Dark matter is a proposed kind of matter that cannot be seen, but that we believe accounts for most of the mass in the universe. Its existence, mass, and properties are inferred from its gravitational effects on visible matter. The most favored hypothesis is that dark matter is not composed of baryons, the basic components of visible matter, but of completely different types of particles. In any case, while the actual nature of dark matter is a mystery, its effect on the universe is well-documented, and the term is quite precise in its usage and meaning.
Biological “dark matter” is quite a different thing, as the term is not original, but a metaphor taken from astronomy. As such, it has been used to mean various different things in different fields. In molecular biology, dark matter has been used to mean junk DNA, and non-coding RNA, among other things. In microbiology it has been used to describe the large number of microbes we are unable to culture and classify, and whose nature we mostly infer from metagenomic data. “Dark matter” has also been used for the shadow biosphere, a microbial world that does not feature any known biochemistry, and whose existence is only hypothesized.
I am uncomfortable with the use of the term dark matter metaphor in biology. First, this term is used to mean so many different things, it ends up meaning none of them. If someone tells me they work on biological dark matter, my first reaction is: “which one?” Second, as metaphors go, it is misused. With the exception of the shadow biosphere metaphor, we do understand what the various “dark matters” are composed of, and in many cases their effects on known biological mechanisms. The components of the various types of non-coding RNA are well-known to us: those are the same nucleotides that make up any RNA molecule. We may not understand the exact effects and how they work, but their nature (nucleic acids which may have information and catalytic ability) is not outside the scope of our current biological worldview. Similarly, in the case of junk DNA: yes, most of the DNA in some eukaryotes does not get transcribed or translated. Some of it may regulate gene expression, some (or a lot) of it is selfish DNA that simply replicates itself. But again, junk DNA is not dark matter as its composition is not alien to our understanding of biology, and there is no biological phenomenon that requires its existence to be explained. In fact, the opposite is true: we are not sure why some organisms have accumulated so much junk in their chromosomes, although we have some interesting hypotheses, and we are pretty sure there is no single underlying cause for the existence of junk DNA. As for the use of dark matter in microbiology: we probably have much to discover about microbial diversity, but it is no dark matter. We do not expect that new microbial species would be fundamentally different than those that we know of now: we expect them to be CHON life with mechanisms fundamentally similar to those we know of. That is not to say we are not hopeful of discovering new and exciting biochemistry and molecular biology in these undiscovered species. I am convinced that there are untold riches there! We may even discover new metabolites, new amino acids, maybe even new epigenetic or genetic mechanisms. But those would be still within the framework of known biochemistry. Even if we discover a radical new biochemistry, the second part of the metaphor does not hold: we do not need, at the moment, to assume a completely different microbial world to explain current life. This brings us to the realm of the shadow biosphere: the whole existence of a shadow biosphere, while intriguing, is hypothetical. It is not as if there are unexplained phenomena in biology that can only be explained by the existence of a shadow biosphere, and we have scant evidence of its existence. One day we may very well discover that we are sharing this planet with microbes of non-classical biochemistry. But, for now, we do not see any effects on our own biospehere that can only be explained by a shadow biosphere.
So is there dark matter in biology? Is there a phenomenon that cannot be explained unless we assume a mysterious new player that explains it?
Biology actually has a history of dark matter hypotheses. Biologists have always strived to explain how life differs from non-life, and for that they had to resort to any one of several mysterious “dark matter-like” (or, more appropriately, dark energy-like) explanations. Over time, the differentiation of life from non-life was explained by anything from the Aristotelian Final Cause to, most recently, vitalism: an unmeasurable force or energy that exists only in living creatures and differentiates a frog from a rock. All of these proposals were used to explain the apparent purposefulness of action, or teleonomy, in anything from microbes to humans. As we grew to understand biochemistry and the complexity of life, vitalism went out the window of respected science. Why? Do we understand the apparent purposefulness life displays? Not really, but we do not need to resort to an overarching force that explains it. Our (still highly imperfect) understanding of life is that organisms are emergent highly complex systems, whose apparent purposefulness is tied to evolution and their ability to self-organize and reproduce.
So while there are plenty of unexplained phenomena in biology, at the moment there is really none that require the stipulation of a dark matter analogous to that which is in astronomy. Tempting as it may be, perhaps we should calm down on the use of the term dark matter in biology. Biology is confusing, complicated, and mysterious enough without it.