Science

The Rev. Dr Stephen Ames completes the series on genes as the language of God:

Our theme is asking if genetics is the language of God. John Wilkins has discussed in what sense can we say that ‘genetics’ is a ‘language’. His main point is that it is an analogy but one that is not illuminating. It evokes the idea of intelligible patterns in the structure of genes and the way they interact with the organism and environment to eventually bring living things into existence. A drawback for John is that it gives too much away to proponents of Intelligent Design (ID). I am not a proponent of ID.

Recall how talk about this discussion of the idea of genes as the language of God came about. On 26 June 2000 at the White House Bill Clinton as the President of the United States pronounced the first survey of the human genome 90 per cent complete. ‘Today,’ said Clinton, ‘we are learning the language in which God created life.’ Standing beside him was Francis Collins the Director of the National Human Genome Research Institute in America and headed an international race against time and commercial interests to sequence the 3.1 billion letters of the human genome.

The question whether genetics is the language of God comes through the religious belief that God is the creator of the universe, who sustains the universe in existence. Evolutionary science provides our best scientific account of how live has evolved, which includes the many new forms of life that have thereby come into existence.

For those who believe the universe is created by God, this is the idea that God creates ex nihilo – not from any previously existing ‘stuff’ – and sustains it in existence. Evolution and particularly genetics is part of how life in all its forms has come into existence. From a theological standpoint this is part of how God has created the life producing universe in which we live. Hence Clinton’s words and Collin’s book The Language of God, A Scientist Presents Evidence For Belief, (New York, Free Press, 2006).

This already provokes many questions. For example, aren’t religion and science in fundamental conflict? See the trials of Galileo – “By stifling the truth that was there for all to see, the Church destroyed its credibility with science.” [David Griffith after playing the lead role in Brecht’s play Life of Galileo in 1994.] Secondly, why supposedly, would God use evolution to bring life into existence? Doesn’t the book of Genesis present God speaking ‘let there be light’ it is was so, and so on for the sun and moon and plants and animals. God speaks and it happens. Another question is, ‘if God created everything, what created God?’ I will say a little about those questions later. For the moment let’s keep with our theme.

Galileo has something relevant to say. In 1615 he was asked by the Grand Duchess Christina to explain how to reconcile his telescopic observations and Copernicus’ sun-centred view of the universe with the Bible’s teaching that the sun, moon moved around the earth. Galileo answered in terms of God being the author of ‘Two Books’: the book of Scripture written in human language, and the book of nature, which God created, written in the language of mathematics and geometry. Because God is the author of both Books they cannot be in fundamental contradiction, when both are read correctly. (Of course how to apply Galileo’s principle will take us into another set of questions.)

Following Galileo’s view, not just genetics but the whole universe (multiverse), with its many levels and forms of intelligibility, including mathematics, may also be thought of as the many ‘languages’ of God. Here ‘language’ is used to highlight an analogy between human language and other different forms of intelligibility needed to understand the natural universe.

A Christian theologian, Maximus the Confessor (b. 580CE), understood the universe to be created through the divine Logos (Word) and as a result all creatures are many different logoi (words). Maximus would probably enjoy an idea shared by Prof. Paul Davies’ and philosopher of science Susan Haack; that scientific theories are analogous to a vast crossword puzzle with the ‘words’ being different theories interlinking, and the ‘clues’ being the empirical data of sciences.

One of John’s concerns is that speaking about genetics as the ‘language of God’ gives aid to the proponents of ID as they attempt to argue to God from the search for intelligent causes operating in nature. I am not a proponent of ID because I think it is a version of the ‘god of the gaps’ argument. By contrast it is quite possible to talk about the ‘fine tuning’ of the physical constants and laws of physics for the production of carbon based life, without presupposing or entailing a ‘Fine Tuner’.

Galileo is not doing this. He starts from the view that natural universe is like a book written by God (who created the universe), who as its ‘author’ has written it in the language of mathematics. This is a theology of nature. It seeks to interpret nature and mathematics in the light of a prior belief in God. It is not a natural theology, which attempts to prove the existence of God from using ordinary human reasoning about ordinary processes including all the natural processes that the natural sciences describe. This is what the ID movement is attempting to do. I think there are better alternatives. In any case, it is quite different from Galileo.

The idea of the ‘language of God’ or the ‘word of God’ meaning the language or word spoken by God is found in different religious traditions. For example for Hinduism Sanscrit is the language of the divine realm. In Islam Arabic is the language God chose to communicate the words of the Qur’an to the Prophet. In Judaism G-D gives speaks to Moses from the Burning Bush giving the divine name. Christianity believes that God has spoken in many different ways but now has spoken to us through his Son.

I have left some questions to be answered now. Let’s start with a very common question: if God created everything what created God? This is asked by Prof Dawkins and by Peter Adam and by students I meet. The answer is that if God created everything then any supposed ‘contender’ for the job of creating God has already been created by God. The atheist physicist Lawrence Krauss made this point in his book A Universe from Nothing, Why There Is Something Rather Than Nothing, (New York, Free Press, 2012,p.173) made the point that if God is the cause of all causes, then you can’t ask what created God. People offer strong reasons for not accepting the idea of God – lack of evidence, the problem of natural evil, irrelevance, among others. But asking what created God is not a reason for rejecting the idea of God.

