Wednesday, October 31, 2012

Hurricane Sandy and the collapse of the Maya

On our whacked society
So, there are those enlightened members among us who have declared in their wisdom that hurricane Sandy is God's punishment for our tolerance of gays, for Obama (naturally--he's the wrong color), for our loose morals, and I forget what else (maybe too many liberals).  What an insight!

This hurricane sent by divine wisdom to punish us for allowing gay marriage was not aimed very precisely, however, and one wonders at His supposed omniscience.  After all, the people displaced or killed were mainly not gay couples or people sinning by the various means suggested.  They were just folks, minding their own business.  That suggests a God who's like a surgeon working with a band saw.  Can't He target his gales and floods to those who really deserve it?  I mean, some whole states that are under water and wind don't even allow the mortal sin of gay marriage.  We should expect more skill from the entity supposedly to be our savior!

Why do we bother to maintain schools in this country?  Obviously, the lessons are not sinking in.  After all, 40% or more of our citizenry thinks evolution didn't happen, and liken Darwin's ideas to misleading fantasies such as the idea of an Easter bunny (like fossils, those eggs in your lawn on Easter were just laid there to mislead you).  Maybe God Himself hasn't got much of an education, as his skill level in aiming floods and hurricanes is about equivalent to  many people who have college degrees these days, perhaps reflecting the slipping standards we in the profession have tolerated.  One begins to wonder whether the Noachian flood was really meant just to drown the Pharaoh's troops or something.  Maybe the Red Sea parted too early and should have drowned the Jews.  Who knows what blunders have been recorded as miracles?

On the other hand, there are those who are saying, after this recent flood, "WHY AREN'T PEOPLE  PAYING ATTENTION??  THIS PROVES WHAT WE'VE BEEN SAYING ABOUT GLOBAL WARMING!!"   Well, this, too reeks of ideology and tribalism, the tendency to see in an event support for one's favorite group's  pre-existing biases.  Does the tidal surge that caused so much damage on the East coast bode poorly for the future, on the grounds of human-induced global warming?  In fact, that does seem to us to be plausible -- certainly more plausible than the idea that the hurricane was God's wrath -- and the extent of the damage could be viewed as a warning sign.  Some analysis seems to suggest that the tide was higher by a foot or so as a result of global warming, than it would have been from the same storm a century ago.  Indeed, the equation that suggests that climate change is exacerbating extreme weather takes into account more moisture in the air, warmer ocean temperatures and so on -- here's an explanation of this.  But one swallow doesn't make a spring and whether this one storm should be given much if any weight, on its own, in the global warming dialog is a relevant question.

The Mayan collapse
The climate-change argument to account for Sandy's destructiveness raises an interesting thing to think about, over and above whether it is evidence of human-caused climate change (or God's wrath).

Archeologists wonder and debate about the causes of the disappearance of major civilizations, of which there are many instances.  One on the American landscape was the collapse of major Mayan urban centers in Central America.  These had declined and largely been deserted, at least as major urban centers, by the time the Spanish arrived--that is, they were not, as were the Aztecs, done in by Spanish swords or by new diseases.

What caused the abandonment of the Mayan cities?  Was it war, a catastrophic event, a decimating conquest?  Or was it gradual, over many generations, due to the diminution of the soil or climate for supporting agriculture?  If slow, did the Mayans even know it was happening, or did each generation just do as best it could, not realizing the decline in population and so on? 

We might get a hint from Sandy and global warming debates.  What if there are more and more frequent incidents like Sandy in the next few years?  Unlike priests who may blame this on the cursed sinfulness of New Yorkers (which is a true characterization of them even if unrelated to hurricanes), climate scientists might correctly blame it on global warming.  At some point, even current skeptics would begin wondering what to do to keep from ruining their shoes several times a year.

A major company might be the first to decide that at the price of sandbags, the cost of staying in Manhattan was no longer good business, and would move to, say, Cleveland where such disasters don't seem imminent.  Banks and the stock exchange might decide to move to greener pastures, so to speak, like Omaha, where George Soros lives and seems to have done very well.  The entertainment media might move to Dallas or Minneapolis.  Once enough major companies did this, in the following decade other large entities might follow suit.  Starbucks and McD would be out of customers, and would close their doors.  Nobody would be there to see Macy's Christmas displays, so they'd move to St Louis.  There could be a kind of sheep-like trend-following by which those entities just decided to do as others have done, with or without good reasons of their own.  Or, it could become apparent that the gravitational center of the whatever-business universe had moved and that anyone hoping to make it in that business had to move to where the action was.

Fencing off of abandoned buildings, closing some subway lines or even, say, the lower tip of Manhattan, could lead the movement of even more away from the City.  After a few decades, New York could become a virtual ghost town.

Of course, we keep extensive records of what we're doing, so unlike our difficulty deconstructing what happened in Central America, future historians of the 4th millennium might know what happened here directly.  Or, records could be lost and they might have to make the  kinds of guesses about New York that archeologists today make about the Mayans:  What happened to the New York civilization to lead to its collapse?  Indeed, if the climate argument is correct, the east coast concentrations of buildings might go the way of Atlantis, submerged into mythology.

Whatever the reason, if there is any particular long-term reason, for what Sandy did, it may give a hint of how events that everyone was aware of at the time led to gradual abandonment of former civilization centers, that thousands of years later could look like sudden catastrophes.

Maybe the Mayans blamed their droughts on God's anger, too.  But whether the reason was that  they had allowed gay marriage is something one can only speculate about.

Tuesday, October 30, 2012

Science funding: what it's really (or at least largely) about

An Op-Ed in Monday's hurricane-nervous NY Times is a plea for more federal science research funding.  It's by a former science adviser and of course it's an advocacy piece.  It makes the attempt to show the benefits to society of university-based federally sponsored research--the usual claim that this leads to new medicines, cleaner energy, and more science jobs.

Of course, these things are true in principle and in some instances actually true.  We'd create more science jobs if we actually did our duty with respect to raising the expectations and standards for our educational programs, especially for undergraduates (but that's not what professors' jobs are all about any more).  The extent we really generate usable research that leads to products is something we don't know much about, because industry loves foisting their responsibility (to do research for their company's products) off on the public, while still being secretive and competitive so that most of the key research is done in house.  Pharmas are trying to cooperate in their support for basic facts which will then be turned over to their own private (and secret) value-added research.

By buying research from universities, companies impose various levels of privatization of the results (and commercial incentives for faculty), which undermines the proper role of public institutions, and in some ways actually privatizes public research.

Federal research is, in a naturally expectable way, bureaucratized to give it inertia so that program officers' portfolios are stable or enlarged, and prominent investigators' labs (and their universities' general funds), have continuity.  That may sound good, but it means safe, incremental work without any serious level of accountability for producing what one promised (here, we refer not just to miracle results, which can't be promised, but things like adequate statistical power to detect what one proposes one has the power to detect, or advances in things like disease therapy that is promised in grant applications.).

One can always crab about this waste of funding generated by the way we know how to work the system in our favor.  We ourselves have been regularly funded for decades, so this post is not  a matter of sour grapes on our part.  But there is, from an anthropological point of view, a broader truth--one that shows in a way the difference between what are called a culture's emics and its etics.  The emics are what we say we're all about, and the etics are what an observer can see we are really up to.  Here, part of the usually unspoken truth about huge government investments is that citizens are given promises by the priests (the recipients) of some specific good in return for investment.  But the momentum and inertia is largely for a different reason.  As the Times author says:
Moreover, the $3.8 billion taxpayers invested in the Human Genome Project between 1988 and 2003 helped create and drive $796 billion in economic activity by industries that now depend on the advances achieved in genetics, according to the Battelle Memorial Institute, a nonprofit group that supports research for the industry. 

