Evaluating students' evaluations

Student evaluations are an important part of the undergraduate experience at most universities. But how effective are they?

You would think that universities might have studied this question and applied critical thinking and evidence-based reasoning to the question. You might think that the popularity of student evaluations at universities is largely because they have proven to be reliable indicators of teaching effectiveness.

Think again. The pedagogical literature contains dozens of studies indicating that student evaluations are not reliable indicators of teaching effectiveness. Here are some recent papers that show you what the experts are thinking and what kind of evidence is being published.

Gormally, C., Evans, M. and Brickman, P. (2014) Feedback about Teaching in Higher Ed: Neglected Opportunities to Promote Change. CBE-Life Sciences Education 13, 187-199. [doi: 10.1187/cbe.13-12-023]

Despite ongoing dissemination of evidence-based teaching strategies, science teaching at the university level is less than reformed. Most college biology instructors could benefit from more sustained support in implementing these strategies. One-time workshops raise awareness of evidence-based practices, but faculty members are more likely to make significant changes in their teaching practices when supported by coaching and feedback. Currently, most instructional feedback occurs via student evaluations, which typically lack specific feedback for improvement and focus on teacher-centered practices, or via drop-in classroom observations and peer evaluation by other instructors, which raise issues for promotion, tenure, and evaluation. The goals of this essay are to summarize the best practices for providing instructional feedback, recommend specific strategies for providing feedback, and suggest areas for further research. Missed opportunities for feedback in teaching are highlighted, and the sharing of instructional expertise is encouraged.

Osborne, D. and Janssen, H. (2014) Flipping the medical school classroom: student acceptance and student evaluation issues (719.4). The FASEB Journal 28, 719.4.

Flipping the classroom has generated improvement on summative exam scores in our first-year medical students; however, faculty members adopting this teaching methodology often receive lower satisfaction rating on student evaluations. In previous years, these same professors received outstanding evaluation ratings when the same topics were presented using standard didactic lectures. We feel that this decreased student satisfaction may be result of two distinct causes. First, students who have been accustomed to didactic lectures often come to class unprepared and therefore are incapable of the critical thinking and problem solving skills need in the flipped classroom. Second, the evaluation tool which was appropriate for didactic lectures is inappropriate for the analyzing the flipped classroom methodology. The student evaluations have improved in that last several years; however, the transition was not accomplished without difficulty. Anyone planning to pursue this teaching approach should be prepared to weather the storm of sub-standard student evaluations and, if possible, prepare their administrators for this potential outcome. Our experience suggests that faculty persistence targeted at changing student culture and expectations can help in this process. Accurately determining student’s acceptance of this relative new teaching methodology is important. Improvements in the teaching methodology can be made only when the evaluation tool is valid. It is felt a new evaluation tool can be developed based on results obtained in student focus-groups coupled with cognitive assessment outcomes.

Wilson, J.H., Beyer, D. and Monteiro, H. (2014) Professor age affects student ratings: halo effect for younger teachers. College Teaching 62, 20-24. [doi: 10.1080/87567555.2013.825574]

Student evaluations of teaching provide valued information about teaching effectiveness, and studies support the reliability and validity of such measures. However, research also illustrates potential moderation of student perceptions based on teacher gender, attractiveness, and even age, although the latter receives little research attention. In the present study, we examined the potential effects of professor age and gender on student perceptions of the teacher as well as their anticipated rapport in the classroom. We also asked students to rate each instructor's attractiveness based on societal beliefs about age and beauty. We expected students to rate a picture of a middle-aged female professor more negatively (and less attractive) than the younger version of the same woman. For the young versus old man offered in a photograph, we expected no age effects. Although age served as a detriment for both genders, evaluations suffered more based on aging for female than male professors.

Blair, E. and Valdez Noel, K. (2014) Improving higher education practice through student evaluation systems: is the student voice being heard? Assessment & Evaluation in Higher Education, 1-16. [doi: 10.1080/02602938.2013.875984]

Many higher education institutions use student evaluation systems as a way of highlighting course and lecturer strengths and areas for improvement. Globally, the student voice has been increasing in volume, and capitalising on student feedback has been proposed as a means to benefit teacher professional development. This paper examines the student evaluations at a university in Trinidad and Tobago in an effort to determine whether the student voice is being heard. The research focused on students’ responses to the question, ‘How do you think this course could be improved?’ Student evaluations were gathered from five purposefully selected courses taught at the university during 2011–2012 and then again one year later, in 2012–2013. This allowed for an analysis of the selected courses. Whilst the literature suggested that student evaluation systems are a valuable aid to lecturer improvement, this research found little evidence that these evaluations actually led to any real significant changes in lecturers’ practice.

Braga, M., Paccagnella, M., and Pellizzari, M. (2014) Evaluating students’ evaluations of professors. Economics of Education 41:71–88. [doi: 10.1016/j.econedurev.2014.04.002]

This paper contrasts measures of teacher effectiveness with the students’ evaluations for the same teachers using administrative data from Bocconi University. The effectiveness measures are estimated by comparing the performance in follow-on coursework of students who are randomly assigned to teachers. We find that teacher quality matters substantially and that our measure of effectiveness is negatively correlated with the students’ evaluations of professors. A simple theory rationalizes this result under the assumption that students evaluate professors based on their realized utility, an assumption that is supported by additional evidence that the evaluations respond to meteorological conditions.

Stark, P.B. and Freishtat, R. (2014) An Evaluation of Course Evaluations. [PDF]

Student ratings of teaching have been used, studied, and debated for almost a century. This article examines student ratings of teaching from a statistical perspective. The common practice of relying on averages of student teaching evaluation scores as the primary measure of teaching effectiveness for promotion and tenure decisions should be abandoned for substantive and statistical reasons: There is strong evidence that student responses to questions of “effectiveness” do not measure teaching effectiveness. Response rates and response variability matter. And comparing averages of categorical responses, even if the categories are represented by numbers, makes little sense. Student ratings of teaching are valuable when they ask the right questions, report response rates and score distributions, and are balanced by a variety of other sources and methods to evaluate teaching....

