by jsomers on 11/18/20, 1:21 PM with 298 comments
by joshuamcginnis on 11/19/20, 4:18 AM
What you can do today from your kitchen or home lab is remarkable. For instance, I taught myself PCR (polymerase chain reaction) and recently published my first genetic sequence at GenBank from fungi that I cultured, extracted, sequenced and aligned. I'm planning to have developed my first GMO yeast in the next 90 days.
If you're interested, I also host the EverymanBio Podcast (YouTube & iTunes) where I talk to folks doing incredible work in the biotech / startup / diybio community.
by Sophistifunk on 11/19/20, 6:15 AM
But most of all, you're being kept out of the house so that both your parents can go back to jobs they don't like.
by nneonneo on 11/19/20, 3:30 AM
I had a dining-table discussion with my dad the other day where the subject of DNA mismatch repair came up. It turns out that, in E. coli, a very simple & widely studied prokaryote, there's a mechanism called DNA mismatch repair which fixes errors which might occur during DNA copying. If an error is detected - a mismatch (e.g. a G paired with a T) - a trio of proteins (MutL, MutS, MutH) spring into action. The original template strand is already methylated - marked with an extra methyl group - at certain points in the genome (usually where there's a C followed by a G). The daughter strand, on the other hand, is usually not methylated yet. So, one of these proteins starts running down the DNA from the mismatch site, looking for a methyl group - up to 1000 base pairs away. When it finds a site with a methyl group on one side but not the other, it nicks (marks) the daughter strand, and another protein complex comes along and chops up everything from the nick to the mismatch site. The DNA polymerase then comes by and resynthesizes the whole strand.
Just three proteins are needed to drive this complex algorithm - a linear search procedure which distinguishes the mother from the daughter strand, a marking procedure which identifies the incision point, and a third to chop up the DNA and prepare it for resynthesis. What's even more bonkers is that E. coli - under stressful situations - will disable certain DNA repair mechanisms to deliberately induce more mutations. And I know that there are thousands more such pathways and complex interactions going on in cells all the time - many of which we simply haven't discovered or probed yet.
I wish that everything in biology could be explained so neatly. Unfortunately, real biology is so incredibly messy. There's just so much we don't know - and so much that we can't neatly slot into an explanation like this. But, I know now that in another life I probably would have been a biologist!
by m463 on 11/19/20, 2:49 AM
I took biology 101 in college and what I thought would be really interesting turned out to be SO unexpectedly meaningless.
Now years later all I recall is the memorization of phylums and kingdoms on one test and cell structures on another test and sitting in a large auditorium looking at the map and not the territory.
The course was so much about WHAT and never about WHY.
I don't know if I was immature, or if the biology course was a "weed out" course designed to filter out all but the most dedicated, or if biology education is off the rails.
I do know that every subject would benefit from a little storytelling, a little excitement and a good helping of why.
by achenatx on 11/19/20, 5:30 AM
There is so much potential for biology to be engineering, but the reality is you can spend your whole life studying one tiny aspect of something esoteric. You can spend your whole life trying to find one amazing cure (or not).
Biology is great if you are interested in learning how the world works, but not so great if you love to create new things.
Even with medicine you are essentially a mechanic for humans instead of cars and the technology improves a lot slower.
I considered doing bioinformatics, but there was essentially no way to make money because grad students were doing everything for 12K/year.
One great thing about biology is that it is easy to understand because everything makes sense and "works" like you think it should. Human created systems often times dont make sense at all.
by ampdepolymerase on 11/19/20, 3:46 AM
by faichai on 11/19/20, 10:42 AM
It was much later in my 30s after buying a book on cellular biology that I learnt that enzymes work by using electro-static forces to bend target molecules to increase their probability of breaking at lower energies. It’s this pattern of +ve and -ve charges on the enzyme that matches the target molecule and provides the basis of the key/lock metaphor.