So science investments not only created jobs in new industries of the time, like the Internet and nanotechnology, but also the rising tax revenues that made budget surpluses possible.
This is both a post-hoc rationale (one can always look backwards and identify successes and thus try to justify the expense, and its continuation, but is not usually compelled to argue what else, or what better, could have been done by government--or by taxpayers keeping their money--had the policies been different.

At the same time, it's a very legitimate argument.  If science investment doesn't lead to a single real advance in health or energy efficiency, but if it does lead to jobs for lots of people, not just including the scientists, but the people who make, transport, market, advertise, and design their gear, their reagents, even their desks and computers, then those funds are circulating in society and in that sense doing good.

It's a poor kind of justification for the investment relative to its purported purpose.  But life is complex.  Sequencing machines or enzymes or petri-dishes are made by people.  The challenge to identify real societal needs (or to decentralize) and achieve success without just building self-interested groups and bureaucracy is a major one.  Often it leads to disasters, like wars or poor agricultural management, and so on.  But it also is part of the engine of a society, whatever that society's emic delusions about what they're up to may be.

Monday, October 29, 2012

The microbiome: competition or cooperation, adaptation or adaptability?

We're just now getting around to blogging about a Perspectives piece in the Oct 12 Science called "Animal Behavior and the Microbiome" by Vanessa Ezenwa et al. It's an overview of current thinking about the role microorganisms play in animal behavior.  The Human Microbiome Project documenting the extent of such organisms in humans, and the essential role these guys play in human health and disease, has found that the genes in the trillions of microorganisms with which we share our bodies outnumber ours by 100 to 1.

Since at least some of these are necessary for life, one offshoot of learning about this is to ask what 'the' human genome really is.  Most bacteria we know of, like the ones in our gut, have to do with rather prosaic, if vital, physiology such as digestion.  These are interesting and important, but they don't involve more sensitive issues such as our personal identity -- our behavior.  The role of microbes in animal behavior is just beginning to be understood, and it may be more profound than had been thought. 

Kudzu bug; Wikipedia
For example, as described in the paper, "the Kudzu bug (Megacopta cribraria), an agricultural pest, is born without any symbionts (species with which both have a mutually necessary affiliation for survival). After birth it acquires a specific symbiont from bacterial capsules left by its mother. If these capsules are removed, the bugs show dramatic wandering behaviors, presumably to search for symbiont capsules left with nearby eggs."

Or, bumble bees acquire gut microbiota either through contact with nest mates or by feeding on feces containing the microbiota required by the gut. Bees without these microbiota were more susceptible to a bumble bee parasite, Crithidia bombi. Fruit flies that share the same diet-acquired microbiota are much more likely to mate with each other than with those that don't.  And then there's the zombie ant, infected by killer fungi, and the rats -- and cat ladies -- infected by Toxoplasma gondii, both of which we described here.  The examples go on and on.

But what does the recognition that we don't go through life alone mean for the usual understanding of social context, ecosystems and the evolution of behavior?  It's tempting to suggest that these are examples of exquisitely fine-tuned co-evolution, and the usual darwinian interpretation would be that every organism is out for itself, selfishly hijacking another's gut, brain, feces, nasal passages, skin, eyes, now manipulating their behavior -- any and everything -- to make a living.  And needing to out-compete all the other microbes fighting for the same territory.  But don't get too greedy or you'll kill your host and then you're in trouble too.  (Reminiscent of how humans feel about climate change -- we have to save the planet so we can continue to exploit it ourselves.) 

But this is rather a stretch, really, and depends on fitting the facts to a preconceived view of the purpose of organismal interactions (apply our take on why people believe microbes will be found on Mars here).  And that preconceived view is that life is all about selfishness, exploitation and competition.

But there's an alternative view, and that is that what this represents is cooperation, one of the fundamental principles of life that we've often written about here and in our book MT.  It's a principle that requires abandoning the long-held belief in the primacy of "survival of the fittest" because that very rarely happens.  A better description would be "failure of the frail" -- it's only the weakest organisms that can't reproduce; most everyone else does just fine.  Plus, much of survival depends to a large degree on luck and has nothing to do with genes or competition or your ability to outwit your neighbor.

So, this Russian doll kind of life-within-life-within-life that's being catalogued is an ongoing documentation of the centrality of cooperation in life.  There's surely some adaptation going on -- the bumble bee is better off without Crithidia bombi than with, but 10-20% of worker bees in hives in the field have been shown to be infected and bees have carried on; it's only now that they're bombarded with infection with multiple parasites and more that it's a problem.  But the bee did not evolve to be infected with gut microbiota to fight off C. bombi, the bee evolved with the ability to host gut microbiota and to fight off the parasite, however that happens. 

Further, some infection was survivable, and the parasite didn't need the bumble bee because it's an equal opportunity infector, infecting other insects.  This brings up another fundamental principle of life, and that's adaptability.  Because it's ubiquitous, we believe adaptability is a characteristic of life that was present very early in evolution. So, humans can't live without a gut full of microbiota, but the species that we host are widely variable, they change when we're ill or pregnant, we can kill them off in great numbers with antibiotics, can add more with probiotics or natural exposures, and we're fine.  The same has to be true for other organisms.

One can say that what's here has to work, or at least to have worked successfully enough in the past to be here today.  But that's only a part of the biology, and there has been a tendency to focus more on how that evolved via competition, than on the interactions themselves.  How cooperation works is turning out to be an elegant but complex business.  Even if Darwinian explanations are 100% correct -- and there are reasons to temper such a view -- understanding how such things work today is in itself a challenge, and a very interesting one at that.  Though, perhaps our very interest in it is because of some microbe in our brains, that makes us sympathetic to the lives of microbes...

Friday, October 26, 2012

The true meaning of "candidate" genes revealed

The biology of behavior
I take a deep breath.  If you were here with me you'd have noticed that it was breath signifying annoyance, annoyance over something I've just read.  The annoyance triggered my brain to trigger my diaphragm to contract and elevate my lower ribs and expand my thoracic cavity vertically, while at the same time my external intercostal muscles and interchondral muscles have elevated my upper rib cage to expand the width of my thoracic cavity to allow the intake of air.  The process is reversed as I breathe out. It's a biological thing.  My annoyance also surely triggered hormonal releases of some sort as well, and other downstream reactions that may or may not catch up with me someday in the form of "stress-related illness."

But ok, that deep breath out of the way now, I start to type.  My brain has begun to formulate sentences in response to what I've just read, and now transferring those sentences to the screen requires a complex interplay between the parts of my brain that think (clearly or not) and the muscles that govern my fingers on the keyboard.

More biology.  Genes are firing all over the place, creating and controlling the complex interactions that make all this, and more, happen simultaneously without me making it happen or even being aware of what's going on.  That's because in many senses I'm nothing but an automaton controlled by my genetic makeup to respond to my environment with biological impulses. 

But I'm also eating a pear as I type.  My hunger is a biological drive -- a genetic predisposition, even -- to which I'm responding.  I have to eat or I can't fulfill my darwinian destiny to survive and reproduce.

But why am I eating a pear and not a durian fruit?  Or a betel nut?  Or a peanut butter and jelly sandwich on Wonder Bread?  Because durians and betel nuts aren't sold at my local grocery stores, or even my local farmers' markets, and I don't like Wonder Bread.  (Have you tried peanut butter and pickle sandwiches though?  My mother's favorite lunch, a taste passed down to me.)  So my clearly biological drive has to be satisfied in culturally specific ways, and based on my own personal taste.  In part taught to me by my mother. 

