The unexamined walk is not worth taking

I've been reading Robert Macfarlane's beautiful book, The Old Ways: A Journey on Foot, about his travels in Britain and beyond, from walks around his home in Cambridge, England, to the bird islands of the north, to ancient seaways where he, no sailor, sails with friends, and on to Spain and even Palestine.  Macfarlane's is a deep, broad, poetic, idiosyncratic and haunting voice and there is much to take in.

His description of his barefoot walks is whimsical (his friend walks barefoot through nettles because it's chili for the feet), his walk across the Broomway, a path in Essex that only when the tide is out, where many a careless wanderer has met his end, shows a bit of a stubborn, defiant nature that I can't help but believe gets him far.  He travels alone, or enlists the aid of wizened sailors or lifelong inhabitants of the moors, he walks with friends.  But he is always observing.

It's an observation that he tosses off when writing of his travels between bird islands in northern Scotland that catches my attention today.  He is sailing from the Isle of Lewis with four experienced sailors on a 75 year old boat, the Jubilee.

I watched gangs of skua pursue single gannets: their method was to fly above a gannet, drop onto its back, force it down onto the sea, smash its skull with their beaks until the gannet was dizzied, then paddle its head underwater with their feet until it vomited up the contents of its stomach, which the skua then ate. 

This is curious indeed and raises many questions.  It's not the most straightforward way to catch fish, after all.  What else do skua eat, and how else do they procure it?  And are they always so brutal?  How on earth could they learn this rather exotic and complex way of dining?

Great Skua; Wikipedia

In my wanderings through what's written about skua, they are most frequently described as "avian pirates."  The fancy word for this is kleptoparasite, but as long as we're anthropomorphizing, "bully" or even "brute" might be more appropriate. Not only do they smash gannets' skulls, but they have been seen to grab them by the wing in mid-flight so that they stall and fall into the sea, whence the poor birds disgorge the fish they've just caught, freeing it for the skua to scavenge.  And it's not just gannets; they also steal from puffins or terns.

Most skua don't always steal what they eat, though.  They do fish themselves, usually splash diving for surface fish, and they often trail fishing boats and scavenge discards or innards.  But they don't live on only fish.  They eat a wide variety of things, including other seabirds; chicks, fledglings and adults, large and small. They also eat eggs, goose barnacles, tons and tons of goose barnacles, and sand eels when they are available, small mammals.

Gannet; Wikipedia

Skua are generalists, omnivores, but individuals also might specialize, preferring sand eels to barnacles, or whitefish to herring. And huge changes in what they eat over time have been documented, so they certainly can adapt to changes in the availability of foods.

Thieves, pirates, kleptoparasites.  Brutes.  Whatever you want to call them, they don't sound like very nice birds.  But are they worse than the gannet, who you might pity given how he is treated by his near-brethren?  The gannet is a hunter, too, hunting fish, that of course it eats alive, often swallowing the poor fish before surfacing after a dive.  And, people on the Isle of Lewis eat gannets, too (though Macfarlane writes: "I know a Lewisian crofter who, when I asked him whether he liked gannet meat, replied, "I gave a piece to the dog and it spent all week licking its arse to take away the taste.")  So we might just be pots calling the kettle black.

It could be, and surely is argued that kleptoparasitic behavior is innate: skua are born to harass gannets.  Not all seabirds treat each other this way, after all, so it must be something in the skua genome that makes them do this.

But, skua aren't only brutes.  Yes, they do treat gannets abominably, and they do dive bomb people who get too close to their nests, which from a person's perspective might seem brutish, but they are doing it to protect their young.  Which means that they do have some warm and fuzzy feelings. Indeed, like other seabirds, skua invest proportionately more in their young than do land birds.

What part of their behavior would be inborn, anyway?  They don't always smash the gannet's skull, they don't always grab their wing, they don't only eat by stealing, they don't only eat fish, indeed their diet can change from year to year, and they aren't always brutes.  So, exactly what kind of protein would a protein-coding gene be coding for to produce this kind of behavior?

Frigate bird; Wikipedia

Perhaps it's something that skua have been teaching their young for millennia, a behavior passed from generation to generation, not inborn at all. But if so, you'd think it might have caught on among other species of seabirds, so everyone would be dive bombing the poor gannet, a particularly skittish bird. Other seabirds are kleptoparasites, most notably the frigate bird, and many will steal another bird's food when the opportunity arises, but the skua version is not a generally shared behavior.  

