How-To: Stage-Structured Matrix Models

Happy Thanksgiving everyone!

So this week I constructed several stage-structured matrix models- aka Lefkovitch models- to estimate the finite and intrinsic rate of increase of the weevils Neochetina eichhorniae and N. bruchi under laboratory simulated Fall and Winter conditions in the Sacramento-San Joaquin River Delta. This work is in conjunction with a postdoctoral researcher- Angelica Reddy and Paul Pratt’s laboratory at the USDA to test the temperature performance of these biological control agents.

As you know, if insects are adapted to warm weather- they don’t perform very well in colder temperatures and this can be very applicable to biological control agents (such as the two Neochetina weevil species) that are brought from their tropical origins to colder regions to control invasive species.  Below is a cute cartoon I had a scientific illustrator Jacki Whisenant draw for me, and for a new children’s book we are writing…stay tuned!

ChillyWeevil
Copyright 2017, illustration by Jacki Whisenant and made for Julie Hopper

Because we are working in the laboratory on these two species we are able to gather a lot of life history parameters of the weevils undergoing Fall and Winter conditions. These parameters include: development time and survivorship of the different insect stages (egg, III instars of larva, pupa, pre-reproductive adult and reproductive adult), as well as the emerging sex-ratios, and longevity and daily and lifetime fecundity of the reproductive female adults.

From these parameters we can conduct several different analyses to approximate the finite rate of increase, intrinsic rate of increase, generation time, doubling time and net reproductive rate of a species to understand more about their potential population growth rates (which of course is important for biological control).

My favorite way to approximate these population growth parameters for insects is to use a stage-structured matrix model (Lefkovitch model). There are other methods you can use as well- but I won’t go into that here. If you would like to read more see the citations at the end of this blog.

Instead, I will provide a how-to tutorial since while I was working on these matrix models as a graduate student- I realized there is a lack of tutorials on the web on how to construct these models in an intuitive manner. I got lucky  as both my PhD adviser and one of my lab mates (whom had already done the research on stage-structured matrix models) helped me understand how to construct and interpret the models. In the name of paying it forward- I am attaching here an excel worksheet that has all of the calculations and formulas that demonstrate how to construct these stage-structured matrix models (see link). 

Julies_tutorial_example_matrix_for_popbio

In my next blog- I will detail how to use this resulting matrix and input it into the package popbio (Stubben and Milligan 2007) for calculation of finite rate of increase (lambda), intrinsic rate of increase (r), doubling time, generation time, net reproductive rate and much more!

Disclaimer- this is for insect stage-structured matrix models only as calculations differ for plants and vertebrates typically.

Here are some of the calculations that are built into the excel formulas: 

Screenshot 2017-11-22 12.53.45

Below is another screenshot of the file: 

Screenshot 2017-11-22 12.57.42

Below is a diagram from the famous study on Loggerhead sea turtles that explains the flow of this matrix better. However be aware that the matrix above and in the attached excel sheet-calculates gamma as 1/duration which is very different than the famous example on turtles (below), and from any matrix with plants- mainly due to life history differences among plant, invertebrates and vertebrates.

Screenshot 2017-11-22 13.10.04.png
A Stage-Based Population Model for Loggerhead Sea Turtles and Implications for Conservation Author(s): Deborah T. Crouse, Larry B. Crowder, Hal Caswell Source: Ecology, Vol. 68, No. 5, (Oct., 1987), pp. 1412-1423

References 

Caswell H (2001) Matrix Population Models: Construction, Analysis, and Interpretation. Sinauer Associates, Sunderland


Resources:

Awesome powerpoint by Chris Free at Rutgers 

Another awesome tutorial on primarily the Leslie matrix from UCSC

 

 

Advertisements

Invasive Weed Alert! Alligatorweed in the Delta and Suisun Marsh, California

I just received word from Louise Conrad (Department of Water Resources) that there have been recent sightings of Alligatorweed (Alternanthera philoxeroides) in both Suisun Marsh and the Tower Bridge marina in the east Delta. This is a new, noxious, weed to the Sacramento-San Joaquin River Delta system and we should all be on the look out (see photo above and below).

