Tag Archives: alan turing

The gene that gives tabby cats their adorable stripes

Credit: Pixabay.

House cats exhibit quite a great deal of diversity in the coloration and patterns of their fur compared to their wild feline relatives. One of the most common coat patterns is the tabby, consisting of undulating swirls, stripes, and dots — a timeless classic. Now, scientists have figured out the development process, showing that the tabby pattern remarkably starts appearing while a kitten is still an embryo.

Greg Barsh, a scientist at the Hudson Alpha Institute for Biotechnology and a professor of genetics and pediatrics at Stanford University, and colleagues collected and examined nearly a thousand house cat embryos from pregnant feral cats admitted to veterinary clinics for spaying. Most of these embryos were between 25 and 28 days old, which is apparently old enough for skin cells to develop.

“Color patterns are one of these unsolved biological mysteries; there’s no go-to model organism to study it — mice don’t have stripes or spots,” said Barsh. “The color patterns and variability that you see in animals like tigers, cheetahs and zebras prompted some central questions for us: What are the developmental genetic mechanisms and the cellular mechanisms that give rise to these patterns and how have they been altered during mammalian evolution to give rise to the amazing diversity of shape and form we see today?”

The gene that signals where stripes, spots, and blotches go

When the researchers examined the embryos under a microscope, they saw thicker skin dispersed across regions with thinner skin. The pattern resembled the tabby coat of an adult cat, which was very surprising considering that, at this stage, the embryos had yet to develop hair follicles and pigments, the most important components that color animal skin and fur.

Upon closer inspection, the team found that cats have at least two different types of skin cells, each of which is expressed by distinct sets of genes. For tabby cats, the DKK4 gene is essential since it is the one responsible for mapping the pattern of thick and thin skin in the developing kitten embryo.

Thick skin had more proteins expressed by the DKK4 gene and would later be covered in darker fur, while the thin patches had less DKK4 expression and would be covered in lighter-colored fur.

These findings nicely complement those from an earlier study, also led by Barsh, which identified a gene that controls coat color variation in tabby cats.

“We knew from studying domestic cats that there were other genes that contributed to color pattern formation; we just didn’t know what they were,” Barsh said. 

Not all tabby cats are the same, though. Mutations always occur, resulting in alterations in coat colors and patterns. For instance, some tabbies have white spots or thinner stripes.

Beyond answering a mere curiosity, the study is extremely valuable because it advances our understanding of one of the most important aspects of developmental biology: pattern formation.

Part of a grander picture

In 1952, British mathematician Alan Turing, regarded as the father of modern computing, published a landmark paper that described how biological cell patterns form and when they know it’s time to stop division.

The brilliant mathematician imagined that biological patterns are formed due to interactions of certain chemicals he called  “morphogens” that initiated and directed patterns by triggering on- or off-switches. Turing used math to show that these morphogens could move in 3-D space, a movement now known as diffusion-reaction, and deconstructed patterns seen in animal fur and leaf shapes.

We now know that Turing’s morphogens are actually activating or inhibiting molecules produced by the expression of genes. Turing patterns in hair follicleschicken feathers, and teeth-like shark “scales” have all directly been shown to be produced by the interaction between an activator and an inhibitor chemical. In the case of tabby cats, the DKK4 gene acts as an inhibitor.

However, Turing patterns can be found everywhere in nature. The diffusion-reaction equations have been used to model countless 2-D and 3-D patterns seen across the natural world, from fingerprints to semi-arid landscapes.

Now that scientists know which gene is important in house cat fur development, they can look for it in other species. They believe the same development process is present in tigers and cheetahs, considering house cats have been bred by humans for only 9,000 years.

But there are also other unanswered questions. The DKK4 gene alone doesn’t explain the rich array of colors sported by the fur of domestic cats.

“This is one of the big unanswered questions in our work — how to connect the process of prepattern formation to the process that implements the pattern later in development,” Barsh said in a statement. “That’s something that we’re actively trying to figure out.”

The findings appeared in the journal Nature Communications.