Let's go back to the source of my annoyance.  It's a commentary in this week's Nature: "Biology and ideology: the anatomy of politics," about how biology shapes our politics.
An increasing number of studies suggest that biology can exert a significant influence on political beliefs and behaviours. Biological factors including genes, hormone levels and neurotransmitter systems may partly shape people's attitudes on political issues such as welfare, immigration, same-sex marriage and war. And shrewd politicians might be able to take advantage of those biological levers through clever advertisements aimed at voters' primal emotions.
Many of the studies linking biology to politics remain controversial and unreplicated. But the overall body of evidence is growing and might alter how people think about their own and others' political attitudes.
Of course biology affects our beliefs and behaviors, in much the same ways that it affects what we choose to eat or our responses to things that annoy us, which in turn have been affected by our culture and upbringing.  The work described in this commentary annoys me but it might strike you as perfectly fine.  We are biological beings, and everything we do and are is affected by genes and hormones and neurotransmitters.  But that is not the same as saying that everything we do is determined by our biology.  I eat a pear but not a durian fruit, if I'm a southerner I voted Democratic in my youth and Republican now.

Genes 'for' 
Genetics is now becoming deeply entrenched in the social sciences; economists, psychologists, sociologists, political scientists are being seduced by the appeal of genetics and Darwin as they try to explain why humans do what they do.  Hell, evolutionary theory is even used to explain why characters in classic novels behave the way they do.

But this shows how little social scientists understand what genetics can actually tell us about complex traits like, well, like all the traits of interest to these disciplines.  We can't even find genes 'for' truly biological traits like type 1 diabetes or clinical depression, even if the commentary assumes we have:
The past few decades have seen a wave of research connecting genes to disorders such as schizophrenia, depression and alcoholism, and to complex outcomes such as sexual orientation and how far people progress in education.
Well, but we have made very little progress in geneticizing such things, and where we've found genetic variants that affect such traits, they usually have very little, and inconsistent, effect.  Indeed, when we throw in the effects of culture and learning, not to mention neuroplasticity of the brain, almost all bets are off in terms of identifying biological forces that shape what we believe or how we behave.

And then there's the question of just what phenotype is being measured anyway.  This is hard enough for biological traits -- what constitutes 'high' blood pressure, obesity, or autism?  Very large studies to find genes for obesity find essentially entirely different candidates depending on the measure being used (e.g., body mass index, waist-hip ratio), or the obesity-related traits like diabetes, hypertension, or Alzheimer's disease.  So how on Earth do you measure political belief in such a way that it is a proxy for some protein coded for by some gene?  

Eugenics
What about this sentence, that you might have just glided over above:
...shrewd politicians might be able to take advantage of those biological levers through clever advertisements aimed at voters' primal emotions.
We've been down this road before.

Once Darwin gave people, especially the noble science class, the idea that Nature not God made people what they were, and that through their insight they the scientists rather than clergy, could divine what was good and bad, they (like clergy) are the ones who should evaluate who was naughty and who was nice, and indeed could help Nature out by doing something about the offenders.  Of course it was all for the good.  Just like clergy helping to save souls, scientists would help save society.  And since Darwin showed that our essence was not our soul, but our biology, which within decades became  genes, their term for their wise engineering was not absolution, but eugenics.

The temptation was of course to believe that they, through their science, could find out people's true essence, and recommend what to do about it.  All for the protection of society.  Does it sound a lot like the inquisition, where clergy decided how to test, and judge, and engineer (get rid of) those who polluted the true and faithful?

Eugenics in its early form, which crept in on little cat's feet, led by the biomedical research establishment, was all for human good, of course.  But of course power corrupts and demagogues are always ready to use it, and scientists as we know very well from the past -- and today -- are easily co-opted by the hands that feed them.  And of course that kind of thinking, in its various guises, led to the Nazi exterminations (and, here and elsewhere, incarcerations, involuntary sterilizations, and the like).  It also led to the abuses of the Stalinist era called Lysenkoism, which was the inverse of Darwinism out of control.

Well, you might say, that was then and this is now.  Yes, the early eugenicists were the well-respected scientists and physicians, but they were misguided.  Now, we know better, and our scientists have only everybody (else's) good at heart, don't they?  Intrusive abuses couldn't happen any more, could they?

Thursday, October 25, 2012

More on Mars life: How are those little green men made?

Why the hype about life on Mars?
We've commented on the talk swirling around these days about the search for life on Mars.  We don't think there is any good evidence that there is any, or was any, such life.  But of course we have no way to know that....yet.

In part, NASA talks up the life-on-Mars scenario because it wants support for extended, extensive Mars missions, a big budget even to include sending people to explore, and eventually colonizing the Red Planet.  It's an understandable desire if you work for NASA, of course.  Nobody will support all this if the place is just a big rock with some polar ice caps.But it goes beyond that.  It has to do with the truly interesting question: Are we alone in the universe?

If life is a commonplace occurrence, a chemical inevitability that occurs all over the place, it will heat up space exploration, and the public's willingness to pay for it. It will be driven by its interplay with philosophy, science, religion, and even the arts. 

What might be found?
Maybe the NASA hype machine will turn its very Disney-like graphical promotions and, yes, its extremely compelling actual footage from Curiosity and prior vehicles, onto some real, wriggling little green worm, at least.  If it does that, we will of course be mesmerized as will everyone else.

Source: Vincedevries
So, given the expectations that this 'life' is vastly most likely to be former life, what do those in the know expect to see?  Basically, it's carcasses of microbes.  This as we suggested in our previous two posts on the topic is based on the purported precedent of microbe-like forms in the ALH84001 meteorite found a few years ago in Antarctica, and on scenarios suggested even by reputable scientists that life on Earth and Mars followed highly parallel courses from the founding of the planets about 4.5 billion years ago, until geologic events killed it all off on Mars roughly 3.5 billion years ago.  Only remnants could be found today (though the hyped hope is included that maybe stuff is still alive in or under the ice or ground there).

The search initially will be for molecules compatible with having been part of life at that time.  That means the expectation that life there is like life here.  Either that's a kind of inevitability belief, or a belief that chemistry has proven that that's the only way life could exist, or it's just a total gullibility on the part of scientists for science fantasy.  If the latter, the only reason we don't still expect complex creatures like little green men is that we have already explored Mars, on the ground and all over the planet by satellite, and haven't seen any, nor even the tracks of their cars and houses (nor their spoors or footprints).

Scientists who seek organic molecules know (and sometimes, when being candid, acknowledge) that these kinds of molecules can arise in many ways and, indeed, have always rained down on Mars (and Earth) from space, having nothing at all to do with life.  But at least one scientist who should know better has suggested in an interview that the similarity to these atoms and molecules and the ingredients in DNA is a relevant fact. As we noted, that makes the humongous leap of faith in parallelism to believe that Mars life would be based on a polymer coding system related to proteins as the basis for its organization.

So, let's suspend judgment and ask what we might find.  Of course, on Earth at least, DNA degrades too rapidly to be conserved for more than a few tens of thousands of years, which is why mammoth and Neandertal, but not dinosaur, DNA can be found.  So of course one can find some carbon and fantasize that into DNA, but let's pretend we core down into the Mars ice (as part of mining it for water to pipeline out to support our space colony there, as is being suggested by NASA's PR office), and do find some DNA.  What might it show?

Well, normally, DNA sequences are basically random strings of nucleotides.  That means there's no formula from the sequence itself by which knowing the nucleotide in one position can predict what the nucleotide will be at any other position.  Yet, bioinformatics is a highly sophisticated science that does identify very non-random aspects of DNA sequence--the location of genes, for example, and their regulatory regions along chromosomes.  We can do this because we can compare species' DNA, and we have a century of experiments that have revealed what bits of sequence do, and why they do it.

