We are Not Us Without The Microbes Within Us

Posted on April 16, 2017  Comments (0)

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 there 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

Posted on April 9, 2017  Comments (0)

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

Posted on April 2, 2017  Comments (1)

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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Bird on the Ice Age National Scenic Trail

Posted on March 22, 2017  Comments (1)

close up photo of a bird

Bird on the Ice Age National Scenic Trail in Wisconsin. Please comment if you know what type of bird this is.

Related: Backyard Wildlife: Blue JayBird Using Bread as Bait to Catch FishFriday Cat Fun: Cat and Crow FriendsBackyard Wildlife: Sharpshinned Hawk

The Amazing Reality of Genes and The History of Scientific Inquiry

Posted on March 4, 2017  Comments (2)

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

Female African-American Mathematicians at NASA in 1961

Posted on February 24, 2017  Comments (0)

Hidden Figures is a film based on the experiences of female African-American mathematicians at NASA in 1961 including Katherine Johnson. It is easy to forget our history if we don’t make an effort to remember.

Popular movie adaptations are not the best source for completely accurate history but they are a great way to raise awareness when they hold somewhat close to historical events.

It is amazing to see what was accomplished and also remember how badly mistaken our society was in important ways. We have made strides as a society, but we still have significant problems we need to address. Movies like Hidden Figures are a positive reminder of what can be accomplished when we give people opportunities. We need to remember that lesson and do what we can to remove the barriers that continue today.

NASA video on Katherine Johnson’s career:

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Backyard Wildlife: Large Lizards

Posted on February 2, 2017  Comments (0)

large thin lizard

Close up of the large, thin, lizard

These photos were taken across the street from my condo in downtown Johor Bahru, Malaysia. From my window I could see Singapore.

It is at least a meter long from head to tail (probably longer, the tail is really long). Still it isn’t huge since it is very narrow (more like a very thick snake with legs than anything else).

A few months before seeing the lizard in the photos I saw a really big lizard 1 block from the Johor Bahru Customs Immigration and Quarantine complex. It was easily 2 meters long (head to end of the tail) and quite large (stout). It was a different species I am pretty sure.

I was standing for awhile looking at a cool patch of wild greenery. All of a sudden I heard a noise and looked down; this large lizard probably got tired of me standing so and moved quickly into the brush. I hadn’t seen it. I would guess it was sunning itself, before I wandered over. Too bad I didn’t have my camera ready.

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WindTree – Harnessing Breezes for Electricity

Posted on January 22, 2017  Comments (2)

This style of wind power looks cool. The WindTree turns small breezes into electricity. Its production varies with the wind speed and its average output ranges between 1,500 kWh and 2,000 kWh. Peak power is 3,500 kWh.

But I don’t see how it can be effective given the large cost. The WindTree is being offered for installation late in 2017 in the USA and Canada at $67,500 – excluding delivery, installation and taxes (they estimate almost $100,000 total). It really seems to me the prices would have to come down by more than 75% to make any real impact in the market.

An average household in the USA uses 901 kWh per month.

The tree is 36 feet tall and 26 feet in width. The first trees were installed in France in 2015, the company is based in France.

It is good to see us investigating numerous ways to generate clean energy. But unless the price of this drastically reduces over time it doesn’t seem likely to contribute much to our energy needs.

Related: Chart of Wind Power Generation Capacity Globally 2005-2012Capture Wind Energy with a Tethered Turbine (2007)Engineering Floating Wind Farms (2010)Sails for Modern Cargo Ships (2008)

14 Year Old Signs $700,000 MOU for a Drone to Detect and Defuse Land Mines

Posted on January 14, 2017  Comments (4)

Harshwardhan Zala, from Gujarat, India has signed an agreement worth Rs. 5 crore (US$733,940) to explore the possibility of commercial production of a drone created by him which can help in detecting and defusing landmines.

Harshwardhan started work on the prototype of the landmine-detecting drone last year after reading in newspapers about high army casualties due to landmines. Aerobotics7 is the company founded by the 14 years old.

Harshwardhan Zala, 14-year-old trends for Rs 5 crore deal at Vibrant Gujarat Global Summit 2017!

Explaining more about the drone, the zealous 14-year-old said, “The drone is designed to send out waves that cover eight sq. mt area while flying two feet above the surface; the waves detect land mines and communicate their location with a base station. The drone also carries a bomb weighing 50 gram that can be used to destroy the landmine.” Harshwardhan Zala’s proud father Pradhyumansinh is an accountant with a plastic company in Naroda, and his mother Nishaba is a homemaker.

[missing video – removed 🙁 ]

The video has Harshwardhan speaking a bit of English but mainly some other language that I don’t understand. If I understand right, his drone is 98% accurate at identifying mines (where the current solutions are 92% accurate – and much more dangerous for those having to walk around testing). His solution is 17 times faster and 22 times cheaper than the current solutions. Once the mine is detected by the drone through an infrared sensor, a 50 gram detonator will complete the task of defusing it (blowing it up).

This video shows a bit of the drone itself (non-English audio)

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Pepper – A Social Robot from Softbank

Posted on January 8, 2017  Comments (2)

Pepper is a social robot developed in France and part of the Japanese conglomerate Softbank.

Pepper robots are at work in retail stores in Asia and Europe as sales associates. The first personal robots have been available in Japan for 2 years now and may be available elsewhere soon.

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Unexpected Risks Found In Editing Genes To Prevent Inherited Disorders

Posted on January 1, 2017  Comments (0)

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