Wednesday, July 31, 2013

Burma in my back yard

I’ve just recently begun my final stretch of field work for my PhD.  The last several years I’ve been travelling in the summers to the Thai-Myanmar border to do field work concerning malaria epidemiology and human demography.  This time I’ve moved my family, my wife Amber and my son Salem, to the field with me, and we’ll be staying until at least March of next year (2014).  We’ve settled into a cheap rent house in a town named Mae Tan in Tha Song Yang District, Tak Province and have spent the last several days trying to get it set up to our liking.  In fact, I’m writing this from my new home over the weekend with the hope that I’ll be able to post it while visiting the malaria clinic down the street (where I have internet access).

My new stove and the view out back of our rent house

From my kitchen window I can look out back over the Moei river, which marks the international border between Myanmar and Thailand.  Down one end of my block is an international border crossing and down the other is the malaria clinic.  While I’ve been working on my Thai, it does me little good in this neighborhood since most of my neighbors are Karen and they seem to know very little Thai.  

Across the Moei River from Tha Song Yang

Across the river there appears to be a simple mosque.  We can’t really see it, but there are several wooden, thatch roof structures and we hear the call to prayer several times during the day.  The river here is sandwiched by mountains on both sides and the resulting canyon makes a perfect echo chamber for carrying the sounds of the Imam’s song.  I don’t know whether the moslem adherents there/here are mostly Karen or if they are Rohingya who are attempting to flee persecution from the other side of Myanmar.  I do know that some of the Rohingya have been making their way to the refugee camps, one of which (Mae La, with about 50,000 people living in it) is a few miles south of here.  

A river ferry transporting someone across a very high Moei River

Over the last several days I’ve been struck by some interesting realities, a few that are related to research areas that I hope to investigate while here.  The most obvious to my family and me has been the openness of households…

Mosquitoes are most apparent at dusk and dawn, but if they get into your dwelling they’ll feed during the night too.  My toes and feet have been pretty thoroughly gnawed.  I brought a mosquito net for my son’s bed, and we’ve all been using some repellant from Mahidol University which appears to be made from lemongrass, but I’ve yet to find a net that will work for our own bed.  Furthermore, almost every house has openings that aren’t covered.  The tops of the walls in our bathroom and kitchen areas have ventilation holes large enough for me to stick my arm through – a feature which actually makes the humid bathroom and kitchen bearable in the humid heat.  

Such openings also make it quite easy for mosquitoes and other creatures to move into the house at will.  Last night we were awakened by a Tokay gecko, probably close to a foot long, that appears to have worked his way in as well.  If you’ve never heard a Tokay gecko’s call before, it isn’t something that is easy to ignore.  My son and I decided to name him Figaro, being that he so loves to sing.   

There has been some question about whether or not malaria transmission here occurs within households or outdoors, perhaps in agricultural fields.  For one species, Plasmodium vivax, infections appear to cluster in younger children.  I take this as potential evidence of exposure in or around the household, with older household members probably still being infected but having some acquired tolerance for vivax infections.  

Last night as I sat out front of my house, drinking a sweaty Chang beer, listening to the call to prayer and the rain that hasn’t stopped now for close to 3 days, I looked down the street and saw almost every household with doors and windows wide open, families sitting inside enjoying each other’s company.  If transmission is occurring within households, it’s going to be near impossible to completely stop.  I’m fortunate to have a relatively well built structure to stay in while living here and I can’t keep the mosquitoes out.  It is more than a little overwhelming to think about the options for the countless others who aren’t as well off as a poor graduate student.  
But even if exposure occurs outside of the household, and I think that for Plasmodium falciparum it does, it will be at least as hard to halt transmission.  Children cannot stay inside their beds or houses forever, it is healthy that they run and play outdoors.  Parents need to tend their agricultural fields, to hunt and fish, so that they can put food on the table.  

Another thing that has become blatantly clear is the effect of the rain on everyday life.  As I write this I believe it has been raining almost non-stop for about 2 ½ days.  The rains don’t make life come to a stand-still, but they do make things more difficult and uncomfortable.  The market was still open early this morning.  The steady stream of Karen migrants walking down our street continues.  A few hours ago I walked down to the border patrol check station, where migrants check in, and found empty, closed buildings (it is Sunday here) and a few boat drivers ferrying people to and from Myanmar from the Thai side of the border.  One jokingly asked if I’d like a ride across the river (and as exciting as that might be, it’s probably a bad idea).  When the Karen here were still at war with the Burmese military, fighting mainly occurred during the dry season – it is too difficult to traverse the countryside during the wet season.  

I frequently find heterogeneities in life to be fascinating fodder for research and theory.  Many of the statistical and mathematical models that population scientists, demographers, and epidemiologists use assume homogeneity in whatever processes we are studying: random mating, random mixing, random contacts, etc.  I think we all know that these things aren’t realities, but frequently that fact gets lost in the simple assumptions that are made, sometimes out of necessity, in research.  

Here I find some interesting heterogeneities in the rainy season.  While I complain that it has basically rained for several days straight, at times the rain slows.  During those times, traffic on the streets picks up.  This isn’t surprising, wading through puddles of muddy water isn’t fun.  Though the countless motorcycle drivers around here are quite adept at driving one-handed while holding an umbrella in the other hand, I imagine they’d much rather the rain stop altogether as well.  

And with the rains here comes malaria.  Tak Province consistently reports the highest number of malaria cases (both vivax and falciparum) of any province in the Kingdom, and within Tak Province, Tha Song Yang District has the heaviest malaria burden.  Cases here are highly seasonal, with only a very few in the dry season.  However, the trickle of infected people at the local malaria clinic isn’t a steady flow throughout the rainy season.  I once fancied a Poisson process of arrivals at the clinic, but this too doesn’t appear to be the pattern.  What is a pattern, however, is that after a rain, the clinic is quite busy.  (The clinic is closed on weekends and so Monday morning is generally a busy time too).  Does this mean that no one feels sick while it’s raining??  Probably not.  Also, it takes approximately 2 weeks from the time of infection until a person actually feels classic malaria symptoms.  So rain can lead to increased mosquito vector populations but infections that have occurred in the last day or two aren’t likely to be symptomatic so quickly.  No, it appears that people who are sick would rather not wade through muddy water, potentially have to illegally cross an international border, and then make their way down to the waiting area of a clinic during a torrential downpour.  

I think this makes perfect sense, but it doesn’t wind up in any model of seasonality in malaria infections that I’ve ever seen.  Rains = more mosquitoes = more malaria.  But rains also mean that people are likely to at least momentarily delay seeking treatment.  Infected people who wait longer before seeking treatment are important in malaria epidemiology because they spend longer amounts of time being infectious – potentially acting as so-called “super spreaders” (individuals who spread infectious disease at higher rates than do others).  

Tuesday, July 30, 2013

You have no genotype, and you have no phenotype, either!

Yesterday we discussed the genomic heterogeneity that comprises each organism, except a single-celled organism during its pre-division lifetime.  When each cell divides into two 'daughter' cells, they both experience some mutations.  Since you are made of many billions of cells, and they are constantly turning over, you do not have a single genotype, and haven't had one since you started life as a single fertilized egg cell.

But, you might say, at least the result is a single phenotype, that is, you.  But that is not true, either.  The mutations in each cell are inherited in the cell's subsequent daughter cells during your life, and cells come and go, and the mutations may sometimes affect gene regions that affect their respective tissue, and hence the behavior of the tissue itself.  So, really, you don't have a specific phenotype, either.

One illustration of that is just the definition of different states.  Monday's NY Times reports a deliberation about 'cancer' and whether the definition or use of the term should change.  Many things, if not everything about you changes during your lifetime.  Cancer as we have called it is a disease resulting from some cells behaving differently from what is 'normal.'  Of course, that's happening all the time in your body, but the idea of cancer is that it is a lineage of abnormally dividing cells that grows without limits and thus threatens your life.  But not all abnormal growth is like that.

We've known this for decades or millennia.  Some growths are benign or haven't even been called cancer.  But even things that have been diagnosed as cancer are highly variable.  The new idea is that many that are slow-growing or not aggressive or not able to metastasize (spread to other parts of the body) are not dangerous and may never become dangerous.  They should not be called 'cancer', a scary word that is also expensive since doctors don't like to just leave it alone.  That's why it is perhaps wrong to screen too widely and diagnose something that will then have to be 'treated'.  But treatments all involve risk, if not also misery or fear, and expense.  So would re-defining be a good idea?

