7 ms·

Alan Turing's 'Morphogenesis' Theory Confirmed 60 Years After His Death

122 points by wrongc0ntinent 13y ago

apsec112 13y ago
An important discovery, but equally important to keep it in proper context: "If you want to get a rough grasp of how the leopard might get its spots, then building a CA model (or something similar) can be very illuminating. It will not tell you whether that's actually how it works. This is an important example, because there is a classic theory of biological pattern formation, or morphogenesis, first formulated by Turing in the 1950s, which lends itself very easily to modeling in CAs, and with a little fine-tuning produces things which look like animal coats, butterfly wings, etc., etc. The problem is that there is absolutely no reason to think that's how those patterns actually form; no one has identified even a single pair of Turing morphogens, despite decades of searching. For a good account of the actual mechanisms of biological pattern formation, as they are being revealed by molecular developmental biology, see John Gerhart and Marc Kirschner, Cells, Embryos and Evolution: Toward a Cellular and Developmental Understanding of Phenotypic Variation and Evolutionary Adaptability (Oxford: Blackwell Scientific, 1997). This book provides an excellent discussion of the interactions between genetic control, self-organization, evolutionary forces and functional adpatations in development. (There is a nice review by Danny Yee.) — The failure of experiment to turn up any biological system working according to Turing's principles was remarked by the late, great John Maynard Smith in his review of Depew and Weber's Darwinism Evolving (in the New York Review of Books, vol. 42, no. 4, 2 March 1995); my search of the subsequent literature doesn't indicate that the situation has changed. Update, 4 March 2012: There is now a fairly convincing example of a pair of Turing morphogens in actual biology: Andrew D. Economou, Atsushi Ohazama, Thantrira Porntaveetus, Paul T Sharpe, Shigeru Kondo, M. Albert Basson, Amel Gritli-Linde, Martyn T. Cobourne and Jeremy B. A. Green, "Periodic stripe formation by a Turing mechanism operating at growth zones in the mammalian palate", Nature Genetics 44 (2012): 348--351 Thanks to a reader for letting me know about this." http://vserver1.cscs.lsa.umich.edu/~crshalizi/reviews/wolfram/ http://vserver1.cscs.lsa.umich.edu/~crshalizi/reviews/wolfra...
- mjn 13y ago
  Yeah, the reporting is a bit strange, though the Turing paper covers a wide range of subjects, so that's not too surprising. Turing's theory is so broad it would be difficult to "confirm" it with any single study, because he proposed a mechanism that he hypothesized could account for an extremely wide range of phenomena. It's not really a theory of one particular mechanism, so much as a meta-theory that many patterns in nature are produced by various physical instantiations of a more general mathematical mechanism. It would be difficult to confirm that in the strong sense with anything short of a wide-ranging survey covering thousands of experiments, showing that an enormous range of physical mechanisms and patterns in nature really are the result of this abstract meta-mechanism. This paper has not done that, so it hasn't really confirmed Turing's hypothesis in the strong sense. On the other hand, one might be looking for a weaker sort of confirmation: not that Turing-style morphogenesis accounts for everything, but that it accounts for at least something, i.e. there is at least one demonstrable instance where a Turing-style explanation can be shown to account for a process as it actually works physically & historically in nature, vs. just being a clever way of mathematically approximating a pattern. In that case, the paper you link above is at least one prior example, and this article adds another domain-specific investigation.
Splendor 13y ago
Turing's paper [PDF]: http://www.dna.caltech.edu/courses/cs191/paperscs191/turing.pdf http://www.dna.caltech.edu/courses/cs191/paperscs191/turing....
- nswanberg 13y ago
  And here is the paper covered in the original post: http://fraden.brandeis.edu/publications/papers/PNAS(2014).pdf http://fraden.brandeis.edu/publications/papers/PNAS(2014).pd... with notes at http://www.pnas.org/content/suppl/2014/03/06/1322005111.DCSupplemental/pnas.201322005SI.pdf#nameddest=STXT http://www.pnas.org/content/suppl/2014/03/06/1322005111.DCSu... It's dense but not impossibly so. One modification they made to Turing's idea was that each cell has the same composition. They found that, to produce the results they expected, they needed to alternate the composition of neighboring cells. (It would be nice if your post was at the top of the thread, since it's the most relevant and useful so far, but it is not very controversial. Next time consider adding something like "Biology professors hate him! Read this man's 1 weird trick for explaining morphogenesis!")
