Alan Turing's 'Morphogenesis' Theory Confirmed 60 Years After His Death | Hacker News Reader

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

huffingtonpost.com

122 pointswrongc0ntinent51 comments

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/wolfra...

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.

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".

Zuse wrote Calculating Space: http://en.wikipedia.org/wiki/Calculating_Space

He couldn't give a single shout out? Considering what a behemoth that book is, that's just poor form!

marktangotango is lying, and almost certainly deliberately. See my sibling comment: https://news.ycombinator.com/item?id=7451765.

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?

How could that be a "simple mistake"? Either the commenter has read the book, in which case such a lapse in memory is inexcusable in the face of such a strong statement of the book's contents, or the commenter has not read the book or even quickly searched its contents, in which case the lie is the result of deliberate ignorance.

If I claimed that the Lord of the Rings trilogy does not contain a character named "Frodo," would you call that a deliberate lie or a simple mistake?

If I claimed that the Lord of the Rings trilogy does not contain a character named "Frodo," would you call that a deliberate lie or a simple mistake?

I'd call it neither.

You'd be wrong, but maybe you were confusing the name, or maybe the book, or maybe it's spelt differently in a different language. Maybe you read it long ago and forgot. Maybe you read a printing done by a little known cult that censored all referenced to hobbits. I have no idea why, but there are an infinite field of possibilities and only some require bad faith.

Or maybe your cat skipped across the keyboard and just happened to type out those exact characters and submit the comment. Fair enough. However, when I read a comment, I tend to infer that it was made intentionally by a human, and that the human intends to claim that the contents of the comment are correct.

the human intends to claim that the contents of the comment are correct

Sure. But I think it is inadvisable to claim to know the reasons or motive behind the comment, and doubly so to claim they are acting in bad faith.

Why do you say deliberately? I don't mean to provoke this thread, but you've made a pretty strong accusation, and you need to either provide evidence, or an apology.

I say deliberately, because it is so specific and so easy to verify. Either the commenter has read the book, in which case such a strong statement could only be confidently made if paired with an extraordinarily bad memory, or the commenter has not read the book (or done a quick search to see if the book contains these references), in which case I consider the lie to be the result of deliberate ignorance.

> in which case I consider the lie to be the result of deliberate ignorance.

It's not a lie, if it is the result of ignorance.

I'm not even sure what "deliberate ignorance" means in this context: he knowingly doesn't know if Wolfram mentioned this, and guessing he probably did, chooses to say he didn't?

Yes. If he knows that he has never read the book and thus doesn't know what is and isn't in it, then I would consider it a deliberate lie to make a confident claim about the contents of the book.

At this point, it's a facile criticism to say that Wolfram doesn't give enough credit to others. Many people have complained about this.

marktangotango extrapolated this trope to assuming that Wolfram doesn't cite the particular authors in question without bothering to check, perhaps because he assumes (incorrectly) that Wolfram never gives credit to others at all.

Maybe assuming you can extrapolate a common criticism of a person in any way that occurs to you, and then presenting the extrapolations as fact isn't "lying," but whatever it is, it shouldn't have a very nice name.

Assume good faith.

Mistakes happen.

Not really clear why we should be incentivizing mistakes. "Just say whatever," you might say, "If someone really cared; they'll do the research for you."

Who said anything about incentivizing?

Corrections and even downvotes are fine. Accusing someone of acting in bad faith is completely different.

It's the same principle behind Cunningham's law.

In this discussion, the mistake was corrected in about an hour and included citations.

You can argue the morality of it, but it gets results.

Well, that's a bit silly. I could just apply that same motto to my comment! and then lambast the people accusing me of being errantly hateful.

I do apply the same motto to your comment. People shouldn't lambaste you over it either.

I believe (hope?) none of my comments in this thread could be regarded has hateful (errantly or otherwise).

> Also interesting, Wolfram mentions none of their work in his book, "A New Kind of Science".

There's one of the most blatant and ridiculous lies I've seen today, with such an obvious agenda. It's disgusting.

Turing and biological pigmentation patterns: https://www.wolframscience.com/nksonline/page-1003g-text

Detailed summary of von Neumann's work in self-replication: https://www.wolframscience.com/nksonline/page-876b-text

An index entry on Zuse and modelling the Universe as a cellular automaton, although the text itself is not freely available: https://www.wolframscience.com/nksonline/index/z.html?Search...

Please don't use bald-faced lies to propagate hatred of anyone.

I stand corrected, I recall searching the index for Zuse, but did not review it for the others. I apologize.

