, then we would expect that the students of Dover Pennsylvania have now come to accept evolution and reject creationism.

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1. I'm using "public" school in the North American sense to refer to schools that are open to the public and supported by government funding.

2. I'm a bit ambivalent about banning post-modernism.

Thinking critically about the Central Dogma of Molecular Biology

Our department is preparing to review our undergraduate courses and programs. Part of the review will be to examine our fundamental goals and objectives and determine if we are meeting them. In preparation for this exercise, I've been going over some papers that have been sitting around my office.

One of them concerns teaching the Central Dogma of Molecular Biology (Wright et al., 2014). It was just published last year. The authors have discovered that students have a "weak conceptual understanding" of information flow. Here's how they describe it in the abstract.

The central dogma of molecular biology, a model that has remained intact for decades, describes the transfer of genetic information from DNA to protein though an RNA intermediate. While recent work has illustrated many exceptions to the central dogma, it is still a common model used to describe and study the relationship between genes and protein products. We investigated understanding of central dogma concepts and found that students are not primed to think about information when presented with the canonical figure of the central dogma. We also uncovered conceptual errors in student interpretation of the meaning of the transcription arrow in the central dogma representation; 36% of students (n = 128; all undergraduate levels) described transcription as a chemical conversion of DNA into RNA or suggested that RNA existed before the process of transcription began. Interviews confirm that students with weak conceptual understanding of information flow find inappropriate meaning in the canonical representation of central dogma. Therefore, we suggest that use of this representation during instruction can be counterproductive unless educators are explicit about the underlying meaning.

How do we teach our students that basic research is important?

There's a fabulous editorial in the Toronto Star today. It's critical of the Prime Minister and the Conservative Party of Canada for the damage they are doing to science in Canada [Canada needs a brighter federal science policy: Editorial].

Here's some excerpts ...

Finding a fan of Canada’s current science policy among those who care about such things would be a discovery worthy of Banting and Best. Few if any would contend that Ottawa’s approach is sound; rather, the debate in 2014 has been over what in the world would possess a government to pursue such a catastrophic course.

According to one school of thought, the answer is simple: the Conservatives are cavemen set on dragging Canada into a dark age in which ideology reigns unencumbered by evidence. Let’s call this the Caveman Theory.

The other, more moderate view holds that Prime Minister Stephen Harper et al are not anti-science – that they at least understand the importance of research and development to their "jobs and growth" agenda – but are instead merely confused about how the enterprise works and about the role government must play to help it flourish. Let’s call this the Incompetence Theory.

The rest of the editorial describes how Stephen Harper and his Conservative buddies have directed funding agencies to concentrate on research that will be of direct benefit to Canadian for-profit companies.

It concludes with ...

Whatever the government’s motives, whatever it understands or does not about how science works, it has over the last eight years devastated Canadian research in a way that will be hard to reverse. Private sector R&D continues to lag, but in our efforts to solve that problem we have seriously reduced our capacity for primary research, squandering a long-held Canadian advantage. Meanwhile, we have earned an international reputation for muzzling scientists, for defunding research that is politically inconvenient and for perversely conflating scientific goals with business ones, thus dooming both. Our current funding system is less well placed than it was in 2006 to promote innovation and our science culture has been so eroded that we are unlikely to attract the top talent we need to compete in the knowledge economy.

Whether it was anti-intellectualism, incompetence or both that led us to this dark place, let this coming election year bring the beginning of a climb back into the light.

How can the government of Canada be so ignorant? It's because they have a huge amount of support from the general public who see all research as technology. They are only willing to support research that helps the economy.

Most people are not interested in research that simply advances our knowledge of the natural world.

What are we doing as educators to reverse this trend? Not very much, as it turns out. Many of our courses in biochemistry focus on how biochemistry can benefit medicine as though this was the only reason for learning about biochemistry.¹ Our department is discussing whether we should have undergraduate courses on drug discovery and how drugs are brought to market. We are considering a co-op program where students will spend some time working in the private sector. We are toying with the idea of creating an entirely new program that will train students to work in the pharmaceutical industry.

It's no wonder that the general public thinks of science as the servant of industry. We are not doing a very good job of teaching undergraduates about the importance of knowledge and the value of scientific thinking. In fact, we are doing the opposite. We are supporting the Stephen Harper agenda.

