A cautionary note: the jiggle can be misleading, making one think motion is fully represented. These are traditional 3D animations, with their profoundly misleading handling of motion, just with a "jiggle filter" added.
For illustration, consider the classic animation of a walking kinesin towing a vesicle. One could jiggle-ify it. But that won't convey that during every step, the vesicle has done a "balloon in a hurricane" exploration of every possible position it can reach while remaining tethered. Won't clarify that the very very misleading "I'm just a peaceful barge" vibe is entirely animation fantasy. Secondary content could have been added to defuse this negative educational impact, but the choice was made to optimize for, and I'm quoting, "pretty".
Jiggle-ification takes perhaps the biggest educational downside of these animations, and makes it even more misleading.
> 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.
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.
I'm currently reading (and enjoying) "How Life Works: A User's Guide to the New Biology" by Philip Ball. It proceeds from the bottom up: the first half is all about cells and smaller structures. Pretty readable but doesn't gloss over complexity.
> 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.
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.
> converting about 40 bases of DNA into its corresponding RNA each second. If an RNA polymerase were scaled up to the size of a human, it would move twice as fast as Usain Bolt's
Hold up, My own inexpert "numerical intuition" is having problems here.
If polymerase converts 40 bases/sec, and travels ~20m
/sec, how on earth is one base pair 2 meters long?
I assume what the author means is that the average conversion work done by each protein is 40 base pairs per second, however it spends most the time "seeking" rather than "converting"?
22 comments
[ 4.5 ms ] story [ 35.1 ms ] threadOne 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
For illustration, consider the classic animation of a walking kinesin towing a vesicle. One could jiggle-ify it. But that won't convey that during every step, the vesicle has done a "balloon in a hurricane" exploration of every possible position it can reach while remaining tethered. Won't clarify that the very very misleading "I'm just a peaceful barge" vibe is entirely animation fantasy. Secondary content could have been added to defuse this negative educational impact, but the choice was made to optimize for, and I'm quoting, "pretty".
Jiggle-ification takes perhaps the biggest educational downside of these animations, and makes it even more misleading.
> 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.
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.
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.
[1] https://commons.wikimedia.org/wiki/File:E._coli_Bacteria_(73...
“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.
There's a searchable database of bionumbers[1], and a draft version of "by the Numbers" officially online[2].
[1] https://bionumbers.hms.harvard.edu/search.aspx [2] https://www.dropbox.com/s/gvpleqtcv8scro4/cellBiologyByTheNu...
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.
Hold up, My own inexpert "numerical intuition" is having problems here.
If polymerase converts 40 bases/sec, and travels ~20m /sec, how on earth is one base pair 2 meters long?
I assume what the author means is that the average conversion work done by each protein is 40 base pairs per second, however it spends most the time "seeking" rather than "converting"?