Climate Change and Global Health

Storm Surge Flooding, Westport, Washington, November 2009

Climate Change and Global Health

Climate change poses a number of risks to global health.  These risks draw our attention to the fact that health issues operate on a scale that transcends our own individual concerns, extending well beyond local communities, state and national boundaries.  

I attended a lecture in February, 2011, by Dr Howard Frumkin, Dean of the University of Washington School of Public Health on the health risks of climate change.  It was an interesting talk, covering many areas where climate change impacts global health. These impacts may be associated with the increased frequency of extreme weather events. 

Extreme weather events discussed included increased heat, cold, melting, freezing, flooding and droughts.  Increased atmospheric instability may give rise to more frequent hurricanes and tornadoes. Extreme weather events can be viewed on various time scales, from 50 to 100 year storms, to events on a more geological time scale.

Heat stress is of particular concern to the elderly, the young and the immune-compromised. Extreme heat, especially in non or inadequately air-conditioned spaces may result in premature mortality during heat waves, in the vulnerable, especially in the city where paved areas draw heat.  Dr Frumkin was concerned about the "harvesting" effect of heat waves on elderly, urban, populations.

Cold, snow, ice and freezing also may become survivability issues, involving issues of heating and interruption of water and electrical service.  Storms may impact travel and thus food supply, transportation of vital supplies to population centers and medical facilities.  

Public health challenges may emerge with air or water quality issues, impacting respiratory, cardiovascular, and other associated systems.  Infectious diseases may spread via the air or water through vectors  such as tic or mosquitoes, or via zoonotic means through human to animal or animal to human spread).  Allergies may develop in response to climate changes, and new pathogens may emerge or spread to different areas.

Air pollution is a problem which affects more than just urban areas.  With experience working in the regulatory air quality sector, I realize the widespread impacts that pollutants such as ozone and other pollutants have.  Photochemical reactions involving products of combustion (e.g. auto exhaust) take place in the atmosphere resulting in ozone levels downwind of major urban areas. As the reactions involve sunlight and heat, the levels on sunny and hot days increase in the summer. In the fall and spring periods of extended air stagnation resulting from stalled high pressure weather systems may increase the respiratory and cardiovascular burden on the vulnerable patient group. Air pollution does not know boundaries, thus residential and industrial pollution from other countries may impact us, as ours impacts theirs.  Forest fires add to the impact.  Extreme weather may impact all these issues.

The impact of climate change, extreme weather events and public health challenges may impact food production, may result in civil conflict, dislocation of impacted people and may increase the expression of mental health issues .

The discussion of climate science drives the discussion on public health impacts as projections are made regarding the manner in which changes will take place in Earth's climate systems.  Modeling climate systems drives downstream weather and public health challenges. These challenges are studied in a variety of settings, including federal government institutions such as NOAA, NASA and the CDC, and at a variety of state and local governmental and, at private institutions.  The Intergovernmental Panel of Climate Change and the National Climate Assessment have comprehensive plans reflecting policy in this area.

Extreme weather events can result in significant mortality and morbidity, as well as impacts to property.  Tornadoes and Hurricanes and wind storms may result in death and injuries from flying objects, falling trees and power lines as well as medical emergencies secondary to the event.  Fires may result from damaged gas lines. 

Increased flooding and storm surge may result in drownings and damage to property. Flooding may increased the spread of infectious diseases, problems with sewage systems and interruptions in drinking supplies

Drought may bring about reductions in food supply.  This is a serious issue as crops may be challenged to grow in areas where they were previously able to.  Vegetation, vectors and pathogens may spread into other areas as a result of warming.  This impacts the latitude at which such impacts occur as well as the altitude above sea level, moving to cooler latitudes and elevations.

More weeds may develop in urban areas in response to climate change and global warming as vegetation adjusts to the changing environment.

Extreme weather events thus may have public health impacts relating to many systems, resulting in dislocation of people and mental health issues as citizens adjust to the events.

The challenge is how to address climate change issues in the context of these public health issues.

Ferguson

What started presumably as a simple theft and an encounter with a marked police car and a uniformed police officer has turned into racial rioting in Ferguson, Missouri and elsewhere around the country.  It is a tragedy that an 18 year old African-American young man was shot and killed by a white police officer.  This young man had a potential future ahead of him, and whether or not he stole some cigarillos from a store, and whatever his encounter may have been with the officer, it is a tragedy that his life had to end so soon.

At the same time we consider the actions and state of mind of the police officer in question, who was not indicted, but who will live with his actions for the rest of his life, and who must have gone through his own private and public hell, taking a life in the course of duty.  This was a life, going through that tenuous period in early adulthood. But there probably was more to it than that.

The riots that have followed the incident in Ferguson and the decision by the Grand Jury are an unfortunate commentary on the manner in which society acts to resolve its problems.  The issues in this case are complex.  The issue goes to the core of what it means to be a police officer in a society where the officer is empowered to use lethal force and must, in some cases, at a moment's notice act to preserve the law and/or to protect his own life and well being.

How can society understand the lessons of the Michael Brown and apply them better?  I will focus on  a few broad areas that I feel led to the situation escalating quickly and then  spiraling out of control into a series of demonstrations.

Cognitive Dissonance

One principle is the principle of cognitive dissonance that the police officer has to deal with in his position, whether it be as a beat cop, a patrol officer in a vehicle, or an undercover officer placed in an extraoardinarily difficult position.  Cognitive Dissonance  according to Wikipedia, is the "mental stress or discomfort discomfort experienced by an individual who holds two or more contradictory beliefs, ideas, or values at the same time, or is confronted by new information that conflicts with existing beliefs, ideas, or values." The officer has to deal with threats to his life, health and well being,  as he balances his actions in enforcing the law and in maintaining a civil society.  When these issues conflict, it creates cognitive dissonance.

Bayesian Thought Processes

Another principle the officer has to deal with is "Bayesian Thought Processes", which refer to a manner in which the brain processes information in order to perceive situations.  The brain tends to be programmed in a fashion in order to do forward thinking threat and risk assessment based on prior probabilities, which are conditional.  These conditional experiences represent the statistical evaluation of past experience in the brain.  If the officer has come to associate the evolution of threats with certain populations, then when a threat situation arises, he will be more likely to act on the basis of that threat when those populations are involved.  The associations may relate to personal experience, exposure to media, training or other exposures.  The key to solving the problem, is to address these underlying associations.  This is a difficult task and it is one that reflect's society's views and prejudices.

