The hen keeps laying (American education shortfalls, continued)

A new survey of high school science teachers, reported in Science (Berkman and Plutzer, Jan 28, 2011, pages 404-405), and described here, shows that many high school teachers do not teach the scientific method or approach it very well in the context of the 'debate' between evolution and creationism.  Many teachers teach outright creationism, while about 60% hedge their bets about the subject.

The authors express it this way:

Creationism has lost every major U.S. federal court case for the past 40 years, and state curricular standards have improved....But considerable research suggests that supporters of evolution, scienfitic methods, and reason itself are losing battles in America's classroom, where instruction in evolutionary biology 'has been absent, cursory, or fraught with misinformation'.

Berkman and Plutzer, Science

We know there is a problem of under-educated teachers generally, low rigor and low admission standards in schools of education, low status and low pay in the jobs.  We know American kids are not getting nearly the rigorous level of training and work ethic that they may need in the future, given what is happening in other nations and the increasingly technological nature of global society.

As scientists, we can't react except with concern about the thin training in evolutionary biology that US students are getting.  But there are two things that all of us should ask, that might make it seem a less dismal situation than it seems.

1.  First, how much does it matter?  The senior generation in this country (of which we're a part) were trained without much, or even specifically with no, high school evolutionary training.  For various reasons, including the pressure from fundamentalist Christian (or so they self-describe, though they may not have read even the Sermon on the Mount which tells what Christians should be about in their lives), evolution was simply omitted from texts.  Even some introductory college Biology courses had relatively little evolution--a chapter, say, along with anatomy, classification, basic physiology, Mendelian genetics, and so on.

Yet this same generation is responsible for what amounts to a massive gain in knowledge across the life sciences, including evolution.  So is our concern about high schools more than just our taking sides in the cultural battle now under way between the 'left' and 'right'?  Does it really matter if most people don't believe in evolution?  For those who need to know or use evolutionary perspectives, things are motoring along very well these days.

2.  Secondly, some people choose to opt out of a purely material, experimental, empirical view of the world.  They depend instead on mysticism, externally derived answers, reassuring dogma, or the comfort of the tribalism of the right.  If that's how they wish to live their lives, and they don't want their kids exposed to what they object to in these very fundamental worldview areas, so what?  Why not recognize that this is the 'age of science' only in some areas of life, for many people?  Wouldn't it be just as good, in this particular sense, to insist that, at least, high school science teachers understood their biology itself?  The things that people need to know about, like how genes work, how infectious organisms work, the diversity of living Nature, structures of human bodies and the nature of plants, etc.

Where are the teachers?
In our Honors class of 19 bright, thoughtful students last fall, in discussing this subject, the students all nodded in agreement as we pointed out the failure of our educational system (some of which they, as college seniors, had experienced only a few years earlier).

Then we asked:  "OK then, so how many of you are going into teaching as your profession?"

The silence was deafening.  The brightest students just aren't going to be teachers.

Whose fault?
It is too easy to feel self-righteous and rue the absence of evolution in school curricula.  But stepping back from our legitimate emotional engagement with the idea that the truth, the whole truth, as seen from the scientific worldview should be taught, suggests that the debate is about other things in our culture than whether the general public really needs to understand evolution as we scientists see it.

After all, within our own families, we have to make up at home for what the less than competent teachers do to or for our kids in all the subjects they are taught.   There doesn't seem to be any legitimate empirical doubt that evolution is a fact of and about life.  Fully educated people should realize that.  But you can live perfectly well without it, as our benighted population shows, and for many the comfort of answers is worth all the truth that Darwin ever wrote.

At least, this is one way to ponder the strangeness of this persistent issue.

Americans lay another egg in science education!

We've posted a number of times before about our educational system.  Here's a blurb from another story on the subject in the New York Times. 

On the most recent nationwide science test, about a third of fourth graders and a fifth of high school seniors scored at or above the level the federal Department of Education calls proficient, according to results released on Tuesday.

 And, a new book, discussed at length again in the NYTimes,

“Academically Adrift: Limited Learning on College Campuses” (University of Chicago Press) by a professor at New York University and another at the University of Virginia, attempts to answer questions [about how much students learn and how they spend their time] in a systematic way — and, as its title suggests, its findings suggest reason for concern.

In the book, and in an accompanying study being released Tuesday, the authors followed more than 2,300 undergraduates at two dozen universities, and concluded that 45 percent “demonstrated no significant gains in critical thinking, analytical reasoning, and written communications during the first two years of college.”

So, we conclude that Americans hardly do any studying, hardly learn anything in college, and can hardly read and write when they graduate from high school.  

Of course, that's an exaggeration, but when our noble society can't agree that climate is changing anomalously, or whether vaccines cause autism, or whether evolution occurred, then it's time to take the problem seriously.  The idea that the wealthiest country at any given time is vulnerable to becoming lazy and self-satisfied is not exactly new.  It was written about even by Romans at the height of the Roman Empire (e.g., in satires by Juvenal, at about 115 AD).

Now, universities are dropping programs that 'don't pay', while pouring money into the 'real' subjects like science while visions of overhead dance in their heads.

We recently saw that to qualify as a teacher in Scandinavian countries, you must graduate in the top third of your university class.  By contrast, who do you think populates our schools of education?

We need to insist that students actually do work and come to class, we must be able to fail them if they don't, to stop having students evaluate whether they 'like' our classes, and to have teacher trainees learn more about science than about how to make science bulletin boards.  We need to de-emphasize the precious 'research' that we flatter ourselves is so important, and return faculty to a concentration on teaching.  And if we can afford 90" TVs for every bathroom in the house, we can afford to pay more taxes to pay teachers enough to encourage good students to become them.  There needs to be a sense of seriousness about this, because in case you haven't noticed, improving K-12 will take 13 years to bear fruit!

Just because a society is technological or scientific doesn't guarantee that it will be a good society, and the history of empires suggests otherwise.  But the odds would at least favor a better quality of life for its citizens.  Maybe if research scientists weren't paid so munificently to do incremental, me-too work, and teachers were paid more to build our capability future, these problems would be ameliorated.

But probably not.  Probably, we are so used to our luxuries that we will let ourselves sink slowly into history.

A big congratulations to Holly!

We want to post a brief message of congratulations to our great co-conspirator on MT, Holly Dunsworth. She has just taken a faculty position at the University of Rhode Island. We wish her well and hope, of course, that she'll continue to have the time to make her very interesting, insightful, and amusing contributions to these conversations.

"and I want no other fame": The tale of the butterfly novelist--Vladimir Nabokov

Lolita may be a story for adults only, but Vladimir Nabokov told another story that can be enjoyed by all.  It appears to be an amateur's triumph, based on a correct guess that was before its time.  No definitive data could have been assembled to tell the tale while Nabokov was alive.  But thanks to the very regular, clocklike way that DNA accumulates variation among descendants over time, the guess seems to have been confirmed with current methods.

