ARIP 2017

Page Contents

Advanced Research
Internship Program 2017

We are in the midst of the Advanced Research Internship Program (ARIP) for 2017, in collaboration with the AGM Institute.

Program participants should refer to this web page (see below the syllabus) for information and assignments for the online week, beginning July 10, 2017.

ARIP 2017 Syllabus

We are following this syllabus, and we will fill in details as events and venues are confirmed. Note that this outline is subject to change as we adapt to program needs.


L = lecture
G = group discussion/activity
F = field collecting
T = tour/trip
R = research lab activity

On-Line July 10–15 Research reading
0 Su 16 July Arrivals in L.A.
G: Welcome dinner and orientation
1 Mo 17 July L: Introduction to the program (in Mark Ridley Thomas Center)
T: Behind-the-scenes tour at Natural History Museum of L.A. County
G: Using the scientific literature
L: Animal diversity
R: Begin sorting samples from seafloor grab
2 Tu 18 July F: Collecting at King Harbor marina floating dock
T: Seafood lunch and crustacea dissection
R: Sample sorting, identification, and processing
3 We 19 July R: DNA extraction from specimens (8am)
T: Visit USC campus and admissions (11:45am – 1:15pm)
T: California Science Center: space shuttle (2pm), ecosystems, IMAX movie (4pm)
R: PCR prep tutorial
4 Th 20 July R: DNA amplification of specimen extracts (8am at USC lab)
G: Scientific communication; research presentation workshop
G: Begin Materials & Methods written activity
R: Sequencing gels (then PCR product sent out for sequencing)
5 Fr 21 July T: Visit Malibu, Pepperdine University
T: Santa Monica Mountains Recreation Area
6 Sa 22 July T: Day trip to Catalina Island — USC Wrigley Marine Science Center
7 Su 23 July R: DNA sequence processing
L: Channel Islands; Chaparral; E/V Nautilus
G: Writing good résumés and getting good letters of recommendation
G: Research presentation discussion
8 Mo 24 July T: Visit La Brea Tar Pits Museum
T: Visit Farmers Market and The Grove
9 Tu 25 July F: Intertidal collecting trip to San Pedro (sunrise 6a, tide -1.0 ft at 5:34)
T: Beach time at Cabrillo Beach
T: Visit Cabrillo Marine Aquarium (noon)
G: Research presentation prep
L: Trees and phylogeny
T: Visit Butterfly Pavilion and visiting exhibit (Extreme Mammals) at NHMLA
10 We 26 July R: Specimen data and specimen photo posting to Barcode of Life Database
G: Research presentation prep
11 Th 27 July R: Molecular sequence and tracefile posting to Barcode of Life Database
G: Getting into U.S. colleges and college life
G: Lunch in the lab
G: Materials & Methods revisions
12 Fr 28 July 10:00a – 11:00a Research talks (5)
11:30a – 12:30p Lunch
12:30a – 01:30p Research talks (5)
01:30p – 02:30p Break
02:30p – 03:15p Research talks (4)
04:00p Closing ceremony (in NHMLA MBC lab)
06:00p Farewell dinner
13 Sa 29 July Departures

Day 11 (Thursday) Documents

Talking Science, Speaking Powerpoint
Reference formatting guidance
Tracefile and sequence uploading

Day 10 (Wednesday) Documents

Sample ImageData.xls spreadsheet contents
Guidance on entering BOLD specimen data

Day 9 (Tuesday) Documents

Trees and phylogeny lecture

Day 3 (Wednesday) Documents

Molecular replication lecture
Polymerase chain reaction (PCR) video I
Polymerase chain reaction (PCR) video II

Here is the paper on the molecular primers (the “Geller primers”) that you will use:
Geller, J., C. Meyer, M. Parker, and H. Hawk. 2013. Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys. Molecular Ecology Resources 13:851–861.

Day 2 (Tuesday) Documents

DNA extraction protocol

Day 1 (Monday) Documents

Introduction to ARIP
The DISCO program
Finding the scientific literature (sample paper)
Animal diversity

First Week Online Activities

During this first, online week of the ARIP program, we have two goals. One is to familiarize you with reading real research papers: the scientific literature. The other goal is to familiarize you with some of the genetic biodiversity concepts you’ll be working with during the on-site two weeks of the internship.

Understanding the content of these papers is very important for doing well in the internship. You will be expected to know these concepts and be able to work with them once you are here. We know they are complex ideas, and we know that learning them directly from the actual research literature (not popular articles) is difficult. But that’s why you are participating in this internship. You will work hard. In return, we will work hard to give you all the help and information you need to do well — that is why we are participating.