This invasive weed, native to South America, forms floating mats but it is rooted in sediment and has submerged, floating, and emergent forms. This invasive weed can survive a wide range of environmental conditions making it particularly threatening to both aquatic and terrestrial ecosystems.    For more information on this weed- please see: http://www.sms.si.edu/irlspec/alternanthera_philoxeroides.htm

In California, currently this weed has been documented near Grizzly Island in August, 2017 and from two other sites further up the Montezuma Slough channel in September.

The introduction point is unknown, but it is clear that this weed is in the Sacramento River and has now moved into Suisun Marsh.  Other naturalized locations can be expected.  A rapid response to the alligator weed in Suisun is warranted before this invasion compromises planned tidal wetland restoration projects.

On a related note, the invasive yellow flag iris (Iris pseudacorus), and  Ludwigia hexapetala  (Uruguayan primrose-wllow) are also spreading in these same areas and should be reported as well if found (see details for contact info below).

 

Alternanthera_philoxeroides_discoverlife.org
High densities of Alligatorweed (Alternanthera philoxeroides), forming dense mats. Also called “Pig Weed”. Photo credit: http://www.discoverlife.org

KEY ACTION POINTS: If you find new populations of alligatorweed (or the other weeds mentioned above) please take photos, GPS points (can be via your smart phone), and a voucher specimen (if possible) to send/email to the State Taxonomist, Genevieve Walden, at CDFA Genevieve.Walden@cdfa.ca.gov

 

It is crucial to notify Genevieve Walden as we need to document the extent of the problem. If we are not able to control the spread of this weed immediately it will result in similar issues and problems resulting from Brazilian Waterweed, Water Hyacinth and Water Primrose.

What happens if this weed spreads you ask?


Biological control is a possibility, and in fact, one of the biological control agents, the alligatorweed flea beetleAgasicles hygrophila, has the distinction of being the first biocontrol insect released in the U.S. in order to combat an invasive aquatic weed!

ahygrophila1
Agasicles hygrophila, Photo Credit: http://www.sms.si.edu/

Overall, management impacts on alligator weed by the alligatorweed flea beetle have resulted in a dramatic decrease in the amount of infested aquatic habitat since the insect was first released.

However, the most effective and easiest solution to combating alligatorweed in the California Delta and Suisun Marsh regions is to prevent it from spreading in the first place!

 

 

 

 

How to Get into Grad School: Part I

The past month has been crazy again (or maybe this is just how I start all my blogs?).

My husband and I made the big move to Los Angeles as he started his PhD program at the University of Southern California (USC). In-between moving,  I’ve been driving back and forth between LA and the Bay Area to finish up my lab work for my current postdoc position so that I can get all of my data and remotely work the rest of the year in LA.

Screenshot 2017-09-29 14.38.51.png

When Im not in the Bay Area living the couch surfing and pipetting life style, I’ve been surveying my favorite coffee shops in the West-Adams area (so far Nature’s Brew and Cafe Ignatius are the winners!) and submitting postdoctoral research proposals for several fellowships as well as applying for jobs.. real big time professor jobs!!! Fingers crossed that something comes out of all of this!

However, while I was working on all of my research and teaching statements, I realized that it might be useful if I posted a blog on the how-to’s of graduate school.. since I have now successfully put that behind me.

For Part I, I will focus on just the ‘admissions’ aspect of graduate school.

I will have a Part II later on with details on how to succeed and survival it all.

Disclaimer: This advice mainly pertains to PhD programs and STEM fields, and may differ slightly if you are applying for a masters degree or other programs (non-STEM).

61BeeTO-NQL._AC_UL130_

Part I: How to Get Into Graduate School


A: What to do as an undergraduate to prepare for applying for Graduate School?

