"Oceans of Trouble," the series by John McQuaid, Bob Marshall, Mark Schleifstein and Ted Jackson that this article was taken from, won the Sigma Delta Chi Award for Excellence In Journalism in the category Public Service in Journalism in 1997 and won a Pulitzer Gold Medal for Public Service in 1998. The series, which was in 8 parts, began on March 21, 1996 and has been posted in its entirety at both the Pulitzer [] and Sigma Delta Chi [] sites.    While not all of the points covered in this very extensive series are universally accepted, it is a tremendous piece of reporting and is well worth examining.

This idea is almost an article of faith among managers and biologists who dominate the field. 

Dozens of government agencies are devoted to it, hundreds of university programs initiate marine biologists into its mysteries, and it is propagated in the attitudes handed down from one generation of scientists to the next. 

So what happens when it doesn’t work? 

Collapsing fish stocks and a rash of mysterious occurrences such as the oxygen-depleted ‘‘dead zone’’ in the Gulf of Mexico have called into question the basic principles used to manage resources since the early 1900s, which say the best way to manage fisheries is to count the fish and control fishing accordingly. 

Fish vs. ecosystem 

Instead of looking at how individual parts of an ecosystem operate in isolation, new disciplines look at the behavior of entire systems. The emerging fields — chaos and complexity theory and ecological science — could ultimately supplant traditional methods. 

They look for ways to explain what traditional scientists consider unexplainable — wild fluctuations in fish populations, for example, that often confound fishery managers and paralyze management. 

Traditional science operates on the assumption that natural systems like fish populations exist in balance. But in reality they are in constant flux — spiking up and down, with many overlapping cycles — and can be upset by even tiny changes. 

That’s where the new approaches come in. Chaos scientists, for example, try to find order in what looks like chaos. 

They have found complex equations, called nonlinear in mathematics jargon, that describe many common, previously inexplicable behaviors. 

An example of chaos science at work involves the relationship between the population of fish spawning and their offspring. 

Most fish release millions of eggs, a fraction of which survive and grow into baby fish. The numbers of baby fish left alive for fishers to catch vary wildly year to year, seemingly independent of the numbers of parents. That makes measuring the total population problematic. 

Most fishery scientists treat the internal dynamics of spawning, affected by thousands of factors such as ocean currents, predators and temperature changes, as random and unknowable. 

‘‘Someone with a standard view would say that all the stuff that I can’t explain is noise. The nonlinear view is, maybe I can get something out of that,’’ said George Sugihara, a biophysicist at the Scripps Institution of Oceanography at the University of California at San Diego. ‘‘Noise is not an objective thing. It’s a statement of our own ignorance.’’ 

Take the case of the damselfish, a common aquarium fish that spawns off Australia’s Great Barrier Reef. 

In a recent study that Sugihara supervised, scientists focused on what happens when fish spawn at their nests, which are clustered on the sea floor, defended by male fish. When the larvae emerged, the scientists measured wind speed and direction, phases of the moon and other factors, then 30 days later observed what happened with the population’s size, repeating the experiment many times. 

They were able to show that the successive shifts in the population of new fish were caused in part by a single environmental factor: wind speed. 

Their equation showed that wind speed accounted for 64 percent of the fluctuations. The statistical analysis used in most fish stock assessments was able to account for only 5 percent. 

If scientists could routinely isolate the environmental factors that influence the size of each year’s crop of fish, they would have a powerful tool to manage fishing. 

Variables infinite 

Some practitioners of chaos theory go the opposite route, seeking to describe not the interactions of just one or two things, but billions. Sometimes, patterns of order emerge even at the global level. They can be described, even predicted, with the right equation. 

Chaos scientist Stephen Guastello of Marquette University in Milwaukee applied predator-prey dynamics to the world fish catch. Predators, in this case, are fishing boats, and prey are fish. 

The relationship between populations of predators and prey can display chaotic cycles in which one rises, then the other falls. No two cycles are alike. 

By tracking catches in 16 regions monitored by the United Nations — most of which have been falling since the late 1980s — he derived a nonlinear equation that showed several possible trends for the future catch. Nonlinear equations can have multiple solutions. 

One showed a decline bottoming out last year, then wobbling at weak levels — not making a recovery for 36 years. Another possible trend showed the catch falling indefinitely. 

Scientists are using other approaches to study dynamic change. Ecologists study ecosystems — marshes, oceans, deserts — where many populations interact with each other and the environment. Sometimes they treat the economy as a part ofhe ecosystem. 

The ecosystem approach is especially useful for the Gulf of Mexico, where almost all commercially important fish species depend on marsh habitats in constant flux. 

‘‘The standard models don’t really address the issue of habitat at all — just fish population,’’ said Robert Costanza, director of the University of Maryland’s Institute for Ecological Economics. ‘‘Particularly in places like Louisiana with a lot of interactions with coastal wetlands, addressing habitats is what you need to do.’’ 

Costanza was the principal designer of a computer model that projected long-term changes in a section of the Atchafalaya marsh. 

The model divided the area into a checkerboard of 2,479 squares, each a square kilometer. 

The scientists took data from detailed maps compiled by the U.S. Fish and Wildlife Service on three occasions over 27 years to map the actual changes in the marsh. They used a weekly record of climate conditions in the area during the same period — rainfall, temperature, wind, river flow, and sediment and nutrient concentrations. 

Plugging all this into the model, they were able to chart a continuous change in each square over decades, and get a picture of how the marsh was evolving. 

To see what the marsh might look like in the future, the scientists plugged in different scenarios for climate, sea level, man-made structures and other factors. One result: The model showed that random, catastrophic events such as hurricanes and floods have a greater cumulative effect on marsh erosion than daily tidal flows and the annual flood cycle. 

Tradition dies hard  

Ecosystem scientists argue for a shift away from just managing fishing toward a more comprehensive approach taking into account habitat, current flow and interactions with other species [to an article indicating that NOAA is finally looking at ecosystem effects]. 

But the new approaches face many obstacles. Scientists violently disagree, for example, on the role of chaotic changes in fish populations. Many fishery scientists say any chaotic changes will almost always be impossible to separate from other factors that aren’t chaotic. 

And while agencies such as the National Marine Fisheries Service employ new techniques as they can, they must function in an era when government is shrinking — not expanding its mandates across entire ecosystems. 

‘‘One reason fish management spends a lot of effort on controlling fishing is that’s what the law allows fish managers to control. That has the most immediate impact, and that’s what the public is most concerned about,’’ said Bradford Brown, director of the Southeast Regional Science Center of the Fisheries Service, who is also an expert on ecosystem modeling. 

But the biggest problem is history. Institutions are set up and budgets are determined the way they are because agencies have been doing it that way for decades, not because their approaches are the best. 

‘‘The people who are the principal proponents of current theory are government scientists who have a large vested interest in it,’’ said James Wilson, a fishery economist at the University of Maine and a proponent of alternative management approaches. 

‘‘From my perspective, there’s a problem in that the government has had a monopoly on the science in this area.’’