Not so long ago I quarrelled with a friend as he lay dying in hospital with leukaemia. He had read an article about new medical research, how the harvesting of cells from early human embryos, which are thereby destroyed, could result in a cure for his disease.

"I wouldn't want to benefit from a cure," he said, "that involves sacrificing another human life."

I hesitated to agree and he grew furious with me.

Scientists, religious believers, ethicists, politicians, governments, are gripped by the worldwide quarrel over human stem-cell research that involves the destruction of the human embryo. Stem cells are those so-called 'mother cells? that can, in theory, be turned into any tissue type, promising cures for serious illnesses like Alzheimer's, cancer and heart disease.

This is a story about new science and new ways of understanding how and when we become human individuals in the womb. Can new thinking about human developmental biology shatter old prejudices to bring religion and science closer together and resolve the most intransigent ethical divide in recent history?

The nub of the current conflict is a battle between "cells" and 'souls", with no prospect for a common language. 'The newly fertilized human egg, a tiny cell one two-hundredth of an inch in diameter, is not a human being. It's a set of instructions set adrift into the cavity of the womb," declares the biologist E O Wilson, hailed as "Darwin's natural heir", and a guru on what biology tells us about human nature. His opinion belongs in a different universe from that of many religious believers: for example, the billion-strong Catholic Church, which maintains that the newly fertilised human egg is a "human individual, body and soul" possessing the "dignity of the person, who is not just something, but someone".

To bypass the moral dilemma, researchers have been striving to develop stem cells that do not depend on the destruction of human embryos. Last month, scientists in the US announced they had at last obtained stem cells by turning back the biological clocks of skin cells in a mouse. This has caused tumult in America, exacerbating the clash between those who think an embryo is a mere bunch of cells, ripe for scientific exploitation, and those, like George Bush, who believe it is a human soul and therefore off limits. The ethics of human embryonic research are set to be the most incendiary issue in the US election.

In Britain, the government recommended the creation of animal-human hybrid embryos to bypass experiments on human embryos. In the view of many ethicists, this has merely replaced one dilemma with another: the prospect of embryo 'monsters". The Bush administration has outlawed hybrid embryos, but believes that the mouse discovery should result in an immediate ban on further embryo exploitation. Researchers in developmental biology insist, however, that human-embryo experiments will remain essential for years to come, in order to study how natural stem cells divide and specialise in human beings from conception. There are many unknowns about stem cells, they warn, not least the possibility of their turning cancerous. In any case, repeating the mouse experiment with human cells could take decades, according to many scientists in the field, and new stem-cell therapies, in the view of clinicians, cannot wait.

Should we be concerned at the continued destruction of human embryos when it may bring unprecedented benefits to future patients? And can the impasse be resolved by fresh thinking?

The brain scientist and Nobel prize winner Gerald Edelman has developed a theory he calls "neural Darwinism?, which is nothing less than a biological explanation as to how you become a uniquely individual brain and mind: what many people have traditionally called a 'soul". Some of his peers think it a work of genius, with the potential to generate new thinking in the human-embryo debate. Others have strong reservations.

Edelman has attempted to encapsulate his life's work in a new book entitled Second Nature: Brain Science and Human Knowledge. He is to be found at the Neurosciences Institute in southern California.

"G-O-D," he tells me, spelling out the letters, "stands in my vocabulary for Generator Of Diversity. Diversity is what drives evolution; and it's what makes each of our brains, literally, physically, significantly, different, even between identical twins." The beginning of human individuality, he asserts, is not marked by a biological threshold: it is an unceasing "process?, a "history", a "journey", whereby huge populations of cells travel and compete in the task of forming your brain, which is the physical basis of your mind, who you are. 'there is no gene that tells cell A to go precisely to point Y in the development of the brain," he explains. While the process is mapped out and constrained by our genes, it involves a dimension of randomness, including the impact on a particular foetus within a particular mother.

Edelman's fascination with the brain began 40 years ago. He was originally a successful teenage violinist in New York ("I gave up when I realised I was past my peak at 16"). Then he became a medical doctor, before turning to immunology research in New York, which culminated in the discovery of a formula that explains how the immune system copes with invasive germs. It was an equation that filled one side of a sheet of A4.

Francis Crick (co-discoverer of the structure of DNA) pledged to eat the paper on which it was written should it be proved correct. But Edelman was right. The formula earned him the Nobel prize for physiology or medicine in 1972. At the award ceremony he is said to have thrust the formula into Crick's hand, growling: "Mayonnaise on me, Francis!" Crick unsportingly demurred.