Recommendations

1. Drop omnibus items about “overall teaching effectiveness” and “value of the course” from teaching evaluations (SET): They are misleading.
2. Do not average or compare averages of SET scores: Such averages do not make sense statistically. Instead, report the distribution of scores, the number of responders, and the response rate.
3. When response rates are low, extrapolating from responders to the whole class is unreliable.
4. Pay attention to student comments—but understand their limitations. Students typically are not well situated to evaluate pedagogy.
5. Avoid comparing teaching in courses of different types, levels, sizes, functions, or disciplines.
6. Use teaching portfolios as part of the review process.
7. Use classroom observation as part of milestone reviews.
8. To improve teaching and evaluate teaching fairly and honestly, spend more time observing the teaching and looking at teaching materials.

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Ann Gauger moves the goalposts

We've been discussing Ann Gauger's claim that evolution is impossible because she was unable to transform a modern enzyme into another related one by changing a small number of amino acids.

I pointed out that this is not how evolution works. In some cases, you can easily show that two enzymes with different specificities can evolve from a common ancestor that could carry out both reactions. Such enzymes are said to be "promiscuous."

Here's Ann Gauger's latest post: In Explaining Proteins (and Life), Here's What Matters Most. She says ...

So now, let's address enzyme evolution and the divergence of enzymes to produce related families and superfamilies. Larry Moran says that modern enzymes evolved by specializing from a promiscuous ancestor. As evidence, he says modern enzymes can sometimes catalyze reactions with several substrates (the chemicals they bind to and change), and that it is possible to shift these enzymes to favor one substrate over another. He gives several examples or provides links to them.

Here's another place where he and I agree. Promiscuous enzymes can be shifted with just a few mutations to a new reaction specificity, provided the capacity for the reaction already exists in the starting enzyme, and each step is small and selectable. They can evolve easily, because they can already carry out the reaction in question. Larry Moran's description of the process is actually quite good, despite the digs he takes at us.

It strikes me that Larry Moran would know we agree with him on these points if he had read our papers.

So, what's the problem?

Turns out that changing one related enzyme into another with a different specificity wasn't the goal of her experiment. Here's what she was really trying to do ...

The Big Problem

Here's the big problem -- the arrival of novelty.

Novelty or innovation means the appearance of something not already present. It's the opposite of promiscuity. So a way to create novelty is absolutely essential to explain modern cells, as I will demonstrate.

...

Here's the heart of the matter. Promiscuity cannot solve the problem of novelty. Mutation, natural selection, and drift cannot drive the creation of novelty of all those new protein folds. That's what Doug Axe and I have been testing all along, from Doug Axe's 2004 paper to this most recent one. Based on our experiments, the problem of how innovation originates remains unsolved.

Now I get it (not). What she and Doug Axe were really trying to do was to intelligently design an entirely new enzyme.

They failed.

Therefore Intelligent Design Creationism is falsified.

That seems logical to me.

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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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How many microRNAs?

MicroRNAs are a special class of small functional RNA molecules. The functional RNA is only about 22 nucleotides long and most of the well-characterized examples bind to mRNA to inhibit translation and/or destabilize the message.

The big questions for many of us are how many different microRNAs are there in a typical cell and how many of them have a real biological function. These questions are, of course, part of the debate over junk DNA. Are there thousands and thousands of microRNA genes in a typical genome and does this mean that there's a lot less junk DNA than some of us claim?

The journal Cell Death and Differentiation has devoted a special issue to microRNAs [Special Issue on microRNAs – the smallest RNA regulators of gene expression]. There are four reviews on the subject but none of them address the big questions.

That didn't stop the journal from leading off with this introduction ...

It is now well recognised that the majority of non-protein-coding genomic DNA is not “junk” but specifies a range of regulatory RNA molecules which finely tune protein expression. This issue of CDD contains an editorial and 5 reviews on a particular class of these regulatory RNAs, the microRNAs (miRs) of around 22 nucleotides, and which exert their effects by binding to consensus sites in the 3'UTRs of mRNAs. The reviews cover the role of miRs from their early association with CLL to other forms of cancer, their importance in the development of the epidermis and their potential as disease biomarkers as secreted in exosomes.

I'm not certain what the editors mean when they say that "it is now well recognised ..." I interpret this to mean that there are a large number of scientists who are completely uniformed about the structure of genomes and the debate over junk DNA. In other words, it is now well recognized that some scientists don't know what they are talking about.

I don't know any expert who would claim that 50% of large genomes consist of genes that specify regulatory RNAs involved in fine-tuning protein expression. Do you?

On a related issue, Wilczynska and Bushell begin their review with ...

Since their discovery 20 years ago, miRNAs have attracted much attention from all areas of biology. These short (~22 nt) non-coding RNA molecules are highly conserved in evolution and are present in nearly all eukaryotes.

Sequence conservation is an important criterion in deciding whether something is functional. In order to use conservation as a measure of function you have to establish some standards that let you distinguish between sequences that are "conserved" by negative selection and those that have drifted apart by random genetic drift.

What do Wilczynska and Bushell mean when they say that microRNAs are "highly conserved"? The most highly conserved genes exhibit about 50% sequence identify between prokaryotes and eukaryotes. They are almost identical within mammals. Other highly conserved genes are about 80% identical within animals (e.g. between insects and mammals). As far as I know, the sequences of most putative microRNAs aren't even similar within mammals and certainly not between mammals and fish.

The phrase "highly conserved" has become meaningless. It's now a synonym for "conserved" because nobody ever wants to just say "conserved" and they certainly don't want to say "moderately conserved" or "weakly conserved" even if it's the truth.

