book review | Chris Aldrich

Brief Review: The Rule of Four by Ian Caldwell and Dustin Thomason

The Rule of Four by Ian Caldwell and Dustin Thomason
My rating: 4 of 5 stars

A nice little thriller about an obscure text from the Renaissance (quattrocento) set in modern times. This falls into the genre of historical fiction that’s similar to Dan Brown‘s Robert Langdon series or films like the Nicolas Cage National Treasure series, though not quite as “rompish.” I have to imagine that those who liked Mr. Penumbra’s 24-Hour Bookstore, Gentlemen and Players, and The Thirteenth Tale will enjoy this quite a lot.

Those who are fans of historical fiction, cryptography, puzzles, books about books, and history in general, are sure to enjoy it.

Spoilers follow:

The Vincent Taft character could have been a better “heavy” but was pretty functional in the story given his limited appearances in the actual plot. I saw the Savonarola portion of the plot a mile away, but to most unaware of this part of history this will be an interesting historical diversion/lesson. I thought the ending was a bit too literary given the more plot-motivated feel of the rest of the narrative, but in all, it was relatively satisfying given Tom’s full back-story. I can see this being adapted into film, but it will take some creative ideas to better linearize the plot and to make the ending a bit bigger for the screen.

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Breaking the code | The Economist

Bookmarked Breaking the code (The Economist)

Brief book overview of Matthew Cobb's "Life’s Greatest Secret" from The Economist.

For those interested in some of the history behind genetics, evolution, biology and information theory, the following book, which I just saw the attached review in The Economist, is likely to be of interest:

Life’s Greatest Secret: The Story of the Race to Crack the Genetic Code. By Matthew Cobb. Basic Books; 434 pages; $29.99. Profile Books; £25.

In 1953 James Watson and Francis Crick, with the help of Rosalind Franklin and Maurice Wilkins, described the structure of the molecule at the heart of life. Deoxyribonucleic acid, better known as DNA, was, they said, a double helix, two spirals joined across the middle by pairs of four chemical bases, like a twisted ladder. That work earned Messrs Crick, Watson and Wilkins a Nobel prize and a place in the history books. The image of the double helix now often stands for biology, or even science, itself.

But this was merely the most visible breakthrough in a long struggle to understand the engine of life—how traits are inherited, mutated and weeded out by natural selection, and how the whole mysterious process works at the biochemical level. It is that lesser-known history that Matthew Cobb, a professor of animal behaviour at the University of Manchester, aims to sketch in his book, which has been shortlisted for the Royal Society’s Winton prize for science writing.

The result is a fascinating reminder of just how hard-won are the seemingly obvious facts of modern biology. The development of genetics was a tale of confusion, accident, frustration and the occasional flash of insight. It was, says Dr Cobb, as important as the Manhattan or Apollo projects, but with no government support and little money, carried out by scientists interested in the question for its own sake.

The researchers started from almost total ignorance. William Harvey, better known for describing the circulation of the blood, wondered in the 17th century what could explain why children’s skin colour was often a blend of their parents’, whereas they share a sex with only one, and can have an eye colour different from either.

In the late 19th century a monk, Gregor Mendel, established, through experiments on pea plants, the basic rules of inherited traits. A Danish biologist, Wilhelm Johannsen, coined the term “gene” in 1909 to describe whatever it was that Mendel had found. But as late as 1933 scientists were still debating whether genes were physical things or just useful abstractions, and how they could transmit traits. Scientists knew that DNA existed, but many considered it a boring bit of scaffolding in the cell. Proteins, which come in zillions of different varieties, were seen by many as the only things exciting enough to account for all the diversity seen in life.

After the second world war, ideas from information theory, arising out of wartime work on computers and automation, percolated into biology. Once the structure of DNA had been established, those ideas helped crack the problem of how the four chemical bases do their job. Proteins are built by stringing together 20 different sorts of amino acid. Strings of three bases within a DNA molecule represent these amino acids, but with 64 such triplets, there is much redundancy which information theory alone could not fully explain. Years of painstaking lab-work were needed to reconcile theory with reality.

Dr Cobb is good on the human side of the story, showing science as fuelled by rivalry, jealousy, competitiveness and wonder. The only downside is that he must marshal hundreds of scientists across several disciplines into around 300 pages of narrative. The results can sometimes be dense, and readers without a command of biological jargon will frequently find themselves consulting the glossary for guidance. But the cracking of the code of life is a great story, of which this is an accomplished telling.

