What's a virus, anyway? The bare-bones basics • Hacker News Board

Re: What's a virus, anyway? The bare-bones basics

#181

Post by martythemaniak » Fri, Apr 03, 2020, 6:38 PM UTC

nikofeyn wrote: post #178

chadcmulligan wrote: post #127

Earlier quoted context omitted.

I picked up a microscope last year - they were on sale, and one of those things I'd always wanted to have a play with. I remember having a look with them in school and never seeing much and it seemed very hard. All you have to do is go to a pond or creek scoop out some weeds, dirt and water and stick it in a jar and there is hours of exploration in front of you. Once you start looking its like seeing an evolutionary…

one of my greatest confusions of "life" is why there is this need to consume or feed off of or battle against other life. what is the purpose of this drive? why is it like this? i suspect the answer lies in thermodybamics and/or information theory, but it would be amazing to understand the reason behind life's battles for survival.

Look into "dissipative structures", which are indeed closely linked to thermodynamics.

In short, energy gradients (ie, on hydrothermal vents) can cause matter to organize itself into structures that more efficiently dissipate this energy. You can see how the creation of this structure would in turn enable the creation of a new kind of structure that lives on top of that.

https://en.wikipedia.org/wiki/Dissipative_system

https://www.youtube.com/watch?v=PqPGOhXoprU

Re: What's a virus, anyway? The bare-bones basics

#182

Post by garmaine » Fri, Apr 03, 2020, 7:18 PM UTC

codekilla wrote: post #172

garmaine wrote: post #148

Earlier quoted context omitted.

Actually it was a terrible critique of nanotechnology, which doesn’t try to make things the same way as biology. But a good overview of the funkiness which comes part and parcel with life’s microbiology.

Not sure which field of bionanotechnology (I assume you meant bionanotechnology ) you work in, but for the one I work in, the metaphor of biology and computer science is extremely intertwined—like very explicitly. Circuits, computation, the whole nine yards. If you’re talking about graphene or something that is an entirely different field. I can’t see how this book was a terrible critique of bionanotechnology—or at l…

I did not mean bionanotechnology, and neither did Smalley. He offered that as a critique against Drexlar’s diamondoid molecular manufacturing, in a successful political coup to claim the billions in research dollars that were promised as part of the National Nanotechnology Initiative.

Because of Richard Smalley that money went towards material science and chemical research instead of the molecular manufacturing it was promised for. Even though, as you point out, in terms of fact the critique only applied to life-like bionanotechnology.

The history of this is laid out pretty well—with a surprisingly minimal amount of sour grapes—in Drexler‘s book Radical Abundance.

Re: What's a virus, anyway? The bare-bones basics

#183

Post by dekhn » Fri, Apr 03, 2020, 7:31 PM UTC

ggm wrote: post #94

Wise words a former cell biology aware PhD said to me once: a cell is at a scale where van der Waals forces means 'water' isn't behaving like you think and the 'liquid' of a cell is possibly more like a matrix than a fluid. Those high school cell models are very misleading. He basically said macro scale intuition was useless for what it means to pierce the cell wall, as an example. What does "pierce" even mean?

The classic intro to this is "Life at Low Reynolds Number", https://science.curie.fr/wp-content/uploads/2016/04/Purcell_...

Another interesting thing: cells are packed so tightly (not just a bag of water) that proteins grind against each other and against their ligands, increasing the "activity" (even the free energy of ATP hydrolysis isn't the standard 7.3kcal/mol.

Yes, macro-scale intuition isn't great (although people pierce cell walls with tiny needles all the time), but if you spend enough time looking at cells under a microscope, you start to build an intuition about cell and molecule behavior.

Re: What's a virus, anyway? The bare-bones basics

#184

Post by effie » Fri, Apr 03, 2020, 9:53 PM UTC

nikofeyn wrote: post #178

chadcmulligan wrote: post #127

Earlier quoted context omitted.

I picked up a microscope last year - they were on sale, and one of those things I'd always wanted to have a play with. I remember having a look with them in school and never seeing much and it seemed very hard. All you have to do is go to a pond or creek scoop out some weeds, dirt and water and stick it in a jar and there is hours of exploration in front of you. Once you start looking its like seeing an evolutionary…

one of my greatest confusions of "life" is why there is this need to consume or feed off of or battle against other life. what is the purpose of this drive? why is it like this? i suspect the answer lies in thermodybamics and/or information theory, but it would be amazing to understand the reason behind life's battles for survival.

There are competing processes in nature even without life (in the usual sense of the word) - atomic nucleus fission/fusion, light absorption/emission, crystal nucleation vs. decay, molecule synthesis vs molecule decay - each process operating towards getting more ground. Life fighting (or helping) other life can be looked upon as a more complex variant of the same process dynamics: one set of atoms and processes interacting with other set of atoms and processes, sometimes this looks like cooperation, sometimes like a battle.

Re: What's a virus, anyway? The bare-bones basics

#185

Post by darkerside » Fri, Apr 03, 2020, 10:20 PM UTC

01100011 wrote: post #88

darkerside wrote: post #84

Earlier quoted context omitted.

So they're a parasite. There are insects that can only reproduce by laying eggs inside of another insect. They don't physically carry their own. Does that mean they're not alive?

You're describing an organism. What about its cells?

