Abstract
This chapter focuses on the interactions between developmental, evolutionary, and genetic considerations in thinking about the structure and content of the genetic material and how it is regulated, with additional attention to the role of genetics in biomedical research. We suggest an approach to teaching non-professionals about genetics by paying attention to these issues and how they have been transformed by molecular tools and doctrines. Our main aim is to debunk the intuitive and widespread notion of “genes for”. The perspective proposed in this chapter should help students engage with the issues raised by contemporary biomedicine and biotechnology. We suggest that in many contexts it is wise to replace the concept of the gene with the concept of the genetic material as a vehicle for integrating developmental, evolutionary, and genetic considerations and for understanding the importance of genetics in biomedicine and biotechnology. In doing so, questions about genes turn into questions about the genetic material, which then can become a tool for integrating knowledge of other biological sciences. This policy should enter into early teaching about genetics in high schools and colleges. In the process, one will be able to develop helpful arguments against overly-narrow versions of genetic determinism and for the importance of a broad understanding of genes and inheritance.
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- 1.
Etymologically, the term ‘gene’ originated in the (Hippocratic) idea of Pangenesis, advanced by Darwin (1868). Darwin thought that gemmules from all parts of the body are transmitted to the reproductive organs and, from there, to the next generation. Hugo de Vries suggested that pangenesis did not involve transportation of gemmules between cells; rather all specification of information was intracellular (de Vries 1910/1889). He called the hereditary elements ‘pangens’, occasionally written ‘pangenes’ in English. It is from this that the term ‘Gene’ was suggested by Wilhelm Johannsen.: ‘it appears simplest to isolate the last syllable, gene, which alone is of interest to us […] The word gene is completely free from any hypotheses’. (Keller 2000, p. 2, quoting from Johannsen 1909).
- 2.
Split genes are DNA sequences which consist of two kinds of sections: (a) those called exons, which are transcribed to corresponding RNA sections that are in turn translated into protein and (b) those called introns which are transcribed to RNA sections that are then excised and not translated; promoters are specific DNA sequences to which RNA polymerase binds; enhancers are specific DNA sequences to which proteins bind which facilitate the binding of RNA polymerase to the promoter (enhancers increase the transcription of genes – other DNA sequences have the opposite effect and are called silencers).
- 3.
We can generally distinguish between protein encoding genes, i.e. genes which are implicated in the synthesis of a particular protein molecule which is directly related to some trait or phenotype, and regulatory genes which are implicated in the synthesis of a particular RNA or protein molecule which in turn affects the expression of other genes.
- 4.
Working the other way round, i.e. from phenotype to gene or genetic material is described as forward genetics. In this case, one attempts to relate an observed phenotype to a DNA sequence. In reverse genetics, DNA sequences are usually altered in order to see which phenotypes are affected and in what way.
- 5.
Frameshift refers to the fact that different proteins can be produced by different readouts of the same DNA sequence. The reading frames are shifted by one or two nucleotides and thus yield entirely different amino acid sequences over the length of the genetic material in which their readouts overlap.
- 6.
Functional domains are segments of a protein (often encoded in single exons) that play a particular well-defined role in different contexts, e.g., attaching the protein to a membrane or facilitating the interaction of the protein with a specific signaling molecule. The fact that many proteins include exons encoding distinct functional domains and that those domains are separated by introns facilitates the evolutionary process by allowing the modular swapping, addition, or subtraction of pieces performing particular functions or subfunctions.
- 7.
Some sections of this chapter draw in part on chapters 7 and 9 of Burian (2005).
- 8.
In sexual reproduction, recombination (exchange of segments of some specific length at matching loci by means of a mechanism called ‘crossing over’) occurs between homologous chromosomes which pair during meiosis, yielding chromosomes that have partially maternal and partially paternal DNA.
- 9.
Carlson (1966, chap. 8) discusses the conceptual importance of Sturtevant’s analysis which provided the key step in recognizing that mutation often involves alteration rather than loss of genes.
- 10.
It is not possible to review the major advancements of that period here but the interested reader may refer to Carlson (1966).
- 11.
Not all parts of the genome turn over at a uniform rate, either within an organism or between organisms. For this reason, the calibration of molecular clocks is tricky and imperfect, but with care they have proved to be very powerful analytical tools.
- 12.
There are other changes within the boundaries of genes that may count as mutations in medical genetics, namely changes in regulatory segments of the gene that alter whether, when, where, or with what intensity the gene is expressed, or, in some cases, which exons encoded by the gene are transcribed and translated.
- 13.
- 14.
The papers by Falk, Fogle, Gifford, Gilbert, Holmes, Rheinberger, and Schwartz in Beurton et al. (2000) are particularly relevant to this point.
- 15.
Johannsen’s attempt at an atheoretical definition (Johannsen 1909) illustrates the point precisely. In Carlson’s translation (Carlson 1966, pp. 20–22): “The word ‘gene’ is completely free from any hypotheses; it expresses only the evident fact that, in any case, many characteristics of the organism are specified in the gametes by means of special conditions, foundations, and determiners which are present in unique, separate, and thereby independent ways – in short, precisely what we wish to call genes.” Genes are thus the differences, whatever they may be, between gametes that cause organisms to have the potential for revealing patent, independently-heritable, traits. Darden (1991) amplifies this point usefully in firmly separating Mendelian genetics as developed after the ‘rediscovery’ of 1900 from the chromosomal theory developed by the Morgan group and others.
- 16.
