Author Archives: curiouscat

How do Plants Grow Into the Sunlight?

Plants are extremely competitive in gaining access to sunlight. A plant’s primary weapon in this fight is the ability to grow towards the light, getting just the amount it needs and shadowing its competition. Now, scientists have determined precisely how leaves tell stems to grow when a plant is caught in a shady place.

Hole in the Wall trail, Olympic National Park, Washington, USA by John Hunter

The researchers discovered that a protein known as phytochrome interacting factor 7 (PIF7) serves as the key messenger between a plant’s cellular light sensors and the production of auxins, hormones that stimulate stem growth.

“We knew how leaves sensed light and that auxins drove growth, but we didn’t understand the pathway that connected these two fundamental systems,” says Joanne Chory, professor and director of the Salk’s Plant Biology Laboratory and a Howard Hughes Medical Institute investigator (HHMI provides huge amounts of funding for scientific research). “Now that we know PIF7 is the relay, we have a new tool to develop crops that optimize field space and thus produce more food or feedstock for biofuels and biorenewable chemicals.”

Plants gather intelligence about their light situation—including whether they are surrounded by other light-thieving plants—through photosensitive molecules in their leaves. These sensors determine whether a plant is in full sunlight or in the shade of other plants, based on the wavelength of red light striking the leaves. This is pretty cool; I love to learn about the brilliant strategies that have evolved.

If a sun-loving plant, such as thale cress (Arabidopsis thaliana), the species Chory studies, finds itself in a shady place, the sensors will tell cells in the stem to elongate, causing the plant to grow upwards towards sunlight.

When a plant remains in the shade for a prolonged period, however, it may flower early and produce fewer seeds in a last ditch effort to help its offspring spread to sunnier real estate. In agriculture, this response, known as shade avoidance syndrome, results in loss of crop yield due to closely planted rows of plants that block each other’s light.

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Bacteria In Cave Isolated for 4 Million Years Highly Resistant to Many Antibiotics

PLoS published an interesting open access research paper on bacteria and their resistance to antibiotics. I am surprised how widespread and strong the antibiotic resistance was is the isolated bacteria that were studied. It raises more interesting questions about the important area of antibiotics.

The lead researcher on this study, Gerry Wright, previously published on antibiotic properties of bacteria found in soil.

Abstract of Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome

Antibiotic resistance is a global challenge that impacts all pharmaceutically used antibiotics. The origin of the genes associated with this resistance is of significant importance to our understanding of the evolution and dissemination of antibiotic resistance in pathogens. A growing body of evidence implicates environmental organisms as reservoirs of these resistance genes; however, the role of anthropogenic use of antibiotics in the emergence of these genes is controversial.

We report a screen of a sample of the culturable microbiome of Lechuguilla Cave, New Mexico, in a region of the cave that has been isolated for over 4 million years. We report that, like surface microbes, these bacteria were highly resistant to antibiotics; some strains were resistant to 14 different commercially available antibiotics. Resistance was detected to a wide range of structurally different antibiotics including daptomycin, an antibiotic of last resort in the treatment of drug resistant Gram-positive pathogens.

Enzyme-mediated mechanisms of resistance were also discovered for natural and semi-synthetic macrolide antibiotics via glycosylation and through a kinase-mediated phosphorylation mechanism. Sequencing of the genome of one of the resistant bacteria identified a macrolide kinase encoding gene and characterization of its product revealed it to be related to a known family of kinases circulating in modern drug resistant pathogens. The implications of this study are significant to our understanding of the prevalence of resistance, even in microbiomes isolated from human use of antibiotics. This supports a growing understanding that antibiotic resistance is natural, ancient, and hard wired in the microbial pangenome.

Baboons Learn to Recognize Hundreds of Words

The (Monkey) Business Of Recognizing Words by Jon Hamilton

[Jonathan Grainger, researcher, Aix-Marseille University] says a baboon named Dan learned more than 300 words. “Dan’s our star baboon,” he says. “He’s a high-performing individual, basically. He does well in most tasks.”

But here’s the amazing thing: Dan and the other baboons also learned to tell whether a string of letters they’d never seen before was an English word. That’s something first-graders learn to do when they start reading, but scientists had assumed that children were simply sounding out the letters to decide whether they make sense.

Of course, the baboons couldn’t do this because they’re not learning to read a language they already speak. They had to rely on a part of the brain that can tell whether objects fit a known pattern.
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Michael Platt, who directs the Duke Institute for Brain Sciences, says he was surprised by what the baboons were able to do.

