Epistemology and genetics: does pervasive transcription happen?

Pervasive transcription

RNA basepairing

It has been known for some time that only 1-5% or so of the mammalian genome actually codes for proteins. It does that by 'transcribing' a copy of a DNA region traditionally called a 'gene' into messenger RNA (mRNA) that was in turn 'translated' into an amino acid sequence (protein, in common parlance).  According to this established theory known as the Central Dogma of Biology (the problems with which we blogged about here), a gene had a transcription start and stop sites, specific sequence elements in DNA from which this canonical (regular) structure of a 'gene' could be identified from DNA sequence (but see below for problems with the definition of a gene).  From that, we got the estimate that our genome contains roughly 25,000 genes.

Not so long ago, the remainder of the genome, the non-coding DNA, was called 'junk DNA' because it wasn't known what, if any function it had.  Then, some of it, generally short regions near genes, was discovered to be sequence elements that, when bound by various proteins in a cell, cause the nearby gene to be transcribed.  So some of that DNA had a function after all.

But then, with various projects such as in 2007, the ENCODE project, a multi-institutional exploration of the function of all aspects of the genome in great detail, it was found that the majority of all the DNA in the genome is in fact transcribed into RNA in a process called 'pervasive transcription'.  As the ENCODE project reported,

First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another.  

What all this RNA did wasn't yet known, because it didn't have the structure that would be translated into protein, but that pervasive transcription happened seemed clear.  Some functions were subsequently discovered, such as 'microRNA' that codes for sequences complementary to mRNA that are used to inhibit the mRNA's translation into protein.  There were types of RNA that had their own functions within the classical idea of a gene, even if not translated into protein (these included ribosomal RNA and transfer RNA).

Or maybe not...
However, the pervasive transcription idea was challenged by van Bakel et al. in PLoS Biology, who said that most of the low-level transcription described by ENCODE was in fact experimental artifact or just meaningless noise, error without a function.

Oh, but it does!
Now, in a tit for tat, just last week a refutation of this refutation, a paper called "The Reality of Pervasive Transcription," appeared in PLoS Biology (on July 12).  Clark et al. confirm that pervasive transcription does in fact happen, and take issue with the van Bakel et al. results.

...we present an evaluation of the analysis and conclusions of van Bakel et al. compared to those of others and show that (1) the existence of pervasive transcription is supported by multiple independent techniques; (2) re-analysis of the van Bakel et al. tiling arrays shows that their results are atypical compared to those of ENCODE and lack independent validation; and (3) the RNA sequencing dataset used by van Bakel et al. suffered from insufficient sequencing depth and poor transcript assembly, compromising their ability to detect the less abundant transcripts outside of protein-coding genes. We conclude that the totality of the evidence strongly supports pervasive transcription of mammalian genomes, although the biological significance of many novel coding and noncoding transcripts remains to be explored.

Clark et al. question van Bakel et al.'s molecular technique as well as their 'logic and analysis'.

These may be summarized as (1) insufficient sequencing depth and breadth and poor transcript assembly, together with the sampling problems that arise as a consequence of the domination of sequence data by highly expressed transcripts; compounded by (2) the dismissal of transcripts derived from introns; (3) a lack of consideration of non-polyadenylated transcripts; (4) an inability to discriminate antisense transcripts; and (5) the questionable assertion that rarer RNAs are not genuine and/or functional transcripts.

They go into detail in the paper about how and why these are serious problems, and conclude that van Bakel et al.'s results are 'atypical' for tiling array data, their tissue samples were not sufficiently extensive, and that pervasive transcription is being detected by a variety of experimental methods.  (Tiling refers to the fact that sequencing is done one stretch at a time, and long stretches and their location on chromosomes from which they were copied is done by finding overlapping ends of these short stretches, that show how they 'tile' together relative to the chromosome as a whole.)

No, no, no! 
And finally (to date), van Bakel et al. respond, also in the July 12 PLoS Biology.

Clark et al. criticize several aspects of our study, and specifically challenge our assertion that the degree of pervasive transcription has previously been overstated. We disagree with much of their reasoning and their interpretation of our work. For example, many of our conclusions are based on overall sequence read distributions, while Clark et al. focus on transcript units and seqfrags (sets of overlapping reads). A key point is that one can derive a robust estimate of the relative amounts of different transcript types without having a complete reconstruction of every single transcript.

