From the publisher’s website, they provide the following synopsis:
This book discusses information theory as a means of extracting data from large amounts of biological sequences. Utilizing the Shannon theory, the book explains using the information theory principles to interpret sequences and extract vital information. It provides a detailed overview of the practical applications in bioinformatics and includes coverage of diversity in nucleotide and amino acid sequences, sing-nucleotide polymorphism (SNP) and indel sites, binding sites in promoter regions, splicing sites, and more.
If I can manage to get an early copy, I’ll provide a review shortly.
Over the holiday I ran across a press release, which follows with web links added, for a new book on systems theory. It promises to be an excellent read on the development and philosophy of systems theory for those interested in cybernetics, information theory, complexity and related topics.
MIAMI, Fla., Dec. 19, 2013 Dr. Darrell Arnold, Assistant Professor of Philosophy and Director of the Institute for World Languages and Cultures at St. Thomas University, has published an edited volume with Routledge entitled Traditions of Systems Theory: Major Figures and Contemporary Developments. Hans-Georg Moeller, of University College Cork, Ireland, notes that the book “provides a state-of-the-art survey of the increasingly influential and fascinating field of systems theory. It is a highly useful resource for a wide range of disciplines and contributes significantly to bringing together current trends in the sciences and the humanities.” The book includes 17 articles from leading theoreticians in the field, including pieces by Ranulph Glanville, the President of the American Society for Cybernetics, as well as Debora Hammond, the former President of the International Society for Systems Sciences. It is the first comprehensive edited volume in English on the major and countervailing developments within systems theory.
Dr. Arnold writes on 19th century German philosophy, contemporary social theory, as well as technology and globalization, with a focus on how these areas relate to the environmental problematic. He has translated numerous books from German, including C. Mantzavinos’s Naturalistic Hermeneutics (Cambridge UP) and Matthias Vogel’s Media of Reason (Columbia UP). Dr. Arnold is also editor-in-chief of the Humanities and Technology Review.
For additional information on St. Thomas University academic programs and faculty publications, please contact Marivi Prado, Chief Marketing Officer, 305.474.6880; mprado@stu.edu
Dr. Darrell P. Arnold
I’ve ordered my copy and will be providing a review shortly.
A good many times I have been present at gatherings of people who, by the standards of the traditional culture, are thought highly educated and who have with considerable gusto been expressing their incredulity of scientists. Once or twice I have been provoked and have asked the company how many of them could describe the Second Law of Thermodynamics. The response was cold: it was also negative. Yet I was asking something which is the scientific equivalent of: Have you read a work of Shakespeare’s?
I now believe that if I had asked an even simpler question — such as, What do you mean by mass, or acceleration, which is the scientific equivalent of saying, Can you read? — not more than one in ten of the highly educated would have felt that I was speaking the same language. So the great edifice of modern physics goes up, and the majority of the cleverest people in the western world have about as much insight into it as their neolithic ancestors would have had.
This year is the progenitor of what appears to be the biggest renaissance for the application of information theory to the area of biology since Hubert Yockey, Henry Quastler, and Robert L. Platzman’s “Symposium on Information Theory in Biology at Gatlinburg, Tennessee” in 1956. (I might argue it’s possibly even bigger than Claude Shannon’s Ph.D. thesis.) It certainly portends to create a movement that will rapidly build upon and far surpass Norbert Weiner’s concept of Cybernetics and Ludwig von Bertalanffy’s concept of General Systems Theory.
The BIRS workshop will be a bit more general in its approach while the NIMBioS workshop has a slightly tighter view specifically on maximum entropy as applied to biology.
Even more telling (and perhaps most promising) about the two workshops is the very heavy mathematical bent both intend to make their focus. I have a theory that the bounds of science are held below the high water level of mathematics (aka are “bounded by” in mathematics-speak), so there is nothing more exciting than to see groups attempting to push the mathematics and its application further. It was both the lack of mathematical rigor and the general youth of biology (and specifically genetics and microbiology) in the 1950’s which heavily hampered the early growth of cybernetics as a movement. Fortunately this is no longer the case on either count. Now we just need more researchers who are more readily conversant in the two realms simultaneously.
Complexity: A Guided Tour
Melanie Mitchell
Popular Science
Oxford University Press
May 28, 2009
Hardcover
366
This book provides an intimate, highly readable tour of the sciences of complexity, which seek to explain how large-scale complex, organized, and adaptive behavior can emerge from simple interactions among myriad individuals. The author, a leading complex systems scientist, describes the history of ideas, current research, and future prospects in this vital scientific effort.