Part of this, for example, is the nucleotide code for amino acids, by which sets of 3 successive nucleotides in DNA code for specific amino acids and hence for the structure of proteins.  That is a primary function of DNA.  But on Mars, leaping to the assumption that DNA is to be expected is the assumption that it will be a protein code  as well, could we read that code?  Is the code, and the set of available amino acids, the same as on Earth?  How much inevitability or parallelism would that imply?

In fact, some analysis has suggested that, to some extent at least, the evolution of the code can be related to primitive RNA/amino acid interactions.  That has been used to explain the specific aspects of the code, like which triplet would code for which amino  acid, and why the redundancy of the code is as it is.  But such ideas, even if correct, don't show that our system is inevitable.  That makes what are almost anti-evolutionary assumptions: that evolution must follow a path that is predictable from the outset, down to its very specifics.

One way we relate species to each other, and infer genetic function here on Earth is to align DNA sequences from different species to find corresponding regions to show, for example, that we are closely related to mice, less so to alligators, and so on.  We can reconstruct the general phylogeny of all life that way, step by step.  On Mars, if we don't know the coding system, and if it were different from Earth's, it would be very difficult to make any sense of fragmentary ancient DNA we would find there.  In fact, unless we struck some kind of miraculously preserved long stretches, and maybe also some corresponding RNA (which doesn't preserve well and is unlikely to be there), it would be nigh impossible to make sense of them--in terms of Earth life.

Suppose it's really there?
But, hell, let's be generous and suppose we found, for example, that Mars microbial DNA had very similar functions to Earth microbes' DNA.  Maybe they used similar respiration and metabolism and so on.  Maybe they had little ring DNA, called plasmids here on Earth, that protect from viruses!  What would the explanation be?

By far, the most likely explanation is not high parallelism or inevitability of Earth-like life!

The most likely explanation will be that Earth and Mars life share the same common ancestry, not that they arose independently.  We could compare Earth and Mars microbial DNA to estimate the date of that common origin, and perhaps from geological and cosmological evidence make a guess as to whether life started here, or there, and was transported by meteorites splattering off one planet and ending up on the other.  Or it might represent stuff raining down from space that, as some have long suggested rather fancifully, could survive the harsh space environment, with some origin 'out there' somewhere in inter-stellar space that we don't know about.  Geez, maybe the newly found planet around Alpha Centauri that has everyone so excited!

The same would be true if we inferred from Mars DNA that it used the same protein code, but we couldn't show species similarities to Earth microbes.  That's because, in 3.5 billion years Earth life has diverged from its primordial forms to the point that one could not argue that the difference from Mars life showed independent origin.

Finding DNA-driven life on Mars would be very interesting, of course, but would not contribute to theories about its inevitability, or that life had to be based on DNA as a protein code, and such finding could work the other way--suggesting that the only way we get life is by being seeded from some unique source.  It won't answer questions about whether life as we know it is a predictable chemical phenomenon.  Or how common it is in the cosmos.

So as we said the other day, in our music analogy to start this little series of comments, the way ideas about extra-terrestrial life are embedded in our current science culture, often subtly and perhaps not in our awareness, is profound.  We mix wishful thinking with limited thinking.  We do it to advance interest and knowledge, and science, based on how we know it today.  In that sense, we don't show enough respect for what we don't know.  Of course, if you did that, perhaps you simply couldn't get anyone to pay for the exploring you want to do.  Because the paying public is at least as deeply rooted in our current culture as scientists are.

Wednesday, October 24, 2012

FOR DOGKIND: Didactic, allegorical, disgusting, and adorable children's book

Just a momentary interruption of our regularly scheduled MT programming ...

My dog Elroy discovered the real origins of dogkind—our evolutionary tale of connectedness and change over deep time—and I recorded it. It's written for dogs, but humans will find that it's manageable from about eight years on up, and it speaks to kids of all ages. Elroy's story engages humans, young and old, in scientific thinking. I'm posting Chapter 1 of the complete manuscript here in hopes of attracting a publisher.

For Dogkind
The Autobiography 
of Elroy Beefstu Stacey 
as told to Holly Dunsworth © 2012

Chapter 1. To the Dogs

This is a story about a story, Kid. It’s about the origin of me, you, and dogs everywhere and how our tale was discovered in the first place. I’m goin on twelve years old and before I get grayer in the face and longer in the tooth, I figure I’d better put this on record. Preserve it. This way, after I’m long gone, dogs can learn about it from the comfort of their pods on the moon or Mars or wherever their spaceships land.
Figure 1.1. Me, now, in my gray-whiskered twilight years. 
Still reekin of rhino droppins, just one of the amazin smells I wanted to share with Bubba and the gang back home, I first realized the magnitude of our tale while standin on the bow of the R.V. Endeavor. We were journeyin from Capetown to Narragansett.

That’s ship’s deck is where, given everything I’d sucked into my eyes, ears, and sniffer and everything I’d smeared all over my fur, it all washed over me like one a those rogue white waves crashin over the gunwale: We’re all connected, not just dogs and prims, but everything. 

Figure 1.2. Connectin up dogs and prims to all the rest like the horned owl, guinea fowl, octopus, platypus, and human. 
(ask HD for sources found by Google)

Speakin a rogue waves, that minor catastrophe’s how Murphy and I nearly lost our chance at comin home on this ship. One a those monsters struck just as we left the harbor. It wasn’t just lucky for us that we weren’t swept overboard. It was lucky for us that the commotion distracted the humans from noticin us stowaways. 

Figure 1.3. R.V. Endeavor: The ship that carried us home to end our three years of globetrottin. (http://techserv.gso.uri.edu/)


We’d learnt from prior sea voyages that we needed to make sure to hide good and tight until land was completely out of sight before emergin to greet the humans. If land’s in sight, they’re liable to throw you overboard. But if it’s not, and you’re all surrounded by lonesome waters, even better, shark-infested waters, their lovin hearts and chefin hands can be manipulated into toleratin your presence and maybe even makin you a first mate. 

Figure 1.4. Murphy, now, in her white-faced twilight years.


The best way to use a human is to be useful to them in return. You gotta reciprocate! The easiest way is to be a source of positivity, love, peace, laughter, those sorts of brightenin things dogs are good at. Charm them with cuteness. Follow them around, but don’t be so annoyin and whiny about it. This warms their cockles like you wouldn’t believe, allowin you safe passage and usually some nice meals too. But even better is if you have some sort of skill to share with the humans to really cement the deal. And on the Endeavor, Murphy and I had somethin almost too good for the humans to believe.

“Ding dong! Here’s another one!” shouted Murphy, already up and at ‘em, out of her sleepy dogball, leanin out over the starboard side of the bow, tail waggin, sniffer to the wind.

“Bow, wow! I got it too. There she blows!” I cried.

It’s unmistakable, that stink. Hot, wet tongue, teeth, saliva, and snot. Microbes, diatoms, fungi, parasites and plaque. Burps, sneezes, blood, DNA, hormones, and dinners past. All expunged and atomized into the air and whisked by the ocean breeze straight into our sensitive sniffers. 

Figure 1.5 Stinky whale blowhole.

We could detect a whale way before the humans could, at least without their fancy glowin beepin machines, and, yes, sometimes even better than those machines. And it was whales they were interested in, even more than they were interested in us. We figured out right quick that when they found whales they were happy and when they were happy we got extra table scraps! Extra cheese. So whales made us happy too.

