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Posts about scientific research and development as well as science and engineering breakthroughs.
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Stanford Research Scientists Discover 99% of the Microbes Inside Us are Unknown to Science

Readers of this blog know I am fascinated by the human microbiome. It is amazing how much of our biology is determined by entities within us that are not us (at least not our DNA) (bacteria, viruses etc.). This whole area of study is very new and we have quite a bit to learn. There are scientists across the globe studying this area and learning a great deal.

Stanford study indicates that more than 99% of the microbes inside us are unknown to science

Of all the non-human DNA fragments the team gathered, 99 percent of them failed to match anything in existing genetic databases the researchers examined.

The “vast majority” of it belonged to a phylum called proteobacteria, which includes, among many other species, pathogens such as E. coli and Salmonella. Previously unidentified viruses in the torque teno family, generally not associated with disease but often found in immunocompromised patients, made up the largest group of viruses.

“We’ve doubled the number of known viruses in that family through this work,” Quake said. Perhaps more important, they’ve found an entirely new group of torque teno viruses. Among the known torque teno viruses, one group infects humans and another infects animals, but many of the ones the researchers found didn’t fit in either group. “We’ve now found a whole new class of human-infecting ones that are closer to the animal class than to the previously known human ones, so quite divergent on the evolutionary scale,” he said.

Related: We are Not Us Without The Microbes Within UsWebcasts on the Human MicrobiomePeople are Superorganisms With Microbiomes of Thousands of Species (2013)We Have Thousands of Viruses In Us All the Time (2015)Tracking the Ecosystem Within Us (2007)

Very Low Frequency Radio Waves Protect Earth

Very Low Frequency (VLF) radio communications signals are transmitted from ground stations at huge powers to communicate with submarines deep in the ocean. While these waves are intended for communications below the surface, they also extend out beyond our atmosphere, shrouding Earth in a VLF bubble. This bubble is even seen by spacecraft high above Earth’s surface, such as NASA’s Van Allen Probes, which study electrons and ions in the near-Earth environment.

The probes have noticed an interesting coincidence – the outward extent of the VLF bubble corresponds almost exactly to the inner edge of the Van Allen radiation belts, a layer of charged particles held in place by Earth’s magnetic fields. Dan Baker, director of the University of Colorado’s Laboratory for Atmospheric and Space Physics in Boulder, coined this lower limit the “impenetrable barrier” and speculates that if there were no human VLF transmissions, the boundary would likely stretch closer to Earth. Indeed, comparisons of the modern extent of the radiation belts from Van Allen Probe data show the inner boundary to be much farther away than its recorded position in satellite data from the 1960s, when VLF transmissions were more limited.

With further study, VLF transmissions may serve as a way to remove excess radiation from the near-Earth environment. Plans are already underway to test VLF transmissions in the upper atmosphere to see if they could remove excess charged particles — which can appear during periods of intense space weather, such as when the sun erupts with giant clouds of particles and energy.

Related: NASA’s Van Allen Probes Spot Man-Made Barrier Shrouding EarthAstronaut SelfieMagnetic Portals Connect Sun and Earth (2008)Webcast of Man Landing on the MoonNASA Biocapsules Deliver Medical Interventions Based Upon What They Detect in the Body (2012)

Dogs and Wolves Share a Sense of Fair Pay

Dogs and wolves share sense of fair play

The scientists tested similarly raised dogs and wolves that lived in packs. Two animals of each species were placed in adjacent cages, equipped with a buzzer apparatus. When the dog or wolf pressed it with their paw, both animals got a reward on some occasions. Other times, the dog or wolf doing the task got nothing while the partner did.

The key finding was that when the partner got a high value treat, the animal doing the task refused to continue with it.

photo of a Gray Wold looking at the camera

Gray Wolf by Gary Kramer (USFWS), public domain

This is a similar result as that found with Capuchin monkeys that don’t like being paid less than others.

The question of social status or hierarchy also played an important role in the experiments with dogs and wolves of higher rank taking umbrage more quickly.

The human impact on dogs isn’t entirely absent though. Pet dogs are less sensitive to being treated unfairly – probably because of their experience with us!

It is fun to see these results mirror aspects of our psychology. It is fun to see how these experiments test out animal’s responses.

Related: Goats Excel at Learning and Remembering a Complex TasksRats Show Empathy-driven BehaviorInsightful Problem Solving in an Asian ElephantsHow Wolves Changed the Yellowstone Ecosystem

Using Scientific Knowledge to Drive Policies that Create a Better World

I have written about the problems of overfishing in the past: Add Over-Fishing to the Huge Government Debt as Examples of How We Are Consuming Beyond Our Means (2012)Fishless Future (2006)North American Fish Threatened (2008)The State of the Oceans is Not Good (2011)European Eels in Crisis After 95% Decline in Last 25 years (2009). This is not a complicated problem. If you just pay attention to the science and make wise decisions with an understanding of systems we can improve the situation.

