Category Archives: Chemistry

Glyphosate, Pesticides, Industrial Poisoning and Resulting Neurological Effects? — and Questions Un-Answered?

Introducing pesticides into agriculture saved countless lives by feeding many of the poorest of the poor. Bountiful harvests have been the hallmark of the late 20th century and part way into the 21st as well. However, there appears an unwanted, if not horrific, effect of pesticides upon human physiology and health.

The pesticides such as glyphosphate (RoundUp [TM] ) and organo-phosphate pesticides (insecticides) are strongly implicated in the physiological and neurological problems in new borns. The evidence strongly suggests that children born of farm workers and children exposed in urban settings (in close proximity to household pesticides) to lice and roach treatments suffer disproportionately in contrast to their more affluent peers.

While the ag-business may not subscribe to such data or conclusions, there may have been  reasons  for the skepticism. In the 1970s, glyphosphate was invented, and much data was generated on the toxicity of the chemical. What was known in that time period was the rapid degradation of the herbicide. It would rapidly degrade in sunlight and seemed to pose little if any harm (references at the end of the post). Thus, it seemed as if the ag- business had invented a miracle —a truly non-toxic herbicide.

That news was greeted by most as cause for celebration, since Agent Orange was a debacle of the Vietnam War (in the early-to-mid 1970s). Many an American Veteran returned from  Vietnam with mysterious symptoms that seemingly defied medical description. All too often, I heard from my uncles, who served during WWII and Korea–it made no sense that they had been exposed to quite a few industrial chemicals during their tours but showed no ill effects. Moreover, their newborn children seemingly escaped harm. — or did they?

A Case of Voodoo Science? –Oral History or Coincidence?

Although the data seems quite spurious and anecdotal, what needs to be investigated— the links between past exposures to generational ancestors and the present day alterations  to the human genome. WWII saw numerous countries turn their economies into war machines–industrial centers like SF-Oakland Bay Area and Detroit, Michigan turned much of their industrial waste back into the Pacific Ocean or the Great Lakes. Much of the industrial area roadways became breeding grounds for chemical sterility. Higher levels of Pb (lead), Cr (chromium), As (arsenic) and other elements are found on the freeways of inner urban areas. It does not take a rocket scientist to surmise — we poisoned our inner cities– but no one understood why aspects of crime, economics, and poor school performance became the hall-marks for their areas. While other factors make it plain that the areas were neglected due to indifference and lack of small business attractiveness–there were other (so-called) reasons.

What may need  to be answered is: how did past toxic chemical exposure (two to three generations prior) affect the whole human genome as we now know it? Is the question relevant or is it ‘fear-mongering’? 0r Is it Voodoo Science?

The Science Speaks!

What can be said for certain– “….  (glyphosate) use has increased approximately 100-fold since the first decade of its use in the 1970s.  … Initial risk assessments of glyphosate assumed a limited hazard to vertebrates because its stated herbicidal mechanism of action targeted a plant enzyme not present in vertebrates. … ”  –taken from:

National Institutes of Health  — Review article:  Concerns over use of glyphosate-based herbicides and risks associated with exposures: a consensus statement

Link between hazardous chemicals and neurological problems — Opens up to YouTube lecture from the University of California, Davis, MIND Institute

Industrial Chemicals and Autism Link — Epidemiological studies    — Exposure studies

environmental study    Metabolism and Degradation of Glyphosate in Soil and Water (1976)


Pesticide Exposure and Effects on Estrogen Receptors — Biochemical study

Toxic Pesticides of the Late 20th Century — Opens up to article



Early agriculture

By Deutsch: Maler der Grabkammer des Sennudem English: Painter of the burial chamber of Sennedjem [Public domain], via Wikimedia Commons




Uneasy Reality of the Zika Virus

The Zika virus promises a new reality for the USA and ‘the rest of the world.’ The virus will be infecting more individuals in the coming months, and ‘the true tragedy’ becomes apparent for those not infected by the virus.

Many of us will do our best eliminate standing water and ‘dangerous hot spots.’

Otherwise, ‘some encouraging words’ come from the researchers–


Purported MECHANISTIC DETAILS of Zika’s Infection in humans and in animal models:

The word mechanism implies that researchers, doctors and most of the ‘informed community’ understands how the virus infects ‘new borns and adults.’ It is also called a ‘mode of action’ — in some circles.

The impaired neurogenesis (in the fetus) is the focus of research and the impaired growth of  ‘neural stem cells.’ The virus causes what is termed as apoptosis–a death of cellular material. The precise ‘chemical mechanism’ is unknown… if it were known, the scientific community would know the best approach for deterrence. The public is justifiably upset, skeptical, confused and frightened. However, research is a slow and a precise affair in which progress –is marked by ‘repeatable and accurate experimentation.’