marktangotango 13y ago
It's interesting to note that Turing, Von Nueman, and Konrad Zuse all moved into studying cellular automata in their later years. Conway is famous for his game of life, but but Turings work consisted of this morphogensis thing, and Von Nueman created a self replicating automata. I don't recall what Zuse's work consisted of. Also interesting, Wolfram mentions none of their work in his book, "A New Kind of Science".
- Splendor 13y ago
  Zuse wrote Calculating Space: http://en.wikipedia.org/wiki/Calculating_Space http://en.wikipedia.org/wiki/Calculating_Space
- adamwong246 13y ago
  He couldn't give a single shout out? Considering what a behemoth that book is, that's just poor form!
  - baddox 13y ago
    marktangotango is lying, and almost certainly deliberately. See my sibling comment: https://news.ycombinator.com/item?id=7451765 https://news.ycombinator.com/item?id=7451765.
    - adamwong246 13y ago
      ummm... that's kind of a leap of logic. Maybe he just made a simple mistake? Why would someone lie about references in computer science book?
      - deleted 13y ago
        [deleted]
        baddox 13y ago
        I infer that you are claiming me to be a Wolfram-cultist. This is not the case. I think Wolfram is a smart and accomplished guy who tends to be too prideful and single-minded about his own accomplishments. But I'm also someone who is able to spend 3 minutes searching the Internet to determine the validity of extraordinary claims regarding the content of Wolfram's book. I don't have to worship a person to think it's inappropriate to use lies to discredit that person. In fact, the more worthy a person is of being discredited, the more important (and elementary) it is to discredit that person using true statements.
joshontheweb 13y ago
I'm curious as to how this explains geometric drug induced hallucinations. That has always puzzled me.
- jes5199 13y ago
  There's a good paper about how some geometric hallucinations are formed: http://people.mbi.ohio-state.edu/golubitsky.4/reprintweb-0.5/output/papers/6120261.pdf http://people.mbi.ohio-state.edu/golubitsky.4/reprintweb-0.5...
  - moments 13y ago
    Thank you, this looks interesting. Also, a guy named Kent has a book on this called: Psychedelic Information Theory. There is a web print of the book floating around.
  - codezero 13y ago
    Interesting, I see geometric patterns when I rub my eyes real hard, always wondered what caused it.
    - 3rd3 13y ago
      I think there is a wiki article explaining this by pressure and heat both activating cells on the retina.
moron4hire 13y ago
"60 years after his suicide..." appreciated they didn't say "death". Would have preferred "apparent suicide", but it's a step in the right direction.
- JoeAltmaier 13y ago
  I'm surprised by the '60 years' part - if not killed, he could be living today! What a stupid loss.
  - moron4hire 13y ago
    Indeed. Maybe he could have made more discoveries. Maybe he could have trained an entire, new generation of mathematicians. Maybe he could have just gotten to live a happy life, as should be the right of all human beings.
bobjordan 13y ago
Here is an interesting semi-technical read relating to how Turing's work helps to explain drug-induced hallucinations: http://plus.maths.org/content/uncoiling-spiral-maths-and-hallucinations http://plus.maths.org/content/uncoiling-spiral-maths-and-hal...
jboynyc 13y ago
A great book on the general context of what counts as an explanation in biology -- and, by extension, why the mathematical biological approach advanced by Turing never really caught on -- is presented in Evelyn Fox Keller's Making Sense of Life: Explaining Biological Development with Models, Metaphors, and Machines (Harvard U.P., 2003). A short version of the argument is presented in this article from Project Syndicate: http://www.project-syndicate.org/commentary/biology-s-clash-of-civilizations http://www.project-syndicate.org/commentary/biology-s-clash-...
Nursie 13y ago
I went to a talk on this paper up at Bletchley Park a few years back. Very cool, not quite what I expected (ie, not compsci theory) but really interesting nonetheless. As I understand it this was his last paper too, before the authorities basically hounded him to death.