Source: Breaking the code | The Economist, Aug 8th 2015

Popular Science Books on Information Theory, Biology, and Complexity

Previously, I had made a large and somewhat random list of books which lie in the intersection of the application of information theory, physics, and engineering practice to the area of biology. Below I’ll begin to do a somewhat better job of providing a finer gradation of technical level for both the hobbyist or the aspiring student who wishes to bring themselves to a higher level of understanding of these areas. In future posts, I’ll try to begin classifying other texts into graduated strata as well. The final list will be maintained here: Books at the Intersection of Information Theory and Biology.

Introductory / General Readership / Popular Science Books

These books are written on a generally non-technical level and give a broad overview of their topics with occasional forays into interesting or intriguing subtopics. They include little, if any, mathematical equations or conceptualization. Typically, any high school student should be able to read, follow, and understand the broad concepts behind these books. Though often non-technical, these texts can give some useful insight into the topics at hand, even for the most advanced researchers.

Complexity: A Guided Tour by Melanie Mitchell (review)

Possibly one of the best places to start, this text gives a great overview of most of the major areas of study related to these fields.

Entropy Demystified: The Second Law Reduced to Plain Common Sense by Arieh Ben-Naim

One of the best books on the concept of entropy out there. It can be read even by middle school students with no exposure to algebra and does a fantastic job of laying out the conceptualization of how entropy underlies large areas of the broader subject. Even those with Ph.D.’s in statistical thermodynamics can gain something useful from this lovely volume.

The Information: A History, a Theory, a Flood by James Gleick (review)

A relatively recent popular science volume covering various conceptualizations of what information is and how it’s been dealt with in science and engineering. Though it has its flaws, its certainly a good introduction to the beginner, particularly with regard to history.

The Origin of Species by Charles Darwin

One of the most influential pieces of writing known to man, this classical text is the basis from which major strides in biology have been made as a result. A must read for everyone on the planet.

Information, Entropy, Life and the Universe: What We Know and What We Do Not Know by Arieh Ben-Naim

Information Theory and Evolution by John Avery

The Touchstone of Life: Molecular Information, Cell Communication, and the Foundations of Life by Werner R. Loewenstein (review)

Information Theory, Evolution, and the Origin of Life by Hubert P. Yockey

The four books above have a significant amount of overlap. Though one could read all of them, I recommend that those pressed for time choose Ben-Naim first. As I write this I’ll note that Ben-Naim’s book is scheduled for release on May 30, 2015, but he’s been kind enough to allow me to read an advance copy while it was in process; it gets my highest recommendation in its class. Loewenstein covers a bit more than Avery who also has a more basic presentation. Most who continue with the subject will later come across Yockey’s Information Theory and Molecular Biology which is similar to his text here but written at a slightly higher level of sophistication. Those who finish at this level of sophistication might want to try Yockey third instead.

The Red Queen: Sex and the Evolution of Human Nature by Matt Ridley

Grammatical Man: Information, Entropy, Language, and Life by Jeremy Campbell

Life’s Ratchet: How Molecular Machines Extract Order from Chaos by Peter M. Hoffmann

Complexity: The Emerging Science at the Edge of Order and Chaos by M. Mitchell Waldrop

The Big Picture: On the Origins of Life, Meaning, and the Universe Itself (Dutton, May 10, 2016)

In the coming weeks/months, I’ll try to continue putting recommended books on the remainder of the rest of the spectrum, the balance of which follows in outline form below. As always, I welcome suggestions and recommendations based on others’ experiences as well. If you’d like to suggest additional resources in any of the sections below, please do so via our suggestion box. For those interested in additional resources, please take a look at the ITBio Resources page which includes information about related research groups; references and journal articles; academic, research institutes, societies, groups, and organizations; and conferences, workshops, and symposia.

Lower Level Undergraduate

These books are written at a level that can be grasped and understood by most with a freshmen or sophomore university level. Coursework in math, science, and engineering will usually presume knowledge of calculus, basic probability theory, introductory physics, chemistry, and basic biology.

Upper Level Undergraduate

These books are written at a level that can be grasped and understood by those at a junior or senor university level. Coursework in math, science, and engineering may presume knowledge of probability theory, differential equations, linear algebra, complex analysis, abstract algebra, signal processing, organic chemistry, molecular biology, evolutionary theory, thermodynamics, advanced physics, and basic information theory.

