Before the quiet of the night gives way to the murmur of morning, while the bedroom is still murky and the alarm clock has yet to cleave a new day, a silent wake-up call ripples through your body. As the signal spreads, you slowly begin to warm up. Your brain twitches with renewed electrical activity and your heart stirs from its night-time idling to an expectant thud. You are still asleep, but your body is gearing up for the start of the day.

The switch from sleep to waking is just one of the tightly choreographed changes that happen in our bodies in any 24-hour stretch. Thanks to a biological clock, almost every region of our body and mind knows when it must work hardest and when it can take a break. But as scientists unravel the mechanisms that make us run like clockwork, they are coming to some alarming conclusions. While optimists claim that understanding our body clocks will lead to better cures for disease, others believe it might undermine decades of medical testing.

Chronobiology, as the study of body clocks is known, has already produced some curiosities. If you want to give your firmest handshake, for example, do it in the few hours after 6pm. If you want to bet on when you might give birth naturally, go for between 4am and 6am. But it's not all light-hearted pub chat fodder. You are more likely to die during certain hours of the morning. If you have osteoarthritis, it will hit you worst in early evening. Your risk of an asthma attack is 300 times higher between 2am and 6am. Each disease, it seems, strikes hardest at a time of its own choosing.

The origin of the biological clock is a tale of evolutionary parsimony. With built-in clocks, we can anticipate what will be required of us in the coming hours, and ramp up the activity of organs we'll need most. Our clocks dictate when our brains are most alert, when our stomachs are ready to break down food, and when we can safely shut down and sleep."It's pointless running your body at top speed all the time if you don't need it, in fact it's impossible," says Russell Foster, a molecular neuroscientist at Imperial College London. "Instead, you use what you need when you need it. It's a wonderful conservation mechanism."

It took decades of investigation for scientists to tease out the location of the body's master clock. Eventually, in mammals at least, it was narrowed down to a clump of just 20,000 cells in a part of the brain called the suprachiasmatic nuclei (SCN), a part of the hypothalamus at the base of the brain. Within the cells, scientists found a series of genes that switched on, off and back on again, over a 24-hour period. This cycle has two knock-on effects: first to send electrical pulses into the nervous system, and second to produce squirts of hormones. Both spread through the body like the chime of a clock.

The role of the SCN in keeping time was demonstrated dramatically in 1990 when Michael Menaker's team at the University of Oregon and Foster, of Imperial, carried out an extraordinary experiment. By chance, during their research they had happened upon a golden hamster with a genetic defect that sent its body clock haywire. Instead of a 24-hour clock, it lived life on a 20-hour cycle. The researchers took babies from the hamster, who had inherited the defective clock, and transplanted their SCNs into hamsters with normal body clocks. To their amazement, when those hamsters recovered, their biological clocks were all running four hours short. "It proved once and for all that the SCN is where the master clock resides. It was remarkable," says Foster.

Scientists have since discovered that while the SCN beats out a standard time for the body, each of our organs uses the signal to set its own individual clock, much as countries set their time by GMT. Many organs, such as the liver and kidneys, are typically on New York time - five hours behind our master body clock.

While molecular biologists pick apart the workings of our body's clocks, others are investigating the darker side of the issue. Their discoveries have shed new light on diseases that some feel is so compelling, it should usher in a medical revolution. Take heart attacks. Thanks to our bodies being told to ramp up blood pressure just before we wake, we are more like to burst a blood vessel in the early hours of the morning. Likewise, the risk of having a stroke increases. Some, known as cerebral infarctions, are 49% more likely to strike between 6am and noon than at any other time of day.

The huge rise in asthma attacks between 2am and 6am is in part due to plummeting levels of cortisol, a hormone commonly associated with stress, but also an anti-inflammatory chemical that prevents the airwaves constricting. The big diseases also have an eye on the clock. Many cancers advance dramatically at specific times, while remaining dormant at others.

Many working at the forefront of chronobiology believe that medicine has missed a trick by failing to take time variations into account. "Look at how we educate doctors and scientists. They're taught that the body is in a constant state over 24 hours, not that you get these cycles," says Michael Smolensky, an expert in body clocks at the University of Texas at Houston.