Don't be surprised if it comes back to bite you in the future.

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1. We teach medical case studies in our introductory biochemistry course for science undergraduates!

How to think about evolution

New Scientist published a short article on How to think about. Evolution. It was written by Michael Le Page who contacted me a few months ago.

I think it's better than most such articles but I may be a little biased. Here's an excerpt.

What's more surprising is that even mutations that don't increase fitness can spread through a population as a result of random genetic drift. And most mutations have little, if any, effect on fitness. They may not affect an animal's body or behaviour at all, or do so in an insignificant way such as slightly altering the shape of the face. In fact, the vast majority of genetic changes in populations – and perhaps many of the physical ones, too – may be due to drift rather than natural selection. "Do not assume that something is an adaptation until you have evidence," says biologist Larry Moran at the University of Toronto, Canada.

So it is wrong to think of evolution only in terms of natural selection; change due to genetic drift counts too. Moran's minimal definition does not specify any particular cause: "Evolution is a process that results in heritable changes in a population spread over many generations."

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On the importance of course evaluations at the University of Toronto

My university (the University of Toronto, Toronto, Canada) recently developed a new policy and new procedures on undergraduate student evaluations [Policy on the Student Evaluation of Teaching in Courses]. The policy was the work of a committee that began with the assumption that student evaluations were a good thing. As far as I can tell, the committee did not spend any time examining the pedagogical literature to see if the evidence supported their assumptions. As you can see from the title of the policy, the assumed purpose of student evaluations is to judge the quality of teaching.

The university has a website: Course Evaluations. Here's what the administrators say ...

Course evaluations are read by many people at UofT, including instructors, chairs, deans, the provost and the president. They are used for a variety of purposes, including:

• To help instructors design and deliver their courses in ways that impact their students’ learning
• To make changes and improvements to individual courses and programs
• To assess instructors for annual reviews
• To assess instructors for tenure and promotion review
• To provide students with summary information about other students’ learning experiences in UofT courses

It is essential that students have a voice in these key decision-making processes and that’s why your course evaluation is so important at the University of Toronto.

Your feedback is used to improve your courses, to better your learning experience and to recognize great teaching.

How to become a better teacher (not)

Here's a video by Dr. Lodge McCammon. He has a website: lodgemccammon.com. Here are his credentials.

Dr. Lodge McCammon is an educational innovator. His career began in 2003 at Wakefield High School in Raleigh, North Carolina, where he taught Civics and AP Economics. McCammon received a Ph.D. from NC State University in 2008 and continued his work by developing innovative practices and sharing them with students, teachers and schools across the world. McCammon is a musician who spends much of his time in the recording studio composing curriculum-based music. His songs and related materials can be found in Discovery Education Streaming. He is also an education consultant who provides professional services, including keynote speeches, presentations, curriculum development, and a variety of training programs.

Watch the video and discuss. I think you can guess what I think. I reject one of the basic premise; namely that online courses are taught by the very best teachers. How do we know who is the best teacher just by watching videos?

Here's a question for your consideration. It concerns "reflective teaching." Imagine that you record yourself teaching an incorrect version of the citric acid cycle or a flawed version of the Central Dogma of Molecular Biology. How many times do you have to watch that video to recognize that what you are teaching is wrong? Is it more than three? Less than ten?

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On the meaning of pH optima for enzyme activity

The students in my lab course measured the activity of trypsin at different pH's. They discovered that the enzyme was most active at a pH of about 8.0-8.5 and that activity fell off rapidly at pH values above and below this optimum. This is consistent with results in the published literature (see figure from Sipsos and Merkel, 1970). Here's the exam question ...

What was the pH optimum of trypsin activity? Can you explain this in terms of the normal biological function of the enzyme and the physiological conditions under which it is active? Do you expect there to be a strong correlation between the optimal pH of an enzyme’s activity and the pH of the cell/environment where it is active?

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Sipos, T., and Merkel, J. R. (1970) An effect of calcium ions on the activity, heat stability, and structure of trypsin. Biochemistry, 9:2766-2775 [doi: 10.1021/bi00816a003]

On the specificity of enzymes

Most biochemistry students are taught that enzymes are highly specific. It's certainly true that the stereospecificity of some enzymes is extraordinary but is it true in general? Here's one of the exam questions that the students in my course had to answer ....