The Marijuana Symbol

Laws are getting more and more complex and this leads by itself to occasions of increased cognitive dissonance for the police officer.  An example of this is that the officer noticed a marijuana symbol on the socks of one of the men and that impacted perception.  Marijuana laws have become more complex, with some states (Washington and Colorado) legalizing it, while other states and the Federal government consider it illegal.  Medical marijuana is allowed in some cases.  For example, Missouri allows it for use for intractable epilepsy.  These laws by themselves add considerable cognitive dissonance to a police officer who may consider marijuana a 'gateway' drug to other more harmful drugs (and it still may be).  It is possible that the marijuana could be used for a medical purpose, a different association entirely.  Did Michael Brown have epilepsy?  I don't know.

An Officer's Sense of Space and Safety

The subjects approached the patrol officer's vehicle from behind, endangering the officer's feeling of control over his own space.  This was probably the key element in the confrontation.

The race and age of the subjects in question, and the perception that they may be subjects in a robbery the officer had heard about probably also contributed to the officer's sense of personal safety. The issue in question, with the demonstrations, however, is the extent to which the officer's perception of risk to his personal safety was based on preconceptions based on race, which may have influenced the outcome.

The Subject's Behavior and the Officer's Behavior

The officer missed one vital point, the subject's behavior.  If Michael Brown had committed a theft, as it appeared, then why did he challenge the police officer?   Was he guided by outside forces to act in a manner inimical to his own feelings of safety? Was his intent to be caught?  He challenged the police officer when his safest approach would have been to simply avoid the situation. Is it possible that the police officer's reaction, when threatened (by being surprised in his vehicle), triggered past memories of racial harassment in Michael Brown?  Did an emotional memory of a past event trigger an action to challenge rather than avoid conflict (fight or flight?).  At the age of eighteen, a number of issues could have been involved, including unknown existential issues.

Did Michael Brown attempt to surrender and the officer fail to recognize it for some reason?  Why?

Perception of Police and Justice System

The issue in the community becomes the perception of the public towards the police and the justice system as they examine the various roles in a tragedy of a life that ended too soon and the feelings of the police themselves.

How to fix this?  It is a good idea for people to have some understanding of police thought processes, especially understanding their concern about protecting their firearms and their physical space.

Police responses are to a certain extent wired into them by training, as in many fields.  Police need to be trained to act very quickly in risky situations, something not necessarily true of all professions.   In fact many of these hardwired thought processes are what have kept them safe in their jobs, so that seeking to change perceptions of police officers is fraught with many challenges, some of which involve the issues of cognitive dissonance alluded to above.

So the mystery of Michael Brown remains, how do you solve the problem?  You can educate the public, but the public is such a large body to educate.  This is a challenge.  Police training needs to continue to incorporate the importance of psychological factors, perceptions, including  the types of issues discussed above.

It is very possible that the subjects anomalous behavior led to a situation of cognitive dissonance in the officer where it generated a 'fight or flight' situation that the officer reacted to and resolved with his training and his capability to protect himself from potential harm.  It's possible the officer resolved the anomalous situation as only a challenge to his authority when there were other factors as well.  Time will tell as analysis of the situation proceeds.

One thing we do know, and that is suppressing a vulnerable, poor and disadvantaged population can have impacts that reverberate beyond the immediate situation in question.

It is difficult to comment on the legal tactics employed with the grand jury proceeding. The results speak for themselves.

A community mourns and it is time to heal and try to fix the problems.

Ebola

Raudfjorden Beach, Svalbard, Norway

The Ebola outbreak has proven to a challenge for worldwide heatlh leaders.  The CDC has information about Ebola on its website, as does the World Health Organization (WHO).  The CDC information is delineated into a number of topical areas of interest to subject audiences.  I'm interested in the etiology of Ebola, its transmission, and issues surrounding its current outbreak.

My interest in Ebola began during my actuarial career, reading the "Hot Zone" , a 1994 non-fiction book about incidents involving viral hemorrhagic fevers, including ebolaviruses and marbug viruses. The memory of the book stayed with me since I was reading it while sailing down the west coast of Vancouver Island in 15 foot swells in a sailing vessel.  I can recall eating copious amounts of ginger cookies to ward off seasickness as I read of hemorrhagic fevers killing off people very quickly, in a very bloody and gory fashion, as all the while I was lurching back and forth in the sea and swell on the Pacific Ocean.  The ginger cookies did their job and the memory is etched in my experience, gone but not forgotten, as Ebola emerges again, this time, expressed  in the news of an outbreak.

These hemorrhagic diseases killed off people before they had a chance to spread extensively, and, were confined to certain areas in Africa and mostly away from major population centers.

According to the CDC, the virus can be spread through direct contact with blood and body fluids of a person infected with Ebola, with objects such as syringes infected with Ebola and infected fruit bats or primates.  The question remains as to factors impacting the geographical distribution of Ebola, how it independently arises, factors of etiology and its potential spread elsewhere.

The recent upswing in the Ebola virus prompted me to question its etiology, transmission and other issues.  For example, because of the increase in number of cases, I wondered if the virus had recombined with another virus to increase its transmission and decrease its mortality, or if there were other factors.   In this blog article I consider a number of issues, and raise some questions relating to the virus.


Etiology

• Does Ebola predate the AIDs/SIV/HIV viruses and does it provide some idea of the origin of these viruses? The CDC expresses that it does not know the origin of the original host of the Ebola Virus;  It is interesting to study the context of the Ebola virus regarding its emergence out of the Kinshasha Highway  across the Congo into Uganda as discussed in "The Hot Zone".  Did the virus have origins in bat habitats such as caves, rock, lava tubes, environments exposed to varying bacteria and archaea?
• The Ebola virus is a negative sense RNA virus. The production of proteins from a negative sense RNA virus require first the production of Messenger RNA (mRNA) and then proteins from mRNA. Ebola does not have reverse transcriptase, which would ordinarily be needed to enable insertion of its genetic contents into the DNA.   Is its 'purpose' then to directly produce mRNA (messenger RNA), and why? Research has shown that the filoviruses behind Ebola are very old and that there is direct insertion of genetic content with indications of evolutionary divergence a long time ago.  - The Lin Edwards article, "Ebola and Marburg viruses may be much older than thought" discusses this subject.
• Does the Ebola virus relate to issues concerning New World Monkeys and Old World Monkeys and the divergence of the two species?  If so, would this tend to indicate the same type of environmental conditions that may have existed at the time of that divergence?
• What is the distribution of the virus?  Does the virus act with regards to specific populations, affecting certain populations in a negative or positive way, and leaving others untouched.  What factors in these populations would account for the outbreak?  Are other populations at risk?