So, of course what this all brings up is the question of whether there are genes for behavior or not. Or, is behavior an emergent property for which the groundwork is laid by genes that give us all the ability to scavenge and steal, care well for our young, and a whole host of things besides?  If so, we aren't going to find genes 'for' kleptoparasitism, just as we aren't going to find genes for good parenting -- or bad.

Life evolved depending on one creature living on the flesh of another, by and large.  It's a fundamental legacy of our common ancestry; we all share the building blocks of life, and get, or steal, them from others to survive.  No plant or animal likes being eaten alive, often in a cruel way (since other than humans, species haven't got abattoirs that are at least somewhat terror-free and quick in their killing).  It may be cruel for us to maim, kill, or torture one another for reasons other than food, as is so often what humans do.  But killing for food is what we have to do, whether we are eating plants or animals.  This was one of the observations that led Darwin to his theory that adaptations arise via harsh competition.  It's not the only fact of life, but it's a fundamental one.

Are there genes 'for' survival? 

Report from the frozen north

I have just returned from co-teaching a course, that we call Logical Reasoning in Human Genetics, in Helsinki, Finland.  As mentioned in an earlier post about 10 days ago, I have done this jointly with Joe Terwilliger several times before, 3 of them also in Helsinki, but also in Berlin, Maricaibo, and Madrid.  There have been some additional lecturers in most of these--this time Joe Lee from Columbia, Markus Perola and Tero Hiekkailinna from Finland.

Our point is to explain why approaches to understanding the nature of genomic causation have run into the difficulties that all but the most glassy-eyed advocate or know-nothing ostriches are willing to acknowledge.  Complexity has evolutionary and mechanistic origins, and the challenge to identify causal elements in this context is serious.  Confirmation criteria, so fundamental to science, are problematic because different samples have different evolutionary  histories and most genetic variants that affect the kinds of disease and behavior traits we want to understand are rare and have individually very small effects.  Standard scientific methods that rest on repeatability and statistical significance criteria are often stymied by these facts.

The 60 students in the mini-course, of various levels of seniority including post-docs, and professionals as well as graduate students, seemed to find the lectures we gave conceptually eye-opening.  If we did our job, the effect reported is because many in biomedical genetics do not have a very sophisticated understanding of evolutionary genetics, and because wishful thinking has led to many types of biased reporting or inadequately interpreted studies.  Also, of course, there is stress on those results that are successful, at the expense of the much greater studies that find very  little of relevance.

We have, of course, our own view of this field, and we post that view often.  But many people seem simply to be unaware of  the issues involved and their implications.  So we think there is merit to continue to critique the field (in the proper sense of the term, meaning to provide as objective an evaluation of strengths and weaknesses, successes and failures, as we can).

This will happen again only after the jet-lag is over!

Disease driven poverty

In a few of my previous blog posts I’ve discussed the relationship between poverty and infectious disease.  Many of the most prevalent and severe infectious diseases in the world disproportionately affect the world’s poor.  Part of the reason is that the necessary resources aren’t available for tackling such diseases.  A lot of money is currently spent (wasted?) on designing biomedical ‘cures’ for diseases that persist in some places (usually economically poor places) while having already been eradicated in other places (usually economically rich).  It is my position that diseases such as malaria and tuberculosis remain major threats to some populations simply because of the way that financial resources are allocated in our extremely heterogeneous world.

But there is another angle to this story.

Not only does poverty lead to poor health, but poor health can also lead to poverty.  Quite frequently, that is, the arrows point both ways and the reality is a system in which there are “positive” feedback loops.  There is a growing literature on this type of system which is frequently referred to as a “poverty trap.”  Much of this literature has been in economics, where mathematical models have indicated that populations with infectious diseases are less able to ‘develop’ economically.

With economic development at the population level, e.g. with the growth of average income levels, we tend to see an increase in overall life expectancy at age 0.  Most likely this indicates a relationship between improved health and increased wealth.  However, most of the models that actually look at this relationship are either ecological (they are looking at the entire population and frequently assume homogeneity within the population) or at an individual level.  A few models have also looked at community or household levels.

One major problem with models of all types is that results can change when we change our unit of scale.  The effects of poverty on disease, for example, might be different if we look at a community level rather than a province/state level or even consider an entire nation to be a single population.  This is a problem known as the ecological fallacy (and is closely related to the modifiable areal unit problem) in which causal relationships at the population level don’t explain what is happening at, say, the individual level.  

