Deciphering a New Enigma: The Genetic Code

When we imagine code breaking, we conjure up images of dingy basements in the 1940s, with mathematicians striving to decipher Nazi communications during the Second World War. Undoubtedly, this is because breaking the German Enigma code became pivotal for clinching the allied victory, subsequently making it the most famous code (and code-breaking event) in modern history. Part of this breakthrough can be attributed to Alan Turing, who recently came back into the limelight due to the centennial anniversary of his birth. Cited as the father of modern computer science, Turing was a brilliant mathematician whose vision of intelligent machines was perhaps way ahead of its time, and his untimely suicide.

An Enigma Machine

Gathering intelligence by the mathematics of code breaking is of course still relevant to us today. However, modern code-breaking is surprisingly important in biology, as we are still yet to fully decipher the meaning of DNA's genetic code in every living cell. Deceptively, at first glance this code appears simple as it only uses four letters; A. C, T and G. DNA is basically a long string of these four letters, which cells read for the instructions to build proteins. Proteins are highly important to the construction of cells, enabling them to grow, divide and carry out their respective functions. Every three letters in the DNA sequence encodes one amino acid – the building-blocks of proteins –with the amino acids joining together in a chain, like beads on a necklace, following the DNA sequence. As there are 20 different amino acids, there can only one of 20 different amino acid ‘beads’ forming the protein ‘necklace’ encoded by the DNA. This amino acid sequence is said to be the primary structure of a protein.

Proteins are not merely chains of amino acids, as the amino acids are attracted to each other due to the properties of the 20 different types. This means that the beads of the necklace will form coils, twists and loops, as some of the amino acids attach to others in the chain. This is said to be the secondary structure of the protein. In turn, these coils and loops interact with each other further, and twist up the chain of amino acids to form an even more distinct three-dimensional shape, making the tertiary structure of the protein. We can picture the final result by imagining the beads of the necklace being scrunched into a tight ball.

The three-dimensional structure of proteins is governed by the sum of the relationships between the amino acids in the protein

Each protein encoded in DNA has its own unique three-dimensional structure, which is crucial for the protein to carry out its function. The three-dimensional shape determines how the protein can interact and attach with other proteins to build the structure of cells within the body, as well as form part of many important proteins like insulin and haemoglobin. If we think of how important the shape of a key is to fitting a lock, this describes a similar situation that we find with the shape of proteins, as when this shape is changed, the protein can no longer perform its allotted task. For instance in haemophilia, we know that a protein called factor VIII intrinsic to the blood-clotting process has a defective shape, resulting in the prolonged bleeding found in these individuals.

A diagram showing how the chain of amino acids in defective factor VIII fold up in haemophiliacs

Thanks to the Human Genome Project, we have found that human DNA encodes about 20,000 different protein sequences, for which deciphering the sequence of amino acids is easy as we know this part of the code; however, deciphering how these will interact to form a protein’s three-dimensional structure is trickier. Traditional techniques can be used, but deciphering the three-dimensional structure of 20,000 proteins by these methods is really not a feasible task for us to undertake, as they are slow and expensive. This is where mathematics and computational biology is now increasingly important.

By the application of mathematics we have been able to predict how the string of amino acids might form coils, twists and turns in a protein’s secondary structure.  In essence, this involves determining the statistical probability of how each amino acid will behave in respect to others on the chain. This is because common amino acid sequences are found in proteins, and we know how those sequences are likely to interact to make particular types of coil or twist. In addition, by looking at the probability of how certain amino acids are likely to interact with others, the most likely secondary structure of a protein can be predicted. This is not entirely accurate because the environment in the cell where the protein is manufactured can also influence its final structure, and common amino acid sequences may coil or twist in slightly different ways. As we all know, probability only gives us the most likely outcome, not a certain one, making these predictions only an approximation. Predicting the three-dimensional tertiary structure is therefore even more difficult; not only are there more amino acid interactions to consider, there may be some error in the secondary structure as well.

This is why the problem of unlocking the three-dimensional structure of proteins is where the code breaking of the human genome still continues. Even though we have unlocked the sequence of amino acids in the 20,000 proteins of the human genome, in many cases their corresponding three-dimensional structure is unknown. This structure is essential to the function of a protein, and can tell us what role that protein might have within the human body; we are effectively at a standstill in deciphering the code until we can do this. This presents itself a considerable problem within contemporary science, but thanks to the recent developments in mathematics and computational power, it is now far less daunting and achievable.