The entry point for the virus can happen at multi-sites –and can happen before, during and after ‘egg fertilization.’ The placenta– a safe haven– is, in this case, susceptible. The plea to the public is–be safe and minimize potential exposure.

Treatment Options (Future)… Detection? Vaccines? and Potential Therapies?

Presently, some in the medical community believe it will find a vaccine within two years while others speculate one year and even three years. The discovery of a vaccine hinges upon poorly understood aspects of the viral replication cycle and diagnosis of infection — an intimate knowledge its bio-chemical and mechanistic details is needed.

Diagnosis of viral infection has returned false negatives in some instances–a terrifying outcome. The reasons for diagnostic problems arise when one understands that Zika–is an arboreal virus– it is similar to Dengue Fever and West Nile with its mode of infection. Mosquitos, the culprits for much death, can carry other viruses. That is a challenge we face…

Presently, the medical community believes its best chance to contain the spread of the illness is through vaccination.

A vaccine for Zika is pursued in at least three ways: targeting DNA replication of Zika, modifying live viruses of Zika and modifying inactive Zika virus. There are a number of different strains of the Virus. Namely, the original 1947 virus (less problematic to people) transformed– aspects of its biochemistry changed from the Zika River Valley in Africa to its infectious form of 2007-08 Micronesia and the present infection of the  Americas.

How a virus transforms  would go far in understanding how to treat the infection. That type of mechanistic detail would expedite the path to vaccination and therapy.

Therapies, presently, are in planning stages. One route of investigation subverting viral replication —

The immuno-suppressor, Rapamycin is one potential candidate for therapeutic success. It subverts the immune system and may interfere with a viral replication.

ChemSpider 2D Image | Sirolimus | C51H79NO13

The anti-biotic macrolide, Rapamycin is a therapeutic candidate for Zika infection. The therapy is in the beginning stages of research. It may be awhile. Credit for Image Chemspider

As with many candidates such as Rapamycin, it is a ‘hot compound– toxic to many vital organs.’ However, in the war against pathogens, humanity can not afford to rest…



Adapting the Stess Response: Viral Subversion of the mTOR Signaling Pathway

The Global Zika virus to pregnancy: epidemiology, clinical perspectives, mechanisms, and impact





Growing Crystals—brief post with link to NY Times

To the un-initiated, crystallization and re-crystallization of a ‘organic molecule’ ignites enchantment and frustration. Enchantment ignites the soul as the molecule ‘drops’ out of solution to re-form a stable state of matter. Frustration tempers the impulse to flee the lab bench while a reticent crystal produces oil after oil rather than the ‘sharp-display of symmetric plates.’ Thus, it bears to be said, crystal-growing needs to be a part of every scientist’s training.

While the growth of crystals produces wonder to the imagination of the student-scientist, watching crystal growth done by a professional induces a sense understanding. The understanding of why we wish to understand nature’s secrets, it is a fundamental desire—a love for the cosmos.


Shuttle Experiments Seek Clues to Building Blocks of Life






LUCA—What does it mean and why is it important? Ruminations upon Life’s Origins

The acronym LUCA stands for—Last Universal Common Ancestor. The term is used by astrobiologists and those interested in the evolutionary biology. The geological period of time in which LUCA existed was a point of demarcation from primitive life forms to more-advanced earth-living entities. The importance of LUCA lies in understanding how the three kingdoms of life came from a universal ancestor.

Description from Source: A phylogenetic tree of living things, based on RNA data and proposed by Carl Woese, showing the separation of bacteria, archaea, and eukaryotes.

Original Source: NASA Astrobiology Institute Attribution: By MPF [Public domain], via Wikimedia Commons

URL Source:

You might ask, why is LUCA so important? (brief interpretation)

Glancing at the phylogenetic tree one gains a sense that there may be a commonality or root to everything. ( It is not an oversimplification as much as it is a functional, mnemonic device.) So for sake of argument, the center point of the tree may be the point of LUCA—the point where red, black and purple branches form a ‘Y.’ It is at the point where RNA-life may have taken the first steps to ‘current’ DNA/RNA commonality. (It would be obvious—to evolutionary biologists, at least—that gaining an understanding of LUCA is tantamount to taking the next step backward to the origins of life.) The complex machinery in present DNA/RNA is like a ‘black box’ problem—one knows what goes in and what comes out–but the manner (or mechanism) is unclear. LUCA is a point of ‘transcendence,’ it is in essence a step in the evolutionary ladder. (Once the mechanism is discerned, the understanding may be harnessed for the betterment of the human condition.) Current evolutionary paradigms utilize a random mutations as a means by which ‘the paradigm advances.’ However, random mutations may literally take eons of time until the fit survive the next step of evolution.

