Category Archives: Evolution

Water, Thermodynamics and Insight

Water, life’s solvent, is the current yardstick by which scientists use to characterize earthly life and is in part the basis for understanding the “Goldilocks zone.” As a result of life’s watermark, it is often assumed that where there is life—water is nearby. That statement, by itself, is more complex than most can appreciate. Early earth did not have “enough” of life’s present necessities—one primary element comes to mind, reduced phosphorous. When one looks for phosphorus—the primary form that is found is in oxidized form. Chemistry, as we know it, needs reduced phosphorus to readily form the phosphate groups in RNA and DNA. The elementary chemistry of nucleotides (that of RNA and DNA) is notoriously difficult in the laboratory—so much so that science at present cannot hope to fully elucidate the origin of life. The oceans of the early earth were far more conducive to forming life’s early molecules and possibly even more so at or around hydrothermal vents (a source of heat energy).

Reduced phosphorus is found in sedimentary layers of the Earth’s crust—and is a predominant mineral found in SNC –meteorites (meteorites that are primarily carbonaceous chondrules that contain iron-nickel-phosphorus minerals). The chemical nature of phosphorus on earth is such that it is in the predominantly oxidized form—as chemical thermodynamics dictates. Thus, examination of phosphorus “thermodynamic phase diagrams” indicates that early earth conditions (specifically during the Archean)—favored the reaction of reduced phosphorus with prebiotic soup of the time period.

In papers by Pasek and others, mounting evidence may point toward the Late Heavy Bombardment of the Archean era as one likely source for reduced phosphorus. Through the sampling of “archean sedimentary rock” it seemed as if prebiotic conditions were conducive to RNA-world life. The reasons for the hypothesis are time of the Late Heavy Bombardment, and presence of schreibersite (nickel-iron-phosphorus containing) meteoritic material in the sedimentary layers. Although further evidence is warranted so as to be conclusive, layers of sediment from Australia are indicative of reduced phosphorus being present.

(At the time of this writing, Dr. Steven Benner at University of Florida announced the intriguing hypothesis that life may owe its origins to Mars due to the relative paucity of water, and readily available metal ions needed stabilize early nucleotides; e.g. RNA and DNA.)—It should be noted that most SNC-meteorites originate from Martian crust.


Pasek, Matthew a, Jelte P Harnmeijer, Roger Buick, Maheen Gull, and Zachary Atlas. 2013. “Evidence for Reactive Reduced Phosphorus Species in the Early Archean Ocean.” Proceedings of the National Academy of Sciences of the United States of America 110 (25) (June 18): 10089–94. doi:10.1073/pnas.1303904110.

Pasek, Matthew a. 2008. “Rethinking Early Earth Phosphorus Geochemistry.” Proceedings of the National Academy of Sciences of the United States of America 105 (3) (January 22): 853–8. doi:10.1073/pnas.0708205105.

Citations regarding Dr. Benner’s announcement:

Pale Blue Blog– Men are from Mars and Women are from Mars, too? By: S. DOMAGAL-GOLDMAN.

The Guardian– Life on earth ‘began on Mars’ Geochemist argues that seeds of life originated on Mars and were blasted to Earth by meteorites or volcanoes. By: Press Association.


Life on Earth and its Tenuous Nature—One Instance

Without doubt researching astrobiological and science-based literature (while coming to a definition for life) and attempting a readable work might have turned into a tall tale.

What makes defining life so hard is the diverse, contrary, and seeming ease with which biological experimentation is performed. As some may atest, life exists in places that would seem inhospitable to the hardiest of souls. One place in particular is in the shallower waters off California at the Farallon islands (a former nuclear waste site). Although some current estimates put the amount of radioactive isotopes as negligible, we have placed ourselves in harm’s way so often to warrant introspection.

Fig. 1 Barrel and Crab from Farallon islands (figure is a composite—photo is available from the website listed in the following paragraph)—

From the website—( –I quote: More than 47,800 drums and other containers of low-level radioactive waste were dumped onto the ocean floor west of San Francisco between 1946 and 1970; many of these are in the Gulf of the Farallones National Marine Sanctuary. . . . The interagency cooperation among the USN, USGS, and Gulf of the Farallones National Marine Sanctuary has provided the technological, scientific, and practical expertise to develop a cost-effective and time-efficient method to locate the barrels of radioactive waste. This method can be used to locate containers of hazardous waste over a regional scale in other ocean areas such as Boston Harbor and the Kara Sea in the Arctic.