So, they defend their methods and interpretation and conclude that "a compelling wealth of evidence now supports our statement that 'the genome is not as pervasively transcribed as previously reported.'"

An epistemological challenge -- what do we know and how do we know it?
What is going on here?  Is most of the genome transcribed or isn't it?  We are intrigued not so much by the details of the argument but by the epistemology, how these researchers know what they think they know.  In the past, of course, a scientist had an hypothesis and set about testing it, and drew conclusions about the hypothesis based on his or her experimental results.  The results were then replicated, or not, by other scientists and the hypothesis accepted or not.  The theory of gravity allowed many kinds of predictions to be made because of its specificity and universality, for example, as do the theories of chemistry in relation to how atoms interact to form molecules.  This is a simplified description of course, but it's more accurate than not.

Molecular genetics these days is by and large not hypothesis driven, but technology driven.  There is no theory of what we should or must find in DNA.  Indeed, there is hardly a rule that, when we look closely, is not routinely violated.  Evolution assembles things in a haphazard, largely chance-driven way.  Rather than testing a hypothesis, masses of data are collected in blanket coverage fashion, mined in the hopes that a meaning will somehow arise.  That this is how much of genetics is now done is evident in this debate.  As first reported by ENCODE, complete genome sequencing seemed to be yielding a lot of DNA that was transcribed from other than protein coding regions, and so they speculated as to what that could mean.  Their speculation wasn't based on anything then known about DNA, or theory, but on results, results produced by then-current technology. That is the reason--and the only reason--that they were surprising.

And van Bakel et al. disagreed, again based on results they were getting and interpreting from their use of the technology.  Then Clark et al. disagreed with van Bakel et al.'s use and interpretation of molecular methods, and described their results as 'atypical'.  And both 'sides' of this debate attempt to strengthen their claim by stating that many others are confirming their findings.  And this is surely not the end of this debate.

We blogged last week about 'technology-driven science', suggesting that often the technology isn't ready for prime time, and thus that many errors that will be hard to ferret out are laced throughout these huge genetic databases that everyone is mining for meaning.  When interpretation of the findings is based on nothing more than whose sequencing methods are better, or whether or not a tissue or organism was sequenced enough times to be credible, or which sequencing platforms seem 'best' for a particular usage (by some criterion) -- meaning that the errors  of the platform are least disturbing to its objective -- rather than on any basic biological theory or prior knowledge, we're left with the curious problem of having no real way to know who's right.  If everyone's using the same methods, it can't be based on whose results are replicated most. If we haven't a clue what is there, even knowing what it means to be 'right' is a challenge!

But we don't even know what a gene is anymore!
These days, even the definition of a gene, our supposedly fundamental inherited functional unit, is in shreds and the suggested definitions in recent years have been almost laughably vague and nondescript.  Try this, by G. Pesole in a 2008 paper in the journal Gene, out for size, if you think we're kidding:

Gene: A discrete genomic region whose transcription is regulated by one or more promoters and distal regulatory elements and which contains the information for the synthesis of functional proteins or non-coding RNAs, related by the sharing of a portion of genetic information at the level of the ultimate products (proteins or RNAs).

Or how about this one, from 2007 (Gerstein et al., Genome Research):

Gene: A union of genomic sequences encoding a coherent set of potentially overlapping functional products.

Not very helpful!!

These definitions show how much we're in trouble.  Ken attended a whole conference on the 'concept of the gene', at the Santa Fe Institute, in 2009, but there was no simple consensus except that, well, there is no consensus and essentially no definition! 

The good old days
When microscopes and telescopes were invented, they opened up whole new previously unknown worlds to scientists.  If anyone doubted the existence of paramecium they had only to peer through the eyepieces of this strange new instrument to be convinced.  When cold fusion was announced by scientists in Utah some years ago, the reaction of disbelief was based on what was known about how atoms work.  That is, there were criteria, and theoretical frameworks, for evaluating the evidence.  Yes, there has always been a learning curve; when Galileo looked at the moon or planets, various optical aberrations actually were misleading, until they were worked out.

And now....
But they were building in an era when fitting theory was the objective.  In biology, we're in new territory here.

The ethics of studying genetic causation

A comment in the current issue of Nature, "Genomics for the world", calls for including non-Europeans in the genomic revolution. 

In the past decade, researchers have dramatically improved our understanding of the genetic basis of complex chronic diseases, such as Alzheimer's disease and type 2 diabetes, through more than 1,000 genome-wide association studies (GWAS). These scan the genomes of thousands of people for known genetic variants, to find out which are associated with a particular condition.

