Winter has long reigned in the globe’s northern latitudes, where
vast expanses of frozen soils called permafrost nurture a rich, if
still mysterious, mix of microbes that can tolerate year-round
subzero temperatures. But as climate change warms the permafrost,
that microbe community is changing in ways scientists are still
trying to understand. Most worrisome is what will happen to the
permafrost’s huge store of long-frozen carbon that newly awakened
microbes can now feast on, and how that may propel further changes
Janet K. Jansson, a microbial ecologist at the
Pacific Northwest National Laboratory in Richland, Washington, was
one of the first scientists to study how the bacterial community in
permafrost has shifted as the soils have thawed. Understanding the
complexity of life in soils — permafrost or other — has long been
made difficult by the fact that scientists are unable to culture a
majority of the species that grow there in the lab. But Jansson and
her collaborators have found a way to take a molecular census of
these exotic organisms to better track changes in soil communities
affected by climate change, including the icy north as well as
grasslands in the south.
CREDIT: JAMES PROVOST (CC BY-ND)
Microbial ecologist Janet K. Jansson
Pacific Northwest National Laboratory
Metagenomics — a technique in which scientists isolate, sequence
and analyze DNA of microbial communities directly from the
environment — and other molecular technologies, termed “omics,” are
offering new insights about underground life and the
transformations wreaked by warming temperatures, Jansson described
earlier this year at a meeting of the American Association for the
Advancement of Science held in Washington, DC, and in a paper she
coauthored in the 2016 Annual Review of Earth and Planetary
She recently spoke with Knowable about soil critters
and how they are adjusting to a warming planet.
This conversation has been edited for length and clarity.
Why is so much still unknown about the soil’s
For a very long time, the microbes that have lived in the soil,
especially in extreme environments, have been difficult to study
because they don’t grow well under laboratory conditions. Now we’re
starting to be able to look into this “black box” — the soil
microbiome — and start to understand what the microbes are doing,
and how they’re influenced by the environment. And that’s exciting
because once we have that knowledge, we can start to use soil
microorganisms to potentially help mitigate the negative impacts of
You’ve spent many years studying one example of an
extreme soil environment — the permafrost. What makes the
microorganisms there distinct?
Permafrost is a special environment. A large fraction of the
terrestrial carbon is trapped in the world’s permafrost — about as
much carbon as is currently in the atmosphere and in plants
combined. The permafrost is like a huge carbon freezer.
What’s really important is that as the permafrost starts to
thaw, the microbes that are there start to become more active and
metabolize the carbon compounds stored in the soil. And as they
degrade them, the microbes produce greenhouse gases like carbon
dioxide and methane, which get released into the atmosphere and can
drive further warming.
Permafrost is covered by a layer of soil active with microbial
life and is characterized by high amounts of carbon (brown) and
liquid water (blue), but low levels of oxygen (green). When
permafrost thaws in lowlands, more water and less oxygen are
available, creating the perfect conditions for anaerobic bacteria
to thrive. As a result, the soil community fixes less nitrogen and
releases more carbon dioxide and methane into the atmosphere. At
higher elevations, however, permafrost thawing can increase soil
porosity, which allows oxygen to penetrate farther down. In this
condition, aerobic bacteria thrive and release carbon dioxide to
the atmosphere. In both scenarios, greenhouse gas output increases
as the frozen soils warm.
Bacteria, in the permafrost or elsewhere, all need carbon to
grow and produce cellular biomass. But they have other ways to get
energy. One of our more unexpected findings were a lot of proteins
for the reduction of iron within the frozen permafrost.
Microbes can reduce iron for energy — it’s a process that can occur
under conditions with no oxygen, but usually requires liquid
We were able to replicate this in the laboratory and show that
iron reduction is carried out by organisms living in frozen soil.
This was key to understand how they survive and — slowly — grow in
such low temperatures with little oxygen. It turns out that at
subzero conditions it is still possible to have liquid water
because salts become concentrated and lower the freezing point of
water. So the proteins we found were probably produced by the
active iron-reducing bacteria living in salt brines.
How is the polar microbial community responding to
We’re doing incubations in the laboratory and monitoring in
field areas where the permafrost has already started to thaw. I
have collaborations with scientists from several different areas in
the Arctic: Svalbard, Greenland and Alaska.
What we and others have found is that, as permafrost thaws, the
microorganisms that are there start
to change — it’s a real turnover. You get a different
composition of microorganisms, more of the ones that are better
adapted to degrading carbon versus other types of metabolisms. We
see a shift in function toward fermentation processes or methane
generation. Methanogens — bacteria that produce methane — often
increase in numbers. And that makes sense because they now have
access to it, if you compare them to the microorganisms in frozen
Using our molecular tools, we see not only which organisms are
there, but also what pathways they’re expressing to be able to
produce these gases. This is important because methane is a potent
greenhouse gas and its production can amplify global warming.
One way to see into the black box that is the soil
microbiome is by using “meta-omics” — a range of different
biological censuses. How can each “omic” help us understand the
Each “omic” technology gives you a slightly
different view. You start, on one end, by looking at the DNA in the
genomes. For these types of organisms, their identity is all about
the total number of genes and the type of genes they have — that’s
how we know who’s there. But you don’t know if those genes are all
expressed or not. The genomic view just shows you what they are
potentially capable of doing.
Scientists use a repertoire of molecular techniques to paint a
more complete picture of the make-up and dynamics of the soil
microbiome. The concept of the metaphenome of the community arises
from combining these separate analyses with information about the
local environment and other factors.
If you go to the next step, you can look at which organisms are
actively transcribing which genes into RNA, what’s
called the transcriptome. This gives us a clue about metabolic
processes that are active at a given time, and which ones are
favored under different conditions.
The next step is the proteome, because not all expressed genes
actually are translated into proteins. So, if you look at the
proteins that’s an even better confirmation that the expressed
genes are dictating the functions that were carried out in that
environment, at that particular point in time.
And then, the last step in this “omic” pipeline would be the
metabolome. Metabolites — the intermediate molecules of microbial
metabolism — are very valuable, because detecting specific metabolites gives
us clues about all the biochemical reactions that are occurring in
the environment. They are the ultimate signature of the metabolic
processes carried out by the microbial community.
To understand how microbes living in one particular
environment change as a whole, you’re looking at something called
the metaphenome. Can you describe what that
The metaphenome is a new concept. It’s a term that represents
the combined biological functions, such as using iron for energy or
carbon for growth, carried out by all the microorganisms living in
a community. You can think of a single organism that has a genome
and depending on the resources available or the environment,
certain genes are expressed into RNA, but not all — it depends on
the situation and can change over time.
If you look at the whole community, that would be a metaphenome:
the product of all of those functions carried out by all the
microorganisms. Studying that will allow us to predict the impact
of environmental change on the microbiome, as well as think of new
ways to manage our soil.
What do we know about the role of viruses and fungi in
We have a big research push right now on the soil virome — the
collection of DNA and RNA from all the viruses in a given spot —
and that is very exciting. We screened for hundreds and hundreds of
soil metagenomes and we were able to find what types of viruses are there. Some of these viruses
contain metabolic genes that could potentially help with nutrient
cycling in soil.
The viruses are probably really important, and we just don’t
know much about them. It is definitely a new frontier because these
viruses outnumber all of the other organisms that you have in
We’re also looking at fungi in grasslands, and one of the things
we’re really interested in is that when the soil starts to dry, the
water no longer connects different locations in the soil. The
microorganisms need water to be able to exchange metabolites and
interact with each other. So, in dry soils, you have these
disconnected “islands” of microorganisms. But fungi can grow these
long filaments, called hyphae, that can bridge these disconnected
islands and serve as the train for carrying nutrients back and
forth between bacteria and to other organisms in the system.
Droughts change the soil microbiome in subtle and not so subtle
ways. In grasslands, for example, groups of soil bacteria normally
communicate with one another by sending chemical messages through
water and through fungal threads called hyphae. In a drought,
however, hyphae may be the only option for communicating across
long distances. Metabolic interactions within the soil community
release carbon dioxide.
The soils of grasslands are another ecosystem you study.
How are the microbes there faring with climate change?
I’m concerned about how climate change will affect these highly
productive regions of the world, especially with increasing
Looking at the metaphenome, and the influence of the soil drying
on the metagenome, we have found that the microbial community
starts to shift its metabolism toward the production of metabolites
that help them survive dryness, like sugars and different kinds of
osmolites, molecules that help keep the cells from bursting when
the soil gets dry.
The thing that really impresses me is that we can now look at a
whole community and dissect what the community is doing in response
What other big questions are you trying to
One of them is: How do these microorganisms across different
kingdoms — the bacteria, viruses and fungi — live together in the
same system and interact? We don’t know how, because most studies
have looked at a single or a couple of organisms in isolation. So
how are they functioning as a community? That’s one of our big
questions. And then, of course, the second one is: How are these
community interactions impacted by climate change or by access to
different kinds of resources, like water?
Have these findings changed your view of the Earth’s
I do not consider soil to be dirt, let’s put it that way. It is
one of our most precious resources on the planet. Improper land
management, such as over-tillage and leaving the soil barren and
free of plants, is a problem because it causes erosion. And that
happens at a faster rate than new soil is being formed.
We have to conserve our soils. They are alive — they carry
billions and billions of microorganisms in a single gram. So, this
is a living resource that we have to protect from being eroded and
A sunny disposition isn’t just good for your mental health. It’s
good for your body, too. It can even add years to your life.
Sarah Pressman, a health psychologist at the
University of California, Irvine, has spent her career
investigating the link between positive emotions and physical
In the 2019 Annual Review of Psychology, she and her
colleagues explore why a positive outlook generates physical health
benefits. Knowable asked her about some of the high
points, and how doctors and their patients can make use of the
knowledge. This conversation has been edited for length and
CREDIT: JAMES PROVOST (CC BY-ND)
Psychologist Sarah Pressman
University of California, Irvine
How did you get interested in studying
For decades, researchers have been studying all the detrimental
ways that stress can make us sick and lead to pain, and minor and
major illness. As a graduate student, I got interested in the
opposite: What can protect our bodies against the harmful effects
of stress? At that time, in the early 2000s, the field of positive
psychology was really just starting. I saw a natural synergy there
— there are these positive factors, and maybe they could be
protective against stress and have health benefits, or at least
protect us against health harm.
And does a positive outlook make a measurable
The negative effect on your health of being socially isolated is
stronger than the effect of being overweight, a regular smoker or a
heavy drinker. That kind of comparison hasn’t been done yet in
positive emotion research. But there’s a host of studies — probably
in the dozens now — that show that people who are
more positive tend to live usually five to 10 years longer than
those individuals who are less positive. That’s a pretty large
What causes this effect?
We have a lot of hypotheses. Positive emotion changes our stress
perception so stressors don’t seem as bad. It changes how we react
to stressors, and it helps us recover. Both our stress reaction and
our stress recovery have been shown to predict important outcomes.
Pick a disease — heart disease, for example. If you feel calmer,
your blood pressure is lower, your heart rate is lower. And we know
one of the things that predicts heart disease is arteries blocked
up with plaques. And where do those plaques come from? Partially,
from damage from high-speed, high-pressure blood. If your blood
pressure is lower, and your heart rate is lower, you have less of
that turbulent blood flow, and therefore over time you might have
less damage to arteries and less plaque.
Positive emotions also change how our immune system works. We
don’t know exactly how, but we do know that if I make you feel
positive, if I make you feel calm, we change the numbers of your
immune cells, and we tend to drop your inflammation level. For
example, there’s a marker of inflammation called interleukin 6, or
IL-6. People who are generally more positive, or who are induced to
feel more positive, have lower levels of IL-6.
But even aside from that, when we are feeling positive, we’re
much more likely to engage in healthier behavior. We take better
care of ourselves, we’re more likely to sleep better and exercise,
we have a better diet. People who are more positive tend to have
more relationships, better-quality relationships. They’re more
likely to be married and stay married for longer. If you have good
relationships, those people will encourage you to take care of
That gives us some really compelling pathways for how this can
happen, both on the behavioral end and by directly altering
cardiovascular function, hormonal function, immune function. If I’m
happy today, that doesn’t mean I’m going to live longer. But if I’m
happy for a few years, that might make a difference.
How do we know that positive emotion causes better
health, rather than the other way around?