Transmission

• Did the Ebola virus recombine with another virus (for example the Corona Mers Virus  , Seasonal Flu Virus or enteroviruses) to allow it to decrease its mortality rate and increase its transmission?  Is it continuing to do so and would further recombination with the current seasonal flu change it further along these lines? 
• A subject of interest to is transmission of Ebola from the natural host to a target population.  Is Ebola being expressed, sustained within the target population or being sequestered?  Does this imply sequestration in a host for transmission or expression later under circumstances that may enable it to be used as a regulatory operator or a mediator of group identity or expression of  immunity systems?  Is it developing a symbiotic relationship with the host or another virus in a toxin/anti-toxin sort of manner (discussed by my blog article on Dr Luis Villarreal and his work on group identity systems)? How does this concept explain the existence of this virus in a reservoir species?
• What is the risk for the spread of Ebola?  To what extent is the risk environmental and to what extent can it be transmitted from person to person? 
• Is Ebola being transmitted in a less than lethal form under our eyes without our knowledge?
• Can Ebola be spread by more species of animals than listed under the CDC website?  
• How might Ebola change to become more transmissible to a greater variety of populations impacted by different environmental factors?  How would this risk change if the Ebola virus were to combine with the seasonal flu in a variety of different ways?

Geological Factors

• What factors in Africa are most significant in the etiology of Ebola?  Heat, humidity, coeexistence with and diversity of animal species, alkaline environments, carbon dioxide sequestration and outgassing (e.g. Lake Nyos), the Archaean basement substrate of the West African bedrock, granite, uranium, endospores such as bacillus anthracis, and  natural nuclear fission reactors from underground uranium (Gabon)? 
• What is the impact of the African mining fields?  Iron, gold, lead, silver, arsenic, mercury , uranium and nickel are among products of mining.  Nickel has a positive feedback impact on inflammatory markers. 
• How do endospores such as bacillus anthracis  fit into the story of Ebola, set in the mining context of West Africa, with its iron, gold, silver, arsenic, uranium, nickel and mercury, and the expression of inflammatory markers and feedback indicators?
• Are these various environmental issues constrained to Africa or are they present in other environments, and where do other similar environmental conditions exist?  Do these conditions have to exist in the same place or can an individual experience them by exposure to a variety of locations? For example, Archaean basement layers of rock exist in the Arctic, in Svalbard, which I visited in 2005. How would exposure to Archaea and other factors present in West Africa differ from the situation in Svalbard where it is much colder! Where else can we find archaea and chiral substances?
• How do increases in solar radiation  and changes in the Earth's magnetic field impact the expression of Ebola in Africa? To what extent would these factors affect the expression of Ebola in other areas of the planet?

Environment and Physiology

•  Does the emergence of a disease that promotes bleeding have significance as it relates to climate change or other planetary or environmental factors?    Is some environmental change occurring that would result in blood clotting more easily, something that would need to be countered by less viscous blood and changes in the coagulation cascade?
• How might the environmental factors in Africa affect blood coagulation?  Through mitochondrial regulation as it is impacted by environment, haplogroups and uncoupling in oxidative phosphorylation?  Through the impacts of oxygen reactive species?  Through solar radiation, geomagnetic storms and cycles?  Through the Warburg effect  (which replaces aerobic respiration with glycolysis)? Through arsenic mining?  Through positive feedback mechanisms involving hypoxemia  and inflammatory responses?  
• Is it possible that the Archaean basement layer of rock in West Africa impacts the blood coagulation cascade  and the blood vasculature through chirality?  Would concepts of fractal dimension  and tortuosity explain concepts of blood coagulation and vascular inflammation and other disorders, including stroke and cancers, including those of the blood and lymphatic systems?  
• What impact does the water people drink (and breathe through water vapor) impact people, including the impact on group identity systems and physiological parameters?
• Does the outgassing  of carbon dioxide  as a result of global warming, the release of iron from iron sequestered in the rock, and the release of endospores from sequestration, explain any of the natural events happening today, as regards vascular and coagulation issues?
• Is it possible that Ebola, as a disorder that promotes bleeding, developed as a feedback mechanism to counter the impact of increased blood coagulation due to the environmental impacts raised above? 
•  Bleeding may increase as blood coagulation factors are used up; does Ebola act to promote such bleeding to counter increases in clotting factors secondary to these environmental issues?  Is it possible that Ebola thus impacts the regulatory mechanisms of the coagulation cascade?

Detection

• Could an easy detection test be done for Ebola using, for example, saliva? This might prove less expensive and easier to measure for initial testing prior to full blood workups if it was sufficiently sensitive and specific.
• Could the d-dimer test and PPT tests be used as early indicators of Ebola.
• Can a series of early indicators, including markers of respiratory and coagulation system function and exposure to certain environmental factors, be developed to ascertain risk patterns for specific populations?  
• Where might the solution to Ebola be found?  Only time will tell.  Are lamprey VLR's a potential solution for isolating, detecting, and finding a cure for Ebola, considering their ability to detect bacillus anthracis and their affinity for carbohydrate glycoproteins?  Considering the age of the filoviruses and the characteristics of Ebola itself, is this a potential area to investigate?

Summary

Does the emergence of Ebola reflect the re-emergence of ancient historical patterns?  Have these patterns been carried by reservoir species from the depths of time to the particular victims of Ebola? Will Ebola adapt and spread elsewhere or re-emerge in other parts of the planet, independently?