Yet the findings from such studies are likely to have less relevance than was previously thought for the world's population as a whole. Ninety-six per cent of subjects included in the GWAS conducted so far are people of European descent. And a recent Nature survey suggests that this bias is likely to persist in the upcoming efforts to sequence people's entire genomes.

Geneticists worldwide must investigate a much broader ensemble of populations, including racial and ethnic minorities. If we do not, a biased picture will emerge of which variants are important, and genomic medicine will largely benefit a privileged few.

And success is always just out of reach -- if only.  If only we have bigger samples, or more heterogeneous samples, or less heterogeneous samples, or more markers, or whole genomes.

The 'missing heritability problem' has led many to become dismissive of GWAS. A danger of this GWAS fatigue is that it deters others from applying the approach to populations where it is likely to yield excellent results. GWAS has proved most successful in relatively small homogeneous populations — in Finland, Iceland and Costa Rica, say, where people generally stay put. Large families and limited migration are common among populations in Latin America, Africa and South Asia — suggesting that new and important associations between diseases and regionally common genetic variants may be found easily in these groups.

Well, yes, the ultimate in relatively homogeneous studies, family studies, have been quite successful in finding genes -- in cases of clearly genetic diseases.  And it has been known for decades that different alleles or even different genes can lead to a similar phenotype.  So it's no surprise that studies in isolated populations might yield results, but if they aren't usually generalizable beyond a single family or a small population, that isn't going to be widely useful.  Nor have the genetic underpinnings of common chronic diseases been reliably or very usefully demonstrated, even in small homogeneous populations, so optimism about finding genes for diseases like heart disease or type 2 diabetes or asthma is pretty much unwarranted.

That said, including non-Europeans in medical studies is a laudable goal.  And yes, genetic variation by geographic ancestry is to be expected.  This was a point made in more than one journal paper by Ken many years ago when one-size-fits-all markers were touted as justification for the HapMap project....but it was an inconvenient, if obvious, truth that was ignored.  The underlying reasons were not very savory and beyond this post.

So who is pushing this now?  Geneticists who want to confirm their belief that GWAS work, that rare variants will explain the 'missing heritability' that isn't being captured by these studies now, and that all we need is bigger or more varied samples to prove it. And, pharmaceuticals pursuing the dream of the 'druggable' genome.  And everyone who wants the largesse to continue pouring into this kind of science (which, not incidentally, will deprive other areas of funds, in the zero-sum game of research funding).  One perhaps cannot blame the researchers for wanting research funds, or biotech firms wanting business, but nobody seems to be watching the priority store.

But even if the world is someday representatively sampled and included in genetic studies, "genomic medicine is going to largely benefit a privileged few" anyway.  First to benefit will be the sequencers and the makers of the sequencers, and they will benefit handsomely, and direct to consumer genome-risk selling firms, followed by the analyzers of the resulting bioinformatics who will be able to mine the data, and apply for grants for follow-up studies when they don't get definitive answers, and then maybe (and, yes, hopefully!) a few people with clearly genetic diseases.  Even in rich countries genomic medicine is going to remain unaffordable for most people for the foreseeable future -- trickle-down doesn't work here either.  And that's assuming that there are benefits to be had!  But, as we write about frequently here, widespread benefits of this kind of research haven't yet been demonstrated, and there are many reasons to believe they will be few and far between anyway, even at best. 

Meanwhile, when it comes to public health, other avoidable disorders go under-attended.   And once again we have to ask whether the largesse being showered on medical genomics could be better spent on prevention.  As a colleague once said to us, it would be a lot cheaper to give everyone at risk of type 2 diabetes a personal trainer than to do all these genetic studies of the disease.  And it would do people a lot more good!  Studies of the genetics of T2D have been ongoing for 40 years -- including in non-European populations -- and have yet to yield significant results.  Or prevent a single case of diabetes.  Even sickle cell and ApoE related diseases are not yet very, if at all, solved in a way that is based on genotype data.  Sickle cell was discovered more than a century ago.  The promises of genetically based genomics may have been sincere, but they have proven to be hollow even in a medium term sense, despite various exceptions that one might cite.  The thousands of GWAS hits are being misrepresented as such exceptions as a rule.