Once they learned how good we were at sniffin out nearby whales, it became such an amusin game for us all, and we earned the spoils for sure. Not the least of which was a trip home to Bubba and the gang.

It wasn’t until after Murphy and I had got round the world, crossed all the wide open spaces, smelt mind-blowin’ly monstrous creatures like those stinky whales; and before that lived with the prims; and before that, done all the silly things you need to do while you’re becomin a dog; it wasn’t until we had all that behind us that it then came rushin back together on the bow of the Endeavor, as if it was before my eyes and inside my sniffer, plain as day: The true story of the origins of dogkind.

And that’s why we have to start this tale at the very beginnin of our lives, eons before we even thought about a trip around the world. And we’ll get right down to that from the first word of Chapter Two.

Now, after hearin this account of mine you might claim that you instead of me could have dreamt up this whole notion of where we came from. And you’d be absolutely right. You may be an extraordinary dog, but I certainly don’t claim to be. Never have.  Despite what all the city tree trunks said. I’m clever, but not exceptionally so. I’m curious, but most dogs I know are. Many to a fault.

Figure 1.6. City tree trunk. Not a tree. 
(http://www.water-waysirrig.com/)
           
“Extraordinary” doesn’t fit me but it certainly describes the stupendous journey I made round the world, and all the circumstances, events, and other dogs in my life, especially Murphy, without which and whom I couldn’t have unraveled and deciphered and translated such a transformative and glorious idea as the one that I’m about to explain to you here.

The real heart of the matter, though, is that this tale was already told long ago. Told by the very nature of its existence. And it’s important to me that you get that. We just needed the right dog in the right place at the right time to sniff it out.  And I suppose that havin a dog like me at this stage in the history of dogkind discover it, well, that’s actually part of the whole ancient process isn’t it?

But for now I’ll leave that thought dangle like drool from your jowls. I don’t want to spoil the ending. Although, come to think of it, you’re probably already well-versed in the origin of dogkind, havin heard it from your elders when you were a wee pup, as I shared it with our little dogglings years ago.

Whatever your level of familiarity, it’s my aim to provide you with just a sliver of a bone or a glimmer of a spark in the followin pages. A spark of what? I can hardly say. But I hope it’s in here somewhere. At the very least, it’s my wish that your experience is pleasant and worth your time.

And to the humans out there who are kind enough to read this story: If I could, I’d lie there with you as you turn these pages, my head on your foot, listenin to you babble, breathe, and bite your flimsy claws, hopin you’ll throw me a gasp, giggle, or grunt—anything I can thump my tail to.

Oh, and go ahead and dog-ear the pages. Makes the book cute. 



***
If we had you at "evolution" or even if you're just potentially interested in helping to get this book published then we hope you contact us at holly_dunsworth at mail.uri.edu so we can send you the whole manuscript for your consideration. In case you'd like to read some details from our proposal, here you go...

Categories: Children’s chapter book, fiction, science, nature, animals, pets, adventure, travel.

Project status: Complete manuscript. Illustrations needed.

Words: ~20,000 (11 chapters plus small appendix "A People's History of Dogkind")

Target age group: 8 years old and up

Style: Didactic and allegorical while disgusting and adorable.

One sentence summary: A wise and charming old dog tells the story of his life in which he discovers the real story of dog origins.

Between the lines: Evolution’s so obvious, anybody who's curious and adventurous can see it.

Sources of inspiration: This is a dog’s mash-up of Darwin’s Origin of Species, Descent of Man, Expression of Emotions, Journal of Researches (Voyage of the Beagle), and, of course, his Autobiography.

Summary: As Elroy learns the ways of doghood he can’t help but wonder how it all began. When he kills a squirrel and loves it, and then when he lives with prims (wolves) and loves it, he’s transformed. He yearns to find out more about other dogs, other animals, and other ways of being around the world. So he and his pal Murphy embark on an expedition circling the globe, sending messages back home via carrier pigeon that reveal their hard-sought conception of a whole new perspective on doghood and its origins—the story that all dogs around the world tell their dogglings to this day! Upon their arrival home, initial reactions to the mutts’ discoveries are mixed. Most in the pack are fascinated and smell immediately how this new angle fits their, admittedly, limited perspective at the animal sanctuary where they’ve lived their whole lives, but other dogs are deeply offended by the notion that they could share common ancestors with those savage, beastly prims. After recounting the highlights of his life, which has been focused on hunting down life’s biggest questions, our curious mutt Elroy shares how his discovery connects dogs to prims to elephants and humans and even to squirrels, all the way back in time as one big family on earth, all working towards something larger than any one dog, and towards something more magnificent than anything anybody can conjure up behind the sniffer.

Format and illustrations: I’m open to ideas, but for now I'm thinking For Dogkind should be modeled after a 1940s-50s classic children’s hardback. The book needs to look epic, simple, and classic. I’d like the drawn illustrations (like Fig. 1.2) to share the spirit of the figure that I made for the title. A nice recent model for the look is Alexander McCall Smith’s The Great Cake Mystery. Ideally the book includes many small, simple line-drawings and one map. Plus three multi-page “notebooks” of sketches, brainstorms, and ideas with arrows, family trees, Venn diagrams, etc. They will be modeled after naturalist's field notebook. (An alternative to drawings is to use photographs from free, open sources on the Internet. But I'm not sure how the printing costs of color photographs compares to hiring an artist for black and white drawings! I also would just love it if it was in color but only in the dog's visible spectrum but I don't want to get my hopes up with costs.)

Story behind the book: As a teacher and also as a member of a core team of educators with the Smithsonian’s Human Origins Program, I’m perpetually facing obstacles to learning and accepting evolution, to seeing humanity’s place in nature for what it is. After a particularly stimulating workshop with my Smithsonian team, it occurred to me how funny and downright ridiculous it would sound if a dog was disgusted to learn that he evolved from wolves, the way that humans are appalled by the notion they evolved from monkeys, fish, and primordial goo. I decided that my dogs, Elroy and Murphy, were the dogs to discover evolution and the ones to share their story, our story, with the rest of us. Thus, For Dogkind was born.

Relevance, needs filled, problems solved, importance: People resist the notion that they’re part of the natural world. It’s certainly a problem, and not just in science education, but in how they make decisions and how they behave, overall, in the sociopolitical realm. Evolution—the fact that over many many generations all life on Earth shares common ancestors—is so controversial, still, that only half of American adults admit to accepting it. For Dogkind is a nice allegory for that obstacle—for the potentially dangerous paradigm of human exceptionalism—that we face as educators, neighbors, citizens, and animals in ecosystems. Additionally, For Dogkind is a tale of discovery—something that we want our children to emulate and to achieve, to sink their teeth into and never ever let go.

When I’m not sharin my stories, Holly tells me hers. They’re not half bad. (credit: Julie Dunsworth)

Elroy tweets (without pigeons) at @ElroyBeefstu 



Thanks everyone for allowing us to interrupt the MT this way!
Much love,


Tuesday, October 23, 2012

Music to your ears

A follow up on Martian life?
This post is a follow up of thoughts that were triggered by the things we hear about the search for life on Mars.  We said that speculation about how to look for life on Mars is couched in terms of what we know about life on Earth and how we know about life on Earth in our present time.  Here is a bit of further musing on the nature of independent thinking--if there is such thing.

The history of music.
One might think that the history of music is pretty far removed from anything useful to thinking about science, but in at least one important way it is quite relevant.  This is triggered by some reading we've been doing--just for interest--about music, and that got our attention.  Here, we're referring to composed music rather than what people were singing in the showers or on the streets.

