Biotechnology and Computing

BIF 101 – Fall 2007

Debra T. Burhans, Ph.D.

Canisius College

burhansd@canisius.edu

What is Biotechnology?

A general definition of biotechnology is the use of biology or biological processes to develop helpful products and services. In this sense, humans have been using biotechnology (biology to create products) for centuries, for example in the breeding of farm animals for offspring with desirable traits and the use of yeast to make bread, beer, and wine. A modern definition of biotechnology is the set of biological techniques originally resulting from basic research, specifically molecular biology and genetic engineering, and now used for research and product development. Alternatively, biotechnology can be defined as the scientific manipulation of organisms at the molecular genetic level to make beneficial products.

http://www.csrees.usda.gov/nea/biotech/biotech_all.html

Biotechnology

• Research to develop new technologies• Includes the application of information developed by that

research to the development of commercial products• Includes all of the business activity that is required to bring

these products to market• Applied in fields from agriculture to aerospace engineering

Bio-technology

• Many high-throughput techniques have been developed that enable biologists to generate tens, even hundreds of thousands of data points with a single experiment

• Some examples include cloning, PCR, sequencing and microarrays

Molecular Biology Tools

Restriction Enzymes

The

• Molecular “scissors”

• Create blunt or sticky ends

• Used singly or in combinations to cleave DNA sequences

Gel Electrophoresis

Blotting

Hybridization

• Labeled fragment of DNA (probe) is allowed to base pair with sample

• Sample DNA may be immobilized on a membrane or may be contained in wells

• Microarrays are small chips containing thousands of samples that are frequently used in today’s biology laboratories

Expression Data

• The context (e.g. tissue type, stage of growth of an organism, etc) of a cell determined its pattern of gene and protein expression

• Expression patterns are measured using microarrays• Each spot on a microarray attracts and binds particular

sequences• The amount of sequence bound to a spot can be quantified• Initially gene expression arrays, now there are protein

expression arrays• “Genome on a chip”, can have tens of thousands of spots on

one chip

Affymetrix Oligonucleotide Chip

Microarray Data

cDNA “spotted” Microarray Chip

Atlantic salmon cDNA microarray

Microarray Data

Microarray Data in Spreadsheet

• Spreadsheet file

Cloning

• General strategy: use a “biological machine” to do the work• Isolate the piece of sequence you want to copy• Insert the sequence into a molecule that can replicate itself• Insert that molecule into (often) a bacterium that multiplies

quickly• Each new generation of bacteria contains copies of your DNA

Making Copies - cloning

The Polymerase Chain Reaction

The reaction is placed in an automated thermal cycler.

Reactions typically have three steps:

- denaturation to separate the DNA strands- approximately 95oC

- annealing to permit primers to bind to target- approximately 60oC- actual temperature depends on composition of primers

- polymerization to permit the enzyme to copy the template

- approximately 72oC

This is repeated 30 or more times.

Making copies - PCR

Sequencing present and future

• Not so long ago it took a year to sequence a few hundred bases, now an entire genome can be sequenced in a day

• The newest technologies will enable sequencing of genomes of individuals – leading the way towards “personalized medicine”

• The ability to easily amplify a DNA sequence using PCR, creating millions of copies, has led to the use of DNA evidence in crime fighting

• The more genomes we sequence the more we learn about how different organisms are related

• The generation of sequence data has far outpaced our ability to analyze the data (at this point in time)

• Data is immediately recorded in a computer and can be displayed as an electropherogram

DNA Sequencing

Modern DNA sequencing is done with an automated sequencer.

