Scientists like to remind us not to confuse cause and effect.
But they're not immune from making that mistake themselves. Last
week, for example, a flurry of sociological headlines emanating
from a conference included the claim that elderly Taiwanese people
who shop every day are 27% less likely to die over 10 years than
those who shop once a week; and the claim that 16-year-olds who
read books at least once a month are more likely to be in
managerial jobs at 33 than those who read no books at 16.
It would be tempting but rash to conclude that shopping prevents
death, rather than that ill health prevents shopping; or that
reading causes career success rather than that a scholarly aptitude
causes both reading and career success.
The nature-nurture debate has long been bedeviled by
cause-effect confusion, as exemplified by the old joke: I'm not
surprised that Johnny comes from a broken home; he would be enough
to break any home.
Whole districts of Freudian theory are confused about cause and
effect. For example, the incest taboo, forbidding people from
mating with close relatives, turned out on closer investigation to
be a codified expression of, rather than a cause of, incest
avoidance. As Freud's rival Edward Westermarck argued, there's an
innate tendency to develop revulsion at the idea of sex with close
childhood contemporaries (who usually are siblings). A taboo turns
this into a rule.
(For more on this see this book by Wolf and Durham.)
Nor is medicine immune. Some years ago epidemiologists found
that women taking hormone replacement therapy had fewer heart
attacks, but controlled trials found that HRT caused more heart
attacks. It turned out that the women taking HRT in the
epidemiological study were from higher socio-economic classes, so
they ate and exercised better. Class caused both HRT and fewer
heart attacks.
Even climate science has encountered cause-effect confusion.
When in 1999 Antarctic ice cores revealed carbon-dioxide
concentrations and temperature marching in lockstep over 400,000
years, many-including me- found this a convincing argument for
attributing past climate change to carbon dioxide. (About 95% of
carbon dioxide in the atmosphere is natural, coming from the
exhalations of living things. In the past, carbon-dioxide levels
rose as the earth warmed at the end of ice ages and fell as it
cooled at the end of interglacial periods.)
Then four years later came clear evidence from finer-grained
analysis of ice cores that temperature
changes preceded carbon-dioxide changes by at least
800 years. Effects cannot precede their causes by eight centuries,
so temperatures must drive carbon dioxide, chiefly by warming the
sea and causing carbon dioxide dissolved in water to "out-gas" into
the air.
(See this chart and the associated post by Frank Lansner at Jo
Nova's site:)

Climate scientists fell back on a "feedback" hypothesis, arguing
that an initial change, probably caused by variations in the
earth's orbit that affect the warmth of the sun, was then amplified
by changes in carbon-dioxide levels. But this made the attribution
argument circular and left the reversal of the trend after a period
of warming (when amplification should be at its strongest) still
harder to explain. If carbon dioxide is still driving the
temperature upward but it falls instead, then other factors must be
stronger than expected.
Some climate scientists see cause-effect confusion at the heart
of climate modeling. Roy Spencer of the National Aeronautics and
Space Administration argues from satellite data that the
conventional view has one thing backward. Changes in cloud cover
are often seen as consequences of changes in temperature. But what
if the amount of cloud cover changes spontaneously, for reasons
still unclear, and then alters the temperature of the world by
reflecting or absorbing sunlight? That is to say, the clouds would
be more cause than consequence. Not many agree with Mr. Spencer,
but it is an intriguing idea.