Category Archives: Biology

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—(http://walrus.wr.usgs.gov/farallon/radwaste.html) –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 ( http://aquaticcommons.org/722/1/Technical_Report_1987_No._55_A.pdf ). 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) http://pubs.usgs.gov/of/2001/of01-062/ 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 (http://www.huffingtonpost.com/2013/02/22/radioactive-fish_n_2743899.html ) because the blame is pointed at the catastrophic earthquake and tsunami in Japan in 2011) and the following news release ( http://news.yahoo.com/fukushimas-radioactive-ocean-plume-reach-us-waters-2014-132118620.html ) 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 ( http://articles.latimes.com/1990-11-19/news/mn-3595_1_radioactive-waste ) 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.

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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:

 

http://www.nasa.gov/vision/universe/starsgalaxies/life’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)

An attempt to understand our Origins


raisons d’être?

Humanity, for the most part, thrives day-in-and –out; they respond, act, adapt, grow, and perhaps learn anew after reflection. Why? How?

What I mean is that most lives are neither meaningless nor without tedium and pain. Those contrasting words signify a larger context in which a person resides—the reasons for life, perhaps? A reason to explore, a reason to learn, a reason to make mistakes, a reason to make war, and a reason to love, as well . . . and in my humble opinion, they are the reasons for life. Perhaps when one attempts to look at their own life, he-or-she may recognize the interconnectedness between moments and individuals. And, when finding the connections on an occasion or two, one may see the grander scheme—raison d’être. (To the science purists—please bear with me.) Whether life originated (for the aforementioned reasons) to affect a grand purpose, the tenets of science currently cannot answer; the approaches to science do not address the notions of “why.” Pure science asks how a phenomenon occurs, what are the interconnections between related phenomena, and eventually—can we harness the phenomenon. The question of “why” lies within the realms of philosophy, ethics, theology, and on occasion, organized religion. When a scientist conducts experiments in an attempt to elucidate certain biological processes associated with Life’s origins, many of us will associate the results and conclusion of the experiment with the concept of “why.” Careful reading of an experimental “write-up” in a journal reveals that “good” science practice never asks “why.” (Perhaps, “why” is a part of our genetic make-up?)

Thus, perhaps no one can readily awake each-and –every-morning and “truly” ask themselves “why” without coming to a realization that to ask why—one must ask: for whom?

Getting past the notions of “why” and “for whom” leads many to eventually ask “how.”

How?

Studying life’s origins is a harsh mistress—the reasons being the depth and scope of subject matter with which one needs to have mastery. Astrobiology is a “new” field and its golden age may not be fully realized until ET life (or fossilized ET life) is discovered with no uncertainty. A specific case study is ALH 84001 (the Alan Hills meteorite), when NASA scientists announced that specific discovery—few armchair astronomers and much of the general public wanted to believe in the veracity of the report. At first, I had many mixed feelings and finally settled upon believing upon its veracity. However, many skeptics denounced the manner in which the finding had been publicized—and it has served them well. Towards that end, there were certain NASA scientists who went out on a limb (so to speak) and performed experiments that seemed to dovetail with the findings—and therein lies the problem. The callow reader cannot reasonably discern whether the “control experiment” was published in the journal article along with the purported result. That, in some ways, is the reason why many of us may have been fooled into “blindly” falling into the “appeal to authority fallacy.” Many of us, perhaps, felt that we were following an “Occam’s razor” form argumentation—however if one re-reads some of the more prominent journal articles of that period—the control experiment was not readily discerned. The “microscopic” images purported to be bacterial had no true control—and the best (and possibly the truest) control would be to venture to Mars and sample similar “rocks.” Case closed and proof or dis-proof —and science marches-on.

Everyday astrobiology is practiced in multiple and interdisciplinary settings by individuals who have a deep-seated drive to understand the foundations of life on Earth and elsewhere. Successful astrobiologists take their cues from the interdisciplinary nature of the discipline—thriving on the diverse characterizations of the science from other astrobiologists.

Life . . . how did it all begin?

