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Citizen Science Quarterly http://citizensciencequarterly.com Mon, 23 Nov 2015 19:43:21 +0000 en-US hourly 1 21770170 Encyclopedia of Life “One Species at a Time” podcast: Giant Squid http://citizensciencequarterly.com/2014/01/encyclopedia-of-life-one-species-at-a-time-podcast-giant-squid/ http://citizensciencequarterly.com/2014/01/encyclopedia-of-life-one-species-at-a-time-podcast-giant-squid/#respond Wed, 22 Jan 2014 16:10:51 +0000 http://citizensciencequarterly.com/?p=4839 Giant Squid live in the deep sea and are rarely seen by humans. Recently, however, some Japanese fishermen accidentally captured a still living Giant Squid (it died soon after being brought to the surface). Although glimpsing a living Giant Squid is more cephalopod excitement than most of us can ever hope for, visitors to the Smithsonian Institution’s Museum of Natural History can see two beautifully preserved and displayed specimens from Spain, a large female and a smaller male. How did they get here? A one-ton, 26-foot squid can’t fit in your carry-on luggage. Listen to Encyclopedia of Life’s One Species at a Time podcast about how museum exhibit designers transported this enormous animal from Spain to Washington, D.C. in an effort dubbed “Operation Calamari”.

Read the news story

Listen to the podcast

Meet the scientists in the podcast

The One Species at a Time podcast series is supported by the Harvard Museum of Comparative Zoology.

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Dolphin Podcast from the Encyclopedia of Life http://citizensciencequarterly.com/2013/11/dolphin-podcast-from-the-encyclopedia-of-life/ http://citizensciencequarterly.com/2013/11/dolphin-podcast-from-the-encyclopedia-of-life/#respond Thu, 14 Nov 2013 16:28:24 +0000 http://citizensciencequarterly.com/?p=4813 Stenella attenuata and Stenella longirostris

You have probably seen cans of tuna in your local supermarket marked “dolphin safe.” That label means the tuna was fished in a way that spares most dolphins from being killed in the tuna fleet’s giant nets. In this podcast, biologist and guest reporter Matt Leslie brings us a story about tuna, the intertwined fate of fisheries and dolphins, and the work of scientists.

Listen to the podcast

The One Species at a Time podcast series is supported by the Harvard Museum of Comparative Zoology.

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(New and Improved) Memory Game from the Encyclopedia of Life! http://citizensciencequarterly.com/2013/10/new-and-improved-memory-game-from-the-encyclopedia-of-life/ http://citizensciencequarterly.com/2013/10/new-and-improved-memory-game-from-the-encyclopedia-of-life/#respond Wed, 23 Oct 2013 14:46:43 +0000 http://citizensciencequarterly.com/?p=4807 This is the classic game of Memory – remember where you saw a species and try to find its match! There is also a quiz that challenges you to match species names with the pictures.
Try one of our marine focused memory games by visiting http://fieldguides.eol.org/memory/ and look under “Featured Games”

You’ll see some changes with the latest update to Memory… in addition to speed improvements, you can now also play against Elephas, the computer with a good memory. Good luck!

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Bat Podcast from the Encyclopedia of Life http://citizensciencequarterly.com/2013/10/bat-podcast-from-the-encyclopedia-of-life/ http://citizensciencequarterly.com/2013/10/bat-podcast-from-the-encyclopedia-of-life/#respond Wed, 02 Oct 2013 19:01:00 +0000 http://citizensciencequarterly.com/?p=4803 The batman of Mexico has his own bat-cave. He just shares it with 4,000
Mexican long-nosed bats. In this podcast, join researcher Rodrigo Medellin as
he descends into the Devil’s Cave just north of Mexico City.

Listen to the podcast

Learn about Bats on EOL

Subscribe to all the EOL podcast on iTunes

 

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M-EOL Mobile App http://citizensciencequarterly.com/2013/09/mobile-app-for-encyclopedia-of-life/ http://citizensciencequarterly.com/2013/09/mobile-app-for-encyclopedia-of-life/#respond Wed, 11 Sep 2013 17:21:18 +0000 http://citizensciencequarterly.com/?p=4797 Introducing M-EOL, a new mobile app and the winner of the EOL Education

Innovation Challenge! Created by Natural Solutions and available on iTunes

and Google Play.

