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Spiegelman's Monster (wikipedia.org)
125 points by ideonexus on June 6, 2016 | hide | past | web | favorite | 34 comments



The Wikipedia page doesn't do the best job at conveying the idea of the experiment, in my opinion.

We've long been searching and wondering about the origin of life (aka abiogenesis). The famous Miller-Urey experiment (https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment) demonstrated that conditions similar to early Earth (plus lightning) spontaneously creates important organic compounds that are necessary for the life we see on Earth (caveat: Miller and Urey may have been wrong about early Earth conditions).

Spiegelman tried to create something closer to what we'd consider living. His "monster" was bootstrapped with an enzyme and some RNA (a simpler version of DNA). The enzyme replicated the RNA many times over. After a "generation" of replication, he'd move a sample of the RNA over to a new test tube. This would be the father of a new generation. And so on, he repeated this process almost 100 times.

The interesting thing is that this extremely simple "monster" ended up evolving in a way. By the end of a few generations, the RNA had adapted to its environment and become much more efficient at replication. Other attempts at the experiment have produced similar results. In effect, Spiegelman created a barebones pseudo-living machine, and demonstrated it undergoing evolution in the process.


Agree that the Wikipedia page doesn't do it justice. Richard Dawkins does an excellent job discussing the "monster" and providing context regarding theories on the origin of life in his book, The Ancestor's Tale. The "monster" comes near the end of the book since it's a backward march through time. It's a 700 page book, but so worth the read.

http://www.amazon.com/Ancestors-Tale-Pilgrimage-Dawn-Evoluti...


If you understand this topic well enough to spot what's missing, why not update the wikipedia page in a way you'd find more satisfying?


One fascinating detail on how the RNA adapted to its environment: Spiegelman was giving each generation very little time to reproduce. This created an environment favorable to RNA strings that could reproduce quickly. These strings were shorter, reducing the amount of time they needed to reproduce.

I learned about this "monster" from reading a Great Courses book on Information Science. Apparently the molecular "organism" is fascinating to information theorists because it evolved to have less information in response to an environment where more information, and the burden of longer-replication times, was unfavorable.


why the pseudo? it seems living rather than pseudo-living. it needs a particular environment, but that's true of a lot of living things.


The monster itself is just a strand of RNA.

The definition of living by most biologists wouldn't include a strand of genetic material. Fire replicates in particular environments, as do viruses. But we don't typically classify either as living.

I think the point you're getting at is that the distinction between living and non-living is a bit arbitrary and meaningless. I agree.


Fire and viruses have an important difference though, when fire replicates, its children don't inherit anything. A better example would be crystals as their structure influences crystals they seed.


Neither fire nor crystals mutate. That's the thing.

A crystals arrangement of its microscopic structure will always be the same, as will the oxidation reaction in fire.

A virus undergoes darwinian evolution and will adapt to its environment


Crystals actually do mutate, the crystallization process is not perfect and introduces defects.


that's not what mutation means.


I thought mutate just meant change?


in biology, mutate has a very specific meaning, and it does not include the formation of imperfect crystals. That area has its own set of terminology.


the operational definition agreed on in mainstream science is that to be living, you have to do regulated metabolism. This definition mainly exists to distinguish viruses from cells; I'm sure there are even cells which don't metabolize, but those are exceptional cases in which the ability to metabolize was lost in a parasitic situation.

Spiegelman's monster isn't alive under any common definition of alive, but it has fascinating properties nonetheless and appears to be an attractor in the RNA sequence space, which is quite interesting on its own.


Presumably because it can't act? There are two relevant paradigms to consider:

- Diamonds move through the earth (since the earth itself is not static), grow, and split. This means they move and reproduce. Are they alive?

- Prions are proteins that reproduce directly, by bumping into other proteins and forming them into prions. Are they alive?

The general run of thought that I'm familiar with is that bacteria are unambiguously alive, viruses are ambiguously alive, and diamonds are unambiguously not alive. Prions would go somewhere on the scale between viruses and diamonds. I would personally rate the monster below prions in terms of "being alive"; it doesn't surprise me to see it called "pseudo-living".


Anyway,the question of "where is the line when life begins" is subjective and scientifically boring. It's only interesting philosophically to people who don't understand the concept of spectrum/gamut/continuum. The interesting question is where specimens fall along the spectrum of completely inert to complex life.


>viruses are ambiguously alive.

Interesting you say that. I was always taught that viruses fell into the "not alive" category.


Viruses are mechanically simple enough that the conceptual toolkit of chemistry is enough to understand them. But the conceptual toolkit of biology, while not necessary, can still be fruitfully applied to them. (Biological understanding is also necessary for explaining why viruses might do what they do.)