Pushing, exaggerating, and hyperbolizing expensive genetics research, even if it will get investiators interesting things study and subsidized visits to exotic places, is a highly, and usually knowingly cynical, way to lobby for funds (because this is often acknowledged in private).  If one is as smart as a  researcher at a privileged university, you could perhaps fairly be asked to use your intelligence to solve important problems on modest budgets and save the megabucks for real, proven public health improvements.

We suggest that we are at a point in our understanding of disease causation where lobbying for increased funding for genetic studies is simply to a great extent unethical.

One gene one .... what? The problem with the 'Centra Dogma'...or any dogmas in science

One thing that has been found in recent years, and about which knowledge has been rapidly expanding is that the grand old 'Central Dogma of Biology', that one gene codes for one protein is, well, substantially wrong (to be kind to it).

Gene transcription, from The Mermaid's Tale, Weiss & Buchanan, 2009

The Central Dogma held that DNA is a string of codes that specifies messenger RNA (mRNA) that is translated in the cell into protein.  One gene, one protein.  That was how it looked when the nature of DNA was first being discovered.  But it's been decades since we knew that was not accurate.

A few of the reasons are

1. genes are interrupted coding sequences (they have non-coding 'introns'),  
2. introns are spliced out of mRNA by particular DNA sequence motifs,  
3. genomes evolve by duplication of whole segments, 
4. much more DNA is transcribed into RNA than was thought; 
5. some of this RNA has complimentary sequences to protein codes and there is an elaborate mechanism for this, which is never translated into protein, to inhibit 'real' genes (this known as microRNA);  
6. some non-protein RNA--copied from genes without the usual gene processing sequence elements, is nonetheless found attached to ribosomes in the cell as if it were being translated anyway; 
7. gene usage is determined in part by the way DNA in the gene's part of a chromosome is packaged and chemically modified ('epigenetics'); 
8. important aspects of variation are due to mutations that happen during the lifetime of the organism; 
9. each cell uses only some of its genes, and sometimes only one of its two copies of a gene that it is using; 
10. genes can be assembled via effects of genes from other chromosomes or even make mRNA that is a composite of pieces from two different chromosomes ; and (so we don't have to keep on and on), 
11. some mRNA is 'edited' after being transcribed, in replicable ways sometimes conserved among distantly related species, in which one nucleotide copied from the DNA template is replaced by a specific other nucleotide, thus changing the function, including the protein code, of the mRNA.

These are among many other things that we now know to be parts of DNA function.  They don't change the basic idea that DNA specifies protein structure, but there are so many details, of so many sorts, that it is clear that the idea of the Central Dogma is essentially wrong.  Yet, why do we still have 'exome' sequencing in so many expensive studies, or gene 'for' this or that trait, in so many expensive studies, when we know how simplistic this is?

There are many answers, and we regularly harp on them.  Here, the main point is that these discoveries are real, their importance highly variable and mainly unknown, and that they always add to, but rarely if ever reduce, the complexity between DNA and the traits that it affects.  Promises of simple prediction have been aided and abetted by the addictive discoveries that really work like the genes Mendel studied in peas.  We do a lot of hand-waving to dismiss complexity, but we cling like drowning sailors to life-rafts to the simple, Central Dogma, in the fervent hope that we'll find the Big Gene Story.   Yet those who are thinking about science itself, rather than about what they have to do to maintain their careers, know very well that we know very little about the nature of genetic function.

Dogma should not be part of science.  But historians and philosophers of science have shown that it certainly is.  A new book, for example, shows how this has affected immunology for decades, as  investigators clung to a 'fictive' theory, the idiotype network theory, even though it never had much basis (the book, The network collective: Rise and fall of a scientific paradigm, edited by Klaus Eichmann, is reviewed in the July issue of Bioessays). There's no place for dogma in science, nor for the tribalism that accompanies it.  But, well, we're only human so purging the motivations that drive dogma, and the careers that are made on its basis, may not be in the cards.

The invasion of the poison parsley

Polymeadows Farm

I spent most of the week visiting my sister and brother-in-law in Vermont.  They are dairy goat farmers, owners of Polymeadows Farm.  They sell their products all over New England; Polymeadows milk and yogurt even make it down to New York City.

I love visiting the farm, even if it means I use muscles that have lain dormant since the last time I was there.  Carrying 60 pound bales of hay and 5 gallon buckets of water takes some getting used to every time, and the 10 gallon milk cans just about defeated me this week.