The way this will work is that there will be a series of daily reading assignments. Each day you will be required to complete a brief quiz about the reading for that day. That quiz will be available for only 24 hours — you must check in here and complete the quiz sometime during the 24 hour window for that day’s reading.

To be completely open with you: the purpose of those quizzes is not to grade or rank your performance, but to ensure that you do some of the reading each day. If you could leave it all to one session at the end, there is no way you could get good comprehension!

All the materials are available to you now (see links lower on this page), so feel free to read ahead! But, again, you will have to return to this web page each day to complete each day’s questions on the assigned day.

What if I have questions about the material or the assignment?
Feel free to send email with questions to me (Dean Pentcheff). I’m managing the online portion of the course (I’ll also be participating in leading the on-site part). You can reach me at: .

What if I will be unavailable or travelling on one or more of the assignment days?
Send me an email (to and I’ll get the day’s questions to you by email so that you can complete them on a different day.

What time of day will the day’s questions become available (and when will they disappear)?
Each day’s questions will become available at 00:01 (one minute into the day) on the day of the assignment, and will close at 23:59 (one minute before midnight) on the day of the assignment. All dates and times will be in Pacific Daylight Time (PDT UTC-7).

Online Day 1 (Monday) July 10 — Reading a scientific paper

We‘re starting easily. Today there are two online articles we‘d like you to read that will help you learn how to (constructively) read a scientific paper.

Reading 1: How to read a scientific paper

Reading 2: How to read and understand a scientific paper: a guide for non-scientists

Read both of these to prepare yourself for reading the scientific papers over the next few days. These guides refer to two kinds of scientific papers: primary research papers and review papers. Most of the papers we‘ll have you read are review papers — they summarize the work reported in many other papers. Because of that, they will not be broken into the structure of a typical primary research paper (Introduction, Materials and Methods, Results, and Discussion). However, the analysis you will need to do as you read (for example, looking up every single word you don‘t understand as you read) is the same for primary and review papers.

This quiz is now closed.

Online Day 2 (Tuesday) July 11 — Genetic barcoding

“Genetic barcoding” is a technique being applied to biodiversity research, and is a core technology you will use and learn in this internship. These two papers give a bit of perspective on the technique. The first was written over a decade ago as barcoding was just being developed. The second looks back over the decade of development and summarizes how the field has grown.

Reading 1: Savolainen, V., R. S. Cowan, A. P. Vogler, G. K. Roderick, and R. Lane. 2005. Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences 360:1805–1811.

Reading 2: Hebert, P. D. N., P. M. Hollingsworth, and M. Hajibabaei. 2016. From writing to reading the encyclopedia of life. Philosophical Transactions of the Royal Society B: Biological Sciences 371:20150321.

This quiz is now closed.

Online Day 3 (Wednesday) July 12 — Metabarcoding entire communities

One of the really exiting ways we can use genetic barcodes is to describe entire marine communities based just on seawater samples (by sequencing and identifying the DNA that organisms shed into the seawater). This paper is a recent example of that kind of work. (Note that this is a primary research paper, a report of novel work, unlike the rest of the papers we are having you read, which are review papers.)

Reading: Kelly, R. P., J. L. O’Donnell, N. C. Lowell, A. O. Shelton, J. F. Samhouri, S. M. Hennessey, B. E. Feist, and G. D. Williams. 2016. Genetic signatures of ecological diversity along an urbanization gradient. PeerJ 4:e2444.

This quiz is now closed.

Online Day 4 (Thursday) July 13 — Barcoding and biomonitoring

A key application of barcoding, particularly of entire communities, is the potential it has for letting us monitor biological changes more frequently, more cheaply, and in more detail than traditional techniques.

Reading: Thomsen, P. F., and E. Willerslev. 2015. Environmental DNA — An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation 183:4–18.

This quiz is now closed.

Online Day 5 (Friday) July 14 — Barcoding and taxonomy

The science of taxonomy is the discipline of classifying organisms into some sort of understandable system. It has taken us a couple of centuries to name and describe about one million species. We think there are something like 10–100 million species on earth. Clearly, we have a lot of work to do. These two papers give a little perspective on how genetic barcoding may help us.

Reading 1: Page, R. D. M. 2016. DNA barcoding and taxonomy: dark taxa and dark texts. Philosophical Transactions of the Royal Society B: Biological Sciences 371:20150334.

Reading 2: Blaxter, M. 2016. Imagining Sisyphus happy: DNA barcoding and the unnamed majority. Philosophical Transactions of the Royal Society B: Biological Sciences 371:20150329.

This quiz is now closed.

Thanks for participating in the online week! We will see you soon in Los Angeles.