Graduate Level

These books are written at a level that can be grasped and understood by most working at the level of a master’s level at most universities. Coursework presumes all the previously mentioned classes, though may require a higher level of sub-specialization in one or more areas of mathematics, physics, biology, or engineering practice. Because of the depth and breadth of disciplines covered here, many may feel the need to delve into areas outside of their particular specialization.

Book Review of Dominic O’Brien’s “Quantum Memory Power”

Quantum Memory Power by Dominic O'Brien — Quantum Memory Power by Dominic O’Brien

I’ve read many of the biggest memory related books over the past three decades and certainly have my favorites among them. I’ve long heard that Dominic O’Brien’s Quantum Memory Power: Learn to Improve Your Memory with the World Memory Champion! audiobook was fairly good, and decided that I’d finally take a peek having known for a while about O’Brien and his eponymous Dominic System.

General Methods

Overall, I was fairly impressed with his layout and positive teaching style, though I don’t particularly need some of the treacly motivation that he provided and which is primarily aimed at the complete novice. While I appreciate that for some, hearing this material may be the most beneficial, I would have preferred to have some of it presented visually. In general, I wouldn’t recommend this as a something to listen to on a commute as he frequently admonishes against doing some of the exercises he outlines while driving or operating heavy machinery.

Given the prevalence of and growth of memory systems from the mid-20th century onwards, I personally find it difficult to believe all of his personal story about “rediscovering” many of the memory methods he outlines, or at least to the extent to which he tempts the reader to believe.

Differences from Other Systems

Based on past experience, I really appreciate his methods for better remembering names with faces as his conceptualizations for doing this seemed better to me than the methods outlined by Bruno Furst. I do however, much prefer the major mnemonic system’s method for numbers over the Dominic system for it’s more logical and complete conversion of consonant sounds for most languages. The links between the letters and numbers in the major system are also much easier to remember and don’t require as much work to remember them. I also appreciate the major system for its deeper historical roots as well as for its precise overlap with the Gregg Shorthand method. The poorer structure of the Dominic system is the only evidence I can find to indicate that he seems to have separately re-discovered some of his memory methods.

I appreciated that most of his focus was on practical tasks like to do lists, personal appointments, names and faces, but wish he’d spent some additional time walking through general knowledge examples like he did for the list of the world’s oceans and seas.

While I appreciated his outlining the ability to calculate what day of the week any particular date falls on (something that most memory books don’t touch upon), he failed to completely specify the entire method. He also used a somewhat non-standard method for coding both the days of the week and the months of the year, though mathematically all of these systems are equivalent. I did appreciate his trying to encode a set up for individual years, which will certainly help many cut down on the mental mathematics, particularly as it relates to the dread many have for long division. Unfortunately, he didn’t go far enough and this is where he also failed to finish supplying the full details for all of the special cases for the years. He also failed to mention the discontinuities with the Gregorian versus the Julian calendar making his method more historically universal. For those interested, Wikipedia outlines some of the more familiar mathematical methods for determining the day of the week that a particular date would fall on.

Instead of having spent the time outlining the calendar, which is inherently difficult to do in audio format compared to printed format, he may have been better off having spent the time going into more depth memorizing poetry or prose as an extension of his small aside on memorizing quotes and presenting speeches.

I could have done without the bulk of the final disk which comprised mostly of tests for the material previously presented. The complete beginner may get more out of these exercises however. The final portion of the disk was more interesting as he did provide some philosophy on how memory systems engage both lobes of the brain within the right-brained/left-brained conceptualizations from neuropsychology.

While O’Brien doesn’t completely draw out his entire system, to many this may be a strong benefit as it forces individuals to create their own system within his framework. This is bound to help many to create stronger personalized links between their numbers and their images. The drawback the beginner may find for this is that they may find themselves ever tinkering with their own customized system, or even more likely rebuilding things from scratch when they discover the list of online resources from others that rely on people having a more standardized system.

O’Brien also provides more emphasis on creativity and visualization than some books, which will be very beneficial to many beginners.

Overall, while I’d generally recommend this to the average mnemonist, I’d recommend they approach it after having delved in a bit and learned the major system from somewhere else.

