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Dr. Steve Goodman’s Work as a Field Biologist in Madagascar

Dr. Steve Goodman‘s work is a legendary Field Biologist and spends 9-10 months out of the year conducting research in other countries, with a focus on Madagascar for nearly 30 years. Learn more about the future of Madagascar’s biodiversity and research.

This video is from the great Brain Scoop channel with Emily Graslie; if you are not following that channel I highly recommend doing so for people interested in science.

Related: The Michael Jordan of Field BiologyInsect ArchitectureNew Life Form Found at South African Truck StopNeil Degrasse Tyson: Scientifically Literate See a Different World

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

Elephants Learn to Cooperate to Reach Their Objective

This clip shows elephants learning to work together to achieve what they can’t achieve alone (from BBC’s Super Smart Animals). It is interesting to see what animals are capable of. See the related post links for more amazing animal behavior.

Related: Insightful Problem Solving in an Asian Elephant (2007)Crows can Perform as Well as 7 to 10-year-olds on cause-and-effect Water Displacement TasksBeehive Fence Protects Farms from ElephantsCapuchin Monkeys Don’t Like Being Paid Less Than Their PeersFriday Fun: Bird Using Bait to Fish

Insect Architecture

In this webcast The Brain Scoop takes an interesting look at the homes of eusocial animals and other insects. The video includes many interesting details including that adult weaver ants can’t produce the silk used to weave leaves together so they pick up their larva and use them like a glue stick.

Related: For Many Crops Ants Can Provide Pest Protection Superior or Equal to Chemicals at a Much Lower CostWhy Don’t All Ant Species Replace Queens in the Colony, Since Some DoSymbiotic relationship between ants and bacteriaHuge Termite Mound in Nigeria

We are Not Us Without The Microbes Within Us

I Contain Multitudes is a wonderful book by Ed Young on the microbes within us.

Time and again, bacteria and other microbes have allowed animals to transcend their basic animalness and wheedle their way into ecological nooks and crannies that would be otherwise inaccessible; to settle into lifestyles that would be otherwise intolerable; to eat what they could not otherwise stomach; to succeed against their fundamental nature. And the most extreme examples of this mutual assured success can be found in the deep oceans, where some microbes supplement their hosts to such a degree that the animals can eat the most impoverished diets of all – nothing.

This is another book exploring the wonders of biology and the complexity of the interaction between animals and microbes.

For hundreds of years, doctors have used dioxin to treat people whose hearts are failing. The drug – a modified version of a chemical from foxglove plants – makes the heart beat more strongly, slowly, and regularly. Or, at least, that’s what it usually does. In one patient out of every ten, digoxin doesnt’ work. Its downfall is a gut bacterium called Eggerthella lenta, which converts the drug to an inactive and medically useless form. Only some strains of E. lenta do this.

The complex interactions within us are constantly at work helping us and occasionally causing problems. This obviously creates enormous challenges in health care and research on human health. See related posts: Introduction to Fractional Factorial Designed Experiments, “Grapefruit Juice Bugs” – A New Term for a Surprisingly Common Type of Surprising Bugs and 200,000 People Die Every Year in Europe from Adverse Drug Effects – How Can We Improve?.

Every person aerosolized around 37 million bacteria per hour. This means that our microbiome isn’t confined to our bodies. It perpetually reaches out into our environment.

Avoiding bacteria is not feasible. Our bodies have evolved with this constant interaction with bacteria for millions of years. When we are healthy bacteria have footholds that make it difficult for other bacteria to gain a foothold (as does our immune system fighting off those bacteria it doesn’t recognize or that it recognized as something to fight).

A few pages later he discusses the problem of hospital rooms that were constantly cleaned to kill bacteria and largely sealed to reduce airflow. What happened is those bacteria the sick people had in them were the bacteria that were flourishing (the number of other bacteria to compete for space was small). Opening the windows to welcome the outside air resulted in better results.

Outdoors, the air was full of harmless microbes from plants and soils. Indoors, it contained a disproportionate number of potential pathogens, which are normally rare or absent in the outside world

Human health is a fascinating topic. It is true antibiotics have provided us great tools in the service of human health. But we have resorted to that “hammer” far too often. And the consequences of doing so is not understood. We need those scientists exploring the complex interactions we contain to continue their great work.

