Archive for the ‘Science’ Category
Lamarck rides again: the inheritability of acquired traits—epigenetics—continues to be a field of study. Michael White has a good article on the topic in Pacific Standard:
You inherit some of your grandmother’s genes, but do you also inherit her experiences? Last month, a group of Swedish researchers at the Karolinska Institute and the University of Umeå released their latest in a series of reports on a long-term health study of people born between 1890 and 1920 in Överkalix, a small town in northern Sweden. These scientists have been making waves for more than a decade with claims that our health is influenced by the experiences of our grandparents. Using statistics of 19th-century harvests in Northern Sweden to determine how much food was available to the ancestors of the residents of Överkalix, the researchers concluded that the risk for cardiovascular disease among their study participants was influenced by the dramatic swings from feast to famine experienced by the participants’ grandparents during childhood.
Studies like this one are part of the hodgepodge of research that gets lumped together in the growing and increasingly ill-defined field of epigenetics. Scientific interest in this field has boomed over the past decade, thanks in part to technological advances that make new types of experiments possible. Epigenetics is hot in the popular press as well. It made the cover of Time in 2010. In Germany, Der Spiegel declared that epigenetics is a “victory over the gene,” illustrating both the victory itself and the sexiness of the science with an image of naked woman emerging from the confines of her gene pool. And of course, epigenetics is touted as the new secret to curing cancer. But the popularity of epigenetics is misplaced: It’s a badly over-hyped field whose recent findings aren’t nearly as revolutionary as many of its practitioners believe.
What is epigenetics? The term was coined in 1942 by British biologist Conrad Waddington, as a name for the study of how genes produce a fully developed organism from a single fertilized egg. More recently, epigenetics is commonly defined as the study of processes that transcend our genes—processes that produce different outcomes from a single, fixed set of genes by controlling how those genes get used. A classic example is a strain of laboratory mice that carry a particular version of a gene that can cause two different coat colors. Two mice may carry identical versions of this gene but nevertheless appear very different, with either light or dark fur, depending on its epigenetic state—whether the gene is in an on or off state.
What is surprising about this gene is that its epigenetic state can be passed from parents to offspring. This is not supposed to happen. Biological development depends on a complex process of switching the epigenetic states of tens of thousands of genes, as a newly fertilized egg gradually transforms itself into an adult organism made up of trillions of cells that come in hundreds of different types. In order for all of this epigenetic switching to happen correctly, genes must reset to a default state at conception. But researchers are finding evidence of exceptions, genes that somehow escape the reset. If states of genes can be inherited, and not just the genes themselves, then life experiences that happen to alter the epigenetic state of your grandparents’ genes can be passed on to you.
Recently developed technologies make it possible for scientists to measure the epigenetic states of genes more comprehensively than ever before. The result is a wave of studies showing how our life experiences impact the state of our genes. These studies are fascinating, but the results shouldn’t be particularly surprising to anyone familiar with the last 60 years of molecular biology. DNA is not a static biological blueprint. Much as your body adapts to a high-altitude environment by ramping up the production of red blood cells, our genomes respond to environmental signals by changing which genes get expressed. This is not news. A trio of French scientists won a Nobel Prize in 1965 for showing how this process works in bacteria, and there have been decades of studies of this phenomenon in humans.
So we shouldn’t be surprised that our physical and even our mental environment can influence the behavior of our genes in many different cells in our body. Epigenetic states of genes are manifestations of DNA doing its job, and many scientists are currently focused on trying to understand what those different epigenetic states mean. This research is important and interesting, but not paradigm-breaking.
The question of inherited epigenetic states is another matter. . .
Ryan Koronowski writes at ThinkProgress:
Alpha Natural Resources, the third-largest coal company in the U.S., agreed to pay a $27.5 million fine after violating water pollution permits in Kentucky, Pennsylvania, Tennessee, Virginia and West Virginia.
Over the last seven years, Alpha and its subsidiaries discharged heavy metals into waterways across those five Appalachian states 6,289 times, through 794 different discharge points, sometimes by as much as 35 times the legal limit.
The pollutants that spilled from the coal mines throughout Appalachia include “iron, pH, total suspended solids, aluminum, manganese, selenium, and salinity,” according to an EPA press release.
The giant coal company will also spend $200 million to stop sending toxic discharge into the nations rivers and streams. According to the AP, which obtained details about the settlement on Wednesday, “under the agreement, the mine operators will install wastewater treatment systems and take other measures aimed at reducing discharges from 79 active coal mines and 25 coal-processing plants in those five states.”
Cynthia Giles, who runs the Environmental Protection Agency’s enforcement office, told the AP that the settlement was “the biggest case for permit violations for numbers of violations and size of the penalty, which reflects the seriousness of violations.”
“This is the largest one, period.”