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Ann Gauger keeps digging

Ann Gauger and her creationist collaborator, Doug Axe, have been swapping amino acid residues in one kind of protein hoping to show that they cannot change it into another. They have deliberately ignored any clues that might be derived from assuming that evolution happened.

They have succeeded in their goal. None of their constructs have a different activity. They conclude that evolution is disproved.

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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A creationist argument against the evolution of new enzymes

Intelligent Design Creationists have found it impossible to make a positive case for intelligent design and the existence of a supernatural designer. Instead, they concentrate on trying to prove that evolution is wrong. Turns out, they're not very good at that either.

The latest attempt is by Ann Gauger posting on the best Intelligent Design Creationist website.¹ She outlines her case at: Is Evolution True? Laying Out the Logic.

On the irrelevance of Michael Behe

Michael Behe is one of the few Intelligent Design Creationists who have come up with reasonable, scientific, defenses of creationism. I give him credit for that and for the fact that it often takes some effort to show why he is wrong.

However, when he has been proven wrong he should admit it and move on. He should instruct his fellow creationists to move on as well. That's not what happened with respect to his book on The Edge of Evolution. Last July he doubled down when a new study appeared that refuted his claims. Amazingly, Behe said that his ideas were vindicated. I questioned his logic in: CCC's and the edge of evolution and Michael Behe's final thoughts on the edge of evolution.

After a thorough discussion, we conclude that Behe is wrong about his edge of evolution. There's nothing in evolutionary theory, or in experimental results, that prevents the evolution of new functions with multiple mutations.

Now Ken Miller has posted an article making many of the same points [Edging towards Irrelevance]. Miller rightly demands an apology from Behe but his main point is that Michael Behe's recent behavior has made him largely irrelevant in the debate over Intelligent Design Creationism. I agree.

What this means is that there is nobody left in the Intelligent Design Creationist community who deserves serious attention from scientists. It will still be fun dealing with them but the game has become more like whac-a-mole than science. PZ Myers¹ makes the same point: Aren’t we all more than a little tired of Michael Behe?.

It's kinda sad.

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1. Unfortunately, PZ weakens his case by misrepresenting Behe's argument. PZ says, The hobby horse he’s been riding for the past few years is the evolution of chloroquine resistance in the malaria parasite: he claims it is mathematically impossible." That's just not true. Behe's entire case rests on the fact that chloroquine resistance is well within the edge of evolution. Behe has no problem with the evolution of chloroquine resistance.

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.

For the King

My son Gordon and his friend Colby are working on a new game called "For the King." It looks really cool. (I'm playing with an early version.)

Check out the website: IronOaks Games. They are also on Facebook: IronOaks Games. Twitter is @IronOakGames where you can make suggestions and follow development.

This is a game that reminds you of Hack and Nethack except with much better graphics. I think all the old people (like me) are going to like it. Ms Sandwalk asked for a carnival and got it (see below) and I'm pumping for a university.

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Nature criticizes science hyperbole and bad science writing

There's a very interesting editorial in the Oct 14, 2014 issues of Nature [see here]. It's about a scientific paper that turned out to be misleading and the role of science writers and journals in promoting that story.

The editors of Nature remind us that ...

Extraordinary claims, as the saying almost goes, demand more scrutiny than usual to make sure they stand up. That is how science works. Claim and counter-claim: intellectual thrust and experimental parry.

They report on an upcoming meeting meeting of the Council for the Advancement of Science Writing in Columbus Ohio. Apparently, this council is composed of scientists and journalists and the goal of the meeting is to search for "lessons learned by scientists and science writers" in light of their publicity campaign promoting the flawed paper.

The Nature editors note that ...

The first thing to highlight is that such a thing as the Council for the Advancement of Science Writing even exists. Too many scientists dismiss the media and journalists as sloppy and unwilling to engage in both detail and ambiguity. In fact, there can be no branch of journalism as self-scrutinizing and anxious about its performance as that which covers science. It is hard to imagine political and sports reporters taking the time to discuss so thoroughly what (if anything) they did wrong after one of their stories went belly-up.

Indeed, that's admirable, but it's another example of journalistic hyperbole. I do not believe that this branch of journalism (science writing) is as "self-scrutinizing" as they would have us believe. I do not believe that science writers usually debate and discuss what they did wrong when a story goes belly-up.

But it may be true that science writers are increasingly "anxious" about their performance. Why are they so "anxious"? It's because they are doing a very sloppy job characterized by parroting press releases written by amateurs whose main goal is to promote their institution or by science journals that want publicity.

Science writers (and journals) used to get away with this but now ...

The (welcome) rise of the science blogger has fuelled this navel-gazing. Some bloggers seem to spend most of their time criticizing other science writers, or at least debunking examples of what they regard as inferior science writing. But they do lots of good stuff too. Although traditionalists lament the decline of science coverage in the mainstream press, a terrific amount of analysis and comment, much of it very technical, is happening online under their noses.

There's an interesting slip of the tongue in that paragraph. If science writers are really interested in self-scrutiny then they should welcome the arrival of a group of bloggers who point out their errors. This should be a "good" thing but the Nature editors clearly contrast this role (criticizing science writers) with other "good stuff" that bloggers do. Apparently the criticism of science writing doesn't count as "good stuff." It just makes science writers anxious—which they weren't before science bloggers came on the scene and pointed out what a bad job they were doing.

Nature then admits its complicity in hyping the event and not doing a proper skeptical analysis of the findings. The editors then get to an important issue.

Some may question the timing of the announcement, made when the paper was released on the Internet, not accepted or published by a journal, but at least the evidence was there to examine. If the scientists and the media both largely acted properly, then what should be discussed at next week’s meeting? It could do worse than start by screening the celebratory online video produced by ... and released to accompany the announcement. Scientists and journalists can include as many academic caveats as they like, but the sounds and images of champagne corks popping tend to render such statements of caution just that — academic.

