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

Scientists Don’t Look Like They Do in Movies

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.

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

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.

How to Walk on Ice

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]).

Open Source Ecology: Using Open Engineering to Create Economic Benefit

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).

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.

Chart of Wind Power Generation Capacity Globally 2005-2012

Chart of installed wind energy capacity by country from 2005 to 2012 by Curious Cat Science and Engineering Blog using data from the Wind Energy Association. 2012 data is for the capacity on June 30, 2012. Chart may be used with attribution as specified.

Wind power generation capacity continues to grow faster than the increase in electricity use. The rate of growth has slowed a bit overall, though China’s growth continues to be large.

From 2005-2012 globally wind power generation capacity increased 330%; lead by China with an increase of 5,250%. Of the leading countries Germany grew the least – just 63%. The percent of global capacity of the 8 countries listed in the chart (the 8 countries with the highest capacity in 2012) has been amazingly consistent given the huge growth: from a low of 79% in 2006 to a high of 82.4% in 2011 (2012 was 82%).

Global growth in wind energy capacity was 66% in 2008-2010. In 2010 to 2012 the increase was 28%. The second period is just 18 months (since the 2012 data is for the first half of the year). Extending the current (2010-2012) rate to the end of 2012 would yield an increase of 37%, which still shows there has been a slowdown compared to the 66% rate in the previous 2 year period. The decrease in government subsidies and incentives is responsible for the slowing of added capacity, though obviously the growth is still strong.

From 2005 to 2012 China’s share of global wind energy capacity increased from 2% to 27%, the USA 15% to 20%, Germany fell from 31% to 12%, India fell from 7.5% to 6.8% (while growing capacity 292%).

Hydro power is by far the largest source of green electricity generation (approximately 5 times the capacity of wind power – but hydro capacity is growing very slowly). And installed solar electricity generation capacity is about 1/5 of wind power capacity.

No Surprise: Engineering Graduates Continue to Reign Supreme

If you want a high paying job upon graduation choosing to major in engineering is a great choice, for those that enjoy it and are able to meet the challenge. This data is for the USA. My guess is that similar results would show up in most locations, but I am just guessing, I don’t have any specific data.

The top average starting salary paid USA under-graduates by major:

major		2012 salary
computer engineering		$70,400
chemical engineering		$66,400
computer science		$64,400
aerospace/aeronautical/astronautical engineering		$64,000
mechanical engineering		$62,900
electrical/electronics and communications engineering		$62,300
civil engineering		$57,600
finance		$57,300
construction science/management		$56,600
information sciences and systems		$56,100

NACE salary survey

This continues a long term trend of engineering major being rewarded: Engineering Majors Hold 8 of Top 10 Highest Paid Majors – Engineering Again Dominates The Highest Paying College Degree Programs – S&P 500 CEO’s: Engineers Stay at the Top – Career Prospect for Engineers Continues to Look Positive.

Overall starting salaries were up 3.4% to $44,455. Engineering major starting salaries increased 3.9%, to $61,913. Computer science is the 2nd highest paid broad major category at $59,221 (up 3.8%). Next is business at $53,900 (up 4.2%). At the bottom of both average pay and increase was humanities and social sciences with $36,988, up 2%.

The highest-paying industry for Class of 2012 graduates in this report is mining, quarrying, and oil and gas extraction; employers in this industry offered starting salaries that averaged $59,400.

The mining, quarrying, and oil and gas extraction industry also has the top-paying occupations for Class of 2012 graduates. Mechanical engineering graduates hired as petroleum, mining, and geological engineers received starting salaries that averaged $77,500.

As I have said before, I believe it is foolish to pursue a career in a field that doesn’t interest you. Pay doesn’t make up for doing something you don’t enjoy. But if you enjoy several things somewhat equally pay is worth paying attention to.

Many Great, Free, Online Courses in Science, Engineering and More

The video, above, provides an overview of an online course, Calculus: Single Variable, via coursera from the University of Pennsylvania. This course provides a brisk, entertaining treatment of differential and integral calculus, with an emphasis on conceptual understanding and applications to the engineering, physical, and social sciences.

Robert Ghrist is the Andrea Mitchell University Professor of Mathematics and Electrical & Systems Engineering at the University of Pennsylvania. Coursera offers many courses in all sorts of disciplines including: Introduction to Genetics and Evolution (Duke), Scientific Computing (University of Washington), Principles of Economics for Scientists (California Institute of Technology), Game Theory (Stanford University and The University of British Columbia), A Beginner’s Guide to Irrational Behavior (Dan Ariely, Duke University), The Modern World: Global History since 1760 (University of Virginia), Microeconomics for Managers (University of California, Irvine), Data Analysis (Johns Hopkins University), Fundamentals of Human Nutrition (University of Florida), Algorithms, Part I (Princeton University), The Ancient Greeks (Wesleyan University), Astrobiology and the Search for Extraterrestrial Life (University of Edinburgh) and Epigenetic Control of Gene Expression, (University of Melbourne).

All the classes are free. These courses, and many more, are extremely appealing. I signed up for 2. I would be interested in signing up for much more but I worry about having the time to commit to keeping up with the coursework. I hope the first two go well and I can sign up for more in the future.

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2012 Gordon Prize for Innovation in Engineering and Technology Education

I have posted on the Olin College of Engineering several times. I really like what they are doing. Innovation in engineering education will pay high dividends, especially providing a focus on the nexus of engineering and entrepreneurship.

Olin College of Engineering’s three founding academic leaders, Richard Miller, David Kerns and Sherra Kerns, received one of engineering’s highest honors – the Bernard M. Gordon Prize. The $500,000 prize is awarded by the National Academy of Engineering to recognize innovation in engineering and technological education.

“This team of educational innovators has had a profound impact on society by improving the way we educate the next generation of engineers,” said NAE President Charles M. Vest. “Olin serves as an exemplar for the rest of the engineering world and a collaborative agent for change.”

Armed with one of the largest gifts in the history of higher education, the F. W. Olin Foundation recruited Richard Miller as Olin’s first employee in 1999. To help build the college from scratch, Miller recruited the founding academic leadership team including David Kerns and Sherra Kerns later that year. Together, they developed a vision for an engaging approach to teaching engineering and a new culture of learning that is intensely student centered.

To insure a fresh approach, Olin does not offer tenure, has no academic departments, offers only degrees in engineering, and provides large merit-based scholarships to all admitted students.

Perhaps the most important contribution the Gordon prize recipients made was the creation of a profoundly inclusive and collaborative process of experimentation and decision-making involving students in every aspect of the invention of the institution. This is illustrated by the decision in 2001 to recruit 30 young students to spend a year as “partners” in residence with the faculty in conducting many experiments together before establishing the first curriculum.

“As entrepreneurs, we learn to listen to our customers. Olin’s innovative approach was co-created by enterprising faculty, inspired students, and a dedicated staff, as well as collecting and integrating innovative approaches from more than 30 other institutions worldwide,” said David Kerns, current faculty at Olin and founding provost and chief academic officer of the college from 1999 to 2007.

With the extensive help of a collaborative team of faculty and students, and the guidance of the late Dr. Michael Moody, a novel academic program emerged. Some of the features include a nearly gender-balanced community, a strong focus on design process throughout all four years, extensive use of team projects, a requirement that students repeatedly “stand and deliver” to the entire community at the end of every semester, an experiential requirement in business and entrepreneurship, a capstone requirement outside of engineering, and a year-long corporate-sponsored design project in which corporations pay $50,000 per project.

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