Answers-Language of Neo-Darwinism

The language of neo-darwinism

This page answers the profound, and fundamental, question whether the language of neo-darwinism has been responsible for, and itself expresses, many of the problems with the way in which 20th century biology has been interpreted.

The short answer is ‘yes’. The discourse of neo-darwinism and twentieth century biology in general is intricately linked to the specific philosophical and scientific viewpoints that they represent. It is necessary to deconstruct this discourse since the associated concepts are not required by the scientific discoveries themselves. In fact it can be shown that no biological experiment could possibly distinguish even between completely opposite metaphorical interpretations. The discourse therefore forms an interpretive veneer that can even hide those discoveries in a web of interpretation.

It is also quite difficult to unravel since it is the whole discourse of neo-darwinism that is the problem. Each metaphor reinforces the overall mind-set until it is almost impossible to stand outside it and to appreciate how beguiling it is. Since it has dominated biological science for over half a century, the metaphysical viewpoint represented by this discourse is now so ingrained in the scientific literature that most biological scientists themselves probably don’t recognise its metaphysical nature. Most would probably subscribe to the view that it is merely an accurate description of what experimental work has shown: the discourse in a nutshell is that genes code for proteins that form organisms via a genetic program inherited by subsequent generations and which defines and determines the organism. What is wrong with that? The answer is that almost everything is wrong with it and, sadly, it is not required by the experimental science itself.

The approach used here is, first, to analyse the main metaphors individually, and then to show how they reinforce each other. At the end, I will ask ‘what could be an alternative and better discourse?’

The main problem words are ‘gene’, ‘selfish’, ‘code’, ‘program’, ‘blueprint’, ‘book of life’. We also need to examine secondary concepts like ‘replicator’ and ‘vehicle’.

‘Gene’

Neo-darwinism is a gene-centred theory of evolution. Yet its central entity, the gene, is an unstable concept. Surprising as it may seem, there is no single agreed definition of ‘gene’. Even more seriously, the different definitions have incompatible consequences for the theory.

The word ‘gene’ itself was coined by Johannsen in 1909, but the concept already existed and was based on “the silent assumption [that] was made almost universally that there is a 1:1 relation between genetic factor (gene) and character” (Mayr 1982). Since then, the concept of a gene has changed fundamentally, and this is a major source of confusion when it comes to the question of causation. Its original biological meaning referred to the cause of an inheritable phenotype characteristic, such as /hair/skin colour, body shape and weight, number of legs/arms/wings, to which we could perhaps add more complex traits such as intelligence, personality and sexuality.

The molecular biological definition of a gene is very different. Following the discovery that DNA forms templates for proteins, the definition shifted to locatable regions of DNA sequences with identifiable beginnings and endings. Complexity was added through the discovery of regulatory elements, but the basic cause of phenotype characteristics was still the DNA sequence since that determined which protein was made, which in turn interacted with the rest of the organism to produce the phenotype.

But unless we subscribe to the view that the inheritance of all phenotype characteristics is attributable entirely to DNA sequences (which is just false: DNA never acts outside the context of a complete cell) then genes, as originally conceived, are not the same as the stretches of DNA. According to the original view, genes were necessarily the cause of inheritable phenotypes since that is how they were defined. The issue of causation is now open precisely because the modern definition identifies them instead with DNA sequences.

The original concept of a gene has therefore been taken over and significantly changed by molecular biology. This has undoubtedly led to a great clarification of molecular mechanisms, surely one of the greatest triumphs of twentieth-century biology, and widely acknowledged as such. But the more philosophical consequences of this change for higher level biology are profound and they are much less widely understood.

The difference between the original and the molecular biological definitions of ‘gene’ can be appreciated by noting that most changes in DNA do not necessarily cause a change in phenotype. Organisms are very good at buffering themselves against genomic change. Further analysis of the difference between the definitions can be found in the answer on Slippery Definitions, which also includes an important diagram of the differences.

Some biological scientists have even given up using the word ‘gene’, except in inverted commas. As Beurton et al. (2008) comment “it seems that a cell’s enzymes are capable of actively manipulating DNA to do this or that. A genome consists largely of semi stable genetic elements that may be rearranged or even moved around in the genome thus modifying the information content of DNA.”

The reason that the original and the molecular biological definitions have incompatible consequences is that only the molecular biological definition could be compatible with a strict separation between the ‘replicator’ and the ‘vehicle’. A definition in terms of inheritable phenotypic characteristics (i.e. the original definition) necessarily includes more than the DNA, so that the distinction between replicator and vehicle is blurred.

‘Selfish’

As the lectures show, no possible biological experiment could conceivably distinguish between the selfish gene ‘theory’ and its opposites, such as prisoner or co-operative genes. See the answer What is wrong with The Selfish Gene. This point was conceded long ago by Richard Dawkins at the beginning of his book The Extended Phenotype: ‘I doubt that there is any experiment that could prove my claim’ (Dawkins, 1982, p. 1).