...cells are definitely alive

Re: What's a virus, anyway? The bare-bones basics

#186

Post by landryraccoon » Fri, Apr 03, 2020, 10:38 PM UTC

nojvek wrote: post #119

Someone who is a molecular biologist, please correct my understanding. DNA is a molecule, made out of 4 amino acids. ACTG. There are 18 different kinds of amino acids. Amino acids are made out of carbon, nitrogen, hydrogen, oxygen. Amino acids make proteins. Proteins are the structural bricks (like LEGO) that are combined in various sequences by enzymes to build more complex machinery. The proteins make up cell organ…

> Do we have a DNA simulator where I can write ACTG code and it tells me what kind of proteins will be made, how those proteins will interact to build complex structures?

Determining the physical structure of a protein from the amino acid sequence is NP-Hard : https://ieeexplore.ieee.org/document/6965037

Without a very significant breakthrough either in computation or some biological discovery that gives a shortcut I don't think a "DNA compiler" will be available anytime soon.

Re: What's a virus, anyway? The bare-bones basics

#187

Post by chadcmulligan » Fri, Apr 03, 2020, 11:57 PM UTC

nikofeyn wrote: post #178

chadcmulligan wrote: post #127

Earlier quoted context omitted.

I picked up a microscope last year - they were on sale, and one of those things I'd always wanted to have a play with. I remember having a look with them in school and never seeing much and it seemed very hard. All you have to do is go to a pond or creek scoop out some weeds, dirt and water and stick it in a jar and there is hours of exploration in front of you. Once you start looking its like seeing an evolutionary…

one of my greatest confusions of "life" is why there is this need to consume or feed off of or battle against other life. what is the purpose of this drive? why is it like this? i suspect the answer lies in thermodybamics and/or information theory, but it would be amazing to understand the reason behind life's battles for survival.

Thats probably the thing I learnt looking through the microscope, or was perhaps made obvious. Life at that level is just chemical gradients and finding bio mass to procreate, so things that don't do this don't procreate and die, the winners are the ones that are the best at this. The asking why is a human thing and is so many layers on this elementary life we can afford to ask these questions, but I don't think life can exist without competition, at least not organic life that has evolved. Maybe we'll make a more pure sort of life that doesn't need competition to grow but not sure about that.

Re: What's a virus, anyway? The bare-bones basics

#188

Post by Cogito » Sat, Apr 04, 2020, 2:51 AM UTC

ethbro wrote: post #174

Cogito wrote: post #151

Earlier quoted context omitted.

You're begging the question here; you need to establish they have any purpose before you can ask if one has more than the other.

No. I'm pointing to the relativity of the term. Anything can be said to have, or not have a purpose, depending on how broadly or narrowly you scope the definition. For use in this conversation, I think it's self evident that the level of purpose exhibited by higher-complexity organisms is several orders of magnitude different than that of basic organisms. Wasn't sure if original poster would agree / disagree.

See, I think this is exactly why you are begging the question.

The word purpose has lots of usages, but the one that seems to be discussed here is some intrinsic purpose that an object or creature has for existing.

I can perform an action with a purpose, which is different to my (personal) purpose for being alive, which is different again for some intrinsic purpose for why I am here in the first place.

It's this last purpose that daseiner1 was referring to when they asked "what’s the purpose of an amoeba? or a mosquito? or a duck? or a chimpanzee?"

They are questioning if that kind of purpose even exists.

Your argument is:

Some things have more purpose than others.

Therefore purpose exists.

In this next response you get closer to defining what purpose is - "level of purpose exhibited by higher-complexity organisms" - but we haven't really established what that purpose is or what it means to have more purpose. At best you seem to be equating complexity of behaviour to level of purpose, but I see no reason why complex behaviour should imbue some kind of purpose; all usages of the word purpose imply intent of some kind, and there are many complex processes that have no intent.

I will say that complex animals seem to be more purposeful than simple creatures, but that just means that they perform actions with more intent than simpler creatures, not that they have some intrinsic purpose themselves.

Re: What's a virus, anyway? The bare-bones basics

#189

Post by jvanderbot » Sat, Apr 04, 2020, 3:13 AM UTC

nikofeyn wrote: post #178

chadcmulligan wrote: post #127

Earlier quoted context omitted.

I picked up a microscope last year - they were on sale, and one of those things I'd always wanted to have a play with. I remember having a look with them in school and never seeing much and it seemed very hard. All you have to do is go to a pond or creek scoop out some weeds, dirt and water and stick it in a jar and there is hours of exploration in front of you. Once you start looking its like seeing an evolutionary…

one of my greatest confusions of "life" is why there is this need to consume or feed off of or battle against other life. what is the purpose of this drive? why is it like this? i suspect the answer lies in thermodybamics and/or information theory, but it would be amazing to understand the reason behind life's battles for survival.

My friend built a house. I wanted a house. It was easier to take the lumber from his house than cut down trees and mine iron for nails. Eating another is no different. Different life evolves to take a niche item (like grass or minerals) and turn it into something useful to them (muscle and fat) that is also useful to others.

Re: What's a virus, anyway? The bare-bones basics

#190

Post by nikofeyn » Sat, Apr 04, 2020, 8:24 AM UTC

jvanderbot wrote: post #189

nikofeyn wrote: post #178

Earlier quoted context omitted.

one of my greatest confusions of "life" is why there is this need to consume or feed off of or battle against other life. what is the purpose of this drive? why is it like this? i suspect the answer lies in thermodybamics and/or information theory, but it would be amazing to understand the reason behind life's battles for survival.

My friend built a house. I wanted a house. It was easier to take the lumber from his house than cut down trees and mine iron for nails. Eating another is no different. Different life evolves to take a niche item (like grass or minerals) and turn it into something useful to them (muscle and fat) that is also useful to others.

i don't think that analogy holds up because it seems to ignore that there are other methods of obtaining energy.

and your last statement isn't getting to why. it's just what happens.