Friday, November 29, 2013

Interesting discussion site...

Here is an interesting online tv website, the Institute for Arts and Ideas (IAI).  There are a variety of discussions involving societal issues, including those related to science.  They are on the philosophical or sociopolitical side, rather than the technical, but interesting.

I don't know if they've done a discussion on big ag and so on, but they have dealt with evolution and medicine.

We just thought we'd point it out.

Thursday, November 28, 2013

Thanksgiving poems

Jim Wood recently introduced me to Edwin Muir, an Orkney poet, a poet of the land.  I love this poem, and here Jim explains why it's so perfect for today.

We give you what we think may be the best Thanksgiving poem ever written. Oddly enough, it’s not by an American, and it doesn’t mention pilgrims or turkeys. It’s by the great Orcadian poet Edwin Muir (1887-1959), born in rural Dearness, raised on the northern isle of Rousay, heir to Orkney’s only semi-important “clearance” (see his poem “The Little General”), lover and fearer of great Clydesdale plow horses (see “Horses” and “The Horses”), and discoverer (as far as the West is concerned) of Franz Kafka. We love “The Difficult Land” because it expresses both the pain and beauty of the traditional rural world. I have now written on the MT about both what we have lost (tragically) by abandoning traditional farming – and what we have gained (thankfully) by abandoning traditional farming. Both are true, and nothing that I know of expresses all this better than this achingly beautiful poem. The perfect Thanksgiving poem: “This is a difficult country, and our home.”

The Difficult Land

This is a difficult land. Here things miscarry
Whether we care, or do not care enough.
The grain may pine, the harlot weed grow haughty,
Sun, rain, and frost alike conspire against us:
You’d think there was malice in the very air.
And the spring floods and summer droughts: our fields
Mile after mile of soft and useless dust.
On dull delusive days presaging rain
We yoke the oxen, go out harrowing,
Walk in the middle of an ochre cloud,
Dust rising before us and falling again behind us,
Slowly and gently settling where it lay.
These days the earth itself looks sad and senseless.
And when next day the sun mounts hot and lusty
We shake our fist and kick the ground in anger.
We have strange dreams: as that, in the early morning
We stand and watch the silver drift of stars
Turn suddenly to a flock of black-birds flying.
And once in a lifetime men from over the border,
In early summer, the season of fresh campaigns,
Come trampling down the corn, and kill our cattle.
These things we know and by good luck or guidance
Either frustrate or, if we must, endure.
We are a people; race and speech support us,
Ancestral rite and custom, roof and tree,
Our songs that tell of our triumphs and disasters
(Fleeting alike), continuance of fold and hearth,
Our names and callings, work and rest and sleep,
And something that, defeated, still endures – 
These things sustain us. Yet there are times
When name, identity, and our very hands,
Senselessly labouring, grow most hateful to us, 
And we would gladly rid us of these burdens,
Enter our darkness through the doors of wheat
And the light veil of grass (leaving behind
 Name, body, country, speech, vocation, faith)
And gather into the secrecy of the earth
Furrowed by broken ploughs lost deep in time.

We have such hours, but are drawn back again
By faces of goodness, faithful masks of sorrow,
Honesty, kindness, courage, fidelity,
The love that lasts a life’s time. And the fields,
Homestead and stall and barn, springtime and autumn.
(For we can love even the wandering seasons
In their inhuman circuit.) And the dead
Who lodge in us so strangely, unremembered,
Yet in their place. For how can we reject
The long last look on the ever-dying face
Turned backward from the other side of time?
And how offend the dead and shame the living
By these despairs? And how refrain from love?
This is a difficult country, and our home.

                                          -- Edwin Muir

One of the things I now look forward to at holidays is the poems that arrive in my inbox from MT reader Ed Hessler a day or two before the event.  Among the poems he sent to a fortunate list of recipients this Thanksgiving was this one by Kenneth Rexroth.

Falling Leaves and Early Snow

In the years to come they will say,
“They fell like the leaves
In the autumn of nineteen thirty-nine.”
November has come to the forest,
To the meadows where we picked the cyclamen.
The year fades with the white frost
On the brown sedge in the hazy meadows,
Where the deer tracks were black in the morning.
Ice forms in the shadows;
Disheveled maples hang over the water;
Deep gold sunlight glistens on the shrunken stream.
Somnolent trout move through pillars of brown and gold.
The yellow maple leaves eddy above them,
The glittering leaves of the cottonwood,
The olive, velvety alder leaves,
The scarlet dogwood leaves,
Most poignant of all.

