Today my blog post will be devoted to a very controversial topic not just in physics, but also in biology. For those who do not know, both biology and physics have what we call “dark matter”. Whereas cosmological dark matter represents the gravitational effects that cannot be explained by known bodies in the universe, genomic dark matter emerged from the application of new technologies to the analysis of the transcriptome (all genes expressed in a genome), and could not have been inferred from any known biological principle. In physics, it represents everything that is not matter (basically, matter is any substance which has mass and occupies space in the universe such as the planets, us, etc; and the “dark matter” represents everything else). In biology, it corresponds to regions of the DNA in living cells, especially humans, which are noncoding or do not code for proteins (our building blocks in the cells). The dark matter in both fields account for more than 90% when compared to matter in the case of physics and to regions of the DNA that produce functional elements such as proteins and regulatory RNAs in molecular biology. The term “dark matter” was postulated by a researcher named Fritz Zwicky in 1934 to account for evidence of “missing mass” in the galaxies. At first, researchers thought that both “dark matters” had no function or did not represent anything important, just something that was there. Nobody knew why. However, it is becoming clear that “dark matter” plays a central role in state-of-the-art modeling of structure formation and galaxy evolution in astronomy. The same way, in biology, parts of DNA that were considered “junk” probably have functional importance. Studies have been showing that more than 50% of eukaryotic genomes is transcribed into RNA, but these are not translated in proteins. A recent editorial piece from BMC Biology (“The noncoding universe”, BMC Biology 2011, 9: 52) have discussed this topic claiming that the “dark matter” of genomes probably have function and are evolutionarily important for humans. Maybe they could also explain human complexity (for more details see the article that I wrote about this topic – “Non-coding RNAs, epigenetics and complexity”. Gene 2008, 410: 9-17). The debate on the functionality of “noncoding” parts of genomes recently took central stage in several debates in the scientific community with articles and editorials covering this topic. Some believe most of the transcribed regions of genomes represent by-products of the transcription itself and have no function. Others believe non-coding regions generating non-coding RNAs are important for gene regulation and even in evolution. Growing evidence with examples of RNAs coming from the “dark matter” of the genome that are functional and have roles similar to that of proteins have surfaced. But what function really means in genomics? What can be a good definition for function? Well, if gene expression control relies on the expression of non-coding regions for genome stability, maybe genome stabilization could be assigned as a function. The controversy will continue for some time, but in my opinion the noncoding regions probably have roles we do not even imagine yet. Similarly to the “dark matter” of the universe in physics, noncoding parts of genomes are still full of mysteries. This is a very philosophical controversy – the same way the universe, which is big, has a “dark matter”, the very small in the cells, specifically the DNA, have the same conundrum. The next years will be very exciting since researchers in these fields will try to understand both “dark matters”. The future is promising for astronomy and molecular biology…I am excited with this debate!