A big part of the reason this settlement was so comprehensive and expensive is because in 2011, Alpha Natural Resources bought a coal company called Massey Energy. Massey’s coal operations account for more than half of the violations represented in Wednesday’s settlement.
Alpha spent $7.1 billion to purchase Massey, and it has been picking up the pieces ever since. Months after the purchase agreement was announced, Massey was still fighting a legal battle over dumping 1.4 billion gallons of toxic coal slurry into old underground coal mines — knowing all the while that the mines leaked into the water supply. Alpha settled the lawsuit with hundreds of West Virginia residents in 2011.
Massey received global headlines for the tragic explosion in 2010 that killed 29 miners, and stayed in the headlines as Massey CEO Don Blankenship’s confrontational relationship with safety regulators prompted shareholder calls for his resignation. In 2009, Blankenship called the idea that safety regulators cared more about coal miners than he did “as silly as global warming.” This despite the small world encompassing coal industry and coal regulators: President Bush appointed a former Massey official to an MSHA review commission in 2002.
In 2012, Massey mine superintendent Gary May pled guilty to charges of criminal conspiracy over deceiving federal safety regulators. When the Mine Safety and Health Administration would come for an inspection, May would warn miners, increase air ventilation, falsify records, and cut corners in order to hide dangerous safety violations.
Though 2014 is barely two months old, the U.S. has seen a raft of coal spills — in West Virginia, North Carolina, West Virginia again, and West Virginia again — signalling the problem of dirty coal is not going away.
Andrew Briner writes at ThinkProgress:
Add attention deficit hyperactivity disorder (ADHD) to the list of ailments attributed to the popular painkiller acetaminophen. A new study in the journal JAMA Pediatrics found that more than half of mothers who took acetaminophen during pregnancy were more likely to have children with ADHD-like behavior or hyperkinetic disorder, a severe form of ADHD.
It’s unclear at this point whether acetaminophen use is actually causing these symptoms or if both are a sign of other unnoticed factors, as the Globe and Mail pointed out. And the long, shameful history of blaming and criminalizing pregnant women for pretty much anything they do during pregnancy means this news should be taken carefully. But even if proof of a causal link is demonstrated, the FDA’s record on regulating over-the-counter (OTC) drugs, specifically acetaminophen, shows it wouldn’t be up to the job of dealing with it.
And this news comes just as the Food and Drug Administration (FDA) announced it would berevamping its process for approving and regulating over-the-counter drugs, in response to just such concerns that it’s too slow to respond to new products and safety issues.
Acetaminophen is one such failure, as ProPublica extensively documented in September. The FDA convened a panel of experts to evaluate its safety in 1977, as the drug was first becoming widely popular. The panel determined it was “obligatory” to include a label warning that acetaminophen could cause “severe liver damage.” The FDA didn’t add that warning until 2009.
Acetaminophen is both one of the most commonly-used pain relief drugs in the United States and the primary cause of acute liver failure, nearly half of all cases. Overdoses kill an estimated 458 Americans each year, and are responsible for more than 56,000 emergency room visits and 2,600 hospitalizations.
No painkiller or drug is without risk. But for comparison, the entire class of drugs that includes ibuprofen, the Advil ingredient that is similarly popular to acetaminophen, was responsible for 15 deaths in 2010, according to CDC data as reported in ProPublica. In the same year acetaminophen killed 321, 166 of which were accidental overdoses.
The main problem is that the difference between a therapeutic dose and a life-threatening one is small. . .
We should focus on eating plants. Rina Shaikh-Lesko notes in The Scientist:
Two studies published March 4 in Cell Metabolism suggest that a low-protein diet may be key for longevity, casting doubt on the widespread dietary trend of reducing carbohydrate intake and loading up on protein.
One study, led by Stephen Simpson at the University of Sydney, looked at the life spans of mice on diets containing varying levels of protein, carbohydrates, and fat. Mice on a high-protein diet were leaner, but mice on a low-protein, high-carbohydrate diet lived much longer. The other study, led by Valter Longo of the University of Southern California, used death certificate data from people 50- to 65-years-old who had participated in the national NHANES nutrition survey. NHANES participants who reported a high-protein diet on NHANES had a higher rate of death, especially from cancer before age 65. However, after age 65, a high-protein diet seemed beneficial.
“If these two studies are really correct, what people in general are trying to do . . . might be completely wrong in terms of maintaining health and even longevity,” Shin-ichiro Imai of Washington University in St. Louis told ScienceNow.
Popular nutrition writer Marion Nestle, who is also a public health professor at New York University, is more skeptical of Longo’s results. “Protein is not, and never has been, an issue in American diets, and the data presented in this study do not convince me to think otherwise,” she told the Washington Post.
Nice to know that a high-protein diet is good for me. (I’m past age 65.) However, I do respect Prof. Nestle’s opinion.
