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The life cycle of HIV in 3D [video]

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Re: The life cycle of HIV in 3D [video]

#61

Post by ASalazarMX »

ekianjo wrote: post #47
cornholio wrote: post #38

As a technologist, I have mixed feelings when I see the fascinating details of life. On one hand, mastering this molecular machine would give us literally God-like powers: we could fabricate, grow or heal anything. We could solve all current problems, we could terraform planets using a few milligrams of DNA and literally redefine what it means to be human. On the other, I see the human body as a completely unsecured…

> power to kill every human on the planet. Truly God-like powers. You can't really design a perfect virus that will wipe out the human race, because anything you do to affect its properties will also affect its ability to spread. I'd be way more concerned about the destructive power of nuclear weapons, still numerous enough to destroy a very large part of humanity and our vital infrastructures.

> You can't really design a perfect virus

Just design several good-enough viruses.

Re: The life cycle of HIV in 3D [video]

#62

Post by godelski »

cryoshon wrote: post #58
mikeash wrote: post #55

Earlier quoted context omitted.

What would prevent the development of something like HIV that’s able to spread through the air like the flu?

slower replication speed, more difficulty infecting the host, requirement of much greater volume of replication to accomplish the same rate of infection. think of it this way: every cool feature you add to a living thing has an overhead. you want your little bacteria to have antibiotic resistance? fine. but it'll need that much more energy to grow relative to the bacteria which don't have the added burden. this means…

What would be the overhead for just something "simple" though? Like making HIV airborne? (Or rather what the lay person perceives as a small change)

It seems like there are plenty of diseases out there where a (apparently) "small" modification could have a dramatic effect on how it spreads. And I'll admit my naivety to the subject and do not know if such small changes are actually small, or the related overhead associated with them.

Re: The life cycle of HIV in 3D [video]

#63

Post by nabla9 »

daveguy wrote: post #60
nabla9 wrote: post #46

Earlier quoted context omitted.

Interestingly the Gene Regulatory Network (GRN) - the interaction of genes and proteins that control the prosess inside the cell is computationally very similar to recurrent neural network. Gene expression levels is controlled by proteins that are produced by active genes. https://en.wikipedia.org/wiki/Gene_regulatory_network Harnessing this mechanism directly for neural computation would be grand project.

I think it's a bit of a stretch to say GRN is "computationally similar" to neural networks. That seems to be a shoehorn of the most popular technology of one field into another field. Just because the GRN contains feedback loops with multiple influences doesn't mean it's suited to NN computation. The GRN is orders of magnitude more complex than computational NNs and it is orders of magnitude slower than signal transd…

> That seems to be a shoehorn of the most popular technology of one field into another field.

Recurrent neural network is used to model gene regulatory network. It's not a shoehorn.

See for example:

[1]: Reconstruction of Gene Regulatory Networks from Gene Expression Data Using Decoupled Recurrent Neural Network Model https://link.springer.com/chapter/10.1007/978-4-431-54394-7_...

[2]: Gene regulatory networks inference with recurrent neural network models https://ieeexplore.ieee.org/document/1555844/

[3]: Recurrent Neural Network Based Modeling of Gene Regulatory Network Using Bat Algorithm https://arxiv.org/pdf/1509.03221.pdf

> The GRN is orders of magnitude more complex than computational NNs and it is orders of magnitude slower than signal transduction of axons.

It's possible that we can reduce relevant complexity to the RNN subset that it useful. Feedback loop speeds are slower but they can be below second.

In many search and optimization problems the ability to run say 100 trillion large stochastic RNN's in parallel in a 100 liter tank could be huge. Especially if all you need is glucose and few cheap nutrients to power it.

Re: The life cycle of HIV in 3D [video]

#64

Post by czardoz »

danielmain wrote: post #48
czardoz wrote: post #26

Hard to believe that no one has programmed this. Evolution is insane.

Seems that you are not a programmer. Even with Intelligence people can write code (much much simpler and buggy) how can chaos build such a complex thing? Can you answer what was first? information (RNA/DNA) or the first cell?

What makes you think I'm not a programmer? I was marveling at how evolution can lead so something so systematic.

> Can you answer what was first? information (RNA/DNA) or the first cell?

No I can't. What are you getting at?

Re: The life cycle of HIV in 3D [video]

#65

Post by cryoshon »

godelski wrote: post #62
cryoshon wrote: post #58

Earlier quoted context omitted.

slower replication speed, more difficulty infecting the host, requirement of much greater volume of replication to accomplish the same rate of infection. think of it this way: every cool feature you add to a living thing has an overhead. you want your little bacteria to have antibiotic resistance? fine. but it'll need that much more energy to grow relative to the bacteria which don't have the added burden. this means…

What would be the overhead for just something "simple" though? Like making HIV airborne? (Or rather what the lay person perceives as a small change) It seems like there are plenty of diseases out there where a (apparently) "small" modification could have a dramatic effect on how it spreads. And I'll admit my naivety to the subject and do not know if such small changes are actually small, or the related overhead assoc…

to answer your question, the overhead is very small for a small change. you can add a bit of noncoding DNA to a virus' genome without ruining its ability to compete in the wild. but the survival margins are very thin. on a population scale, natural selection is very harsh. anything that is superfluous given the environment is an inefficiency which eventually results in extinction. of course, between organisms this isn't that frightening because there are different niches, so sometimes a large change can be more viable than a small change even if it's a lot more expensive, provided that the large change lets the organism live in a new niche.

making HIV airborne isn't a simple change, however. it's more like a massive change of niche. it's a change in the transmission modality of the virus -- for comparison, consider the scale of the changes you'd need to make to turn a car into a plane. or maybe a car into a boat.

it's doable, artificially. but the result won't be as good at being a car, plane, or boat as something which was purpose-built for that application and didn't have to carry the features of something intended for a different purpose.

many of the "small" changes that make a disease spread more easily are actually mutations which don't change the ability of the disease to weather external conditions, but rather change the ability of the disease to survive first contact with the host's immune system.

the flu is a great example here. we need a new flu vaccine every year because the flu mutates constantly and drastically. the flu never becomes capable of surviving outside a host for longer than before, though. it just becomes more effective at evading the immune systems of most hosts.

