DNA Digest - Breaking the bottlenecks of research for faster treatments in genetic disease. (5 mins read)
DNA Digest is a new scientific non-profit organisation that is tackling the issue of data sharing, an issue that could affect you and countless others. I am part of DNA DIgest and we need your support .
Genetic disease can affect anyone at any time. These diseases include anything from Cancer to Alkaptonuria. The frustrating thing about these diseases is that they are caused by your own genome (your entire personal DNA code) because unfortunately your DNA had a variant/mutation in anything from a single base to across a chromosome. A further unfair twist is that these mutations could occur at any time, of course likelihoods increase with some environmental exposures, but the overall potential remains quite at random.
Now the problem with treating these diseases is they are incredibly individual, to the extent that we might need to sequence your genome to try to understand what the issue is. This sequence data is vital to develop a treatment but in reality it’s only the first step as this data only gains real value when compared to other data. So couldn’t we just share data amongst each other to begin working towards treatments?
Unfortunately not, because it’s individual and personal data. To share this we need to overcome hurdles of privacy, security and confidentiality. The current process in gaining access to this data is long and complex, often with multiple applications and permissions. This is in place to protect individuals but conversely this also means that the patients, ordinary people with genetic diseases, are suffering.
This is where DNA Digest steps in, we understand that data needs to be protected but we also realise current methods are too drawn out resulting in greater suffering. Lack of data sharing means data remains locked in separate institutions. By not being available for reuse it reduces the value of the time and effort invested to create that data. Further the focus is still on technological breakthroughs for faster data generation. But these won’t bring us new diagnostics and treatments for cancer and other rare diseases. Because data interpretation not data generation is the major bottleneck for research.
What DNA Digest is doing to solve these issues bringing people together to discuss data issues and prototyping/developing tools to enable researchers to gain secure and ethical access to genetics data. We believe the answers lie in collaboration and cooperation between stakeholders everywhere. We have a new video further explaining what we do and our first solution that retains patient privacy whilst sharing genetics data.
If we succeed in our campaigns we could have a huge impact across science and peoples lives. Because we would break the crucial bottleneck in comparing sequence data and access to the data itself.
The way we use and think about data needs to change, but for this to succeed we need your support and feedback to make it happen. We have the necessary technology to start building one of our first solutions as a prototype, what we need right now is your support to enable this. Please join us on our campaign on thunderclap to lend your social voice and on indiegogo to contribute to DNA Digest. The launch of our campaign officially goes live on the 13th of March we have so many big plans and your support would go a long long way. Overall for better data sharing and impact on genetic disease please #supportdnadigest.
A New Phytopia - Visualising the structures of life.
That title may have read as a rather grand statement but put simply without plants, life as we know it would not exist. From food, to fibre, to the air we breathe we are quite dependent on plants. The unique photos above are the babies of many different plants AKA seeds. This work has been created by academic/artist Rob Kesseler in partnership with the Kew Gardens Millenium Seed Bank.
Phytopia reveals a hidden world lying beyond the scope of the human eye. Working in the liminal territory between Art and Science. Rob K
There are many ways this work is special. First is the location, these seeds are live specimens forming a genetic bank of sorts within the Kew Millennium Seed Bank it’s quite a similar initiative to the Svalbard seed bank. Here these seeds remain protected, stocked in numbers to potentially restore plant populations if required.
Second is due to the way they are photographed by using a scanning electron microscope. Which basically uses a beam of electrons instead of light, giving the extremely fine details we can see above. These images then have layers of colour, specific to their mother plant, added to them. Rob describes this artistic process akin to how plants attract insects to attracting an audience.
Finally is the individual characteristics the photos highlight. Each seed has been honed through hundreds of years of evolution, adapting each one to succeed in a particular strategy of dispersal and growth. This brings home the fact that these plant babies are alive and individual as you or me.
Plants babies under microscope = eye & brain candy.
Magnetism by Ling Meng - "What I am trying to focus on recently, is combining Art and Science somehow."
Created by Ling Meng a Shanghai based artist these atmospheric photos visualise the invisible force of magnetism. What we are observing acting on these iron filings in these photos is specifically known as ferromagnetism.
The iron filings have domains scattered through them, which can be thought of as smaller magnets in themselves. When a magnetic field is applied these domains they turn their poles in the same direction, referred to as a dipole dipole alignment, resulting in a net magnetization. A really nice video explaining this and its function in transformers is here. There are lots more artistic ways of applying these fields have a look at this ferrofluid sculptre video for example.
Past posts on magnetic levitation.
New Images of Saturn’s Hexagon North Pole.
The Hexagon is a six sided jet stream that occurs on Saturn’s North Pole, due to the lack of solid geographic landforms the hexagon may have been occurring for centuries. It’s diameter is wider than two Earth’s and contains at the very center, a storm which has an eye 50 times larger anything observed on Earth. NASA’s Cassini spacecraft has recently gained an opportunity to better view this phenomenon due to the movement of the sun in 2012, illuminating the interior of Saturn.