Brief Review: The Swerve: How the World Became Modern by Stephen Greenblatt

The Swerve: How the World Became Modern by Stephen Greenblatt

My rating: 4 of 5 stars

Stephen Greenblatt provides an interesting synthesis of history and philosophy. Greenblatt’s love of the humanities certainly shines through. This stands as an almost over-exciting commercial for not only reading Lucretius’s “De Rerum Natura” (“On the Nature of Things”), but in motivating the reader to actually go out to learn Latin to appreciate it properly.

I would have loved more direct analysis and evidence of the immediate impact of Lucretius in the 1400’s as well as a longer in-depth analysis of the continuing impact through the 1700’s.

The first half of the book is excellent at painting a vivid portrait of the life and times of Poggio Bracciolini which one doesn’t commonly encounter. I’m almost reminded of Stacy Schiff’s Cleopatra: A Life, though Greenblatt has far more historical material with which to paint the picture. I may also be biased that I’m more interested in the mechanics of the scholarship of the resurgence of the classics in the Renaissance than I was of that particular political portion of the first century BCE. Though my background on the history of the time periods involved is reasonably advanced, I fear that Greenblatt may be leaving out a tad too much for the broader reading public who may not be so well versed. The fact that he does bring so many clear specifics to the forefront may more than compensate for this however.

In some interesting respects, this could be considered the humanities counterpart to the more science-centric story of Owen Gingerich’s The Book Nobody Read: Chasing the Revolutions of Nicolaus Copernicus. Though Simon Winchester is still by far my favorite nonfiction writer, Greenblatt does an exceedingly good job of narrating what isn’t necessarily a very linear story.

Greenblatt includes lots of interesting tidbits and some great history. I wish it had continued on longer… I’d love to have the spare time to lose myself in the extensive bibliography. Though the footnotes, bibliography, and index account for about 40% of the book, the average reader should take a reasonable look at the quarter or so of the footnotes which add some interesting additional background an subtleties to the text as well as to some of the translations that are discussed therein.

I am definitely very interested in the science behind textual preservation which is presented as the underlying motivation for the action in this book. I wish that Greenblatt had covered some of these aspects in the same vivid detail he exhibited for other portions of the story. Perhaps summarizing some more of the relevant scholarship involved in transmitting and restoring old texts as presented in Bart Ehrman and Bruce Metzter’s The Text of the New Testament: Its Transmission, Corruption & Restoration would have been a welcome addition given the audience of the book. It might also have presented a more nuanced picture of the character of the Church and their predicament presented in the text as well.

Though I only caught one small reference to modern day politics (a prison statistic for America which was obscured in a footnote), I find myself wishing that Greenblatt had spent at least a few paragraphs or even a short chapter drawing direct parallels to our present-day political landscape. I understand why he didn’t broach the subject as it would tend to date an otherwise timeless feeling text and generally serve to dissuade a portion of his readership and in particular, the portion which most needs to read such a book. I can certainly see a strong need for having another short burst of popularity for “On the Nature of Things” to assist with the anti-science and overly pro-religion climate we’re facing in American politics.

For those interested in the topic, I might suggest that this text has some flavor of Big History in its DNA. It covers not only a fairly significant chunk of recorded human history, but has some broader influential philosophical themes that underlie a potential change in the direction of history which we’ve been living for the past 300 years. There’s also an intriguing overlap of multidisciplinary studies going on in terms of the history, science, philosophy, and technology involved in the multiple time periods discussed.

This review was originally posted on GoodReads.com on 7/8/2014. View all my reviews

Lecture Series Review: “Augustine: Philosopher and Saint” by Phillip Cary

Augustine: Philosopher and Saint (Great Courses, #611)

Augustine: Philosopher and Saint byProfessor Phillip Cary, Ph.D., Eastern University (The Learning Company, 1997)

My rating: 4 of 5 stars

This series of 12 audio lectures is an excellent little overview of Augustine, his life, times, and philosophy. Most of the series focuses on his writings and philosophy as well as their evolution over time, often with discussion of the historical context in which they were created as well as some useful comparing/contrasting to extant philosophies of the day (and particularly Platonism.)

Early in the series there were some interesting and important re-definitions of some contemporary words. Cary pushes them back to an earlier time with slightly different meanings compared to their modern ones which certainly helps to frame the overarching philosophy presented. Without a close study of this vocabulary, many modern readers will become lost or certainly misdirected when reading modern translations. As examples, words like perverse, righteousness, and justice (or more specifically their Latin counterparts) have subtly different meanings in the late Roman empire than they do today, even in modern day religious settings.

