Cocoa, Coffee and Caffeine: How Helpful (or Harmful) is a Cup of Joe?

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Americans gulp nearly 400 million cups of coffee every day, so it’s time to understand what all of that java is doing to our brains and bodies.

For many, coffee is a morning eye-opener, thanks to the stimulating effects of caffeine, but other compounds native to the coffee bean include antioxidants that have been linked to a lower risk of skin cancerAlzheimer’sheart disease and diabetes. Just a few weeks ago, a Harvard School of Public Health study found that java may even prevent suicide; individuals who drank two to four cups of coffee every day were less likely to commit suicide than those who didn’t drink it.

(MORE: How Coffee Could Save Your Life)

But unfortunately, studies touting the benefits of coffee are often followed by others that highlight its adverse effects on health. The latest, published in the journal Mayo Clinic Proceedings, studied health records of 45,000 people who reported their coffee-drinking habits and concluded that younger people under age 55 who drank more than 28 cups a week were 21% more likely to die prematurely during the 17 year study than those who drank less. (Older coffee drinkers didn’t show such an increased risk of early mortality.)

While the heavy coffee drinkers were also more likely to be less fit and to smoke cigarettes — both factors that can contribute to early death — the relationship between more coffee and earlier death continued to hold even after the scientists adjusted for these effects.

So is that morning cup of coffee a health-booster or a health hazard?

That answer depends on how the studies that examine this question are designed, and the type of coffee in question — as well as who is doing the drinking. Unlike the latest analysis above, some studies in the past did not adjust for factors other than coffee that could affect outcomes like mortality, cancer rates or cognitive measures. A 1981 study, for example, connected coffee to an increased risk of pancreatic cancer, but other analyses showed conflicting associations. Later research concluded that these contrary findings were due to the fact that some of the studies failed to control for potentially confounding factors such as smoking, while others were subject to the errors of having drinkers recall how much they consumed.

It’s also important to understand what the studies are designed to measure. When it comes to brain function, for example, it turns out that caffeine in coffee acts as a stimulant that can sharpen cognitive function but doesn’t necessarily improve memory or learning; the distinction, however, isn’t often made in media reports on coffee studies involving cognition or even the risk of Alzheimer’s disease.

The effects of coffee on the body can also change over time, and studies don’t always tease apart the different health outcomes of participants by age. A long-term java habit’s effect on the hearts and brains of older drinkers, for instance, may differ from that of a short-term one as cells and tissues become tolerated to the chemicals in the coffee. For example, frequent and long-term coffee drinking — about four or more cups a day — has consistently been linked to a nearly 50% lower risk of type 2 diabetes compared to non-drinkers, while the effect of fewer cups is less consistent. Such a coffee habit isn’t all beneficial, however; high consumption among pregnant women has been linked to a lower birth rate.

How the coffee is prepared can also make a difference; some studies found that unfiltered coffee—like French Press—increased cholesterol levels while paper-filtered coffee did not, but most studies of coffee drinkers don’t distinguish between different preparations.

(MORE: Coffee: Drink More, Live Longer?)

“Back when I was in medical school in the 70s, I was taught that coffee is bad for you,” says Dr. Peter Martin, director of the Institute for Coffee Studies at Vanderbilt University. “There was strong data showing it was associated with excess mortality and unfortunately statistical studies were done without taking into consideration a whole bunch of covariates. It’s also true people who drink coffee tend to smoke. By statistically removing these lifestyle variables, then coffee starts looking quite healthy. I think that coffee is basically good for you unless there is a specific reason you shouldn’t drink it.”

And like anything else we put in our bodies, figuring out whether it will help or harm our health is about understanding the balance of ingredients packed into each cup. While the antioxidants in coffee can protect the heart and combat diabetes, those benefits need to be balanced against risks like the over-stimulation that caffeine can cause. “Coffee contains hundreds of compounds including caffeine, phenolic acids, minerals, and vitamin B3 that can vary by coffee bean, degree of roasting and brewing method. All of which may have different health effects,” says Dr. Robert van Dam, an assistant professor in the Department of Nutrition at the Harvard School of Public Health.

(MOREStudy: Caffeine May Alter Estrogen Levels in Women)

To complicate matters even more, these effects can greatly vary from person to person. Plus, our bodies tend to adapt to the various components in coffee, including caffeine, so each individual’s response to it may even change over time. “Only after consumption of more than a week [does] tolerance to the effects of caffeine develop,” says van Dam. “Even then there is a large variation in how fast people metabolize caffeine which is partly genetically determined and there will thus be large differences in how much caffeine people can consume without unpleasant side effects.”

Martin, however, says that there are some simple ways to determine if coffee is likely to be doing you more harm or good. If your java habit is disrupting your sleep, then cut back on the last cup of the day so the stimulating effects of caffeine aren’t making you anxious or impeding your ability to concentrate and focus. “If caffeine intake affects sleeping habits, induces irritability etc. then you are probably consuming too much,” says van Dam.

And if you aren’t a coffee drinker, there’s no need to pick up the habit in the hopes of reaping some of the benefits associated with coffee, since it’s not clear that those benefits outweigh the risks associated with drinking it — especially in large amounts.