Amazon rank\ mathematics of biology

Amazon rank\ mathematics of biology

Sorry It's been a while. A new year is upon us. The holidays are over and its time to get back regular time.

In 1936  Alan Turing famed code breaker and mathematician published his now famous paper, "Computable numbers with an application to the Entscheidungs problem." In it he lays the groundwork for all future computers by introducing the idea of data formatted into a binary code.   He laid out in theory how by using a simple switching device and a counting machine or processor  problems of great complexity could be quickly and easily calculated. Few of us born in the 1960’s could have foreseen the changes brought upon society by the revolution born of this technology. Everything from our cars to toasters  now possess some level of calculating ability. The age of complex mechanization is dead. For all but the most rudimentary of technologies is so to speak on the grid.

http://www.cs.virginia.edu/~robins/Turing_Paper_1936.pdf

It is true that with each passing year we grow more dependent upon our personal devices. So much so that they are becoming more like appendages than the tools they were originally intended to be. This is not to say that it is such  bad thing. For in the past other life changing technologies have had their opponents. Who among us would consider indoor plumbing, automobiles and airplanes to be inherently detrimental.Though some problems from each over time have been identified, all have in their own way tended to improve the overall quality of each of our lives. Despite this each in its time had drawn the ire of vocal detractors.

                                                                                     

I am among other things an artist and a writer. For those like myself who feel the urge to create the burgeoning changes have offered both challenges and opportunities. For those who in the past who had been rejected by the traditional arbiters of culture for reasons of either of taste or content have discovered new avenues of expression.  Some categorize this changing landscape as a democratization for its ability to be inclusive. Others are less convinced and feel that these entities have to some extent have for better or worse taken the place of more traditional productions. Still others on the fringe believe that the artificial intelligence behind the likes of Amazon and Google have far more ominous consequences for our future. Regardless however how one might feel In the age of amazon  those who aspire to make a literary name for themselves must contend with the algorithms of rank. This system designed to reflect the hidden desires of those about to purchase has emerged as the king of the digital media marketplace.

http://www.amazon.com/dp/B00LLI4ZPQ

http://www.amazon.com/dp/B005EC705M

In 1952  attempting to explain the phenomenon morphogenesis Alan Turing again published another revolutionary  set of equations that in time came to be the basis of modern mathematical biology. In essence Turing by trying solve the riddle of how a tiger got  its spots,  created a logical model to describe the process through which patterns arise in biological systems.

http://vagueterrain.net/journal14/jonathan-mccabe/01
http://www.wired.com/2011/02/turing-patterns/
http://www.jstor.org/discover/10.2307/92463?sid=21105633002693&uid=3739864&uid=4&uid=3739256&uid=2

In a sense by using algorithms similar to those used in mathematical biology, entities such as Amazon and the like are trying to predict the purchasing pattern of millions of  their paying consumers.  Is it possible that hidden within the nature  from which springs our complex behavior that there exist patterns akin to that of spots on an octopus or the stripes on a cat. Despite how fiercely we defend the concept of each of us possessing a unique individuality our behavior patterns as it turns are highly predictable. From a roughly homogeneous set the buying public will seize, and their attentions coalesce upon a particular product, song, film or book. Hidden in this behavior as in all things there must be patterns. At first glance one might surmise that these patterns appear randomly. There is however in both  instances  a hidden structure that can only be realized in highly evolved computer systems.

So then as these systems continue evolve there will no doubt that there should be corresponding effects be them good or bad upon our everyday lives. I for one see no reason why one should not feel optimistic about the societal changes wrought by these burgeoning technologies. May I recommend however that we retain the off switch just in case. For as these technologies advance and their deployments become ever more seamless, could we one day find ourselves being exploited in ways we can't now imagine?

An Accumulation of Errors

This week I read an article which described how Astronomers at observatory high in the Andes had for the first time visualized with their telescopes the clearest images yet available of the formation of a solar system similar to our own. In this haunting image in concentric bands of blank space are seen as the proto planets are caught in the act of clearing away from their own region of space of the vast clouds of cosmic debris. It was in a manner similar to this our own Earth came to be.

http://www.newsweek.com/image-captures-planet-formation-striking-detail-282793

It had not always been so. Long ago in a relative instant all that was to become the universe was set in motion by a singular chain of chaotic events. In an incalculable release of energy one by one the laws of nature unfolded from the singularity to form all that we know and see.  Space itself from some infinitely small point expanded into the void. To some it may seem that our existence from that point was merely a matter of consequence. All however is not as it would seems for this planetary system in which you and I exist is anomalous to the vast majority of this violent and chaotic universe. There had been no uniform means of creation its is by laughing chance that we find ourselves here on this island of relative stability, by chance a kind of order had arisen and where the laws of nature tend to make a kind of intuitive sense. Perhaps it is due to the favorable nature that stability provides many a grand and mysterious set of circumstances have since evolved. Chief among these of course, is life itself. 

