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cheap linux hostingHere we report a new cell
Image: J Craig Venter Institutue / NCMIR/Thomas Deerinck/Mark Ellisman
Cells are the fundamental units of life. The genome sequence of a cell may be thought of as its operating system. It carries the code that specifies all of the genetic functions of the cell, which in turn determine the cellular chemistry, structure, replication, and other characteristics. Each genome contains instructions for universal functions that are common to all forms of life, as well as instructions that are specific to the particular species. The genome is dependent on the functions of the cell cytoplasm for its expression. In turn, the properties of the cytoplasm are determined by the instructions encoded in the genome. – Venter Institute, 2016
Sixty-three years ago Francis Crick wrote a letter to his 12 year-old son, Michael, and explained that he and his research-partner (James D. Watson) had constructed a model of how DNA molecules could hold encoded information inside the cell. The very concept of a molecule holding encoded information was scientifically and philosophically fascinating; we had discovered the “stuff of heredity”. Fifty-eight years ago we discovered the necessary "interpreter" molecules that allowed the translation of this encoded information into concrete physical effects. Without these interpreter molecules, the information contained in DNA would be completely useless. Life would simply not exist. Fifty-five years ago we demonstrated experimentally that the information contained in the genome was held in an actual reading-frame code. We readily recognized the utility of a reading-frame code, given that our own recorded language is the (only) other place in the cosmos we can find such a thing. In that same year, Marshall Nirenberg and Heinrich Matthaei began the process of finally breaking the code, the Genetic Code, which holds the information of life inside the cell.
And just last month in March 2016 ...
Irreducible Complexity: the primordial condition of biology
Irreducible Complexity:
The primordial condition of biology
In 1996, Lehigh University professor of biochemistry, Michael Behe, published his first book Darwin’s Black Box, which famously advanced the concept of irreducible complexity (IC) to prominent status in the conversation of design in biology. In his book, Professor Behe described irreducible complexity as: A single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning.
In illustrating his point, Behe used the idea of a simple mousetrap -- with its base and spring and holding bar -- as an example of an IC system, where the removal of any of these parts would render the mousetrap incapable of its intended purpose of trapping a mouse. Further, he provided examples of biological IC systems; each one dependent on several distinct parts in order to accomplish its task. Behe's point in all this was that ALL the parts of the mouse trap are simultaneously necessary in order for a mousetrap to trap mice. And in a biological sense, if critical functions require several parts, then those functions would not occur until the various parts became available.
An encounter with a critic of biological semiosis
For those who are unfamiliar with The Royal Society, it’s an academic organization whose membership includes many of the world’s most eminent scientists, and is “the oldest scientific academy in continuous existence”. In loose terms, they are a British forbearer to many of the various Academies of Science sprinkled throughout the nations of the world. From their mission statement:
The Society’s fundamental purpose, reflected in its founding Charters of the 1660s, is to recognize, promote, and support excellence in science and to encourage the development and use of science for the benefit of humanity.
This article isn’t necessarily about the Royal Society, except for the fact that it serves as the genesis of the story, and also a proper backdrop to frame the issues at hand.
What is at issue is the void that seems to exist between the average working biologist and the fundamental reality that DNA (the genome) is a genuine representational medium. It operates in a system that translates the representations it uses to encode information into long-term memory. It is not sort-of-like information; it is not kind-of-like information.
From a physics perspective, it functions exactly like the words you are reading right now. In fact -- again from a physical systems perspective -- only genetic encoding can match the variety and open-ended content of the words on this page. The genetic code and recorded language are the only two physical systems like this in the entire cosmos. They use spatially-oriented representations and a reading-frame code. It is the organization of arbitrary constraints that enables the combinatorial encoding of effects. In the total sum of human knowledge, they are a set of two – with no others.
Writing Biosemiosis.org
Writing Biosemiosis.org
In September of 2009 I started a new document on my computer entitled “A System of Symbols”, where I was going to write about the part of design theory that interested me the most – that is, the representations that are required for self-replication (von Neumann, Pattee). My goal was to inventory all the physical conditions necessary for one thing to represent another thing in a material universe. I wrote and rewrote that essay for more than four years -- reading, learning, and sharing along the way. As it turns out, writing that essay was my way of coming to understand the issues, and I spent a great deal of that time trying to articulate things I had come to understand conceptually, but could not yet put into words. Eventually I came into contact with the types of scientists and researchers who had substantial experience with these issues, up to and including those who had spent their entire careers on the subject. It was a humbling experience to share my thoughts with people of that caliber, and have them respond by sending me papers of their own that reflected the same concepts.
Then In 2014, I retired that essay and began writing Biosemiosis.org in its place. Since that work is available to any reader, I won’t recapitulate it here, but there are a couple of concepts I’d like to highlight – particularly the discontinuity found in the translation of recorded information.