EXPERIENCE EXPERIENCE EXPERIENCE! Get involved in whatever research opportunities that you can. Don’t be too picky if it is your first research experience, since opportunities lead to more opportunities and every opportunity will give you a little bit more insight on what you are passionate about. Furthermore.. every research project should have the same fundamental scientific process (or it should anyhow) and so you will learn about science and how to conduct research by taking advantage of research opportunities that are available. After you have a little bit of experience, try to conduct your own independent projects either in a class setting, under the mentorship of a professor, postdoc or graduate student and/or apply for undergraduate research fellowships.                      

MAKE CONNECTIONS WITH PROFESSORS & RESEARCHERS- In addition to going to office hours and talking with researchers at your University, research experience will also help you establish real connections to professors, postdocs, and graduate students. Connections are critical for meaningful letters of recommendation, as well as getting advice on your next steps, regarding what research programs, advisers and universities are a good fit for YOU!

GRADES AND GRE SCORES…do they matter? 

phd120902s          Short answer: Yes, but don’t kill yourself over it. Long answer: As long as you don’t have horrible grades and GRE scores (e.g. B’s are fine, and being in the average range is fine), your research experience and personal character will be just as important to the graduate admissions committee.  Regardless, since you still have to take the GRE for most university programs, start studying at least 6 months in advance of your test date.

B: How the Heck do you Choose a Graduate Program and/or Adviser?

  1. Figure out what you are passionate about!!! Think about what research projects and what types of courses inspired you? The ones you liked studying for? Maybe this is a clue to what you are passionate about!Hopefully your research experience and courses as an undergraduate can give you a head start on this critical component. If you need more help on finding out what really moves you- go to your school library and sit down with some various peer-reviewed research journals (Science, Nature, Ecology, PNAS, etc) and browse through them until a topic hits your interest. You can also browse an Internet research browser such as ISI web of science, but this is a bit harder if you don’t know where to start!
  2. Do you have any location limitations for graduate school? Write out a list of places you would be willing to live (or not to live in).
  3. Browse the faculty members and their research profiles at prospective Universities that you would like to go to.
    1. Look at their CVs, and the publications they have produced
    2. Look at how many graduate students they have mentored and how many students have graduated.
    3. Read several publications and see what they are currently working on.
    4. If any of their research interests you: EMAIL THE PROFESSOR!!
  4. Email the Professor of interest and think about Applying to the University 

The email should go something like this: (substitute specific and personal items for XYZ)

 Dear Professor XYZ,

            I am very interested in your research on XYZ because I have experience with xyz ….. I read your article entitled “XYZ” and was particularly intrigued in the fact that… ……I would love to focus on this research area for my PhD at the University of XYZ in your laboratory. Would you have any time to discuss the potential for working in your laboratory? If you do not have available funding or positions, would you be willing to work with me to apply for funding or able to recommend another laboratory in this field of research?

I have also attached my resume for your review. 

Thank you for your time, XYZ

  1. Email a ton of other professors as well (don’t put all your eggs in one basket!)
  2. Look at other research profiles at various Universities
  3. Think about possible grant-writing opportunities and come up with a rough-draft proposal if you think you need to take this direction.
  4. Email professors again (in two weeks) if they haven’t responded.
  5. Don’t take a lack of response or rejections personal
  6. Schedule interviews (phone, Skype or In-Person) for yourself with the professors you emailed if they respond positively. I actually scheduled my own meetings with professors I wanted to work with at UC Berkeley since I was in town for a week coincidentally, and I think that helped! 

5. Have an Interview?! Dress nicely (even in on the phone!) be on time, and come prepared (e.g. read all the papers you can in the area of research you plan on discussing with the Professor.. particularly the articles the professor authored!). Provide your thoughts on some of the theory in the field and ask lots of questions.

C: How do you apply to a graduate program? and When?

****Establish Connections****Hopefully from the above, you can see how important it is to establish a connection with one or more professors from the program and university of your interest.

PUT A LOT OF EFFORT INTO YOUR PERSONAL STATEMENT and/or STATEMENT OF PURPOSE: You should be passionate about something and this should be very apparent in your  statements. Be careful and stay honest. Don’t say you have experience with things that you don’t, and don’t propose an area of research that you are not interested in. Also, if you are interested in Ecology, Evolution and/or Environmental Science- it is beneficial to list specific faculty that you have already made contact with, and state how your interests align with their research. For MCB/Chemistry and maybe some other departments- my understanding is that they mainly do lab rotations, and so you would want to list several faculty at least.

