Category: Evolution
Book Review: Gregory Chaitin’s “Proving Darwin: Making Biology Mathematical”
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.
Review of “Major Transitions In Evolution” by Anthony Martin and John Hawks
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.)
You and I Are Not Much Different from Cans of Soup
Book Review: Werner Loewenstein’s “The Touchstone of Life: Molecular Information, Cell Communication, and the Foundations of Life”
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.
David Christian’s “Maps of Time” and “Big History” – a Profound Thesis
David Christian, a trained historian, is one of the leading proponents of the relatively new concept of Big History, which I view as a sea-change in the way humans will begin to view not only the world but our place in it and what we might expect to come in the future. His work presents a truly monumental and profound thesis and a drastically new framework for where humankind fits into the universe. Of the broad variety of works I’ve read in the past several decades, it is simply one of the most interesting and cohesive theses I’ve come across, and I highly and unreservedly recommend it to everyone I know. I’d put it on par or above works like Jared Diamond’s Guns, Germs, and Steel and Matt Ridley’s The Rational Optimist among others for its broad impact on how I now view the world. For scientists and researchers it has the potential to be the philosophical equivalent of The Bible and in fact, like many religious texts, it is in effect a modern day “creation myth,” albeit one with a scientific underpinning.
Christian’s work was initially brought to my attention by an article in the Chronicle of Higher Education by Jeffrey R. Young in which he mentioned that Bill Gates was a big fan of Christian’s work and had recommended it himself at a TED conference. (Gates is now also a financial supporter of Christian’s Big History Project.) I myself was aware of the Learning Company’s generally excellent coursework offerings and within a few weeks got an audio copy of the course of forty-eight lectures to listen to on my daily commute.
I’ve now devoured both his rather large text on the subject as well as a lecture series he created for a course on the subject. Below are brief reviews of the two works.The magnum written opus Maps of Time: An Introduction to Big History is an interesting change of reference from a historical perspective combining the disciplines of physics, cosmology, astronomy, geology, chemistry, microbiology, evolutionary theory, archaeology, politics, religion, economics, sociology, and history into one big area of contiguous study based upon much larger timescales than those traditionally taken in the study of historical time periods. Though it takes pieces from many disciplines, it provides for an interesting, fresh, and much needed perspective on who humans are and their place in not only the world, but the entire universe.
By looking at history from a much broader viewpoint (billions of years versus the more common decades or even just a few centuries) one comes away with a drastically different perspective on the universe and life.
I’d highly recommend this to any general reader as early as they can find time to read through it, particularly because it provides such an excellent base for a variety of disciplines thereby better framing their future studies. I wish I had been able to read this book in the ninth or tenth grade or certainly at the latest by my freshman year in college – alas the general conception of the topic itself didn’t exist until after I had graduated from university.
Although I have significant backgrounds in most, if not all, of the disciplines which comprise the tapestry of big history, the background included in the book is more than adequate to give the general reader the requisite introductions to these subjects to make big history a coherent subject on its own.
This could be an extremely fundamental and life-changing book for common summer reading programs of incoming college freshman. If I could, I would make it required reading for all students at the high school level. Fortunately Bill Gates and others are helping to fund David Christian’s work to help introduce it more broadly at the high school and other educational levels.
Within David Christian’s opus, there is also a collection of audio lectures produced by The Learning Company as part of their Great Courses series which I listened to as well. The collection of forty-eight lectures is entitled Big History: The Big Bang, Life on Earth, and the Rise of Humanity (Great Courses, Course No. 8050). It provides a much quicker philosophical overview of the subject and doesn’t delve as deeply into the individual disciplines as the text does, but still provides a very cohesive presentation of the overall thesis. In fact, for me, the introduction to the topic was much better in these audio lectures than it was in the written book. Christian’s lecture style is fantastic and even better than his already excellent writing style.
In the audio lectures Christian highlights eight major thresholds which he uses as a framework by which to view the 13.4 billion years of history which the Universe has presently traversed. Then within those he uses the conceptualization of disparities in power/energy as the major driving forces/factors in history in a unique and enlightening way which provides a wealth of perspective on almost every topic (scientific or historical) one can consider. This allows one to see parallels and connections between seemingly disparate topics like the creations of stars and the first building of cities or how the big bang is similar to the invention of agriculture.
I can easily say that David Christian’s works on big history are some of the most influential works I’ve ever come across – and having experienced them, I can never see our universe in the same naive way again.
For those interested in taking a short and immediate look at Christian’s work, I can recommend his Ted Talk “The History of Our World in 18 Minutes” which only begins to scratch the surface of his much deeper and profound thesis: [ted id=1118]
Given how profound the topic of big history is, I’m sure I’ll be writing about and referring to it often. Posts in relation to it can be found here with the tag: “big history“.
Added material below on 21-October-2016
Reading Progress
- 03/11/2011 marked as: want to read after reading Bill Gates Promotes Professor’s Online Course at TED by Jeffrey R. Young in The Chronicle of Higher Education
- 08/26/11 started reading
- 08/27/11
- 03/01/12 “Reread some of the beginning this morning as I get back into David Christian’s audio lectures.”
- 04/28/12
- 04/30/12
- 05/03/12
- 05/05/12
- 05/23/12
- 06/02/12
- 06/14/12
- 06/17/12 ; “Technically finished reading, but need to still go through the endnotes.”
- 10/21/12
Added material below on 23-October-2016
Highlights, Quotes, & Marginalia
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
Editor’s Note: Data relating to reading progress was added to this post on 10/21/16. Data relating to highlights, quotes, and marginalia added on 10/23/16.
