Welcome to Biology Welcome to Biology 181 Lab!181 Lab!

Glad to have you here, and I do Glad to have you here, and I do hope you are glad (or at least hope you are glad (or at least marginally glad) to be here!marginally glad) to be here!

Are you where you are Are you where you are supposed to be?supposed to be?

Quick check: If you are registered Quick check: If you are registered for Biol181L section 53 which meets for Biol181L section 53 which meets on Thursdays from 5:00 to 8:00 pm on Thursdays from 5:00 to 8:00 pm in Koffler 420, then you are in the in Koffler 420, then you are in the right spot. If not, you best hurry to right spot. If not, you best hurry to one of the other 3 rooms teaching one of the other 3 rooms teaching this course right now! this course right now!

About me...

• Day Job = Genetic Researcher/Instructor

• Poet & Photographer/Artist

• (I really am a writer and an artist first, but ask me sometime about how strongly I believe the creative process is integral to success in scientific work!)

• I have been with this University for 14 years, prior to coming here I was a Park Ranger in Glacier National Park, Montana (the naturalist kind, not the gun-toting kind.)

Where to find me• My office hours are before class on Thursdays in

room 422 (Koffler) from 9:50 to 10:50. Please call or email if you plan on stopping by, if not… I may step out for caffeine or something.

• Otherwise, I am more than willing to make myself available to you pretty much any time (other than Thursdays) in my genetics lab at UMC. Email me if you would like to stop by and I will “show you the way.” My lab number is 626-2314.

• It would be helpful if you prefaced all emails with “Bio181” in the title.

About you?

• I’d really like to know a bit about you before we begin this biology journey together.

• Please take an index card, if the colors offend you terribly, feel free to select a white one

• Now write the following information:

Index Card Info• Full name and the name you would prefer to go

by

• Where you are from (Born, grew up…)

• Why you are taking this class & college major/minor

• Email address you would prefer that I use

• Something interesting about you…

• Anything else you care to jot down

Our goals & path

• We have a lot to talk about here, it might be best if you turned to page xi of your Lab Manual and we will go over that information quickly.

• We will also revisit this topic a little later…

• We’ll work together to help you truly understand scientific processes and concepts. My wish for you is to leave this class with real problem solving skills, not just facts and figures stored away someplace in the brain.

• You should leave this class with an understanding of how all of biology arises from molecular properties, and how all of the “core concepts” in biology are interrelated, and in all truth, function hand in hand in every aspect of life as we know it.

• You should know…

But it really all boils down to this…

How biology is an eternal part of the world

around us

How understanding biology can help us help others, be it for the benefit of

humankind or the benefit of pigeons everywhere.

How biology and genetics can help us understand some of the

differences and sameness between us.

And finally, how “better living through biology” enables us to

ferment foods and create other such delicacies.

Really, it’s important… so Really, it’s important… so now, The fine print.now, The fine print.

Policies & Grading

• Syllabus (Linked on course homepage)

• Attendance & related

• Honor code & Plagiarism (Manual, p. xiii)

• Assignment Breakdown

• On-line homework

• In-class quizzes

• Lab assignments (LABAs--Lab Activity Based Assignments)

• Lab reports

Continued…• The course syllabus may be found here:

http://blc.arizona.edu/courses/181Lab/ in the upper right side of the course homepage. You should reference this for all of the nuts and bolts of attendance/absence/late work, etc… policies.

• Attendance is absolutely mandatory. In a course with so few class periods (meeting once a week), more than two absences will result in an administrative drop and a failing grade for the class.

And a little more…

• Arrival 20 minutes late to class (or more) will count as an absence unless you have a darn good reason and/or a verified excuse.

• Plagiarism and cheating are taken very seriously, please fill out the form on page xiii of your lab manual and hand in the top portion by the end of class today.

Lastly… tidying up

• Cell Phones

• Food/Drinks

• Attire

• General disrespectful/annoying behavior

• Resources (BLC, Office hours, other…)

Lab I: the Scientific Lab I: the Scientific ApproachApproach

or why Chemistry outlasted Magickor why Chemistry outlasted Magick

"Science walks forward on two feet, "Science walks forward on two feet, namely theory and experiment. Sometimes namely theory and experiment. Sometimes it is one foot which is put forward first, it is one foot which is put forward first, sometimes the other, but continuous sometimes the other, but continuous progress is only made by the use of both - progress is only made by the use of both - by theorizing and then testing, or by by theorizing and then testing, or by finding new relations in the process of finding new relations in the process of experimenting and then bringing the experimenting and then bringing the theoretical foot up and pushing it beyond, theoretical foot up and pushing it beyond, and so on in unending alternation."and so on in unending alternation."