Alan Turing to feature on new £50 note

The mathematician cracked the Nazi Enigma code and is widely credited as the father of computer science — but he was persecuted for his homosexuality. He will now be featured on the £50 note.

The UK continues its tradition of featuring scientists on banknotes. After Charles Darwin was featured on the £10 from 2000 to 2018, now Alan Turing will feature on the £50 note (the equivalent of approximately $62).

The announcement was made by the Bank of England governor, Mark Carney, at the Science and Industry Museum in Manchester. Turing was selected from a list of around 1,000 scientists, to celebrate his role in World War II, his pivotal work in computational science, as well as the impact of his homosexuality persecution. Carney commented:

Alan Turing was an outstanding mathematician whose work has had an enormous impact on how we live today. As the father of computer science and artificial intelligence, as well as [a] war hero, Alan Turing’s contributions were far ranging and path breaking. Turing is a giant on whose shoulders so many now stand.”

Alan Turing was a British scientist and a pioneer in computer science. He laid the groundwork for modern computing and produced important theories about artificial intelligence. The Turing test, developed in 1950, is still a landmark test to assess a machine’s ability to exhibit intelligent behavior indistinguishable to that of a human. During World War II, his work was instrumental in breaking the German Enigma code.

But Turing’s life took a turn for the worst when he was prosecuted for his sexual orientation. Turing was prosecuted in 1952 for homosexual acts and had to choose whether to go to prison or accept chemical castration. He opted for the latter, which caused dramatic health consequences, including causing breast tissue to form. At the time, Turing wrote that “no doubt I shall emerge from it all a different man, but quite who I’ve not found out.”

Due to intense distress caused by this, Turing committed suicide two years after the “treatment”. Despite his immense contributions to society, his life ended in utter misery.

“He set the foundations for work on artificial intelligence by considering the question of whether machines could think,” the Bank said. “Turing was homosexual and was posthumously pardoned by the Queen, having been convicted of gross indecency for his relationship with a man. His legacy continues to have an impact on both science and society today.”

Turing’s face will appear on the new £50 polymer note starting in 2021.

Alan Turing. Credit: Public Domain.

Alan Turing’s final paper inspires new way to desalinate water

Alan Turing. Credit: Public Domain.

Alan Turing. Credit: Public Domain.

Alan Turing is famous as the father of computer science and artificial intelligence, as well as a WWII code breaker. However, Turing was also heavily involved in what was, at the time, an obscure field of science: mathematical biology. In 1952, just two years before his death, the brilliant British scientist published a paper in which he proposed a mathematical model that finally described how embryonic cells turn into complex structures like organs or bones. Now, Chinese researchers have built a unique nanostructure of tubular strands inspired by Turing’s work in mathematical biology. They’ve incorporated the structure into a filter that removes salt from water three times faster than some conventional filters.

Dot-based and tube-based Turing-type membranes (imaged with electron microcope). Credit: Z. Tan et al./Science

Dot-based and tube-based Turing-type membranes (imaged with electron microcope). Credit: Z. Tan et al./Science

Turing structures arise when imbalances in diffusion rates make a stable steady-state system sensitive to small heterogeneous perturbations. For example, Turing patterns occur in chemical reactions when a fast-moving inhibitor controls the motion of a slower-moving activator. The motion causes the inhibitor to push back the activator, causing a pattern of spots or stripes to appear on the product. It’s not clear whether this reaction-diffusion process does indeed take place at the cellular level, but previously scientists have used it to explain zebra stripes, sand ripples, and the movements of financial markets.

Attempts to synthesize such structures have so far been confined to 2D patterns. Now, thanks to the marvels of 3D printing, a team of researchers at Zhejiang University in Hangzhou, China have created a 3D Turing structure out of a polyamid (a material similar to nylon). The substance is the result of the reaction between piperazine and trimesoyl chloride. In typical conditions, trimesoyl chloride diffuses faster than piperazine but not fast enough to result in a Turing structure. The researchers, led by material scientist Lin Zhang, used a nifty trick: they added polyvinyl alcohol to the piperazine, further lowering its diffusion rate and allowing it to act as the activator to the trimesoyl chloride’s inhibitor.

