Toward Personal Biodigital :

Bio Appstore, Voice Control Biofab, and Augmented Biology

When I think of biotechnology, the music “Biotech is Godzilla” by Sepultura always comes to my mind. Perhaps the Godzilla in the song provokes my inner dinosaur fanatic or maybe because of the roaring beat of the song that keeps slamming me like the new advancement in biotechnology. One thing for sure is that we have now passed the era where biotech was a Godzilla mainframe computer to the modern era where biotech is democratized, everywhere, and anytime like our personal computer.

Bio is the new Digital

Being part of MIT Media Lab’s Biosummit reminds me of the quote by Nicholas Negroponte, the co-founder of the place. Negroponte argues:

“Biotech is the new Digital”

as biological building blocks are becoming the new infrastructure for designing and building new gadgets, technology, arts, and business, in the same way, that digital system has been integrated seamlessly with our life. “Bio as the new Digital” paradigm gives us the modularized lego of biological system “biobricks” for building many applications as shown in the international genetically engineered machine (iGEM) [1], to the stunning bio-arts such as Adam Zaretsky’s works on doing human gene-editing as sculpting [2]. And also companies that apply synthetic biology to design and fabricate organisms from the ground up such as, Ginkgo Bioworks [3].

Family photo from the Global Community Bio Summit by David Kong

Digital is the new Bio

However, there is also the notion that “Digital is the new Bio.” This year, a team of researchers developed a new type of soft robot that has plant-like tendril, which can grows across long distances without moving its whole body using pressurization in a thin-walled vessel body [4].

This concept is inspired by the organisms that cover the distance by growing — such as vines, fungi and nerve cells, with the potential applications in search and rescue operations as well as medical applications. Beyond that, the bio-inspired technologies are becoming more and more common. Even one of the most complicated system such as human’s intelligence can be recreated (partially) using learning algorithm. Even though, the intelligent robots that pass the Turing test only demonstrates machine’s ability to express intelligent behaviors, which is far from the real human intelligence; The perception of robots as living creature is being more acceptance as Saudi Arabia recently grants the citizenship to robots [5].

Toward Biodigital

Therefore, as much as we are using biological elements as design elements, converting bio to digital; digital systems also gain new biological abilities from growing to learning and are becoming the new bio.

It is funny for me thinking about this recalling my peers at IBM computational biology group that have published paper around their studies of AI from the biological science perspective.

After seeing exciting stuff that people have been working on at the biosummit, It is becoming clearer to me that we cannot separate this two notions from one another as they have a close symbiotic relationship. The democratization of DIY (Do it yourself) electronic devices give rise to the DIY tools for manipulating the biological system, people have created a different kind of projects that do not necessarily get categorized since the makers are neither affiliated with the department of biology or school of engineering in the university. These projects are just at the intersection of two systems: bio and digital working together. Therefore, I would use the term “Biodigital” to represents the superposition properties of bio + digital system.

As the accessibility of biotechnology is now shifted from a time when it was like a mainframe computer, to now where it is reasonably accessible like a personal computer, we should be able to imagine a variety of the future possibilities out there. Even though, the prediction about the future is always off the mark as Thomas Watson, president of IBM in 1943 has said : “I think there is a world market for maybe five computers.” However, It is fun to think and prototype about it as I always believe in the process of prototyping the impossible things!

Voice Control Biofab

Since the race in human genome sequencing, I believe that the next breakthrough in biotechnology is the creation of a device that allows for the real-time reading, writing, and fabricating of biological materials. This kind of device will allow for the live modification of the living things in the same way that human edit computer code and see the sudden changes.

Historically, reading DNA sequence requires a lot of resources in term of the hardware and reagents. Now, the biotech company such as Oxford Nanopore Technologies had developed a pocket-size USB-powered sequencer called the MinION utilizing the nanopore sequencing approach that looks at the change of electrochemistry signal when DNA passed through the pores [6]. This device is part of the first wave of tools that democratize the process of reading DNA information allowing the process to happen outside the lab.

A pocket-size USB-powered sequencer called the MinION

For writing DNA and fabricating biological materials, researchers have developed various methods for assembling biologics. From developing inexpensive 3D printed microfluidics chip that facilitates DNA assembly[7]

DNA Assembly in 3D Printed Fluidics :

to the development of a portable on-demand biomolecular manufacturing using freeze-dried cell-free transcription and translation machinery, “which can be easily hydrated and utilized for biosynthesis through the addition of DNA encoding of the desired output” [8].

Portable Biomolecular Manufacturing :

The combination of this three parts (reading, writing, and fabricating) is the primary functions of the biological input/output system. This “bio i/o” system will have tremendous applications as input/output of computers are essentials to many software applications. For example, George Church has shared his imagination with me during the summit about the “wearable DNA sequencer” that can read surrounding organism’s information in real-time allowing the person wearing the device to know the species of his/her/their food or beware of the pathogens in the air.

