Posts tagged ‘Sam Kean’

January 24, 2013

#Book #Review – The Violinist’s Thumb by Sam Kean

by C. Michael Eliasz-Solomon

The Violinist’s Thumb by  Sam Kean -

contact:  samkean.com/contact

KeanCoversStanczyk is a BIG reader, definitely a bibliophile. My background is a computer scientist which means I am both a mathematician and computer specialist, with a school of engineering training. I have had a life-long affinity for science as well as mathematics (of which I view computers as just a branch thereof). However, in the spirit of this era’s memes, specifically, the STEM meme – we separate S.T.E.M. into constituent parts as: Science, Technology (computers no?), Engineering  and Mathematics. I had always thought of STEM as just Science & Mathematics (Ummm S&M ??) with Engineering being the School within which these topics were taught and Engineering being the rigorous discipline that is applied to various fields (Chemical Engineer, Construction Engineer, Electrical Engineer, Computer Engineer, Mechanical Engineer, etc.) and technology just an ubiquitous part. So Stanczyk considers himself a STEM knowledge worker.

Computers (Technology) often borrow concepts from other disciplines. For example, there are a whole set of “genetic” algorithms: cross-over, insertion, deletion, duplication, mutation, etc. Obviously, all branches of mathematics are represented in a wide swath of computer programs. So I have always viewed that a computer scientist would be a better professional by being well read and being able to borrow concepts from other fields to be able to bring to bear the broadest toolset to solve the great variety of challenges that a software developer is often faced with.

So now I come to this blog’s topic for today … a new book I read, The Violinist’s Thumb by  Sam Kean.

As a genealogist, I am fascinated by the thought of using genetics/DNA as another tool – however I do have some reservations (another blog post, another time). So when I saw this Kean book (published July 2012) I was intrigued. Perhaps you already know Sam Kean from his prior book, The Disappearing Spoon.

When I read a book or even before I decide to read a book, I examine a book’s “DNA” (cover, table of contents, author, etc.) to form an opinion of whether I want to invest myself in the effort. A quick scan of the book yields … the book’s organization: Introduction, Chapters (16), Epilogue, Acknowledgement, End Notes, Selected Bibliography, Index, spanning 401 pages including the index. Do not skip past the title page so quickly here. Part of the charm was the page after the title and before the table contents. It prodded my curiosity (see for yourself, I won’t ruin the surprise in this blog post, but I will email the author). Examining these parts, I linked this book in my mind to  Lewis CarrollDouglas Hofstadter and especially Stephen Jay Gould (a favorite science author of mine). So all-in-all, I decided to invest myself.

What is The Violinist’s Thumb About?

It is right there on the first page of the Introduction (which is actually page 3 – where is page 1 and 2 ??). The book is about DNA. Do not let that dissuade you. There is an interesting narrative about science and scientists and the history of DNA thought/understanding and how that understanding  evolved. The book is not bogged down in science jargon and your eyes will not gloss over with a baffling “scientific paper and statistical data” send-up. If you have read Stephen Jay Gould, then that is the tone and style of Sam Kean’s writing and it is comfortable for the non-scientist (like Stanczyk) and engaging with interesting stories and anecdotes while presenting the topic and the teaching/learning is subtle – this is not a text book nor scientific abstract, just an enjoyable read on a science topic that you may have an interest in or a curiosity about.

Criticism

Let me state up front, that my literary criticisms are slight and should not dissuade you from reading this book nor does it invalidate any of the author’s points.

[1]  ‘*’ -> look in Notes & Errata for that chapter;

It would be much better if Kean had numbered each ‘*’ note as  1,2,3 …

[2]  Page 216 referring to chimps & gorillas as “monkeys” instead of apes

[3] Chapter 14 is not about its title at all; No answer, nary any mention of the 3Billion and does not answer the title’s question

[4] 25,947 genes was lowest guess, but the actual number was not given. Was this the actual, exact number of genes?

Chap. 14, page 312.

[5] DNA debases???? I say no. The proper analogy is DNA is a historian/scribe. However, DNA history is not flattering.

