Participant Handbook Summer Science Program - Astrophysics Biochemistry in or - The Summer Science Program
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Participant Handbook
for the 62nd annual
Summer Science Program
in
Astrophysics
or
Biochemistry
SummerScience.org
This document is online at www.ssp.org/files/SSP Participant Handbook 2020.pdfContents Program Description (formal version) ........................................................................................ 1 Program Description Part 2 – For Participants Only .................................................................... 3 Faculty ...................................................................................................................................... 5 Honor Code ............................................................................................................................... 7 Digital Citizenship ..............................................................................................................................8 Advance Academic Preparation ................................................................................................. 8 Astrophysics ......................................................................................................................................8 Biochemistry.................................................................................................................................... 10 About Evaluation ............................................................................................................................. 10
Welcome! This Handbook is designed to tell you everything you need to know to launch your SSP experience successfully. Be sure to share it with your parent or guardian. If you or your parent have questions, do not hesitate to ask, by email or phone. As you know, the COVID-19 pandemic has forced a crash program to move in-person educa- tional programs online. Our faculty will do their best to keep a fast pace and maintain our traditions, including research teams of three, a Talent Show, and many others. We will ask for your flexibility as the schedule evolves this summer. Especially, we will ask you to reach out to your faculty and peers without hesitation, for camaraderie and support. No one does SSP alone. By August you will become an alum and voting member for life, and your SSP community will en- large to encompass 2,500 alumni around the world of all ages, every one of them smart and inter- esting … like you. SSP is the only summer program operated by its own alumni. That matters. We know exactly what it’s like to be a really smart and motivated teenager. SSP is designed to meet your needs at this spe- cific stage of life, and beyond. We hope and expect you will benefit from, and contribute to, this unique nonprofit organization for the rest of your life. Your faculty and I are looking forward to meeting you virtually. It will be a great summer! Best regards, Richard D. Bowdon SSP '74 Executive Director rbowdon@ssp.org
SSP Participant Handbook page 1 Program Description (formal version) The Summer Science Program is one of the longest-running pre-college, research-based enrichment programs for highly gifted high school students. Applicants choose a research project in Astro- physics or Biochemistry. There are two programs for each project; enrollment at each program is limited to 36, mostly rising high school seniors from around the U.S. and the world. The original programs in Astrophysics were held from 1959 through 1999 at Thacher School in Ojai, California. In 2000, Thacher decided to end the program. Alumni organized to form an inde- pendent 501(c)3 nonprofit and take over the operation, moving it to a different campus. SSP has cooperation agreements with its host campuses, plus academic partners Harvey Mudd Col- lege, Caltech, and MIT. Its governing body is a volunteer Board of Trustees, elected by alumni and former faculty. All participants and faculty become voting members for life upon completion of the Program. A second Astrophysics program opened in 2003, a Biochemistry program in 2017, and a second Biochem program in 2019. The coronavirus pandemic in 2020 forced the program to move online for that summer. Design and Goals The Program’s goal is to accelerate the development and raise the aspirations of its participants. Applicants are evaluated through a holistic process very similar to that of highly selective colleges. We admit roughly 10% of applicants, those excelling in the most challenging math & science courses available to them, and showing evidence of maturity and motivation, especially in the face of obstacles. These young people have great potential; SSP inspires them to “realize” that potential in both senses of the word. Participants do research themselves from start to finish, working in teams of three. In the Astro- physics project, each team uses a series of images of a near-earth asteroid to calculate its orbit and predict its future position. Teams in the Biochemistry project model an enzyme from a particular fungal crop pathogen, then hypothesize an inhibitor molecule that could become the active ingredi- ent of a safe fungicide. Participants find collaborative research to be a refreshing and motivating contrast to the competi- tive, individualized coursework of high school. Many are surprised to discover that working closely with equally bright and interesting peers is as rewarding socially as it is intellectually. Indeed, cul- tivating a supportive community of scholars is another primary goal of SSP. The spirit of coopera- tion and collaboration is reinforced by an Honor Code and an absence of exams, grades, or formal credit; the experience itself is the reward. Inspired by this intense immersion in a scientific community, most SSP alumni choose STEM ma- jors at leading colleges and universities. Many have gone on to become leaders their chosen profes- sions, and cite the Program as “the educational experience of a lifetime.” Faculty Each program employs seven full-time faculty. Mentoring and collaboration happen continuously. The Academic Director and Associate Academic Director are experienced, PhD-level scientist / educators. They lead the classroom time, make assignments, and monitor progress in the research. The Site Director is responsible for non-academic aspects of the program, and acts as our liaison with parents.
