Biology’s Birthday present for Alan Turing: Father of computer science and artificial intelligence, mathematician, cryptographer and…..biologist? 60 years after Turing published a hypothesis for pattern formation (such as zebra stripes) in biology, using math and simple diffusion, scientists have found evidence to support it. Like the yin and yang of Eastern philosophy, Turing proposed interactions between an activator (working over a short range) and an inhibitor (working over long range).
In a paper published in Nature Genetics, researchers discovered that two morphogens worked as an activator-inhibitor pair to develop striped ridges in the roof of a mouse’s mouth. Consider the reaction in Image 2 : A + B react to form C + D, where the product C feeds back autocatalytically to speed its production. C also activates an inhibitor, X*, which inhibits the reaction. Suppose these factors can regulate the genes that make skin pigment, then this interaction can give rise to the Turing patterns shown in the image.
To understand, look at Image 3: As the tissue expands,levels of the inhibitor diffusing from the stripes fall below a threshold (dashed line) so that the activator now gets back to work and produces a new stripe (dashed bar). The other panels show real data from the Nature Gen paper. Notice the appearance of the new stripe r3, first between r8 and r2 and then another (r4) between r8 and r3 both in the excised tissue and in the animal (in vivo). If diffusion of the inhibitor is blocked by making a cut next to the stripe, a new stripe emerges.
Image 4 shows the wonderful range of patterns that can be generated: A) Zebra stripes. B) Fish skin patterning. C) Phyllotaxis (leaf positioning). D) Developmental fields of leg segmentation in Drosophila. E) Cardiac arrhythmias (spiral/scroll waves).
What a neat 100 year birthday present for Alan Turing!
Sources: 1) Nature Genetics Abstract (image 3): http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.1090.html
2) A good free read (images 2, 4): http://www.fasebj.org/content/17/1/1.full
3) Turing’s 1952 paper: http://www.dna.caltech.edu/courses/cs191/paperscs191/turing.pdf
Excerpt from Turing’s Abstract : “The purpose of this paper is to discuss a possible mechanism by which the genes of a zygote may determine the anatomical structure of the resulting organism. The theory does not make any new hypotheses; it merely suggests that certain well-known physical laws are sufficient to account for many of the facts.”
Hah, I did not know that connection between Turing and morphogens – thanks for making this very informative post!
Buddhini Samarasinghe , you may have heard of this particular pair of morphogens: FGF (fibroblast growth factor) and Shh (Sonic Hedgehog) that are the activator and inhibitor respectively.
Rajini Rao There is no escaping Shh. I’ve never worked with it, but yes I know them 🙂 I’ve been meaning to make a post about Drosophila gene names, I think they’re awesome! My favourite is ‘tinman’, the mutation of which leads to flies with no heart 😀
Are Turing jokes permitted on this day?
Marc Ponomareff you are permitted any joke on any day.
Buddhini Samarasinghe , PLEASE do a post on Drosophila names! That is the one model organism envy I have, no cool names for human or yeast genes 🙂
How cool is Sonic Hedgehog (mutations make more bristles on the fly). I love the K+ channel gene, eag , which stands for ether-a-go-go . The flies develop the shakes when anesthetized.
A Turing machine walks into a bar. The bartender says- No, I can’t go on, it would be disrespectful. The “busy beaver function” can wait ’til another day:)
Marc Ponomareff , he couldn’t decide? 🙂 I found another, although I admit to knowing nothing about the Church-Turing thesis: Turing came up with a machine containing an infinite tape to store state, and something to modify that state.
Church thought he needed even less: his theoretical machine was just a single function (lambda) which didn’t require any state to do all that Turing’s machine could do. Thus began the separation of Church and state.
And he did all this including numerical examples without a computer. But he thought about it:
“It might be possible, however, to treat a few particular cases in detail with the aid of a digital computer. This method has the advantage that it is not so necessary to make simplifying assumptions as it is when doing a more theoretical type of analysis.”
OK Turing lovers – has anyone read the recent novel about his life? Turing (A Novel about Computation) by Christos Papadimitriou. He’s the same guy who wrote Logicomix, about the philosophical struggles around math (and other things) in the first half the 20th century, featuring Bertrand Russell and Ludwig Wittgenstein as his protagonists. Having studied the issues of that era pretty extensively from both a mathematical and philosophical point of view, I have to say that Logicomix was superb – and heart-breaking.
Wittgenstein wrestled with mathematics? Interesting …
Not so much as mathematics as what it means (and whether it is possible) to lay an absolutely certain foundation for mathematics and thereby for all human knowledge. This idea of “foundation” was one of Bertrand Russell’s obsessions, along with Alfred Whitehead, though they later went their own way so to speak. Both were more philosophers than mathematicians. There were other efforts during the same time period, many were purely mathematical (eg Hilbert). But then Goedel shot them all out of the water sometime in the 30s. Turing came of age after Goedel’s Theorem had hit like a bomb.