This is handily one of the best, most interesting, and (to me at least) the most useful popularly written science books I’ve yet to come across. Most popular science books usually bore me to tears and end up being only pedantic for their historical backgrounds, but this one is very succinct with some interesting viewpoints (some of which I agree with and some of which my intuition says are terribly wrong) on the overall structure presented.
For those interested in a general and easily readable high-level overview of some of the areas of research I’ve been interested in (information theory, thermodynamics, entropy, microbiology, evolution, genetics, along with computation, dynamics, chaos, complexity, genetic algorithms, cellular automata, etc.) for the past two decades, this is really a lovely and thought-provoking book.
At the start I was disappointed that there were almost no equations in the book to speak of – and perhaps this is why I had purchased it when it came out and it’s subsequently been sitting on my shelf for so long. The other factor that prevented me from reading it was the depth and breadth of other more technical material I’ve read which covers the majority of topics in the book. I ultimately found myself not minding so much that there weren’t any/many supporting equations aside from a few hidden in the notes at the end of the text in most part because Dr. Mitchell does a fantastic job of pointing out some great subtleties within the various subjects which comprise the broader concept of complexity which one generally would take several years to come to on one’s own and at far greater expense of their time. Here she provides a much stronger picture of the overall subjects covered and this far outweighed the lack of specificity. I honestly wished I had read the book when it was released and it may have helped me to me more specific in my own research. Fortunately she does bring up several areas I will need to delve more deeply into and raised several questions which will significantly inform my future work.
In general, I wish there were more references I hadn’t read or been aware of yet, but towards the end there were a handful of topics relating to fractals, chaos, computer science, and cellular automata which I have been either ignorant of or which are further down my reading lists and may need to move closer to the top. I look forward to delving into many of these shortly. As a simple example, I’ve seen Zipf’s law separately from the perspectives of information theory, linguistics, and even evolution, but this is the first time I’ve seen it related to power laws and fractals.
I definitely appreciated the fact that Dr. Mitchell took the time to point out her own personal feelings on several topics and more so that she explicitly pointed them out as her own gut instincts instead of mentioning them passingly as if they were provable science which is what far too many other authors would have likely done. There are many viewpoints she takes which I certainly don’t agree with, but I suspect that it’s because I’m coming at things from the viewpoint of an electrical engineer with a stronger background in information theory and microbiology while hers is closer to that of computer science. She does mention that her undergraduate background was in mathematics, but I’m curious what areas she specifically studied to have a better understanding of her specific viewpoints.
Her final chapter looking at some of the pros and cons of the topic(s) was very welcome, particularly in light of previous philosophic attempts like cybernetics and general systems theory which I (also) think failed because of their lack of specificity. These caveats certainly help to place the scientific philosophy of complexity into a much larger context. I will generally heartily agree with her viewpoint (and that of others) that there needs to be a more rigorous mathematical theory underpinning the overall effort. I’m sure we’re all wondering “Where is our Newton?” or to use her clever aphorism that we’re “waiting for Carnot.” (Sounds like it should be a Tom Stoppard play title, doesn’t it?)
I might question her brief inclusion of her own Ph.D. thesis work in the text, but it did actually provide a nice specific and self-contained example within the broader context and also helped to tie several of the chapters together.
My one slight criticism of the work would be the lack of better footnoting within the text. Though many feel that footnote numbers within the text or inclusion at the bottom of the pages detracts from the “flow” of the work, I found myself wishing that she had done so here, particularly as I’m one of the few who actually cares about the footnotes and wants to know the specific references as I read. I hope that Oxford eventually publishes an e-book version that includes cross-linked footnotes in the future for the benefit of others.
I can heartily recommend this book to any fan of science, but I would specifically recommend it to any undergraduate science or engineering major who is unsure of what they’d specifically like to study and might need some interesting areas to take a look at. I will mention that one of the tough parts of the concept of complexity is that it is so broad and general that it encompasses over a dozen other fields of study each of which one could get a Ph.D. in without completely knowing the full depth of just one of them much less the full depth of all of them. The book is so well written that I’d even recommend it to senior researchers in any of the above mentioned fields as it is certainly sure to provide not only some excellent overview history of each, but it is sure to bring up questions and thoughts that they’ll want to include in their future researches in their own specific sub-areas of expertise.
Apparently Starbucks has learned well from big tobacco and they’re getting ahead of the whole cancer thing whether or not they really need to. This morning while picking up my morning tea (and apple fritter), I ran across a Prop 65 warning very prominently posted–ironically above the aspartame, though that wasn’t mentioned specifically in the notice–about the cancer risks of acrylamide.
