Biology would be much more interesting if it were explained from a mechanical point of view. At the smallest scale it is a form of nanotechnology after all.
I should have loved biology
141–150 of 282 posts
Re: I should have loved biology
#142Earlier quoted context omitted.
I recall the same "everything coming together" feeling, but for me it didn't happen until Applied Biochemistry in grad school. I recall the final exam being only a single question, with a bunch of blank lined pages to write your answer, and the question was something like "You just ate a ham sandwich. What happens to it?" A good answer needed to include everything down to the molecular/chemical level and tie it toget…
The two questions I really remember from my neuroscience grad program are: "You discover a mouse that can sense radiation. How does it do it?" "You are riding a bicycle. Explain." We had to do it in 2 pages, NSF grant rules on spacing and margins.
>You are riding a bicycle. Explain
Oh man, where do I even start? Sensory input from the inner ear to balance, the networks that handle feedback from afferent signals from the periphery, efferent pathways to control motor movement. I don't even know all the details but it's mind bogglingly complex. Do I explain the molecular basis of action potentials? The modulating effects of inhibitory feedback within the networks? I feel like all of that barely scratches the surface of the insane complexity of neuronal networks
And how does one even begin to talk about our desire and internal drive to do things like ride a bicycle
Re: I should have loved biology
#143Earlier quoted context omitted.
Except it seems like a way harder question!
... it'll be fun if you start from what happens when the enter key is pressed- the mechanics and electronics involved in submitting that URL (and some chemistry and physics behind what your eyes see on the screen), the physical transmission of the signal from your computer to through the interwebs and some error correction protocols to ensure your signals are still useful. Maybe toss a line or two in about the comple…
When we start looking at life at the level of physics, chemistry, and biochemistry, the absolute beauty of the system begins to appear. The complexity is on a scale that's difficult to imagine or even unimaginable even to those trained in the fields, and there is a feeling of wonder that words can't capture
Re: I should have loved biology
#144Earlier quoted context omitted.
I worked for a professor (James Milner-White) who was interested in early protein evolution and I remember a conversation we had about the possibility that proteins could have evolved from large to small. Not sure if it was from a published paper, but the idea was that early proteins might have been large - say several hundred residues - but mostly disordered. The smaller, more ordered 'domains' would then have evolv…
wow ... it makes sense ... more of a top down approach.
Its actually top down and bottom up at the same time. All of biochemistry operates on the basic rules of physics which determine how the chemistry happens with feedback from the surroundings/system as the top down part
Re: I should have loved biology
#145Earlier quoted context omitted.
I must be running on slower code, as I can't quite unpack that. So the code in life is the DNA which is also the 'runtime'?
Proteins are the runtime on which DNA is executed, because they are the mechanism that "reads" DNA. But proteins are the compiled output of DNA, because they are the result of "reading" DNA. So the DNA defines the runtime environment that is necessary for DNA to run.
RNA actually has a large role to play in going from DNA to protein. Its been suspected that the first life was RNA based because RNA can actually form functional site similar to proteins to do enzymatic reactions. RNA is some of the secret sauce to many of these systems
Re: I should have loved biology
#146During the first part of the pandemic I watched the lectures for the Introductory Biology course [1] from MIT OpenCourseWare. I cannot recommend those highly enough! Almost every lecture brought up and highlighted something really cool and fascinating. Like how RNA sequencing over the last couple of years has gone from expensive to almost free, and what its uses are. Or time-lapse of bacteria adapting to antibiotics.…
To anyone who watches these, watch the basic chemistry series and organic chemistry lectures if you can find them. Follow that up with biochemistry to get a deeper understanding of the mechanisms of life
Re: I should have loved biology
#147Earlier quoted context omitted.
Hard disagree. We understand biology for the most part. The issue is in the exact implementations. An analogy would be like understanding how a computer works. We know how chips are made, the physics behind them. We know how bits are stored and processing steps are executed. We also know generally how operating systems work. We have the full compiled code as assembly instructions. But we don’t have the source code of…
Having done a lot of biology, I'd disagree that we understand biology. My background is neuro, so take that into account. But in neuro, we've nearly no idea about the larger parts of how it all works. Sure, yeah, electrically active neurons, we have that down. But the non electrically active parts? I mean, we're still debating about how much of the brain is glia. Like, we can't even agree on how to count. Don't get m…
I don't even think we understand software, much less biology :-) We can only hope to understand the pieces that are most relevant to the business domain we're trying to solve (like curing a disease or expanding an online business). The complexity of both types of systems is just increasing exponentially over time, so there's little hope (or even need) to understand the whole thing. The challenge is, of course, to understand what's relevant in the first place.
And just like in software, we can only hope to come with the right levels of abstraction and disregard the irrelevant parts at each level of understanding.
Re: I should have loved biology
#148Earlier quoted context omitted.
I would argue that depends on your definition of deep - we are certainly getting better at developing both genetic and chemical tools that allow us to probe specific pathways/sub-systems of biology, and read out the resulting perturbed phenotype(s). > There's a huge gap between the fundamental units of biology (biochemistry) and the resulting emergent behaviour (living things). We don't have a good bottom-up system t…
> (perhaps if program behavior depended on the size of indents, font, variable names, how many lines of code you wrote, the proximity in source location of different functions, etc) I think I've seen all of those functionalities implemented in esoteric programming languages! Nice comparison.
What you haven't seen is a CD-ROM sized program with no abstraction, encapsulation, or modularization, all implemented on a language that has all of those.
Oh, and that is being interpreted by more than one incompatible interpreter at the same time.
Re: I should have loved biology
#149There is a large gap between the mechanisms of chemistry and the magic of biology that most people do not see closed until late in their education. It's a real shame that this gap cannot be closed sooner. In undergrad I took a bunch of biology and chemistry classes. It wasn't until I took Biochemistry (a senior level class) that everything came together. The biochemistry class I took was a re-telling of all the stori…
I majored in biochemistry as well. I was so unbelievably hooked. The ground up principles. It led me to medicine
Re: I should have loved biology
#150Earlier quoted context omitted.
Hard disagree. We understand biology for the most part. The issue is in the exact implementations. An analogy would be like understanding how a computer works. We know how chips are made, the physics behind them. We know how bits are stored and processing steps are executed. We also know generally how operating systems work. We have the full compiled code as assembly instructions. But we don’t have the source code of…
Biology is incomparable to computers, or to any other man-made machine. In computers the components interact in well-defined separable and independent roles. In a biological organism, all components depend heavily on not just one or two other components, but many. The role we impute for each mechanism often interfere and/or collaborate with other seemingly unrelated mechanisms, often in hierarchical and nonlinear fas…
> Context and interdependency are everywhere.
Very much applicable to software as well :-) Modern systems are so complex there're very few people (if at all) who understand everything in them, even though they were man-made over time.