There is no "not alive" category; that is the long-discredited philosophy of vitalism. It's purely a question of how you choose to do your analysis.

But I'll leave you with a selection from the wikipedia article "Virus":

Opinions differ on whether viruses are a form of life, or organic structures that interact with living organisms. They have been described as "organisms at the edge of life", since they resemble organisms in that they possess genes, evolve by natural selection, and reproduce by creating multiple copies of themselves through self-assembly. Although they have genes, they do not have a cellular structure, which is often seen as the basic unit of life. Viruses do not have their own metabolism, and require a host cell to make new products. They therefore cannot naturally reproduce outside a host cell – although bacterial species such as rickettsia and chlamydia are considered living organisms despite the same limitation. Accepted forms of life use cell division to reproduce, whereas viruses spontaneously assemble within cells. They differ from autonomous growth of crystals as they inherit genetic mutations while being subject to natural selection.


It's a _very_ particular environment, because it includes RNA replicase, which is a complex protein.


Sure, but one could make the same argument about any life on Earth. If considered in the context of the galaxy, our planet is pretty much as rare and well tailored for us as a test tube is for the monster.


"Living" is one of those things that is hard to pin down an exact definition for because there are so many edge cases.

Is life on earth everything that processes sunlight, directly or indirectly? Well solar panels do and microbes subsisting on energy released from deep sea vents don't. Is sexual reproduction the defining characteristic of life? Plenty of examples to the contrary of life forms reproducing in other ways.

It's actually really hard to find a precise definition that doesn't have an exception.

As for the Spielgelman's Monster, if this were to be described as living, that would mean man had created "life" from non-living matter, that would be rather big news.


Well the article says its not even self replicating. It requires humans to do much of the work of providing specific machinery and materials that it needs to make copies of itself.

But it also doesn't do much. That's a nebulous, hard to pin down statement. But I mean it doesn't have all the complex machinery and behaviors of living cells. It's static and kind of just floats around. Until things happen to bump into it and stick.

It's not fundamentally different than a virus. Which are also self replicating, but I don't think they are considered "living".


Heh, we must have been posting at the same time. Good point that the RNA monster doesn't do much; even some bacteria can "smell" chemicals and move along a gradient, a "behavior" that makes us think of them as alive. I wonder if you could get behavior like that with just rna


I haven't read anything about this besides the Wiki but I would say the RNA monster's not alive because it only reproduces when a scientist adds the right enzyme to the test tube. It can't actually reproduce itself. Viruses on the other hand contain genes in their rna for proteins (both enzymes and the structural proteins that make up their shells) and so they can reproduce by hijacking some cell's protein synthesis pathways.


Agree. Probably would have been better to submit something clearer than the Wikipedia page. That being said, the concept is awesome. I'm amazed it is not better known.


Interesting that it's the informational equivalent of 109 bytes, which is around the same order of magnitude as some of the earliest computer viruses that did nothing but replicate.


For reference the human genome is around 800MB.


1 nucleotide = 2 bits,

218 nucleotides = 436 bits = 54.5 bytes


Still bigger than a fork bomb !


Let's make DNAduino and start doing this kind of thing at home. Best science project.

I wonder what the current state of the art of homemade bioexperimentation is.


For those who are interested in this space, I'd strongly recommend first looking at options outside of your home.

If you're in the bay area, here's a hacker/maker space for biology:

http://biocurious.org/

If you're not, you could investigate joining an iGEM team. It's an annual synthetic biology competition, where competitors engineer biological "machines" and are encouraged to factor their work into standard, reusable biological components, called BioBricks (see: http://parts.igem.org/Catalog). I participated for some time in college, and it was really exciting and I was able to contribute via mathematical/in silica modeling with only a handful of undergraduate biology courses under my belt.

If you're set on your own biohacking space, you're going to need to get some equipment. A non-exhaustive list of what you'll likely need in no particular order, are: reaction vessels, pipettes + tips, plates + medium, incubators, autoclave, fridge/freezer, restriction enzymes & ligase, electrophoresis chamber + gel, PCR machine + polymerase, centrifuge, microscope, and of course, some e. coli.

Please do your research and if you don't have lab experience or are uncertain about something, find someone who has worked in a lab to help you. Most of this stuff isn't as scary as it seems, but if you mishandle the equipment&chemicals, you can do real damage, to yourself, to property, and to the environment. It's not something you should "move fast and break things" with.


For those in NYC:

http://genspace.org/




Amazing! Douglas Hofstadter's "Goedel, Escher, Bach" introduces a formal system called Typogenetics designed to resemble the system of RNA and DNA and its replication. He poses the question of the shortest psuedo-RNA chain that can self-replicate. He doesn't provide a solution in the book but plenty have been found online. I had no idea there was also a solution for the _real thing_!




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