Are the issues happening in West Africa an early indicator ('Canary in a Coal Mine')  of planetary changes?  These changes include changes in Earth's magnetic field, climate change, global warming and solar radiation, and downstream effects including release of sequestered minerals and gases such as carbon dioxide and methane from rock and oceans.  These are all areas of concern.  Historical examples of changes in Earth's magnetic field are shown over longer periods of time and more recent geologic time periods in this Wikipedia article on the Earth's Magnetic Field.

Finally, I am reminded of the childhood game, "Animal, vegetable or mineral" and associations with the "Tree of Life" (and probably, by extension, "The Tree of Good and Evil").  Ebola is a disease with a past, reflecting deep phylogeny and the rivers of time as embedded in the history of our rocks.

Sources:

marilyndunstan.blogspot.com
Evolution of Adaptive Immunity

Wikipedia:
Ebola virus disease
"The Hot Zone"
Kinshasha Highway
Archaea
Sense (molecular biology)
Messenger RNA
Reverse Transcriptase
Filoviridae
New World Monkey
Lake Nyos
Endospore
Bacillus Anthracis
Natural nuclear fission reactor
Nickel
Chirality
Sunlight
Earth's Magnetic Field
Oxidative Phosphorylation
Reactive Oxygen Species
Geomagnetic Storm
Warburg Effect
Glycolysis
Coagulation Cascade
Fractal Dimension
Tortuosity
Outgassing
Carbon Sequestion
Animal Sentinel
Earth's Magnetic Field-Geomagnetic Polarity
Earth's Magnetic Field-Brunhes Geomagnetism
Earth's Magnetic Field

World Health Organization:
Ebola Virus Disease

CDC:
CDC
Ebola (Ebola Virus Disease
2014 Ebola Outbreak in West Africa (Outbreak Distribution Map)

Phys Org: 
Ebola and Marburg Viruses May be Much Older Than Thought

JoVE Visualize: Anthrax lethal toxin inhibits translation of hypoxia inducible factor 1? and causes decreased tolerance to hypoxic stress

Geology and Mineral Resources of West Africa - The Archaean Basement

National Academy of Sciences: High-affinity lamprey VLRA and VLRB monoclonal antibodies

Berkeley Lab: Structure of the Ebola Virus Glycoprotein Bound to an Antibody from a Human Survivor

NASA Science News - Earth's Inconsistent Magnetic Field

Evolution of Adaptive Immunity

Two Trees (creative digital image)

I attended a "Weiser Endowed Lecture in Immunology" featuring Dr Max Cooper of the Emory University School of Medicine, speaking on "Evolution of adaptive immunity" at the University of Washington in 2012.  Dr Cooper's work is foundational in this subject area.

It is interesting that immunity systems follow a phylogenetic pathway much as the phylogeny of species themselves do. The evolutionary pathway of jawless vertebrates (of whom hagfish and lampreys are surviving members), possess differences in comparison to the common evolutionary pathway followed by other vertebrates.

Lampreys and hagfish do not possess a thymus , nor do they possess a spleen.    Lampreys and hagfish do not possess Major Histocompatibility Complex (MHC) 1 or 2, T-cell receptors or recombination activating genes (RAG 1 and 2) which play an active role in the recombination of T-cell and immunoglobulin  receptors. Lampreys and hagfish posses hematopoietic tissue, the former in the intestine and the latter in the portal vein.  With these changes, the lampreys and hagfish diverged off the common immune system evolutionary pathway prior to the development of certain MHC class immunity in other species.  This is an important benchmark due to the major role that the MHC class plays in vertebrates.  It is a vital aspect which makes the concept of a separate phylogenetic pathway earmarked for the immune system so interesting.  If lampreys do not possess a thymus, then what substitutes in its place?

Lampreys and hagfish utilize a system of leucine-rich repeats )(LRR's) to mediate immune system responses using Variable Lymphocyte Receptor (VLRs), (VLRA's, VLRB's and VLRC's).  The interesting aspect of the jawless vertebrate immune system function is comparing its action in structure and function to the immune systems we are familiar with.  VLRB's have structures similar to toll like receptors (proteins that play a key role in the innate immune system), while their functions are similar to those of antibodies,  and they possess humoral characteristics (using macromolecules in extracellular fluids in immunity systems). They act using discrete populations of lymphocytes (types of white blood cells) .

VLRBs act as an adaptive immune system and can differentiate foreign from self in recognizing lymphocytes.

Lampreys posses a diverse variety of leucine-rich repeats which code for germline and mature genes. They possess a specificity for carbohydrate and protein receptors on bacterial and mammalian cells. They bind antigens with high avidity and affinity, describing the binding capacity of multiple versus single interactions of antibodies with antigenic epitopes.

 In "Evolutionary implications of a third lymphocyte lineage in lamprey", the authors find a thymoid source for VLRA and VLRC assembly in the lamprey gill tips, while VLRB assembly occurs in hematopoietic typhosole and kidney tissues.  VLRC appeared more numerous than VLRA, and predominated in the skin.  They conclude that a similar body plan of two T-cell type lymphocytes in a thymoid type structure and one B-cell type lymphocyte in the blood and kidneys shows some similarity in basic structure to the immune system for jawed vertebrate, while achieving adaptive immunity through different means.

Monclonal VLRB antibodies  from immunized lamprey larvae can recognize plasma cells from myeloma patients.  VLR4, a monoclonal VLRB specific for BclA, the bacillus collagen-like protein, has shown to be specific for B. Anthracis spores.  Information on B. Anthracis can be obtained from the US Centers for Disease Control (CDC) CDC - Anthrax and the World Health Organization (WHO) WHO - Anthrax.

Research indicates a number of applications where VLR's can recognize certain immumogens  An immunogen is any antigen that is capable of inducing humoral and/or cell-mediated immune response rather than immunological tolerance.  These applications include diagnosis, research and bioterrorism investigations.

PANSPERMIA and EVOLUTION

Mars Spirit Lander and Bonneville Crater in Color

 Image Credit: NASA/JPL-Caltech/Univ. of Arizona 

Panspermia  is a concept which portrays how life might be distributed throughout the universe.  These means include a wide variety of astronomical or celestrial objects  including meteors, comets, asteroids, and factors such as the solar wind.  The theory of panspermia, however does not really address how life began in the first place.