A second question: Isn’t there a ‘warfare’ or an inherent conflict between science and religion? This is known as the ‘conflict thesis’. It goes back to John W. Draper’s History of the Conflict of Science and Religion (1875) and Andrew D. White’s A History of Warfare of Science with Theology in Christendom (1896). Historians of science since the 1960s have forced a profound rethink of this ‘conflict thesis’. Historical scholarship shows that deep theological commitments and motives underpinned the work of figures like Kepler, Descartes, Newton, Boyle who were the leading lights of the rise of early modern Science in Europe (16th–17th Century).

This brings us back to the Galileo Affair. It is very complex event set in the context of the Protestant Reformation and the Counter Reformation by the Catholic Church. When the Affair is used to promote the ‘conflict thesis’ a key point is the claim that Galileo showed us the truth about the solar system but the Church stifled this truth and destroyed its credibility with science. Galileo made stunning telescopic observations which certainly contradicted the old earth centred model of the heavens, with the sun and moon and planets circling the earth. However this didn’t prove the sun centred view of Copernicus. This is because all of Galileo’s telescopic observations could be explained by the famous Danish astronomer Tycho Brahe (1546-1601). In his model the sun circled the earth while all the planets circled the sun. The Jesuit astronomers of the day reproduced all of Galileo’s observations but espoused Tycho’s model. Galileo also supported his view with an explanation of the tides, which predicted a 24 hour cycle, not the observed 12 hour cycle. Galileo was alerted to this discrepancy but thought it could be explained by the odd shapes and varying depths of the ocean floor. The Galileo Affair does not support the ‘conflict thesis’.

Another question was why would God create a universe for some purpose and then use evolution to bring life into existence? For a fuller answer see my paper ‘Why Would God Use Evolution?’ in, J. Arnould OP, ed., Darwin and Evolution Interfaith Perspectives, (Adelaide, ATF Press, 2010), 105–128. Here are the ‘bare bones’. For some readers it may be the first time you have encountered theological reasoning. Here I am starting with a traditional idea of God that God is all powerful, all knowing and all good, who freely creates the universe ex nihilo and sustains it in existence. (This will be a theology of nature not a natural theology.) I am working towards understanding what kind of universe we might expect such a God to create (should such a God exist), by reasoning largely from the idea of God.

I draw on the work of a theological ‘giant’ Thomas Aquinas from the 13th century (see his Summa Theologiae 1a,103.6; 1a, 105.5). Aquinas asked whether God would create a universe in which things had their own real powers or would God be the only power in the world? Would it be the fire that warmed you or God in the fire that warmed you? Aquinas’ view was that God is the primary cause, creating from nothing and (continually) sustaining in existence all the secondary causes we see operating in the world. For Aquinas, God is that than which there is none greater. Therefore we should prefer to say that God creates things, with real causal powers, rather than with no real powers. This is because it is a greater exercise of power, which creates things that are not only good in themselves but the cause of good in others.

For Aquinas, God creates things in such a way that things have the dignity of also being causes, rather than, so I would add, the indignity of also not being causes. In God’s creation there are no ‘wall flowers’ – everything has a part, everything is a ‘player’.

On similar reasoning I should say that God maximises these features of creation, rather than minimises them. I should therefore prefer to say that this God creates a life producing universe, which is better than only producing an inert universe, or a merely mechanically interactive universe. Therefore we should expect that things make other things and overall creation makes itself as much as possible as a life producing universe. Of course this is easily extended to a life producing universe that produces intelligent life. This understanding of God claims to express at least one thing that is of value to God as creator: creatures as co-creators and that God maximises the realisation of that value in a created universe.

Now let’s pause here and ask what this theoretical idea of the God created universe might look like in fact. Can theology take us that far? The answer is ‘no’. Here is why. On the idea of God we are working with, God freely creates the universe ex nihilo. Because it is freely created we cannot derive in detail what the creation will look like from the idea of God. We should expect it to be an intelligible universe and open to rational explanations because God is all knowing and all powerful. Because the universe is created ex nihilo it means there was no prior ‘stuff’ that God used, so we can’t figure out from the ‘stuff’ what the universe might look like since there was no ‘stuff’. How could we find out what this God created universe might look like in fact? We would have to go and look, use all our senses to gather data and use our reason to understand it in different ways.

If you think that our universe is created by such a God then this would be the way to find out what kind of universe it is. This could take at least three quite different forms. One is scientific, another is theological and the other poetic. For example Charles Darwin, naturalist extraordinaire, did go and look and after gathering lots of data and lots of hard thinking came up with the theory of evolution by natural selection about the evolution of life by natural selection. He showed we are living in life producing universe. Secondly, If we used the ideas drawn from Aquinas then we could say that God uses evolution because what is of value to God is creatures as co-creators, all the way from the simplest to the most complex creatures. Perhaps one or more of the exoplanets astronomers are finding will have the ‘signature’ of life. Thirdly, an example of a poet extraordinaire is Gerard Manley Hopkins (see for example his poems, God’s Grandeur, and, The Windhover).

Finally, we come back to the question about what the Bible says on God creating the world. Everyone quickly turns to Genesis chapters 1 and 2. (A helpful book is S. C. Barton, and D. Wilkinson, eds., Reading Genesis After Darwin, Oxford, Oxford University Press, 2009). The above discussion seems very different. There are three brief points to make.

