The Effect of Environment on Genes

The Effect of Environment on Genes

The Effect of Environment on Genes

Lab experiments show how sensitive genes can be to small differences in the environment

Many genes have consistent, powerful effects, but far more of them show a marked environmental dependency than most scientists had previously anticipated.

Many genes have consistent, powerful effects, but far more of them show a marked environmental dependency than most scientists had previously anticipated.Illustration: Getty Images

I just read a wonderfully obscure paper entitled “Factors in the Selection of Surface Disinfectants for Use in a Laboratory Animal Setting,” published in the Journal of the American Association for Laboratory Animal Science in March, by Michael Campagna and colleagues at the University of California, Los Angeles. They studied, well, disinfectants. Various kinds are used in labs, and the scientists examined, among other things, which ones have odors that lab mice find aversive. Why study that? Because it’s a small piece of a big issue related to genes and behavior: the role of the environment.

Suppose scientists want to know what a gene—let’s call it Gene Z—has to do with behavior. Using genetic-engineering wizardry, they generate a line of mice lacking Gene Z (“knockout” mice), plus another line with an extra copy of Gene Z (“transgenic overexpression” mice). Then they see if there’s something different about the behavior of either group when compared with unmanipulated control mice.

So a lab discovers that Gene Z is pertinent to, say, anxiety. Knock out the gene, and mice don’t get anxious; overexpress the gene, and they’re more prone to anxiety. (How can you measure mouse anxiety? Mice, being nocturnal, are afraid of light. Researchers might put food in the middle of a brightly lighted arena and see how long it takes for a hungry mouse to leave a comforting, shaded corner to get the food.)

With the results in, other labs get some of the Gene Z mice, eager to study different aspects of anxiety. And surprisingly often, something disquieting occurs. Another group confirms the link between Gene Z and anxiety, but they don’t see as big of an effect. Then another lab reports that the gene has no effect on anxiety. Yet another finds that Gene Z decreases anxiety.

Yikes. Everyone wonders if the scientists don’t know what they’re doing, or if the test is reliable. But research started in the 1990s by neuroscientist John Crabbe of the Oregon Health and Science University suggests a different explanation.

Genes like our fictional Gene Z, with “neurogenetic” effects on behavior, are often sensitive to small differences in the environment. Gene Z’s effects on anxiety might differ between two labs because the mice in the two are fed different kinds of food; nutrition influences brain chemistry and thus potentially Gene Z’s effects on the brain. Or maybe one of the labs uses a caustic disinfectant, or its doors bang loudly, and the mice there secrete more stress hormones, which alter the brain. Likewise with different temperatures, producing different levels of thyroid hormone.

People are often impressed with the deterministic power of genes, believing they explain everything about our biology and behavior. Many genes do indeed have consistent, powerful effects, but far more of them show a marked environmental dependency than most scientists had previously anticipated. Thus, what Dr. Crabbe and others show is that in many cases, you can’t really say what a gene generically “does”—so perhaps be a bit skeptical about such pronouncements. Instead, you can only safely say what a gene does in the environment(s) in which it has been studied.

This is pertinent to mice living in different laboratories. But just imagine how much that would apply to a species that can live in dramatically different environments—in deserts, tundra and rain forests, in hunter-gatherer bands and in dense cities, in close-knit communities or as hermits. There is no species that matches humans in the range of ecosystems, habitats and social system in which it lives. And that suggests there is no species freer from the power of genes than humans.

By Robert M. Sapolsky

Aug. 11, 2016 2:08 p.m. ET

wsj

The Effect of Environment on Genes

Advertisements

Scientists are studying ant colonies to create better network analysis

Scientists are studying ant colonies to create better network analysis

Ants are really good at lots of things. Lifting, communicating, ruining picnics. Turns out they’ve got the whole voting thing down to a science, too. When time comes to move nests, the plucky little insects vote by quorum. The democratic process is determined, at least in part, by how often they bump into one another.

Scientists believe that ants have a knack for determining their own population density based on how often they collide while exploring their environments. It’s a random exploration that turns out to be a really good method for figuring out how many are present in a space.

“What we’re doing is giving a rigorous analysis behind that intuition, and also saying that the estimate is a very good estimate, rather than some coarse estimate,” MIT electrical engineering and computer science grad student Cameron Musco explains, previewing a new paper on the subject. “As a function of time, it gets more and more accurate, and it goes nearly as fast as you would expect you could ever do.”

The paper argues that these sorts of “random walk” explorations could provide the basis for network communication algorithms used to estimate everything from social to ad hoc device networks, determining data when random sampling isn’t available for various reasons. In the random walk scenario, the ant or other “explorer” is equally likely to visit any adjacent cell on a graph. Much to the researchers’ surprise, this method is nearly as fast at determining population density as sampling.

Musco again, “If you’re randomly walking around a grid, you’re not going to bump into everybody, because you’re not going to cross the whole grid. So there’s somebody on the far side of the grid that I have pretty much a zero percent chance of bumping into. But while I’ll bump into those guys less, I’ll bump into local guys more. I need to count all my interactions with the local guys to make up for the fact that there are these faraway guys that I’m never going to bump into.”

Scientists are studying ant colonies to create better network analysis

The biggest scientific breakthrough of the year will reshape life as we know it

Gene Editing Technology

The biggest scientific breakthrough of the year will reshape life as we know it

This wasn’t the year the most powerful gene editing technology we’ve ever known — CRISPR — was discovered, but it was the year the world started to see just how much this tool would transform life as we know it.