That's a clinical question we're not qualified to answer.  But we did think it relevant to the way we characterize people, and in particular, ways that could be dangerous to them.  We have in mind behavioral characterizations, especially when purportedly based on estimates of a person's genotype when s/he was a single cell, as estimated from a cheek swab or blood sample.  Not only do our cells' genotypes change with time, and due to environmental exposures, but our behavior is not nearly all hard-wired.  So really we don't have a clear-cut immutable phenotype, physically or behaviorally.

Of course, we are not completely changeable, so the challenge is to know what limits there are to change and how they are expressed or could be predicted.  The cancer story led us to raise this, as something to think about.  There is a tendency to simplify things beyond what is appropriate.

Monday, July 29, 2013

What is 'your' genotype? There's no answer because you have millions of them!

No one has a single genotype.  We begin life as a single cell, a fertilized egg containing two human genome copies, one inherited from each parent.  It also contains hundreds or thousands of mitochondrial DNA molecules that were in the egg cell.  They will not all be identical.  Then the initial cell divides to begin the process by which we formed an embryo that grew its many tissues and organs.  This involved billions of cell divisions.

Human blastocyst; Wikimedia

Each time a cell divides, some mutations occur.  These are not germline (sperm or egg) mutations, differences between your parents and you, the usual notion of mutation.  Instead, they are somatic (body cell) mutations.  The embryo forms a tree of cell descent (and, in that sense, so do you), and mutational changes in a cell are inherited when it divides into two daughter cells and their descendant cells throughout the rest of your life.  So that the earlier a mutation occurs in the embryo the greater the number of cells that will have that change.

As a result, each person is a genotypic mosaic.  When people talk about a genotype, they usually and sloppily refer to what would be sequenced in a sample of blood or cheek cells.  Most of this will be the inherited sequence but there will be a mix of cells with rarer changes (that the sequence-reading software may regard as sequencing errors and ignore), and mutations that may be common in other tissues from different embryonic cell branches will not be seen.

Somatic mutations can have no effect or great effect depending on when and where they occur.  You can have a BRCA1 mutation that arose during your development but that was not inherited and/or isn't in the sample that was sequenced to determine 'your' genotype.  Since your cells are always dying and dividing, you don't really have 'a' genotype!

A recent commentary in Science points out the potential importance of somatic mutations and the complexities they introduce into trying to infer genetic causation in medicine.  This is quite important, and is well-explained.  But there is a deeper history to this than covered in the piece.

Indeed, people had realized by the 1970s that somatic mutation was probably a contributor to cancer, because one transformed cell that had misbehaving behavior as a result of mutant genes could grow into a life-threatening tumor.  The idea was bruited in a wonderful and famous paper by Al Knudsen at the University of Texas in Houston (my Dean, where I was at the time) in the early '70s, in relation to the eye cancer retinoblastoma.  He showed the potential joint impact of inherited and somatic variation.  That conceptually led various people to pursue the idea of multistage somatically based tumorigenesis, and work largely by Bert Vogelstein and colleagues at Johns Hopkins established early ways of genomic screens to compare tumor cells with the patient's normal cells to show this.

Many of us were writing about the implications of somatic mutation at that time.  It was explicit in articles, book chapters, and books.  I myself attempted to awaken people to the potentially broader and challenging impact of somatic mutation (e.g., in Trends in Genetics in 2005).  Ranajit Chakraborty and I wrote many papers in the '80s about the way somatic mutation might explain why cancer is not usually present at birth and to account for the age of onset patterns of cancer, and in my 1993 book Genetic Variation and Human Disease (20 years ago!) and elsewhere I provided a speculative account of how this could apply to age-related diseases (most diseases) more widely.

There were and are many other examples and instances of the importance of somatic mutation, in humans and other animals (and plants).  But the bemused human genetics establishment, anchored in early 20th century concepts of simple inheritance, established its juggernaut of GWAS and the idea of relating 'the' genome of a person to his/her fate, paying conveniently little attention to somatic mutation.

Because the situation is so clear in regard to cancer, cancer research has gone to great lengths to understand somatic mutation, as has some smattering of other work here and there, such as attempts to account for some effects of aging in terms of mitochondrial somatic mutation.  In a way, the idea of genomewide 'expression profiling'--looking for cell-specific gene expression in specific tissues--is related to the idea that you can't describe a person from an inherited genotype.

The challenge is outlined well in the current paper, even if the author decided or neglected to cite the earlier literature or note that somatic mutation has been widely ignored out of convenience or culpable unawareness (pick your favorite explanation).  Until we face up to the problem, we will be wastefully pouring funds down the GWAS and sequence database drain. 

The issues are complex.  We know now that the same inherited mutation has variable effects depending on the rest of a person's genotype--and that's why the effectiveness of personalized genomic medicine is heavily misrepresented by various hopeful and/or vested interests.  Similarly, a person's somatic mutations will interact with each other, and with his/her inherited genotype to produce resulting traits, normal as well as disease.  That two-set pattern 'squares' the amount of complication we have to deal with.

Working out how to handle what we know about genotypic variation will not be easy, but we should slow down the train while we try to work out a useful strategy, or at least stop over-promising.  However, the likelihood is that most people who read the article (or, indeed, this post!) will say "Hmm, that's interesting," and then, feeling satisfied about their new awareness, finish their coffee....and go back to business as usual.

Friday, July 26, 2013

We're all psychopaths sometimes

A paper just published in the journal Brain reports that psychopathic individuals are less empathic than controls, but that empathy can be turned on on command.  The study is reported on the BBC website here. Researchers recorded fMRI images of 20 incarcerated males diagnosed as psychopaths and 26 non-prisoner controls as they watched video clips of hands interacting "in a loving, painful, neutral or rejecting way". The researchers report that the fMRI images are evidence that psychopathic individuals are less empathic than controls but that when they are encouraged to imagine what the actors in the videos were feeling, the active brain regions are more similar to those of the controls.

Experimental paradigm. (A) Three still frames from example videos of each condition. Each video included a receiving (1) and an approaching (2) hand. (B) Photo of hand interactions during the experience. (C) Design of the three experiments (always performed in this order). Source: Brain Vol 136, Issue 8, Pp 2550-2562
The researchers note that incarcerated psychopaths may not be representative of all psychopaths, and that the 20 subjects in their study were less educated and less wealthy than controls, and they can't be sure that these differences don't explain the differences observed between the two groups before the first were instructed to be empathetic.  And, the sample size is small.  Nonetheless they conclude that rather than having no empathy, as is apparently widely supposed, psychopaths simply have a 'reduced propensity' to empathize rather than an inability.  What 'reduced' means in other than some statistical value related to this particular study isn't clear, at least to us.

There are several interesting points here.  If it's true that people who have been thought to be unable to feel other people's pain actually can, this would mean that psychopathy is but a point on the spectrum of human affective behaviors, not to mention judgments we individually make about other people.  The ability to empathize is essentially distributed from none to total empathy, and as with blood pressure or height or blood glucose or many other traits, we (our culture or some assigned experts) define the extremes of the distributions, beyond some chosen value, as pathologies.

But it's not surprising that psychopaths, however defined, can switch on their empathy on command or under specific circumstances.  Few of us have equal amounts of empathy at all times -- we might identify more with someone we love than someone we dislike, or even cats more than dogs, if soldiers didn't turn off their empathy on the battlefield, they couldn't do their job, and we often listen to news about yet another war or famine in a far off place with no emotion.  Indeed, if the definition of psychopathy is lack of empathy, we're all psychopaths sometimes.

This study brings up many questions.  Can psychopathy be prevented?  Is it really a category?  Are psychopaths people who weren't taught empathy as children?  Will genes for psychopathy be sought, with the aim of identifying at-risk children and intervening (teaching empathy) before it's too late, and, disturbingly, where might that lead?  Is it ever too late, if even psychopaths who are hardened criminals can empathize on command?  Is the switchability something that we need to or will have studied for some assumed genetic basis?  If psychopaths can turn empathy on and off, what keeps them from turning it on more often? This seems to us to be the biggest challenge, no matter how clear it is that they can empathize.