Firstly, it is a question of how to understand the text. St. Augustine (354–450CE) in his On The Literal Meaning of Genesis interpreted Genesis as saying the earth received the causal power to bring forth plants and trees, not that plants and trees were specially created. The above account expands this idea.

Secondly, there are many other accounts of creation in the Bible. For example John’s Gospel (1:1–4) speaks about the divine Word through whom all things were created (this was mentioned above in the work of Maximus the Confessor.) The above discussion fits well within that account of creation.

Thirdly, Galileo’s ‘Two Books’ principle says that if we are confident of our scientific knowledge of some part of God’s creation we ought to allow that knowledge to inform biblical passages that are speaking about the same part of creation. Galileo’s principle calls all who accept it to seek the theological message that God give us through the biblical passage.

 

 

Genes are more commonly regarded as information than as a language, and in fact the informational metaphor underpins the language metaphor. In this post I will consider how genes came to be called information (that is, how the Dawkins view of genes as computer messages came to the fore), and what it can and cannot mean.

In The Blind Watchmaker (1986), Richard Dawkins compared DNA to computer programs (instructions for building organisms):

It is raining DNA outside. … [downy seeds from willow trees] The cotton wool is mostly made of cellulose, and it dwarfs the tiny capsule that contains the DNA, the genetic information. The DNA content must be a small proportion of the total, so why did I say that it was raining DNA rather than cellulose? The answer is that it is the DNA that matters… whose coded characters spell out specific instructions for building willow trees… It is raining instructions out there, it’s raining programs; it’s raining tree-growing, fluff spreading, algorithms. That is not a metaphor, it is the plain truth. It couldn’t be any plainer if it were raining floppy disks. [Chapter 5, p 111]

Floppy disks have been superseded by USB thumb drives, but the point is clear enough – DNA is information, not just a molecule. It’s not a metaphor.

However, many have tried to make this “plain truth” work, and failed. There are many reasons for this, but first let us look into the history of the idea that DNA is information.

As I noted in the first post of this series, the notion that inheritance is about information long precedes the discovery of DNA, let alone its structure and role in inheritance. But the idea that DNA is information goes back to the two discoverers of how DNA was structured, Francis Crick and James Watson. At first, back in 1952, the structure did not give the way DNA made proteins; it took some time to figure this out. In 1958, Crick published what came to be known as the “Central Dogma” of genetics:

Central Dogma Crick 1970 combined

[From Sandwalk’s excellent essay on the Central Dogma.] On the left Crick diagrammed all the possible ways sequence information could be passed on between DNA, RNA and proteins. DNA could copy itself, pass sequential information to RNA molecules or to proteins or all three; and the same was true for the other two types of molecules. In fact, Crick said, it only is passed on according to the right hand graph. Later, we discovered that some RNA sequences can be reverse transcribed into DNA, especially through the medium of what are now called retroviruses. Crick gave the following definition of the Central Dogma:

… once (sequential) information has passed into protein it cannot get out again.

It is very important to note that the “information” here is the linear sequence of the base pairs matching up to a linear sequence, first of RNA (tRNA), and then later of the proteins (through intermediary molecules of mRNA). Nothing beyond this is implied by the Central Dogma, and we can usefully call this “Crick information”, as Griffiths and Stotz do in their book. The passing of sequential or Crick information is thus a kind of templating from a sequence in the DNA to the [often edited] sequence in the RNA to the finished protein. It is not as “instructions” that Crick posited information. You lose nothing if you drop the word “information” in favour of “structure”, and I will argue there are good reasons for this.

When Crick was writing, information was all the rage. In 1948, the so-called Communications Theory of Information, made mathematical by Claude Shannon at IBM, was published, and many scientists thought this was a fruitful way to approach scientific problems. Inheritance seemed like a transmission of information, and so it was natural that Shannon’s scheme would be brought to bear. However, it was ultimately rather fruitless.

Another information idea, coincidentally published the next year by Norbert Wiener, is called Cybernetics. Here the information is about control of one thing by another, through signals. Cybernetic ideas about genes have been more fruitful, but in the end they turn out to be just analogies that are not terribly deep (in my opinion).

The code aspect of genes: what it is and isn’t

Code language is widely used when talking about how DNA causes proteins. Terms like editing, reading, transcribing, and expressing are all used in the technical literature. DNA is “expressed”, and “edited”; a gene is regarded as an “open reading frame”; DNA is “copied” or “replicated”. Such terms point up the leading property of DNA – it is both long lasting and its structure can be duplicated, not unlike a document. For this reason, some scientists refer to genetics as a “codical domain”.

But what is happening physically is that DNA molecules are split into two strands by helicases, and then either transcribed by polymerases, and RNA made from it, or that new DNA is made. The DNA and the RNA are just as physical as the proteins they produce. As Weiner noted in his book:

Information is information, not matter or energy. No materialism which does not admit this can survive at the present day. [p132]

Following Weiner here, DNA is a physical structure, and it is not “information” in the sense used by communications or computation theories. That sort of information is an abstract entity, a property of mathematics, not physics. Genes are not that kind of information. A mathematical model of genetics, especially population genetics which describes how genes change in populations, contains information about genes, but that’s a different kind of information too; it isn’t what those who say genes are information mean by it.

