Reddit reviews Physical Biology of the Cell

[Physics PhD, theoretical soft condensed matter physics/active matter]
In short, I think interdisciplinary research is always a good thing. Both sides benefit from different ways of thinking and different methodology, which leads to an even greater understanding.

Long version:
Biology (unlike physics or mathematics) contains an “-ology” suffix, which means it is the study of something, specifically life. Whereas physics is more of way understanding and distilling nature through universal principles, and mathematics is a tool or a language to develop those principles and more. Physics/mathematics and biology meet most commonly when biologists borrow physics/math tools to understand new biology. For example, the use of optical tweezers (part of this year’s physics Nobel prize) to accurately control proteins in the subcellular environment in vivo is a vital tool in understanding vesicle transport (if I’m not mistaken). Or in general, the use of more mathematics to make biology more quantitative may help make biology experiments more reproducible.

A second way biology and physics meet is when physicist use biology as a system to understand new physics of things out of equilibrium (or active), complex/adaptive networks, or living. For example, William Bialek and Jeremy England develop general theories for living systems. Mathematics is used as a language to think about these theories. One of my favorite analogies is, “if mathematics is the language of nature, physics is the poetry”.

As for mathematics and biology without physics, ecology is a field that has been a fruitful endeavor for both math and biology.

Lastly, I’d like to add that biology is not being replaced by physics/math. The goals of the fields are inherently different. But where there’s some overlap in these goals, teams collaborate and even more can be achieved/understood than separately. This is beautiful science.

P.S. Two great textbooks where biology, math and physics (and some chemistry) meet are “Biophysics” and “Physical Biology of the Cell”.

My favorite undergrad course that I ever took was biophysics (under the physics dept). The course used this textbook: http://www.amazon.com/Physical-Biology-Cell-Rob-Phillips/dp/0815344503/ref=dp_ob_title_bk. I highly recommend it for a first look at biophysics.

If you want a textbook, I would recommend one of two books:

Biological Physics by Philip Nelson is a pretty good starting point. The author tried to write a book that is both as accessible as possible and introduces only the most important topics. He covers a lot of interesting, but important material like random walks and molecular machines assuming that the reader does not have a very strong background in either biology or physics. The advantage to this is that he covers only the most important ideas, and in a way that someone with only introductory physics and calculus can understand. The downside is that some of the results are not general, focussing on one dimension instead of three for example, and for the experienced his introductions can be a little redundant. Nelson tries to get around this by having an optional “Track 2” that goes into greater detail and looks are tough problems and original papers.

Physical Biology of the Cell by Rob Phillips is also very good. This book is much longer than the Nelson book and goes into greater detail on a lot of the material. Where Nelson was trying to include only the most important topics, Phillips tries to include everything. The upside is that this book covers more examples and often includes more general results, but it makes for a long read at over a thousand pages. A fairly strong background in some higher level physics, like knowing how to set up and use a partition function, makes reading this book much easier.

I personally like the Phillips book more than the Nelson book, but it depends on where you are at in your major. If you have just taken introductory physics, the Nelson book might be better, if you have taken some higher level courses (especially thermodynamics/statistical mechanics) the Phillips book would be better. Either way I recommend checking them out from the library before you buy them.

Edit: How could I forget this little gem: Can a Biologist Fix a Radio? by Lazebnik. If you want a nice introduction into the philosophy of biophysics, I strongly recommend this well written article.

A good introductory text on the statistical mechanics of biopolymers (including a number of models of DNA) is Ken Dill's Molecular Driving Forces. Much of it is undergraduate level, and it will necessarily include simple models that are primarily pedagogical, but they are nonetheless incredibly useful tools for connecting to the literature in a deeper way. For example, two state models can deliver some surprising results despite how simple they are -- such models show up in the literature in the form of elastic network models (ENMs), where two well-defined configurations are used to construct harmonic approximations to the state space. These can then be used to model transitions between states across the potential surface. ENMs aren't as relevant to DNA, as far as I know (I work on a membrane transporter at the moment), but is representative of the simpler tools used in the field.

Additionally, Rob Phillips has some very useful texts (that emphasize an intuition of the length- and time-scales involved): Physical Biology of the Cell and Cell Biology by the Numbers.

Hope that helps!

If you look online you can find pdfs of

"Physical Biology of the Cell"

https://www.amazon.co.uk/Physical-Biology-Cell-Rob-Phillips/dp/0815344503

This is a book that basically looks at biology through a physicist's lens, rather than a biochemist's.

You could also try "Biological Physics" by Nelson.


These books spend a good chunk of time dealing with topics such as Statistical Mechanics, Self-assembling structures, Polymer Physics, etc...

I think Physical Biology of the Cell is quite good.

Book in question https://www.amazon.com/Physical-Biology-Cell-Rob-Phillips/dp/0815344503

I mostly learned from a variety of sources, as there's not an ideal single text on this avenue of research, IMO.

I found general small-angle scattering references for free here and here, the latter being a PDF document from the EMBL small-angle scattering group. For NSE experiments on these sorts of systems, it's pretty much expected you've already done characterization of your samples via small-angle x-ray and/or neutron scattering

I'd also recommend the NIST Summer School course materials as a good and inexpensive way to get started on the neutron spectroscopy side of things. Most of what I'd seen in terms of texts tended to be fairly pricey monographs when starting out, so I'd either borrow stuff from coworkers or my institutional library. There are advanced undergrad/starting grad student texts on x-ray & neutron scattering - e.g., 1 and 2 - but I didn't find out about them until a bit further into my studies.

As might be obvious, there's definitely inspiration and foundational work to be found in the polymer science literature. I went running to Doi and Edwards, for example, when I realized that I needed more background reading in this area, but I'm sure others have their particular favorites in this and related areas.

Insofar as the bio-side of things, well, I've been doing biophysically oriented research since I was an undergrad. I'd suggest a popular biophysics text as well (either Nelson's Biological Physics or Physical Biology of the Cell ) as a starting point/reference. These are aimed towards advanced undergraduates or new grad students as well, mostly due to the interdisciplinary nature of the topics. Speaking of PBoC, one of the authors maintains a publications page where you can check out the PDFs of his group's work.

I think I'll end there, as I think that should be enough pleasure reading for a little while, at least.

i did my phd in a related field. it seems like you will have enough math and that some more computer programming could be a good thing. the main pitfall in this kind of stuff is that people want to do a bunch of math that is more complicated than it needs to be without tying it back to the biological system.

obviously you will need help from senior people with that, but it seems to me that the best thing you could do to prepare is read a bunch about motor proteins and the cytoskeleton. every cell-biology textbook should have a few chapters on this. i recommend this book if you want something with a bit of math.

if you want, PM me the name of the person you'll be working for. odds are good i know a bit about what they are doing.