Category Archives: Technology

You can help biological research from home

by Piter Kehoma Boll

There are a lot of people around the world that, although not being scientists, are science enthusiasts. I guess many of you reading this article fit in this category. You may be a housemaid, a lawyer, a taxi driver, or simply a young student, but you have a big interest in science.

Well, what if you could help science from home? That’s actually possible in several ways. There are plenty of programs, applications or websites in which you can help to do research on several different areas. Here, I’ll focus on biological research, since biology is the subject of this blog.

So, let’s start! See below how you can help.

1. Take photographs of wildlife and make them available online

A lot of people love to take photographs of wildlife. Some websites, such as flickr, are crowded with amazing images of all kinds of lifeforms. Unfortunately, most people protect their work under copyright laws that prevent the photographs to be used without direct permission from the author or by buying it.

But you can be more generous and distribute your work under a creative commons license. This makes sure that you have to be mentioned as the author of the work while still allowing others to use it. There are several different creative commons licenses. Choose the one that suits you! The important thing is to allow your works to be used on other websites, on books, scientific articles, etc, and thus helping to spread scientific knowledge.

You can upload your photographs on flickr, Wikimedia Commons, or even on your own website, as long as you indicate the right creative commons license. Be generous!

wikimediacommonsplanarians

I’ve uploaded many of my photos of land planarians on Wikimedia Commons.

2. Record the lifeforms you see

More than only sharing your pictures, you can record the location where you found the species. Thus, you will help the scientific community to improve the knowledge on species distribution around the world. A wonderful place to do that is the website iNaturalist.org. Even if you don’t know the identity of the species you found, you may upload your records there and someone will eventually identify the species for you. Likewise, you may help identify records from other users.

inaturalist

I’ve uploaded many records on iNaturalist.org

3. Share your bibliographic research on Wikipedia and EOL

If you are an undergraduate or graduate student, an academic researcher, or simply someone who loves science, and you read a lot of scientific articles, books, encyclopedias, etc, do not lock your knowledge within yourself. Make it available to others! And a wonderful way to do that is by editing Wikipedia.

I guess everyone knows Wikipedia, the free encyclopedia that anyone can edit. If you have been reading about the sexual behavior of earthworms, or the use of a plant extract in the tratment of cervical cancer, just check the Wikipedia’s article on the subject and, if the information is not there already, do not hesitate and add it and, of course, cite the source! Wikipedia may be a little confusing to handle at first, but once you understand it and get excited, no one can stop you!

Furthermore, if you information on a subject that does not have an article on Wikipedia yet, simply start a new article!

wikipediarsp

The article Reproductive system of planarians is one of my contributions to Wikipedia.

Another project that you can help is the EOL (Encyclopedia of Life), a website that aims to gather information on all lifeforms and let them available in a single place. After you have registered, you will have some limited freedom to add new content, but eventually you may ask for a higher position that will give you access to a greater number of features.

Do you know other ways to help biological research from home? Let a comment to share it with us!

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Friday Fellow: Taq

by Piter Kehoma Boll

It’s time for us to start to look at the tiny little creatures living with us in this world. We haven’t featured any bacterium yet, so here comes the first one, the magnificent Taq!

Taq stands for Thermus aquaticus, the bacterium’s scientific name. It was initially discovered in hot springs of the Yellowstone National Park, but certainly no one could guess how it would impact science as a whole.

The Great Fountain Geyser in Yellowstone National Park is located near the place where Taq was first found. Photo by Paul Kordwig.*

The Great Fountain Geyser in Yellowstone National Park is located near the place where Taq was first found. Photo by Paul Kordwig.*

Usually with a small rod shape less than 1 µm in diameter and up to 10 µm in length, Taq can also reach more than 200 µm in length when acquiring a filament shape. Living in hot springs all around the world, it thrives at about 70°C. It produces its own food via chemosynthesis by oxydizing inorganic elements in the environment, but it can also associate with some cyanobacteria living in the same habitat to obtain food from their photosynthesis.

Taq under the microscope. The scale corresponds to 1µm. Photo by Diane Montpetit.

Taq under the microscope. The scale corresponds to 1µm. Photo by Diane Montpetit.

But what impact did it have in science? Well, because it lives in such high temperatures, Taq’s proteins need higher temperatures to denature, so they are useful to perform biochemical processes in high temperatures, such as in DNA amplification.