There’s a lot more to viruses than we thought. Didier Raoult reports in The Scientist:
The theory of evolution was first proposed based on visual observations of animals and plants. Then, in the latter half of the 19th century, the invention of the modern optical microscope helped scientists begin to systematically explore the vast world of previously invisible organisms, dubbed “microbes” by the late, great Louis Pasteur, and led to a rethinking of the classification of living things.
In the mid-1970s, based on the analysis of the ribosomal genes of these organisms, Carl Woese and others proposed a classification that divided living organisms into three domains: eukaryotes, bacteria, and archaea. (See “Discovering Archaea, 1977,” The Scientist, March 2014) Even though viruses were by that time visible using electron microscopes, they were left off the tree of life because they did not possess the ribosomal genes typically used in phylogenetic analyses. And viruses are still largely considered to be nonliving biomolecules—a characterization spurred, in part, by the work of 1946 Nobel laureate Wendell Meredith Stanley, who in 1935 succeeded in crystallizing the tobacco mosaic virus. Even after crystallization, the virus maintained its biological properties, such as its ability to infect cells, suggesting to Stanley that the virus could not be truly alive.
Recently, however, the discovery of numerous giant virus species—with dimensions and genome sizes that rival those of many microbes—has challenged these views. (See illustration.) In 2003, my colleagues and I announced the discovery of Mimivirus, a parasite of amoebae that researchers had for years considered a bacterium.1 With a diameter of 0.4 micrometers (μm) and a 1.2-megabase-pair DNA genome, the virus defied the predominant notion that viruses could never exceed 0.2 μm. Since then, a number of other startlingly large viruses have been discovered, most recently two Pandoraviruses in July 2013, also inside amoebas. Those viruses harbor genomes of 1.9 million and 2.5 million bases, and for more than 15 years had been considered parasitic eukaryotes that infected amoebas.2
Now, with the advent of whole-genome sequencing, researchers are beginning to realize that most organisms are in fact chimeras containing genes from many different sources—eukaryotic, prokaryotic, and viral alike—leading us to rethink evolution, especially the extent of gene flow between the visible and microscopic worlds. Genomic analysis has, for example, suggested that eukaryotes are the result of ancient interactions between bacteria and archaea. In this context, viruses are becoming more widely recognized as shuttles of genetic material, with metagenomic studies suggesting that the billions of viruses on Earth harbor more genetic information than the rest of the living world combined. (See “Going Viral,” The Scientist, September 2013.) These studies point to viruses being at least as critical in the evolution of life as all the other organisms on Earth.
A giant discovery
Despite the fact that viruses use the same genetic code as verifiably living things, science long classified them as mere collections of biomolecules. And because scientists assumed that viruses had both an upper size limit of just 0.2 μm and a parasitic nature, they classified them in a not-quite-biological world of their own.
That thinking started to change in the early 2000s, when my colleagues and I identified an unknown virus living inside an amoeba. It was as big as some bacteria and archaea and was visible under an optical microscope—qualifying it as a microbe under Pasteur’s original definition. I named it Mimivirus as a personal joke about the stories that my father, a biomedical scientist, told me when I was a child to explain evolution; the stories were based on the life of “Mimi the amoeba.” I initially disguised the true source of this name, however, pretending that Mimivirus came from “MiMicking microbe.”
Researchers had first noticed Mimivirus in 1992, but based on its appearance under light microscopy it had been considered an intracellular bacterium for several years. Transmission electron microscopy images depicting its ultrastructure, along with the determination of its genome sequence in 2004,3however, confirmed that it was, in fact, part of the viral world. Mimivirus has no ribosomal genes, but its genome contains more than 1,200 genes—three times more than any virus known at the time. Its genome is larger than that of many bacteria and archaea and comparable to some eukaryotic genomes. Mimivirus was no ordinary virus.
Unlike most other viruses, Mimivirus carries genes that encode . . .
Rep. Rush Holt (D-NJ) is a scientist who is perfectly willing to take on climate change denialists using evidence and studies. The Salon article at the link is interesting and Rep. Holt is quite convincing—which, as it turns out, will make denialists cling even more fiercely to their idea that climate change is a gigantic hoax engineered by climate scientists eager to cash in—scientists so desperate for grant money that (presumably) they have actually heated up the Earth!
And, unfortunately, that’s what humans are like. As Aaron Carroll writes in a summary of efforts to counter the harmful and erroneous idea that vaccines are harmful:
When they gave evidence that vaccines aren’t linked to autism, that actually made parents who were already skittish about vaccines less likely to get their child one in the future. When they showed images of sick children to parents it increased their belief that vaccines caused autism. When they told a dramatic story about an infant in danger because he wasn’t immunized, it increased parents’ beliefs that vaccines had serious side effects.
Basically, it was all depressing. Nothing was effective.
And check out this Slate article.