122 points by wrongc0ntinent 13y ago

An important discovery, but equally important to keep it in proper context: "If you want to get a rough grasp of how the leopard might get its spots, then building a CA model (or something similar) can be very illuminating. It will not tell you whether that's actually how it works. This is an important example, because there is a classic theory of biological pattern formation, or morphogenesis, first formulated by Turing in the 1950s, which lends itself very easily to modeling in CAs, and with a little fine-tuning produces things which look like animal coats, butterfly wings, etc., etc. The problem is that there is absolutely no reason to think that's how those patterns actually form; no one has identified even a single pair of Turing morphogens, despite decades of searching. For a good account of the actual mechanisms of biological pattern formation, as they are being revealed by molecular developmental biology, see John Gerhart and Marc Kirschner, Cells, Embryos and Evolution: Toward a Cellular and Developmental Understanding of Phenotypic Variation and Evolutionary Adaptability (Oxford: Blackwell Scientific, 1997). This book provides an excellent discussion of the interactions between genetic control, self-organization, evolutionary forces and functional adpatations in development. (There is a nice review by Danny Yee.) — The failure of experiment to turn up any biological system working according to Turing's principles was remarked by the late, great John Maynard Smith in his review of Depew and Weber's Darwinism Evolving (in the New York Review of Books, vol. 42, no. 4, 2 March 1995); my search of the subsequent literature doesn't indicate that the situation has changed. Update, 4 March 2012: There is now a fairly convincing example of a pair of Turing morphogens in actual biology: Andrew D. Economou, Atsushi Ohazama, Thantrira Porntaveetus, Paul T Sharpe, Shigeru Kondo, M. Albert Basson, Amel Gritli-Linde, Martyn T. Cobourne and Jeremy B. A. Green, "Periodic stripe formation by a Turing mechanism operating at growth zones in the mammalian palate", Nature Genetics 44 (2012): 348--351 Thanks to a reader for letting me know about this." http://vserver1.cscs.lsa.umich.edu/~crshalizi/reviews/wolfram/ http://vserver1.cscs.lsa.umich.edu/~crshalizi/reviews/wolfra...

mjn 13y ago
Yeah, the reporting is a bit strange, though the Turing paper covers a wide range of subjects, so that's not too surprising. Turing's theory is so broad it would be difficult to "confirm" it with any single study, because he proposed a mechanism that he hypothesized could account for an extremely wide range of phenomena. It's not really a theory of one particular mechanism, so much as a meta-theory that many patterns in nature are produced by various physical instantiations of a more general mathematical mechanism. It would be difficult to confirm that in the strong sense with anything short of a wide-ranging survey covering thousands of experiments, showing that an enormous range of physical mechanisms and patterns in nature really are the result of this abstract meta-mechanism. This paper has not done that, so it hasn't really confirmed Turing's hypothesis in the strong sense. On the other hand, one might be looking for a weaker sort of confirmation: not that Turing-style morphogenesis accounts for everything, but that it accounts for at least something, i.e. there is at least one demonstrable instance where a Turing-style explanation can be shown to account for a process as it actually works physically & historically in nature, vs. just being a clever way of mathematically approximating a pattern. In that case, the paper you link above is at least one prior example, and this article adds another domain-specific investigation.

Splendor 13y ago

Turing's paper [PDF]: http://www.dna.caltech.edu/courses/cs191/paperscs191/turing.pdf http://www.dna.caltech.edu/courses/cs191/paperscs191/turing....

nswanberg 13y ago
And here is the paper covered in the original post: http://fraden.brandeis.edu/publications/papers/PNAS(2014).pdf http://fraden.brandeis.edu/publications/papers/PNAS(2014).pd... with notes at http://www.pnas.org/content/suppl/2014/03/06/1322005111.DCSupplemental/pnas.201322005SI.pdf#nameddest=STXT http://www.pnas.org/content/suppl/2014/03/06/1322005111.DCSu... It's dense but not impossibly so. One modification they made to Turing's idea was that each cell has the same composition. They found that, to produce the results they expected, they needed to alternate the composition of neighboring cells. (It would be nice if your post was at the top of the thread, since it's the most relevant and useful so far, but it is not very controversial. Next time consider adding something like "Biology professors hate him! Read this man's 1 weird trick for explaining morphogenesis!")