A technical report from the California Fish & Game Department (from 1986) tells of different species fish that have been seen to dwell at or near the dump site ( ). The report details that while some species exclusively dwell within a 100 mile radius of the site, there are other species of fish that make all the North American coast their “home.” By the lack of public outcry, it would seem that the three cited sources paint a benign picture of the site. And, a report authored by the USGS, NOAA, EPA and the British Geological Survey (2001) again paints the same ambiguously benign picture of the site—with the exceptions being a higher-than-normal amount of certain isotopes and the majority of dump was not or could not be accessed. All of this bears mention due to the recent news of “radioactive” tuna off the California coast ( ) because the blame is pointed at the catastrophic earthquake and tsunami in Japan in 2011) and the following news release ( ) points to a 2014-2016 peak of radioactive water reaching United States.

In spite of the furor spawned from the Fukushima disaster, we seem to ignore that there may have been prior precedent? It is as if one had overlooked past failure—only to repeat it in the near future. Further investigation reveals an article from the 1990 L.A. Times ( ) confirming the presence of radioactive waste off the coast of Northern California.

Analytically speaking, it is hard to place a specific causal factor for the tuna catch, but it should be noted that we really didn’t learn our lesson the first time around.

The reasons for the above approach is to demarcate the public perception of (1) how science fails to protect the public (2) how the public (in general) has lulled itself into a complacent state around science and education. The issue of the Farallon island nuclear dump
site was common knowledge to many in the San Francisco Bay Area in the mid-to-late 1970s; I can personally recall reading of the issue in the San Francisco Chronicle newspaper. My personal take (as a callow teenager) was that the incident was sensational and it had a certain coolness factor to it. Little did I know (as a 13 year old) of the implications to the food chain nor of the larger perspective to how science can serve the public interest. But, where and how didn’t the public as a whole or the “govt” protect us more fully from ourselves? It may take a village to raise a child—but who teaches the village to think—other than the previous villagers? The inane nuances of the problem points to an “almost catastrophic breakdown in the normal functioning of society.”

I am not faulting the generation that believed in “Atoms for Peace,” but this news item came about during the height of 1970s environmental movement—a full twenty years after President Eisenhower’s ground breaking proposal.

The above work was what I had been laboring on—before realizing that I personally did not have the answer. . . .

One may ask in what way do the above paragraphs pertain to the astrobiological nature of life—it is just one view of possibly “billions and billions” of which I need to fully understand. It reminds me of the riddle of the raven—how do you know that all ravens are black? You assume that all will be black—and to prove otherwise may(?) take multiple lifetimes.

Follow-up post

As  I worked through parts of my Saturday and very early Sunday morning–I realized that I that I don’t know the answer. I respectfully refer you to the following link:’s_working_definition.html


I apologize —

PREVIEW for Saturday’s post: Further Defining Life

Finding a consensus for a working definition of life is among the hardest problems which astrobiologists tackle; for every nuanced school of thought there seems to exist a different definition. For those who don’t understand—

Take the following result as an example (using Google scholar):

Note that the search took less than a tenth of a second to produce 14,000 results. The current state of cutting edge research does not fair better (as the comments to my previous post may be indicative), and some mainstream scientists would insist that to define life exposes science to the “slippery slope argumentation of theology.” And, what is meant by the terms slippery slope is the definitions become devoid of empirical evidence (and meaning)—which is a cardinal sin in the pantheon of science.

So, can we give new insight to the scientific definition of life? Perhaps, we should look at how various scientific disciplines define life and the way the in which definitions are utilized.

concluding on Saturday (8/31/2013)



Fig 1. STS 132 –May 14, 2010. Launch pad 39 Cape Kennedy. Source URL:

(Retrieved 6-28-2013).

So it has been more than 50 years since the Sputnik launch—there have been both milestones and setbacks. And, if we can take one thing and put it in our proverbial books of wisdom—it would be to learn how to continually better ourselves. However, each subsequent generation seemingly experiences identical growing pains that the previous generation experienced. These growing pains may be summed in the following pithy aphorism—failing to learn the mistakes of history forces one to repeat similar mistakes ad nauseum. Life, in general, seems cyclical whenever the subsequent generation does not successfully learn from previous generation.

Fig 2. Some Medical Objectives of Skylab Mission and their interrelationships, a briefing chart used at NASA Headquarters In 1971. ML7 1-5271

Source URL: (Retrieved 6-28-2013).


The way to the stars is paved with a lot of growth and no one “seems” to like the pain associated with the eventual golden opportunities of space. Quite a few sacrifices have been given to the citizens of the world—and here is one that bears mention: Biosatellite program of the late 1960s.