For your personal statement, let the admissions committee see who you are as a person, and how this has contributed to your passion in the field that you are applying to. What sets you apart from others? Bring in your personal story- how you grew up, your cultural and economic background (the latter only if you had disadvantage and you overcame it).

These statements are tremendously important, so proof read your statements (grammar/spellcheck!). Send your statements out to former grad students, postdocs and faculty that you worked with during your undergraduate years for more feedback. Don’t forget to tailor the statements to each of the schools you are applying to and be careful if you are copying and pasting to not list a different school for the current school you are submitting your essay to.

Do not underestimate the power of these statements. 

Timeline: You should be studying for the GRE’s around June-August, Take the GRE early in case you need to retake it, make contact with prospective advisers/labs around August-October, working on your statements in November/December and applying for Schools in December/January. * Note this is mainly from my experience with schools in the USA and may vary across the globe.

D: Congrats- you got in to multiple places! How do you choose?

phd0406s

If you get into multiple places- make sure you visit each University and each prospective lab that you would want to work in. For the University level: Do you like the location? e.g- would you be happy with  climate and surrounding area? Does it suit your personal life? e.g. If you have a partner- how do they feel about relocating to that area? How does the University compare to your other options in terms of reputation and funding?

For the Department Level: What is the funding situation like? How much money will you make and is it enough to live off of in the surrounding area? Do you need to teach? If so how much would you teach? Teaching is great,  but you don’t want it to interfere so much with your research that it takes you 10 years to graduate! Will you have health insurance? How are the benefits compared to your other options? Also- how is the social culture in the department? Do faculty, postdocs and graduate students all work together well? Are there at least some social events that the Department hosts? Do graduate students seem happy? What are the career support options? (eg. do they have a career center or folks that can help you with job applications when the time comes?)

Lastly and perhaps the most important:  At the Lab/Adviser level:

What is the adviser like? Is he/she hands-on or hands-off? Which of these suits you best? Are there lab meetings or does the professor (adviser) schedule one-on-one meetings with the students? How available is the professor? e.g. – Are they chair of the Department? If so then just keep in mind they might be more busy than other professors and might be more hands-off while they have that position (doesn’t always hold true, but something to ask them about at least if they do have a demanding position).

Are the graduate students in the lab relatively happy and productive? Have the graduate students published papers in a timely manner? Have former graduate students secured relevant jobs (government/academia/biotech)? Does everyone in the lab seem to work well together?

What are the laboratory facilities like? Do you have access to all of the equipment/materials that you need (either in the prospective lab or in willing labs nearby?) Are things relatively organized, clean and safe?

Does the research still interest you when compared to your other options? Lastly- is the research in an area of high funding? This might be important if the Department can’t pull together enough funds for your research or stipend.

Weigh all of your pros and cons and then go with your gut feeling! Good Luck!

 

 

 

Society for Invertebrate Pathology, 2017

This week has been intense and fun, as yesterday was the last day of the five-day SIP Conference  (Society for Invertebrate Pathology) in San Diego California!

This society and conference focuses on invertebrate pathogens, with seven different divisions, and works in conjunction with the Journal of Invertebrate Pathology.

Divisions
The seven divisions that make up the Society for Invertebrate Pathology (source: http://www.sipweb.org/)

Personally I am the most involved in the Microsporidia division, but have been attending some tremendously interesting talks across all of the divisions!

As my current postdoc work is not focused on pathogens, I presented a poster at this meeting on a side project that I did in 2013 where I surveyed local honey bees for Nosema apis and Nosema ceranae (microsporidia) in Mo’orea and Tahiti, French Polynesia. Below is a clip of my poster!