And this year I was using muscles that I haven't used since my kids were small, because my sister's one year old grandson is there now and I carried him around a lot.  He loves doing chores with his grandmother.  They go out together every morning.  He sometimes gets a little frustrated when she won't let him carry the eggs he finds in the chicken coop, but that quickly passes and he delights in feeding the goats, filling the water buckets and the baby goats' milk bottles in the milk house, and sprinkling grain for the roosters that wander around the yard.  One day he's hoping he'll actually touch one.  He's learning to do chores in Spanish, so he points at the goats, and each morning smiles as though it's the first time he's seeing them, and says, "Cabras, cabras!"

The three of us wandered up the lane one morning after breakfast to pick black raspberries.  They were at the peak of ripeness and there were a lot of them, and that made a one-year old very happy.  We all picked for half an hour or so, some of us eating a lot more than the others of us and turning blue.  When our helper got tired I brought him back to the house, and went back up the lane to do some more picking.  The berries are all in the hedgerows between hay fields, where the mower doesn't reach, richly biodiverse strips of land.  There are grape vines there too, climbing over the aging, gnarled trees that haven't yet died and been split for fuel for the outdoor furnace that heats the houses in the winter.  My sister makes jam from the grapes and black raspberries every year, and it's the best. 


Invaders

Giant Hogweed

We walked over the hill and down through two or three fields looking for berries where she's found them in years past.  The berries and grapes all happily co-habit, along with the cherry, spruce, ash, oak, maple, and poplar trees there.  Or they did until two invasive species came along, taking root up and down the hedgerows and slowly suffocating much that has been living there for centuries.  These are oriental bittersweet and poison parsley (also known as poison parsnip).  Many of the black raspberry bushes my sister once knew to be fruitful are no longer bearing, or aren't even there any more, and more and more of the grapevines are being crowded out.

Invasives are species that are particularly aggressive when introduced to habitats outside of their usual range.  They often out-compete local species because there are no predators in the adopted habitat or because they grow faster, or in a more diverse habitat.  Ultimately, invasives can choke out native species, leading to reduced biodiversity. 

There is apparently a fledgling movement afoot to beat invasives by eating them -- invading fish, animals, plants beware.  Here's the Top 10 edible invasives list.  Note that neither poison parsley nor oriental bittersweet is on the list.  Poison parsley is in the carrot/parsnip family, related to Queen Anne's lace (also called wild carrot) and the very toxic Giant Hogweed.  Apparently, some parts of the plant can be lethal if eaten -- there are stories about cows and people killed by this stuff, but the roots are edible.  They're parsnips, much like the parsnips you buy at the store -- this is one invasive that escaped from horticulture.  The sap, though, can cause severe burning to the skin, but it's phototoxic, so it only burns where it touches you on a sunny day.


Poison parsnip, wild edible.

My brother-in-law says that years ago when his father was growing corn in the same fields where he now mows hay, and dosing it with herbicides, it was the 'superweeds' that survived.  Then it was velvet weed, and when they stopped growing corn and planted things like alfalfa and orchard grass instead, and stopped using herbicides, the velvet weed disappeared.  The poison parsley has been up in those hedgerows for a long time, and he thinks it probably took hold in the old corn days.  It's not in the fields because they get mown and it needs to go to seed to propagate, but it sure is happy in the hedgerows. He knows about superweeds from experience, but he's not the only one who says this.  Herbicide-resistant weeds are an ever increasing problem, one we blogged about here.   

Invasives and evolution
In competitive Darwinian terms, in the short run, invasives can win and win big.  That is, those introduced plants that do get a foot-hold.  Most incomers might be driven to local extinction. But if an invasive has some advantage, they garner the most resources, reproduce best, spread the fastest, and out-compete many of the native plants in a given habitat.  Perhaps they have ways to extract resources, or avoid competitors or predators, that plants in the local stable ecosystem didn't have and hence were not equipped to resist.

The resulting reduction in biodiversity that can happen when a highly successful invasive takes hold explains why there is such intense interest in getting rid of them, or preventing their spread in the first place. Their success isn't necessarily because they adapt to their new environment with genetic changes, but rather it can be a combination of not being very picky about where they live and having no predators in the new habitat.

Rather like humans, as we elbow our way into every corner of the globe.  We can live in very different environments because we are able to exploit many different food sources, and because we have tools and culture and can find ways to survive in many different climates.