This is a unique weather feature not observed anywhere else in the solar system, due to its consistent shape and location. It is proposed that its structure is maintained due to a difference in aerosol sizes inside and outside of the hexagon creating a situation similar to the Antarctic Ozone Hole. Inside the hexagon there are a larger concentration of small haze particles, while outside the hexagon a greater concentration of larger haze particles exist. Combined with a fast moving jet stream the larger aerosols act like a barrier.
Although it has been occurring for centuries, scientists are now excited to observe the changes to the Hexagon as lighting conditions over Saturn’s north pole improve culminating in it’s summer solstice in 2017. Research into a phenomenon like this may help in future analysis of weather patterns on Earth. You can see the hexagon in a video form here.
Cracking an egg underwater for Science.
A raw egg is cracked open by a researcher from the Bermuda Institute of Ocean Sciences at approximately 60 feet (20 meters) underwater. It’s interesting to note that the egg’s yolk retains a spherical shape and doesn’t become flatter due to the water pressure. Also whats shown in the original video is that the egg actually begins to sink and needs to be pulled upwards by a vortex action from the researchers finger showing the higher density of the egg.
Admittedly this is a negligible experiment but the Bermuda Institute of Ocean Science does great research on ocean sciences for human good. They have programmes of research exploring healthier oceans, climate change and coral reefs.
Water droplets covered in hydrophobic aerogel powder.
These water droplets have been rolled over a “superhydrophobic” aerogel powder which coats the water forming a jacket allowing for the water to be rolled like a squishy marble.
So anything hydrophobic repel water but this one is unique by being a powdered form of an aerogel. Instead of containing liquids, aerogels contains gas imagine a Swiss cheese (or any kind of porous structure) in which the center has been pumped full of gas. These aerogels are made even more special by having their polar groups replaced (in this case mainly oxygen and hydrogen) with non-polar groups (silica, carbon, and hydrogen). Replacing just a small of amount of these groups turns the aerogel powder hydrophobic.
It works because water is a polar molecule, having both positive and negative charges. Having the gels polar elements replaced it becomes hydrophobic and wont mix with the water instead surrounding its surface. Adding drops of water to this powdered gel will cause the water to ball up to minimize their contact with the aerogel surface.
These water droplets hold together and resist popping as above as the water molecules hold on to each other and pull the droplet into a sphere. The above gifs show two colored droplets close to each other on a normal white paper sheet rolling around resisting being popped. The droplets are only about 2-4 mm in diameter and the needle in the video is needle from a normal syringe.
A drone in agriculture - Monitoring and generating data.
This week I’ll be writing about robotics past, present and future. This post falls into the present, spotlighting a new initiative to use machines to monitor crops and agricultural experiments.
Behold the Octocopter (see first 3 photos) an 8 rotor battery powered unmanned aerial vehicle (UAV). Although usually used within the film industry this drone has been equipped with 4 specialised cameras to collect data from experimental plots. Funded by the BBSRC for Rothamsted Research this data collection methods strengths lie in its rapidity and the unique perspectives offered on crop growth and plant functionality.
It’s eyes are the key allowing remote visibility, video and photo capture simultaneously whilst also allowing more informative images through its thermal infra red camera and a hyperspectral camera (4th and 5th photos). That technology is similar to the infragram technologies developed by the Public Laboratory. The speed at which this technique would allow data collection would extend capabilities for screening and comparing crops of different genetic background for performance, nutrition, stress, pathogen and disease responses.
The real benefits will come once the process is more automated and more streamlined with pre-programmed low level flights. By doing so the speed of data generated could be compared to the principles of Next Generation Sequencing. Due to the potential to allow thousands of plots to be monitored sequentially or in parallel. Rothamsted aim to utilise the Octocopter in multiple of its programmes including 20:20 Wheat® to its Wheat Improvement Strategic Programme.
A significant point is that this type of technology is increasing in use around the world, the last photo is from the University of Tasmania from 2011 and many more examples can be found. As the director of Rothamstead puts it, “this technology will compliment ground-based measurements initially but eventually aerial-based observation will replace the need for low throughput non-automated manual measurement” and by non-automated manual measurements he means less human eyes. This is a theme that’s going to be more prevalent as we progress.
Robots, from science to society to the future.
This coming week I’ll be writing about robotics. From it’s early beginnings to the current applications and the future of our interactions with robots. The projects above are a quick glimpse in to the types of things robots are currently involved in from the quirky Eggbot (first photo) to the serious deployment RAF Bomb Disposal Robot (third photo).
A recent Japanese project took KIROBO The Robot Astronaut (fifth photo) into space to research how machines can lend emotional support to people. Another project saw the development of GROVER The Autonomous Rover (last photo) to monitor ice sheets. Overall robots are increasingly involved in how we live this trend is set to increase in the future, it makes for great science and philosophical thought.
Identify wild animals and help science. Snapshot Serengeti.
The Serengeti is a large beautiful geographic area in Africa spanning Northern Tanzania and Southern Kenya. These huge plains encompass a large ecosystem consisting of some of the best known animals on the planet. Snapshot Serengeti began as a project looking to monitor the Lions of the plains but now has become significantly larger hosted on the Zoo Universe platform to study how species are distributed across the land and how they interact with each other the middle six photos of some of the animals.
