August 28, 2014, by Brigitte Nerlich
Dark matter: A mystery metaphor that turns genomic junk into gold
I have become intrigued by a new metaphor, most recently used in an interesting Aeon Magazine article. The authors state that the human genome can’t be, as was so long assumed, a blueprint for building a human being, as “science has served up the confounding paradox that the bulk of our genome appears to be dead wood, biologically inert junk.” They then ask: “Could all this mysterious ‘dark matter’ in our genome really be non-functional?” Dead wood, junk, dark matter… what’s the connection between these metaphors? I’ll explore this by focusing on the dark matter metaphor.
Metaphors usually map a familiar or known domain of knowledge onto an unfamiliar and unknown one. In this case, curiously, we seem to map something lots of people know not very much about (relating to physics) onto something lots of people know not very much about (relating to genomics)!
From blueprint to junk
The blueprint metaphor emerged around the time when scientists set out to decipher the human genome, that is, in the 1990s. In 1999, for example, Francis Collins, one of the directors of the Human Genome Project indicated that mankind was about to see ‘its own blueprint’ somewhat earlier than had been originally scheduled. And during the White House press conference in 2000 announcing the draft decipherment of the human genome, the draft sequence was referred to as ‘the working blueprint of the human race’ (see Zwart, 2009). However, the blueprint metaphor began to lose popularity as scientists discovered that the human genome contained much fewer genes than expected and a lot more ‘junk’; in fact it seems that 99% of the human genome is ‘junk’ – and it is this junk that has come to be known as ‘dark matter’. But when did people begin to use this metaphor and how did they use it? To explore these issues I delved first into Google.
The genome’s dark matter on Google
When I put ‘dark matter’ plus ‘genome’ into Google I got 1,010,000 results (27 August, 2014). The first five URLs read like this:
One of the earliest articles using this metaphor that I could find by googling a bit more was from 2005, but most of the articles I saw were much more recent. The 2005 article was entitled ‘Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments’. That title frightened me a bit, so I began to look into more ‘popular’ uses of the metaphor which might give me some clues as to how it emerged, how it was used and how it could be understood by laypeople like myself. Of course some of the five links I listed above also provide more popular accounts of the ‘matter’. So please follow the links, if you want to know more.
The genome’s dark matter in the press
To find more popular representations of genomic ‘dark matter’, I searched the news database Lexis Nexis. This was not easy, as dark matter and genomics are often mentioned together in articles about science (advances, breakthroughs, and, of course, mysteries). I used dark matter as a key word plus gene or genome in the same paragraph but not particles (I couldn’t exclude any other terms). This gave me 48 articles. Not a lot, but nicely readable.
The oldest article was from 2001 and entitled ‘Tiny genes may have big effects on hearts’ (UPI). It cites Gary Ruvkun of Harvard Medical School in Boston who talks about ‘tiny RNA genes’ and surmises that they “may be the biological equivalent of dark matter, all around us but almost escaping detection”. The journalist then adds that Ruvkun was “speaking of the as-yet undetected matter that physicists say must exist to explain the shape of the universe.”
The next article appeared in The New York Times in 2003, that is, in the year that the human genome was finally fully deciphered. In the following quote Francis Collins appears and than another biologist: “Though there is now a rough consensus that humans have about 30,000 genes, the number is far from solid. Dr. Francis S. Collins, director of the National Human Genome Research Institute in Bethesda, Md., said last week that the number might range from 25,000 to 30,000. But researchers using more reliable methods of gene prediction have started saying the number could be double that. Other biologists, cribbing a page from the astronomers’ book of stratagems, are talking of ‘dark matter’ genes, mystery objects that are surely out there but invisible to current methods of detection.”
In 2010 Francis Collins himself uses the dark matter metaphor and says: “There is this dark matter of the genome that is lurking out there, waiting to be uncovered.” The important thing about the dark matter metaphor is it works not because we know what dark matter is but because we know that we don’t know what dark matter is. It’s a mystery! And so is 99% of the human genome. This then means that great efforts have to be made ot find out what ‘lurks’ there.
