In this sense, the proper practice of philosophy has to involve science—and by that I mean evidence— if the results are going to produce knowledge. There's lots to debate on this topic, including discussions about the meaning of "knowledge" [Is science the only way of knowing?].
But that's not what I want to talk about today. Today's topic is about the contribution that philosophers can make to science. I'll focus on philosophers of biology and on scientific topics that I'm knowledgeable about and I'll assume that most philosophers agree with Elisabeth Lloyd when she says, "As a philosopher of science, I have always been oriented towards addressing problems that scientists have, not so much problems that philosophers have. That is how to do good philosophy of science."1
Now, let me be clear about the issue. It is blindingly obvious that philosophers could use their deep understanding of logic and argumentation to make significant contributions to biology, especially in cases where scientists are misusing logic. The question is not whether philosophy is incapable of ever contributing to biology but whether it is actually fulfilling that potential.
There are all kinds of conflicts and controversies in evolution including issues such as the relative contribution of drift and selection (adaptationism), the importance of a null hypothesis, mutationism, genetic load, and the molecular clock, just to name a few. There are also lots of controversies in molecular biology including alternative splicing, epigenetics, defining genes, junk DNA, and the proper interpretation of the Central Dogma of molecular biology.
Some of the scientists holding strange views on these topics are just stupid and ignorant may not have very good arguments. This is where philosophers could step in and make a contribution but in order to do so they would have to be very knowledgeable about the subject. They would also have to be very knowledgeable about the history of the subject.
Take genes, for example. Philosophers have been attracted to arguments over the definition of "gene" and they often quote conflicting definitions from biologists. But some biologists use stupid definitions that should properly be ignored. For example, many biologists are sloppy and they often describe genes only in terms of protein-coding genes.
This is wrong, of course, because there are also non-coding genes. The question philosophers should be asking is whether biologists who refer to genes only as protein-coding are really prepared to defend the idea that regions specifying ribosomal RNA or tRNA are not genes. Of course they aren't. They just got sloppy and we shouldn't make a big deal out of the fact that they didn't think carefully about their definition. It's not a fundamental problem in biology.
Philosophers should know whether scientists who describe evolution as a change in the frequency of genes are really serious about that definition. Do they really mean "genes" or did they just get sloppy when they should have said "alleles"?
Recognizing these sorts of errors are what philosophers should be good at. Philosophers should be able to clarify concepts like "what is a gene?" But are they? Do they? [Definition of a gene (again)].
Elisabeth Lloyd is a good example of a philosopher who has made significant contributions to understanding scientific issues but she's not the only one. I won't list all the philosphers I admire but it would be remiss of me not to mention Stefan Linquist.
Most of the scientific controversies I mentioned have been extensively discussed in the scientific literature and it's quite common to see some harsh criticism of scientists who defend controversial views. Think of how Richard Dawkins and Stephen Jay Gould have been treated, for example. And think of the very harsh criticism aimed at the ENCODE researchers for their ridiculous unusual views on junk DNA.
I don't usually see that kind of criticism in the philosophy literature; for example, even though Evelyn Fox Keller was clearly wrong about some of her statements on genes, genomes and junk DNA there wasn't much pushback from other philosophers until recently. That's puzzling since philosophers claim to be experts in the history of science and in analyzing the logic of scientific arguments. We're supposed to look to them for help.
There are other examples. In my opinion, the writings of philosophers on molecular issues often suffer from a lack of understanding of the true history of the subject and a lack of in depth knowledge about the subject. Here (below) are a few examples taken from the Stanford Encyclopedia of Philosophy but you can also find examples from some of the books in my library: The Cambridge Companion to the Philosophy of Biology (2007), Keywords in Evolutionary Biology (1992), Philosophy of Biology (1989), Genetics and Philosophy ((2013), Philosophy of Pseudoscience (2013), Biology, Ethics, and the Origin of Life (1995), Science Unlimited (2017), Scientific Knowledge (1987), The Gene from Genetics to Postgenomics (2017), Nonsence on Stilts (2010), and The Black Box of Biology: A History of the Molecular Revolution (2020).2
I'm disappointed that philosophers haven't tackled some important controversies; for example, there are no separate entries in The Stanford Encyclopedia of Philosophy on alternative splicing, junk DNA, mutationism, neutral theory, or the origin of life. Some of those topics could really use help from philosophers on logic and argumentation because the debates are full of logical fallacies in addition to often being short on evidence.
Molecular Biology
As previously stated, there is a strong scientific consensus that most of the human genome consists of DNA whose nucleotide sequence is not relevant to biological function—being the so-called junk.