With successful invasives there is no 'adaptation' of the usual kind needed: the incomers' nature simply allows them their advantage, without the need for new mutations or variation to be selected for over generations.  That may apply to mutations in viruses or bacteria, where selection and spread are very fast.  But if classical 'Darwinian' evolutionary adaptation were required, most incomers would be driven back out long before they could adapt, or their adaptation would take much longer than documented recent invasions.  Perhaps that history is very misleading about the dynamics of invasions not made possible by quick human transport and so on. 

But perspective is important here.  In the long run, the picture can be quite different; the invaded habitat might itself adapt to the invader.  This has been true, e.g., after invading fire ants have decimated an area of other insect life.  In the short-term, it looks like the fire ant has won, but years later the local insect populations that had been reduced in number may well bounce back, to co-exist with the invaders.  Or co-exist because the invader was a selective force that molded changes in the host-land species.

But how long does a species have to be in a place before it's considered 'native'?  Many species that we think of as native were once invaders. Again, including humans.  So, many 'native' habitats are only so by our short-term definition.

I hope the grapevines up the lane behind the barn at Polymeadows, native or not, aren't squeezed out entirely by the invaders.  Wild concord grapes make much better jam than do parsnips.

Bioinformatics: the more we look, the more we find

I'm at a bioinformatics summer course in Poznan, Poland this week.  There are lecturers and students from many places, and Poznan is a very fine setting and this is a very fine program organized by Woitech Makalowski and Elizabeta Makalowska.  The topics cover many areas of the information sciences that try to deal with the huge amount of information being revealed about many different species of animal, plant and bacteria (among others) as a result of high-throughput, automated DNA sequencing and other techniques of similar power.

The old models are falling rapidly.  We now know very clearly that genomes are more than 20-some thousand protein coding units strung together along an otherwise inert DNA sequence.  Instead, many more functions are being discovered, even if their functions are only partly known.  DNA is copied into RNA, and the RNA has many different uses, and is even processed in many different ways.

The bottom line is that for the relatively few and straightforward causal functions in DNA, there is now an expanding array of newly found functions.  Some of these are clear, major, and easy to characterize.  But much of the evidence is for things that seem to have some function (for example, the same elements are found in similar elements of the genome in multiple species, suggesting that they have been conserved by natural selection).  For most of this, bioinformatics provides statistical evidence from reams of data, and some confirmatory experiments support the data-base analysis findings, but what the function is, or how important it is, or how variable it is, are still quite unknown.

Part of the problem is that this ever-expanding amount of complexity, of types we had not at all anticipated, makes general evolutionary sense but makes the idea of prediction from genes to traits much more problematic than we have hoped.  The complexity makes evolutionary sense if you are willing to abandon the hyper-simplistic idea that gene makes protein makes trait and selection definitively removes the bad and advances the good versions of the trait.  Instead clearly selection is very tolerant of variation, that is redundancy all over the place, and each element of a genome has function that depends on what's in the rest of the organism's genome, and its living environment.

This suggests a much less causally definitive view of life than is the general theory, and also reveals how very little most people--even most biologists--are aware of when it comes to the complexity of genomes and their relation to the traits we care about.

There are no solid answers beyond simply noting how complex and internally variable organisms are, and it is not clear even what kinds of answers will be needed for better explanations.  It is clear that most people will propose purely technological answers: generate more data and more sophisticated computer programs to process it....and hope some deeper truths, if there are any, will emerge from the results.

Maybe it will work that way.  But except for a subset of things that follow the simple theories we thought applied to all of life, promises of quick or simple answers don't seem in the offing, no matter how much we may hunger for them.  So, too much to say in any detail in a blog post, but very stimulating and humbling to hear about even more sources of complexity than I was aware of!

Technology driven science

Ever since around Galileo's time, which was also the origin of modern science, empiricism replaced deductive reasoning as the core of basic knowledge.  This changed worldview was stimulated by many things, but largely by instrumentation.  In particular optics drove fundamental realizations about the world that could not have been made previously.  One thinks of the vast new worlds of facts revealed by telescopes and microscopes, but other things came along as well, such as the discovery of vacuums, basic findings in chemistry, anatomy, and geology among others.  Navigation with the aid of improved astrolabes and, especially, reliable clocks, opened the world to faster, safer navigation.  Steam power led to trains and improved mining and factories.

