FORTUNE — Few ecological disasters have been as confounding as the
massive and devastating die-off of the world’s honeybees. The phenomenon
of Colony Collapse Disorder (CCD) — in which disoriented honeybees die
far from their hives — has kept scientists, beekeepers, and regulators
desperately seeking the cause. After all, the honeybee, nature’s
ultimate utility player, pollinates a third of all the food we eat and
contributes an estimated $15 billion in annual agriculture revenue to
the U.S. economy.

The long list of possible suspects has included
pests, viruses, fungi, and also pesticides, particularly so-called
neonicotinoids, a class of neurotoxins that kills insects by attacking
their nervous systems. For years, their leading manufacturer, Bayer Crop
Science, a subsidiary of the German pharmaceutical giant Bayer AG (BAYRY),
has tangled with regulators and fended off lawsuits from angry
beekeepers who allege that the pesticides have disoriented and
ultimately killed their bees. The company has countered that, when used
correctly, the pesticides pose little risk.

A cheer must have gone up at Bayer on Thursday when a front-page New York Times article,
under the headline "Scientists and Soldiers Solve a Bee Mystery,"
described how a newly released study pinpoints a different cause for the
die-off: "a fungus tag-teaming with a virus." The study, written in
collaboration with Army scientists at the Edgewood Chemical Biological
Center outside Baltimore, analyzed the proteins of afflicted bees using a
new Army software system. The Bayer pesticides, however, go
unmentioned.

What the Times article did not explore — nor
did the study disclose — was the relationship between the study’s lead
author, Montana bee researcher Dr. Jerry Bromenshenk, and Bayer Crop
Science. In recent years Bromenshenk has received a significant research
grant from Bayer to study bee pollination. Indeed, before receiving the
Bayer funding, Bromenshenk was lined up on the opposite side: He had
signed on to serve as an expert witness for beekeepers who brought a
class-action lawsuit against Bayer in 2003. He then dropped out and
received the grant.

Reporter: scientist "did not volunteer" funding sources

Bromenshenk’s
company, Bee Alert Technology, which is developing hand-held acoustic
scanners that use sound to detect various bee ailments, will profit more
from a finding that disease, and not pesticides, is harming bees. Two
years ago Bromenshenk acknowledged as much to me when I was reporting on
the possible neonicotinoid/CCD connection for Conde Nast Portfolio magazine, which folded before I completed my reporting.

Bromenshenk
defends the study and emphasized that it did not examine the impact of
pesticides. "It wasn’t on the table because others are funded to do
that," he says, noting that no Bayer funds were used on the new study.
Bromenshenk vociferously denies that receiving funding from Bayer (to
study bee pollination of onions) had anything to do with his decision to
withdraw from the plaintiff’s side in the litigation against Bayer. "We
got no money from Bayer," he says. "We did no work for Bayer; Bayer was
sending us warning letters by lawyers."

A Bayer publicist reached
last night said she was not authorized to comment on the topic but was
trying to reach an official company spokesperson.

The Times
reporter who authored the recent article, Kirk Johnson, responded in an
e-mail that Dr. Bromenshenk "did not volunteer his funding sources."
Johnson’s e-mail notes that he found the peer-reviewed scientific paper
cautious and that he "tried to convey that caution in my story." Adds
Johnson: The study "doesn’t say pesticides aren’t a cause of the
underlying vulnerability that the virus-fungus combo then exploits…."

At
least one scientist questions the new study. Dr. James Frazier,
professor of entomology at Penn State University, who is currently
researching the sublethal impact of pesticides on bees, said that while
Bromenshenk’s study generated some useful data, Bromenshenk has a
conflict of interest as CEO of a company developing scanners to diagnose
bee diseases. "He could benefit financially from that if this thing
gets popularized," Frazier says, "so it’s a difficult situation to deal
with." He adds that his own research has shown that pesticides affect
bees "absolutely, in multiple ways."

Underlying cause of bee deaths still unclear

Dr.
Jennifer Sass, a senior scientist with the health group at the Natural
Resources Defense Council, says that while the Bromenshenk/Army study is
interesting, it fails to ask the underlying question "Why are colonies
dying? Is it because they’re getting weak? People who have HIV don’t die
of HIV. They die of other diseases they get because their immune
systems are knocked off, making them more susceptible." In other words,
pesticides could weaken the bees — and then the virus/fungus
combination finishes them off. That notion, however, is not explored in
the new study.

In 2008 the NRDC sued the Environmental Protection
Agency after it failed to release Bayer’s underlying studies on the
safety of its neonicotinoids. The federal agency has since changed
course, and NRDC researchers are being allowed to sift through the Bayer
studies, an NRDC spokesman says.