We are not qualified to judge the degree to which fMRI is a modern form of phrenology with little in the way of rigorous underpinnings in circumstances like these, but there certainly are vocal skeptics about the usefulness of this new toy.  But it is likely that the much harder, if less glamorous slogging to work out the day-to-day behavior or behavior-changing approaches will take longer, and probably because they are more vague, the low-tech studies will struggle harder to get funding, and will get less news coverage.

The problem of understanding things like this, which we've said many times before, is that we don't know all of the potential triggers or vulnerabilities, inherent and environmental.  For that reason, even thinking of lifelong therapy, such as psychotropic drugging, is problematic.  Perhaps we just don't yet have the appropriate resesarch strategies, or even aren't asking the right kinds of questions.

Thursday, July 25, 2013

The extent of what we can't know about gene function is infinite

A paper in Cell reports preliminary results of an effort to systematically mutate each of the genes in a mouse genome, one at a time, to determine the function of every gene ("Genome-wide Generation and Systematic Phenotyping of Knockout Mice Reveals New Roles for Many Genes," White et al.).  It's the Sanger Institute Mouse Genetics Project.

This isn't the first such effort, nor is the mouse the only organism on which this has been done, but the authors write that the advantages of their project are that all mice have a common genetic background (which actually is both good and bad; genetic background is controlled, but results will differ in other strains of mice), they've used a standard protocol for constructing the alleles they introduce, and the lines they produce are readily available to other researchers.  In addition, White et al. note that other mutagenesis projects have focused on a subset of known and previously characterized genes.  This precludes discovery of novel gene function, and can shed no light on previously uncharacterized genes.  

The method used in this project is targeted mutagenesis of embryonic stem cells, to knock out expression of specific genes. The cells are inserted into the embryonic mouse and its viability, fertility and the effect of the knockout "on a broad range of traits" are then assessed.  Many mouse knockout experiments have been reported to show "no phenotype", that is, have no effect on the mouse, but the authors suggest that other researchers didn't look hard enough.

In the paper, White et al. report statistics for the first 900 or so genes they've done.  
We found that hitherto unpublished genes were as likely to reveal phenotypes as known genes, suggesting that novel genes represent a rich resource for investigating the molecular basis of disease. We found many unexpected phenotypes detected only because we screened for them, emphasizing the value of screening all mutants for a wide range of traits. Haploinsufficiency and pleiotropy were both surprisingly common. Forty-two percent of genes were essential for viability, and these were less likely to have a paralog and more likely to contribute to a protein complex than other genes.
Really, not at all surprising and should not be interpreted as such, but it is nice to have this additional documentation.  The finding that unexpected phenotypes will be uncovered if you screen for them brings to mind developmental biologist Lewis Wolpert's query after yet another experiment showed "no phenotype" in a knockout mouse, "But have you taken it to the opera?".  (Is this apocryphal I ask, finding no documentation other than the last time we blogged it.  If he didn't say it, at least someone did, and it's perfect.)

That novel genes (or functional elements in genomes of various types) are still to be found, and are as likely to affect phenotype as well-characterized genes is, again, no surprise.  We've blogged several times (here and here, e.g.) about a craniofacial genetics project we've been working on, particularly the gene mapping phase.  Gene mapping, or the effort to identify a gene or genes within a chromosomal region statistically associated with a trait or disease of interest, sounds straightforward enough.  But, as we said in our posts on the subject, choosing candidate genes within what can be chromosomal regions that contain tens or hundreds of genes, many of them as yet uncharacterized, is often more of an art than a science.  Or, indeed, a crap shoot.  

Mapping problems are exacerbated by the fact that of the subset of genes that have been characterized, most are known only for a single function, or even a disease with which it's associated. And, investigators gravitate to known genes as they contemplate candidates -- the drunk under the lamp post effect.  White et al. very appropriately call attention to this in the paper, but the extent of the problem is even greater than they indicate.  Yes, they are characterizing the effect of gene knockouts on a broad range of traits, but, well, are they taking their mice to the opera?  Changing the environment; food, temperature, lighting, cage conditions, etc.?  

Indeed, no matter how well-intentioned, they can't expose these mice to all possible environments, and so can't observe all possible phenotypes. There is no way to relate many of these effects to what the same mice would be like in the wild, and until many mice of each genotype are studied the amount of variation even under controlled lab conditions can't be known--so it is only tentative to assign trait effects to the mutant strain.  

And as importantly, they can't do their knockouts in every strain of mice, although genetic background is known to be a huge factor affecting gene expression and effects, which may range from none to lethal.  Genetic background is probably a given mutant gene's most proximal environmental factor there is.  

So, the project reported in this paper is interesting as far as it goes, particularly as it makes clear how much we still don't know about the function of most genes, and why.  But because environments are endlessly changing and every genome is unique, no finite set of experiments can do much more than make it clear how much we'll never know, or be able to predict. The danger is that while digesting what was found we not become bemused by mega-studies of this type into thinking that they show more than they really do.

Wednesday, July 24, 2013

What is an organism? Lessons from bacteria on cooperation in life

The battle against antibiotic resistance is in the news a lot lately, because if our over-use of antibiotics causes resistance to evolve, we and our livestock will be in deep trouble.  Resistant strains of pathogenic bacteria are already proving to be a serious problem.  Major pandemics could be in the offing.  Even the simplest of surgical procedures could become dangerous again. 

From what we read, pharmaceutical research is rather stalled in this respect.  New drugs coming onto the market are mainly minor tinkering with older approaches, and are both costly to develop and test but also have diminishing effectiveness.  Yet entirely novel approaches seem hard to come by as well as prohibitively costly to develop. 

Part of the apparent reason for the problem of increasing resistance is that to be economically viable, antibiotics tend to be broad-spectrum. That is, they work against whole classes of bacteria, which means that eventually they don't work against whole classes of bacteria.  Developing an antibiotic directly against a specific bacterial type gets too costly for the potential payoff.  At least that's the argument that's often made.

But might there be a wholly different approach?  The BBC Radio 4 program Discovery on July 8 (here for download) took a refreshing and clever approach to this challenging subject.  And it's based on a rather little-known characteristic of bacteria that has been part of their lives for about 3.5 billion years.

Bacteria societies.
Bacteria are single-celled organisms that live and reproduce on their own (though sometimes a version of sexual reproduction is undertaken).  Because of the way we've studied them in science, cell by cell, we have tended to think of them as lone wolves, but they are not.  At least under some conditions, they live in large social groups (sometimes including members of more than one species).  They form layered structures of large numbers of bacteria, called biofilms (or, in the fossil record, their mineralized remains are called stromatolites).

Stromatolites in Shark Bay, Australia; Wikimedia

A phenomenon associated with this environmental monitoring is called quorum sensing.  Like all cells--and indeed all organisms including you and me--bacteria are constantly monitoring their environment.  They secrete substances that they can also detect, and they can assess the concentration of these substances in their environment.  This means they can sense how many of each other there are in the vicinity.  This among other triggers is used to stimulate the formulation of a biofilm when there are enough bacteria in the vicinity to make that work.

Five stages of biofilm development: (1) Initial attachment, (2) Irreversible attachment, (3) Maturation I, (4) Maturation II, and (5) Dispersion. Each stage of development in the diagram is paired with a photomicrograph of a developing P. aeruginosa biofilm. All photomicrographs are shown to same scale. Wikipedia

Under some conditions, they respond to these signals by aggregating, huddling together and even forming physical connections among each other.  Their gene expression pattern changes as well.  Sometimes this is a protective means of herding in hostile environments.  But other times, they aggregate because together they can mine a food source that an individual cell can't effectively access.

Unfortunately, sometimes that food source is you!

As the story was told on the BBC program, individual bacteria often are rather quiescent because too much activity could trigger an immune response and that means curtains to the bug.  For example, if they were to attack your cells--and that, after all, is their menu!--the materials leaking from the cells would be detected by your immune system.  But when there are enough bacteria, they decide to go ahead with their attack, and they activate mechanisms that lead to the lancing of your cells, releasing its cornucopia of nutrients.  By then, there may be enough of them to overwhelm your immune reactions, and survive to live another day.

A stealth attack
The idea for a new approach is to design chemotherapeutic agents that interfere with the quorum sensing mechanism, not even trying to kill the bacteria but just preventing them from ganging up on you and eating away.  If this works, and experimental trials are under way, then bacteria will face a very subtle attack: they won't 'know' that they're being targeted because all their cells and those of their fellow travelers' will be normal and unaffected.  They just will never know that there are enough of them around to make a frontal assault possible.