Become an explorer, discovering different plant and animal species by
travelling around the world. Improve your knowledge about each species
through descriptions, images, distribution information, and conservation
status from the Encyclopedia of Life website. Explore how organisms in each
game collection are related to each other by browsing a dynamic, interactive
graph.

Features:

Discover: Explore species classification (taxonomy) and develop a deep
understanding of each species through descriptions, images, and the IUCN
conservation status.

Game: Play with funny collections of species to improve your knowledge and
beat your previous records!

M-EOL App on iTunes
https://itunes.apple.com/us/app/meol/id679021914?mt=8

M-EOL App on Google Play:
https://play.google.com/store/apps/details?id=eu.NaturalSolutions.Meol

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New Species in the Old World Podcast http://citizensciencequarterly.com/2013/09/new-species-in-the-old-world-podcast/ http://citizensciencequarterly.com/2013/09/new-species-in-the-old-world-podcast/#respond Thu, 05 Sep 2013 09:20:08 +0000 http://citizensciencequarterly.com/?p=4793 You don’t always have to venture into the heart of a rain forest to discover a new species. Sometimes all you have to do is look more closely, right where you are. In Europe, experts and enthusiasts alike are looking high and low, from alpine meadows to underground caves, in search of Old World species new to science.

Listen to the podcast

This podcast is part of the One Species at a Time Podcast series from the Encyclopedia of Life. Funded by the Harvard Museum of Comparative Zoology.

 

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3D-printed adjustable volume straw pipette http://citizensciencequarterly.com/2013/08/3d-printed-adjustable-volume-straw-pipette/ http://citizensciencequarterly.com/2013/08/3d-printed-adjustable-volume-straw-pipette/#respond Wed, 14 Aug 2013 00:36:52 +0000 http://citizensciencequarterly.com/?p=4783 Pippettes, a tool for dispersing specific volumes of liquid, are quite possibly the most used tool in any bio lab. Most biologists buy their pipettes from a manufacture and they’ll usually set you back $500-$1000 for a set*. Or you can do what Kwalus did and make your own using a 3D printer, a balloon, a bit of duct tape and a spring.

3D Printed Pipette

Check out this video of it in action:

Via: Thingiverse

*Note: If you’re in need of quality(read:calibrated) micropipettes, I highly recommend genefoo, they’re DIYbio friendly and affordable.

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Learn Python for Science – Numpy, SciPy and Matplotlib http://citizensciencequarterly.com/2013/08/learn-python-for-science-numpy-scipy-and-matplotlib/ http://citizensciencequarterly.com/2013/08/learn-python-for-science-numpy-scipy-and-matplotlib/#respond Tue, 13 Aug 2013 22:46:02 +0000 http://citizensciencequarterly.com/?p=4779

 

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Spare a Thought for the Scientist http://citizensciencequarterly.com/2013/08/spare-a-thought-for-the-scientist/ http://citizensciencequarterly.com/2013/08/spare-a-thought-for-the-scientist/#respond Mon, 12 Aug 2013 22:27:36 +0000 http://citizensciencequarterly.com/?p=4774 An assertion that is often made by the more scientifically inclined is that it’s a great shame that the vast majority of people don’t know or apply basic scientific principles to their everyday life. Not in an over complicated sense, but rather to help overcome simple tasks, to aid getting to grips with new and possibly complex concepts, or figuring out how to work some newfangled piece of technology.

Let me illustrate this point by way of a story. A friend of mine (this is completely true) once lived with a physicist, and couldn’t relate to his way of thinking at all. One day when their toilet broke my friends natural response was to simply call in the plumber. When he returned from work to make the call however, he found to his dismay that his scientist house mate had disassembled the toilet. Parts were strewn everywhere, and the physicist was looking rather pleased with himself. ‘Have you managed to fix it then?’ my friend asked. ‘No.’ The physicist replied, ‘but I’ve worked out what the problem was, and have ordered a new part. Should arrive tomorrow.’ My friend stood aghast, transfixed at what he found to be a different breed of person.

As the Philosopher of science Karl Popper remarked ‘Science may be described as the art of systematic over-simplification’, and it is with this in mind that scientists can cut through the extraneous details and get to the heart of a concept rapidly, laying the foundation for a solid understanding in any undertaking. Discover what is known, and what isn’t known, and how ignorance can attempt to be overcome. It is this systematic framework that has eradicated small pox, extended life expectancy, put man on the Moon and an iPhone in his pocket.