Bach's Violin Sonata No. 1 in G minor
Musical styles change through history.  Medieval music was church-based and had to follow lots of rules.  It was almost strictly vocal.  Then, in the Renaissance, more secular and more a mix of voice and instrumental accompaniment.  In the Baroque period, there were formal structures that were followed, by the likes of Bach and others.  And then came modern style opera and orchestral music.

The genius of his time was Bach, but later it was Mozart, then Haydn, then Beethoven, then....  One can ask, if they had exchanged time periods, could Mozart or Beethoven have written the works they did?  The answer is no.

Albert Schweitzer (1875-1965) was a famous organist, theologian, philosopher, dedicated medical missionary in Africa--and a Nobel Peace Prize winner.  Among things that he did in his life, was to write a detailed biography of Bach, first published in 1911.  I was browsing this, and came across the following:
The more we look into the development of things, in any field whatever, the more we become conscious that to each epoch there are set certain limits of knowledge, before which it has to come to a halt, and always at the very moment when it was apparently bound to advance to a higher and definitive knowledge that seemed just within its grasp. The real history of progress in physics, philosophy...is the history of incomprehensible cessations, of conceptions that were unattainable by a given epoch, in spite of all that happened to lead it up to them, -- of the thoughts that it did not think, not because it could not, but because there was some mysterious command upon it not to.
JS Bach
In music the constraints included both the understanding of theory, of chords, harmonies, and how they 'sound' to listeners, but also they involved the economics--concert halls for the middle class replaced recitals in wealthy homes, or the church constrained what was legitimate; they involved technology, including the very instruments that existed. Without pianos, subtle keyboard music wasn't possible, without modern string instruments, a whole range of emotions and ensemble playing wasn't in the cards.

Why can we have a history of music, of art, of architecture...or of science?  It is because of the chain of evolving context.  What we are now is a product of what we (or our ancestors) were.  We are constrained by the legacy, and we can't live in our future, even if we do live in the future of all the people who once lived.  Unlike a perfect law-like world in which the present could predict the future, for example, as you can predict the path a thrown ball will take, we cannot predict the future of art, or of science.

When we struggle against the unknowns of our own day, we do so in the context of what we know, of the technologies we have available, of the social context of jobs, approvals, status, and a sense of meaning.  We need funding, and that means we must appeal to the contexts of our own day.

Unlike the arts, science purportedly deals with the objective nature of Nature.  Presumably that is a given, we are born to observe and try to understand it.  In the arts, we think more of inspiration and open creativity, not constrained in the same sense with the realities of the physical world.  But the two areas are not so different.  Both science and music build on the shoulders of giants, as Newton put it, but they stray too far from the giant at their own risk.  Mavericks don't generally fare well.  Most of us inch along, even when we are well aware that that's just what we're doing (no matter how much we may trumpet our worth).  Many who succeed had some unpleasant, disturbing, unusual or quirky childhood or circumstances that led them to see further.  It was rarely (if ever) due to what they learned in school--many of the greats in any field were not the products of institutionalized schooling.

Usually, even the transforming geniuses of any age are building on, by departing from, the context they inherited.  That's why, for example, even in science we can find inklings of transformative ideas in the murmurings of predecessors.  Often, indeed, we can find a maverick or two who said what the genius said, but in an unprepared soil so the message was lost.  Partly conservatism and normal-science, partly the reality that we can only do what we can do, even if we know there are problems that go beyond just the fact that much is still unknown--there are problems with the entire approach, etc.

So when we complain about the modus operandi of our era, we understand that first, most scientists can't just invent something totally new; second, they could not have careers if they tried to; third that they would  most likely fail if they did; yet fourth, one cannot order up genius the way you order a hamburger; but, nonetheless, it is important for at least some in the field to harp on its limitations to try to stimulate new thinking.

And Mars....
So this brings us back to life--on Mars. The ideas about what that must be like--the expectation that we'll find 'microbes' or, perhaps more revealing, the interpretation of structures in a Mars meteor as microbes, shows how we interpret even something so alien (so to speak) as life elsewhere, from the lenses of our current experience.  In the past, even among scientists, when we didn't have the DNA and biochemical focus we have today, nor any satellite or huge telescopic reconnaissance directly from the planet, much more dramatic and well-developed forms of life were imagined.

Life today has some basic characteristics, that we discussed yesterday. If we were to discover a quivering slime somewhere, that was clearly a form of life, or some other form that's foreign to Earth life, then our speculations will change accordingly.  Just as we think it laughably far-fetched to imagine little green men on Mars, future scientists may think it was laughably naive to suggest such parallelism between Earth and Mars as is done today.

It's possible as we said yesterday that our understanding of chemistry is so complete that we can rule out truly different kinds of 'life.'  But that would be remarkable, given the history of science to date.  We always think we know the parameters as well as the perimeters of Nature.  The 'end of science' has been proclaimed before.  But so far, we've been wrong because we've always been very limited in our understanding.

Similarly, no one can say what kind of music here on earth will please our descendants.

Monday, October 22, 2012

Life on Mars: Why microbes?

Tropes of our time
When the proponents of costly explorations of Mars start justifying these projects, they usually reduce the reason to the objective of finding life there.  That's good space-travel-as-Disney imagery that will get the public to open up their wallets.

In fact, even the most hyperbolic NASA proponents don't promise 'advanced' life like humans (or, even, little green men) there.  No, they are always referring to microbes, so tiny that we can't see them from telescopes or cameras aloft in orbiting spacecraft.  We have to land, and indeed we have to land guys with shovels to find it.

The argument that Mars life must be primitive is based on the geological history of Mars which suggests that it and the Earth originated at similar times, but about 4 billion years ago the smaller Mars settled down to a nearly atmosphere-free, more hostile environment unlike the hospitable environments here.  But if life had begun on Mars at about the same time as it seems to have begun here, so the tale goes, it would have reached a comparable stage of primitive forms, the kind that evidence from 3.5 billion year old rocks shows was then here on Earth....life that the newly hostile Martian environment killed off.  At best, if there are any surviving forms, they'll have to be hiding, protected, under the ice or huddling inside rocks.

That's a pretty powerful belief in parallel histories up to that point, as if life is nearly inevitable.  It seems like quite a stretch, but that's not all.  Even purportedly knowledgeable scientists speak of carbon and oxygen and so on in Mars rocks, in the context of noting that these are the building blocks of life, and especially of DNA.  This shows how deeply the flash-words, or 'tropes' of our time control our thinking, although we know that it's by far more likely that RNA came first (here on Earth, at least).  But this is how current science is embedded in current culture.  RNA has very similar molecular contents, but the implied idea is that a DNA-based protein code must be the way life works.  That's how it is here, and it's the core of current life science, so it must be that way there, too!

NASA will be peeking with great Curiosity everywhere it can look for anything it could claim suggests life, and eventually exploratory vehicles will try to bore down to find life, shivering modestly, in or under the Martian ice.  Again, we look there because, with its unshielded solar radiation, cold temperature, and little atmosphere, Martian life can't live on the surface--or that is, earth life couldn't--and assuming the same about Martians provides a convenient escape clause for why we we haven't actually seen any Mars life.

Principles of Life
Although our current scientific culture, and its popular image, is centered on or even obsessed by Darwinian competition as the essence of life, there are many other principles that are much more pervasive and important.  We described these at great length in our book MT, and in other papers.  Not only do we argue that cooperation (that is, functionally successful interactions) among many contributing elements is the rule, but the same fact fits with other aspects of life.  Among them are that life, from genes on up, is organized around modular functional units that interact in partially isolated or compartmentalized structures.