The question of life is “thorny.” Why? The answer is simple enough to seem too trivial. No one was present to understand the processes—but current geology is far different from the origins geochemistry. However, what may be surmised is that “first life” chemistry may have resembled early Earth geochemistry, and because of weathering and plate tectonics many potential fossil remains are lost.

What can currently be said?

Since attempts to emulate life’s origins have failed—what have systematic efforts revealed: (1) Darwinian evolution is the rule of order, (2) RNA World is one primary paradigm of Life’s Origins, (3) given current knowledge—life (and evolution itself) may be based upon information theory—and I will attempt expound upon the aforementioned points—

The above-points are a “synthesis” of 60-plus years of “Origins research”—from the Miller-Urey experiments of 1950s to “Neural Darwinism” and “Information Theory paradigms for Life” of the present generation—so

Can Meaning be Extracted?

The gap between “chemistry” and “origins biology/chemistry” is far greater than most are able to imagine—chemical reactivity and its processes do not adequately approximate how inanimate matter (carbon-based molecules of life—CHNOPS) could have organized and re-produced in life’s fashion. And, as with most problems that appear intractable, solutions lie outside of the box. A recent solution by Walker, Davies, and others posit that life may be no more than an algorithmic process—in essence, life may be characterized in a “pseudo-top-down-bottom-up-algorithm.” Molecules and the processes of life take shape as bits of information, and “life” and “environment” with its “evolutionary complexity” interact in the following way—

The chemical and physical processes of life form an initial “scaffold” or “architecture” from which evolutionary processes take form. Information and its instructions (molecules and processes) communicate with each from-the-top-down, as well as, from-the-bottom-up possibly due to environmental forces. The origin of life may (?) be formulated when the scaffolding responds to outside forces “conservatively.” Thus, a utilization of standard thermodynamic laws, in effect, precludes the un-raveling of the scaffolding, and original scaffolding responds to outside forces through the “internal algorithm.” Evolutionary changes occur to accommodate the given architecture of life from outside forces (e.g. physical processes: temperature, climate, or over-population).

Thus, the original molecules of life—as important and fascinating they may appear—would have (for the time being) reacted in the same manner that molecules react today, but as most synthetic chemists may attest—the products of any reaction depend the initial and final physical conditions.

__

REFERENCES

Fernando, Chrisantha, Eörs Szathmáry, and Phil Husbands. 2012. “Selectionist and Evolutionary Approaches to Brain Function: a Critical Appraisal.” Frontiers in Computational Neuroscience 6 (April) (January): 24. doi:10.3389/fncom.2012.00024.

Abstract
We consider approaches to brain dynamics and function that have been claimed to be Darwinian. These include Edelman’s theory of neuronal group selection, Changeux’s theory of synaptic selection and selective stabilization of pre-representations, Seung’s Darwinian synapse, Loewenstein’s synaptic melioration, Adam’s selfish synapse, and Calvin’s replicating activity patterns. Except for the last two, the proposed mechanisms are selectionist but not truly Darwinian, because no replicators with information transfer to copies and hereditary variation can be identified in them. All of them fit, however, a generalized selectionist framework conforming to the picture of Price’s covariance formulation, which deliberately was not specific even to selection in biology, and therefore does not imply an algorithmic picture of biological evolution. Bayesian models and reinforcement learning are formally in agreement with selection dynamics. A classification of search algorithms is shown to include Darwinian replicators (evolutionary units with multiplication, heredity, and variability) as the most powerful mechanism for search in a sparsely occupied search space. Examples are given of cases where parallel competitive search with information transfer among the units is more efficient than search without information transfer between units. Finally, we review our recent attempts to construct and analyze simple models of true Darwinian evolutionary units in the brain in terms of connectivity and activity copying of neuronal groups. Although none of the proposed neuronal replicators include miraculous mechanisms, their identification remains a challenge but also a great promise.

Joyce, Gerald F. 2012. “Bit by Bit: The Darwinian Basis of Life.” PLoS Biology 10 (5) (January): e1001323. doi:10.1371/journal.pbio.1001323.