The idea here is that resistance won't evolve because you're not putting the bacteria under any sort of stress.  By contrast, antibiotics kill all vulnerable cells but that means that they open a clear path for any cells in which mutation has led to resistance to the agents.  This makes evolution work against our epidemiological hopes, and (sorry, creationists) evolution works!

A limitation will be that different species of bacteria use different quorum sensing compounds or receptors and the like, so drugs may have to be more species-specific and less broad spectrum--and hence much more costly to develop.  We'll see if this clever strategy works.

However, in the interview at least, the investigators seemed to be very naive about evolution, and as a result perhaps highly over-optimistic.

How evolution works and why it will again
Resistance to lethal attack is easy to understand.  When a bacterial gene undergoes a mutation that, say, makes the cell no longer able to be bound by some chemical (an antibiotic), then the chemical will be harmless.  Since mutations are always happening, and antibiotics work by molecule-to-molecule interactions, mutations leading to bacterial proteins that no longer bind to the antibiotic, and hence to resistance, are all too common.

This is one, rather classical, view of evolution.  But there are others, and perhaps they are more subtle.  After all there are differences among bacterial species in how they do their quorum sensing or what conditions trigger the formation of their biofilms.  Since these vary among species, this must occur by mutational chance.  Whether or not selection is involved, variants have become established.

Thus, even if you devise a way to confuse the current quorum sensing mechanism, without killing the bacteria, they won't be eating you (that's the idea), but will just continue to flit about singly and in rather a dormant state.  But the food source (i.e., your cells) are still there as a waiting harvest.  So it is inevitable that mutations in quorum sensing will lead some bacteria to be able to detect each other or to modify their predatory behavior.  They will feast while their confused fellows die out.

This may take longer and be more complex an adaptive scenario, but it is hard to imagine that it would not occur.  The BBC interviewees seemed unaware of this aspect of evolution, thinking that if you don't try to kill the bacteria you don't put adaptive selective pressure on them, but that is only one way that adaptation works.  If there are other reasons to argue that bacteria can't adapt to interfering with their quorum sensing mechanisms, that wasn't stated.

Cooperation: a rigorous, vigorous, ubiquitous part of life
Our book, after which this blog was named, was written to take obsessive attention away from a competition-is-everything worldview that is so common in biology and biomedicine.  Cooperation takes many forms and is far, far more widespread and ever-present than is competition (which, of course, does occur).  The way bacteria join together to find a meal, and cause big problems, is an interesting example of cooperation even at the simplest level of life.

Tuesday, July 23, 2013

Why is the cause of X (or Y or Z) so hard to find?

£1.1m to find the answer -- will it?
Acute Oak Decline (AOD) is killing England's oak trees, and no one knows exactly why.  The story is in the news (here at The Guardian, e.g., and on the BBC radio program "Farming Today" on July 15) because a government-funded research project into the cause and the cure, to the tune of £1.1m, has just been announced. AOD came on fast, kills quickly, and seems like it should be easy to understand.  But it isn't.

'Decline' is a generic term for a category of tree diseases with multifactorial causation.  There are several forms of oak decline, acute and chronic, and cause can differ.  There was an outbreak of Acute Oak Decline in the 1920s in Britain, attributed to "over-riding effects of successive first flush defoliations by the caterpillar of the oak roller moth (Tortrix viridana), followed by damage to summer leaves by powdery mildew (Erysiphe alphitoides)," according to a 2010 paper describing the current epidemic ("Description of Gibbsiella quercinecans gen. nov., sp. nov., associated with Acute Oak Decline," Brady et al.).  That is, the cause was completely different from that of the current epidemic.

The new wave of the disease, which first appeared about 20 years ago, is characterized by attack on oak stems, with small cracks appearing in the bark, from which a gooey exudate bleeds heavily.  The disease hits mature trees, and they can die within 3 years, a quick death for a large tree that can otherwise take 200 years to die.  Some trees do seem to recover, though why they do is another unknown.

Thousands of trees have been affected, predominantly in the English Midlands, but the disease is spreading and is now in the south and south east of England and in Wales, and the number of trees with the disease in Britain could rise significantly in years to come. 

Stem bleeding in an AOD affected tree; Wikipedia
Although the cause of this epidemic is not yet understood with certainty, as Brady et al. report, several bacteria are consistently found in the exudate from affected trees, and indeed in trees with AOD in Spain.  Based on genetic analyses of various house keeping genes and of 16S rRNA (which is the stretch of bacterial ribosomal RNA that is conventionally used for constructing phylogenies, the historical ancestral connections between organisms) of nine different Gram-negative strains of bacteria from affected trees, Brady et al. found the bugs to be within the family of Enterobacteriaceae, but no match to previously known strains. They thus concluded that the bacteria affecting oak trees were novel species. (I say this in one short sentence; web searching shows that this was a long and involved process, with extensive sequencing and statistical analysis, culminating in petitions to classify and reclassify these bacteria based on genetic distance from other known bacteria.)

So, why aren't investigators satisfied that the cause of AOD has been found? Because, for one thing, the same bacteria aren't found in all affected trees. And, the larva of the jewel beetle (buprestid beetle) has been found in the infected cracks of over 90% of affected trees. The beetle lays its eggs in the tree, which creates tiny holes and cracks, and it's here that the disease is found. So, do the beetle and the bacteria together cause the disease? Maybe, but if so, why aren't beetles and the same bacteria always found in affected trees? Is it the interaction between the adult beetles, their larvae and bacteria that is causal? Or does the disease come first, and the beetle or the bacteria (or both) follow?

Haven't we heard this before?
This all sounds hauntingly reminiscent of Colony Collapse Disorder (CCD) in honey bees -- bees started dying about a decade ago, it seemed that it should be a quick puzzle to solve; find the infectious agent, or the pesticide and then just fix it, but the pieces are still lying all over the table.  One study makes it look like it's obviously a virus -- or a mite, or insecticides, or pesticides, or a combination of factors -- but then colonies affected by none of these things will die off and we're back to the beginning.  And white-nose syndrome that's killing bats. What causes that?

Little brown bat with white nose syndrome; Wikipedia
But then, this is hauntingly reminiscent of the hunt for the cause of the asthma epidemic that began in the 1980's in the US and much of Europe, or the heart disease epidemic that waxed and waned (well, ebbed) in the last century still without an explanation, or the type 2 diabetes epidemic in Native Americans, or the obesity epidemic throughout the world, or the rise in autism, or ADHD, or.... We're dismally bad at figuring out causation when it isn't simple and sharp.

But no need to stop at disease.  What caused the financial crisis of the last 5 years?  Why such exacerbated disorder in the fiscal houses of Spain or Italy or Greece?  Why is Syria in flames?  These are all questions that legions of experts -- epidemiologists, geneticists, sociologists, economists, psychologists, etc. -- have been trained to answer, but no amount of training makes the answering easy.  Or often, even possible. For example, these are things due to human behavior, but are they in any serious sense biologically related phenomena?  If not, how can we treat 'society' or 'culture' as phenomena?  These are questions that were long seriously debated, and sometimes still are.

And what about predicting the next AOD, or influenza epidemic, or financial crisis?  Or even who'll be unlucky enough to become demented in old age, or die of heart disease?  We're even worse at that.  We aren't stupid.  But perhaps our methods are.

But it used to work!
Epidemiology and genetics had noble beginnings.  Both were good at finding single causes with strong effects.  Smoking, the genes that code for wrinkled or yellow peas in Mendel's garden, or cystic fibrosis or Tay Sachs, or the bacterium that causes cholera or Legionnaire's Disease, asbestos -- these were found with good robust methods.  These are sharp, single or 'point' causes: one cause, and if you're exposed to it you manifest the effects.  These successes went to their heads and the fields got cocky.

But then the questions got harder.  With infectious diseases knocked (so we thought), the landscape changed.  When cause is multifaceted, like the complex chronic diseases that will eventually get most of us, or when there were multiple causes for what look like the same disease, and so on, our methods fail us.  So, looking for 'the genes for' asthma, or heart disease, or autism, or major explanatory environmental risk factors, have not panned out.  These, and many others, are diseases that would surely have been easily cracked, if they had a single major cause.  We treated them as though they do -- we still treat them as though they are, looking for genes for everything that afflicts us -- because those methods worked so well before.  But that's now the wrong model.