Everything I’ve read about how he was treated is heart breaking, including his “chemical castration” and his ultimate suicide. The House of Lords has refused to grant him a posthumous pardon for his conviction for so called indecency, even though Britain is celebrating the centennial of his birth.
That is tragic … Wittgenstein also had a weird life – three brothers committed suicide. When Wittgenstein inherited his father’s estate he became one of the richest people in Europe. He gave the entire fortune to his remaining siblings.
Alan Turing is the true genius in devicing a method to decipher the codes of enigma, he is the first programmer, and because of him we have many software code writers
Gnotic Pasta , stick with us, scientists have a great sense of humor. Some classic experiments on how fruit fly (Drosophila) developed segments led to a gene called hedgehog because mutations in this gene resulted in spiny projections all over the fly (actually, the scientists went on to win the Nobel prize). When the same genes were found in humans and other mammals, the fun began. I’m just pasting this from Wiki 🙂 “Investigations aimed at finding a hedgehog equivalent in mammals revealed three homologous genes. The first two discovered, desert hedgehog and Indian hedgehog, were named for species of hedgehogs, while sonic hedgehog was named after Sega’s video game character Sonic the Hedgehog. In zebrafish, the orthologues of the three mammalian hh genes are: shh a, shh b, (formerly described as tiggywinkle hedgehog named for Mrs. Tiggy-Winkle, a character from Beatrix Potter’s books for children), and indian hedgehog b (formerly described as echidna hedgehog, named for the spiny anteater, though this may have also been a playful reference to Knuckles the Echidna, another character from the Sonic the Hedgehog series of video games).”
Many of the thinkers in this nebulous area between mathematics & philosophy were “weird” – if not tragic. Of course, Turing had the added burden of being a fairly open gay man at a pretty bad point in cultural history. (Maybe some of the others were also homosexual, but entirely closeted. I’m pretty sure there are suggestions that this is true of Ludwig. Bertrand, on the other hand, was a notorious womanizer and as I recall at least one of his wives committed suicide … but don’t quote me on that.)
Martha E Fay I tried reading Philosophical Investigations and … the only part of Wittgenstein’s philosophy that I understand is, “Whereof one cannot speak, thereof one must be silent.”
“I believe that at the end of the century the use of words and general educated opinion will have altered so much that one will be able to speak of machines thinking without expecting to be contradicted.”
— Alan Turing
Wish he knew how awesomely right he was !!!
LOL, Matt Kuenzel , that’s a keeper..committing it to memory right now 🙂
Correction: B Russell’s eldest son committed suicide, not one of his wives.
Matt Kuenzel “Whereof one cannot speak, thereof one must be silent.” And this statement was the beginning of quite a few interesting strands in philosophy. Jacques Derrida, for example, takes this kind of statement and turns it on its head, philosophically speaking – one ends up realizing that Derrida did his best for speaking about the kinds of things that mid-century philosophy (many lines of thought lumped together here) told us that we could not talk about in philosophy or in science. (I’m not sure that other readers of Derrida have had the same reaction, but to me, his project was mostly about opening this space … without speaking of it. Brilliant.)
Martha E Fay On this topic I must remain silent.
Matt Kuenzel at this point, I should remain silent as well. My inner philosopher is chomping at the bit, but it’s bedtime for this old lady. But it’s a wonderful topic, don’t you think? Or maybe not. Many “hard” scientists (as their philosophical apologists, who dominated philosophy when I was a philosopher, called them) would, at this point, simply do their best to extricate themselves from the conversation.
Martha E Fay Matt Kuenzel on a silly note: M.A. Numminen sings Wittgenstein
Paradoxically, (collectively) not speaking about anything you don’t know about would stop progress. As making errors and then weeding them out is central to evolution / the scientific method.
So very true Henk Poley – trial and error is the essence of scientific method. The same method, in its essentials that little babies use as they try to figure out their parents, not to mention the rest of their world!
(I wish there were subtitles)
M.A. Numminen sings “Whereof one cannot speak, thereof one must be silent.” in German, Wittgenstein’s native language: “Wovon man nicht sprechen kann darüber muss man schweigen”
A serious text in a silly voice .
The absurdity cracks me up every time I hear it.
Awesome post! Information overload for my system, but awesome nonetheless!
Great to see – thanks for the post/link.
very 9ce post Rajini Rao…………..
You may enjoy the links to Turing’s 1952 paper and images in this post, Kevin Clift !
Yes thanks, Rajini Rao.
Have you read Enigma by Andrew Hodges? It may appeal more to the Maths side but is an excellent biography. http://www.amazon.com/Alan-Turing-Enigma-Centenary-Edition/dp/069115564X/ref=sr_1_1?s=books
I’ve created a Gdrive file from the Turing paper if like me people prefer that format to that of pdfs: https://docs.google.com/open?id=0B5w87B1C–aKV3Fseld3czJGX0E
Thanks, Kevin Clift . I haven’t read Enigma..about his war time decrypting efforts, I’m guessing. Sounds like a good read!