‘Code’

After the discovery of the double helical structure of DNA, it was found that each sequence of three bases in DNA or RNA corresponds to a single amino acid in a protein sequence (see What does DNA do?). These triplet patterns are formed from any combination of the four bases U, C, A and G in RNA and T, C, A and G in DNA. They are often described as the genetic ‘code’, but it is important to understand that this usage of the word ‘code’ is metaphorical and can be confusing.

A real code is an intentional encryption used by humans to communicate. The genetic ‘code’ is not intentional in that sense. The word ‘code’ has unfortunately reinforced the idea that genes are active causes, in much the same way as a computer program directs the computer to obey instructions. The more neutral word ‘template’ would be better. It also expresses the fact that templates are used only when required (activated); they are not themselves active causes. The active causes lie within the cells themselves since they determine the expression patterns for the different cell types and states. These patterns are communicated to the DNA by transcription factors, by methylation patterns and by binding to the tails of histones, all of which influence the pattern and speed of transcription of different parts of the genome. If the word ‘instruction’ is useful at all, it is rather that the cell instructs the genome. As the Nobel-prize winner, Barbara McClintock said, the genome is an ‘organ of the cell’, not the other way round.

Getting the direction of causality in biology wrong is a fundamental mistake with far-reaching consequences. These consequences include the frequent characterisation of genes as the genes ‘for’ this and that.

‘Program’

The idea of ‘le programme génétique’ (‘genetic program’) was first introduced by the French Nobel laureates, Jacques Monod and Francois Jacob. They specifically referred to the way in which early electronic computers were programmed by paper or magnetic tapes: “The programme is a model borrowed from electronic computers. It equates the genetic material with the magnetic tape of a computer” (Jacob 1982).  The analogy was that DNA ‘programs’ the cell, tissues and organs of the body just as the code on a computer program determines what the computer does. In principle, the code is independent of the machine that implements it, in the sense that the code itself is sufficient to specify what will happen when the instructions are obeyed. If the program specifies a mathematical computation, for example, it would contain a complete specification of the computation to be performed in the form of complete algorithms. The problem is that no such algorithms can be found in the DNA sequences. What we find is better characterised as a mixture of templates and switches. The ‘templates’ are the triplet sequences that specify the amino acid sequences or the RNA sequences. The ‘switches’ are the locations on the DNA or histones where transcription factors, methylation processes and other controlling processes occur.

Since what we find in the genome sequences are templates and switches, where does the full algorithmic logic of a program lie? Where, for example, do we find the equivalent of ‘IF-THEN-ELSE’ type instructions? The answer is in the cell or organism as a whole, not just in the genome.

Take as an example circadian rhythm. The simplest version of this process depends on a gene that is used as a template for the production of a protein whose concentration then builds up in the cytoplasm. It diffuses through the nuclear membrane and, as the nuclear level increases, it inhibits the transcription process of its own gene. This is a negative feedback loop of the kind that can be represented as implementing a ‘program’ like IF LEVEL X EXCEEDS Y STOP PRODUCING X, BUT IF LEVEL X IS SMALLER THAN Y CONTINUE PRODUCING X. But it is important to note that the implementation of this ‘program’ to produce a 24 hour rhythm depends on rates of protein production by ribosomes, rate of change of concentrations within the cytoplasm, rate of transport across the nuclear membrane, and interaction with the gene transcription control site (the switch). All of this is necessary to produce a feedback circuit that depends on much more than the genome. It depends also on the intricate cellular, tissue and organ structures that are not specified by DNA sequences, which replicate themselves via self-templating, and which are also essential to inheritance across cell and organism generations.

This is true of all such ‘programs’. To call them ‘genetic programs’ is to fuel the misconception that all the logic lies in the one-dimensional DNA sequences. It doesn’t. It also lies in the three dimensional static and dynamic structures of the cells, tissues and organs.

The phrase ‘genetic program’ has therefore encouraged the idea that an organism is fully defined by its genome, whereas in fact it is also defined by its inheritance of cell structure as well as the genome. Moreover, this structure is specific to different species. Cross-species clones do not generally work, and when they do (very rarely) the outcome is determined both by the cytoplasmic structures as well as the DNA – see Immortal genes.

A debate on the motion “No privileged level of causation: An organism is not defined by its genome” was held in Leipzig in July 2012. See

http://www.virtual-liver.de/wordpress/en/2012/07/16/the-virtual-liver-network-keynote-debate/.

The protagonists were Sydney Brenner and Denis Noble. But the remarkable thing about this debate is that, on the central theme, they were both in agreement with the motion. There was no real debate!

‘Blueprint’

‘Blueprint’ is a variation on the idea of a program. Blueprints, for example as architectural designs for construction of buildings and other structures, existed before the modern idea of a computer program. The word suffers from a similar problem to the concept of a ‘program’, which is that it implies that all the information necessary for the construction of an organism lies in the DNA. This is clearly not true. The complete cell is also required, and its complex structures are inherited by self-templating. The ‘blueprint’, therefore, is the cell as a whole. But that destroys the whole idea of the genome being the full specification.