Alberts et al. (2022)
Molecular Biology of the Cell
7th ed. p. 231
The Stanford Encyclopedia of Philosophy entry on Molecular Biology was updated in 2024. It repeats the old myth about the number of genes being a surprise when the human genome sequence was published. There's a considerable literature on this so there's no excuse for presumed experts in the history of biology to get it wrong.
The entry also has an extensive discussion about the meaning of the word "gene" but it never mentions the common molecular biology textbook definition and why that definition is useful. The authors only had to check the Wikipedia entry to get up-to-date. There's no discussion of the controversies surrounding alternative splicing and junk DNA.
Genomics and Postgenomics
You might think that defining what a genome is would be an important topic in an entry on Genomics and Postgenomics. You would be correct. The authors put down a lot of words on this topic but although they criticize some of the more ridiculous definitions, they don't really come up with the definition they are going to use in the rest of the article. Instead, they worry about whether histones are part of the genome (not in viruses or bacteria!), whether methylation confuses the issue, or whether epigenetics is important. After all that, the first sentence of the next section is "The first genome to be sequenced was that of a virus, namely bacteriophage ΦX174." The discussion about junk DNA is embarrassing.
Gene
The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce RNA. There are two types of molecular genes: protein-coding genes and non-coding genes.
Wikipedia: Gene
The entry on Gene was written in 2022. The opening sentence is "Many biologists and commentators from the humanities and social sciences have questioned whether the gene is still a useful category in biology."
It's pretty much downhill from there. The article gives an adequate history of the Mendelian gene but when it gets to the molecular gene the history goes astray. The authors make the same mistake as a number of scientists in assuming that the "classical molecular gene" only encodes protein in spite of the fact that non-coding genes have permeated the molecular biology literature since the mid-1960s. These philosophers are not contributing to clarifying the misconceptions of scientists.
The authors then fall down a deep rabbit hole created by ENCODE workers and they even highlight the ridiculous definition of a gene promoted by Mark Gernstein back in 2007. The don't mention any of the scientists who refute that definition or any of the recent textbooks that have been using a perfectly adequate definition for the past four decades—the same one we worked out in the Wikipedia article [Gene]. They don't even seem to recognize the existence of non-coding genes since they use the term "DNA regions transcribed to non-coding, but functional RNA." This means they avoid bringing their philosophical expertise to bear on the important controversy over the number of non-coding genes in the human genome.
In my opinion, this is a clear example of where philosophers have not followed Elisabeth Lloyd's advice. Instead, they have created a whole separate world of philosophers arguing among themselves about genes in a way that's almost completely disconnected from the real issues that biologists face.
The Human Genome Project
This article was substantively revised in 2023. It seems like this is a place where an expert philosopher in the history of biology could shine and indeed she does. The description of the human genome project from its beginning to the publication of the draft sequence in 2001 is excellent and it contains many insightful comments that are well worth reading.
The discussion of the aftermath begins with a very good analysis of HGP's impact on genetic diseases including the important point that it was very much oversold as a contribution to medicine. That's another example of a philosopher who makes a contribution to understanding biology although it would have been enhanced by recognizing that many scientists where fully aware of the fact that hype about the HGP's impact on medicine was necessary in order to convince politicians that it should be funded. Many of them didn't really believe the hype.
Unfortunately, the very brief discussion about the actual genome results isn't as good. It's another example of philosphers who don't dig deeply into statements about the number of genes that were expected and the the basic understanding of gene expression prior to completion of the human genome project. There's nothing in the article about the controvesies surrounding junk DNA and how to identify function even though this has attracted the attention of several philosphers.
Molecular Genetics
I think of molecular genetics as a field of study similar to biochemistry or molecular biology. Scientists who work in this field often study genes and how they are expressed but also other functional and non-functional regions of the genome. These scientists work on all kinds of organisms including bacteria, yeast, fruit flies, plants, mice and, of course, humans.
The article on molecular genetics was substantively revised just a few weeks ago (March 2026). Here's how it begins.
The term molecular genetics sometimes refers to (1) a fundamental theory alleging that genes direct all life processes through the production of proteins and RNAs (ribonucleic acids), sometimes to (2) a more modest, basic theory about the replication and expression of DNA (deoxyribonucleic acid), and sometimes to (3) an investigative approach applied throughout biomedical science that is based on investigative strategies grounded in the basic theory about genes.
Some of the article isn't about what molecular geneticists study. It's about genetics and whether the field of genetics can be reduced to the molecular level. It delves into the philosophical literature about reductionism. There may be some scientists who want to keep up with that debate but I lost interest in it about 40 years ago when it didn't seem to be going anywhere. Still isn't.