Edelman's insight about the immune system became the basis of an extensive theory about how the human brain develops and works. It had long been thought that antigens (invading germs) "instructed"? antibodies (the immune system's frontline defence) to adopt appropriate molecular structures to respond to viruses and infections. But it was discovered in the late 1960s that the immune system is a "library" of existing antibodies supplied by the organism's environment and evolution, from which a match for the invasive germ is "looked up"? or 'selected', prompting the immune response. Edelman's formula explained how the selection process works.

He now turned to the mysteries of the human brain. He wanted to know whether the brain also develops and works by a similar selection process. 'the brain," he says, "is in no sense like any kind of instruction machine, like a computer. Each individual's brain is more like a unique rainforest, teeming with growth, decay, competition, diversity, and selection."

Development of the embryo is critical in his theory, suggesting new perspectives on the status of human life in the womb and the ethics of intervention. It was thought until well into the 19th century that a minuscule man, a "homunculus?, was folded up inside a human sperm waiting to attach itself to the mother's womb. We now know that 200m to 300m sperm, containing a set of the father's genes in each, are normally discharged in a single ejaculation.

Instead of the successful sperm penetrating the egg, new perspectives describe it as being engulfed, selected, by one of the surviving 6m eggs the mother possessed at her birth. Despite E O Wilson's minimalist description of a human egg (he describes it as no more than a "corpuscle"), an egg is large: 250 times larger than a red blood cell and weighing a hundredfold more. It has the appearance of a living planet whose landscape is being approached by vast hordes of explorers: the searching sperm. After a sperm is taken into the egg, chemical signals go to work to prevent the approach of further ambitious sperm. Describing the development of the individual brain, Edelman emphasises its sheer numerosity: "The human brain contains more than 100 billion neurons, or nerve cells, and a trillion supporting brain cells that form the special scaffolding and pathways of the neurons as they travel prodigious distances for their size."

Each neuron is like an individual creature in its own right, working according to communicating connective impulses employing both electrical charges and chemical messengers. The body of a single neuron (of which there are at least 50 kinds) looks like an exotic tropical tree with myriad fronds. It measures up to 250 microns (250 thousandths of a millimetre) in diameter. The tip of its axon, a main communicating extension, like the tendril of a vine, grows great distances before settling at its optimum destination. Some axons are a metre in length, which would be the equivalent of a single strand of a vine creeper growing through London for seven miles from a precise spot at Waterloo station, say, through streets, parks and buildings, to arrive at a precise spot in Mill Hill.

Sprouting from each neuron are branches of bushy 'dendrites?, which make contact with immediate, or remote, neighbouring neurons. Magnified by an electron microscope, they look like luxuriant, gently swaying kelp. The bafflingly complex combinations of connections produced by the dendrites of the 100 billion neurons in one person's brain are said to exceed the number of particles in the universe.

During the development of the embryo, a huge excess of neurons is generated - twice as many as necessary - to cope with the selection processes, involving massive wastage, as the brain strengthens certain connections between populations of neurons at the expense of others. In order to supply adequate cells for selection, for the benign wastage, the embryo generates cascades of neurons at a rate of 50,000 every second throughout development in the uterus. Twenty per cent of an individual's energy is dedicated to maintaining a brain that is only 2% of the average bodily weight - about 3lb. More than half of an individual adult's genome (the full complement of human genes) will be dedicated to the continuing process of regulating the brain after birth. If an individual's entire genetic code within all the cells of a single human body were to be stretched out in a single line, it would reach to the moon and back 100 times.

Can the awesome facts of individual human development challenge religious notions about the soul? Even among Christian theologians, the idea of instant divine "ensoulment" at conception, and indeed the idea that a person is a spiritual soul dwelling within a physical body (known as body-soul dualism), has undergone drastic revision. Many scholars argue that body-soul dualism has no basis in early Christianity and Judaism, which maintained only the vaguest notion of 'soul', as simply "life". Body-soul dualism, they maintain, is a relatively modern view of human beings, deriving from the influence of the philosopher René Descartes in the 17th century. In the absence of "body-soul? talk, new perspectives, such as Edelman's neural Darwinism, become significant.

At fertilisation, the zygote (from the Greek zugos, meaning "yoked"), has a complete set of genes, half of them from the father and half from the mother. In the first 24 hours after fertilisation, the cell divides into two 'daughter' cells. After another 18-24 hours it becomes four cells. Cell division continues in this exponential way for about a fortnight, forming a mulberry-like ball until a groove known as the "primitive streak" forms on the surface of the embryo. When the groove is fully complete, a thickened node develops at one end, containing a sort of chemical production unit, which triggers chemical signals for the next stage of development.

