Shared publicly  - 
 
Frankenstein's monster was just a story, but Spiegelman's monster is real!    Professor Spiegelman took the genome of a virus and put it in an environment where it could reproduce itself with almost no work.  It evolved to become simpler and simpler, dropping all genes that were no longer needed.   Eventually it became a tiny, ultra-fast self-replicating machine. 

In his book The Fifth Miracle, Paul Davies wrote:

"The Qb virus doesn't need anything as complicated as a cell in order to replicate: a test tube full of suitable chemicals is enough. The experiment, conducted by Sol Spiegelman of the University of Illinois, consisted of introducing the viral RNA into a medium containing the RNA's own replication enzyme, plus a supply of raw materials and some salts, and incubating the mixture. When Spiegelman did this, the system obligingly replicated the strands of naked RNA. Spiegelman then extracted some of the freshly synthesized RNA, put it in a separate nutrient solution, and let it multiply. He then decanted some of that RNA into yet another solution, and so on, in a series of steps."

"The effect of allowing unrestricted replication was that the RNA that multiplied fastest won out, and got passed on to the "next generation" in the series. The decanting operation therefore replaced, in a highly accelerated way, the basic competition process of Darwinian evolution, acting directly on the RNA. In this respect it resembled an RNA world."

[The RNA world hypothesis is a theory that life started out as self-reproducing RNA.]

"Spiegelman's results were spectacular. As anticipated, copying errors occurred during replication. Relieved of the responsibility of working for a living and the need to manufacture protein coats, the spoon-fed RNA strands began to slim down, shedding parts of the genome that were no longer required and merely proved to be an encumbrance. The RNA molecules that could replicate the fastest simply out-multiplied the competition. After seventy-four generations, what started out as an RNA strand with 4,500 nucleotide bases ended up as a dwarf genome with only 220 bases. This raw replicator with no frills attached could replicate very fast. It was dubbed Spiegelman's monster."

"Incredible though Spiegelman's results were, an even bigger surprise lay in store. In 1974, Manfred Eigen and his colleagues also experimented with a chemical broth containing Qb replication enzyme and salts, and an energized form of the four bases that make up the building blocks of RNA. They tried varying the quantity of viral RNA initially added to the mixture. As the amount of input RNA was progressively reduced, the experimenters found that, with little competition, it enjoyed untrammeled exponential growth. Even a single RNA molecule added to the broth was enough to trigger a population explosion."

"But then something truly amazing was discovered. Replicating strands of RNA were still produced even when not a single molecule of viral RNA was added! To return to my architectural analogy, it was rather like throwing a pile of bricks into a giant mixer and producing, if not a house, then at least a garage. At first Eigen found the results hard to believe, and checked to see whether accidental contamination had occurred. Soon the experimenters convinced themselves that they were witnessing for the first time the spontaneous synthesis of RNA strands form their basic building blocks. Analysis revealed that under some experimental conditions the created RNA resembled Spiegelman's monster."

But that's not all!   In 1997, further experiments by Eigen and Oehlenschlager showed that Spiegelman's monster eventually evolves under the same unnatural conditions to two kinds of RNA, one consisting of 54 bases and one consisting of only 48!

• Paul Davies, The Fifth Miracle, Simon and Schuster, New York, 1999, pp. 127-128.

• M. Eigen and F. Oehlenschlager, 30 years later - a new approach to Sol Spiegelman's and Leslie Orgel's in vitro evolutionary studies: dedicated to Leslie Orgel on the occasion of his 70th birthday, Orig. Life Evol. Biosph. 5-6 (1997), 437-457.

Manfred Eigen, a mathematical biologist, is famous for his work on the origin of life.  He's also the invented an important concept called the Eigen vector

#ScienceSunday
48
26
Jim Wilbur's profile photoSergey Ten's profile photoKaj Sotala's profile photoJames Griffin's profile photo
65 comments
 
This is pretty fascinating and does it point to the very origins of life?
 
It may indeed help us understand the origin of life.  Manfred Eigen is famous for his work on that question.
John Baez
+
1
0
1
0
 
I'll warn people that my post contains a joke, near the very end.
 
No problem here - I don't get jokes about Eigenvectors. :-)
 
Devolution or biological reverse engineering?
 
+Zetetic Elench wrote: "did they put a name to the process of stripping features in this way?"

Not that I know of.  Parasites tend to lose features as they rely more and more on their hosts - that process may have a name that can be used here too, but I don't know it.
 
How long until that joke finds its way into Wikipedia as fact?
 