As man has ventured out into space, with human space travel, or has used unmanned spaceflight, the issue of man (or machine) as a vector or agent of panspermia has become an issue.  This issue parallels the concept of jet travel and airports as a vector in spreading contagion. Migratory birds have been vectors for centuries, landing in Qinghai Lake, China, a saline and alkaline lake and migratory crossroads  or in the Izembek National Wildlife Refuge in Alaska, along the Bering Sea. . Such bird migratory pathways provide fertile ground for recombination and spread of various contagions.

The NASA photo of the Bonneville Crater and Mars Spirit Lander depicts an impact crater on Mars.  Such an impact would have created a large amount of energy upon impact.  Many theories of life involve the discussion of how reorganization and complexity arises as energy is input into a system.  The Miller and Urey experiment in 1953 attempted to address this issue through recreation of a primordial atmosphere laced with water, methane and lightning storms.
 
Henry Eyring, a chemist, discovered Actual Rate Theory or Transition State Theory, which discusses reaction rates of chemicals in the context of potential energy states, complexes activated by chemical reactions, entropy considerations and products formed by the chemical reaction. In considering the input of exogenous energy into a system, this theory would be important in examining the potential reactions that might take place, as the reaction may change the system through transformational change.

In considering the issue of panspermia, therefore, there are a couple of issues; the development of a system and then the spread of that system.  Issues of energy and mixing concern the development or the boot-strapping of a system through transformational change, while panspermia addresses the spread.  Where panspermia occurs through media that spread via impact, the two issues (bootstrapping and spread) tend to co-exist to some extent.

The concept of panspermia requires a vector that is resilient.  It must be able to adapt to environmental factors such as extremes of temperature, must be able to resist impact as well as radiation and other factors such as high levels of salinity.   Such organisms, extremophiles  fit a profile as a candidate for panspermia.

Santa Catalina Mountains seen from Saguaro National Park, Arizona

Recently, I came across an article in Applied and Environmental Microbiology (AEM) on Bacillus Endospores,  written by Patricia Fajardo-Cavazos and Wayne Nicholson, "Bacillus Endospores Isolated from Granite: Close Molecular Relationships to Globally Distributed Bacillus spp. from Endolithic and Extreme Environments".   This article discusses the issue of the diversity of Bacillus spp. populations, and specifically certain endolithic spore populations obtained from near surface granite from the Santa Catalina mountains near Tucson, Arizona.

An endospore is a tough non-reproductive surface that lies dormant for an extended period of time, and can be later revived after many years to a vegetative state.

Anthrax is a bacillus, and may exist in the dormant state as an endospore.  According to a World Health Organization document on studies of anthrax endospores (bacillus anthracis),  "Sporulation requires the presence of free oxygen. In the natural situation, this means the vegetative cycles occur within the low oxygen environment of the infected host and, within the host, the organism is exclusively in the vegetative form. Once outside the host, sporulation commences upon exposure to the air and the spore forms are essentially the exclusive phase in the environment."  Spores are thus spread by release of spores by the dying host into the environment where they are taken up by another animal.

 The focus of the AEM article is on the very issue of panspermia, the issue of transference of microbes through spaceflight, It concerns the measurement of characteristics of various endolithic spore populations obtained through a variety of near surface granites and basalts and even the ultra clean environments of spacecraft assembly facilities.

Blue fluorescence obtained through medium wavelength UV illumination, distinguished certain endospores obtained from near surface granites.  Endospores were grouped into species or strains based on their rRNA  gene sequences. Numbers and diversity of endospores from granite were greater than those obtained from basalts.  This may be due to the lower porosity of basalt versus granite. Limited subsets of Bacillus spp. appeared to occur in certain rock environments that favored them and not other strains. Certain bacillus strains (bacillus subtilis) were used as proxies for bacillus anthracis fluorescence properties in the study.

The issue of panspermia is a very important one, set in the context of space exploration and in consideration of how extraterrestrial impacts may have impacted (and may still be impacting) human life.  The AEM study provides interesting results as to the diversity and characteristics of Bacillus spp. from a variety of environments, including, importantly, granite, set in the context of fluorescence properties.   A bacillus such as anthrax, as studied by the World Health Organization (WHO) or the CDC may provide clues as to how bacillus and endospores fit into our evolutionary framework.

Trinity Nuclear Test

Bosque del Apache National Wildlife Refuge

near San Antonio, New Mexico

On July 16, 1945, the first atomic bomb test was performed at a site about 35 southeast of Soccorro, New Mexico.  The test was code named 'Trinity' by Dr Robert Oppenheimer, director of the Los Alamos Laboratory involved in the Manhattan Project.  It used a 20 kiloton Plutonium implosion device, of a similar design to what would ultimately be dropped over Nagasaki on August 9, 1945, less than a month later.  The Manhattan Project was a war-time effort to develop an atomic bomb, which occurred over a time period from 1942 to 1946.  The effort extended to a number of facilities, including Hanford, Washington and Oak Ridge, Tennessee in addition to the Los Alamos, New Mexico  site where major design work occurred.  Ultimately testing would be done in a number of areas, including Nevada and the Pacific Islands, including Bikini Atoll, after World War II.

The Trinity test differed in nature from that used on the first atomic blast at Hiroshima.  The Hiroshima blast used a gun type, or projectile type detonation of uranium while the Nagasaki and Trinity Blast involved implosion of a plutonium core.

The Trinity atomic bomb test followed a period of development of nuclear expertise in a number of areas, from study of the atom itself, to study of high energy collisions and the study of nuclear chain reactions. A key development was a letter by physicists Eugene Szilard  and Albert Einstein,   expressing their concern that Germany could develop an atomic bomb.  The result of their efforts, which included collaborations with other physicists such as Eugene Wigner and Edward Teller , was that President Franklin Delano Roosevelt accelerated scientific research with a new committee on June 28, 1941 and approved the atomic program on October 9, 1941.  The response to their letter came on October 19, 1941.

This timeline is interesting, taken in the context of the historical evolution, from World War I, in 1914-1918 to World War II and its aftermath in the nuclear arms race.  The historical context included the 1918 Flu Pandemic (Spanish Flu), aided by a World War I fought in the trenches, the Great Depression,  and the ever continuing battle between commercialization, globalization and nationalist interests.  The development of nuclear weapons ratcheted up the stakes, due to the wider implications of their use and the attendant risks.