Slide1

Some of my favorite talks have ranged from discussing the ‘Pathobiome (discussed briefly in this linked article)‘ to Biological Control of Bed-Bugs using Beauveria bassiana (in video form here) to Nematode behavior and host searching (nematodes are so cool!), to the talks in the symposium featuring Ann Hajek and David Shapiro Ilan’s new book “Ecology of Invertebrate Diseases” with many of the great authors highlighting findings of their specific chapters (release date is November 2017!).  I also of course enjoyed hearing all of the famous microsporidian researchers discuss their work in the Microsporidian Symposium, including the work of four microsporidian researchers I hadn’t met in person prior to the meeting: Charles Vossbrinck and his work on the phylogenetics of microsporidia, Joe Maddox, John Henry (his work on the biological control of grasshoppers with Nosema locustae) and Louis Weiss’s work on human microsporidia (and of course on the similarities/differences to microsporidia in invertebrates). Here is the full meeting program from this year.

IMG_7541
Most of the participating Microsporidian researchers after our symposium

I also attended a workshop on RNAseq and Bioinformatics on Monday evening, and learned about the wonderful online GUI platform: Galaxy. This is a great platform to upload your RNAseq data and to do bioinformatics WITHOUT ANY CODING! WOW!

As the Student and Postdoctoral Chair for SIP, I was also responsible this year for organizing the youtube video contest (see all the winners here!), and the workshops and meetings for the students and postdocs. For the Student Workshop this year, we had a workshop on Science Communication- including how to work with the press and media, giving an elevator talk, and using social media to your advantage. (If you are interested- you can read more about some tips for science communication here). Then for the student business meeting, all of the students and postdocs (myself included) discussed what they would like to see in future SIP meetings (workshops on career opportunities, and scientific writing seemed to be the most popular requests!).

It was fun interacting with all of the students and postdocs, but definitely resulted in a busier conference than I’ve ever had before… it was difficult to get in my workouts- but nevertheless I succeeded with fitting some short workouts in and still have my ~ 10 year streak going (haven’t missed a day since Oct. 2007.. and that was because I was on a plane to New Zealand for almost 24 hours…)…

The other awesome part about this conference is that every year we spend half of a day going on group excursions. This year we went to the San Diego Zoo (and some folks did the Midway Excursion) – and it was a great chance to catch up with other researchers about both life and science!

In addition, every night we have social events ranging from a BBQ (this year there was no BBQ meat though which was funny- but we had fantastic tacos!), A Welcome Banquet and a Goodbye Banquet with Dancing (the last night is always the best!).

We also have a 5K run/walk every year- which I  usually attend but this year I stayed at a friend’s house a bit far away from the conference and couldn’t manage to get up early enough for that… ha (5:30am wake up I think not!).

And with that, I look forward to next year’s SIP conference in Australia (I’m trying to research potential fellowships for that as I will not have my current fellowship at this time next year).

Traveling in Cuba as an American

Cubacarte2015
Photo from cubacasas.net

I haven’t posted for awhile as in addition to recently getting back from our 10 day honeymoon in Cuba (followed by a cousin’s wedding in the DR)- we are preparing to move to LA (my husband is starting his PhD program at USC soon)!  This past month has been a whirlwind- but all in all a good time and Cuba was certainly an adventure (complete with ups and downs!).

Cuba isn’t one of those places you go to just flop down on a beach chair and drink all you can drink piña coladas while you relax. In my opinion -Cuba is a place you go to understand and appreciate the culture, and to learn more about how a socialist society operates.

I’ll detail our trip in my next blog- but first here is some of my advice, How-tos, and insights on traveling in Cuba. 