One of the virtues that emerges from scientific training, which amounts to years spent in learning and research, is a way of thinking that is lauded by those that have it. Decried as more important even than the knowledge it imparts, the scientific perspective that moulds its practitioners changes the way they see the world. But is it really so hard to achieve?

At its most basic level, science demands scepticism in its users. This is not, however, to be confused with cynicism. Optimism is critical to overcome the countless intellectual brick walls that researchers in scientific disciplines come up against. Without a doubt, it is doubtitself which is crucial to begin to understand what is going on in nature. Starting with a blank slate, and incrementally building from the bottom up a simplistic picture of reality one begins to form a working model to learn from. It may be slow, but if the price for progressing more quickly is not being sure of what you know such action is surely rendered pointless.

Experts that arise from persistent exploration of their chosen field, and continued high impact research, are not to be confused with authority figures. The only thing that carries weight in science is the data and the evidence. If some unheard of and unpublished slack-jawed researcher generates findings contrary to the accepted theories of the day, then it is the theory that needs to be modified or dispensed with. Whatever experts were saying is trumped, and immediately outdated.

Indeed, the Physicist Richard Feynman surmised that ‘science is the belief in the ignorance of experts’. In other words take nothing for granted, there are no sacred cows, no areas one shouldn’t question or attempt to overturn the accepted thinking on. Professors, being the old and accomplished hands in their subjects, are still of course better placed to interpret the revelation to a deeper level. And more often than not would be happy to do so, for there are no hard feelings about being proved wrong. The cosmologist Lawrence Krauss has even gone as far as to state that the best place one can be in science is wrong, because once something is known to be wrong this offers up an opportunity to learn.

So there we have the scientific mindset: scepticism, doubt, curiosity and an acceptance of an underlying order in the universe. All of this seems obvious. Humans naturally seek out order to make sense of their surroundings, so how can science claim these universal traits as its own? While such an acquisition is true, the propensity to which a trained scientist confirms to such a way of thinking in rigid terms is perhaps what sets them apart from the non-scientist. Consequently it is the ardency with which they approach the world that can lead them to be irked with their non-scientific contemporaries.

The vice of the scientific outlook, as perceived in general, is that its practitioners can come across as cold, seeing the world as a collection of parts which can be broken down and understood. With Nobel prize winning Theoretical Physicist Paul Dirac making statements such as ‘In science one tries to tell people, in such a way as to be understood by everyone, something that no one ever knew before. But in the case of poetry, it’s the exact opposite!’ it is little wonder such resentment can build up.

But rather than strip nature of its resounding beauty, deeper levels of understanding only serves to open up new dimensions to the world which can all be appropriated concordantly. No one would ever make the claim that Professors of Music can no longer listen to and enjoy a symphony, or that their analytical knowledge and academic understanding of music gets in the way of their enjoyment of it. Rather we are left to envy them, as they can enjoy aspects of it we aren’t even privy to.

A key difference between the Professor of Music and the Scientist is that the scientific method is infinitely easier to grasp and employ. So next time you can’t work the printer, the TV won’t tune in properly, or you need to make a course correction for your satellite to successfully slingshot around an upcoming planet while still maintaining the correct trajectory to reach its desired destination, take a cool breath, try and get to the root of the problem, and assume there is an underlying logic at play which can be reasoned out into the open.

 

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UK Government Cultivates Synthetic Biology with Cash Grants http://citizensciencequarterly.com/2013/08/uk-government-cultivate-synthetic-biology-with-grants/ http://citizensciencequarterly.com/2013/08/uk-government-cultivate-synthetic-biology-with-grants/#respond Fri, 02 Aug 2013 21:10:26 +0000 http://citizensciencequarterly.com/?p=4749 July 11th saw the UK government’s announcement to pledge almost £1 million to fund several university research groups’ participation in an international collaboration to create the world’s first synthetic yeast. David Willets, the UK’s science minister, made the announcement during the week of the sixth Synthetic Biology conference which is this year being hosted by Imperial College London.

Willets is expected to make further announcements about a £60 million investment into the field as a whole, some of which will go towards the creation of a centre of ‘innovation and knowledge’ in order to find uses for the deluge of synthetic organisms set to be created in the coming years. Areas among those expected to benefit from the emergent field of synthetic biology include vaccine design and production, biofuels, crops, diagnostic medicine, and nanotechnology.

