People are Superorganisms With Microbiomes of Thousands of Species

Posted on February 25, 2013  Comments (2)

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 Methé, 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

Related: Tracking the Ecosystem Within Us – What Happens If the Overuse of Antibiotics Leads to Them No Longer Working? – Antibacterial Products May Do More Harm Than Good – Antibiotics Too Often Prescribed for Sinus Woes

Scientists Don’t Look Like They Do in Movies

Posted on February 20, 2013  Comments (4)

The Myth of the Scientist: Crystal Dilworth at TEDxYouth@Caltech

Scientists don’t fit the stereotypical mold some people think they do. It doesn’t take much to replace those views. The main point, in my opinion, is to let kids know they can be a scientists even if they are not like the stereotypical examples – though it will take a lot of work.

Related: Movie Aims to Inspire College Students With Tales of Successful Minority Scientists – Women Working in Science – Citizen Scientists – Scientists Singing About Science

Read more

Human Gene Origins: 37% Bacterial, 35% Animal, 28% Eukaryotic

Posted on February 17, 2013  Comments (3)

The percent of human genes that emerged in various stages of evolution: 37% bacterial, 28% eukaryotic, 16% animal, 13% vertebrate, 6% primate. The history that brought us to where we are is amazing. Eukaryotes include animals, plants, amoebae, flagellates, amoeboflagellates, fungi and plastids (including algae). So eukaryotic genes are those common to us and other non-animal eukaryotes while those classified as animal genes are shared by animals but not non-animal eukaryotes.

We are living in a bacterial world, and it’s impacting us more than previously thought by Lisa Zyga

Bacterial signaling is not only essential for development, it also helps animals maintain homeostasis, keeping us healthy and happy. As research has shown, bacteria in the gut can communicate with the brain through the central nervous system. Studies have found that mice without certain bacteria have defects in brain regions that control anxiety and depression-like behavior. Bacterial signaling also plays an essential role in guarding an animal’s immune system. Disturbing these bacterial signaling pathways can lead to diseases such as diabetes, inflammatory bowel disease, and infections. Studies also suggest that many of the pathogens that cause disease in animals have “hijacked” these bacterial communication channels that originally evolved to maintain a balance between the animal and hundreds of beneficial bacterial species.
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Scientists have also discovered that bacteria in the human gut adapts to changing diets. For example, most Americans have a gut microbiome that is optimized for digesting a high-fat, high-protein diet, while people in rural Amazonas, Venezuela, have gut microbes better suited for breaking down complex carbohydrates. Some people in Japan even have a gut bacterium that can digest seaweed. Researchers think the gut microbiome adapts in two ways: by adding or removing certain bacteria species, and by transferring the desired genes from one bacterium to another through horizontal gene transfer. Both host and bacteria benefit from this kind of symbiotic relationship, which researchers think is much more widespread than previously thought.
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We want badly for the message in ‘Animals in a bacterial world,’ to be a call for the necessary disappearance of the old boundaries between life science departments (e.g., Depts of Zoology, Botany, Microbiology, etc.) in universities, and societies (e.g., the American Society for Microbiology, etc.). We also want the message disseminated in college and university classes from introductory biology to advanced courses in the various topic areas of our paper.”

Very cool stuff. This amazing facts scientists discover provide an amazing view of the world we live in and how interconnected we are to other life forms in ways we don’t normally think of.

Related: People’s Bodies Carry More Bacterial Cells than Human Cells – Microbes Flourish In Healthy People – Tracking the Ecosystem Within Us – Foreign Cells Outnumber Human Cells in Our Bodies – Bacteria Beneficial to Human Health

How to Walk on Ice

Posted on February 12, 2013  Comments (6)

infographic explaining how to walk on ice - walk like a penguin

Infographic by Tablet. Falling on ice leads to many injuries and even 60 deaths a year in the USA (about the number that will die due to tornados). The graphic encourages thinking like a penguin. Penguins walk well on ice (in some ways) and they also fall well.

Seeking to keep your weight well supported (short strides) is wise (and sliding instead of picking up your feet can help). Falling well is also important. It is basic physics, you want to lower your center of gravity if you are start to slip and avoid any excessive force (so sliding is better than trying to stick out your hand and support all your weight). The elderly are especially susceptible to injuries – avoiding taking direct shocks to the wrist, knees or hips is wise). It does seem kind of silly to learn how to fall but it is very helpful in avoiding injuries.

On sidewalks if you are going to fall and there is snow piled up off the sidewalk, falling into the pile of snow may well be softer than falling directly onto the sidewalk.

On ice you have lower friction so strategies that require friction are not useful – quick moves often rely on very sturdy bases (which are based on the friction of our shoe on for example concrete [which normally is good - though business shoes are not very good] and on ice [where it is very poor - sliding and gradual moves are better]).

Related: Falling Safely – Ministry of Silly Walks – Make Crosswalks More Visible – Why Wasn’t the Earth Covered in Ice 4 Billion Years Ago – When the Sun was Dimmer – Science Toys You Can Make With Your Kids

Open Source Ecology: Using Open Engineering to Create Economic Benefit

Posted on February 7, 2013  Comments (0)

Open Source Philosophy. from Open Source Ecology on Vimeo.

I think the video’s message is overly simplistic and unrealistic (great innovations often seem unrealistic so I don’t mind people trying things I don’t think are likely to succeed in the ways they imagine). But I believe in the concepts of using our knowledge to use appropriate technology to make the standard of living better for everyone. Open access to scientific knowledge is important to such efforts and to the economic well being of modern society.

Open Source Ecology provides a modular, DIY (open access), low-cost, high-performance platform that allows for the easy fabrication of the 50 different Industrial Machines that it takes to build a small, sustainable civilization with modern comforts. The are recruiting for an Operations Manager, and an Executive Team (based in Kansas City or New York City in the USA).

Related: Pay as You Go Solar in India – Student Engineers Without Borders Project: Learning While Making a Difference in Kenya – Reducing Poverty Through Entrepreneurism

Homing Pigeons May Use Low Frequency Sound Maps To Locate Home

Posted on February 1, 2013  Comments (3)

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.

Related: Pigeon Solves Box and Banana Problem – Cool Research on Crows – Bird Using Bait to Fish – Moth Jams Bat Sonar