Earlier quoted context omitted.
The patterns will be understood, by machines in whole and by people in part. To think it’s impossible seems ... religious
irrationality is not religiosity. You can calculate digits of Pi, but can't understand why Pi is the way it is ... Do you call the assumption that humans and computers can never understand why Pi is the way it is, and that you cannot extract understandable patterns from Pi (or any irrational number for that matter) a religious idea?
New universe of miniproteins is upending cell biology and genetics
71–80 of 121 posts
Re: New universe of miniproteins is upending cell biology and genetics
#72Earlier quoted context omitted.
Melatonin and Melanin are closely related chemicals that are used all over the body and are synthesized in the body through related mechanisms and pathways. Melatonin is used in the sleep-wake cycle and melanin is used by the skin to darken it and protect from solar radiation. When you need to sleep and when you need solar protection tend to be inversely related. The interaction between these processes is still being…
While I agree personally, I am comfortable letting others experiment with new drugs and take on that risk with the potential to discover things a bit faster than traditional medicine. Regardless of what you think of CBD, it has garnered steam because of non-medical use and I think brought it up to popular culture which researchers are then hearing about and interested in researching more. At the end of the day, in th…
One of the big changes for researchers (in the US) is that it's a lot easier to obtain materials, but it's still really onerous.
Re: New universe of miniproteins is upending cell biology and genetics
#73Earlier quoted context omitted.
I wouldn't be surprised in the slightest that it is easier to build a brain scanning machine and simulate you in a computer than to "solve aging". And don't think I underestimate the difficulty of that, either.
Wow. I understand that you are a layperson, but that’s a very strong statement in my view. What do you base it on? Or did you just pull it ”out of a hat”?
When understanding a complicated existing system, like a program, with the intention of making changes to it or fixing it, I find there are characteristic phases to it. There's the part where you have no handle on it at all. At this point you think there maybe isn't that much to the system. Then you get a handle, and you view the whole system through that handle for a while, and everywhere you look you see new stuff. Every time you find something new, your estimate of the size of the task grows. Slowly, but surely, you begin to go more places and look at more things and you encounter stuff you've already seen before. Your estimate of how much work you have to do goes up, but the rate of change starts to decrease. You find more useful handles to understand more bits of the system as you encounter new subsystems and bunches of code. There's a long period of consolidation, where your understanding finally starts matching the complexity and you start getting to the point you know what you are doing, and the rate of surprises you encounter slopes off, perhaps never quite reaching zero, but certainly dropping off. You then have the long slog of actually doing the work, because now you understand it.
In biology, you can argue about exactly where we are, but we are certainly not at the "long period of consolidation" yet, because we keep finding entirely new subsystems that we weren't even aware of. For the past several decades, it seems like every 5 or 10 years we keep finding new subsystems and the apparently complexity of what's going on keeps going up. The ratio of "things we know" over "things we know we don't know" has been steadily going down over the past decades, even as the "things we know" may be increasing in absolute terms. At this point I would have no confidence in anyone's claim that "no, this is the last complication we'll find, we're on our way now!"
Trying to get into that mess and fix it for the long term may just be an unrealistic goal entirely. I suspect modern research into fixing senescence and this or that promising treatment option (oh, look, maybe if we supplement with this, oh, look, maybe if we supplement with that!) may be the equivalent of trying to fix an architectural issue in a large-scale code base armed with the equivalent of three letter "a"s you can insert into the code base, or trying to reassemble a supernova armed with a BB gun.
Not that brain simulation is easy either. In fact, I'm not even convinced the simulating is the hard part. It's the reader I can't hardly imagine how we're going to build without some serious borderline-magic nanotech. You need to be able to read millions of neurons in parallel if you have any hope of finishing before the patient being scanned dies of old age. (And what does "reading" a neuron even mean? Can a "reader" fit into the space between neurons? If not you've got some serious scheduling problems with how to cover everything. And it's not like 'a neuron' is a point, either... one of their major purposes is to spread.) There's also a chance you'll have to be dynamically simulating the already-scanned parts as you go, since the system is changing as you scan it and it's basically the equivalent of a stroke if everything scanned is just dead afterwards, and who would want to be scanned that way? It's an insane machine to build.
It's really hard to tell which is harder, because they are both insanely hard. Neither would particularly surprise me. It's like an ant trying to judge which Redwood is higher.
Re: New universe of miniproteins is upending cell biology and genetics
#74Earlier quoted context omitted.
