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Biological EngineeringAn engineering in the context of Biology
Institute of Biological Engineering Western Regional Meeting
Utah State UniversityOctober 28, 2011
Brahm P. VermaThe University of [email protected]
“Emerging Discipline/Fluency between Boundaries"
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
• views on biological engineering• how I was motivated • the vision of biological engineering that led to the formation
of IBE• engineering in the context of biology should incorporate
such features as self-organization, emergent properties,
systems, etc.• a need to develop basic principles of biological engineering• couple of research examples• challenges for the future
Presentation goals
We stay in comfortable structures, travel on roads and in air reliably, communicate across the globe instantly, produce food and deliver water safely, see inside body non-invasively, monitor treatment remotely, innovate tools for science and new worlds creatively,… our life is so much freer from the drudgery of the past.
Just look around; engineer’s work is pervasive. Tomorrow’s technology-savvy, global economy is an engineer’s paradise.
Engineering… an enabling science and profession
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
“Engineering is a profoundly creative process. A most elegant description is that engineering is about design under constraint.
The engineer designs devices, components, subsystems, and systems and, to create a successful design, in the sense that it leads directly or indirectly to an improvement in our quality of life, must work within the constraints provided by technical, economic, business, political, social, and ethical issues.”
National Academy of EngineeringThe Engineer of 2020
Engineering… a creative process
Engineering is a combination of science and practical art learned from
• Scientific knowledge transforming theory as a means to operational ends
• Mathematical logic objective logic as a means to quantitatively predict
• Experiential knowledge from practical designinescapably unique and context-dependent by
domain of application
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Engineering
A Brief History
6000 BC – Canals, flood control, buildings
1818 – Institute of Civil Engineering; 1852 – Am. Soc. of Civil Engineers1847 – Institute of Mechanical Engineers1880 – Am. Soc. of Mechanical Engineers1884 – Inst. Elec. & Electronic Engineers1907 – Am. Soc. of Agricultural Engineers1908 – Am. Institute of Chem. Engineers
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
1. A distinct branch of knowledge
2. Distinct practices/methods
Two Characteristics of a Discipline
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
1. Science-based – relies heavily on a distinct body of knowledge based on a branch of natural science, and
2. Application-focused – draws from all engineering disciplines for designing solution applied to fulfill for a domain needs.
Classes of Engineering Disciplines
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Discipline & Application
Mechanical
Agric
ultu
ral
Food
Fore
st
Petro
leum
Aero
spac
e
Med
ical
Materials
Envi
ronm
enta
l
Chemical
Electrical
ECONOMIC USE - ENTERPRISE - APPLICATION DOMAIN
ENG
INEE
RIN
G D
ISCI
PLIN
E
Phar
mac
eutic
al
Adapted From Jim Dooley, IBE President, 2000
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
A Brief History – Biological Engineering
1930’s – E.O. Reed - Agricultural Engineering is based on the science of biology
1960’s – Agricultural Engineers were challenged to enter the world of living things
1968Mississippi State University
Undergraduate curriculum in Biol. Engr.Rose-Hulman
Biomedical Engineering DepartmentBioMedical Engineering Society (BMES)
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Personal motivation
October 26-28, 1987Academic Heads of Agricultural Engineers, OSU
Dr. Carl HallDeputy Assistant Director of Engineering, NSF“The Age of Biology – Impact of Engineering”
He said that basic engineering sciences are strong in physical sciences; they must equally be strong in biological sciences. If we have engineering based on physics then why should we not have engineering based on biology.
Mechanical
Agric
ultu
ral
Food
Fore
st
Petro
leum
Aero
spac
e
Biological
Med
ical
Materials
Envi
ronm
enta
l
Chemical
Electrical
ECONOMIC USE - ENTERPRISE - APPLICATION DOMAIN
ENG
INEE
RIN
G D
ISCI
PLIN
E
Phar
mac
eutic
al
Biol
ogica
l Sys
tem
s
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Discipline & ApplicationAdapted From Jim Dooley, IBE President, 2000
1. An application-focused engineering discipline with special knowledge and interest in problems related to biological organisms, materials, processes andsystems.
2. A biological sciences-based, ubiquitous application engineering discipline.
Biological Engineering Worldviews
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
“In physical science a first essential step in the direction of learning any subject is to find principles of numerical reckoning and practicable methods for measuring some quality connected to it.
I often say that when you can measure what you are speaking about and express it in numbers, you know something about it; but when you cannot measure it, when you cannot express it in numbers, your knowledge is of a meager and unsatisfactory kind; it may be the beginning of knowledge but you have scarcely in your thought, advanced to the state of science, whatever the matter may be.”
Lord Kelvin, 1883Brahm Verma
Biological Engineering – An engineering in the context of BiologyIBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
When do we know?