And the USA has done so. The USA has more work to do, but by taking sensible steps based on an understanding of science we have made significant progress.

How the world can stop overfishing – A case study of U.S. fishery success

By 1996, the US had declared 86 species overfished. Fast forward twenty years, and only 29 species in US waters are classified as overfished. That’s a decrease of 66% from the peak of overfishing in the 1990s.

One year after President Clinton declared the New England ground fishery a federal disaster, congress met in Washington to amend and renew the 20-year-old Fishery Conservation and Management Act. The result was the Magnuson-Stevens Act, a major bipartisan commitment to end overfishing in US waters and promote fish stock recovery.

The goal of the Magnuson-Stevens Act was to create a framework for rebuilding overfished stocks in as short a time as possible. The timeframe for rebuilding a fish stock under the act is typically ten years or less.

To accomplish such a goal, scientists established fishery management plans for each overfished stock and instituted annual catch limits to control overfishing.

By the end of 2015, 89% of fisheries with annual catch limits in place had halted overfishing.

While 64% of the fish stocks managed by the Magnuson-Stevens Act are now rebuilt or recovering, success hasn’t been universal. Certain regional fisheries, such as those in the Gulf of Mexico and New England, have struggled to control overfishing under existing regulations. The act also does a poor job of protecting highly migratory species, such as tuna, swordfish, and sharks, which move freely between different regulatory areas.

We need to build on our successful use of scientific knowledge to make wise decisions and implement wise government policy. Sadly there is an alarming lack of appropriate thinking by many of those we elect to office, in the USA and around the globe. We can’t afford to elect people that don’t have an understanding of how to make wise decisions and how to ensure scientific knowledge forms the basis of policy when it should, such as: overfishing, pollution, global warming, the health care benefits vaccines provide when they are used properly, the dangers of abusing antibiotics, etc..

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The Amazing Reality of Genes and The History of Scientific Inquiry

cover of The Gene

The Gene by Siddhartha Mukherjee is a wonderful book. He does a great job of explaining the history of scientists learning about genes as well as providing understandable explanations for the current scientific understanding of genes and how they impact our lives.

As I have mentioned before, I find biology fascinating even though I found biology classes utterly boring and painful. I wish everyone could learn about biology with the insight people like Siddhartha Mukherjee provide. I realize not everyone is going to find the history and understanding of genes to be fascinating but for those who might this book is a great read. And don’t rule the idea out just because you found biology classes painful.

Life may be chemistry, but it’s a special circumstance of chemistry. Organisms exist not because of reactions that are possible, but because of reactions that are barely possible. Too much reactivity and we would spontaneously combust. Too little, and we would turn cold and die. Proteins enable these barely possible reactions, allowing us to live on the edges of chemical entropy – skating perilously, but never falling in.
– page 134

Whether it is the physics of our solar system or our biology there is a precarious band that allowed beings such as ourselves to evolve.

most genes, as Richard Dawkins describes them, are not “blueprints” but “recipes.” They do not specify parts, but processes; they are formulas, not forms. If you change a blueprint, the final product is change in a perfectly predictable manner: eliminate a widget specified in the plan, and you get a machine with a missing widget. But alteration of a recipe or formula doesn’t not change the product in a predictable manner: if you quadruple the amount of butter in a cake, the eventual effect is more complicated than just a quadruply buttered cake (try it; the whole thing collapses in an oily mess).
– page 454

The is a powerful idea. And when combined with turning genes on and off it is understandable how complex determining genetic impacts on biology and disease are. A few diseases or results (e.g. blue eyes) are nearly as simple as 1 or a few genes being altered in a specific way but most are not nearly so easy. And it isn’t like even that is so easy but with the amazing efforts scientists have made and the advanced tools those scientists created it can now seem simple to identify some such diseases.

The genetic code is universal. A gene from a blue whale can be inserted into a microscopic bacterium and it will be deciphered accurately and with near perfect fidelity. A corollary: there is nothing particularly special about human genes.
– page 480

This is something I have known and understood but it is still amazing. Genes and proteins and how they act to create the incredible diversity of life is something that is awe inspiring.

This book is a wonderful adventure for those interested in life and scientific inquiry.