marktangotango 13y ago

It's interesting to note that Turing, Von Nueman, and Konrad Zuse all moved into studying cellular automata in their later years. Conway is famous for his game of life, but but Turings work consisted of this morphogensis thing, and Von Nueman created a self replicating automata. I don't recall what Zuse's work consisted of. Also interesting, Wolfram mentions none of their work in his book, "A New Kind of Science".

Splendor 13y ago
Zuse wrote Calculating Space: http://en.wikipedia.org/wiki/Calculating_Space http://en.wikipedia.org/wiki/Calculating_Space
adamwong246 13y ago
He couldn't give a single shout out? Considering what a behemoth that book is, that's just poor form!
- baddox 13y ago
  marktangotango is lying, and almost certainly deliberately. See my sibling comment: https://news.ycombinator.com/item?id=7451765 https://news.ycombinator.com/item?id=7451765.
  - adamwong246 13y ago
    ummm... that's kind of a leap of logic. Maybe he just made a simple mistake? Why would someone lie about references in computer science book?
    - deleted 13y ago
      [deleted]
      - baddox 13y ago
        I infer that you are claiming me to be a Wolfram-cultist. This is not the case. I think Wolfram is a smart and accomplished guy who tends to be too prideful and single-minded about his own accomplishments. But I'm also someone who is able to spend 3 minutes searching the Internet to determine the validity of extraordinary claims regarding the content of Wolfram's book. I don't have to worship a person to think it's inappropriate to use lies to discredit that person. In fact, the more worthy a person is of being discredited, the more important (and elementary) it is to discredit that person using true statements.

joshontheweb 13y ago

I'm curious as to how this explains geometric drug induced hallucinations. That has always puzzled me.

jes5199 13y ago
There's a good paper about how some geometric hallucinations are formed: http://people.mbi.ohio-state.edu/golubitsky.4/reprintweb-0.5/output/papers/6120261.pdf http://people.mbi.ohio-state.edu/golubitsky.4/reprintweb-0.5...
- moments 13y ago
  Thank you, this looks interesting. Also, a guy named Kent has a book on this called: Psychedelic Information Theory. There is a web print of the book floating around.
- codezero 13y ago
  Interesting, I see geometric patterns when I rub my eyes real hard, always wondered what caused it.
  - 3rd3 13y ago
    I think there is a wiki article explaining this by pressure and heat both activating cells on the retina.

moron4hire 13y ago

"60 years after his suicide..." appreciated they didn't say "death". Would have preferred "apparent suicide", but it's a step in the right direction.

JoeAltmaier 13y ago
I'm surprised by the '60 years' part - if not killed, he could be living today! What a stupid loss.
- moron4hire 13y ago
  Indeed. Maybe he could have made more discoveries. Maybe he could have trained an entire, new generation of mathematicians. Maybe he could have just gotten to live a happy life, as should be the right of all human beings.

bobjordan 13y ago

Here is an interesting semi-technical read relating to how Turing's work helps to explain drug-induced hallucinations: http://plus.maths.org/content/uncoiling-spiral-maths-and-hallucinations http://plus.maths.org/content/uncoiling-spiral-maths-and-hal...

jboynyc 13y ago

A great book on the general context of what counts as an explanation in biology -- and, by extension, why the mathematical biological approach advanced by Turing never really caught on -- is presented in Evelyn Fox Keller's Making Sense of Life: Explaining Biological Development with Models, Metaphors, and Machines (Harvard U.P., 2003). A short version of the argument is presented in this article from Project Syndicate: http://www.project-syndicate.org/commentary/biology-s-clash-of-civilizations http://www.project-syndicate.org/commentary/biology-s-clash-...

Nursie 13y ago

I went to a talk on this paper up at Bletchley Park a few years back. Very cool, not quite what I expected (ie, not compsci theory) but really interesting nonetheless. As I understand it this was his last paper too, before the authorities basically hounded him to death.