It's possible to identify many different components, as in the oak and colony collapse story.  But with very rapid change, is it more likely that there is a single major cause, and some minor passengers along for the ride?  Or should we search for numerous highly correlated causal elements?  There is basically no theory for this!

The fact that incidence rises quickly should take the hunting dog off the genetic trail and alert him to an environmental scent, because genes don't change quickly but environments can.  Quickly rising incidence would seem to suggest some single environmental change.  So why aren't the causes of CCD, or AOD, or asthma or autism, each of which might be characterized as epidemics with fairly quick onset and rapid rise, simple and easy to identify?

Well, even that question deserves a multifaceted answer.  It could be that what we're calling a single disease -- heart disease, asthma, autism, schizophrenia etc. -- is in fact a collection of diseases, with different causes.  This kind of phenotypic heterogeneity can wreak havoc with the best of study designs.  This is true looking for genes or environmental factors.

And cause may in fact be (fairly) simple, but there are so many potentially causal environmental factors that it's exquisitely hard to find the needle in the haystack.  Or, there are multiple ways to kill off a bee colony, or to get asthma -- that kind of genotypic or environmental heterogeneity can easily do in a study.  You think you've identified the cause -- neonicotinoids, for example -- but the next dead colony you look at was never exposed.

And if it's so hard to characterize causation, and causation is complex anyway, and we don't know how to capture all the relevant factors in the environment, how can we possibly predict disease (or the next economic downturn, or whether this way of teaching kids will work) in a completely unpredictable environment?

We don't have the answers.  But the questions keep on coming.

Monday, July 22, 2013

Giving in.....and cashing in? The state of social sciences

To put it bluntly, the social sciences have largely been a scientific flop.  Despite ample funding for decades and claims to be science, no one can say that as a result of the knowledge gained through social science research, our society is socially healthier or happier or really even more self-understanding than decades ago.  One could ask why we still bother to invest in anything other than the most safe and useful kinds of social science (like, perhaps, demography or economic statistics that are measurements rather than 'theories' of social life).  Perhaps we should close down the departments and let the jobs go to fields that better deliver the goods?

Never!  An article  in the NY Times suggests that, yes, social sciences have failed -- or rather, have accomplished what they set out to do a century ago, describe society, and are now stagnating -- but that shifting to hypertech approaches will save them, and that this will require dissassembling current departmental structure in favor of new-fangled ones, as was done in the hard sciences.

The author says that we've now long known that, for example, too much concentration of power in a few money oligarchs leads to social disparity, and that racism is part of human nature, and that health disparities exist, other things of that sort  Instead of continuing the relentless, but unproductive restudy of this litany of topics, what we need is to set up departments for these new get-with-the-modern-program technologies.
... social scientists should devote a small palace guard to settled subjects and redeploy most of their forces to new fields like social neuroscience, behavioral economics, evolutionary psychology and social epigenetics, most of which, not coincidentally, lie at the intersection of the natural and social sciences. Behavioral economics, for example, has used psychology to radically reshape classical economics.
But what is the point of any academic department, especially in the sciences?  One might say that it is to learn truths and teach them to students who will live better and/or more edifying lives.  But is it simply to document what researchers see, such as that racism and health disparities exist, as the author suggests the social sciences have done very well?  In the case of 'science', we also expect research to lead to solving or at least ameliorating problems we face, and this is particulary true of the social sciences -- they should help us improve group and economic behavior, political and intercultural relations, improve education and social well-being, and relieve mental anguish, etc., should they not?  And we look, whether properly or not, to university faculty to take a leading role in this. 

From this point of view, the problem is not that we have now long known basic facts about society, psychology, economics, and politics, but that there has not been the dividend to the society that's been paying the bills to keep these fields in business. The state of our society these days is prima facie evidence that social sciences, despite a half-century of substantial funding (including by NIH), have not been delivering the goods.

Now one source of troubles in the social sciences has been a strong anti-science movement that has gone under various names, in various disciplines.  One term is 'postmodernism', whose advocates basically argue that personal subjective impressions exist but that social phenomena aren't being or can't be subject to ideas like laws of Nature.  This has been very divisive, and like many things became an ideology of its own, that has driven some departments to hive off scientific branches in a mutually desired separation from militant subjectivism.  But that rift doesn't seem to be the author of this article's problem--at least it's not so stated, whose argument is that social sciences have been successful up to a point, but then stalled.  Why it stalled is not explained.  Is it that what is settled are just some bland generalizations rather than precise predictions?

From its beginning in the Enlightenment period, an important and explicit goal and criterion of science has been to manipulate and control Nature.  In that light, it is not easy to see the failure of social sciences when it comes to many social issues we face.  We have an unbudgable drug problem -- illegal substance abuse as well as pervasive lifetime meds including mood-related therapy.  Those in the lower classes (why are there still lower classes?) are in jail, unemployed, poorly educated and hovering fearfully, to the sound of gunshots, in their locked tenements at night.  Hm, and there still seems to be a race problem.  Everyone in the middle class has to have a permanent personal therapist, and belong to a gym to get some exercize and relief from their daily cubicles.  Kids are overwhelmingly not receiving good educations.  Our governments are spying on everyone and democracy is retreating, with fewer participants and private interests buying influence.  And we need not mention the general gun problem.

What about teen sex and pregnancy?  Or, how about our diet, and its health consequences, not to mention our failure to accept a social contract by which we agree to care for each other (as in, for example, nationalized health care and decent welfare programs that give funds to the actual needy)?  Are increasing economic disparity and unconstrained greed by bankers and boom-and-bust cycles signs of a successful social science program -- when we've known the underlying social facts, as the author says, for a long time?  And what about crime cycles?  They occur, but nobody knows why.

And, well, is being gay a disease, a genetic trait, or suddenly (and historically, again) simply part of the normal range that needs to be recognized?  Why was it unconstitutional to have same-sex marriage a few years ago but suddenly it's constitutional and just fine...but only in some societies?  And then how about the world's 7 billion population, and growing, or the choking air and warming climate due to uncontrolled urbanization, exurbanization, suburbanization, and paving over of farmland (and uncontrolled soil erosion)?  We can think internationally, and that brings us to militant Islam (cf, formerly militant Christianity), to genocide (e.g., Rwanda, Congo, Yugoslavia).  Or blood diamonds?

One cannot fault the social sciences for not solving all the world's problems.  The problems are hard and there isn't agrement on what is wrong or what to do (some people benefit from blood diamonds, inequity, and recreational drugs and would not want the system to change).  And after all, even if biomedical sciences are sciences, people still get diseases--with few exceptions the same diseases we got before NIH started pouring money into biomedical research.  We have said much here in our blog about the over-promises of medicine, but there is, at least, a direct mandate to try to do something about the problems studied, and in many areas it actually gets done.  But if the successes in social sciences are true, then why have things stalled in the progress department?

This a sad situation, because in many ways the social sciences are far, far more important to our lives, and life-long, than even medical science. After all, we do all have to die of some cause some day, but that is usually brief relative to a lifetime, unlike the long-lasting effects of war, poverty, social discrimination, endless mental anguish, poor education, uncontrollable economies and their job and other consequences.  Knowing this and knowing about human cultures and their behavior, change, and structure, and about human behavior, are very important and it would be a major tragedy if, universities chuck them for venal reasons, (investing in chemistry because it brings in grant money), because every student should hear their wisdom.  That's certainly true in anthropology, our particular field.

But perhaps the social sciences should level with us more openly and with less selfishness: universities do have every right to ask whether they should shift resources to more effective areas of research.  Instead of disemboweling the Times author's field, he wants a bunch of new tech-based departments formed, which among other things is usually another way to acquire buildings, administrative staff, and lower teaching responsibilities, but as what?  a reward for a history of failure?  There is nothing wrong with arguing that, say, network analysis or game theory, or what-you-will could improve the yield, but those could be (and already are) studied in social science departments without having special centers, and many of these research areas have actually been around for a long time, again, without much yield.  For example, the idea of social networks, one of the author's recommended new disciplines, isn't exactly new.

The issues we rattled off above are ones whose nature and prevalence have changed dramatically in all sorts of ways, even just during your and our lifetimes, and repeatedly over known history.   They have not changed because of what professors at universities say, as a rule, but as a result of the internal workings of societies in the real world.  Indeed, that cultures evolves on their own, with humans being relatively biologically constant, has long been known.