Regardless of these problems and issues, there does appear to be a feedback loop between poverty and disease.

And this is an interesting thing from an anthropological view.  First off, poverty can mean different things to different people.  For example, to some, poverty means “not modern.”  Some indigenous groups actually choose to live in a traditional house rather than a more modern one.  In my opinion, “traditional” (or not modern) does not equal poverty, but it does get mistaken as poverty.  Poverty can also be a relative thing; something that becomes apparent when you don’t have as much stuff as the people with whom you are coming into contact.  Clearly this may lead to psychological and sociological issues, but it might also explain gradients in outcomes (relative health?)  Finally, there is a type of poverty that exists where people are simply unable to put food on the table.  While there can be some argument about the effects of modernization and relative poverty, I would suggest that this final type of poverty is unambiguous and its negative effects are less debatable.  

In poverty trap models we are frequently interested in investigating and understanding threshold levels under or above which equilibria are reached.  (There are quite a few relatively new papers out that are excellent references (see: Bonds, Keenan, Rohani, & Sachs, 2010; Plucinski, Ngonghala, Getz, & Bonds, 2013; Wood, n.d.)).  Perhaps it is easiest to consider at the unit of the household.

An already poor or marginally poor household in which the major breadwinner is afflicted by severe disease is plagued with multiple problems.  For example, aside from the risk of infection for other household members, if that person is afflicted by malaria or dengue fever, they may not be able to work for several weeks.  A house on the margin of poverty may then fall just enough behind in household money and/or food to fall into true poverty.  Households that are already poor may fall even further.

And an important aspect of this situation is that not only is the person who is actually infected met with further troubles; the entire house is also afflicted.  Furthermore, there tends to be heterogeneity in these effects even within households.  That is, poor households may see things such as greater infant mortality, and this effect may be exacerbated when there is a shortage of food or resources in the household.

In poverty trap models, there are usually equilibrium points in poverty levels that, once reached, are quite difficult to break.  From Bonds et al. (2010):

What may be most important in these debates is therefore not whether the effect of health on poverty is more significant than that of poverty on health, but whether the combined effect is powerful enough to generate self-perpetuating patterns of development or the persistence of poverty.  

Children who grow up in households with frequent food shortages may not have the same physical or cognitive abilities as others.  Their immune systems, already taxed by years of exposure to pathogens, may not be able to fight off diseases as well as their healthy counterparts.  Therefore, when they begin their own households, they are already behind in the nutrition, health, and economic game.  And once again, when adults in the new household fall ill and cannot put food on the table, the children will be disproportionately affected.  

This cyclical pattern, where disease leads to poverty and poverty can lead to disproportionate disease, provides a perfect storm in which there aren’t enough resources to keep from getting sick, where once sick you are likely to fall further into poverty, and once you fall further into poverty you are even further away from pulling yourself and your family out.  This leads to the maintenance of poverty and sickness across the generations.

And this story could perhaps get even more complicated when we consider some evolutionary implications.  For example, populations that have historically been afflicted with malaria also tend to have high proportions of blood and blood-related disorders that seem to protect against malaria.  Almost all of these disorders are harmful in some cases (for example, in homozygotes).  Therefore the evolutionary history of disease can lead to a situation where some individuals are actually plagued with sickness from the very beginning of life.  Paradoxically, under situations of heavy malaria burden, some people with these disorders will apparently be healthier than their non-affected counterparts.  I don’t know whether the side effects of these disorders are enough to lead to poverty traps on their own.

Finally, in an age when many scientists appear to be looking “for the gene for (fill in your favorite thing to study)”, poverty traps and households are an interesting thing to ponder.  Poverty and the apparent predisposition of household members toward succumbing to disease can look like a genetic effect.  If it runs in families, and certainly both poverty and sickness do, then it can look a whole lot like there is a genetic reason for it.  I think that poverty trap models are therefore a nice illustration of how we could arrive at the same phenotype (poverty and sickness) from purely socio-economic and ecological factors.  