 If we examine this closely there we may be some comparative analogies drawn. Though life and consciousness have for eons continually driven from chaos the creation of temporary pockets of complexity these however hand remained in the context of time as fleeting as a spark from a flame. From a perspective within the sphere of influence of these sparks time is marked out in the scale to which we are all familiar. Entire lives are lived and generations pass and our inheritance like a string are drawn out from the past through the present into the future. This inheritance being the sole survivor of this experience exists then simultaneously in all three. The fire itself is order from disorder.

 From this chaos here in the relative calm of our stable celestial neighborhood a fragile balance has then existed for eons. It is well known that in any sufficiently complex system there the cumulative effects of entropy will over time become apparent.  In respect to the human body it is through an accumulation of errors in our genetic code where this tendency toward degradation and our own individual mortalities are made evident.

http://gifsoup.com/view/4580486/dna-replication.html

It would seem logical that through the accumulation of these errors that this process would in due course cause all to turn ultimately to dust. However this has proven to not be the case for therein a contradiction exists. During the duplication a genetic trait’s code an error on occasion will occur during the process of transcription where in an advantage in survivability can be bestowed into a line of inheritance. 

http://www.science20.com/news_articles/genetics_show_how_earliest_europeans_weathered_the_last_ice_age-148658

Is it thereby through this accumulation of errors that both dissolution and rebirth are mitigated?  It would seem that by these means that despite the obstacles that life muddles on in an ever evolving pageant. 

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The Parasitic Arms Race

The parasitic arms race

Though it may appear to some that we feel secure in our domination over nature it is important on occasion to recall that this was not always the case. Certainly the news of late should serve as a reminder to this. Throughout all of the kingdoms of life that have ever existed on Earth there has been an ongoing arms race the prize of which is survival. This arms race has left within each us all a lasting legacy of immunologic memory of biological battles fought well before anyone alive was ever born.

In a previous creatures log “the realms of the very small” I wrote about the microscopic creatures such as demodex that make themselves at home upon the surface of our bodies. For the most part these fellow travelers tend to cause us no harm. There are however whole legions of viruses, bacteria and parasites that are far less benign. As early man wandered around the coasts until he literally walk out of Africa into Eurasia he took with him only the parasites that came along for the journey. However there in the African cradle of human evolution there remains in the environment hosts of creatures that evolved specifically to parasitize us. 

Ebola was discovered by the outside world only in 1976. Hidden there on the fringes of man’s territory it had surely lingered for millennia. Since that time in contained remote areas in central Africa there have been limited outbreaks in which entire villages have fallen in its wake. In the decades since it has elicited within us a nascent fear. Reminiscent of all the plagues of our nightmares it kills indiscriminately as jumps from host to host.Here in the west perhaps because we live far from the region of our natural evolution we erroneously feel we have had little to fear from our ancient nemesis. However there are no more “contained areas”, for anywhere in the world is now accessible within a day’s time. As our populations swell and technology everyday makes the world a little smaller, we should abandon this notion of invincibility in the face of a very old and sophisticated enemy.

                                                      A heart effected by Chagas disease



http://phenomena.nationalgeographic.com/2010/02/14/genes-from-chagas-parasite-can-transfer-to-humans-and-be-passed-on-to-children/

Are we headed toward a perfect storm to which we will one day become extinct like all previous occupants of the top of the food chain throne? I would say not. The plagues that have for eons besieged our bodies are doing just as nature had evolved them to do and they have done it well. However despite this almost constant battle, along the way humans have not only survived but have thrived. Hidden within each of us transcribed within the strands of our DNA is the story of many a hard fought battle of survival. The evidence of which can be seen in the traces of parasitic bacterial and viral DNA sequences that abound intermingled with our native code. Some of these splices possibly date back to the beginnings of life on earth. These battles have undoubtedly influenced our own evolution.  Some of these subsequent adaptations may have greatly improved our survivability. However we should not fool ourselves that we should go unscathed this time. We will survive as we have done before.  This time we possess the advantage of foresight.   Armed with the latest that medical science can provide we should take the responsibility to do all we can.  We must remember while doing so to maintain a healthy respect for our enemy and an eye on our own frailty.

