Friday, November 21, 2014

Serial science

Are you hooked on Serial yet?  The current season of this radio series from the makers of This American Life explores whether Adnan Syed, in jail for the last 15 years and sentenced to life for killing his ex-girlfriend Hae Min Lee when they were both 18, really did it.  He says he didn't.  His friend Jay says he did.  The question comes down to, what happened in those crucial 21 minutes when his whereabouts are unknown and undocumented, and Hae was strangled?

Sarah Koenig, presenter of this series, and a producer of This American Life, describes herself as having been obsessed with this case for the past year.  She probes every angle, reads every report she can find, listens to the police interview tapes, talks to anyone who will speak to her about what they saw or what they know, revisits the supposed scene of the crime, tests whether Adnan could have gotten there in the 21 minute window of opportunity, challenges Adnan with her thoughts, doubts and questions in hundreds of phone calls, and so much more.
What she realized is that the trial covered up a far more complicated story, which neither the jury nor the public got to hear. The high school scene, the shifting statements to police, the prejudices, the sketchy alibis, the scant forensic evidence - all of it leads back to the most basic questions: How can you know a person’s character? How can you tell what they’re capable of? In Season One of Serial, she looks for answers.
Some weeks Koenig is convinced Adnan is guilty, some weeks she's not so sure. We don't yet know what she concludes, or indeed whether she concludes anything other than that it's impossible to reach a conclusion, but, perhaps because it's possible to weigh the evidence from various angles, it's a gripping series.

Scales of justice; Wikipedia

A compelling story.  Not because we really care about Adnan -- unless he's innocent, in which case of course, the injustice is a tragedy.  Indeed, it's Hae one really cares about, a bright young woman whose future was violently and callously taken from her.  And, the idea that, to compound this tragedy, a young man's life may have been ruined by a system that didn't do it's job is also part of the emotional hook that keeps us listening.  But more, to me the show is fascinating because of what it tells us about truth, and how we know what we know.

Starting with the Enlightenment around 400 years ago, the gold standard for science has been empirical evidence, the equivalent of fingerprints, witness stories and DNA.  Naturalists collected then, scientists collect now, observational or experimental data, to try to make sense of, and build a story with.  As Koenig does, scientists assume there's a truth, and that evidence can lead us to it.  Yes, the evidence needs to be tested and weighed, and evaluated and re-evaluated, but the assumption is that with evidence we can know the truth.

But that's science. Koenig is talking about a legal question -- this crime happened, who did it? Lawyers aren't necessarily looking for the truth, even though they know there is one, because they know they can't necessarily know what it is.  The evidence often can be interpreted in numerous ways, used by a canny defense attorney as well as a canny prosecutor in support of either guilt or innocence.  Or, as in Adnan Syed's case, it seems that what would be crucial evidence just doesn't exist, so he was convicted on circumstantial evidence instead.

And of course sometimes pieces of evidence are omitted in the pursuit of a consistent story, which is often what lawyers are really after.  Many times, defense lawyers don't know whether their client is guilty or innocent, but they simply (or not so simply) build whatever exculpatory story the evidence (or some of the evidence) will support.  So, Koenig is being an ace reporter in this series, and a great storyteller as she unpeels layer after layer after layer of evidence in her search for the truth, but she's not necessarily being a winning lawyer.  But that's ok; she is a reporter.  By contrast, in our system a lawyer's job is to take sides, not to seek truth, which is different from science and might seem strange unless you realize that there may not be a better way, to determine guilt or innocence  when truth can't be tested directly.

Chemical balance; Indica Scientific

Scientists are telling stories from evidence, too, with the hope that there's a knowable truth to be found.  As much evidence as they can get.  Should they be impartial?  Yes and no.  Building evidence is what the whole push for Big Data, and meta-analyses is about; building stories from enough data that we can assume we're approaching the truth.  Evidence that should be weighed impartially.  This seems like the new path to truth but, to be fair, Darwin collected Big Data in his way, too, observing more pigeons, barnacles, and orchids than most of us would have had the stomach for.  He was a diligent, patient observer, who also built a consistent story from the evidence -- but with various theories in mind.  Not impartially.  So, scientists are reporters of the natural world, but the synthesizer scientists are lawyers, too, piecing together the evidence to make a good, consistent story, taking a side.

But, it's never clear how close we are to the truth, even if or when we think we can assume there is a single truth.  Understanding what genes are and what they do, for example, took a lot of sleuthing, building a story, from the circumstantial evidence that Mendel so diligently provided, to the discovery that chromosomes were an important actor, and the discovery of DNA, and so on.

But geneticists understood what genes were a lot more definitively in the beginning than they do now. Ironically that was because it was before there was so much evidence.  Ask 5 of them now what a gene is, and if any of them actually give you an answer it will be vague, and it's likely that it won't agree with any of the others you get.  Ken always told his Human Genetics students each semester that much of what he was going to tell them wasn't going to be true the next year.  They seemed surprised or nonplussed, but he then explained about our growing knowledge and understanding.  Presumably there's a truth, and presumably we're heading toward it, but often it seems we have no idea how close we are getting to it.  Of course, the goal keeps changing as discoveries keep happening, and that doesn't help.