PCR (polymerase chain reaction) is a process used for amplifying short segments of an organism’s DNA. It needs to be performed in high temperatures in order to denaturate the DNA chain so that the primers can align. Primers are very short modified DNA fragments that determinate the beginning and the end of the segments that one wants to amplify. Amplifying a DNA segment means producing a large amount of copies of that segment. The problem in earlier PCRs was that the high temperatures needed to denaturate the DNA also denature the enzyme that produces the copies, called DNA polymerase. As a result, there was a need to add enzyme after every cycle of thermal denaturation. The DNA polymerase of Taq, called Taq polymerase, can resist the high temperatures of denaturation, so that it needs to be added only once.

Thanks to Taq polymerase, DNA amplification has become a much more efficient process, accelerating researches in molecular biology.

Sometimes revolution beginns with the tiniest things.

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References:

Brock, T. D. 1997. The value of basic research: discovery of Thermus aquaticus and other extreme thermophiles. Genetics, 146(4): 1207-1210.

Wikipedia. Thermus aquaticus. Available at: <https://en.wikipedia.org/wiki/Thermus_aquaticus&gt;. Access on January 21, 2016.

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Paleontology, biology and human life in face of 3D Printing

by Carlos Augusto Chamarelli

Hi there folks! After a long time absent I finally gathered enough willpower and decent topic material to post something in this humble site of ours. In this article I’ll talk about a relatively recent technology that is quickly growing and can revolutionize the way we study fossils and other biological subjects, as well as the way we can help humanity in an applicable way.

But first, some shameless advertising because it’s always good to spread this kind of thing around: if you missed Bill Nye’s debate against that other guy you can watch it in its entirety clicking here. Regardless of whether you believe Bill inadvertently helped the Creation Museum go ahead in building its replica of Noah’s Ark (until they run out of money again, that is) or not, it’s still a great source of entertainment to watch and show your kids, teaching them the difference between spouting nonsense that vaguely sounds convincing to actual debating using facts and that’s okay to not know something rather than pretending you know all. Second but not less important, Cosmos: an Space Time Odyssey episodes are available online by clicking here. As of now I myself couldn’t watch because my internet lets me down, but for those who missed it or don’t live where it’s airing, go ahead and watch it for your brain’s content.

Now for my topic properly, the astounding technology in question is 3D printing. If you’re unfamiliar with 3D printing: it’s the process to which a tridimensional model made in a computer is transformed into a physical object by means of a machine – the 3D printer – that will sculpt the desired object. In 3D. I first came to know of this technology sometime during 2006; it was during the development of Spore, and Maxis considered offering a service to which players could import their creations and receive it as physical miniature, and it did come live two years later when the game was released. It had some limitations such as not being able to reproduce overly thin features and a very grainy texture thanks to the material used, which also made the model incredibly fragile. Since then 3D printing became more refined and widespread. Nowadays there are several online services to which you can order your very own 3D models such as Shapeways, i.Materialise, Sculpteo and so on, and make them in better details and made of more durable materials than before.

Yup, EBA is out of business.

Yup, EBA is out of business.

Apart from the alluring prospect of printing your favorite video game characters and prototyping for engineers (my priorities are set right), 3D printing also offer some interesting possibilities when it come to the study and teaching of biology – specially paleontology – and the development of prosthetics. For instance, regarding the former, it can help paleontologists in the extraction of fossils. As of now, the process to which fossils are dug up and prepared to be analyzed properly in a lab is something along the lines of:

Find fossil bed -> very carefully excavate the site -> find fossil embedded in rock -> very carefully excavate fossil -> shed tears as you accidently damage the fossil while excavating -> wrap fossil in plaster and ship it to the lab and hope it arrives safely -> receive fossil in lab -> very carefully remove plaster not to damage fossil -> shed tears as you accidently damage fossil while removing plaster with saw-> further shed tears as you accidently damage the fossil during analysis.

Pictured: shed tears.

For the reasons above, it’s understandable that methods that allow studying these fossils while minimizing risks are very welcome. One such method that quickly gained notoriety was the use of CT scans, which generated 3D models of the specimens to which scientists could peek at their inner structures without actually cracking open the fossil. It was by this very technique we came to know that Pachycephalosaurus had a sturdier helmeted skull than previously thought, making the old assumption that they butted heads just a little bit more plausible. While this was an amazing step forward in the study of fossils, the next step came soon after; this technique was mostly used on fossils already cleaned up of sediments, but the same method proved to be just as effective to fossils still encased in rock slabs.