All three of the enzymes (trypsin, alcohol oxidase, β-galactosidase) that you assayed in the past three months are active with several different substrates substrates. Is this behaviour typical or are most enzymes highly specific? Aminoacyl tRNA synthetases are the classic examples of enzymes that are highly specific. Why? Do aminoacyl-tRNA synthetases ever make mistakes?

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Using mass spec to find out how many protein-encoding genes we have

One of the other exam questions is based on an experiment students did with an enzyme they purified. They digested the enzyme with trypsin and then analyzed the peptides by mass spectrometry. They were able to match the peptides to the sequence databases to identify the protein and the species. The exam question is ...

Nobody knows for sure how many functional protein-encoding genes there are in the human genome. About 20,000 potential protein-encoding genes have been identified based on open reading frames and sequence conservation but it is not known if all of them are actually expressed. How can you use Mass Spec to find out how many functional protein encoding genes we have? [see the cover of Nature from May 29, 2014: click on about the cover]

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King Dick and PCR

The students in my lab course are writing their final exam. Prior to the exam they were given 22 questions and they knew that five of them would be on the exam. I thought that Sandwalk readers might enjoy coming up with answers to some of the questions.

The possible remains of King Richard III of England have recently been discovered. His identity has been confirmed by DNA PCR analysis. Descendants of his mother in the female line have the same mitochondrial DNA as King Richard. However, the results with the Y chromosome were surprising. None of the descendants in the all-male lineage had the same Y chromosome markers as King Richard. This is almost certainly due to something called a "false-paternity" event. (There are other ways of describing this event.) Given what you know about PCR, what are some possible sources of error in this analysis? Would you be prepared to go back in time and accuse one of the Kings of England of being a bastard? [Identification of the remains of King Richard III]

(The lab experiment was to analyze various foods to see if they were made from genetically modified plants.)

Note: It's extremely unlikely that the "false-paternity" event occurred in the lineage leading directly to any of the Kings and Queens of England.

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Why fund basic science?

This video was the winner in the 2013 FASEB competition for "Stand Up for Science." The title was "Funding Basic Science to Revolutionize Medicine."

I'm sure their hearts are in the right place but I fear that videos like this are really just contributing to the problem. It makes the case that basic research should be funded because ultimately it will pay off in technologies to improve human health. If you buy into that logic then it's hard to see why you should fund research on black holes or studies of plate tectonics.

Don't we have a duty to stand up for ALL basic research and not just research that may become relevant to medicine? Besides, if the only important basic research that deserves funding is that which has the potential to contribute to medicine, then shouldn't funding be directed toward the kind of "basic research" that's most likely to pay off in the future? Is that what we want? I don't think evolutionary biologists would be happy but everyone working with cancer cells will be happy.

The best argument for basic research, in my opinion, is that it contributes to our knowledge of the natural world and knowledge is always better than ignorance. This argument works for black holes, music theory, and for research on the history of ancient India. We should not be promoting arguments that only apply to our kind of biological research to the exclusion of other kinds of basic research. And we should not be using arguments that reinforce the widespread belief that basic research is only valuable if it leads to something useful.

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How to revolutionize education

I believe that we need to change the way we teach. But not the way you probably think. Watch this video to see what's really important about teaching.

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Hat Tip: Alex Palazzo, who I hope will help us make the transition to 21st century teaching.

How not to teach biochemistry

One of my friends is teaching introductory biochemistry and he thinks this video (below) is worth posting on his blog [here]. I do not want MY students to think that this is the right way to understand glycolysis and the citric acid cycle.


Theme

Better Biochemistry

1. Accuracy: The top three criteria for effective teaching are; accuracy, accuracy, and accuracy. If what you are saying isn't factually correct then nothing else matters. The citric acid cycle shown in the diagram is pretty good. It avoids the most important error (using FADH₂ as the product of the succinate dehdrogenase reaction) but it commits the three other, less significant, common errors [Biochemistry on the Web: The Citric Acid Cycle].
   