IMG_7293


  1. You have to designate your travel under one of the 12 reasons for travel. 
    • We went under the “People to People” travel which falls under the ‘Educational activities and exchanges’ category I believe. We were required to keep a journal documenting our daily activities and exchanges with the Cuban people. We did things like teaching capoeira to Cuban children in Habana, Beach Cleanups (and talking to the locals about the trash on the beaches), and just talking with everyone that we possibly could (taxi drivers, airbnb owners, shop owners, musicians, folks walking on the street, etc. ) Note- travel is subject to change under the new rulings under thou who shall not be named, but you should be good to go in the next couple months still and see more details here if you plan to fly via Southwest like we did
  2. You should pre-budget everything and bring all cash with you (Euros or Canadian dollars are best). American credit cards/debit cards don’t work. Really.. I tried. I even called Navy Federal Credit union which allows for cards to be used in Cuba… but looks like Cuba still didn’t let my card go through regardless. Don’t bring US dollars because Cuba charges you 10-13% for exchanging Dollars for CUCs… Just bring EUROs and you will have an easier time. Also bring about 200 EUROs more than you think you will need… more on that later.
  3. If you want to travel around cheaply- reserve a Viazul Bus about 10 days ahead of time online. Or you should plan on getting lucky hitchhiking, taking a local taxi ‘collectivo’, or paying a ton of money out-of-pocket for a tourist taxi. (I’ll write more about this in my next blog …ugh).
  4. Practice your Spanish before going if you are not fluent already. I speak portuguese and had a decent enough vocabulary in “Portenol” to get around and have conversations with folks- and it helped us out a lot. I used DuoLingo to brush up before I left.
  5. Airbnb reservations are likely the best way to reserve places for Americans.  This and online reservations with anything really will help with lowering the amount of cash you carry on you while in Cuba. Many Cubans rent their “casa-particular” out with personal websites, in-person advertisements in Cuba, and on Airbnb. Typically the Airbnb rates are a bit more than what you would pay in-person, but again the online pre-pay feature of Airbnb is worth it.
    IMG_7057
  6. There are two currencies in Cuba: Cuban Pesos (CUP) and CUC. Pesos are worth way less than CUCs (25 CUP is worth 1 CUC about). Don’t exchange money with people on the street- this is the easiest way to get scammed, as they can hand you back pesos instead of CUCs for your Euros. See photos below. Keep in mind there are coins also that differ between these currencies but look similar to a new tourist. 
  7. The down-low on food:
    • Do Not expect great food at hotels/resorts. Your best meals will likely be at the most random unexpected places, and not necessarily in your Cuba Guide Book. We stayed at the Maria la Gorda Hotel for three days to go scuba diving and have time at the beach, and the buffet breakfast was not good. They tried their best, but the unfortunate truth is that the government limits how much hotels and resorts can obtain/spend on food and facilities. We did find that the shrimp at their dinner restaurant was great!
    • The best food we had was:  eating fresh fruit from the local market (pineapples and large mangos are 10 pesos each (CUP) which is almost 1/3 of a CUC, avocados are 8 pesos and limes are 2 pesos), fresh bread from the bakery (price varies depending on size of bread- but about 10 pesos will get you enough bread for two people), and fresh eggs (10 pesos each) from the egg man (notice how there are little shops for everything). A full and large breakfast (eggs,bread, fresh fruit and coffee) for two people was less than 2 CUC. You can also just grab an egg and bread sandwich for 10 pesos from a street corner ‘cafeteria’.
    • And the best restaurant we ate at was actually someone’s house.  We ate on the footsteps of this woman’s (Cari) house in Habana Vieja. Beans, Rice, Fried Chicken and Salad for 30 pesos (about 1.10 CUC which is about 1.10$ Us dollar)… It was fantastic, not to mention the amazing sights and sounds of the neighborhood coming alive in the evening. The address for her restaurant/house is:  105 Santa Clara, Habana Vieja Cuba. Below is a picture of me and Cari in her house after a wonderful meal. She even wrote me out the recipe for the Cuban Beans and wouldn’t even accept a tip after we came back the second night. You have to go here and have a meal and tell her that Julie and Gerid recommended her restaurant. And no we did not get sick.

