If you have a background in IT, and are modestly comfortable with statistics, the following foundational paper on algorithms to reconstruct the tree of life from genetic data should actually be understandable: http://science.sciencemag.org/content/311/5765/1283

The statistics really only ever amount to Occam’s Razor, I. e. fewer differences in the genome means closer relationship.

Edit: actually free full-text link: http://bioinformatics.bio.uu.nl/pdf/Ciccarelli.s06-311.pdf

I am a statistician (although as I confessed nowhere near computational biology), so, uh, yeah this is up my alley.

One more thing: Jared Diamond (of “Guns, Germs, Steel” fame) transferred the exact, same method to linguistics, using it to discover the ancestry of Pacific Islanders using features of their respective languages instead of letters of DNA. The result is both a tree of their (cultural) ancestry, and a map of their migration/expansion from island to island.

Yet another thing: Julien d’Huy uses these methods to analyze folk literature and myths. Very, very interesting research.

Excellent! I believe I remember a far longer version of the paper, and interactive widgets to explore the tree. Couldn’t find those right now and am on the road, unfortunately.

In any case, the process consists of basically two steps:

“Align” the DNA of all the species you have sequenced. That’s done using algorithms such as smith-waterman, which minimize the number of edits needed to go from one species’ version of a gene to another.

That number defines a metric that measures all the distances between the species. So, Orang-Utan to Homo Sapiens may be, say, “450”, while Homo Sapiens to Ficus Benjamini is, say “12321”.

(The difference may also be measured on the level of protein sequences. The process is basically the same, only that edits may be assigned different distance scores, because some result in more functional differences, while others are functionally “silent”. Evolutionary pressure would make the first rarer than the latter)

The metric is unitless (I. e. It doesn’t allow translation into, say, “years since species diverged”. But it should fulfill the triangle equality).

Once you have a (triangle) matrix with all the difference, all that’s needed to reconstruct a binary tree that maximizes plausibility, I. E. minimizes the sum of difference at each branching point.

Richard Dawkins’ The Ancestors Tale is a great layman introduction, on par with Bill Bryson’s as mentioned a few posts up. I’ve read both. Both cover similar subject matter, but approach it from opposite chronological orders.

Bill Bryson's "A Short History of Nearly Everything" is an amazing layman start.

It's a little dated (the first edition came out in 2004!) but to be honest, if you're interested in a "human-focused" intro and how the concepts fit together, things haven't really changed that much.

I really, really, really loathe Bill Bryson, because every time he touches on something I actually know about, there are invariably glaring, awful mistakes, including repetitions of urban legends and just the sort of 'facts' you'd expect to find on a "AMAZING TRUE FACTS" diner placemat.

And so I'm real reluctant to read what he has to say about other fields, because I've got to assume it's all that bad.

You've got to understand the purpose of those books.

You, dmd, are not going to do anything with the knowledge gleaned from those books, except possibly one of two things: Peruse further study, or inspire others (usually children) to be interested in the field. The book opens up the field, the basic concepts of the field, and a bit of history of the field to you. You now have the tools to go off and either learn more or inspire others. You can even get into conversations and debates with those well-versed in the field.

The book is a gateway into a field, not a path to follow in the field.

Can you list some examples (or are examples collected somewhere?)

Many of the errors were corrected in later editions (it's been in print for 14 years!).

You can see the original errata here:

http://errata.wikidot.com/0767908171

I leave it to your judgement whether this makes you "really, really, really loathe" the author :-) Note the book had 20 pages of just bibliography.

You know this is a problem for the layman like me. I need to get educated on the general aspects of so many things in life. But with science and knowledge always progressing at a fast pace, the "truth" is always evolving. And this makes it a problem because I cannot be 24/7 invested in every single area of my interest, which are many. So I appreciate Jared Diamond and Bill Bryson because they make available to me (random person with a lot of interests but limited time) a quick overview of things, which I gladly accept at a high enough accuracy. It's sort of like Wikipedia, yes not the be-all-end-all reference but gets you started.

Only bio class I took was in high school. The Vital Question is tricky in some places (I don't pretend to understand all of the details), but accessible, interesting, and one of my favorite books of the last few years. Of course, YMMV, but don't let that hold you back.

I would say it's accessible, yes. My background is CS and math, and I have managed to follow most of it, though I have occasionally got lost on some of the chemistry.

"If I know nothing beyond high school biology about taxonomy and nothing beyond a reasonably educated layperson about biology generally, is "The Vital Question" accessible?"

I have not yet read _The Vital Question_ but I have read his previous books and I highly, highly recommend:

_Power, Sex, Suicide_ _Oxygen_

If I had to pick just one, it would be PSS.

I'd avoid it because it is a rather misleading book whether or not it is accessible. Many people (but especially Carl Woese) led to our modern understanding of molecular phylogeny. Lane's main contact for his book was Bill Martin, who was a rival to Woese, which is fine, but the result is a story in which Martin made all the major discoveries and Woese literally gets one sentence. I'd strongly recommend Quammen's "The Tangled Tree" instead, which is a more balanced book.

IIRC, Woese gets a fair bit of credit in TVQ. Certainly far more than a sentence.

accessible!!