I'm not too worried about that - plenty of mathematicians known that 'eigenvalue' comes from the German 'Eigenwert', meaning 'characteristic value', and similarly for 'eigenvector' - and these folks keep those Wikipedia articles pretty darn accurate.   By the way, most of my math colleagues (including myself) really love the amount of high-quality information you can find on math on Wikipedia.  A lot of those articles are impossible to understand unless you're a mathematician, but the info tends to correct.  It's made it a lot easier for mathematicians to learn more math - just what the world needs, eh?
 
So if you can get self-replicating RNA to appear spontaneously in a mixture of bases and replication enzyme, I suppose an interesting question to explore next would be what it takes to get out something with some more bits to it: a protein coat, say. Probably much harder, but a step closer to the appearance of living things.
 
Possibly thinking of self-replicating RNA experiments as being pointers to the origins of life tends to be too speculative without taking into account protein development?
 
Couldn't agree more about the math content on Wikipedia, although sometimes PlanetMath is better.  I always check Wikipedia first.
 
+Charlie Ebert That's not fair asking anyone to explain the Chia-pet as there can be no explanation for that.
 
+Matt McIrvin - I imagine a protein coat and other things will only evolve when they're evolutionarily useful.  It might be interesting to start with this extremely 'coddled' RNA that's given plenty of the bases and an enzyme necessary for its self-replication, and somehow gradually make life more difficult for it, and see how it evolves.  But this would be going in the other direction than the experiment described here, where we coddle the RNA of a virus as much as possible and watch it 'devolve' to a minimal self-replicating unit.
 
Just the idea of a minimal self replicating unit like that is really interesting.
 
+John Baez wrote >>" plenty of mathematicians known that 'eigenvalue' comes from the German 'Eigenwert', meaning 'characteristic value', and similarly for 'eigenvalue. By the way, most of my math colleagues (including myself) really love the amount of high-quality information you can find on math on Wikipedia.'"  ????


You probably wanted to write "Eigen", which means various things centered around the word property, like a person which is "eigen" is a person who is somewhat a little bit centered around him/herself and is even eventually a little odd. "Eigentum" (the noun to "eigen") means property. An Eigner is an owner, "eignen" means to be appropriate for a purpose. "Dies is mein Eigen" means "this belongs to me", so Eigenvector means rather a strange vector which belongs to a matrix etc., I would say.

Wikipedia changed my information life quite dramatically.

Regarding the RNA experiments: the fact that you loose somewhat control about whats actually happening is one of the biggest problems with bio- and other technology. so I find enthusiastic reports about recreating some complex thing in the lab (like a bacteria or so) sometimes even rather disturbing. There is a  big difference between rebuilding something and fundamentally understanding why this works in this way and what it would mean to change little things in the process (like they could happen in certain lab mutations)
 
I meant "plenty of mathematicians known that 'eigenvalue' comes from the German 'Eigenwert', meaning 'characteristic value', and similarly for 'eigenvector'."
 
Cell-free replication systems are fascinating. The origin of life stuff always struck me as sketchy. Much more interesting to me is how this sort of system can be tweaked, tinkered with or downright subverted- then we are in the realms of synthetic biology.
 
This is fascinating staff. Wiki point that the key element of replication here is enzyme called "RNA replicase", which is very complex by itself.
http://en.wikipedia.org/wiki/RNA_replicase
So virus is kind of shifing complexity from itself to environment, or more  exactly compress itself using context (dictionary) of environment.
Even more fascinating (and ominous) is that the same "RNA replicase" is related to telomeres, who are responsible for aging and death.
http://en.wikipedia.org/wiki/Telomere
 
+Sergey Ten I wouldn't worry about the connection to telomerases- sounds like something buried in evolutionary history. Also telomerases are good- they stop your DNA from fraying.
 
+John Baez I meant "plenty of mathematicians known that 'eigenvalue' comes from the German 'Eigenwert', meaning 'characteristic value' and similarly for 'eigenvector'."

The strange word eigenvalue comes probably from PARTIALLY TRANSLATING the german word eigenwert. But usually one wouldnt say that the english word "value" "comes from" the german word "Wert" (at least not in front of a general audience), but rather that the word "value" is used in this context because it is a direct translation of the word "Wert", and that this word was previously used in german texts in this context.
In particular it looked to me as if you where originally setting out to explain the strange word "eigen" and may be what it could mean or why it wasnt translated so thats why I was irritated.
 
