Super interesting. On a side note the disappearing / reappearing top bar on the science site is incredibly annoying.
New universe of miniproteins is upending cell biology and genetics
81–90 of 121 posts
Re: New universe of miniproteins is upending cell biology and genetics
#82Earlier quoted context omitted.
We aren't curing aging any time soon are we :(?
I recommend reading "Being Mortal" by Atul Gawande to get a good sense of how hopeless "curing aging" is. Although that's not the focus of the book it does a wonderful job describing the challenge. The way it reads to me as a lay person, the body just falls apart. Things go wrong. It's not one thing going wrong, it's a very long list of disparate problems that ultimately aren't survivable. Aging isn't a losing battle…
For a more hopeful picture: Ending Aging, by Aubrey de Grey. He organizes that long list of disparate problems and propose a possible path for their solution. Doesn't make it sound any easier, but at least it is a hopeful reading.
Re: New universe of miniproteins is upending cell biology and genetics
#83* 'Small proteins also promise to revise the current understanding of the genome. Many appear to be encoded in stretches of DNA—and RNA—that were not thought to help build proteins of any sort. Some researchers speculate that the short stretches of DNA could be newborn genes, on their way to evolving into larger genes that make full-size proteins. Thanks in part to small proteins, "We need to rethink what genes are,"…
This is why you should be very skeptical of anyone who claims transparency between genetics and complex phenotypes.
Which is why I have zero interest in things like 23 and me. I worked in a genetics lab and the longer I worked there, the more I realized how little we understand.
Re: New universe of miniproteins is upending cell biology and genetics
#84Earlier quoted context omitted.
This is why you should be very skeptical of anyone who claims transparency between genetics and complex phenotypes.
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...
> But people and genetic testing companies seem to want to keep it going.
You can still get alot of mileage out of a simplified, inaccurate model. If you just say to yourself, "well, this whole gene thing is hopelessly complex", then you'll never get anywhere outside of a lab or personal project. Applied biology especially, and medicine in particular, seems to require grossly simplifying assumptions in order to make any problem tractable.
I would think that would be understood by people on HN. One of the biggest impediments to smart people starting companies is an inability to set aside the inherent, irreducible complexity that they, alone, see and appreciate. The people who succeed in business tend to be those ignorant of the complexity[1], or those able to come to terms with the reality that any practical, marketable solution is necessarily built on an inaccurate model of the world and is doomed to eventually crumble for its inherent flaws.
The old adage that ignorance is bliss is more insightful and meaningful than people give it credit for. Knowledge, especially epistemic knowledge, can be debilitating.
[1] Which doesn't imply being stupid or incurious. Willful ignorance seems like a potentially useful strategy.
Re: New universe of miniproteins is upending cell biology and genetics
#85Imagine trying to understand biology like we try to understand what we code day to day. I would need a brain at least 100x as large and efficient.
There are early efforts under way to do just that: https://www.youtube.com/watch?v=RjD1aLm4Thg
This is one of the most mind-blowing talks I've ever seen. I recommend it to everyone reading this. Thanks for sharing.
Re: New universe of miniproteins is upending cell biology and genetics
#86Earlier quoted context omitted.
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.
Can you elaborate - I’ve always been fascinated hearing CS interpretations of biological processes.
DNA methylation acts as a form of error correction analogous to parity.
Re: New universe of miniproteins is upending cell biology and genetics
#87Earlier quoted context omitted.
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…
I...doubt that's an accurate characterization, because the things that you are describing lead to fragile software. Biological systems are hard to understand and to modify, but maybe that's more due to redundancy that has evolved than to systems that are coupled like bad software systems. After all, if they broke like buggy software, we wouldn't have so many diseases to study; living things would just crash and stop.
Biological systems mostly make up for the brittleness by being, if they survive, very redundant. You might be made up out of spaghetti code, but damn if we can't monkeypatch that shit on the fly!
Re: New universe of miniproteins is upending cell biology and genetics
#88* 'Small proteins also promise to revise the current understanding of the genome. Many appear to be encoded in stretches of DNA—and RNA—that were not thought to help build proteins of any sort. Some researchers speculate that the short stretches of DNA could be newborn genes, on their way to evolving into larger genes that make full-size proteins. Thanks in part to small proteins, "We need to rethink what genes are,"…
This is why you should be very skeptical of anyone who claims transparency between genetics and complex phenotypes.
That doesn't really follow. We don't need to have a complete map genotype to phenotype in order to have an understanding of the weight of genetic component of certain traits. Just because we don't know exactly which genes cause a certain hair color doesn't mean we can't guess which parents are more likely to have children with that hair color. The same goes for behavior that can be measured and predicted. As long as that prediction is more accurate than a random guess, the prediction has value.
Re: New universe of miniproteins is upending cell biology and genetics
#89Earlier 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.
Making a very crude analysis based on the size of data, I would say solving aging is a piece of cake comparing to scanning someone's brain content. Our proteins that eventually break down with aging are coded by the DNA. The DNA is a few GB across. Sure there are mutations, folding and other complexities, but it is still mostly digital data. The brain has 80B neurons, each with thousands of dendrites. You'd need to scan not only the (real valued) state of the neurotransmitters in each of these dendrites, but also the topology of the (varying) connection to other neurons. Not that it isn't a daunting challege, but I would bet my money on beating aging, rather than scanning the brain.
Re: New universe of miniproteins is upending cell biology and genetics
#90I love these discoveries.
Are proteins easy to detect and isolate? How does one tell where a protein begins and ends and if one megs protein is not just a bunch of smaller proteins.
Also how do they discover the functions of proteins? Just turn them off and on and try to see what effect it has on the body?
This is such a super interesting field; Any one have good resources (youtube) that show how this stuff is done in the lab?