An introduction to systems biology

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. MajimasEyepatchApr 2024
   Absolutely right. These basic concepts like the central dogma aren't especially hard to learn, but it's important to really understand them deeply if you want anything to make sense.

   Among textbooks, Molecular Biology of the Gene by James Watson et al. is a good starting point to understand the central dogma: DNA -> RNA -> Protein. Likewise Molecular Biology of the Cell by Alberts et al. for cell biology.

   An Introduction to Systems Biology by Uri Alon is good for the more mathematically inclined once you're ready to get more advanced, though you should really have a solid grasp on the fundamentals of molecular and cellular biology first.

   None of this is for the faint of heart, but it's not especially difficult either. It's unfortunate that it's hard to get hands-on experience with biology once you've graduated from college, which helps a lot to connect the dots, but there are still plenty of great resources out there.

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3. signal_spaceApr 2024
   check out uri alon’s introduction to systems biology
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4. bglazerMar 2023
   I’d say it’s a pretty even mix of matlab and python. My advisor would be upset if I didn’t plug his framework: https://pysb.org/

   As far as textbooks go, I guess I’d recommend Uri Alon’s book: https://www.routledge.com/An-Introduction-to-Systems-Biology...

   Full disclosure, I haven’t read it, but I like his research and he’s a good communicator.

   It’s tough because it’s a newish field and not super well defined. The frustrating answer is that the best way to understand the field is maybe to read a book about biology, then a book about computational modeling, then a few papers where they put those together.

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5. ampdepolymeraseJul 2022
   Voit looks gimmicky. Uri Alon's treatment (An Introduction to Systems Biology) is much better.
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6. nextosJul 2022
   > [...] where we mostly learned things from outdated books

   I can recommend 3 really good books, SICP-level good:

   1. Biological Sequence Analysis by Durbin et al.

   How to model DNA, RNA and proteins as probabilistic languages / generative models. There is also a companion book with all exercises solved.

   2. Physical Biology of the Cell by Phillips et al.

   A massive amount of quantitative cell biology models that use simple undergrad physics.

   Originated from a Caltech course. After reading this book, all other intro to biology books look like a bag of tricks.

   3. An Introduction to Systems Biology: Design Principles of Biological Circuits by Alon.

   Bacterial circuits from the perspective of an electrical engineer.

   Sadly, NSF discontinued funding for a totally epic Cold Spring Harbor Summer school for postdocs that taught [2,3].

   A shame, we need more quantitative biology and less bags of tricks.

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