To do the perfect study would require that we experimentally
assign people to an intervention that makes them happier, or less
happy, and see if that affects longevity. That has not been done.
But we have a lot of studies of groups of people where we know the
health and the emotional state of each person at the start. We
control for sociodemographic factors, we control for medications
and immune function. So we know that those people who were less
happy at the beginning weren’t less happy because they were already more
Then we can look over time. If you control for smoking and
health at the start and you still see the effect of positive
emotion five or 10 years later, it’s more suggestive than a study
looking at people at just one point in time and just saying, “Oh,
happy people feel healthier.”
In a classic study, people with a more positive outlook were
less likely to get sick after experimenters introduced cold viruses
into their noses. The researchers measured the volunteers’ sickness
both objectively (by weighing a day’s worth of used tissues) and
subjectively (by asking the volunteers if they had a cold).
Have you also done experiments?
We measured people’s naturally occurring positive emotions. Then
they were experimentally wounded. It was kind of a nasty study,
actually. We damaged their skin by putting tape on it over and over
and ripping the tape off. We monitored to see how quickly water was
being lost from the skin surface. As that water loss decreases, we
know the skin cells are healing. This is really an immune-system
function test, because the more quickly your immune system is able
to traffic white blood cells to the injury, the faster you will
heal. We saw about a 20 percent shorter healing time for those individuals who were more
positive versus those who were less positive.
There is another study, not yet published, where we manipulated
positive emotion. There’s something called the facial feedback
hypothesis, where if you fake an emotion, it sends a message to
your brain that you’re feeling that emotion. If we trick people
into smiling by holding things in their mouth, it can trigger a
So we had people smile while getting a fake flu shot. Some
people were smiling and others were not. Those who were smiling had
about 40 percent less pain from that needle, and their heart rate
recovered faster from the stress of it.
Do we know that positive emotions — and not just the
absence of negative ones — are causing the benefit?
That we actually know really, really well. Through the last 20
years of research, almost every study does a good job of accounting
for that by controlling for negative emotions.
Time and time again, you see that it really does seem to be the
presence of positivity, independent of negativity,
that’s driving health effects. It’s the presence of positive
emotions, not the absence of negative ones, that can help undo
stress. If I have to give a talk and I’m feeling neutral, that
isn’t helping me — but if I can say, “Actually, I’m really excited
about giving this talk,” that can change my stress trajectory. That’s
very different than the absence of a negative emotion.
Are there health conditions where a positive attitude
For individuals who have a serious chronic illness that’s far
gone — stage 4 cancer, end-stage kidney disease — the data are
inconsistent. Some studies show benefit, some show harm, some show
no effect. If we’re talking about a minute immunological change
from laughing, that’s not going to kill millions of cancer
On the other hand, if you are feeling hopeful and positive, and
able to adhere to your doctor’s recommendations, and take the
medications that you’re supposed to, and exercise when you’re
supposed to, and quit smoking, those things are helped by positive
emotions, and can have an important role in helping at earlier
This is something we have to work on, because if people want to
design positive interventions for these severe illnesses, we have
to really understand when it will be helpful. That’s a really
important next step for the field.
Isn’t there a risk that people with serious diseases
will be stigmatized into thinking it’s their own fault for not
being more positive?
We certainly don’t want to say that. There’s absolutely no
evidence in health psychology that being unhappy causes cancer, or
causes disease to happen. If someone gets diagnosed with cancer,
you don’t want to tell them to be happy all the time. There’s good
evidence that keeping negative feelings locked up inside is harmful
to our health. They have to go somewhere. You have to let it out —
express your negativity and process it. Once you’ve accomplished
that, we can try to teach you how to find benefit.
It is very important for people to deeply understand the power
of mind over body, because if you are depressed and you are
stressed it can be hurting you, and we want to help you cope with
that. There is value in pursuing happiness. It’s not a selfish,
silly, soft thing that you don’t have to do. This is actually an
important piece of being a healthy human. And at a time when your
health is compromised it can be especially important.
Are there ways to change people’s happiness level?
Aren’t some people innately Eeyores and others Poohs?
Some work suggests that as much as 40 percent to 50 percent of
happiness is based on genetics — you just luck into being born a
more positive person. But that leaves a lot of room to
Although some people naturally tend toward a more positive or
negative outlook — like Winnie the Pooh and Eeyore — studies
suggest that happiness is based on much more than genetics or
innate setpoints. Exercise, relationships and personally meaningful
activities can help an Eeyore see the bright side, which may also
CREDIT: TANUHA2001 / SHUTTERSTOCK
A good amount of our day-to-day wellbeing — maybe 30 percent to
40 percent — is due to how we choose to spend our time. We can
choose to spend our time on things we know improve positive
emotion, like spending time with the people we love, having good
relationships, getting enough sleep, exercising.
But on top of that, there are some specific, well-researched
interventions — little tweaks that can help you focus on positive
things. We can train our brains to hang onto positive emotions,
which should help promote that positive emotion in our daily lives.
Some of the more popular activities are gratitude exercises, where
before you go to bed you write down three things you’re grateful
for, and meditation.
The nice thing about happiness is you don’t have to buy some
expensive medicine. Much of this is free. Happiness is not just a
luxury that rich people should be pursuing — it’s something that
absolutely everyone should be investing time in every day.
Alfalfa, oats and red clover are soaking up the sunlight in long
narrow plots, breaking up the sea of maize and soybeans that
dominates this landscape in the heart of the US farm belt. The
18-by-85-meter sections are part of an experimental farm in Boone
County, Iowa, where agronomists are testing an alternative approach
to agriculture that just may be part of a greener, more bountiful
Organic agriculture is often thought of as green and good for
nature. Conventional agriculture, in contrast, is cast as big and
bad. And, yes, conventional agriculture may appear more
environmentally harmful at first glance, with its appetite for
synthetic pesticides and fertilizers, its systems devoted to one or
two massive crops and not a tree or hedge in sight to nurture
wildlife. As typically defined, organic agriculture is free of
synthetic inputs, using only organic material such as manure to
feed the soil. The organic creed calls for caring for that soil and
protecting the organisms within it through methods like planting
cover crops such as red clover that add nitrogen and fight
But scientists bent on finding ways to produce more food
globally with as little environmental impact as possible are
finding that organic farming is not as green as it seems. In a
simple contest of local environmental benefits, organic
wins hands down. That doesn’t hold true on a global scale, though,
because organic farming can’t match the high-yield muscle of big
agriculture. A widespread shift to organic would leave billions
hungry, researchers predict, unless farmers put more land to work
by turning now-unfarmed habitats into food-producing fields — doing
more harm than good to natural ecosystems.
Red clover (foreground) grows alongside corn (background) in a
crop rotation experiment at Iowa State University’s experimental
farm in Boone County.
CREDIT: PAULA R. WESTERMAN
“Organic farming is often seen as synonymous with sustainable
farming, but it is not the Holy Grail of sustainable agriculture,”
says Verena Seufert, an environmental geographer at VU Amsterdam
who studies sustainable food systems. But the strategies being
tested in those fields in Iowa, and similar methods finding their
way onto hundreds of millions of acres of farmland globally, might
just be. In experiments in Europe and across North America,
agronomists are testing hybrid approaches that weave together the
green touch of organic farming with a dash of chemical fertilizer
and pesticide applied only when needed — an approach known as
low-input agriculture. They hope that this cocktail of farming
techniques will steer future farming to a truly sustainable
This shift toward fusion farming comes at a time of increasing
political interest in greener, more productive agriculture. Heads
of state and governments will meet in September at the United
Nations in New York for a summit to discuss progress toward 17
global sustainability targets to be met by 2030. Producing more
food with fewer impacts is key to reaching many of these goals,
which include ending hunger and slashing water pollution. That’s
also in line with meeting a separate set of targets that countries
party to the Convention on Biological Diversity are working
Many experts worry that little progress has been made,
particularly on saving biodiversity. But others are confident that
a greener agricultural revolution is not far off. “It’s optimistic,
but it’s not a pipe dream,” says Jules Pretty, an agroecologist at
the University of Essex in the UK, who studies sustainable
agriculture. “Agriculture could be at a turning point.”
And turn it must, says Andrew Balmford, a conservation scientist
who studies farming’s impacts on biodiversity at the University of
Cambridge in the UK. “Agriculture is by far the biggest threat to
biodiversity, and that will only get worse as we try to feed 10
billion people in the future.”
Many studies show that organic farming is beneficial to
biodiversity, especially for creatures like birds, spiders and some
soil-dwelling insects. The effect is less pronounced for animals
like butterflies. Outcomes for other critters, such as beetles, are
more uncertain, with individual studies showing a breadth of
Over the next 30 years, agricultural economists estimate, food
production will need to at least double to feed billions of extra
bellies as the global population grows. But the current farming
system cannot carry on as it is without wreaking great damage,
experts conclude. The International Union for Conservation of
Nature, a science-based conservation organization, says that of the 8,500 threatened species it has
studied, agriculture alone imperils 62 percent, ranging from
the elegant African cheetah to California’s lovable Fresno kangaroo
rat. Fertilizers running off farmland and into rivers and lakes are
fueling toxic algal blooms across the world, suffocating fish and
damaging ecosystems. And agriculture has its hand in around
80 percent of global deforestation.
The organic movement was sparked, in part, from similar
environmental concerns in the early twentieth century. With its
roots in Europe and the US, organic farming grew from the idea that
soils nurtured with compost rather than synthetic fertilizers could
safeguard the soil and biodiversity while producing more nutritious
food. Today, organic produce is a must-have stock on the shelves of
many major Western supermarkets, and organic farming is practiced
in more than 180 countries, on more than 172 million acres of
farmland. Although this is still just 1.4 percent of global
agricultural land, land farmed organically has increased more than
sixfold since 1999 and is rising.
Organic farming could easily spread further and help put more
food on the global dinner table, says John Reganold, an
agroecologist at Washington State University. “In many ways,
organic farming is leading the way towards food security and
sustainability because it is a well-recognized farming system that
is economically successful — and so more farmers want to try it. I
think we owe credit to organic for that,” he says. But he and many
others who have studied the issue say that without a massive change
in diet, organic could never grow enough food globally on existing
farmland despite its demonstrated pluses.
Many studies have shown that organic farming has benefits for
biodiversity on farms. For example, in an assessment comparing organic and conventional
farming published in Science Advances in 2017, Seufert
reported that organic farms host up to 50 percent more organisms
such as bees and birds than conventional farms. They nurture
greater biodiversity largely because they don’t use synthetic
herbicides and pesticides, allowing plants, insects and other
animals to thrive. Farm workers also benefit from lower pesticide
exposure, Seufert says.
The benefits of organic farming depend a lot on what is being
measured. For a variable like low pesticide residues, organic
farming has clear benefits over conventional farming, as indicated
by the petal extending beyond the red circle, which demarks where
organic performance equals that of conventional farming. But for a
variable like low nitrogen loss, organic farming’s benefit
diminishes when output is assessed (right) rather than area
Organic farms also take better care of soil than average
conventional farms, studies show. Enriched with compost from rotted
animal manure or plant matter, organic soils can contain up to 7 percent more
organic matter than their chemically enhanced counterparts,
according to Matin Qaim, an agricultural economist at the
University of Goettingen in Germany, and colleague Eva-Marie
Meemken, writing in the 2018 Annual Review of Resource
Economics. Organic matter, rich in diverse microbes, is key to
the health and structure of soil, helping it hold on to water and
Qaim and Meemken report that, acre for acre, organic farming
consumes less energy largely because it doesn’t use synthetic
fertilizers. It also releases lower levels of some greenhouse gases
such as carbon dioxide and methane, and leaches fewer polluting
nutrients such as nitrates from fertilizers into rivers and
groundwater. Organic fields are also an experimental ground for
greener farming techniques, such as planting cover crops including
the leguminous hay crop red clover (Trifolium pratense).
Cover crops help suppress weeds and guard against erosion.
Yield is the one crucial feature where organic farming falls
short, Qaim concludes. Organic yields are on average up to 25
percent lower than conventional farming yields. Some crops grow
better than others under organic conditions: Legumes, which fix
nitrogen from the air and thus can meet some of their own nitrogen
needs, tend to produce deficits of just 10 to 15 percent. But
yields of nitrogen-thirsty cereals are 21 percent to 26 percent
lower on organic soils, due to limited nutrient supply as well as
greater susceptibility to pest outbreaks and encroachment by weeds,
“The facts are not in favor of organic — the observation that
organic yields are lower than in conventional practices cannot be
denied,” he says.