      IMG_7210.jpg
      Cari and I at her restaurant: 105 Santa Clara Ave, Habana Vieja, Cuba
  8. Bring a water filter! We brought this gravity-operating water filter (gift from my cousins!) and hardly ever bought water. Although the water in Habana (Havana) is supposedly safe for tourists we did not try it and did not meet any other tourists that tried it either. However after seeing all the construction going on and pipes being worked on- I’m glad we did not try it. We saved a ton of money and did not get sick from the water we filtered (I did get sick however from eating an egg-sandwich at the Jose-Marti Airport.. ugh).
  9. Souvenirs: Make sure your artwork comes with a valid certificate (otherwise you will pay 40 CUC at the airport for it). We paid 45 CUC including the certificates each for two nice and large paintings. If you buy cigars on the street (not recommended, but if you have someone trustworthy then it is cheaper than the factory)- make sure that the cigars have a seal on the box so that you can take them home.
  10. Racism exists in Cuba… but most of the light-skinned Cubans will deny this. Not all  Cubans are racist by any means, but my husband (who is African-American) was treated miserably by our first Airbnb host lady, and was stared at on the street a lot by many Cubans (and no it wasn’t because they couldn’t believe how handsome he is). For example-our first airbnb lady made breakfast for us everyday and was super nice to me, but barely looked at my husband in his eyes and couldn’t reply hello or goodbye to him most of the mornings (and she spoke perfect English). My husband and I weren’t the only ones to notice the covert racism. We went to this amazing ARt/Music/Dance collective: Fabrica del Arte in Vedado, Habana (a must-see if you visit Habana!)- and were struck by the art piece below. We even had a conversation with a local Afro-Cuban that was so ecstatic that finally someone was conversing about the issue of racism in Cuba.

    IMG_7177
    My husband and I mad about racism in Cuba.. this piece of art at the Fabrica del Arte Cubano (FAC) in Vedado, Habana, Cuba depicts this perfectly.
  11. Scams are everywhere and are incredibly annoying: Some of the scams that we encountered (and did not fall for) were: 1) overpriced taxis, 2) currency exchanges on the street –and giving you back pesos instead of CUC (see above note on the currency), 3) ‘The Cigar Festival’... People will tell you ‘its the last day for the cigar festival, you should go and get good prices on the cigars’.. we never went to check it out but we know it was a scam because four days later someone said “today is the last day for the cuban cigar festival”..ugh!, 4) overpriced paintings that are not certified (They try to sell these paintings for 130 CUC instead of 45-60, and then in addition to that they do not have the certificates and lie to you saying that the certificates are 40 CUC… The truth is that the certificates are only 2-3 CUC, and if you don’t get a certificate with your artwork, then you will have to pay 40 CUC at the airport. My husband and I had two main rules to avoid scams: Do not let anyone lead you anywhere, and do not agree to anything right away.  Just tell them thank you and that you will check it out later. That will give you time to research whatever it is they are trying to sell you and discuss the pros/cons.
  12. Online Cuban agencies will likely rip you off. We used the CubanTravelNetwork to book our Maria la Gorda hotel and scuba diving (to not have to bring as much cash with us once we were there)- and they majorly ripped us off on the scuba diving packages. We overpaid them for scuba diving compared to what the hotel charged in person, and then on top of it our scuba diving equipment was not even included (which they did not tell us during the online purchase)- so we had to pay for that in person which we did not budget for.. ugh.
  13. Segregation of tourists and locals exists everywhere from the taxis to the Coppelia ice cream place (Vedado, Havana, Cuba)They have security guards which actually force you to go to the tourist sections of the ice-cream parlor (where they charge you more money). No thank you. In the end, we got our ice-cream at a small spot in Vedado for < 1 CUC each elsewhere. I’m all for giving to the local Cuban economy, but I prefer to do it via tipping rather than segregation.
  14. Socialism: Yes it is a socialist country- and it is evident in the fact that even the poor people are well taken care of in terms of housing, food, water, health care and education. I only saw one homeless person the whole 10 days we were there, and even all of the stray dogs and cats were fed every night via food on cardboard paper (I’m not sure who went around feeding them at night). I think this is also why all of the strays were  very nice and well-behave. However, in my opinion- if you want anything aside from the basic necessities- it is hard to do so in Cuba (unless you have family sending you money, or an extra house you can rent out as an air-bnb/casa particular). We did meet some people who felt trapped by the system. The  government has a lot of control on everything- evident from the rationed food at hotels/resorts, and from the fact that if you are born in the east of Cuba you cannot immigrate to Havana unless you become a police officer (thus many folks seek out that job). Coincidentally (or not) eastern Cuba is also the more Afro-Cuban region… again.. racism is very apparent in this country. 

