8 ms·

Spiegelman's Monster

125 points by ideonexus 10y ago

sillysaurus3 10y ago
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.
- Zigurd 10y ago
  CRISPR kit https://www.indiegogo.com/projects/diy-crispr-kits-learn-modern-science-by-doing https://www.indiegogo.com/projects/diy-crispr-kits-learn-mod...
- cjhveal 10y ago
  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/ 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 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.
  - teod 10y ago
    For those in NYC: http://genspace.org/ http://genspace.org/
- fernly 10y ago
  BioBricks: http://parts.igem.org/Help:An_Introduction_to_BioBricks http://parts.igem.org/Help:An_Introduction_to_BioBricks
mfav 10y ago
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 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.
- brashrat 10y ago
  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.
  - mfav 10y ago
    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.
    - adrianN 10y ago
      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.
deleted 10y ago
[deleted]
userbinator 10y ago
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.
- nenreme 10y ago
  1 nucleotide = 2 bits, 218 nucleotides = 436 bits = 54.5 bytes
  - bbrizzi 10y ago
    Still bigger than a fork bomb !
- jon_richards 10y ago
  For reference the human genome is around 800MB.
bjackman 10y ago
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_!

125 points by ideonexus 10y ago

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.

Zigurd 10y ago
CRISPR kit https://www.indiegogo.com/projects/diy-crispr-kits-learn-modern-science-by-doing https://www.indiegogo.com/projects/diy-crispr-kits-learn-mod...
cjhveal 10y ago
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/ 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 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.
- teod 10y ago
  For those in NYC: http://genspace.org/ http://genspace.org/
fernly 10y ago
BioBricks: http://parts.igem.org/Help:An_Introduction_to_BioBricks http://parts.igem.org/Help:An_Introduction_to_BioBricks

mfav 10y ago

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 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.

brashrat 10y ago
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.
- mfav 10y ago
  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.
  - adrianN 10y ago
    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.

deleted 10y ago

[deleted]

userbinator 10y ago

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.

nenreme 10y ago
1 nucleotide = 2 bits, 218 nucleotides = 436 bits = 54.5 bytes
- bbrizzi 10y ago
  Still bigger than a fork bomb !
jon_richards 10y ago
For reference the human genome is around 800MB.

bjackman 10y ago

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_!