Nuclear risks include the potential manufacture, storage, transportation, testing and potential use of nuclear weapons in conflict (including WWII).  These risks are in addition to risks arising from nuclear usages in other areas, such as power generation and medical usages.  We have seen impacts from the Three Mile Island, Chernobyl and Fukushima nuclear power plant incidents.  I've discussed some of these issues in other blog articles, including: Nuclear Balance of Risks, Chernobyl 25th Anniversary and Energy Choices and Risk.

Development, testing and use of nuclear weapons has left a long lasting radiological footprint on the landscape in areas such as Hanford and the Pacific Northwest, the Trinity Site and White Sands and the Southwest, the Pacific Islands, including Japan during WWII, and downwind (and water) areas.

The above photograph is taken at Bosque Del Apache National Wildlife Refuge, near San Antonio, New Mexico in February, 2009, about 20 -30 miles from the Trinity Test Site, some 63-64 years after the test.  Another image, taken at Valley of the Fires State Park, New Mexico, was taken near Carrizozo, New Mexico, one of the areas harder hit by the Trinity plume.

The Odd Couple: The Mitochondria and the Cell Nucleus

Mitochondrion (Creative Image)

Mitochondria are key to understanding many life processes, in the body, in nature,
and in our environment.

Years ago, the Eukaryotic cell   developed as a symbiotic relationship between a prokaryotic cell and a proteobacteria.  The prokaryotic cell may have been an archaea. The proteobacteria was was incorporated into the cell as an endosymbiont.  As gene transfer took place between mitochondrial DNA  and the cell's nuclear DNA, the extent of the  mitochondrial DNA (mtDNA) decreased and the nuclear DNA incorporated more of the functions performed previously by mitochondrial DNA.  As this occured, the relationship changed from being symbiotic to the development of the mitochondrion as an organelle within the cell.

Much of the work developing the theory of symbiogenesis was done by Lynn Margulis in a 1967 paper..  The theory behind symbiogenesis is a very important topic with wide ranging implications due to the complexities involved in the interoperablity of nuclear DNA and mitochondrial DNA.  These issues are ongoing and represent a major challenge in understanding a wide range of scientific issues confronting our society today.

Mitochondria are present in most living cells that include DNA.  Mitochondria are responsible for  a large portion of the energy generated by the cell.  Mitochondria are responsible for the generation of adenosine triphosphate (ATP) from adenosine diphosphate (ADP)  through aerobic processes using its electron transport chain (ETC).  The energy generated as ATP is many times greater than the energy generated through anaerboic glycolysis, which is an energy generation process that does not use oxygen.

The use by the cell of anaerobic  vs aerobic respiration has significance in studying various physiological processes which occur throughout the body.  These issues have implications in wide ranging areas from cancer to the relationship between sleep and wakefulness.

As energy is generated throughout the body, principles of conservation of energy must be satisfied.  Whether energy is generated through aerobic respiration and Oxidative Phosphoylation (OXPHOS)  using the mitochondrial electron transport chain (ETC), energy generation requires inputs and outputs that must be balanced.  This is a principle called "conservation of energy".  OXPHOS generates ATP,  the "energy equivalent of currency" in the body, energy in the form of heat, and outputs such as oxygen radicals (Reactive Oxygen Species (ROS))  as a byproduct of the process.

Oxygen Canisters

Oxygen reactive species such as superoxide (O-), hydrogen peroxide (H202) and the hydroxyl radical (OH-) can be generated depending upon a number of factors.   This includes natural process in the body involving signaling and homeostasis and also exposure to a number of environmental factors which may increase their generation.  Antioxidants may help the cell counter some of the impacts of reactive species.

Exposure to pollution, chemicals, toxins and radiation may increase oxygen reactive species exposure.  Radiation exposure may include ionizing radiation or non-ionizing radiation  such as cosmic rays  (e.g. gamma rays ).  Geomagnetic storms  and reduced ozone layer  protection at polar regions as Antarctica and the Arctic may increase such exposure, with greater historical ozone depletion  over the Antarctic.

I photographed in Antarctica in November/December 2004, and in October 2006 and photographed in the Arctic in July 2005.  The year 2006 saw the worst levels of depletion (2004 Image-Halley Bay Station, Antarctica) in recorded history.

Cellular processes guide apoptosis, or programmed cell death under a number of circumstances, generating  an intrinsic pathway or extrinsic pathway for cell death.  Reactive species play key roles in this process, as signaling mechanisms, and also in promoting cell death, as free radicals generated by a variety of situations trigger apoptosis.

Mitochondria play a large role in enforcing 'group identity' in a cell. The mitochondria helps to sustain certain energy needs within the body and when certain system parameters (group identity system requirements) are not fulfilled, the process of apoptosis or programmed cell death is intended to kill off certain cells that do not meet those system parameters.

Mitochondria can be loosely or tightly coupled; this means that they can "leak" protons so that more heat is produced (uncoupled) relative to amount of ATP produced;  there are certain uncoupling proteins  that aid in this process, which decreases  the generation of potentially damaging oxygen radicals.  A highly coupled system will thus be more efficient in the generation of energy, less efficient in generating heat, and will generate more oxygen radicals, which can cause damage to the system.  A more loosely coupled system will produce more heat, will generate less oxygen radicals, and will be less efficient in generating energy.  A loosely coupled system will be more valuable in colder climates due to the greater heat protection.  A tightly coupled one will result in more conditions, such as diabetes, which are impacted by the generation of oxygen reactive species.

The generation of reactive oxygen species is a significant issue in DNA damage  and mutations involving mutagenesis.  Mitochondrial DNA (mtDNA) are much less protected from the generation of reactive species than nuclear DNA.  In the proverbial sense, they sit at the edge of the  oxidative phosphorylation 'fiery furnace' and absorb more damage than nuclear DNA.  Nuclear DNA has greater protection from reactive species, being protected by histones   and telomeres.

Mitochondria can be damaged by reactive species, however, there is a certain amount of punishment that mitochondria can take before a process called heteroplasmy  takes place. Heteroplasmy in the mitochondria is a process where, due to mutation, mitochondrial damage or other process, more than one mitochondrial genome can exist.  This process may be associated with mitochondrial disease and be more extensive the greater the degree of heteroplasmy.  However some individuals may live to long ages with some degree of heteroplasmy.