But what is synthetic biology? Arguably just a decade old, it’s a discipline in its infancy whose implications could be more far researching than anyone could realistically envisage at present. Just the name, synthetic biology, comes across to many as a puzzling oxymoron; biology: the study of living things that emerge as part of the natural order; synthetic: artificial and man made. How does one make fake life, and if something artificial can come to life, then in what way could it then be perceived, or indeed distinguished, as being synthetic? Such thoughts sound like they belong to the realm of science fiction and conjure images such as Frankenstein’s creation, but this isn’t something that may one day come to fruition – this is happening now, and it’s changing the way biologists do biology.

The go to analogy that best explains both what synthetic biology is attempting to achieve and how it intends to do so is by thinking of a car. One way of trying to understand how the inner workings of a car come together to give rise to its functionality is by disassembling it entirely and rebuilding it piece by piece. This allows a deeper awareness of the role each part plays and its role in relation to the whole.

The legendary physicist Richard Feynman famously stated ‘What I cannot create, I cannot understand.’, and it is with this sentiment the field aims to more acutely determine the nuances that conspire together to make living matter from no living matter. An ultimate long term goal of synthetic biology is often touted as having such a complete understanding of how each part of a living system works one would simply be able to sit at a computer and redesign it to improve its functionality, or even better: design new organisms from scratch.

The obvious problem with the car comparison however is that living things, even the simplest, are infinitely more complex than any smart car you’re ever going to run into. The parts that go into the make-up of them interact on the nano-scale, the number and variety of them are mind boggling and their design has arisen over the course of billions of years through the process of evolution. In spite of these challenges, real progress has been made by researchers working in the field.

Notable examples are the range of medical biosensors now coming to market. By a process called gene ‘tagging’, bacteria can be modified to light up in response to specific external stimuli. This is done by attaching the gene for a light emitting florescent protein to the end of the protein which would ordinarily be output in response to the stimulus under scrutiny. Rather than being subject to often invasive testing, the results of which can take a good deal of time to process, gels embedded with such synthesised biosensors can be simply smeared onto the area of concern on the patient and a diagnosis made within minutes on the basis of whether or not the gel lights up.

A novel approach to clearing land mines was pioneered by altering thale cress’s genetic code so that the pigment in the leaves would grow as purple as opposed to the ordinary green when grown in the presence of nitrogen dioxide, a gas given off by the buried mines. Rather than prod along the ground with a stick hoping not to be blown apart, the seeds of such a plant could be scattered upon the ground of land suspected to contain mines and returned to when the plants have reached maturity in order to identify the dangerous locations.

In order to quell the spread of malaria in Sub-Saharan Africa, which is estimated to kill more than half a million people annually, swarms of mosquitoes were created with without the ability to carry the disease. Such flies would compete for the resources of those that could, so while not combating the cause of the disease completely such measures seek to drastically reduce the effectiveness of it spreading by these means.

Unsettling concerns which spring to mind with the latter two examples are the possibility, if not the probability, that these organisms could cross contaminate species already in the wild, giving rise to disastrous and wholly unforeseeable consequences. The beauty of redesigning life at the genetic level is that safeguards to exclude such eventualities can be built in. For instance, their reproductive capabilities can be written out, thus ensuring they can’t mix with nature. However, film buffs may recall this is similar to what was done in ‘Jurassic Park’ and (SPOILER ALERT!) it failed.

The timeliness of these developments being able to be made now are twofold, the cost and ease of nucleotide sequencing and synthesis, and the current level of computing power.

In the wake of the Human Genome Project the speed at which it was possible to read off and write nucleotides, the chemicals on the double helix backbone of DNA whose sequences act as a store of genetic information, became ever more quick, accurate and the cost involved diminished to incredible levels. The total cost of the Human Genome Genome project came in at approximately £3 billion, but thanks to the technology it employed and the invigorating blaze it conferred to the entirety of this domain of science it would now cost less than £1000 if carried out tomorrow. Such progress renders the famous ‘Moore’s law’, which observes the continual doubling of computer power every eighteen months and which has been obeyed for the past forty years now, as looking almost sloth-like. However, without Moore’s law continually driving computing power to ever new bounds the design, virtual representation, and most importantly the ability to model biological systems would be severely limited.

