Tag Archives: Research

People are Superorganisms With Microbiomes of Thousands of Species

In a recent article in National Geographic Carl Zimmer has again done a good job of explaining the complex interaction between our bodies and the bacteria and microbes that make us sick, and keep us healthy.

The damage done by our indiscriminate use of antibiotics is not just the long term resistance that we create in bacteria (making the future more dangerous for people) that I have written about numerous times but it also endangers the person taking the anti-biotics in the short term. Sometimes the other damage is a tradeoff that should be accepted. But far too often we ignore the damage taking antibiotics too often does.

When You Swallow A Grenade

While antibiotics can discriminate between us and them, however, they can’t discriminate between them and them–between the bacteria that are making us sick and then ones we carry when we’re healthy. When we take a pill of vancomycin, it’s like swallowing a grenade. It may kill our enemy, but it kills a lot of bystanders, too.
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If you think of the human genome as all the genes it takes to run a human body, the 20,000 protein-coding genes found in our own DNA are not enough. We are a superorganism that deploys as many as 20 million genes.
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Before he started taking antibiotics, the scientists identified 41 species in a stool sample. By day 11, they only found 13. Six weeks after the antibiotics, the man was back up to 38 species. But the species he carried six weeks after the antibiotics did not represent that same kind of diversity he had before he took them. A number of major groups of bacteria were still missing.
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They found that children who took antibiotics were at greater risk of developing inflammatory bowel disease later in life. The more antibiotics they took, the greater the risk. Similar studies have found a potential link to asthma as well.

The human body contains trillions of microorganisms — outnumbering human cells by 10 to 1. Because of their small size, however, microorganisms make up only about 1% to 3% of the body’s mass, but play a vital role in human health.

Where doctors had previously isolated only a few hundred bacterial species from the body, Human Microbiome Project (HMP) researchers now calculate that more than 10,000 microbial species occupy the human ecosystem. Moreover, researchers calculate that they have identified between 81% and 99% of all microorganismal genera in healthy adults.

“Humans don’t have all the enzymes we need to digest our own diet,” said Lita Proctor, Ph.D., NHGRI’s HMP program manager. “Microbes in the gut break down many of the proteins, lipids and carbohydrates in our diet into nutrients that we can then absorb. Moreover, the microbes produce beneficial compounds, like vitamins and anti-inflammatories that our genome cannot produce.” Anti-inflammatories are compounds that regulate some of the immune system’s response to disease, such as swelling.

“Enabling disease-specific studies is the whole point of the Human Microbiome Project,” said Barbara MethÃ©, Ph.D., of the J. Craig Venter Institute, Rockville, MD, and lead co-author of the Nature paper on the framework for current and future human microbiome research. “Now that we understand what the normal human microbiome looks like, we should be able to understand how changes in the microbiome are associated with, or even cause, illnesses.”

Read the full NIH press release on the normal bacterial makeup of the body

Homing Pigeons May Use Low Frequency Sound Maps To Locate Home

Mystery of Lost Homing Pigeons Finally Solved

Prior research had shown that birds hear incredibly low-frequency sound waves of about 0.1 Hertz, or a tenth of a cycle per second. These infrasound waves may emanate from in the ocean and create tiny disturbances in the atmosphere. Hagstrum began to think the birds used infrasound for navigation.
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on the odd day when the birds reached home from Jersey Hill without problems, the infrasound traveled between the two locations. At the other locations where pigeons headed off in the wrong direction, he showed that wind currents channeled the infrasound waves in that direction.

The explanation may solve other mysteries about pigeons — for instance, why they circle around before heading off in one direction. Because the sound waves are so long, but the birds’ ear canals are tiny, they need to circle to reconstruct the wave and figure out which way they are oriented, he said.

More interesting scientific inquiry. It is very interesting to learn what scientists are learning about our world – even when the conclusions are still preliminary and may be adjusted or refuted.

Evolution Follows a Predictable Genetic Pattern

Far from random, evolution follows a predictable genetic pattern

The researchers carried out a survey of DNA sequences from 29 distantly related insect species, the largest sample of organisms yet examined for a single evolutionary trait. Fourteen of these species have evolved a nearly identical characteristic due to one external influence — they feed on plants that produce cardenolides, a class of steroid-like cardiotoxins that are a natural defense for plants such as milkweed and dogbane.

Though separated by 300 million years of evolution, these diverse insects — which include beetles, butterflies and aphids — experienced changes to a key protein called sodium-potassium adenosine triphosphatase, or the sodium-potassium pump, which regulates a cell’s crucial sodium-to-potassium ratio. The protein in these insects eventually evolved a resistance to cardenolides, which usually cripple the protein’s ability to “pump” potassium into cells and excess sodium out.
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Andolfatto and his co-authors examined the sodium-potassium pump protein because of its well-known sensitivity to cardenolides. In order to function properly in a wide variety of physiological contexts, cells must be able to control levels of potassium and sodium. Situated on the cell membrane, the protein generates a desired potassium to sodium ratio by “pumping” three sodium atoms out of the cell for every two potassium atoms it brings in.