Different crops grown in the same field at the same time can
boost yields and help control weeds and pests. Here, strips of corn
grow alongside alfalfa and soybeans in test plots at the US
Department of Agriculture’s Agricultural Research Service Farming
System project, in Beltsville, Maryland.
CREDIT: MICHEL CAVIGELLI / USDA-ARS
Small yields add up to a big problem. Switching all the world to
organic would mean turning 24 percent more natural habitats into
agricultural land to meet future demands, researchers
calculate. Small yields also drive up greenhouse gas emissions
produced by organic farming because land must stay working rather
than being allowed to regularly go fallow. Organic’s land-use costs
would undo much of the ecological good that organic brings locally,
Organic advocates, however, question the size of yield gaps
reported in much of the scientific work. The Rodale
Institute, an organic advocacy and research center in Kutztown,
Pennsylvania, says its own work shows that under certain conditions
organic farming can match or exceed conventional yields. Andrew
Smith, the institute’s chief scientist, acknowledges that organic
yields are overall lower. But he says they have plenty of scope to
grow if greater investment is made in developing crop and animal
breeds better suited to organic’s challenges, and in doing more
research on best practices. Global funding for research on organic
farming is less than 1 percent of that spent on conventional
farming and food, according to a 2017 report from the International Federation of
Organic Agriculture Movements.
Conventional farming’s failures
The researchers who conclude that organic could not feed the
globe’s growing population also recognize that conventional
agriculture can’t carry on as it is, either. So agronomists are
doubling down on the middle road, testing a fusion of techniques
where farmers use green practices topped with synthetic inputs when
necessary. Many of these green techniques, such as planting cover
crops and growing different crops in the same field one year to the
next, were once routinely used in agriculture to manage weeds and
soil health but fell out of favor after World War II when the cost
of synthetic fertilizers and herbicides dropped. These methods are
now making a supercharged comeback in the low-input agriculture
Studies are starting to show that low-input fusion farming comes
up trumps for both yields and the environment. After an eight-year
experiment ending in 2016, agronomists at the universities of
Minnesota and Iowa State reported promising results from three-crop rotation
systems on a 22-acre experimental farm at Iowa State. The crops
were switched over periods of two, three or four years and assessed
for yield, profit and environmental effects such as soil erosion
and nitrogen leaching into rivers and groundwater.
Average yields in the Marsden Farm crop rotation experiments are
higher than that of conventional commercial farms in Boone
In the two-year crop rotation, researchers planted maize and
soybeans in alternating years, but added a mixed crop in the
three-year rotation, planting oats and red clover together for year
three. They planted oats along with a different legume, alfalfa, in
year three of the four-year rotation field, then let the alfalfa
keep growing into the fourth year, after the oats were
The team was able to slash the input of synthetic chemicals.
Researchers added fertilizers in the two-year rotation plots at
rates typical of conventional farms, but used substantially less in
the three- and four-year rotation plots: on average 85 percent and
91 percent less synthetic nitrogen (13 and 8 kilograms per hectare
per year, respectively). The researchers added manure to boost
nitrogen but it contained about half the amount of nitrogen that a
full application of synthetic fertilizer supplies. They also added
substantially less herbicide active ingredient to the low-input
maize and soybean crops: 94.8 percent (0.06 kg/ha) and 92.5 percent
(0.12 kg/ha), respectively. Herbicide application did not differ
across the longer and shorter rotations.
Yields rose as the number of rotations increased and were
unaffected by the lower herbicide use in the longer rotations. On
average, maize yields were 4.5 percent higher and soybean yields 25
percent higher in the three- and four-year rotations compared with
the two-year rotations. The alfalfa and clover steps are key for
this effect, says Matt Liebman, an agronomist at Iowa State and one
of the study’s authors. “You begin to see big changes in nutrient
dynamics because the hay crops like alfalfa and clover take
atmospheric nitrogen and put it into the soil” for the crops that
follow, he says. “So you don’t have to have anywhere near as much
Problems with weeds and disease also looked somewhat better.
Despite a lower use of herbicide in the three- and four-year
rotations, weeds intruded equally in the two- and four-year
rotation plots. And soybeans grown in the longer rotations
succumbed less often to soybean sudden death syndrome, a fungal
infection common to the Midwestern farm belt. “The crop rotations
typically result in much more effective management of insect
disease and weed pests with much lower investment in chemical
pesticides because you disrupt the life cycles of many of the pests
that are specialized for particular crops,” Liebman says.
Finally, the low-input, longer rotation strategies also had
environmental benefits. The potential harm to freshwater ecosystems
caused by the herbicide (known as toxicity load) was 99.9 percent lower in the low-input maize plots than
in the conventional maize plots. And though the longer rotations
required more labor, profits for all three rotation systems were
Narrow plots of corn (m), soybeans (sb/s), oats (g), and alfalfa
(a) grow at Iowa State University’s Marsden Farm where agronomists
tested how crop rotations and low levels of synthetic inputs, like
herbicides and fertilizers, affect yields. All three crop rotations
(2-year, 3-year and 4-year) were tested in four replicate blocks
(1, 2, 3, 4). The more diverse crop rotations had yields that were
equal to or better than the conventional system, despite receiving
fewer synthetic inputs.
CREDIT: A. DAVIS ET AL / PLOS
Balancing yields and pollution
Other studies in Europe and across the US are reporting similar
results. A meta-analysis of 15 studies done in the US, Canada,
France, Sweden, Switzerland and Norway concluded that yields of
maize grown under low-input conditions were equal to those produced
under conventional conditions, and 24 percent higher than organic
crops. Wheat yields were 12 percent lower than conventional, but 43
percent higher than organic, according to the analysis, published in 2016 in Agronomy Journal.
On average, crops grown under low-input conditions received less
than half the synthetic pesticide applied to conventionally grown
crops and were often cultivated as part of a crop rotation that
included more plant species than in conventional systems.
Agronomist Laure Hossard of the Montpellier campus of the French
National Institute for Agricultural Research, a coauthor of the
meta-analysis, says it’s unclear why wheat yields dropped but maize
yields didn’t under low-input conditions. Perhaps wheat succumbed
more to uncontrolled disease or needed more fertilizer. Still, the
low-input wheat yield losses were small, and the study’s overall
conclusion is that low-input farming can dramatically cut back on
pesticide use without drastically harming yields.
There are some potential downsides to low-input farming, Hossard
says. Money spent on pesticides and fertilizers may not always
compensate for lost income from slightly lower yields. Although
studies have shown that it is possible to cut pesticide use by around 30 percent without
reducing farmers’ income, these calculations may vary from year
to year as prices for crops and synthetic inputs fluctuate. Also,
low-input crops don’t command higher prices like organic products
do, so they may be less profitable than conventional products, she
Even as researchers fine-tune low-input strategies in
experimental plots, farmers are beginning to apply these tactics in
their own fields. It’s unclear how many farmers are taking on a
fusion farming approach, but a survey of 2,012 farmers across the
US found they are increasingly using green techniques, such as
planting cover crops, and that acreage planted in cover crops
nearly doubled between 2012 and 2016.
Organic crops such as corn (pictured) typically produce lower
yields than their conventionally grown counterparts. That casts
doubt on the ability of organic farming to feed the world’s growing
population. But fusion farming techniques, which combine organic
and conventional approaches, have higher yields, providing a path
to feed more people while reducing environmental impacts.
Plant biologist Pamela Ronald is concerned with the pressing
problem of feeding the world without destroying it. The question of
how to grow enough food for an expanding global population has
grown more urgent in the face of climate change. And it’s only made
harder, she says, by the push-back against the use of the genetic
tools now at scientists’ disposal.
Ronald’s views have emerged from nearly 30 years of research on
how plants resist disease and tolerate stress, work that is ongoing
in her lab at the University of California, Davis. Much of that
work has focused on rice, a staple crop that feeds nearly half the
globe. While she’s an outspoken advocate for using genetic
engineering to modify crops — her TED Talk The Case for Engineering Our Food has
been translated into 26 languages and watched more than 1.7 million
times — she’s also married to an organic farmer, Raoul Adamchak.
Together, they wrote the book Tomorrow’s Table: Organic Farming, Genetics,
and the Future of Food , exploring how the best of both
approaches might be needed for long-term sustainability.
CREDIT: JAMES PROVOST (CC BY-ND)
Plant biologist Pamela Ronald
University of California, Davis
We spoke with Ronald about her research and her views on genetic
modification and its place in the sustainable agriculture toolbox.
This conversation has been edited for length and clarity.
How do genetically modified crops fit into the
sustainable agriculture landscape?
Sustainable agriculture has three pillars: social, economic and
environmental. It creates food that’s nutritious, it allows farmers
to reduce the amount of land and water they use, to foster soil
fertility and genetic diversity, and to reduce toxic inputs. And it
enhances food security for the very poorest farmers and families in
the world. So, for example, if you can breed resistance into a plant, whether through
conventional or genetic engineering, and that means you can reduce
the amount of sprayed chemicals you use, that’s part of sustainable
Any type of agriculture is pretty challenging. Most farmers are
trying to move their farm toward more sustainable approaches.
Unfortunately, there’s no magic bullet because farmers in different
regions of the world face different challenges, grow different
crops and have different markets.
The book you and your husband cowrote is titled
Tomorrow’s Table. What does tomorrow’s table look like to
In the book, we describe what’s on our table and explain how the
foods were developed — the kinds of genetic techniques and organic
farming techniques used to produce that food. We try to give the
reader an idea of what geneticists do and what organic farmers do.
We have a number of recipes.
But the book isn’t about nutrition, it’s about: How do we
produce and provide that nutritious food with minimal environmental
impacts? How do we ensure that farmers and rural communities can
afford the food? How do we address this critical challenge of our
time: to produce sufficient, nourishing food without further
devastating the environment? There are a lot of issues, a lot of
people on the globe right now, and even more in the future. They
all need to eat.
Sticky “mutant” rice, included in this recipe from the book
Pamela Ronald and her husband wrote, came into being more than a
thousand years ago. The stickiness arose thanks to a spontaneous
genetic mutation that disrupted the gene for making the starch
amylose, which helps make non-sticky rice fluffy. The recipe
juxtaposes that ancient genetic modification with a more modern
one: genetically engineered papaya, which farmers began planting in
the late 1990s after papaya ringspot virus decimated orchards.
Does your husband have a different view of the future of
It’s a shared view. We both think people should focus on the
challenges and not get distracted by the concept of genes in our
food. We really want to use all the tools that are available and
use scientific-based farming practices, such as those that minimize
pests and disease. There are many organic farming practices that
are very useful, such as crop rotation.
It’s the combination of farming strategies and genetic
strategies that are going to continue to be quite important for
producing our food and moving forward to a sustainable farming
future. Farming is destructive. But, as my husband says, we farm
because we have to eat. Some people say, well, let’s change our
diets, or reduce waste. Those are both important, but we still need
technological change. All these aspects are even more critical as
the population continues to grow.
A lot of your research has focused on rice, a hugely
important staple crop. Did you always want to work on
I was working on peppers and tomatoes as a graduate student at
UC Berkeley and as I was making the transition to a postdoc, I
thought, what do I want to do, because this may last my whole
career. And I decided to work on rice because it feeds half the
world’s people. It’s also a very good genetic system; it’s easy to
do genetic analysis of rice. So I thought if we can make any kind
of incremental advance we could potentially help millions of
One of those advances has been the development of
flood-resistant rice. I’ve seen so many photos of rice paddies
flooded with water, doesn’t rice tolerate flooding?
The rice plants that many of us are familiar with grow well in
standing water. But most rice plants will die if they are
completely submerged for more than three days. When the leaves are
submerged, they can’t carry out photosynthesis. My UC Davis
colleague David Mackill was working with this ancient variety of
rice, discovered at the International Rice Research Institute, that could be
completely submerged in water for two weeks, and then can start to
grow again when the water is removed. So this was very, very
Breeders then tried to use conventional breeding to introduce
this trait from the ancient variety into varieties grown by
farmers. But when you cross-pollinate with another variety, even
though it has a nice trait, you can bring a lot of other traits you
don’t want. So, the result from conventional breeding were rice
varieties that were rejected by farmers because they had traits
that the farmers did not want such as reduced yield, or a change in
the texture of the rice grain.
