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Sunday, January 01, 2023

The function wars are over

In order to have a productive discussion about junk DNA we needed to agree on how to define "function" and "junk." Disagreements over the definitions spawned the Function Wars that became intense over the past decade. That war is over and now it's time to move beyond nitpicking about terminology.

The idea that most of the human genome is composed of junk DNA arose gradually in the late 1960s and early 1970s. The concept was based on a lot of evidence dating back to the 1940s and it gained support with the discovery of massive amounts of repetitive DNA.

Various classes of functional DNA were known back then including: regulatory sequences, protein-coding genes, noncoding genes, centromeres, and origins of replication. Other categories have been added since then but the total amount of functional DNA was not thought to be more than 10% of the genome. This was confirmed with the publication of the human genome sequence.

From the very beginning, the distinction between functional DNA and junk DNA was based on evolutionary principles. Functional DNA was the product of natural selection and junk DNA was not constrained by selection. The genetic load argument was a key feature of Susumu Ohno's conclusion that 90% of our genome is junk (Ohno, 1972a; Ohno, 1972b).

All that changed in 2007 when the ENCODE Consortium published their preliminary results and suggested that most of the human genome was functional because it was transcribed. They doubled down on this claim in 2012 by claiming that 80% of the genome was functional and the concept of junk DNA was dead. ENCODE ignored the standard evolutionary arguments for function and junk and substituted a new definition based on whether DNA was transcribed and whether it was bound by transcription factors. It didn't matter whether you could assign a real biological function to this DNA or whether it was conserved.

The ENCODE II results were published on Sept. 5, 2012 and by the end of that day there had already been substantial push back from knowledgeable scientists who strongly objected to the misuse of the term "function." This prompted immediate response the next day from some ENCODE leaders and from the editorial staff at Nature. Their defense was that scientists can have legitimate disagreements over the meaning of "function" and "junk" and the correct definition has not been decided.

That kicked off the most intense years of the function wars when scientists and philosphers combined to work out a reasonable definition of function based on evolutionary principles and, at the same time, demonstrate the uselessness of a definition based entirely on some sort of activity that may or may not be indicative of real function.

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]

Brzović, Z., and Šustar, P. (2020) Postgenomics function monism. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 101243. [doi: 10.1016/j.shpsc.2019.101243]

Doolittle, W. F. (2018) We simply cannot go on being so vague about ‘function’. Genome biology, 19:1-3. [doi: 10.1186/s13059-018-1600-4]

Doolittle, W. F., and Brunet, T. D. (2017) On causal roles and selected effects: our genome is mostly junk. BMC biology, 15:116. [doi: 10.1186/s12915-017-0460-9]

Doolittle, W. F., Brunet, T. D., Linquist, S., and Gregory, T. R. (2014) Distinguishing between “function” and “effect” in genome biology. Genome Biology and Evolution, 6:1234-1237. [doi: 10.1093/gbe/evu098]

Graur, D., Zheng, Y., Price, N., Azevedo, R. B., Zufall, R. A., and Elhaik, E. (2013) On the immortality of television sets:“function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution, 5:578-590. [doi: 10.1093/gbe/evt028]

Linquist, S. (2022) Causal-role myopia and the functional investigation of junk DNA. Biology & Philosophy, 37:1-23. [doi: 10.1007/s10539-022-09853-2]

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. (2014) Genome as a Multipurpose Structure Built by Evolution. Perspectives in Biology and Medicine, 57:162-171. [doi: 10.1353/pbm.2014.000]

Niu, D.-K., and Jiang, L. (2013) Can ENCODE tell us how much junk DNA we carry in our genome? Biochemical and biophysical research communications, 430:1340-1343. [doi: 10.1016/j.bbrc.2012.12.074]

Palazzo, A. F., and Gregory, T. R. (2014) The Case for Junk DNA. PLOS Genetics, 10:e1004351. [doi: 10.1371/journal.pgen.1004351]

The world is not inhabited exclusively by fools and when a subject arouses intense interest and debate, as this one has, something other than semantics is usually at stake.
Stephan Jay Gould (1982)

By the time the dust had settled, we were right back to the original definitions from 50 years ago. Functional DNA is DNA that is currently under purifying selection - it is being maintained by natural selection. This is the "maintenance function" definition [Identifying functional DNA (and junk) by purifying selection]. It not only applies to the sequence of functional DNA but in some cases to just the size (e.g. spacer DNA). There are no other definitions of function that stand up to close scrutiny, especially those that cannot distinguish between gene transcripts and spurious transcripts and between true regulatory sites and fortuitous transcription factor binding sites in junk DNA.

The ENCODE researchers have lost the Function Wars and conceded defeat. The official ENCODE position now refers to "candidate" functional sites or "potential" functional sites [ENCODE and their current definition of "function"]. However, I should note here that many junk DNA opponents refuse to adopt those terms and they continue to make irrational claims for abundant function without defining what they mean by function. When pressed, they usually fall back on some version of, "There is still a lot of debate about the proper meaning of function," which is code for "I don't accept the opinion of the experts who have published numerous papers on this topic."