This realisation was so beautiful, astonishing and illuminating that I can’t for the life of me understand why it was left out, particularly as we were learning about the physics and chemistry of the related concepts anyway.
by locallost on 11/19/20, 8:50 AM
His complaint about calculating the surface of a triangle is fair, but actually I do remember that in 5th/6th grade we had to derive things like the height of an even sided triangle give the length of the side, and subsequently the surface. But the Pythagorean theorem was kind of just given. Is there a way to provide a proof that children will understand and thus understand better in general? I think that's really non trivial (and I hope people are working on it).
by madrox on 11/19/20, 8:45 AM
"You can know the name of a bird in all the languages of the world, but when you're finished, you'll know absolutely nothing whatever about the bird... So let's look at the bird and see what it's doing — that's what counts. I learned very early the difference between knowing the name of something and knowing something."
I knew this intuitively at a very young age, which made me a poor public school student. Unfortunately, there are some subjects that are easy to learn on your own, and some that are only easy with a good teacher. Biology is one of the latter. However, that may be different these days.
by emmanueloga_ on 11/19/20, 4:12 AM
This is a common complaint when learning many subjects, and many teachers don't explain why the names are needed.
Take music theory, it has an insane amount of vocabulary and concepts to assimilate, but if you watch any of the popular music theory videos on YouTube around these days, you get a glimpse of what mastering those terms looks like.
So, extrapolating to other areas, it seems like school needs to do a much better job of explaining the focus on vocabulary. The language of Algebra, the language of Organic Chemistry, the language of Music Theory, etc, etc ... what superpowers does mastering those languages unlock?
To me, watching someone work who already mastered those languages in action can be very inspiring, even if haven't reached that level of understanding yet.
by teekert on 11/19/20, 8:09 AM
Over time I learned that if you can imagine some process, it's likely you'll find it somewhere in biology (keep the laws of physics in mind though ;)).
by dekhn on 11/19/20, 3:18 PM
I continued to pursue biology in undergrad, learning some excellent underlying basis (that Roche Biochemistry pathways poster? I had it memorized by the end of my junior year) and getting some experience in the new field of sequence analysis (at the time, E.Coli was being sequenced, and you could FTP the new sequences when the showed up on the server). I worked with some very early machine learning in '95 to build gene classifiers.
This seemed like a good area to work in ("molecular biologists make $70K/year!") so I went to grad school and continued to learn deep biology and work in computational biology along with some wet lab work (whcih I'm terrible at). Postdoc as well- I was on my way to being a Professor of Biology. But, realistically, I couldn't compete with high end postdocs and decided instead to go into industry as a computer scientist.
I've still dabbled in biology- my long term passion is still to build a warehouse-scale biology lab with a tightly coupled robotic experiment framework and machine learning system to do automated biology. A number of people are working in this area and all failing, but writing wonderful PR that makes it sound like they're solving the world's problems. Biology has a huge hype problem- remember when it was promised that genomics was going to cure all human diseases?
I've dropped all biology and returned to computers (with some hardware hacking). It's a real relief- everything makes sense, the engineering is straightforward, you can do it in your garage without contaminating all your surfaces.
by orobinson on 11/19/20, 7:13 AM
I think another root cause is modern schooling does a pretty terrible job of teaching a passion for learning (unless of course you’re lucky enough to have some amazing teachers). I didn’t really completely discover the joy of learning until I did my degree and since then I’ve had a renewed interest in subjects I paid less attention to in school because the thought of learning new things excites me a whole lot more than it used to.
by bartread on 11/19/20, 12:59 PM
This opening sentence resonated hard with me.
For reasons now too obscure to go into I decided to study biochemistry at university and whilst, at the time, it sounded like it should be exciting, what I found instead was that it was substantially an uninspiring exercise in memorization from beginning to end. No interesting general principles or profound insights.
I hated it. Not exactly from the beginning, but certainly after the first year novelty wore off, and I despised it ever more as time went on. In the end - surprise, surprise - I didn't do that brilliantly. A total waste of time but sometimes you only learn by making quite expensive mistakes.
I probably would have been a lot happier had I studied physics, or even maths, or - as I ended up converting into with a post-grad masters, and thankfully I at least managed to do well enough to qualify for that course - computer science.
by Upvoter33 on 11/19/20, 3:58 AM
by stef25 on 11/19/20, 6:12 AM
Also wanted to mention the differentiation of cells in an embryo (how the f*ck can that even work ... not in a lab, but our own bodies?!) - it's explained really well in "The Gene" (hormonal gradients in the embryonic fluid). Author also mentions this.