We don't yet know how Sarah Koenig is going to conclude her story.  She will have plowed through masses of evidence, but if the truth was in there to be found, I think it would have been found 15 years ago.  She's talking to a lot of people who knew Hae and know Adnan, and perhaps she'll dig up something new and significant that might change the story.  But so far, the crucial evidence is missing; only Adnan, Jay and Hae know what happened, but Hae can no longer speak, there were no witnesses, and Adnan and Jay are telling different stories.  Or, maybe someone else killed Hae.

This is an imperfect metaphor for science, of course, because no one person is holding out on us on whether there are multiverses, or dark matter, or something crucial missing from our understanding of biology, or even how antimalarials work.  But the elusiveness of these kinds of truths, the difficulty of interpreting the evidence and the idea that we might need to re-evaluate the data from time to time certainly pertain to science.

Thursday, November 20, 2014

K13 and the spread (or simultaneous emergence) of drug resistance in malaria parasites

We’ve mentioned this before, but the malaria and evolution story is complicated by multiple evolutionary tales:

  • Humans adapt to parasites
  • Parasites adapt to humans
  • Mosquitoes adapt to both

Parasites may adapt to mosquitoes too – and humans have adaptations to mosquitoes…

Malaria parasites bursting from red blood cells.  From National Geographic, June 1986 - scanned and shared online by Centuron: http://imgur.com/a/nBJb6
This post is a story about parasites developing responses to some of the things we do to get rid of them.  Malaria parasites appear to have a real knack for survival, or at least the ones that survive and spread do.  Time and time again they have developed immune responses to our antimalarials.  Sometimes it happens quickly, sometimes it seems to take decades, but each time a new antimalarial is used, parasite strains emerge that are resistant to that antimalarial drug.

Southeast Asia appears to be a “special” place with regard to the evolution of antimalarial resistance.  For whatever reason, parasites that are resistant to new antimalarials always seem to be first documented here and then sometimes appear to subsequently spread globally.  (See Klein 2013 for a nice review of some theory around this problem (2)).  For example, chloroquine resistance in falciparum malaria seems to have independently emerged in both South America and Southeast Asia, but then seems to have spread globally from Southeast Asia (3).

Plasmodium falciparum parasites are almost globally resistant now to all antimalarials except for artemisinin.  In an attempt to keep these drugs effective, there has been a huge push to only use them in combination with other antimalarials.  The mechanisms of action of most antimalarials aren’t well understood, but the hope has been that by using different drugs, with different half-lifes, and probably different modes of action, then it will be much more difficult for parasites to develop resistance when compared to monotherapy (only using a single drug).

However, despite these efforts, artemisinin resistance has emerged in Southeast Asia (4).  It is not normally complete treatment failure at this point, but rather increased clearance times.  For example, while it would once take at most two days for parasites to be cleared from a patient’s blood stream after taking a dose of artemisinin, it now can take five.  Occasionally the treatment doesn’t work at all.   This is even occurring with artemisinin combination therapy.  Strains of parasites with “reduced sensitivity” have been found in Cambodia, in part of Vietnam, and along both sides of the Thailand-Myanmar border.

Some work has attempted to understand the genetics behind artemisinin resistance but many results, including a few I’ve been a part of, have contradicted each other.  However, one region on the parasite’s chromosome 13 keeps popping up in analyses.   Earlier this year, mutations in a particular gene (Kelch 13 (K13)-propeller) were identified as being potentially important in artemisinin resistance.  The function of this gene in the parasites isn’t well understood, but it is related to protein interactions.  And it isn’t a single point mutation that seems to confer resistance.  It appears that a wide variety of mutations, any of which are occurring in this gene, lead to parasites that are less sensitive to artemisinins – and this has now been confirmed both in vitro and in vivo.

The in vitro portion of this work began with a lab strain of falciparum malaria (3d7) which was intermittently exposed to artemisinins over a period of five years(5).  Doses of the drug were applied, then removed, then applied at higher proportions over this period of time.  Parasites from each dose cycle were sequenced so that the origin of mutations could be documented and so that mutations could be compared between case and control strains.  Ultimately the researchers narrowed their search down to a mutation in a single gene that corresponded to a point in time where some of the lab parasites seemed to no longer have strong, negative reactions to the antimalarial.

[It is important, I think, to remember that drug resistance isn’t usually an all or nothing type of trait, it is much more a trait of degree.  Even in situations where an antimalarial no longer works, it is likely that by increasing the dose of that antimalarial, there will be a point at which the parasites are still sensitive.  The problem is that it also becomes toxic to the human at some point.]

Next the researchers began looking at field isolates, across space and time, in Southeast Asia.   While they didn’t always find the same point mutations, they did find mutations in the same gene, in geographic areas where parasites are known to be less sensitive to artemisinins.  In areas where parasites still appear to be sensitive to the drug, they did not find mutations in this gene.  Furthermore, the prevalence of these mutations appears to have increased in certain regions (the ones that now have artemisinin resistance) over time.  

These findings are interesting I think for several reasons.
Here we have a gene in which mutations are somehow related to artemisinin resistance in malaria parasites.  But there isn’t a single mutation that leads to this resistance phenotype – rather it seems that just about any mutation(s) in this “gene” leads to resistance.  Does that make this a gene for resistance?

Another major finding, this time from a paper that came out in September 2014 (6), is that these mutations may not be spreading in the same way that other resistant strains (like chloroquine resistant falciparum malaria, for example) seem to have.  By analyzing the flanking regions of the K13 gene, analyzing patterns of linkage disequilibrium, the authors noted that several mutations in the K13 gene appear to have emerged independently and almost simultaneously both in Cambodia and along the Thailand-Myanmar border.