Three layers of different kinds of tissue now emerge in the embryo, like three living geological strata. One produces cells that make skin, hair, nails, nerves and the brain; this layer is known as the ectoderm (or outer skin). The next, the mesoderm (middle skin), produces muscles, heart, blood vessels, lungs, stomach and bones. And a third, the endoderm (inner skin), includes all the cell systems that line our organs and vessels. These layers now create themselves into a cylindrical structure, replicating the evolutionary transition that took place as invertebrates became vertebrates 600m years ago. Then a streak of tissue appears, running longitudinally down the cylinder. Known as the notochord, it releases complex chemicals prompting cell proliferation in the ectoderm sheet. As the embryo begins to lengthen, a crease known as the "neural groove? appears, which eventually becomes another tube.

An extraordinary development now takes place on the walls of this tube. What was a single-cell layer of primitive cells becomes a highly fertile field for the growth of cells that will build the central nervous system, brain and spinal cord. The process of cell production, mitosis (meaning division), involves a fascinating pattern of behaviour. Each cell first gets plumped up with sustaining energy molecules before entering a multiplication zone, a kind of nursery where cells are dividing rapidly. Some of the cells will become neurons, while others are destined to become glial cells (brain cells that will provide scaffolding and pathways in the brain). Now begins "cell migration". Cells move forward in large numbers from the multiplication zone. Some, as if acting altruistically, offer themselves as a 'rope ladder' along which the primitive nerve cells climb, adopting co-operative interactions whereby the cells know when and where to get off.

The foundation work on brain-cell migration in the primate embryo was originally performed by the Yugoslav neuroscientist Pasko Rakic of Yale University. In the 1970s, Rakic injected 200 rhesus monkeys with radioactive dye. The experiment, which would be controversial today, was set up so that only replicating cells took up the radioactive marker, hence he was able to trace the lineage of the brain cells as they migrated at different stages of embryonic development. After the monkeys' deaths, he and his team sliced the entire brain of each one to create 7,000 sections tracing neural-cell migration.

The most dramatic of the migratory voyages, and the longest and most complex, occurs with the formation of the cereral hemispheres - the two sides of the brain that will become the cortex, where high-level intelligence, like perception and cognition, are generated. The cerebral cortex of a human being is made up of six types of cell layers, each with its own distinct pattern of organisation and connections. The migrating cells initially form the deepest or sixth layer. Then each successive migration wave ascends further away from the field of original production, progressively forming more superficial layers (fifth, fourth, third, second and first) beyond the layer that was initially laid down. Thus each group of migrating cells must pass through the layers already laid down by the earlier arrivals, thereby following an inside-out sequence of development. One sees the guards doing this kind of fancy movement in Trooping the Colour. The later-arriving cells appear to migrate out along the same rope ladders used by the earlier migrants. Reminiscent of troops scaling complicated cliffs at the D-Day landings, it is crucial that the earlier populations alight from the rope ladders before the next wave of migrants attempts to come up and through.

It is still a mystery how the cells co-operate with each other on the rope ladders. As Professor Arnold Scheibel of the University of California, Los Angeles, explains, "It should be clear that unless they do release their hold, the next wave of cells coming up the ladder may not be able to get by on their way to a more distant destination. When this happens, the ensuing traffic pile-up produces developmental anomalies which can lead to abnormal neuronal connections and disturbed behaviours such as schizophrenia, temporal-lobe epilepsy and perhaps some forms of dyslexia."

When the migrant neurons have reached their habitat, they begin to grow their dendrite branches from many points along their bodies. This gives each neuron a larger surface area for communication with other neurons at points known as synapses. Professor Geoffrey Raisman of University College London discovered as a researcher in Oxford 40 years ago what he terms "plasticity" of the dendrites. He showed that when the connections to a dendrite from one set of nerve fibres is lost, an adjacent group of nerve fibres grows in to take its place.

For Edelman, the principle of selection in embryonic development "not only guarantees a common pattern in a species, but also results in individual diversity at the level of the finest neural networks". And, as Scheibel puts it, "The remarkable combination of gene-controlled factors, some of them conserved for over a billion years, together with an enormous range of idiosyncratic, non-genetic factors, both internal and external, help account for the uniqueness of each individual."

Even within the womb, the environment is significant for development. For example, researchers have discovered that visual impulses from the darkness of the womb on the growing optic nerve create signals that affect the optic nerve's subtle developmental journey to the brain. Meanwhile the placenta, measuring 11 square metres of exchange surface between mother and foetus at its fullest development, also gives rise to selection. A recent study in the magazine Nature argues that 'the fetus, although entirely dependent on its mother's nutrients, is not just a passive recipient, but influences its own development and growth? indeed it subverts many of the mother's physiological activities to its own end, to ensure adequate mobilization of nutrients and oxygen health and nutrition of the mother". The competition between foetus and mother at certain points arises from gene expressions that at times pitch the interest of the foetus against that of the parent: the interest of the foetus to become "a large fit baby versus the [mother's] desire to withhold resources for future offspring".