It does appear that there are a limited number of ways that all twenty amino acids can interact to form particular structures, and it is believed that there about 2,000 types of interaction which are common to the majority of proteins. In addition, we do know that proteins can only fold in limited ways forming specific geometrical structures, as when they do bend at certain angles or turn with specific twists, they cannot form a stable shape and would not naturally form. These rules that govern the three-dimensional structure of proteins have resulted in several mathematical algorithms that can predict the most probable protein shape from a DNA sequence. However, the drawback is these require hefty amounts of computational power, far beyond that which was present at the time of Alan Turing and the Enigma Code – only modern supercomputers have the ability to calculate all the feasible protein structures within an acceptable time from amino acid sequences. Nevertheless, there is an alternative method; by utilising the internet and the computing power of thousands of small computers across the globe. Like the millions that downloaded the SETI@home project to search for intelligent life on other planets, we all can be code-breakers like Alan Turing by downloading protein structure prediction software from projects such as the Human Proteome Project, Rosetta@home and Folding@home.

Knowing how all 20,000 proteins in the human genome form their three-dimensional structure will be incredibly important in combating complex diseases which have so far proven very difficult to treat. The huge amount of proteins that may change in conditions such as cancer, diabetes and heart disease may provide new and effective targets for drugs which can be used to treat and prevent these conditions. Not only this, we will know much more about ourselves as we will have completely decoded the DNA message in every cell in our bodies. Due to the plummeting costs of sequencing DNA, we may be able to obtain a sequence for every person on the planet, and therefore the structure of every protein within that individual – both when they are functional and when they are defective. This means that drugs may be designed for each specific individual, unique like their DNA, meaning that we may all be able to live longer, disease-free lives, all by the power of mathematics and code breaking.

Obviously, we should still celebrate the famous efforts that were needed to decipher the Enigma code, as they were pivotal to events in the 20^th Century and the Second World War. However, in the 21^st Century, we are still fighting a war that requires the mathematics of code-breaking – the battle against diseases with a real human cost. As we have celebrated the centenary of the famous code-breaker Alan Turing, perhaps in another century we will be celebrating the birth of another great code-breaking event: breaking the code that is found within DNA. Not only this, but it may have been an effort from millions of people across the world, thanks to mathematics and modern computing.

Further Reading:

The Human Genome: Book of Essential Knowledge, John Quackenbush (2011)

The $1000 Genome: The Revolution in DNA Sequencing and the New Era in Personalised Medicine, Kevin Davies (2010)

Printing Human Organs: While-U-Wait

In the film, ‘The Fifth Element’, Mila Jovovich’s character is in a pretty bad state. After her spaceship is shot down and crashes on Mars, all that can be recovered from the wreckage is a solitary hand.  There is no cause for alarm (although cue spoiler alert), because thanks to the magic of science fiction she is saved! In the following scenes, government scientists from the year 2263 place the surviving limb in a perspex tube, and use DNA from the cells clinging on to life to completely reconstruct her body, albeit without clothing. In mere minutes, her modesty is hidden by a few strategically placed bandages, and she fights on as the female protagonist till the end of the film.

All operations in the year 2263 allow you to emerge looking like a supermodel.

Could science fiction ever become fact? Perhaps not at this scale or speed, but human organs may one day be manufactured simply by using 3D-printing. Traditionally used with plastics and polymers, 3D-printing is particularly special because at the stroke of a few computer keys, objects are easily customised and made unique. Besides the manufacture of bespoke and on-demand plastics, other ‘inks’ have been formulated for these machines to produce clothing, food and even buildings. Specially adapted 3D-printers can now use living cells as a ‘bio-ink’, and are close to being capable of printing entire human organs for transplantation. By using cells harvested from an individual, organ donations, organ rejection and immunosuppressant drugs may one day be a thing of the past.

Several names have been coined for the fledgling technology, such as ‘bio-printing’ or ‘organ-printing’, as well as ‘computer-aided tissue engineering’. This multitude of names reflects the numerous approaches to building complex organs out of living raw materials. In general, temporary scaffolding materials such as agarose gel or starch, are printed alongside a bio-ink containing cells to form the working organ, such as liver or kidney cells. As layers are printed consecutively on top of one another, the cells anchor around the scaffolding, forming the 3D structure. The scaffolding is then simply dissolved away, leaving the tissue in a formation that mimics that of the organ. Producing vascular structures, such as blood vessels and capillaries is critical to surmount the greatest challenge in bio-printing fully-sized organs: keeping cells alive. After printing layers of cells on top of each other, the cells buried within the tissue are cut off from nutrients and oxygen supplies, causing them to die. Bio-printing blood vessels and capillaries in organs can evade this problem, and allows the production of bigger tissues that stay alive.

Printing something less complex than a supermodel using an agarose scaffolding.