   However, when the song gets to the succinate dehydrogenase reaction (at 1:55) it points to QH₂ and calls it FADH₂. If you are going to teach about these reactions then get them right.
   
   
2. The Evolutionary Approach: There are several ways of teaching biochemistry. The American Society of Biochemistry and Molecular Biology (ASBMB) recommends an emphasis on evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution]. This may seem obvious in the 21st century but very few biochemistry courses are taught this way. Most of them adopt some version of the "fuel metabolism"¹ approach to teaching biochemistry. This approach focuses on human metabolism without putting it into the large context. The video is all about "popping carbs" as though converting carbohydrates (glucose) to energy was the only reason for having these pathways.
   
   This approach caters to the biases of the students and to the pre-meds in the class. It does not take the opportunity to correct some of those biases.
   
   

3. Basic Concepts: ASBMB has come out strongly in favor of teaching core concepts rather than memorize/regurgitate [ASBMB Core Concepts in Biochemistry and Molecular Biology]. While I don't always agree with their core concepts, I strongly support this way of teaching biochemistry. The emphasis in a course should be on understanding the basic principles and not on memorizing the details. When I was teaching this material, I allowed students to bring their notes to the exam so they could refer to the specific reactions of the various pathways. They did not have to memorize them.
   
   The core concepts here are things like the importance of gluconeogenesis and why some species have evolved ways of "reversing" that pathway. It's also important to understand the thermodynamics of the reactions in a pathway and the fact that most reactions are at equilibrium. This leads to an emphasis on flux. With respect to the citric acid cycle, the core concepts are that all of the intermediates are involved in multiple reactions and in most species there's no simple "spinning" of the cycle spewing out CO₂. Once they grasp that, you can teach teach them what happens in active mammalian muscle cells. It's harder to make a rap video about core concepts.
   
   You should never, ever, ask students to memorize these reactions for exam questions. No only is that a waste of time but it detracts from the main goal, which should be learning fundamental principles and concepts.

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1. Also known as "rat liver biochemistry" since most of the information comes from studies on rat livers.

Are "science" fairs really about science?

Another year, another "Science" Fair. The winners of the Google Science Fair 2014 have just been announced. Congratulations to all the winners.

It's time for my regular tirade about the difference between science and technology. Look at the list of projects (below). Most of these studies would be carried out in Engineering Faculties or in Clinical Departments at hospitals. Most of them are better described as engineering or technology and not science.

I think there should be two categories at most "science" fairs: one should be "science" and the other should be "engineering and technology."

What's amazing about the list is the tiny number of projects that are actually investigating the basics of how the universe works (naturalism). There's only one project on astronomy and none on geology. There's a couple that may count as chemistry. I don't see any that are looking at basic concepts in biochemistry. Most of physics isn't represented. There's hardly any mention of evolution.

I do understand why students are interested in the applications of scientific knowledge but I fear that we are not spending enough time teaching about the value of fundamental research (basic science). Is there something we can do to change this?

1. Efficient management and use of rain in the Tilacancha basin, Chachapoyas, Amazonas, Peru.
   
2. FABRICATION AND CHARACTERIZATION OF CARBON NANOTUBE DOPED ORGANIC SOLAR CELLS
   
3. The Synthesis of Oleic Acid Core Silica Nanoparticles for the Safe Delivery of Enzymes
   
4. Determining the ideal pendulum tuned mass damper length for optimal reduction of building earthquake resonance
   
5. UTILISATION OF SOLAR ENERGY BY MAKING SOLAR WATER SPRINKLER
   
6. Quantifying the Carbon Footprint of Academic Institutions to Address Systemic Inefficiencies
   
7. Fruit Fly-Inspired Flying Robots
   
8. "Krishak": Empowering farmers for better agriculture outcomes!
   