Re: The life cycle of HIV in 3D [video]

#66

Post by mikeash »

cryoshon wrote: post #65
godelski wrote: post #62

Earlier quoted context omitted.

What would be the overhead for just something "simple" though? Like making HIV airborne? (Or rather what the lay person perceives as a small change) It seems like there are plenty of diseases out there where a (apparently) "small" modification could have a dramatic effect on how it spreads. And I'll admit my naivety to the subject and do not know if such small changes are actually small, or the related overhead assoc…

to answer your question, the overhead is very small for a small change. you can add a bit of noncoding DNA to a virus' genome without ruining its ability to compete in the wild. but the survival margins are very thin. on a population scale, natural selection is very harsh. anything that is superfluous given the environment is an inefficiency which eventually results in extinction. of course, between organisms this is…

What about starting with the flu and giving it an HIV-like ability to wreck your immune system? Is the “attack” part too intertwined with everything else to be able to do that sort of mix-and-match operation?

Re: The life cycle of HIV in 3D [video]

#67

Post by sizzle »

This is why I'll never go on tinder or screw around, frightened about getting stds. My friends act like STDs are no big deal and joke around about the times they've contracted chlamydia and gonorrhea etc like it's a cost of doing business (getting laid).

I'll stick to long term relationship.

Re: The life cycle of HIV in 3D [video]

#68

Post by sizzle »

cornholio wrote: post #54
ekianjo wrote: post #47

Earlier quoted context omitted.

> power to kill every human on the planet. Truly God-like powers. You can't really design a perfect virus that will wipe out the human race, because anything you do to affect its properties will also affect its ability to spread. I'd be way more concerned about the destructive power of nuclear weapons, still numerous enough to destroy a very large part of humanity and our vital infrastructures.

Are you sure you aren't still thinking in the conventional, evolutionary paradigm? A highly engineered bioweapon could circumvent such problems by separating the infection phase (which could be completely silent and airborne) from the eradication phase. The payload could be triggered deliberately at a later date when a certain secret artificial protein is released in the environment - and then produced in industrial…

Wow these are novel concepts, do you read a lot of sci fi? How did you come up with these interesting scenarios?

Re: The life cycle of HIV in 3D [video]

#69

Post by cornholio »

sizzle wrote: post #68
cornholio wrote: post #54

Earlier quoted context omitted.

Are you sure you aren't still thinking in the conventional, evolutionary paradigm? A highly engineered bioweapon could circumvent such problems by separating the infection phase (which could be completely silent and airborne) from the eradication phase. The payload could be triggered deliberately at a later date when a certain secret artificial protein is released in the environment - and then produced in industrial…

Wow these are novel concepts, do you read a lot of sci fi? How did you come up with these interesting scenarios?

I'm not really inspired by scifi - but I'm sure some authors have had similar and probably much wilder ideas.

Been thinking for years about the human body as a cybernetic attack surface with no engineered cyberdefense. Most people seem not able to make that mental leap; no, the human body can't behave like a vulnerable Windows 95 machine giving kernel privileges to any ActiveX control it can download, because reasons.

But once you see the biological world like a hacker and DNA like a programming medium, as opposed to a representation of what evolution produced, an endless array of nefarious possibilities become obvious. The rational power of our minds far exceeds what evolution could ever concoct - or defend against.

Re: The life cycle of HIV in 3D [video]

#70

Post by cryoshon »

mikeash wrote: post #66
cryoshon wrote: post #65

Earlier quoted context omitted.

to answer your question, the overhead is very small for a small change. you can add a bit of noncoding DNA to a virus' genome without ruining its ability to compete in the wild. but the survival margins are very thin. on a population scale, natural selection is very harsh. anything that is superfluous given the environment is an inefficiency which eventually results in extinction. of course, between organisms this is…

What about starting with the flu and giving it an HIV-like ability to wreck your immune system? Is the “attack” part too intertwined with everything else to be able to do that sort of mix-and-match operation?

the flu gaining deadlier characteristics via engineering is more realistic. unfortunately, i believe that is well within the scope of our present capability. the exact magnitude of how dangerous such engineering could make a virus based on the flu is unclear to me, but i'd estimate somewhere between "globally apocalyptic" and "continentally destabilizing".

the mixing and matching of attack characteristics is probably possible under certain circumstances, but i don't know of any specific instances where it has been done. theoretically, it's easy to swap A for B, but making such changes nearly always has unintended downstream problems.

in the lab we used to do all sorts of mixing and matching, but for defensive characteristics (mostly to see if certain isomorphs were more vulnerable than others).

long story short, generating virus and isolating it is a real PITA for a slew of reasons. experimental cycles might be as long as a week for each trial of "mixing and matching".

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