Once again the implications are quite interesting, if also scary.
One is that the evolutionary response seems less rare and unique if it can happen independently and simultaneously in different regions.  Does this mean that combination therapy is not working the way we hoped it would?

Another is more directly related to public health.  Right now there are several small scale elimination attempts occurring throughout Southeast Asia.  In fact, I’m working with one of the teams doing this (briefly discussed here).  Our hope is that we can wipe out resistant strains before they spread (via mosquitoes or humans) to other regions – perhaps especially Africa.  If resistance is likely to evolve anywhere that artemisinins are being used, we may not be able to halt this spread.  I would argue that our intentions to eliminate malaria in targeted subregions are worthwhile regardless.  But, it is a bit scary nevertheless.  




*** My opinions are my own!  This post and my opinions do not necessarily reflect those of Shoklo Malaria Research Unit, Mahidol Oxford Tropical Medicine Research Unit, or the Wellcome Trust.  


1. Network MGE. Reappraisal of known malaria resistance loci in a large multicenter study. Nat Genet. 2014;46(11):1197–205.

2. Klein EY. Antimalarial drug resistance: a review of the biology and strategies to delay emergence and spread. Int J Antimicrob Agents [Internet]. Elsevier B.V.; 2013 Feb 7 [cited 2013 Mar 8];41(4):311–7. Available from: http://www.ncbi.nlm.nih.gov/pubmed/23394809

3. Payne D. Spread of chloroquine resistance in Plasmodium falciparum. Parasitol Today [Internet]. 1987 Aug;3(8):241–6. Available from: http://www.ncbi.nlm.nih.gov/pubmed/15463062

4. Dondorp A, Nosten F, Yi P. Artemisinin resistance in Plasmodium falciparum malaria. New Engl J Med J … [Internet]. 2009 [cited 2013 Nov 17];455–67. Available from: http://www.nejm.org/doi/full/10.1056/nejmoa0808859

5. Ariey F, Witkowski B, Amaratunga C, Beghain J, Langlois A-C, Khim N, et al. A molecular marker of artemisinin- resistant Plasmodium falciparum malaria. Nature. 2014;505(7481):50–5.

6. Takala-harrison S, Jacob CG, Arze C, Cummings MP, Silva JC, Khanthavong M, et al. Independent Emergence of Artemisinin Resistance Mutations Among Plasmodium falciparum in Southeast Asia. J Infect Dis. 2014;491:1–10.

Wednesday, November 19, 2014

"Save the planet": a meaningless slogan?

What is all this talk about sustainability and so on?  What does the term mean and do we have historical precedents to turn to for an answer?  These days, in relation to the concept of sustainability we also hear a debate about how to 'save the planet' in the face of climate change, global warming, CO2 emissions, fossil fuels, overpopulation, industrial agriculture and erosion, antibiotic overuse, loss of clean water, and so on.  We're on various email lists that almost every day send us stories bemoaning the course of things that are not 'sustainable'.

Nothing specific triggers this post other than musing about a set of issues that may be of critical importance to 'us'--whoever 'us' is.  These various terms and slogans make sense to many people and indeed even hearing them puts others' hair on fire, because they oppose what those who want to save the planet are assumed to be advocating.  But these terms are in themselves almost without clear meaning, if any meaning at all, and that can be a problem, given how polarized society is on the issues.

Generally speaking, those on the political left express urgent fear about the current problems that are being discussed, recognized, or claimed.  The left wants to save the planet by cutting back on the use of fossil fuels and big-scale agriculture, human overpopulation, the destruction of natural habitats, and so on.

In reaction, generally those on the political right say that if there really is a problem (they tend to doubt sensory reality and science as its formalizer), then industrial innovation and the capitalist seizing on opportunity will fix it, so not to worry.  Even more, they often argue that the crises are being over-stated or data being misunderstood (or fabricated) so that, in truth, the planet doesn't need 'saving' anyway.  Global warming is either being misinterpreted or it's just part of the normal cycling on Earth and the pendulum will swing back in time.  Industrial capitalism will feed and warm us all, if we but give it the time and enough rein to do its job. The planet, in a sense, will 'save' itself.


Earth; What exactly does one want to 'save'?  Source: Wikipedia


But if you think about it, none of this has much meaning at all, no matter that it sounds like it does.
To see this, we ask in particular what, exactly, save the planet means?

1.  Does it mean save our current way of life?  Do we want to cut back on fossil fuels enough to stop or reverse global warming and resource exhaustion, but not so much that even liberals would complain?  I don't hear them saying we need to outlaw18-wheelers, or trains, tractors, air conditioners, golf carts, power leaf-blowers, backyard pools, or personal cars.  'Cutting back' generally seems to mean to people that we can have a bit less, though not a whole lot less, and still keep our lifestyle and reverse climate change, loss of topsoil, and so on.  Of course, if we really wanted to 'save' the planet in these terms, perhaps we should be advocating global equity in resources and living conditions, but nobody is actually serious about that because if we evened out the income distribution we'd all be in the soup.  Indeed, of course, we're concerned that the Chinese, Indians, Brazilians et al. want to wait til they have cars and A/Cs before they start to save the planet.