Also, imagine the convergence of the bio i/o system and the intelligence system to enhance human’s capability; we might see a kind of closed-loop healthcare on-chip device that takes the biological information of a person to fabricate pharmaceutical compounds that are personalized to that person.

Beyond that, It is also interesting to think about different alternative ways in which human can interfaces with the “bio i/o” system. In a project I did with my friends Brandon Dorr, and Professor Hilary Harps, we explore the idea of voice control gene editing as a form of modern magical incantation. The incantation is a charm or spells created using words. For instance, the modern day fantasy “Harry Potter” has a “Colour Change Charm” where a character can change the color of the object by saying :

“Sunshine, daisies,
butter mellow,
turn this stupid,
fat rat yellow.”

In this case, the charm would change the color of a cat to yellow.

What if we can change the color of bacteria in the way that we cast spell on animal?

Expressing color through genetic engineering has been an area of interest by researchers. The Nobel Prize in Chemistry in 2008 has been awarded to the isolation of Green Fluorescence Protein (GFP) and the discovery of the gene responsible for the production of GFP. Since then, such genes that express specific colors have been used as the reporters for gene expressions.

In the voice-control gene editing project, we built a system that has syringes containing genes that would change the color of the bacteria to red (RFP), green(GFP), blue (lacZ). These syringes are connected to motors and computer that would activate when certain phrases are said. We built this prototype to explore the future of HCI, where the digital system mediates the complexity of the biological system, in the sense that the bacteria cells act as pixels that receive a command from the human voice.

The design of the voice control gene editing device

This project freaks many people out, which I think was cool! As it gives us a glimpse of the future of the biodigital world. In a gathering of the Minority Report futurists that I attended, one of my favorite conclusion is that

“Imagining dystopian is a child play. It is easy to think of different ways that the world might come to an end, but finding the positive side in the future is the real challenge that requires greater imagination.”

Bio Appstore

The spreading of smartphones decentralizes the creation process of mobile apps. The method of app making became a shared discourse that is no longer bounded by the specific type of job; students, business owners, artists, scientists, and people from all walks of life can now make apps and share them with others [9]. These apps are circulated and presented to millions of potential users through application store or “app store,” which serve as the space for showcasing new ideas and exchanging feedbacks; where the users can directly post comments for the app makers to see. Therefore, the app store does not only break down the bureaucracy of the app making by allowing anybody to submit their apps to the app store, but also breakdown the barrier between the users and the creator, creating the community where the ideas and knowledge flow in the circle.

Moving from the interaction between human and “bio i/o” system to a bigger picture. I believe that the platform for sharing practices is essential in the process of “bio is the new digital” paradigm. We have seen an open platform such as : iGEM that contains an extensive collection of standard biological parts, protocols, codes that have grown in number every years, Metafluidics — platform that decentralize the knowledges of microfluidics device, Dream challenge — open science, crowdsourcing platform for solving biological/medicine challenges, thriving in post-internet era.

Last month, Josiah Zayner, a practitioner of the biohacking community became the first person known to have edited his genes with CRISPR [10]. The process involved injecting CRISPR machinery with the guide RNA (gRNA) that target the exon of the Myostatin gene into the forearm. Myostatin inhibits muscle growth, so in theory, this edit should increase muscle mass of the person after the experiment [11].

Zayner said on his blog

“the point of this experiment is not whether the CRISPR gene editing changed my muscles(too early to tell). Or that the efficiency was 100% and better than anything available. The point is that we are on the cusp of humanity changing. This is the first of many people who will change their genomes. This will happen for medical reason, for science, athletics or maybe just because people wanted to or were bored.”

To extend this trajectory it is Interesting to think about the platform that would allow human to download genes that would change or alter their body like what Zayner did. This platform in somewhat similar to the concept of the app store, where download apps to enhance the capability their smartphones.

As I always do (prototyping weird stuff), I and the futuristic research group (Freak Lab, KMUTT) created “” a biological app store that allows people to submit and download genes as applications. So far, there are some speculative bio app ideas that have been posted. But, it is just the beginning. This project is no way close to finish, and I am always looking forward to collaborators and folks that are interested in this topic.

Augmented Biology

Beyond the relationship between digital and biological systems. The conversion between the two systems is also fascinating. The researcher at Autodesk Life Sciences has introduced the concept of “generative design for biology” [12]. In general, the generative design is a computational process that mimics biological evolutionary approach to design. This method is used for finding forms that best fit the design goal by generating a variety of forms or design choices and evolving them through cycle iterations. Autodesk Researchers can apply this bio-inspired generative design approach on the biological design challenge; the team developed a strategy to efficiently search the large possibilities for a genetic system built from combinations of genetic parts using iterative and interchangeable algorithm [13].‏ This approach bridges the gap and converts the product of computational evolution with the product of biological evolution.