In the afternoon thin blades of cloud
Move over the mountains;
The storm clouds follow them;
Fine rain falls without wind.
The forest is filled with wet resonant silence.
When the rain pauses the clouds
Cling to the cliffs and the waterfalls.
In the evening the wind changes;
Snow falls in the sunset.
We stand in the snowy twilight
And watch the moon rise in a breach of cloud.
Between the black pines lie narrow bands of moonlight,
Glimmering with floating snow.
An owl cries in the sifting darkness.
The moon has a sheen like a glacier.

                                --Kenneth Rexroth

Wednesday, November 27, 2013

Is science that different from other forms of ideology?

We in science are convinced that, whatever our failings, greed, and ignorance, the systematic approach to understanding the actual cosmos we're in is the only one that will do that.  Religion and other mysticism won't.  That is our motto, and it's our cant.

We lambaste religion--those who are just plain wrong--as grasping at every evidential straw it can to support its unsupportable belief-system.  Defenders of the faith will point to every statement of uncertainty, every mistake, and every missing puzzle-piece with sneering dismissal.  They use any lever they can find, even culpably misrepresenting science.  And, what is probably worse, they invoke the patently false logic that if a particular science explanation is wrong that implies that their particular explanation is therefore right. That is, if evolutionists make a mistake, that implies not just that there is much that we don't know about evolution, but that biblical literalism must therefore be right instead.

This is ideology in action.  For the religious (that is, those with the major nominal religious faiths), their belief brings comfort against the fears of life--its injustices, cruelty and its end.  A rewarding life ever after drives much of such belief.  Scientists don't get that comfort, even if we sometimes wax forcedly poetic about the grandeur of life's panoply.  But we feel edified, if not arrogant, that at least we have a finger on the way to Truth.  But are we so different?

What about science?
Science is a form of ideology.  It is tribal, with its secret jargon, its oracles of wisdom, beatified by symbols like Nobel prizes.  We become the experts who know.

But we usually do that based on our own canonical beliefs.  We call it a theory rather than an ideology or faith, but it amounts to more of the same than we like to think.  For example, if our ideology is that natural selection is the cause of all things present today and genetics their immediate cause, then counter-facts are dismissed.  We say that we may not know the explanation for those facts, but that with more work (and, of course, more funding) we will find it.

This defensive ideological behavior has political and economic implications of many sorts.  We often write about the vested interests and the inertia they defend with invocations of their mantras, such as that of genetic determination of our traits like disease and behavior.

Climate change is an excellent example.  Politicians routinely invoke climate change in their rhetoric if it serves their arguments in favor of some policy.  Deniers do the same, invoking science's lack of definitive results as if that falsifies the whole theory. We now routinely hear statements about typhoons as manifestations of climate change and then, "See, I told you!  Now we need a law to xxxxx".   Not all climate scientists themselves do this, but climate-change science has its lobbying for funds and attention, like all sciences do.

Typhoon Usagi, Sept 19, 2013; Wikimedia
 The NYTimes last week had a very cogent editorial that relates to this issue in the context of climate change. The author points out that the data suggest that we in fact may face fewer super-storms with global warming.  He criticizes politicians who blindly invoke climate-change rationales, and notes that even advocates sometimes slip into arguing the big-storm rationale.  Scientists seem reluctant to point out that non-commonsense phenomena may exist and things may not be well-known, but that that does not undermine our ideology.  And the fact that, say, big storms may not be a result of climate change after all, does not suggest that climate change is being imagined.

If both sides of arguments rely on selective citation and selective amnesia, then we as a society are not having a debate about the facts, but instead are in a tribal conflict for material as well as symbolic territory of one kind or another.  That may be how culture works, with science far from being as neutral and objective as we scientists like to fancy. But if science really is about the material rather than cultural/tribal world, we should learn to recognize that, and act accordingly in a more responsible way.