DNA sequencers use new technologies:

-fluorescent tags for each base-permit machine basecalling

-dideoxy chain termination chemistry-efficient and amenable to automation

-capillary electrophoresis-permits analysis of small samples

-direct output to computer-minimizes errors and speeds process

Sequencing: figuring out what the letters are

dideoxy chain termination

Sequencing

• Sequences are passed through a capillary electrophoresis apparatus that arranges them by length

• The result is that one labeled nucleotide at a time passes through the capillary tube

• Labeled nucleotides are excited by a laser and emit a light signal corresponding to A, C, G, or T

Electropherogram

Sequencing Facility – Whitehead Institute

Pyro Sequencing

• This newest of technologies is the latest standard in sequences• As bases are incorporated they emit light signals, allowing a

single reconstruction of an original sequence to yield all of its letters

• http://www.personalchemistry.com/DynPage.aspx?id=8726&mn1=1366

Sequencing tied to physical maps

• HGP (Human Genome Project) • Sequencing video

Shotgun approach

DNA sequence is obtained through a “shotgun” approach:

-DNA is fragmented by shooting it out of a small opening, e.g. the end of a syringe

-fragments are cloned in suitable bacterial vectors

-fragments are sequenced using primers flanking fragment in plasmid

- sequence of fragments must be reassembled which relies on the existence of very fast, large computing resources

- there are no physical maps to help with reassembly

Computing

B.C.

• Around 1600 BC the abacus, the first mechanical calculating device, was created by the Chinese (image http://www.johnnapier.com/abacus.htm)

• 300-400 BC – Aristotle invented syllogistic logic, the first formal deductive reasoning system

A, A B (modus ponens)

B

Early A.D.

• 780-850 Algorithm – Idea invented by Mohammed ibn-Musa al-Khwarizmi, who was part of the royal court in Baghdad. – The notion of an algorithm is fundamental to computing. An

algorithm is a step by step procedure for solving a problem that is guaranteed to find the right answer after a finite number of steps.

• 13th century – Ramom Llull, a Spanish theologian, invented a machine (Ars Magna) for discovering nonmathematical truths through “eccentric” logic (he wanted to prove the truth of the bible)

• 1434 –self striking water clock• 15th century – Gutenberg and the printing press

1500s

• 1500 Leonardo DaVinci’s mechanical calculator (designed, has since been built and works). DaVinci also designed a mechanical knight

• Early 1500s Hans Bullmann creates the first androids – simulated people that play musical instruments

• Clock makers create mechanical animals• 1533 Johann Muller, aka Regiomontanus, created an iron fly

and an iron eagle both of which were purported to fly• 1580 Rabbi Loew of Prague invented the Golem, a clay figure

that could be brought to life

1600s

• Descartes proposed that bodies of animal were nothing more than complex machines

• Hobbes published The Leviathan, describing a material and combinatorial theory of thinking

• Early 1600s Napier created Napier’s bones, carved wooden strips for mechanically computing logarithms

• 1621 Oughtred invented the slide rule based on what Napier had done

• 1642 Pascal created the first mechanical digital calculating machine

• 1673 Leibniz invented the multiplier

1800s - I

• 1801 – Jacquard invents a loom where the pattern is controlled using punched “cards” made out of wood (http://en.wikipedia.org/wiki/Jacquard_loom)

• 1811-1816 Ned Ludd leads the Luddite movement to destroy machinery (England)

• 1822 – Charles Babbage designed the Difference Engine – using Newton’s method of differences it could approximate the value of a given polynomial using only subtraction (http://en.wikipedia.org/wiki/Difference_engine)

1800s - II

• Ada Byron (Lady Lovelace) worked with Babbage on his designs and is considered to be the first computer programmer

• 1833 Babbage designs the Analytical Engine, considered to be the first programmable computer – it was never built

– The analytical engine was to be powered by a steam engine and would have been over 30 meters long and 10 meters wide. The input (programs and data) was to be provided to the machine via punch cards, a method being used at the time to direct mechanical looms. For output, the machine would have a printer, a curve plotter and a bell. The machine would also be able to punch numbers onto cards to be read in later. It employed ordinary base-10 fixed-point arithmetic. There was a store (i.e., a memory) capable of holding 1,000 numbers of 50 digits each. An arithmetical unit (the "mill") would be able to perform all four arithmetical operations.

