Awesome ‘Possum

Today I received a copy of Awesome ‘Possom volume 3 in my mail from Angela Boyle, a natural science illustrator and cartoonist who has curated and edited the fourth volume of Awesome ‘Possum. Before I had laid my hands on the book, I had imagined it to be a few-pages-long book that I would sit down and devour in the evening. Boy I was wrong. When I opened my mailbox, I was pleasantly surprised by a 400 page beast of a book. I flipped a few pages and was blown by thinking about the amount of cumulative effort and coordination that must have gone in realizing this book.

Excited, I sat down and started reading every word from the cover and beyond. Not having ever read an illustrated book, I had judged them to be the books for children. I was too old to enjoy them I had thought. When I sent the pictures of the book to my friends, “Aww that’s such a sweet children’s book” is what I got from these other engineers too. I think this is a disease we engineers have, assuming cartoons = children.

Not having experienced something like this, if that’s you, let me tell you, you should get a volume of Awesome ‘Possum to get rid of that delusion. It is indeed a fantastic book for children of all ages. But it is equally good, if not better, for adults! Adults would definitely extract a lot of great experience and knowledge out of it. That is exactly what I told my friends too.

First of course was a beautiful introduction by Ursula Vernon who has a peculiar hobby of taking pictures of moths, and does it despite being a not-so-great photographer or etymologist. With these hobbies in her life she has managed to do big things which I think will touch you better if you read the actual introduction yourself. Maybe, this book right here was a gateway to my own peculiar hobby I thought, and turned the page.

Being an engineer I honestly do now know a lot about animals. A few general things and when I manage to dig few obscure facts, I get excited, do more research and often write about them on my blog here. My point is that the natural world is inherently very fascinating. If you think it is not, you have not known a lot about it.

Awesome ‘Possom was a perfect exposure of the natural world for me. It talks to me about things like, how I should be thankful for little known scientists like Philip Henry Gosse, Anna Thynne and Jeanne Willepreux Power because of whom we are able to decorate our homes with glass boxes (aquariums) with little alien worlds in them. Or things like how rolling bees in sugar could sometimes be a better way to do a mite count and figure if the mite infection is above the threshold to proceed with a treatment. Because alcohol kills the bees.

I noticed a stark difference in the illustration style of each comic and conveniently found the name of the cartoonist or natural science illustrator on top of every page of that chapter. The works of these talented people from across the North America and the world, compiled into this book, refresh you with a diverse subject matter and illustration style every few minutes. And this is just the volume 3 I’m talking about. Then there’s 1, 2 and 4 which is up on kickstarter right now. Volume 4 includes cover art by Eisner-nominated Tillie Walden, creator of Spinning (First Second, 2017) and a foreword by Jon Chad, creator of Volcanoes: Fire and Life (First Second, 2016). I for sure am going to read all of them. In my free time I have been exploring the amazing works of various artists mentioned on this kickstarter page.

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Say, Elise Smorczewski for example. She grew up on a farm that fostered a lifelong fascination with animals of all kinds. And Spratty, a cartoonist living near Philadelphia with their various human companions, two snakes, and two cats. They think reptiles are great. More importantly they have had first hand experiences and deep insights to share from their own experiences. Also, they are a wonderfully reliable to get your science facts from!

Chicken Scratch, by Elise Smorcsewski

I have been finding that the snippets of wisdom I get out of illustrations actually stick as if I someone had told me about them. That’s because everything is so visual and is delivered in a way that is easy to digest. You do not get this out of reading dense textbooks. Especially true for people like me who are not directly involved in natural sciences research. We are not great at extracting knowledge out of reference texts without a significant amount of experience in that particularly narrow field. Just within the first few pages I had extracted enough things to delve deeper into and to write about them on my blog. I will be doing that as I go.

I know that the book / scholar world thrives on criticism. That’s not me. i get my style from reading people like Maria Popova of Brain Pickings who believes in book recommendations rather than book reviews. I want to do that. I do not deem myself capable to criticize the work that I myself am not capable of producing. The only thing I see is the endless value in the thousands of human-hours spent in producing carefully curated work for me.

