COEP Technological University, Pune

A Unitary Public University of Government of Maharashtra

Department of Applied Sciences & Humanities
(School of Transdisciplinary Sciences & Management)
Wellesley Road, Chhatrapati Shivajinagar, Pune - 411005.

BIOLOGY FOR ENGINEERS - CLASSNOTES

UNIT V: APPLICATION AREAS OF BIOENGINEERING

Distributed Information Processing in Biological and Computational Systems

Biological systems, ranging from the molecular to the cellular to the organism level, are
distributed and in most cases operate without central control. Such systems must solve
information processing problems that are often very similar to problems faced by
computational systems, including coordinated decision making, leader election, routing and
navigation, and more. Over the last few years our ability to study and model biological systems
has improved dramatically. Using advanced sequencing technologies we can now determine
the composition of the genomes of hundreds of organisms. For specific cells and tissues we can
query the set of active genes, their expression levels, and how their responses change in
different conditions and over time. We can also determine which molecules within cells interact
and how such interactions are wired to form the control diagram regulating cellular activity.
Using this data we can build models of information processing within and between cells and
answer questions regarding the methods biological systems use to achieve their goals that were
out of reach even a few years ago. This data can also help us understand what computational
problems are being solved by biological systems and how, which in turn can lead to specific
algorithms that may also benefit computational systems.
Video: Distributed Information Processing in Biological and Computational Systems on Vimeo

Biological computing All biological

organisms, be it primates, snails, plants or
single-celled amoebas, sense their
environment and internal state, and process,
integrate and prioritise this information to
compute which action to take next. Figure
inspired on earlier work in Scheres and van
der Putten
(Reference Scheres and van der Putten2017).

Defense system in Yeast: The robust defenses that yeast cells have evolved to protect
themselves from environmental threats hold lessons that can be used to design computer
networks and analyze how secure they are (Computer scientists at Carnegie Mellon University).
Environmental “noise” is a key evolutionary pressure that shapes the interconnections within
cells, as well as those of neural networks and bacterial/ecological networks. The researchers
factored this into an established model for the evolution of molecular connections, resulting in
an algorithm that gives rise to a rich range of architectures found in biological, computer and
other types of networks.

It is said that this approach is particularly helpful in understanding how networks respond to
cascading failures, whether it be an overloaded power grid or a computer network being
overwhelmed by fake identities in a so-called sybil attack.

The generative model the CMU team developed can be used to tailor networks to the
environments in which they are expected to operate. These strike a balance between highly
connected networks that are efficient and fast but are prone to infections and cascading
failures, such as the Internet and its large service providers, and more sparsely connected
elements that are less efficient, requiring more time to relay information, but can better
tolerate failures and attacks, such as peer to peer networks.

That’s a balance that evolution already has achieved in yeast. A yeast cell has about 6,000
genes, of which 20 percent are considered essential — that is, if the gene is removed, the cell
dies. But Ziv Bar-Joseph, an associate professor in the Machine Learning Department and the
Lane Center for Computational Biology, said that view of what is essential and what isn’t
reflects how scientists study genes — by noting their effects on an organism when a gene is
removed — not necessarily the gene’s importance.
“The cell did not evolve to protect itself against the deletion of these ‘essential’ genes,” Bar-
Joseph said, noting that’s an event that doesn’t often occur in nature.
Rather, the fragility of genes, proteins and other cell components may reflect exposure to their
environment. Those that lie near the cell surface, for instance, can expect to encounter lots of
environmental stress, so the cell has evolved to tolerate the loss of some of them. Those
involved in DNA duplication, on the other hand, normally don’t experience that kind of
exposure to noise and so don’t have the same robust interconnections. That’s why the cell dies
if one of those genes is removed, Bar-Joseph noted.
Just as biologists study genes by knocking them out, one by one, computer scientists often
evaluate network security by removing a server and seeing how the network responds. But
Navlakha said that’s not always realistic; many attacks or failures of computer and electrical
networks can involve the loss of multiple, neighboring nodes.
To better understand the significance of how various networks are interconnected, the
Carnegie Mellon researchers, including Christos Faloutsos, professor of computer science, and
Xin He, a Lane Fellow in computational biology, modified the well-known duplication-
divergence model used to explain the evolution of molecular networks. The concept is that
gene duplication can result in two equivalent proteins that, over time, diverge to develop
specialized subtasks, while also maintaining common connections.
By adjusting the duplication-divergence model to account for the pressure of environmental
noise, the researchers developed a method that can be used to generate or evaluate the
interconnection, or topology, of networks that work in a variety of environments. A military
network, for instance, might not worry about malevolent viruses and noise because access is
restricted, while a wireless sensor network deployed over a wide area might need to tolerate
continual losses of random nodes.
At the same time, the evolutionary role of external noise might well prove to be an insight that
will enhance the understanding of biological networks, Bar-Joseph added.

A comparative approach for the investigation of biological information processing: an

examination of the structure and function of computer hard drives and DNA
Background: The robust storage, updating and utilization of information are necessary for the
maintenance and perpetuation of dynamic systems. These systems can exist as constructs of
metal-oxide semiconductors and silicon, as in a digital computer, or in the "wetware" of organic
compounds, proteins and nucleic acids that make up biological organisms. We propose that
there are essential functional properties of centralized information-processing systems; for
digital computers these properties reside in the computer's hard drive, and for eukaryotic cells
they are manifest in the DNA and associated structures.

