Comments on: minimal cells

minimal cells

kliuless — Tue, 20 Apr 2021 05:43:08 -0800

Scientists Create Simple Synthetic Cell That Grows and Divides Normally - "New findings shed light on mechanisms controlling the most basic processes of life."[1]

Five years ago, scientists created a single-celled synthetic organism that, with only 473 genes, was the simplest living cell ever known. However, this bacteria-like organism behaved strangely when growing and dividing, producing cells with wildly different shapes and sizes.[2] Now, scientists have identified seven genes that can be added to tame the cells' unruly nature, causing them to neatly divide into uniform orbs... Identifying these genes is an important step toward engineering synthetic cells that do useful things. Such cells could act as small factories that produce drugs, foods and fuels; detect disease and produce drugs to treat it while living inside the body; and function as tiny computers.

also btw...

An on-off switch for gene editing - "New, reversible CRISPR method can control gene expression while leaving underlying DNA sequence unchanged."[3]
The incredible bacterial 'homing missiles' that scientists want to harness - "A Berkeley Lab-led team is digging into the bizarre bacteria-produced nanomachines that could fast-track microbiome science."[4]
Kati Kariko Helped Shield the World From the Coronavirus - "Collaborating with devoted colleagues, Dr. Kariko laid the groundwork for the mRNA vaccines turning the tide of the pandemic."[5]

By: polymodus

polymodus — Tue, 20 Apr 2021 05:49:25 -0800

So can they replicate out in the real world? Press release does not address this

By: dances_with_sneetches

dances_with_sneetches — Tue, 20 Apr 2021 06:03:05 -0800

It's ALIVE!

By: AzraelBrown

AzraelBrown — Tue, 20 Apr 2021 06:36:17 -0800

So can they replicate out in the real world? The press release was announced in a press conference emcee'd by a trenchcoat with a fedora pulled low so you can't see it's "face" and when asked about replicating in the wild it replied "cease asking us such meaningless questions, human"

By: Modest House

Modest House — Tue, 20 Apr 2021 06:45:05 -0800

By: GenjiandProust

GenjiandProust — Tue, 20 Apr 2021 07:02:23 -0800

This is how you get shoggoths, you know. At first it's cool, then you end up as cruel masters of subjugated intelligent beings, crushed under... ... ... righ, so business as usual then. Yay, humans!

By: Aardvark Cheeselog

Aardvark Cheeselog — Tue, 20 Apr 2021 07:04:01 -0800

In all seriousness, I hope someone will tell the less biologically literate among us how this differs from "creating life". Have these scientists replicated or paralleled the primordial circumstances that brought about the first cell?

My biology training was decades ago so I don't know how literate I am, but the short answer is "no." Nobody knows what exactly those primordial circumstances were, so any claim to have replicated them would be suspect. TFA says

Scientists at JCVI constructed the first cell with a synthetic genome in 2010. They didn't build that cell completely from scratch. Instead, they started with cells from a very simple type of bacteria called a mycoplasma. They destroyed the DNA in those cells and replaced it with DNA that was designed on a computer and synthesized in a lab. This was the first organism in the history of life on Earth to have an entirely synthetic genome. They called it JCVI-syn1.0.

So at no point was there a cell-free system from which these replicating objects were derived. They started with a living cell (of just about the simplest kind) and replaced its genome with a vastly simplified synthetic one, and this story is about an advance on that synthetic genome that makes the resulting chimera look a lot more like a natural organism, in terms of its ability to reproduce itself.

By: lalochezia

lalochezia — Tue, 20 Apr 2021 07:06:34 -0800

tl;dr ship of theseus, molecular biology edition

By: GenjiandProust

GenjiandProust — Tue, 20 Apr 2021 07:12:07 -0800

In all seriousness, I hope someone will tell the less biologically literate among us how this differs from "creating life". Have these scientists replicated or paralleled the primordial circumstances that brought about the first cell? Aardvark Cheeselog got there before me, but (from my limited understanding) they didn't remotely parallel how life might have actually arisen, more cut back to the minimum operational system and then started adding and subtracting stuff. Remembering back to some discussions with geologists working on very very small fossils, these sound like they are a little too small to have all the machinery they really need to be "alive." They may need regular adjustments to keep dividing, they may not have reliable mechanisms for taking in nutrients, etc. What the scientists seem to have done is get a better idea of how cells replicated themselves in a standard way, which is very exciting, but it's not creating life.