How did you tackle the problem?
First, we carried out the initial work of isolating the flood-tolerance gene, called
Sub1a, from the ancient variety. Then we introduced the
gene into a model rice plant using genetic engineering. We then
grew up those plants and submerged them, in large tanks in our
greenhouses for two weeks.
The plants that carried the Sub1a gene were very
robust; you could see the difference right away. Plants without
Sub1a turned yellow, had very long leaves and soon died.
This is because when the leaves try to grow out of the water, they
deplete their chlorophyll content and energy reserves. But the
plants that carry the Sub1a gene just stay kind of
metabolically inert — they don’t grow very fast, they just kind of
wait out the flood. And when the flood’s gone, they start to
regrow. The Sub1 plants remained green and healthy, indicating we
had indeed isolated the correct gene.
Is Sub1 rice now being grown by farmers?
Yes. As I described we used genetic engineering tools to isolate
and validate the submergence-tolerance gene in the greenhouse. That
genetic knowledge was then used to develop a flood-tolerant variety through a
different approach called marker-assisted breeding. That work
was done by the International Rice Research Institute. The ancient,
flood-tolerant variety was cross-pollinated with a modern variety
that farmers like because of its flavor and high yields. Seeds
derived from those hybrids were planted, and tested for the
preferred genetic fingerprint that included Sub1a but did
not carry genes from the ancient variety that affected traits
important to the farmers.
Rice bred to contain the Sub1a gene can survive even
when completely submerged for 17 days. This flood-tolerant rice
yielded 3.8 tons per hectare (pile on left), compared with 1.4 tons
per hectare for the same variety lacking the flood-tolerant gene
(pile on right).
CREDIT: INTERNATIONAL RICE RESEARCH INSTITUTE
Marker-assisted breeding is very focused, you don’t drag in
genes that you don’t want, you can just drag in a very small region
of a chromosome. And because the genetic fingerprint can be
determined at the seedling stage, it saves a lot of time and labor
that would normally be spent on submerging hundreds of plants.
Farmers have now been growing Sub1 varieties for several years.
In 2017, more than 5 million farmers grew it. Sub1 rice is
disproportionately benefiting the poorest farmers in the world, who often have the
most flood-prone land. Compared with conventional rice varieties,
farmers growing Sub1 rice are able to harvest three- to fivefold
more grain after floods. The Intergovernmental Panel on Climate
Change predicts that flooding will become more
frequent and last longer as the climate changes.
These various breeding approaches underscore the
difficulty in defining “genetically modified” crops. How do you
The term “genetically modified” is scientifically meaningless,
and so it’s not useful. The FDA does not use the term.
With Sub1 rice, for example, scientists can introduce the
Sub1a gene with either genetic engineering or
marker-assisted breeding. In each of these cases, the genetic
region that’s introduced is smaller than the huge number of genes
that you bring in with conventional breeding, in which you are
mixing two genomes together.
Grafting is another kind of conventional breeding that mixes two
genomes. There are a lot of grafted varieties on farms in
California. The walnuts harvested in California are actually a
graft of two different species where the rootstock is a different
species than the top part of the plant. Then there are foods that
we eat that have been developed through radiation and chemical
mutagenesis, like grapefruit. Those approaches create many random
uncharacterized changes in the genome and are not regulated. They
can also be sold as “certified organic.”
What do you think most consumers mean when they say
genetically modified organism or GMO?
I think some consumers are concerned only about plants
engineered to contain genes from another species, like the
bacterial Bt gene. It sounds a little strange to put
bacterial genes into a plant, but it is important to consider the
risks versus the benefits. Organic farmers spray Bt to prevent
insect damage to their crops. It is safe to use. But spraying Bt is
not always effective. In Bangladesh, for example, there is an
insect that can destroy an entire eggplant crop and spraying
doesn’t keep the insect from getting into the plant. And the Bt
sprays are expensive and difficult to get. So Bangladeshi and
Cornell scientists engineered eggplants with the bacterial gene
so that the plants produce the Bt organic
insecticide in the crop. And it’s been tremendously successful
over the last five years, allowing farmers to reduce their
insecticide sprays dramatically.
Among the challenges to feeding the world’s growing population
is crops lost to disease. Developing rice strains that can resist
infection by the extremely destructive rice blast fungus (spores
shown) is an active area of research.
CREDIT: DONALD GROTH, USDA FOREST SERVICE
One reason that the FDA and many scientists don’t find the term
“GMO” useful is because it means different things to different
people. You can’t really compare an eggplant engineered for farmers
in Bangladesh that has allowed them to reduce insecticide use to,
say, the “Golden Rice” plants engineered to have higher amounts of
provitamin A to help save the lives of children in developing
countries, or herbicide-tolerant canola grown in developed
countries. These are different traits, different crops, and
different people benefit.
Why do you think there is so much distrust of modern
I think part of the issue is that less than 2 percent of people
in the US are farmers and are somewhat removed from food
production. Many people aren’t familiar with the challenges faced
by farmers and may not understand that Bt crops have massively
reduced the use of insecticides in the US and globally. The World
Health Organization estimates that 200,000 people die every year
from misuse or overuse of insecticides, primarily in less developed
The use of genetic technologies has become very politicized like
several other issues in science — vaccines, climate change. The
major scientific organizations have concluded that the climate is
changing, that vaccines can save lives, and that genetically
engineered crops are safe to eat and safe for the environment.
I think most of us know someone who has been very sick and we
would do anything to help them. Often that means using a
genetically engineered drug. Or maybe we know someone with diabetes
who uses genetically engineered insulin. We accept that use of the
technology, most consumers accept it, because they have some
understanding of it in their own world. But I think very few
Americans have seen a malnourished Bangladeshi kid, so it’s not in
their world. It’s not that they aren’t compassionate, it’s that at
some level they don’t understand or see it. They don’t really
understand why farmers need genetically improved crops.
I think people understand with computer technology that there
are different applications of that single technology. People
wouldn’t say “computers are bad.” But somehow it gets confusing to
people when it comes to agriculture, maybe because so many of us
are so removed from actual farming.
A frog the size of a fingernail. A poncho-clad farmer leading
his mule. A tree, some intertwining leaves, a silhouetted figure
holding a pot. Such logos are stamped on labels of coffee, cocoa,
mangoes, jeans and myriad other products, certifying that the
object for sale is in some way “sustainable” — made, in other
words, in a way that meets humanity’s needs without jeopardizing
the ability of future generations to meet their own.
The idea of sustainable economic development was first proposed
in the 1980s, when a commission established by the United Nations
concluded that human activities were exhausting
natural resources and launched efforts to tackle the problem. The concept spans three
dimensions: social (for example, ensuring workers are treated
fairly), economic (increasing profits, improving quality of life)
and environmental (managing land, water and biodiversity so they
aren’t lost to future generations). And over the years, a slew of
standards that focus on these dimensions in different ways have
been implemented by nonprofits and multinational companies.
CREDIT: JAMES PROVOST (CC BY-ND)
Environmental scientist Eric Lambin
Consider coffee farms. The Rainforest Alliance standard (that
little green frog) requires coffee farmers to increase tree cover
on their plantations and ensure fair treatment of workers, among
other things. Fair-trade certifications — there are a variety, with logos of leafy
yin-yangs, dancing figures and more — require farmers to use water
efficiently, prohibit bonded labor and offer safe working
conditions. The Smithsonian Migratory Bird Center’s Bird Friendly
certification checklist requires a coffee farm to have at
least 10 different tree species and at least 40 percent of the
plantation covered in shade. Farmers who comply can then sell their
certified products at a higher price.
These efforts have led to a deluge of more than 400 ways to
certify various goods and services — and much confusion for those
consumers who want to choose responsibly. (At my local grocery
store, I couldn’t find a single package of coffee without one of
these many symbols, or at least the word “sustainable,” printed on
it.) What’s more, the data are still unclear on which
certifications truly make a product better for the planet or for
farmers, says environmental scientist Eric Lambin of Stanford
University and the Catholic University of Louvain, who co-authored an article on the topic in the 2018
Annual Review of Environment and Resources.
Lambin says that one thing is clear: Certifications are most
likely to work when, in addition to consumers following through on
their green intentions by buying certified products, nonprofits put
significant muscle into the effort and governments offer their
support. This conversation has been edited for length and
Why are there so many different ways for a product to
get certified as sustainable?
In the 1980s, it was largely thought that sustainability
objectives would be achieved via government policies that would
mandate certain basic sustainability practices. Over the years it
became clear that most states — especially developing countries —
were not able to do this effectively because they had other
priorities and limited capacity. This whole realm of voluntary
sustainability standards emerged when private actors, such as
non-governmental organizations, various societies and private
companies, stepped in. The goal at that stage — was to achieve
“governance without government,” a slogan at the time.
This history explains why each certification emerged
independently, rather than in an organized fashion. The traders or
a local non-governmental organization might start an initiative to
make timber or coffee production more sustainable. Someone else
might look at golf courses, or water consumption. A lot of these
certifications are specific to one commodity, or to a place, such
as the tropical rainforest. It’s an uncoordinated, sort of
Sustainability standards can emerge from a number of different
routes and players. Variables include who sets the standards, such
as an NGO or private company, and who verifies compliance: the firm
who set the standard (first party), a party associated with the
firm (second party), or an independent group (third party).
Is it useful to have so many standards?
Yes and no. Some level of competition forces standards to
demonstrate effectiveness. But too much duplication leads to wasted
resources in terms of transaction costs, manpower, verification
work, fundraising and advertising.
The other problem is that when you have many organizations that
do exactly the same thing, one of them might create a very easy
sustainability certification that anyone can get because it doesn’t
require much change. And that leads to a race to the bottom. But
some do try to be more effective and demonstrate real impact.
Are some standards emerging as clear
We are only starting to have reliable evidence on this. Until
four or five years ago, most studies trying to evaluate the impact
of the standards were not sufficiently rigorous. Even now, the
evidence is still very mixed.
For example, we found that in one province of Colombia, coffee
farmers who were Rainforest Alliance–certified planted more trees
on their farms compared to neighbors who were not certified. We
also noticed that these farmers’ children had studied more years at
school than the kids of their neighbors who were not certified.
There was a significant difference between the two groups.
It turned out that because a farm must meet 90 criteria to
receive the certification, many of these farmers, who were not
literate, were quite happy to keep the kids at school for a few
more years so they could help with the administrative work of
reading forms and filing reports to get certified. In this way, the
certification provided more than just environmental benefits
— it provided social and potentially economic benefits, too. When
kids get a few additional years of schooling, it has a positive
impact — not just on farming, but also on job opportunities and
But when another research group studied coffee certification in Honduras, they
came up with slightly different results: While few Rainforest
Alliance–certified farmers were expanding their fields into
forests, farmers certified by Fairtrade, UTZ and 4C were still
Growing coffee under a tree canopy, as shown here in Nicaragua,
benefits farmers and is more environmentally friendly than coffee
grown in open fields.
CREDIT: JOHN MITCHELL / ALAMY STOCK PHOTO
Why the difference?
Mostly because the social and policy context in Honduras is
different. Also, these studies are done by different teams, and we
use slightly different methods and definitions, making it tough to
compare results. In Honduras, they surveyed farmers to ask about
forest clearing but not about tree planting, whereas in Colombia,
we used satellite data to find out. The field is only starting to
adopt a systematic approach to compare and evaluate the
effectiveness of eco-certification.
But these nuanced findings led me to look beyond evaluating the
effectiveness of a single standard. In more recent work, we have
found that these sustainability certification standards become clearly successful and transformative
when they are supported by, or get integrated into, public
How does a voluntary certification become public
Here’s an example: Bolivia was reforming its forestry code a few
years ago. A few forest concessions [public lands that timber
companies lease from the state for wood extraction] were
eco-certified under the label of the Forest Stewardship Council
(FSC), and they were more productive and profitable. So the
government decided that rather than write a forestry code from
scratch, they would reuse entire segments of the FSC guidelines as
the new code.
Suddenly this certification system that was purely voluntary was
now public policy.
Large multinational companies also contribute to such upscaling.