Natural selection ... is our DNA some kind of cosmic RAM memory that stores all this information over millions of years?
The other day I went to get my hearing checked and the doc explained to me how sound is captured by the ear drum and transferred to the brain through a few bones and along hairs & nerves. It's basic high school stuff but if you take a step back and think about how this mechanism makes us perceive the beauty of our favorite sounds (music, hearing our children laugh), how complex it must actually be and that this ... "evolved", out of a cosmic chemical soup, it's just incomprehensible.
Biology, genes, brains are nothing short of amazing. I'm not a religious person but if something points to the existence of a god then you'll find it in biology.
by hnmm23 on 11/19/20, 3:56 AM
It took us years and years and years, tons of shot gun approaches by doctors with treatments, diagnoses, and medications that treat the symptoms but not the underlying cause til we finally figured out what could possibly be wrong with her!
And that was only after she started working in the health field herself and had physicians and specialists that care about her take into consideration everything about her and run expensive tests.
All this to say, I've been researching others' experiences with what my partner is inflicted with and those who are doing better or have some understanding had to figure a lot of it out on their own with countless medical research and studies they pore over - a lot of these success stories are from physicians inflicted with these diseases themselves!
But, how am i supposed to understand the studies, and papers, and drug mechanism of action sheets?
Do I start at ground 0 and start learning biology? What are some good resources?
And how do I know where to go from there?
All this is really troubling me and i feel so powerless.
by skybrian on 11/19/20, 5:50 AM
Scientists Surprised to Find No Two Neurons Are Genetically Alike https://www.scientificamerican.com/article/scientists-surpri...
by VonBlue on 11/19/20, 1:15 PM
Incidentally, the only things I remember from biology are pictures, or the demonstration that a teacher made when someone “stretched” her “intestines” across the room.
by anm89 on 11/19/20, 4:29 PM
Seeing the mechanical nature of gene transciption and chemical signaling blew my mind.
https://www.youtube.com/watch?v=7Hk9jct2ozY&t=170
https://www.youtube.com/watch?v=LQmTKxI4Wn4
On the other hand, I don't buy his thing about wishing his high school teacher had presented it differently. No on else can make you interested in this stuff. The best they can do is provide resources like the ones above.
by leto_ii on 11/19/20, 12:59 PM
The key thought of the article comes right at the top. The distance between the astonishing nature of reality and the dry tedious way it's taught to people is present in all subjects, but seems greatest in biology. What seems to always be missing is what Chomsky calls a 'willingness to be puzzled'.
In fact I think this ability to be puzzled or amazed is there to begin with, but is beaten out of us by the educational system.
by xrd on 11/19/20, 5:17 AM
Does anyone have suggestions on starting down this path as someone that understands programming but has forgotten all the high school biology I learned?
I love the way I can now learn new programming frameworks. Read small bit by bit projects that build up slowly and teach the important components. Svelte for example. Solving problems and practicing the techniques are the best way for me to memorize things and then apply them to my own projects.
Is there anything similar that could start me down this path?
I'm less interested in videos like the Ninja Nerd. They look great, but it isn't a way of learning that sticks with me.
by stonogo on 11/19/20, 7:22 AM
by kashyapc on 11/19/20, 11:51 AM
So far my only quibble is that Sapolsky cites the infamous "priming" study from 'Thinking, Fast and Slow', which the author, Daniel Kahneman, himself has retracted it elsewhere. This is forgivable, as the retraction from Kahneman (Feb 2017) and the release of 'Behave' (May 2017) were too close. Though I'll keep an eye for other transgressions.
Regardless of my quibbling, 'Behave' has so far been an exhilarating read; it covers an insane amount of ground, all while not losing sight of its goal—a better understanding of human nature.