I mean, if we polluted ourselves out of supermarkets and personal cars, we would still survive, though there would be a lot fewer of us, and perhaps no global transport and even, heaven forbid, no electronic entertainment.  Some would survive all the fracking anyone could possibly imagine.  So, here, 'saving' really means something akin to delaying the demise of our way of life.

2.  Save human life on Earth?  That is an understandable if selfish thing to advocate.  The Earth would not miss us were we to go extinct.  And we will eventually be gone, of course.  So as far as that goes, again what is being advocated is not save the planet, but delaying our specific species' demise.  Likewise, saving species from extinction is, as any ecologist or evolutionary biologist (or cosmologist) knows, quite illusory.  All species become extinct and only a fraction of lineages do that by evolving into new species.  In the long term, of course, the Earth will be swallowed up by the exploding dying Sun.  So 'saving' again means 'delaying' something we, personally, in our very short-sighted, egocentric lives value.

Even more than that, we want our own lives to have some sort of long-term meaning. That's of course also an illusion, unless perhaps you have expectations of an infinite afterlife.  It's just that when we are returned to ashes, some new future ashes will harbor similar thoughts (about their own lives).

3.  Save the 'planet' as a whole?  It means little to talk about 'saving' the planet.  First, evolution has always adapted life to our planet's conditions, and there is absolutely no reason to think it won't adapt to whatever humans do to the place, including nuclear holocaust.  But since Earth is doomed to destruction eventually, what, exactly, does 'saving the planet' mean?  I think it probably means some cuddly short-term view of things, rather than a carefully considered view, unless it means preserving for the moment things we happen to like, like pandas, our kids and grandchildren or fellow countrymen and the like.  There's of course absolutely nothing wrong with that, but one should be clear, because not saving 'the planet' doesn't mean there'd be nothing; it just means it'd be different.

Our planet is not in danger and doesn't need 'saving'.  The Earth is one huge biochemical reaction and its 'Gaia', its physico-chemical unity is based on its components, energy, and so on.  When or whether or for how long people, or any given lifestyle, or any lifestyle exists is part of that.  We may try to preserve what we like, or enough of what we like, in a state that for our limited lifespan and egocentric purposes seems permanent, if that's how we wish to define 'save'.

4.   Go back to swidden hand-hoed agriculture?
There are many arguments, apparently quite valid, that we are rapidly exhausting our soil in various ways having to do with large-scale industrialized commercially capitalized agriculture.  Does save the planet mean to find and implement ways, that apparently do exist, to grow enough to feed the human population without this being forced upon us when naturally developed soils are drained away?  This might be a good objective, but it is a political one, obviously, because from the 'planet's point of view, maybe its overall sustainability would be better off if we did exhaust the agricultural soil and starved ourselves out of existence or at least back to less resource-demanding numbers. But save the planet as a slogan probably isn't advocating this.  Does it just mean we don't like the way Kansas is being farmed, that Big Ag's like Monsanto are very rich, and that we (most of us who've never really seen a farm first-hand) are venting some nostalgia about things we don't really personally even know much about?

5.  Develop 'sustainability'?
This word is as vague and in a way naive as save the planet.  Nothing in human (much less evolutionary) history is eternally sustainable.  Change is part of Nature and its geological-historical processes.  Human agriculture has more or less from its beginning gone through periods of growth, resource over-use, and decline.  That ours will do the same should come as no surprise.  Is that bad? From the point of view of our own personal nostalgia and sentimentality, perhaps.  From the point of view of 'the planet', there is no reason to impose such a purely human judgment.

In a NY Times editorial on the Canadian tar sands XL pipeline debate, Andrew Nikiforuk concludes:
"The American social critic Lewis Mumford described mining as barbaric to land and soul. By any definition, Keystone XL grants license to an earth-destroying economy."
The editorial is in itself a good discussion of the tar sands and how they are extracted and what that will do to large tracts of forest.  But the final description is just naive, in the sense I am discussing.  No matter what the ramifications in the short term, mining won't actually destroy the earth.

Yet, of course, there is something here--but what is it?  Esthetics about primeval forest?  Global warming and forest destruction?  Dislike of greedy BigOil?  Failure of society to come to grips with the potential traumas whose seeds short-term convenience and greed will lead to?

Do as I say, not as I do?
A new book by Naomi Klein called This Changes Everything, is getting rave reviews these days.  She makes a case that current global capitalism is responsible for climate change that is soon to be disastrous (not good for saving the planet!).  We must cut back, way back, on our energy consumption in the developed world.  Citing conservation advocates' estimates, for global sustainability and to curb or reverse global warming, we must, if we are humanitarian, share the wealth, that is, share the per-capita Wattage expended.  We here in the developed world need to cut back by something like 80%, and let those in the developed world grow, for humanitarian reasons, a few-fold.

Sounds nice.  I haven't read the book, and I am writing based on reviews, including an excellent recent one (OA) by Elizabeth Kolbert in the December 4th issue of The New York Review of Books.  From the reviews, I probably will agree with the book's argument, but that's not the point here.  The review notes in passing that Klein has traveled the globe so much that she's an 'elite' frequent flyer club member, that she has been flying over the world to visit places where relevant activities to curb resource extraction are taking place, that she got ideas when dining in Geneva, and that she and her husband are making a film to go with her book.  The book is printed on paper and distributed around the world.  It's not freely downloadable.  Will the film involve air travel, or a lot of resource consumption, or be free on line?