The Green Hills Of Mars

The Green Hills of Mars

Since the earliest days of astronomy and indeed into the deep recesses of history there has remained within the human psyche an abiding desire to know what life might inhabit the worlds that share our solar system. Looking into the night sky with the naked eye upon Venus and Mars our ancestors wondered how and why these stars behaved differently than those of the background. These stars like the others of their kind in time came to be known as planets.  In our imaginations they took upon the names and characteristics of whatever local god seemed appropriate. There in the sky the planets of love and war dominated their arena in the same ways that these aspects of life dominated us. Later as notions of what it really meant to be a planet grew more mature so too did the imagery used to depict them had become.  

 

However in the absence of true knowledge so deep was this desire to know these unknowable places that men began in their imaginations to create visions of ornate fantasy. On these worlds fantastical realms there in existed, each populated by dragons, fairy kingdoms, and hot steamy jungles. And in the case of Mars, there even existed a worldwide system of canals. All of these were readily created to fill the void left by these knowledge gaps.  

 We now know much to our disappointment that Venus and Mars are for the time being uninhabitable. One has a shrouded atmosphere many times denser than our own with temperatures hundreds of degrees hotter than our own. And the other is a barren lifeless dessert with little if any atmosphere to speak of.  Despite how much we have learned the most basic questions have remained unanswered. Is it possible that even in these most desolate environments, can and does life exist beyond the Earth?

Let’s look at the evidence so far. We do not because of the extreme environments on Venus yet possess the technology that would make such a voyage possible. Perhaps in a future time we will make that leap. But for purely practical reasons we must focus on Mars.

                                                  Mars Then and Now 
                Credit & Copyright: Tom Ruen, Eugene Antoniadi, Lowell Hess,  

                 Roy  A.Gallant, HST, NASA 

I’m old enough to remember references from science texts to the green seasons on mars. Maps indicting the dry and wet cycles were considered by some to be of sound theory. It was  astronomers like Schiaparelli and  Percival Lowell who in the late nineteenth and early twentieth century s  who popularized such notions. Though extrapolations on grand canals and advanced cultures had maye missed the mark had they perhaps in the world before color photography visualized a rare and anomalous greening event?

By the nineteen seventies these ideas had been firmly dismissed by science.  Imagery of Mars showing it to be the arid and cold wasteland that we know today had existed for some time.  By the time the twin Viking landers had touched down in 1976 the consensus was that Mars was a dead world. The mission would be one of confirmation rather than discovery. To their credit however a number of biological experiments were conducted.

 When the results of these experiments were released to the general pubic Mars was officially declared dead. There were however within the details contradictory results that some say  showed just the opposite. In particular the Viking biology package GEX/LR/PR designed to capture the telltale signs of chemical metabolism in soil found some interesting results. However in the absence of earth-like organic compounds these results were considered to be no more than an aberration.

http://apod.nasa.gov/apod/ap031112.html

Viking chemistry of life soil experiments

http://www.spacedaily.com/news/mars-life-00g.html

http://www.nytimes.com/2010/09/04/science/space/04mars.html?_r=0

Since that time four rover missions have successfully touched down on the red planet. What they have discovered there along with what we now know about extremophiles on earth has been revolutionary in the field of planetary science. With the use of rovers and satellites have found conclusive evidence of past and possible current water that could be trapped below the  frozen surface. We are forced now to reevaluate and replicate those early experiments.

 

 1996 an announcement was released which made headlines around the world. What they discovered within  a 4-billion-year-old Martian meteorite found in Antarctica was shocking. Under microscopic examination they discovered  there what appeared to be fossilized bacteria. The excitement that followed this amazing news was however short lived as this evidence was deemed once again to be inconclusive.

 The other day I read of another discovery this time from a meteorite that struck Egypt in 1911. The article describes a find similar to those of the Allen hills discovery of 1996. In this case however structures more similar to what would be described as cellular or similar to earth biology was found. Now however because such Ideas are chastised within the scientific community they are all but ignored. I not being a scientist do not have a professional reputaion to throw away by advocating such notions.

http://www.techtimes.com/articles/15761/20140917/1-3-billion-years-old-martian-meteorite-yields-cradle-of-life-can-alien-life-on-mars-exist.htm

                      http://www.newsledge.com/mars-life-martian-meteorite-pushing-case-life-9602

additional reading

http://www.extremetech.com/extreme/150417-astrobiologists-discover-fossils-in-meteorite-fragments-confirming-extraterrestrial-life

http://www2.jpl.nasa.gov/snc/nasa1.html

I could make the case that there is now sufficient evidence to place a manned mission to Mars squarely at the top of our scientific priority list. We as humans have a deep seated desire to make the discoveries that answer these questions. However in the last fifty years the arbiters of science have stalled this human urge by continually denying the possibilities on the grounds of insufficient evidence.  Currently there are grand plans on the boards at NASA yet as always they remain twenty years or more away. The unfortunate truth is there is no political will to make the commitment to use the necessary resources. Are we doomed to be a one planet species?