It may be the case where an understanding of the transcendence of RNA life to DNA/RNA informs the human condition of how to better utilize life for itself and its progeny.

Source for thoughts and further introspection:

Frontiers of Astrobiology, edited by Impey, Lunine and Funes

Cambridge University Press, 2012

Brief notes on viruses

Virus: ‘A piece of bad news wrapped in a protein’

-Sir Peter Medawar

Source: Wikimedia

Diagram of the HIV virus. US National Institute of Health (redrawn by en:User:Carl Henderson)

U.S. Gov URLs:


It is no secret that viruses are a bane of modern life—prior to the Bird Flu, Ebola, and HIV most individuals did not put much worry in catching a cold nor the influenza. However, the arrival of HIV in the late 1970s opened the eyes of many people—(and HIV’s source seemingly came from ‘monkey meat.’) While all along, the question as to whether viruses were a form of life was hotly debated and still remains partly solved (with the mainstream regarding viruses as non-life). Truth be told, the definition of life is a thorny issue to the majority of biologists.

The lack of understanding of viruses plagues the field of astrobiology as well. Googling the terms—viral life and astrobiology will nearly turn up an empty cache. One other remarkable fact is the number of viruses are said to outnumber bacteria by one order of magnitude. (Estimates put the number of viruses at 1031and the number of bacteria at 1030. That is the number 10 with 31 zeros behind it.) Any place there is humanity, you may well find a virus feeding as a parasite. In fact, there are viruses that feed on other viruses.

The discipline of astrobiology is studying viruses, and it may help discern the puzzle of fossilized life on the side (see note at end of post). However more to point, I will speak of ‘virus fundamentals.’ Viruses trick their host into ‘believing’ that their chemistry is a part of host’s biochemistry. The virus will attach itself to the ‘wall of its host’ and insert its DNA (or RNA) to make more copies of itself. It is correctly pointed out that viruses play a prominent role in life’s present and past evolution. (Viruses have been a part of the Earth’s biology since near the beginning of life.) And, it is pointed out that by finding ET-viruses it will help us to understand how life may have arisen elsewhere. That argument is put forth because viruses are now found in archaea, the bacterial communities that survive under extreme conditions. It has also has been reported that archaeal viruses may survive for extended periods by coating their exteriors with a glassy silica (related to sand).

The likelihood of finding ET-viruses is one which intrigues the astrobiology community. However, scenarios posed show a murky picture at best. If viral entities are found everywhere, it may be nearly impossible to discern ‘infected-life’ from ‘non-infected-life.’ Further clouding the scenario is the mainstream view that viruses are not alive but collections of chemical bags that bear little similarity to conventional life.



Matti Jalasvuori, Anni-Maria Örmälä and Jaana K.H. Bamford (2009). On the astrobiological relevance of viruses in extraterrestrial ecosystems. International Journal of Astrobiology, 8, pp 95-100. doi:10.1017/S1473550409004479.

Griffin D.W. (2013). The quest for extraterrestrial life: what about the viruses? Astrobiology. 2013 Aug;13(8):774-83. doi: 10.1089/ast.2012.0959.

REFERENCE related to fossils and biosignatures: &

Laidler, J., Shugart, J., Cady, S., Bahjat, K., Stedman, K. “Reversible Inactivation and Desiccation Tolerance of Silicified Viruses.” J. Virol. 10.1128/JVL.02825-13.





‘Space age innovation’

Space Shuttle Atlantis's three Block II RS-25D main engines at liftoff during the launch of STS-110. This image was extracted from engineering motion picture footage taken by a tracking camera. Source URL:

Space Shuttle Atlantis’s three Block II RS-25D main engines at liftoff during the launch of STS-110. This image was extracted from engineering motion picture footage taken by a tracking camera.
Source URL:




The retired-Space Shuttle program (like its predecessor Apollo) ushered much innovation to the public. And, if one were to ‘google’ the terms, nasa spinoff database –one may get lucky enough to see a lot of which many take for granted. The database is chock full with the ‘fruits of our labor;’ we truly hit the proverbial jackpot by going into space. For instance, I draw attention to the utilization of ‘photochemistry;’ to those of us who are not familiar with the terminology I give a quick definition:

Photochemistry is utilizing light (e.g. the Sun) to generate a desired (or needed) outcome. Sounds simple enough. . . .