Robert Millikan (Nobel Prize in Physics Robert Millikan (Nobel Prize in Physics 1946) 1946)

Or perhaps better said…Or perhaps better said… You’ll get mixed up, of course, as you You’ll get mixed up, of course, as you

already know. You’ll get mixed up with already know. You’ll get mixed up with many strange birds as you go. So be sure many strange birds as you go. So be sure when you step. Step with care and great when you step. Step with care and great tact and remember that Life’s a Great tact and remember that Life’s a Great Balancing Act. Just never forget to be Balancing Act. Just never forget to be dexterous and deft. And never mix up dexterous and deft. And never mix up your right foot with your left.your right foot with your left.

Dr Seuss (genius in every respect)Dr Seuss (genius in every respect)

“The datura is sacred (to certain cultists) because of its content of atropine, a powerful narcotic of the alkaloid group capable of inducing visionary hallucinations, as the Indians discovered long before the psychedelic craze began. How they could have made such a discovery without poisoning themselves to death nobody knows; but then nobody knows how so-called primitive man made his many other discoveries. We must concede that science is nothing new, that research, empirical logic, the courage to experiment are as old as humanity.”

-Edward Abbey, excerpt from

Desert Solitaire: A Season in the Wilderness

www.plantoftheweek.org/week090.shtml

Let’s think about scientific Let’s think about scientific thinking in action…thinking in action…

Illuminating Darkness

• You stumble out of your room at 4 a.m. and turn on a lamp

• Nothing happens

• Now what? Curse the darkness?

So what is the scientific approach anyhow?

•Is there a right way and a wrong way to come to any kind of conclusion?

Hypothesis testingHypothesis testingRead, Observe, Consider, Intuit

Create/Embrace an explanation (model)

Derive predictions

Create tests to which you ‘know’ the answer**Because of insights from your model

Execute tests

Reject/modify modelGain confidence

Repeat

Sometimes we miss, for Sometimes we miss, for better or worse… (but learn better or worse… (but learn

things all the same)things all the same) See Lab manual 1-See Lab manual 1-

44%A%A %T%T %G%G %C%C

MycobacteriuMycobacteriumm

15.115.1 14.614.6 34.934.9 35.435.4

YeastYeast 31.331.3 32.932.9 18.718.7 17.117.1

WheatWheat 27.327.3 27.127.1 22.722.7 22.822.8

Sea UrchinSea Urchin 32.832.8 32.132.1 17.717.7 17.317.3

Marine CrabMarine Crab 47.347.3 47.347.3 2.72.7 2.72.7

TurtleTurtle 29.729.7 27.927.9 2222 21.321.3

RatRat 28.628.6 28.428.4 21.421.4 21.521.5

HumanHuman 30.930.9 29.429.4 19.919.9 19.819.8

A brief tour of the semesterA brief tour of the semester

Choosing & Defining a Choosing & Defining a ProblemProblem

Lab 2: Tao of MoleculesLab 2: Tao of Molecules Slimy Biology experimentsSlimy Biology experiments

Discerning the RulesDiscerning the Rules

Lab 3: CodingLab 3: Coding Lab 5: TranslationLab 5: Translation Lab 7: Molecular DetectingLab 7: Molecular Detecting

Experimental DesignExperimental Design

Lab 2: Tao of MoleculesLab 2: Tao of Molecules Lab 4: Meiosis & MendelLab 4: Meiosis & Mendel Lab 8: FermentationLab 8: Fermentation Lab 9: Tools of LightLab 9: Tools of Light Lab 11: Electron TransportLab 11: Electron Transport Slimy BiologySlimy Biology

Gathering, Gathering, interpreting datainterpreting data

Lab 6: Pedigrees Lab 6: Pedigrees Lab 8: FermentationLab 8: Fermentation Lab 10: Colors & PhotosynthesisLab 10: Colors & Photosynthesis Lab 11: Electron Transport Lab 11: Electron Transport

Sharing & PersuadingSharing & Persuading

Lab 2: Tao of moleculesLab 2: Tao of molecules Lab 7: Molecular DetectingLab 7: Molecular Detecting Lab 8: Glycolysis and FermentationLab 8: Glycolysis and Fermentation (etc.) (etc.)