It’s a biography in general written sympathetically by a mathematician who happens to be gay. It may have had an Enigma spin when it was first published as, if I remember rightly, these machines were in the news at the time due to some declassification.
Did Britain finally overturn the criminal conviction against this poor man? I thought not..then I saw this: http://www.parliament.uk/edm/2010-12/2660
My goodness, this post is still going on?? I’ve read Enigma and a whole lot more. Going from mathematics in college to philosophy in grad school, we joked a lot about how do I know I’m not just a Turing machine? Recently read the novel Turing (forget the author) which I did not much follow or even enjoy, but I did understand it as an embodiment of that same question.
Only briefly revived, Martha E Fay , because Kevin Clift also posted on Turing’s contribution to patterning. Good to see you here.
I am much more on FB these days, Rajini Rao, as you know, because, for me, at any rate, there’s more going on. But I do miss this environment – it is very different!
I enjoy your shares on FB, keep them coming! Just remember to stop by here once in a while, Martha E Fay .
Thanks Rajini Rao. I can get pretty rabid sometimes! There seems to be more of an audience for my political posts on FB – less so here. (Although I get followers pretty much every day, here.)
Martha E Fay : Here is my theory on your different experiences: On FB, they are mostly friends IRL, so they will respond to your posts. However, the standard FB post is a witty remark or cartoon. Nothing in depth, but you get the Likes (no complex responses either).
On G+, most are virtual friends so they are only obliged to respond if you reciprocate actively. The more you engage with others, the more they will with you. I bet they see your posts here as well, it’s just that it flows by one’s stream so quickly, that unless you build a strong circle of interactors, there is only an off chance that someone will comment. If the post is particularly angsty, people will be compelled to engage here.
Rajini Rao Your theory about FB is not quite true, in my experience. I have a lot of virtual friends on FB. I’ve never met them. And believe me, I often rant on FB. OK, maybe not so much as here – you be the judge, as one of my virtual friends in both spaces.
But here on G+, if no-one responds to a post, I admit – I feel defeated. Interestingly, though, someone I met here (Ron K Jeffries) has begun paying attention on FB (thanks Ron!). And it’s true, I often just pass on stuff I’ve seen or read (rarely cartoons, thank you very much).
Even when I am at my most angsty, though, I often feel as though I am speaking into a vacuum – except for a few very good virtual friends who would be IRL friends if they were somewhere on this continent.
That may mean the next time I visit DC (where I went to college and have more than a few IRL friends), I may need to visit JH.
Of course! Come visit me Martha E Fay , so we can dissect the finer points of social networks, and much much more 🙂 Ron K Jeffries is in my circles too, on G+.
Very good point about rants, Gnotic Pasta . One only responds if the emotions evoked are strong. Also, Martha E Fay is brave enough to rant. I, on the other hand, am still at a phase where I actively avoid conflict. Even though I have plenty of strong opinions, I’m cautious about airing them. Give me a few more years, and I’ll give Martha a run for her money 🙂
Gnotic Pasta You’re right, whether on FB or G+, those who would rant in the opposite direction will not respond. But, it seems to me, that in either space, there’s some gender politics. In both spaces, responding to a rant – with one’s own rant – seems to be a male-to-male phenomenon. What do you think?
I see plenty of rants that get lots of oppositional rants in response. Of course, if I got a real live flaming rant, what would I do? Hmmm.
I think I would try to find questions to ask the other ranter.
In my own IRL environment, my rants are considered, well, cute. When I was younger, maybe not so much – but still, tolerated.
I will have to figure out “gnotic”, which at first I took to be “gnostic”. And given the pasta, I thought of gnocchi, which I had once in my life, hand-made, in high school by the mother of a good friend.
Dan says he goofed typing Gnostic 🙂
Phew, the only gnotic references I can find are misspellings of gnostic. Which is a loaded word for some of us (read: Elaine Pagels). On the other hand, my brain is definitely not noodles. (But this has to do with glucose intolerance.).
When it comes to weird epiphanies, mine led to “Red Shoes”. Go figure.
As a cradle catholic (a curse, let me tell you), Elaine Pagels was an eye opener.
As for Red Shoes. Nothing like what you have in mind.
After I signed my divorce papers (25+ years into the relationship, and two amazing sons), I needed – yes needed to have red shoes. That was something like 10? 12? years ago. I have lots of red shoes now.
Gnotic Pasta Just need to clarify – I have been on G+ for about a year. Yup, an early adopter (thanks to my kids).
(Now I am embarrassed by my need to establish this.)
As for religions, including my own, it’s all mysticism. Which is hard, when one needs some concrete symbols/rituals. It’s the smells & bells!