SSP Participant Handbook page 2 Teaching Assistants and Residential Mentors, as the title implies, integrate academic and resi- dential/social roles. Graduate or upper-class college students majoring in a related field, many are alumni returning to SSP. They assist participants in their research, and organize social events. They are role models and front-line supervisors. Beyond the Research A series of guest scientists and professionals make a presentation not directly related to the re- search, followed by questions and open-ended discussions. Rounding out the schedule are organized social events including games and a talent show. Daily Routine Participants stay very busy, spending several hours each day on learning new material, data collec- tion, analysis, assignments, and social activities. The schedule for 2020 will be evolving before and during the program. There will be a mix of scheduled and spontaneous, synchronous and asynchro- nous activities, involving larger (up to 72) and smaller groupings. Topics Covered SSP is not coursework; most of the material taught, and reinforced with regular assignments, is in- tegral to the research. Topics overlap parts of several standard courses, and are presented at a brisk college sophomore/junior pace and level. Participants keep a scientific notebook and write a final report. They are encouraged to collaborate on assignments, as long as what they submit reflects their own understanding. Topics covered typically include: Astrophysics Project Astronomy: celestial coordinates, digital observational techniques, astrometry; brief introductions to planetary science, cosmology Physics: gravitation, celestial mechanics; brief introductions to the electromagnetic spectrum, rela- tivity, quantum mechanics Mathematics: interpolation, coordinate transformations, differential and integral vector calculus, numerical methods, differential equations Scientific Programming in Python Biochemistry Project Biochemistry: protein purification, gel electrophoresis, enzyme assays, kinetics, and inhibition, drug screening Molecular Modeling: homology modeling, ligand docking, molecular dynamics simulations, in- hibitor optimization Mathematics: rate equations, linear and non-linear curve fitting, biostatistics Bioinformatics: Sequence similarity searching, multiple sequence alignment, secondary structure and binding motif prediction
SSP Participant Handbook page 3 Program Description Part 2 – For Participants Only So that’s the formal description. But what will SSP really be like, from your perspective? Why is it designed the way it is, and why has this design lasted for over six decades? SSP is an opportunity to work in an academically rigorous, socially supportive community of scholars. The experience is similar to a research group of professional scientists. The research you will do was carefully chosen for its intrinsic value, as an archetype of experi- mental science, and as a tool for self-discovery and personal growth. Let’s unpack all of that. Science classes teach you to regurgitate what (mostly dead) scientists learned in the past. That’s not what working scientists do. At SSP you will learn some science, yes, but also what it feels like to do science, where there is not a “right answer” known in advance, there is instead the result of a carefully run experiment. Our goal is that everyone, no matter how brilliant and/or well-prepared, will feel challenged at least some of the time. The pace is much faster than high school. The meta- phor is “drinking from a fire hose”… you will not be able to absorb all of the information “fire- hosed” at you. No one can! That’s right: unlike a school, we intentionally throw more at you than anyone can possibly absorb. Why? Because that is the only way you can learn how fast you can learn. Another metaphor: you are like a sports car that has been circling around a parking lot in second gear. SSP is an open free- way with no speed limit. Let's see how fast you can go! You can go very fast, and yes, that will feel thrilling. But there’s another side to that … even a fast race car has a maximum speed. At SSP you will find yours. We actually want you to experience (temporarily) how it feels to be lost and confused, to not understand something right away. That may feel very discouraging, especially if this has never happened to you before (which is the norm for SSPers). When it does, you’ll learn to ask for help from your peers and from the faculty, without embarrassment, even if you’ve never had to ask for academic help from anyone before. The goal is to give you practice in overcoming frustration and confusion. You will learn that asking questions and reaching out for help is not a sign of weakness or stupidity … it is a habit practiced by all successful people. We want you to collaborate with your classmates on everything, while learning and respecting the line between collaboration and plagiarism. You will learn how rewarding it can be to work in a col- laborative team with others just as bright as you are. Alumni often say that college is “easy” compared to SSP … even Harvard, MIT, or Caltech. That’s because these skills – how to absorb new material quickly, when to ask for help, how to tackle con- fusing problems that seem insurmountable – will be very valuable in college, no matter where you go or what you study. Besides challenging, SSP is designed to be immersive. You will not have much time for other ac- tivities with your school, friends, or family. To manage these challenges, we want you to build strong bonds of support with one another. To keep up your energy and ability to learn efficiently, we encourage everyone to make healthy life- style choices, including enough sleep and daily exercise. So plan to break out of your usual routine during SSP, and make the most of this socially rich environment. Spend the time interacting with these smart, interesting colleagues and faculty from around the world, talking about science or college or Life. So that’s what SSP is really like. After Closing Exercises, you will join an elite worldwide alumni network that spans over sixty years. SSP meant so much to us that we still donate time and money
SSP Participant Handbook page 4 to keep the program going … for you, and for those who will come after you. As you will notice, some of your faculty are alumni too. The alumni who fund and operate SSP hope that you find this program as life-changing as we did. At Closing Exercises, we will welcome you as a lifetime, voting member of the Summer Science Program! But first … buckle your seat belt.
