Did Charles Darwin get it wrong?

The Darwin anniversary celebrations last year were the most lavish ever for a British scientist. Now, with the garlands and bunting stored away, comes the party pooper, in the form of Jerry Fodor and Massimo Piattelli-Palmarini's book What Darwin Got Wrong (Profile, £20). Richard Dawkins's friend, the US philosopher Daniel Dennett, once noted to him that if he ever fell on hard times he could make a million dollars in a week by proposing to author a book entitled "Confessions of an Ex-Darwinian". Hence the inflammatory and tendentious title of this book.

Perhaps there was a risk in making such a fuss of the great man that what is known about evolution now and what Darwin wrote 150 years ago should become confused in the popular mind. Darwin was writing speculatively, before there was any scientific knowledge of genetics or the chemistry of life.

We are living in the golden age of biology, with discoveries pouring from the genome projects and even the prospect of personal, consumer genomes available at a modest price within five to ten years. Science honours Darwin as a pioneer, at the very beginning of modern biology, not the man who brought the holy tablets and whose writ must run for evermore.

So why would Jerry Fodor (philosopher) and Massimo Piattelli-Palmarini (cognitive scientist) be so concerned to refute aspects of Darwin's theory? Their book makes it very clear that an academic turf war lies behind it all. The stimulus was the outrage Fodor and Piattelli-Palmarini felt for what they see as the misuse of Darwinism in the social sciences. Evolutionary psychology, in particular, gets their goat.

Evolutionary psychologists claim that the human mind was essentially formed by our life as hunter-gatherers in the Pleistocene ice age: we were adapted to that so aren't very well adapted to life in the shopping mall. These stories are fascinating, maybe true in some cases, but are untestable. The book includes a 15-page dossier of quotes from the culprits, the star turn being Steven Pinker.

Fodor and Piattelli-Palmarini think that the best way to clear these pesky theorists from the campuses is to attack the idea of adaptive evolution at its root. Their title suggests that it is Darwin himself they are gunning for but, in fact, their target is an updated Darwinism enshrined around 50 years ago as the Modern Synthesis or Neo-Darwinism.

Beginning with the rediscovery of Mendel's work in 1900, genetics had posed some problems for the theory of natural selection. The Modern Synthesis was an amalgam of natural selection and Mendelian genetics.

Its leading contributors were Theodosius Dobzhansky, Ernst Mayr, Julian Huxley, and JBS Haldane. The result was somewhat bland, usually summarised as: "Evolution is considered to have occurred if the frequencies of genes change in a population". It was abstract, statistical, and left out the living creatures themselves, their flesh and bones and chemistry.

Now that the facts about the living creature and its genes are pouring from biology's horn of plenty, scientists are divided on whether the new findings shake the old Modern Synthesis. Polling some biologists and science writers and scanning the literature reveals that about half believe that the new findings can be harmonised with the old.

Richard Dawkins says: "Population genetics' ideas of evolution always treated development as a black box that would one day have to be opened. It is a very good thing that the box is now finally being opened... but the Modern Synthesis still stands." Professor Steven Rose at the Open University disagrees: "If by the Modern Synthesis you mean the reduction of the definition of evolution to changes in gene frequency in a population, I would say no."

Dawkins also stresses that natural selection "is the principal driver (indeed, probably the only) driver of adaptive evolution." Adaptive evolution, for Dawkins, is the result of very many infinitesimally small random variations, but huge changes in the genome are common. The wheat in your bread underwent a six-fold genome copy before it became the crop we know. And natural selection mostly acts to eliminate harmful mutations; it does not seem to be the principle source of new body plans.

Taking account of all this, in a recent Darwin celebratory article, Eugene Koonin, researcher at the US National Institutes of Health, calls for a New Extended Synthesis, writing: "The edifice of the Modern Synthesis has crumbled, apparently beyond repair." Lynn Margulis, James Lovelock's collaborator on the Gaia Theory and "science's unruly earth mother" according to Science magazine, expressed this even more pungently almost 20 years ago. She called Neo-Darwinism "a minor 20th-century religious sect within the sprawling religious persuasion of Anglo-Saxon Biology... Neo-Darwinism is in a complete funk."