The german word "Ei" by the way seems to be ethymologically related to the french word "a" or "ai" which means "to have".
As a side remark the german word "Ei" means "egg" and also "ovum" but also "awe" or "ah" and it is pronounced as the english word "I". The german word "Gen" means "gene" but it sounds also like the german word "gehn" (go). So the word "Eigen" may have come from something as "to become property". So the word "Igon" (in +Allen Knutson  link) in the sense of "I" -"going" seems therefore actually not such a far "translation" or "interpretation" of the word "Eigen" .
 
While he's not really behind eigenvalues, Manfred Eigen's book with Ruth Winkler : The Laws Of The Game: How The Principles Of Nature Govern Chance first published 1975 in the German edition, is the first place I ever met any idea of a Singularity, in the form of the observation that the human demography curve was better fitted by an hyperbolic curve with a vertical asymptote than by an exponential.
 
The stars of the show are really the RNA-dependent RNA polymerases. I find that of the Φ6 phage of Pseudomonas syringae particularly striking - Wikipedia says:

The recombinant Φ6 RdRP is highly active in vitro, possesses RNA replication and transcription activities, and is capable of using both homologous and heterologous RNA molecules as templates. The crystal structure of the Φ6 polymerase, solved in complex with a number of ligands, provides insights towards understanding the mechanism of primer-independent initiation of RNA-dependent RNA polymerization. Interestingly, this RNA polymerase appears to operate without a sigma factor/subunit. The purified Φ6 RdRP displays processive elongation in vitro and self-assembles along with polymerase complex proteins into subviral particles that are fully functional.
 
In the german special edition of 1978 (which I got from my father some weeks ago) Manfred Eigen and Ruthild Winkler-Oswatitsch write on p. 287:

"Gewiß die Lage der Menschheit ist heute gefährlicher, als sie jemals war. Potentiell aber ist unsere Kultur durch die von ihrer Naturwissenschaft geleistete Reflexion in die Lage versetzt, dem Untergange zu entgehen, dem bisher alle Hochkulturen zum Opfer gefallen sind. Zum ERSTENMAL in der Weltgeschichte ist das so. Wir wollen uns im folgenden weniger mit Inhalt und Grenzen der Welten auseinandersetzen, als vielmehr nach den Regeln fragen nach denen das Spiel der Selbstorganisation auf den verschiedenen Ebenen abläuft."

translation without guarantee:
Sure, the position of humankind is more dangerous then ever. However our culture is - due to the of the natural sciences achieved reflection - in the position to escape the fall, which had made all high cultures fall prey. For the FIRST TIME this is so in the world's history.
In the following we want to care less about the content and the boundaries of the worlds, but ask for the rules which guide the game of self-organization on the various levels.

By the way +Boris Borcic how do you do cursive here on google+?
 
+John Baez I hadn't heard that story before, thank you!  

I wonder how directly this can process be modelled.  One could replace the RNA by sequences of 0's and 1's and the "replicase" by a computer program.  The whole system could be replaced by a stochastic process which runs the computer program on randomly chosen sequences adding the output to the data set.  

Maybe this model is missing something about the system, or maybe the RNA should be computer programs and the "replicase" should be a Turing machine.
 
+Nadja Kutz cursive, strikethrough and bold are obtained by framing the word or text with underscores, dashes and asterisks respectively. But it sometimes fails, God knows why.
 
+Nadja Kutz -- German ‘eigen’ (and its cognate, English ‘own’) are usually thought to derive from a proto-Indo-European verb ‘aik’.  (The ‘n’ is a past participle suffix.)
 
+Boris Borcic -- Wikipedia reports that the human population growth rate has been declining since the 1960s (logarithmic scale) or the 1980s (linear scale).
 
+Boris Borcic -  Thanks, I'll have to learn about the Φ6 phage!  I don't know what a 'sigma factor' is.
 
I like to use italics and boldface here, but they're very fragile.  They seem to work differently on comments than in posts, they've worked differently at different times, and they tend not to work if you try to include periods, commas, exclamation marks, question marks or parentheses at one or the other end of the string you're trying to affect. 

Let me see how it works today:

This should be boldface, including the period.

This should be boldface, not including the period.

This should be boldface, including the exclamation mark!

This should be boldface, not including the exclamation mark!
 
Okay, all four worked in comments.  Unfortunately they tend to work worse in posts, where I really want them.
 
IME, things break down if there are punctuation marks on both sides.

Each copy of ‘test’ is individually italicised:
test (test test) (test)

Wow, even the last one worked!  That used to be guaranteed to fail.  Maybe Google+ is getting better?
 
OK, so what I learn from this is that, in the presence of an appropriate enzyme, RNA that can use this enzyme will appear spontaneously (as long as the bases are around, but we already know that those are easy to come by).  As far as implications for the origin of life go, I conclude that the protein-first scenario is more likely than it otherwise would be.
 
