Welcome to Biology 181
Lab!

Glad to have you here, and I do hope you
are glad (or at least marginally glad) to be
here!
Are you where you are supposed to
be?

Quick check: If you are registered for Biol181L
section 53 which meets on Thursdays from 5:00
to 8:00 pm in Koffler 420, then you are in the
right spot. If not, you best hurry to one of the
other 3 rooms teaching 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…
But it really all boils down to this…
•
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…
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
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
Approach

or why Chemistry outlasted Magick
"Science walks forward on two feet, namely
theory and experiment. Sometimes it is one
foot which is put forward first, sometimes the
other, but continuous progress is only made
by the use of both - by theorizing and then
testing, or by finding new relations in the
process of experimenting and then bringing
the theoretical foot up and pushing it beyond,
and so on in unending alternation."
Robert Millikan (Nobel Prize in Physics 1946)

Or perhaps better said…

You’ll get mixed up, of course, as you already
know. You’ll get mixed up with many strange
birds as you go. So be sure when you step. Step
with care and great tact and remember that Life’s
a Great Balancing Act. Just never forget to be
dexterous and deft. And never mix up your right
foot with your left.
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.”
www.plantoftheweek.org/week090.shtml
-Edward Abbey, excerpt from
Desert Solitaire: A Season in the Wilderness
Let’s think about scientific 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 testing
Read, 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
Gain confidence
Repeat
Reject/modify model
Sometimes we miss, for better or
worse… (but learn things all the same)

See Lab manual 1-4
Mycobacterium
Yeast
Wheat
Sea Urchin
Marine Crab
Turtle
Rat
Human
%A
%T
%G
%C
15.1
31.3
27.3
32.8
47.3
29.7
28.6
30.9
14.6
32.9
27.1
32.1
47.3
27.9
28.4
29.4
34.9
18.7
22.7
17.7
2.7
22
21.4
19.9
35.4
17.1
22.8
17.3
2.7
21.3
21.5
19.8
A brief tour of the semester
Choosing & Defining a
Problem


Lab 2: Tao of Molecules
Slimy Biology experiments
Discerning the Rules



Lab 3: Coding
Lab 5: Translation
Lab 7: Molecular Detecting
Experimental Design






Lab 2: Tao of Molecules
Lab 4: Meiosis & Mendel
Lab 8: Fermentation
Lab 9: Tools of Light
Lab 11: Electron Transport
Slimy Biology
Gathering, interpreting data




Lab 6: Pedigrees
Lab 8: Fermentation
Lab 10: Colors & Photosynthesis
Lab 11: Electron Transport
Sharing & Persuading




Lab 2: Tao of molecules
Lab 7: Molecular Detecting
Lab 8: Glycolysis and Fermentation
(etc.)
Wounded soldiers not
killed by wounds
“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.”
http://www-gap.dcs.st-and.ac.uk/~history/Biographies/Nightingale.html
Content



Molecules & Properties

Surfaces, feels

Interactions--pH, redox, color
Life’s polymers

DNA & how it carries (and loses) information

Protein: the machine maker
Processes

Energetics: Capturing, storing, releasing energy

Inheritance: Where the genes are & where they go
Quantum Mine Assignment



Scientifically approaching black box
This can be tricky so I would advise you to start
early, not the eve before it is due!
Really the purpose of this computer module is
to get you thinking in a “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 part
You 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.
PatternMaster




A quest for the rules that order a system
Again, this can be tricky so I would advise you
to start early, not the eve before it is due!
Also again, really the purpose of this computer
module is to get you thinking in a “problem
solving” sort of manner.
If you care to tackle the harder versions, extra
credit points will be awarded.
Rule Quest
Given 1-step clockwise*...
•Perimeter to top inner color
•Top inner color to lower left color
•Lower right color to lower left color
NEIGHBOR definitions are clockwise, counterclockwise
Take a look
Homepage => 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-Do

Quantum Mine: Solution & (written) approach

Pattern Master: Solution & (written) description

181 Intro Quiz (Assessor)

Molecular World Tutorial (Assessor)
**All Due 10 p.m. night before class two weeks hence**
Extra Credit Option





Design your own “light bulb” experiment.
Include a scenario, possible hypotheses and
ways in which to test your hypothesis.
Be as creative as you would like!
This will be worth up to 5 points.
Drop it in my box or hand it in next class
period.