By: jjray

jjray — Tue, 20 Apr 2021 07:14:24 -0800

In all seriousness, I hope someone will tell the less biologically literate among us how this differs from "creating life". Have these scientists replicated or paralleled the primordial circumstances that brought about the first cell? This study is not really creating primordial life because they are adding modern genes to the cells to get them to act more normally. The result is really cool because it shows us in more detail what the most basic building blocks of cell growth and division are. This is closer to an empty chassis that engineers can use to build up living cells that do what we engineer them to do without wasting unnecessary energy on functions evolved in nature and irrelevant to growing in the conditions needed for the engineered cells. There are many such pathways in workhorses like E. coli and baker's yeast that reduce yields of metabolite production. Oh and also they stripped out all the immunity, stress response functions, ability to shift to utilize alternate nutrient sources, etc. It would never survive in nature.

By: condour75

condour75 — Tue, 20 Apr 2021 07:20:27 -0800

Oh and also they stripped out all the immunity, stress response functions, ability to shift to utilize alternate nutrient sources, etc. It would never survive in nature. It's like the todo app in a tutorial for a new JavaScript framework.

By: Aardvark Cheeselog

Aardvark Cheeselog — Tue, 20 Apr 2021 07:23:21 -0800

Reading TFA more carefully, and looking at the thing it links (and at the original publication about the 1.0 organism), it appears that the 1.0 version of the synthetic genome was a synthetic copy of the natural one and the 1.0 organism was close to a straight-up copy of the natural one. Subsequently the researchers started knocking out bits of the copied genome to see what parts were required for replication. Of the ca. 900 genes in the 1.0 organism they found a subset of 473 genes that were required for the things to grow at all, though the resulting new cells had abnormal sizes and shapes. This is the 3.0 organism. TFA is a report on how adding back 7 of the knocked-out genes results in a 3.0A organism that grows (apparently) normally. TFA is also about a neat-o bit of gear that was invented at NIST, which allowed the researchers to visualize the living cells under light microscopy as they grew.

By: exlotuseater

exlotuseater — Tue, 20 Apr 2021 07:36:58 -0800

Oh and also they stripped out all the immunity, stress response functions, ability to shift to utilize alternate nutrient sources, etc. It would never survive in nature. This is what I came in here to see. I had a bit of a Gray Goo panic, I'm afraid. Otherwise, this is really cool.

By: clawsoon

clawsoon — Tue, 20 Apr 2021 08:10:32 -0800

Of the seven genes added to this organism for normal cell division, scientists know what only two of them do. The roles that the other five play in cell division are not yet known.

Interesting how much we still have to learn. Anybody know what kind of no-doubt-painstaking work will have to be done to figure out the function of those five genes?

By: justsomebodythatyouusedtoknow

justsomebodythatyouusedtoknow — Tue, 20 Apr 2021 08:34:50 -0800

Have these scientists replicated or paralleled the primordial circumstances that brought about the first cell? "They destroyed the DNA in those cells and replaced it with DNA that was designed on a computer and synthesized in a lab." So no, this is an artificial manufacturing process completely unlike the circumstances under which life arose on Earth. Unless... unless... I'm not saying it's aliens, but...

By: benzenedream

benzenedream — Tue, 20 Apr 2021 08:41:13 -0800

Think of this as taking a Lexus, and removing parts until you just barely had a chassis and engine that was capable of puttering along at 3 mph. Then the press issues stories declaring you have found the basis of transportation. And people worry that Skelet-o-chassis may take over the highways.

By: clew

clew — Tue, 20 Apr 2021 08:54:27 -0800

how this differs from "creating life" Many microbiologists can spend hours fascinatingly argue-explaining how "life" is a foggy-boundaried category. That's the precedent this reminds me of - DNA is expensive, so it's common for parasites and commensals to lose it. As the commensals simplify and their hosts depend on them, it can get arguable whether we're looking at two living organisms or one. Which is a great metaphor for the likely human coëxistence with such creatures. We have commensal microbes in our breast milk , probably to boot up our immune systems, but chosen/adapted to be harmless to us. Synthetic microbes could be commensals outside us.

By: njohnson23

njohnson23 — Tue, 20 Apr 2021 09:51:44 -0800

There was a TV brand in the 50's (don't remember the name, but it started with a D) where they took an RCA TV and started stripping out parts. If it stopped working, put it back, if it kept working, leave it out. Thus they came up with a much cheaper TV, that sort of worked, for awhile. Doesn't sound like intelligent design to me.