Abstract
All known examples of life belong to the same biology, but there is increasing enthusiasm among astronomers, astrobiologists, and synthetic biologists that other forms of life may soon be discovered or synthesized. This enthusiasm should be tempered by the fact that the probability for life to originate is not known. As a guiding principle in parsing potential examples of alternative life, one should ask: How many heritable “bits” of information are involved, and where did they come from? A genetic system that contains more bits than the number that were required to initiate its operation might reasonably be considered a new form of life.

Joyce, Gerald F. 2002. “The Antiquity of RNA-based Evolution.” Nature 418 (6894) (July 11): 214–21. doi:10.1038/418214a.

Abstract
All life that is known to exist on Earth today and all life for which there is evidence in the geological record seems to be of the same form–one based on DNA genomes and protein enzymes. Yet there are strong reasons to conclude that DNA- and protein-based life was preceded by a simpler life form based primarily on RNA. This earlier era is referred to as the ‘RNA world’, during which the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA.

Walker, Sara Imari, Luis Cisneros, and Paul C W Davies. . “Evolutionary Transitions and Top-Down Causation.” arXiv 1207.4808v1 [nlin.AO] 19 Jul 2012

Sara Imari Walker and Paul C. W. Davies. 2012. 2013 “The algorithmic origins of life” J. R. Soc. Interface ( 6 February) vol. 10 no. 79 20120869: doi: 10.1098/​rsif.2012.0869

Abstract
Although it has been notoriously difficult to pin down precisely what is it that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique informational narrative of living systems suggests that life may be characterized by context-dependent causal influences, and, in particular, that top-down (or downward) causation—where higher levels influence and constrain the dynamics of lower levels in organizational hierarchies—may be a major contributor to the hierarchal structure of living systems. Here, we propose that the emergence of life may correspond to a physical transition associated with a shift in the causal structure, where information gains direct and context-dependent causal efficacy over the matter in which it is instantiated. Such a transition may be akin to more traditional physical transitions (e.g. thermodynamic phase transitions), with the crucial distinction that determining which phase (non-life or life) a given system is in requires dynamical information and therefore can only be inferred by identifying causal architecture. We discuss some novel research directions based on this hypothesis, including potential measures of such a transition that may be amenable to laboratory study, and how the proposed mechanism corresponds to the onset of the unique mode of (algorithmic) information processing characteristic of living systems.

Who or What is Astrobiology?


Earthrise Apollo 8, the first manned mission to the moon, entered lunar orbit on Christmas Eve, Dec. 24, 1968. That evening, the astronauts-Commander Frank Borman, Command Module Pilot Jim Lovell, and Lunar Module Pilot William Anders-held a live broadcast from lunar orbit, in which they showed pictures of the Earth and moon as seen from their spacecraft. Said Lovell, "The vast loneliness is awe-inspiring and it makes you realize just what you have back there on Earth." They ended the broadcast with the crew taking turns reading from the book of Genesis. Image Credit: NASA

Earthrise
Apollo 8, the first manned mission to the moon, entered lunar orbit on Christmas Eve, Dec. 24, 1968. That evening, the astronauts-Commander Frank Borman, Command Module Pilot Jim Lovell, and Lunar Module Pilot William Anders-held a live broadcast from lunar orbit, in which they showed pictures of the Earth and moon as seen from their spacecraft. Said Lovell, “The vast loneliness is awe-inspiring and it makes you realize just what you have back there on Earth.” They ended the broadcast with the crew taking turns reading from the book of Genesis.
Image Credit: NASA

What is Astrobiology?

“Astrobiology, the study of life as planetary phenomenon, aims to understand the fundamental nature of life on Earth and the possibility of life elsewhere. To achieve this goal, astrobiologists initiated unprecedented communications among the disciplines of astronomy biology, chemistry, and geology. . . . “
(1)

Who is an Astrobiologist?

Perhaps, an Astrobiologist is best described as a scientist whose primary roles fall within three definite areas:

  • Concerned about how life began and evolved
  • Concerned about questions of life beyond Earth
  • Concerned about the future of life (on Earth and beyond)

Beyond the major roles in Astrobiology, the scientist acknowledges the need for an interdisciplinary and collaborative effort among the disciplines. Perhaps it is best stated in the following manner—”it is not a practice of a lone scientist, but the interdependence between all parties.”

