A Skeptics guide to the mind and Montaigne: the just seem to go together

Just finished reading:

Robert Burton's: "A Skeptic's Guide to the Mind" (still have to watch this talk).

& 
Stephen Greenblatt on Shakespeare's debt to Montaigne 

& 

reasonably happy that 

18th century Swedish biologist Carl Linnaeus is bigger than Jesus (on Wikipedia anyway)

Reading list

As I am working on updating the Biofundamentals course (and turning the web notes into a book), I find myself reading and rereading a number of great books.    Mostly so that I do not forget, I will list them here.   On the off chance anyone cares, I have linked them to reviews.

THE UNDERGROWTH OF SCIENCE: Delusion, Self-Deception and Human Frailty’ By Walter Gratzer, Oxford University Press  [a review here] Quite amazing how often weird ideas become accepted or accepted (at least for a time), until reason prevails.


Black Mass: Apocalyptic Religion and the Death of Utopia by John Gray Allen Lane  The main idea is that apocalyptic (religious) thinking is pervasive among people, even those who claim to be complete secularists - and it least to some truly stupid and tragic consequences (as if tragedy can be avoided in this life).

Beyond the Hoax: Science, Philosophy and Culture by Alan Sokal  An oldy but goody on how people can stop thinking and get lost in the ozone.

The fanaticism of the apocalypse by Pascal Bruckner

Religion explained by Pascal Boyer

The theory of evolution by John Maynard Smith

The age of wonder: How the romantic generation discovered the beauty and terror of science by Richard Holmes

Principles of social evolution by Andrew F.G. Bourke

The Ancestor's Tale by Richard Dawkins

The evolution of physics (yet again) by Albert Einstein and Leopold Infeld

Farewell to reality: How modern physics has betrayed the search for scientific truth by Jim Baggott

To save everything, click here: the folly of technological solutionism by Evgeny Morozov

Religion in human evolutionL from the paleolithic to the axial age by Robert Bellah

Darwin's Lost world: The hidden history of animal life by Martin Brasier:

The Rocks don't lie: A geologists investigates Noah's Flood by David Montgomery:

Microbes and evolution: the world that Darwin never sawL Stanley Maloy

The first crusade by Steven Runciman

Academic Freedom, Monty Python & Loretta.

Neither faculty or "Students do not shed their constitutional rights...at the schoolhouse gate." Tinker v. Des Moines Independent Community School District, 393 U.S. 503 (1969).

Having read Professor Hayward’s now notorious October 2013 blog post^[1], it is clear he takes delight in rattling cages. Nevertheless, some of the issues raised could serve as interesting jumping off points for discussion. For example, I have always objected to being lumped together with other Caucasians when it comes to ethnic identity. But assuming that he maintains an atmosphere of civility, it is difficult to understand how it is even imaginable that his comments rise to the level of “hate speech”. That said, I would love to listen to the debate that might ensue if students were asked to critically consider the Loretta sketch from Monty Python’s Life of Brian [http://youtu.be/sFBOQzSk14c]. One wonders whether this video (or even showing this video in class) is a form of hate speech? 

But really, that is not the issue here, rather there are two issues: the defense of academic freedom and the importance of training our students to learn to defend their positions, and critique the positions of others, based on empirical evidence and rigorous and logical argument.

Why does this matter?  Primarily because as faculty we are called upon to present and analyze a wide range of potentially disconcerting (and perhaps even threatening) facts, phenomena, and their implications. A short list, off the top of my head, includes the evolutionary bases and outcomes of sexual selection and the various forms of social organization^[2], the dynamics of immunity and the social outcomes arising from the refusal to vaccinate children (which could be seen as a form of child abuse), the origin of the universe and the elements of life, not to mention evolutionary mechanisms in general (which could offend a range of more literalist religious groups), the generation, costs and benefits of genetically modified organisms (including, in the future, humans), as well as the implications of social policy in the context of feeding the world’s population, the ramifications, positive, negative, economic and sociopolitical of climate change. Given the importance of social biology in species as deeply socialized as humans, one might even imagine a discussion of the origins of customs ranging from “honor” killings to the personal and political subjugation of women or the origins of slavery and its modern variants (which could be seen as “disrespecting” certain cultures.)  What will the position of the BFA be if faculty are publicly denounced by a group of devout students demanding retraction or the punishment of the faculty member?  