9. Novel Artificial Neural Networks For 3D Chromosome Reconstruction Bias Correction
   
10. Using Measures of Diversity and Disturbance to Assess Eelgrass Restoration Sites
    
11. The ThereNIM: A Touchless Respiratory Monitor
    
12. The Effect of Water Salinity on the Vitamin C in Radishes
    
13. MASE – Selective Absorption Membrane
    
14. Device for Associating Colors with Sounds
    
15. Preparation of PS/PMMA Polymer Nanocomposites containing Ag Nanoparticles and their Physical Properties
    
16. Stopping the Sahara: Building a Barrier against Desertification
    
17. Developing Arginine as Inhibitor of alpha-synuclein aggregation- Innovative Therapy to Combat Parkinson's Disease
    
18. Caloric Content of Zoo Animal Food
    
19. The Effects Of Atmospheric Circulation On The Water Balance in Boulder, Colorado
    
20. Effect of UV and Infrared light irradiated chitosan on Cu2+ and Ni2+ ions performance adsorption
    
21. The SMART System - Stroke Management with Augmented Reality Technology
    
22. Acidic pH determines if Cryptococcus neoformans can survive in the environment and within the host
    
23. The great significance of small insects, or the impact of large earth bumblebees on tomato plants
    
24. Effect of Amylase on Different Grains
    
25. Development of TCO-less Dye Sensitized Solar cell: An approach to low cost solar cell
    
26. DETECTION AND VISUALIZATION OF THE QUANTIZED BEHAVIOR OF RESISTANCE AND CONDUCTIVITY IN GOLD WIRE
    
27. Ion Culture: Using Microbial Fuel Cells to Stimulate Plant Growth and Electricity with Kimchi
    
28. Cleaning the world with sunscreen & pencils!
    
29. Sustainable Electricity Generation and Water Purification
    
30. Improving Power Plant Efficiency by Recovering Waste Heat
    
31. The Olfactory Awakening
    
32. Photo-realistic 3D rendering using Path tracing with dynamic recursion depth
    
33. Study of children's fears.
    
34. Converting Breath to Speech for the Disabled
    
35. Smart Portable Interactive Whiteboard: A Novel HMI using 3D Vision, SVMs, and Kalman Filters
    
36. A Novel Approach for the Rapid Detection of Food-Borne Pathogens Using Cell Imprinted Polymers
    
37. Wheelchair Controlled by Eye Movements
    
38. NOS ∞ [computer operating system)
    
39. Wearable Sensors for Aging Society
    
40. One Cent Test for Toxicity
    
41. Rethink: Effectively Stopping Cyberbullying
    
42. Can Learning Vocabulary Words Be Made More Efficient?
    
43. Binaural Navigation for the Visually Impaired with a Smartphone
    
44. Harvesting Energy From Human Interactions The Future of Renewable Energy
    
45. Electricity Harvesting Footwear
    
46. Virtual jogging - interactive network with Google Streetview
    
47. Parking Pigeon: Application for Enhanced Localisation in Multi-Story Parking Lots
    
48. A Method for the Mobile Study of Fracking Sites
    
49. Predicting Alcohol Dependence Genetically
    
50. Lowering costs for algae biofuel
    
51. Computationally-Predicted Structure of Human DP Prostaglandin G-protein Coupled Receptor-Bound to Medications to Combat Cardiovascular Disease
    
52. Using Machine Learning to Create an Efficient Irrigation Controller
    
53. Ultrasonic burner
    
54. An Intelligent Power Switching Device with an Energy-Saving Protocol
    
55. A Real Time Map Based Approach to Emergency Management Systems
    
56. Server to User Energy Infrastructure for Wireless Microwave Power Transmission
    
57. Quiet Eye: A novel way to improve accuracy in badminton
    
58. Construction of a light sensor to measure the light level in the surroundings and the section of the sky being observed in the telescope
    
59. Dynamic Support Surface (Bed) for Effective Pressure Ulcer Prevention
    
60. Sustainable Future for Endangered Species? Predicting the Impacts of Wilmar's Policy on Bornean Orangutan Populations
    
61. The Correlation Between Highway Proximity and the Photosynthetic Rate of the Shinus terebinthifolius (Brazilian Pepper)
    
62. Development of a cash-free cashier system
    
63. Soil moisture sensor for plant watering
    
64. KL_AS_YOL [painting asphalt roads with chlorophyll]
    
65. An Enhanced Weather Forecast Model Based on Studies of Forecasted vs. Observed Weather
    
66. Superconducting Levitation and Propulsion Control System
    
67. A Modular House incorporating a MFC and a MEC to initiate efficient usage of resources
    
68. Inzeolation! How zeolite and cellulose make a perfect combination for ecological, recyclable, multi-efficient thermal insulation?
    