REFERENCES:

Bonds, M. H., Keenan, D. C., Rohani, P., & Sachs, J. D. (2010). Poverty trap formed by the ecology of infectious diseases. Proceedings of the Royal Society B: Biological Sciences, 277(1685), 1185–92. doi:10.1098/rspb.2009.1778

Plucinski, M. M., Ngonghala, C. N., Getz, W. M., & Bonds, M. H. (2013). Clusters of poverty and disease emerge from feedbacks on an epidemiological network. Journal of The Royal Society Interface, 10(80), doi: 10.1098/rsif.2012.0656.

Wood, J. (in press). The Biodemography of Subsistence Farming: Population, Food and Family. Cambridge University Press.

Burrowing into the unending nature vs nurture debate

Behavior modules
Two interesting stories about behavior this week.  You've probably read about the mouse that builds its nest in a stereotypical way.  The Nature paper (Weber, Peterson, and Hoekstra) describing this was reported in The New York Times, as a story about how genes control complex behavior. 

The research was motivated by the question of how genetics influences the evolution of complex behaviors, but the researchers also wonder whether the environment influences variation in heritable behavior, and whether many or few genetic changes affect behavioral evolution.

The authors describe the burrow built by oldfield mice as having a long entrance and escape tunnels, and they say that the length is consistent wherever these mice build them, although tunnel depth depends on the soil in which they build.




Deer mice make a smaller, simpler burrow, and when the two species are interbred in the lab, the offspring reproduce the more complex burrow of the oldfield mouse, though with varying length.  First generation backcross mice (offspring of the interbreeding then bred with the parental strain) build burrows of varying length, and not all built escape tunnels, which suggests to the researchers that these behaviors are separately determined. 

The researchers then looked for genetic loci that might be influencing these behaviors and found three different loci that seem to contribute to tunnel length, and another that influences the building of escape tunnels.  As explained in the NYT:

All complicated behaviors are affected by many things, Dr. Hoekstra said, so these regions of DNA do not determine tunnel architecture and length by themselves. But tunnel length is about 30 percent inherited, she said, and the three locations account for about half of that variation. The rest is determined by many tiny genetic effects. As for the one location that affected whether or not mice dug an escape tunnel, if a short-burrow mouse had the long-burrow DNA region, it was 40 percent more likely to dig a complete escape tunnel. 

Well, if tunnel length is about 30 percent inherited (and there is variation in tunnel length; average length is 181 cm, with a standard deviation of ± 53), and the three locations account for about half of that variation, or perhaps 15% of the variation in tunnel-building, then the rest of the causation is not due to a few major genes.  Though, if it's 70% non-genetic, then one wonders how the environment specifies that a tunnel will have an escape hatch.

The authors conclude that "discrete genetic modules" control complex behaviors and that, "Together, these results suggest that complex behaviours—in this case, a classic ‘extended phenotype'—can evolve through multiple genetic changes each affecting distinct behaviour modules."  One could challenge this rather strong genetic-determinism view.  But how genes (much less environments) determine this type of thing is interesting and challenging to think about.

Overcoming behavior modules

Manduca sexta, or Hawkmoth;
Wikimedia Commons

The second story this week is from a paper in Science reporting that while the hawkmoth seems to innately prefer the nectar of night-blooming flowers, it can learn to collect nectar from other sources.  These moths seem to innately prefer flowers that give off a specific class of aromatic compounds, or at least the aromatics of their preferred flowers are processed similarly by the moth's olfactory response.

But the researchers wondered whether olfactory response necessarily reflects the moth's preference.  To test this, they exposed naive moths to paper flowers scented with different classes of compounds from those they generally prefer.  The moths were then observed to visit flowers emitting these scents at similar frequencies to those they innately prefer.  The authors conclude that "olfactory conditioning provided moths with flexibility in their foraging behavior but did not extinguish their innate preferences for scents from the moth-pollinated flowers." They suggest that "olfactory conditioning may operate in an olfactory "channel" separate from, but parallel to, that involved in the innate responses."  Modularity again. 

So much for exquisitely fine-tuned co-evolution of flower and pollinator. 

Glass half full/half empty
There's something for everyone here. The mouse researchers conclude that behavior is modular and evolves by the mixing and matching of genetic modules. Maybe, but there's plenty of non-heritable influence on mouse burrowing behavior as well, if tunnel length is only "about 30 percent inherited."