Prop 65 Warning at Starbucks All the fine print boils down to saying that coffee might cause cancer.
I’ve read a fair amount about acrylamide in the past two years following the news that just about anything cooked or fried has small trace amounts of the substance, so I know there’s not too much to be worried about. The biggest “scare” was apparently over french fries–particularly those served at fast food restaurants. Apparently after the scare blew over the general public – the subject just didn’t seem to catch any traction aside from a few snippets in the mainstream press–Starbucks has decided to get out ahead of this “non-issue” just in case. (I will admit that the State of California has actually sued and won against major corporations under the Safe Drinking Water and Toxic Enforcement Act of 1986, Health and Safety Code section 25249.6, also known as “Proposition 65,” that businesses must provide persons with a “clear and reasonable warning” before exposing individuals to these chemicals which includes acrylamide.)
As an aside, I will mention that placing the warning on the condiments counter which I visit only after I’ve made my purchase seems a bit after-the-fact – it would have done me more good in front of the cash register. For the ambulance chasers, this is probably great “grounds”–pun intended–for a major class action.
PROP 65 WARNING
Chemicals known to the State of California to cause cancer and reproductive toxicity, including acrylamide, are present in coffee, baked goods, and other foods or beverages sold here. Acrylamide is not added to our products, but results from cooking, such as when coffee beans are roasted or baked goods are baked. As a result acrylamide is present in our brewed coffee, including coffe made at home or elsewhere from our beans, ground or instant coffee, baked goods or other foods sold here, in grocery stores or other retail locations.
Your personal cancer risk is affected by a wide variety of factors. For more information regarding acrylamide, see www.fda.gov. For more information about acrylamide and Proposition 65, visit www.oehha.ca.gov/prop65/acrylamide.html.
As posted in Starbucks Coffee, Lake Avenue, Pasadena, CA
While I laud their savvy general counsel, do we really need this type of notice in our lives? Humankind has been living with acrylamide cancer risk since the dawn of the Holocene when man first learned to use fire to cook, is there any reason to worry about it now?
I’m reminded of Jared Diamond’s bookThe World Until Yesterday and some of the things that primitive societies simply learn to live with, but which our overly litigious society just can’t seem to deal with logically. Simple things didn’t fool primitive societies like: don’t sleep under trees that look like they are dead or possibly rotting–just in case the tree falls over and kills you in the night while you’re sleeping. Yet somehow some of us need additional warnings about our coffee from McDonald’s being served hot or cautions not to operate our toasters in the bathtub.
Next I fear that we’ll discover we need signs telling us that pinecones might fall out of pine trees.
“Caution Falling Cones” Photo taken about 20 miles from Jared Diamond’s home in Los Angeles.
I sure hope that Henny Penny copyrighted, registered, and patented everything about the concept of “The Sky is Falling” as I’m sure it’ll have made her the richest chicken in the world.
Surely, God could have caused birds to fly with their bones made of solid gold, with their veins full of quicksilver, with their flesh heavier than lead, and with their wings exceedingly small. He did not, and that ought to show something. It is only in order to shield your ignorance that you put the Lord at every turn.
Salviati’s (Galileo’s voice) response to Simplicio (Pope Urban VIII)
Galileo Galilei in Dialogue Concerning the Two Chief World Systems
In the publishing industry there is a general rule-of-thumb that every mathematical equation included in a book will cut the audience of science books written for a popular audience in half – presumably in a geometric progression. This typically means that including even a handful of equations will give you an effective readership of zero – something no author and certainly no editor or publisher wants.
I suspect that there is a corollary to this that every picture included in the text will help to increase your readership, though possibly not by as proportionally a large amount.
In any case, while reading Melanie Mitchell’s text Complexity: A Guided Tour [Cambridge University Press, 2009] this weekend, I noticed that, in what appears to be a concerted effort to include an equation without technically writing it into the text and to simultaneously increase readership by including a picture, she cleverly used a picture of Boltzmann’s tombstone in Vienna! Most fans of thermodynamics will immediately recognize Boltzmann’s equation for entropy, , which appears engraved on the tombstone over his bust.
Page 51 of Melanie Mitchell’s book “Complexity: A Guided Tour” featuring Boltzmann’s tombstone in Vienna.
I hope that future mathematicians, scientists, and engineers will keep this in mind and have their tombstones engraved with key formulae to assist future authors in doing the same – hopefully this will help to increase the amount of mathematics that is deemed “acceptable” by the general public.