The Central Dogma of Molecular Biology
Book Review: Matt Ridley’s “The Rational Optimist: How Prosperity Evolves”
I am now going to recommend it to everyone that I meet and have already begun proselytizing its thesis. Certainly worth a second, third, and a successive rereads given the broad array of topics it covers in such a cohesive way. Simply and truly SPECTACULAR!
Dare to be an optimist…
For those interested in short tangential video related to the broader thesis take a look at Matt Ridley’s related TedX talk:
Reading Progress
- 06/05/11 marked as: currently reading
- 06/06/11 10:37 pm Page 98 22.0% “I love the thought of ideas having sex! Evolution in a whole different framework…”
- Finished book on 07/05/11
Darwin Library, Now Online, Reveals Mind of 19th-Century Naturalist | The Chronicle
A portion of Charles Darwin’s vast scientific library—including handwritten notes that the 19-century English naturalist scribbled in the margins of his books—has been digitized and is available online. Readers can now get a firsthand look into the mind of the man behind the theory of evolution.
The project to digitize Darwin’s extensive library, which includes 1,480 scientific books, was a joint effort with the University of Cambridge, the Darwin Manuscripts Project at the American Museum of Natural History, the Natural History Museum in Britain, and the Biodiversity Heritage Library.
The digital library, which includes 330 of the most heavily annotated books in the collection, is fully indexed—allowing readers to search through transcriptions of the naturalist’s handwritten notes that were compiled by the Darwin scholars Mario A. Di Gregorio and Nick Gill in 1990.
We describe the evolution of macromolecules as an information transmission process and apply tools from Shannon information theory to it. This allows us to isolate three independent, competing selective pressures that we term compression, transmission, and neutrality selection. The first two affect genome length: the pressure to conserve resources by compressing the code, and the pressure to acquire additional information that improves the channel, increasing the rate of information transmission into each offspring. Noisy transmission channels (replication with mutations) gives rise to a third pressure that acts on the actual encoding of information; it maximizes the fraction of mutations that are neutral with respect to the phenotype. This neutrality selection has important implications for the evolution of evolvability. We demonstrate each selective pressure in experiments with digital organisms.
To be published in J. theor. Biology 222 (2003) 477-483
DOI: 10.1016/S0022-5193(03)00062-6
Bill Davenhall at TEDMED 2009 on Geomedicine: How Your Environment May Affect Your Health
Does where you live have an impact on your overhall health? Bill Davenhall believes that the location of our homes is critical to our medical history.
This is the third in a series of three papers devoted to energy flow and entropy changes in chemical and biological processes, and their relations to the thermodynamics of computation. The previous two papers have developed reversible chemical transformations as idealizations for studying physiology and natural selection, and derived bounds from the second law of thermodynamics, between information gain in an ensemble and the chemical work required to produce it. This paper concerns the explicit mapping of chemistry to computation, and particularly the Landauer decomposition of irreversible computations, in which reversible logical operations generating no heat are separated from heat-generating erasure steps which are logically irreversible but thermodynamically reversible. The Landauer arrangement of computation is shown to produce the same entropy-flow diagram as that of the chemical Carnot cycles used in the second paper of the series to idealize physiological cycles. The specific application of computation to data compression and error-correcting encoding also makes possible a Landauer analysis of the somewhat different problem of optimal molecular recognition, which has been considered as an information theory problem. It is shown here that bounds on maximum sequence discrimination from the enthalpy of complex formation, although derived from the same logical model as the Shannon theorem for channel capacity, arise from exactly the opposite model for erasure.
https://doi.org/10.1016/j.jtbi.2008.02.013
This is the second in a series of three papers devoted to energy flow and entropy changes in chemical and biological processes, and to their relations to the thermodynamics of computation. In the first paper of the series, it was shown that a general-form dimensional argument from the second law of thermodynamics captures a number of scaling relations governing growth and development across many domains of life. It was also argued that models of physiology based on reversible transformations provide sensible approximations within which the second-law scaling is realized. This paper provides a formal basis for decomposing general cyclic, fixed-temperature chemical reactions, in terms of the chemical equivalent of Carnot's cycle for heat engines. It is shown that the second law relates the minimal chemical work required to perform a cycle to the Kullback–Leibler divergence produced in its chemical output ensemble from that of a Gibbs equilibrium. Reversible models of physiology are used to create reversible models of natural selection, which relate metabolic energy requirements to information gain under optimal conditions. When dissipation is added to models of selection, the second-law constraint is generalized to a relation between metabolic work and the combined energies of growth and maintenance.
https://doi.org/10.1016/j.jtbi.2008.02.008
This is the first of three papers analyzing the representation of information in the biosphere, and the energetic constraints limiting the imposition or maintenance of that information. Biological information is inherently a chemical property, but is equally an aspect of control flow and a result of processes equivalent to computation. The current paper develops the constraints on a theory of biological information capable of incorporating these three characterizations and their quantitative consequences. The paper illustrates the need for a theory linking energy and information by considering the problem of existence and reslience of the biosphere, and presents empirical evidence from growth and development at the organismal level suggesting that the theory developed will capture relevant constraints on real systems. The main result of the paper is that the limits on the minimal energetic cost of information flow will be tractable and universal whereas the assembly of more literal process models into a system-level description often is not. The second paper in the series then goes on to construct reversible models of energy and information flow in chemistry which achieve the idealized limits, and the third paper relates these to fundamental operations of computation.
https://doi.org/10.1016/j.jtbi.2008.02.010
The most significant legacy of philosophical skepticism is the realization that our concepts, beliefs and theories are social constructs. This belief has led to epistemological relativism, or the thesis that since there is no ultimate truth about the world, theory preferences are only a matter of opinion. In this book, William Harms seeks to develop the conceptual foundations and tools for a science of knowledge through the application of evolutionary theory, thus allowing us to acknowledge the legacy of skepticism while denying its relativistic offspring.