The resulting material is a rough, porous mesh with a nanostructure resembling a Turing pattern. The Chinese researchers were even able to print two variants: dots and tubes. These are the two types of self-organizing structure predicted by Turing’s model.

The primary objective of the new study was to produce 3D Turing structures. However, the researchers were amazed to learn that membranes fashioned this way were incredibly efficient water filters. Due to the filter’s tubular structure, water can pass through a much larger surface area compared to conventional filters. In experiments, the amount of table-salt inside a slightly saline solution passing through the Turing filter was reduced by half. The Turing filter proved much more efficient with other salts: magnesium chloride was reduced by more than 90%, and magnesium sulfate (aka Epsom salt) was reduced by more than 99%, as reported in the journal  Science.

The membranes may be impractical on their own for desalinating seawater due to the rather low effectiveness for this purpose. Zhang, however, says it could be used to pretreat the seawater before eliminating the rest of the salt via reverse osmosis, which would make the overall process much more efficient. The tubular Turin filter could also be useful for purifying brackish water and industrial wastewater. And perhaps, in the future, the tubular Turing structures could be used to fashion artificial veins or bones. Turing would have been so proud!

‘I Detest America’ — trove of Alan Turing letters give unique insight to his life

Legendary computer scientist and mathematician Alan Turing was a complex figure. These newly discovered letters add even more depth to what we know about him.

Image credits: University of Manchester.

Wrapped in plain paper, lying inconspicuously at the back of an old filing cabinet somewhere in the University of Manchester, are 148 never-before seen documents and letters from Turing’s personal and professional life.

“When I first found it I initially thought, ‘that can’t be what I think it is’, but a quick inspection showed it was,” says computer engineer Jim Miles from the university’s School of Computer Science.

“I was astonished such a thing had remained hidden out of sight for so long. No one who now works in the School or at the university knew they even existed.”

Few people can claim to have offered as much to the world as Alan Turing. Already a respected scientist, he rose to international fame when he cracked the Enigma Code Nazi Germany leaders used to command their armies — “because no one else was doing anything about it and I could have it to myself”.

Turing also developed the first computer chess algorithm. Image credits: University of Manchester.

Despite living before computers really became a thing, Turing greatly contributed to computer science, and we are just now proving some of his theories. But for all his contributions, he suffered an unfair and tragic fate. Turing was homosexual, something which he confessed in an unrelated police investigation (someone had robbed his house). Homosexual acts were criminal offenses in the United Kingdom at that time and he was sentenced to hormonal treatment which, among other side effects, made him grow breasts. He was also eliminated from any relevant research and ultimately committed suicide.

Naturally, Turing’s life is of great interest, and this gives us a rare insight into how he felt about some things. For instance, his response to a conference invitation to the US in April 1953 is simply, “I would not like the journey, and I detest America”.

Another interesting letter conversation was between Turing and one of his old war-era collaborators from 1952. The mathematician was being asked for a photo portrait of himself for a history Bletchley Park that was being compiled by the American cryptographer William Friedman. In his characteristic style, Turing agreed to send a picture for the “American rogues gallery”.

But more of his letters focus on his pioneering, groundbreaking research in AI, computing, and mathematics. For instance, one interesting document from the collection is a handwritten draft for a BBC radio programme on artificial intelligence, titled “Can machines think?” from July 1951.

We can’t make up for the injustice that Turing was subjected to, but the very least we can do is respect and cherish his memory. This might add a whole new dimension to the man’s legacy, James says.

“The letters mostly confirm what is already known about Turing’s work at Manchester, but they do add an extra dimension to our understanding of the man himself and his research. As there is so little actual archive on this period of his life, this is a very important find in that context. There really is nothing else like it.”

The least we can do is respect his legacy.