Polyommatous blue, by Lilly M.,
Wikimedia Commons

The immediate story is told by Carl Zimmer in the NY Times, but is based on a paper just published in the Proceedings of the Royal Society.  If Lolita was about a man in pursuit of a (too-)young person he obsessively adores, the story of the Polyommatous blue butterflies is one of a man chasing a group of old species that he obsessively adores.

It has long been widely known that Nabokov was a persistent, knowledgeable, dedicated if technically amateur butterfly enthusiast.   It was also long known that he did extensive work on the structures and relationships of the species that came years ago to be known as 'Nabokov blues'.  You can read about this, with maps and illustrations, in a fine book by Kurt Johnson and Steve Coates, Nabokov's Blues: The Scientific Odyssey of a Literary Genius, Zoland Books, 1999.  Johnson is a lepidopterist, expert in these butterflies.

They write "Where South American temperate life-forms had come from became a compelling question from the earliest stages of the continent's exploration." Much of their book, which is a readable, popularized narrative, tells of the efforts by Nabokov and others then and since, to understand the taxonomy--species relationships--among the South American blues and their relatives elsewhere. 

The traits of species available to Nabokov and others did not neatly correlate with their locations in the Andes or down into warmer environments.  That meant that some nearby species seemed too different to have had an evolutionarily recent common ancestor.  And, if they did not, and for the group as a whole, where were their origins then?

This issue had arisen out of the work of many naturalists going back at least to the early 1800s.  From an evolutionary point of view a couple of explanations were plausible.  One is polyphenism: species can have very different morphology or behavior depending on the individuals' local environment or genotypes.  And there is mimicry: distantly related species can come to resemble each other by natural selection. But that will only affect the mimicked trait, leaving the species' other traits less similar.  But in any case how did these butterflies get into the Americas?  There were various suggestions.  One possibility that Nabokov entertained was that the species had expanded into the Americas from Asia, by way of the Bering land bridge--that is, into South America from the north, what is now the Arctic.  The North American ancestral species may then have died out, leaving only their South American descendants.

The story in the Times, like news stories tend to do, makes this seem as if Nabokov got this 'blues' story out of the blue, so to speak, and was insistent on this view.  Indeed, Vila et al. in the Proceedings of the Royal Society paper, do the same:

The radiation of Polyommatus blues in the New World was first appreciated by the famous writer Vladimir Nabokov when he was working as curator in the Museum of Comparative Zoology at Harvard in the early 1940s.

And:

Our results show that Nabokov’s inferences based on morphological characters (primarily of the male genitalia) were uncannily correct in delineating not only species relationships but also the historical ordering of these five key events in the evolution of New World blues.

But even brilliant discoveries occur in a context, and people rarely take immovable positions when the evidence is ambiguous. Johnson and Coates go to great lengths to describe the long history of South American biogeography--the distribution of species over space and how it gets that way.  Ideas of species rafting across vast oceans had been suggested, and when continental drift was discovered, land connections between South America and Asia and Africa provided a possible explanation.  But climate change and a northern connection was another possibility.

There's no taking away from Nabokov that he was diligent and insightful, but others were thinking similar kinds of things, about the biogeography of many different species besides butterflies.  As he said in our title quote, he wanted to be known for this work, and properly so.  But at least Johnson and Coates present the history as one of many widely discussed possibilities by many different investigators--including the Northern origin of South American species generally.  Nabakov appears to have weighed different possibilities, and his preferred hunch, given the set of specimens and knowledge available to him, appears to have been right. 

The new paper uses extensive DNA sequence to resolve these tales in detail, data that of course was unavailable in the past.  The authors draw species-relationship trees based on the degree of sequence identity.  The times of splitting among the species were estimated by the number of DNA sequence differences that had arisen.  Many of the branches were  deep--large numbers of sequence variants, suggesting ancient splits, relative to other nearby species in South America.  Since the nearest relations in these instances were in Asia, the American species must more than once--in different expansion waves--have come from Asia.

Paleoclimatology and continental drift, and known climate tolerance patterns in the butterflies made it possible for the butterflies, over many generations, to expand here from Asia and survive in the warmer climes that existed episodically over an estimated period of 10 million years.  DNA analysis can even work when there has been selection for polyphenism or mimicry.  That's because such selection would distort relationships only at the genes involved in those particular traits, but genomewide variation will accumulate in a pattern that corresponds to the species' histories.  Indeed, DNA evidence could provide evidence for it, by showing that though some species looked similar, they really were not very close relatives overall (genomewide).

Here is an application of genetics that is entirely appropriate, that makes it possible to draw convincing inferences, when morphological or behavioral analysis may not.  A tree of descendant genomes accumulates variation probabilistically, so little can be said from observation of just a few nucleotides.  But these erratic patterns even out when thousands of nucleotides are compared, as these authors did.

Even so, let's keep in mind that genetic analysis is not exactly a scientific miracle.  If genes cause traits, then traits will diverge over evolutionary time in ways that generally reflect underlying genetic divergence.  That is why, in effect, Nabokov was indirectly using genomewide genetics to draw his conclusions--he just couldn't see the genes directly.  This is in essence how Darwin did what he did, too, without a good understanding of what inheritance really was.  But what we now have is explicit genetics to replace Nabokov's inferences from aggregate, implicit genetics. And this can get around problems of phenotypes that don't fit the history.

DNA is more specific and in the sense of time estimation much more rigorously useful than morphology and behavior.  As in forensic applications of genetics, that match sequences to their owners as in crime investigations, analysis that relies on the clear properties of genomes can tell stories that are as powerful as the compelling novels that Vladimir Nabokov wrote.  And he is justly famed for both!

Western intellectual history....all roads did not lead to Rome

As the old saying goes, you may be able to sit sipping espresso on the Via Veneto in Rome and eventually everyone you ever knew will pass by.  All roads may once have led to Rome, but it didn't stay that way.  In terms of knowledge, intellectual pursuits, and science, for many centuries no roads led to Rome.  Instead, those activities occurred elsewhere.

We posted some time ago (here and here) about an Islamic philosopher born in the 14th century in Tunisia, Ibn Khaldun.  He had a lot to say about what we now call social science, as well as about evolution, and he hasn't been forgotten.

Here, for example, is a picture taken just the other day in Ramallah, Palestine, where our daughter, a violinist, and her friend, a cellist and photographer, are teaching at a music conservatory for kids for the year.  We like this photo because it can be read in a way that is both droll and draws attention to the history of scientific thought.

In the early Christian through the Middle Ages, theological dogma replaced the kind of open investigation in areas of thought and science.  That is one reason that long time period is called the Dark Ages.  Classic writings were lost, or lost to the awareness of Europeans.  But the rise of the major Islamic caliphates led to the rescue, study, and translation of those classic texts (some of this in Corcoba, the Spanish Islamic center).  But translation was not all that happened in the height of Islamic culture.

