March, 2019 | Chris Aldrich

👓 Dr. Hubert Yockey of Bel Air, Director of APG Reactor; Manhattan Project Nuclear Physicist, Dies at 99 | The Dagger

Read Dr. Hubert Yockey of Bel Air, Director of APG Reactor; Manhattan Project Nuclear Physicist, Dies at 99 (The Dagger - Local News with an Edge)

Hubert Palmer Yockey, 99, died peacefully under hospice care at his home in Bel Air, MD, on January 31, 2016, with his daughter, Cynthia Yockey, at his side. Born in Alexandria, Minnesota, he was t…

Acquired The Emergence of Biological Organization by Henry Quastler

Acquired The Emergence of Biological Organization by Henry Quastler (Yale Univ Press; First Edition edition (1964))

In 1964 Quastler's book The Emergence of Biological Organization was published posthumously. In 2002, Harold J. Morowitz described it as a "remarkably prescient book" which is "surprisingly contemporary in outlook". In it Quastler pioneers a theory of emergence, developing model of "a series of emergences from probionts to prokaryotes".

The work is based on lectures given by Quastler during the spring term of 1963, when he was Visiting Professor of Theoretical Biology at Yale University. In these lectures Quastler argued that the formation of single-stranded polynucleotides was well within the limits of probability of what could have occurred during the pre-biologic period of the Earth. However, he noted that polymerization of a single-stranded polymer from mononucleotides is slow, and its hydrolysis is fast; therefore in a closed system consisting only of mononucleotides and their single-stranded polymers, only a small fraction of the available molecules will be polymerized. However, a single-stranded polymer may form a double-stranded one by complementary polymerization, using a single-stranded polynucleotide as a template. Such a process is relatively fast and the resulting double-stranded polynucleotide is much more stable than the single single-stranded one since each monomer is bound not only along the sugar phosphate backbone, but also through inter-strand bonding between the bases.

The capability for self-replication, a fundamental feature of life, emerged when double-stranded polynucleotides disassociated into single-stranded ones and each of these served as a template for synthesis of a complementary strand, producing two double-stranded copies. Such a system is mutable since random changes of individual bases may occur and be propagated. Individual replicators with different nucleotide sequences may also compete with each other for nucleotide precursors. Mutations that influence the folding state of polynucleotides may affect the ratio of association of strands to dissociation and thus the ability to replicate. The folding state would also affect the stability of the molecule. These ideas were then developed to speculate on the emergence of genetic information, protein synthesis and other general features of life.

Lily E. Kay says that Quastler's works "are an illuminating example of a well reasoned epistemic quest and a curious disciplinary failure". Quastler's aspiration to create an information based biology was innovative, but his work was "plagued by problems: outdated data, unwarranted assumptions, some dubious numerology, and, most importantly, an inability to generate an experimental agenda." However Quastler's "discursive framework" survived.

Forty-five years after Quastler's 1964 proposal, Lincoln and Joyce described a cross-catalytic system that involves two RNA enzymes (ribosymes) that catalyze each other's synthesis from a total of four component substrates. This synthesis occurred in the absence of protein and could provide the basis for an artificial genetic system.

There was a single used copy in the UK for $12.49 and all the rest are $149.00+ so I snapped it up. Should be an interesting read in and of itself, but I suspect it’s got an interesting niche of the history of science covered with respect to bit history, complexity, and biological organization.

Should arrive some time between March 13 – March 25.

👓 Book review by Nicolas Rashevsky of Information theory in biology | The bulletin of mathematical biophysics

Read Book review of Information theory in biology by Nicolas Rashevsky (The bulletin of mathematical biophysics, June 1954, Volume 16, Issue 2, pp 183–185)

While sifting through some old bookmarks from CiteULike which is going to disappear from the web soon, I ran across one for this book review of Henry Quastler’s book Information Theory in Biology (1953).

The last page of the review had an interesting information theoretical take on not only book reviews, but the level of information they contain with respect for improved teaching and learning in an era prior to Mihaly Csikszentmihalyi’s ideas about “flow”.

As it isn’t the easiest thing to track down, I’ll quote the relevant paragraphs from page 185:

The purpose of a scientific book (we at least hope!) is to store and convey information in a given field. The purpose of a review is to convey information about a book. It is therefore legitimate to attempt a mathematical theory of writing books and to find the optimal conditions which make a book good. At first it may seem that the optimal conditions consist of maximizing the amount of information per page, that is, in minimizing the redundancy. But a certain amount of redundancy may not only be desirable, but necessary. When presenting a new subject to young students who have never heard of it, a judicious amount of repetition is good pedagogy. Giving an exact abstract definition and then illustrating it by an example already constitutes a logical redundancy. But how useful it frequently is! The minimum of redundancy that is found in some well-known and excellent mathematical books (nomina sunt odiosa!) occasionally makes those books difficult to read even for mathematicians.
The optimum amount of redundancy is a function of the information and intelligence of the reader for whom the book is written. The analytical form of this function is to be determined by an appropriate mathematical theory of learning. Writing a book even in a field which belongs entirely to the domains of Her Majesty the Queen of Sciences is, alas, still more an art than a science. Is it not possible, however, that in the future it may become an exact science?
If a reviewer’s information and intelligence are exactly equal to the value for which the book has been optimized, then he will perceive as defects in the book only deviations from the optimal conditions. His criticism will be objective and unbiased. If, however, the reviewer’s information and intelligence deviate in any direction from the value for which the book is intended, then he will perceive shortcomings which are not due to the deviation of the book from the optimum, but to the reviewer’s personal characteristics. He may also perceive some advantages in the same way. If in the society of the future every individual will be tagged, through appropriate tests, as to his information and intelligence at a given time, expressed in appropriate units, then a reviewer will be able to calculate the correction for his personal bias. These are fantastic dreams of today, which may become reality in the future.

Some of this is very indicative of why one has to spend some significant time finding and recommending the right textbooks ^[1][2] for students and why things like personalized learning and improvements in pedagogy are so painfully difficult. Sadly on the pedagogy side we haven’t come as far as he may have hoped in nearly 70 ears, and, in fact, we may have regressed.

I’ve often seen web developers in the IndieWeb community mention the idea that “naming things is hard”, so I can’t help but noticing that this 1950’s reviewer uses the Latin catchphrase nomina sunt odiosa which translates as “names are odious”, which has a very similar, but far older sentiment about naming. It was apparently a problem for the ancients as well.

📑 Walter Pitts by Neil Smalheiser | Journal Perspectives in Biology and Medicine

Bookmarked Walter Pitts by

Neil Smalheiser (Journal Perspectives in Biology and Medicine. Volume 43. Issue 2. Page 217 - 226.)

Walter Pitts was pivotal in establishing the revolutionary notion of the brain as a computer, which was seminal in the development of computer design, cybernetics, artificial intelligence, and theoretical neuroscience. He was also a participant in a large number of key advances in 20th-century science. ❧

This looks like an interesting bio to read.

📑 A logical calculus of the ideas immanent in nervous activity by Warren S. McCulloch, Walter Pitts

Bookmarked A logical calculus of the ideas immanent in nervous activity by Warren S. McCulloch, Walter Pitts (The bulletin of mathematical biophysics December 1943, Volume 5, Issue 4, pp 115–133)

Because of the “all-or-none” character of nervous activity, neural events and the relations among them can be treated by means of propositional logic. It is found that the behavior of every net can be described in these terms, with the addition of more complicated logical means for nets containing circles; and that for any logical expression satisfying certain conditions, one can find a net behaving in the fashion it describes. It is shown that many particular choices among possible neurophysiological assumptions are equivalent, in the sense that for every net behaving under one assumption, there exists another net which behaves under the other and gives the same results, although perhaps not in the same time. Various applications of the calculus are discussed.

Found reference to this journal article in a review of Henry Quastler’s book Information Theory in Biology. It said:

A more serious thing, in the reviewer’s opinion, is the complete absence of contributions dealing with information theory and the central nervous system, which may be the field par excellence for the use of such a theory. Although no explicit reference to information theory is made in the well-known paper of W. McCulloch and W. Pitts (1943), the connection is quite obvious. This is made explicit in the systematic elaboration of the McCulloch-Pitts’ approach by J. von Neumann (1952). In his interesting book J. T. Culbertson (1950) discussed possible neural mechanisms for recognition of visual patterns, and particularly investigated the problems of how greatly a pattern may be deformed without ceasing to be recognizable. The connection between this problem and the problem of distortion in the theory of information is obvious. The work of Anatol Rapoport and his associates on random nets, and especially on their applications to rumor spread (see the series of papers which appeared in this Journal during the past four years), is also closely connected with problems of information theory.

Electronic copy available at: http://www.cse.chalmers.se/~coquand/AUTOMATA/mcp.pdf

🔖 Information Theory in Biology by Henry Quastler (editor) | University of Illinois Press (1953)

Bookmarked Information Theory in Biology (University of Illinois Press (1953))

I’d love to have a copy of this book that I don’t think I’d heard of before. I’ve got his later Symposium of Information Theory In Biology (1958) already. That volume gives credit to this prior book as inspiration for the symposium.

I suspect based on the Wikipedia article for Quastler that this may also be the same book as the slightly differently titled Essays on the Use of Information Theory in Biology. (Urbana: University of Illinois Press, 1953). There’s also a 1955 review of the text with this name available as well.

Google uses the first title with 273 pages and the Symposium text specifically cites Information Theory in Biology as the correct title several times.

The tough part seems to be that there are very few copies available online and the ones that are are certainly used, in poor condition, and priced at $100+. Ugh…