It's an ethical dilemma and by no means new.  Authors and film-makers, like missionaries for causes back through history, must make a living.  The justification for high consumption on their part is a kind of executive privilege: it's a nasty job being holier than thou, but somebody's got to to it.  This is similar to what has always been heard from powerful, pious, or privileged as they squeeze the rest of the population, exhorting them to bite this or that bullet.

Yet, obviously, authors do have to make a living, just as preachers, earls and kings do, and maybe it's simply true that someone abusing the resource issue is needed if masses are to be informed so they won't abuse the resources.  Masses need leaders.  You can make your own assessment as to what's fair, whether there are other ways than experts and spokespersons to carry a banner, and so on.  There are no easy answers (and, certainly, yours truly drives, has a warm house, travels to Europe to lecture or visit family, eats fresh food in winter shipped from the tropics, and so on).  It's very hard not to be hypocritical.  The human track record isn't very good in this respect.  Indeed, even many of today's arguments were au courant only a few decades ago--if you're old enough, you'll remember 'the population bomb' and 'small is beautiful' and daisy-painted VW buses parked in drop-out, live- naturally communes.

Is change as we are experiencing it these days any more threatening than it has been to prior human generations, albeit each in its own particular way, with likely negative as well as positive consequences?  If we individually or collectively want to alter things to satisfy some goal, and want to rally others behind that view, is the simple, catchy save the planet banner the kind of rallying point that works?

OMG, this is what really matters!
While finishing this post, nibbling a chocolate covered hazelnut, we came across this horrifying story that in an incredibly timely way showed in stark relief just the very disastrous things we face, to make our entire point.

From http://www.globalpost.com/dispatch/news/regions/africa/141118/chocolate

A new story apparently reports iron-clad proof that what we are doing to the earth is going to make its most precious resource disappear completely: chocolate!  Horror of horrors, now here is some thing that really does threaten anybody and everybody in every way and that even the most rabid Republican capitalist can agree on!  This shows why we really do need to save the planet and it clearly shows that that slogan has unambiguous, and unquestionable meaning.

Well, take a breath (if you can!).  Should we be clearer and more precise about what, exactly, that might be, and why, that a consensus could agree on?  Can we be clearer?  Maybe nostalgia is enough, but otherwise, save the planet is more an advertising slogan for a vague, essentially ideological point of view than a clear statement of some objective goal.  There are serious issues for us, or at least our living descendants. Is it possible to have agreement an agenda or are people just too different in what they think about themselves and the world, whether you want to call that selfishness or whatever?

Tuesday, November 18, 2014

Darwin and the evolution of my brain

 My drawing ability stalled out at the second grade level.  To wit, this drawing of an imaginary place that I did in reply to a request from my daughter just 3 months ago.




It is embarrassingly bad, and it perfectly illustrates why I didn't draw for my entire life.  At least by hand.  (What are those green blobs in the pond? Frogs? Lily pads?)  Ok, yes, somehow I did manage to produce illustrations for two different, 'serious' books, but I thought of that as 90% Adobe Illustrator and 10% me.  But I did learn as I went along, or maybe AI and I trained each other.

Here's one of my first Illustrator drawings, from our earlier book.


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



I remember how much I struggled just to make this simple line drawing.

And then one of my favorites, which not coincidentally was among the last I did for The Mermaid's Tale.

From The Mermaid's Tale; Weiss and Buchanan, 2009



Ok, two of my favorites.

C. elegans body plan; The Mermaid's Tale; Weiss and Buchanan, 2009


I learned a lot about using AI by the time that book was finished.  But see drawing above as to how much that applied to hand drawing.

And then a few months ago, by chance I saw that a painter at the local art co-op was offering a beginning drawing class. On a whim, I decided to sign up.  I knew someone in college who drew her way through Norway on a postcard-sized sketchbook, and I always thought it would be wonderful to be able to do that, though I had no illusion that I would ever be able to.  Still, I liked the idea of perhaps being able to improve my drawing at least to the point of being able to enjoy doing it.

I took the list of supplies we'd need to the art store before the first class, bought the pencils, erasers, pencil sharpener, and the suggested sketch pad, which was so large that it was unwieldy to carry.  I was embarrassed to walk out of the store with that 18 x 24" sketch pad under my arm.  I felt a total fraud.




The first class was a bit intimidating -- one woman was already seated at her easel, half-way through copying a da Vinci drawing, which didn't help.  As it turned out, she was a private student but I didn't know that at the time.  I sat down at one of the free drawing tables and opened the sketch pad to the first yawningly empty sheet of paper.  I laid my 2HB pencils and my erasers and my sharpener next to the paper, and looked around at the 6 other students doing the same.  What if they were all as good as the woman copying the master?

Introductions followed -- relief, the rest of us really were beginners -- and then the instructor sat down to demonstrate what he was asking us to do.  He put a simple box on the pedestal that was the hub of the circle of tables and nervous students, and began to draw.  Yes, he did put up his thumb to measure the size of the object.  It was in fact a revelation to me that artists actually do that -- and the beginning of the evolution of my brain.

After watching how it was supposed to be done, I sat back down to try to draw the box myself.  Huge blank sheet, everyday object, render to paper.  Just picking up the pencil was awkward, and the act of putting the first line to paper felt like it was being done by someone else's arm, driven by someone else's brain.  But I did it, and this is what I drew.




Ok, tentative lines, no attention to technical issues, but there are lines on paper.  That was good enough for day 1.