The same MT principles are even more deeply, if subtly and even implicitly, at work in surmises about Mars life.  The assumption that we're looking for 'microbes' is that Martians will look like bacteria. This expectation was whetted by the idea, fostered a few years ago, that rod-like remnants of 'microbes' were found in a Mars meteorite named ALH84001, found in Antarctica in 1984. Whether this is biogenetic or biobulldroppings is beyond our expertise.  But the interpretation that it was life rests to a great extent on the tacit assumption that sequestered modularized structures--cells with internal structures that sequester the inside from the outside--is a universal feature of life, wherever we may find it.

The reference to DNA reflects also the assumption that life at the molecular level is a polymer phenomenon--a string of units (assumed to be nucleotides) that are grouped into local, distinct, functional parts).  That means life is not just a reaction among identical molecules, even a 'cooperative' one like the formation of crystals, but is instead based on cooperative interaction.

These kinds of statements about Mars life show the latent assumptions about life, not just or even not mainly about evolution but about how it must be organized. It is an implicit reflection of the kinds of principles we discussed in MT. 

At the same time, it reflects a lack of imagination or much thought.  It is embedded in our current culture, here on Earth, where we are focused on DNA and bacteria as the primitive detectable form of life, because that's what we see here and that's the current theme of the life sciences.

Could life be other than something than this?  And here we mean something beyond the question of whether life must involve carbon or water, etc.  Rather, we ask whether the laws of physics and chemistry mean that to be an evolvable builder of orderly but non-homogeneous complexity--forms built up with variable subunits, the way we are built of cells, organs, organ systems, and populations--must be based on spatial relationships among polymer-like molecules, whose combinatorial presence enables structures to be built.  If that is the case, it is probably a rather profound truth.

And yet, can that be the case?  It would seem not likely, since even our understanding of life as it happened here is that it arose merely as chemical reactions in a primordial soup in some lakes, ponds or oceans.  That is, it was initially some open reactions, not encased in membrane compartments, not diversified based on an array of 'instruction' molecules (RNA or proteins).
 
If not, if there could be very different ways of what we would classify as 'life', then we could be in for some startling surprises as space is explored. And it would show how rooted human thinking is in its cultural context, no matter how objective science tries to be.

Friday, October 19, 2012

Social Malaria

My name is Daniel Parker and I am a PhD candidate at Penn State University in the Anthropology and Demography Departments.  I consider myself to be a population scientist and my research concerns a range of population scales, from the microscopic level to human metapopulations (populations of populations).  Humans are my favorite study organism; however I am also very interested in the microparasites and invertebrate vectors that plague humans.  My dissertation research looks at human migration and malaria in Southeast Asia.  Anne and Ken invited me to write a guest post on this subject, and this is it.
--------------------------------



Are there social determinants to malaria infection?

If you’re a social scientist you might be quick to say yes, but if you understand the biology of the disease the question may not make much sense to you.

A female anopheline mosquito feeds on someone carrying the sexual stage of the parasite.  The blood meal gives her the nutrition necessary for laying her eggs.  Assuming that the parasite has successfully undergone another transformation in the mosquito gut, and that the mosquito feeds on another person, she may transfer the infection.  Mosquitoes probably don’t care about the socio-economic status of the people on which they feed (though they do seem to prefer people with stinky feet and pregnant women).  It is probably safe to say that all other things being equal, mosquitoes really don’t care who they bite.  But are all other things equal?  Not even close…

Let’s consider our not-too-distant history with malaria in the U.S. since it was a plague of non-trivial proportions for a large swath of our nation.  During the 1860s a prominent scientist (one of the first to publicly suggest that malaria may come from mosquitoes) argued for having a giant screen placed around Washington D.C. (which was a swampy, malaria infested city up until the mid 1900s).[1]  Several of our presidents seem to have suffered from the disease.  George Washington suffered throughout much of his life with bouts of fever that were likely malaria.  Presidents Monroe, Jackson, Lincoln, Grant, and Garfield also may have suffered from malaria.  On a personal note, both of my grandparents contracted malaria growing up in modern day Oklahoma (at that time it was still Indian Territory).  My grandmother still drinks tonic water, which contains the antimalarial Quinine, when she feels a headache or chills today.    The following maps (I apologize for the poor resolution) come from a CDC webpage about the history of malaria in the U.S.

 
CDC Malaria History

A question, then, is: How were we so successful at eradicating malaria here?  Furthermore, why didn’t we do that everywhere else?!!!

A favorite story for many anti-environmentalists is that it was all or mostly because we used DDT.  And beginning in the 1930s we did use the hell out of DDT.  Apparently it was common practice for parents in the Southern U.S. to encourage their children to run behind DDT fog trucks as they drove down streets.  (See this blog post for some related stories).  But some real problems with DDT are that it doesn’t just target mosquitoes, probably also targets the predators that would feed on mosquitoes and other pests, and can potentially cause all sorts of troubles (with regard to bioaccumulation and/or biomagnifications) as it works its way through trophic levels.  A few people noticed this could be a problem (see Silent Spring by Rachel Carson) and DDT production was halted in the U.S in 1972.  (Soon after there were global efforts at banning its use for agricultural purposes).

But DDT wasn’t the only thing that changed in the U.S. during the Second Great War.  The U.S. was just coming out of the Great Depression and there were some interesting demographic things going on too.  For example, lots of working-aged males were away for the war, returned in masse, and then some major baby-making ensued.  The economy was rebounding and suburbia was born, meaning that many of those baby-makers could afford houses (increasingly with air conditioning units) that wouldn’t have been possible in previous years.  There were major public works projects aimed at building and improving drainage systems and sanitation.

During this same time period chloroquine, a major antimalarial drug with some important improvements on quinine, went into wide-spread use (mostly in the 1940s) but by the 1950s there were drug resistant parasite strains in Southeast Asia and South America.  This isn’t a surprising occurrence.  Antimalarials provide a pretty heavy selective force against the parasites.  Furthermore, those parasites undergo both clonal and sexual reproduction, meaning they can potentially generate a lot of novel variants and strains.  This has been the curse of antimalarials ever since, soon after they are rolled out the parasites develop resistance and resistant strains quickly spread globally.

Eradication of malaria in the U.S. occurred during a time when we were using heavy amounts of DDT, when we had access to relatively cheap antimalarials, and when we were undergoing some major socio-economic, structural, and demographic changes.  However the DDT was becoming an issue of its own and wasn't working as well as it once did.  The antimalarials weren't working as well as they once did either.  Despite this fact, and despite the fact that mosquito vectors for malaria still exist in the U.S., we still don’t have a real malaria problem.  And while it is almost impossible to tease out all of the contributors to our current malaria-free status, I argue that the social and economic factors that changed during this time period are the main reason why malaria is no longer a problem for us here in the U.S.  If that weren't the case, we’d be back to using insecticides and antimalarials to try to eradicate it once again.

I’m certainly not the first to notice such things.  A study on dengue fever (a mosquito-borne viral disease) in a Southern Texas/Northern Mexico town split by the international border (los dos Laredos) found that people without air conditioning units seem to have more dengue infections when compared to people who do.[2]  Poor people, living on the Mexico side of the border, tended to leave their largely unscreened windows open since they didn't have AC units to combat the sometimes brutal heat in that part of the world.  This is a clear example of how socio-economic factors can influence mosquito-borne disease transmission, but it plays out in other ways in other environments and parts of the world.

