Abstract
What is a gene? Does it represent a natural kind, or is it just a tool for genomics? A clear answer to these questions has been challenged by postgenomic discoveries. In response, I will argue that the gene can be deemed a natural kind as it satisfies some requirements for genuine kindhood. Specifically, natural kinds are projectible categories in our best scientific theories, and they represent nodes in the causal network of the world (as in Khalidi. Natural Categories and Human Kinds: Classification in the Natural and Social Sciences. Cambridge University Press, Cambridge, 2013; Khalidi. Synthese 195: 1379–1396, 2018; Khalidi. Are Sexes Natural Kinds, In: Dasgupta S, Weslake B (eds) Current Controversies in Philosophy of Science. Routledge, New York, 2020; Khalidi. Philos Sci 88:1–21, 2021). In Sect. 2, I will present a brief history of the gene and the controversy over its status. In Sect. 3, I will introduce the account of natural kinds considered in this paper. In Sect. 4, I will first present the relevant definition of genes and how they can be classified. Then, I will argue that the gene can be considered a natural kind as it satisfies the criteria for natural kindhood. Section 5 concludes.
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Notes
- 1.
- 2.
This does not imply that a given gene can never be considered within actual scientific practice as a precise and contiguous stretch of nucleotide sequences, such as in prokaryotes. Nevertheless, a strict identity relation between genes and genomic stretches excludes many genetic phenomena (see Fogle 2010; Griffiths and Stotz 2013).
- 3.
- 4.
Havstad (2021) defines three classificatory practices concerning kinds: classificatory characterization or definition, individuation and organisation (2021). The first—which is the one we are concerned with—focuses on the definition of the kind. The second focuses on identifying which tokens belong to a given kind. The last focuses on organizing taxonomies.
- 5.
The ENCODE project is a project with the aim to identify all the “functional elements” in the human genome sequence. It represents an important project for the gene concept as it elucidated some complex phenomena that compromised the simple identification of the genes with contiguous stretches of DNA. Reference: https://www.encodeproject.org/about/2012-integrative-analysis
- 6.
I thank reviewer 1 for the helpful comments on this section.
- 7.
We can identify four main models that aim at identifying the precise material basis of genes. Model A presents the material basis of the gene as the transcribed region of the DNA plus all neighboring sequences which play a role in the process; Model B considers only the transcribed region, with introns and exons; Model C further restricts the basis and includes only the set of exons derived from a pre-mRNA; lastly, Model D limits the gene to only the coding exons of a primary transcript (Fogle 1990, El-Hani 2007, 3). Here, I leave open the question about the exact material component of the gene as it should be determined by scientific practice.
- 8.
As will be further clarified in Sect. 4.1, the functional component of the gene definition allows for both multiple realisation and multiple composition (in contrast with a materialist only view). A gene would be any entity that is composed of the relevant material aspect, nucleic acids—either DNA or RNA—and that has the relevant function. However, for individual genes the correspondence does not need to be 1 stretch: 1 function, as the function could be multiply realised by any stretch that realises it. For further references, see Bellazzi 2022.
- 9.
These sequences can either be of DNA or RNA according to the genes considered.
- 10.
For an overview on the debate on universals, consider Bird and Tobin 2022.
- 11.
This question can also be referred to as the “taxonomy question”. However, I prefer to avoid this terminology as it seems to constrain natural kinds to biological taxonomies or to identify kinds with taxonomical classifications.
- 12.
See Magnus’ definition of deep realism (2018) or Khalidi’s definition of Realism (2013) for which one has to commit to the existence of some fundamental categories.
- 13.
A summary of the status of the species controversy can be found in Ereshefsky (2017).
- 14.
Khalidi’s account has also been applied to a variety of kinds from the life sciences, such as viruses, cancer cells, biological species and ADHD, making this approach even more suitable to consider the gene case (Khalidi 2013, 2021).The validity of Khalidi’s view of natural kinds is discussed also in Tahko (2022).
- 15.
This view is contrasted with a stronger form of Realism in which kinds correspond either to sui generis universals or to second-order universals.
- 16.
These are based on a re-elaboration of the simple theory of natural kinds proposed by Craver (2009) for which kinds refer to the causal structure of the world.
- 17.
It is important to notice that the natural kinds display a role in the causal network which can be seen when considering instances of the kinds due to the nature of the causal relation. I thank Jessica Wilson for suggesting this important clarification and reviewer 2 for insisting on this aspect.
- 18.
For the importance of functional similarity of products in gene classification, see Fogle 2010.
- 19.
Despite the importance of the functional aspects of the genes, genes are not mere functional kinds, because the material component they present as union of genomic sequences is also relevant in determining their identity.
- 20.
For the database on S. cerevisiae genome and the relevant articles, see www.yeastgenome.org
- 21.
For Gene Ontology, see www.geneontology.org
- 22.
In order to appreciate how the definition allows for multiple realisability and composition, it is important to consider that the gene type is the one that can be multiply composed, while each gene token is going to be composed by specific nucleic acid sequences. Accordingly, for the gene definition we just need to identify which specific token nucleic acids could compose it while maintaining that the relevant function is realised. For further analysis of the complexity of the relations between the properties of the gene, see Bellazzi 2022.
- 23.
The purpose of this section is not to show that “DCS2” is a gene, but rather that the properties that genes display (and are present in DCS2) respect the requirements for the naturalness of kinds. Moreover, the causal component required by the naturalness claim supports using an instance of the kind to explore whether it is natural. I thank reviewer 2 for insisting on this clarificatory point.
- 24.
Further reference can be found at yeastgenome.com.
- 25.
I thank both reviewer 1 and reviewer 2 for the suggestion to clarify the relation between the example of gene considered in the paper and the general kind “gene”. The definition of gene defended in the paper allows the generalisation from simple to more complex case studies, as the definition presented here is compatible with both multiple realisation and composition. Accordingly, we can generalise it to cases such as those involving alternative splicing because it is possible to identify the two core properties of the kind “gene” also in those cases (see Bellazzi 2022 for more discussion on this).
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Acknowledgements
I would like to thank Tuomas Tahko, Samir Okasha and Elle Chilton-Knight for reading and reviewing multiple versions of this paper. For the helpful and constructive comments that have substantially improved the paper, I would like to thank the anonymous reviewers. I am sincerely grateful to Maurizio Zuccotti and his team for the insightful discussions on the genetics case studies. Thanks also to the members of the ERC MetaScience Project – Toby Friend, Vanessa Seifert, Samuel Kimpton-Nye – and to Jessica Wilson, Giacomo Zanotti, Margarida Heremida and Luca Zanetti for the helpful discussion, advices and feedback. Lastly, I would like to thank deeply the editors and the organisers of the PBCS X workshop and the audiences where I have presented the main ideas of the paper.
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Bellazzi, F. (2023). The Gene as a Natural Kind. In: Viejo, J.M., Sanjuán, M. (eds) Life and Mind. Interdisciplinary Evolution Research, vol 8. Springer, Cham. https://doi.org/10.1007/978-3-031-30304-3_12
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