For example, a company such as Unilever might say that by 2020 or
2030, they commit to completely eliminating tropical deforestation
from their supply chain. That means the property of every producer
from whom they buy palm oil has to be deforestation-free. With a
large company, that’s a significant proportion of the global palm
But then how does the multinational meet that goal? They might
try to implement a change by mandating a certification by the
nonprofit Roundtable on Sustainable Palm Oil (RSPO) for all
their palm oil suppliers. So now suddenly every producer who wants
to sell to Unilever has to be RSPO-certified. Again, you have this
powerful upscaling mechanism of a voluntary certification system.
And that’s when you start to have a big impact.
It’s almost as if the idea of governance without
government doesn’t really work.
Exactly — and for another reason that’s even more fundamental.
One of the reasons the Rainforest Alliance coffee certification was
successful in Colombia, or RSPO for palm oil is more likely to work
in the Sabah state in Malaysia, is because these governments made
sustainability a goal with a range of supportive policies.
At a palm oil plantation in Malaysia, workers transport fruit by
hand to trucks at the ends of rows of trees. This plantation is
certified by the Roundtable on Sustainable Palm Oil, a nonprofit
organization that develops and implements global standards for
sustainable palm oil.
CREDIT: ELIZABETH FITT / ALAMY STOCK PHOTO
In Colombia, for example, the Colombian Coffee Growers
Federation supported cooperatives of producers to help smallholders
meet sustainability standards. These cooperatives then promoted new
varieties of plants, introduced technology and explained the
benefits of certification to farmers. The government also worked to
develop an export market, boosting the reputation of — and demand
for — Colombian coffee as this high-quality, eco-certified
These supportive policies are necessary for a certification
system to succeed. It’s not just that you need the government to
upscale a voluntary certification, it’s that government
intervention is necessary to make efforts successful in the first
place, beyond the most progressive producers.
Do consumers also contribute to the success of
For example, you or I make an individual decision to buy this
pack of coffee or chocolate over another one, perhaps based on
packaging marked with a “certified sustainable” label. For these
products, there’s a very short supply chain linking the producer to
you, the consumer. So the pressure from the consumers on retailers
— and therefore on the whole supply chain — is much more direct,
and there’s a greater incentive for producers to make this claim of
The products that sport these seals have been manufactured in
ways that are considered sustainable from an economic,
environmental or social standpoint, but measuring the success of
these certification programs is difficult and the labels can be
confusing for consumers.
But that’s not the case for other types of products. Take palm
oil, for example — about half the goods that you find in a
supermarket have some palm oil in them. It’s in your shampoo, your
biscuits, your soap, etc. But you never go and buy a bottle of palm
oil. Because it’s just one of many ingredients in a product, it’s
difficult to check whether the palm oil has been certified. So
there’s also less direct consumer pressure on companies to improve
Can consumers play a part in improving the
Yes, it’s a combination of consumers and non-governmental
organizations. Consumers often have a very poor understanding of
the nitty gritty of a certification. But large companies conduct
marketing campaigns, and the companies clearly sense that, at least
in Europe and North America, there is a new wave of consumer demand
for sustainably produced items.
Pressure is especially effective when the supply chain is very
concentrated, meaning a few companies hold a large market share.
For example, five large companies control about 90 percent of the
global trade in palm oil. When it’s that concentrated, consumers
and nonprofits can campaign hard, name and shame the companies
into taking action on sustainability, like Greenpeace has been
doing with Nestlé, Unilever and more. Companies tend to quickly
adopt sustainability standards just to protect their reputation
What are some choices or actions consumers can take to
support sustainability efforts?
Just buying certified products and pushing for more stringent
standards helps. Consider coffee: Only 25 percent of the coffee
that’s produced under some certification label is sold with a
certified label. The rest is just sold as conventional coffee with
no price premium, which suggests that consumer demand still doesn’t
match production. In surveys, consumers say sustainability is very
important to them, but studies of actual market behavior show that
their purchasing of certified products is still very low. They
don’t translate the preferences they express into actual buying
It’s really a paradox. Think about it, these smallholder coffee
farmers in remote areas are quite poor. They make all the effort to
comply with 90 different criteria and get audited every year. It’s
a lot of work. And if there’s little consumer demand for certified
coffee, the price premium for producers decreases over time. In our
Colombia study, for example, the price premium decreased from 20
percent to 2 percent above the price of conventional coffee, and
some farmers were abandoning the certification because it was too
much work for 2 percent more income.
And most coffee or chocolate consumers are wealthy people in
rich countries. All that’s needed is for them to take a second,
check on the package whether the product is certified, and pay a
few extra cents for it. And too few of them do it.
His Twilight Zone was a dimension of imagination, a dimension of
sight and sound and mind, a dimension as vast as space and timeless
as infinity. It was all very clear except for the space and time
part, the dimensions of real life. Serling never explained
Of course, ever since Einstein, scientists have also been
scratching their heads about how to make sense of space and time.
Before then, almost everybody thought Isaac Newton had figured it
all out. Time “flows equably without relation to anything
external,” he declared. Absolute space is also its own thing,
“always similar and immovable.” Nothing to see there. Events of
physical reality performed independently on a neutral stage where
actors strutted and fretted without influencing the rest of the
But Einstein’s theories turned Newton’s absolute space and time
into a relativistic mash-up — his equations suggested a merged
spacetime, a new sort of arena in which the players altered the
space of the playing field. It was a physics game changer. No
longer did space and time provide a featureless backdrop for matter
and energy. Formerly independent and uniform, space and time became
inseparable and variable. And as Einstein showed in his general
theory of relativity, matter and energy warped the spacetime
surrounding it. That simple (hah!) truth explained gravity.
Newton’s apparent force of attraction became an illusion
perpetrated by spacetime geometry. It was the shape of spacetime
that dictated the motion of massive bodies, a symmetric justice
since massive bodies determined spacetime’s shape.
“The emergence of spacetime and gravity is a mysterious
phenomenon of quantum many-body physics that we would like to
Verification of Einstein’s spacetime revolution came a century
ago, when an eclipse expedition confirmed his general theory’s
prime prediction (a precise amount of bending of light passing near
the edge of a massive body, in this case the sun). But spacetime
remained mysterious. Since it was something rather than nothing, it
was natural to wonder where it came from.
Now a new revolution is on the verge of answering that question,
based on insights from the other great physics surprise of the last
century: quantum mechanics. Today’s revolution offers the potential
for yet another rewrite of spacetime’s résumé, with the bonus of
perhaps explaining why quantum mechanics seems so weird.
“Spacetime and gravity must ultimately emerge from something
else,” writes physicist Brian Swingle in the 2018 Annual Review of Condensed Matter
Physics. Otherwise it’s hard to see how Einstein’s gravity
and the math of quantum mechanics can reconcile their longstanding
incompatibility. Einstein’s view of gravity as the manifestation of
spacetime geometry has been enormously successful. But so also has
been quantum mechanics, which describes the machinations of matter
and energy on the atomic scale with unerring accuracy. Attempts to
find coherent math that accommodates quantum weirdness with
geometric gravity, though, have met formidable technical and
At least that has long been so for attempts to understand
ordinary spacetime. But clues to a possible path to progress have
emerged from the theoretical study of alternate spacetime
geometries, thinkable in principle but with unusual properties. One
such alternate, known as anti de Sitter space, is weirdly curved
and tends to collapse on itself, rather than expanding as the
universe we live in does. It wouldn’t be a nice place to live. But
as a laboratory for studying theories of quantum gravity, it has a
lot to offer. “Quantum gravity is sufficiently rich and confusing
that even toy universes can shed enormous light on the physics,”
writes Swingle, of the University of Maryland.
A strange type of spacetime with unusual curvature known as anti
de Sitter space, illustrated here, is nothing like the universe we
live in, but could nevertheless provide clues to the quantum
processes that may be responsible for producing ordinary
SOURCE: U. MOSCHELLA / SÉMINAIRE
Studies of anti de Sitter space suggest, for instance, that the
math describing gravity (that is, spacetime geometry) can be
equivalent to the math of quantum physics in a space of one less
dimension. Think of a hologram — a flat, two-dimensional surface
that incorporates a three-dimensional image. In a similar way,
perhaps the four-dimensional geometry of spacetime could be encoded
in the math of quantum physics operating in three-dimensions. Or
maybe you need more dimensions — how many dimensions are required
is part of the problem to be solved.
In any case, investigations along these lines have revealed a
surprising possibility: Spacetime itself may be generated by
quantum physics, specifically by the baffling phenomenon known as
As popularly explained, entanglement is a spooky connection
linking particles separated even by great distances. If emitted
from a common source, such particles remain entangled no matter how
far they fly away from each other. If you measure a property (such
as spin or polarization) for one of them, you then know what the
result of the same measurement would be for the other. But before
the measurement, those properties are not already determined, a
counterintuitive fact verified by many experiments. It seems like
the measurement at one place determines what the measurement will
be at another distant location.
That sounds like entangled particles must be able to communicate
faster than light. Otherwise it’s impossible to imagine how one of
them could know what was happening to the other across a vast
spacetime expanse. But they actually don’t send any message at all.
So how do entangled particles transcend the spacetime gulf
separating them? Perhaps the answer is they don’t have to — because
entanglement doesn’t happen in spacetime. Entanglement
At least that’s the proposal that current research in toy
universes has inspired. “The emergence of spacetime and gravity is
a mysterious phenomenon of quantum many-body physics that we would
like to understand,” Swingle suggests in his Annual Review
paper. Vigorous effort by several top-flight physicists has
produced theoretical evidence that networks of entangled quantum
states weave the spacetime fabric. These quantum states are often
described as “qubits” — bits of quantum information (like ordinary
computer bits, but existing in a mix of 1 and 0, not
simply either 1 or 0). Entangled qubits create networks
with geometry in space with an extra dimension beyond the number of
dimensions that the qubits live in. So the quantum physics of
qubits can then be equated to the geometry of a space with an extra
dimension. Best of all, the geometry created by the entangled
qubits may very well obey the equations from Einstein’s general
relativity that describe motion due to gravity — at least the
latest research points in that direction. “Apparently, a geometry
with the right properties built from entanglement has to obey the
gravitational equations of motion,” Swingle writes. “This result
further justifies the claim that spacetime arises from
Still, it remains to be shown that the clues found in toy
universes with extra dimensions will lead to the true story for the
ordinary spacetime in which real physicists strut and fret. Nobody
really knows exactly what quantum processes in the real world would
be responsible for weaving spacetime’s fabric. Maybe some of the
assumptions made in calculations so far will turn out to be faulty.
But it could be that physics is on the brink of peering more deeply
into nature’s foundations than ever before, into an existence
containing previously unknown dimensions of space and time (or
sight and sound) that might end up making The Twilight
Zone into Reality TV.
Call it the body’s postal system. Cells package goodies into
little envelopes made of membranes. Then these packages cruise the
bloodstream — billions of them in every milliliter of blood — to
recipient cells far and near, delivering freight such as genetic
material and proteins.
These little bubbles, known as extracellular vesicles, or EVs,
tell the receiving cell to change its biology, with far-reaching
consequences, potentially influencing how we learn, the timing of
childbirth, where diseases like cancer spread to, and more.
The cellular packages called exosomes have membranes studded
with various sets of proteins, fats and other particles (center).
Ranging from 30 to 100 nanometers across, exosomes travel to
distant cells in a variety of body fluids.
EVs are a mixed bag; scientists are still finding new varieties
and figuring out how to categorize them. Different types originate
in different cellular packaging plants. They vary in size from 20
to 1,000 nanometers, or up to about one-thousandth of a millimeter.
On the smaller side, types called exosomes are created inside
specialized cellular factories and then exported. Others that pinch
off from a cell’s own membrane are called microvesicles or
ectosomes, and tend to be larger.
The contents vary too, but one frequent cargo is small molecules
of RNA — snippets of genetic material that can turn genes on or off
in the cells they are dispatched to.
In many cases, scientists are just starting to figure out how
the cells that send out EVs package their specific cargoes, what
those cargoes are and how the EVs influence the cells where they
end up. Medical applications are under investigation too, by
companies like Codiak BioSciences, ReNeuron, Exosomics and Exosome Sciences. Specific EVs found in body fluids
might help doctors diagnose diseases, for example, and lab-created
EVs might package and deliver drugs to therapeutic targets.
Here’s a taste of some of the things that EVs do — and how
scientists could harness them for novel purposes.
EVs known as exosomes are generated in a special cellular depot
called the multivesicular body and sent out for delivery to
recipient cells, which can take up the contents or the entire
vesicle and use the proteins or genetic material inside.