Otherwise, I take the following quotation from (Workshop on the Societal Implications of Astrobiology, Final Report—2000):

“Interdisciplinary and multidisciplinary work is imperative. There must be close coordination between the scientists who conduct the research and those who can shed light on the social implications…Thoughtful and effective collaboration may
break down the barriers that separate different intellectual fields and move us in the direction of consilience, or the unification of knowledge.”(2)

 Illustration Comparing Apparent Sizes of Moons This illustration provides a comparison for how big the moons of Mars appear to be, as seen from the surface of Mars, in relation to the size that Earth's moon appears to be when seen from the surface of Earth.  Earth's moon actually has a diameter more than 100 times greater than the larger Martian moon, Phobos. However, the Martian moons orbit much closer to their planet than the distance between Earth and Earth's moon. Deimos, at far left, and Phobos, beside it, are shown together as they actually were photographed by the Mast Camera (Mastcam) NASA's Mars rover Curiosity on Aug. 1, 2013.  The images are oriented so that north is up. The size-comparison image of Earth's moon, on the right, is also oriented with north up. Deimos has a diameter of 7.5 miles (12 kilometers) and was 12,800 miles (20,500 kilometers) from the rover at the time of the image. Phobos has a diameter 14 miles (22 kilometers) and was 3,900 miles (6,240 kilometers) from the rover at the time of the image. Earth's moon has a diameter of 2,159 miles (3,474 kilometers) and is typically about 238,000 miles (380,000 kilometers) from an observer on Earth. Image credit: NASA/JPL-Caltech/Malin Space Science Systems/Texas A&M Univ.


Illustration Comparing Apparent Sizes of Moons
This illustration provides a comparison for how big the moons of Mars appear to be, as seen from the surface of Mars, in relation to the size that Earth’s moon appears to be when seen from the surface of Earth. Earth’s moon actually has a diameter more than 100 times greater than the larger Martian moon, Phobos. However, the Martian moons orbit much closer to their planet than the distance between Earth and Earth’s moon. Deimos, at far left, and Phobos, beside it, are shown together as they actually were photographed by the Mast Camera (Mastcam) NASA’s Mars rover Curiosity on Aug. 1, 2013. The images are oriented so that north is up. The size-comparison image of Earth’s moon, on the right, is also oriented with north up. Deimos has a diameter of 7.5 miles (12 kilometers) and was 12,800 miles (20,500 kilometers) from the rover at the time of the image. Phobos has a diameter 14 miles (22 kilometers) and was 3,900 miles (6,240 kilometers) from the rover at the time of the image. Earth’s moon has a diameter of 2,159 miles (3,474 kilometers) and is typically about 238,000 miles (380,000 kilometers) from an observer on Earth. Image credit: NASA/JPL-Caltech/Malin Space Science Systems/Texas A&M Univ.

NOTES:

  1. Billings, L, V Cameron, M Claire, G J Dick, S D Domagal-Goldman, E J Javaux, O J Johnson, et al. 2006. “The Astrobiology Primer: An Outline of General Knowledge–version 1, 2006.” Astrobiology 6 (5) (October): 735–813. doi:10.1089/ast.2006.6.735. http://www.ncbi.nlm.nih.gov/pubmed/17067259.
  2. Connell, K., Dick, S.J., and Rose,K. (2000) Workshop on the Societal Implications of Astrobiology, Final Report, NASA Technical Memorandum, NASA Ames Research Center, Moffett Field, CA.: http://astrobiology.arc.nasa.gov/workshops/societal.
  3. Image Credit: Earthrise–http://www.nasa.gov/multimedia/imagegallery/image_feature_1249.html#.Ug6pRZK1GSo
  4. Final Image Credit: Moons–http://www.nasa.gov/mission_pages/msl/multimedia/gallery-indexEvents.html#.Ug6q_JK1GSp