So the Crick information model – that genes are templates for the structure of RNA and through them of proteins – seems to be the only meaningful sense in which one can say genes are information.

Other types of information in genes

There are some other senses in which genes are supposed to have an informational aspect. They are the program sense, and the game theory sense.

Program/recipe: genetic control versus genetic involvement

The program or receipt metaphor has been used by many evolutionary biologists, including Ernst Mayr and Richard Dawkins. It is used in Dawkins’ quote above: genes are instructions. There can be no doubt that genes are involved, either directly or indirectly (say, by building molecules that have functions) in the development of living things. They are “first among equals”. But how can they be “instructions”?

Recall the mnemonic

G & E -> O

from the last post. In order for genes to be instructions, there would need to be a “computer” to “run” the instructions (or in the case of a recipe metaphor, a cook and kitchen to make the recipe). What could do this for genes? It would need to be not only the cellular machinery that expresses genes – ribosomes and so forth – but also the organism itself, which turns on and turns off genes, and the environment that provides the source material. So the mnemonic would have to become

G & O[<tE -> O[t]

or, the genes G, together with the state of the organism before now O[<t], together with the environment E, gives the organism now O[t]. While this is true enough, the metaphor no longer seems to hold up. Why not just say that genes and organisms and the environment gives the later organism? There is no temptation to talk about some abstract program, and ascribe to genomes powers they do not have.

Incidentally, while the Human Genome Project delivered the entire genome in 2000 (it’s been revised a bit since), we have yet to discover what sorts of effects most of the expressed genes actually have, and it will probably be another century before we finish that. And of course most of the genome is unused junk.

Game theory: genes as bookkeepers

There is one final metaphor that is possibly more than a metaphor that we should look at. It is yet another view that is found in Richard Dawkins’ work: genes are strategies in a game. Here the metaphor is backed up by extensive mathematics: a field known as “game theory”, developed to deal with Cold War threats and counter threats, turns out to be very useful to model how genetics changes in certain conditions (when the fitness of genes and their propensity to work together to against each other within a single population are known).

This was the basic underlying metaphor of The Selfish Gene: genes have interests, and behave (evolutionarily) like self-interested players of a game known as The Prisoner’s Dilemma. The details are not important here.

Game theory treats genes as “players” or agents. But genes have no strategies themselves; it is just that the mathematics of games can transfer to genetics. This often happens, that mathematics developed for one field get used in other fields. It doesn’t mean that the properties of that first field (where game players are rational and selfish) apply to the new field, only that the maths applies.

In fact, the game theory view has been called by Stephen J. Gould a “bookkeeping” view of evolution; you track the “wins” and “losses” of a given gene in a mathematical scorecard. In other words, selfish genes exist only in how you record the outcomes of the evolving population. It’s useful, but it doesn’t mean genes actually are strategies, nor that they have them.

Next I will discuss why genes are not a language.

Further information:

Molecular Biology (Stanford Encyclopedia of Philosophy)

Biological information (Stanford Encyclopedia of Philosophy)

A video on epigenetics:

There are a number of other metaphors used by the media and explainers when communicating about genes. Some of them have an acceptable interpretation, but may mislead; others only mislead. Before we consider the genes-as-information issue (next post), let’s look at some of these:

Genes as the essence of an organism

A while back I was contacted by a philosopher who specialises in metaphysics, which is the study of what ideas are necessary to make sense of the world. He asked me (as a philosopher of biology) whether, if a coat was made of my own DNA, I would become “bigger” than without that coat on. The idea that he seemed to have was that in modern biology, DNA was my “essence”, what made me who and what I am.

This is a fundamental mistake. DNA does contribute to some of my traits, and it may even contribute to how I develop my personality over time. But it is not my “essence”. The reason I quote mark “essence” is that it is a vague and largely meaningless term. In philosophy it means the properties that make some individual thing what it is: humans, for example, were held to be rational animals, which meant that they had an essential nature that was rational, along with the essential natures of animals (sensitivity to the environment, ability to move), along with the essential natures of all living things (ability to eat and grow, ability to reproduce).

But while DNA is implicated in how all organisms (of which we know) develop and mature, it is not their “essence”. DNA in a test tube will slowly denature (lose its structure and breakdown into its components, called monomers). DNA in an organism that lacks the right conditions (egg, maternal environment, atmosphere) will not enable that organism to continue. A newborn animal placed in a hard vacuum will do little apart from drying out. In short, the relationship between genes and the organism and its environment is summed up with the standard mnemonic:

G & E ? O

or, Genes plus Environment gives you the Organism.

What counts as the environment, however, is a complicated issue. Not only does the environment (for genes) include the ecosystem, as well as the maternal resources (egg yolk, placenta), it also includes the cell mechanisms of the fertilised egg as well; this means the mitochondria, the nuclear membrane, transport mechanisms like the actin cytoskeleton, and a host of other thing, not least ribosomes and cell membrane (or wall in plants). As well as this, it also includes the non-genetic structures that are needed to “express” genes – the polymerases and spliceosomes that are used in the process of making proteins. Finally, the environment for genes includes the machinery that replicates the genes themselves when cells divide – helicases and proteins that initiate replication.