This has been successful in many applications, such as the creation of artificial liver tissue at the University of Pennsylvania using a scaffolding of sugars (1); dissolving the sugar leaves ‘holes’ where blood vessels are required. Other techniques to create blood vessels have also been explored. For instance, artificial capillaries have been constructed in Germany at the Fraunhofer Institute, using photons to stimulate scaffolding materials into fine flexible structures. This allows the capillary to infiltrate surrounding tissue, alongside a bio-molecular coating to subdue rejection by the immune system (2). However, in addition to their structure, capillaries contain layers of different cell types like the endothelium, which all perform important functions for vascularisation. At Harvard University, an approach where the holes in bio-printed organs are ‘seeded’ with endothelial cells has been successful, as the cells spontaneously cover the lining of artificial blood vessels if the right conditions are provided (3).

The innate self-organising abilities of cells are enabling this technology to go even further towards bio-printing entire organs. Simply by using several bio-inks containing the constituent cells of vascular structures like the endothelium, including smooth muscle cells and fibroblasts, complete capillaries can be printed within organs. Like the endothelial cell-seeding approach, when these cell types are printed around artificial capillaries, they autonomously organise themselves into the distinct layers found in vascular structures. Finally, bio-printing is coming of age, and is now commercially available from the biotechnology firm Organovo, with their ‘Novogen’ bio-printers. However, many researchers have produced bio-printing machines of a similar calibre, many of which are ‘hacked’ 3D-printers. Unfortunately, they all share the same caveat; no bio-printers can produce anything on the scale of human organs, and are only readily useful to researchers who require home-grown tissues for experimental work, rather than using cells cultured in the traditional way.

Even with the small-scale capabilities of bio-printing, it is already set to revolutionise medical care. A bio-printing spray from the Wake Forest Institute for Regenerative Medicine has shown great promise in animal studies. By directly spraying cells onto wounds, this may speed up the healing process and eliminate the need for painful skin grafts (4). A scanning laser directly analyses the exposed tissue in the wound, and a 3D map is generated to determine where certain cell types are appropriate to print directly onto the area. A future development for this technology promises even greater things; it may be possible to have ‘tissue on demand’ within the operating theatre, not unlike the donated blood that is readily available today.

Further uses for bio-printing technology – even at this small scale – are also revolutionising other fields of medical science. Complete human organs may be many years away, but the ‘body-on-a-chip’ concept is rapidly becoming reality, and is also under development at the Wake Forest Institute (5). This technology is a tiny bio-printed collection of human organ chambers, connected with a minute blood system. These bio-printed systems could provide a more valuable drug testing environment, as they would both imitate the effects of disease or chemical agents on the entire human body, and also reproduce the effects of any potential drugs, including any side-effects. Furthermore, if the body-on-a-chip originated from one person, the efficacy of medicines could be tailored to the individual, making a highly personalised treatment.

Even without personalising medicine to this extent, the body-on-a-chip could make drugs more specific to our species. Animal testing has been a mainstay of drug development, as drugs can have considerably different effects within organ systems in comparison to cells in a petri dish. This means any drug approved for clinical trials must demonstrate both safety and effectiveness in animals, which is not completely fool-proof. Investigated treatments can become tailored to animals rather than humans (with potentially fatal consequences), or may be effective in humans but fail animal tests. As it is made from human cells, the body-on-a-chip could circumvent these problems, and may even replace the need for animals altogether. There are many possibilities, ripe for exploration.

All of these prospective applications would revolutionise medicine, but bio-printing entire organs for transplantation is urgently needed. From the first kidney transplant in the 1950s to today, organ transplants have undoubtedly saved countless lives, but sadly many die before reaching the end of the waiting list for a suitable donor. Even those that are successful face a lifetime of immunosuppressants, and the threat of organ rejection. Hopefully, thanks to the magic of real science, by the middle of the 21^st Century these lives can all be saved, like Mila Jovovich. Saying that, I’d avoid flying around in spaceships when someone clearly wants to kill you, as complete bodily reconstruction might take a little longer to develop.