Don't let the page count discourage you—you'll quickly warm up to Sapolsky's loquacious writing style, peppered with tasteful humor and a deep love for science. And don't skip the footnotes; plenty of interesting bits in there. (Get the hardcover edition if you can, it's much less unwieldy during back-and-forth flipping, among other benefits.)
by wombatmobile on 11/19/20, 9:20 AM
But yeah, you might never get into it if it were taught to you as dry mumbo jumbo, like
Type 4 secretion system: ii- Pilus biogenesis
That's why they invented computer visualisations. Check out the molecular apparatus on the surface of the bacterium. It uses it to inject DNA into another nearby bacterium!
by whatshisface on 11/19/20, 2:58 AM
Just a minor point, electrophoresis uses electric fields not magnetic fields - hence its name, "electro-" as opposed to "magneto-".
by vfinn on 11/19/20, 5:54 AM
by Rochus on 11/19/20, 9:40 AM
The biggest books I ever bought were those on molecular biology and biochemistry. Huge and weighing several kilos. Until then I did not know that it was possible to produce such large paperbacks at all. Some of these books are also among the best I have ever seen in terms of design and didactics. This is also necessary because the area is so big that you can easily spend several lives with it.
I agree with the author that molecular biology is neglected in school or is often not taught in a very motivating way. But this is true for many fields of knowledge, not only for molecular biology.
My entry into the field was when I did a PhD in molecular biology and biophysics after ten years of professional experience as a computer scientist. That was almost twenty years ago now, and I still have the feeling that I'm only scratching the surface.
by ricardo81 on 11/19/20, 10:21 AM
At that time I could put ads on the page to effectively make it a full time job developing the site, which I did. It was massively rewarding knowing that 5000 people a day were reading something I wrote. I'd like to think someone managed to get their degree/job based on stuff they learned on there.
My personal belief is that biodiversity and preserving it should be one of our top priorities this century, nature has inspired a lot of our ideas and there's going to be many more. For all our advancements, we're just part of a larger tapestry. Great subject.
by pdm55 on 11/19/20, 6:52 AM
They also have diagrams of the internal structure of cells. Maybe, one day, they will add explanations beyond the succinct labels that they presently have:
https://www.cellsignal.com/contents/science/cellular-landsca...
by koeng on 11/19/20, 4:55 AM
If there is one takeaway from working in both fields, I think it is that a lot of computer scientists believe their systems are deep - it is nothing compared to biology.
Biotechnology also has a fundamentally different culture than tech, and so there can be some culture shock between the two. This is improving - I think the author would have loved synthetic biology :)
by watwut on 11/19/20, 7:47 AM
Why is that crazy? I had years when I liked biology and years when I did not liked it, but imo, the wish for mystification does not lead to knowledge. Well done any topic can be interesting, badly done it will be boring.
But, that wish to have everything framed in mystique is something I cant comprehend or really stand by. Like, I did not wanted to be manipulated that way as a kid and teachers who overdone it came across as untrustworthy or pathetic.
by LockAndLol on 11/19/20, 3:30 PM
My anguish for the worldwide state of education is abysmal. School and university are necessary, but the goal isn't to make us curious and wonder about things or excited to learn. The education system packages us up for work and is heavily focused on knowledge, not understanding. If you fail school, or uni - or look like you failed - people think you're dumb and unintelligent.
You can be lucky sometimes and get a teacher who's actually passionate about their subject AND is able to teach. Most teachers and professors I had were just I'm the system and mentally done. I can't blame most of them. The salary is often miserable, the curriculum bad, the books boring, administration annoying and the parents... good grief. Of course some really shouldn't have become teachers or let near kids, but that's the minority.
Anyway, I'm really glad the pandemic happened. Studying biology and physics at home has been rewarding and highly interesting. If only school and uni were/had been the same...
(1): https://www.youtube.com/playlist?list=PLGhmZX2NKiNldpyRUBBEz...
by neurostimulant on 11/19/20, 7:16 AM
When people asked me why a person that loves computer like me is getting into biology so much, my answer is how come anyone not getting crazy over biology? The rabbit hole is so deep, I can't help but dig and dig just to satisfy my curiosity. When people heard about biology they always imagine endless recitation on taxonomy and stuff but like the author wrote, that's not what biology is all about.