EVs in cancer: A tool for tracking
David Lyden, a cancer biologist at Weill Cornell Medicine in New
York, studies how cancer spreads from one tumor to other parts of
the body — say, when a melanoma in the skin sends out cells to set
up shop in the lungs and form a secondary malignancy.
Working with mice that had melanoma, Lyden and colleagues first
used a technical trick to tag blood cells and tumor cells so they
glowed green and red, respectively. Observing the mice over time,
they noticed that the green
blood cells got to the lungs before the red tumor cells arrived
there, findings reported in Nature in 2005. Moreover,
as described in 2012 in Nature Medicine, the team saw tiny
red specks joining those blood cells early on, indicating that the
tumors were sending in EVs to prepare the area. EVs
seem to build up blood flow, change immune responses and remodel
the environment outside cells to better support the incoming cancer
Cells from mouse connective tissue take up human-derived EVs
(green) and concentrate them around the nucleus (blue); part of the
cellular skeleton (red) is also visible. Many cells in the body
make EVs, including tumor cells, so tracking the spread of EVs
could help with the targeting of cancer therapies.
CREDIT: AYUKO HOSHINO AND DAVID LYDEN
The team also analyzed EVs extracted from the blood of people
with advanced melanoma. They discovered that EVs from tumors
carried a complement of proteins, fats and genetic material
entirely distinct from vesicles coming from healthy tissues.
EVs could help doctors diagnose and track cancer, as well as
predict if it will spread. One of Lyden’s collaborators, Johan
Skog, cofounded Exosome Diagnostics, a company that has developed
urine and blood tests for cancer-derived vesicles. For example, if
patients have tumors removed but still have cancer EVs in their
blood, it would suggest there’s still some cancer around, sending
out seeds for its next move. The patients could then receive more
EVs from parasites: Preparing a niche?
Trypanosomes are slug-shaped protozoans that cause African
sleeping sickness. Transmitted by the bite of the tsetse fly, they
cause fevers, rashes and anemia, followed by seizures, personality
changes and daytime sleepiness as the illness worsens.
Trypanosomes have tail-like structures, but scientists didn’t
think much about those tails until recent work by the lab of
Stephen Hajduk, a biochemist at the University of Georgia in
Athens. “They actually look like beads on a string,” Hajduk says.
When the beads reach the end of the string, they pinch off and float away as EVs called ectosomes,
Hajduk’s group reported in the journal Cell in 2016.
A super-resolution microscope image of three trypanosomes, the
cause of African sleeping sickness. The parasites may use EVs to
prepare their favorite body niches for invasion.
CREDIT: JUSTIN WIEDEMAN
Hajduk isn’t sure what the EVs do for the trypanosomes in
infected people, but he thinks they act much like tumor EVs,
preparing far-off regions of the body for future colonization, in
this case by the parasite. To nail down that theory, he’s working
in mice to see if the ectosomes reach sites where trypanosomes like
to settle: the reproductive organs, fat tissue and the brain. He’s
also collaborating with the US Centers for Disease Control and
Prevention to use trypanosome EVs as a potential means to diagnose
EVs may also explain why trypanosomes cause anemia. The
researchers found that the ectosomes fuse with red blood cells,
making their membranes less flexible. Immune cells, scouting for
broken-down old blood cells, recognize this membrane rigidity as a
sign of aging and clear the cells away.
EVs on your mind: Sharing memories
The brain has its own EVs. At the University of Utah in Salt
Lake City, neuroscientist Jason Shepherd studies a gene called
Arc, which carries instructions for a protein that’s key
for long-term memory. His team reported in Cell in 2018
that this Arc protein assembles to form containers similar to the shells of
viruses. Once assembled, these structures pop out of nerve
cells, picking up a membrane coat along the way.
“This was a real surprise,” recalls Shepherd. He wasn’t
expecting a gene in nerve cells to make something that looked like
a virus. “It’s kind of a crazy biology.”
The team also found that these Arc EVs carry RNAs inside them —
ones bearing instructions to make the Arc protein itself, and
perhaps others — that seem to be used by the cells that take them
up. Given Arc’s known function in memory and the ability of EVs to
transfer materials from cell to cell, he suspects that the
Arc-based EVs help nerve cells communicate with each other so that
memories can form.
Shepherd is also investigating other, unshelled, EVs in the
brain. These can cause problems, too, in diseases such as
Alzheimer’s and Parkinson’s, where cells fill up with toxic,
malformed proteins. “The garbage disposal is sort of blocked, or it
can’t work anymore,” Shepherd says. EVs may then carry the
dangerous proteins from cell to cell, across the nervous system,
bringing the disease along with them.
Incorporating a fluorescent tag into genetic material allowed
researchers to follow the fate of glowing exosomes delivered via
breast milk from mother mice to their pups’ organs, such as the
brain and liver (left). Organs from a control mouse pup, without
such genetic tagging, are also shown (right).
CREDIT: JANOS ZEMPLENI AND BIJAYA UPADHYAYA, U OF
So what does this mean for the human infant diet? Zempleni and
other researchers have tested formulas made from either soybean or
cow milk proteins, and neither contained many exosomes, he says.
Still, he suspects that children in developed nations get such rich
nutrition that any exosome deficiency doesn’t make much of a
difference to long-term brain development. But a lack of exosomes
might be a problem for children in developing nations.
EVs in pregnancy: Bringing babies to term
Speaking of babies, exosomes have key roles in childbirth as
At the University of Texas Medical Branch in Galveston,
reproductive biologist Ramkumar Menon is trying to understand how
the fetus signals to the mother that it’s time to come out.
The membranes surrounding a fetus begin to age as the end of
term approaches. They release exosomes, filled with cellular
garbage, that incite inflammation in the mother.
Those junk-filled exosomes are enough to cause labor, Menon’s team reported this
year in Scientific Reports. In mice, pregnancy lasts for
19 to 20 days. The researchers collected exosomes from the blood of
mice that had been pregnant for 18 days — close to term — and
injected them into mice that were 15 days pregnant. “And boom, they
went into preterm labor,” typically delivering a day or two earlier than normal, Menon
Menon hopes that this work could lead to exosome-based tests for
women at risk for preterm labor, or treatments to prevent preterm
EVs in your heart: Delivering the goods
Cardiologist and researcher Eduardo Marbán also has treatments
in mind: He wants to repair people’s tickers after heart attacks.
He hoped that stem cells — blank-slate cells that can develop into
a broad variety of tissues — would be able to rebuild heart muscle.
And indeed, cardiac stem cells did help build up heart tissue after
scientists in Marbán’s lab, at Cedars-Sinai Medical Center in Los
Angeles, induced heart attacks in mice.
Scientists envision using EVs derived from stem cells as
medicine-delivery vehicles. Large quantities of ready-to-use
vesicles could be used to treat any patient (top), or EVs could be
harvested from specific patients, their contents customized and
then delivered back to that patient (bottom).
In another recent study in Stem Cell Reports, Marbán’s
group used EVs to treat heart failure in mice
engineered to mimic the muscle-wasting disease Duchenne muscular
dystrophy. Not only did the EVs help the heart work better, they
also helped skeletal muscles.
EVs loaded with therapeutic cargos would be much easier to use
as a treatment than stem cells, Marbán says. They could deliver
RNAs, genes, proteins —whatever scientists load them with. Unlike
most stem cells, the EVs can be freeze-dried for convenient
storage. And they can cross into the brain, making them potential
delivery trucks to treat neurological conditions such as
EVs in plants: Killing invaders
Plants make EVs, too. They appear to use them for defense,
fighting off fungi and bacteria.
These EVs stick to fungi, and the fungal cells take them up.
That can be a fatal mistake, because some of the cargoes seem to
comprise a two-part anti-fungus poison. Innes has evidence that
some EVs contain chemicals called glucosinolates, which are
harmless on their own. Other EVs hold enzymes that act like
molecular scissors, slicing those glucosinolates in half. That
slicing produces a killer molecule that prevents fungal cells from
making energy, so they die. (Glucosinolates are also responsible
for the characteristic odor of plants like mustard and
To take advantage of plant EVs, scientists might engineer them
to carry small RNAs that would improve crops’ resistance to pests
and disease, Innes says. He also sees applications for plant EVs in
medicine, because animals
can take up EVs from the plants they eat. He thinks it would be
easier and cheaper to engineer plants to make therapeutic EVs, and
to grow entire fields full of medicinal crops, than to make
drug-toting EVs in a lab.
But before we get to enjoy salads laden with beneficial EVs,
scientists have a long way to go. Researchers don’t fully
understand how cells shunt specific cargoes into EVs as they’re
made. In many cases, they still don’t know what those cargoes are,
and how they influence the cells that receive and open the
Another major mystery is how these vesicles are addressed so
they’re delivered to the right cell recipients. Researchers do know
that some exosomes are studded with proteins that hook up with ones
on the membranes of target tissues. To create therapeutic EVs,
Marbán and others are working on ways to put artificial addresses on the vesicles, modifying
their membranes so they find the right place in the body.
Though EV research is just getting started, it has already built
a picture of a bloodstream packed with letters and packages of
diverse sizes bobbing along in the flow, somehow finding their
addressees amid the chaos. It’s like the most hectic post office on
the day before Christmas — all day and all night, all over our
In the murky darkness, blue and green blobs are dancing.
Sometimes they keep decorous distances from each other, but other
times they go cheek to cheek — and when that happens, other colors
The video, reported last year, is fuzzy and a few seconds long,
but it wowed the scientists who saw it. For the first time, they
were witnessing details of an early step — long
unseen, just cleverly inferred — in a central event in biology: the
act of turning on a gene. Those blue and green blobs were two key
bits of DNA called an enhancer and a promoter (labeled to
fluoresce). When they touched, a gene powered up, as revealed by
bursts of red.
Enhancers, promoters and mRNA - YouTube
Activation of a gene — transcription — is kicked off when
proteins called transcription factors bind to two key bits of DNA,
an enhancer and a promoter. These are far from each other, and no
one knew how close they had to come for transcription to happen.
Here, working with fly cells, researchers labeled enhancers blue
and promoters green and watched in real time. Also tweaked was the
gene itself, such that mRNA copies, hot off the press, would glow
red. The red flare is so bright it's almost white, because several
mRNAs at a time are being made. The study found that the enhancer
and the promoter have to practically touch in order to kick off
CREDIT: H. CHEN AND T. GREGOR / PRINCETON
The event is all-important. All the cells in our body contain by
and large the same set of around 20,000 distinct genes, encoded in
several billion building blocks (nucleotides) that string together
in long strands of DNA. By awakening subsets of genes in different
combinations and at different times, cells take on specialized
identities and build startlingly different tissues: heart, kidney,
bone, brain. Yet until recently, researchers had no way of directly
seeing just what happens during gene activation.
They’ve long known the broad outlines of the process, called
transcription. Proteins aptly called transcription factors bind to
a place in the gene — a promoter — as well as to a more distant DNA
spot, an enhancer. Those two bindings allow an enzyme called RNA
polymerase to glom onto the gene and make a copy of it.
That copy is processed a bit and then makes its way to the
cytoplasm as messenger RNA (mRNA). There, the cellular machinery
uses the mRNA instructions to create proteins with specific jobs:
catalyzing metabolic reactions, say, or sensing chemical signals
from outside the cell.
This textbook take is true as far as it goes, but it raises many
questions: What tells a given gene to turn on or off? How do
transcription factors find the right sites to bind to? How does a
gene know how much mRNA to make? How do enhancers influence gene
activity when they can be a million DNA building blocks away from
the gene itself?
For decades, scientists had only blunt and indirect tools to
probe these questions. Ideas about DNA, RNA and proteins came from
grinding up cells and separating components. Then, in the 1980s,
scientists began using a game-changing technique called FISH (short
for fluorescence in situ hybridization) to see DNA and RNA
directly, right in the cell. Other methods followed — microscopes
with better resolution, new ways to tag (and thus track) players in
this molecular symphony as it played out. Researchers could parse
transcription as it happened, in detail.
Before, it was like trying to hear the symphony by looking at a
static picture of the orchestra, says Zhe Liu, a molecular
biologist at the Howard Hughes Medical Institute's Janelia Research
Campus in Virginia. “You would never figure out what they are
playing,” he says. “You could never appreciate how beautiful the
Here’s a taste of what molecular biologists are learning by
spying on this key, nanoscopic process — increasingly in real time,
in living cells.