Cardenolides disrupt the exchange of potassium and sodium, essentially shutting down the protein, Andolfatto said. The human genome contains four copies of the pump protein, and it is a candidate gene for a number of human genetic disorders, including salt-sensitive hypertension and migraines. In addition, humans have long used low doses of cardenolides medicinally for purposes such as controlling heart arrhythmia and congestive heart failure.

Cool stuff. It makes sense to me which is nice (it is nice to get confirmation that I find what actually exists is sensible). When things that are true just seem crazy it is a bit disconcerting – like quantum mechanics. It is fun to read stuff that totally shakes up preconceived notions, but even then it is nice once I think understand it to find it sensible.

Add Over-Fishing to the Huge Government Debt as Examples of How We Are Consuming Beyond Our Means

Fish are hidden under the water so the unsustainable harvesting isn’t quite as obvious as the unsustainable government debt but they both are a result of us living beyond our sustainable production. You can live well by consuming past wealth and condemning your decedents to do without. That is the way we continue to live. Over-fishing a century ago was not as obviously dangerous as it is today. But we have witnessed many instances of overfishing devastating the fishing economy (when the fishing is unsustainable the inevitable result is collapse and elimination of the vast majority of the food and income that previous generations enjoyed).

The normal pattern has been to turn to more aggressive fishing methods and new technology to try and collect fish as over-fishing devastates yields. This, of course, further devastates the state of the resources and makes it so recovery will take much much longer (decades – or more).

New research shows the existing problems and the potential if we apply science and planning to manage fisheries effectively.

Using new methods to estimate thousands of unassessed fisheries, a new comprehensive study provides a new view of global fish stocks. The results show that the overall state of fisheries is worse than previously thought. Unassessed stocks, which are often left out of global analyses because of a lack of data, are declining at disturbing rates. When these fisheries are taken into account, the results indicate that over 40 percent of fisheries have crashed or are overfished, producing economic losses in excess of $50 billion per year.

The good news is that this decline is not universal: fisheries are starting to rebound in many areas across the globe and we can learn from these examples. Recovery trends are strongest for fisheries where data on the status of the fishery exists, and in which managers and fishermen have made science-based decisions and stuck with them in the face of political pressure.
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The amount of fish brought to shore could increase 40 percent on average – and double in some areas – compared to yields predicted if we continue current fishing trends.
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The management solutions to overfishing are well known, tested and proven to work. While these solutions are not “one-size-fits-all” for fisheries, there are common themes. Specifically, managers and fishermen must: 1. Reduce fishing to allow stocks to rebuild; 2. Set catches at a sustainable level that is based on the best available scientific and economic information rather than short-term political pressures; and 3. Prevent dangerous fishing activities that destroy habitat, wildlife, or breeding fish.

The over fishing problem is difficult because our nature is to ignore problems that are not immediate. But the costs of doing so are very large. If we don’t behave more wisely our children will pay the price. And, in fact, this problem is so acute now that those of us that expect to live a couple decades can expect to pay the price. In rich countries this will be tolerable, a bit less fish at much higher prices. In rich countries food prices are a minor expense compared to the billions of those not living in rich countries. They will suffer the most. As will those that have jobs directly dependent on fishing.

Toyota Human Support Robot

Toyota continues to develop their partner robot initiative. Demographics in Japan make a compelling case for the need to provide solutions to those who need assistance to support independent living.

The aim is to contribute to the maintenance and improvement of quality of life.

In cooperation of the Yokohama Rehabilitation Center, Toyota conducted experiments for disabled people, using HSR in their homes, in 2011. Toyota has been integrating the feedback to the design, based on actual user experience.

The Human Support Robot (HSR) can pick up something on and bring it to the person. Also it can do small tasks such as opening the curtains.

Controlling the robot can be done easily, by using the voice recognition function or using a tablet control. In addition, Toyota is designing it to directly assist the person, helping them get into and out of a bathtub, for example.

They are also developing new features for remote viewing and remote operation (to provide off site help to make the robot more useful). They are working with health care professionals, including nurses, and research institutions aimed at practical use for such a robot.

Toyota, along with several other Japanese companies, continue to invest a great deal to create personal care robots.

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Did a massive comet explode over Canada 12,900 years ago and start an ice age?

I think it is important to increase scientific literacy. One thing that is greatly misunderstood is the process for new scientific explanations being accepted by the scientific community. It is often quite a drawn out process over years (and for the explanation provided in this paper the debate is certainly still ongoing). And for issues that really shake up past explanations it can take decades and be quite contentious. I think posts tagged with “scientific inquiry” are a very interesting collection to explore.