Modularity is a fundamental principle of life, and the idea that behavior, as well as morphological traits, can be modular is certainly a possibility -- every 4th grade class has its clown and its bully and its teacher's pet, after all.  But this doesn't mean that it must be genetically determined.  It could be, but the evidence isn't yet there. Maybe the non-mapped variation has to do with general cognitive function and how an animal scopes out its environment and decides what would be a good strategy for living in it.

We are all ultimately reducible to genes, in the sense that they are the basis of who and what we are.  But, as the hawkmoth study shows, the fact that even a lowly moth can easily overcome "innate" behavior with a whiff of something it wasn't born to crave is yet further evidence that organisms are inherently adaptable, a fundamental principle of life.  Given that environments can change quickly and unpredictably, that's a good thing. 

The height of fashion: fMRI and high-impact publishing

Are some parts of the brain sexier than others?  Apparently there's no small amount of suspicion in fMRI labs that this is true, so Tim Behrens, neuroscientist at the Wellcome Trust Centre for Neuroimaging, University College London and the Functional MRI of the Brain Centre, University of Oxford and colleagues set out to answer this question.  Behrens talked about his study the other day with Quentin Cooper on BBC4's "Material World." The results were also published in the January Trends in Cognitive Sciences.  

You'd think all parts of the brain would be equally interesting, but apparently some labs are right to be suspicious that this isn't so. Behrens and colleagues analysed over 7000 brain imaging studies and concluded that some regions are indeed sexier than others, and studies of these regions tend to be published in higher impact journals than others.

Behrens et al. correlated the area of the brain subjected to fMRI in each of these 7000 papers with the impact factor of the journal in which the paper was published.

The champion of the popularity contest was the presupplementary motor area (pre-SMA), defeating its nearest contender, the dorsolateral prefrontal cortex, by the considerable margin of 25%. Further lowering the frequency threshold to ‘half-a-pre-SMA’ revealed a network of brain regions commonly activated in studies of attention and executive function, including the frontal operculum and/or insula, and the intraparietal sulcus. The only intruders on this cognitive panacea were the hand area of primary motor cortex and Broca’s area, both in the left hemisphere only.

As Behrens explained it to Cooper, the most fashionable region is the anterior insula, the part of the brain that seems to be associated with empathy.  Further, studies of the parts of the brain that are associated with, in Behrens' example, how you might fall in love are more inherently interesting and thus more likely to be published in a top-tier journal than a study of which part of the brain is involved in controlling, say, movement of your little finger.

Behrens and company were also able to identify the least fashionable parts of the brain.  

Leading the way in ignominy was the secondary somatosensory area (Z = 4.4, P < 5 x 10^-6), but the supplementary motor area was almost equally disgraced (Z = 4.25, P < 5 x 10^-6).  Researchers unfortunate enough to find activity in these regions can expect to be published in a journal with approximately half the impact of their most celebrated colleagues (mean impact factors of approximately 5 compared with approximately 9).

They also looked at keyword associations with impact factor.  Words like emotion, semantic, reward, recognition, attention, face, explicit, and recall clustered together, as did execution, fixation, vibrotactile, inhibition, stroop, saccades, covert and so on.  And, as the authors wrote, "We leave it to the reader to ... decide which set of words was positively correlated with impact factor, and which exhibited a negative correlation."

fMRI of the less sexy primary visual cortex, 

extrastriate visual cortex and lateral 

geniculate body; Wikimedia

Cooper tried to argue that some of this apparent fashionability might actually follow function.  Any kind of study of the human body, he suggested, would focus on the more significant functions.  The left side of the chest rather than the right side, e.g. But Behrens reminded him that it isn't just that there's more research into the big questions, which there is, but that it's primarily papers about some of the big questions that are published in the fashionable journals. Maybe, he suggested, because some are harder to sell to Radio 4. 

Indeed, there is a broader issue, which Cooper also pointed out, and that is that there are certainly funding fads.  "Nano-science," "climate change," "translational medicine," and so on are perhaps buzzwords that help your chances of funding and publication in top-tier journals.  There have been times when it has been best not to include the word "evolution" in your grant title.

But, who is setting the fashions and who is following?  Are journal editors, funding agencies, technological innovation the trendsetters?  Scientists themselves?  Is the idea to game the system? The rewards of publishing in top-tier journals are great, after all -- further funding, raises and promotions -- so, why not?  Anyone can do in their own field what Behrens et al. did with fMRI studies; figure out the key keywords and follow the money.  Some people surely will and do make their next grant decisions like this, maybe particularly in big money fields like genetics.