To suggest that the issues in understanding social phenomena are genetic is really preposterous.  The societal changes have been major, but the gene pool hasn't changed!  Certainly some genotypes may make someone a bit more likely to do this or that, but the predictive power to date has generally been poor, and cultural context is manifestly and vastly more important than genotype, as we've said many times and about which there is even widespread agreement.   Let those who advocate new-tech for old problems demonstrate that it will actually make a real difference, without making promises (as does genetics) that this will solve all ills.  After all, if it's science it should lead to rigorous theory with predictive powers, and those then should be translatable into policy and amelioration of problems.  This seems to be what the author is claiming.

Rigorous understanding of its problems is very difficult and the social sciences probably need a good dose of slow-down, scale-back and rethinking their basic epistemology -- their way of understanding the world or posing well-posed questions.  If students had a better understanding of society and its issues (i.e., the faculty were teaching more and doing less multivariate regression on social survey data, or fMRI scans, or computer-based observations on paid undergraduate volunteers, etc.), there might be some at least edification in their lives, perhaps even some new understandings (if knowledge is even relevant to human social behavior).

Technology is challenging to learn and use, but that's often a rather mechanical process, and it is trivially easy to invoke technology as if that by itself will lead to answers.  We see this in genetics and other omics fields every day.  Anyone can buy a DNA sequencer or software to analyze brain scans.  So is the plea to shift social science to such areas a sideways glance at where the money is, and the societal will to spend it?  Maybe not, but it certainly has a familiar ring, that we hear all the time in biomedical circles.  It rings of physics envy, which goes all the way back at least to Herbert Spencer and Karl Marx (and, in some ways, Darwin himself).

Maybe our society is falling for snake-oil promises by biomedical sciences, NIH, the journals, and the media.  But it is not hard to think that the suggestion that the answer for social science problems is the same technologies, and invoking evolution and behavior genetics, is either very shallow, very gullible, or a very cynical strategy to get at the public purse.  And anyone over the age of consent should be aware of the history of abuse that a fervor for geneticizing or Darwinizing behavior leads to.  It is naive not to be concerned that the gushing rush in this direction today does not pose risks of some sorts of repeat of the mind-set of the eugenics era.  Change a few terms here and there, and the conceptual rhetoric is very similar.

Fortunately, it's not very likely that the social sciences' lobbying will shift much money their way. After all, the new genomics itself, despite decades of hype and billions of dollars, has not made much of a dent even in major health problems. Most of our health gains have been due to things like environmental changes (exercise, better diet, etc.), rather than most of the kinds of research that's been so publicized. Besides that, geneticists are already grabbing the behavior genetics/evolutionary psychology brass ring.   But the lack of dramatic progress even in medicine suggests that there seems to be no precedent or natural success-based momentum to draw money, already getting so tight that geneticists are crying in their champagne, away into the historically low-yielding fields that have been floundering.  For that to happen, we need to hear some actual ideas, not a list of current fads or technologies, nor a plea for new research centers in times of fiscal stress.

What is needed is to examine everything, root and branch, and resource deprivation rather than largesse is most likely to engender it.  Just to take some illustrative examples of business as usual issues that should be considered seriously, is multivariate regression using off the shelf software packages, standard practice in the social sciences, the best way to understand social behavior?  Are experiments on college students, the best way to understand society as a whole?  Is survey research reliable?  If society is changing so that the same kinds of surveys have to be done again and again, then something is wanting in the explanatory realm.  Will 'experts' on campuses, publishing in journals few people read, change political vested interests, eliminate the many emotional seeds of racism or greed for differential wealth, other peoples' resources, or political power?  Even in principle, how can social science, or behavior genetics for that matter, change smug, hypocritical religions and their willingness to slaughter each other?  Or are these things simply beyond the realm of what our society views as 'research' and not well suited to the type of activities we call 'science'?

As we said above, in our opinion the issues and problems in the social sciences' purview are, in truth, more important to more people in more ways and for more years than most of those in the hard sciences, even including much of medical science.  How should they be addressed?

You be the judge!

Friday, July 19, 2013

When a fly's smell is bad, its life stinks.

Is the system by which humans detect odors, olfaction, as deeply conserved through evolution as we've long assumed?  Olfaction presents an important chemosensory challenge to organisms, like us, that evaluate their environment by picking up some subset of its chemical aspects.  A wide diversity of animals smell with a series of more or less randomly varying cell-surface receptors on the olfactory tissue which is exposed to the outside world (e.g., the lining of your nose). 

Human olfactory system; 1: Olfactory bulb 2: Mitral cells 3: Bone 4: Nasal Epithelium 5: Glomerulus 6: Olfactory receptor cells; Wikimedia

Olfactory receptor neuron; Wikimedia
Neurons express olfactory receptor (OR) molecules, which are proteins (and hence coded by specific genes) that have a binding pocket in the part that sticks outside of the olfactory neuron.  There are hundreds of different OR genes in the genome, and they vary in their amino acid content so that the binding pocket of each responds only to specific aspects of an odorant molecule.  A given odorant will be detected by only a subset of ORs; this has been known for a long time, but how it happens is still unknown and debated.  Recent arguments suggest that certain aspects of quantum entanglement (rather than molecular binding) are responsible.

Now, if all ORs were expressed by each olfactory neuron, each cell would respond to every odorant, sending "I detect this!" messages to the brain.  Whether you were smelling lion or chocolate, your brain would get the same message--a 'bell' rung by each neuron.

Instead, through various mechanisms each neuron only expresses one of these many OR gene products.  The mechanism is very specific, though currently basically not understood, but that is not our topic today.  The point is that when chocolate molecules waft through your nose, they 'ding' only some of the neurons.  Lion smell dings others.  Indeed, the wiring to the brain's detection center, the olfactory bulb, sends signals from cells using the same OR to the same places in the brain.  This allows your brain to do the bookkeeping and keep an orderly account of what's out there; as a result you can tell if you are about to become a meal or partake of one. 

Insects have a very different repertoire of OR genes, but have similar one-gene mode of using them.  Well, that at least is the story as it has been believed since the whole single-gene per neuron expression and highly variable, numerous OR genome was discovered--a striking finding for which Axel and Buck deservedly won a Nobel prize in 2004.  But does the system actually work that way?

Flies, the standard laboratory Drosophila species, are easy and quick to work with compared to mammals, and one can do genetic engineering to test ideas like these.  And a recent paper in PLoS One by Tharada et al. reports just that, their test of whether the single-neuron unique-address system actually works in insects as has been thought.

Dorsal view of a cutaway fly head showing the main elements of the olfactory pathway. Odours are sensed by olfactory receptor neurons in the antennae and maxillary palps. These neurons project axons along the antennal nerve to the antennal lobe glomeruli, where they are sorted according to chemosensitivity. From there the information is relayed by projection neurons in the inner and medial antennocerebral tract (iACT and mACT) to the mushroom body and to the lateral horn. Gustatory stimuli are sensed by gustatory receptor neurons in the labellum on the tip of the proboscis, the elongated fly mouthpiece.  Source: Nature Reviews Neuroscience, Keene and Waddell 2007
Basically, they found that flies engineered to co-express more than one OR in a given neuron were less able to detect and find a secondary food source in their experimental chamber, compared to control flies expressing only a single OR per neuron (the normal pattern). The experimental group that were forced to search for secondary food had lower survivorship and were thus less fit.
While any experimental study of this sort is somewhat artificial relative to the real world, and perhaps specialists will raise various methodological questions beyond our ability to judge the study, this does seem to be the first direct evidence that the presumed single-expression neural bookkeeping hypothesis about odorant detection, and its evolutionary basis, are supportable.

This is important first to the degree that it confirms prior ideas, suggesting that we understand at least major elements of this system.  More importantly, perhaps, it further opens doors towards understanding the mechanism by which single gene per cell expression patterns are achieved.  One can't automatically extrapolate from flies to vertebrates, but the similarity in gene families and expression pattern suggest that such extrapolations are  not entirely fanciful.

Or, put another way, when a fly's smell is bad, its life stinks!

Thursday, July 18, 2013

When the answer is, "It's hard to say...."

Often in science, physical as well as biological, when one asks an important question, the answer given by the expert who may be expounding on his/her research or on the state of play in the field, is "Oh, it's hard to say!".

Examples would be how much risk will be associated with a given environmental exposure, how much life expectancy will change by the year 2050, how many planets there are per galaxy, or how high ocean levels will be by 2050, and so forth.