Margulis's credibility rests on her achievement (generously recognised by Richard Dawkins) in demonstrating that the single-celled ancestor of all multi-celled life on earth was the result of one bacterial cell swallowing another (the two lived happily together ever after). One small gulp for a bacterium; a giant gobble for the future of life on earth. And about as far from a minor mutation as you can get.

But the biologist and science writer Matt Ridley sees no problem in achieving a New Extended Synthesis: "It is not that it is 'needed'; it 'is happening'. Modern evolutionary developmental biology is replete with examples of discovering both developmental changes and the ways they are being selected, for example in Darwin's finches".

Fodor and Piattelli-Palmarini use a two-pronged attack to try to undermine Neo-Darwinism. First, they detail some of those modern examples. Secondly, they attack the logic of Neo-Darwinism. In their philosophical assault, Fodor and Piattelli-Palmarini pursue several lines, one of which boils down to the old conundrum: natural selection demonstrates the survival of the fittest. What are the fittest? Those that survive. Scientists know that this is a trivial linguistic trick but Fodor and Piattelli-Palmarini pursue this wrangling for 68 pages. At the nadir, Fodor facetiously proposes a research programme to enquire into how objects perfectly fit their hole in space.

What Darwin Got Wrong concludes that there can be no unifying theory of evolution. For Fodor and Piattelli-Palmarini, the story of evolution is an historical one, just like human history. Everything only happens once and can be interpreted after the event - but not predicted. But, unremarked by Fodor and Piattelli-Palmarini, it has been shown that some traits – wing patterns in fruit flies, body armour in sticklebacks – have been gained and lost several times in the course of evolution.

Fodor is a philosophical flâneur: he loves cheap jokes and affects a kind of provocative insouciance. His 2003 book on Hume states at the outset that he "could even write a book on Hume without actually knowing anything about him," and then claims to have done so. Philosophers and scientists could not be further apart. For geneticist and science writer Professor Steve Jones, "philosophy is to science what pornography is to sex."

No, the problems for evolutionary theory are not philosophical. The problem is that the source of novelty is so dammed elusive. Most genes don't change very much at all, even the body-plan genes seem to be very similar in the mouse and blue whale. Or, to compare even less similar creatures: a mouse gene essential for building the eye can be inserted into the fruit fly to produce a fly eye! This refutes a key prediction of Neo-Darwinism, Ernst's Mayr's statement that it would be futile to look for similar genes in different creatures. Neo-Darwinism predicted that random mutations would pile up until the genes of mice and men were as different as, say, the Finno-Ugric and the English languages.

The best bet at the moment seems to lie in the altered timing of processes involving cascades of many genes. And what alters the timing? Well, now we're at the frontline of research, and there are candidates but no certainties. One of the most dramatic possibilities is that elements of DNA have entered the germline from viruses. Putting this together with Margulis's ideas on the evolution of the ancestral single cell, we can see that viruses and bacteria are starting to loom very large in the picture of evolution.

This primacy-of-microbes idea has already entered fiction in one of David Eagleman's short stories from his cult collection Sum (2009). In "Microbe", God made the world in his own image and He is a microbe. All of the multicellular creatures who think themselves the lords of creation are invisible to him, their much vaunted actions as lost to record as a bacterium we might accidentally smear from a surface and carry across the world. The evolution of viruses and bacteria clearly evinces very different principles to the evolution of the multi-celled creatures that followed.

Unlike physics, biology is the science of exceptions. Fodor and Piattelli-Palmarini come to the same conclusion but mostly for the wrong reasons.

Given the provocative title, it's important to stress what Fodor and Piattelli-Palmarini's polemic is not. From the outset, they assert that they have no quarrel with the course of evolution and its timescale, only its mechanism. Furthermore, they affirm that they are "outright, card-carrying, signed-up, dyed-in-the-wool, no-holds-barred atheists." For that small relief, much thanks.

Peter Forbes's 'Dazzled and Deceived: mimicry and camouflage' is published by Yale University Press