The question, of course, is why does evidence work to convince some people while having no effect on others? Is it a matter of genetics? of education? of prior experience?
That would be a good question to answer.
UPDATE: Kevin Drum also has a post on this issue.
Fascinating article at Pacific Standard by Ethan Watters:
One morning last fall, the evolutionary biologist Randy Thornhill was standing with me in front of the gorilla enclosure at the Albuquerque zoo. He was explaining a new theory about the origins of human culture when Mashudu, a 10-year-old western lowland gorilla, decided to help illustrate a point. In a very deliberate way, Mashudu sauntered over to the deep cement ravine at the front of his enclosure, perched his rear end over the edge, and did his morning business.
Mashudu, I suspected, had just displayed what evolutionary theorists call a “behavioral immune response”—a concept central to Thornhill’s big theory. So I asked him whether I was right about Mashudu. “Pooping downhill is pretty smart,” Thornhill said after some consideration. “He got his waste as far away from him as possible. I think that would probably count as a disease avoidance behavior.”
It might seem strange to fixate on how a gorilla goes about answering the call of nature. But according to Thornhill’s hypothesis, much of what we humans like to think of as politics, morality, and culture is motivated by the same kind of subconscious instinct that likely drove Mashudu to that ledge.
Anyone with a basic grasp of biology knows that all animals have immune systems that battle pathogens—be they viruses, bacteria, parasites, or fungi—on the cellular level. And it’s also fairly well understood that animals sometimes exhibit outward behaviors that serve to ward off disease. Just around the corner from the fastidious Mashudu, Thornhill and I watched an orangutan named Sarah grooming her six-month-old son Pixel, poring through his hair for parasites. Some species of primate, Thornhill told me, will ostracize sick members of the group to avoid the spread of disease. Cows and other ungulates are known to rotate their movements among pastures in such a way as to avoid the larvae of intestinal worms that hatch in their waste. And in ant societies, only a small number of workers are given the task of hauling away the dead, while sick ants will sometimes leave the nest to die apart from the group.
At the most quotidian level, Thornhill finds it easy to convince people that humans likewise manifest such instinctual behaviors to avoid infection and illness. Some of these habits very much parallel those seen in other creatures. I admitted to Thornhill that I had recently been displaying a bit of grooming behavior myself after the youngest primate in my care came home from preschool itching with head lice. Like Mashudu, we humans remove waste from our living quarters. We ostracize our sick, at least to the extent that we expect those with the flu to stay home from work or school. And similar to the lowly ant, we assign a small number of our fellows the solemn duty of hauling away and disposing of our dead. On examination, everyday life is full of small defensive moves against contamination, some motivated by feelings, like disgust, that arise without conscious reflection. When you open the door of a gas station bathroom only to decide you can hold it for a few more miles, or when you put as much distance as possible between yourself and a person who is coughing and sneezing in a waiting room, you are displaying a behavioral immune response.
But these individual actions are just the tip of the iceberg, according to Thornhill and a growing camp of evolutionary theorists. Our moment-to-moment psychological reactions to the threat of illness, they suggest, have a huge cumulative effect on culture. Not only that—and here’s where Thornhill’s theory really starts to fire the imagination—these deep interactions between local pathogens and human social evolution may explain many of the basic differences we observe between cultures. How does your culture behave toward strangers? What kind of government do you live under? Who are your sexual partners? What values do you share? All of these questions may mask a more fundamental one: What germs are you warding off?
The threat of disease is not uniform around the world. In general, higher, colder, and drier regions have fewer infectious diseases than warmer, wetter climates. To survive, people in this latter sort of terrain must withstand a higher degree of “pathogen stress.” Thornhill and his colleagues theorize that, over time, the pathogen stress endemic to a place tends to steer a culture in distinct ways. Research has long shown that people in tropical climates with high pathogen loads, for example, are more likely to develop a taste for spicy food, because certain compounds in these foods have antimicrobial properties. They are also prone to value physical attractiveness—a signal of health and “immunocompetence,” according to evolutionary theorists—more highly in mates than people living in cooler latitudes do. But the implications don’t stop there. According to the “pathogen stress theory of values,” the evolutionary case that Thornhill and his colleagues have put forward, our behavioral immune systems—our group responses to local disease threats—play a decisive role in shaping our various political systems, religions, and shared moral views.
If they are right, Thornhill and his colleagues may be on their way to unlocking some of the most stubborn mysteries of human behavior. Their theory may help explain why authoritarian governments tend to persist in certain latitudes while democracies rise in others; why some cultures are xenophobic and others are relatively open to strangers; why certain peoples value equality and individuality while others prize hierarchical structures and strict adherence to tradition. What’s more, their work may offer a clear insight into how societies change. According to Thornhill’s findings, striking at the root of infectious disease threats is by far the most effective form of social engineering available to any would-be reformer.
