Evolutionary Dynamics

What Hacker News says

1. natarilMay 2026
   > engineering first-principles intro to cell bio

   Very true, these books are qualitative. There's a bit of basic math around delta-G for reactions and Chi-sq tests for genetic associations, but the conventional undergraduate introductory biology course is 99% descriptive.

   There are reasonable arguments for taking that approach. These courses are foundations for subsequent study, with the intended outcome that students have a broad but shallow understanding of core basic ideas. Lots of biology makes intuitive, mechanistic, and visual sense, much like introductory computer science and introductory chemistry.

   Obviously applied math plays a key role in biology but it tends to address specific needs like protein structure prediction, dynamic modeling of transcription/translation and metabolism, inferring phylogeny, high-throughput 'omics analysis, network simulation of epidemic outbreaks, and so on. These are great to study, but without the broader context the understanding would be relatively fragmented, lacking the big picture.

   Rereading OP's question:

   > good modern starting points to someone who would want to learn more about how living beings work (from bottom up)?

   I interpret that as wanting a general understanding, starting with chemistry and working upwards towards evolution and populations. That's all in the standard two-semester introductory course, hence my book recommendation.

   If that's wrong and OP wants a math-centric approach, here are a few gems:

   Physical Biology of the Cell, Phillips, et. al

   An Introduction to Systems Biology, Alon

   Evolutionary Dynamics, Nowack

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2. martingoodsonMar 2020
   A wonderful book that answers this and many other questions is 'Evolutionary Dynamics: Exploring the Equations of Life' by Martin Nowak.
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3. mnemonicslothJul 2016
   tldr: malware evolves into superintelligence. I'm afraid evolution doesn't work like that. Here's a good book (some math):

   https://www.amazon.com/Evolutionary-Dynamics-Exploring-Equat...

   The long and the short of it is that software can't evolve because too much of its genome space is lethal, and the non-lethal parts are non-contiguous, so the quasispecies decoheres -- if it survives at all -- instead of climbing to the top of the fitness landscape.

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4. apiAug 2012
   I don't think it can yet. My point was just that such things should be studied, and are being studied.

   The link I provided is of particular interest in the area of moral theory. There is a good book called Evolutionary Dynamics that summarizes this group's work and contains, among other things, a rather beautiful equation predicting the optimal rate of forgiveness in cooperating populations.

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5. jballancJun 2009
   Oh man...I was totally with him until I saw "Selfish Gene". Please, speaking as an evolutionary biologist, don't read that book. Dawkins oversimplifies the important and complicates the obvious. If you want a good book on an analytical approach to evolution, might I recommend "Evolutionary Dynamics" by Nowak in its place.
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6. jballancApr 2009
   Ok, while I understand that this sort of article might be interesting, honestly it's only scratching the surface of the current state of the art (and the idea of TE's acting as fodder for evolution isn't exactly new).

   Short reply -- Get Martin Nowak's book Evolutionary Dynamics

   Long reply -- Even Nowak's work is just the beginning (disclaimer: my current Ph.D. thesis work is building off of Nowak's start). Let's start with this notion that TE's are vital for evolution. Real answer: sort of. You see, there's an awful lot of species that don't have an overabundance of "junk" DNA, yet are still able to adapt and evolve. The reason that TE's at least seem to be more important in higher order plants and animals is because of how such organisms organize their genomes.

   Ok, before I get carried away on a long rant, here's the heart of the matter for the hacker audience:

   Proteins fold into domains. These are compact structures with a rough upper limit to their size that typically can carry out one biochemical function. In E. coli, most genes code for proteins with only one domain. So, E. coli can evolve by grabbing new genes, turning genes on or off, or in some circumstances, evolve new functionality from existing domains through random mutation. (In reality, random mutation takes a long time to produce anything useful, and the creation of novel domains appears to no occur. There's a theory growing in prominence that all of the protein domain folds that exist today were present when life began, and may even represent independent life originating events...but I'm getting off track.)

   In humans, most of our proteins are multi-domain. Not all of these domains, however, are catalytic. That is, in a human protein with 5 domains, maybe only one actually has biochemical activity. The function of the rest is to modulate that activity or localize the protein to one part of the cell or another. Also, the mechanisms controlling when genes get turned on and off in humans is much more complex than in bacteria. Therefore, evolution in higher order plants and animals is much more likely to occur through a "shuffling" of domains and regulatory elements. Because TE's are good at "shuffling" DNA, it's not surprising that having a healthy dose of this sort of "junk" DNA is advantageous. Of course, that's not all...there's also neutral evolution and pseudo-genes and epigenetic inheritance, etc. Biology is really on the cusp of exploding (oh, and I'm writing a book about that too ;-).

   tl;dr -- The genetics of higher order plants and animals is not unlike a program which relies heavily on many libraries. If you swap out one XML parser for a better XML parser, you'll get better performance (and more customers!). Transposable elements function (sort of) like biology's equivalent of a linker, and can help organisms swap in and out libraries/protein domains.

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