Rattle snakes have infrared detectors on them. How is that not cool, especially for a person who works with infrared spectra on a daily basis.  I realize the importance of having specialized detectors for getting the right information at the right wavelength range. And that reminds me of how a son and dad open up the rattle of a rattle snake in their youtube video to see how it works. And who would have known that rattle snakes also are great parents. The rattle snake illustrations making it easier for me to understand actual rattle snake research also inspires me to look for, or think about making illustrated research papers for the layman to understand my own field! This source of inspiration does not stop for hundreds of pages.

Do not forget to go explore the kickstarter to help the artists get their fair share for their hard work. 

Spider Eyes are Nature’s Marvels

Now I do not exactly remember where and how I started my journey down this rabbit hole. But the deeper I went the more interesting it became. It was a great learning experience. I’m clearly not an expert. Here I share the understanding I developed of the spider eye over the few hours of exploration. For this I referred to various sources all of which are mentioned in the links. And if you know more or would like to add something interesting to the article please let me know in the comments below.

The  first thing about spider eyes is that 99% of spiders have 8 eyes. A little less than 1% of them have 6 eyes. In some fringe species there are 4, 2 or no eyes at all. Apparently, based on the pattern these eyes are arranged in, on their cephalothorax (let us mortals call it the ‘head’ to make things simple), the family to which the spider belongs can be determined. Some blessed human, made the following schematic to help us do exactly that. In case you ever feel the need to do so, here it is:

And in much greater detail, right here.

For their small size and the limited number of photocells, spider eyes, especially the jumping spider’s (Salticids) eyes perform surprisingly well. Their resolution is better compared with larger mammals than with insects. In the human world a camera of such standards this would simply be an engineering miracle. You will understand why I say that soon…

In the image above if you locate the family Salticidae, you will see those two large eye in the front which are particularly very interesting. These are called the principal eyes (or anterior median eyes) and are the ones that allow high resolution vision. So much that the spider would be able to resolve two spots on a screen 20 cm away from the spider, sitting just 0.12 mm apart from each other. An acuity of about ten times that of a dragonfly – 0.04°.

The brain of this spider, show in blue in the image below is pretty big for its size. The proportion of the volume of brain to body is more or less similar to that of human beings. The brain of Salticids also have a rather large region dedicated for visual processing.

The principal eyes we are talking about are in the shape of elongated tubes as seen below, in the front of which is a hard lens and at the other end is a layer of photocells. Inside the tube, near the retina is another little lens which moves back and forth along the tube like a telephoto lens system. These elongated tubes are like the tubes of a binocular which allow for a higher resolution using a small package.

However the downside of such a tube like architecture is that it limits the field of vision. Here’s how that problem is dealt with.

The front part, with the big corneal lens is fixed. It has a long fixed focal length. The farther end where the retina is located, is connected to these muscles shown in red. These muscles allow for the tube’s farther end to move around in several degrees of freedom to make quick movements and scan a larger image in its head, one small field of view at a time.

In the video below you can see the retinal end of the black tubes moving around inside the translucent exoskeleton of the spider as the spider forms a high resolution complete image of its surroundings, one small field of view at a time.

If you peer deep into their eyes you will see a dark (black) when you are looking into the small retina. However when the farther end of the tube moves, you see a honey brown color with spots. This is the inner wall of the tube that you are seeing in the following video.

Then the retina itself is another biological marvel. Unlike our single layered retina, the Salticid’s retina is made up of four layers. The four layers are arranged one behind the other. This lets the nature pack more photocells in a smaller area and also helps the spider see in color as different colors (different wavelengths) with different refractive indices are focused in different planes.

Counting from the rear end, the spider uses different layers of retina to obtain different colors of the image. The retina’s layer 1 and 2 to get the green color (~580 nm – 520 nm wavelengths), blue color using the layer 3 (~480 – 500 nm wavelengths) and layer 4 for ultraviolet (~360 nm).