A first step of learning any subject is to find:
1. principles of numerical reckoning and
2. practicable methods for measuring some quality connected to it.
Lord Kelvin, 1883
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Simply, when do we first know we know
© Brahm Verma, July 15, 2002
Physics
Chemistry
Biolog
y
Scientific MethodsScientific Methods
Biological
Chemical
“General”
Use-Focused
Engineering Sciences
NatureNature
• Agriculture• Environment• Information• Marine• Medical• Pharmacy• Science•
Quantitative MethodsQuantitative Methods
Cultural ValuesCultural Values
Social
Economic
Politica
l
Designed Products, Processes & SystemsDesigned Products, Processes & Systems
“General” Engineering + Mechanical+ Electrical + Electronics+ Structural
Schematic Illustration ofPerspective of Engineering Disciplines
Design Methods
PHYSICAL SYSTEMS BIOLOGICAL/LIVING SYSTEMS
Static Adaptable
Fixed Self-organizing
Same for ever Autopoietic (self-making)
Cause and effect Pattern, structure, process
Relationship among static components (crystal)
Relationship is among processes
Structurally rigid and organizationally closed
Structurally open but organizationally closed
Stable near equilibrium Stable far from equilibrium
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Physical versus Biological Systems
Discipline & Application
Mechanical
Agric
ultu
ral
Food
Fore
st
Petr
oleu
mAe
rosp
ace
Biological
Med
ical
Materials
Envi
ronm
enta
l
Chemical
Electrical
ECONOMIC USE - ENTERPRISE - APPLICATION DOMAIN
ENG
INEE
RIN
G D
ISCI
PLIN
E
Phar
mac
eutic
al
Biol
ogica
l Sys
tem
s
Adapted From Jim Dooley, IBE President, 2000Modified Brahm Verma, 2011
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
•Agricultural Engineering departments added “bio” to their names
• Other engineering programs introduce biology in their disciplines
• Nearly 35 new Biomedical engineering departments formed• 1995 – Institute of Biological Engineering
within ASAE• 1998 – Institute of Biological Engineering
become an independent society
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
The 1990’s
OBJECT
“. . . shall encourage, in the broadest and most liberal manner, interest and inquiry in biological engineering, fostering international cooperation among engineers, scientists, technologists, and allied professionals . . .”
The Institute of Biological Engineering
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
IBE Established, June 1995
A Living System Perspective
Include appropriate mathematical sciences for non-mechanistic, post-Cartesian understanding of living systems.
• Combine reductionism and systems approach• Combine stability and fluidity to change• Combine structure, pattern and process of organization for self organization/design • Combine boundaries and fluency across boundaries • Combine numeric and non-numeric patterns in the mathematical language• Similitude across object-levels (nano- to eco-level) must deal with “emergent properties”
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
One feature of Biological Engineering is the ability to consider the entire system (of internal and external influences) on the actions of living things.
To avoid having to determine specific responses of each living thing to these influences, it is important for Biological Engineers to understand the connections (syllogism, similitude, fractal natures, or other descriptors) among various levels of living things. Information known about one level should, in many cases, be generalizable to other levels, as well. It is important, therefore, for
Biological Engineers to discover basic principles that can guide an engineering approach to utilization of biology for useful purposes.
Art Johnson, U of MD, 2010
© Brahm Verma, July 15, 2002
Physics
Chemistry
Biolog
y
Scientific MethodsScientific Methods
Biological
Chemical
“General”
Use-Focused
Engineering Sciences
NatureNature
• Agriculture• Environment• Information• Marine• Medical• Pharmacy• Science•
Quantitative MethodsQuantitative Methods
Cultural ValuesCultural Values
Social
Economic
Politica
l
Designed Products, Processes & SystemsDesigned Products, Processes & Systems
“General” Engineering + Mechanical+ Electrical + Electronics+ Structural
Schematic Illustration ofPerspective of Engineering Disciplines
Design Methods
DevelopBasic Principles
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
How do we represent bio-complexity?
Quantitative representation of biological processes requires many approaches
Multi-value set theoryFuzzy LogicSoft computingNetwork theoryStatistical methods Dimensional AnalysisTheory of SimilitudeModeling
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
LOTFI A. ZADEH AND BRAHM VERMA AT THE FIRST ANNUAL MEETING OFTHE INSTITUTE OF BIOLOGICAL ENGINEERING, AUGUST, 14, 1996, PHOENIX,AZ
LOTFI A. ZADEH AND BRAHM VERMA AT THE FIRST ANNUAL MEETING OFTHE INSTITUTE OF BIOLOGICAL ENGINEERING, AUGUST, 14, 1996, PHOENIX,AZ
Lofti Zadeh and Brahm Verma
First Annual Meeting of IBE, Phoenix, AZ - August 14, 1996
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
A Fuzzy Photosynthesis Model for Tomato
Brian Center and Brahm Verma
Trans. ASAE 40(3):815-821, 1997
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
'Fuzzy logic' reveals cells' inner workings
Living cells are bombarded with messages from the outside world -- hormones and other chemicals tell them to grow, migrate, die or do nothing. Inside the cell, complex signaling networks interpret these cues and make life-and-death decisions.
