A New Way of Understanding What Might Kill Us

It has been more than half a century since the discovery of penicillin revolutionized our ability to control communicable disease. Since that time a lot of progress has been made on all kinds of diseases, although the emphasis has been more on degenerative diseases--treatments for cardiovascular conditions, cancer, and other issues that are associated especially with an aging population. But, a story in today's New York Times puts the control of bacteria and viruses back in the spotlight. The story focuses on the work of Dr. James M. Musser, chairman of pathology and genomic medicine at the Methodist Hospital System in Houston.

It is the start of a new age in microbiology, Dr. Musser and others say. And the sort of molecular epidemiology he and his colleagues wanted to do is only a small part of it. New methods of quickly sequencing entire microbial genomes are revolutionizing the field.

The first bacterial genome was sequenced in 1995 — a triumph at the time, requiring 13 months of work. Today researchers can sequence the DNA that constitutes a micro-organism’s genome in a few days or even, with the latest equipment, a day. (Analyzing it takes a bit longer, though.) They can simultaneously get sequences of all the microbes on a tooth or in saliva or in a sample of sewage. And the cost has dropped to about $1,000 per genome, from more than $1 million.

With rapid genome sequencing, “we are able to look at the master blueprint of a microbe,” Dr. Relman [from Stanford University] said in a telephone interview. It is “like being given the operating manual for your car after you have been trying to trouble-shoot a problem with it for some time.” Dr. Matthew K. Waldor of Harvard Medical School said the new technology “is changing all aspects of microbiology — it’s just transformative.”

One group is starting to develop what it calls disease weather maps. The idea is to get swabs or samples from sewage treatment plants or places like subways or hospitals and quickly sequence the genomes of all the micro-organisms. That will tell them exactly what bacteria and viruses are present and how prevalent they are.

Knowledge is power and we seem to be gaining at an increasing rate on these bugs that still can kill us.

Federal Judge Blocks Alabama Immigration Law--For the Moment

A Federal District Judge in Alabama has temporarily blocked the implementation of the new anti-immigrant legislation that was scheduled to take effect this week in Alabama. She blocked it only to give herself more time to study the law, so both sides apparently took comfort in that fact:

The ruling was cheered both by Republican leaders who were pleased the judge didn't gut the law and by opponents who compare it to old Jim Crow-era statutes against racial integration.
Blackburn didn't address whether the law is constitutional, and she could still let all or parts of the law take effect later. Instead, she said she needed more time to consider lawsuits filed by the Justice Department, private groups and individuals that claim the state is overstepping its bounds.

The judge said she will issue a longer ruling by Sept. 28, and her temporary order will remain in effect until the day after. She heard arguments from the Justice Department and others during a daylong hearing last week.

 While I certainly understand the frustration at the local level that the federal government has not implemented any kind of immigration reform, we can only hope that these egregiously punitive laws will be held back.

Similar laws have been passed in Arizona, Utah, Indiana and Georgia. Federal judges already have blocked all or parts of the laws in those states.

Urbanization is a Major Source of Environmental Degradation

An important new study has just been published in the academic journal PLoS One summarizing our knowledge of what growing urban populations mean for the environment. The authors--Karen Seto, Michail Fragkias, Burag Guneralp, and Michael Reilly--drew the following major conclusions:

The conversion of Earth's land surface to urban uses is one of the most irreversible human impacts on the global biosphere. It drives the loss of farmland, affects local climate, fragments habitats, and threatens biodiversity. Here we present a meta-analysis of 326 studies that have used remotely sensed images to map urban land conversion. We report a worldwide observed increase in urban land area of 58,000 km² from 1970 to 2000. India, China, and Africa have experienced the highest rates of urban land expansion, and the largest change in total urban extent has occurred in North America. Across all regions and for all three decades, urban land expansion rates are higher than or equal to urban population growth rates, suggesting that urban growth is becoming more expansive than compact. 

The New York Times picked up on the story and noted that:

While shifting variables make predictions about future growth difficult, the authors write, a few things are clear: because two-thirds of urban areas with populations exceeding five million are in coastal zones at risk from sea-level rise, “inadequate responses to protecting coastal urban areas would be devastating to the economies and infrastructure of 13 percent of the world’s urban population.”

These are obviously important issues since the UN Population Division projects that virtually all of the world's population growth in the next few decades will be in or show up in cities, especially cities of developing nations. Furthermore, note that this refers only to the land near cities. It does not take into account the extensive ecological footprint of urban residents that extends to literally all corners of the earth.