Research has also confirmed that the mother's environment (including recreation, such as listening to music), state of mind, and contact with potentially toxic substances such as tobacco and alcohol, have consequences for the embryo. Data gathered by Professor Vivette Glover at Imperial College London suggests that women who suffer stress during pregnancy affect the unborn child from as early as 17 weeks. Measurements of raised levels of stress hormones in the mother's blood have revealed corresponding raised levels in the amniotic fluid around the baby. Glover has also shown a link between high levels of stress in pregnancy and a lower IQ in the child.

What difference does it make for human individuality to be seen as a continuing process rather than the result of a particular threshold or event in development? Edelman believes that if the assumptions of neural Darwinism are correct, "We cannot think of a clear starting point of human individuality after conception". He stresses, moreover, that individuality is a continuing process throughout development in the womb and throughout a person's life: "Every act of perception is to some degree an act of new creation, and every act of memory is to some degree an act of imagination."

His overview is not applauded by all his peers. Many, such as the philosopher Dan Dennett and the distinguished husband-and-wife "neurophilosophy" team Professors Patricia and Paul Churchland, prefer the computer model for the mind, rather than Edelman's rainforest image. Meanwhile, Britain's eminent expert on the embryo, Professor Lewis Wolpert, disagrees with Edelman on the non-genetic random process involved in the formation of the unique brain. "In my view," he says, "the genes are supremely important, and any non-genetic activity or variation from genetic instructions is mere noise."

"No," responds Edelman. 'this is not noise. Cell migration and cell death in development are stochastic, or statistical - they have unpredictable consequences at the level of individual cells. These statistical processes oblige individual brains, unlike computers, to be individual."

As the work of cognitive neuroscience goes forward, the mind-brain picture of a vast aggregate of living and dying interactive events in a jungle is becoming clearer. And the implications for ethics, and the notion of what it means to be a human, are becoming increasingly irresistible. For one noted Cambridge ethicist and lawyer, Peter Glazebrook, "It is hard to see a fixed point at which you can say now the organism is not a person, and now it is.

The more we see individual life as a process the more the ethical problem is about caution, and about slippery moral slopes as you enter grey areas, for example the early stages of life after conception." For another philosopher, one specialising in religion, Dr Michael McGhee of Liverpool University,

"It seems that process is crucial, but so is the status of the embryo within the mother. Once an embryo has been extracted and put inside a Petri dish, it is not the same thing at all." In other words, the partnership between mother and embryo is what gives the embryo its human sustenance, potential for becoming a person, and therefore humanity. Hence there is an argument, in his view, for using spare embryos from IVF treatment for medical research.

The debate continues; but the notion of personhood occurring with an instantaneous, divine infusion of a spiritual substance seems increasingly just as implausible, in the light of new development biology, as its creationist parallel: the idea that God created the world in a series of six instants spread over six days.

Can the discovery of individuality as an embodied and continuing endowment of nature bring the antagonists in the debate closer together? A significant new point of agreement should be to focus more on caution and respect, and less on dogma and prejudice. Unease over human embryonic research is not restricted to notions of soul creation. The lessons of history, shared by both religious believers and scientists, are also important guides to ethical behaviour. Germany and Japan, for example, are wary of biotech research that evokes national memories of past abuses of human life. Research aimed at the future good of patients, moreover, while being a crucial aspect of weighing ethical consequences, often obscures other motives - not least the commercial prospects, worth billions of pounds, in intellectual-property rights. For this reason, the ethical debate should not be monopolised by a single medical-scientific interest group, nor impelled exclusively by governmental and commercial anxieties about falling behind in the biotech-industry race.

The remarkable process of human individuation should serve to prompt new thinking about human-embryo research, based on the ascertainable wonders of biology, its unknowns and its continuing processes, rather than hard-and-fast convictions about instantaneous spiritual ensoulment, or arguments based on future therapies and commercial profits.

In a world of endangered and ever-diminishing life forms, scientists and religious believers should work to find common ground. Neither side in the debate can afford to claim a monopoly of truth, or exclude itself from the discussion. 'think," says Edelman, "about the idea that each individual's soul is truly embodied, rather than a spirit; precious because it is unique in its physicality, and consciousness; unpredictable in its creativity, and mortal." In other words, each of us comes this way only once, and each of us is uniquely precious by nature from start to finish. Such thoughts are not a prelude to an erosion of ethics and of choices, but a deepening and maturing of respect for human life.