Related: People are Superorganisms With Microbiomes of Thousands of Species (2013)Bacteria are Always Living in Our Bodies (2014)Gut Bacteria Explored as Medical Treatment – even for Cancer

Solar Storm Could Do $2 Trillion in Damage

I read an interesting article from NASA recently, Near Miss: The Solar Superstorm of July 2012

According to a study by the National Academy of Sciences, the total economic impact could exceed $2 trillion or 20 times greater than the costs of a Hurricane Katrina. Multi-ton transformers damaged by such a storm might take years to repair.

By extrapolating the frequency of ordinary storms to the extreme, he calculated the odds that a Carrington-class storm would hit Earth in the next ten years.

The answer: 12%.

Our high technology is far more at risk than most people appreciate. I don’t understand why the odds are so high (given that the last such event was in 1859 but I would guess there are sensible reasons for them to calculate such high odds. Others (in a quick web search) offer lower odds, but still 7 or 8% of such an event in the next 10 years.

The 2012 event would have done a great deal of damage. Luckily it was directed away from the sun in a direction away from where the earth was at the time. NASA has satellites arrayed around the sun (even where the earth isn’t) and one of those was able to capture data on the event.

There is also disagreement about how much damage such a solar storm would cause on earth. The main direct damage is expected to be done to the power system (of the USA and the rest of the world).

Related: Solar Storm (2006)photo of Solar Eruption (2006)Solar Flares May Threaten GPS (2007)Magnetic Portals Connect Sun and Earth (2008)

NASA explored this idea in a webcast:

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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

Unexpected Risks Found In Editing Genes To Prevent Inherited Disorders

Mitochondrial replacement seeks to remove genes known to cause genetic defects from embryos in order to allow for a baby to avoid inheriting the defect.

Mitochondrial Replacement Techniques: Ethical, Social, and Policy Considerations from the USA National Academy of Sciences

Accordingly, the committee recommends that any initial MRT clinical investigations focus on minimizing the future child’s exposure to risk while ascertaining the safety and efficacy of the techniques. The recommended restrictions and conditions for initial clinical investigations include

  • limiting clinical investigations to women who are otherwise at risk of transmitting a serious mtDNA disease, where the mutation’s pathogenicity is undisputed, and the clinical presentation of the disease is predicted to be severe, as characterized by early mortality or substantial impairment of basic function; and
  • transferring only male embryos for gestation to avoid introducing heritable genetic modification during initial clinical investigations.

Following successful initial investigations of MRT in males, the committee recommends that FDA could consider extending MRT research to include the transfer of female embryos if clear evidence of safety and efficacy from male cohorts, using identical MRT procedures, were available, regardless of how long it took to collect this evidence; preclinical research in animals had shown evidence of intergenerational safety and efficacy; and FDA’s decisions were consistent with the outcomes of public and scientific deliberations to establish a shared framework concerning the acceptability of and moral limits on heritable genetic modification.

The research in this area is interesting and our ability to help achieve healthy lives continues to grow. The path to a bright future though is not without risk. It requires careful action to pursue breakthrough improvements while minimizing the risks we take to achieve better lives for us all.

Unexpected Risks Found In Editing Genes To Prevent Inherited Disorders

Earlier this month, a study published in Nature by Shoukhrat Mitalipov, head of the Center for Embryonic Cell and Gene Therapy at the Oregon Health and Science University in Portland, suggested that in roughly 15 percent of cases, the mitochondrial replacement could fail and allow fatal defects to return, or even increase a child’s vulnerability to new ailments.

The findings confirmed the suspicions of many researchers, and the conclusions drawn by Mitalipov and his team were unequivocal: The potential for conflicts between transplanted and original mitochondrial genomes is real, and more sophisticated matching of donor and recipient eggs — pairing mothers whose mitochondria share genetic similarities, for example — is needed to avoid potential tragedies.

“This study shows the potential as well as the risks of gene therapy in the germline,” Mitalipov says. This is especially true of mitochondria, because its genomes are so different than the genomes in the nucleus of cells. Slight variations between mitochondrial genomes, he adds, “turn out to matter a great deal.”

Related: Gene Duplication and EvolutionThe Challenge of Protecting Us from Evolving Bacterial ThreatsOne Species’ Genome Discovered Inside Another’s (2007)Looking Inside Living Cells

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