Without all this machinery, genes would do nothing much. So, they are not, on their own, the “essence” of the organism.

Genes “for” a trait

The media often uses the phrase “the gene for” this or that trait, such as language, homosexuality, religion, rape, and so on. This is always misleading, and should never be said, by teachers or the media.

For a start, no gene does anything in isolation from other genes, so finding out that a gene like FOXP2 is implicated in the development and evolution of language is like finding out that 3/4 inch bolts are used in bridge building. They are crucial to the integrity of the bridge, but the bridge is a lot more than those bolts.

Second almost every gene has some other role in the body. Non-biologists will often talk about “the” function of a gene or other body part, but in fact parts of organisms, including genes, will always have many different roles in the normal function of an organism, and claims that “the” function is X are usually based upon what happens when a gene goes wrong. Delete or impair that gene, and language won’t develop. These are called “knockout studies”, because geneticists often remove the gene (knock them out of the organism being studied) to see what effects this has on the physiology of the organism.

Rather than saying FOXP2 is a “gene for language” it would be better to say it is a gene “involved in the development and evolution of language”. It takes longer to say, but it is at least accurate.

Genetic reductionism: it’s all about the genes

In 1976, Richard Dawkins published a book entitled The Selfish Gene. In this book, Dawkins argued that modern evolutionary theory considered that it was the gene, not the organism, that evolved. Critics pointed out some difficulties with this view, and today the consensus is that evolution occurs at all levels from genes to colonies or populations. But one outcome of Dawkins’ book was the introduction of what has come to be called genetic reductionism. Most people think this is a bad idea.

To reduce one level of talk about the world to another used to be considered progress in science. For example, we reduced talk about chemistry to physics when we developed quantum mechanics. Now we know that the reason why molecules for in reactions is that the molecules are made of smaller particles which attract each other and have certain energies that are reduced when a reaction takes place (roughly).

Dawkins seemed to be reducing talk about organisms, and their behaviour, to talk about the interests of genes (which were like selfish economists, trying to maximise their return on investment). However, many people objected to this, because it suggested that only genes were the beneficiaries in evolution, and that all that happened in evolution was adaptation by natural selection.

A philosopher once noted that in philosophy, “there’s the bit where you say it, and the bit where you take it back”. Dawkins expanded his view in subsequent books until he did not differ much from other evolutionary thinkers, but he remained convinced that natural selection was the main engine of evolution. Most evolutionary biologists will argue that much that happens to genes in evolution is anything but adaptive, and that much of what is important in evolution is anything but genetic. This leads us to the next metaphor:

Genetic determinism: biology is destiny

One thing genetic reductionism is thought to imply is genetic determinism. Sometimes summarised as “biology is destiny”, this is the idea that everything you do is directly determined by your genes. Dawkins wrote something like this in the Selfish Gene:

Was there to be any end to the gradual improvement in the techniques and artifices used by the replicators to ensure their own continuation in the world? There would be plenty of time for improvement. What weird engines of self-preservation would the millennia bring forth? Four thousand million years on, what was to be the fate of the ancient replicators?

They did not die out, for they are past masters of the survival arts. But do not look for them floating loose in the sea; they gave up that cavalier freedom long ago. Now they swarm in huge colonies, safe inside gigantic lumbering robots, sealed off from the outside world, communicating with it by tortuous indirect routes, manipulating it by remote control.

They are in you and in me; they created us, body and mind; and their preservation is the ultimate rationale for our existence. They have come a long way, those replicators. Now they go by the name of genes, and we are their survival machines.

The implication is that “we” (as bodies) are just what genes “program” us to do and be, and the genes determine our fate.

This idea is much older than genetics. Plato [in The Republic] thought we were all born with gold, iron or bronze souls, and our fates were determined at birth. Likewise, in the middle ages people thought that one’s “blood” determined one’s social rank (as an aristocrat or a peasant).

In the late nineteenth century this became the foundation for “eugenics”, which sought to breed humans the way a farmer breeds cattle or horses. This was then turned to justifying the extermination of millions by the Nazis, who followed the United States and Canada and Australia in its eugenics program.

Genes don’t “hardwire” people to behave in particular ways. Studies of psychopaths show that many of them live perfectly normal and law-abiding lives, because the negative side of their genetic dispositions was never triggered as they grew (see above, genes-as-essence). Just as people with a metabolic genetic disease can develop normally by avoiding the triggers (phenylketonuria can be prevented by avoiding phenylalanines in their food), pathological behavioural traits don’t always cause particular behaviours. But they can bias how a person responds to the environment as they develop.

In short, biology is not destiny, but it is an influence. Genetic conditions do not force behaviours, but they make some behaviours more likely to develop,

Common genes: what we share with chimps and mice (and bananas)

You will often see “similar DNA” numbers like this: Humans share 99.5% of their genes with chimps, 90% with cats, 82% with dogs, 80% with cows, 75% with mice, 60% with flies, and so on, and supposedly 50% with bananas.

While these percentages scale roughly with the amount of time since we shared a last common ancestor with them, the numbers are often wildly varying. Why?

It all hinges upon the notion of “similar”. There are three main kinds and several minor kinds of ways in which the DNA of one species can be similar to another’s.