My favorite part, however, has to have been the examples discussing mathematics as an extended metaphor for God and divinity to help to clarify some of Augustine’s thought. These were not only very useful, but very entertaining to me.

As an aside for those interested in mnemotechnic tradition, I’ll also mention that I’ve (re)discovered (see the reference to the Tell paper below) an excellent reference to the modern day “memory palace” (referenced most recently in the book Moonwalking with Einstein: The Art and Science of Remembering Everything) squirreled away in Book X of Confessions where Augustine discusses memory as:

“fields and spacious palaces” “…where are the treasures of innumerable images, brought into it from things of all sorts perceived by the senses. There is stored up, whatsoever besides we think, either by enlarging or diminishing, or any other way varying those things which the sense hath come to; and whatever else hath been committed and laid up, which forgetfulness hath not yet swallowed up and buried.”

Those interested in memes and the history of “memoria ex locis” (of which I don’t even find a reference explicitly written in the original Rhetorica ad Herrenium) would appreciate an additional reference I subsequently found in the opening (and somewhat poetic) paragraph of a paper written by David Tell on JSTOR. The earliest specific reference to a “memory palace” I’m aware of is Matteo Ricci’s in the 16th century, but certainly other references to the construct may have come earlier. Given that Ricci was a Jesuit priest, it’s nearly certain that he would have been familiar with Augustine’s writings at the time, and it’s possible that his modification of Augustine’s mention brought the concept into its current use. Many will know memory as one of the major underpinnings of rhetoric (of which Augustine was a diligent student) as part of the original trivium.

Some may shy away from Augustine because of the religious overtones which go along with his work, but though there were occasional “preachy sounding” sections in the material, they were present only to clarify the philosophy.

I’d certainly recommend this series of lectures to anyone not closely familiar with Augustine’s work as it has had a profound and continuing affect on Western philosophy, thought, and politics.

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Brief Book Review: “Make Your Own Soda: Syrup Recipes for All-natural Pop, Floats, Cocktails, and More”

Make Your Own Soda: Syrup Recipes for All-Natural Pop, Floats, Cocktails, and More by Anton Nocito
My rating: 3 of 5 stars

I ran across this at random and picked it up on a whim as I often do with books about concocting drinks–particularly having recently picked up a SodaStream machine for fashioning my own seltzer and sodas at the beginning of the new year. Certainly with some lovely photographs it does a reasonable job of harkening back to an older time. There are a handful of small asides and historical facts – though not nearly enough in my mind and it could have included some photos of early and mid-century soda fountains for all its talk about them. The real star of the book has to be the litany of recipes of which I’ll begin trying a few (and hopefully posting up reviews of those over time.)

I’d put this book in a similar league with my all-time favorite Charles Schumann‘s American Bar: The Artistry of Mixing Drinks which is dense with some great information and recipes for the bartender. This book isn’t quite as “hard core” as Schumann’s, but seems to come pretty close to his rigor for the art of mixology. I read an e-book version, which was generally passable, but I would likely have given it 4 stars had I read what I’m sure is a richer experience in print.

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Review of The Signal and the Noise: Why So Many Predictions Fail – But Some Don’t

Read The Signal and the Noise: Why So Many Predictions Fail - But Some Don't by

Nate Silver (Amazon.com)

The Signal and the Noise: Why So Many Predictions Fail, But Some Don't Book Cover

Title: The Signal and the Noise: Why So Many Predictions Fail, But Some Don't
Author: Nate Silver
Genre: Business & Economics
Publisher: Penguin Press HC
Release Date: September 27, 2012
Format: Hardcover
Pages: 534
Source: personal library

The founder of FiveThirtyEight.com challenges myths about predictions in subjects ranging from the financial market and weather to sports and politics, profiling the world of prediction to explain how readers can distinguish true signals from hype, in a report that also reveals the sources and societal costs of wrongful predictions.

Amazon

Started Reading: May 25, 2013
Finished Reading: October 13, 2013

Given the technical nature of what Nate Silver does, and some of the early mentions of the book, I had higher hopes for the technical portions of the book. As usual for a popular text, I was left wanting a lot more. Again, the lack of any math left a lot to desire. I wish technical writers could get away with even a handful of equations, but wishing just won’t make it so.