Instrumentation led to a wealth of new data, and that stimulated thinking both in theoretical science (e.g., gravitation, the sun-centered planetary system, and so on).  Partly this was driven by the desire to control commerce and global political power.  Engineering and 'science' became more part of each other.  This led to understanding the law-like nature of Nature, and stimulated evolutionary and even social science thinking.

Today, we are driven even faster--much faster--by technology.  Technology people to dream of having an advantage over research competitors, and companies push their gear to feed their own interests but also those of their academic and industry customers.  Genetics exemplifies these trends.  But are we  paying a fair price for the gains?

I'm at a meeting in bioinformatics, in Poland right now, and the new DNA sequencing and other technologies feature prominently.  The technologies are mentioned almost as much as the results, and talk after talk is about what 'can now be done' with the latest computer or sequencing powers.

Clearly, as we've said countless times here on MT, we are not getting the results we dreamed of when it comes to genetic causation and the prevention of all known human ills.  We are just as clearly learning new things--such as the discovery of all sorts of RNA that wasn't supposed to be there according to previous genetic 'theory' (one gene, one protein, for example).  Were it not for the misleading hype by which the system is driven, one might feel less like complaining.  But even advocates realize that these tools have neither revealed a new theory of life nor reaped their promised miracles.

One problem, widely recognized, is that the new technologies are pushed on the marked before they are really properly ready and battle-tested.  The drive, perhaps especially in the US but spreading around the world, to have the newest machinery, is largely responsible.  Don't wait for the stuff to work really well--get it now and get a jump on your competitors!  You can publish results and shamelessly acknowledge then, or at least later, that you know or knew there were plenty of problems, but it was, after all, only exploratory or pilot or tentative data.

One thing this impatience does, besides cost a lot, is fund the companies for years while they make their gear actually work.  New types of DNA sequencers are widely acknowledged to produce many errors on the sequence they report.  Extensive and expensive efforts, paid for by grants to a great extent, are made to use the stuff and document the errors and attempt to correct for them.  But they are not removed, and genomic and other data bases are now loaded with sequence and other types of data that have too many errors, and they are often inscrutable.  How do we decide what data to use, and what data we have to ignore (or ask the public to pay for again, now with updated technology)?

We keep the tech companies afloat by buying products that are flashy but not yet ready for prime time.  It's one thing to acknowledge that anything highly sophisticated will improve over time, but it's another to go in too far, too fast which is what we're doing.  In part, I think (though I'm no business expert of any sort!) that the companies are often start-ups that don't have huge amounts of up-front investment: they have to sell sooner rather than be more patient, because they're not building on top of other mainstream things that they sell.

It's a problem in this field, and it has many consequences.  Not only the cost, but the loading up of massive data bases with suspect data, tentative but erroneous conclusions that lead to large numbers of follow up studies by investigators eager to jump on bandwagons, follow the latest trends, or get better information on some important problem such a serious disease, are examples.

Better and more restricted focus, less 'omics' and more theoretical understanding and basic science, and a slowed down pace would help.  But these seem impossible in our current heated-up system, unless the funds dry up.  If that happens, it will be bad in some ways because some of these new technologies really are important, but it may be good if it forces us to think more before we act.

Sorting out the vitamin D story needs better data, not religious fervor

If even a tenth of what's being said about vitamin D these days is true, those of us astute enough to supplement what we get from the sun are destined for a ripe old age.  Or, if we're already old, and female, taking vitamin D might extend our lives even further.

The idea that vitamin D promotes bone density is based on solid evidence, but beyond that it's effectiveness is not entirely clear.  Advocates say that vitamin D prevents prostate, breast and other cancers, multiple sclerosis, diabetes, heart disease, osteoporosis, allergies, inflammation, fights the common cold and the flu, and boosts fertility, just to name a few of the benefits being touted.  And, limited sun exposure for mothers during pregnancy could be condemning children to a lifetime of illnesses.  According to a new study,

We have known for some time that mums-to-be with low vitamin D levels during pregnancy run the risk of having ­a child that may develop diabetes.

This latest study concluded that other conditions like asthma, autism, multiple sclerosis (MS) and Alzheimer’s could be related to low levels of maternal vitamin D.

Yes, Vitamin D is "Summer's Superhero"!

“Vitamin D deficiencies are rampant amidst our nation and could possibly lead to an increase in the most troubling diseases of our time,” said Steven Hotze, M.D., founder and CEO of PPVS [Physicians Preference, vitamins and supplements].

Indeed, Mozart may have died of vitamin D deficiency!  Think what music the world is missing because he slept during the day when he should have been sitting in the sun, and composed and caroused all night.