One is “base pair similarity”. If each species has a gene X with around 10000 base pairs (“letters” A, T, C and G), and 400 differ, then they are (in that gene alone) 96% similar. However, gene X may be “the same” in its place in the genome and functions despite these differences, and so it can be 100% similar between the two species. Then you have the overall structure of the genome, which is arranged in chromosomes.

If each species has the same chromosome structure, then it can be 100% similar even if many genes are different between the species. But differences can arise when multiple copies of genes are made between species. If Gene X has three copies in species A but only one copy in species B, that can change the “similarity” measure.

Finally, chromosomes can be duplicated even in one species (this is called polyploidy): a species can have 1, 2, 3 or more copies of each chromosome. Obviously whether these count as differences or not depends on whether you are counting the genes, the base pairs, or the chromosome numbers.

So take care. A banana can have a whole host of genes that humans and other eukaryotes (roughly, plants, animals and fungi) have because they are basic genes for organisms to survive. But it will be very unlikely to have the same genes at a finer level of detail (base pair sequence, position, chromosomal arrangement).

Genome mapping sequence

A common way to talk about genes is as things that have meaning, either as a kind of language (or code, or recipe), or as information about the bodies of the organisms they generate. This has led some, for example, Francis Collins (2010), to speak of genes as the language of the living universe, in much the same way that some physicists talk about the mathematical laws of physics as the language of the physical universe. In this series, I will discuss this way of talking about genes, and consider (1) if it is true or helpful, and (2) what problems arise from thinking about genes as language. Towards the end, Stephen Ames will discuss what this means for thinking about God and genes, responding to Collins’ 2006 book The language of God. As I am not a believer, I cannot say anything helpful to believers about this topic.

Let us look at some examples of genes-as-language talk.

In 1966, George Beadle entitled a book on genetics – then still new to most readers – The Language of Life. It was a metaphor of course, and he did not employ it much in the textbook, but the idea that genes are something language like is very old. The historian of science, Donald Forsdyke, has traced similar ideas back to Darwin’s contemporary, Samuel Butler.

Because we are most familiar with language, describing and explaining things in terms of language and language-like features has real power to convey ideas about science. However, since these things science describes are not actually language, there is a risk that it will cause confusion, and it does.

Collins’ use of this terminology is wildly overblown. For example, he writes, in a chapter he titled “Deciphering God’s Instruction Book”, “I found myself standing next to the President of the United States in the East Room of the White House on June 26, 2000, announcing that the first draft of the human instruction book had been determined. The language of God was revealed.” [2006, 122] Later, he writes “For me as a believer, the uncovering of the human genome held additional significance. This book was written in the DNA language by which God spoke life into being.” [2006, 123]

If these are metaphors, they might be harmless. A metaphor is a figure of speech, in which what we know of one thing can be carried over to another (the Greek word metaphoros today means a shopping trolley!), and the use of metaphors in learning and teaching is unavoidable. But a metaphor is at best the first step up to knowledge. Once you take that step, then you have to understand the new item in its own terms. Here are some other language and informational metaphors regarding genes:

  • Genes as a code. Since the structure of DNA was discovered in 1952, the idea that the DNA is a code for proteins was taken up enthusiastically. By the mid-1960s, biochemists had worked out which three-“letter” combinations “stood for” which amino acids. But, once “the code” was worked out, it turned out in short order there were up to 17 alternate variations. There is nothing about the triplet letter codes that must create the amino acids that they do; in fact what causes the triplet to create an amino acid chain is more to do with the ribosome; all the RNA that the DNA makes does is to trigger the ribosome to add a particular amino acid to the peptide, or chain.
  • Genes as a program or recipe. The computer metaphor and the cook metaphor have been used at different times. The computer metaphor is based on the idea that DNA is an algorithm that is “executed” by the cellular machinery to build a cell or organism. The cook using a recipe metaphor is slightly older, but often these two are used interchangeably. Both involve the idea there is a sequence of steps that is specified by genes to create (“cook” or “output”) an organism.
  • Genes as information. Genes are the patterns of DNA that are “transmitted” from one generation to the next.
  • Genes as a language. Genes “describe” organisms in some fashion.

A metaphor can systematically mislead us. It can mislead members of the general population who think that the Higgs boson really is the “god particle” or that the Big Bang really was an explosion. This might be unavoidable if we don’t teach the facts early enough; and it may be harmless. But consider some other metaphors: we “stimulate” the immune system with this or that drug or vitamin. This dysmetaphor, so to speak, causes people to spend literally billions of dollars on useless vitamin supplements or to avoid vaccination so their kids are “stimulated” by actually contracting measles, which can kill.

These dysmetaphors can have more subtle effects. Some, such as George Lakoff, argue that the metaphors by which we frame issues subtly changes how we process the issues. While it may not be that framing effects really sharply change our thinking, nevertheless, even scientists can be misled by metaphors. I would say that the idea genes are linguistic things – symbols – misleads a great many scientists in a great many ways. It moves our attention from the physical properties of genes and their organisms to abstract properties. We will return to this. And of course there is the misleading such metaphors cause when philosophers take them up.