Gregory Chaitin’s book Proving Darwin: Making Biology Mathematical combining biology, microbiology, mathematics, evolution and even information theory is directly in my wheelhouse. I had delayed reading it following a few initial poor reviews, and sadly I must confirm that I’m ultimately disappointed in the direct effort shown here, though there is some very significant value buried within. Unfortunately the full value is buried so deeply that very few, if any, will actually make the concerted effort to find it.
This effort does seem to make a more high-minded and noble attempt than what I would call the “Brian Greene method” in which an academic seemingly gives up on serious science to publish multiple texts on a popular topic to cash in on public interest in that topic through sales of books. In this respect Chaitin is closer to Neil deGrasse Tyson in his effort to expound an interesting theory to the broader public and improve the public discourse, though I would admit he’s probably a bit more (self-) interested in pushing his own theory and selling books (or giving him the benefit of the doubt, perhaps the publisher has pushed him to this).
Though there is a reasonable stab at providing some philosophical background to fit the topic into the broader fabric of science and theory in the later chapters, most of it is rather poorly motivated and is covered far better in other non-technical works. While it is nice to have some semblance of Chaitin’s philosophy and feelings, the inclusion of this type of material only tends to soften the blow of his theoretical work and makes the text read more like pseudo-science or simple base philosophy without any actual rigorous underpinning.
I’m assuming that his purpose in writing the book is to make the theories he’s come up with in his primary paper on the topic more accessible to the broader community of science as well as the public itself. It’s easy for a groundbreaking piece of work to be hidden in the broader scientific literature, but Chaitin seems to be taking his pedestal as a reasonably popular science writer to increase the visibility of his work here. He admittedly mentions that his effort stems from his hobby as his primary area is algorithmic information theory and computer science and not biology or evolution, though his meager references in the text do at least indicate some facility with some of the “right” sources in these latter areas.
Speaking from a broad public perspective, there is certainly interest in this general topic to warrant such a book, though based on the reviews of others via Amazon, Goodreads, etc. the book has sadly missed it’s mark. He unfortunately sticks too closely to the rule that inclusion of mathematical equations is detrimental to the sale of ones books. Sadly, his broader point is seemingly lost on the broader public as his ability to analogize his work isn’t as strong as that of Brian Greene with respect to theoretical physics (string theory).
From the a higher perspective of a researcher who does work in all of the relevant areas relating to the topic, I was even more underwhelmed with the present text aside from the single URL link to the original much more technical paper which Chaitin wrote in 2010. To me this was the most valuable part of the entire text though he did provide some small amount of reasonable detail in his appendix.
I can certainly appreciate Chaitin’s enthusiastic following of John von Neumann but I’m disappointed in his lack of acknowledgement of Norbert Weiner or Claude Shannon who all collaborated in the mid part of the 20th century. I’m sure Chaitin is more than well aware of the father of information theory, but I’ll be willing to bet that although he’s probably read his infamous master’s thesis and his highly influential Bell Labs article on “A/The Mathematical Theory of Communication”, he is, like most, shamefully and wholly unaware of Shannon’s MIT doctoral thesis.
Given Chaitin’s own personal aim to further the acceptance of his own theories and work and the goal of the publisher to sell more copies, I would mention a few recommendations for future potential editions:
The greater majority of his broader audience will have at least a passably reasonable understanding of biology and evolution, but very little, if any, understanding of algorithmic information theory. He would be better off expounding upon this subject to bring people up to speed to better understand his viewpoint and his subsequent proof. Though I understand the need to be relatively light in regard to the number of equations and technicalities included, Chaitin could follow some of his heroes of mathematical exposition and do a slightly better job of explaining what is going on here. He could also go a long way toward adding some significant material to the appendices to help the higher end general readers and the specifically the biologists understand more of the technicalities of algorithmic information theory to better follow his proof which should appear in intricate glory in the appendix as well. I might also recommend excising some of the more philosophical material which tends to undermine his scientific “weight.” Though I found it interesting that he gives a mathematical definition of “intelligent design”, I have a feeling its intricacies were lost on most of his readership — this point alone could go a long way towards solidifying the position of evolution amongst non-scientists, particularly in America, and win the support of heavyweights like Dawkins himself.