The EPA has based its approval
of neonicotinoids on the fact that the amounts found in pollen and
nectar were low enough to not be lethal to the bees — the only metric
they have to measure whether to approve a pesticide or not. But studies
have shown that at low doses, the neonicotinoids have sublethal effects
that impair bees’ learning and memory. The USDA’s chief researcher, Jeff
Pettis, told me in 2008 that pesticides were definitely "on the list"
as a primary stressor that could make bees more vulnerable to other
factors, like pests and bacteria.

In 1999, France banned
Imidacloprid after the death of a third of its honeybees. A subsequent
report prepared for the French agricultural ministry found that even
tiny sublethal amounts could disorient bees, diminish their foraging
activities, and thus endanger the entire colony. Other countries,
including Italy, have banned certain neonicotinoids.

Bayer v. beekeepers

As
for the Bayer-Bromenshenk connection, in 2003 a group of 13 North
Dakota beekeepers brought a class-action lawsuit against Bayer, alleging
that the company’s neonicotinoid, Imidacloprid, which had been used in
nearby fields, was responsible for the loss of more than 60% of their
hives. "My bees were getting drunk," Chris Charles, a beekeeper in
Carrington, N.D., and a plaintiff in the lawsuit, told me in 2008. "They
couldn’t walk a white line anymore — they just hung around outside the
hive. They couldn’t work."

Charles and the other North Dakota
beekeepers hired Bromenshenk as an expert witness. Bayer did not dispute
that Imidacloprid was found among the bees and their hives. The company
simply argued that the amount had not been enough to kill them.

As
the North Dakota lawsuit moved forward, an expert witness for the
beekeepers, Dr. Daniel Mayer, a now retired bee expert from Washington
State University, traveled to 17 different bee yards in North Dakota and
observed dead bees and bees in the throes of what looked like
Imidacloprid poisoning, he told me in 2008. He theorized that after
foraging in planted fields where the seeds had been treated with
Imidacloprid, the bees then brought the pesticide back to the hive,
where it built up in the wax combs.

The beekeepers tried to enlist
more expert witnesses, but others declined, according to two of the
beekeeper plaintiffs, in large part because they had taken research
money from Bayer and did not want to testify against the company. One
who agreed — Bromenshenk — subsequently backed out and got a research
grant from Bayer. Bromenshenk insists the two actions were unrelated.
"It was a personal decision," he says. "I, in good conscience, couldn’t
charge beekeepers for services when I couldn’t help them." He adds,
"Eventually, the lawyers stopped calling. I didn’t quit. They just
stopped calling."

In June 2008 a district court judge in
Pennsylvania defanged the beekeepers’ lawsuit by siding with Bayer to
exclude Mayer’s testimony and the initial test results from a laboratory
in Jacksonville, Fla., that had found significant amounts of
Imidacloprid in the honeybee samples.

That same year Bromenshenk
brokered a meeting between Bayer and beekeepers. When I interviewed
Bromenshenk that year, he said that increasing frustration with the
accusations against Bayer, which he described as a "runaway train," led
him to contact the company in an effort to create a dialogue between
Bayer and the beekeepers. Because of his efforts, in November 2008,
Bayer scientists sat down in Lake Tahoe, Nev., with a small group of
American beekeepers to establish a dialogue. The issues discussed were
"trust and transparency," Bromenshenk told me. "How did Bayer do its
testing, and do we trust the results?" Generally beekeepers and
scientists have been highly critical of the design of Bayer’s studies
and deeply suspicious over who is or isn’t on Bayer’s payroll.

After
the meeting, Bayer tentatively agreed to appoint a beekeeper advisory
board to help redesign studies so that beekeepers could trust the
results. But many beekeepers see the advisory board and grant money as a
ruse on Bayer’s part to silence its enemies by holding them close.
"They have the bee industry so un-united," says Jim Doan, once New York
State’s busiest beekeeper until CCD decimated his business. "Even the
researchers are off working on anything but the pesticide issue."

Bromenshenk’s
study acknowledges that the research does not "clearly define" whether
the concurrent virus and fungus, which were found in all the afflicted
bee samples, is "a marker, a cause, or a consequence of CCD." It also
notes uncertainty as to how, exactly, the combination kills the bees,
and whether other factors like weather and bee digestion play a role.
Scientists like Sass at NRDC believe the mystery is far from resolved:
"We’re even concerned that based on this, beekeepers will use more
pesticides trying to treat these viruses," says Sass.