Islamic scholars of all types, including the social and anthropological thinker Ibn Khaldun, wrote works that were later influential when the 'west' awoke, and broke out of Catholic dogmatism in the Renaissance period.

Of course, Khaldun is still highly and rightfully honored, and perhaps more so in Islamic lands than elsewhere (though he certainly is known to Anthropology). As we described in our earlier posts, Khaldun developed one of the first systematic theories of sociocultural evolution, and wrote presciently about the origin of life and biological evolution, too.  Here, unintentionally of course, the sign suggests that Rome is 'that way', far away, while enlightenment represented by Khaldun, is everywhere!

The genetics of olfaction -- is a rose a rose by any other nose?

Laura Spinney writes about the genetics of olfaction in The Independent this week, and about population variation in what we can smell.  The genetics of olfaction have been pretty well worked out; in fact, the 2004 Nobel Prize in Physiology or Medicine went to Linda Buck and Richard Axel for this work.  But there is much still left to understand. 

Genes for olfactory receptors (ORs) comprise the largest gene family in the mammalian genome -- at about 900 genes and pseudogenes in humans, they make up approximately 3% of our total genome. On average, we've each got about 400 working olfactory receptor genes, and the rest have accumulated enough mutations to no longer be functional, and are now pseudogenes.  This is not quite accurate, because we are diploid so that we actually have about 800 OR genes, 2 copies of the 400.  Of the hundreds of these genes, many are polymorphically pseudogenes, meaning their sequence works in some copies in the population, but has been mutated out of function in others.

In addition, the copies we each have of each of our functional OR are themselves highly variable in their odorant binding pockets (the part of the receptor that binds to odorant molecules that float by in the nose).

"When I give talks, I always say that everybody in this room smells the world with a different set of receptors, and therefore it smells different to everybody," says Andreas Keller, a geneticist working at the Rockefeller University in New York City. He also suspects that every individual has at least one odorant he or she cannot detect at all – one specific anosmia, or olfactory "blind spot", which is inherited along with his or her olfactory apparatus.

Each olfactory receptor responds to several odorants.  But with so many genes, how on earth could we actually distinguish what we're smelling?  The answer is remarkable and one of the most interesting unsolved problems in genetics.  Our hundreds of OR genes are located in many different clusters of a few to hundreds of adjacent duplicate OR genes.  And we have two copies of each.  But in each individual olfactory neuron, only one of these hundreds of genes is expressed!  The other 799 genes, all over the genome, are inactive.

From Genetics and the
Logic of Evolution,
Weiss and Buchanan, 2004

Further, neurons expressing a given OR are in some way guided by that choice to collect in OR-specific locations in the olfactory bulb of the brain.  That's what makes it possible for the brain to tally what specific receptors have been triggered.  That is, the binding of an odorant to its receptor triggers its perception in the brain.  The wiring pattern is to some extent, at least, conserved among individuals, so in that sense we may share not only the ability to identify, say, 'lemon', but to experience it in somewhat similar ways.

Most odor perception involves a combination of signals from a number of different receptors.  And, some of those receptors may be non-functioning pseudogenes in some people, and if the subset of pseudogenes differs, the odor perceived will be different.

That genetic variability is reflected in behavioural variability, as Keller, with colleague Leslie Vosshall and others, recently demonstrated when they asked 500 people to rate 66 odours for intensity and pleasantness. The responses covered the full range from intense to weak, and from pleasant to unpleasant, with most falling in the moderate range – a classic bell curve in each case.

There is also variation in how intensely people can smell.  Some people are born with no ability to smell, while others are acutely aware of odors.  This may have nothing to do with odorant receptors, but instead how efficiently the odorant signal is transmitted to the brain.

One of us (Ken) spent a sabbatical in England working with Manolis Dermitzakis at the Sanger genome institute outside of Cambridge, trying to find genomic DNA sequence 'signals' that might help explain the extensive monoallelic and monogenic expression of only one OR per olfactory neuron.  Unfortunately, the search was frustratingly unfruitful. In fact, earlier we had done a study in the Pennsylvania Amish, collaborating with one of the experts cited in the Spinney story to see if, in this classic founder-effect population, we could work out the genetics of the ability to identify specific odorants, for which the ability to smell seemed, in other studies, to be polymorphic.  We couldn't find any pattern, because essentially everyone could smell all the test odorants.

The unusual expression pattern of this huge gene family, and the bookkeeping by which its detection of complex odorants allows us to identify our surroundings with a great deal of reliability (and, much more so in other species like dogs, who use the same system) is one of the remarkable, and incompletely understood, facts of genetic life.

The value of education?

Here is another instance of the relationship -- or not -- between education and an educated public.

Just a slim majority of Americans -- 52 percent -- think vaccines don't cause autism, a new Harris Interactive/HealthDay poll found. 

Conversely, 18 percent are convinced that vaccines, like the measles-mumps-rubella (MMR) vaccine, can cause the disorder, and another 30 percent aren't sure. 

The poll was conducted last week, following news reports that said the lead researcher of a controversial 1998 study linking autism to the MMR vaccine had used fraudulent research to come to his conclusion.

The poll also found that parents who have lingering doubts about the vaccine were less likely to say that their children were fully vaccinated (86 percent), compared to 98 percent of parents who believe in the safety of vaccines.

For many years many people did not have their children vaccinated against childhood diseases like measles, mumps, or pertussis (whooping cough) because there were allegations that the vaccines were toxic in some ways and could cause autism.  Mercury is in thimerosol, a vaccine preservative, and the MMR vaccine was said to have some other brain-damaging properties.

Figure from BBCnews.com

The absolute risk was low but the consequences when the problem arises are lifelong and can be devastating.  So children were going unvaccinated, but this itself had consequences.  Directly, the unprotected child could suffer harm from disease itself, and some children have apparently died as a result.  Indirectly, a large unvaccinated subpopulation could provide a transmission reservoir for the pathogens.

Many expensive studies were carried out to see if the evidence for the connection between vaccination and autism was real -- which meant a lot of research energy thus diverted from other problems.  Lawsuits were instigated by angry and devastated parents against the producers of the vaccine, who naturally denied any liability.

Well, as we've posted earlier and you've seen in the news, the original Lancet paper was apparently very flawed, if not indeed a fraud, with faked or at least incompetently analyzed data.  The Lancet withdrew the paper, the author was disbarred from medical practice in Britain, and so on.  It seems now that there is consensus about the false nature of the first result.  This has been widely publicized, with great sighs of relief by the established infectious disease community: now, finally, we can get with the modern program and have every child vaccinated and remove the burden of these various diseases!

But no!  This new survey shows that a substantial fraction of the population still believes that the vaccines are dangerous.  Some may feel there's an Establishment conspiracy to silence the risk to feed the greed of Big Pharma.  Some may just not accept the recent outcome because they're so fearful for their children in regard to autism.  And there is the contributing problem that the actual causes of autism remain largely unknown.