The function wars are over. If you want to claim that our favorite DNA sequence has a biologically relevant function then the burden of proof is on you to show that it is currently being constrained by purifying selection. If you can't do that then you can't claim that it's functional. The best you can do is claim that it's still junk but it might eventually turn out to be functional when there's more evidence for function.

Ford Doolittle: [U]ntil we actually have some agreement about what we mean by words we are going to get into these arguments, and in my mind, there are two devastating things you can say about the ENCODE people.

One is that they completely ignored all that history about junk DNA and selfish DNA. There was a huge body of evidence that excess DNA might serve some structural role in the chromosomes, but not informational. They also ignored what philosophers of biology have spent a lot of time asking: what do you mean by “function?” And you can mean one of two things: we might mean either what natural selection favored, which is what I think most biologists mean, or we might mean what it does. Some people might say, “Well the function of this gene is in the development of cancer,” but they don’t really mean that natural selection put it there so that it would cause cancer. These are not-so-subtle differences.

I think many molecular biologists and genomicists, in particular, think that each and every nucleotide is there for a reason, that we are perfect organisms. It is almost as if we were still theists thinking God doesn’t make junk; we just now think natural selection doesn’t make junk. I think there is a deep issue about the extent to which we are noisy creatures and the extent to which we are finely honed machines. I think the latter view informs much of genomics, and I think it is false. (Gitschier, 2015)

Gitschier, J. (2015) The philosophical approach: an interview with Ford Doolittle. PLoS Genet, 11(5), e1005173. [doi: 10.1371/journal.pgen.1005173]

Ohno, S. (1972a) So much "junk" DNA in our genome. In H. H. Smith (Ed.), Evolution of genetic systems (Vol. 23, pp. 366-370): Brookhaven symposia in biology.

Ohno, S. (1972b) An argument for the genetic simplicity of man and other mammals. Journal of Human Evolution, 1:651-662. [doi: 10.1016/0047-2484(72)90011-5]


Georgi Marinov said...

Unfortunately, there will still be articles written about how junk DNA has been debunked a decade from now...

jb said...

The definition, "Functional DNA is DNA that is currently under purifying selection - it is being maintained by natural selection" seems very adaptationist. Surely you're not suggesting neutral evolution only affects non-functional DNA.

What am I missing?

Larry Moran said...

jb asks, "What am I missing"

You're missing the point. When I say that functional DNA is maintained by purifying selection I'm speaking in "big picture" language. I never meant to imply that every single nucleotide in a functional region is resistant to change. I thought that was obvious but I'm glad of the opportunity to make it clear.

Conserved regions of DNA are not absolutely conserved. They are simply more conserved than regions that evolve at the neutral rate. There are many nucleotides within conserved regions that can change due to mutation and fixation by random genetic drift. That's why homologous genes in distant species are only 70% similar or 30% similar and not 100% similar.

In cases where it's the size of the region that's important and not the sequence, it doesn't mean that the exact size is conserved. There can be considerable variation as long as a minimum, or maximum, size of spacer DNA is maintained.


Lamarck said...

Hi Larry Moran,

in my capacity as the bulldog of modern synthesis, a few minor science theory references:

i. “Functional DNA is DNA that is currently under purifying selection”

This “definition of the conservation function” uses circular logic. Another circular argument is contained in the word “currently”. By the way, the real “maintenance function” is called adaptation.

ii. As a systems biology approach, functional genomics looks at the interaction of genes and proteins (structure, function, regulation) at the level of the entire genome. Against the background of functional genomics, junk DNA would then have the function of having no function [sic!]. Functions do not know evolution; they are present or not. If the adaptive properties depicted in the structure of a sequence are indispensable, then all other sequence segments are play money of evolution: mutation catcher AKA potential preadaptation.

iii. “Some people might say, “Well the function of this gene is in the development of cancer,” but they don’t really mean that natural selection put it there so that it would cause cancer.”

Ford Doolittle is much closer to me here than you are. Nevertheless: It is indeed not impossible that natural selection could prefer the development of cancer. If this were otherwise, there would be neither p53, sickle cell disease, asexual reproduction via dieback in Volvox, nor infectious cancer in Tasmanian devils. Of course, natural selection also makes junk!

iv. “That kicked off the most intense years of the function wars when scientists and philosophers combined to work out a reasonable definition of function based on evolutionary principles and, at the same time, demonstrate the uselessness of a definition based entirely on some sort of activity that may or may not be indicative of real function.”

Formally, functions are left-total. For example, it can be said that a bird's wing serves to fly. This does not mean that the wings of flightless birds have the function of being able to fly. This is vivid proof that functions - of whatever kind - cannot be based on evolutionary principles. Bird wings, however, have evolved by adaptive means.