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From what I collected, coffee is a magical potion that lets you feel energetic, and essentially not-sleepy. But are there any tradeoffs? I mean, if it was so beneficial, wouldn't the human body produce caffeine naturally?

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First of all, the fact that a substance is beneficial does not mean that our body will, perforce, produce it naturally. Think of oxygen and water for example1.

As for the negative effects of coffee drinking, yes there are many although coffee has both a positive and a detrimental effect on human health. The main active ingredient in coffee is caffeine which can have the following negative effects:

  • Caffeine can increase blood pressure in non-habitual consumers.
  • High blood pressure is associated with an increase in strokes, and cerebral vascular disease, which in turn increase the risk of multi-infarct dementia.
  • Caffeine may reduce control of fine motor movements (e.g., producing shaky hands)
  • Caffeine can stimulate urination.
  • Caffeine can increase cortisol secretion, some tolerance is developed.
  • Caffeine can contribute to increased insomnia and sleep latency.
  • Caffeine withdrawal produces headache, fatigue and decreased alertness.
  • Caffeine is addictive.
  • High doses of caffeine (300 mg or higher) can cause anxiety.
  • High caffeine consumption has been linked to an increase in the likelihood of experiencing auditory hallucinations. A study conducted by the La Trobe University School of Psychological Sciences revealed that as few as five cups of coffee a day could trigger the phenomenon.
  • High caffeine consumption accelerates bone loss at the spine in elderly postmenopausal women.

The list above comes from the very comprehensive wikipedia page on the health effects of caffeine. In fact, wikipedia is particularly good on this subject, see the following pages:

http://en.wikipedia.org/wiki/Caffeine

http://en.wikipedia.org/wiki/Health_effects_of_caffeine

http://en.wikipedia.org/wiki/Health_effects_of_coffee

1 Our bodies do produce both Oxygen and water as byproducts of various reactions but nowhere near enough to satisfy our need for these substances.

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    $\begingroup$ I understand the need of writing a generic answer but... it all depends on doses, frequency of assumption and the person who drinks the coffee. Caffeine has very different effects at the molecular level depending on its concentration, so it is very difficult to generalize. For instance, 300 mg of caffeine are ~4 cups of espresso, which you generally don't drink at the same time. $\endgroup$ – nico Oct 11 '12 at 21:27
  • $\begingroup$ @nico, of course it does, everything is dosage dependent. However, the question was not about what the effect of a specific dose of coffee is, it was about coffee in general. All I said was that caffeine can produce the listed effects. if you can give an answer listing different effects of long term cofee consumption at different doses please do, considering how much of the stuff I drink, I would very much like to read it :). $\endgroup$ – terdon Oct 11 '12 at 21:33
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As always, it depends.

To be more precise, let's presume you are asking about habitual coffee consumption. Thus, for people asking: "I really like to drink several cups of coffee per day, but I have heard this might be unhealthy. Should I be worried?"

Based on my reading of O'Keefe, J. H. et al. (2013), overarching results indicate you should not be overly worried (but exception cases will follow):

a growing body of data suggests that habitual coffee consumption is neutral to beneficial regarding the risks of a variety of adverse CV outcomes including coronary heart disease, congestive heart failure, arrhythmias, and stroke. Moreover, large epidemiological studies suggest that regular coffee drinkers have reduced risks of mortality, both CV and all-cause. The potential benefits also include protection against neurodegenerative diseases, improved asthma control, and lower risk of select gastrointestinal diseases. A daily intake of ∼2 to 3 cups of coffee appears to be safe and is associated with neutral to beneficial effects for most of the studied health outcomes.

However, you might want to be cautious in regards to:

... potential risks (which are mostly related to its high caffeine content) including anxiety, insomnia, tremulousness, and palpitations, as well as bone loss and possibly increased risk of fractures.

And ...

Those with dyslipidemia may consider brewed and filtered coffee as opposed to preparations made from boiling beans without filtering.

So if you have trouble sleeping, already have an overly anxious personality, are prone to fractures, or have dyslipidemia, you might want to consult your doctor about your coffee intake.

A systematic review and meta-analysis investigates the effects of coffee on blood pressure and cardiovascular disease (CVD) in hypertensive individuals (Mesas, A. E. et al., 2011) and concludes:

The results of this review have clinical implications for the control of hypertensive patients. On the one hand, the acute increase in BP may temporarily increase the risk of a cardiovascular event (10, 11). This is consistent with the increased risk of coronary disease and stroke in the hours after coffee consumption. Thus, hypertensive patients with uncontrolled BP should avoid consuming large doses of caffeine. ... However, we found no evidence to justify avoidance of habitual coffee consumption in well-controlled hypertensive patients; therefore, in these patients, medical recommendations should prioritize modification of other lifestyles, such as quitting smoking, controlling weight, and increasing physical activity.

O'Keefe, J. H., Bhatti, S. K., Patil, H. R., DiNicolantonio, J. J., Lucan, S. C., & Lavie, C. J. (2013). Effects of habitual coffee consumption on cardiometabolic disease, cardiovascular health, and all-cause mortality. Journal of the American College of Cardiology, 62(12), 1043-1051.
Mesas, A. E., Leon-Muñoz, L. M., Rodriguez-Artalejo, F., & Lopez-Garcia, E. (2011). The effect of coffee on blood pressure and cardiovascular disease in hypertensive individuals: a systematic review and meta-analysis. The American journal of clinical nutrition, 94(4), 1113-1126.

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There are copious studies on the health effects of coffee. The overall conclusion is that people who drink coffee have slightly less health issues than people that don't.

BMJ: The umbrella review identified 201 meta-analyses of observational research with 67 unique health outcomes and 17 meta-analyses of interventional research with nine unique outcomes. Coffee consumption was more often associated with benefit than harm for a range of health outcomes across exposures including high versus low, any versus none, and one extra cup a day. https://www.bmj.com/content/359/bmj.j5024

For adults consuming moderate amounts of coffee (3-4 cups/d providing 300-400 mg/d of caffeine), there is little evidence of health risks and some evidence of health benefits. https://www.ncbi.nlm.nih.gov/pubmed/16507475

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