[6] It took me really until Chapter 12 to understand the book title (was a reference to Paganini and his thumb)

Things I Learned

  • Radiation can be used to create mutations on demand
  • Lack of Variety in Human Genes (compared to the great apes)
  • 1815 Tambora Eruption caused 1816 year with no summer
  • Toba super-volcano Eruption 70,000 years BCE exacerbated that Ice Age, possibly causing a dire near-extinction event of humans (that did not affect the apes as much because the apes were further inland, away from Toba).
  • Zipf distributions in languages – DNA as a human language or Musical language
  • The greater the language diversity, the greater the DNA diversity. That is language diversity and DNA diversity go hand-in-hand (i.e. 1:1 correspondence). Click languages 100 sounds, English 40+ sounds, Hawaiian  around a dozen
  • mtDNA – mutation rate: once every 3,500 years
  • Mitochondrial Eve lived 170K years ago (see Wells book for a differing estimate)
  • At the DNA level, humans are 99.9 identical. So humans have less variability than the great apes.
  • Contrary to the Book of Mormon’s theological tenets, Native Americans were NOT descended from a Jewish tribe.

Things I Liked

  • Chapter 4 – The Musical Score of DNA  – DNA as a language, music (music as DNA), distribution of amino acids
  • Chapter 4 – Palindromes, in particular,  the palindrome square (from Pompeii)
  • Chapter 14 – The Human Genome Project – Science Race and Craig Venter’s impact
  • Epilogue – Craig Venter mapping his own genome

Things That Made Me Laugh

  • Craig Venter’s surprising chimp DNA (Chapter 14, page 313)
  • Chapter 8, pages 173-174 – The “gay bomb”
  • Lewis Carroll’s Mock Turtle appearance in Chapter 4
  • Bolsheviks & Humanzees (Stalin was a very naughty boy)

Things I Was Horrified By

  • Chapter 3 and  nijyuu hibakusha (Tsutomu Yamaguchi)
  • Chapter 7 and Machiavelli Microbe – Toxo (Toxoplasma gondii)
  • 8% of human genome is not human at all. It is virus DNA !
  • Human DNA suggests widespread cannibalism in all Haplotypes – although maybe that is explained by an early occurence in Africa >100,000 years ago before the diaspora/migration of modern humans [2014: I corrected this when I thought the canabilism referred to  must have happened after Haplotype diversity for this to be STILL true]
  • Chapter 12 and Paganini’s Thumb – ah the raison d’etre

Impressions

I decided to go back and re-read Deep Ancestry by Spencer Wells in parallel with this book. I wanted to consider Haplotypes and the historical migrations as it impacted and documented the human DNA’s evolution. I wish Sam Kean had included something on this – not a criticism, just a wish. I wanted a book about the human genome, its DNA and how it evolved. For me I wanted to form in my mind the DNA that is genealogy related and what that DNA implies. Kean’s book definitely gives the reader a flavor for the Human Genome Project (HGP).

Therefore, I needed to supplement Kean’s book with Deep Ancestry by Spencer Wells to answer my question about the parallel to Mitochondrial Eve (i.e. Y-Chromosome Adam ??). It turns out that Y-Chromosome Adam dates back to 60K years ago. Now I had to explain why Eve’s DNA goes back 40,000-110,000 more years than Adam’s DNA. So I needed the following factoids from Deep Ancestry :

  1. The Human genome contains about 30,000 genes
  2. 2.9-3.0 Billion  base-pairs (nucleotides) make up the human genome
  3. An average gene is 47.5K nucleotides in length (paired up in an helix) giving 95K on average in each gene. [derived by CME-S]
  4. Chromosomes vary in length from about 47M to 247M nucleotides
  5. There are 46 chromosomes. [derived, Ergo each Chromosome has on average nearly 62M nucleotides.]
  6. The Y chromosome (male sex indicator) does not recombine and is passed down intact (identical). [How often does mutation affect Y chromosome?]
  7. mtDNA (mitochondrial DNA, female lineage) has  16,569 nucleotides
  8. mtDNA has 37 genes (<448 nucleotides/gene)
  9. mtDNA is circular, while nuclear DNA (DNA from the cell nucleus) is linear
  10. mtDNA (DNA from the cytoplasm) is purely a copy of maternal mtDNA
  11. In nature only bacterial DNA is circular
  12. Mitochondrial Eve dates back to about 100K years ago
  13. Y-Chromosome Adam dates back to 60K years ago
  14. Modern humans date back to 200K years ago.

