Juliana & Fiammetta
Fiammetta: I’ve been reading Juliana’s text from the point of view of a non-expert. What I’d like to do is to “decrypt” making it easily understandable, to raise awareness about worldwide initiatives to fight the pandemics, even among undergraduate students!
My idea is to start from Juliana’s text and create short, digestible pieces of information and illustrate them to make them more clear and compelling, and create a short visual lesson.
Juliana is now working on a series of sketches to represent each “mini chapter”. Here are some notes I took while discussing with her about the possible visualizations.
Synthetic Biology against the Pandemic
Juliana: Synthetic biology is such a versatile area, last year there were many initiatives around it to combat COVID19! That is why I want to bring you the ones that I found most interesting in the area of diagnosis, therapy, and prevention that were developed by undergraduate students for the largest International Competition that surrounds Synthetic Biology, Igem. Go for it!
F: IMAGE: Juliana in a lab coat, talking and introducing the topic.
Rapidemic (Netherlands Team)
J: During the first weeks of the pandemic and we still saw very clearly the lack of diagnostic tests in different countries, among the most affected third world and developing countries for not having access to the infrastructure and reagents that require PCR diagnostic tests.
F: IMAGE: Person positive to COVID19 (e.g. having the virus “hidden”, masked in her). This should represent the main problem; the following illustrations will illustrate alternative solutions.
J: That is why Rapidemic offers a Diagnostic option based on nucleic acids (which are the tests that have the highest sensitivity) engineered from generic kits with small and accessible interchangeable pieces of DNA called primers (which are specific for each pathogen) with the great potential to offer diagnostic solutions.
F: IMAGE: the actual kit from Rapidemic. Use the reference with different tubes of different colors: The greener the liquid, the more likely the positivity
But how does it work? All organisms have unique DNA sequences that can be identified and employing enzymes, these enzymes multiply DNA to obtain many copies, this is how most diagnostics work at the molecular level. PCR has this principle, however, these copies of the pathogen of interest can only be visualized by very expensive and specialized equipment that detects this signal of fluorophores in these sequences, so this group devised a way to detect microorganisms in a sample in which they find the DNA of the pathogen of interest and through DNAZymes generate a colorimetric reaction visible to the human eye !!!! Amazing, right?
F: IMAGE: ??? Here Juliana will help me to visualize something!
For more information visit:
MotBox (USA Team)
J: This therapeutic solution is inspired by origami and uses Artificial Intelligence (AI) to create mRNA sequences (which is responsible for carrying the message to synthesize proteins, including antibodies) from a virus. This AI has the form of the antigen (which in our case would be the covid19 virus) and generates an mRNA sequence with which antibodies could be generated to fight the disease. The antibodies work by binding to the protein S of the virus, which is The entry key for the virus to the cells it infects, obstructing the entry of the virus and at the same time marking the virus so that the cells of the immune response can destroy it.
F: IMAGE: Need Juliana’s input here, but for sure the origami reference is a promising one and as we can transform it in an understandable visual analogy.
For more information visit: https://2020.igem.org/Team:Harvard
ACT Technology (Israel Team)
J: This group had a preventive approach to the disease that aims to reduce transfer by methods other than face masks and gloves that cause contamination or chemical agents that are usually abrasive to human skin. This is how this group designed a hydrogel-based skin screen that contains proteins that act as "decoy proteins", the objective of which is to block the infection of host cells by the SARS-CoV-2 virus from bacterial spores. Bacillus subtilis (BSSD). Thus, when bacillus produces bait proteins, it begins to sporulate and bind the bait proteins to a microgel-pearl that we can spread on our skin!
F: IMAGE: The gel should be the main character here, with a “zoom in” on what’s happening inside it, at a microscopic level, when the skin gets in touch with the virus.
For more information visit: https://2020.igem.org/Team:Technion-Israel/Description
Taking a breath!!!
This year has been one of the changes for everyone, that is why I took a break from the laboratory and came to Laguna de Tota, the second largest lagoon in Latin America and a beautiful place.