Indeed. The whole "One Gene, One Protein [One Phenotype]" [1] dogma went out quite some time ago. ... But people and genetic testing companies seem to want to keep it going. [1] - https://embryo.asu.edu/pages/george-w-beadles-one-gene-one-e...
We will eventually find that there's the equivalent of JPEG encoding (plus SSL and ECC) and that today we're doing the equivalent of someone with no knowledge of SSL or JPEG staring at a tcpdump trace of a browser loading an image over https, trying to make sense of the resulting hex dump.
Re: New universe of miniproteins is upending cell biology and genetics
#75Earlier quoted context omitted.
Indeed. The whole "One Gene, One Protein [One Phenotype]" [1] dogma went out quite some time ago. ... But people and genetic testing companies seem to want to keep it going. [1] - https://embryo.asu.edu/pages/george-w-beadles-one-gene-one-e...
We will eventually find that there's the equivalent of JPEG encoding (plus SSL and ECC) and that today we're doing the equivalent of someone with no knowledge of SSL or JPEG staring at a tcpdump trace of a browser loading an image over https, trying to make sense of the resulting hex dump.
Re: New universe of miniproteins is upending cell biology and genetics
#76Earlier quoted context omitted.
We aren't curing aging any time soon are we :(?
I wouldn't be surprised in the slightest that it is easier to build a brain scanning machine and simulate you in a computer than to "solve aging". And don't think I underestimate the difficulty of that, either.
Re: New universe of miniproteins is upending cell biology and genetics
#77I've noticed when I take magnesium that my muscles really relax, and jaw doesnt tighten as much when I sleep. this is from what i understand, because Magnesium acts as a natural calcium blocker, helping your muscle cells relax after contracting preventing excess muscle contraction (tightness). An interesting avenue i've started exploring is attacking the problem from another angle and instead of using mg, lying on a grounding mat plugged into a wall, which after reading this, is providing extra grounding for the "ion pump" described above? After sleeping on that mat, i feel even more relaxed than downing 500mg of magensium, i can even feel like the inner heart area be able to relax, which otherwise felt uncommandable to relax.
Ben greenfield, a biohacker whos pumped his entire body full of stemcells at one point (including the netherregions), has recently been investing it [1]
I can imagine since we know _so little_ about how even proteins and now these mini proteins work... how is the underlying electric system affecting the whole interaction a couple of abstraction levels up!?! what happens when the entire system is operating under a slight electric potential for 80% of lifetime, as opposed to being grounded? (static in a television signal)
[1] https://bengreenfieldfitness.com/podcast/biohacking-podcasts...
Re: New universe of miniproteins is upending cell biology and genetics
#78Earlier quoted context omitted.
> while peptides usually are too short to have a defined fold. That's not strictly true. My PhD project has looked at an entire class of peptides that are known to fold in to alpha-helices when bound to a cell membrane e.g. https://www.rcsb.org/structure/2k9b . There are many others that are known to fold into beta-sheets too.
Fair, but I would not really call a single helix a 'fold', either! Ok, so I'm playing with definitions here a bit. Clearly 2k9b adopts a helical structure so it is 'folded' in some sense. However it has no tertiary structure. Structural proteins like collagen are different again. They have a simple fold that could be described as quaternary (multichain), although that is again an abuse of terminology. There are also…
WW domains[1] fold stably into a three-stranded sheet. Also, not strictly a sheet, but beta hairpin motifs (e.g. tryptophan zippers[2]) are known to be stable isolated from their parental domains.
Re: New universe of miniproteins is upending cell biology and genetics
#79Earlier quoted context omitted.
We are just in the debugging phase.
i've been doing biological/biomedical research for about 20 years now (god, that's a scary thought...) I don't think that biology is well modeled by "being a meat computer", in general, but as far as the analogy goes ... : What we are debugging is 4.5 billion years of grad student code in at least a few dozen languages, with no documentation, method names that are outright lies, no separation of concerns at all, the…
Re: New universe of miniproteins is upending cell biology and genetics
#80Earlier quoted context omitted.
This is "the andy grove fallacy": it's not clear that you actually can , because code and computational hardware was designed by humans and biology emphatically was not. http://blogs.sciencemag.org/pipeline/archives/2007/11/06/and...
I'm starting to wonder if there are physical limits to cognition and if we've already hit them. Maybe it's impossible for the physical universe to understand its own complexity.
I.e. the good old divide-and-conquer principle.