At first impression, the two groups of children were hard to tell apart: just regular kindergarten kids from different neighbourhoods in Kamloops, B.C. Yet, when they visited a mobile lab as part of population study he collaborated on, Clyde Hertzman remembers how their young brains revealed a striking contrast.

Both groups were asked to focus their attention on a series of sounds while researchers monitored their neural activity. Not only did one group tend to have a harder time with the task, Dr. Hertzman recalls, it " had a systematically different pattern of brain responses to the test."

How could children drawn from a city of just 85,000 people end up with wiring that was essentially different? They had grown up with any number of genetic and environmental influences affecting their brain development and behaviour, but one variable stood out: affluence. Those who did not perform as well tended to be from the poorer of the two neighbourhoods. Somehow their socio-economic status was showing up in the architecture of their thoughts.

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The result was a particularly vivid example of something scientists who specialize in early childhood development have seen again and again. Kids from communities that are underresourced and subject to economic stress think differently than their wealthier counterparts in ways that can ultimately affect behaviour.

Five years later, Dr. Hertzman – who teaches at the University of British Columbia's School of Population and Public Health and was Canada's health researcher of the year in 2010 – is part of a rapid evolution of the field that has grown from merely recording the demographics of cognitive disparities to building a bottom-up understanding of the molecular changes that cause them.

The change has gathered momentum in recent months, fuelled by a bounty of new findings that bolster the long-observed link between social environment and development with a newly emerging biological perspective.

It also underscores the stunning human cost of what is called the "socio-economic gradient." Only 3 to 4 per cent of Canadian children are born with inherited differences that will limit their physical, emotional or intellectual growth, yet an average of 25 to 30 per cent exhibit some level of developmental vulnerability that could include a cognitive "deficit."

In some communities, the figure may reach 70 per cent, and by adolescence, the resulting deficits can translate into a range of mental-health issues, substance abuse and diminished opportunities for education and employment.

The Royal Society of Canada and the Canadian Academy of Health Sciences issued a report in November that surveys the new research on how socio-economic factors can affect someone's biological makeup – and warning of "dire consequences for the individual and society" if nothing is done. The report concludes by calling for a broad strategy of investment in early childhood.

"If a society wants to ensure the best trajectory for its children, its policy focus should be on those early years," says Alan Bernstein, president of the Canadian Institute for Advanced Research (CIFAR), which supports several leading scientists in the field.

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A key feature of the emerging connection between brain and poverty is stress. While economic status does not necessarily spell bad news for a given child's development, it tends to dovetail with parental stress and family stability in a way that can strongly shape how a young brain experiences the world.

At the extreme end, low socio-economic status and the stress that underlies it can mean higher incidences of physical and emotional abuse. But it can also lead to a broader, more subtle type of social adversity – parents or caregivers have less time, or are less inclined, to nurture their children.

The potential risk is illuminated by a proliferation of genetic studies that, by comparing the DNA, uncover hidden variants that could affect how children develop in response to adversity.

But genes are hardly the development dictators they are sometimes made out to be. Instead, the quality of the nurturing environment, often through the presence or absence of stress, can determine whether a genetic difference actually matters.

"The genes, in a sense, are listening to the environment," says Marla Sokolowski, who specializes in genetics and behavioural neurology at the University of Toronto.

Researchers have long recognized that not everyone abused or neglected as a child goes on to have problems. In some cases, genes can buffer against environmental effects and allow the brain to develop normally; in others, those that might otherwise be silent are triggered by adversity in early childhood and so influence brain development.

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As an analog for more complex human behaviour, Prof. Sokolowski studies fruit flies that naturally carry one of two possible variants of a gene that affects food-foraging habits. The genes, dubbed "rover" and "sitter," will either lead a fly to wander around a food source or stay put and feed. Fruit flies that are genetically predisposed to be rovers nevertheless become sitters if they are nutritionally deprived during development. The effect of the scarcity is to ramp down the activity of the rover gene, thereby maximizing food intake over other kinds of behaviour.

At McGill University, a powerful set of studies by behavioural scientist Michael Meaney and his colleagues has been especially important at showing how the interplay of genes and social environment can program the behaviour of mammals.