There is a deeper issue here: science not by press conference but presented as an event. What in reality is a long, messy and convoluted process of three steps forward and two steps back is too easily presented as giant leaps between states of confusion and blinding revelation. At the heart of this theatre is the artificial landmark of a peer-reviewed paper. Fixed print schedules and releases to journalists under embargo (with or without champagne videos) help to lend the impression that the publication of a paper is the final word on a question — the end-of-term report on a scientific project that details all that was achieved.

I bet you're thinking that this is all about the ENCODE publicity campaign and how Nature was totally at fault for misrepresenting the data and hyping the false claims of the ENCODE Consortium.

Nope. It's about the discovery of gravitational waves—a paper that turns out to have been wrong because scientists didn't do the proper controls.

Meanwhile, Nature, and science writers in general, have yet to admit that they failed massively in September 2012 and they have done little to convince us "bad" bloggers that they are capable of self-scrutiny. This is serious because in this case Nature and its editors were very active participants in the making of videos and holding press releases [see How does Nature deal with the ENCODE publicity hype that it created?]. Let me remind you of the video PRODUCED BY NATURE featuring Senior Editor Magdalena Skipper in which she promotes the idea that most of the human genome is functional. [Note: I'm getting error messages when I try to run this video.]


Maybe there are other things that the Council for the Advancement of Science Writing could be talking about? Maybe there are other examples of bad science journalism that the editors of Nature should be addressing?

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Creationists trash Denmark

Denmark present a real problem for many Christians. It appears to be a successful secular society that has all but abandoned extreme forms of religion. These Christians can't figure out how a country could be moral if it's full of nonbelievers.

Vincent Joseph Torley (vjtorley) has found the answer [Is something rotten in the state of Denmark?]. He's responding to claims by Jerry Coyne that Denmark is a successful country.

Perhaps Coyne might be interested to read an eye-opening article by Carol Brown over at American Thinker on what is happening in Denmark. Ms. Brown paints a terrifying portrait of a society which is falling apart under the influence of religiously motivated violence. Crime in Denmark has exploded, and street gangs "have taken over large parts of Danish towns and cities. There are numerous "no go" zones where even the police are afraid to venture. Is this Coyne’s idea of a successful secular society?

Some morals to be drawn from Brown’s article:

1. Not all forms of religion are good; some are toxic.

2. Nature abhors a vacuum. Secularism is powerless to drive out toxic forms of religion.

3. The only proven way to drive out toxic forms of religion, and keep them out, is with wholesome forms of religion.

I was in Denmark for seven days and I never saw any sign of this sort of lawlessness or even heard about it. But maybe I was just in the wrong places? Or maybe it's not true? (Heavens!)

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BREAKING NEWS!!! A creationist doesn't understand evolution

Last March, I dissected the views of James Tour, a chemist who doesn't understand evolution [A chemist who doesn't understand evolution]. Apparently he didn't listen because he's at it again and still being promoted by IDiots [Detective Columbo of Chemistry: "I Don't Understand Evolution"].

I don't know who wrote that post but here's the punchline ...

Tour signed Discovery's Scientific Dissent from Darwinism years ago when the National Center for Science Education asserted that only a handful of scientists doubt Darwin's theory. Our list of dissenters started at 100, then grew to 800. At that point we stopped inviting people to sign it because their names on the list were used by Darwinists to persecute them professionally. Some lost their jobs.

However, Tour doesn't seem to have been hurt. Is that possibly because chemists are more open-minded than biologists? Or is the dirty little secret about Darwinism -- that it has more public advocates in science than private believers -- becoming more apparent?

Maybe we should consider the possibility that that a synthetic organic chemist is not an expert on biology? Naw, that would require the application of skepticism [How to use selective hyperskepticism to debate Darwinists].

You just can't make this stuff up.

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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.

Razib Khan defends old-fashioned evolution theory

Razib Khan writes at Gene Expression. He's a big fan of personal genetics and genome sequencing and, in the past, has been a defender of the Modern Synthesis version of evolutionary theory. In light of the recent Nature discussion on "Does evolutionary theory need a rethink?" (Laland et al. 2014), Razib thought he would re-state his position [Evolution Ever Evolves].

I laid out my position in: Rethinking evolutionary theory. I don't think any of the new ideas like epigenetics, plasticity, facilitated variation etc. are about to change evolutionary theory significantly. However, I do think that the standard version of the 1940s Modern Synthesis was far too rigid and that a modern emphasis on population genetics (including Neutral Theory and more emphasis on random genetic drift) have significantly changed evolutionary theory—something close to a "revolution." The problem is that many scientists, and even many evolutionary biologists, haven't really integrated this change into their way of thinking. This resistance was very well described in a paper by Stephen J. Gould and Richard Lewontin over 45 year ago (Gould and Lewontin, 1978) [What Does San Marco Basilica Have to do with Evolution?]

I think there's already been a "revolution" but most people didn't notice and are still stuck in the 1940s adhering to an old-fashioned version of evolutionary theory that emphasizes adaptation.

Razib Khan doesn't like Gould and doesn't like new-fangled ideas like "neutralism" and "random genetic drift". Let's see what he thinks of the latest kerfluffle.

It seems that rather regularly there is a debate within evolutionary biology, or at least in public about evolutionary biology, where something new and bright and shiny is going to revolutionize the field. In general this does not pan out. I would argue there hasn’t been a true revolution in evolutionary biology since Mendelian genetics and classical Darwinism were fused in the 1920s and 1930s during the period when population genetics as a field was developed, and the famous "synthesis" developed out of the interaction of the geneticists with other domains of evolutionary relevance. This does not mean that there have not been pretenders to the throne. Richard Goldschmidt put forward his "hopeful monsters," neutralism reared its head in the 1970s, and evo-devo was all the rage in the 2000s. Developments that bore scientific fruit, such as neutralism, were integrated seamlessly into evolutionary biology, while those that did not, such as Goldschmidt’s saltationism fell by the wayside. This is how normal science works.