And just like other big lagoons and uninhabited places, the legends of cryptid beings that inhabit these places abound, and the analogy with science is always inevitable! So I want to talk a little about metagenomics, the technique with which we microbe hunters look for microorganisms with extraordinary qualities, BigFoots bacteria, Nessies yeast, and microscopic marine snakes.
Before metagenomics studies and the discovery of wonderful creatures and where they live, researchers had to cultivate microorganisms, which grew in a laboratory environment, and once there they were studied. However, this assumed that we could cultivate all microorganisms and it is estimated that only 1% is cultivable because we do not know their nutritional needs, live in symbiosis with other living beings, or are simply very labile for an environment such as the laboratory.
Thus, after the sequencing of the human genome, interest in microorganisms and the area that we call metagenomics was developed, this area basically studies all the genetic material obtained from environmental samples and from there, identifies all the genomes (living organisms) that are found there and classify them. This involved the discovery of microbial communities with various emergent properties that could be exploited for different applications.
Among them, metagenomics researchers discovered that we were missing out on dragon microorganisms (which could withstand temperatures up to 340 C), Yetis bacteria (which develop mechanisms to protect themselves at temperatures down to -12 C without freezing), Microscopic Marine Snakes (capable of growing at very acidic pHs in lakes inhabited by other living beings) among other cryptid microorganisms that have been exploited for applications in medicine, biotechnology and especially bioremediation. These cryptid microorganisms eluded us for a while. But thanks to new technologies these are being unveiled and used for our benefit!!
Synthetic biology entered our homes!!!
Today I want to show you what the products made with microorganisms that Fia showed us in her illustration!
And there was light! For bacteria, these lamps are made with microorganisms, the initiative of Ecovative Design made with Mycelia (which is basically the vegetative part of a fungus).
Another of the materials that can grow thanks to Synthetic Biology are the walls of a house! This is what the HyFi tower looks like, made with mycelia and recycled organic material exhibited in 2019 at MoMA.
And clearly the furniture in the house could also be made with microorganisms, this is the initiative of Ecovative Design that brings a proposal of cozy furniture for a sustainable house.
Microorganisms are also invading the closet, Brewed Protein is a company that makes garments made from protein materials produced from plant-derived biomass using Spiber's proprietary fermentation process. With which there have been numerous collaborations with brands such as Adidas, The North Face and even the designer Yuima Nakazato made a collection with these fabrics for Autumn 2019.
Continuing with the closet, the "ethical leather" could not be absent. This is the idea of the company Bold Threads that offers bags, gloves and shoes made from leather made by engineered fungi.
And we also ferment our shoes, the Genomatica company, in collaboration with some big companies that make shoes to produce BioMylon free of petrochemicals takes old fishing nets, textile scraps and other forms of nylon waste and transforms them into new yarn that is so good. as virgin raw material.
And now let's go to the kitchen, Impossible Food, in which they produce the heme group with yeast to give the flavor of vegetable meat that of an animal, this in response to contamination with ammonia, de-killing, use indiscriminate use of antibiotics and animal abuse in this food industry.
This week I uploaded a first version of the small animation we created with Juliana. It is a recap of all things we can today do with synthetic biology: the list was put down by Juliana as well as the first sketch which served as inspiration for the animation. Next step involves adding a music background or some kind of audio design.
Our collaboration is now half way, and we are discussing about the next steps!
Hope in the form of a Vaccine!
This week with Fia, we are still very interested in COVID-19, which as we said brings us a break! Fiametta interviewed some very important researchers in the area and collected very important information and I wanted to show a little how this new type of vaccine works, which promises us a very high efficacy in its first preliminary data from phase III!
With Juliana we decided to take a break from synbio for one week - we will go back to it next Monday. Just for this week we would like to talk about vaccines, as the news of Pfizer's vaccine 90% efficacy spread.
Without writing too much, I will share three graphic recordings, a form of visual note taking, about vaccine testing in times of coronavirus. The information is coming from three scientists working on vaccines: Anne Moore (UCC Cork), Jeremy Rossman (University of Kent) and Zania Stamataki (University of Birmingham) answering three main questions: how fast are we going, what kind of vaccines are being tested (The Pfizer / BioNTech vaccine kind is #4, very promising and never done on a global scale), and how are people reacting.