Quick Overview: Mission To Mars 2020


m31_comolli_2193

Fig. 1 via Wikimedia This mission is being designed to launch in 2020 and to enable surface operations lasting one Martian year (about 687 Earth days). Source URL:  http://en.wikipedia.org/wiki/File:Mars2020MissionTimeline-20130710.jpg  Accessed July 30, 2013

The Mars 2020 mission promises to further humanity’s efforts to understand Mars’ history and pave the way for eventual human exploration. The report that outlines the mission was released early July of this year.  (In some senses it reminds me of the way in which the moon-shot was planned.) The prior missions to the eventual 2020 landing painstakingly laid down a foundation of what will be the important areas for investigation. (see Fig. 2)

In a nutshell, the mission priorities were summarized in the SDT 2020 Mars here: (Available at the following website: http://mars.jpl.nasa.gov/m2020/ )

  • Explore an astrobiologically relevant ancient environment on Mars to decipher its geological processes and history, including the assessment of past habitability.
  • Assess biosignature preservation potential within the selected geological environment and search for potential biosignatures.
  • Demonstrate significant technical progress towards the future return of scientifically selected, well-documented samples to Earth.
  • Provide an opportunity for contributed Human Exploration & Operations Mission Directorate or Space Technology Participation, compatible with the science payload and within the mission’s payload capacity.

mars2020b-e1375224802331c

Fig. 2 From Mars 2020 Report (Prior missions paved the way for the upcoming 2020 exploration.)

Original illustration to appear in the following :

Fraeman et al (2013) “Detection and Mapping of Hematite Capping Ridge in Gayle Crater, Mars and Implications for Past Aqueous Conditions.” Geology  (submitted by report authors)

OPINION—EVOLUTION and CLIMATE CHANGE


Fig. 1 Image taken from APOD–Astronomy Picture of the Day -Accessed July 17, 2013 [URL Source: http://apod.nasa.gov/apod/ap130626.html ]

M31: The Andromeda Galaxy

Image Credit & Copyright: Lorenzo Comolli

Explanation: Andromeda is the nearest major galaxy to our own Milky Way Galaxy. Our Galaxy is thought to look much like Andromeda. Together these two galaxies dominate the Local Group of galaxies. The diffuse light from Andromeda is caused by the hundreds of billions of stars that compose it. The several distinct stars that surround Andromeda’s image are actually stars in our Galaxy that are well in front of the background object. Andromeda is frequently referred to as M31 since it is the 31st object on Messier’s list of diffuse sky objects. M31 is so distant it takes about two million years for light to reach us from there. Although visible without aid, the above image of M31 was taken with a small telescope. Much about M31 remains unknown, including how it acquired its unusual double-peaked center.

Evolution may be the limiting factor that stands before us in our journey to the next nearest habitable zone. The brightest minds of evolutionary biology note that it takes millions of years for our species to ascend to the next rung of sophistication. That, at least, seems to be the trend by which evolution has taken for humanity. As a frustrated, singular observer, I often hope for a logarithmic scale of advancement. The reason for my wishful thinking is, as our current existence dictates, the transition from the industrial age to the information age has enabled us to control the face of our own planet. Past trends indicate that we may face a hard road ahead because of our changing climate. Past civilizations have disappeared when drastic changes to their micro-climates produced prolonged drought (e.g. the Mayan civilization and the Anasazi aboriginals). However, the current state of affairs affects not just the micro-climate but all of the Earth. Intelligence and free will (?) seemingly gives us control over our own lives—but how do we respond to ourselves. Moreover, our current actions affect the climate of not just half a world away, but global circulation will bring the storms to our backyards as well. And, we (together) advance slowly as a species; almost imperceptibly we advance.

My current observation comes from trends of that our planet seems to adopt—I am unsure if my description qualifies as the Gaia hypothesis. However, it is life that has shaped the forces of nature. Perhaps we need to understand how our actions affect the climate of the world and our actions affect our neighbors 10,000 miles away. Whether by free market forces or altruism, (in my humble opinion) we may need to address imbalances in our ecological perceptions of climate change. I believe that our evolution points in that direction—a path which can also sustain a long trip from the Solar System.