The main point here is whether Neutral Theory and an increased emphasis on random genetic drift "were integrated seamlessly" into the Modern Synthesis view that was popular in the 1960s. Is it true that the way modern population geneticists look at evolution is just a little bit different from the way evolutionary biologists thought about evolution in the 1920s, 1930s, and 1940s? I don't think so. I think there's been a significant shift—so much so that we can no longer refer to the "Modern Synthesis" as the most modern version of evolutionary theory.

Unlike Razib Khan, I am not convinced that most evolutionary biologists have made the shift. At my university, for example, the students must take a first-year course on evolution taught by members of the Dept. of Evolution & Ecology. I see these students in subsequent years and they don't understand the basics of population genetics. Nor do they appreciate the role of neutral alleles and random genetic drift. They are being taught the evolutionary theory of the Modern Synthesis (circa 1960).

Also the debates we are having over junk DNA suggests strongly that most scientists are not familiar with modern population genetics and Neutral Theory.

But every now and then you have a self-declared tribune of the plebs declaring that the revolution is nigh. For decades the late Stephen Jay Gould played this role to the hilt, decrying "ultra-Darwinism," and frankly misrepresenting the state of evolutionary theory to the masses from his perch as a great popularizer. More recently you have had more muted and conventional revisionists, such as Sean Carroll, who promote a variant of evo-devo that acclimates rather well to the climes of conventional evolutionary biology.

I do not believe that Gould misrepresented evolutionary theory to the masses. I believe that Richard Dawkins misrepresented evolutionary theory to the masses.

Like Razib, I'm not a big fan of evo-devo and I don't think it contributes much to fundamental evolutionary theory.

Nature now has a piece out which seems to herald the launching of another salvo in this forever war, Does evolutionary theory need a rethink? It’s written in the form of opposing dialogues. I’m very much in the camp of those believe that there’s no reason to overturn old terms and expectations. Evolutionary biology is advancing slowly but surely into new territory. There’s no problem to solve. The one major issue where I might have to make a stand is that it focusing on genetics is critical to understanding evolution, and dethroning inheritance from the center of the story would eviscerate the major thread driving the plot. The fact that evolutionary biologists have the conceptual and concrete gene as a discrete unit of information and inheritance which they can inspect is the critical fact which distinguishes them from fields which employ similar formalisms but have never made comparable advances (such as economics).

I agree with Razib Khan that genetics (population genetics) is the key to understanding evolutionary theory at the population level. I think we disagree on exactly what version of population genetics we support and on the importance of adaptation.

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Gould, S.J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. Proceedings of the Royal Society of London. Series B, Biological Sciences, Vol. 205, No. 1161, The Evolution of Adaptation by Natural Selection (Sep. 21, 1979), pp. 581-598. [AAAS reprint] [printable version]

Laland, K., Uller, T., Feldman, M., Sterelny, K., Müller, G. B., Moczek, A., Jablonka, E., Odling-Smee, J., Wray, G. A., Hoekstra, H. E., Futuyma, D. J., Lenski, R. E., Mackay, T. F. C., Schluter, D. and Strassmann, J. E. (2014) Does evolutionary theory need a rethink? Nature 514, 163-165. [PDF]

How to use selective hyperskepticism to debate Darwinists

Gordon Elliot Mullings (kairosfocus) is explaining to his fellow creationists how to debate evolution. His latest post focuses on the techniques of "selective hyperskepticism" and "close-mindedness" [Darwinian Debating Devices # 12: Selective Hyperskepticism, closed-mindedness (and “extraordinary claims require extraordinary evidence”)].

Here's how he describes selective hyperskepticism. He's quoting someone who comment on Uncommon Descent.

... hyper-skepticism (which is certainly not a term we made up … just google it) is virtually never equitable. Rather it is highly selective. Selective Hyper-Skepticism results when one requires a much higher degree of warrant in order to accept things that they prefer weren’t true. It most often comes up when worldview issues are at stake. It’s the application of a double-standard where one demands sufficient evidence to support absolute certainty (which is generally impossible) on certain facts they’d rather not have to believe, but they are willing to accept a much more lax standard of evidence and argumentation on matters of a very similar profile that don’t threaten their worldview. It also happens that someone demonstrating hyper-skepticism on these types of worldview issues often displays hyper-credulity towards arguments and evidence on the matter that is consistent with their own worldview. This isn’t really an accident, because the hyper-skepticism applied on one side of the equation often leaves the person grasping for any contrary evidence or argument at all on the other side of the equation, no matter how implausible or unsubstantiated.

Now, Gordon Elliot Mullings doesn't give any examples of how to use this technique to debate Darwinists but I can think of a few examples.

Let's take the formation of bacterial flagella as a good illustration of how they use selective hyperskepticism. They begin with the unshakeable assumption that gods exist that that they must have created life. They then find an example of something complex where the exact evolutionary pathway hasn't been worked out and declare that the gods made it. They refuse to answer any questions about how, when, where, and why and they refuse to present any evidence that gods did it.

When evolutionary biologists present some evidence that bacterial flagella could have arisen by evolution the creationists turn into selective hyperskepticists by demanding a detailed blow-by-blow account of the historical process complete with reams of scientific evidence. Of course, they would never think of applying these same criteria to their own worldview.

I didn't read the rest of the post or the other ones put up by Gordon Elliot Mullings so I'm not sure why he's exposing this tactic to the public. It makes creationists look bad.

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Do you believe that drinking carbonated beverages containing sugar will cause your telomeres to shorten and hasten your death?