We had eight classes, three hours long, each utterly basic but utterly eye-opening to someone stuck in second grade drawing mode.  Perspective! Oh, that's why I could draw the diagrammatic figures for the books that I did with Illustrator!  No need to make them look life-like.  Oh, we're supposed to draw what we see, not what we think we see!  Revolution.  Negative space! A whole new way of seeing.  Organizational lines, vanishing points, units; all basic, all essential.

As I practiced, somehow the rust fell away, and my muscles started to be willing to move.  Not just arm muscles, but the seeing, rendering muscles.  We went outside to draw houses for one class, and here's the one I drew.




Still tentative, still technical issues, and the house looks rather more haunted in my rendering than it does on the street (it's a very tidy, well-kept house, in fact), but still, progress I thought.  I started to sort of like what I drew, so I kept drawing.

And then the other day I woke up wondering if I could draw Darwin.  Who does that?  So, me, online photo of Darwin, sketchbook and a pencil.  I wish I'd taken more photos as I worked, because the fascinating thing, to me, is that at some point early on, my lines on paper began to actually look like the famously familiar photo of this man.  This absolutely amazed me, and continues to.

Here's a photo of just the face, before I added the trimmings, which turn out not to be necessary for the effect.  I actually kind of like this picture better than the 'finished' one.  But the thing is, it was Darwin after just the first eye was done.



Now, 'finished' (which brings up another artistic problem: how do you know when you're finished?)




How does the brain turn lines on paper into a sense of a three-dimensional person?  Is it because we know this image so well that we excuse my raw attempt at rendering it, and fill in the blanks?  Simple (or not so simple) pattern recognition?  That could be.

And, to pull this tale back to the beginning of evolutionary time, at the end of each drawing class we looked at all of our drawings, and 'critiqued' them.  To me the fascinating thing, each week, was how very differently each of the seven of us put pencil to paper; same beginnings, usually the same object, totally different renderings.  One woman drew a bird's-eye view of the house she was sitting in front of, in the beautiful dark confident lines she used for everything; another man drew every shingle on the roof of his chosen house.  Speciation in action.

As well as evolution of the mind.  My mind, my understanding, my confidence and ability to tell my muscles what to do.  I have a long way to go, having drawn my way into a number of technical corners in just this one Darwin drawing, and I have no idea where to even begin working with color, but I've learned a lot.  Not least about what this optical illusion, this effect of graphite on paper, tells us about the power of the brain, of its constant, effortless brilliance at solving 'the binding problem', the putting together of the results of what so many different parts of the brain are perceiving and making final sense of it.  Indeed, to the brain, this isn't a 'problem' at all.  Even ants and bees and crows and dolphin brains can do it.  It's a 'problem' only for those who want to put it into words.

Friday, November 14, 2014

A Groundhog Day blog redux

Someone wondered the other day why we keep saying the same thing over and over on our blog.  "Ok, ok, we know things are complex, get on with your life." We, of course, wonder why we have to keep repeating ourselves.  But his query reminded me that we've dealt with this issue before, so we're rerunning a post from 2012.

The Groundhog Day blog?

Sometimes it seems that we're posting the same story over and over again.  Here are some new study results, here's what the authors say they mean, and here's what we think they really mean.  Usually a lot less than the authors report.  Just this week, does aspirin prevent cancer?  Should we eat eggs?  And a post asking simply how we can tell if results are credible.  If you read us regularly you know we don't just pick on epidemiology.  We give genetics the same treatment -- why should we believe any GWAS results, e.g.?  And should we expect to find genes 'for' most diseases?  Or behaviors?  The same for all those adaptive stories that 'explain' the reason some trait evolved.  And Holly is equally circumspect about claims in paleoanthropology, which of course is why we love her posts!

Is it just being curmudgeonly to ask these questions?  Or is it that where some see irreducible complexity others see a simple explanation that actually works?

An isomorphic problem
The important thing about these various issues in modern science is that from the point of view of gaining knowledge about the causal world, they are isomorphic problems.  They have similar characteristics and are (currently) addressed by approaches with similar logic--in terms of study design, and similar assumptions on which both study design, data collection, and methods of analysis are based.  The similarities in underlying causal structure include the following:
  1. Many different factors contribute causally to the outcome
  2. Most of the individual factors contribute only a small amount
  3. The effect of a given factor depends in various ways on the other factors in the individual
  4. The frequency of exposure to the factors varies greatly among individuals
  5. Sampling conditions (how we get the data we use to identify causal elements) vary or can't really be standardized
  6. The conditions change all the time
  7. The evidence for causation is often indirect (esp. in reconstructing evolution)
  8. We have no underlying theory that is adequate to the task, and so we use 'internal' criteria
These days, we use the word 'complexity' to describe such situations.  That word is often used in a way that seems to imply wisdom or even understanding on the part of those who use it, so it has become a professionalized flash-word often with little content.

Often, people use the word, but persist in applying enumerative, reductionist approaches that we inherited over the past 400 years largely from the physical sciences (we've posted on this subject before).  This is based essentially on the repeatability of experiments or situations.  We try to identify individual causal elements and study them on their own.  But if the nature of causation is the integrated effects of uniquely varying individuals, then only the individual strong (often rare) factors will be easily identified and characterized in this way.