Related: Epigenetics, Scientific Inquiry and UncertaintyHuman Gene Origins: 37% Bacterial, 35% Animal, 28% EukaryoticUnexpected Risks Found In Editing Genes To Prevent Inherited DisordersEpigenetic Effects on DNA from Living Conditions in Childhood Persist Well Into Middle AgeWhy Don’t All Ant Species Replace Queens in the Colony, Since Some Do

Eating Nuts May Reduce the Risk of Heart Disease, Cancer and Other Diseases

A large analysis of current research shows that people who eat at least 20g of nuts a day have a lower risk of heart disease, cancer and other diseases. The analysis of all current studies on nut consumption and disease risk has revealed that 20g a day – equivalent to a handful – can cut people’s risk of coronary heart disease by nearly 30%, their risk of cancer by 15%, and their risk of premature death by 22%.

While this is reassuring news to those of us (like me) that frequently eat nuts I am not sold on their evidence. Heath research is prone to overstating the benefits. Still there is little reason to avoid making nuts part of a healthy diet. That is a big part of the reason I have. They offer benefits and maybe even great ones (as indicated in this research) without much risk.

An average of at least 20g of nut consumption was also associated with a reduced risk of dying from respiratory disease by about a half, and diabetes by nearly 40 percent, although the researchers note that there is less data about these diseases in relation to nut consumption.

The study, led by researchers from Imperial College London and the Norwegian University of Science and Technology, is published in the journal BMC Medicine, Nut consumption and risk of cardiovascular disease, total cancer, all-cause and cause-specific mortality: a systematic review and dose-response meta-analysis of prospective studies (open access paper).

The research team analysed 29 published studies from around the world that involved up to 819,000 participants, including more than 12,000 cases of coronary heart disease, 9,000 cases of stroke, 18,000 cases of cardiovascular disease and cancer, and more than 85,000 deaths.

While there was some variation between the populations that were studied, such as between men and women, people living in different regions, or people with different risk factors, the researchers found that nut consumption was associated with a reduction in disease risk across most of them.

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Chimpanzees Solving Numerical Memory Test Better Than People

I can’t even see all the numbers before they disappear. But chimpanzees are shown seeing a flash of 9 numbers on a screen and then pointing to where they were on the screen in order from 1 to 9. Human test subjects can’t even do 5 numbers most of the time.

Related: Chimpanzees Use Spears to Hunt Bush BabiesOrangutan Attempts to Hunt Fish with SpearCrows can Perform as Well as 7 to 10-year-olds on cause-and-effect Water Displacement TasksTropical Lizards Can Solve Novel Problems and Remember the Solutions

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The Challenge of Protecting Us from Evolving Bacterial Threats

I have long been concerned about the practices we continue to use increasing the risks of “superbugs.” I have written about this many times, including: The Overuse of Antibiotics Carries Large Long Term Risks (2005)Are you ready for a world without antibiotics? (2010), Antibiotics Breed Superbugs Faster Than Expected (2010), Entirely New Antibiotic (platensimycin) Developed (2006), Our Poor Antibiotic Practices Have Sped the Evolution of Resistance to Our Last-Resort Antibiotic (2015).

I do also believe the wonderful breakthroughs we make when we invest in science and engineering have made our lives much better and have the potential to continue to do so in many ways, including in dealing with the risks of superbugs. But this is something that requires great effort by many smart people and a great deal of money. It will only happen if we put in the effort.

Winning war against ‘superbugs’

hey won this particular battle, or at least gained some critical intelligence, not by designing a new antibiotic, but by interfering with the metabolism of the bacterial “bugs” — E. coli in this case — and rendering them weaker in the face of existing antibiotics

ROS, or “reactive oxygen species,” include molecules like superoxide and hydrogen peroxide that are natural byproducts of normal metabolic activity. Bacteria usually cope just fine with them, but too many can cause serious damage or even kill the cell. In fact, Collins’ team revealed a few years ago the true antibiotic modus operandi: they kill bacteria in part by ramping up ROS production.

We need to continue to pursue many paths to protecting us from rapidly evolving bacterial risks. Many promising research results will fail to produce usable solutions. We need to try many promising ideas to find useful tools and strategies to protect human health.

Promoting Open Science

As I have written many times in the past we need to take back science from the closed-science journals. Historically journals were useful (before the internet). With the advent of the internet (and its spread) instead of maintaining the mission they started with the journals sought to maximize their profit and their own pay and jobs at the expense of sharing scientific knowledge with the world.

Elsevier — my part in its downfall by Timothy Gowers provides another good look at what can be done to promote science, math and engineering by addressing the damage to that goal being done by closed science publishers.