If you were looking for a paradigm-shifting theory about human behavior, . . .
Both fascinating and useful. Pennebaker is also the author of Opening Up, a practical guide to recovering from (and making sense of) personal tragedy. He discovered (he’s a scientist, so he’s tested his ideas) an effective approach that you can do easily on your own—and he pretty much demolishes the idea of talking a lot about the event immediately after it happens—the usual “grief counseling” approach, which turns out to be counter-productive in fact.
The Secret Life of Pronouns: What Our Words Say About Us: $1.99 for a little while. (Obviously, the subtitle might well have been “What People’s Words Tell Us About Them.”)
You are not a beautiful and unique snowflake – but these are. Film-makerVyacheslav Ivanov used a high-speed camera to record these individual snowflakes blooming into being like chilly flowers.
Ivanov’s snowflakes grow into stars with six-fold symmetry because water molecules join together into hexagon shapes as they freeze. Starting with a small crystal, more and more molecules attach to the sides of the hexagon, and it grows in six directions. Each arm of the snowflake closely matches the others because they form in near-identical conditions. . .
Trip Gabriel reports in the NY Times:
Last June, state employees in charge of stopping water pollution were given updated marching orders on behalf of North Carolina’s new Republican governor and conservative lawmakers.
“The General Assembly doesn’t like you,” an official in the Department of Environment and Natural Resources told supervisors, who had been called from across the state to a drab meeting room here. “They cut your budget, but you didn’t get the message. And they cut your budget again, and you still didn’t get the message.”
From now on, regulators were told, they must focus on customer service, meaning issuing environmental permits for businesses as quickly as possible. Big changes are coming, the official said, according to three people in the meeting, two of whom took notes. “If you don’t like change, you’ll be gone.”
But when the nation’s largest utility, Duke Energy, spilled 39,000 tons of coal ash into the Dan River in early February, those big changes were suddenly playing out in a different light. Federal prosecutors have begun a criminal investigation into the spill and the relations between Duke and regulators at the environmental agency.
The spill, which coated the river bottom 70 miles downstream and threatened drinking water and aquatic life, drew wide attention to a deal that the environmental department’s new leadership reached with Duke last year over pollution from coal ash ponds. It included a minimal fine but no order that Duke remove ash — the waste from burning coal to generate electricity — from its leaky, unlined ponds near drinking water. Environmental groups said the arrangement protected a powerful utility rather than the environment or the public.
Current and former state regulators said the watchdog agency, once among the most aggressive in the Southeast, has been transformed under Gov. Pat McCrory into a weak sentry that plays down science, has abandoned its regulatory role and suffers from politicized decision-making.
The episode is a huge embarrassment for Mr. McCrory, who worked at Duke Energy for 28 years and is a former mayor of Charlotte, where the company is based. And it has become yet another point of contention in North Carolina, where Republicans who took control of the General Assembly in 2011 and the governor’s mansion last year have passed sweeping laws in line with conservative principles. They have affected voting rights and unemployment benefits, as well as what Republicans called “job-killing” environmental regulations, which have received less notice.
Critics say the accident, the third-largest coal ash spill on record, is inextricably linked to the state’s new environmental politics and reflects an enforcement agency led by a secretary who suggested that oil was a renewable resource and an assistant secretary who, as a state lawmaker, drew a bull’s-eye on a window in his office framing the environmental agency’s headquarters.
“They’re terrified,” said John Dorney, a retired supervisor who keeps in touch with many current employees. “Now these people have to take a deep breath and say, ‘I know what the rules require, but what does the political process want me to do?’ ”
Duke has apologized for the Dan River spill and says it is now committed to cleaning up some of its 32 coal ash ponds across the state. The company has also been subpoenaed in the federal investigation.
A spokesman for Governor McCrory said the governor had no role in the state’s proposed settlement with Duke. . .
Continue reading. The story at the link includes a video. And the comments are worth reading. People are becoming increasingly angry at the downfall of the US.
Interesting note by Kerry Grens in The Scientist on a long-running experiment in evolution:
In 1988, when evolutionary biologist Richard Lenski was an assistant professor at the University of California, Irvine, he started a simple experiment: toss E. coli into a new environment and watch what happens. He wanted to know how reproducible evolution would be, so he put the same strain of the bacteria into 12 flasks with the same simple medium and waited to see how they would evolve. E. coli normally lives in the guts of animals, so the experiment would allow for a way to observe adaptations to a new environment.
After about a year and 2,000 E. coli generations, Lenski and his colleagues published the first results of what they then considered to be a long-term experiment in evolution. Little did they know that 25 years and 50,000 generations later, the experiment would still be chugging along—those 12 flasks representing alternate universes of bacterial existence. “I guess I didn’t view it as [being as] open-ended as it clearly has become, not only as an experiment but in terms of the ability of the organisms to keep improving,” says Lenski.