Alas, I ended up not having a career in biology-related field though. I'm a programmer through-and-through. But I did meet my wife through these event so it's not all for nothing, and I still like biology.
by lambdatronics on 11/19/20, 5:30 AM
It's about the role of energy in the emergence of life (pre-biotic -> single-cell -> multicellular -> animals). You'll see some chemical names, but it also tells interesting human stories too.
by wombatmobile on 11/19/20, 11:03 AM
The Machinery of Life, David Goodsell
A Computer Scientist’s Guide to Cell Biology, William W. Cohen
by xingyzt on 11/19/20, 4:04 AM
by srom on 11/19/20, 10:03 AM
The course is outstanding and anything but a "lifeless recitation of names". Prof Eric Lander (key researcher on the Human Genome Project) goes through two centuries of research and takes the time to explain how and why discoveries came into existence. It goes from the early days of biochemistry to recent major advancement such as CRISPR/Cas9.
I'm looking to apply my ML expertise to the field of biology and this course was a real windfall, I highly recommend it.
[1] https://www.edx.org/course/introduction-to-biology-the-secre...
by minhaz23 on 11/19/20, 3:57 AM
does anyone have any other articles, books, courses, lectures, youtubers, key people, papers, journals, interesting links/talks/podcasts/quotes they'd like to share to help others on their journy to understand biology better?
Thank you!
by kernoble on 11/19/20, 3:53 AM
With programming and computers this is so much closer, because these things are made my humans. Millions of man-years of effort, but still man-made. So, at least with computers I know I can learn how it's all done, and I know the steps needed to make all this technology are also known.
by julius_set on 11/19/20, 2:57 PM
by olau on 11/19/20, 10:10 AM
I have an older sister who majored in biology long time ago. The some time later while visiting her I borrowed one of her university books (introduction to zoology or something like that). It was actually written in the style suggested here, and yes, it was just amazing to read about people having studied and eked out mysteries of life. For instance, why do you have a front side?
I think I ended up reading 5 of her books. If you're the kind of person who could pick up a book on physics just because you're curious about the world, this will definitely appeal to you.
by FrankyHollywood on 11/19/20, 12:46 PM
Only in my 20s I read biography's from people like Feynman (1) and Erdös (2). Great reads! Really make you exited about math or physics. I wonder if high-school teachers even know these persons. And if they do, why not talk about them?
(1) Surely you're joking mr Feynman
(2) The man who loved only numbers
by medymed on 11/19/20, 3:14 AM
by b34r on 11/19/20, 5:07 AM
by Rastonbury on 11/20/20, 6:55 PM
by jmiskovic on 11/19/20, 8:18 AM
I thought the last part would resonate more with HN crowd. We have means and opportunity to build better tools for visualizing and communicating complex diagrams. Is anyone working on something similar?
by felnasire on 11/19/20, 2:34 PM
by ramraj07 on 11/19/20, 7:05 AM
by acomjean on 11/19/20, 5:13 PM
things like this in the boston area.. They have talks, offer classes, have some equipment and such. BOSlabs in cambridge MA is one such. I'm sure there are lots of others.
by cee_el123 on 11/19/20, 2:57 AM
today I'm obsessed with understanding proteins because predicting protein structure, behaviour, interaction are really hard problems that would unlock huge medical advances if fully solved
by awinter-py on 11/19/20, 5:08 AM
his 'there's a gold rush on and I'm the shovel' article about his decision to leave programming for writing has always stuck with me
and nothing he's written since then has betrayed that voice (especially the post on 'you're using the wrong dictionary')
by codecaveman on 11/19/20, 1:16 PM
by kls on 11/19/20, 11:13 AM
by sjg007 on 11/19/20, 6:07 PM
by k__ on 11/19/20, 1:31 PM
I have the feeling it being "a lifeless recitation of names" was the reason, yes.
by dannykwells on 11/19/20, 3:10 AM
by xwdv on 11/19/20, 11:18 AM
by vagrantJin on 11/19/20, 8:33 AM
by zelly on 11/19/20, 5:27 AM
by nahuel0x on 11/19/20, 7:44 PM
by FrankyHollywood on 11/19/20, 2:00 PM
by iron0013 on 11/19/20, 2:37 PM
by known on 11/19/20, 7:58 AM