Tuesday, November 26, 2013

The Nair-do-wells, and their evolutionary message

In what, if you'll forgive the pun, is a barely visible revolution, it appears that women are throwing away their razors (sorry, Nair!).  As Beverley Turner put it in The Telegraph last week, "Ladies, breaking news: it is time to step away from the molten wax and let our lady gardens grow free." Maybe it's because Gwyneth Paltrow told Ellen DeGeneres that she "rocks a 70s vibe down there", or maybe it's just, like clothing, another changing fashion, but pubic hair is back.  Whether this is caused by, or will be followed by the porn industry is something that, surely, many university professors will be seeking grants to study.

This should be especially interesting to the evolutionary psychology industry, because of their determination to document the Darwinian reasons for the hard-wiring for every element of behavior.  In the old, naive days, their academic ancestors showed how clearly pubic hair evolved as a sexual-display trait, to ensure that males would be interested (as if that were necessary!).  Otherwise, if it were not all about mate choice and sexual selection, what was it doing there?

Well, perhaps it wasn't just a sexual attractant, but instead, a signal by the females that they were no longer girls, but women, ready and able to mate and conceive.  No wasted sperm by males who would otherwise be attempting to make the Shakespearean beast with two backs with those who couldn't yield the offspring by which the promiscuous males were so driven to propagate.  Or maybe it "aids in the wafting of human pheromones", never mind that there's no uncontroversial evidence that humans even have much in the way of active vomeronasal organs, or pheromone receptors. 

Whatever the explanation, strong sexual selection clearly mandated this particular patch.

But if so, how could it possibly be that for the past generation the fashion was no pubic hair at all?  After all, why would looking like a pre-pubescent girl attract men?  How could any woman give up her come-on signal, that so clearly, we were told, evolved as a fundamental necessity for evolutionary existence?  We haven't tried to explore what the evolutionary behavior people said about this patchwork trend in patchwork, but given it's lascivious appeal surely there are articles and books galore, retrofitting Darwinian explanations to that once-new (and now obsolescing) hirsute reality.

But that doesn't really work if we are hard-wired to respond to that View.  It may be a conundrum.

This is not (only) a prurient post!
We must leave this mesmerizing topic, to show that we ourselves are not dwelling on it for its reader-appeal.  There are many similar issues, that generalize the point, and it is in fact an evolutionary one!

Nov 24's NY Times book review section reviews two new books dealing with the philosophy of dilemmas, specifically the trolley dilemmas, which goes like this: If you could divert a trolley from its current track, knowing that if it continued on that track it would be derailed, killing all on board, to a spur that was safer for all on board but someone was tied across the tracks and sure to be killed if the trolley goes in that direction, what would you do?  Intentionally kill someone, or kill one to save many more?

You might think this a strange thing to consider along with the now you see it, now you don't pubic hair issue, but it's actually very similar.  The reviewer notes that the book reports research showing that what people choose to do in such a Hobson’s-choice situation is not hard-wired.  It depends upon the individual, how the choice is presented to them, their gender, and aspects of their recent lives.  They are not programmed to evaluate whether the person to be killed is one they would normally have affinity with, nor asked whether they would sacrifice themselves by jumping on the track in front of the trolley to save everyone else.  Their decision was contextual and specific to individuals. 

You might think this could be the biggest ‘so what?’ item one can imagine.  Duh!  People make different choices!  But given the tenor of the behavioral evolution literature, such optional thinking should not be optional at all: people should use their hard-wired game-theory neurons to make the self-interested decision that Darwinian selection mandated them, by eons of filtering right decisions from wrong ones, to do.

The real evolutionary problem, harder and so easily being ignored
There are countless other examples of similar issues that we could cite.  They have one aspect in common:  humans are generally not hard-wired for our behavioral repertoire.  Instead, we are hard-wired not to be hard-wired.  And how that could be is the real evolutionary problem we should be trying to understand.

Now you might defend the ev-psych Darwinian point of view by saying that since Eve ate the forbidden apple, it was cover-up time with the proverbial fig leaves, which thwarted the Vital View that men needed to see to know that what they wanted was ready.  Thus clothing put all bets off, and since men can't know what's hidden until the action actually starts, they now have to respond to something else, and women provide it with, say, tight clothing or makeup or hanging out in bars, or whatever.  