So what is the role of education in this kind of situation?  Risks are low (even if they exist) and that means it is difficult to estimate, assess, or dismiss them.  And peoples' sociopolitical views, including suspicion of government, are deeply entrenched.  Conspiracy theories, and advocacy group solidarity, conspire to reinforce tribal feelings of us vs. them.  Since everyone, even scientists (believe it or not) have their own vested interests, it is not easy to define what is 'education' and what is 'propaganda'.  The emotional side of this keeps people in their camps.  Unclear causation is partly responsible.  Low risks or slow risks are very problematic and play into the hands of all of us, in the way we view the world: climate change, evolution, environmental pollutants, and so many other similar issues reflect this.

When we give a lecture in class or write papers, we believe that by educating our students or readers, we are helping in societal progress and enlightenment.  But we're flattering ourselves, at least to some extent.  Knowledge, and action based on knowledge, are vague areas in society and the tide of action is the result of many factors, of which our teaching and writing are but a part, and sometimes perhaps even just a small part.

Bacterial husbandry

Even amoeba are more complex than we generally think.  A paper in this week's Nature, written about on the BBC site among other places, describes the social bacterium Dictyostelium discoideum, as having 'a primitive farming symbiosis that includes dispersal and prudent harvesting of the crop.'  That is, they farm bacteria. 

D. discoideum life cycle, from
Weiss and Buchanan, 2009

D. discoideum are a slime mold.  These amoeba live singly apparently quite satisfactorily until they sense a dangerous depletion in the local bacterial food source, at which time they signal to each other that it's time to get together and move to a lusher site.  They do this by amassing into a multi-celled organism, a slug, that then migrates -- and now it turns out that some of the cells take their own food source with them.

When they reach greener pastures, they form a fruiting body, the stage in the life cycle that produces spores. Among other things these creatures do that requires cooperation, a fair number of the cells (20%, according to the Nature paper) of the fruiting body undergo apoptosis, programmed cell death, to sculpt the organism, which means that not every cell -- and the cells come from different clones, so are not all identical -- gets to donate genes to the next generation. Why a single-celled autonomous bacterium would apparently give up so much to contribute to the greater good is a bit of a mystery to strict Darwinians, just as altruism among primates remains a mystery, but it is certainly good for the group.  There is some evidence (from Joan Strassmann's lab, the same lab that reports this farming behavior) that cells from some clones are more likely to 'cheat' than others, by contributing fewer cells to the part of the body that is most likely to undergo apoptosis, but this is apparently a rather complex trait genetically.  Other investigators have looked for this kind of behavior (we think it is a big mistake to use culture-bound terms like 'cheating' -- or even 'farming', which is less loaded but still anthropomorphic -- but that's another matter).

In any case, all of this complex behavior requires signaling and communication -- cooperation -- and this has long been known.  But the fact that they also practice bacterial husbandry has not.

We show that about one-third of wild-collected clones husband bacteria through the sporulation and dispersal process. We call these clones farmers because they carry, seed and prudently harvest their food, but the farming is primitive because no active cultivation is known.

Strassmann et al. confirmed that infection of the amoebae they called farmers was not simply accidental by treating farmers and non-farmers with an antibiotic and then assessing their consequent behavior when placed in an infected site again.  The farmers took up bacteria again, and the non-farmers remained bacteria-free.

Carrying bacteria seems to be a clone-specific trait, and there are other differences between farmer and non-farmer clones, such as that farmers consume less of the bacteria in a given site before they signal that it's ready to go, presumably to retain sufficient bacteria for transport to their next site.  And, farmer clones migrate shorter distances than non-farmers. 

This is all very interesting, in light of recent stories about leaf cutter ant colonies that accommodate their aging colony mates, and bees that can learn, and a recent story about dogs' ability to learn hundreds of words.

With this kind of demonstrated complexity -- 'well over 100 diverse genes' for cheating in tiny slime mold, for heavens' sake! -- it is surprising that anyone could find, much less would advocate the idea that there were genes 'for' behavior.  And that is particularly true in an organism with culture and learning and the plasticity that comes with learning that is known to happen in humans.  At the same time, with many contributing genes, the common story is that there may always be genes that if inactivated can 'break' the trait, or that can have minor effects on it.  Working out the distribution and importance of such effects, and their evolution, is a substantial challenge now that we can identify the variation at the gene level.

Eugenics and other genetic risks, continued

Again, we return to a topic we said months ago we'd follow up on, but never did.  Holly touched on it here recently in her post about genetics and intelligence -- and, in fact, here's a quick followup on that subject; in particular, scroll down a bit in that link and read the sidebar on what happens to the brains of London cabbies -- and we wrote about it yesterday.  But, as the issues won't go away, and yet another paper is out this week in PNAS by the same characters using the same set of data, we think a topic we began to write about months ago is worth another look.  Especially given our focus this week on randomness and probability, and once again on genetic determinism and eugenics. 

Back in October, we, and many others, blogged about the paper by Fowler et al. that reported that genes largely determine political ideology.  The data set Fowler et al. mined for that paper, have mined before, and mine again for their PNAS paper this week, is the 2,600 subjects included in the National Longitudinal Study of Adolescent Health, a study of 20,000 adolescents in grades 7-12 in 1994, and followed up in 2001-2002 when students were 17-24 years old, and a subset more recently followed up with biomarkers, including DNA.  The study was designed to look at the effects of social context on health behaviors like seat belt use, drug use, sexual activity, nutrition and so on.  

The small subset who donated DNA were genotyped for 7 candidate polymorphisms. 

The initially targeted candidates are the dopamine transporter (DAT1), the dopamine D4 receptor (DRD4), the serotonin transporter (5HTT), monoamine oxidase A (MAOA), monoamine oxidase B (MAOB), the dopamine D2 receptor (DRD2), and the dopamine D5 receptor (DRD5).

Why these particular genes were   chosen is not something we could easily find but presumably it has to do with previous reports of their association with particular behaviors.

A cursory literature review shows that using these genetic data, researchers have, to date, found 'the warrior gene', that is, an association with DAT1 or DRD2 and gang behavior and serious delinquency, a link with low grades and DAT1, a dopaminergic gene, and that "students with a single, DRD4 variant had significantly lower grades in English and math, but only marginally lower grades in history and science", the genetic basis of victimization, the genetic basis of our place in a social network, that is, popularity, an association with genes and smoking behavior, as well as the links with political behavior and ideology reported by Professor Fowler et al.  And, the new study by Fowler et al. reports that people who share the same DRD2 allele associated with alcoholism tend to be friends.  

Ok, let's just take the DRD4 gene.  This gene that has been associated with numerous behaviors previously, including attention deficit disorder (the association is with a 48 basepair VNTR, or variable number of tandem repeats, in exon 3), novelty-seeking (that exon 3 VNTR again), externalizing behavior in toddlers (exon 3 VNTR), temperament in children with the exon 3 repeat allele if they are given poor quality parenting (or 'differential susceptibility to child rearing'), aggression at age 4 (long repeat), attachment disorganization in infants (48 bp repeat), to cite just a few of the studies reporting an association of behavior with this long repeat in this dopamine receptor gene.  And there are plenty more.