Indeed there are Ribozymes, RNA molecules with enough tertiary structure to act protein-style as enzymes. There are even RNA polymerase ribozymes, but if I read Wikipedia correctly, their performance is far from stellar.
 
Now if we can get that to arise spontaneously too, then we're set!
 
Trouble is, it might be an event of very low probability. As far as we know, we might be the only life in the observable universe which means there is no empirical lower bound on this probability. In an infinite universe, life would form infinitely many times however small the chances. 
 
At low enough probability, you have to start considering alternatives, whether DNA-first, panspermia, or even a creator god or other extraterrestrial intelligence.
 
BTW, a good reason for underscores and the like to fail time to time to produce cursive etc in G+, [could be] to allow failures show how the effect is commanded, and to help the knowledge propagate both from the illustrative failures and the discussions their mysterious causes provoke.

Meanwhile, the insecurity of the commands helps the style of using them sparingly.
 
+Boris Borcic - I think that theory assumes that Google is optimizing everything; in fact I believe that like most other organizations they screw up, especially when it comes to things they consider unimportant, like the use of italics in Google+ posts.
 
+John Baez You are really mistaken - although on second reading I must admit my revised version leaned to the tone of what you say, but that was more simplifying for clarity than intention. I really, to start with, only meant to tell (what sums up to) why Google could find it perfect to leave it as it is.
 
+John Baez And in fact this find (of beautifully plausible motive where there are likely none) strongly reminds me of a similar find I made one year ago, of a plausible enough (but clearly fictional) hidden agenda to the FTL neutrinos of the Opera experiment (trying to sell colliders to HFT).

I mean, these are miraculously plausible plots to rationalize (probable) accidents, plots that do no wrong by just retro-fitting intelligence where only stupidity (presumably) reigned.
 
Conspiracy theories usually assume more intelligence, more ability to cooperate, and more ability to keep secrets than people actually have.  At least, that's what I think: if there are lots of conspiracies that never get discovered, I wouldn't know about that!  The Fermi Paradox could be solved by positing a very, very large conspiracy.
 
There are lots of real conspiracies about. The thing that distinguishes a stupid conspiracy theory from a plausible claim is whether the absence of evidence for the conspiracy is explained by enlarging the conspiracy.
 
I feel conspiration theories (or fictional conspiracies) vary also by the quality of their irony, with the more low-grade and common sort similar to brutal sarcasm, and the better sort shining by the way they take extant polarized attitudes by surprise (by being inconsistent with the partisan script typical of the former sort), while efficiently conveying some good background information or principles.

Hum, this reminds me of a blog post draft of mine that's been sleeping for months, explaining that Climate Change is really only Arctic Melting, and that the latter was willed by God to make it easier for Creationists to verify the transformation of species in the case of the flagship ring species of arctic seagulls. It would be about right to publish now. "Arctic Melting As Intelligent Design Enacted".
 
+Boris Borcic - Please don't help silly people of bad intent come up with the next fallback excuse.  You may mean your story as parody, but these people don't have a sense of irony.   We can expect very soon a bunch of people to start talking about how great it is that the Arctic ice is gone.
 
+John Baez The gist of the piece, though, also has a fascinating way of facing the challenge of an ethically clean interpretation of some biblical passage - but it's logical you end up opposing that some "people don't have a sense of irony", since the particularity of the singular central verse is that it inescapably implies irony if only both author and reader are assumed to be (humans, and) in possession of a complete enough sense of perspective.

(To mellow the above, I'd be ready to negotiate that in the abstract "complete enough sense of perspective" could refer to concentric russian dolls; implying unstable non-completions around/above any (meta)stable "completion" - as well as, perhaps, the converse).
 
There are already a bunch of people talking (at least privately) about how great it is that the Arctic ice is melting: the people running energy companies (and their government sponsors).  More oil and natural gas under there!
 
I see that. I don't see why censoring non-standard opportunistic interpretations of the opening of the Arctic should slow down the rise of the standard opportunistic interpretations.
 
I wasn't "censoring" anything.  I was giving some un-asked-for advice.  I'll make it more explicit: I think your energy would be better spent constructing narratives that would lead people to come up with ways to combat global warming.   But do whatever you want, of course.
 
I guess I've been tripped by the cultural gap vs the 1st amendment - my use of "censoring" was meant as more technical and impersonal than accusatory. Maybe there's a more adequate verb. Anyway, my audience is tiny and I have other reasons not to feel quite comfortable about the move, so we'll see. Thanks in any case for the polite advise.
 