But that doesn't wash as an escape, because if we really were hard-wired to respond to the View, we would not be able to substitute it with something else.  For reproduction to occur and our species to survive, even clothed women would have to wear a see-through triangle (that, in freezing winter, could be double-glazed).  And women, hard-wired to be fearful that they would not be properly recognized, would never, ever, ever reach for the razor.  And of course all this male mate choice talk doesn't explain why they have pubic hair.

No, the obvious truth is that the View is not necessary--men and women can alter their landscape and still succeed.  And that raises the key point.

The hunger for competition-based, simple, dramatic and telegenic stories about how this or that behavior must have evolved to wire us to behave as we do, makes it easy to write grants, publish papers, tell stories on television and the like.  Also, it is easy, and hence convenient, to imagine and hypothesize hard-wiring of a clockwork organism, and how the trait could evolve:  if the incoming retinal signal-carrying nerve from the eye synapses in a fixed neural arc with some relevant behavioral neuron that connects with some muscle activating neurons, one can easily imagine evolution favoring this hard-wiring--when the signal comes in, the behavior goes out.  Such a generic story doesn't make a specific invocation of it true nor even easy to find the neurons, but at least it fits in a highly selection-based, model of the body as a machine.  

It sounds so simple that it sounds as if it simply must be true.  So one can see why it's easy to take this approach even when, hidden in plain sight, is the massive evidence that such pat stories are at the very best great exaggerations and usually little more than speculation. That is, one can do studies about how this particular experimental set-up or study shows what people in particular circumstances do, or how often, and even guessing at why they do it.  You can be a professor, have sage-sounding things to say, publish papers and so on.  

But it is damnably difficult to have much confidence in reconstruction of (1) the specific way, if there is one, in which genes actually affect the behavior, and (2) the evolutionary reason for it--that is, when, where, and how natural selection molded whatever the genetic basis of the trait is--if, indeed, natural selection was involved in the determinative ways usually invoked.

The real challenge
In fact, from an evolutionary and genetic point of view, the question is not whether our behavior has an evolutionary, genetic, or neural basis.  That seems rather obvious.  The challenge, and where the research ought to be being invested, is in the much more complex, longer-term, less exotic and sexy understanding of how our brains evolved not to be hard-wired.

Empirically, we use our senses and our thinking powers to evaluate circumstances in which we find ourselves, and determine how to act.  Our reasons usually seem to be quite abstract or indirect compared to simplistic Darwinian stories of immediate reproductive success.  We differ in how we assess situations, the options available, and their likely outcomes.  There is no one wiring diagram, nor one that everybody has.  Indeed, even ev-psych studies use statistical methods to argue that this or that behavior, under some controlled conditions, will occur--and statistical methods mean the behavior is, at best, only sometimes true (e.g., happens more often in some subjects shown some particular image or asked some particular questions, than in some group of controls), and at most only partially wired-in.

Instead, the real question is how can a brain be structured to do this sort of very complex evaluation and integration of many different sensory input systems, in circumstances that are always partly if not largely unique (now, to us, or to our ancestors)?  Answering that is a challenge!

If you think of it that way, you may not have the answer but you will have more respect for the difficult nature of this important biological and evolutionary problem.  You'll have more respect for science as it is supposed to be.  And you'll see that our species seems to continue to proliferate, with or without its razors.

Monday, November 25, 2013

the border

Sometimes people ask me why I work on malaria in Thailand.  Most of the malaria in the world, most of the deaths from malaria in the world, occur in Africa.  So if I want to study malaria, why not study in Africa?  An honest answer would have to include the opportunities that happened to fall in place, but there are real substantive reasons to be very interested in malaria in Thailand.

What I actually study is what we sometimes call “border malaria” – a strange pattern where malaria clusters along international borders.  This is the pattern in Thailand, where malaria is almost completely absent in the central plains.

Probably the easiest way to think about these maps is: A. is where the falciparum malaria is, and B. is where it could be.  Maps from the Malaria Atlas Project:

Understanding why this pattern occurs isn’t easy.

If you look at a elevation map of Western and Northwestern Thailand you’ll see that much of that border consists of mountains and hills.  You can't tell from this map, but those same areas are also heavily forested.  This aspect of the landscape has a whole lot to do with the persistence of malaria in this area.  It has a lot to do with ecology (both human and mosquito), politics, demography, economics, and a few other sociocultural factors.