69. Predicting Cancer Drug Response Using Nuclear Norm Multi-Task Learning
    
70. Somnolence Detection And Aiding System For Better Driving Conditions
    
71. Effect of different organics on seed germination and growth of Indian economical seeds
    
72. Correlation Analysis and Smartphone Terminals to Monitor and Analyze Geographic Relevance the of PM2.5
    
73. The Accident Detection and Location System (ADLS)
    
74. Identification of Gravitationally Lensed Quasars
    
75. COMPLETE ORGANIC FARMING WITHOUT ANY MEDICINE OR HORMONE, WITH ONLY WASTE PROPOLIS
    
76. A Simple Method for Simultaneous Wastewater Treatment and Chemical Recovery Using Temperature and Pressure Changes
    
77. Kindling Cracker [an easy way to cut kindling]
    
78. Detection of gamma hydroxybutyrate in acidic and sugary drinks
    
79. Intellectual Device Capable of Diagnosing Cardiovascular Diseases
    
80. Cleaning Up Oil Sands Waste
    
81. Development of a Computer-Based Multi-Sensory System to Better Relay Pharmacotherapy Information
    
82. Braille E-Book
    
83. Enabling Situational Awareness: A Hat-Based Hands-Free Haptic Navigational Aid for the Visually Impaired
    
84. The Charging Pan [harvesting heat waste from a kitchen stove]
    
85. Natural Bacteria Combatting World Hunger {GRAND PRIZE WINNER!)
    
86. Multidecadal Changes in Warm Season Convective Storms over the Northeastern United States
    
87. Seeing Hands
    
88. Frictionless Pedal Power Electromagnetic Induction Generator (for USB charging devices)
    
89. Breaking the AGE Barrier! Inhibiting Advanced Glycation End-products to Combat Atherosclerosis, Cancer and Diabetic Disorders
    
90. Common dandelion, as an indicator of geomedium well-being
    
91. Analysis on the acute-toxicity of CeO2 nano particle
    
92. Non-invasive Search for Optimal Cancer Treatment
    
93. Two-hit Approach Blocking Alzheimer's β-amyloid Toxicity: Fibril Formation and Inhibition of newly characterized Oxygenase activity
    
94. Vehicle for disabled people
    
95. Novel Automated Next-Generation Multijunction Quantum Dot Solar Cell Designs Using Monte Carlo Modeling
    
96. P.E.ACE (Portable.Evasive.AssistanCE)
    
97. Haptic Feedback e-Reader for the Visually Impaired
    
98. A Microbial Fuel Cell for the Eco-Friendly Processing of Acid Whey and Power Generation
    
99. Jute-reinforced Polyester to Replace Steel Manhole Covers
    
100. Remote controlled school presentation microscope
     
101. Photovoltaic additive for paint and varnish
     
102. Possibility of removing oil products from the water surface by means of magnetic fields
     
103. A New Class of Pluripotent Stem Cell Cytotoxic Small Molecule
     
104. Detergents in the lakes of Zainsk municipal area and their impact on the buoyancy of the aquatic birds
     
105. Improving Raloxifene’s Affinity with ER-Beta Through Synergy with S-Equol as a Novel Chemopreventive Treatment
     
106. Using the Soapnut, Spaindus Mukorossi, to prevent mosquito breeding
     
107. Tomatricity - converged electricity
     
108. Enhancing Solar Hydrogen Generation via Computer-Aided Development of Novel Metal Nanostructures
     
109. Oil in the Soil
     
110. BIOTECHNOLOGICAL METHOD DEVELOPMENT BASED ON AFFINITY MEMBRANE SYSTEM FOR ANTIBODY RECOGNITION
     
111. Instant curd using Wrightia tinctoria plant latex as starter
     
112. Technology of processing foliage, plastic bottles and waste paper into paper
     
113. Advancing Cancer Research with an Integrated Repository and Search Engine for Gene Regulatory Networks
     
114. Automated Lip-Reading Technique For Speech Disabilities By Converting Identified Visemes Into Direct Speech
     
115. The effect of dormancy on poplar tree remediation of nitrates, phosphates, and fecal coliform
     

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