The idea, as proposed by Hamer et al. in 1996 in the precedent-setting Novelty Seeking study, was that the number of repeats in the gene affects the structure of the receptor, thus how dopamine binds to it, and so the efficiency of neurotransmission.

But now there's this, a 2010 genomewide association study by Verweij et al.:

Variation in personality traits is 30–60% attributed to genetic influences. Attempts to unravel these genetic influences at the molecular level have, so far, been inconclusive. We performed the first genome-wide association study of Cloninger's temperament scales in a sample of 5117 individuals, in order to identify common genetic variants underlying variation in personality. Participants’ scores on Harm Avoidance, Novelty Seeking, Reward Dependence, and Persistence were tested for association with 1,252,387 genetic markers. We also performed gene-based association tests and biological pathway analyses. No genetic variants that significantly contribute to personality variation were identified, while our sample provides over 90% power to detect variants that explain only 1% of the trait variance. This indicates that individual common genetic variants of this size or greater do not contribute to personality trait variation, which has important implications regarding the genetic architecture of personality and the evolutionary mechanisms by which heritable variation is maintained.

No association with DRD4 and Novelty Seeking.  And no association with DRD4 and Novelty Seeking was found in 2 samples in New Zealand, and while some studies in birds have shown an association with a DRD4 variant and exploratory behavior, it isn't consistently reported.  A study of one of these repeat polymorphism has shown that the effect of the variation depends on your socioeconomic status: negative for low SES, positive for high SES.  Context determines what the genotype determines.

Now, all the usual caveats that we mention over and over again apply here -- the definition of the trait may vary enough between studies that they are comparing apples and oranges, and the association may in fact be real in some populations and not in others.  But GWAS should find genes with large effects, and the Verweij et al. study did not.

What if that's because the trait is due not just to a single gene but to gene-and-environment interaction? Would a GWAS still pick it up?  This would depend in part on the size of the study sample and the amount of environmental variation among those sampled.  GWAS detects net results, basically, especially if the environmental factors are not known or measured.  Large effects found in a GWAS may be because there was some tractably invariant environment among the sampled people, that may not be present in another sample, and the same allele may not have its purported effect in those data.

The association of this gene with political ideology could be real.  Or it could be a chance positive result due to multiple testing or other statistical aspects of the sample.  Or it could be real....but only ephemeral, changing rapidly with societal context.  The notion that we can predict these kinds of things very meaningfully is one we should be very circumspect about.  Even after extensive (and expensive), very technically sophisticated studies (unlike many of the behavior one-gene studies mentioned here), we can't make good predictions of very clearly genetically-affected traits like how tall you are or whether you'll have diabetes (and if so, what its particular characteristics, severity, response to treatment, etc. will be).

Every trait you can name probably has at least some heritability; that is, genetic variation contributes to variation in the trait.  Heritability is usually substantial.  But so are chance and the various aspects of lifestyle and environment.  High heritability means that genes are relative important in the population, but does not mean that an individual genotype predicts that person's trait reliably.  GWAS experience, which is now extensive, shows that high penetrating power of single (or even a few) genetic variants is not common.  Often, the trait definition is crude (like 'intelligence' or 'IQ', or 'asthma' or 'autism' or even obesity), but the definitions are changeable and cultural, the measures sometimes arbitrary, and people can have the same value for different reasons.  People with high intelligence measures can have better ability to memorize, or to learn quickly from one exposure to a fact or challenge, or to integrate repetitive exposure, or to do mental work by visualization or by other means, and so on.  

Change the environment or the measuring criterion and you can change the result.  Different approaches to modifying the achieved trait, like therapy for a disease, can apply differently to different people with similar measurement value.  People with similar glucose levels have different ways in which the 'same' trait is manifest during their respective lives.  This should be obvious, since diabetes and IQ have both increased substantially in recent decades, but the underlying genetic variation hasn't.


This is in rough terms why things can be genetically affected in real and substantial ways but, we would say, not genetically determined.  Again, the problem lies in overstating the latter and putting it into policy.  This is where the idea of 'eugenics', that is, of using ideas about inherited worth to make policy to 'improve' the human species and its genome, become heavily sociopolitical rather than scientific.  Historically this has led to discrimination against individuals and against whole groups.  One might be tempted to say that it's 'right wing' to believe in genetic determination of traits like ability or behavior, or the inherent value of one race vs another.  But this would be vague at best and misleading at worst.


To caricature affiliations, we can say that it's not just rapid right-wing behavior genetics that we should be wary of.  The rabid left has left its own trail.  While the Nazis were gassing people who were inherently 'inferior', the Soviets were starving people because, under the influence of one Trofem Lysenko, they believed life was improvable by experience alone rather than by inheritance (a view generally attributed originally to Lamarck in 1813).  In both cases, categorical beliefs about the role of inheritance led to disaster on a major scale.


That is why, despite the fact that of course genetic variation contributes to all biological variation, we should be very careful about making pronouncements that could be used for societal policy.  Today that policy might be favorable to you....but what about tomorrow?  Even if nothing untoward is being done with genetic data these days, prevention is the better part of valor.

Of course, if you want to make strong statements about the genetic determinants and evolution of ostrich knees, feel free, because only a few 'experts' in the world will care one way or the other.

Eugenics, or a new regime for beneficent science, or the fox in the henhouse once again?

Finally we return to a subject we promised months ago to write a bit more about.  It's an issue that pervades much of what we write about here on MT much of the time, but that we don't often address specifically.

Like it or not, we're in an age of genetic determinism, from the promises that risk of disease is readily predictable from genes to the easy way people have of, metaphorically or not, talking about traits that are "in my DNA".  Even in a nation's DNA.

Of course, few acknowledge that they are genetic determinists, because that sounds a lot like the bad old days of eugenics, when you were what your genes made you, inescapably and inherently.  If society could identify that, then it could do something about it.  It could be clothed in, and even to a great extent be, attempts to better mankind or even you as an individual.  But it had its very dark side.

Determinists of course acknowledge that evidence about genetic effects is statistical: few genotypes perfectly predict traits--they're generally not completely 'penetrant' they way Mendel's pea traits were.  But if you listen to how this is often expressed, you can tell that the underlying belief often is that if we identify a manageably small number of genetic variants our predictive power will be great....that in the main genotypes really do determine traits.

Today, there is a fervor for genetic Gotcha! like we have not seen since about 1945 (in case that year might ring a bell).  It starts with medicine, perhaps archetypically with Francis Collins' promise of 'personalized' genomic medicine. But it's spilling rapidly into the social sciences, where how you vote and whether you're in a gang or tolerate child abuse or make retirement investments well is going to be pronounced by your genome--indeed, by a few simple tests. We've been posting about this recently.

