For me, eating healthily doesn't necessarily mean giving up all our little treats. My personal dietary vice is coffee, and I indulge myself with a cafetiere of organic Guatemalan brew most mornings. From a purist's point of view, drinking coffee is nutritional heresy: there's a stack of research linking caffeine consumption with all manner of health issues including heart rhythm irregularities, high blood pressure and insomnia. However, I have always consoled myself with the fact that science seems to show that it generally requires more than one or two cups of coffee a day to bring on these sort of problems. Besides, I wouldn't want to miss out on the caffeine-induced jolt that helps get my day off to a rip-roaring start.

So this week I resolved to dig out the positive research on the energy and mood-enhancing effects of moderate amounts of caffeine. And I was heartened to find that there is indeed good evidence for caffeine's stimulant effects on both the body and mind; in experimental studies caffeine increases energy and alertness, and it has been proven to be useful for counteracting flagging energy levels. Cheap, legal and freely available to all, caffeine does seem at face value to be the ideal pick-me-up. Much to my dismay though, a closer look at the research reveals that this is not the whole story.

While caffeine may well enliven us when it's whooshing around our blood stream, trouble can start when levels drop off. Caffeine withdrawal is a recognised phenomenon characterised by undesirable symptoms such as fatigue, anxiety and headache, but I had always imagined that these problems were only relevant to the dozen-cups-a-day brigade. It appears I have been labouring under an illusion. Contrary to popular opinion, the amount of caffeine that gives rise to problems with withdrawal can be surprisingly small. Withdrawal from daily intakes as low as 2-3 cups of coffee have been shown to cause significant problems. Research also shows that we don't need to go cold turkey for too long before symptoms of caffeine withdrawal kick in. In one study, habitual coffee drinkers unknowingly deprived of caffeine for just four hours felt significant withdrawal effects like sleepiness and fatigue.

With growing recognition of caffeine withdrawal, scientists are now beginning to question whether caffeine's energy-boosting effects are merely a chemical confidence trick. Some researchers argue that the feel-good effects of caffeine are really nothing more than a sense of relief that comes when the body is delivered from caffeine withdrawal. In other words, for habitual consumers, a caffeine fix essentially returns the body to the state it would have been in if it had not had caffeine in the first place. Paradoxically, it seems that by eschewing caffeine we can enjoy its mood- and energy-boosting benefits all day long.

If you want to cut down on caffeine, I suggest you opt first to cut out soft targets such as instant and machine-delivered coffee and tea. A useful trick is to take a cup of such stuff and imagine you are drinking it for the very first time. You might be surprised by what an affront it is to your taste buds. I'm convinced that the major driving force behind our drinking of crappola coffee and tea is simply habit, and most people find they can kiss goodbye to much of it without too much heartache. If complete abstinence from caffeine is your preference, you can expect any withdrawal symptoms to settle in about a week.

Of the alternatives, naturally caffeine-free herb and fruit teas are a good choice. However, for those who find these a little insipid and not altogether satisfying, there are other options. Rooibosch (Redbush) tea bears more than a passing resemblance to regular tea, but contains no caffeine. Decaffeinated coffee or tea, though, turns out for many to be a palatable compromise. Some decaffeination processes use suspect chemicals that may come into direct contact with the coffee beans. To be on the safe side, it might be just as well to opt for more naturally decaffeinated brews. Look for labels that state the product is decaffeinated using the 'Swiss water' or 'carbon dioxide' method. Personally, I feel better for having recently taken the decaf route. Mind you, I'm keeping some high-octane stuff in the cupboard in case of emergencies.

Dear John...

I am 27 and am soon to have my third round of treatment for kidney stones. Could you recommend anything that might help protect me from further problems?
Ben Hills-Jones, Brighton

The vast majority of kidney stones are made out of calcium and oxalate. Higher concentrations of these substances in the urine will tend to predispose to stone formation. The simplest way of protecting yourself is to drink plenty of water.

Although low-calcium diets are sometimes advocated for stone prevention, there is evidence that higher calcium intakes can be protective by binding with oxalate in the gut, reducing its absorption and subsequent appearance in the urine. A better tactic might be to reduce your intake of high-oxalate foods (rhubarb, spinach, tea and citrus fruits). Also, avoid too much meat and cheese. Animal protein does seem to increase calcium levels in the urine, and this can increase the risk of kidney stones.

Supplementation may also help. Higher levels of magnesium in the urine appear to help prevent the formation of calcium-based stones. Try 300-500mg magnesium a day. Also, Vitamin B6 (20 mg per day) is thought to help in the conversion of oxalate into a less troublesome substance.

One natural substance that might help dissolve an existing stone is the South American herb Quebra pedra. Take three capsules a day for about a month. Quebra pedra is available by mail order from Rio Trading on 01273 570 987.

Nutrition news: The whole picture

A high intake of wholegrain foods, such as oats, wholemeal bread, wholewheat pasta and brown rice, is often advocated for its disease-protective benefits in adults. Recent research from the University of Minnesota suggests wholegrains have benefits for younger folk, too. A higher consumption of these appears to reduce the risk of weight problems in children. Plus, wholegrain intake was associated with a reduced risk of a condition known as insulin resistance. This problem, in which the body fails to respond properly to the blood-sugar-regulating hormone insulin, is linked with an increased risk of heart disease and diabetes in the longer term. The latest evidence suggests that opting for wholegrain foods is good news for adults and children alike.

· If you have any issues you would like Dr John Briffa to address in this column, please contact him by email on life@observer.co.uk. Please note that Dr Briffa cannot enter into any personal correspondence.