These mountain areas aren’t heavily populated in the sense that Bangkok or Chiang Mai are, but they have been inhabited for a long time.  Along with the Thai who live in this area, most of the inhabitants consist of what are commonly called Hill Tribes.  These are groups of ethnic minorities who live, both literally and metaphorically, on the margins of Thai society.  They have different cultures, different languages, different houses, slightly different ways of making a living, and ultimately different health problems.

They also live in a vastly different ecology than does most of the rest of the country.  The farther away you get from big cities, the more the roads and other forms of infrastructure (including hospitals and clinics) crumble away.  In the wet season everything is soaking wet and the rivers spill over their edges while in the dry season it can be quite hot.  But it’s also a beautiful place, one of my favorite in the world.  I find both the landscape and the people to be awe-inspiring.  

My main study population here is the Karen.  Living along the international border, on the edges of both Thai and Burmese society, things have been quite difficult for the Karen for a long time.  They spent well over half a century at war with the Burmese military and the symptoms of this warfare are far reaching.  The Burmese military would sometimes attack Karen villages, rebel fighters, farmers, school children, monks and all – and villagers would flee across the border into the relative safety of Thailand.  Some set up makeshift refugee camps while others settled into official camps that have existed now for decades.  At times these camps, with huts built almost on top of each other and constructed of bamboo and dried heliconia leaves, would be set ablaze by the Burmese.  (Here is a nice publication about some of this history, from The Border Consortium).

Mae La camp, which is about 30 kilometers south of where I live, has around 50,000 people living in it, including some who are third generation camp inhabitants. Image from:     
Many things were lost during these years.  Don’t get me wrong, plenty of Karen remained resilient and strong throughout these hard times – they are a lively and outwardly happy people who love to sing and dance, but Karen elders and their knowledge were killed.  People lost limbs to the many land mines that litter this border region.  Some lost their sanity and others lost their hope.  Children lost their chances at education.  All of this for over half a century.  Seriously, imagine a society that hasn’t been able to settle down and focus on families and communities for over 50 years.  Perhaps the greatest loss in this time has been the cohesiveness of such social institutions.

Malaria has been a major cause of both death and sickness for the Karen throughout this time, but these types of conditions make it difficult to focus on a single problem or to even do anything about it.  As malaria researchers have found all over the world, when people have more pressing "for sure" problems (like needing to fill their bellies with food), it is hard for them to worry about invisible parasites in tiny mosquitoes.  Also, preventing malaria means that communities and households need to be working together for this goal.  Community members must work together to ensure people are educated about where the disease comes from and how to prevent it.  Standing water needs to be covered, villages should be well drained, people need to use mosquito nets and they need to seek treatment when they’re sick.  But these are all things that don’t happen when communities are frequently uprooted in the middle of the night only to be forced to move somewhere else, perhaps deeper into mosquito infested forests and hills, to get away from soldiers who wish them harm.  After having to do this several times, people are likely to give up on building permanent communities.  What’s the point when you’ll probably just have to move again one night?  

On the other hand, the Thai have been in a comparatively better position to handle the malaria problem and for most of the country that is exactly what they’ve done.  For most Thais, malaria is a concern of the past.  While I can’t speak for the Thais, I also think many feel as though their neighbors frequently weigh them down.  Thailand is more economically developed than its mainland neighbors (especially Cambodia, Myanmar, and Laos).  Many migrants from these economically poor regions come to Thailand seeking work.  The Burmese are their ancient enemies and while the Karen certainly aren’t the Burmese, they still come from across that border and use the resources (including health care) that are available in Thailand.  The situation is in some ways quite reminiscent of the Southwestern United States, complete with the ill-feelings that some have for the migrants that come across the Mexico border.  The malaria researchers who’ve worked here for a long period of time also have fresh memories of this border area as a dangerous place, where even elephants and water buffalo sometimes step on landmines that were buried years ago and where mortars inadvertently wind up sunk in neighbors front yards.