The life and times of transcription factors
Though scientists have long known that transcription factors
dictate whether or not a gene powers up, it’s been mysterious how
these proteins navigate the ridiculously crowded space in the
nucleus to find their binding sites.
Consider that, uncoiled, the DNA in a human cell would run a
meter or two long. The nucleus is about 5 to 10 micrometers in
diameter, so the packaging of our genome is akin to stuffing a
string that could wrap 10 times around the Earth inside a chicken
egg, Liu says.
Researchers are just starting to tackle how this coiling and
looping affects gene transcription. For one thing, they suspect it
could help explain how enhancers can influence a gene’s activity
from a great distance — because something far away when DNA is
stretched out may be a lot closer when the genetic material is
And if it seems miraculous that transcription factors know where
they are going — well, most of them don't. By tracking these
proteins in a single cell over time, researchers find that they
spend fully 97 percent of their life jiggling hither and thither,
bouncing off of whatever bits of DNA they encounter until they luck
out. (A few types may act as leaders, scanning the genome, latching on
to their target and setting up the right conditions for a larger
pack to follow.)
Transcription factors in action - YouTube
To see how transcription factors move around inside the nucleus,
researchers watched one specific transcription factor, Sox2, in
living cells taken from mouse embryos. Shown are Sox2 molecules
labeled with fluorescence, in a 3-D grid. Researchers recorded the
movements of several Sox2 molecules within a single cell nucleus
using a special microscopy approach that stacks 2-D images to make
a 3D one. Each of the traces represents the movement of a separate
CREDIT: J. CHEN ET AL / CELL 2014
One would imagine, at least, that when a transcription factor
finally found its binding site, it could stay stuck and do its job
for hours. Scientists used to believe so from experiments with
dead, preserved cells.
But studies on live cells show that’s far from true. Liu’s lab
and others have shown over the past five years that transcription factors bind only for seconds, and that
high concentrations of them congregate near the binding site,
helping each other glom on. “It’s mind-boggling how transcription
factors actually work,” Liu says.
And there are a lot of them: Up to 10 percent of the genes in a
mammal carry instructions for making ones of different flavors.
Recent evidence suggests that this affords huge precision to the
cell. For any given gene, varied combinations of transcription
factors can ramp up or tamp down the process, potentially making
the system exquisitely tunable.
Hooking up at the polymerase party
If transcription factors are the gas pedal and brakes, the
engine is RNA polymerase. In the basic model, RNA polymerase pulls
apart a gene’s two strands, then slithers down one of them to make
an mRNA copy of it. Turns out things are a hair more
Last year, the same team of scientists spotted gatherings of other proteins as they
congregated to help RNA polymerase do its job. These beasts — known
as mediator proteins — form giant clusters numbering in the
hundreds that join the RNA polymerases on the DNA.
Mediator proteins and RNA polymerases - YouTube
Specialized groups of proteins called the mediator complex
(green) gather around a gene to help RNA polymerase do its job of
copying DNA into mRNA (magenta). The box outline marks a
3-dimensional region surrounding the gene. The study showed that
the two clusters fuse together and interact directly with the gene
CREDIT: W. CHO ET AL / SCIENCE 2018
The two gaggles seem to concentrate into distinct droplets, like
blobs of oil in water. Then they fuse, perhaps creating a kind of
self-assembling, cordoned-off transcription mill. A lesson from
this? “Beyond the biochemistry, there are all these physical
phenomena that may have a role in telling us how genes get turned
on,” says biophysicist Ibrahim Cissé of MIT, who led the work.
Messenger RNA is made in fits and starts
For decades, researchers assumed that when a gene is active,
transcription simply goes into “on” mode and cranks out mRNA at a
steady clip. But a breakthrough technique called MS2 tagging, first
developed in 1998 and still widely used, has radically changed that
Invented by cell biologist and microscopist Robert Singer and
colleagues at the Albert Einstein College of Medicine in New York,
MS2 tagging allowed scientists to see mRNAs in living cells for the
very first time. (Key ingredients of the method come from a virus
called MS2 — hence the technology’s name.)
In a nutshell, scientists use engineering tricks so that mRNA
made from a specific gene bears distinctive structures called
stem-loops. Through a second trick, those stem-loop locations are
made to glow fluorescently so researchers can “see” mRNA from the
gene of their choice whenever it is made and wherever it travels
to, under a microscope and in real time.
Singer, who coauthored a 2018 article about mRNA imaging in the
Annual Review of Biophysics, used MS2 tagging to show,
with his colleagues, that the production rate of mRNAs from a gene fluctuates
wildly over 25 minutes or so. It turned out that the size of
these bursts doesn’t vary much, but their frequency does, and
that’s what dictates how energetically a gene pumps out its mRNA
product. Increasing or decreasing the rate of this transcriptional
“bursting” may allow the system to ramp up or slow down a gene’s
activity to meet the cell’s needs.
Researchers think that the on-off kinetics of transcription
factors, meaning the rate at which they pop on and off of their
binding sites, somehow regulates transcriptional bursting. But they
don’t yet know how.
Trekking towards translation
Making mRNA is just the first step in a gene’s strutting its
stuff. Next comes translating instructions in that mRNA to make
proteins. For that to happen, the mRNA must journey out of the
nucleus and into the cytoplasm where the protein-making factories
Scientists had assumed that the cell’s molecular machinery
carefully transported mRNA to the nucleus’s membrane and then
pumped it out into the cytoplasm. Using the same MS2 method,
Singer’s lab found that wasn’t so. Instead, mRNAs bounce around — “buzzing around in the nucleus like a
swarm of angry bees,” as Singer terms it — until they happen to hit
a pore in the nuclear membrane. Only then does the cell’s machinery
lift a finger and actively shuttle mRNA through this gate.
mRNAs departing the nucleus - YouTube
In this video, proteins in the pores of the nuclear membrane are
labeled red, and mRNA is labeled green. Using a special microscope
designed to record at a very fast frame rate, researchers could
watch individual mRNAs as they zipped around the nucleus until they
hit a pore and passed through the pore into the cytoplasm, where
protein synthesis takes place.
CREDIT: D. GRÜNWALD AND R.H. SINGER / NATURE,
More recently, Singer and colleagues created mutant mice that
enabled them to watch as mRNA shuttled up and
down a nerve cell’s delicate dendrites, the structures that receive
signals from other nerves. The team even got to spy on memory-making in action. The mRNAs
they were tracking carried instructions for making a protein —
β-actin — that is abundant in nerve cells and is thought to help
bolster connections when memories are made in the brain. In a video
that looks like a network of roads at nighttime, within 10 minutes
after a nerve cell was activated, mRNAs cruised to points of
contact with other nerves, ready for actin production to shore up
those nerve-nerve connections.
The Molecular Basis of Memory: Tracking mRNA in Brain Cells in Real Time - YouTube
Researchers devised a way to track mRNAs of a gene crucial for
making memories as they traveled through living brain cells. The
team engineered a mouse so that all the mRNA copied from this gene,
which codes for a protein called β-actin, was labeled. β-actin
helps neurons reshape tiny protrusions called spines that other
neurons connect to, a process thought to be important in learning
and memory. When neurons grown in a dish were stimulated, β-actin
mRNAs were produced in the nucleus within 10 to 15 minutes. In this
video, you can see about 6 seconds of β-actin mRNAs cruising
through the neuron's branches, or dendrites, after stimulation. The
researchers believe that these mRNAs are searching the dendrites
for spines that have just made connections, so that they can
synthesize β-actin protein right there on the spot.
CREDIT: HYE YOON PARK
Scads of details about gene activity remain mysterious still,
but it’s already clear that the process is far more dynamic than
once assumed. “The change has been phenomenal, and it’s
accelerating rapidly,” Singer says. “There’s a lot of information
to be gleaned just by watching.”
Whether a business model is built on gigabytes, interest rates
or the latest innovations in aluminum siding, every company
ultimately depends on its people — some more than others.
Businesses of any size have stars that drive productivity and get
results, but look beyond those high achievers — the break room
might be one place to check — and you’ll find others who drag the
company down with shoddy performance.
The ultimate success or failure of a company often comes down to
the quality of employees. As Jack Welch, former chairman of General
Electric, once said, “the team with the best players wins.” But as
CEOs and managers try to set up winning companies, they face a
surprisingly difficult task: sorting the good employees from the
bad ones. Baseball pitchers have earned run averages and
quarterbacks have touchdowns, but the value of a given coder or
salesperson can be much harder to define. Companies spend millions
of dollars and burn countless hours conducting performance reviews
and devising checklists to assess their employees, and business
scholars have studied the issue with great urgency and
The results so far? By all available evidence, formal attempts
to rate employees don’t seem to meaningfully improve employee
performance or give companies any sort of competitive advantage,
says Elaine Pulakos, a management expert and CEO of PDRI, a
management consulting company based in Arlington, Virginia. “They
end up being extremely costly and have no impact on productivity,”
she says. Pulakos discussed the science of employee evaluation in
a 2018 issue of the Annual Review of Organizational Psychology
and Organizational Behavior.
CREDIT: MARTHA GRADISHER / CARTOONSTOCK.COM
Despite many efforts, no one has been able to come up with a
rating system that can reliably discern which companies are blessed
with a deep bench of high performers and which brim with
mediocrity. You certainly can’t tell simply by looking at the
bottom line. Pulakos cites a 2012 report that gathered more than
23,000 employee ratings from 40 companies and found no sign that ratings had any effect on
profits or losses. “Performance ratings have no relation to
organizational performance whatsoever,” she says.
Out of all of the methods used to rate and grade employees, the
dreaded annual or semiannual performance reviews are especially
unhelpful and potentially harmful, Pulakos says. “They’re really
toxic and people hate them,” she says. “You’re creating artificial
steps just to check a box.” Pulakos points to brain imaging
research positing that even high-performing employees automatically go into a
defense mode during performance reviews, turning a supposedly
productive meeting into a fight-or-flight scenario.
Formal annual performance reviews can be extremely damaging to a
company’s culture, says Herman Aguinis, the Avram Tucker
Distinguished Scholar and professor of management at George
Washington University in Washington, DC. “It’s a soul-crushing
enterprise,” he says. “The employee doesn’t know what they’re
supposed to do, and the manager doesn’t see any value in it.
They’re only doing it because human resources told them to.”
All too often, Aguinis says, formal performance reviews become a
self-serving exercise in politics, not a realistic examination of
an employee’s strengths and weaknesses. “Some managers will give
biased ratings on purpose,” he says. “I have personally seen a
supervisor giving a bad employee a good rating just so that
employee could get promoted out of his unit.”
CREDIT: MIKE SEDDON / CARTOONSTOCK.COM
Still, some HR experts continue to see some value in annual
performance reviews. In a February post on her popular Evil HR Lady
blog, Suzanne Lucas says “annual performance reviews aren’t all bad.
Formal ratings provide a macro-view of performance and engagement
levels across the company. If the results of any group (department,
experience level, etc.) stick out — it can indicate a bright spot
or potential problem worth looking into.”
Businesses that abandon formal performance reviews still have to
keep tabs on employees, Aguinis says: “Companies that say they are
getting rid of ratings are still using ratings. They just have
different labels.” For one thing, managers must have some rationale
for assigning promotions and raises. If there’s no data on
performance, the process of handing out promotions and raises can
turn chaotic. In some cases, companies could be vulnerable to
lawsuits if they don’t have a way to justify decisions.
To really understand the value of their employees, Aguinis says,
managers should double down on the practice of everyday management.
That means checking in on employees every day and giving them
real-time feedback on things they’re doing well and areas where
they can improve. “When performance is a conversation, when it’s
not something that happens just once a year, the measurement
becomes very easy and straightforward with no surprises,” he says.
He adds that it’s important to gather input from many different
people within the system — peers as well as supervisors. “The best
source of data is often not the manager,” he says.
When rating employees, it’s best to keep things simple, says
Seymour Adler, a talent and rewards partner at Aon, a management
and HR consulting firm headquartered in London. He ruefully
remembers a mistake early in his career, when he was part of a team
that came up with a 40-point scale to rate employees. “That’s an
over-engineered solution in my view,” he says.