Recently he announced the launch of Discrete Analysis, a new journal that publishes to arXiv.

Disrupting the subscription journals’ business model for the necessary large-scale transformation to open access from the Max Planck Digital Library provides some good ideas for how to promote science in spite of the closed science journals fighting that goal.

There needs to be a shared understanding that the money currently locked in the journal subscription system must be withdrawn and re-purposed for open access publishing services. The current library acquisition budgets are the ultimate reservoir for enabling the transformation without financial or other risks.

Related: The Architecture of Access to Scientific KnowledgeWhy Copyright Extension is a Very Bad IdeaPublishers Continue to Fight Open Access to Science (2007)Harvard Steps Up Defense Against Abusive Journal Publishers (2012)

An Eukaryote that Completely Lacks Mitochondria

If you don’t have any idea what the title means that is ok. I probably wouldn’t have until the last 15 years when I found how interesting biology is thanks to the internet and wonderful resources online making biology interesting. I hope you find learning about biology as interesting as I do.

Look, Ma! No Mitochondria

Mitochondria have their own DNA, and scientists believe they were once free-living bacteria that got engulfed by primitive, ancient cells that were evolving to become the complex life forms we know and love today.

What they learned is that instead of relying on mitochondria to assemble iron-sulfur clusters, these cells use a different kind of machinery. And it looks like they acquired it from bacteria.

The researchers say this is the first example of any eukaryote that completely lacks mitochondria.

However, the results do not negate the idea that the acquisition of a mitochondrion was an important and perhaps defining event in the evolution of eukaryotic cells, he adds.

That’s because it seems clear that this organism’s ancestors had mitochondria that were then lost after the cells acquired their non-mitochondrial system for making iron-sulfur clusters.

Biology is amazing and mitochondria are one of the many amazing details. I wish so much that my education could have given biology a tiny fraction of the interest I have found it in after school.

Related: Human Gene Origins: 37% Bacterial, 35% Animal, 28% EukaryoticOne Species’ Genome Discovered Inside Another’sParasite Evolved from Cnidarians (Jellyfish etc.)Plants, Unikonts, Excavates and SARs

Healthy Living Greatly Reduces Likelihood of Dying from Cancer

Lifestyle choices can greatly reduce the incidence and death rates from cancer. 4 factors can reduce the incidence of cancer by up to 40% and death rate by 50%: don’t smoke, don’t drink alcohol in excess, maintain a BMI between 18.5 and 27.5, and exercising at a moderate intensity for at least 150 minutes or at a vigorous intensity for at least 75 minutes every week.

Preventable Incidence and Mortality of Carcinoma Associated With Lifestyle Factors Among White Adults in the United States

A substantial cancer burden may be prevented through lifestyle modification. Primary prevention should remain a priority for cancer control.

Cancer is the second leading cause of death in the United States, with 1.6 million new cancer cases and 0.6 million cancer deaths projected to occur in 2016.1 The cancer mortality rate, age-standardized to the 2000 US standard population, decreased from 199 to 163 per 100”¯000 between 1969 and 2013.2 However, this decline (17.9%) has been modest compared with the dramatic decrease in heart disease mortality (67.5%) during the same period, highlighting the need for further efforts in cancer prevention and treatment.

The study reviewed previous studies and the makeup of the previous studies and available statistics. As they state in the paper: “Because our cohorts’ participants were predominantly whites, to avoid any influence of different racial distributions on the comparison with the general population, we only included whites in the analysis.” They also excluded about 10% of cancers that are believed to have strong environmental factors.

Table Showing a Comparison of Lifestyle Factors in the Low- and High-Risk Groups

In the 2 cohort studies of US white individuals, we found that overall, 20% to 40% of carcinoma cases and about half of carcinoma deaths can be potentially prevented through lifestyle modification. Not surprisingly, these figures increased to 40% to 70% when assessed with regard to the broader US population of whites, which has a much worse lifestyle pattern than our cohorts.

Notably, approximately 80% to 90% of lung cancer deaths could be avoided if Americans adopted the lifestyle of the low-risk group, mainly by quitting smoking. For other cancers, from 10% to 70% of deaths could be prevented. These results provide strong support for the importance of environmental factors in cancer risk and reinforce the enormous potential of primary prevention for cancer control.

Related: A Healthy Lifestyle is More About Health Care than the Sickness Management That We Call Health Care IsBetter Health Through: Exercise, Not Smoking, Low Weight, Healthy Diet and Low Alcohol Intake (2013)Exercise Is Really Really Good for YouPhysical Activity for Adults: Inactivity Leads to 5.3 Million Early Deaths a Year (2012)

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