For that reason, the journal Science named CRISPR its “2015 Breakthrough of the Year.”

As John Travis of Science explains, CRISPR has appeared as a runner up for the top breakthrough before, in combination with other tools that scientists use to manipulate and edit the building blocks of life.

“[T]his is the year it broke away from the pack, revealing its true power in a series of spectacular achievements,” Travis writes.

As Jennifer Doudna, the Berkeley biologist who was one of the pioneers of using CRISPR, explained to us earlier this year, the tool basically allows us to find specific sections of our genetic code and either cut them out or even more dramatically, replace them.

“We’re basically now able to have a molecular scalpel for genomes,” she said.

There are hundreds of potential uses for this, ranging from creating genetically edited animals — cows that don’t grow horns or super-muscled dogs — to creating algae that can function as a sustainable energy source to perhaps even changing our own DNA to become disease resistant or super strong.

But there were two things done with CRISPR this year that gave it that breakthrough of the year status: the editing of (nonviable) human embryos and the creation of a “gene drive.”

When researchers at Sun Yat-sen University announced they had made changes to the DNA of human embryos it caused waves around the world. Even though they were doing something that researchers knew was possible with gene editing tools and even though there were a lot of errors, they’d still actually changed the genes of humans in ways that would have been passed on if those embryos were implanted and brought to term.

That would be the equivalent of making designer babies; it would be taking an active hand in human evolution.

To demonstrate the ability of CRISPR to create what’s known as a “gene drive,” researchers at the University of California engineered a gene that would forcibly spread throughout a population. In a study published in Science, they showed that within two generations, their mutation had found its way into 97% of a population of fruit flies.

The ability to force a gene to spread through a population could be a way to eliminate mosquitoes that spread malaria, for example. But releasing something into the wild that has the ability to wipe out a population also frightens researchers, as it might lead to unexpected side effects that can’t be taken back.

Both of these developments show the control that CRISPR gives us over life’s building blocks. And as Travis explains, there’s so much more this tool is helping scientists do. By using it to turn genes on and off, researchers are figuring out how those genes interact and what effects they have. It’s a tool that’s helping unlock the secrets of cancer. Other scientists are creating pigs that grow organs that can be transplanted into humans.

As Dustin Rubinstein, the head of a lab working with CRISPR and other genetic engineering tools at the University of Wisconsin–Madison, told us earlier this year, “it’s really going to just empower us to have more creativity … to get into the sandbox and have more control over what you build.”

“You’re only limited by your imagination.”

TECHINSIDER

The biggest scientific breakthrough of the year will reshape life as we know it

The Myth of Basic Science

Does scientific research drive innovation? Not very often, argues Matt Ridley: Technological evolution has a momentum of its own, and it has little to do with the abstractions of the lab.

Innovation is a mysteriously difficult thing to dictate. Technology seems to change by a sort of inexorable, evolutionary progress, which we probably cannot stop—or speed up much either. And it’s not much the product of science. Most technological breakthroughs come from technologists tinkering, not from researchers chasing hypotheses. Heretical as it may sound, “basic science” isn’t nearly as productive of new inventions as we tend to think.

The Myth of Basic Science

Genomics: What You Should Know

Personalized medicine. Predictive medicine. Targeted medicine. These are just some of the descriptors being applied to “genomic medicine,” a field of medical research generating much fanfare and hope for the future.

Genomics, according to the Centers for Disease Control and Prevention (CDC), is the study of all the genes in the human genome – that double-stranded DNA helix that defines who we are and what we’re made of. Building on classical genetics, it focuses on gene variations, the genetic code we inherit, the environment we live in, and the range of diseases we develop.

The promise of genomics is huge. It could someday help us maximize personal health and discover the best medical care for any condition. It could help in the development of new therapies that alter the human genome and prevent (or even reverse) complications from the diseases we inherit.

Genomics: What You Should Know.

Masters of the Universe

Masters of the Universe: Picturing Space - WSJ - WSJ

The new book ‘Cosmigraphics’ chronicles the history of how humans have depicted space.

Masters of the Universe: Picturing Space - WSJ - WSJ

Masters of the Universe: Picturing Space - WSJ - WSJ

Masters of the Universe: Picturing Space - WSJ - WSJ

Masters of the Universe: Picturing Space – WSJ – WSJ.

The Map of Mars

Scientists have compiled the most comprehensive map of Mars we’ve ever seen.

Thanks to advances in imaging and four spacecraft that have been orbiting Mars since the late 1990s, the new map improves upon the earliest global maps of Mars, which were made back in the 1970s and 1980s, according to USGS.

Scientists have compiled the most comprehensive map of Mars we’ve ever seen – The Washington Post.

Beyond Energy, Matter, Time and Space

Though he probably didn’t intend anything so jarring, Nicolaus Copernicus, in a 16th-century treatise, gave rise to the idea that human beings do not occupy a special place in the heavens. Nearly 500 years after replacing the Earth with the sun as the center of the cosmic swirl, we’ve come to see ourselves as just another species on a planet orbiting a star in the boondocks of a galaxy in the universe we call home. And this may be just one of many universes — what cosmologists, some more skeptically than others, have named the multiverse.

Beyond Energy, Matter, Time and Space – NYTimes.com.