The first few chapters were a bit more technical sounding, but eventually devolved into a more journalistic viewpoint of statistics, prediction, and forecasting in general within the areas of economics, political elections, weather forecasting, earthquakes, baseball, poker, chess, and terrorism. I have a feeling he lost a large part of his audience in the first few chapters by discussing the economic meltdown of 2008 first instead of baseball or poker and then getting into politics and economics.

While some of the discussion around each of these bigger topics are all intrinsically interesting and there were a few interesting tidbits I hadn’t heard or read about previously, on the whole it wasn’t really as novel as I had hoped it would be. I think it should be required reading for all politicians however, as I too often get the feeling that none of them think at this level.

There was some reasonably good philosophical discussion of Bayesian statistics versus Fisherian, but it was all too short and could have been fleshed out more significantly. I still prefer David Applebaum’s historical and philosophical discussion of probability in Probability and Information: An Integrated Approach though he surprisingly didn’t mention R.A. Fisher directly himself in his coverage.

It was interesting to run across additional mentions of power laws in the realms of earthquakes and terrorism after reading Melanie Mitchell’s Complexity: A Guided Tour (review here), but I’ll have to find some texts which describe the mathematics in full detail. There was surprisingly large amount of discussion skirting around the topics within complexity without delving into it in any substantive form.

For those with a pre-existing background in science and especially probability theory, I’d recommend skipping this and simply reading Daniel Kahneman’s book Thinking, Fast and Slow. Kahneman’s work is referenced several times and his book seems less intuitive than some of the material Silver presents here.

This is the kind of text which should be required reading in high school civics classes. Perhaps it might motivate more students to be interested in statistics and science related pursuits as these are almost always at the root of most political and policy related questions at the end of the day.

For me, I’d personally give this three stars, but the broader public should view it with at least four stars if not five as there is some truly great stuff here. Unfortunately a lot of it is old hat or retreaded material for me.

Book Review: “Complexity: A Guided Tour” by Melanie Mitchell

Read Complexity: A Guided Tour by

Melanie Mitchell (amzn.to)

Title: Complexity: A Guided Tour
Author: Melanie Mitchell
Genre: Popular Science
Publisher: Oxford University Press
Release Date: May 28, 2009
Format: Hardcover
Pages: 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.

Amazon

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.

Book Review: Gregory Chaitin’s “Proving Darwin: Making Biology Mathematical”

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.

For the technically interested reader, save yourself some time and simply skim through chapter five and a portion of the appendix relating to his proof and then move on to his actual paper. For the non-technical reader, I expect you’ll get more out of reading Richard Dawkins’ early work (The Selfish Gene) or possibly Werner R. Loewenstein’s The Touchstone of Life: Molecular Information, Cell Communication, and the Foundations of Life.

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.

This review was originally published on June 17, 2013.

Book Review: Jared Diamond’s “The World Until Yesterday: What Can We Learn from Traditional Societies?”

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.

Brief Notes on “Consider the Fork”

Consider the Fork: How Technology Transforms the Way We Cook and Eat by Bee Wilson was one of my favorite Christmas presents this year. It covered my loves of history, gadgets, food, technology, entomology, popular culture and even evolution and anthropology. The major broad themes were very interesting and enlightening while being very well researched.

There were a few short sections on individual technologies which did feel a bit throw in almost as afterthoughts or which were related to the bigger topics, but just didn’t stand up on their own. Fortunately these didn’t detract from the overall work, though I did feel a bit more on these could have been written.

This is one of the most interesting books on food which I’ve had the pleasure of reading.

Book Review: The Man Who Loved China: The Fantastic Story of the Eccentric Scientist Who Unlocked the Mysteries of the Middle Kingdom by Simon Winchester

Read The Man Who Loved China: The Fantastic Story of the Eccentric Scientist Who Unlocked the Mysteries of the Middle Kingdom by Simon Winchester (Harper Perennial)

The Man Who Loved China: The Fantastic Story of the Eccentric Scientist Who Unlocked the Mysteries of the Middle Kingdom Book Cover

Title: The Man Who Loved China: The Fantastic Story of the Eccentric Scientist Who Unlocked the Mysteries of the Middle Kingdom
Author: Simon Winchester
Genre: Biography & Autobiography
Publisher: Harper Perennial
Release Date: April 28, 2009
Format: Paperback
Pages: 352

In sumptuous and illuminating detail, Simon Winchester, bestselling author of The Professor and the Madman, brings to life the extraordinary story of Joseph Needham—the brilliant Cambridge scientist, freethinking intellectual, and practicing nudist who unlocked the most closely held secrets of China, once the world's most technologically advanced country.