There is a basic problem with mitochondrial damage and mutation in so far as the mtDNA and the nuclear DNA interoperate in the OXPHOS process.  This is because, as mentioned earlier in the article, some mitochondrial functions ages ago were shifted into the nuclear DNA through the process of gene transfer.  Cytochrome C belongs to the cytochrome c family of proteins and is an integral part of the ETC.  Cytochrome C has a long history, which goes back to time periods when the Earth was subject to heavy amounts of radiation.  Illnesses associated with Cytochrome C may involve both nuclear DNA and mitochondrial DNA.

Since Nuclear DNA has greater protection than mitochondrial DNA (mtDNA) from the insult of reactive species, the degree of damage in each case will differ, or in the case of nuclear DNA, there may be minimal or no damage.  This will lead to interoperability issues as mutations and damage occurs. Interoperability is the ability of systems to work together.  As oxidative stress occurs at different rates and to different but  inter-operating parts of the cell (mtDNA and nuclear DNA), illness and damage occurs, and potentially mutations.  This occurs in systems requiring heavier use of energy, including muscles.  Respiratory muscles bear the burden of oxidative stress, as these muscles are those subject to the greatest use during sleep.  Sleep apnea may be associated with higher levels of exposure to oxidative stress.

As we are subject to greater and greater levels of substances that create oxygen reactive species, we can see that problems can add up.  There are greater and greater chances of damage and mutations, the probability of heteroplasmy increases, the levels of heteroplasmy in the cell may come closer to the levels of heteroplasmy that may be tolerated in the cell without incurring mitochondrial disease.

We can see, therefore, that exposure to reactive species such as environmental toxins and radiation may provide for mutations in both nuclear and mitochondrial DNA, that these processes may occur at different rates, and that past a certain point, mitochondrial disorders may develop as the result of such exposure. At the same time, mutations that are beneficial may sometimes occur, and mutations and damage that are harmful may indeed result.  The ability for mutations that are adaptive to occur may reflect the ability of the mitochondrial DNA and the nuclear DNA to inter-operate, which is statistically difficult, considering the conditions under which each of these processes work.

Thus any process which seeks to advance a species by introducing mutagenic factors via the use of the creation of oxygen radicals must take into consideration that mutations and damage may result in the process and that individuals may be harmed in such process.  Due consideration must exist for who is subject to such exposure, and when the risk of subjecting certain individuals to such exposure constitutes a material risk that makes such experimentation untenable in  a civilized society.

 The risks of exposure to reactive species increases with the degree and length of the exposure, impacting the risk of early morbidity and mortality. Mutagenesis is more effective when it occurs in germ line cells which can pass mutations, either favorable, or unfavorable on to the next generation

Where such experiments are conducted, they must be conducted in an ethical fashion, they must be done with full informed consent of those involved, they must adhere to the law of civilized nations, and the ongoing experience of such studies must be monitored and measured so that those involved are not unduly harmed and the patient population put at excessive risk.

It must be made abundantly clear that if our society depends upon mutations to adapt the species to future environmental (or other) challenges, that those who have been subject to environmental (or other) assaults for such purpose be treated with due respect, that their contributions be valued, and their condition be measured, monitored and treated. It is clear that what these individuals are doing on a collective basis is aiding the future development of humanity. They are test subjects in a process that will benefit others, later.

What are our future ecological and planetary challenges and how can we adapt to them?  How do these challenges impact our exposure to environment risks and how we deal with them?  These are all important issues.

The mitochondria, as a vital cog in the production of energy has a very important part of the story that must be told as we seek to deal with the environment, climate change and other planetary challenges that we face.

Leptin

Butter

I attended a lecture in 2008 about leptin signaling given at Harborview Medical Center through their research programs on diabetes, metabolism and obesity.  The lecture, although highly technical, was  interesting and it gave me plenty to think and read about.

Leptin is what is called a signal transducer.  A signal transducer is an extracellular  signaling molecule that activates a receptor inside or on the cell surface, initiating a series of events, biochemical reactions.    Leptin signaling is involved in a number of areas relating to the management of energy throughout the body, regulating or giving permission for the use of energy for a variety of vital functions.  As I read more about leptin, it led me into a labyrinth of other, associated issues.

Leptin is involved in signaling relating to mesolimbic (dopaminergic) reward centers, food, satisfaction, glycemic control, saiety and reproduction.  Leptin deals with long term energy storage, provision of energy to the brain and gives permission for the use of energy falling within its defined duties.  Intuitively, one wonders what happens if energy demands are requested for things that aren't associated with its associated duties.

Leptin acts to communicate to the Central Nervous System the availability of energy stores.  It acts to restrain food intake and induce energy expenditure, when necessary.   Leptin acts with other systems, such as the Sympathetic Nervous System,  and with factors such as thyroid hormone  and insulin,  in regulating energy use throughout the body and in insuring the thermodynamic  efficiency of skeletal muscle, for example.  Leptin is also involved involved in the cardiovascular system, for example in cardiac hypertrophy.

Leptin is increased, or up-regulated, in obese people.  It increases appetite, generates a low metabolic rate, decreases thyroid function and is impacted by sleep apnea  issues.  Dysregulation of leptin adversely impacts fertility.  Leptin acts on lipid and glucose metabolism.  Leptin also regulates bone metabolism.  This may serve to improve structure with increasing weight by regulating the allocation of higher density bone development.    Leptin resistance occurs during obesity when increasing leptin levels do not have an impact.

Leptin acts in the brain in a neuroprotective  fashion that may also impact memory.  Leptin may be necessary to protect the cell against cell death (apoptosis).

Leptin plays a key role in thermoregulation, working through diverse systems such as the brain's preoptic area and hypothalamus.  Studies in the brown adipose tissue (BAT)  of mice injected by virus indicated involvement of leptin in regulating BAT circuits.  Severely obese mice that lack leptin or its receptor show decreased BAT thermogenesis, and are thus challenged to maintain their body temperature and adapt to cold temperatures.