This week I took a Break from the world of Bacteria and art to talk about a topic that has knocked on everyone's door this year, the coronavirus. Unfortunately, my country, Colombia, has just reached one million cases and 30,000 deaths from this disease. So today I wanted to bring a little hope.
I compiled the vaccine initiatives that exist around the world and I wanted to show you in this infographic the stages of vaccine approval and the types that exist so that we understand a little and see that light at the end of the road.
During this week Juliana sent me several examples, links and images of synbio items. I was very surprised by the looks and quality. They go from lamps to food, from brick walls to dresses. In the spirit of showing at a glance all this great variety of possibilities, Juliana had the idea of condensing what they have in common is that being everyday objects they can be found in one single room.
Juliana sent me a sketch of the visual she was imagining (image 1) and suggested to me a title for the piece we are preparing: “Synthetic biology entered our homes!”
I have been playing a bit with the sketch by Juliana and I produced the first visual (image 2). As I mentioned in the previous post, I was thinking about ways to animate it, and I added motion guidelines for the synbio objects: dresses, sugar in cookies, Impossible © meat, lamps of every shape and color, brick walls, furniture.
The first color palette I chose was supposed to be “cozy” and homely (image 3), because I didn’t want to associate bacteria with a scary or too futuristic visual scheme. But looking at it a few days later I realized I wasn’t very happy with it and I thought, well, I can give myself permission to go a little fluo because, bacteria! So I changed the colors of the illustrations (image 4) and I’m now working on animating the synbio items.
Synthetic biology entered our homes!!!
Synthetic biology is an area with mind-blowing applications. Biohackers in conjunction with bio-designers have brought this Sci-Fi-like area into our homes. As we know most of the things we use in our daily lives demand a great expenditure of energy and resources. And, these researchers-artists-creators understood that we must not deprive ourselves of these comforts, but rather that we must create sustainable solutions that replace them.
For this, bioinspiration in systems found in nature plays a central role. Thus, the manipulation of organisms for our benefit and that of the planet with initiatives that reach our home are increasingly close to all of us, this thanks to the fact that synthetic biology is also an area in which all its members seek the democratization of the use of all its tools with open source elements, development of cheap tools in what they have called the Frugal Science aspect and in the constant search for increasingly sustainable and healthy applications.
The first of the applications I want to talk about is one of the most ancient that we have applied, food! The fermentation processes have been extensively studied and for centuries they are being refined, this is how the Brazilian company Amyrs wants to come up with organizations specialized in the fermentation of the RebM compound in stevia and its obtaining process to give options of a sweetener that mimics the true taste of sugar but calorie-free. This to give a range of candy, chocolate, and cake options to the 450 million people with diabetes around the world. Another of the great applications in the food industry is the Impossible Food, in which they produce the heme group with yeast to give the flavor of vegetable meat that of an animal, this in response to contamination with ammonia, de-killing, use indiscriminate use of antibiotics and animal abuse in this food industry. And of course, it is healthy and sustainable food made by microorganisms is also served in plates made free of plastic derived from petroleum and if made with fungi and bacteria that biodegrade. Isn't this amazing?
And going from the table to our closet!! Did you know that the dyes in jeans are derived from petroleum and each pair of jeans we use uses more than 450 liters of water to be produced? Synthetic biologists in search of a more sustainable fashion industry have been inspired by the diverse colors of nature to color fabrics with pigments produced by fungi and bacteria as well as to create beautiful and elegant pieces with bacteria capable of forming biofilms that function as fabrics for clothing or even leather for clothing, shoes, and accessories.
Finally, I am going to sit on some furniture made with microorganisms!!! In my house made with mushroom bricks to end the day!! Incredibly, a whole space can be filled with things made by microorganisms.
During this week Juliana and I have been talking about everyday use of bacteria as initiative in the synbio field. I was astounded to learn that bacteria can be used for daily applications and in creating objects such as textiles, food and decorations. We have been talking about making an illustration representing in one piece several possible bacteria-based items. I think it’s a funny and light idea, also useful to escape the current heavy climate.