Amazon

Winchester really is a magnificent writer. Although I am a bigger fan of some of his other works, this certainly fits well into the rest of his life’s opus. Somehow he manages to cover bits of science, technology, philosophy, history, (his love) geology, archaeology, culture, politics and even uses his flair for travel writing with great ethos and pathos to tell an interesting story.

Aside from the breadth of topics he covers while telling the story of one man’s life’s work, he writes about and discusses topics which should be part of everyone’s personal cultural knowledge. As a small example, he makes mention of one of the real life archaeologists who served as a model for Indiana Jones – though sadly he only makes the direct connection in a footnote which many may not likely read.

Though I had originally picked up the book out of general curiosity (not to diminish the fact that I’m on a quest to read every word Winchester has written), I find that it also neatly fits into providing some spectacular background on the concept of “Big History” (see Maps of Time: An Introduction to Big History) as it relates to China’s place in the world. In particular “Needham’s question” (briefly: Why, given China’s illustrious past, did modern science not develop there after the 1500’s?) turned around becomes a interesting illustration on the course of human history and the rises and falls of cultures and societies since the Holocene.

For those who may miss the significance, I was particularly impressed with the overall literary power imbued to the book by the use of the book-ended contrasts of Needham’s Chongqing at the opening of the work and modern day Chongqing at the close. This is one of the few times that the mechanics behind how Winchester, the master of telling often non-linear stories, has been patently obvious to me. I hope one day to unravel all of his other secrets. I can only imagine that in his heavy research of his topics, he somehow internally sees the ultimately magical ways in which he will present the information.

I will note that, in contrast to some of his past works, this one had some better physical maps and photos to go along with the text, although I was highly disappointed in their unusable presentation in the e-book version of the book. (Higher dpi versions would have gone a long way, particularly with the ability to zoom in on them in most e-readers.) For those unfortunate enough to have the e-book copy, I commend picking up a physical copy of the book for better interpretations of the photos and maps included.

Finally, perhaps for Winchester’s benefit, I’ll note that typically I would give this book a full five stars in comparing it will all others, but I’m comparing it only with Winchester’s other works and, so it stands at four, and that only because there isn’t the ability to give tenths or hundredths.

Reading Progress

12/17/09 marked as: want to read; “Purchased copy from Amazon.com.”
12/27/09 Purchased copy from Amazon.com.
02/05/10 started reading
04/24/10 started reading again
04/24/2010 8.81% done or on page 31 of 316; “Simon Winchester has such a lovely writing style and grasp of language. I’m depressed that I’ve finished reading most of his works.”
12/03/12 started reading again from the beginning
12/03/2012 09.0% done
12/10/2012 20.0% done
12/17/2012 30.0% done
12/20/2012 40.0% done
12/31/12 Finished book

Highlights, Quotes, & Marginalia

John Hay, America’s secretary of state at the turn of the twentieth century, remarked in 1899 that China was now the “storm center of the world,” and that whoever took the time and trouble to understand “this mighty empire” would have “a key to politics for the next five centuries.”

Highlight (blue) – Location XXX

China – storm center of the world;
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Guide to highlight colors

Yellow–general highlights and highlights which don’t fit under another category below
Orange–Vocabulary word; interesting and/or rare word
Green–Reference to read
Blue–Interesting Quote
Gray–Typography Problem
Red–Example to work through

Book Review: Werner Loewenstein’s “The Touchstone of Life: Molecular Information, Cell Communication, and the Foundations of Life”

The Touchstone of Life: Molecular Information, Cell Communication, and the Foundations of Life by Werner R. Loewenstein

Though there is a paucity of equations, particularly on the information theoretic side, Loewenstein does a fantastic job of discussing the theory and philosophy of what is going on in the overlapping fields of information theory and microbiology. (I will note that it is commonly held wisdom within publishing, particularly for books for the broader public, that the number of equations in a text is inversely proportional to the number of sales and I’m sure this is the reason for the lack of mathematical substantiation which he could easily have supplied.)