It's very difficult to teach students to be skeptical of the scientific literature and how it's reported. I read this press release from the University of California, San Francisco (San Francisco, USA) and dismissed it as ridiculous but I can't really tell you why. It's from one of the top research universities in the world.

What do you think? Do you believe this study? If not, why not? How do you explain why you are skeptical about this research but not about other research?

Kim Krisberg, who describes herself as "freelance public health writer" writes at The Pump Handle [New research finds that drinking soda may lead to cell aging and disease, regardless of obesity]. She doesn't appear to be skeptical.

UCSF scientists find shorter telomeres in immune cells of soda drinkers

Sugar-sweetened soda consumption might promote disease independently from its role in obesity, according to UC San Francisco researchers who found in a new study that drinking sugary drinks was associated with cell aging.

The study revealed that telomeres — the protective units of DNA that cap the ends of chromosomes in cells — were shorter in the white blood cells of survey participants who reported drinking more soda. The findings were reported online October 16, 2014 in the American Journal of Public Health.

The length of telomeres within white blood cells — where it can most easily be measured — has previously been associated with human lifespan. Short telomeres also have been associated with the development of chronic diseases of aging, including heart disease, diabetes, and some types of cancer.

"Regular consumption of sugar-sweetened sodas might influence disease development, not only by straining the body's metabolic control of sugars, but also through accelerated cellular aging of tissues," said Elissa Epel, PhD, professor of psychiatry at UCSF and senior author of the study.

"This is the first demonstration that soda is associated with telomere shortness," Epel said. "This finding held regardless of age, race, income and education level. Telomere shortening starts long before disease onset. Further, although we only studied adults here, it is possible that soda consumption is associated with telomere shortening in children, as well."

The authors cautioned that they only compared telomere length and sugar-sweetened soda consumption for each participant at a single time point, and that an association does not demonstrate causation. Epel is co-leading a new study in which participants will be tracked for weeks in real time to look for effects of sugar-sweetened soda consumption on aspects of cellular aging. Telomere shortening has previously been associated with oxidative damage to tissue, to inflammation, and to insulin resistance.

Based on the way telomere length shortens on average with chronological age, the UCSF researchers calculated that daily consumption of a 20-ounce soda was associated with 4.6 years of additional biological aging. This effect on telomere length is comparable to the effect of smoking, or to the effect of regular exercise in the opposite, anti-aging direction, according to UCSF postdoctoral fellow Cindy Leung, ScD, from the UCSF Center for Health and Community and the lead author of the newly published study.

The average sugar-sweetened soda consumption for all survey participants was 12 ounces. About 21 percent in this nationally representative sample reported drinking at least 20 ounces of sugar-sweetened soda a day.

"It is critical to understand both dietary factors that may shorten telomeres, as well as dietary factors that may lengthen telomeres," Leung said. "Here it appeared that the only beverage consumption that had a measurable negative association with telomere length was consumption of sugared soda."

The finding adds a new consideration to the list of links that has tied sugary beverages to obesity, metabolic syndrome, type 2 diabetes, and cardiovascular disease, and that has driven legislators and activists in several U.S. jurisdictions to champion ballet initiatives that would tax sugar-sweetened beverage purchases with the goal of discouraging consumption and improving public health.

The UCSF researchers measured telomeres after obtaining stored DNA from 5,309 participants, ages 20 to 65, with no history of diabetes or cardiovascular disease, who had participated in the nation's largest ongoing health survey, called the National Health and Nutrition Examination Survey, during the years 1999 through 2002. They found that the amount of sugar-sweetened soda a person consumed was associated with telomere length, as measured in the laboratory of Elizabeth Blackburn, PhD, professor of biochemistry at UCSF and a winner of the 2009 Nobel Prize in Physiology or Medicine for her telomere-related discoveries.

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Additional study authors include, from UCSF, Nancy E. Adler, PhD, professor of psychiatry and director of the Center for Health and Community, and Jue Lin, PhD, an associate researcher with Blackburn's lab; from UC Berkeley, Barbara A. Laraia, PhD, director of public health nutrition; from the University of Michigan, Belinda Needham, PhD, assistant professor of epidemiology; and from Stanford University, David H. Rehkopf, ScD, assistant professor of medicine.

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Fixing CO2 fixation

How biochemistry students can become multi-millionaires by making plants more efficient. Has someone finally succeeded?

Living organisms need carbon to grow and divide. Many get their carbon atoms from organic molecules such as glucose or acetate that have been synthesized in other species.

Most organisms can fix carbon directly from carbon dioxide by a variety of different reactions but this isn't necessarily the primary source of carbon atoms. (We can fix carbon using pyruvate dehydrogenase, isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, and phosphoenolpyruvate carboxykinase (PEPCK) among others.)

Non-coding half of human genome unlocked

This is another story about press releases. In this case, it's an article published by ScienceDaily: Non-coding half of human genome unlocked with novel sequencing technique. It's almost a direct copy of a press release put out by Texas A&M University (Texas, USA): Texas A&M Biologists Unlock Non-Coding Half of Human Genome with Novel DNA Sequencing Technique.

Let's begin by looking at the actual paper (Aldrich and Maggert, 2014). Here's the abstract.

Heterochromatin is a significant component of the human genome and the genomes of most model organisms. Although heterochromatin is thought to be largely non-coding, it is clear that it plays an important role in chromosome structure and gene regulation. Despite a growing awareness of its functional significance, the repetitive sequences underlying some heterochromatin remain relatively uncharacterized. We have developed a real-time quantitative PCR-based method for quantifying simple repetitive satellite sequences and have used this technique to characterize the heterochromatic Y chromosome of Drosophila melanogaster. In this report, we validate the approach, identify previously unknown satellite sequence copy number polymorphisms in Y chromosomes from different geographic sources, and show that a defect in heterochromatin formation can induce similar copy number polymorphisms in a laboratory strain. These findings provide a simple method to investigate the dynamic nature of repetitive sequences and characterize conditions which might give rise to long-lasting alterations in DNA sequence.