Why Are We Still Even Talking About Vitamin A?

The BBC News today highlights a paper just published in the British Medical Journal that extols the virtue of Vitamin A supplements for children.

UK and Pakistani experts assessed 43 studies involving 200,000 children, and found deaths were cut by 24% if children were given the vitamin. And they say taking it would also cut rates of measles and diarrhoea. The body needs vitamin A for the visual and immune systems to work properly. It is found in foods including cheese, eggs, liver and oily fish.

The incredibly sad part of this is that we have to keep talking about it in order to get the world to remember how important Vitamin A is for children. A very nice history of the discovery of how important Vitamin A can be is told in the PBS special of "Rx for Survival--Back to the Basics." Dr. Alfred Sommer at The Johns Hopkins Bloomberg School of Public Health is interviewed in this program, which I highly recommend to you:

In the early 1970s, Sommer, an ophthalmologist by training, was working in some of the poorest countries on Earth for the Epidemic Intelligence Service of the Centers for Disease Control. There he began to focus his work on a devastating, startlingly prevalent eye condition called nightblindness.
"A child who is night-blind in a village in India or Bangladesh or Nepal literally can't fend for him- or herself," Sommer explains. "While other kids are walking around the village or playing with toys, these children huddle in a corner."
Sommer saw firsthand the tragic consequences of leaving the condition untreated. "The children will go truly blind, because what happens is the cornea, that clear front of the eye, just melts away. And it can melt away in the course of one day." Millions of children were losing their vision permanently, Sommer learned, because of a simple lack of vitamin A in their diet.

Discovered in 1913 by nutritionist EV McCollum, vitamin A was one of the first essential "micronutrients" to be identified. One of its functions is to produce a light-sensitive chemical called rhodopsin in the retina, which allows us to see in low light. This is why carrots help us see in the dark, along with liver and dark green leafy vegetables like spinach — all foods that were missing from the diets of the children Sommer encountered.

There was only one way to find out. Sommer and his team gave an oral dose of vitamin A to 10,000 children and compared them with children not getting vitamin A. The results were astounding: Just two cents' worth of vitamin A given twice a year reduced childhood mortality by a third. "We were absolutely elated," he recalls. "Suddenly you have a very inexpensive, practical way to save more than a million lives a year of young children, year in and year out, and prevent half a million children from going blind."

But critics dismissed Sommer's results as too good to be true, and he couldn't convince them that such a simple solution could save so many lives. "What was most frustrating of all was when you present the hard data and people just say they don't believe it. I mean, how do you deal with that?"

And so it is that decades later we are still having to convince the world that we need to get Vitamin A to children, instead of it just being an automatic thing to do. And don't get me going on people who don't want to give their children vaccinations...

Researchers Have Linked Climate Change and Conflict

A new research paper in Nature is reported to be the first to find a statistically significant relationship between climate change and conflict. The researchers, Solomon M. Hsaing, Kyle C. Meng, and Mark A. Crane, from Princeton and Columbia Universities, "looked at data on conflicts between 1950 and 2004 that killed more than 25 people in a year. They compared El Niño years, which happen roughly every five years, with La Niña years. El Niño tends to bring hotter, drier conditions - and La Niña cooler ones - to tropical countries, but both have less of an influence on temperate countries. The analysis included 175 countries and 234 conflicts, over half of which caused more than 1000 deaths. It found that the risk of conflict in tropical countries rose from 3 per cent during La Niña years to 6 per cent during El Niño years. The effect was absent from countries only weakly affected by these climate cycles."


The link between climate change and conflict is probably not a direct one, and the researchers were not able to nail down cause-and-effect relationships, but they do have some possible explanations in mind:

Lead author Solomon Hsiang of Columbia's Earth Institute said El Nino was an invisible factor -- but not the only one -- in driving intra-border conflict.By causing crop losses, hurricane damage or helping to spread epidemics of water-borne disease, it amplified hunger, loss, unemployment and inequality, which in turn fuelled resentment and division.
Other factors that could affect risk and the outcome are the country's population growth and prosperity and whether its government is able to manage El Nino events properly.
"Even though we control for all of these factors simultaneously, we still find that there's a large and pervasive El Nino effect on civil conflicts," Hsiang said in a teleconference.
Although the current crisis in the Horn of Africa occurred beyond the parameters of the study, it was a "perfect example" of the hidden destruction of an El Nino.
"Forecasters two years ago predicted that there would be a famine in Somalia this year, but donors in the international aid community did not take that forecast seriously," said Hsiang.