+Toby Bartels  wrote:  -- German ‘eigen’ (and its cognate, English ‘own’) are usually thought to derive from a proto-Indo-European verb ‘aik’.  (The ‘n’ is a past participle suffix.)

What is the meaning of aik? So if I understand you correctly then you say that "eigen" should not be understood as arising from two words, but just one word, namly "aik" and a suffix, which gives it a temporal indication? (which means that aik'n is a verb??!)
I am no linguist, so my suggestion is probably wrong. But to defend my thoughts about the origin of the word "eigen" (namely that it could have stemmed from the word "property" and the word "ge(h)n" to mean something as "to become property") I would like to add that in the ethymology dictionary of F. Kluge the old indian word "ishe" means to own, to have the property, to rule. In this word there is no "k" or "g" sound.
 
The Online Etymology Dictionary ([entry for English ‘owe’](http://www.etymonline.com/index.php?term=owe)) translates ‘aik’ as ‘to be master of, possess’ and lists among its other descendents Sanskrit ‘ise’ (which seems to be a third person singular of Kluge's verb).  I'm no linguist either, but I know that Indo-European /k/ often became /s/ in Indo-Iranian languages (and became a guttural fricative in Germanic, as with ‘owe’ and the root of ‘eigen’); compare ‘hundert’ (German), ‘cent’ (Latin root), ‘shat’ (Sanskrit root).

But I am only reporting what etymologists say.
 
It's only called a "gutteral" fricative if you learned your linguistics on the streets.
 
Imagine that there's a German word ‘eigen’ (infinitive now) meaning something like Indo-European ‘aik’ or English ‘own’ (as a verb).  And imagine that it's a strong verb.  Then its past participle might be ‘geeigen’.  But the ‘ge’ prefix on past participles is a relatively recent development, so 1000 or 1500 years ago it would just be ‘eigen’ (now a past participle, not an infinitive).  Then if the verb is lost except for this past participle, people won't add ‘ge’ to it later, and it becomes the modern German adjective ‘eigen’ (from which the noun ‘Eigen’ descends).  This is my impression as to what really happend, but since this comes from reading the comparative material in English etymologies rather than German etymologies directly, I may be confused.

Much the same thing happened in English, where the verb was ‘owe’ (anachronistically leaving the ‘n’ suffix off of English infinitives) and the past participle is ‘owen’ or ‘own’ (here the ‘n’ suffix survives).  But then a funny thing happened to this verb: although we didn't lose it entirely, it shifted meaning from ‘have’ to ‘have to pay’.  (In fact, there was a phrase ‘owe to yield’, meaning verbatim ‘have to pay’, and somehow that dwindled to only the first word.)  Yet ‘own’ retained its original meaning, becoming (like ‘eigen’) an adjective in its own right.  And then we quite unnecessarily expanded the meaning of this adjective to a verb with the same meaning as the original verb ‘owe’, creating the modern English verb ‘own’!

Etymology is crazy.
 
+Toby Bartels wrote: "Then its past participle might be ‘geeigen’."

But Toby above you wrote: "(The ‘n’ is a past participle suffix.)" ???

I could live with a past participle suffix or prefix "ge", because "go, gehn" indicates a temporal process, so it would be no wonder if this would be used for a "temporalization" of a verb (i.e. here the process to make a verb into a past participle).

I was actually thinking in this context about the word "some", but I am not sure if John wants me to turn his Spiegelman-self replicating- Frankenstein post into a linguistic thread. So I'll try to be short: the word "some" (http://www.etymonline.com/index.php?allowed_in_frame=0&search=some&searchmode=none) seems to me to be related to the german word "samen", which means semen, but also sperm.
So somebody seems to be a "body with sperm " . Interestingly the german word manche(r) (which means "some" for which Kluge holds not so much information about the root, but more about similarities to other languages) could be interpreted as the diminuitive of man, since the suffix "chen" ist a possible diminuitive in german (like my father used to call me Nadjachen). So "manche" could mean "little men".
However if you follow this line of argumentation (see also my explanation about the word "Ei") then e.g. "awesome" gets a rather sexual annotation. I may interpret a little bit to much into this, but looking at the german translation of "awesome" which is "überwältigend" (which literal translation is something like "more than force", i.e. "overpowering") or lovesome, which tranlation is "entzückend" (which literally means "to stop quivering") doesn't help too much to refute the association.
 
>I am not sure if John wants me to turn his Spiegelman-self replicating- Frankenstein post into a linguistic thread.

Yes, good point.  I'll make no more comments.
Add a comment...