Generative Design for Biology :

Beyond optimization, the conversion between biological and digital information can also have a practical application. For example, researchers can now create a 3D model of a human face by jointly modeling sex, genomic ancestry, and genotype [14]. The result of using a set of 20 genes showing significant effects on facial features can be used for criminal investigation and other applications. However, this research also raises an ethical concern around the privacy of the biological data, since the facial model constructed from a random DNA sample can be used to track down and search for the person.

Individuals’ faces compared with Dr. Shriver’s computer-generated DNA predictions. See more comparisons. Credit The New York Times; Images and renderings by Mark D. Shriver/Penn State University

To extend our thinking further, I would like to connect this notion of the bio-digital conversion with the prior notion of bio i/o system and purpose four potential use cases :

1) Redesign human face through generative algorithm and CRISPR

Base on the research that uses DNA to construct the face, it is possible to create an app that allows the user to take a picture of his/her/their face, and modify it in 3D (changing hair color, make the nose smaller, etc.). Then use the algorithm that constructs the face and the generative design approach to simulate the necessary steps needed to transform the current look of a person to the designed condition. Then create the CRISPR construct that is needed to inject to achieve the design goal.

2) Augmented Biology & Augmented Reality

The making of Dragog

Disney has developed a method that allows human to seamlessly interact with the digital character in the augmented reality platform [15]. It is interesting to also think about the blend of augmented reality and augmented biology. Imagine designing the future animal pet, we can create and use genetics engineering to modify certain body parts (this is a thought experiment, I am not suggesting that this should be done! ), but can also use AR to add digital body on top of it. For example, one might design a Dragog (a Dragon/Dog hybrid) pet. The person might add a gene that produces green pigment to turn a regular dog green, and also use AR app to add digital body parts such as horns and wings on top of it.

3) I want to eat a dinosaur leg!

At the futuristic research group (Freak Lab), one of the research focuses is on the future of food. The group has experimented with the variety of ways to make food in the future form the process of making personalized food in space [16] to a device that allows people to make food with their mind [17]. I imagine the process of augmenting the biological process of eating by laying digital information on top of it. For example, one might use an AR app to align the 3D shape of a stir-fried dinosaur leg on of the real chicken leg. I am curious to know how might it change the feeling of the person eating it.

4) Generative Microfluidic Design

The development of microfluidic methodology is novel for drug screening and biomolecular diagnostics [18]. This platform can be used for the conventional 2D cell cultures, 3D culture, and organ on chip, which offers a route to personalized medical care [19]. The open repository platform for microfluidic devices such as allows the sharing of blueprints and protocols among researchers. However, it can also serve as the holder of data set which can be used to train machine learning algorithm to extract feature of each devices in order to create a new one. The application of applying generative approach to microfluidics design is for the doctor and healthcare provider to personalize the design for diagnostic and testing device for each patients. For example, a patient with cystic fibrosis would require a module that simulate oxygen tension in cell, anaerobic module, antibiotic essay module, and cell culture module [20]. Thus, the generative model would design a new microfluidics device based on the combination of known blueprint in the data set for this patient.

What is not digital?

As much as I am excited about the notions that “Bio is the new Digital,” “Digital is the new Bio,” and the conversion between Bio and Digital, I would post my final question here: What is NOT digital? Normally, we would associate digital things with being virtual, artificial, and futuristic. Therefore, the opposite of digital is natural, tangible, traditional things. In this essay, we already explored how the natural and biological system is now becoming the new digital system. So what is left NOT digital is tangible and traditional things?

That is also not true. The works around tangible computing by Hiroshi Ishii’s Tangible Interfaces group demonstrate how a human can interface with the digital computer through tangible objects. Ishii and his group developed the idea of “Radical Atoms” to represent their vision of human interaction with future dynamic materials that are computationally reconfigurable [21].

Tangible User Interfaces by Ishii’s research group

Finally, the notion of Digital also expands to traditional things as well. Researchers have used technology transform and revisited classical knowledge and practices. For example, researches have used “Big data” approach in performing clinical research of traditional Chinese medicine [22], recreated a painting from a departed artist from the Renaissance period using machine learning algorithm [23], and much more.

The entanglement between digital system and everything else makes it very difficult to think about “What is NOT digital?”

Well, I think there is still one thing that is NOT digital? Professor Sha Xin Wei, the author of the book “Poiesis and Enchantment in Topological Matter,” have discussed this question with me a lot, and I have concluded that even though Bio is the new Digital, Life is NOT and should not be digital? Professor Xin Wei reminds me that there is something beautiful yet simple about life that in the core is incomputable, and I shall hope for that.

As I write this essay, I realized the social construction that forced humanity to believe that our power is in the ability to modify, design, and make things. However, I also think that the real power of humanity is the ability to critically think through decisions before taking those actions critically. I believe in prototyping and making of things that not only work, but also make people think, push the boundary of possibility, and explore different futures. I wish that this essay not only give us the glimpse of the of biodigital future but also serves as a reminder of our responsibility to nature as we manipulate them as the new digital. May the freak force be with you :)


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