Leptin may be a key component in considering survival issues under a variety of scenarios or projections associated with climate change modeling.  It may react to a variety of seasonal (zeitgeber) cues, as well as sexual cues regarding melatonin , odor and reproduction.  It will react to hedonistic feelings regarding food, appetite and to the allocation of resources regarding shorter term versus longer term energy needs.

Leptin plays its role along with a host of other players in this complicated web of life.

Book Review:
Group Immunity Systems

 "From Bacteria to Belief: Immunity and Security by Dr Luis P. Villarreal, UC Irvine
in "Natural Security, A Darwinian Approach to a Dangerous World"
edited by by Raphael D Sagarin and Terence Taylor

Fractal Julia Design (creative digit image)

I attended a guest lecture by Dr Luis Villarreal, University of California, Irvine, given at the University of Washington . Dr Villarreal gave a very interesting talk about viruses, which got me interested in reading some of his work on the role of viral evolution in life.

Dr Villarreal's work appears in,  "Natural Security, A Darwinian Approach to a Dangerous World" Edited by Raphael D Sagarin and Terence Taylor.  The book discusses applications of security systems which exist in  evolutionary biology,  to solve security based problems in the risky world that we humans have to deal with.  In this blog post I discuss Dr Villarreal's article, in which he discusses immunity systems.  

Dr Villarreal develops his concept of group immunity based on bacterial models, discussing the colonization of genetic parasites such as viruses.  Systems bind individual units to the group using a "carrot or stick" approach to enforce group identity.   His model employs the term Addiction Model for this approach.  This model uses the term "antitoxin" for protective aspects of the system which draw and retain members, and "toxin" for aspects which are destructive or harmful to nonmembers or members who violate the group identity system rules. Together these aspects constitute a security system which is the basis for his discussion.

Biological based concepts are extended to higher level human biological models by asking how we identify members of a group, how we identify self versus foreign entities and how we respond to threats. Human cognitive sensory systems using visual or pheromone based cues are employed.   

Dr Villarreal tackles the very difficult topic of death of the individual for the good of the whole in the context of programmed cell death (apoptosis) where many cells must die in the process of developing a specific specialized tissue, giving specific biological-based examples.   He discusses the issue of genetic parasites which create an addiction state within a host cell whereby the host cannot lose the parasite and still remain alive.  Competition between group identity systems is also important as Dr Villarreal discusses how group identity systems may kill off individual E. Coli cells if one of them is co-opted by another organism.   

Dr Villarreal goes on to discuss adaptive immune systems.  He discusses the worm C. Elegans, whose neural system and ability to protect against endogenous retroviruses is of evolutionary interest.  He discusses the recognition of self versus foreign, the reigning in of an over-reactive immune system that erroneously attacks itself,and the development and training of group identity.  He discusses how evolutionary features of the immune system can be extended to the social activity of humans based on long standing biological evolutionary principles.

Dr Villarreal discusses the creation of a stable group identity system using sensory based systems that may exclude input from non-members.   "Colonization" and imprinting (of language or group identity) is described as a process through which group identity is established and maintained.  The assignment of meanings to words, through language, and the stability of memories are important in such systems.

Dr Villarreal's work is an interesting discussion of the use of evolutionary biology techniques applied to the phylogenetic "tree of life" and one is left wondering the extant implications for the "tree of the garden of good and evil".  

"Natural Security, A Darwinian Approach to a Dangerous World" can be found  through the California Scholarship Online and on Amazon, with interesting contributions from a variety of authors on the topic of natural security and biological based models.

Fractals 

Portion of a Mandelbrot Set

A fractal is an entity that exhibits a repeating pattern.  Many patterns in nature exhibit fractal phenomenon and computer simulations are used to generate fractal patterns artificially.  Natural phenomena such as coastlines  exhibit a fractal pattern, as the pattern displayed may be exact (self-similar) or perhaps just similar at various levels of detail or magnification.  Snowflakes and trees property of continuing detail at higher levels of magnification.  Because of this, fractals are considered "nowhere differentiable" because of their inability to be measured traditionally.

Fractals are used in many fields, including physics, biology, medicine and physiology, imaging and financial fields. Fractals may apply in economic contexts such as the stock market Standard and Poors 500 Index, when examining longer term patterns (years) vs shorter terms (months, days, intra-day trading).  Fractals may be used in cinema, advertising, graphic design and climate science .  Fractals are a beautiful representation of art in their own way, in the visual arts, including the Droste effect, which is a picture within a picture. 

Fibonacci numbers, the basis of the Fibonacci Sequence appears in fractal geometry in a wide variety of ways.  Fractal dimension is a measure used to quantify complexity.  It measures  how detail changes with scale and the capacity of the fractal to fill space.  Various definitions of fractals and mathematical indicators exist, including a definition by mathematician Benoit Mandelbrot  who characterized a fractal as an object whose Hausdorff-Besicovitch dimension  is greater than its topological dimension. 

Wikipedia lists the Hausdorff-Besicovitch dimensions of a number of common fractals, including the Koch snowflake, Sierpinski Triangle, Quadric Cross, Julia Set and the Boundary of the Mandelbrot Set. Values for natural processes such as  the Coastline of Ireland , Great Britain and Norway are listed, as are values for various Brownian motion and random walk processes.  Dimensions are shown for biological models such as Cauliflower, Broccoli, the surface of the Human Brain , and the Human Lung.  Higher numbers indicate increasing complexity.

Fractals may be use in diagnostic medicine and physiology.  For example, blood vessels may exhibit fractal characteristics, as may the lung and surface of the human brain.  Tortuosity, another metric, relates the ratio of the actual length of a curve or segments of a curve to the distance between the two ends. Tortuosity may also reflect the degree to which a curve crosses over itself.  
  
Tortuosity was used for characterizing animal trails of mites  with regards to Brownian motion pathways.  Fractal dimension and tortuosity may both be used in measurement of blood vessels, as is shown in this article from the medical journal PubMed in a study of pulmonary hypertension.  In that study, distance metric, a measurement of tortuosity, was statistically more significant than the fractal dimension in correlating clinical patient parameters with the particular metric.   This goes to show that the use of different metrics may produce differing correlations, perhaps a clue in itself to underlying characteristic studied.

Fractals  form the basis of many aspects of life and the world around us, igniting our curiosity, aiding our research, informing us, and conveying a sense of beauty, form and function.