So we have been discussing how to highlight the bacteria-based items, not only with Juliana but also with Kate. Among the ideas that came up, there was a classic visual hyperlink structure and a point and click game structure. One thing that I begin to appreciate a lot about The Bridge is that there is no pressure to decide one thing and then go for it, as a lot of space is left to experimentation and to enjoy the creativity process. So once we exchanged mail with Juliana I began to play around with the idea of an animated illustration. As I was quite interested about the idea of books made with bacteria, I began drawing a woman reading a book, imagining it as just a part of a bigger animation. To animate her I used the very old technique of rotoscoping, meaning that I filmed myself browsing the pages of a book and then traced some lines representing the movement in a digital drawing. I came up with what is called “boiling lines”, which are basically little deviations from the actual line; they used to be a “mistake” done by people rotoscoping back in the days (the technique has been used since the beginning of the XX century). But since then boiling lines have become an artistic choice often used by animators, to give elements more life. And speaking of life, I thought that boiling lines could be a nice idea to highlight bacteria-based objects in a complex illustration. Their movement is exactly the one I imagine in a petri dish! So for the next week I think I’ll explore this idea. What is still to be discussed is, since we are headed for a science communication and outreach piece, how to communicate the “how” and “why” of bacteria-based manufacturing, and this is going to be the next step.
As a scientist, it is easy to think about pragmatism and how you can explain to your colleagues what you do in a presentation with a piece of data that is ultimately translated into a number. However. In the last decade, the first generations of professionals who are active in art, design, and biotechnology are emerging. I see that these people, in addition to considering the pragmatic or creating theories that are intrinsic to scientists, involve aesthetics in their work. These things have made scientific divulgation to develop the interest of the public and the dialogue; Researchers or artists who understand this concept are more creative and it is these types of people who are now democratizing science, creating global networks and inspiring others to do increasingly incredible projects in which the barrier of knowledge and the imagination is blurred.
Seeing the work of Fiammetta and her desire to divulgate through her art has been an incredible experience, I have seen the various areas it covers and how it explains for people like me that are not familiar with physics to understand phenomena that seem complex and distant to our understanding. I show her a bit of our work in SSLAB what and why we do with bacteria (Image 1, Image 2). We also talk about how synthetic biology was created from the natural step of manipulating DNA once the humans understand natural systems and how synthetic biologists work at the boundary between engineering and biology to reassemble parts of organisms to perform new functions, recreating unnatural chemical systems to reveal emerging properties of the original systems and give information to predict the behavior of the cells in which DNA was synthetically introduced. We are certainly very eager to start this journey by joining Synbio to art.
“If you can’t explain what you’re doing and why you’re doing it to any intelligent layman, that really means that you don’t understand it yourself”
I have been working in science communication since almost 10 years now, but before that, I wanted to be a researcher myself. Whilst I’ve always loved drawing and reading comics, I was not sure about the research field I should specialize in. Eventually I wrote my PhD thesis about bistable perception, that is to say the perceptual phenomenon that takes place in the brain when we see ambiguous images. Ambiguous images are a specific kind of optical illusion that you have surely witnessed, where the same image can be interpreted in two different ways, like the lady who is young and old at the same time, or the animal which is a rabbit and a duck simultaneously. Our brain cannot decide which interpretation is the “right one” - because there isn’t one - and goes back and forth interpreting the images in one way or another, changing the “interpretation” every few minutes.
Just after discussing my thesis, I decided not to pursue a career as a researcher but rather to dive deeper in my interest for drawing and comics, orienting it towards science communication, thus creating a science comics project, ERCcOMICS and founding a science illustration agency, RIVA Illustrations. But this is another story.
The first images that Juliana sent me where pictures of petri dishes representing artworks and patterns (I even discovered an annual competition of bacteria design!).
This images reminded me, in a way, of my thesis. They made me think of these biological paintings are like ambiguous images: you can interpret them simultaneously as artworks and as a demonstration of the scientific concepts behind Juliana’s work in synthetic biology; art interpretation, science interpretation - both of them are valid. What I would love to do now is to better look at the “science interpretation", to better understand the concepts and the implications of Juliana’s work, and to incorporate it in the “art interpretation” that I will try to give. The back and forth between these two is “The Bridge”!