“I was really looking for holes to poke in this study, but it was very difficult to find any because it was really beautifully done,” he says. “And I think the linchpin here was that the baboons, once they had learned the rule, could generalize to new words that they had not seen before.”

Platt says when you think about it, the finding makes sense, given what’s known about human and animal brains. “Brains are always looking for patterns,” he says. “They are always looking to make some statistical pattern analysis of the features and events that are in the environment. And this would just be one of those.”

Platt says that’s a big departure from the idea that reading is a direct extension of spoken language.

One questions I have, is why the experiment done in France tested wether the Baboons could recognize English words?

Pay as You Go Solar in India

Farmers Foil Utilities Using Cell Phones to Access Solar

In October, Bangalore-based Simpa Networks Inc. installed a solar panel on Anand’s whitewashed adobe house along with a small metal box in his living room to monitor electricity usage. The 25-year-old rice farmer, who goes by one name, purchases energy credits to unlock the system via his mobile phone on a pay-as-you-go model.

When his balance runs low, Anand pays 50 rupees ($1) — money he would have otherwise spent on kerosene. Then he receives a text message with a code to punch into the box, giving him about another week of electric light.
When he pays off the full cost of the system in about three years, it will be unlocked and he will get free power.
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Across India and Africa, startups and mobile phone companies are developing so-called microgrids, in which stand- alone generators power clusters of homes and businesses in places where electric utilities have never operated.

Very cool. Worldwide, approximately 1.6 billion people have no access to electricity and another 1 billion have extremely unreliable access. The poorest spending up to 30% of their income on inefficient and expensive means of providing light and accessing electricity. Solutions like this, finding engineering solutions for basic needs that are market based, are great.

That the poor end up owning their solar system after just 3 years is great.

Creating great benefit to society with the smart adoption of technology and sustainable economics is something I love.

Flavonoids Reduce Instances of Parkinson’s Disease in Men

Men who eat flavonoid-rich foods such as berries, tea, apples and red wine significantly reduce their risk of developing Parkinson’s disease, according to new research by Harvard University and the University of East Anglia.

The findings add to the growing body of evidence that regular consumption of some flavonoids can have a marked effect on human health. Recent studies have shown that these compounds can offer protection against a wide range of diseases including heart disease, hypertension, some cancers and dementia.

This latest study is the first study in humans to show that flavonoids can protect neurons against diseases of the brain such as Parkinson’s.

Around 130,000 men and women took part in the research. More than 800 had developed Parkinson’s disease within 20 years of follow-up. After a detailed analysis of their diets and adjusting for age and lifestyle, male participants who ate the most flavonoids were shown to be 40 per cent less likely to develop the disease than those who ate the least. No similar link was found for total flavonoid intake in women.

“These exciting findings provide further confirmation that regular consumption of flavonoids can have potential health benefits,” said Prof Aedin Cassidy of the Department of Nutrition, Norwich Medical School at UEA.

“This is the first study in humans to look at the associations between the range of flavonoids in the diet and the risk of developing Parkinson’s disease and our findings suggest that a sub-class of flavonoids called anthocyanins may have neuroprotective effects.”

Prof Gao said: “Interestingly, anthocyanins and berry fruits, which are rich in anthocyanins, seem to be associated with a lower risk of Parkinson’s disease in pooled analyses. Participants who consumed one or more portions of berry fruits each week were around 25 per cent less likely to develop Parkinson’s disease, relative to those who did not eat berry fruits. Given the other potential health effects of berry fruits, such as lowering risk of hypertension as reported in our previous studies, it is good to regularly add these fruits to your diet.”

Flavonoids are a group of naturally occurring, bioactive compounds found in many plant-based foods and drinks. In this study the main protective effect was from higher intake of anthocyanins, which are present in berries and other fruits and vegetables including aubergines, blackcurrants and blackberries. Those who consumed the most anthocyanins had a 24% reduction in risk of developing Parkinson’s disease.

The findings must now be confirmed by other large epidemiological studies and clinical trials.

Parkinson’s disease is a progresssive neurological condition affecting one in 500 people. There are few effective drug therapies available.

The result is far from conclusive and even if the result were confirmed the 24% reduction is hardly huge. But since berries are yummy there seem little reason to not tilt toward more berries in your diet.

Backyard Wildlife: Mountain Lion

Sadly this isn’t my backyard. I would love to see a mountain lion like this. So close. A real wild mountain lion. And I am safe.

Citizen Science

Citizen science enters a new era

Another online program, Phylo, is advancing scientists’ knowledge of genetics by making a game out of DNA matching. If areas of genetic sequence are roughly similar between species, it suggests strongly that they could have an important function. Finding them has been beyond the scope of computer algorithms. But earlier this month, researchers published a study where gamers outsmarted the best computers – they made the best possible DNA sequence match between up to eight species at a time.