But money for malaria control and prevention flows into Thailand from lots of different sources (more on that in a future post).  Aid that is specifically geared toward these border populations, frequently channeled through the numerous NGOs in this area, also flows in from many parts of the world.  Yet while the problem almost certainly won’t be fixed in the absence of money, the money must be efficiently directed.  The money doesn’t always make it to the people that need it the most.  Very remote populations that are still on the Burmese side have long been neglected, if for no other reason than because they’re very difficult to reach.  More recently though, there are signs of peace (this is a big point of contention among the Karen!)  More foreigners are allowed into Myanmar/Burma and this means that medical teams have better access to some of these communities.  Even while this is occurring though, there are remote Karen populations on the Thai side that remain ignored.  When I first began working on malaria in Thailand, the story I heard was that most of it came from Burma via migrants.  While that does sometimes happen, it is increasingly obvious to me that small pockets of very high malaria transmission on the Thai side of the border remain.  It’s just that those communities with the most malaria seem to mostly be  non-Thais (for that matter, a lot of people in these areas have no official nationality at all).

And since political reforms have begun in Myanmar, and outside nations have been dropping their sanctions, funding for border related NGOs and other groups has been drying up (see here, here, and here, for example).  I suppose that it was only sexy to donate money when there was an active war going on.  I assure you that the war zone here on the border, and all of its implications, still exists today.  (To be fair, many people want to move their funds into Myanmar.  With that comes the likelihood that some of that money will go to the government.  In my opinion, it also means that many people on the Thai side are abandoned).

I admit that I've only worked on malaria in a few places, but I can't imagine a place in the world where malaria is more obviously linked to social, economic, and political factors.

Now, back to the question that I began this post with: Why do I study malaria here?  Aside from the fact that I just really love this part of the world – there is hope on the horizon and that hope keeps me going.  At one point I was a starry eyed anthropology student who wanted to do something about infectious diseases.  I went to where some of those infectious diseases were, began working with other people in public health (not just Thais), and I found out that not everyone was as passionate as I.  In fact, public health work is a job.  Those malaria funds that flood into this part of Thailand create jobs for people, and some of those people aren’t necessarily concerned about malaria control, prevention, or eradication - some of them just want a job.  And I think this gets at a deeper, more troubling problem that must exist anywhere where there are people who work with health problems.  If you are completely effective, if you actually get rid of a disease, you've actually worked yourself out of a job...

But malaria incidence in Thailand has decreased dramatically since the 1960s and it may even be going down in parts of Burma/Myanmar.  Political changes in Burma/Myanmar mean that there is much less fighting, in this region anyway, than there has been for a very long time.  The resources are here, even if I don’t think they’re always directed in the most efficient way.  I think that many of the young Karen adults are now in a place to learn new skills, take leadership roles, and to gain back much of what they’ve had to do without for so long.  The implication of these things, in particular the latter, I think is that we will see very real changes in the overall health and well-being of the Karen in the very near future.  I’d love to be a part of that.

Friday, November 22, 2013

The nut study -- the good, the bad, and the ugly

We take rare pleasure in praising an Associated Press piece about a paper just out in the New England Journal of Medicine ("Association of Nut Consumption with Total and Cause-Specific Mortality", Bao et al., NEJM 2013 369: 2001-2011).  The paper reports a study showing that risk of death from all causes is reduced among study participants who frequently eat nuts and author Marilynn Marchione does a nice job pointing out the caveats (well, apart from the suggestion that nut eaters are less likely to die).

Why might nuts be protective of your health?  Boa et al. note that "Nuts are nutrient-dense foods that are rich in unsaturated fatty acids, fiber, vitamins, minerals, and many other bioactive substances, such as phenolic antioxidants and phytosterols."

Boa et al. used data from the longstanding Nurses Health Study and the Health Professionals Follow-up Study, looking at the dietary intake and disease history of a total of 119,000 people. Dietary intake was assessed with food-frequency questionnaires sent to study participants every 2 to 4 years.  And the primary endpoint was death from any cause. 
In two large prospective U.S. cohorts, we found a significant, dose-dependent inverse association between nut consumption and total mortality, after adjusting for potential confounders. As compared with participants who did not eat nuts, those who consumed nuts seven or more times per week had a 20% lower death rate. Inverse associations were observed for most major causes of death, including heart disease, cancer, and respiratory diseases. Results were similar for peanuts and tree nuts, and the inverse association persisted across all subgroups.
Other studies have reported similar findings.  Bao et al. suggest several alternative explanations for these findings, other than the apparent protective effects of nuts.  The findings could reflect "confounding by unmeasured or poorly measured variables", although the authors believe this is unlikely because so much data have been collected on these study participants that they feel they could control for most potential confounders.  Unknown confounders can't be controlled for, as they point out.