But, in fact, most people won't.  There were 7000 fMRI studies published, after all (whatever you think of the value of such work), most of them in lower tier journals, which means that a lot of people are interested in parts of the brain that are not fashionable (well, ok, fMRI itself is fashionable, in the fashionable field of neuroscience).  As long as there's money for a topic, someone's going to be studying it.  Some scientists must still be doing what they do for the love of the science.  Backwaters can have their appeal.  And scientists in those backwaters, self-selected to avoid the rapids as they are, might well be happier for it. 

Epigenetics -- what else don't we know?

Epigenetics -- a hot topic
Epigenetics* is a buzzword these days, in genetics, yes, but it is appealing enough that it is trending in general usage as well. For better or worse.  While the idea that factors other than changes in DNA can affect development was hypothesized almost a century ago, and called epigenesis by CH Waddington, epigenetics is now more often considered to be changes in the genome that don't involve changes in DNA sequence. Generally this involves chemical modification of nucleotides that causes a gene to be silenced, and many instances have been documented, pathological and not.

Epigenetic mechanisms. Source: Wikimedia Commons

But, much as, say, political scientists invoke genetics to explain why we vote the way we do, or economists to explain our economic behavior, people are invoking epigenetics to explain things like the 'culture of poverty' (due to epigenetic changes because of maternal malnutrition during pregnancy), or psychiatric diseases that seem to be genetic but for which genes have not been identified, or even homosexuality (due to epigenetic signaling that is usually beneficial to the parent, but can be transferred to a fetus of the opposite sex, affecting subsequent sexual behavior). 

Epigenetics is appealing because it's not strict genetic reductionism, and finding genes 'for' traits, particularly behaviors, has proven to be frustratingly difficult (well, at least when done properly), and yet epigenetics explains traits in terms of tractable biological markers, such as methylation of mRNA or histone modification. Whether epigenetics is always correctly applied is another matter.

Epigenetics documented
But the actual, documentable science of epigenetics marches on.  A paper in the Dec 14 issue of Science ("Epigenetic Regulation by Long Noncoding RNAs," Lee) adds a new twist to the epigenetic story, addressing long noncoding RNAs and asks about their function.  Thousands of lncRNAs have been found in the last five years, and their function is just beginning to be documented.

The ENCODE project has shown that 70-90% of the mammalian genome is transcribed, yielding a very large 'transcriptome' of long (defined as greater than 100 nucleotides) noncoding RNA (lncRNA), and that this 'pervasive transcription' actually happens seems to be emerging as the consensus view (though, see this post on differences of opinion on this).

ENCODE, again, has shown that there are about 10 "isoforms overlapping any previously annotated genes, thereby challenging the traditional definition of a gene."  That is, whereas the classic view of messenger RNA is that it is transcribed from coding regions within protein-coding genes -- which comprise only about 1% of the genome -- now it seems that most of the non-coding genome is also transcribed, and that the transcripts start and stop in unexpected places, given accepted wisdom.  These transcripts are "often poorly conserved, unstable, and/or present in few copies" and whether they always have a function is unknown, though Lee suggests that much of this RNA is involved in epigenetic regulation of gene expression. 

lncRNAs were first seen to play a role in genomic imprinting and inactivation of the X-chromosome, with the X-inactive-specific transcript (XIST/Xist) being among the first lncRNAs to be identified in mammals.  Males have 1 X chromosome and females have 2, which means that genes on the X chromosome could be expressed twice as much in females than in males.  This doesn't happen, however, and lncRNA is part of the reason for this.

Nowhere is the abundance of lncRNA more evident than the X-inactivation center (Xic). To balance X-chromosome gene expression between males and females, the Xic on the mammalian X chromosome controls the initiation steps of XCI through a series of RNA-based switches. Today, the Xic serves as a model for understanding epigenetic regulation by lncRNA.

Xist codes for a long piece of RNA that is never translated; the RNA coats the inactive X-chromosome, which results in the silencing of its genes, though it is complicated -- Xist itself is regulated by two other lncRNAs, with downstream effects.  

Lee writes that

"[A]lthough lncRNAs now dominate the Xic, this region was once coding.  Evolution of random XCI 150 million years ago in eutherian mammals coincided with a shift from coding to noncoding space, suggesting that lncRNAs offer distinct advantages over proteins for some forms of epigenetic regulation." 

