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Animals as Chemical Factories

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Re: Animals as Chemical Factories

#31

Post by tomohelix »

lblume wrote: post #24
daemonk wrote: post #4

Cell-free synthesis is the next step. Theres slow progress, but very interesting operational models if it works.

I once visited a lab near Berlin where they told me that cell-free synthesis is basically like cell-based synthesis, just that they kill the cells first and use what's inside. The major benefit, I was told, was that you don't have to keep the cells alive. It sounds very odd at first glance but seems very fascinating to me (and I know way less about biology than I would like to), this idea of dissecting a system into…

I don't like that description very much. The cell being "alive" is literally the top reason the cellular machineries work so well. By being "alive" it is keeping the environment optimal and perfect for the enzymes to run and being productive. Taking this away and then seeing problems about efficiency is like taking off the wheels and then asking why the car is not running well.

They are trying to fix it by maintaining the same cytoplasmic conditions using all the machines and sensors in a bioreactor. But that can scale is a different question. The narrow ranges of conditions biological processes require is already hard to maintain while the cells itself is still whole and using more than half of its enzymes to do this.

Re: Animals as Chemical Factories

#32

Post by [deleted] »

tomohelix wrote: post #27
daemonk wrote: post #4

Cell-free synthesis is the next step. Theres slow progress, but very interesting operational models if it works.

I have strong doubt it will work. On paper we are just removing an arbitrary boundary that is the cell membrane/wall and combine trillions of cells together to form a giant cell. So it sounds very reasonable and attractive in engineering terms. But these are biological systems inherently designed/evolved to work in one special condition that is the cytoplasm of the host... Any engineer would know the kind of troubles…

[deleted]

Re: Animals as Chemical Factories

#33

Post by throw939494 »

benchmarkist wrote: post #5

Yet another instance of how people view the biosphere as a resource to be exploited for their own monetary profit and short-term benefit. That type of logic and thinking is a dead end. I've never had a silk robe and I doubt I would be any better off if I did have one. I'd much prefer clean air, water, and unpoisoned land for growing nutritious food.

Silk worm industry is the definition of long-term sustainable exploitation of biosphere. It was done for thousand years, with minimal resources, no polution, it captures CO2... It only takes a few worms and some leafs! Chemical alternatives are poluting and poising, land air and waters!

Re: Animals as Chemical Factories

#34

Post by benchmarkist »

throw939494 wrote: post #33
benchmarkist wrote: post #5

Yet another instance of how people view the biosphere as a resource to be exploited for their own monetary profit and short-term benefit. That type of logic and thinking is a dead end. I've never had a silk robe and I doubt I would be any better off if I did have one. I'd much prefer clean air, water, and unpoisoned land for growing nutritious food.

Silk worm industry is the definition of long-term sustainable exploitation of biosphere. It was done for thousand years, with minimal resources, no polution, it captures CO2... It only takes a few worms and some leafs! Chemical alternatives are poluting and poising, land air and waters!

How about we leave the silk worms alone.

Re: Animals as Chemical Factories

#35

Post by asdff »

tomohelix wrote: post #27
daemonk wrote: post #4

Cell-free synthesis is the next step. Theres slow progress, but very interesting operational models if it works.

I have strong doubt it will work. On paper we are just removing an arbitrary boundary that is the cell membrane/wall and combine trillions of cells together to form a giant cell. So it sounds very reasonable and attractive in engineering terms. But these are biological systems inherently designed/evolved to work in one special condition that is the cytoplasm of the host... Any engineer would know the kind of troubles…

All that matters is that it works and is easier or cheaper than existing cell based techniques. If it does, whats the harm then? This is why people are figuring this out on grant funded work after all, to see if it is in fact cheaper than existing techniques. This is how we have found many optimizations to lab work and other processes through basic research in the past.

Re: Animals as Chemical Factories

#36

Post by asdff »

lblume wrote: post #24
daemonk wrote: post #4

Cell-free synthesis is the next step. Theres slow progress, but very interesting operational models if it works.