In his latest publication on the experiment, Lenski reported that the bacteria continually become more fit. His team pitted bacteria from various evolutionary time points (from each flask, a sample is frozen every 500 generations) against one another to see which would grow better when combined in the same container. “I like to think of this project as time travel because we’re comparing organisms that lived at different points in the past, resurrecting them, and comparing them head to head,” says Lenski.
Lenski and his collaborators can distinguish the competitor populations from different flasks because of color-coded genetic markers. For instance, they would pit a sample taken from one flask of red bacteria at 50,000 generations against an ancestral sample from another flask housing white bacteria. To make sure the resurrected bacteria weren’t at a dis-advantage, they would give the organisms time to acclimate after being thawed. Lenski’s team found that bacteria that had evolved for a greater length of time—those from later generations—appeared more fit than those resurrected from earlier generations; fitness never peaked (Science, 342:1364-67, 2013). Their data suggest that, at least in this situation, evolutionary fitness is ever increasing.
Rees Kassen of the University of Ottawa says the most interesting finding is that most adaptations happened early on in the experiment. “That means [initially] there are lots of opportunities for [the bacteria] to get better,” he says. “Even though beneficial mutations are still very rare events, there are still different ways they could get better, and they also are likely to improve fitness by a large amount.”
The results came as a surprise to Lenski, who expected fitness to plateau. It’s not the first time his bacterial cells have proven unpredictable, such as when they began to utilize a new food source. In 2008, one of the strains evolved to metabolize citrate, which is ordinarily just a buffer in the medium. “It was a quantum leap in the evolution of this species, and it was totally unexpected,” says Tadeusz Kawecki of the University of Lausanne.
John Thompson, an evolutionary biologist at the University of California, Santa Cruz, says that the results show there are many adaptive solutions, even in a simple environment. “It is, then, no wonder that life has evolved to be so diverse,” Thompson writes in an e-mail. “That does not mean, though, that all populations in nature will always continually evolve increases in adaptation.” In cases where the environment is changing rapidly, for instance, slow increases in fitness will not be able to continue.
The finding contradicts the “naive” view that an organism will cease getting fitter once it’s well adapted to an environment, says Kassen. Without Lenski’s experiment, there wouldn’t be much empirical data to show that. “The fact of the matter is, it’s the only experiment we can test,” he says. “No other experiments have gone on as long.” . . .
Jerome Groopman has an interesting book review in the NY Review of Books. Just one quotation in the article:
To put it bluntly, marijuana works. Not dazzlingly, but about as well as opioids. That is, it can reduce chronic pain by more than 30 percent. And with fewer serious side effects. To be sure, some researchers think it’s too soon to declare marijuana and synthetic cannabinoids a first-line treatment for pain, arguing that other drugs should be tried first. But that may be too cautious a view.
Would a corporation deliberately harm the health of the public, including not merely illness but many deaths, merely for the sake of profit? Need I ask? (cf. cigarettes for a prime example—and it’s still going on)
Mark Bittman has a good column in the NY Times:
In the last few years, it’s become increasingly clear that food companies engineer hyperprocessed foods in ways precisely geared to most appeal to our tastes. This technologically advanced engineering is done, of course, with the goal of maximizing profits, regardless of the effects of the resulting foods on consumer health, natural resources, the environment or anything else.
But the issues go way beyond food, as the City University of New York professor Nicholas Freudenberg discusses in his new book, “Lethal but Legal: Corporations, Consumption, and Protecting Public Health.” Freudenberg’s case is that the food industry is but one example of the threat to public health posed by what he calls “the corporate consumption complex,” an alliance of corporations, banks, marketers and others that essentially promote and benefit from unhealthy lifestyles.
It sounds creepy; it is creepy. But it’s also plain to see. Yes, it’s unlikely there’s a cabal that sits down and asks, “How can we kill more kids tomorrow?” But Freudenberg details how six industries — food and beverage, tobacco, alcohol, firearms, pharmaceutical and automotive — use pretty much the same playbook to defend the sales of health-threatening products. This playbook, largely developed by the tobacco industry, disregards human health and poses greater threats to our existence than any communicable disease you can name.
All of these industries work hard to defend our “right” — to smoke, feed our children junk, carry handguns and so on — as matters of choice, freedom and responsibility. Their unified line is that anything that restricts those “rights” is un-American.
Yet each industry, as it (mostly) legally can, designs products that are difficult to resist and sometimes addictive. This may be obvious, if only in retrospect: The food industry has created combinations that most appeal to our brains’ instinctual and learned responses, although we were eating those foods long before we realized that. It may be hidden (and borderline illegal), as when tobacco companies upped the nicotine quotient of tobacco. Sometimes, as Freudenberg points out, the appeals may be subtle: Knowing full well that S.U.V.’s were less safe and more environmentally damaging than standard cars, manufacturers nevertheless marketed them as safer, appealing to our “unconscious ‘reptilian instincts’ for survival and reproduction and to advertise S.U.V.’s as both protection against crime and unsafe drivers and as a means to escape from civilization.”