You haven't yet deleted the false statements. Please do so, to avoid misleading readers.

Normally an edit would be good, if the post can't be edited any more, deleting it would just remove context from the concise rebuttal.

His wasn't an informed comment but it's best responded to with just the links you posted.

Turing seems to be sort of a personal hero to Wolfram, so I'm sure that he'd have some interest in the results in the post.

And for anyone interested in modeling nature with computers more generally, A New Kind of Science is wonderful reading and gives a great conceptual framework on how to go about it. It's sad that the Shalizi review is the first thing people refer to (it's sort of the Huffington Post of reviews).

It's sad that the Shalizi review is the first thing people refer to (it's sort of the Huffington Post of reviews).

Do you base this on just this one review, or more generally? I've mostly found his reviews informative and much better researched than most online reviews. They have opinions, but the opinions are more informative to me than "I like this" or "I don't like this". I usually feel that I learn something from the reviews, including finding new books and articles to read because they're cited in the review. That's not exactly something that happens at HuffPo.

I meant to refer to that particular review, not his reviews in general. It's been a long time since I've poked through those, and they seem reasonable, which makes the review of Wolfram's work that much stranger.

Anyway, the history of cellular automata is sort of interesting, and the notion of using computation to explain biological markings is also interesting. Thought after skimming Turing's paper it looks like while Turing makes many simplifying assumptions, did some basic computer modeling, and is literally about biological cells, his model is not as abstract as the cellular automata von Neumann, Conway, or Wolfram studied--unlike the others Turing's model uses linear equations to transmit "state" from cell to cell instead of rules. In fact Wolfram's contribution was to remove as many details as possible from cellular automata, enumerate all the possibilities, and observe what happens.

The bummer about referring to that review in other threads or in this case mischaracterizing Wolfram's work is that it distracts from creating more interesting discussions about this stuff. There are currently about 16 comments effectively discussing attribution, and precious few about what sort of model Turing proposed.

Sorry to go meta, but is there a review of that review which lays out some or most of the things you object to in it?

Here you go: https://news.ycombinator.com/item?id=3972635#up_3974503

My personal single biggest objection, though, is that the review appears to be used as a sort of conversation-ending trump card, usually posted with very little comment, sort of like you might see from a fan of talk radio posting in a newspaper comment section.

https://hn.algolia.com/?q=http%3A%2F%2Fwww.cscs.umich.edu%2F...

https://hn.algolia.com/?q=http%3A%2F%2Fvserver1.cscs.lsa.umi...

It's about as bad as bringing up Wolfram's ego--the consequent discussion never leads to anything interesting. Witness this thread that marktangotango started. I don't believe he was being malicious, but it's clear that rather than start a discussion about cellular automata like he intended it spawned a wasteland thread about attribution.

Why must we talk about TMZ-level bullshit when we could be talking about Turing's paper and the original paper in the post? Why is that discussion losing out to gossip?

I was eagerly anticipating A New Kind of Science and bought it when it was first available. But it was a tremendously aggravating read. It was repetitive, inconclusive, and far longer than the material merited. I came away thinking Wolfram must have set some kind of record for use of the personal pronoun "I" in a book, including autobiographies. The egotism shines through that much. Perhaps this accounts for the perception that nobody else gets credit in Wolfram's book.

This was how I thought before I read any reviews or heard anything other than laudatory things about Wolfram. Until I read the reviews I thought there might be something terribly wrong with my understanding of what I just read.

That's a strangely hostile response. I went through all of marktangotango's previous comments and didn't see one mention of Wolfram. Am I missing something?

The last sentence of his original comment.

No, (unless there was some edit that has been very cleverly camouflaged) -- an erroneous comment was taken as some kind of attack on Wolfram. I can't see any reasonable reading of that comment as "hate", though.

I'm unable to imagine an interpretation of that comment that isn't an attack on Wolfram.

Von Nueman? Is he related to von Neumann? ;)

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

And here is the paper covered in the original post: http://fraden.brandeis.edu/publications/papers/PNAS(2014).pd... with notes at 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!")

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-hal...

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-...

"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.

I'm surprised by the '60 years' part - if not killed, he could be living today! What a stupid loss.

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.

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

There's a good paper about how some geometric hallucinations are formed: http://people.mbi.ohio-state.edu/golubitsky.4/reprintweb-0.5...

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.

Interesting, I see geometric patterns when I rub my eyes real hard, always wondered what caused it.

I think there is a wiki article explaining this by pressure and heat both activating cells on the retina.

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.

Reply on news.ycombinator.com