Meet Joe Felsenstein

Here's some other little known facts about Joe Felsenstein. He doesn't like Tim Hortons. He likes beaver tails. He knows a lot about sex.

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Faculty of Medicine at the University of Toronto supports quackery

Our Dean of Medicine, Catharine Whiteside, announced recently that the Faculty of Medicine and the Faculty of Pharmacy are entering into a joint program for
Evaluating Complementary and Alternative Medicine. They will collaborate with a new Centre for Integrative Medicine (CIM) run by Lynda Balneaves.

It's not clear what form of "Complementary Medicine" (i.e. non-evidence based medicine) she (Lynda Balneaves) supports but it seems to include "natural health products (e.g., vitamins and herbal therapies), manipulative physical treatments (e.g., massage), and mindbody therapies (e.g., meditation)" [CAMEO]. Other websites mention acupuncture.¹

"Alternative Medicine" is also another word for medical care that has not been proven effective by standard clinical trials. Otherwise it wouldn't be "alternative." What this means is that the Faculties of Medicine and Pharmacy have abandoned the ideal of evidenced-based medicine.² You may want to take that into account next time you are choosing a physician.

Rethinking evolutionary theory

I believe that Gould was correct when he pronounced the death of the Modern Synthesis [Is the "Modern Synthesis" effectively dead?] [Razib Khan doesn't like Gould and doesn't like new-fangled ideas like "neutralism" and "random genetic drift"] [Die, selfish gene, die!] [Gould on Darwinism and Nonadaptive Change] [Extending the Modern Synthesis at the Molecular Level ].

I agree with Arlin Stoltzfus in his description of the Modern Synthesis [Arlin Stoltzfus explains evolutionary theory]. I agree with him, and with Masatoshi Nei, that mutation and mutationism were downplayed in the Modern Synthesis [The Mutationism Myth, VI: Back to the Future] [Mutation-Driven Evolution]. That's one example of why the old-fashioned Modern Synthesis should be abandoned as a description of modern evolutionary theory.

Explaining Intelligent Design Creationism: Who is the designer?

I'm told that the Mark IX irony meter is still being tested. It's been almost two years and those of us with the older Mark VIII meter have to be very cautious. There are just too many IDiot posts that will fry them [Turn Off Your Irony Meters Before Reading This!!!].

Here's one, for example. It's a post on Uncommon Descent that begins with a quote from a reader and is completed by Barry Arrington [Quote of the Day]. I'm not sure if either part will be safe for the Mark IX but I know my Mark VIII can't survive.

Let's look first at the quote from a reader named "logically_speaking." You need a little background in order to understand the quote.

Recall that Intelligent Design Creationism is relatively new even though some of the basic ideas have been around for centuries. It's only been about fifteen years since they claim to have developed proof of design in nature. What that means is that before about 1995 nobody was ever convinced about design so nobody ever though about a possible designer.

Here's how logically_speaking explains it ....

logically_speaking says:

In my opinion questions such as who was the designer and who designed the designer are only important after design has been detected. In fact this is how many branches of scientific endeavor must proceed. Ask any detective at a crime scene, do they ask who was the murderer before answering the question of was any murder committed in the first place.

I wonder how that's working out? If design was only detected by Bill Dembski and Michael Behe then they've only had a few years to think about who the designer might be. I wonder what they've come up with? Who are the leading suspects?

It can't be anyone from the past since, according to logically_speaking, it would have been silly to speculate about the designer before design was detected.

Or is it possible that people believed that design was detected hundreds of years ago so they have already identified the designer using the scientific endeavor? If that's true then the modern Intelligent Design Creationism detection unit has wasted its time.

Barry Arrington clarifies ....

There are two separate questions (1) was there design and (2) who was the designer. It really is a common sense observation that the second question is logically downstream from the first. It is a corollary to that common sense observation that anyone who insists that one cannot address the upstream question until one has resolved the downstream question is either deeply confused or has an agenda unconnected with discovering the truth of the matter.

Imagine that! Some people have an agenda that's unconnected with discovering the truth!

Who knew?

Don't say I didn't warn you about turning off your irony meter.

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Bruce Alberts awarded the National Medal of Science

The National Science Foundation (USA) selected this year's recipients of the National Medal of Science. President Obama made the announcement last Friday [President Obama Honors Nation’s Top Scientists and Innovators].

One of the winners is Bruce Alberts. Congratulations Bruce!

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The 2014 Nobel Prize in Physiology or Medicine

Who are these people? I pride myself on being a generalist so I think I've heard of any important discoveries in biology. I may not always agree that they are ground-breaking discoveries but at least I know about them.

I think this is the very first time that I learned of an important discovery only when the Nobel Prizes are announced.

I must be getting too old for this game. From The 2014 Nobel Prize in Physiology or Medicine ...

The Nobel Prize in Physiology or Medicine 2014 was awarded with one half to John O'Keefe and the other half jointly to May-Britt Moser and Edvard I. Moser "for their discoveries of cells that constitute a positioning system in the brain".

How do we know where we are? How can we find the way from one place to another? And how can we store this information in such a way that we can immediately find the way the next time we trace the same path? This year´s Nobel Laureates have discovered a positioning system, an “inner GPS” in the brain that makes it possible to orient ourselves in space, demonstrating a cellular basis for higher cognitive function.

In 1971, John O´Keefe discovered the first component of this positioning system. He found that a type of nerve cell in an area of the brain called the hippocampus that was always activated when a rat was at a certain place in a room. Other nerve cells were activated when the rat was at other places. O´Keefe concluded that these “place cells” formed a map of the room.

