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Saturday, October 25, 2014

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?

Monday, October 20, 2014

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!)

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.

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.


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.

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

Sunday, October 19, 2014

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.

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]

Saturday, October 18, 2014

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.

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.


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.

Friday, October 10, 2014

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.

Thursday, October 09, 2014

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.

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.

Monday, October 06, 2014

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.

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!

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?

Sunday, October 05, 2014

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."

Friday, October 03, 2014

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.

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]

Thursday, October 02, 2014

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?