SSP Participant Handbook page 5
Faculty
SSP 2020 in Astrophysics @ New Mexico Tech
Name Position Education
Ph.D. Astronomy, Indiana Univ.; B.S.
Dr. Adam Rengstorf Academic Director
Physics, Binghamton Univ.
Associate Academic Ph.D. Nuclear Physics, MIT; B.S.
Dr. William Andersen
Director Physics, Baylor Univ.
M.S. Science Teaching, New Mexico
Barbara Martinez Site Director Tech; B.A. Elementary Education, Univ.
of Santa Fe
Ph.D. Computer Science, Univ. of WA,
Adjunct Faculty for
Aaron Bauer '06 ’19; B.A. Computer Science, Williams
Programming
College
SSP 2020 in Astrophysics @ CU Boulder
Name Position Education
Ph.D. Astrophysics, Univ. of Texas; B.S.
Dr. Agnès Kim Academic Director
Physics, Iowa State Univ.
Associate Academic Ph.D. Physics, Cornell Univ.; B.S.
Dr. Michael Dubson '73
Director Physics, Univ. of Illinois
Masters in Teaching, Univ. of California,
Mark Greenberg Site Director Irvine; B.S. Business Administration,
MIS, Univ. Illinois, Urbana-Champaign
Ph.D. Computer Science, Univ. of WA,
Adjunct Faculty for
Aaron Bauer '06 ’19; B.A. Computer Science, Williams
Programming
College
Teaching assistants will be listed on the website when finalized.SSP Participant Handbook page 6
SSP 2020 in Biochemistry @ Purdue
Name Position Education
Ph.D. Molecular Biology, Univ. of North
Dr. Mark Hall Academic Director
Carolina; B.S. Biology, Trinity College
Associate Academic
Dr. Chittaranjan Das Ph.D. Indian Institute of Science
Director
Ph.D. Mathematics Education, Univ. of
Georgia; M.Ed., Mathematics Education,
Nicole Ice Site Director
Georgia State Univ.; B.S. Mathematics,
Georgia State Univ.
SSP 2020 in Biochemistry @ Indiana University
Name Position Education
Dr. Martha Oakley Academic Director Ph.D. Chemistry, Caltech
Associate Academic Ph.D. Biological Chemistry, Indiana
Dr. Jessica Hollenbeck
Director Univ.; B.S. Chemistry, Univ. of Michigan
BS - Biology, Univ. of Texas at Tyler,
Christin Latus Site Director
2017
Teaching assistants will be listed on the website when finalized.SSP Participant Handbook page 7
Honor Code
What to Do
Inspired by the Honor Codes at Caltech and Haverford College, the Honor Code at SSP expresses
the shared values that promote the smooth functioning of the whole community. It is the keystone
of our culture.
You will be a trusted and respected member of a diverse community, in which we embrace our dif-
ferences, care about each another, and resolve conflicts through respectful communication.
Every member of the Summer Science Program community is expected to practice personal and
academic integrity, including honesty, trust, consideration, and mutual respect, and to take respon-
sibility for his or her words and actions. No one will denigrate or take unfair advantage of any other
person.
Trust. Responsibility. Nice words, but what do they mean in practice?
All of us will practice behaviors that promote the smooth functioning of the community, and avoid
behaviors that disrupt it. Anyone whose actions cause him or her to lose the trust of the community
will have to leave.
For example, quoting Haverford’s Code: “A participant commits an act of plagiarism … by repre-
senting another person’s ideas or scholarship as that participant’s own work. [This] constitutes a
withdrawal from the commitment to academic honesty required by the Honor Code ….”
As one participant wrote:
“The honor code was new and interesting for me. I really appreciated the level of trust it put in me
to be responsible for myself and my actions. It kind of changed the way that I thought of myself in
an academic setting: more responsible for my own successes and failures.”