It is important to note that as we develop an account of the relevant causal chains, we may come to adjust what we count as a trait or, at least, what we count as a trait caused in a particular, stably inherited, manner. Think, for instance, of the multiplication of distinct disease entities, e.g., some of the cancers formerly believed to be a single disease, as we have learned to distinguish different underlying ways in which, e.g., the regulatory apparatus of certain types of cells can be disrupted so as to yield phenotypically similar outcomes. It is also important to recognize that the schematic definition may require specification in a great variety of ways. Thus the specification of ‘modifier genes’ (i.e., genes that have the function of altering the expression or function of other genes) and ‘regulatory genes’ may be relative to a specific gene or control pathway carried by some, but not all, conspecifics affecting their manifestation of the relevant traits affected by the modified gene. Again, transmission genetics requires the specification of a chromosomal location for the gene over and above the rest of its Mendelian characterization.
- 17.
This claim is, of course, contentious, but we believe it is correct. Consider the sorts of substantially false conceptual commitments that have commonly been made: genes are discrete particles, genes are composed of proteins, they are located only on chromosomes, they are linearly contiguous, they are non-overlapping, etc. Note that our claim that such commitments of detail have been built into gene concepts and are substantially false, does not imply that genetics is based on fundamental mistakes.
- 18.
Chapters 11 and 12 in Burian (2005) contain illustrations that will help the reader unfamiliar with the technical terminology to understand Singer and Berg’s text.
- 19.
- 20.
This is also the reason for which the amino acid sequence cannot be determined (or determined up to permutations) by an examination of the structure of DNA or mRNA molecules alone. In different cellular contexts (nucleus vs. mitochondria, some species of organisms vs. others), there are sometimes some regular differences in the transfer RNAs. Thus, in a few cases, the same codon in different contexts codes for a different amino acid or for a stop signal instead of an amino acid.
- 21.
A brief technical description of such a case is given by Singer and Berg (1991, pp. 705–706) for introns in the mitochondria of yeast.
- 22.
Alternative splicing, i.e. the production of different mature mRNAs from the same primary RNA transcript through differential excision of introns, is just one of many relevant post-transcriptional phenomena that are relevant here. Gilbert (2000) and Singer and Berg (1991, pp. 578) provide helpful accounts of alternative splicing and other technicalities discussed below. This phenomenon again demonstrates the impossibility of employing the intrinsic features of the DNA or RNA alone to determine which stretches of a DNA or RNA molecule produce “biologically active RNA.” For further explanation of many of the issues discussed below, see Burian 2005 chap. 12.
- 23.
The abbreviation stands for “Open reading frame,” which is the name for the nucleotide sequence that signals (in many but not all contexts) a place at which to initiate the readout of DNA.
- 24.
Chapter 5 of (Gilbert 2000), which covers differential gene expression, includes useful reviews of differential RNA processing (pp. 130–133) and of (contextually variable) translational and post-translational controls of the end products of the expression of nucleotides sequences (pp. 134–136).
- 25.
- 26.
It should be noted that (to the best of current knowledge) sequences of nucleotides in plasmids, viruses, mitochondria, and plastids do not replicate or reproduce outside of the laboratory except in cellular contexts. Thus, for practical purposes, the only contexts in which these entities have functional genes are when they are in some sort of cellular context.
- 27.
This is Crick’s version of the ‘Central Dogma of Genetics’. Watson’s, version was different: he interpreted the Central Dogma as claiming that information flows from DNA to RNA to protein, and not backward. Watson’s formulation was especially influential thanks to the importance of his textbook The Molecular Biology of the Gene (Watson 1965), but it was mistaken and caused a lot of the resistance to reverse transcription (see Strasser 2006; Morange 2008; Olby 1972, 1975). Unfortunately, although in practice geneticists often use the term information in accordance with Crick’s account, they often present Watson’s account of the Central Dogma when they discuss it, a situation that has caused much misunderstanding, even by geneticists, of their discourse about genetic information. The confusion has been exacerbated by confusion between claims about sequence information with claims about information, in some more general sense, e.g., as it is used in cybernetics or information theory.
- 28.
A recent study (Djebali et al. 2012) found that a shocking 85 % of 492 protein-encoding transcripts for human chromosomes 21 and 22 were chimeric in the sense that they contained transcripts from more than one gene, using the standard boundary definitions for genes. However, as the authors warn, the technical tools involved may yield a significant number of false positives and the proportion of these transcripts that are translated and actually yield proteins is not yet known. These authors, like some others, suggest that the appropriate functional units that should be investigated are transcripts rather than genes, a stance that would be justified if, as they argue is likely, a substantial proportion of the chimeric transcripts they examined are functional.
- 29.
Scientists should, and must, have a role in communicating contemporary knowledge about genetics to the public (see Reydon et al. 2012 for a relevant proposal, which also includes some of the arguments made here).
- 30.
In an important footnote, Peter Godfrey-Smith sketches a calculation that shows that after 40 cell divisions any two cells of an adult human would, on average, differ by about 144 point mutations. Most of these mutations would be in non-coding regions and have no phenotypic effects. Nonetheless, it is important to recognize that the casual assumption that most human cells within a human body are genetically identical is simply false (Godfrey-Smith 2009, fn. 9, pp. 82–83). Additionally, within a human body there are about ten times more bacterial and archaeal cells than human cells, some of which are required for proper development (Gilbert and Epel 2009), further undermining simplistic accounts of the genetic uniformity of the cells within our bodies that are essential for our normal functioning.
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Burian, R.M., Kampourakis, K. (2013). Against “Genes For”: Could an Inclusive Concept of Genetic Material Effectively Replace Gene Concepts?. In: Kampourakis, K. (eds) The Philosophy of Biology. History, Philosophy and Theory of the Life Sciences, vol 1. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6537-5_26
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