The problems are clear, but grouping these industries gives us a better way to look at the struggle of consumers, of ordinary people, to regain the upper hand.The issues of auto and gun safety, of drug, alcohol and tobacco addiction, and of hyperconsumption of unhealthy food are not as distinct as we’ve long believed; really, they’re quite similar. For example, the argument for protecting people against marketers of junk food relies in part on the fact that antismoking regulations and seatbelt laws were initially attacked as robbing us of choice; now we know they’re lifesavers.
Thus the most novel and interesting parts of Freudenberg’s book are those that rephrase the discussion of rights and choice, because we need more than seatbelt and antismoking laws, more than a few policies nudging people toward better health. . .
The comments to the article are quite interesting, although not always well thought out.
The food industry always opposes any effort to inform the consumer. Food companies, for whatever reason, VERY much do not want consumers to have information about the foods they are buying. But the proposed improvements look good to me:
Tara Culp-Pressler writes in ThinkProgress:
Later this week, the White House is set to unveil the first update to FDA-approved nutrition labels in more than two decades. Politico reports that First Lady Michelle Obama will announce the changes on Thursday, as part of her larger focus on encouraging healthy habits and tackling childhood obesity.
At the beginning of this year, the Food and Drug Administration indicated that updating nutrition labels would be a top priority for the agency in 2014. But officials didn’t confirm a timeline for rolling out the new requirements.
The move has the potential to impact a considerable number of Americans. A recent studyconducted by the U.S. Department of Agriculture found that the number of people who rely on nutrition labels when they’re grocery shopping is on the rise. About 42 percent of working-age adults and 57 percent of older adults now say they consider the FDA’s labelwhen they’re selecting their food — and nearly three fourths of all adults report they would use similar information in restaurants if it were available.
The Center for Science in the Public Interest (CSPI), a nonprofit organization dedicated to nutrition and food policy, has repeatedly urged the FDA to “bring food labeling into the 21st century.” Back in 2010, the organization released a report entitled “Food Labeling Chaos” that detailed the lack of industry-wide regulations in this area to hold companies accountable. The report urged the agency to crack down on brands that made overreaching claims about their products, establish a consistent standard for the foods labeled as “natural,” and make several updates to the current nutrition labels.
CSPI’s report put forth several suggestions for improving nutrition labels — like . . .
Interesting essay by Luís A. Nunes Amaral in The Scientist:
The United States currently spends about 2.7 percent of its gross domestic product (GDP) on research and development, about half of which comes from federal sources. This amount is comparable to annual expenditures on transportation and water infrastructure (3 percent of GDP) and on education (5.5 percent). The magnitude of the investments required for maintaining the scientific enterprise have resulted in calls for a quantitative assessment of the impact of the contributions of individuals and institutions, so that policy makers are persuaded that resources are being used effectively.
Despite its importance, whether and how to quantify scientific impact remains a source of controversy within the research community. For example, the San Francisco Declaration on Research Assessment has promoted “the need to eliminate the use of journal-based metrics, such as journal Impact Factors, in funding, appointment, and promotion considerations.” I find it surprising that a scientist would propose a move away from measurement and quantification when these activities are at the core of science itself. I believe that when considering an imperfect but necessary tool, the right course of action is to seek to improve it, rather than to discard it. The scientific community—and especially the funding agencies—should support the development of better bibliometric evaluation tools rather than oppose their use altogether.
There is a long history of using bibliometric-based measures to quantify scientific production and impact. Opponents of such measures, including many prominent scientists, have recently urged the scientific community to return to the “gold standard” of peer review. Underlying this recommendation is the “hypothesis” that, if two intelligent, unbiased evaluators were to read the papers of, say, applicants for a faculty position, they would draw the same conclusion about which candidate was best for the job.
This is a naive, unsustainable position. Anyone working as an editor of a journal, or as a member of a selection or promotion and tenure committee, knows how broadly the ratings of papers, individuals, or proposals vary across reviewers. Indeed, Case Western Reserve University’s David Kaplan and his colleagues have demonstrated that one would need tens of thousands of independent unbiased peer-evaluations in order to obtain an accurate ranking. And the number of reviewers needed is not the only limitation of peer review as a measurement process. Like all humans, scientists have biased views of students, collaborators and competitors. Sadly, being an expert is not a guarantee that those biases will be absent; it is only a guarantee that one will be convinced that one is right.
Scientists are already being evaluated using bibliometric-based measures such as . . .
