5th December 2019
Hasan Baig is an Assistant Professor in the Department of Electrical and Computer Engineering at Habib University. He holds a PhD from the Denmark Technical University, where he worked on developing methods and tools for the analysis, verification and synthesis of genetic logic circuits. He has previously worked in various industries of Pakistan, South Korea and the United States as a Hardware and Design Engineer, specialising in system on chip development. He owns patents of the fault-tolerant FPGA architecture and has to his name, several published articles in reputable journals, conferences and workshops.
In his session, Dr. Baig introduced the public lecture series audience to genetic engineering, specifically by discussing genetic circuits in comparison to electrical circuits. He broke down the idea of genetic circuit systems by first elaborating on the composition of programmes that work through electrical systems. Programmes are purposed so they can follow a set of command instructions as input and execute operations towards an output. Embedded systems as in smart phones are an example of electrical systems on chip, designed to perform desired functions through the cell device. The phenomenon Dr. Baig brought to light was the possibility that electrical components in embedded system circuits could also be biological in nature. Genetic engineering has been an area of research that has conceived programmable genetic systems, which includes circuits comprising of programmable DNA.
Dr. Baig gave a very basic overview of how a genetic circuit works by contrasting it alongside the electrical circuit. He pointed out that in the biotech field, embedded systems notably see application in pacemakers and chemotherapy, where high radiation aims to destroy harmful cells. However, it also causes other cells to be compromised, resulting in side effects like hair loss. In these cases genetic systems may prove more efficient. Genetic circuits, though similar to electrical ones, have different inputs and outputs. For instance, in the treatment of defective cells if the circuit is satisfied in its multiple conditions of i) a living cell and ii) a defective cell, it can then as an output release a protein to destroy them. As opposed to electrical circuits, the genetic ones have DNA components, varying inputs and outputs depending on type of protein and high signal interference owing to molecule movement. It is of note that while we know the right conditions for electrical circuits, from the appropriate temperature to type of component, it is difficult to determine in genetic circuits as its preconditions may vary depending on the scenario.
The design flow of genetic circuits requires more detailed specification. Dr. Baig highlighted some tools that are helpful in this regard, for instance genetic programming can be coded in a systems biology markup language called ‘spml 5’. Much of his work comprised of developing tools and programmes to analyse different genetic models through simulations, optimization and synthesis optimisation technology mapping.
Working in virtual experimentation where models were tested through real-time interaction with its genetic systems, Dr. Baig helped implement an improved system. They designed a specialised labortary environment for experimenting and observing genetic models as well as a tool, the Dynamic Virtual Analyzer and Simulator (DVA-Sim) that is able to generate virtual tools in suitable to each individual genetic model. The DVA-Sim is an automated analysis and verification system that can check models functionality in varying parameters to determine the level of input it requires. So the threshold value or minimum concentration of a protein that is needed by a genetic model under changing conditions can be tested for through the DVA-Sim. Dr Baig reported he was able to apply the algorithm he made on 15 different models at the University of Utah and MIT. He named another one of their applications, the GeneTech is a technology mapping tool that along with the DVA-Sim is available for download online and has received encouraging response. Combining the two tools in their functionalities is the next goal for Dr. Baig and his team.
Towards the end he gave credit to all the collaborators that are making possible advanced technology like genetic circuits a more concrete reality. Along with bio technologists and experts from institutions in South Korea and across the world, he also listed a group of Habib University students that have been assisting him in the ambitious projects. Dr. Baig introduced a unique side of the advancing field of engineering that shows a lot of potential for changing how we live life and in effect, the world. If DNA can be programmed, then there are a lot more revolutionalising technologies to be expected.