CREDIT: TERRY LABAN. THIS CARTOON WAS ORIGINALLY
PUBLISHED IN REWORK
Rating employees solely on objective measures such as sales
numbers, absentee days, or customer calls may seem like a winning
strategy, but those data points can be wildly misleading, Adler
says. A salesperson with the most sales may have a better territory
or better luck than others, not more talent or drive. “Objective
measures may seem straightforward, but you have to think about all
the factors that are beyond an employee’s control,” he says.
Daily evaluation and feedback may sound like an onerous task,
but Adler says there’s an important loophole: Most employees do
just fine without constant scrutiny. “When I work with companies, I
encourage them to get away from ratings and start managing by
exception,” he says, meaning that the exceptional employees need
the most attention. Out of 100 employees, there might be three or
four who are struggling so mightily that they need an intervention
or a career change. At the other end, there might be five or so
excellent employees who should get special treatment because they
drive the company’s success. A 2012 study by Aguinis and coauthor
Ernest O’Boyle Jr. found that the
top 1 percent of workers account for 10 percent of a company’s
productivity. The hardworking, competent but unexceptional
workers in between the extremes — Adler calls them “the Mighty
Middle” — are going to make about the same contribution to a
company’s bottom line regardless of how much time they spend in
Some companies have taken appreciation of superstar employees to
extremes. In his 2015 book Work Rules!, former Google executive
Laszlo Bock reveals that the company routinely pays high-performing employees five or six times as
much as other employees at the same level, maybe even more. He
also cites such instances as one worker’s receiving a $1 million
stock bonus while another received just $10,000.
Of course, Google is an industry outlier in many ways. Pulakos
notes that the company lives on data, and it has methods for rating
and ranking employees that just wouldn’t work anywhere else. That’s
one of the big lessons of modern business scholarship: Every
company has to figure out its own approach to getting the most out
of its employees. “You have to evaluate your own strategic goals,”
she says. “What works for Google is not going to work the same way
for anyone that is not Google.”
In the world of business, there aren’t many universal truths.
Just one, really: Annual performance reviews are the worst.
The suicide rate in the United States continues to spiral
upward, with seemingly no end in sight. More than 45,000 Americans take their own lives each
year, 33 percent more than did so in 1999, according to the most
recent federal data.
It’s a national public health crisis — one that researchers and
clinicians have struggled to thwart because the triggers of suicide
are so poorly understood. People may wrestle with suicidal thoughts
for years, but not follow through. Depression and other mental
health conditions are clearly risk factors, but such diagnoses
aren’t linked to roughly half of all US suicides. Some prevention
efforts, such as asking a patient to sign a “contract” to not
commit suicide, have proved to be largely useless.
But there’s been some encouraging progress in recent years, both
in understanding the suicidal thought process and in developing
individual and societal interventions to better assist those caught
in the crucible of such a crisis. Instead of encouraging people to
sign no-suicide contracts, clinicians now are more likely to work
with a patient to design a personalized prevention plan to use when
suicidal thoughts flare. Clinicians and suicide prevention experts
are tackling how suicide is portrayed in the media, working to
debunk misunderstandings and trying to slow access to pills, guns
and other means, particularly for individuals who have expressed
“From a clinical perspective, we can do a lot better than just
leaving people on their own to figure out how to deal with not
killing themselves,” says Barbara Stanley, a clinical psychologist
at New York City’s Columbia University. “We can give them
strategies and skills.”
Across the United States, suicide rates are rising. Here are the
percentage increases for different states from 1999 through 2016.
Read more about the statistics at the CDC’s website.
What turns thought to action?
Some 15 years ago, researchers began to view suicide as two
distinct processes —suicidal thoughts, also called ideation, and
the progression that can lead to an attempt. That shift in thinking
has spawned research on when and how ideation leads to action, and
the risk factors involved.
David Klonsky, a psychologist at the University of British
Columbia, and Alexis May, then a graduate student and now at
Connecticut’s Wesleyan University, posited that three steps tip the
balance from ideation to action. They explore their Three-Step Theory, and several others with overlapping
elements, as part of a look at suicidal ideation and attempts in
the 2016 Annual Review of Clinical
The first step — the psychological groundwork — is laid when
someone is living with unremitting emotional or physical pain,
which is further amplified if it’s overlaid by a sense of
hopelessness: a feeling that there’s no way out. “Another way to
think about step one,” Klonsky says, “is that it’s creating that
desire to not want to be alive.”
The second step in the theory rests on the degree to which that
pain and hopelessness is ameliorated by connectedness to others or
to a broader community. Those ties might be rooted not just in
personal relationships — a challenge in today’s America where
loneliness appears to be on the upswing — but
also connections to a job, a personal cause or even the outcome of
the current football season.
The National Suicide Prevention Lifeline (1-800-273-8255) is
open 24 hours a day. Prefer to chat online? Go to the Lifeline’s
homepage and click on the “chat” button in the top
If bleakness and disconnectedness align, a person becomes
vulnerable to taking the critical third step: the leap from
thoughts to action. Basic personality plays a role here: Someone
less squeamish about blood and violence will have lowered
sensitivity to inflicting pain and harm on themselves. But in large
part, the leap to step three is a matter of practical capability —
access to lethal means and the knowledge to use them. In America,
that often means guns. “If someone is living with a firearm and
they … know how to use it, their practical capability is very, very
high,” Klonsky says.
Heightened practical capability can also figure in the emergence
of apparently related suicides, such as the unsettling deaths this
March involving survivors of the Parkland school shootings. Knowing
that someone you know, or who appears similar to you, has committed
suicide can make taking one’s own life seem more feasible, suicide
prevention experts say.
A troubling influence
For this reason, experts were highly critical of the popular
Netflix dramatic series “13 Reasons Why,” which first aired in 2017
and featured a teenage girl who, after her suicide, released 13
score-settling tapes describing the ways people in her life had
failed her. Not only could other teens identify with the girl, but
the program also showed the method in graphic detail, presenting
suicidally inclined viewers with a means.
“That was a lot of the backlash with the show,” says Catherine
Glenn, who studies self-injury risk factors in adolescents at the
University of Rochester in New York. “That played out [the method]
in almost a step-by-step fashion.” And hospitalizations for
suicide attempts and suicidal thoughts did indeed
increase after the show aired, according to a recent study in
the Journal of Adolescent Health.
Of the people who think about suicide, relatively few go the
next step and translate their thoughts into action. This image
depicts the path by which suicidal thoughts (also known as suicidal
ideation) lead to follow-through. Pain and hopelessness without a
counterbalancing connectedness to people and other valued things
intensify the ideation. Then comes “capacity” to act, which is
somewhat influenced by personality but even more by easy access to,
and knowhow about, the means to carry out an attempt.
But there is a surprising safety net for all potential suicide
victims: time. It’s on their side if they can be kept away from
guns or other immediately lethal means. Research shows again and
again that the window of peak suicide risk is narrow, frequently just an hour or so, and sometimes less
than 20 minutes. “The choice to take one’s life is rarely a
long-term stable choice,” Klonsky says. “It’s usually made in the
moment of crisis that’s not as bad even five or six hours
Keeping the window to life open
Still, clinicians are frequently faced with a longer-term
dilemma: what to do if patients are considered suicidal — either
because they’ve attempted suicide or admit to suicidal thoughts —
but not ill enough to be hospitalized. How best to keep them safe
in the weeks and months to come?
“By and large, if someone is in your office or in an emergency
room, they at least have mixed feelings about killing themselves,”
says Stanley. “As a clinician, you align with the part of them that
wants to stay alive.”
Previously, and sometimes even today, patients who have
expressed suicidal thoughts or attempted suicide have been asked to
sign a contract promising not to try again. Research into this
contractual approach has been limited, but what data exist don’t
show benefit. There also are some practical reasons why this
approach has proved to be a non-starter, Stanley says. Patients
have described the paperwork as little more than a way to shield
clinicians and clinicians’ employers against future liability.
Plus, a contract by definition requires that both parties “have
skin in the game,” Stanley points out. “For a no-suicide contract,
the only person giving is the patient.”
Instead, clinicians have begun working with at-risk patients to
create individual prevention plans. Working together, they design a
concrete series of steps for recognizing a burgeoning suicidal
crisis and heading it off.
The crisis moment triggering a suicide attempt can be very
brief, and measures to deter action can make the difference between
a life fully lived and one cut short. The safety net shown in this
artist's rendering is under construction at San Francisco’s Golden
Gate Bridge, where almost 1,700 people have died by suicide since
it was built in 1937. The nets will be installed 20 feet below the
sidewalk and extend out 20 feet, retaining views from the bridge
and the structure’s iconic appearance, while making it harder to
jump into the water.
CREDIT: COURTESY OF THE GOLDEN GATE BRIDGE,
HIGHWAY AND TRANSPORTATION DISTRICT
Patients identify warning signs, such as drinking more, or
spending a lot of time alone. With clinicians, they brainstorm
coping strategies and ways to distract from or soothe their mood,
such as doing chores or listening to music. For times when they
need outside help, they list names of close friends, family members
and mental health clinicians.
The plans are not a substitute for treating underlying risk
factors such as depression or post-traumatic stress disorder, but
they do provide something tangible to rely on during a person’s
darkest moments, says Stanley, co-developer of one such approach
called the Safety Planning Intervention. “When you’re in a
suicide crisis, you’re not thinking straight — you don’t want to
have to think.”
Stanley says she has many examples in which the plan made a
difference — such as, one time, “somebody going to the George
Washington Bridge, realizing that the safety plan was in his
pocket, feeling it, and saying, ‘OK, let me try this first instead
A recent study in JAMA Psychiatry of the Safety
Planning Intervention reported that it cut short-term suicidal
behaviors nearly in half. It looked at 1,640 patients getting care
at Veterans Affairs emergency departments, finding that among 1,186
who completed a plan and got at least two follow-up phone calls
shortly after hospital discharge, the rate of attempts or near attempts in the
subsequent six months was 3 percent, versus 5.3 percent for 454
patients getting usual care, which was typically referral to a
mental health clinician.
How guns make a difference
These prevention plans often also involve restricting access to
suicidal means. Researchers affiliated with Means Matter, a Harvard
School of Public Health campaign, have promoted this approach with
strategies that include reducing access to dangerous or lethal
doses of medications and storing guns away from at-risk individuals or,
at a minimum, locking them up. The campaign is working with an
array of gun owner groups and gun shops across the country to
promote suicide prevention as a basic tenet of firearm safety.
One frequently cited study in the 2007 Journal of
Trauma found that access to guns does make a difference. It compared a
group of states with high rates of gun ownership to a second group
with low ownership, and found suicides in the first group were
nearly twice as high. Virtually all of that disparity was
attributable to firearm suicides; there was scant difference in
non-firearm suicides between the two groups. The pattern remained
in a study published in 2013.
A 2013 study found sharply higher rates of suicide in a group of
US states with high levels of gun ownership compared to another
group of states with low gun ownership levels. Total suicide rates,
not just suicides by firearms, were lower in the states with fewer
guns, while rates of non-firearm suicides were about the same.
Ready access to a means for suicide make it more likely that
someone in crisis will follow through, say mental health experts.
(Data are for total numbers of suicides in 2008 and 2009;
population sizes of the high-gun and low-gun groups were close to
“When you try with a gun, you usually don’t get a second
chance,” says Matthew Miller, one of the studies’ authors and a
suicide researcher at Boston’s Northeastern University who has
studied access to firearms.
A graph shows dips in suicide rates in Sri Lanka after it
outlawed various poisonous pesticides. Read more about it in
a 2017 paper in the Lancet.
CREDIT: D.K. KNIPE ET AL / THE LANCET GLOBAL
There’s good reason to be hopeful about interventions like
these, particularly because the popular perception that someone
contemplating suicide is nearly unstoppable is wrong, Miller says.
A 2006 study he was involved with, based on a survey of 2,770
members of the public, found that 34 percent didn’t believe
installing a barrier at the Golden Gate Bridge would avert even a
single death. In other words, they believed that 100 percent of
potential jumpers would have found another way. “That just shows
you in some sense how fatalistic people are,” Miller says.
In reality, most people’s unsuccessful suicide attempts do not
ultimately lead to a later death by suicide — a fact that offers
hope. One analysis of 90 studies, which followed people who had
been treated for self-harm, found that while some had gone on to
attempt again, more than nine years later just 7 percent had taken their own lives.
“If people have a suicidal crisis and don’t die,” Klonsky says,
“they’re overwhelmingly likely to live a life that does not end in