Item #8 above is important.  In physics we have strongly formal theory which yields precise predictions under given conditions.   There is measurement error, and the predictions are sometimes probabilistic, but the probabilities involved and the statistics of analyzing error, were designed for such situations.  We compare actual data to predictions from that externally derived theory.  That is, we have a theory not derived from the data itself.  It is critical to science that the theory is largely derived not just in our heads but from prior data.  But it's external to new data that we use to test the theory's accuracy.

In the situations we are facing in genetics, evolution, biomedicine, and health, we have little similar theory, and the predictions of what we have are not precise or our assumptions too general.  Even the statistical aspects of measurement error or probabilistic causation are not based on rigorously specified expectations from theory.  Our theory is simply too vague at this stage.  So what do we do?

We use internal test criteria.  That is, we test the data against itself.  We compare cases and controls, or different species of apes' skeletons, or different diets.  We don't use some serious-level theory to predict that so many eggs per day, or some specific genotype at many sites in the genome will have some specific effect based on primary biological theory, but only that there is a per-egg outcome. We don't know why, so we can't really test the idea that eggs really are causal, because we know there are many variables we just aren't adequately measuring or understanding.  When we do find strong causal effects, however, which does happen and is our goal of this kind of research, then subsequently we can perhaps develop a real theoretical base for our ideas.  But the track record of this approach is mixed.

This is also often called a hypothesis-free approach.  For most of the glory period in science, the scientific method was specifically designed to force you to declare your idea in a controlled way, and test it (the 'scientific method').  But when this didn't work very well, as in the above areas, we adopted a hypothesis-free approach that allowed internal controls and tests: our 'hypothesis' is just that eggs do something: we don't have to specify how or why.  In that sense, we are simply ignoring the rules of historically real science, and even boasting that we are doing science anyway, by just collecting as much data as we can, as comprehensively as we can, in the hopes that some truth will fall out.

The central tenet of science for the last 400 years has been the idea that a given cause will always produce the same effect.  Even if the world is not deterministic, and the result will not be the same exact one, it will at least have some probability distribution specifying the relative frequency with which we'll observe a given outcome (like Heads vs Tails in coin-flipping).  But we really don't even have such criteria in the problems we're writing about.  Even when we try to replicate, we often don't get the same answer, and do not have good explanations for that.
When we're in this situation, of course we can expect to get the morass of internally inconsistent results that we see in these areas, and it's for the same basic epistemologicalreason!  That is, the same reason relative to the logic of our study designs and testing in these very different circumstances (genetics, epidemiology, etc.).  Yet that doesn't seem to slow down the machine that cranks out cranky results: our system is not designed to let us slow down to do that.  We have to keep the funds coming in and the papers coming out.

And then of course there's cause #9. Most of us have some underlying ideology that shapes our interpretation of results.

This is all a fault of us and the system.  We can't be faulted for Nature's complexity.  The issues are much more--yes--complex than we've described here, but we think this captures the gist of the problem.  Scientific methods are very good when we have a good theory, or when we are dealing with collections of identical objects (like oxygen or water molecules, etc.), but not when the objects and their behavior are not identical and we can't specify how they aren't.  We all clearly see the problem.  But we haven't yet developed an adequate way to deal with it.

Comet: it's not just a cleanser any more!


  

Thursday, November 13, 2014

Evolution of malaria resistance: 70 years on...and on....and on

It was about 70 years ago that the complex problem of anemia, malaria, and genetic interactions, with their relation to hemoglobin was first beginning to be understood.  Sickle cell anemia and its association with a globin gene variant, and similar associations between malarial susceptibility and other genes (such as G6PD and Duffy and other globin gene mutations) were also rapidly identified in roughly the same decades.  The findings were showing that in areas of the world with long-endemic malaria, various gene mutations seemed to be at high frequency as if they protected against malaria.  I was never involved in this directly, but I studied under Frank Livingstone and James V Neel at Michigan, two of the leaders in understanding the evolution of the protective mechanisms.

For decades we have had direct clinical evidence, mainly in Africa, but also in Sardinia, and then later in other places including southeast Asia, that at least some of the putatively protective mutations in the alpha and beta globin, and other genes did in fact protect against malaria, but that they had side effects such as various forms of anemia or other problems.  Even then most of the evidence was circumstantial and based on geographic correlations.

The idea of a balanced polymorphism was suggested in regard to these variants.  If you had two 'malaria-protective' alleles at the gene (one in each copy of the gene that you have), you were vulnerable to anemia, but if you had two 'normal' alleles you were susceptible to malaria; however, having one of each (a heterozygote genotype) you had some protection against both malaria and anemia.  Evolution favored keeping both variants in the population, because selection worked against both homozygotes.

Plasmodium falciparum lifestyle; Wikipedia

Far beyond malaria: Relationship to fundamental evolutionary questions
The idea of balanced polymorphisms played into a major theoretical argument among evolutionary biologists at the time, and sickle cell anemia became a central case in point, and a stereotypical classroom example. But the broader question was quite central to evolutionary theory.  Balancing selection was, for many biologists who held a strongly selectionist version of Darwinism, the explanation for why there was so much apparently standing genetic variation in humans, but  generally in all, species.