            It is in this context that Paul Chinowsky’s remarks (presumably made as chair of the BFA rather than as an individual faculty member) - assuming that they have been accurately reported (“If any (other) faculty member said this, we would find ourselves in a dean’s office or possibly on suspension for writing this. ... The question is, are we going to allow this or condone this from someone in our own faculty?” ), seem, at least to me, to be overtly threatening, and certainly not dispassionately supportive of faculty who hold potentially unpopular or contrarian views. 

Is this an appropriate role or position for a BFA chair to take, given that this a chair rather than a CEO position. Am I to be marched to the Dean’s office (perhaps even by the BFA chair) or not allowed to teach until my views become consistent with the current orthodoxy, or rather the orthodoxy imposed by a vocal subgroup of the student body?  I suggest that these are extremely serious questions that strike at the heart of faculty freedom, and the viability of intelectual life on campus, and I am shocked that they have been addressed in such a cavalier manner — when speaking for the BFA (and the faculty at large) a more circumspect and supportive stance would seem appropriate.

---

^[1] http://www.powerlineblog.com/archives/2013/10/off-on-a-gender-bender.php

^[2] Pity for example the poor slime mold that becomes part of the stalk rather than a spore cell, and so sacrifices itself for the good of the community.  Of course we probably should also talk about the internal and external mechanisms involved in the suppression of social cheating, but that is another course.

Restore the balance (in Boulder and beyond)

Recently, I came across a sticker advocating "restoring the balance" by bringing back the wolf.  Great idea, I thought, but perhaps not daring enough. What about following the lead of those who refuse to vaccinate their children!  Given the complete absence of empirical evidence that vaccination increases the odds of autism or other diseases, one must conclude that these brave  souls are working to restore the balance in their own small way.  We can help them by bringing back smallpox, plague, and other potentially lethal (but currently avoidable) diseases. What right do we have to drive viruses like polio to extinction? To be perfectly consistent, however, we might also want to refuse expensive medical care to those unvaccinated children who fall ill. Of course children rarely make their own decisions about vaccination (and perhaps water and waste treatment plants as well), but it seems reasonable that they share the costs of their parents semi-religious beliefs. While we are at it, we might also outlaw antibiotics, as this would lead to a dramatic increase in avoidable deaths, another balancing move. After all, in a balanced system viruses and bacteria have as much of a right to infect us as we have avoid infection.

Latest MadScientist post: Does random mutation alone account for the complete diversity of life?

Does random mutation alone account for the complete diversity of life?

Emotional versus dry science

Here is an extremely interesting article, particular in the light of thinking about how to teach evolutionary biology effectively:  The science of why we don't believe science

Autism, Mice, and the Dangers of Scientific Hype

Another day, another PR barrage centered on a scientific paper and a real danger that people will be tempted to treat a serious human disease with untried, ineffective, and potentially harmful “cures.” The paper, published in the prestigious magazine Cell, reports that some autism-like symptoms in mice, generated by treating pregnant animals with a compound that mimics viral infection, can be ameliorated by treating their offspring with the bacteria Bacterioides fragilis (1).  Rob Knight, a major player in the “American Gut” project, claims that, “The broader potential of this research is obviously an analogous probiotic that could treat subsets of individuals with autism spectrum disorder.”(2)  This is a truly remarkable claim given the multiple inherent and substantial limitations of the original study.  

So what are these limitations and why do they lead to significant doubts about whether their “promise” is either misguided or likely to be fulfilled?  The first and most obvious issue is whether mice, no matter how experimentally manipulated, can actually be autistic or, better put, whether the symptoms such manipulated mice display are related in any useful way to developing an understanding of autism or the more general “autism spectrum disorder” (ASD) in humans, yet alone alleviate the symptoms displayed by people diagnosed with ASD.  

Let us begin with what autism is currently defined to be.  According to the National Institute of Neurological Disorders and Stroke, “The hallmark feature of ASD is impaired social interaction.”(3)   Because people are so deeply and inherently social, ASD is a serious condition. That said, it remains unclear whether ASD is one or a number of distinct diseases that produce similar symptoms.