Why lncRNAs rather than the usual, ubiquitous regulatory elements that turn genes on?  LncRNAs are so large that they seem to address only a unique location in the genome.  Transcription factors, on the other hand, are short and bind with short DNA sequences that often are found in thousands of places in the genome.

Lee presents several classes of lncRNA, those involved in genomic imprinting, which is when only one of the two inherited copies of a gene is expressed; lncRNAs that are involved in non-allelically regulated loci; lncRNAs can activate gene expression as well as repress it; lncRNAs may be found as parts of pseudogenes, from whence they silence or activate the still functional form of the gene.  Lee concludes that much is yet to be discovered about these molecules.  "Indeed, the Wild West is a rich landscape waiting to unfold."

And it is unfolding at a fast rate.  E.g., two papers in the last week's issue of Science document epigenetic involvement in embryonic stem cell pluripotency (here), and epigenetic influences on gene expression as a response to metabolic state (here).  Epigenetics is being over- and too often improperly applied, by people who'd like a simple yet rigorous, scientific explanation for a complex trait, but, like genetics itself, the field is developing to the point where it is possible to begin to sort fact from fiction.

What we don't know
But, just as single genes aren't the explanation for every trait or illness, epigenetics isn't going to be the explanation either.  Naturally enough, we always try to make complete stories from incomplete data -- before we knew about short RNAs or DNA methylation, we thought we understood gene expression.  But, every age has its 'normal science,' as Thomas Kuhn called it in "The Structure of Scientific Revolutions."  It's only when enough challenges arise to that normal science that understanding can broaden and build those challenges into a new and different picture.  The picture may change to encompass new data, but the sense that we actually understand does not; we always think we do.  We never know how much we don't know. 

------------------------------------
*Nice introductions to epigenetics:
Neuroscientist Kevin Mitchell nicely sums up the history of epigenetics, and its current trendiness -- and misapplication -- in a two-part blog series starting here.

Here's a quick YouTube discussion.

Not to defend fast food, but does it really cause asthma?

Here's a case for confounding variables if there ever was one: a new study suggests that 'fast foods' cause asthma, rhinoconjunctivitis and eczema.  Indeed, the BBC tells us that teens who eat fast foods three or more times a week are 39% more likely to have severe asthma than kids who eat three or more servings of fruit each week. Sounds pretty clearly causal, doesn't it?  Well, maybe not.

The results are from a long-standing international study of asthma, begun in 1991 because of concern over increasing asthma rates.  Called ISAAC, the International Study of Asthma and Allergies in Childhood, the study is based in New Zealand but is associated with centers all over the world.  Asthma incidence began to rise in the mid 1980's and the trend has yet to be satisfactorily explained by environmental epidemiology.  And of course, many tens of millions of dollars have been spent looking for a genetic cause, without success.   

An ISAAC study published in 2004 reported that eating hamburgers was associated with increased risk.  Other studies have found some association with maternal diet during pregnancy, as well as childhood diet. 

Results from the latest paper relied on questionnaires translated into 53 languages, and included more than 500,000 children from 54 countries. Along with lifestyle questions, teenagers, and parents of younger children, were asked about symptoms of asthma, watery itchy eyes and eczema.  And, quoting from the paper, they were asked the following about their diet: ‘In the past 12 months, how often, on average, did you (did your child) eat or drink the following: meat; seafood; fruit; vegetables (green and root); pulses (peas, beans, lentils); cereal; pasta (including bread); rice; butter; margarine; nuts; potatoes; milk; eggs and fast food/burgers?’.  They could choose 'never or occasionally,' 'once or twice per week,' or ' ≥3 times per week.'

Covariates considered included exercise, television watching, maternal education, maternal smoking in the first year of life and current maternal smoking.

While the BBC story makes a case for fast food being the cause of asthma, rhinoconjunctivitis and eczema, the story is much less clear if you look at the details actually presented in the paper. In teenagers, fruits are 'protective' if eaten once or twice, or 3 or more times a week,

[m]ilk was inversely associated with current wheeze once or twice per week, severe asthma ≥3 times per week, VQ [current wheeze], current and severe rhinoconjunctivitis once or twice per week and current and severe eczema once or twice per week as well as ≥3 times per week for current eczema. Vegetable consumption was also inversely associated with current wheeze ≥3 times per week and VQ once or twice per week and ≥3 times per week.