The potential for regular people contributing to science is great. This has a long history. For most of human history science was done by non-scientists since there were no scientists. Calling is science might be a stretch but to me it was (passing on what health cures worked for various sicknesses, how to use various tools, how to grow crops…). As scientists came into being they were primarily unprofessional – that is they practiced science but were doing so as a hobby, they were not paid and had no requirements to get a PhD or anything.

Today regular people help by collecting data (counting birds, documenting plant growth [time of year], migration data, weather data…) sharing knowledge with scientists who ask, sharing their computer to be used to analyze data, analyzing data (for example, in astronomy hobbyists often make new discoveries) and the latest way people help is through games (that essentially tap human brainpower to analyze data – such as Foldit, which I have posted about previously).

I like the contributions people can make to science but I think the biggest value is the scientific understanding people gain while participating. As Neil Degrasse Tyson says the scientifically literate see a different world.

Cornell University provides an online tool to find opporunities participate in scientific research.

And we shouldn’t forget the amazing science done by students like those honored with Intel Talent Search, though the work those winning the awards do I would lump with science by “real scientists” (I believe now most of those who win are working on projects with university scientists).

Friday Fun: Elephant Playing with a Smart Phone

An elephant plays with a smart phone (Samsung Galaxy Note).

Dangerous Drug-Resistant Strains of TB are a Growing Threat

Drug-resistant strains of TB are out of control

The fight against new, antibiotic-resistant strains of tuberculosis has already been lost in some parts of the world, according to a senior World Health Organisation expert.
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Dr Paul Nunn, head of the WHO’s global TB response team, is leading the efforts against multi-drug resistant TB (MDR-TB). Nunn said that, while TB is preventable and curable, a combination of bad management and misdiagnosis was leaving pharmaceutical companies struggling to keep up. Meanwhile, the disease kills millions every year.

“It occurs basically when the health system screws up,” said Nunn. “Treating TB requires a carefully followed regime of medication over six months. In places where health services are fragmented or underfunded, or patients poor and health professionals ill-trained, that treatment can fall short, which can in turn lead to patients developing drug-resistant strains. It’s been estimated that an undiagnosed TB-infected person can infect 10 others a year.

We tend to do a poor job of dealing with systemic effects of poorly functioning systems. Direct present threats get out attention. And we are decent at directing brain power and resources to find solutions. We are not very good at dealing with failures that put us in much worse shape in the long term. For small threats we can wait until it becomes a present threat and then deal with it. There are costs to doing this (economic and personal) but it can be done.

Some problems though become enormously complicated to deal with once they become obvious. Global climate change, for example. And often, even once they are obvious, we won’t act until the costs (economic and in human lives) are very large. It is possible that once we decide to get serious about dealing with some of these issues that the costs (economic and in human lives) will be catastrophic.

The failure to use anti-biotics medicine properly is a very serious threat to become one of these catastrophic societal failures. While tuberculosis failures may be larger in poorer countries, rich countries are failing probably much more critically in the misuse of anti-biotics (I would guess, without having much evidence at my fingertips to back up my opinion. I believe the evidence exists I am just not an expert). These failures have huge costs for all of humanity but we are risking many premature deaths because we systemically fail to deal with issues until the consequences are immediate.

Google Lets Servers Stay Hot, Saving Air Conditioning Costs

The electricity to run huge server farms is enormous. One of the significant cost is air conditioning to cool down the server rooms.

Too Hot for Humans, But Google Servers Keep Humming

Google’s data center in Belgium, which was the company’s first facility to rely entirely upon fresh air for cooling, instead of energy-hungry chillers.
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For the vast majority of the year, the climate in Belgium is cool enough that this design works with no problems. When it gets hot in Belgium, the temperature inside Google’s data center warms beyond the facility’s desired operating range
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During these periods, the temperature inside the data center can rise above 95 degrees.
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“We’ve had very few excursion hours, and they don’t last long, so we let the site run right through them. We ask our employees to go in and do office work. It’s too warm for people, but the machines do just fine.”

Google’s experience is the latest affirmation that servers are much tougher than we think. Many data centers feel like meat lockers, as servers are maintained in cool environments to offset the heat thrown off by components inside the chassis. Typical temperature ranges in data centers often range from 68 and 72 degrees.

In recent years, rising power bills have prompted data center managers to try and reduce the amount of power used in cooling systems.

The temperatures in Fahrenheit obviously. I was surprised that the servers don’t seem to need to be chilled to perform well.