Reverse causality is another possible explanation for their findings -- unhealthy people might stop eating nuts, for example, rather than that people who don't eat nuts become unhealthy.  But the researchers excluded people from the study once they reported illness, in order to limit this potential problem.

Bao et al. note that because their study is observational, they haven't demonstrated cause and effect, but they also note that their results are consistent with many other reports of the health benefits of eating nuts.  Indeed, the authors are, to an usual but praiseworthy extent, responsibly circumspect in their reporting of their results.

So, the ground was well-laid for Marchione to write a responsible story in turn, and she did. Among other issues, she points out, for example,
Researchers don't know why nuts may boost health. It could be that their unsaturated fatty acids, minerals and other nutrients lower cholesterol and inflammation and reduce other problems, as earlier studies seemed to show.
Observational studies like this one can't prove cause and effect, only suggest a connection. Research on diets is especially tough, because it can be difficult to single out the effects of any one food.
People who eat more nuts may eat them on salads, for example, and some of the benefit may come from the leafy greens, said Dr. Robert Eckel, a University of Colorado cardiologist and former president of the American Heart Association.

Read more here:
.So, kudos to Marchione for pointing out that there are limitations to this kind of study.  The evidence seems to be building in favor of the protective role of nuts, and this study adds to the evidence, but it is not definitive.

Funder bias
Marchione notes rather in passing that one of the funders of the study was the International Tree Nut Council Nutrition Research and Education Foundation, but she says that they had no role in designing or reporting the results.  This, of course, raises the question of whether they were involved in analysis, but let's assume they were not.  Marchione was correct to mention this bit of information because studies funded by industry are much more likely to report findings in the funder's favor than are independently funded studies -- this is common enough that there's a Wikipedia entry for "funding bias".

Knowing that the Tree Nut people weren't involved in study design or reporting is not entirely reassuring about there being no conflict of interest.  A study published in PLoS Medicine in 2007 ("Relationship between Funding Source and Conclusion among Nutrition-Related Scientific Articles", Lesser et al.) reported the results of an examination of the relationship between sponsorship and conclusions of studies of the health effects of non-alcoholic beverages. 
206 articles were included in the study, of which 111 declared financial sponsorship. Of these, 22% had all industry funding, 47% had no industry funding, and 32% had mixed funding. Funding source was significantly related to conclusions when considering all article types (p = 0.037). For interventional studies, the proportion with unfavorable conclusions was 0% for all industry funding versus 37% for no industry funding (p = 0.009). The odds ratio of a favorable versus unfavorable conclusion was 7.61 (95% confidence interval 1.27 to 45.73), comparing articles with all industry funding to no industry funding.
The authors conclude that this has "potentially significant implications for public health."

Why this bias exists isn't clear, and there are probably multiple causes. Some of it is perhaps malfeasance or bad science, industry buying results, but it can't all be that. It's possible that when results are negative they just aren't published, and, ok, it can be argued that that's a clear sort of malfeasance. Or Lesser et al. suggest that perhaps industry funds only studies that they believe will favor their product.  But then the prior knowledge should be reported accurately and built into the testing (e.g., in a 'Bayesian' way), rather than pretending that one has a true 'null' hypothesis.  Or investigators, knowingly or not, propose studies that are likely to show that a sponsor's product is beneficial.

Lesser et al. also suggest that all investigators are biased somehow -- e.g., they want to support their favorite hypothesis -- but that financial conflict of interest is a separate animal.  "We contend that financial conflict of interest is qualitatively different, producing selective bias that acts consistently in one direction over time." This is certainly true in clinical trials funded by pharmaceutical companies.  Cosgrove and Wheeler, for example, go so far as to call the involvement of pharmaceuticals in drug testing corruption in a paper published this year in the Journal of Law, Medicine and Ethics.

The problem here is that the nut study might well have been devised, conducted and analyzed in exactly the same way without industry funding.   But it might well not have, and we have no way of knowing.  Again, Marchione was right to bring this up, but stating conflict of interest doesn't automatically prevent it.