Mice, and in fact the vast majority of animals, are very, very much less social than humans, and in so far as they are social, they are social in dramatically different ways.  Moreover, mice often differ quite dramatically from humans in their responses to various physiological insults and how diseases arise and progress.  Unless carefully taken into account, these differences can make observations in mice more or less irrelevant to humans. This has been revealed most recently in the course of comparative studies on sepsis, the life threatening consequence of a wide-spread bacterial infection, where “… researchers report evidence that the mouse has been totally misleading as a model system to investigate at least three major killers – sepsis, burns, and trauma. As a result, years and billions of dollars have been wasted following false leads, they say.” (Kolata, 2013).

Let us consider the mouse as a model for autism/ASD used in the Cell study.  The investigators used an inbred line called C57BL/6N. To induce autism/ASD-like symptoms, pregnant mice were injected on embryonic day 12.5 (birth occurs between 19-21 days) with the compound poly(I:C); this treatment mimics an acute viral infection.  Administration of this compound hyper-stimulates the mother’s immune system, leading to a condition known as “maternal immune activation” (MIA) associated with elevated levels of inflammatory factors in the maternal blood, placenta, and amniotic fluid.  These changes have dramatic effects on fetal development and the affected offspring often display behaviors seemingly analogous to some of those displayed by people with ASD. Of course, since mice never display the types of social behaviors that normal people do, whether the symptoms mice from MIA mothers display are relevant to individuals diagnosed with ASD is speculative at best. 

What the authors of the Cell paper focused on were changes in the behavior of the gut, that is primarily changes in cellular behavior affecting the gut’s permeability in MIA-derived mice and the possibility of repairing these behaviors through treatment of afflicted mice with bacteria. There have been some reports that humans with autism/ASD have gastrointestinal abnormalities, but the data is unclear. A small study, published in the British Medical Journal, found no relationship between an ASD diagnosis and gastrointestinal symptoms (4) while a larger study by the Autism Microbiome Consortium reported “significant enrichment of bowel symptoms and disorders in patients with ASD (11.74% vs. 4.5%, p<0.0001 by chi-square test)”, perhaps not a completely unexpected result from a project centered on the relationship between autism and gut bacteria, but these authors note that their conclusions “may well be affected by the limitations of our study,” which relate to the specific population of patients examined. Here it is worth noting that only a minority (~12%) of individuals with ASD appeared to display gastrointestinal symptoms.

The authors of the Cell paper pursued the hypothesis that autistic/ASD-like symptoms displayed by mice might well arise directly from the defects in their gastrointestinal tract associated with MIA treatment. They found changes in the relative abundance of intestinal microbes between normal and MIA mice. We know that the interaction between intestinal microbes and gut is critical for the normal “development, maintenance, and repair of the intestinal epithelium.”  Following on they tested whether feeding mice B. fragilis, a microbe also found in humans and previously shown to ameliorate experimental colitis, could influence the effects of MIA. Their observation was a striking yes. This treatment also corrected some, but not all of the autism/ASD-linked behavioral effects found in MIA offspring mice. Most interestingly, however, from the perspective of the defining social aspects of autism and ASD, “they (the B. fragilis treated MIA mice) retain deficits in sociability and social preference” (emphasis added). Now given that autism/ASD is primarily a disease of social interactions, together with the rather dramatic differences between human and mouse immune systems brought to our attention by the sepsis studies, these observations suggest that this study’s results may well not be relevant to ASD. Moreover, from a practical perspective “B. fragilis, which accounts for only 0.5% of the human colonic flora, is the most commonly isolated anaerobic pathogen due, in part, to its potent virulence factors. Species of the genus Bacteroides have the most antibiotic resistance mechanisms and the highest resistance rates of all anaerobic pathogens. Clinically, Bacteroides species have exhibited increasing resistance to many antibiotics.” (6)  This suggests that the use of B. fragilis as a “probiotic” treatment in humans might be actively dangerous.    