Science is stuck with what we know today, and we don't know what we'll know tomorrow.  But our society has high regard for experts (perhaps, experts favoring a given person's personal interests or viewpoint), and of course in many areas we need to make policy.

But we scientists are proud and we don't advance our careers by saying what the truth is in these circumstances:  "We don't know!"   Most of the time, that is how we should properly translate "It's hard to say."  Or, perhaps, better, "It is currently impossible to know that."  That is the honest answer and if we did our jobs better we'd be saying that, clearly, more often.

One might respond to this by arguing that while we don't literally know the answer, we at least can give some estimate of it, some approximation.  So the typical hedging answer isn't all that wrong.  Indeed, often the expert in question would say something like  "It's hard to say, but based on current data it will be about xxx...."  Or they'll give a range of possibilities ("it will likely be between xxx and yyy...").

Now, there is nothing ethically wrong with giving such vague or approximate answers, but in many if not most situations, the expert doesn't really even know these xxx and yyy values and is just giving his/her personal opinion.  Sometimes the answer is simply a very wild guess (how many planets in the stars in an average galaxy?), with almost no connection to real data.  How did upright posture evolve?  We typically can't predict the future values of causal variables, or really know what they were in the past (as in evolutionary adaptation reconstructions), or what new technology might let us see.  Often, we can't predict such things even in principle.  Yet we see such things said almost every day in the popular media and even in Discussion sections of science journal articles and the like.

Science is largely about what we don't know.  We should acknowledge that so that the public is aware of it, and so we keep ourselves aware of it.  Instead, too often we act as if "hard to tell" means we basically know but not very precisely, and too often that kind of connotation is used for self-interested purposes.

It is unnerving to realize how much we don't know, even if it is rather inspiring to realize how much science has learned, and even how much for the first time just in our own lifetimes.  But a more sober, slow and carefully considered examination of what we don't know--and why we don't know it--might lead to even more inspiring attempts to push ahead.

Of course, it's hard to tell how well that might work!

Wednesday, July 17, 2013

The deep epistemological problem in 'personalized genomic medicine' . . . that nobody wants to acknowledge

Two recent studies, both published in The Lancet, one from Denmark, and reported in this BBC story, and the other from England and reported by Gina Kolata in The New York Times, clearly illustrate one of the most important issues in personalized genomic medicine. The BBC writes, "People born in 1915 scored higher in cognitive tests in their 90s compared with those born a decade earlier, according to the study in The Lancet."  People now living into their 90s are experiencing a substantially higher quality of life than in the recent past, or that could have been predicted in any reliable way.  They are experiencing much less loss of mental function as well.  And the story in the NY Times says dementia rates are dropping as 'predicted'.  Senility, clearly, is not inherent in the human genome.

Also on the BBC site there's a story reporting that air pollution is harmful for people with at-risk hearts.  This is tragic for those people, and had been suspected but not specifically predicted.  The point is not just that we should pay heed to the quality of our air, but that we can't really predict where there will be more, or less air pollution, nor pollution by what mix of agents, and so on.   Yet, if there are genomic factors affecting heart vulnerability (regardless of whether there are other genomic factors related to how we respond to airborne pollution), we cannot reliably estimate the risk associated with those genomic factors.

These stories are interesting, given that we are being promised, with few and often rather hidden caveats, that if you just let investigators sequence your genome, they'll be able to predict your future disease risks (and companies and various advocates of genomics-everywhere, promise that other personal traits like academic ability, musical or athletic ability, or tendency to abuse drugs or commit violent crimes etc., will also be predictable from your DNA sequence).

The longevity study is great news for those of us in the dotage range!  But it has much deeper meaning when it comes to the promises being made by the genomics industry.  The aging experiences of two cohorts were very different, but surely their genotypes were not.  Thus, the genotypes of neither cohort, those born in 1905 or those born in 1915, could have been used to predict either healthy or less healthy aging.  That is, neither result was predictable from genes.  That the result was 'predicted' as described in the NY Times story doesn't mean that it was or could have been predicted in any precise way, for the reasons we discuss here, and of course this has nothing to do with specific genetically based predictions, nor can it, in any useful way.

This is what it means to point out that environment, whatever that includes, is not just a trivial variable to be regressed out in terms of genotype effects.  It also shows the hollowness of the rationale that epidemiologists often use to justify big genomics studies, that they just want to be able to regress out genotype effects so as to identify the more important environmental effects.  That assumes, inherently, that genotype-based risks are stable and well-estimated.

Clearly, and to an important extent, most predictions based on GWAS and other related omics approaches, cannot be taken seriously except for very clear-cut strong effects--most of which do not and did not require massive genome-wide studies to identify.

Since environments--physical and lifestyle, etc.--cannot be predicted, not even in principle, this is why we  repeatedly say that the promises used to justify much that is going on today in genomics and biomedical genetics is more to satisfy the investigators than to deliver the promised benefits.  The point that environmental effects are estimated retrospectively (based on today's GWAS subjects' past history), but personalized medicine is about prospective (future) risk, and that future risk cannot be predicted when environments are important.

Every week there are studies showing these points.  This is not mysterious, nor new, nor technically subtle.  But the problem is fundamental.  So is it being conveniently ignored by those who want to continue with current approaches?  Is it wrong to question their underlying motives?

Tuesday, July 16, 2013

Progress in gene therapy: a promise that could come to pass?

We often write about the excesses and over-promising of human genetics, but here are two stories on something genetics seems to have gotten right.  Successful gene therapy stories both, they represent, to us, a use of money and expertise that fulfills the promises of the field and actually changes lives.

Both reports are in the July 11 issue of Science.  The first (paywalled, but here's one summary and here's another) describes gene therapy for MLD, metachromatic leukodystrophy, an inherited neurological disease caused by deficiency in an enzyme that is required for maintenance of the myelin sheath, the protective lipid layer around nerve fibers.

The disorder is caused by variants in the ARSA gene, as described in the paper:
ARSA deficiency causes accumulation of the enzyme substrate, sulfatide, in oligodendrocytes, microglia and certain neurons of the Central Nervous System (CNS), and in Schwann cells and macrophages of the Peripheral Nervous System (PNS). This build-up of sulfatide leads to widespread demyelination and neuro-degeneration, which is ultimately manifested in patients as severe progressive motor and cognitive impairment.
Without myelin, nerves in the central and peripheral nervous systems eventually cease to function properly.  MLD becomes progressively worse and patients usually die not many years after onset.  Incidence is from 1 in 40,000 to 1 in 160,000 worldwide, with some populations having much higher rates.  

Researchers used a lentivirus to introduce the corrected form of the gene into cells, first demonstrating proof-of-principle in their mouse model of MLD in which they showed that disease could be both prevented and corrected.  They report that transferring the strategy to people was a challenge, and one major potential set-back is leukemia as a consequence of the treatment, although they have altered the method for introducing the virus into cells in an effort to circumvent this.

They have now treated 9 patients with early-onset MLD, and report the outcome for the first three patients after 24 months for one and 18 months for the other two. The children's cognitive and motor skills development is currently age-appropriate, they have no signs of demyelination and no signs of leukemia. That's very encouraging.

The other report is of gene therapy in children with Wiskott-Aldrich syndrome, an immunodeficiency disorder caused by mutations in the WASp gene, which codes for a protein that regulates the cytoskeleton of the cell.  The platelets of affected children are small and function improperly, and children are at high risk of autoimmune disorders and malignancies.

Researchers used the same method of introducing the functioning version of the gene into patients and report results after 20-32 months of follow-up, and again, they are encouraging.  The patients now have healthy immune systems and no signs of leukemia.

This is good news for people with these disorders, but it's also good news for the field of gene therapy.  The field has held great promise for decades, but the challenge has been to develop methods for safely introducing genes into the cells where they are needed.  It sounds as though progress has been made.

Engineering: Where science really works
Science as an exploration of the unknown has to juggle various aspects of its agenda.  These include the difficulties of the problems themselves, technological limitations, costs, and of course various professional and other vested interests. Sometimes 'we like sheep' follow fads and current thinking without really considering what we're doing.  When nature is complex, or causation unclear or highly complicated, we often falter.  And we sometimes wish that things were actually simple, even when we know very well that's incorrect.

But one thing that can be said about human beings: we are great at technology.  Technology tends to work.  So when a cause really is known, and there is a clear objective, there's a good chance we can figure out how to achieve it.  We are terrific at engineering solutions for known problems. That's the case with strong genetic causation of a disease.  The objective is to intervene to prevent or treat the disease.