– The programming language to be employed was akin to modern day assembly languages. Loops and conditional branching were possible and so the language as conceived would have been Turing-complete long before Alan Turing's concept. Three different types of punch cards were used: one for arithmetical operations, one for numerical constants, and one for load and store operations, transferring numbers from the store to the arithmetical unit or back. There were three separate readers for the three types of cards. (From Wikipedia, http://en.wikipedia.org/wiki/Analytical_engine)

1800s - III

• 1847 George Boole developed a binary logic that could be used to represent (some) “laws of thought”

• 1887 Hollerith developed the modern-day punched card to tabulate the US Census, he went on to found a company that ultimately became IBM

20th Century

• 1910-1913 Russell and Whitehead’s Principia Mathematica – leads philosophy into the logical analysis of knowledge

• 1936 Alan Turing published his paper On Computable Numbers which describes the concept of a Turing Machine

• 1943 The term “cybernetics” is coined in a paper • 1943 – McCulloch and Pitts do pioneering work on neural

networks• 1950 – Alan Turing proposed the Turing Test to determine

machine intelligence

Turing Test

• The Turing Test is considered by some to be the “gold standard” for determining whether a machine is intelligent

• Many, however, regard it as an unsatisfactory way to define intelligence

• Turing predicated that by the year 2000 a general machine intelligence would pass the test

• Ray Kurzweil believes this will happen by 2020• The Loebner competition is a limited version of the TT• Image: http://www-user.tu-chemnitz.de/~rima/PsyLin/hausarbeit/img8.png

First generation electronic computers1937 - 1953

• vacuum tubes; punched cards or magnetic tape; machine language; magnetic core memory

• 1941 Atanasoff and Berry (Iowa State) build the ABC which could solve partial differential equations with many unknowns, it was not, however, programmable

• 1943 Turing – Colossus used by British military to crack the German code in WWII

• 1945 ENIAC – first general purpose programmable computer (Eckert, Mauchly, vonNeumann)

• 1945 – first computer bug, discovered by Grace Hopper• 1948 – transistor invented• 1955 EDVAC – stored program concept, program and data can both be

stored• 1950s IBM mainframe computers

More Generations of Computing Machines

• Second generation electronic computersmid 50s – mid 60s

– transistors; punched cards or magnetic tape; assembly language and some high level languages; magnetic core memory

• Third generation computers: mid 60s – early 70s – integrated circuits; silicon chips; punched cards, magnetic tape, magnetic

disks; magnetic core, some semiconductor memory; e.g. IBM System/360– 1968 microprocessor invented

• Fourth generation computers: 1972 – 1984– VLSI (very large scale integration); microprocessor chip; magnetic disks,

floppy disks; high level languages; user-friendly software; semiconductor memory

• 1976 Apple II

• 1981 IBM PC

Computing Revolution

• Computers have been steadily and precipitously decreasing in price and increasing in power and storage space

• Moore’s Law: number of transistors on chips doubles every two years

• Update of Moore’s law: data density on chips doubles every 18 months

• Computer science researchers continue to find new ways of solving problems

Programming

• A program is a set of instructions a computer can follow• There are many different programming languages

– Machine language (binary)

– Assembly language (primitive instructions, e.g. ADD)

– High Level language (Java, Fortran, Perl, etc.)

• Programs are what make computers behave in a certain manner

• Algorithms can be realized as programs

Limits to computation

• P = polynomial time• NP = non-deterministic polynomial time• Problems whose solutions involve NP algorithms are effectively

“not computable”• There are problems for which no computer can find a solution• This is related to a mapping between algorithms (computer

programs) and the integers• There are more real numbers than integers, therefore there are

noncomputable “numbers” (i.e. problems)• Until a fundamental change in the design of computers happens

this will continue to be the case (possibly quantum computing)

Computer System Components(Von Neumann architecture)

INPUT

MEMORY

PROCESSOR OUTPUT