I’ll agree wholeheartedly with one reviewer who said that Chaitin tends to “state small ideas repeatedly, and every time at the same shallow level with astonishing amount of redundancy (mostly consisting of chit-chat and self congratulations)”. This certainly detracted from my enjoyment of the work. Chaitin also includes an awful lot of name dropping of significant scientific figures tangential to the subject at hand. This may have been more impressive if he included the results of his discussions with them about the subject, but I’m left with the impression that he simply said hello, shook their hands, and at best was simply inspired by his having met them. It’s nice that he’s had these experiences, but it doesn’t help me to believe or follow his own work.
Though I would certainly agree that we could use a mathematical proof of evolution, and that Chaitin has made a reasonable theoretical stab, this book sadly wasn’t the best one to motivate broader interest in such an effort. I’ll give him five stars for effort, three for general content, but in the end, for most it will have to be at most a 2 star work overall.
I’m honestly shocked that no one else has written a book similar to The World Until Yesterday: What Can We Learn from Traditional Societies prior to now. It’s certainly a wonderful synthesis and a fantastic resulting thesis based on an incredibly broad array of areas of study over a lifetime of work.
I personally don’t think that it is as significant as Guns, Germs, and Steel: The Fates of Human Societies was, though perhaps it should be just as (if not more) ground shaking for modern society. As a long-time student of evolutionary biology and other fields related to this work, I’m not as impressed with the effort as I might otherwise be since most of the overarching thesis is second nature to me. It does however have some superb anecdotes and broad reviews of large areas of literature to provide some excellent motivation that I might not otherwise have spent the time to find thus giving it some excellent value to me.
As for others in the general public, I highly recommend it for it’s simple and clear examples and the ultimate thesis which are exceptionally worth reading (and implementing) into one’s life as well as into broader areas of modern society. If nothing else, it points out how drastically life has changed for human societies even in the last 150 years, much less the last 10,000.
For those in the field or with an interest in Big History, this is certainly a must-read and possibly an excellent place to start for those without any background at all.
Based on my own personal background, I’d give this 3 stars (in terms of it’s direct value to me), but for the general public it’s easily a 5 star work. I do wish that it had been more traditionally and extensively footnoted, but for a broader audience I certainly understand Dr. Diamond’s reasons for publishing it as he did.
Overall this series of 24 video lectures from The Teaching Company as part of their Great Courses series is a great introduction to evolution and many of its interdisciplinary sub-fields. I particularly enjoyed seeing the perspective of a geologist/paleontologist to start things off and then the tag-team to cover human evolution from primates.
Professor at Emory University; Ph.D., from University of GeorgiaProfessor at University of Wisconsin–Madison; Ph.D., from University of Michigan
I especially loved the philosophical conceptualization of “deep time” (in analogy with “deep space”) particularly as one considers the even broader idea of “Big History“. Though the professors here don’t delve into Big History directly, they’re covering a large portion of the cross-disciplinary and inter-disciplinary studies which underpin a large portion of the field. More specifically taking the general viewpoint of “transitions” in evolution underlines this conceptualization.
Though the transitional viewpoint seems to be a very natural and highly illustrative one to take, I would be curious in seeing alternate presentations of evolution from a pedagogical standpoint. It was nice to hear a bit of alternate discussion in the final lecture as well as discussion of where things might “go from here.”
I do wish that there were additional follow-on lectures that covered additional material in more depth. It would also have been nice to have included a handful of lectures from a microbiologist’s viewpoint and background to give some additional rounding out of the material and this could have been done either in the early parts of the material or certainly around the discussions of primate evolution. Overall all though, these are wonderfully self-contained and don’t require a huge prior background in material to understand well.
It’s always great to see lecturers who truly love their fields and have the ability to relate that through their lectures and infect their students.
From a purely technical standpoint, I’m glad to see that The Teaching Company only offers a video version of (as opposed to their usual additional offering of audio-only) as having pictures of the fossils and organisms under discussion and their relative physiological structures was very helpful. Additionally having the recurring timecharts of the portions of geological time under discussion was very useful and generally reinforcing of the chronology. Somewhat monotonous from a visual perspective was the almost programmatic back and forth pacing between two cameras during the lectures which at times became distracting in and of itself. Certainly including a third camera would have added some variety as would having had camera operators to zoom in or move the camera around while the lecturers stand relatively stationary. (Though the production value here is exceptionally high, small details like this over the span of several hours of watching become important. As an example of better execution, I prefer Glenn Holland’s “Religion in the Ancient Mediterranean World” as a model – though there wasn’t as much additional visual material there, the lectures were simply more “watchable” because of the camera work.)
Melanie Mitchell
, which appears engraved on the tombstone over his bust.