I once visited a lab near Berlin where they told me that cell-free synthesis is basically like cell-based synthesis, just that they kill the cells first and use what's inside. The major benefit, I was told, was that you don't have to keep the cells alive. It sounds very odd at first glance but seems very fascinating to me (and I know way less about biology than I would like to), this idea of dissecting a system into…

Think of it more as just getting to the one function that you are using. I think a cell free technique that people might have heard of even in high school biology at this point is the polymerase chain reaction. Rather than have some cell we grow in some growth media under certain conditions optimal for cell growth and harvest cloned DNA from these cells, we have isolated the involved protein directly (DNA Polymerase). We know exactly what temperature is most optimal for each step, and infact depending on what targets of DNA we are looking at certain temperatures may be more optimal for these targets. We know the exact pH that these molecules are most effective at and this might not even be a pH found in the cell but one determined empirically by measuring enzyme activity across a gradient of pH and/or temperature ranges among other potential conditions. We know the inputs and reaction and can supply just enough of these molecules as we need to drive satisfactory yield in order to decrease our costs. We can optimize the timing of this temperature-dependent reaction again to the specifics of the DNA molecule that we are amplifying. We can change how quickly this reaction is heated up or cooled down to optimize for product yield. We can change out components of this reaction such as our enzyme for ones that might operate faster with less accuracy, or ones that operate slower with higher fidelity, or ones found from other species that might have these properties, or engineered proteins that might have these properties.

Many reasons why you'd want to go cell free. You are no longer binned into the cell but are now just throwing things into a tube where you can control all the parameters that matter for your desired function.

Re: Animals as Chemical Factories

#37

Post by throw939494 »

benchmarkist wrote: post #34
throw939494 wrote: post #33

Earlier quoted context omitted.

Silk worm industry is the definition of long-term sustainable exploitation of biosphere. It was done for thousand years, with minimal resources, no polution, it captures CO2... It only takes a few worms and some leafs! Chemical alternatives are poluting and poising, land air and waters!

How about we leave the silk worms alone.

Silk worms would starve to death if left alone.

Re: Animals as Chemical Factories

#38

Post by kylehotchkiss »

MrMcCall wrote: post #15
kylehotchkiss wrote: post #3

Make EColi Productive Again

TBF, it's been producing all kinds of chemical effects for longer than human beings have existed ;-) And, now it's proving its survivor's brutally superior intelligence by going from just procreating within our misery, to now tricking us into propagating it willingly and in likely far more beneficial conditions! Is that our petri dishes softly chuckling?

Petri dishes? I thought we let those suckers spawn in giant vats when we need to produce sizable amounts of proteins

Re: Animals as Chemical Factories

#39

Post by MrMcCall »

scythe wrote: post #29
MrMcCall wrote: post #11

Note that this is another difference between we human beings and the rest of the animals. Yes, non-human animals can take advantage of other animals' chemical factories (ants' use of aphids' sugar excretions come to my mind), but only we human beings can use our abstract conceptual thinking ability and scientific process to discover the nature of nature's chemistry and then put that knowledge to use. After my first-g…

The problem with spider silk is that it isn't just a chemical. We can make spider silk. There are plenty of papers where the spider silk proteins are produced by bacteria and spun into a fiber. The problem is that this fiber basically behaves like regular silk. Spider silk is partially crystallized and partially amorphous in a semi-disordered pattern that maximizes the toughness of the finished product. The way the s…

That's an all-time great comment. Thank you very much.

Yeah, it makes sense that, because Nature wastes nothing, the entire system is required to produce that wonder material. Our focusing just on the chemical structure of what is produced in its "glands" (?) is indicative of our having only a shallow grasp of the intricacies of our world, especially of its life.

Nature grows ever more wondrous the more we learn about it.

Re: Animals as Chemical Factories

#40

Post by alphan0n »

benchmarkist wrote: post #34
throw939494 wrote: post #33

Earlier quoted context omitted.

Silk worm industry is the definition of long-term sustainable exploitation of biosphere. It was done for thousand years, with minimal resources, no polution, it captures CO2... It only takes a few worms and some leafs! Chemical alternatives are poluting and poising, land air and waters!

How about we leave the silk worms alone.

Pretty rich coming from someone sending virtue signals from a device I presume isn’t constructed from twigs and berries.

Must be difficult as a person who doesn’t exploit the biosphere.. you’ll have to let us know how you mastered photosynthesis.

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