It is important to understand the difficulty in providing evidence that satisfies the overwhelming majority of the scientific experts in any area. And it is important to understand the claims in one (or numerous papers) are not the accepted proven wisdom of the scientific community. Thankfully the process is rigorous. While mistakes can still be made, the evidence needed to substantiate a scientific hypothesis is significant. Their is still plenty of room for position to color accepted scientific wisdom. A respected professor is often able to make a claim that is more readily accepted and even more-so for to insist the new claims do not provide enough evidence in support of them to accept the new claims and have there position accepted (even when it really shouldn’t be looking just at the facts).

Topper site in middle of comet controversy

Firestone found concentrations of spherules (micro-sized balls) of metals and nano-sized diamonds in a layer of sediment dating 12,900 years ago at 10 of 12 archaeological sites that his team examined. The mix of particles is thought to be the result of an extraterrestrial object, such as a comet or meteorite, exploding in the earth’s atmosphere. Among the sites examined was USC’s Topper, one of the most pristine U.S. sites for research on Clovis, one of the earliest ancient peoples.
“This independent study is yet another example of how the Topper site with its various interdisciplinary studies has connected ancient human archaeology with significant studies of the Pleistocene,” said Goodyear, who began excavating Clovis artifacts in 1984 at the Topper site in Allendale, S.C. “It’s both exciting and gratifying.”
Younger-Dryas is what scientists refer to as the period of extreme cooling that began around 12,900 years ago and lasted 1,300 years. While that brief ice age has been well-documented – occurring during a period of progressive solar warming after the last ice age – the reasons for it have long remained unclear.

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The Eagle Has Landed

Neil Armstrong and Buzz Aldren land on the moon: July 20, 1969. As Neil Armstrong took humanity’s first step onto the Moon he said:

That’s one small step for man, one giant leap for mankind.

Domestic Cats Remain Successful Predators

House cats kill more critters than thought by Elizabeth Weise

While only 30% of roaming house cats kill prey — two animals a week on average — they are still slaying more wildlife than previously believed, according to research from the University of Georgia.
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The cats brought home just under a quarter of what they killed, ate 30% and left 49% to rot where they died.

The carnage cuts across species. Lizards, snakes and frogs made up 41% of the animals killed, Loyd and fellow researcher Sonia Hernandez found. Mammals such as chipmunks and voles were 25%, insects and worms 20% and birds 12%.
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Seeking a window into the hidden lives of cats, the researchers recruited 60 owners in the Athens, Ga., area. Each owner put a small video camera mounted on a break-away collar on the cat in the morning and let the cat out, then removed the camera and downloaded the footage each night.

Interesting data. As I wrote about before you can get your very own cat cam and see what your cat is up to. I posted an interview I did with the engineer that designs and sells the cat cams.

High School Student Creates: Test That is Much More Accurate and 26,000 Times Cheaper Than Existing Pancreatic Cancer Tests

Seeing what these kids come up with is so refreshing after being so disappointed by the actions fo our leaders (politicians, business leaders, financiers, law enforcement [spying on citizens because they feel electronic privacy is fine to invade, taking away liberty…], health care in the USA [twice as expensive as elsewhere with no better results, 10 of millions without coverage]…). These kids make me feel hopeful, unfortunately the actions of the powerful leave me less hopeful.

Jack Andraka created a new paper based test for diagnosing pancreatic cancer that is 50% more accurate, 400 times more sensitive, and 26,000 times less expensive than existing methods. His method uses carbon nanotubes and can catch the disease in very early stages which is critical to treatment success. The test also covers other forms of cancer very effectively (he concentrated on the results for pancreatic cancer given the low survival rates for that cancer). Jack Andraka: “I actually love single-walled carbon nanotubes; they’re like the superheroes of material science.”

His results are great. Often initial results can be difficult to actually turn into such positive results in the real world. But this is a great step and it is great to see what young minds can do. The claims for how much better, cheaper etc. are wildly different in various places on the International Science and Engineering Fair (ISEF) site.

Jack Andraka was awarded $75,000 for his development of a new method to detect pancreatic cancer as the winner of the top prize at the Intel ISEF (I believe it is new this year to call the winner the Gordon E. Moore Award).

A Novel Paper Sensor for the Detection of Pancreatic Cancer by Jack Andraka
North County High School, Glen Burnie, MD

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Using Robots to Collect Data on our Oceans

Interesting idea to use self propelled robots to provide data on the oceans. They use no fuel to move, they use wave energy. They also have solar panels on the top. The wave gliders can travel to a distant area, collect data, and return to base. One of the big problems with convention methods of collecting data on the oceans is the large costs of placing the buoys (and the cost of servicing them).