This would seem to be fertile ground for philosophers of biology and, indeed, there are some philosophers who have made a significant contribution, mostly in sorting out how to define function (Brunet et al., 2021; Linquist et al., 2020). Also, many philosophers are interested in the history of biology and some (e.g. Morange, 2020) have done a good job of describing the history of the junk DNA concept.
In spite of these significant contributions, it seems to me that the majority of philosophers lack an understanding of the history and the science behind the junk DNA controversy. This may not seem to be surprising since most scientists are in the same boat—they are prone to widespread misinformation about junk DNA.
However, one could make the case that philosophers are supposed to be better at recognizing problems and difficulties in interpreting data and dealing with controversies. Philosophers claim to be good at that sort of thing. This is why they say that scientists need philosophers to help them sort out conceptual issues and definitions.
In order to get a feel for how philosophers are interpreting their colleagues and dealing with the junk DNA controversy, I thought I'd take a look at entries in the Stanford Encyclopedia of Philosophy to see what they say about junk DNA.
It's interesting that the article on The Human Genome Project doesn't have anything on junk DNA and neither does the article on Adaptationism. There are only two articles that address the junk DNA controversy—let's look at what they say.
Genomics and Postgenomics
I was expecting to see a lengthy discussion of the junk DNA controversy because it underlies many issues in genomics. There's a section devoted to junk DNA but it begins with a discussion of the C-value paradox and it states that the concept of junk DNA was based on the idea that humans had far more DNA than expected given the early estimates of gene number. This is not inaccurate but it ignores the mutation load issue and the data showing that mRNA only covered about 2% of the genome.
The description then shifts to the "G-value paradox" and the discrepancy between the expected number of genes and the number discovered when the human genome sequence was published.
The problem that the junk DNA discussion brings up has also been referred to as the ‘G-value paradox’ (‘G’ stands for ‘gene’), which directly concerns the discrepancy between the number of genes in an organism and its complexity (Hahn & Wray 2002). This paradox has been reinforced by the findings of the HGP. As Gregory (2005) and other commentators have pointed out, the finding that the human genome contains many fewer genes than expected was one of the most surprising outcomes of the HGP. Initial estimates from before the project were in the range of 50,000 to 150,000. These were reduced to about 30,000—35,000 after the publication of the first sequence draft in 2001 and have now been further revised to the order of 20,000 (Gregory 2001).
The problem here is that the authors reference Ohno's classic paper (Ohno, 1972) in an earlier paragraph. In that paper, Ohno estimates that there are about 30,000 genes and he references other workers who support that estimate. Such estimates were common in the period leading up to the publication of the human genome project. It's fair to say that the leading experts correctly predicted the number of genes that would be found. Proponents of junk DNA were not surprised when the human genome sequence was published.
It's unfortunate that the authors who wrote this article didn't bother to do a more thorough job of researching the history.
Molecular Biology
This article has a single paragraph devoted to the junk DNA controversy. It focuses on a philosophical issue; namely, how to classify junk DNA. The authors don't seem to be interested in how much junk DNA is present in the human genome.
Related to the debate about the causal distinctiveness of DNA has been the question of how to classify so-called junk DNA. Most biologists and philosophers of biology do not consider junk-DNA to be on causal par with coding DNA, because mutations in junk-DNA do not affect function (although for an alternate account of junk-DNA’s non-coding function see Doolittle 2013). However, Joyce Havstad and Alexander Palazzo (2022) have argued that despite its paradigmatically non-functional role, junk DNA meets the criteria of being an actual difference maker. But since junk-DNA is not considered to be on causal par with coding DNA, this suggests that Waters’ account of what makes coding DNA causally distinctive is incomplete. According to Havstad and Palazzo, the missing components are ‘causal reach’ and ‘causal efficacy.’ While junk DNA can indeed produce causally specific proximate effects, its causal specificity has limited reach and efficacy, which is why it is not considered to be on par with coding DNA in terms of causality. Nonetheless, Havstad and Palazzo maintain that the diminished causal status of junk-DNA in relation to coding DNA does not diminish its significance within the cell.
I'm not much interested in whether junk DNA is on a "causal par" with coding DNA (or regulatory DNA, or non-coding genes, or origins of replication, or centromeres, or telomeres, or SARs). What's interesting is that the authors picked out one paper by a philosopher (Joyce Havstad) who collaborated with my biochemistry colleague, Alex Palazzo. I warned Alex that his paper would be interpreted as a critique of junk DNA.
There are plenty of other papers that discuss function and the fact that junk DNA is non-functional but the philosophers who wrote the molecular biology article decided not to reference them. This seems to be a case where the philosophers aren't interested in the scientific problem of junk DNA but only in the philosophical issue of causal distinctiveness.
Brunet, T.D., Doolittle, W.F. and Bielawski, J.P. (2021) The role of purifying selection in the origin and maintenance of complex function. Studies in History and Philosophy of Science Part A 87:125-135. [doi: 10.1016/j.shpsa.2021.03.005]
Havstad, J.C. and Palazzo, A.F. (2022) Not functional yet a difference maker: junk DNA as a case study. Biology & Philosophy 37:29. [doi: 10.1007/s10539-022-09854-1]
Linquist, S., Doolittle, W.F. and Palazzo, A.F. (2020) Getting clear about the F-word in genomics. PLOS Genetics 16:e1008702. [doi: 10.1371/journal.pgen.1008702]
Morange, M. (2020) The Black Box of Biology: A History of the Molecular Revolution. Harvard University Press
Ohno, S. (1972) So much "junk" DNA in our genome. Evolution of genetic systems. H. H. Smith, Brookhaven symposia in biology. 23: 366-370.
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