‘Book of Life’

The genome is often described as the ‘book of life’. This was one of the colourful metaphors used when projecting the idea of sequencing the complete human genome. It was a brilliant public relations move. Who could not be intrigued by reading the ‘book of life’ and unravelling its secrets? And who could resist the promise that, within about a decade, that book would reveal how to treat cancer, heart disease, nervous diseases, diabetes, with a new era of pharmaceutical targets. As we all know, it didn’t happen. Two editorials in 2010 (ten years after the first full draft of the human genome) spelt this out:

“Ten years ago, the first draft of the sequence of the human genome was heralded as the dawn of a new era of genetic medicine………. You might have noticed that it hasn’t [happened]. The medical impact of the human genome project (HGP) has so far been negligible.” (Editorial, Prospect, June 2010).

“The activity of genes is affected by many things not explicitly encoded in the genome, such as how the chromosomal material is packaged up and how it is labelled with chemical markers. Even for diseases like diabetes, which have a clear inherited component, the known genes involved seem to account for only a small proportion of the inheritance…… the failure to anticipate such complexity in the genome must be blamed partly on the cosy fallacies of genetic research. After Francis Crick and James Watson cracked the riddle of DNA’s molecular structure in 1953, geneticists could not resist assuming it was all over bar the shouting. They began to see DNA as the “book of life,” which could be read like an instruction manual. It now seems that the genome might be less like a list of parts and more like the weather system, full of complicated feedbacks and interdependencies.” (Editorial, Nature, 2010).

In response to these editorials I wrote (Noble 2012):

“In 2002 I wrote an article for the magazine of The Physiological Society, Physiology News, explaining why the genome is not the “Book of Life” (Noble, 2002). A reader was so enthused by it that he approached the Editor of Prospect to insist that it deserved a much wider readership and thought that Prospect was the ideal medium. It would have been, but the offer was turned down without question. Probably it didn’t fit the mind set of that time, full of confidence that molecular biology was going, finally, to deliver the goods through exploitation of the genome data.”

“What has changed in the subsequent 8 years, so that even a staff writer for Prospect now expresses the main message of the 2002 article? The answer is that 2010 is the ten year watermark after the sequencing of the genome, when we were promised by the leaders of the Human Genome Project that the benefits for health care would have arrived. Diabetes, hypertension and mental illness were amongst the targets. Science journalists are therefore becoming uneasy that they bought into a promise that has not and, I would argue, could not have been delivered. And they are not alone. The drug industry also bought in, literally so since start-up genomics companies were bought up for hundreds of millions of dollars. The sequencing of genomes has been of great value for basic science, particularly in studies on comparison of genomes for the purposes of evolutionary biology, but the interpretation of the genome data in terms of biological functions (phenotypes) has proved vastly more difficult than anticipated.”

‘The Book of Life’ represents the high watermark of the enthusiasm with which the discourse of neo-darwinism was developed. Its failure speaks volumes: the discourse was not only unnecessary, it was seriously misleading. Yes, there was a good scientific reason for sequencing whole genomes. The benefits to evolutionary biology in particular have been immense. But the discourse promising a peep into the ‘book of life’ and a cure for all diseases was a mistake.

The discourse as a whole

All parts of the discourse of neo-darwinism encourage the use and acceptance of the other parts. Once people have bought in to the idea that the DNA and RNA templates form a ‘code’, the idea of the ‘genetic program’ follows naturally. That leads on to statements like “they [genes] created us body and mind” (The Selfish Gene, 1976). In turn, that leads to the distinction between replicators and vehicles. The mistake lies in accepting the first step, the idea that there is a ‘code’.

The distinction between the replicator and the vehicle can be seen as the culmination of the neo-darwinist discourse. It follows on from accepting the ideas of a code and a program in the genome. If all the algorithms for the logic of life lie in the genome then the rest of the organism does seem to be a disposable vehicle. Only the genome needs to replicate, leaving any old vehicle to carry it.

The distinction however is a linguistic confusion and it is incorrect experimentally. It is a linguistic confusion since the word replicate means to reproduce. Cells also replicate in this sense. They also use templates to do so. The templates are the cell structures themselves. The process is therefore called self-templating and it is just as necessary and just as robust as genome replication. Indeed, faithful genome replication depends on the prior ability of the cell to replicate itself since it is the cell that contains the necessary structures and processes to enable errors in DNA replication to be corrected. See the answer Immortal genes?

The distinction is incorrect experimentally since cross-species cloning shows that cytoplasmic inheritance exists. Another way to make the same point is that the interpretation of the genome depends on the rest of the organism. To use the ‘program’ metaphor, the program is distributed between the genome and the cell.

Notice that the whole discourse is strongly anthropomorphic. This is strange, given that most subscribers to the discourse would wish to avoid anthropomorphising scientific discovery. As Dawkins wrote about the selfish gene metaphor: “I believe it is the literal truth.” When anthropomorphic language becomes confused with ‘literal truth’ we know we are in linguistic trouble.

An alternative discourse