More than three decades later, in 2005, May-Britt and Edvard Moser discovered another key component of the brain’s positioning system. They identified another type of nerve cell, which they called “grid cells”, that generate a coordinate system and allow for precise positioning and pathfinding. Their subsequent research showed how place and grid cells make it possible to determine position and to navigate.

The discoveries of John O´Keefe, May-Britt Moser and Edvard Moser have solved a problem that has occupied philosophers and scientists for centuries – how does the brain create a map of the space surrounding us and how can we navigate our way through a complex environment?

Is this going to be controversial?

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The ten commandments of faitheism

An accommodationist is an atheist who generally believes that religion and science are compatible but certainly believes that other atheists should go easy on those who believe in gods. Jerry Coyne doesn't like some words (e.g. bl*g, d*g)) so he invented another word for accommodationists—he calls them "faithiests." I'm going to stick with accommodationist.

Alex Chituc posts at "Nonprophet Status" on the patheos website ("Hosting the Conversation on Faith"). He defends the accommodationist position and tries to lay out their position [Our 10 Commandments of Faitheism].

Here's how he explains it ...

In most debates, especially arguments over the internet, each side brings along a list of premises, premises that originally gave rise to their conclusions and often go unaddressed. Unless a counter argument addresses any of these often unstated premises, all it accomplishes is bringing in a whole new set of premises to be addressed, and nobody gets anywhere.

Given a recent list I saw floating around twitter titled "10 commandments of faitheism," which is nothing but a list of things nobody associated with the term "faitheist" actually believes, I thought it would be a good exercise to try to list all of premises that we at NPS, at least, bring to the table. I should state upfront that, obviously, only Chris Stedman can speak for Chris Stedman, but since most people lump us at NPS in with him anyway and “faitheist” is the most convenient term on hand right now, I decided to use it.

This is a laudable objective. I fully support the concept.

Let's see how he interprets his opponents (I am one) and let's see whether his accomodationist premises stand up to close scrutiny. Here's Alex Chitic's "10 Premises of Faitheism."

Metabolism first and the origin of life

There are many ideas about the origin of life but the only ones that concern me are the scientific ones. The 21st century debate mostly involves smokers vs. soupers [Changing Ideas About The Origin Of Life].

Soupers are people who believe in some version of the primordial soup. They believe that life originated in a solution of organic molecules and the most primitive way of getting energy was by oxidizing these molecules. For them, the first biochemical pathways were like glycolysis. Most of them think that complex organic molecules were delivered to Earth by asteroids [see NASA Confusion About the Origin of Life].

Smokers, on the other hand, promote an origin of life scenario that relies on the chemistry surrounding hydrothermal vents on the ocean floor. These environments favor reactions that build up organic molecules from inorganic substrates like hydrogen and carbon dioxide. In this case, the most primitive reactions are simple oxidation-reduction reactions and the most primitive pathways are biosynthesis pathways, not catabolism. This view is often referred to as "metabolism first" [Metabolism First and the Origin of Life].

I'm a big fan of metabolism first and especially the versions promoted by Bill Martin and Nick Lane. I think it's the only reasonable model for the origin of life.

A reader alerted me to a paper published last year by all the big names in metabolism first [Sousa et al., 2013]. It's an excellent paper. You should read this paper if you really want to learn about modern thinking on the origin of life problem. The biochemistry is complicated but well worth the effort.

I don't have time to explain it all. Here's a teaser ...

At first sight, the idea that chemiosmosis is a very ancient means of energy transduction might seem counterintuitive. More familiar to many is the old (and popular) doctrine that the most ancient pathway of energy metabolism is a fermentation such as glycolysis [77], an idea that goes back at least to Haldane [2] and hence arose long before anyone had a clue that biological energy can be harnessed in a manner that does not involve substrate-level phosphorylations and ‘high-energy’ bonds [149,150]. In modern life, all biological energy in the form of ATP comes ultimately from chemiosmotic coupling [151], the process of charge separation from the inside of the cell to the outside, and the harnessing of that electrochemical gradient via a coupling factor, an ATPase of the rotor–stator-type. It was not until the 1970s that it became generally apparent that Mitchell [152] was right, his Nobel prize coming in 1978, and it is hard to say when it became clear to microbiologists that all fermentative organisms are derived from chemiosmotic ancestors. We also note that Mitchell's consideration of the problem of the origin of life introduced key concepts of his later chemiosmotic hypothesis, including a definition of life as process, and the idea of vectorial catalysis across a membrane boundary that is inseparable either from the environment or from the organism itself [153].

The maxim that glycolysis is ancient might be an artefact of experience, since it was the first pathway both to be discovered and that we learned in college; in that sense, it really is the oldest. When one suggests that chemiosmotic coupling in methanogens or acetogens might be ancient, many listeners and readers shy away, mainly because the pathways are unfamiliar and often entail dreaded cofactor names.

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Sousa, F.L., Thiergart, T., Landan, G., Nelson-Sathi, S., Pereira, I. A., Allen, J.F., Lane, N. and Martin, W.F. (2013) Early bioenergetic evolution. Philosophical Transactions of the Royal Society B: Biological Sciences 368:20130088. [doi: 10.1098/rstb.2013.0088]

Germany abolishes tuition fees

There used to be a federal law in Germany that forbade charging tuition at German universities. The court decided in 2005 that it was okay to charge a moderate fee (€1,000). Gradually, over the next few years, 10 states introduced moderate tuition fees.

This proved so unpopular that parties supporting no tuition won elections in most of those states and next year the last state charging tuition (Lower Saxony) will stop. There will be no charge to students to attend university at every German university [Germany’s great tuition fees U-turn].

Germany is not alone. There are many European countries that provide a public university education at no charge to the student. (It's not "free"—the government pays and taxes cover the cost.)

Why can't we do this in Canada? Why can't they do it in the USA?

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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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