A very interesting interview, well worth reading. From the interview, a clue to the obesity epidemic:
The USDA has tracked America’s eating habits beginning in 1909. The average American in 1909 ate just under 124 pounds of meat, per year. That slowly–but steadily–went up and hit a peak in 2004, when it hit 201 pounds per person. That is an increase of 75 pounds of meat per person, per year. In the same interval, cheese intake, which was less than 4 pounds per person back in 1909, shot up to about 34 pounds per person, per year. And sugar intake went up, as well. You put all this together, and what do you do with a person who, year after year, is eating 75 more pounds of meat, 30 more pounds of cheese, 40 to 50 more pounds of sugar? The problem is, they will become overweight and have many health problems.
The USDA has been severely compromised by unrelenting industry pressure. Wenonah Hauter givens an example in the Progressive Populist:
Earlier this year, Food & Water Watch received information that USDA’s Food Safety and Inspection Service (FSIS) was going to permit a trade association — the National Chicken Council — to collect data in poultry plants to assess the rate of foodborne pathogens in chicken parts. The information came in the form of an e-mail from the Assistant FSIS Administrator for Field Operations Daniel Engeljohn, informing his district managers that he was aware of the effort and gave his full blessing to the project. What was troubling about the e-mail was that it told the district managers that the purpose of the data collection was for the industry to develop its own voluntary pathogen performance standards that it was going to enforce on poultry processing plants. It went on to say that FSIS inspection personnel assigned to the plants were not to interfere with the National Chicken Council data collection and that they had no right to look at the data that was collected.
In other words, the poultry industry would create the standards for pathogen levels in chicken parts, and they would only “voluntarily” stick with them. Not only would the industry be able to decide how much salmonella or campylobacter there is on your chicken, but there would be no USDA enforcement of the standard.
Welcome to the latest in privatization of chicken inspections that the industry is pushing, with the USDA’s blessing. Another example is the “Modernization of Poultry Slaughter Inspection,” the proposed plan whose “modern” twist is to turn most poultry inspection over to the very companies that produce our poultry, leaving only one government inspector per plant to inspect over 175 birds per minute — or three birds per second.
This hasn’t happened overnight. The industry has been chipping away at the USDA’s mandate to protect our food system for over a decade. Since the late 1990s, . . .
Continue reading. I would feel better if industry were not driven solely by a drive to cut costs and increase profits. That motivation is insufficient to protect our health and the quality of our food supply—indeed, our health and the quality of the food supply often get in the way, which is why we get industry postures as the above.
Chelsea Parsons writes at ThinkProgress:
Guns kill a lot of young people in the United States. Not just in school shootings or horrific “accidents” between toddlers that tend to garner the most media attention, but in every day shootings in communities around the country that result in the deaths of thousands of children and teenagers.
In 2010, 6,201 young people between the ages of 15 and 24 died by gunfire. Guns were a close second to the leading cause of death among this age group, car accidents, which took the lives of 7,024 young people that year. But, while car accident deaths among young people have been steadily declining over the past decade, gun deaths have remained relatively unchanged. And, as described in a new Center for American Progress reportreleased Friday, if current trends continue, gun deaths will surpass car accident deaths among young people sometime in 2015:
How can we explain these numbers? For car accident deaths, these numbers represent a significant victory. Deaths of young people as a result of car accidents have dropped dramatically in the last two decades, from a high of more than 12,000 deaths among this age group in 1990. This decline is not an accident: billions of dollars have been spent on public health and safety research to understand motor vehicle accidents and how to prevent them from becoming fatal. This research has resulted in design innovation, changes to cars and roadways, and new laws that have led to a significant and steady decline in such fatalities among all age groups, including young people. There was no silver bullet for reducing vehicular death: airbags, seatbelt laws, anti-lock brakes, better signage, and tough drunk driving laws all contributed to it. But, in combination these measures have saved tens of thousands of American lives.
For guns, these numbers represent an enormous failure. The United States has experienced a dramatic decline in violent crime over the last two decades, yet the rate of gun violence, particularly among young people, has barely moved. Why? We don’t know.
Unfortunately, since the early 1990s, very few public health researchers have been trying to find out. Restrictions on such research imposed by Congress have had a substantial chilling effect, which has resulted in the almost total abandonment of this issue by our nation’s public health research institutions. Without this research, policymakers, legislators, community leaders, and parents are left without much direction regarding how to best protect children and teenagers from gun violence.
As we approach that morbid milestone next year when gun violence kills more American children and teenagers than car accidents, it’s time to start approaching this problem in the same manner as we addressed car accident deaths. We know how to do this –-through a combination of public health research, technological innovation, legislative change, enhanced enforcement, and transforming cultural norms we were able to make motor vehicle transportation safer while at the same time preserving American’s unique car culture. We can do the same thing with gun violence by adopting laws and policies designed to prevent gun deaths while protecting the rights of law-abiding gun owners.
Emphasis added. The wholehearted embrace of ignorance seems to be a special feature of the GOP.