Once genome sequencing and testing become inexpensive, and because of their technological flash irresistible, there are many interests (besides professors needing grants or to be seen as deep thinkers revealing the true nature of Nature) who will want to know your genomic Destiny.  What will they do with that information?  Who will be given access?  Will they have your, or their, interests at heart? Will you know about it?

It is mistaken to take the spirit behind our asking these kinds of questions as merely reflecting our politics.  They do that, certainly.  But that's because science in areas like this is politics.  We've had two centuries of innocent proclamations that "we're just trying to understand how the world really is, regardless of human (i.e., religious etc.) illusions.  We scientists don't control what the world does with this knowledge!"  But anyone paying attention knows what society can do and has done with this kind of knowledge.  Some of it is good, surely, such as using knowledge to develop better medical care.  But that is for people who voluntarily show up at doctors' offices asking for help.  Other uses are not so good, as when people are typed genetically by others, such as government, insurers, schools, employers, the military or police, and so on.  Then, there is less control over what is good and what is bad for the people being categorized by their genes.

Maybe those with the information won't misuse it for selfish gain.  But the opportunity that they might do so is sufficient to make it so that they can't do so.  Why we have to learn this lesson again, or what those with good intentions can do about it, are serious questions.   But one thing needs to be understood: the logic of the reasoning in this area, and its implications.....and its history.  This will require understanding what 'determinism,'  invoking 'Darwin' or 'evolutionary' mean in this context.   And whether investigators' intentions matter in terms of the broader issues.

In fact, the lurking potentially ominous nature of these  issues can be readily seen in the resurgence of a classical view--going back centuries--that we should not help the unworthy, because they're that way inherently and thus the attempt is a waste of time and money.  In Britain, there was an effort to  use genetics to identify immigrants from a particular African region.  In Germany, the Chancellor declared multiculturalism dead on arrival, and pointed fingers at non-assimilating Muslim immigrants.  Jim Watson made the statement that it's wasting money to give foreign aid to Africans because they simply aren't capable of living up to standard and we've read that he also said that anyone who has employed African Americans knows what he's talking about.  In the US the Tea Party doesn't like helping those who over-borrowed for their mortgages (but they aren't as mad at the banks that lured people to make the loans).  Growing since Reagan and Thatcher is resentment against welfare-queens.  Why should my hard-earned money go to pay for some wastrel's health care?

These things are relevant because they involve, enable, or incite anger of groups against each other, and the classificatory nature of the accusations that goes with a deterministic view of human inherent value, or selfish retrenchment often couched in religious terms.  And this is without the intervention of actual genetic knowledge--but the easy way in which genetic claims are bought by the public these days reveals the mood, and the possibility that we're about to revisit a grievous history, including two chapters of opposite kinds, known as eugenics and Lysenkoism.

But it is easy to rant against this and one (we) must keep aware of the risk that we just do that without attempting to address the issues, carefully, themselves.  We'll try in the next post.

When your guess is (literally) as good as mine

Randomness is one of the most important concepts in modern science, and yet one of the most difficult to understand.  It seems that no one gave it much thought until the 18th or 19th century, when some founding mathematicians began to study probabilities and their meaning.  Mathematicians cared. Gamblers cared.  Mathematicians who gambled cared. But most people accepted that Nature was governed by wholly deterministic laws.  That idea in its modern form was largely the legacy of Galileo (but see NOTE) and Newton.

This is still debated--that is, is randomness just a concept of mathematics that in the real world is only an illusory manifestation of our lack of sufficient data about things, or could there be things that are really, truly, no-kidding random?  Quantum physics is held by many to be the only area in which that may be the case.  Rolling dice and flipping coins only appear random in this view.  But even if truly random, many argue that quantum effects are so small and numerous that they even out and simply have no bearing on things at the monstrous level of animals and plants, and can be ignored.

Randomness is usually viewed as just a matter of sampling and experimental measurement error.  In the long run, with big enough samples, things will 'even out'. That is, this kind of randomness is just statistical 'noise' that we have to deal with in sampling the real world to understand it.

But in evolution and genetics, since the next generation emerges only from the current one, and what is dead and gone can't come back, randomness (if it exists) can have a permanent effect.

Just the other day we heard an otherwise sophisticated evolutionary geneticist say, of genome mapping kinds of searches for evidence of adaptation, that the problems we are facing these days are just a matter of using the right statistics (i.e., to detect what's significant).  Amazingly, we heard that at least one statistics instructor here at Penn State (where the statistics program has long been a leading one), told a student that the .05 significance cutoff level had something fundamentally meaningful other than being a wholly conventional, subjective, arbitrarily decided criterion for making decisions about evidence.

Using and properly interpreting the right statistics is certainly important, and failure to do that is responsible for a lot of problems in genetics and evolutionary interpretation, as it is in many other areas of life and of science.

But in areas like GWAS and genomic scale analysis, the problem is not all in the statistics.  It's in the phenomena themselves.  Even when nothing causally genetic is going on, genome-scale analysis with open-ended, unconstrained data mining, is almost guaranteed to find something that will appear to be 'significant'.  And we know theoretically and empirically that important evolutionary things can be going on, but not be detectable.  In fact, we can't actually prove that 'nothing causally genetic is going on', either!

GWAS Manhattan plot

Randomness is studied intensely but remains a fundamentally very elusive concept, and everyone should have at least some grasp of why this is true.  Policy that affects daily life depends on the use (or misuse) of statistics and concepts of randomness.  We are not alone in saying this: You might enjoy and benefit from listening to a very clear discussion of the issues on BBC Radio 4's In Our Time from January 13.

This program points out what we said yesterday about astrology: if the world is truly deterministic, then everything is so connected to everything else -- as is often said, the universe is just a clockwork phenomenon -- that everything in a sense can predict everything else.  If that is actually true, than Darwinian evolution, premised on the idea that some genetic variation has a greater chance of success (that's how Darwin himself phrased it around 40 times in the Origin of Species), is a sham: because it's all predictable.  The poor rabbit is destined to be eaten, not because its slowness reduces its chance of escape from the wolf.

Think how arrogant we so often are in making strong assertions with the great data limitations that we have, or in some ways cannot completely overcome.  This is especially important, in a subtle way, because modern science largely rests on concepts of statistical significance and formal 'hypothesis testing', in processes that are either probabilistic as far as we can tell, or that we are forced to study by, but hopefully appropriately structured (random?), sampling.  And to realize that much of Nature could be entirely non-random, even controlled by very simple processes, and yet appear random by every known test.  Those processes can be totally non-random, for example as the BBC discussion mentions, the sequence of digits in the value of pi (circumference divided by diameter of any circle in the universe), are indistinguishable from randomness.

Indeed, often our belief in deterministic laws of Nature may lead us to assume determinism, and treat the probabilistic aspect of data as just a practical impediment, and using 'significance tests' (with arbitrarily agreed-on cutoff values) as if that proves it, when the process itself could be inherently probabilistic.