Some paleontologists were afraid that excavating the rock would damage the skeletons they work so hard to retrieve. As a solution, they simply extracted the rock around with the fossil inside, scanned it thus generating a 3D model like its predecessor, and then printed it. The result was a near perfect replica of what was encased in the rock. I can’t stress enough of how amazing this is: the remains of a creature, extinct for millions and millions of years, reproduced as if removed from its mineral tomb for everyone to look and touch.

In this case, shed tears of joy.

All seems to be favorable evidence that printing fossils might become an even bigger part of paleontology in the future. While I personally don’t believe this process would come to replace the usual method of digging up fossils entirely, as foreshadowed by the nameless paleontologist in Grant’s team in Jurassic Park, – in fact, even if the 3D print is a perfect replica, it still doesn’t beat the real thing – I do believe that employing this technique would minimize the risks of damaging specimens; the fossils would still need to be removed from their locations lest they continue to erode and be affected by earthquakes, rains and whatnot as was the case of the forelimbs of the baby Chasmosaurus unearthed just a few months ago in Canada, which could have been further damaged had it not been removed. Not only it would help knowing exactly where paleontologists should remove the sediments if they judge it to be necessary, the 3D model generated could help in both having a bigger picture of the creature they’re dealing with, as in arranging the pieces to form a posture if the animal was alive (assuming that it’s possible for them to fit in the machines), as well as aiding museums show said findings to the public.

The process to which fossil replicas are made for museum exhibitions is just as risky and labor intensive as the digging of fossils: a team of artisans is employed to make castings out of the original fossils – very carefully not to shed tears as they accidently damage the fossil in the process- and once ready probably months later the skeleton is assembled and put to the public’s delight. The problem is, because of its complexity and requirement for skilled workmanship to achieve maximum quality, these replicas are hard to come by, and so the museums that get to expose them take extra care that they’re not damaged, in the form of a polite sign asking visitors not to touch it when in reality they really want to punch whoever break them in the face. The problem of interchangeability is minimized if the museum makes more replicas intended to other museums, as it was the case of the dodo skeleton offered by the Royal Ontario Museum.

Say “thanks, Royal Ontario Museum”.

While the dodo skeleton was a very nice gesture for other museums, it is a rather small specimen. It’s one thing to make a replica of a bird’s skeleton and ship it to other museums while still providing an affordable price. It’s quite another trying to do the same with a huge dinosaur skeleton like an 85 feet long Brachiosaurus. But imagine if museums could print these skeletons, regardless of their size and complexity. I don’t want to be mean to the people in the trade of fossil replicas, but the idea that a museum could print their own skeletons to their exhibitions using the skeleton models created by MRI scanning is a fascinating one, and advantageous not only to the museum but those who study in it. It’s not something still in the realm of imagination: there is already the employment of 3D printing to reproduce animal’s skeletons for educational purposes (as well as other areas, but we are a biology-centered blog), so plans to make an actual exhibition out of entirely 3D printed specimens seems to me to be just as far out in the future as the use of 3D printed skeletons in biology classrooms that give students a more tangible and interactive tool for learning.

Another interesting use of 3D printing in the field of biology is its medical use. Somewhere in the world someone thought that using polymers and metal to make miniatures was too mundane, and skin tissue was a better material. Whatever the case is that brought about the use of this technology in the medical area, 3D printing functional organs seems to be a new reality, and anything from functional ears, hearts, livers, even eyes are being worked on to aid patients in need of transplants or face reconstructions. More recently, only few days ago, a woman successfully got a 3D printed skull replacement.

I don’t want to post a picture of it here, so here’s a picture of Gummy instead.

I don’t want to post a picture of that here, so have a picture of Gummy instead.

So while more complex organs are still on their developmental phase, there’s this immediate use where 3D print can be used to replace bone structures, even prosthetic limbs. In order words, not only 3D printing opens ups possibilities to print miniatures of your favorite Pokémon and learn about prehistory, it also gives a bright future to those struggling in the line of organ donations. Instead of waiting in line, medics could simply print a new organ.

I just want to finish this post by saying that this is what I find most fascinating about technological advancement: you start out with a simple tool with maybe one or two uses, and then people will create new forms of this tool, for uses one couldn’t possibly imagine. Something that started as a printer that didn’t use paper came to be the door to many other wonderful developments. The downsides of the modern 3D printers regarding their price, operation and general availability are really only temporary.

Well then, I hope you have enjoyed my blabbering article and, as usual, comments and questions are appreciated!

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Filed under Paleontology, Technology