An important detail in the above image reveals how spiders manage to keep focus on different objects at different depths, in focus. The layer one has photocells arranged in a step fashion, with varying distance from the lens which makes sure that all objects are focused on at least one part of the layer 1.

The other problem of distance estimation which matters a lot for jumping spiders is again solved rather elegantly by the same apparatus. Humans use their stereo vision – two eyes which are far apart to estimate distance. Other animals move heads to do the same but I’m not getting into that.

Jumping spiders employ a completely different algorithm, utilizing degree of blur cues. For which the second layer plays a crucial role. The second layer would have received a sharp blue image, but they are not sensitive to blue light like I mentioned above. The green they detect is rather blurred at that plane. It turns out that the amount of blur depends on the distance of the object and helps the spider determine the depth by processing the amount of blur in the image. Hence allowing it to jump and hunt accurately.

If you are a university student with free access to journals, I think a quick look at the paper titled: “‘Eight-legged cats’ and how they see – a review of recent research on jumping spiders,” will help you delve into greater detail.

Psst: Someone has it uploaded on research gate for free access for I don’t know how long: here.

Please leave a comment below to let me know your thoughts on this, or if you have any ideas for future posts. I plan to reward the top commentators every month so do not forget to say something.

Frozen Tissue Array Methodology, Applications and Benefits

Frozen tissue array is a methodology that is used in modern molecular and clinical research to analyze hundreds of tumor samples on a single slide. It allows a high throughput analysis of proteins and genes in a huge unit. It consists of frozen tissues where separate tissue cores are lumped together to allow simultaneous histological analysis. It has made it easy to streamline several research projects thus saving significant time. It also conserves precious reagents for analysis numerous slides that contain a single section per slide. It is an ideal screening tool that is used before

embarking on extensive research and analysis.

Preparation of frozen tissue array

Each product is produced using the state-of-the-art preparation technique by the use of the finest quality specimens. Upon excision, the tissues are then placed in liquid nitrogen and then sorted meticulously by an expert pathologist. Cores from 20 different tissues or more or with pathologically relevant tumors are then combined in a single block. With the use of unique staining methods, the quality of each
slide is selected. Tissues with a diameter of 2 mm from the region of interest
are sorted from frozen tissue OCT blocks by varying their freezing temperatures, see more here.

Features of frozen tissue array

Every product is designed to conform to the FDA guidelines and must meet the requirements of therapeutic antibody validation and vitro diagnostic device certification. There is a vast range of tissues in every array. The technique is suitable for both radioactive and non-radioactive detection. It combines arrays from variety human donors. Compared to paraffin-embedded tissues, frozen array tissue contains better antigen exposure.

Frozen Tissue array applications

The technique has been employed in various areas such:

  • Rapid screening of protein expression or novel gene against a large panel of tissues
  • Diagnostic and high throughput therapeutic analysis in antibody
    variations
  • Analysis of gene expression patterns
  • In situ hybridization and used together with immunohistochemistry
  • Novel gene and protein expression comparison
  • It is also an excellent approach in FISH-based experiments in the
    analysis of DNA. In summary, frozen tissue array provides an excellent target
    material for an effective study of RNA, DNA, and proteins.

Samples of DNA, RNA, and certain antibodies don’t perform optimally when used in pre-fixed paraffin-embedded tissues. However, they work pretty well when used in frozen tissue array. Again, the procedures that require fixation can be identified and conducted in an appropriate manner. This means it is possible for you to include a wide array of samples in your final analysis than when using the paraffin-embedded
procedure
The only drawback with frozen tissue array is that some cell morphology and tissue architecture distortion is likely to occur. This can be seen by comparing it with the sections from paraffin-embedded. Additionally, a limited number of samples can be embedded in one array. This is due to the fact that there may be a tendency of OCT compound cracking or bending particularly when samples are placed one millimeter apart.

Conclusion 

The invention of this technique has become a boon to many scientists from around the world. It has saved scientists and pathologists significant time when conducting several tests. It also has numerous potential applications in basic research,
prognostic oncology, and drug discovery.