Wounded soldiers not killed by wounds

http://www-gap.dcs.st-and.ac.uk/~history/Biographies/Nightingale.html

“The area of each coloured wedge, measured from the centre as a common point, is in proportion to the statistic it represents. The blue outer wedges represent the deaths from:-

... preventable or mitigable zymotic diseases

or in other words contagious diseases such as cholera and typhus. The central red wedges show the deaths from wounds. The black wedges in between represent deaths from all other causes.”

ContentContent

Molecules & PropertiesMolecules & Properties Surfaces, feelsSurfaces, feels

Interactions--pH, redox, colorInteractions--pH, redox, color

Life’s polymersLife’s polymers DNA & how it carries (and loses) informationDNA & how it carries (and loses) information

Protein: the machine makerProtein: the machine maker

ProcessesProcesses Energetics: Capturing, storing, releasing energyEnergetics: Capturing, storing, releasing energy

Inheritance: Where the genes are & where they go Inheritance: Where the genes are & where they go

Quantum Mine Quantum Mine AssignmentAssignment

Scientifically approaching black boxScientifically approaching black box This can be tricky so I would advise This can be tricky so I would advise

you to start early, not the eve before you to start early, not the eve before it is due!it is due!

Really the purpose of this computer Really the purpose of this computer module is to get you thinking in a module is to get you thinking in a “problem solving” sort of manner.“problem solving” sort of manner.

Rules of the Mine

Taking it for a ride

Homepage (then Software then QMine)

Once you have a login you will be able to play the game for credit, prior to that you may practice

“for fun”

Remember you have an unlimited number of times to play the game, however it is your LAST

score that counts for a grade.

The game portion of the assignment is worth 80 points.

The written partYou may complete your write-up in the computer program itself or you may write it by hand and turn it in to my mailbox in room BSE 109 the day BEFORE it is due.

Your write-up should clearly identify 3 aspects/steps of the Scientific Approach and should clearly illustrate how these steps were used to solve Quantum Mine experiment.

The write-up portion of the assignment is worth 20 points.

PatternMasterPatternMaster A quest for the rules that order a systemA quest for the rules that order a system Again, this can be tricky so I would Again, this can be tricky so I would

advise you to start early, not the eve advise you to start early, not the eve before it is due!before it is due!

Also again, really the purpose of this Also again, really the purpose of this computer module is to get you thinking computer module is to get you thinking in a “problem solving” sort of manner.in a “problem solving” sort of manner.

If you care to tackle the harder versions, If you care to tackle the harder versions, extra credit points will be awarded.extra credit points will be awarded.

Rule Quest

NEIGHBOR definitions are clockwise, counterclockwise

Given 1-step clockwise*...

•Perimeter to top inner color

•Top inner color to lower left color

•Lower right color to lower left color

Take a lookHomepage => Software => PatternMaster for Credit=>

Enter a random number=> Chose a challenge.

Remember, you may take this as many times as necessary and it is the last score that counts (not the best

score.)

The 1’s are the easiest, 6’s are more challenging, and 11’s even more so.

For extra credit: Completion of a “6” challenge is worth 5 extra points and completion of an “11” (for the truly

brave) is worth an extra 10 points.

Solver• After exposure, ask: which is easier to figure

out--WHAT is making a given block happy, or WHO

• I would really recommend keeping a pen and paper by your side and keeping track of any patterns you do or do not see while you work through this puzzle.

• Again, the grading on this is 80/20 for the puzzle/write-up. You have the same options for turning in the written portion of the assignment, either online or in my mail box.

The written part

Description clearly explains the rule of the puzzle, supplemented with examples and allows puzzle to be solved by an inexperienced person.

CREATE 181 ACCOUNTS

Two week To-DoTwo week To-Do

Quantum Mine: Solution & (written) Quantum Mine: Solution & (written) approachapproach

Pattern Master: Solution & (written) Pattern Master: Solution & (written) descriptiondescription

181 Intro Quiz (Assessor)181 Intro Quiz (Assessor)

Molecular World Tutorial (Assessor)Molecular World Tutorial (Assessor)**All Due 10 p.m. night before class two weeks

hence**

Extra Credit OptionExtra Credit Option Design your own “light bulb” Design your own “light bulb”

experiment.experiment. Include a scenario, possible Include a scenario, possible

hypotheses and ways in which to test hypotheses and ways in which to test your hypothesis.your hypothesis.

Be as creative as you would like!Be as creative as you would like! This will be worth up to 5 points.This will be worth up to 5 points. Drop it in my box or hand it in next Drop it in my box or hand it in next

class period.class period.