The challenge may be great, but we have a way of getting there eventually with technological advances.  The two examples we see in the current literature seem hopeful in that sense.  They also constitute what we think are unexceptionably good ways to invest health-related funds.

This won't change the fact that Nature is not compelled to yield easily to us, even in engineering.  Nor is there any reason that success in engineering will guarantee that the rest of science will yield to what are essentially engineering approaches that, as is these days so often basically the case.

But it is gratifying that many times we are able to solve problems, once we have properly identified them.

Monday, July 15, 2013

Aeon essay

For today's post we're sending you over to Aeon Magazine, a new, free, open access, online publication that posts a new essay every weekday.  The essays fit one of five themes, from science to memoir to musings on society. The editors have done a stellar job inviting pieces from an incredibly diverse and talented group of writers.

It's a fine publication.  And I am honored to say that today's essay is mine.

This article is for my sister and brother-in-law, dairy goat farmers in Vermont.  The hardest working people I know.

Friday, July 12, 2013

Music and synchronized heartbeats

I once heard the otherworldly baroque cellist Anner Bylsma in concert.  It was many years ago, but I remember that he played some of the Bach cello suites, some of the most challenging and beautiful pieces of music that a cellist can play.  He commented with bemusement that he found it ironic that soloists were expected to sound like many musicians at once, while the many musicians in an orchestra section are expected to sound as one.

Here he is playing Suite no 1. It is simply majestic.  I know people who want to hear Bach as they lay dying, and this is why. 

Now comes a paper saying that musicians together may do more than sound as one.  Their hearts may beat as one.  Or rather, synchronize.  This is choir members, who apparently control their breathing enough that it affects their heart beat, and when they are singing in unison their hearts accelerate and decelerate together.  The authors of this paper discuss the implications of this for the health and well-being of the singers, but I prefer to think of it less prosaically.

Dictyostelium discoideum, slime mold, are amoeba that live in the soil. Their life cycles are interesting; at some stages they are single celled organisms going it alone, but when conditions are right (or wrong -- when the individuals sense that nutrients are being depleted, generally because there are too many amoeba consuming them), the individuals mass together, eventually becoming a fruiting body that releases spores and starts the cycle again. 

Dicty life cycle; Wikimedia Commons

Each aggregate may be comprised of multiple species.  Once they've come together, some cells will undergo apoptosis (that is, programmed cell death -- kill themselves) for the good of the group, even when it includes cells they aren't as close kin to as others.

But this phenomenon is not just a strange evolutionary quirk of slime mold.  Most if not all bacteria can do this.  They have what's called "quorum sensing" which allows them to detect the population density around them.  They respond to high population density in numerous ways, but one common response is to group together into a biofilm, a group of often diverse bacterial species that has a modicum of structure, and can do things that each cell cannot do alone, such as better resist antibiotics.  They have been doing this since before there were multicellular organisms as we know them.

Hive insects, ants, termites, wasps, bees, and so on, are similar.  Individual insects each contributing to the good of the hive, and each surviving only because of the hive.  Enough so that hives are often considered to be superorganisms.  This behavior probably evolved before vertebrates like us did.

Maybe choirs are superorganisms too.  As singers aggregate into groups, specializing as bass, alto, tenor, soprano, they can reach ethereal heights that those of us who sing in the shower cannot.  Perhaps it is good for the singers' health, but I think more, it is good for our souls. 

Thursday, July 11, 2013

Pleiotropy, genomic background, and complexity

A recent paper in Nature Reviews: Genetics, "Pleiotropy in complex traits: challenges and strategies" (Solovieff et al.) raises some interesting questions (it's paywalled, so we'll try to summarize succinctly).  Genomewide association studies (GWAS), they say, have identified numerous gene variants that seem to have effects on multiple traits (they call these "cross phenotype" or CP effects).  This seems to be particularly true for autoimmune disorders, neuropsychiatric disorders and cancers.

In some instances this strengthens epidemiological evidence for what seem to be clinically related traits -- schizophrenia and bipolar disorder, for example, have been found to be familial and GWAS results suggest that they share genetic risk factors as well.  A single genetic variant, protein tyrosine phosphatase non-receptor type 22 (PTPN22), has been linked with "rheumatoid arthritis, Crohn's disease, systemic lupus erythematosus and type 1 diabetes", all autoimmune diseases.  The telomerase reverse transcriptase (TERT)–CLPTM1-like (CLPTM1L) locus has been linked with glioma, bladder and lung cancers.

So, it seems that the different traits share a common genetic pathway. 
At first glance, several scenarios fit these observations: distinct effects of the same allele in different cell populations underlying associations with different diseases or disease groups; a single molecular effect having multiple morphological or physiological consequences; or a CP effect tagging two different causal variants within the same gene that result in different functions and affect different phenotypes.
CP effects, the association of a single locus with multiple traits, can be due to other than true pleiotropy, the term referring to the effect of a locus on more than one trait.  Instead they could be reflecting a shared genetic pathway, or they could be spurious, but in any case the paper addresses the question of how to distinguish biological from spurious pleitropy, and describes various statistical approaches for determining CP.

Interesting, but not the most interesting issues, to us.  Humans have only 20-25,000 protein-coding genes and we've defined many thousands of illnesses, and we've got many thousands of normal traits, and there can't be a gene 'for' every disease or trait.  Indeed, it is we the researchers who sometimes create categories of disease that make sense phenotypically but aren't biologically distinct -- while also lumping traits that are biologically distinct.  So, it must be that sometimes pleiotropy is a social construct, so to speak.   

But multigene pathways help to sculpt traits and diseases, and genes that aren't end-product genes (genes that code for mineralization or the lens of the eye, e.g.) have been recruited by multiple pathways for multiple purposes.  So if a gene variant interrupts the production of a protein in one pathway, it's likely to do so in all the pathways it's used in.

Except that that doesn't seem to always be true, which we find more curious than pleiotropy.  Why can a known mutation in, say, fibroblast growth factor receptor 2 (FGFR2) be associated with something as localized as premature closure of cranial sutures (craniosynostosis) but have no apparent effect in other pathways in which it's clearly shown to be expressed?  Half of all the FGFR2's an affected individual's cells make (assuming one copy of the gene is defective, the other normal) will be equally disrupted, after all, wherever they are.  So each cell expressing the gene should be comparably abnormal.  Why do inbred littermates with known  craniosynostosis-associated FGFR2 receptor mutations have different phenotypes, from no effect to several fused sutures?  (Here's a paper describing this.)

There are several issues here.  First, it is assumed but often not true that both copies of a gene that a person has are expressed in the cell that uses the gene.  It is further assumed, but rarely tested and indeed difficult to test, that each copy of the gene is expressed at the same level in the cell.  Second, somatic mutation may mean that the gene is not identical in the cells in an individual and depending on when such a mutation occurred during embryonic development there can be different fractions of descendant, affected cells.

Third, what happens as a consequence of  FGFR2 expression depends on the rest of the animal's genotype -- because the FGFR2 protein is related to signaling (communication) between cells.  Since somatic mutations are occurring all across the genome, and since there are probabilistic aspects of the signal sending and detecting, each animal will be somewhat different -- even with the same genotype.  Another way to see it is the very well known variation between different inbred mouse strains in which the same genetic mutation has been engineered.  This shows clearly that genomic background affects the result.

Indeed, it is of course quite interesting and important to understand if there are any deeper reasons why there are families in which one member has a severe disorder while others with the same genetic variant remain completely unaffected.  Hemochromotosis is an example, periodic paralyses are other examples, but there are many.  For this, the escape-valve term 'penetrance' was invented long ago, to mean a gene that does something every time....except when it doesn't.  It tends to connote weak effects or stochastic effects (since penetrance 'probabilities' are estimated), but it is at least as likely to reflect genomic background variation; in that case it is improper to consider it to be a probability since that suggests a fixed, stochastic effect rather than one highly dependent but perhaps specific, on context.

So the explanation for variable 'penetrance' is presumably genetic background.  That's a very challenging issue, for which we have inadequate means of addressing.  Each of us has his/her own unique background, and it responds differently to external environmental insults, stimuli, and other factors, as well as what's going on inside our cells.  GWAS gives us some evidence, but does not provide a good conceptual way to understand genomic causation.