Welcome to 20.109 Laboratory Fundamentals of Biological Engineering

Welcome to 20.109Welcome to 20.109

Laboratory Fundamentals of Laboratory Fundamentals of Biological EngineeringBiological Engineering

Orientation LectureSpring 2008

Introducing 20.109

• Why you’re here– course mission– the art of investigation

• What you’ll do– three experimental modules– assessments/communication– course logistics

Course Mission

20.109 Laboratory Fundamentals of Biological Engineering

To teach cutting edge research skill and technology through authentic investigation

To prepare students to be the future of Biological Engineering

To inspire rigorous data analysis and its thoughtful communication

Course Mission

20.109 Laboratory Fundamentals of Biological Engineering

To prepare students to be the future of Biological Engineering

Course Mission

20.109 Laboratory Fundamentals of Biological Engineering

To prepare students to be the future of Biological Engineering

We inform, you create!

Your goals and interests?

Engineering Principles + Modern Biology

Manipulate

Make stuff!

pdb.org

Measure Model

How Doctors(*) People Think

Bias leads investigations astray

Hindsight bias

Attribution error

Framing effect

Scientists are like detectives

…even engineers!

(*) J. Groopman

Puzzles: hindsight bias

A woman had two sons who were born on the same hour of the same day of the same year. But they were not twins. How could this be so?

Why is it better to have round manhole covers than square ones?

They were triplets!

Round covers cannot be dropped down the manhole, no matter how you turn them.

(cf. invention of PCR)

Rote learning: attribution error

Your school district must drive 1128 kids to school each day, and 36 kids can fit on a bus. How many buses do you need?

Most popular answer: 31 remainder 12!

31

10848

36 1128

Framing effect

Politics: “tax cuts” vs. “tax relief” vs. “tax responsibility”

Science policy: GM foods or nanotechnologybenefits frame vs. risks frame

Science: what carries and controls genetic information? (The Canon, N. Angier; Images all from public domain)

1

2

3

4 ?5?

How Engineers Succeed

Bias leads investigations astray

How do we fight bias?

“Your data should be true even if your story is wrong.”

~ Darcy Kelley, Columbia(The Canon, N. Angier)

Appropriate controls

Reluctant interpretation

Community vigilance

- + ?

?+-

Course Mission

20.109 Laboratory Fundamentals of Biological Engineering

To prepare students to be the future of Biological Engineering

To teach cutting edge research skill and technology through authentic investigation

To inspire rigorous data analysis and its thoughtful communication

DNA Engineering (B. Engelward)

Protein Engineering (A. Jasanoff)

Biomaterials Engineering (A. Stachowiak)

Module 1Module 2Module 3

openwetware.org/wiki/20.109(S08)

Lab+Analytical Skills

DNA manipulation: PCR, recombination, gels

Cell culturebacterial ( DNA)mammalian ( protein)

Flow cytometrystatistical analysis

Discuss primary research article

Experimental Goals

Design: PCR primers Truncate EGFP gene (5’) Make and test 5 plasmid Transfect mouse cells with EGFPs (full and ) Test for spontaneous DNA recombination by fluorescence

DNA Engineering: EGFP recombination

web.mit.edu/engelward-lab/animations/DSBR.htmlRecombocell image from Dominika Wiktor, Engelward lab.

Experimental Goals

Design: protein modificationDesign: protein modification Mutagenize wild-type plasmid Express and purify protein in a bacterial host Assess effect of mutation on protein production and behaviour

Protein Engineering: Calcium sensor redesign

Lab+Analytical Skills

Assess protein features DNA mutagenesis and sequencing Characterize protein

identity, amount, fluorescence More error analysis

low vs. high-throughputMATLAB modeling

Lab+Analytical Skills

3D cell culture Fluorescence microscopy Measure message

isolate RNART-PCR

Measure one protein (from mixture)ELISA

Experimental Goals

Design: Culture conditions Study how cell environment affects viability and morphology. Measure collagen contents for chondrocytes cultured differently.

Biomaterials Engineering: Cartilage gel

Communication and Grading

Major Assessments

30% Oral Presentations Module 2 - journal article

Module 3 - research proposal

50% Written Work Module 1 - lab report

Module 2 - portfolio

Module 3 - essay

10% Homework Assignments

5% In-lab Daily Quizzes

5% Lab Notebooks

Day-to-day Assessments

Neal Lerner

Atissa Banuazizi

After 20.109, you should be able to…

• Implement laboratory protocols

• Design novel experiments with

• Examine the scientific literature

• Communicate to various audiences, in various styles

• Present salient points of your own and others’ ideas

appropriate controls

• Organize a lab notebook

• Interpret qualitative data

• Analyze quantitative data

• Recognize utility of models

- + ?

?+-

Course Logistics

Lecture Tuesdays and Thursdays 11-12, 13-3101

Lab Tuesdays and Thursdays 1-5, 13-3095

Wednesdays and Fridays 1-5, 13-3095

There are no “make-up” labs

You will perform experiments in pairs.

Collaboration with integrity is encouraged: assignments

can be worked on together but must be submitted individually.

Work must be turn in on time:

lab notebooks - end of lab

assignments - beginning of lab or lecture