Two books that I highly recommend to give you a visual and numbers view of the cell:
“The Machinery of Life” by David Goodsell is full of illustrations like the ones show in the article and really gave me a sense of what k might imagine when reading about the cell.
“Cell Biology by the Numbers” by Ron Milo and Rob Philips is full of order of magnitude calculations of about the processes of the cell. How fast are they, over what distance, how much, etc.
> For many years, I had an intense aversion to mathematics. Biology was my refuge because it was simple: Read the textbook, memorize the facts, and ace the exam. (The only reason I majored in biochemistry as a college student was because it didn't have a multivariable calculus requirement.)
Every part of this passage is a shockingly accurate description of myself. I felt that I was bad at math and did a biochem degree because it meant I could skip Cal III. Now, I'm a computational biologist and I've mostly made up with math.
Looks fascinating. Related: The Machinery of Life https://link.springer.com/book/10.1007/978-0-387-84925-6 (actually it is the book of the person who drew the first illustration in the article but I could not see any mention of the book).
I feel that, too. And the speeds those move at! There's a spot in the video where it refers to "real-time" replication of DNA, but that has got to be more like "sped up until smooth". Miles of DNA aren't getting reproduced in a few minutes at that speed.
One thing that these animations always remind me of is that speeds at that level are tied to size. We're use to a world where birds and cars are faster than pollen and insects (mostly), but the fidgety twerking of all those big proteins is due to collisions with higher-velocity, invisibly small molecules like water (Brownian motion). When was the last time a pollen grain made you flinch? Everything is kinetic/EM energy exchange; everything is in the gray area between Newtonian and quantum physics. (Shout out to Einstein, but also Boltzmann through Dirac.)
> Miles of DNA aren't getting reproduced in a few minutes at that speed.
I didn't get the "miles of DNA" reference. A single strand of DNA is approx 3 meter in length when uncoiled. Now I'm thinking how many strands may be replicated at a time.
Life is amazing. Can anyone recommend good modern starting points to someone who would want to learn more about how living beings work (from bottom up)? It has been a while since I actively delved into Biology (my school days).
Get any modern undergraduate Intro Biology textbook like Campbell. These are fantastic books: beautifully illustrated and clearly written, and way better than popular science books at the mall bookstore.
The first few Units cover all the basics: chemistry of life and energy, molecular biology, cell biology, and genetics. From there you can branch out into anything.
The research into the origen of life looks at bottom up fundamentals (how they work) of all cells since the solar system was formed. You could start with the slides in this lecture and read the underlying papers and all the references in all those papers. You probably can find these references also in all the books he wrote. https://www.youtube.com/watch?v=vBiIDwBOqQA
Maybe an educational text for the laymen has summarised this recently but I'm not aware of one. Most Biology from your school days have been rewritten.
I will have to re-read Molecular Biology of the Cell, 7th Edition, 2022. I read the 3th edition and it has changed dramatically since.
I can recommend "The song of the cell" as a starting point. If you prefer textbooks, maybe "Life: The Science of Biology". I have a translated non-english copy and besides some math issues it's a nice overview, but I'm not a biologist.
> It's a wonder that cells get anything done at all.
> The first time I did these calculations, I felt an intense appreciation for biology. And now, I want everyone else to feel the same. We ought to teach students of biology to think as mathematicians: to carefully quantify biology, to think in absolute units, and to develop a feeling for the organism.
It was interesting to read this article, but I think I would’ve understood a lot more if this entire piece had been (or were) an animated video that described it. Text and a few animations don’t do enough justice for the passion, knowledge and detail that’s in this article, IMO.
> A typical E. coli cell, after all, measures about one micrometer across.
Bit nitpicky here but ... he wrote a typical E. coli cell.
Naturally bacteria have different size ranges, depending on many factors -
nutrients, temperature, genome and so forth; e. g. look at how huge Thiomargarita namibiensis is.
But the 1 µm as average here given for E. coli, is
not correct:
So while +/- at the lower end may be 1.24 µm, the max range here would be
2.42 µm, which is what I had more in mind (e. g. roughly about 2µm). I don't
have all of the data to be able to say which is the exact value, but I think
the website at bionumbers.hms.harvard.ed is more realistic, so I would say
that E. coli's best average is more at 2µm than 1µm.
“The Machinery of Life” by David Goodsell is full of illustrations like the ones show in the article and really gave me a sense of what k might imagine when reading about the cell.
“Cell Biology by the Numbers” by Ron Milo and Rob Philips is full of order of magnitude calculations of about the processes of the cell. How fast are they, over what distance, how much, etc.
Every part of this passage is a shockingly accurate description of myself. I felt that I was bad at math and did a biochem degree because it meant I could skip Cal III. Now, I'm a computational biologist and I've mostly made up with math.
One of the most fascinating parts to me was DNA transcription. The engineering is quite precise.
Found the video I was referring to: https://www.youtube.com/watch?v=7Hk9jct2ozY
One thing that these animations always remind me of is that speeds at that level are tied to size. We're use to a world where birds and cars are faster than pollen and insects (mostly), but the fidgety twerking of all those big proteins is due to collisions with higher-velocity, invisibly small molecules like water (Brownian motion). When was the last time a pollen grain made you flinch? Everything is kinetic/EM energy exchange; everything is in the gray area between Newtonian and quantum physics. (Shout out to Einstein, but also Boltzmann through Dirac.)
I didn't get the "miles of DNA" reference. A single strand of DNA is approx 3 meter in length when uncoiled. Now I'm thinking how many strands may be replicated at a time.
The painting is wonderful. Yes, it's a snapshot in time of a dynamic state. All paintings are!
The first few Units cover all the basics: chemistry of life and energy, molecular biology, cell biology, and genetics. From there you can branch out into anything.
Maybe an educational text for the laymen has summarised this recently but I'm not aware of one. Most Biology from your school days have been rewritten.
I will have to re-read Molecular Biology of the Cell, 7th Edition, 2022. I read the 3th edition and it has changed dramatically since.
You can download it on Anna's Archive or order it at the usual suspects https://www.amazon.com/s?k=Molecular+Biology+of+the+Cell%2C+...
> The first time I did these calculations, I felt an intense appreciation for biology. And now, I want everyone else to feel the same. We ought to teach students of biology to think as mathematicians: to carefully quantify biology, to think in absolute units, and to develop a feeling for the organism.
It was interesting to read this article, but I think I would’ve understood a lot more if this entire piece had been (or were) an animated video that described it. Text and a few animations don’t do enough justice for the passion, knowledge and detail that’s in this article, IMO.
Bit nitpicky here but ... he wrote a typical E. coli cell.
Naturally bacteria have different size ranges, depending on many factors - nutrients, temperature, genome and so forth; e. g. look at how huge Thiomargarita namibiensis is.
But the 1 µm as average here given for E. coli, is not correct:
https://bionumbers.hms.harvard.edu/bionumber.aspx?id=117344&...
Length 1.78±0.54 μm
So while +/- at the lower end may be 1.24 µm, the max range here would be 2.42 µm, which is what I had more in mind (e. g. roughly about 2µm). I don't have all of the data to be able to say which is the exact value, but I think the website at bionumbers.hms.harvard.ed is more realistic, so I would say that E. coli's best average is more at 2µm than 1µm.