Alan Turing Enigma

Decisions are reached in the brain by the same method used to crack the Nazi Enigma code

The highlight of the award winning film, “The Imitation Game”, is when Alan Turing and colleagues devise an ingenious statistical method that eventually helped decipher the Nazis’ Enigma code. This breakthrough allowed Allied intelligence to read previously unavailable German military positions and actions, vastly shortening World War II. Interestingly, a team of neuroscientists at Columbia University found that more or less the same statistical method applied by Turing and co. is used by the brain to make any kind of decision, be it going left instead of right in an intersection or placing a higher bet during a high raise power game instead of folding.

Enigmatic Brain

Alan Turing Enigma

Image: BBC

German military messages enciphered on the Enigma machine were first broken by the Polish Cipher Bureau, beginning in December 1932. Later versions, however, were of increased complexity and by the time the war broke out, cracking Enigma proved to be a cumbersome riddle. But while the machine was great at encrypting messages, its operators were not necessarily so. The British intelligence had their breakthrough after they systematically exploited German Enigma operator flaws. For instance, the Nazis had the bad habit of broadcasting messages which began with the same text, depending on the situation, like ‘The weather report for today is’. Knowing this, they could take the coded text and know how the first characters would decode. With the knowledge that no letter encrypted could be the same letter decrypted, the number of combinations possible was massively reduced.

Even so, the volume of work needed to break the codes by brute force alone was immense. It simply took too much time. Time they didn’t have. Eventually, Turing employed several statistical techniques to crack Enigma like Banburismus, which is a highly intensive, Bayesian system that allowed Turing and colleagues to guess a stretch of letters in an Enigma message, measure their belief in the validity of these guesses – using Bayesian methods to assess the probabilities – and add more clues as they arrived. Basically, this statistical test decided if two messages were similar enough then decide if these formed a pair, or not.

The animated GIF below gives you an idea of how the system worked. Corresponding pairs of letters from the two messages are aligned one above the other. At first glance, it all looks like gibberish, but the British WWII researchers knew they could preserve the matching probabilities of the original messages, as some letters are more common than others. So in any two messages, any matching pairs of letter were given a positive value and unmatched ones a negative value. When a positive threshold was researched, the code was deemed broken.

tuiring test

Michael Shadlen, MD, PhD, professor of neuroscience at Columbia draws an interesting parallel between the process employed in solving Enigma and the way the brain fires neurons to reach a decision. His team recorded the activity of neurons in the brains of two monkeys as they made a simple decision: choose between two spots for a reward. The decision had to be made fast, since the symbols – right and decoys – appeared in short 250 millisecond-long sequences. To reach the correct decision, the monkeys had to weigh different clues encoded in the symbols that flashed onto the screen. Some of the eight symbols were unreliable clues about the reward’s location; others were more dependable.

Meanwhile, researchers studied how the monkeys’ brains came to a decision by studying the neural activity. If a symbol was tied to a reward it would be assigned a positive value. Conversely a symbol was assigned a negative value if it wasn’t associated to a reward. Together, these amounted to the accumulated evidence range which was represented in the neuron’s firing rate. The more reliable the symbols were, the larger the impact on the firing rate. So, just like in Turing’s test once a positive – or negative, for that matter – threshold was reached, the monkey would come to a decision. The findings appeared in the journal Neuron.

Shadlen believes it’s sensible to claim the human brain works much in the same way to come to a decision.

“It’s the basis of a very basic kind of rationality,” he says.

“They’re decisions like, ‘I’m going to pick up a book,’ or ‘I’m going to walk toward the left of the coffee table, not the right,’” Dr. Shadlen adds.

“We make lots of these decisions every day, and it turns out, we’re making them by using the laws of probability in a way that statisticians think is optimal.”

I think we all knew all along there’s an ‘enigma’ tucked inside our minds somewhere. Now we know you can break it – you just need the right code.

Alan Turing's stripe pattern theory may explain how embryonic fingers are formed. Photo: webmd.com

Alan Turing’s 1952 mathematical model that explains finger formation confirmed

Alan Turing's stripe pattern theory may explain how embryonic fingers are formed. Photo: webmd.com

Alan Turing’s stripe pattern theory may explain how embryonic fingers are formed. Photo: webmd.com

One of the last century’s most accomplished thinkers, British mathematician Alan Turing lived a life full of scientific accomplishments, as well as persecution. He is most famous for being the founding father of computer science and also the inventor of the Enigma machine used to crack Nazi military codes, giving the Allies an upper hand in the war. Less known are his contributions to molecular biology, but of no less importance. A group from the Multicellular Systems Biology lab at the Center for Genomic Regulation confirmed one of Turing’s findings from a biology paper published in 1952, which discusses how fingers are formed.

