biological engineering an engineering in the context of biology institute of biological engineering...

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





• 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









“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





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





1. A distinct branch of knowledge

2. Distinct practices/methods

Two Characteristics of a Discipline





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





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





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)









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


ENG

INEE

RIN

G D

ISCI

PLIN

E

Phar

mac

eutic

al

Biol

ogica

l Sys

tem

s





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





“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



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





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





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


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





•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





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





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”









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





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





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





A Fuzzy Photosynthesis Model for Tomato

Brian Center and Brahm Verma

Trans. ASAE 40(3):815-821, 1997





'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





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





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?





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.)





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





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!!!









To students

Mantra for a successful career:

Find your passionTry hard, hardestFollow your passion.

Steve Jobs:“Stay hungry, stay foolish”

Thank you





biological engineering an engineering in the context of biology institute of biological engineering...

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