Based on the lack of compelling evidence i) that mice really can, in any meaningful sense, be made to be autistic, ii) that there are substantial differences between mice and humans, particularly with respect to their immune systems, which is critical to these studies, and iii) that treatment of mice with B. fragilis fails to reverse the social symptoms of MIA mice, one might well have expected that objective, disinterested scientists would refrain from excessive hyperbole until more relevant and DEFINITIVE data is available. This would not be of great concern if confined to the scientific community but the danger is that such sanguine interpretations in the public press will lead parents or caretakers of people with ASD  to “medicate” affected children with unproven, ineffective, and potentially hazardous  “probiotic” treatments.  This concern is not a theoretical one when one considers how ubiquitous self-medication is in our society.  Any trip to the grocery store or Costco will reveal the widespread availability of dietary supplements including probiotics and other “alternative” medicines that claimed to prevent or treat a wide array of disorders, real or imagined, including gastrointestinal ailments. In the absence of a sober evaluation of the soundness of the observations made in mice and, more importantly, their relevance to humans, the essential question is whether it is socially irresponsible not to include clear and appropriate caveats directed to a scientifically-naïve population who may rightly assume the experiments described represent established fact and therefore, give license to self-directed probiotic treatment of affected individuals, or included in diets of unaffected children as a prophylactic measure.   

1. “Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders,” http://www.ncbi.nlm.nih.gov/pubmed/24315484. 

2.  http://www.dailycamera.com/cu-news/ci_24756593/cu-boulder-professor-says-study-carries-groundbreaking-potential

3. http://www.ninds.nih.gov/disorders/autism/detail_autism.htm 

4. http://www.bmj.com/content/325/7361/419 

5. Kohane et al., 2012. PLoS One DOI: 10.1371/journal.pone.0033224

6. Wexler, 2007: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2176045/ 

Further reading.

Engber, D. 2011. The Mouse Trap. Slate: http://www.slate.com/articles/health_and_science/the_mouse_trap/2011/11/lab_mice_are_they_limiting_our_understanding_of_human_disease_.html

Kolata, G. 2013. Mice Fall Short as Test Subjects for Some of Humans’ Deadly Ills. New York Times. http://www.nytimes.com/2013/02/12/science/testing-of-some-deadly-diseases-on-mice-mislead-report-says.html?_r=1&

Measuring learning: identify effective courses through data analysis.

Higher education faces serious challenges, not the least of which is how to provide compelling evidence that the learning attained is worth the cost, particularly since a number of studies suggest learning is often less impressive than many colleges might wish to portray. There is a growing interest in more effective and efficient educational practices and companies that claim to provide it. Lurking In the background is a “college ranking” industry that rarely uses objective measures of student learning. Altogether, this raises the question, what would evidence-based higher education look like? 

We became interested in how to improve educational outcomes as professors of molecular biology and chemistry, respectively. We, and others, have come to the conclusion that there is a need to change both the way students are taught and what they are taught. Lecturing alone, an anti-Socratic strategy, often presents a fire-hose of information that is, at best, superficially understood. While students can pass exams, the extent of their understanding remains problematic, since it is often unclear what the exams used actually measure.

So how to use evidence-based practices to monitor educational outcomes?  Clearly, what is missing is an objective method to characterize what a particular course claims and what it actually delivers in terms of student learning. At the same time, it is critical to recognize that monitoring educational outcomes is a complex task and easily manipulated for a variety of non-educational purposes. Various “accountability” projects, including both the Bush and Obama administrations’ “No Child Left Behind/Race to the Top” schemes, tend to approach assessment in a ham-fisted, one-size-fits-all manner, with the pernicious effect of eroding support for public education.

Our suggestion builds on the growing ubiquity of the digital collection of student assessment data. With access to the questions students are asked, the answers the students generate, and how these answers were graded, which we refer to collectively as a student’s “ed-data”, it is possible to describe what a particular course aims to teach and what it actually delivers. It enables us to distinguish between memorization-based assessments, that monitor who is paying attention, and assessments that require an accurate working understanding of the materials presented. Using student’s ed-data we can, for the first time, describe courses on their own terms rather than through what may be seen as, and often are, irrelevant or arbitrary assessments. We can focus attention on what the instructor or institution deems important. An ed-data-based analysis would reveal what types of answers are acceptable and so provide direct evidence of the rigor of a class. Evaluating evaluations uncovers what a particular course actually values and delivers.      