What Not to Do
Most prohibited behaviors follow from the Honor Code. For example:
a) Any behavior that disrupts the smooth operation of the community by requiring repeated in-
tervention or correction or close supervision. Our faculty don’t have time or energy for that.
b) Words or actions that are reasonably perceived by others in the community as disrespectful,
insulting, or threatening, including: hostility, disrespect, verbal abuse, bullying, sexism, sex-
ting, racism, demeaning jokes, and other "put-downs.”
c) Untruthfulness in any form: lying, cheating, withholding, distorting, or concealing the truth.
Intellectual dishonesty: plagiarism or falsification of data. While collaboration is encour-
aged and necessary, all work you submit must reflect your own understanding.
If the nature of the violation allows, we would prefer to give you the opportunity to correct your
behavior and make better decisions. However, if in our judgment the behavior is serious or repeti-
tive, your dismissal from the program will be necessary to protect the community from further dis-
ruption. This decision will be made by the Site Director in consultation with other faculty and staff.
If you are dismissed, you will not receive a certificate of completion nor be considered an alumnus.
No portion of your program fee will be refunded.SSP Participant Handbook page 8
Digital Citizenship
[adapted from Duke Talent Identification Program eStudies, used with permission]
We will use a variety of online resources, platforms, and software that require you to post, share,
and publish work online in both protected and open environments. The following serves as a re-
source to help you maintain safety and privacy while interacting online.
Your SSP community consists of your peer participants, faculty members, and SSP staff. You
must protect the privacy, security, and intellectual property rights of others by not sharing any-
thing from or about your work at SSP with anyone outside of this community. This includes
participant or faculty contact information, SSP-produced educational materials, or the work of
other participants.
Manage your own passwords. Create a unique password for every site, and never share that
password. You are responsible for remembering your passwords.
After SSP concludes, you are responsible for maintaining or deleting, at your option, any online
accounts or profiles you created for or during SSP.
Exhibit appropriate behavior online. Every comment, discussion, and share you post online is a
reflection of you, and should be treated as both permanent and public. Be smart about how you
want to be perceived by others now and in the future. Post and share only appropriate and re-
spectful content. Don’t engage with or respond to inappropriate or disrespectful posts or imag-
es.
You have the right to feel safe when utilizing online tools and resources. If at any time you feel
uncomfortable, or experience or witness instances of bullying, harassment, inappropriate lan-
guage or content, contact a TA or the Site Director immediately.
Respect the intellectual property of others, including your peers. Never use another’s work or
software without permission, and always credit the original producer of the work. This includes
computer code, text from books or websites, images, videos, and any other resource. If you are
unsure of whether you might be using copyrighted materials, or how to make an attribution, ask
the faculty. “I didn’t know” is not an excuse for plagiarism or copyright infringement. Your
faculty can explain the difference between collaboration and plagiarism.
Advance Academic Preparation
It is very important that you review the following areas before the program starts. You do not need
to purchase any textbooks.
Astrophysics
Programming
There are many types of programming. At SSP you will do what many scientists and engineers do:
write your own software to analyze your own data. We use the free, open-source, general-purpose
Python language. You will need to learn as much as you can about Python before you arrive.
If you are completely new to programming, don’t be surprised if you find it to be totally incompre-
hensible at first (like a whole other language, haha). It mixes elements of math, logic, and creative
writing; it’s all three put together. Over the years a quite a few people have had their very first ex-
posure to programming at SSP, then later gone on to become professional programmers, computer
science professors, and software entrepreneurs. (For example, Mitch Kapor SSP ’66. Try Googling
him.)SSP Participant Handbook page 9
We will use Python version 3. Install the latest version from www.python.org, accepting all the de-
faults.
Then use the free online Python textbook CS Principles: Big Ideas in Programming by Mark Guz-
dial, Prof. of in Computing at Georgia Institute of Technology:
http://interactivepython.org/runestone/static/StudentCSP/index.html.
If you are new to programming:
o Study chapters 3, 6, 7, 8, and 12. Expect to spend at least 2-3 hours per chapter.
o For each section, read the material, answer the questions, and experiment with the code
samples.
o Do the exercises at the end of each chapter (skip the exam question sections in chap-
ters 6 and 8).
If you have some programming experience:
o Skim chapter 3, then follow the instructions above for chapters 6,7,8,12.
If you are an experienced, veteran programmer who has written hundreds or thousands of lines
of code in some other general-purpose language, skim chapters 6, 7, 8, and 12 to get a sense of
how Python is different than what you're used to. Do some of the exercises as you think neces-
sary to get you up to speed in Python.
Other chapters contain interesting and useful material, but are not as integral to the programming
you'll do at SSP.