I happened to find mention of the program during my research for the post—and it is both important and (definitely) heartbreaking for animal lovers. As most of us know—the first life into space were animals. And, the early days of manned-space flight were indicative that our evolution had not prepared us for our aspirations. Exploration of other planets and a permanence in the Solar System required different thinking. [The problems which “man” would have encountered on a trip to Mars (circa 1975) would have made the Challenger and Columbia disasters look like a day at the local playground by current standards. As an illustration of just one possible problem in low-gravity (the perception of tumbling motion)—I draw upon Neil Armstrong’s account of this “emergency” during Gemini VIII (8) –not Apollo. During the first docking maneuver ever performed—an engine (of Gemini VIII) continuously (miss)-fired and sent the capsules “rolling and yawing.” Armstrong reportedly described not possessing the ability to find the appropriate controls that (normally) were in his field of vision. At Mission Control—his pulse recorded 156 and his reflexes could not respond to the rolling and yawing motion of the capsule.] The physiological mechanisms of Armstrong’s responses are a complex set of neurological patterns that have been hard-wired for our Earthly benefit. I believe the description of Biosatellite program (satellite number 3) that follows below is a chilling reminder of just a “smattering of what awaits the un-prepared.”


The preliminary findings were published in the journal Science. A healthy macaque monkey was trained for a 30 day orbit of Earth. There were only two specific tasks which were duly rewarded with food: (1) “a delayed matching of symbols (DM task) and (2) a test of eye/hand coordination of two rapidly rotating objects (VM task).” The macaque performed them flawlessly pre-flight—but the monkey failed ‘miserably’ once the satellite was off the ground. The macaque did manage to eat almost continuously while in orbit—and the monkey show to be fairly alert for the most part until day 8. On that day the macaque displayed the a marked slowing of heart rate, a slowing of brain waves similar to sleep (while still awake), a sharp drop in blood pressure, and a fall in brain temperature—all indicative of a comatose state. The experiment was halted and the capsule commenced “re-entry.” Recovery operations were promising at first— Within the twelve hours of recovery, the macaque showed signs of a “want” to amble (walk like his fellow monkeys) but the effects of the flight were too severe. The macaque perished soon afterward.

Autopsy results showed little—but all the data from the flight were indicative of an extreme response due to weightlessness. The macaque had been restrained in a “sitting position” throughout the flight—to make matters even more revealing.


We long for the stars—why? Perhaps it is our true destiny. However, as the trail-blazing experiments show, we as a species have more to overcome than meets the eye at first blush.




Adey, W. R. (1969). Biosatellite III: Preliminary Findings, Science. 166, 492-493.

Wagner, B. M. (1971). Beyond the moon some problems in space medicine, Journal of Clinical Pathology. 24, 289–294.

An Intriguing Subtlety of Porphyrin Bio-Chemistry—Part II

The intriguing chemistry of porphyrins comes, in part, from the seemingly ease of synthesis with simple starting materials. Many University-level chemistry majors perform the lab work in their elementary sophomore/junior classes. The lab work is an adaptation of Paul Rothemund’s synthesis from 1935. A simplified (?) reaction scheme is illustrated in Fig. 1: (The beauty of the scheme is the “set-up” takes place in one reaction “vessel.” The major drawback is the low amount of desired product at the end of the lab.) The low “yield” at the other end (of the equation) seems to characterize a majority of attempts to emulate nature (?) in one reaction vessel. The reason for the statement is—try to imagine the length of time in which “life” itself seemed to utilize porphyrin-like structures—early bacteria utilizing chlorophyll or porphyrin-like structures. According to most estimates—it is in the ballpark of 500,000,000 years (1/2 of a billion years). The illustrated reaction takes approximately 30 minutes to complete—or one lab session.

Fig. 1 Source Wikipedia—One “pot” synthesis of a porphyrin

The attempts to understand (or bio-mimic) nature hinge upon certain aspects of classical chemistry (e.g. thermodynamics—the study of heat, temperature, energy and “randomness or dis-order.”) The important aspect of “randomness” is better termed—entropy. In a nutshell, entropy is a (major) controlling factor which might be stated: as time goes by . . . disorder increases. Entropy is a difficult concept (in part) because most of us think of the world as being readily determined—without complication. (Aside: entropy is just one reason why an internal combustion engine may get only 35 miles to a gallon of gasoline while it should, hypothetically, attain 45 miles to the gallon.)

The subtle bio-chemistry that utilizes porphyrins for respiration or sensory processes evolved a long, long time ago—it may not easily surrender the mechanistic detail of its origins. However, piecing the puzzle of our origins is a magnificent journey that appreciates with time.


References and Links:

Porphyrin lab synthesis

  • P. Rothemund (1935). “Formation of Porphyrins from Pyrrole and Aldehydes”. J. Am. Chem. Soc.
    57 (10): 2010–2011. doi:10.1021/ja01313a510.


Thermodynamics for all

  • P. W. Atkins (2010). The Laws of Thermodynamics: A Very Short Introduction. Oxford University Press.

    (Available from Amazon or Barnes & Noble)


An Approach to Physical Law

  • R. Feynman (1964). The Character of Physical Law (The Messenger Lectures). MIT Press.

    (Available from Amazon or Barnes & Noble)