It is very sobering.


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NOTE: Actually, Galileo did many experiments.  These are described in his Dialogues Concerning Two New Sciences (1638), he showed laws of motion and gravity by rolling a ball down inclined planes of various steepness.  He had to do that because time measurement, done by a water-clock, was not precise enough for dropping things off the Leaning Tower.  But he also recognized that he needed replication, and repeated these experiments 100 times: an acknowledgment of random measurement error.

Signs of the times, or Is Astrology True After All?

Well, well, here's a sobering lesson for all of us who have sneered at astrology!  It's not just that some famous scientists dabbled in astrology.  No, it's more serious than that and, in a sense, a great relief! 

There's a story just out  (the story is from the New York Times, but reports on a story in a Minneapolis paper) that says that the signs of the zodiac have traditionally been a month off what they should have been.  Yes, believe it or not, after all this time, you aren't what you always thought.

It appears that because of the moon's effect on the earth's behavior, ancient zodiac/month assignments are now off by about a month.  Now, we're not technical experts, so we can only steer you to the story itself, rather than attempt to interpret the scientific evidence for you.  But this figure and legend from the Times report may  help:

What gets our interest is the relevance of this fundamental flaw to basic questions about how we know the facts of science, and how our theories fit the facts (or don't).  In fact, we really must sincerely apologize for having denigrated as pseudo-science such fields as astrology.  Many famous scientists have held various levels of acceptance of astrology.  But what we thought we knew, in this modern age, is that those horoscopic predictions that people read in the paper every day are bogus: they seem to come true because they're so generic that, like GWAS (genomic association studies), you can always find some apparent truth in their predictions, even if there's nothing really there--and claim success!  That is the skill of the astrologer (or GWAS analyst).

This is a problem, because for those who believe that their genome will predict their life (the way your horoscope does), the world is assumed to be a deterministic one.  If it is perfectly deterministic, then what appear to be probabilistic aspects of the world are simply illusions based on our not yet having figured out all the causal factors at play.  That was Einstein's skeptical take on those who insisted that quantum mechanics showed the universe to be truly probabilistic.  Even when never stated so baldly, that also is the effective worldview of personalized genomic medicine gurus (we're surprised none of them yet has a daily column on the comics page like astrologers do).

Now, think about this:  suppose the world really is, in fact, perfectly Newtonian and deterministic.  Then everything must always affect everything else by way of space-time gravity and so on (including the 'entanglement' of quantum mechanics recently preferred as the explanation for extra-sensory perception).  Like a ball on a string, if you know where the string is you know where the ball is, and vice versa.  In such a world astrology simply must be true: the positions of the stars simply must be completely connected to everything in your life, past or present!  If you observe some set of facts, you can know all other facts!

Thus the fault really is in your stars, if you feel you are an underling.  (We'll skip over the fact that the same must be true of patterns in tea leaves, or even in the flakes of dandruff on your shoulder, or even your dog's dandruff) rarely bear out more than what would be expected by chance (this applies, we skeptically believe, even to the late, lamented octopus who supposedly predicted the outcome of the World Cup).  Since the stuff never really comes true, of course, the science of astrology just isn't a science.  Or so we thought!

What the new story now shows is exactly why astrology hasn't been working: because we weren't observing the facts we thought we were observing.  Pisces aren't Pisces after all.  No wonder the horoscopes were always wrong!  But with the new correction, we should be able to look forward to perfect predictions.

Sadly, for us in genetics and biomedical sciences, this will not be good for business.  Because if everything is predictable by everything else, a quick glance at the Daily Horoscope will tell you all you need to know about your future, including your disease fates and the talents of your children.   You won't need to bother with the cost and effort of getting your genome sequenced by  ZodiGenetics.

And that's bad for us professors, too, because it'll mean we're of no use, since once this realization sinks in there won't be any need for public funds to be spent on genetics research, and universities will certainly dismiss us if we stop bringing in the moolah.

Science, Technology, and Unconstraint

We have to note, with sadness, that in its budget-cutting effort, Penn State has decided to close its STS  (Science, Technology, and Society) program.   This is a group of faculty members who were expert and/or interested in the history, philosophy, or societal impact of science.  Among other things, STS was to be at the heart of a bioethics degree  program here, and we have a number of really first-class faculty who would have provided it.  This may have complex reasons, but at its core it is another sign of the corporatization of universities, dumping things that don't bring in  money.

STS doesn't bring in a lot of money, and it may in fact have little if any influence on what goes on here, much less in wider society, but that's not really the point. It has the potential to remind us that science is not as detached or objective and society-neutral as scientists like to fancy they are and to show us the evidence and the way science is a part of our culture.

STS here deals with issues of many kinds, including disabilities, food and agriculture, evolution, climate and environment, and genetics to name but a few.  This field should help foster a better societal understanding of science among students and future citizens, especially in contentious areas.  At best, perhaps, STS work on the context of science and the history of its effect on society, could help advise on policy in regard to research priorities, and perhaps help put some brakes on what scientists do where that is relevant.  Of course, scientists don't like anyone looking over their shoulder; nobody does, and we naturally want to be able to do whatever we want to do.  Certainly some studies of the context of science are done by meddlers with little understanding of science.  But most of the work is informative and informed, and there are good reasons for any field to be under scrutiny not just for its inherent interest and technical ethics, but its societal ethics as well, though our STS program here is not a Gotcha! operation.  

All scientists are vulnerable to self-promotion, to selective study design and data interpretation, and to advancing their particular worldview or vested interests.  It's part of life.  Part of education of scientists and citizens alike should be to understand these things.  But in some areas, science directly impacts people far beyond the laboratory.  Proper understanding of evolution and climate change are examples where science should have a positive influence, and STS people could help.  Proper understanding of the limitations of the role of genes in our normal as well as health- and agriculture-related lives is also important, in an era of fervid enthusiasm for genetics, even in social sciences, when genetics has a long history of being used to justify major societal abuse.  Yet universities are trephaning their humanities programs .

The implications of science for the society that pays for it should be scrutinized carefully.  To us this is a sad reflection of loss of mission by universities in their desperate hunt for money (even in a time of acknowledged belt-tightening), this kind of program,  that might help faculty and students to understand their world should be cut.  We wonder if a biochemistry, electrical engineering, economics, or chemistry department has ever been cut in this way.  The walk away from these important core areas of university life, and of what it means to lead an informed life, should be resisted where that's possible.

When it comes to IQ and evolution.....

There was a story on the BBC last week, reporting on findings that leaf-cutter ants have socially age-related division of labor that is beyond their genetically programmed cast structure.  This comes from a paper in Behavioral Ecology and Sociobiology.  When their leaf-cutting jaws wear dull, the ants change jobs, from cutting to transporting the cuttings of others back to the nest. It isn't clear if this is done by choice or by some sort of coercion by sharper ants, but seems to the investigators to be voluntary.  It's finding a useful role for the good of the society.