By: Made of Star Stuff

Made of Star Stuff — Tue, 20 Apr 2021 09:59:45 -0800

I am extremely interested in what exactly these seven genes are and why they are necessary for cell division to proceed normally. I'm also extremely interested in Weirdly Dividing Cell. Why you do beads on a string, cell? Is all your actin on the other side and you can't reach it? *imagines sad confused cell* As usual, spermist preformationists declare DNA to be the sum total of life and completely ignore the necessary continuity of the cellular membrane. There is only one membrane. It is all. #Ovism #Malebranche

By: They sucked his brains out!

They sucked his brains out! — Tue, 20 Apr 2021 10:27:24 -0800

Craig Venter's lab used a transplantation technique to discover what minimum set of genes are required for viability in an engineered bacteria. There have been a few revisions made in the lab that refine this minimum set. Interestingly, there's a jump between the presumably initially amino-acid-free "RNA world", to the DNA-based life that uses a variety of peptides. Some recent research suggests RNA and peptides could have evolved together along the way to modern life. Adding genes is interesting, but it perhaps moves the work forwards in the timeline, as opposed to backwards. Going back to Venter's v3 organism, its genome is 531 kb long and is made up of 432 protein-coding genes, which use 20 amino acids, some of which are chemically similar. It would be interesting to see if those redundancies could be pushed further, to make a viable organism that uses proteins made from a smaller set of peptides. That might get us closer to a model that is simpler to understand, and perhaps closer to modeling how life originated and how it got us here.

By: biogeo

biogeo — Tue, 20 Apr 2021 10:37:00 -0800

I had a bit of a Gray Goo panic, I'm afraid. Don't worry about the "gray goo" thing. It already happened, and you're part of it.

By: The Tensor

The Tensor — Tue, 20 Apr 2021 10:48:57 -0800

It would never survive in nature. "Hey, remember last month when we said NovoBacter could never survive outside the laboratory? Well, funny story, we reanalyzed our data and... [gestures at pulsating layer of translucent protoplasm covering the landscape to the horizon]."

By: polymodus

polymodus — Tue, 20 Apr 2021 12:29:12 -0800

I think I watched some movies about life, uh, finding a way

By: unearthed

unearthed — Tue, 20 Apr 2021 12:37:42 -0800

Aardvark - sound a bit basic ".. started knocking out bits ..", I had a car like that once, when something stopped working I yanked it out and carried on, doing it with with genomics sounds really haphazard..

By: darkstar

darkstar — Tue, 20 Apr 2021 12:38:19 -0800

And people worry that Skelet-o-chassis may take over the highways. Well, they'd be somewhat justified in their concerns if Skelet-o-chassis had been designed to self-replicate, and observed doing so, even if it were only under extremely specific, controlled conditions. That said, yeah, not a worry with this organism. And that said, it's not entirely an irrational concern that we might one day devise some minimal organism that is particularly (or even catastrophically) efficient at self-replicating in conditions other than those strictly controlled in the lab...

By: Jon Mitchell

Jon Mitchell — Tue, 20 Apr 2021 12:49:09 -0800

And that said, it's not entirely an irrational concern Any programmer who has made a simple mistake causing, say, an infinite cascade of error windows to pop up all shrieking for attention is rightly a little skittish about engineered self-replicating objects, but maybe the biologists are more careful than they are. Hopefully.

By: automatronic

automatronic — Tue, 20 Apr 2021 12:58:19 -0800

Worrying about new self-replicating organisms seems a bit over the top, when every one of us is already carrying around about 39 trillion of them which evolved completely randomly and are still constantly mutating.

By: clawsoon

clawsoon — Tue, 20 Apr 2021 13:24:34 -0800

We are basically the disaster scenario for life, aren't we? We're the experiment that "got out of the lab" and is in the process of destroying a bunch of the other life on earth, right?

By: clawsoon

clawsoon — Tue, 20 Apr 2021 16:51:44 -0800

I hope someone does a version of the Long Term Evolution Experiment with these. E. coli has already seen everything and has 4000 genes worth of ways to deal with it. What would a minimal organism like this come up with, and how long would it take?

By: GCU Sweet and Full of Grace

GCU Sweet and Full of Grace — Tue, 20 Apr 2021 17:18:38 -0800

Gotta admit the Greg Bear, wet-nano future always seemed more interesting than the Drexler/Neal Stephenson one.