At this point, the non-academic might object: don’t all courses with a given title, say genetics or chemistry, teach similar content and don’t all students passing such courses learn more or less the same things, together with the critical thinking skills needed to apply that knowledge productively? Sadly, there is little evidence to support this conclusion. A systematic analysis of student’s ed-data would help identify those courses, curricula, or institutions that value and help foster critical thinking and subject mastery.  

Using student’s ed-data raises a practical question.  Who owns this data–the student, the institution, or the instructor?  We would argue that a student’s ed-data, like medical data, is the property of the student or that, at the very least, they have a right to its fair use. For example, it could be used to establish that courses delivered by less prestigious institutions produced levels of subject mastery similar to more expensive and exclusive alternatives. 

We suspect that instructors and their institutions will robustly defend their claims of exclusive ownership over student’s ed-data. The problem is that analysis of ed-data is the only objective and economical way to establish that a course has, or could have, delivered what it purports to teach, that is, what the student paid for. The issue becomes one of a product claim, a claim that, in the educational arena, must surely be based on what has been learned. 

Assuming ownership and use issues can be resolved, we are left with the practical question, who would perform and assume of cost of such analyses?  There are extant commercial entities, and perhaps a start up or two, that may be willing to provide such services. The cost could even be part of an institution’s accreditation process or third party ranking schemes.

The analysis of student ed-data provides a unique opportunity to distinguish educational excellence from mediocrity and outright malpractice. It would enable low-cost education providers to establish their quality, provide an impetus for traditional institutions to improve on their efforts, and establish a valuable criteria by which to evaluate educational enterprises. 

Mike Klymkowsky is a professor of molecular, cellular and developmental biology at the University of Colorado Boulder and co-director of the CU Teach science and math teacher preparation program.  Melanie Cooper is the Lappan-Phillips Professor of Science Education and a professor of chemistry at Michigan State University. Both are fellows of the American Association for Advancement of Science and recipients of the Outstanding Undergraduate Science Teacher Award from the Society for College Science Teachers/National Science Teachers Association.  Many of the ideas expressed here emerged through a workshop on student education data held at ETH Zurich in June 2013.

Scientific hype, self-aggrandizement and the integrity

Just beginning to think about this topic: clearly related to science education, public gullibility, and pressures that promote careerism over integrity.

In case you are interested, some recent readings:

Trouble at the lab  &  How to Read About Science

Let us (accurately) label everything

There is a call to label foods as to whether they contain ingredients derived from genetically modified organisms (GMOs.)  Not to concern ourselves for the moment with the fact that all modern foods are GMOs, the result of centuries to millennia of human interventions, Craig Schiesley (speaking on the opinion page of the Daily Camera, apparently in his role as a vice-president of a company that stands to gain from such labeling), raises a particularly interesting question, why shouldn’t all foods, that is, anything people are expected to eat, be accurately labelled?

So where is this not done?  Well most obviously in the nutraceutical and nutritional supplement industry, in large part due to (successful) industry lobbying against product labeling and quality control measures.  In fact these groups succeeded with the passage of a 1994 Federal Law that allows nutritional supplements to “be sold and marketed with little regulatory oversight, and they are pulled from shelves generally only after complaints of serious injury.” 

 Two recent reports point out the problem quite dramatically, and one suspects in a way that the “natural foods” industry would rather ignore.  

The first is a scary report in the New York Times (http://nyti.ms/1hbvTk6) that summarizes an article by Newmaster et al  (http://www.biomedcentral.com/1741-7015/11/222/abstract) that reports that a high percentage of herbal supplements samples not only did not contain the herbs claimed, but often had replaced them with toxic alternatives.  

The second, a paper by Bruce Ames and co-workers some years ago (see http://www.pnas.org/content/87/19/7777.full.pdf, see also http://www.science20.com/) concluded that “99.99% (by weight) of the pesticides in the American diet are chemicals that plants produce (quite naturally!) to defend themselves.”  Since many of these chemicals are, in fact, proven carcinogens while to date no GMO-derived substance has been found to significantly impact human health, shouldn’t the presence of these natural, but carcinogenic, chemicals be disclosed?   