Different spatial organisations of information

processing in biological systems.
Left: centralised information processing based
on a central dominant brain in primates
Middle: hybrid information processing in an
octopus that combines a central brain with
semi-autonomous information processing in its
arms.
Right: fully distributed information processing
with no central processing organ in plants

A descriptive framework is presented herein that compares DNA and its associated proteins
and sub-nuclear structure with the structure and function of the computer hard drive. We can
identify four essential properties of information for a centralized storage and processing
system: (1) orthogonal uniqueness, (2) low level formatting, (3) high level formatting and (4)
translation of stored to usable form. The corresponding aspects of the DNA complex and a
computer hard drive are categorized using this classification. This is intended to demonstrate a
functional equivalence between the components of the two systems, and thus the systems
themselves.

Both the DNA complex and the computer hard drive contain components that fulfill the
essential properties of a centralized information storage and processing system. The functional
equivalence of these components provides insight into both the design process of engineered
systems and the evolved solutions addressing similar system requirements. However, there are
points where the comparison breaks down, particularly when there are externally imposed
information-organizing structures on the computer hard drive.

A specific example of this is the imposition of the File Allocation Table (FAT) during high level
formatting of the computer hard drive and the subsequent loading of an operating system (OS).
Biological systems do not have an external source for a map of their stored information or for
an operational instruction set; rather, they must contain an organizational template conserved
within their intra-nuclear architecture that "manipulates" the laws of chemistry and physics
into a highly robust instruction set. We propose that the epigenetic structure of the intra-
nuclear environment and the non-coding RNA may play the roles of a Biological File Allocation
Table (BFAT) and biological operating system (Bio-OS) in eukaryotic cells.

The comparison of functional and structural characteristics of the DNA complex and the
computer hard drive leads to a new descriptive paradigm that identifies the DNA as a dynamic
storage system of biological information. This system is embodied in an autonomous operating
system that inductively follows organizational structures, data hierarchy and executable
operations that are well understood in the computer science industry. Characterizing the "DNA
hard drive" in this fashion can lead to insights arising from discrepancies in the descriptive
framework, particularly with respect to positing the role of epigenetic processes in an
information-processing context. Further expansions arising from this comparison include the
view of cells as parallel computing machines and a new approach towards characterizing
cellular control systems.

Storage of spatial environmental

information. Top: in the solid brain setting
of a plant root, environmental information
regarding the direction of a salt gradient
can be stored internally in the shape of an
auxin asymmetry. Bottom: in the liquid
brain setting of an ant colony,
environmental information regarding the
direction and shortest path towards a food
source is stored externally through a
pheromone trail.
Source: A review article by Saket Navlakha, Ziv Bar-Joseph Communications of the ACM,
January 2015, Vol. 58 No. 1, Pages 94-102
AI in healthcare

1. Surgery a. Micro dissections and access tiny areas b. Robert arm- brain and heart, absolute
accuracy c. Lessen complications and minimise blood loss d. All procedures can be stored in
digital media hence helps in Surgeon education and training.

2. Medical Imaging a. Support labour intensive image scanning and case triage by surfacing
valid insights to help Radiologists identify critical cases first b. Accurate diagnosis c. Health care
sector for patterns and algorithms

3. Disease diagnosis and treatment

4. Accelerated drug development a. Example, in 2007 a robot called Adam could combine
billions of data points and investigate the diverse roles of yeast. It identified 19 genes that
made up yeast and forecasted 9 new precise ideas. b. Another robot EVE, discovered that
triclosan, a substance present in toothpaste is efficient against parasites related to malaria c.
Accelerates medication making process and makes it cost efficient

5. Expanding access to healthcare a. Lack of radiologists and ultrasound technologists can

restrict access to proper healthcare in underdeveloped countries b. Take over some diagnostic
tasks. c. AI imaging may achieve an accuracy equivalent to people when screening for chest
xrays for indication of tuberculosis

6. Clinical decision making a. Faster response b. Can speed up diagnosis and reduce errors

7. Data collection and administrative tasks a. Doctors spend a lot of time doing paperwork and
documentation b. For administrative tasks, i. Prioritisation and schedule optimization ii. Prior
authorization iii. Clinical recording iv. Revenue management v. Medical record management vi.
Billing and claim process vii. Identify health plan viii. Medical benefits and services ix. Assist with
gathering of paperwork

8. Getting real time data a. Make critical therapeutic decisions more quickly and effectively by
using real time precise data. i. Reduce patient wait times ii. Improve preventive actions iii.
Reduce costs b. Support stronger physician patient relationships c. Patients will be more
involved in their treatments if this is made available through multiple devices d. Wearables i.
Monitor heartbeat ii. Step trackers

9. Providing virtual nursing assistants a. Keeping track of patient health metrics, prescription
usage and lifestyle choices b. Tracks a patient’s weight, blood pressure and other parameters. c.
Example- MOLLY

10. Research a. Gather data from numerous sources b. More precise analysis of fatal disease