This will be a series of posts for a secondary school seminar run at St Paul’s Cathedral in Melbourne during the ‘National Science Week’ This is the fifth such event at St.Paul’s.  It is led the Rev. Dr Stephen Ames and Associate Prof. Lachlan Thompson from RMIT University, Ms Anne Brumfitt, Science Educator, and Emeritus Prof. John Pilbrow from Monash University.  Stephen, with Dr. Kristian Camilleri, runs the second-year subject, ‘God and the Natural Sciences’ as part of the History and Philosophy of Science Programme at the University of Melbourne.

Stephen has doctorates in physics and in philosophy of science. He and I have spent many happy hours arguing about everything over lunch, and almost never agreeing with each other. He is Brodie Innes to my Darwin: “Brodie Innes and I have been fast friends for thirty years, and we never thoroughly agreed on any subject but once, and then we stared hard at each other, and thought one of us must be very ill.”

Stephen is presenting this seminar for years 11 and 12 students of the International Baccalaureate and in the VCE, and has asked me to prepare material and be part of the Q/A Panel on the day. Asking whether DNA is the language of God is founded upon a book by Francis Collins in 2006, The Language of God. I leave it to others to argue if that book succeeds in making a case for God. I am merely concerned in this series to look at the metaphor of DNA or genes as a language. I will rely heavily upon Paul Griffiths’ and Karola Stotz’ recent book Genetics and Philosophy: An Introduction.

This series will be revised and added to as we come across more information and links. Readers are encouraged to add in the comments and raise questions the students might like to ask themselves.

Contents

1: Genes as Language

2: Other popular gene myths and metaphors

3: Why genes aren’t information

4: Why genes aren’t a language

5: God and genes

6: Summary and conclusions

I have been mulling over the philosophical works that were of most influence upon me when I was developing into the warped and twisted thing I am now. Add your own in the comments.:

Herbert Marcuse, One Dimensional Man. This book got me interested in philosophy and social issues. I was 16 when I read it.

David Oldroyd, Arch of Knowledge. This book gave me a historical approach to the philosophy of science that has never left me. Although badly typeset, it is rich with information and context of scientific philosophy. I wish it were reissued, properly set.

Antony Flew, An Introduction to Western Philosophy: Ideas and Argument from Plato to Popper. This book grounded me in the traditions of western philosophy in a way nothing else did. Flew attends to the core arguments in their own words. This is a book to buy and reread, and I have gone through several copies giving them away to students and interested lay folk.

Stephen Toulmin, Human Understanding. This was the first evolutionary epistemology I ever read, and to my mind Toulmin got most things pretty well right. It took me thirty years to find a copy of my own.

David Hull, Science as a Process. I did my masters on this book, and David became a mentor. I still think his conceptual inclusive fitness account of science is correct, although I now do not think he entirely got the history of systematics all that right.

In addition to these are the usual canon fodder: Wittgenstein’s Tractatus Logicophilosophicus, Philosophical Investigations, and On Certainty; Locke’s Essay; Hume (anything of Hume, really, but especially the Treatise); and a few deviants, like F. H. Bradley’s Ethical Studies, and Zen and the Art of Motorcycle Maintenance (I read it as a lad of 14. I now disagree with almost everything it in apart from the joy of riding motorcycles).

What philosophical books warped you?

NotDead

Coming soon as a movie to a philosophy department near you.

Lately there has been a slew of physicists making claims like this:

Traditionally, these are questions for philosophy, but philosophy is dead. Philosophy has not kept up with modern developments in science, particularly physics. [Hawking and Mlodinow, The Grand Design 2011, p5]

My concern here is that the philosophers believe they are actually asking deep questions about nature. And to the scientist it’s, what are you doing? Why are you concerning yourself with the meaning of meaning? [Neil deGrasse Tyson]

… physics has encroached on philosophy. Philosophy used to be a field that had content, but then “natural philosophy” became physics, and physics has only continued to make inroads. Every time there’s a leap in physics, it encroaches on these areas that philosophers have carefully sequestered away to themselves, and so then you have this natural resentment on the part of philosophers. This sense that somehow physicists, because they can’t spell the word “philosophy,” aren’t justified in talking about these things, or haven’t thought deeply about them. … Philosophy is a field that, unfortunately, reminds me of that old Woody Allen joke, “those that can’t do, teach, and those that can’t teach, teach gym.” And the worst part of philosophy is the philosophy of science; the only people, as far as I can tell, that read work by philosophers of science are other philosophers of science. It has no impact on physics what so ever, and I doubt that other philosophers read it because it’s fairly technical. And so it’s really hard to understand what justifies it. And so I’d say that this tension occurs because people in philosophy feel threatened, and they have every right to feel threatened, because science progresses and philosophy doesn’t. [Lawrence Krauss]

Physicists do of course carry around with them a working philosophy. For most of us, it is a rough-and-ready realism, a belief in the objective reality of the ingredients of our scientific theories. But this has been learned through the experience of scientific research and rarely from the teachings of philosophers. This is not to deny all value to philosophy, much of which has nothing to do with science. I do not even mean to deny all value to the philosophy of science, which at its best seems to me a pleasing gloss on the history and discoveries of science. But we should not expect it to provide today’s scientists with any useful guidance about how to go about their work or about what they are likely to find. [Steve Weinberg, Dreams of a Final Theory, p167]