The classifying of animals happens at the Serengeti National Park using images gathered from 225 camera traps located in a grid across the park. The cameras are activated using infrared sensors, when a warmer object walks in front of it (usually an animal, note the word usually). The photographs from these cameras when identified (first photo) and correlated with geographical information (final photo) allow researchers to monitor how animals are distributed across the park and begin to understand how they interact with lions and one another.
The data from the project is looking to understand how competing species coexist. This has important implications for the planet from biodiversity, to the sustainability of life on Earth, to humans (we are arguably the biggest competing species on the planet). Much of the projects current research focuses on how carnivores coexist with carnivores, herbivores with herbivores, and the joint dynamics of predators and their prey, read more here.
The first data from the photos have been taken, so findings are hopefully on their way. There are still plenty of photos to categorize and identify. The snapshot community is active with some fascinating photos and discussions being shared. More photos from Snapshot Serengeti should be on their way.
Glass Microbiology - Alternative Representations of Disease by Luke Jerram
The sculptures above are of some of the most deadliest diseases known to mankind. They were designed by Luke Jerram in consultation with scientists using a combination of scientific photographs and models.
What’s really great about this work is that it can bring you face to face with pathogens, something none of us would have the opportunity to unless under high magnification (see here for a sense of scale). Additionally these sculptures gives us a sense of the alien structures of these pathogens all of which individually could lead to disease and death upon infection.
The pathogens shown above are: Ecoli, HIV, Avian Influenza, Malaria, Swine Influenza, Small Pox, SARS Coronovirus, Giardia and Salmonella. The works have gone on to be housed in several museums and collections worldwide see here for more.
Tree Mountain - 11,000 Trees planted by 11,000 People, protected for 400 years.
In 1996 Finland,Ylöjärvi the Tree Mountain project led by Agnes Denes was completed. A huge ecological and artistic work based around the plantation of 11,000 trees in a complex geometric pattern (see third photo) by 11,000 people. Upon completion Martti Ahtisaari the then president of Finland declared the area protected land to be maintained for four centuries, eventually creating a virgin forest. The trees were planted in an mathematical pattern derived from a combination of the golden ratio and the fibonacci numbers. The mountain has since then been allowed to grow evolving and growing from the original pattern (see last four images).
“The forest will be kept for the next 400 years, thereby creating the first manmade virgin forest. It will take that long for the environment to re-create itself. The 11,000 people who came to plant the trees received a certificate valid for four centuries that they can leave to their children as custodians of the trees. My forests are mathematical in order to combine the human intellect with the majesty of nature. I restore the land, rejuvenate it, and fill it with wonders of new human understanding.” Agnes Denes
Agnes Denes is certainly a visionary managing to incorporate science, mathematics and philosophy into her work. The site itself was created from refuse material from a gravel pit further enhancing the sustainable ethos.
It would great to visit the site on the 20th anniversary in 2016 to carry out ecological analysis of the entire site. Answering questions regarding the biodiversity of the forest, the amount of carbon captured/stored, the air quality and perhaps also contributions to the water quality of the forest.This forest continues to grow and will hopefully be protected till 2396. Read more American Scientist Regeneration on Tree Mountain.
More Microorganisms under the Microscope.
An old school but critical instrument for biologists is the Microscope. Like the telescope for the distant objects without the Microscope we wouldn’t be able to focus on the tiny but important things in biology, like bacteria, fungi, algae, protozoa and other microorganisms.
These gifs were originally recorded in a microworld video under high magnifications I separated them into gifs available here. The video has been carefully rested on one “tiny razor-thin plane" of focus with the rest of in a blurry state. To be recorded it has also overcome a second limitation of transparency of the organisms themselves. Overall they are placed in order of size, the Mosquito larvae being the biggest, the copepod (recognize this character) and tiny rotifer being the smallest of the organisms.
Tardigrades - Microscopic Water Bears
They may look cute but Tardigrades are one of the hardiest creatures on the planet. They are considered under a distinction of life as an extremophile, meaning they can survive in a hostile environment examples include the arctic, deserts, hydrothermal vents and more.
However Tardigrades have a gained a further fame of their own as a polyextremophile by being able to survive not only intense heat, but cold, radiation, desiccation and even the vacuum of space! It’s important to remember that we are considering extreme measured against human abilities, nevertheless these abilities make Tardigrades of great scientific interest.
What researchers believe allows Tardigrades these extreme abilities is their ability to effectively shutdown internally going into stasis and their remarkable repair mechanisms when in this state. Overall they can dehydrate themselves completely known as an anhydrobiotic state a form of Cryptobiosis and survive without a metabolism for months.
Why Tardigrades can do this might be due to how their environments have shaped them. Being less than 1mm in size exposes these organisms to a dynamic and harsh environment. Meaning they have been selected to be able to cope with sudden drastic changes such as loss of water, extreme changes in temperature, similar to the conditions of space. In fact these organisms have multiple forms of existence further refining their abilities to survive in extreme environments. Although eventually every organism needs to eat and when they do their preferred diet consists of algae perhaps filling stores to survive future conditions. Researchers have ongoing research into these creatures in Italy & NASA.