The study leaves many questions open, since the investigators appear to have compared lab ants' jaws to those in the wild, and they say that those with really blunt (90% reduced) cutter jaws 'exclusively' transported things back home.  Naturally, rather than stick with an interesting story, the authors have to start speculating about what this was adapted for and all that.  Like the idea that the ants 'may' have longer life spans than solitary species (so many questions about what comparisons to make and what kind of data actually count, and what determines lifespan in the wild and how strongly, are opened that we'll pass on further comments).

But why this blunt before the retirement from cutting, if this is an evolutionary adaptation?  Why wait?  And do ants always transport what they cut, or do they cut and transport in mixed behavior, transporting when their jaws get tired, and if so, perhaps the dull ants actually keep trying to cut but then when jaw-rest time arrives they pick up a piece and haul it home?  To make darwinian speculation, questions like these must be answered, and undoubtedly we could think of others.  But that won't dull the interest in the role-playing observations themselves.

This facultative action shows yet again the sophisticated abilities of the miniscule brains (if that's where the decision is made) of these amazing creatures. It's another chapter in the antidote for the narcissstic view we have, even in science, of our abilities and the notion of our uniqueness in Nature.  Yes, we're unique, but so are crabs, ants, and oaks.

The Rohrshach Test that is Tucson

We normally don't do politics here, unless it's the politics of science, but this week's tragedy in Tucson and all the resulting uproar over whose fault it was have gotten us thinking in a way that may be relevant to something we write about a lot on MT, and that is how to determine causation.

As we see it, this is all another Rohrshach Test -- there are those on the left blaming Sarah Palin and lack of gun control, and those on the right reminding us that the Democrats had maps with targets, too, and anyway guns don't kill people, people do.  Sadly, all predicable. 

So the politics of this tragedy are absolutely not new, everyone is trying to harness it to their own cause and view of the world.  Though, some, such as David Brooks in the New York Times, do remind us that it seems that the shooter was insane, which means there are no politics to be discussed, this is about mental health.  Though of course that doesn't take the politics of gun control or mental health care off the table, but that's not what everyone is exercised about at this moment, it's all about that damn map with the cross hairs.

Well, but how would anyone know what caused this guy to shoot a bunch of people, anyway?  And how could this be anything but a Rohrshach Test?  There's no way for science to figure out the underlying cause; we can't do a controlled experiment asking whether those exposed to Palin's map were more likely to shoot people than those not exposed; we don't have a large enough sample from which to make generalizations or draw conclusions; and anyway, if the accused shooter is as mentally ill as he seems, should we believe him even if he tells us Sarah Palin bought him the gun?  Or could we believe he wasn't aware of the right wing's vitriol against 'liberal' politicians or government in general?  Or that that message didn't percolate unaware among his insanities?  And, this abuts the larger question of how much sane people are the product of their times, and what that says about our responsibility for our actions.   

In truth, though, all we know for certain about this event is that it is a tragedy for a number of families, and for the country, at a polarized time in our history.

But are we in fact more polarized than ever before?  It is arguable that the Democratic and Republican parties are closer together ideologically than they've ever been.  Yes, there are some issues that aren't open to compromise -- the death penalty, abortion, war, e.g. -- but where you come down on these issues isn't necessarily a mark of your party affiliation.  Perhaps in fact we are more polarized culturally than politically -- religious affiliation, NASCAR, no NASCAR, tennis or football, Thai food or hamburgers, etc., and that's what is behind this "political" discussion.  It's not unique or particular to us to have political assassinations, so in that sense the hand-wringing could be misplaced by trying to make this specific rather than about generic aspects of human tragedy--both political and medical--that litter our history as a species. 

To connect this incident (somewhat forcedly, we admit) to MT's biology theme, in his Malay Archipelago, Alfred Wallace, Darwin's evolutionary co-conspirator, wrote about incidents of people running amok in the Indonesian islands he visited in his many years collecting specimens in the region.  Although commonly used in a colloquial and less-violent sense, the phrase is particularly associated with a specific sociopathic culture-bound syndrome in Malaysia. In a typical case of running amok, a male who has shown no previous sign of anger or any inclination to violence will acquire a weapon and, in a sudden frenzy, will attempt to kill or seriously injure anyone he encounters. Amok episodes of this kind normally end with the attacker being killed by bystanders, or committing suicide.

So we here in our time didn't invent this. And the 'debate' over what really caused the tragedy in Tucson will never be resolved.  All we'll ever know for certain is that someone with a gun pulled the trigger, people were killed or wounded and lives were irrevocably, tragically changed.  But the nature of politics and people is such that the narrative by which we will all continue to explain this particular event to ourselves, often to suit our own personal narratives, was largely predetermined.

Art forgeries are better than science forgery

A big challenge for modern biomedical science (and for others, like climate change, for example) is that the evidence is often that effects may be real  but they are slow, slight, or statistical.  What is barely observable year by year can turn into an ice age--or an epidemic after much time or many exposures have occurred.

False ideas under such circumstances can be very costly.  That's why what now appears to have been outright fraud in associating autism with somehow-toxic childhood vaccines has been so serious.  Countless parents shunned vaccine protection because they believed the vaccines were dangerous.  Huge amounts have been spent on the diseases that would have been prevented, on morbidity and serious ill effects, and of research dollars and resources.

The problem became public and political, with parents advocacy groups, lawyers, and politicians getting into the act.  Other problems might have been addressed with the same funds.

The physician who has been accused, Andrew Wakefield, naturally denies the allegations.  Accusations fly back and forth, and those who believe (or hope) in the conspiracy theory that the attack on  him is from Big Pharma trying to protect their profits or from lawsuits, include advocacy groups that have been attacking the vaccines for some time.  Every side, as usual, sticks to its story. We're not in a position to judge, of course, but there's a deeper point.

There is no easy answer for these situations in which causation is statistical and causal effects small.  We have to work out various criteria for making inference about what causes the ill outcome, or what its mechanism or cause-effect pattern is.  We have to work out societal risk-benefit assessments.  So it is very serious indeed when we can't trust the good faith of the evidence as well as its epistemological shakiness.

No matter how much we criticize science today, and no matter how much hyperbole, dissembling, shading and stretching of truths goes on, it is assumed to stay within the lines at least of technical accuracy.  So when there is fraud as has been claimed in this case, or data cover-ups as has been repeatedly claimed for drug trials, the crime is a crime against society and is very serious.

Fortunately real fraud of the data-faking kind seems to be very rare.  When it happens, sanctions have to be strong, to make as sure as we can that it stays very rare.  In situations where the truth is easy to find, fakery has little chance of getting the faker anywhere.  But in the common situation of complex causation, cheating can pay off.  So we have to be rigorous in preventing it.  Generally, we seem to be doing well, and part of the evidence is the degree of publicity that the occasions of real dishonest science receive.