So, milk was protective if consumed once or twice per week, but not if consumed three or more times per week.

'Risk factor foods' were butter, fast food, margarine and pasta ≥3 times per week.  And seafood was positively associated with 'severe asthma, current and severe rhinoconjunctivitis and current and severe eczema. Butter, margarine, nuts, pasta and pulses [legumes] were positively associated with one or more conditions.'  If there is some consistent causal factor -- dairy fat, say, why butter but not milk?  Why not eggs of meat, if it's just fat that's the risk factor?

In younger children (6-7),

For all centres combined, eggs, fruit, meat and milk ≥3 times per week were inversely associated with all three conditions, current and severe. Cereal ≥3 times per week was inversely associated with severe asthma. Vegetables once or twice per week and ≥3 times per week were inversely associated with current and severe wheeze as well as current and severe rhinoconjunctivitis and ≥3 times per week with current eczema.

So, eggs and meat are protective, whereas they aren't for older children (aged 13-14).  Indeed, risk factor food for younger children is fast food only.  And, the only food category both age groups have in common is fast food.  Which, of course, could include a large variety of things. 

To add to the difficulty making sense of these data, "there is considerable variation for some foods between centres within countries."  Indeed, take a look at the odds ratios (ORs), the measure of the strength of association between variables and outcome, for fruits and fast foods by age and country.  They are, by and large, all over the place.  So, the odds of having severe eczema if you eat fruit in Mexico, say, vs. never eating fruit are 0.15, or 2.0.  That is, risk ranges from much lower than never eating fruit, to twice as high. The odds of having current wheeze if you eat fruit in Spain are 0.50 or 2.0.  The overall data may well suggest a trend, but it's not one that is reliably evident center by center, or even within each country. 

So, apart from the question of why this story has been picked up by the media (well, we know why -- anything that indicts fast food has the potential to be sensational), how is it that these results can be all over the place like this?

For one thing, and we've said this numerous times in numerous posts, food questionnaires are notoriously unreliable.  Do you know how many times per week you consumed pasta in the past 12 months?  Or fruit? 

And, who is likely to eat more fast food?  Kids in cities.  Higher risk of asthma in cities has been documented over and over again.  It isn't clear why that is, though allergy to cockroaches has been suggested, or proximity to asthmagenic industry, although this contradicts the other widely held hypothesis that too much cleanliness is causal (this is the Hygiene Hypothesis, which we blogged about here), and kids on farms have frequently been found to be at lower risk of asthma, for whatever reason.  Ok, it's possible that fast food is the reason, but it's also possible (and we'd say likely) that it's a confounding variable, a factor that stands in for an actual but unknown and unmeasured risk factor that kids in cities are more exposed to than kids in rural areas.  We aren't saying that's so, just suggesting it's a possibility; whether this study shows this rural/urban disparity is not clear. 

The asthma epidemic is relatively recent.  Having fresh fruits and vegetables year-round is also relatively recent, so most grand and great-grandparents were disease-free for some other reason.  Unless, of course, fruit and veg are cancelling out the effect of fast foods in kids who eat both, which we can't tell from the report, but that does seem to be a rather contorted explanation, if so.

It is not our purpose to defend fast food here, but really, how unhealthy is it, relatively speaking?  Yes, it packs a lot of calories, and for a lot of people that's not a good thing, but what else might be wrong with fast food?  And we are talking about fast food as a whole -- Big Macs, fries, fish sandwiches, milk shakes; everything lumped into one.  The authors write, 'Biologically plausible mechanisms for the relationship between fast food consumption and asthma and allergic disease could be related to higher saturated fatty acids, trans fatty acids, sodium, carbohydrates and sugar levels of fast food and possibly preservatives.'  Maybe, but if so, what have fast foods got that bacon, beef, any desserts, and so on don't?

And, the authors suggest that fruits and vegetables are loaded with antioxidants, which are said to be protective -- against almost everything.  Except that multiple large double blind studies have found that they aren't.  So, again, it's possible that fruit and vegetable consumption is a proxy for some other unidentified protective factor.  Or not. 

Given that the data used in this study are recall data, the diseases self-reported, the causal reasoning purely speculative, and that there's a possible problem with multiple confounding variables, we're going to go out on a limb here and suggest that, based on this study, the diet/asthma-eczema-rhinoconjunctivitis connection is a tenuous one at best.