Well, how much of this hype is actually true?   And how would we know?  A Nature News Feature published online on July 6 details an ongoing debate on this question.  Recent recommendations have been that we are all vitamin D deficient, and should be boosting our vitamin D with sometimes megadoses of D3 supplements.  Naturally, many scientists who've been researching this subject now have vested interests in plugging supplements, and, as always, this makes it harder to separate the wheat from the chaff.

In response to all the hype, an 'expert panel' was convened by the Institute of Medicine (a non-profit affiliated with the US National Academy of Sciences) to soberly assess the evidence and make recommendations about healthy vitamin D levels, and who should be taking supplements.  They issued their report last November saying that vitamin D levels recommended by current conventional wisdom were too high, and in fact could even be harmful.  But the report has not gone down easily; panel members have been sent abusive and threatening emails, and so on.  As Nature says,

Much is at stake. By 2009, the amount spent on vitamin-D supplements in the United States had risen tenfold in ten years (see 'Raising the stakes'). Medical practitioners and public-health officials worldwide look to the IOM for guidance on how to interpret the conflicting claims about vitamin D. Yet several vitamin-D proponents say that the IOM's methods, which involved a systematic review of the literature, were flawed. They have accused the panel of misinterpreting data and over-emphasizing the danger of heavy supplementation. Just last month, the Endocrine Society, a professional association of 14,000 researchers and clinicians based in Chevy Chase, Maryland, released guidelines that recommend higher doses than the IOM did.

Why, instead of clearing confusion as was the IOM's goal, has the report sown division and unrest? "The IOM was too definitive in its recommendations," says Michael Holick, an endocrinologist at Boston University School of Medicine in Massachusetts, and an outspoken critic of the IOM panel's conclusions. "Basically, the vitamin-D recommendations are based on low-quality evidence," says Gordon Guyatt, a clinician researcher at McMaster University in Hamilton, Ontario, who has been a consultant on various guidelines. "I think admitting that would have made some of the angst disappear."

(For the record, Holick is not only an outspoken critic of the IOM recommendations, but he has been one of the leading drivers of the vitamin-D-cures-all train for some time, and has a lot to lose if it turns out he has been wrong.)

Indeed, many observers, interested and disinterested alike, recognize that there's a lot of questionable science in the vitamin D field.  It's hard to figure out how recommended levels have been set, there have been few if any prospective studies starting with a cohort of healthy people and following them forward, and many that look at vitamin D in people who are already ill.  Such studies are confounded by the fact that people who are ill tend to stay indoors, out of the sun and thus not synthesizing vitamin D, so it's not possible to know whether the vitamin D deficiency (deficiency according to current standards, however they were determined) preceded and thus led to the illness, or was a result.  Many studies have too few subjects for results to be robust, and so on.

Members of the now disbanded IOM panel are calling for large, multi-year prospective studies, in recognition of the fact that much of the data are from studies that are less credible than they should be.  But this too has generated heated dissent.  As the Nature piece says,

Perhaps IOM panel members underestimated the passion present in the vitamin-D field. Physicians who recommend high doses of vitamin D might not want to believe that the evidence they have trusted isn't quite up to par. "One thing I wasn't aware of before, is the tremendous pressure from industry and investigators who are tied to their religious belief in vitamin D," says Rosen.

So given all of this, why would one ever think of pouring more research funding down this sink-hole, to identify the obviously minor if not trivial effects over which these debates are centered?  Clear vitamin D deficiencies are not at issue.

Several years ago, we did an extensive review of the vitamin D literature and we, too, were unassailably convinced that most conclusions, from recommended blood levels to the diseases caused by deficiencies, were based on questionable to poor data.  As far as we could tell, basic questions are still unanswered, including almost everything about mechanisms of action.  This is another instance of correlations being assumed to be causation without biological justification.

To put it bluntly, the idea that we are all vitamin D deficient is manifest, blatant biological, and evolutionary clap-trap.  It is at the very least extremely naive and superficial thinking.  We live hugely longer and in better health than our ancestors did, when natural selection--to the extent that it cared--established the required levels for successful survival and reproduction.  So the assertion of pandemic deficiency really can mean no more than that we might be somewhat better off, or live even longer, if we doped up on the advocates' dietary supplements.  Such panacea talk is not new to human society, but in an age of science should be roundly stamped out, because it is misleading.