Actually I was dissatisfied by the rough figure of 30,000 genes in the human genome. Kean’s book had left me hanging with the winning pool guess of 25,947 genes (the lowest guess). But the actual number was not given.  So I had to go to Wikipedia, and on the Chromosome article I found the breakdown of the genes by chromosome and then I understood. Women have 31,731 genes and men have 30,339 genes (since the Y-chromosome of men is nearly 1400 less genes than a woman’s X-chromosome).

Stanczyk is an avid wrestler of numbers. Even though I am highly numerate, the numbers are at once boggling and also breathtaking to consider. How would I tackle the computer storage requirements of this science and the parallel processing requirements of analyzing the data. How do we go further with this data? How do you manage this data? How do you detect data errors and correct them?

Stanczyk also loved trying to construct a theory on the huge gap in years between Mitochondrial Eve and Y-Chromosome Adam. Modern humans date back to 200K years ago. Both male and female DNA has gone extinct and whole branches of modern humans’ family tree are gone. Modern humans left Africa about 100K years ago. So Y-Chromosome Adam (only 60K years ago) only dates back to the time after the human diaspora/migration began and Haplotype diversity had already begun. Since male DNA does not go back as far as the female DNA it must be something in men’s DNA or men’s nature that causes their more frequent DNA extinction. My theory is that warfare in tandem with consequences from wars (pestilence, violence, disruption of living standards, etc.) and any global natural disasters that preceded the wars or followed the wars to cause a “bottle-necking” of the human population to near extinction levels. Possibly this bottle-necking occurred a number of times over the 200,000 year history of the modern human species (before and after the human diaspora/migration out of Africa. The fact that female DNA goes further back may be explained, if they were taken as slaves/property to the victors of these wars, while the males (including male children) were eliminated thus extinguishing their male DNA Haplotypes. This demonstrates that some human DNA has been lost, since neither male nor female DNA goes back the full 200K years of modern humanity’s arrival. Ergo, some of the original ADAM/EVE DNA is now lost. We have become less diverse. This shows in comparing the diversity of HUMANS to the Great Apes (chimps/gorillas). Apparently, the DNA or behavior of the great apes is less warlike or by their lifestyle was less prone to extinction events in the past. None the less, the loss of diversity does not mean that humans are more likely to become extinct than the great apes. Indeed, our numbers and adaptability to more diverse habitats actually mean that now it is more likely that the great apes will become extinct before humans even though human DNA is less diverse, relatively speaking. The probability of humans out-surviving apes was not always so at various times over the last 200K years and could still change again.

Recommendation.

Read the Kean book. If you only have time for two chapters, then read chapter 4 and chapter 14. If you have a bit more time, also read chapter 7 too. Read the whole book. You do not need to read it sequentially, just jump in where your interest takes you. I did find reading the Introduction and the first two chapters provided me with a good starting point to jump around from. They gave me a sense of what was the author’s narrative that he was developing.

I would also recommend a quick read of  Deep Ancestry by Spencer Wells in parallel with (or before/after) reading The Violinist’s Thumb by Sean Kean.

On a lark, I also read Douglas Hofstadter’s book, Metamagical Themas. Metamagical Themas is a set of material derived from the 2.5 years that Douglas Hofstadter wrote for Scientific American (overlapping with and following after Martin Gardner (whose column Mathematical Games was anagrammed to create Hofstadter’s Metamagical Themas). In the book, Metamagical Themas, is a Chapter 27, written originally in March 1982, asking the question,  is the genetic code arbitrary (entitled, “The Genetic Code: Arbitrary?”). I found this material also extremely helpful in rounding out my knowledge of DNA. So I recommend you read all three sources:

These should whet your appetite for more and instill in you a gnawing sense of more interesting questions that still need answers.  All three sources are readable by the lay-science person or any person with an interest in science or science history.

So where did I, Stanczyk, get left at? I had read these books to learn more about evolution and science vs. religion boundaries. What I was left at is some kind of cross between those topics and a crossover with computational biology and DNA/Human Genome. Four broad topics viewed through my lenses of computers and genealogy. What an interesting Gordian Knot to unravel !

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