When we do trek beyond our solar system, it may be necessary to grow foodstuffs. Sunlight has guided our days and helped to fill our nights with dreams. So, in the quest to grow foodstuffs, we are learning to utilize artificial light sources aboard the shuttle and the ISS. The ‘spinoff’ of utilizing light stands to benefit us in many novel ways—

From the NASA technologies website:

Red light-emitting diodes are growing plants in space and healing humans on Earth. The LED technology used in NASA space shuttle plant growth experiments has contributed to the development of medical devices such as award-winning WARP 10, a hand-held, high-intensity, LED unit developed by Quantum Devices Inc. The WARP 10 is intended for the temporary relief of minor muscle and joint pain, arthritis, stiffness, and muscle spasms, and also promotes muscle relaxation and increases local blood circulation. The WARP 10 is being used by the U.S. Department of Defense and U.S. Navy as a noninvasive “soldier self-care” device that aids front-line forces with first aid for minor injuries and pain, thereby improving endurance in combat. The next-generation WARP 75 has been used to relieve pain in bone marrow transplant patients, and will be used to combat the symptoms of bone atrophy, multiple sclerosis, diabetic complications, Parkinson’s disease, and in a variety of ocular applications. (Spinoff 2005, 2008)

A major innovation (IMO), however, is the ‘direct’ utilization of light in cancer chemotherapy. A few years back, scientists recognized that certain drugs are active only when shined upon by light—so in other words, if one were to give a cancer patient a drug—it would act against the cancer cells when ‘shined upon.’ Thus, the targeting of cancer cells (in certain cases) became more efficient. (see the cited Nature article at the end of the post)

Most of us utilize space age technology and conjure our own versions of the technology, as well. For instance when one looks at instances of invention, one notices a cluttered path (at times). It is at those times we gain a sense of personal innovation and possibly inspiration. What could be more inspiring than to gain a mastery over the natural world? Science and engineering journals display articles of genius, innovation and refined curiosity.

Often it is not that one has a good idea—we may stumble while implementing the idea. So, given a fertile environment, I contend that we become innovators and tinkerers within our realm. I further contend we can become innovators in wider circle of influence (beyond ourselves) if we desire to do so. The path, then, cannot be so liberally littered by our personal insights as much as getting to the gist of all concerned. Moreover, we need a clarity of purpose.

Ideas become reality in instances where one stands upon the shoulders of giants.


Specific cancer citation– : Cancer cell-selective in vivo near infrared photoimmunotherapy targeting specific membrane molecules Nature Medicine 17, 1685–1691 (2011) doi:10.1038/nm.2554 (the lead author(s) for the work–Hisataka Kobayashi)

READINGS LIST (in no particular order)

Costa, Liliana, Maria Amparo F Faustino, Maria Graça P M S Neves, Angela Cunha, and Adelaide Almeida. “Photodynamic Inactivation of Mammalian Viruses and Bacteriophages.” Viruses 4, no. 7 (July 2012): 1034–74. doi:10.3390/v4071034.

Goodrich, R P, N R Yerram, B H Tay-Goodrich, P Forster, M S Platz, C Kasturi, S C Park, N J Aebischer, S Rai, and L Kulaga. “Selective Inactivation of Viruses in the Presence of Human Platelets: UV Sensitization with Psoralen Derivatives.” Proceedings of the National Academy of Sciences of the United States of America 91, no. 12 (June 07, 1994): 5552–6.

Kiesslich, Tobias, Anita Gollmer, Tim Maisch, Mark Berneburg, and Kristjan Plaetzer. “A Comprehensive Tutorial on in Vitro Characterization of New Photosensitizers for Photodynamic Antitumor Therapy and Photodynamic Inactivation of Microorganisms.” BioMed Research International 2013 (January 2013): 840417. doi:10.1155/2013/840417.

O’Brien, J M, D K Gaffney, T P Wang, and F Sieber. “Merocyanine 540-Sensitized Photoinactivation of Enveloped Viruses in Blood Products: Site and Mechanism of Phototoxicity.” Blood 80, no. 1 (July 01, 1992): 277–85.

Novo, E, and J Esparza. “Tetracycline-Mediated Photodynamic Inactivation of Animal Viruses.” The Journal of General Virology 45, no. 2 (November 1979): 323–9.

Simonet, Julien, and Christophe Gantzer. “Inactivation of Poliovirus 1 and F-Specific RNA Phages and Degradation of Their Genomes by UV Irradiation at 254 Nanometers.” Applied and Environmental Microbiology 72, no. 12 (December 2006): 7671–7. doi:10.1128/AEM.01106-06.

Vigant, Frederic, Jihye Lee, Axel Hollmann, Lukas B Tanner, Zeynep Akyol Ataman, Tatyana Yun, Guanghou Shui, et al. “A Mechanistic Paradigm for Broad-Spectrum Antivirals That Target Virus-Cell Fusion.” PLoS Pathogens 9, no. 4 (April 2013): e1003297. doi:10.1371/journal.ppat.1003297.