In his only ever published biology paper, Turing sparked a novel debate over pattern formation. He developed a mathematical model which showed a system with just 2 molecules could, at least in theory, create spotty or stripy patterns if they diffused and chemically interacted in just the right way. Over time, this theory has come to be accepted as a viable explanation for zebra stripes and even the ridges on sand dunes. As far as embryology is concerned, like the formation of fingers, the theory has been met with skepticism.

[ALSO READ] Robot passes the Turing test for the first time in history

This is the detailed embryo limb and the network topology of the Bmp-Sox9-Wnt (BSW) model. Credit: Luciano Marcon and Jelena Raspopovic.

This is the detailed embryo limb and the network topology of the Bmp-Sox9-Wnt (BSW) model.
Credit: Luciano Marcon and Jelena Raspopovic.

The two lead authors, Jelena Raspopovic and Luciano Marcon, combined empirical data and numerical computations in an integrated form known as systems biology – the experimental findings were correlated with the models and found to be accurate. Previously, the team found evidence the that the fingers and toes are patterned by a Turing mechanism, but the Turing molecules themselves escaped them at the time.

In the present study, the researchers identified these molecules after screening for the expression of many different genes. Two signalling pathways stood out: BMPs and WNTs. They then ran a model which sought to find which was the most efficient compatibility between the two; results showed a third molecule, the non-diffusing Sox9, linked the the other two. Yet another model was made to predict what would happened if BMP and WNT were inhibited, namely how would this effect finger development. Strikingly, when the same experiments were done on small pieces of limb bud tissue cultured in a petri dish the same alterations in embryonic finger pattern were observed, confirming the computational prediction.

Ever wondered how the cells in your body know how to lineup perfectly, so they might form a macroscopic structure? Think of your organs, the brain, your hands, every cell in your body knows where it’s supposed to know and when to stop expanding. One idea proposed by Lewis Wolpert states that cells know what to do because they all receive information about their “coordinates” in space. The present findings suggests that local self-organization is far more important.

As a mental note, I find it absolutely stunning that Turing’s work has been proven right 62 years later using computers, which he fathered one way or the other. If he only had lived to see these times.

Findings were reported in the journal Science.

Robot passes the Turing Test for the first time in history

The 65 year-old iconic Turing Test was passed for the very first time by a supercomputer program named Eugene Goostman. Eugene managed to convince 33% of the human judges that it too was human.

The Turing Test

The Turing test is a test of a machine’s ability to exhibit intelligent behaviour equivalent to, or indistinguishable from, that of a human (via Wikipedia). In this test, a human judge engages in natural language conversations with a human and a machine. If the judge can’t tell which is the human and which is the program, the machine passes the test. The test itself doesn’t check the robot’s ability to give straight or correct answers, but rather its human-like behavior.

The test was introduced by Alan Turing in his 1950 paper “Computing Machinery and Intelligence,” which opens with the words:

“I propose to consider the question, ‘Can machines think?'” Because “thinking” is difficult to define, Turing chooses to “replace the question by another, which is closely related to it and is expressed in relatively unambiguous words.”

Turing, who was a genious way ahead of his time, believed that sooner or later his test would be passed, but he was a bit off. He estimated that in the year 2000, machines with around 100 MB of storage would be able to fool 30% of human judges in a five-minute test. Futurist Ray Kurzweil estimated in 1990 that a machine will pass it by 2020, but in 2005, he changed the date to 2029. He even made a bet with Mitch Kapor about when the Turing test will be passed – but nobody was expecting it to happen so soon.