Assuming for the moment that White Wave, Whole Foods, and other companies are sincere in the efforts in support of GMO labeling, when will they begin lobbying for the accurate labeling of “natural foods” as well?  

now published in the Boulder Daily Camera:  

On reading Lee Smolin's Time Reborn and thinking about the interactions between biology and physics

Having read the book, and a few reviews, I find myself particularly surprised by the disconnect between what (at least theoretical) physicists are concerned about and what I understand to be the concerns of most scientists, and perhaps most educated citizens.  

It seems rather too obvious that we live in the universe we live in, and that is (apparently) the only universe that we know with any certainty to exist.  

If other universes exist but are inaccessible to study, it is a waste of time (scientifically) to think about them. What does "fine tuning" initial conditions mean unless there is direct evidence that alternatives are actually possible? 

Perhaps I think this way because my prosaic mind is engaged by the real rather than the imaginary.  Such digressions are found everywhere in Smolin's book (and it writing of other physics popularizers), but they seem more like empty and pointless philosophizing, not science

This can be see in speculation of the universe and life.  As far as we know life, and intelligent life, is unique to earth, and arose only once; so speculation and generalization about the implications of life elsewhere in the universe seems premature at best (and descends into magical thinking at its worst.  

That said, it is imaginable that actual evidence of life outside the earth could be found and that would be a truly revolutionary discovery.  

As a snippy aside, there does not appear to be much understanding about how evolution works (and its basis on reproduction) and some of the digressions into the chemical seem incorrect.  All atoms do attract one another (through London Dispersion Forces / van der Waals interactions) and molecular systems are structured at the microscopic level (which gives rise to various entropic drivers)(see Chapter 17).   

Aside from that, there is just too much "wishful disembodied thinking" which, outside of silly science fiction, is neither interesting or compelling.  

Learning analytics, formative assessment and student data banking

If there are no targeted hints that students can ask for, if there is no targeted feedback, if there is no well-designed question, there is no semantic data.

There is a very interesting blog post (and an entry into the learning analytics universe that makes a number of important points about the types of data we need to capture from students in order to i) help them learn through coherent and useful suggestions, as well as to ii) to generate objective measures of what learning outcomes various courses and curricula (including MOOCs) actually achieve, as opposed to what they claim or presume to achieve.    

What can we do when we are empowered with this sort of semantic data and analysis?  Here are just some examples:  ... Use semantic analyses like learning curve analysis to identify areas where content needs to be improved

It also highlights the need for formative assessments that go beyond multiple choice questions, something that beSocratic is uniquely suited to do.  

Clearly something we need to incorporate into a useful educational tools (and student education bank) system. 

Thinking about inheritance and epigenetics

There is an interesting RadioLab podcast on inheritance that is worth listening to.  It discusses the differences between Darwinian and Lemarckian mechanisms of inheritance and more.  

They discuss the case of the midwife toad and the work of Paul Kammerer.  One part of this involved work that suggests the role of epigenetic inheritance (changes that do not involve mutations in the DNA, but rather hereditable changes in gene expression.)   

The whole idea of the "Central Dogma" associated with molecular biology (namely that information moves from DNA to RNA to protein, but not backward from protein to nucleic acid, seems pretty clear.  BUT, it is also true that a behavior can influence selection.  This is the topic of the book and the video lecture: Evolution in four dimensions. by Eva Jablonka and Marion J. Lamb.

Sadly, there are some errors in the Radiolab: Inheritance pod cast.  For example that methyl groups are "sticky", and that the transcription factors "knock off" methyl groups is weird (and wrong, at the molecular level).  Both processes are mediated by enzymes (histone methyltransferases and demethylases).  In fact, there are a number of modifications of chromatin, all of which are enzymatically mediated.  

Also interesting is the RadioLab episode on Stochasticity.  The section that starts around 43 minutes in is relevant to gene expression.  

MadSci Network: Does the DNA contain the codes needed for shaping body organs?

I love composing answers for the MadSci Network and here is my latest here [link].

The challenge to answering such questions is to try and place the answer in a coherent and accessible context.  While it is hard to know whether a particular answer actually succeeds in doing that, it certainly gets one thinking about how to address complex questions and looking around for compelling references and resources.

For this answer, I found an amazing video on polydactyl, which could be viewed as a beneficial mutation (assuming that six fingers and toes are better than five!) 

As usual, the Onion get it right!

link to the article!