From junk to switches
In a 2007 article relating to heterochromatin (regions of chromosomes previously thought to be junk), a biologist elaborates the dark matter metaphor a bit further and says: “We don’t know what holds the galaxies together, and the same is true of the genome. We’re pretty good at understanding how individual genes work, but we don’t understand, for example, how the large-scale structure of genomes affects cellular processes. We hear too much about the ‘post-genomic era’ – it’s underappreciated that we don’t understand the genome yet.”
The article then makes a link to epigenetics, a topic that runs through quite a few subsequent articles in this small corpus of articles and field that is becoming increasingly popular. “The heterochromatin sequence of Drosophila will provide an essential foundation for identifying the proteins and components involved in epigenetic inheritance, as well as other mysteries surrounding the genome’s ‘dark matter.’”
After 2010 links between dark matter and epigenetics are made more frequently, especially in an interview with the famous science writer Gina Kolata about the ENCODE project and in a review of a popular epigenetics book by Tim Spector which came out in 2012. In the process, the dark matter metaphor becomes linked to a much more mundane metaphor, that of ‘genetic switches’, a metaphor that itself is linked to speculating about what actually controls genes and enables them to make certain cells in the body. Kolata refers to dark matter as “the thing that controls other genes” and the interviewer then says: “A regulator or a kind of switch”. Another article on a study published in 2013 points out that the dark matter contained in the genome makes “sure that genes are ‘switched on’ at the right time and in the right part of the body”.
Most of the later articles speculate about using insights into the function of genome’s dark matter in order to find cures to human diseases. Over time then the dark matter metaphor has enabled researchers to gain insight into ‘junk DNA’ in terms of ‘regulator switches’. This makes genomic dark matter much less mysterious and potentially more amenable to being used in future healthcare. So while ‘real’ dark matter in physics still eludes detection and remains largely a mystery, the genome’s dark matter is, as my son explained to me, “several orders of magnitude less mysterious”.
From big physics to big genomics
A 2010 article in The Independent goes beyond previous elaborations of the dark matter metaphor (in terms of mapping what we don’t know about the universe onto what we don’t know about the genome) and establishes connections between the whole genomic enterprise, that is to say, between ‘big genomics’ and ‘big physics’: “Ever since the Human Genome Project was first mooted at the end of the 1980s, scientists realised that it would be a mega-informatics project, akin to the ‘big physics’ experiments that have enjoyed huge public financing. Genomics researchers have even adopted the same language of their physical science colleagues, hence the phrase ‘missing heritability’, which is taken directly from the astronomer’s lexicon describing the ‘missing mass’ of the Universe. Equally, ‘dark matter’ – to the genomics researcher – refers not to the cosmological phenomenon but the immense proportion of the genome whose function is unknown. The genomic dark matter is the vast proportion of the genome not directly involved in what genes are supposed to do – code for proteins. This form of dark matter, comprising some 90 per cent of the genome, has no apparent function, but few scientists would now describe it under its old nickname of ‘junk DNA’.” Junk is out, dark matter is in, and, most importantly it can be used to attract funding.
Dark matter turns junk into gold – possibly
As we have seen, at the beginning of the millennium the ‘dark matter’ metaphor began to be used to refer to puzzling junk DNA found in the human genome. Scientists are now beginning to understand how this dark matter might work in terms of regulating and controlling genes and gene expression — in a way they are beginning to see the pot of gold at the end of the rainbow. To stimulate sustained search for this pot of gold, the mystery metaphor of dark matter will probably still be useful for quite a while though.
However, is this new genomic metaphor useful when communicating advances in genomics to the wider public? It is certainly less ‘deterministic’ than the blueprint metaphor was, but it is not really enlightening – rather the opposite – endarkening? For purposes of communicating genomics it might be better to go back to some older metaphors. As Jon Turney pointed out in an essay on genetic and genomic metaphors: “Perhaps one can see the genome as a commune, [John Avise] suggests—a tightly bound organization with an intricate division of labour (Avise, 2001)”, where genes and junk work together in building and rebuilding us as biological beings.
Image: Cosmos 3D Dark Matter Map