The nice thing about this article is that the author clearly understands that one good definition of a gene is a DNA sequence that is transcribed and he knows that there are two kinds of genes; protein-coding genes and genes that specify functional RNA molecules. It's a shame that philosophers don't talk to each other.
We define a gene as a DNA sequence that is transcribed. This definition includes genes that do not encode proteins (not all transcripts are messenger RNA).
Moran et al. (2012)
Principles of Biochemistry,
5th ed. p. 633
However, when we get to the part of the article that discusses gene concepts, things begin to go awry. This philosopher, like many scientists, is hung up on the idea that before 1965 genes were traditionally described as segments of DNA that encode proteins.
He even goes so far as to say that the most common textbook definition is "that a gene is the fundamental unit that codes for a polypeptide." Not in any of my textbooks beginning in 1987 and not in many others, especially the best ones. And not in the first textbook on the molecular biology of the gene published by James Watson in 1965.
Scientists frequently demonstrate their ignorance of this history by repeating the cannard about protein-coding genes being thought of as the only kind of gene but this is where philosophers could make a contribution by correcting their false view of the history of biochemistry and molecular biology instead of reinforcing it. Also, some biologists use the word gene in ridiculous ways that are not logically defensible. That doesn't mean that the definition of "gene" is a serious problem and philosophers need to get over the idea that knowledgeable scientists pay any heed to those unknowledgeable scientists.
Genetics
The introduction to this article points out that there are more than 100 entries that discuss genetics and the philosophical issues that arise from genetic discoveries.
You can skip this article if you are a scientist who knows anything about genes or genetics. It will only make you angry. This article is only for philosophers who enjoy arguing about whether the image on the right is a pipe.
1. This quote is from a very interesting video on the philosophy of biology [Why Philosophy of Biology?].
2. I wonder how many philosophers have a copy of one of my biochemistry textbooks or What's in Your Genome?.
5 comments :
Don't you define a gene as a DNA sequence that's transcribed *to produce a functional product*? It seems as if the second part is missing here, and that makes all the ENCODE genes fit the definition.
We creationists are a pain in the ass but good natured. A way of knowing i guewss means accurate conclusions. Knowledge that is accurate. however in a God created universe, or the option of it, and in Genesis having been written and claimed to be a accurate witness then there are other ways of knowing. Science, if done accurately and is accurate, is just. another way of knowing. Yet this investigative tactic is relevant to the abiluty of the investigator, tailless primates for some, and a question of ability of investigators was breached here in this article. thoughy with a line through it but not really cancelled.
The only relevance of a philosopher to science is either to do it or hold everyone to the rules of play. methodology. We creationists cry foul that bevolutionary biology or genetics does not play by these rules. Leading in a spectrum to them complaining about eaxh others methodology when wrong conclusions are made as they see it. I see no modern philospher understanding or enforcing rules and so are really just people who memoruzed things and got a degree. AI could do it. HEY what does AI say about inhouse controversies?
I enjoyed this, which came out a few weeks ago: DiFrisco, James, and Steven Hecht Orzack. "Biology Needs Philosophy, But What Philosophy?." BioScience (2026): biag016.
It has recommendations for both biologists and philosophers.
@John Harshman: I wrote that definition about thirty years ago. At the time I didn't think it was necessary to qualify it by mentioning that the transcript had to have a function.
I still felt the same way when I finished writing the last draft of my textbook in early 2011.
Now I know better. It turns out that there are a significant number of real scientists who think that spurious transcription of a stretch of DNA means that that DNA is a gene. Who would have guessed?
The important point here is that this seems to me to be a clear example of an issue that philosophers should care about but most philosophers of biology don't care. I think most of them they aren't even aware of the problem because they are not vey knowledgeable about things at the molecular level.
@Anonymous: Whoever you are, I thank you for posting a link to that article by DiFrisco and Orzack. It is fantastic! It's full of all kinds of provocative statements that we should discuss.
DiFrisco, J. and Orzack, S.H. (2026) Biology Needs Philosophy, But What Philosophy? BioScience:biag016. [doi: 10.1093/biosci/biag016]
"Philosophy of biology has the potential to contribute to biology by improving scientific reasoning. However, this potential is largely unrealized because of the lack of awareness by most biologists of what philosophy can offer, because of deficits of biological expertise among most philosophers, and because of adherence to disciplinary norms in philosophy that render much work in philosophy of biology irrelevant to biologists. We believe that philosophy of biology will contribute little to biology without a change of practice. We provide guidelines (“comments” sensu Slobodkin 1975, “commandments” sensu Kornberg 2000, 2003, Francis et al. 2007) for how biologists can better engage with philosophy and for how philosophers can better engage with biology so as to create a “philosophical biology” that improves our biological understanding."
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