Viruses within Viruses & the politics of Anti-Science

One of the more amazing discoveries of late are the giant viruses (first identified in 2003)(for more details, read reviews here and here).  These miniviruses have been found to infect various types of amoeba.  

More amazing still, these giant viruses have their own parasites [read general description here and a scientific description here.]   Cells infected with the giant virus are infected with a second type of virus, known as a virophage, which replicates only in virus infected cells.  Another example of how ecological niches, no matter how small or obscure, can be populated by replicating entities.  

On another, less intellectually entertainingly front, it is increasingly amazing how both scientific denialism and active anti-scientific posturing and policies are coming to dominate American political discourse, particularly in situations where they are seen to threaten fundamentalist religious doctrine (or in Boulder, CO, self-centered ignorance, as illustrated by the anti-vaccine and anti-GMO movements)[check out the panic virus blog].  

This recent article Shawn Otto in Scientific American (Antiscience beliefs jeopardize U.S. democracy) is particularly cogent.  In part scientific denialism may arise from the naive view that science equals truth, and so poses a direct threat to belief and in part from a failure of our education system to help students understand the process by which science accumulates and integrates useful knowledge into a coherent world view. Perhaps more emphasis on critical analysis and less on often superficial "inquiry" would help here.  

In any case, it is scary to see the US return (at least in certain regions) to medieval patterns of thought -- I wonder when witch burning will become part of a political party's platform.  Probably not long, given political positions that explicitly deny global warming [read more here].   

Is embryology a lie "straight from the pit of hell"?

Two remarkable stories from today's paper, one about a Republican Georgia representative  Paul Broun who appears to believe that, 

"All that stuff I was taught about evolution and embryology and Big Bang theory, all that is lies straight from the pit of hell. "

What is truly bizarre is that this person on the House Science, Space and Technology committee.    I am particularly confused by, and would love to understand the logic behind, the  relationship between embryology and hell.  

The second is a quote from an Arkansas state representative John Hubbard that slavery was a blessing in disguise and that all Muslims should be deported, similar views appear to be held by Republican state house candidate Charlie Fuqua.  Their views on Mormons, Jews, atheists, and perhaps all Democrats, etc, are not recorded, but Fuqua claims that 

"I think my views are fairly well-accepted by most people".

Also finished an interesting book that is relevant, "The Rocks Don't Lie: A Geologist Investigates Noah's Flood" by D.R. Montgomery.   

Evolutionary contingency (in the lab)

Bount et al (2012) describes a very interesting study of the appearance (evolution) of the ability of the common gut bacteria, E. coli, to utilize citrate in the presence of O2, something that E. coli normally cannot do. This work was based on the original observation that described the evolutionary origin of citrate utilizing E. coli (Bount et al., 2008).  The Lenski lab has been growing (and freezing) samples of this population for over 40,000 generations (here is an interesting paper on how these populations have been used to study competition within a population (Le Gac et al., 2012).  

The evolution of the ability to utilize citrate in the presence of O2 in E. coli involved "potentiating mutations", which occurred in one specific lineage somewhere around the 20000th generation of the experiment.  These mutations have no (as yet discovered) overt phenotype on their own. 

Later on in this lineage, around the 31,000th generation, there was a mutation that involved the duplication and generation of a novel fusion protein derived from the citrate-succinate antiporter (a membrane-transport protein of a type we discuss generically here in biofundamentals).  This mutation allows the cell's carrying it to import and grow (albeit) poorly on citrate.  Subsequent mutations improve the efficiency of citrate metabolism.  

What is interesting is that because they had "frozen ancestors", Blout et al could "replay" their evolution, and ask, when new citrate utilizing lines arose (which they did), whether they had similar (although not identical) mutations to that found in the originally identified lines.  Interestingly, they did.  

Now it becomes an interesting question whether, given that E. coli is usually defined in part by its inability to grow on citrate under aerobic conditions, whether the appearance of cells, derived from E. coli, but able to grow on citrate in the presence of O2 represents a new species or not.  

Evolutionary thinking and "just so" stories

It is all to easy to tell satisfying stories about how various traits have come to be:  here Anthony Gottlieb in the New Yorker writes about just so stories about the origins of human behavior (and consciousness).

The essay makes a number of points that I have tried to emphasize in class and is worth reading.