The upshot is that many in the medical profession, though aware that physiology changes with time, do not appreciate the implications. A recent survey of more than 300 American GPs carried out by Smolensky found that 55% did not know when blood pressure rises. Only 26% knew when asthma was most likely to strike, and less than a quarter knew when migraine was most likely.

Many experts in the field are convinced that if doctors and pharmaceutical companies appreciated how diseases vary with time, they could significantly improve their treatments. Studies have already shown that, in the case of certain diseases, taking drugs at different times has a marked influence on how effective they are. Last year, Ramon Hermida at the University of Vigo in Spain showed that advising pregnant women to take aspirin to prevent high blood pressure and pre-eclampsia was meaningless unless they were told exactly when to take it. His study showed that taking aspirin either first thing or in the afternoon had little or no benefit, whereas taking the drug before bedtime markedly reduced blood pressure. "Just this little thing, like when you take an aspirin, turned out to make a big difference," says Smolensky.

The revelation that drugs work better at certain times has raised deep concerns among some in the scientific community who believe that it undermines how common chemical tests are performed.

Before a drug gets anywhere near a human, it is tested on animals, usually rodents. And your typical lab mouse is nocturnal. "It means we've been testing chemicals, and not just drugs, on animals whose physiology is 12 hours out of synch with our own," says Foster. "Does this mean we need to redo all of our toxicity testing? It's not out of the question."

Foster believes that the pharmaceutical industry could benefit from investigating how time affects the workings of its drugs. Doing so could not only reveal the best time to take a drug, but also when not to. "Say you test a new anticancer drug and it causes appalling side-effects and kills lots of animals. You decide you can't use that drug and move on to another one," Foster says. "But if that drug had been tested at another time, say 12 hours later, it may have caused very few side-effects. So it could well be the case that not only are we giving drugs that cause more damage than necessary, but we are missing out on other very valuable drugs because they are nasty at the time they are tested."

At the Hopital Paul Brousse near Paris, Francis Levi, a world expert on what is now called "chronotherapeutics" is testing whether cancer drugs work more effectively at different times of day and night. Already, he has discovered that certain drugs used to treat pancreatic cancer are best given at 4am. At this time, the side-effects are easier to tolerate, because levels of a key enzyme that protects healthy cells are highest. "It means that patients can tolerate higher doses," he says.

"The increase in dose you can go to is somewhere between 30% and 50%." But what works for one drug and one form of cancer does not work for all. By the end of the year, Levi hopes to have concluded similar trials on drugs for breast and colorectal cancer.

According to Smolensky, there are probably something in the region of 30 different diseases that could be hit harder by carefully timed medication rather than the standardised once-, twice- or four-times-a-day advice doctors usually state. But while admitting that time is a factor, some argue that carefully timing all drugs for every patient may be actually taking it too far. Some of the time, in clinical practice, it may not make much difference, says Peter Redfern, a pharmacologist at the University of Bath and author of the Royal Pharmaceutical Society's book, Chronotherapeutics. Redfern argues that other factors, such as the time it takes to absorb a drug, vary so much that any benefits from carefully choosing when a drug is taken are likely to be lost.

Despite emphasising the shortcomings though, Redfern doesn't rule out chronotherapeutics. "There may well be conditions like cancer, asthma, cardiovascular disease and epilepsy where this is worth looking at," he says.

"It's not like 10 years ago, when this was considered a bit off-the-wall. It's taken a lot more seriously now. We know it isn't fantasy."

Further Reading

· Rhythms of Life, Russell Foster and Leon Kreitzman, Profile Books, 2004, ISBN 1861972350

· Chronotherapeutics, Peter Redfern, Pharmaceutical Press, 2003, ISBN 0853694885

· The Body Clock Guide to Better Health, Michael Smolensky and Lynne Lamberg, Owl Books, 2001, ISBN 0805056629

· Chronobiology, Jay C Dunlap et al, Sinauer Associates, 2003, ISBN 087893149X