The theory had been that harmful mutations (the majority) are quickly purged, so the finding that there was widespread variation (polymorphism) in nature at gene after gene, the result of the type of genotyping possible then (based on protein variation), demanded explanation; balanced polymorphism provided it.  This was countered by a largely new, opposing view called 'non-Darwinian' evolution, or the 'neutral' theory; it held that much or even most genetic variation had no effect on reproductive success, and the frequency of such variants changed over time by chance alone, that is, experience 'genetic drift'.  This seemed heretically anti-Darwinian, though that was a wrong reaction and only the most recalcitrant or rabid Darwinist today denies that much of observed genomic variation evolves basically neutrally.  But many saw the frequency of variants associated with what were seen as serious recessive diseases, like PKU and Cystic Fibrosis (and others) as the result of balancing selection.

In support of the selectionist view, many variants have been found in the globin and other genes for which the frequency of one or more alleles is correlated geographically with the presence (today, at least) of endemic malaria.  But there are lots of variants that might be correlated with other things geographic because the latter are themselves often correlated with population history.  Thus, the correlations are often empirical but not clearly causal.  Indeed, not many variants have been clearly shown experimentally or clinically actually to be functionally related to malaria resistance.

In this light it is interesting to see a rather large-scale attempt at testing whether putative malaria-associated variants really are protective. The paper ("Reappraisal of known malaria resistance loci in a large multi center study") by a large consortium of authors is in the November 2014 Nature Genetics; it is paywalled so if you don't have direct access but would like to read it, I'd be happy to email a pdf.

These authors compiled large data sets from different areas of the world which have endemic malaria caused by the specific falciparum subtype of parasite, and compared the frequency of the many candidate gene variants in sufferers of severe malaria to a large set of unaffected controls (of course some of them may later become affected).

A long time coming...and the clock still ticking
Even now, 70 years after the first ideas were suggested, we still have scant direct clinical data showing protection at a mechanistic level, so the results of this paper are still statistical.  But they are at least from a reasonably designed and specific study.  The authors found positive statistical association for some of the most clear-cut classical risk alleles (sickle cell, G6PD, O-blood group), but ambiguous or variable evidence even for some of these, and no statistical evidence for many other putative causal, or protective variants.  Further, they found that some variants had different effects in males and females, and one SNP, in the CD40LG gene, previously found to be associated with severe malaria, was associated with reduced risk in The Gambia, but significantly increased risk in Kenya.  Whether this is just statistical variation or indicators of other aspects of these local-area genomes isn't clear.

The evidence in the positive instances is persuasive, even if just statistical, but the conflicting results and the surprising lack of findings for so many is curious as well as discouraging.  How can it be that so long on, we still basically don't even know if a genetic variant is protective or not, other than the most classical ones? This shows how very challenging even 'simple' causation can be.

This raises the basic evolutionary issue in a different way. Darwin was convinced that adaptive evolution was very slow.  One major reason was that rapid changes of species or adaptations were rarely observed (still true), and if they occurred they could be interpreted as creationist rather than natural events.  Adaptive evolution under human direction, as in agricultural breeding, clearly brings about easily measured change.  But some forms of natural selection could be quite strong.  Adaptive coloration is one, but malaria should be another because it is so common and strong a negative effect on health.  So basic evolutionary arguments ought, it was long hoped, demonstrate that, in this instance, balancing selection was a correct explanation of at least these polymorphisms.

In past work, one hemoglobin variant (called hemoglobin E) has apparently been sweeping across southeast Asia because there was no down side to being an EE homozygote, and it protected against malaria.  But generally, the actual selective effect has been very hard to prove.  The new study shows this in a sobering way.  Is the story right?  Have prior speculations about protective mutations been too superficially offered, and incorrect?  Is the selective effect so small even in relation to malaria, that we can't see it even with samples large enough that 'nature' could have made a detectable selective difference?  Or, if so gradual in a Darwinian sense, do these other mutations really make an evolutionary difference?

Several relevant points are, first, that this study only looked at one form of malaria (P. falciparum), and second, that the different putative protective genes are involved in different physiological pathways.  And, as even the authors note, current patterns of disease, when antimalarial drugs are widely used, may not reflect patterns in the past, and thus it may not be possible to conclude that P. falciparum was the selective force these results suggest it may have been, plausible though that seems to be.  These points suggest that even here, complexity and subtlety are involved.

Beyond evolutionary theory
More sobering than the reality of detecting evolutionary or even genuine physiological differences among these various genotypes, is the further fact that even for these major and rather clear causal sites, there is still basically no progress in effective gene-based therapy.  After all, the target cells are in blood (generally, red cells), among the most easily accessible of all tissues.  Given the unrestrained promises repeatedly being made by the genomewide-do-everything industry, this is (or should be) a very sobering thought.  Our technological tools should, one might expect, have been able to solve such comparatively clear-cut problems.

To us, this 'failure' indicates the subtlety of genome physiology.  Given the hundreds of putatively causal single-gene findings by GWAS and other means, where the evidence has seemed strong, we should be showing that genomic data are, after all the expense and effort, really worth gathering.  We should be making a definitive, and one might say systematic, march toward elimination of these genetic threats, perhaps the way vaccines have done against many infectious diseases.  If we could actually do that, and speak of cures and prevention rather than just risk-estimation of countless minor factors, then nobody would disagree that further genomic big-science efforts were worth the investment.

Meanwhile, more than 70 years on, the largely failed effort to use that knowledge directly to rid our species of a disease that has been estimated to have killed more human beings than any other single cause, shows how far we have to go--and how important new sorts of thinking could potentially be to the effort.

And, into the bargain, perhaps we're learning a lot about how adaptive evolution works, reinforcing Darwin's ideas about its slowness, about multiple alternative or interactive pathways, and more.