The international effort towards creating synthetic yeast by 2018 sees researchers at the Universities of Cambridge, Edinburgh and Imperial College working on chromosome 13 of the yeast strain of Saccharomyces Cerevisiae, which contains 16 chromosomes in total (we humans have 46). More commonly known as Brewers’ yeast, it has been used in brewing and wine making for thousands of years.

A more thorough understanding of this yeast could allow it to be modified in the future to create cells giving rise to higher alcohol yields, and more robust to external factors such as temperature and water quality the alcohol is brewed in. If the efficiency rises sufficiently, in such a way to allow a scaled up production to take place it is not unreasonable to this giving rise to a sustainable source of biofuel. The primary output of the process may even be changed to a different product entirely; such as medicinal drugs, vaccines, fertilisers, or various chemicals for all manner of industrial purposes. The possibilities could be potentially endless.

As Saccharomyces Cerevisiae was the first eukaryote cell (cells with a major step up in complexity when compared bacterial cells, and crucially having a membrane surrounding their genetic material in an area called the nucleus) to be sequenced in the mid-nineties, it quite fittingly is set to be the first synthetic cell as well.

The claim to creating the first artificial life form was made by a team led by the pioneering US geneticist Craig Ventor in 2010. There the genome of Mycoplasma Mycoides, a parasitic bacterium which commonly resides in the lungs of cows and goats, was synthesised in its entirety and inserted into the vacated nucleus of another host cell of the same species. True to theory the cell then ‘booted up’ and worked as any other Mycoplasma Mycoide would.

However, it could be argued that this exercise, which took a team of 20 scientists ten years at a cost of forty million dollars, was somewhat unremarkable. Given that they removed the actual genetic code from a host cell only to replace it with an exact replica created in the lab, it shouldn’t have been all too surprising to find that it worked. However, one must bear a philosophical attitude when considering the implication of this experiment. Consider that the team had synthesised some inanimate chemicals, inserted them into some other (arguably) inanimate chemicals, and somehow everything conspired to cross the boundary from the non-living living to the living. A Pandora’s crate worth of questions is unearthed, each of which presents many challenges in even attempting to begin to answer, the chief one being: what is life?

On the scales we’re used to living in, such a question seems trivial. It is reasonably clear that dogs, trees and Putin are alive, while pianos, stones and Lenin are not. But when one delves down to the scales probed by synthetic biology the point at which non-living matter becomes living matter becomes a mire of grey area. When do interacting chemicals take on the extra dimensionality which renders them no longer inert? It is very difficult to tell, and is so fiddly to ascribe a definition to in fact that mainstream science long ago gave up on trying to come up with one. It was hard enough ten years ago, but with the rise of this field the goal posts for what life may be are shifting at break neck speed.

The strides being made by the field though are not without controversy, and has met a non-negligible ground swell of opposition. As one could imagine, when tampering with nature – and moreover, when modifying organisms at the genetic level – concerns that come to the fore include public safety, environmental impacts, level of controls in place, and the ethical implications that are raised. On the basis of such reservations over one hundred environmental and civil society groups, such as ‘Friends of the Earth’, ‘International Center for Technological Assessment’ and the ‘ETC Group’, together issued the publication [source] The Principles for the Oversight of Synthetic Biology in 2012. In it, they call for a global moratorium on the release and commercial use of synthetic organisms until more rigorous and robust biosafety measures can be more firmly established.

Such scepticism is understandably warranted, and particularly interesting is the extent to which those in the field are interested in public awareness of their work. Philosophers of science and academics working in science ethics are being closely involved in the field as it progresses, as the scientists are keen to ensure misunderstandings about the nature of synthetic biology don’t take root and result in the PR disaster that befell GM foods in the UK. Given that the science employed in synthetic biology makes GM techniques look like childs’ play, such reservations are not unfounded in the least.

The most cliché of phrases that undoubtedly rears its well worn face in any popular article one is likely to see chronicling developments in the field is the extent to which researchers are playing ‘god’. Though such accusations could be levelled at anyone in history using newly discovered or partially understood laws of nature to make practical applications, the fact that this is fundamental biology where new life can be created outside the bounds of evolution are acts more usually associated with a deities, perhaps the authors can be excused.

Calum Grant is a freelance writer based in London. He has a background in physics and biology research, and also works in science and mathematics teaching.

Photos by SLU Madrid Campus  

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