Unraveling these networks is critical to understanding human diseases, especially cancer, and to predicting how cells will react to potential treatments. Using a "fuzzy logic" approach, a team of MIT biological engineers has created a new model that reveals different and novel information about these inner cell workings than traditional computational models.
MIT News, April 3, 2009
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Logic-based tools for systems biology
Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli Authors: Melody Morris, Julio Saez Rodriguez, David C. Clarke, Peter K. Sorger, Douglas Lauffenburger
We introduce constrained fuzzy logic to systematically compare interaction networks constructed from the literature or databases to experimental data of activities of many proteins in a biochemical network under different conditions of cellular stimulation and perturbation.
PLoS Computational Biology, March 3, 2011
log (Df/Ds)
-4 -3 -2 -1 0 1 2
PR
or
DR
0
1
2
3
4
5
6
ProliferationDifferentiation
PR
= P
rolife
rati
on
Rati
o
DR
= D
iffere
nti
ati
on
Rati
o
Df = Characteristic diameter of material featureDs = Diameter of the cell type
Cell typesrMSC mNSChMSC rNSCrBMSC rbMSC
Scaffold surfaceNanotubeHoneycombElectrospun fibers
Relationship between structure architecture and cell fate
Structure architecture =
Cell f
ate
=
From William Kisaalita, UGA
2D and 3D Cell culture
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Essential Concepts for Biological EngineersArt Johnson, Biological Engineering 3(1)3-15, 2010 ASABE
Survival and Reproduction of the Genes
Modularity and Incremental Change
Form is Related to Function
Environment Influences Outcomes
Physical Limits cannot be Exceeded
Energy, Order, Entropy, and Information
Reversible Chemical Reactions
Molecular Shapes & Chemical Mass Action
Osmosis
Redundancy & Alternative Pathways
Adaptation Requires Energy & Resources
Competition for Limited Resources
Antagonistic Mechanisms Give Precise Control
Optimization Saves Energy
Directed Evolution
Analogical Thinking
Looping and Successive Approximation
Reliability Curves
Circulation Provides Immediate Availability
Proportional Plus Derivative Sensors
Weber-Fetchner Law
Young’s Principle
Hagen-Poiseuille Formula
The Law of Laplace
Class 3 Levers
Additional Concepts?
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Historically, engineering sciences have evolved from the need to design practical systems
Civil Engineering – the oldest need for designing civil structures, roads, waterways, etc.Mechanical Engineering – for designing blast furnaces for processing iron ore, machinesMining and Materials Engineering – designing for the need to extract raw materials from the depth of the earth and producing new materialsElectrical Engineering – need for producing electricity (energy) and its distribution to power machinesChemical Engineering – need to design for changes in materials during manufacturing operations (heat and mass transfer, reaction kinetics, etc.)
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
From specific applications to general principals
IBE’s vision is to bring professionals from these domainsfor identifying basic principles of biological engineering
•Bio-Materials•Bio-Chemical•Bio-Physical•Bio-Informatics•Computation Biology•Synthetic Biology•Bio-Medical•Bio-Agricultural•Bio-Systems•Systems Biology
Basic Principals
ofBiological
Engineering
Biological,Physical,Chemical,Ecological,
MathematicalSciences
Evolutionary path for BE and IBE
We stay in comfortable structures, travel on roads and in air reliably, communicate across the globe instantly, produce food and deliver water safely, see inside body non-invasively, monitor treatment remotely, innovate tools for science and new worlds creatively,… our life is so much freer from the drudgery of the past.
Just look around; engineer’s work is pervasive. Tomorrow’s technology-savvy, global economy is an engineer’s paradise.
Biological Engineers must prepare for this future.
Engineering… an enabling science and profession
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Engineers, over the centuries, have replaced work of humans by machines; now the time has come for work of machines to be replaced by biological organisms and systems.
Concluding Thoughts!!!
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
Brahm VermaBiological Engineering – An engineering in the context of Biology
IBE Western Region Conference, Utah State University, October 28, 2011, 2005
The Institute of Biological Engineering: “Biology-Inspired Engineering”
Faculty of Engineering The University of Georgia
To students
Mantra for a successful career:
Find your passionTry hard, hardestFollow your passion.
Steve Jobs:“Stay hungry, stay foolish”