If you have extra time, find some other Python tutorials online. Also, try installing and playing
around with a superset of Python called Visual Python (www.vpython.org). It adds a cool, easy 3-D
graphics library that you might use to create an animation of your asteroid’s orbit. Finally, as a bo-
nus challenge, download www.ssp.org/files/visualizing_orbital_elements.py. It was written using
Visual Python and version 2.7. Can you get it running in v3?
Bottom line: it is crucial that you begin SSP familiar with programming in general and Py-
thon in particular. Then you’ll be less likely to get stuck for hours and hours of frustration, trying
to debug your program. In case you need more convincing, heed this advice from recent alumni:
“I wish it had been made mandatory or more urgently stated to learn program-
ming beforehand, because I didn’t think it would be that important, and ended up
struggling with programming because I was so unprepared.”
“LEARN PYTHON BEFOREHAND! I am not kidding!!! I saw the advice in the
Handbook, I didn't listen, and as a result, I struggled with Python throughout
SSP. At least 75% of the time you spend on p-sets will be programming. Also,
learn VECTORS and MATRICES!”
Math & Physics
Study or review as necessary and time permits:
Trigonometry: arrive with a very thorough understanding of trig functions
Vectors: cross products, dot products, and their uses
Introductory Calculus: We’ll devote one lecture to a review of differential calculus, and an-
other to integral calculus, plus an optional tutorial or two. If you have not taken calculus,
study the basics before you arrive. Ask your math teacher for help.
Introductory Physics: the relevant topics to learn or review are mechanics and gravity, and
the laws of Newton and Kepler.SSP Participant Handbook page 10 Astronomy Few participants arrive knowing much about astronomy beyond the names of the planets. SSP is a hands-on research program and not a regular course in astronomy (or anything else). We teach the concepts needed for observational astronomy: celestial coordinates, the ecliptic, celestial equator, sidereal time, etc. Learn about that before you arrive. Start with the introduction to asteroids at http://b612foundation.org/asteroids-101, and explore the links there. Then visit the JPL Small-Body Database Browser to display the orbit and current posi- tion of the asteroid named after SSP: “6962 summerscience”. Visit http://neo.jpl.nasa.gov/orbits/ and enter “summerscience” as the object name.) Online college courses might be of benefit. Edx.org hosts four classes from Australian National University that are approximately equivalent to the first year of the required courses in an astro- physics major. Univ. of California at Berkeley (webcast.berkeley.edu) offers a series of ~25 video lectures for Introductory Astronomy. Within Astronomy C12, these topics are the most relevant: Gravity Force, Newton's Laws Tides, Energy, Momentum Asteroids, Comets, Pluto and Kuiper Belt MIT Open Courseware has two courses of note at ocw.mit.edu: 12.400 The Solar System and 12.409 Hands-On Astronomy: Observing Stars and Planets. The “study materials” in 12.400 in- cludes a PDF titled “Orbital Elements” describing the six orbital elements that you will calculate for your asteroid. Finally, check out this free, online Astronomy textbook from Openstax. Biochemistry Read selected sections (listed below) from Biochemistry Free For All by Kevin Ahern, Indira Ra- jagopal, and Taralyn Tan. This book is available free from Oregon State’s website. Kevin, Indira and Taralyn's latest (FREE) electronic book is aimed at helping students at all levels of biochemistry to learn in a fun and engaging format. The iBooks version can run on an iPad or a Mac running iBooks. The PDF version can be used on any computer. Please note that the file is VERY large and will take considerable time to download. Required study from this textbook: Introduction: Basic Chemistry (pp 24-29) Introduction: Water and Buffers (pp 33-48) Chapter 2: Structure and Function (pp 52-93) Chapter 4: Catalysis (pp 335-389) Basic Techniques (pp 855-884) For your convenience, selected pages are saved in this PDF. Study this material carefully and thoroughly, as you will need to know it when you arrive. If you have time, read other sections of the book – but not at the expense of skimming through the re- quired sections. Fair warning: the entire textbook has 3,500 pages!! About Evaluation During SSP you will not be tested nor graded. Problem sets and reports are checked and returned to give you useful feedback.
SSP Participant Handbook page 11 Throughout the program, the faculty will pay close attention to your attitude, motivation, team- work, and observance of the Honor Code … how you treat others. Such informal, continuous eval- uations are common in organizations of all kinds. And, you will evaluate the faculty in an anony- mous exit survey. In these ways, we are again modeling a professional workplace. Following your successful completion of SSP, you will receive a letter of completion suitable to include with college applications. It will describe SSP, but will not include any evaluation of your own work. You may later request a letter of recommendation from any faculty member. They are not obligated to write one. Whether they will write a letter for you, and what they will write, will be based on the entire faculty’s observations of your attitude and conduct during the program.
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