In Southeast Asia, where I do malaria research, many if not most of the people who are afflicted with malaria are poor, ethnic minorities and migrants who have been marginalized by governments and rival ethnic groups.[3]  Constant, low-grade warfare in Myanmar (Burma) for the last half century has left many of the residents of that nation in a state of public health crisis.  And, since pathogens don’t normally respect international borders, malaria remains a problem for neighboring countries such as Thailand (which is mostly malaria free when you exclude its border regions).  The story is the same along China’s border with Myanmar in Yunnan Province.  Mosquitoes don’t target people because they’re poor disenfranchised ethnic minorities.  But a lot of those ethnic minorities do happen to live in conditions that allow malaria to persist, and the mosquitoes who pick up malaria go on to feed on other potential human hosts, regardless of their economic status.  This means that your neighbor’s poverty can actually be bad for you too.

Arguably, most (not all!) public health advances can be largely attributed to socio-economic change (google: McKeown hypothesis).  Increasing the standard of living for entire populations tends to increase the health of populations too.  In Asia, nations such as Taiwan, Japan, most of South Korea (excluding its border zone with North Korea), and Singapore are malaria free.  Obviously, it isn’t always an easy task to increase the standard of living for a population, but the benefits go far beyond putting some extra cash in peoples’ pockets and letting them have nice homes.  The benefits include decreases in diseases of many types, not just malaria, and that is good for everyone.

Consider, now, the amount of money that is dumped into attempts at creating new antimalarials or that ever elusive malaria vaccine.  Consider the amount of money that has been dumped into genome sequencing and countless other really expensive scientific endeavors.  And then consider whether or not they actually have a lot of promise for eliminating or controlling malaria in places that are still plagued by this disease.  Sure, sequencing can provide insight into the evolutionary dynamics associated with the emergence and spread of drug resistance (and that is really exciting).  Some people believe that genomics will lead to personalized medicine, but even if this is true then I am skeptical that it will ever trickle down to the people that most need medical attention.  New antimalarials and new combinations of antimalarials may work for a while.  But it seems pretty obvious to me that what actually works over the long term, regardless of parasite evolution and genetics, is what we did right here in the U.S.  So, at the risk of jeopardizing my own future in malaria research, I've got to ask:

From a public health standpoint, is it possible that it’s cheaper to attack socio-economic problems in malarious places rather than to have thousands and thousands of labs spending millions and millions of dollars for cures that seem to always be short lived?  

Wouldn't we all get more bang for our buck if we took an approach that doesn't only address one specific parasite?       

1. Charles, S. T. Albert F. A. King (1841-1914), an armchair scientist. Journal of the history of medicine and allied sciences 24, 22–36 (1969).
2. Reiter, P. et al. Texas lifestyle limits transmission of dengue virus. Emerging Infectious Diseases 9, 86 (2003).
3. WHO, Strengthening malaria control for ethnic minorities in the Greater Mekong Subregion. 2011, (2008).

Thursday, October 18, 2012

Science and social policy

We recently blogged about science denial being a trait we can't just attribute to creationists, but one that we scientists share as well.  We said that to a great extent political views can determine how we pick and choose the evidence we believe.  Right-wingers tend to deny climate change but climate change can make left-wingers very anxious; to a right-winger IQ is real and even a genetically determined group characteristic while to a left-winger it's impossible to measure and is environmentally determined.  So in this light, a story at the BBC website on Tuesday was of interest.

Entitled "Childhood adversity affects adult brain and body functions, researchers find," and written by Alok Jha, the piece describes a number of studies presented at the Society of Neuroscience meetings this week in New Orleans.  The papers aren't yet published but the abstracts are online, and here's the first sentence of one example (E. Pakulak, Y. Yamada et al.):
A large and growing literature documents the profound impact of lower socioeconomic status (SES) on cognitive skills and brain structures and functions in children (Hackman, Farah, & Meaney, 2010).
Well, so if you're a believer in IQ being genetically determined and the idea that people earn their socioeconomic status by virtue of their IQ, this isn't right.  That's because you think the cause and effect are the other way around: cognitive skills have a profound impact on where we end up in the SES hierarchy, children inherit their cognitive abilities and therefore they inherit their place in the order of things.  But if you believe that the brain is plastic, and can be affected by experience, you're perfectly ok with how this abstract begins.  In fact, probably you liked the presentation title and that's why you kept reading.

So, say you wanted to sort out which comes first, cognitive ability or SES (and just as importantly, who's right), how would you do it?  Clearly just declaring the order in which you think things happen isn't enough.  A lot of work on neuroplasticity has been published in the last decade or so, much of which is pretty convincing, which may or may not predispose you to believe findings that brains can respond to environment, but even so let's think about it.  Since it's impossible to determine cause and effect just by looking at outcome, what's required is an intervention study.

You'd need to look at the IQ/brain structure/cognitive abilities -- whatever you think the right measure/outcome is -- before and after some kind of intensive training/attention/input.  Anything from a repeat IQ test to determine whether cognitive abilities have changed to a follow-up MRI or fMRI or PET scan to assess changes in brain structure or functioning.  Though, if you did see improved IQ scores, you'd have to worry about whether repeat testing itself is what improved the scores.  And you then have to do the genome sequencing of each individual to be able, in principle, to separate out prior inborn, and later experiential effects, assuming inborn factors are identifiable.  Clearly, these kinds of studies have to be carefully planned and interpreted, at best. 

Judging from the abstract, the study described by Pakulak et al. was an intervention.  They gave adults from a number of SES backgrounds a battery of memory and language proficiency tests and found that childhood SES was strongly predictive of working memory, language proficiency and attention span.  But, see above as to cause and effect.  Then they did an intervention with parents of lower SES children, after which they measured "attention/executive function" in this group and in controls and found attention improved. They conclude that cognitive abilities are malleable and that neuroplasticity extends into adulthood. They did not test the role of genetics.

At the same meeting, Suzanne Houston reported that
...the size of different parts of the brain could be affected by growing up in different homes. "We found higher parent education, smaller amygdala. The higher the income, the larger the hippocampus."
Her interest is in determining which environmental factors affect brain growth.   Others reported that excessive stress or abuse in childhood affects the functioning of the brain and is associated with ill health in adulthood. And so on. 

Does all this work resolve this debate?  Of course not.  If you think IQ is fixed at birth, you wonder first whether the executive function Pakulak et al. measured improved, and if not why not.  That's not addressed in their  abstract. Does something other than improved cognition explain improved attention?  Say, the desire to please the researchers?  You might wonder whether the sample size (72) was large enough.  A researcher can't do the experiment of having a child grow up in one home and then another and measure the difference in the brain.  Nor adequately control for confounders in studies of, say, stress and adult morbidity and mortality. So, you might think this is all yet more evidence that we should stop pouring public money into programs based on the principle of equal opportunity for all when they clearly can't work for everyone. 

But, if you already like the idea of neuroplasticity, and believe that society has a responsibility to let everyone live up to his or her potential and that everyone shares the same potential, you think this kind of study is yet more evidence of neuroplasticity, that social programs can improve the lot of those in the lower SES and that tax money should be spent equally on everyone.

In all of this, we also know that uterine experience can affect growth, development, gene expression and physiological states, and these themselves can be inherited.  Whether this applies to traits like IQ is an open question today, as far as we know, and indeed gene expression would have to be tested for each relevant tissue, and whether this was only relevant during gestation or remains so during life. The point here is just that uterine experience adds another potentially major source of variables that would have to be measured.

It's much easier to pick apart a study we disagree with than one we like, even if we don't recognize that's what's going on.  We all have our subtle biases and may not even be aware of them.  And then there are the not-so-subtle biases.  And, since there's no such thing as a perfect experiment, any study can be criticized.  Rarely do we learn, when we're taught the scientific method, how much our evaluation of the evidence depends on what we already believe rather than how well the experiment is done.