This is a much more specific and therefore much better – in my mind – book than John Avery’s Information Theory and Evolution which covers some similar ground. Loewenstein has a much better and more specific grasp of the material in my opinion. Those who feel overwhelmed by Loewenstein may prefer to take a step back to Avery’s more facile presentation.

Loewenstein has a deft ability to describe what is going on and give both an up-close view with many examples as well as a spectacular view of the broader picture – something which is often missing in general science books of this sort. Readers with no mathematical or microbiology background can benefit from it as much as those with more experience.

One thing which sets it apart from much of its competition, even in the broader general science area of non-fiction, is that the author has a quirky but adept ability to add some flowery language and analogy to clarify his points. Though many will find this off-putting, it really does add some additional flavor to what might be dry and dull explication to many. His range of background knowledge, philosophy and vocabulary are second only (and possibly even on par or exceeding in some cases) that of Simon Winchester.

I’d highly recommend this book to people prior to their academic studies of biochemistry or molecular cell biology or to budding biomedical engineers prior to their junior year of study. I truly wish I had read this in 1994 myself, but alas it didn’t exist until a few years after. I lament that I hadn’t picked it up and been able to read it thoroughly until now.

For my part, his drastically differing viewpoint of the way in which biology should be viewed moving forward, is spot on. I am firmly a member of this new “school”. His final chapter on this concept is truly illuminating from a philosophical and theoretical view and I encourage people to read it first instead of last.

I’ll also note briefly that I’ve seen some reviews of this book which make mention of creationism or intelligent design and whether or not proponents of those philosophies feel that Loewenstein’s work here supports them or not, particularly since Loewenstein appeared on a panel with Dembski once. I will state for those who take a purely scientific viewpoint of things, that this book is written in full support of evolution and microbiology and doesn’t use the concept of “information” to muddy the waters the way many ID arguments are typically made.

Original review posted to GoodReads.com on 9/4/12

Book Review: Charles Seife’s “Proofiness: The Dark Arts of Mathematical Deception”

Read Proofiness: The Dark Arts of Mathematical Deception (Penguin)

Proofiness: The Dark Arts of Mathematical Deception Book Cover

Title: Proofiness: The Dark Arts of Mathematical Deception
Author: Charles Seife
Genre: Mathematics, Popular Science
Publisher: Penguin
Release Date: September 23, 2010
Format: Hardcover
Pages: 320

The bestselling author of Zero shows how mathematical misinformation pervades-and shapes-our daily lives. According to MSNBC, having a child makes you stupid. You actually lose IQ points. Good Morning America has announced that natural blondes will be extinct within two hundred years. Pundits estimated that there were more than a million demonstrators at a tea party rally in Washington, D.C., even though roughly sixty thousand were there. Numbers have peculiar powers-they can disarm skeptics, befuddle journalists, and hoodwink the public into believing almost anything. "Proofiness," as Charles Seife explains in this eye-opening book, is the art of using pure mathematics for impure ends, and he reminds readers that bad mathematics has a dark side. It is used to bring down beloved government officials and to appoint undeserving ones (both Democratic and Republican), to convict the innocent and acquit the guilty, to ruin our economy, and to fix the outcomes of future elections. This penetrating look at the intersection of math and society will appeal to readers of Freakonomics and the books of Malcolm Gladwell.

Amazon

Charles Seife doesn’t prove that mathematics is essential for a democracy, but he certainly shows how the lack of proper use of mathematics can fray heavily at the edges!

Proofiness was a great book to have read over a long Fourth of July holiday. Though many people may realize some of the broad general concepts in the book, it’s great to have a better structure for talking about concepts like Potemkin numbers, disestimation, fruit packing, cherry picking, apple polishing, comparing apples to oranges, causuistry, randnumbness, regression to the moon, tragedy of the commons, and moral hazard among others. If you didn’t think mathematics was important to daily life or our democratic society, this book will certainly change your mind.

Seife covers everything from polls, voting, politics, economics, marketing, law, and even health to show how numbers are misused in a modern world that can ill-afford to ignore what is really going on around us.

This is a fantastic book for nearly everyone in the general public, but I’d highly recommend it for high school students while taking civics.

Reading Progress

07/07/12 marked as: currently reading
07/07/12 23.0% #
07/09/12 52.0%
07/09/12 Finished book