Turing, meet Eugene

Eugene is a computer programme that simulates a 13 year old boy, developed in Saint Petersburg by Vladimir Veselov, who was born in Russia and now lives in the United States, and Ukrainian born Eugene Demchenko who now lives in Russia. Eugene managed to pass the test and convince 33% of the judges that he is human in a 5 minute chat discussion (a score of 30% is needed to pass the test). The event was organized by the University’s School of Systems Engineering in partnership with RoboLaw, an EU-funded organisation focused on the development of robotics. Professor Kevin Warwick, a Visiting Professor at the University of Reading and Deputy Vice-Chancellor for Research at Coventry University, said:

“In the field of Artificial Intelligence there is no more iconic and controversial milestone than the Turing Test, when a computer convinces a sufficient number of interrogators into believing that it is not a machine but rather is a human. It is fitting that such an important landmark has been reached at the Royal Society in London, the home of British Science and the scene of many great advances in human understanding over the centuries. This milestone will go down in history as one of the most exciting.”

Still, there are of course some contradictory discussions about this achievement. Some claim that the program’s task was eased by the fact that it mimics a 13 year old boy from Odessa – which can’t be expected to have the same level of knowledge as a grown man, and can be excused for small grammar errors. Veselov stated:

“Eugene was ‘born’ in 2001. Our main idea was that he can claim that he knows anything, but his age also makes it perfectly reasonable that he doesn’t know everything. We spent a lot of time developing a character with a believable personality. This year we improved the ‘dialog controller’ which makes the conversation far more human-like when compared to programs that just answer questions. Going forward we plan to make Eugene smarter and continue working on improving what we refer to as ‘conversation logic’.”

 

Alan Turing’s 1950 tiger stripe theory proven

Alan Turing is considered by most to be the father of the computer; the British mathematician had one of the most tragic fates ever suffered by scientists. Aside from defining concepts such as ‘algorithm’ and ‘artificial intelligence’, he also put up an idea that repetitive biological patterns are generated by a pair of morphogens that work together as an ‘activator’ and ‘inhibitor’. Now, researchers from the King’s College London have managed to provide the first evidence that this theory is true.

In order to prove this, they studied the development of the regularly spaced ridges found in the roof of the mouth in mice and carried experiments on mice embryos, practically identifying how the team or morphogens worked together and how they could predict where ridges would appear. They were able to pinpoint the specific morphogens responsible for the ridge pattern (Fibroblast Growth Factor) and Shh (Sonic Hedgehog). They proved that if their activity is increased or decreased, the ridge pattern suffers modifications predicted by the Turing equations. For the first time, biologists have been able to prove and observe the direct implications of this 60 year old theory.

Alan Turing

Dr Jeremy Green from the Department of Craniofacial Development at King’s Dental Institute explains :

‘Regularly spaced structures, from vertebrae and hair follicles to the stripes on a tiger or zebrafish, are a fundamental motif in biology. There are several theories about how patterns in nature are formed, but until now there was only circumstantial evidence for Turing’s mechanism. Our study provides the first experimental identification of an activator-inhibitor system at work in the generation of stripes – in this case, in the ridges of the mouth palate.’

‘Although important in feeling and tasting food, ridges in the mouth are not of great medical significance. However, they have proven extremely valuable here in validating an old theory of the activator-inhibitor model first put forward by Alan Turing in the 50s. Not only does this show us how patterns such as stripes are formed, but it provides confidence that these morphogens (chemicals) can be used in future regenerative medicine to regenerate structure and pattern when differentiating stem cells into other tissues.’

Alan Turing, despite being instrumental in breaking the Enigma code in World War II, saving countless lives in the process, was condemned for indecency because he was a homosexual. This, at the time, was illegal in Great Britain, so he was given a hormonal treatment, designed to reduce libido. Practically, he was chemically castrated – the process was so severe he actually started growing breasts. Thus, one of the world’s brightest minds was defeated, and less than two years after this, he committed suicide, swallowing cyanide.

Still, researchers and people throughout the whole world pay homage to him, and this year is actually the Turing centenary – marking 100 years since his birth.

‘As this year marks Turing’s centenary, it is a fitting tribute to this great mathematician and computer scientist that we should now be able to prove that his theory was right all along!’