1)      Miller, J.S. et al. (2012) Rapid casting of patterned vascular networks for perfusable engineered three-dimensional tissues. Nature Materials. 11 (9): 768-74
2)  Moskvich, Katia (2011) Artificial blood vessels created on a 3D printer. BBC News. [Online]Available at: http://www.bbc.co.uk/news/technology-14946808 [Accessed February 25th, 2014]
3)Kolesky, D.B. et al. (2014) 3D Bioprinting of Vascularized, Heterogeneous Cell-LadenTissue Constructs. Advanced Materials. 26 (8): pp 1-7
4)Rosenblatt, Dana (2011) Researchers aim to ‘print’ human skin. CNN. [Online]Available at: http://edition.cnn.com/2011/TECH/innovation/02/19/bioprinting.wounded.soldiers/ [Accessed February 25th, 2014]
5)Hsu, J. (2013) Tiny 3D-Printed Organs Aim for ‘Body on a chip’. LiveScience. [Online]Available at: http://www.livescience.com/39660-3d-printed-body-on-a-chip.html [Accessed February 25th, 2014]

Wandering Worlds

Throughout the aeons, we have looked up at the sky and seen the 'wandering stars'- the planets - giving them personae and even divinity, perhaps as a means to explain their unusual movements. In keeping with this tradition, we have named all the current planets and other larger objects after gods; Roman, mostly. These objects have not changed over any conceivable period, even since the dawn of humanity itself. Although the recent change from having nine solar planets to eight was academic (pluto didn't disappear), over the last century or so, the existence of past planets has materialised and vanished - many never to be accepted within science. This recent video, released by OxfordSparks on YouTube, details the existence of another giant planet, dubbed 'Sol i' which was thrown out of the solar system earlier in it's history.

Various anomalous features of the solar system, such as the tilt of Jupiter could have resulted from this event. It also appears that this may not be a rare event; many free-floating 'orphan' planets may be out there. This has been confirmed by a recent discovery of a huge free-floating planet very close to our solar system, which is six times the mass of Jupiter. There are now many of these objects catalogued. You do wonder if some of our own planets in our solar system were free-floating once, and were caught up into the newly-formed solar system never to travel alone again.

The March of the Orphans

Free-floating planets are not a new idea, and have also contributed to much of the hype surrounding the infamous date; 21st of December, 2012. Nibiru or 'Planet X', first sprang in the emerging internet in 1995, with hordes of doom-mongers saying that an orphan exoplanet would have a cataclysmic collision with Earth. As we all know, this didn't happen - nor is it very likely. Though the website from which these claims originated would like to have you believing otherwise (the images of 'Planet X' are the most baffling), they are not the first, nor the most fascinating ideas about other objects that may be associated with our Sun. In fact, the history of these supposed missing planets probably spurred the search and discovery of a few of the larger objects in our solar system, and one of the current eight canonical planets.

The Giants and the Dwarves 

Dwarf planets became a better-known term after the demotion of Pluto in 2006 from the ninth planet in our solar system to one of several in the lesser pantheon of planets. Pluto's discovery was driven by the hypothesis of there being a ninth 'planet X' - though this term was coined well before the pseudo-scientific belief in a 'Nibiru'. In fact, another planet discovered by mathematical prediction - Neptune - aided in finding this tiny, icy world. Fluctuations in Neptune's orbit led to the search continuing even further out into the sticks of the solar system. This next planet was believed to be another gas giant, after all, the trend from Jupiter outwards did not hint at anything other than the status quo of the outer solar system. This made Pluto serve only to be a sad disappointment for these predictions.The planet's estimated size shrank ever downwards over the resulting years, and it's bizarre orbit (where it actually becomes closer to the sun than Neptune for 20 years of its 248-year orbit) led to this object finally being demoted. Although the biggest object in the Kuiper Belt, it appears to be a small component of a large body of objects that circulate the sun in this vicinity.

Dwarf planets also exist (or have been proposed) much closer to home. Ceres, a large dwarf planet in the asteroid belt between Mars and Jupiter was also classified as a planet for a time, although it shares its orbit with many other asteroids, making up only a third of the mass of the belt. Again, Ceres was discovered by the belief that there would be a planet in this location. However, the final discovery of objects after postulating their existence does not always occur (see above). Vulcan was proposed to be between Mercury and the sun, with an active search for Vulcan continuing well into the 20th Century. Small objects are known to orbit closer to the sun than Mercury, but nothing on the scale of a planet 'zero'. It would pretty hard to identify anything in this vicinity due to the Sun's glare. You would hope that modern planet-hunting techniques have eliminated any hope of their being a scorched rock on the scale of anything planetary. Even the claims that a 'counter-Earth' exists have been completely debunked.

No doubt there will continue to be objects on the same scale as Jupiter found outside of our solar system - this seems certain. However, the search for any other planets which are closer to home is probably never going to be productive. What lies outside our solar system that isn't on the scale of a star (or producing light - more on this soon) now provides a new focus for planet hunting. However, if we go back in time, maybe there were other planets that have now gone off to pastures new, wandering the galaxy looking for a new home.

Chasing Thoth might not be the usual science blog. No doubt I'll be mentioning any recent discoveries and their significance, but also give things a bit of a philosophical slant.

Comments will be appreciated, as will suggestions for any posts.

I thank you....