Mother rats who lick and groom their babies less often tend to produce offspring more sensitive to stress. The effect is thought to be "epigenetic" – the underlying DNA sequence of the baby rats is unchanged, but a cascade of biochemical signals triggered by the grooming affects the activity of a gene that is crucial for regulating stress response.

The experiments suggest how the social adversity that can come with low socio-economic status may work on human children, Prof. Sokolowski says, by reducing the signals of key genes that guide brain development "like a dimmer switch." This, in turn, affects cognition and behaviour with consequences that can reverberate through a lifetime.

Such vulnerability may showcase a fundamental weakness in the way our brains work. It may even be evolution's way of preparing brains for the environments they are growing up in.

"The brain is not fragile; the brain is adaptive," Dr. Herztman says. "The question is whether or not those adaptations will allow you to cope with the world you are then going to live in."

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Thus, a developing brain that has been influenced by a stressful or chaotic social environment at an early age may lead to a child with serious attention issues in the classroom years later.

But a behaviour pattern that is perceived as a deficit in the school setting may be there precisely because the child, as an infant, was shaped by social circumstances to pay more attention to distractions that could warn of sudden danger.

"It's a kind of vigilance – the brain is searching for threatening stimuli to thwart," Dr. Hertzman says. But the epigenetic fine-tuning comes at a cost, he adds, because the brain is less able to concentrate on high-order functions, such as math or reading.

"The problem is that the developmental signals and the demands of modern society become a mismatch."

Symptoms of such cognitive disorders as attention deficit and hyperactivity disorder (ADHD) are not restricted to children of low socio-economic status, of course, and do not always relate to parenting. However, evidence that the environment plays a role in the prevalence of such symptoms is reinforced by studies that track individuals over the course of their lives.

One such study, based in Wisconsin, has followed more than 500 children from the second trimester of pregnancy through high-school graduation.

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Those who were in preschool at a time when their parents reported high levels of economic and social stress bear the scars of that stress in the form of epigenetic marks on their DNA. These marks will persist for life, inhibiting genes that might otherwise be more active.

Thomas Boyce, a professor of pediatrics at UBC, has collaborated with the team behind the Wisconsin study, and says its findings could guide strategies to head off the negative impact of cognitive differences even before it becomes apparent.

Prof. Boyce (who leads with Prof. Sokolowski a long-running program in experience-based brain and biological development sponsored by CIFAR) and his colleagues at UBC are currently studying children from different socio-economic backgrounds in the Vancouver area.

To find epigenetic changes, they will compare their subjects' genetic profiles at ages 8 to 10 with DNA from blood spots banked when they were newborns. These changes can be correlated with cognitive perform- ance and environmental stress.

"The whole idea behind pursuing these epigenetic markers is to develop better indicators of how a child is doing before problems become salient," Dr. Boyce says.

Amedeo D'Angiulli, a developmental cognitive neuroscientist at Carleton University in Ottawa, welcomes the new tools that enable direct eavesdropping on the brain-gene dialogue.

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He is also keen to test measures that may aid children with attention and focus issues, and counterbalance some of the effects of growing up on the low end of the socio-economic spectrum.

In one study, being conducted with the Leading Note Foundation, which teaches music to children in underserved communities, Dr. D'Angiulli will track cognitive function and stress levels as youngsters embark on an intense period of musical training and performance.

He suspects the program can bolster the brain. Children's "short-term memory improves, their focus improves, and it's reinforced because they're doing it as an ensemble," he says.

Ultimately, the research points to what many early childhood education advocates have long maintained: Directing resources toward the social and cognitive health of young minds can help to counter the long-term costs of economic disparity.

"All of the new insights we're getting into how the interactions of genes and environment drive development reinforce the importance of a society that helps families," says Dr. Hertzman, who points to data showing a link between a population's mental health and its economic output.

"If we were to invest according to what the biology of brain development is telling us, there would be a lot more investment in children early on."

Editor's note: A study of the cognitive performance of children in Kamloops, B.C., mentioned in a story on Saturday, was led by Dr. Amedeo D'Angiulli, who was then Canada Research Chair in early childhood education and development at Thompson Rivers University in Kamloops. Unclear information about the study appeared in an earlier version of this article. This online version has been corrected.