Huge Human Population Boom 40,000 to 50,000 Years Ago
Posted on March 14, 2013 Comments (1)
Interesting open access paper on looking at the Y-chromosome to explore our ancestry: A calibrated human Y-chromosomal phylogeny based on resequencing. I can’t understand all the details but the basic idea isn’t that complicated. It is interesting to see these details as are the conclusions that can be drawn: that we had a big explosion of human population o 41,000–52,000 years ago.
This population explosion occurred, between the first expansion of modern humans out of Africa 60,000 to 70,000 years ago and the Neolithic expansions of people in several parts of the world starting 10,000 years ago.
“We think this second, previously unknown population boom, may have occurred as humans adapted to their new environment after the first out-of-Africa expansion,” says Dr Qasim Ayub, lead author from the Wellcome Trust Sanger institute. “We think that when humans moved from the horn of Africa to Asia, Australia and eventually Europe, they remained in small groups by the coasts. It took them tens of thousands of years to adapt to the mountainous, forested surroundings on the inner continents. However, once their genetic makeup was suited to these new environments, the population increased extremely rapidly as the groups travelled inland and took advantage of the abundance of space and food.”
The work highlights how it is now possible to obtain new biological insights from existing DNA sequencing data sets, and the value of sharing data. The majority of the DNA information used for this study was obtained from freely-available online data-sets.
This is the first time researchers have used the information from large-scale DNA sequencing to create an accurate family tree of the Y chromosome, from which the inferences about human population history could be made.
CDC Again Stresses Urgent Need to Adjust Practices or Pay a Steep Price
Posted on March 8, 2013 Comments (0)
Untreatable and hard-to-treat infections from Carbapenem-resistant Enterobacteriaceae (CRE) germs are on the rise among patients in medical facilities. CRE germs have become resistant to all or nearly all the antibiotics we have today. Types of CRE include Klebsiella pneumoniae Carbapenemase (KPC) and New Delhi metallo-beta-lactamase (NDM). By following the United States Center for Disease Control (CDC) guidelines, we can slow the penetration of CRE infections in hospitals and other medical facilities and potentially spread to otherwise healthy people outside of medical facilities.
The CDC has worked with hospitals to successfully apply these measures. The CDC worked with Florida to stop a year-long CRE outbreak in a long-term acute care hospital. With the improved use of CDC recommendations (such as educating staff; dedicating staff, rooms, and equipment to patients with CRE; and improving use of gloves and gowns) the percentage of patients who got CRE at the facility dropped from 44% to 0.
One travesty has been how poorly health care professionals have been about prescribe antibiotics wisely We need to improve and follow CDC antibiotics guidelines (stop the overuse of antibiotics) and use culture results (for patients undergoing treatment) to modify prescriptions, if needed. Antibiotic overuse contributes to the growing problems of Clostridium difficile (c-diff) infection and antibiotic resistance in healthcare facilities. Studies indicate that nearly 50% of antimicrobial use in hospitals is unnecessary or inappropriate (per CDC web site).
Israel decreased CRE infection rates in all 27 of its hospitals by more than 70% in one year with a coordinated prevention program. The USA is at a critical time in which CRE infections could be controlled if addressed in a rapid, coordinated, and consistent effort by doctors, nurses, lab staff, medical facility leadership, health departments/states, policy makers, and the federal government.
As I have been saying for years the damage we are creating due to our actions around the use and abuse of antibiotics is likely to kill tens of thousands, or more people. Because the deaths are delayed and often not dramatic we have continued dangerous practices for years when we know better. It is a shame we are condemning so many to increased risks. The CDC, and others, are doing good work, unfortunately too much bad work is continuing in the face of evidence of how dangerous that is.
Related: CDC Urges Increased Effort to Reduce Drug-Resistant Infections (2006) – Key scientific articles on Healthcare Associated Infections via CDC – Our Dangerous Antibiotic Practices Carry Great Risks – Dangerous Drug-Resistant Strains of TB are a Growing Threat
Introduction Video on 3D Printing
Posted on March 3, 2013 Comments (9)
3D printing is an amazing technology that opens up great opportunities for us to enjoy life. The future is great. It is exciting to see how quickly advances are being made in this area. I think the ability to print replacement parts is a huge benefit. And the creative uses people will put these printers too will be a joy to see.
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.
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.
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.
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 (3)
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.
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.
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.
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 (5)
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)
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
Posted on February 1, 2013 Comments (3)
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
Posted on January 28, 2013 Comments (5)
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
Posted on January 24, 2013 Comments (7)
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:
|electrical/electronics and communications engineering||$62,300|
|information sciences and systems||$56,100|
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.