My son is taking a course in philosophy, and last night we were looking at something by Spinoza and there was the most childish reasoning! There were all these attributes, and Substances, and all this meaningless chewing around, and we started to laugh. Now how could we do that? Here’s this great Dutch philosopher, and we’re laughing at him. It’s because there’s no excuse for it! In the same period there was Newton, there was Harvey studying the circulation of the blood, there were people with methods of analysis by which progress was being made! You can take every one of Spinoza’s propositions, and take the contrary propositions, and look at the world and you can’t tell which is right.” [Richard P. Feynman, The Pleasure of Finding Things Out, p195]

Philosophy of science is about as useful to scientists as ornithology is to birds. [Ascribed to Feynman, but probably from Weinberg]

What is all this? Physicists used to not only value philosophy but do it. Einstein is a case in point; his contributions to his Schillp volume in Library of Living Philosophers are straight-out philosophical discussions of his theories and their implication for epistemology. Heisenberg is another example. Schrödinger another. Sometime after the second world war, however, physicists shifted from philosophical reflections about physics to cant against philosophy.

We might see this as a shift in education. Physicists after the nuclear and quantum age had to specialise much earlier and do more math than before. The liberal education of older physicists was trimmed down so that philosophy had almost no place in their training.

Or we might see it as a case of the industrialisation of physics. As “big science” took root, physics became more technological and high cost, and the practical exigencies of running accelerators and colliders became important. Industrial activities are rarely reflective.

Or we might see it as the hegemony of American pragmatism, eschewing theoretical problems in favour of just getting the job done.

But I think that the main reason is what we might think of as disciplinary over-reach. The deeper physics gets to fundamental realities, the less inclined physicists are to think that anything is beyond their reach. Philosophical problems abound in physics, of course. Krauss’ claim that “something comes from nothing” turns out to be a standard reductionist account: so-called particles are nothing but quantum fields and energy. The causes of quantum fields are not addressed, so something still has to be (philosophically) accounted for. Likewise the often made claim that philosophy makes no progress is simply the result of not thinking that progress is anything but physics. Debates over metaphysics, epistemology and aesthetics have definitely made progress. What the physicists want, however, are fixed and final answers. And the irony here is that they don’t seem to get there either. While we are sure enough about some (not all) of the properties of fundamental particles and fields, there are an indefinitely large number of possible theories about them (10500, at last count, and rising). What was that about progress, again?

Disciplines in academe tend to compete for a decreasing amount of funding and resources, both in terms of money and students, and physics is very big business. The notion that people might do work that is relevant to what they do who are not physicists is seriously objectionable to some physicists. An old joke (due to Asimov, I think) is that while physicists need instruments, mathematicians only need pencils, paper and erasers, and the philosophers don’t even need erasers. But this is a real caricature of philosophy. Three days ago, I attended a talk by a philosopher who started out by saying that he had been wrong on a philosophical claim and was now recanting, and this is not uncommon. Philosophy’s standards of error, however, are conceptual, not empirical (although even philosophers make empirical claims from time to time), and the criteria for error correction have to do with such things as conceptual coherence, consistency with premises (which might in fact be empirical or scientific), and the plausibility of the conclusion.

As to the quite silly claim by Hawking and Mlodinow that philosophy – especially of science and most especially of physics – hasn’t kept up with recent developments, take a browse through journals like Philosophy of Science, The British Journal for the Philosophy of Science, Erkenntnis or Studies in History and Philosophy of Science and tell me that philosophy is not keeping up (and, what is more, relating it to history of these disciplines, something the physicists do not do very well themselves often). Yes, there is also a lot of philosophy in these journals – they are after all philosophical journals – but often the physics being discussed is very up to date, much more so than the physicists’ grasp of philosophy.

That being said, there are two reasons why physicists might dislike philosophy.

One is that for a very long time, up until the late 1960s, philosophers of science attempted not only to analyse the ways science came to know the world, and to discuss the implications of science, but to establish scientific method. Although some of these philosophers were themselves very au fait with modern science, mostly physics, they were rarely active physicists, and some of their strictures, in particular those of Karl Popper, were faintly absurd. Popper denied that science could use induction, for example, and that discovery was a matter of chance or taste or inspiration. This of course is quite contrary to the experience of many scientists who do their discovery the old fashioned way, by gathering data and generalising from that.

When some philosophers started to say things like “Science is as valid as creationism” (as Feyerabend did), this understandably got up scientists’ noses, although this particular comment occurred in a philosophical debate about authority. But in the 1970s, the so-called postmodernists became prominent, and eventually predominant, and some postmodernists took Kant too far and asserted that we create our own worlds.Scientists, who deal with a recalcitrant world (as Huxley said, nature whispers ‘yes’ but shouts ‘No!’), found this ridiculous.

But it isn’t even the postmodern challenge that soured philosophy for scientists. It is, instead, the worst cases of that kind of philosophy. The antiscience movement took root and began to attack the very idea of science for a variety of good and bad reasons. Some, such as Sokal and Bricmont, attacked it as “Fashionable Nonsense”. Of course, every discipline has good and bad examples, and one can get a totally skewed view of philosophy if you rely upon popularisations or self-appointed media stars. Let me tell you, philosophy looks very different within the discipline than it does in the media.

It seems to me that it is time to stop these silly pissing contests. Philosophy is philosophy and physics is physics, and each can equitably accommodate the other with a bit of good will and charity.