  15. The Environment: I was a bit surprised when I got to Cuba because I had heard so many good things about all of their marine and land preserves, and about their efforts to preserve the environment. I did in fact go scuba diving in one of the marine reserves in Maria La Gorda- which was spectacular (lots of live corals and fish while scuba diving), but I was disappointed by all of the trash on the beaches, and even one of the scuba diving instructors threw his cup overboard on the boat ;(. The snorkeling was only so-so however at Maria la Gorda (lots of dead coral), but had some fish, and new coral growth on the docks was apparent. There are lots of land and marine reserves in Cuba.. it is true and these reserves are beautiful from what I saw, but in my opinion littering is a huge problem for Cuba. There was trash everywhere we went– from the streets in Havana, to the Malecon (a strip along the ocean in Havana), and on the beaches. Not to mention the fumes from all of the old cars. However in contrast, I did see a public outreach center in Havana about preserving native species, and the negative effects of littering, fumes from cars, and invasive species. So one can only hope that more public outreach and education will preserve Cuba’s natural beauty. Speaking of invasive species – I did see water hyacinth in Pinar Del Rio, Cuba! I wasn’t surprised though since I knew that biological control using the weevils (Neochetina spp.) has been used in Cuba for controlling this invasive weed.

All in all, I still immensely enjoyed our trip in Cuba- and definitely saw some of the positive aspects of a socialist society. I fully recommend visiting Cuba, and experiencing it for yourself (Just bring enough money!).

IMG_7275
View of Havana, Cuba from ‘El Morro’ on our last night

Academia and Work-Life Balance

fwp-A-Healthy-Work-Life-Balance-webIn Academia, there is often a lot of chatter and inner-struggle concerning the ideal Work-Life Balance. Although it may be too early for me to comment on this (since I’m only a postdoc and I don’t have kids), I feel that I have a decent work-life balance. After all, I finished a PhD program with both my physical and mental health intact afterwards- so here goes some of my opinions on this much sought after balance.

First off – let’s address the statement “Academics are Work-A-Holics”: 


I always hear folks (including academics) complain about how academics work all the time. I experienced this firsthand since I grew up in an academic household and I saw how much both of my parents worked (my own dad even labeled my mom as a ‘work-a-holic’). Both of my parents are/were tenured professors and scientists, and my mom was Departmental Chair at one point at the Ohio State University.

I also saw how much my parents (and other academics) enjoyed their work, which I think is one of the main reasons of why academics ‘work’ a lot. I will linger on this for a second because: if you enjoy your work – is it truly ‘work’? Is this any different than an olympic athlete that trains constantly to achieve their goals/dreams? (Don’t worry.. Im still going to talk about enjoying life below this also). 

The concept of enjoying your work, and waking up excited to start your work day is more than most people outside of academia can say about their jobs. And yes, I realize that academia is a privileged job position to hold because of this very reason.

However even though academics self-identify as work-a-holics- I also see and appreciate the huge amount of flexibility that academics have for when and where they choose to do their work. My parents for example always made time for all of the important things- my gymnastics competitions, birthdays, family vacations… the list goes on, and of course they could take off work whenever I got sick. When one parent was writing a grant- the other parent would take me to a bookstore or to the amusement park (weather pending). My dad was actually the main chef, and we would have family dinners together almost every single night!

Now compare this lifestyle to the working family where both parents hold down more than one full or part time job… Or to a family of lawyers or doctors.. or business CEOs….How many family dinners do these families have? How many times are they able to take off work without penalties for when their kids get sick or have a special event?

If you keep this perspective – then maybe you will see my first main point.. that academia might actually be the most perfect job (if you can get a tenure-track position of course) to feed your soul and to have a decent work-life balance (with a little bit of effort of course).

In fact for me this hit home when recently my dad got terminally sick during my postdoc (metastatic cancer from a brain tumor) and I was able to work remotely in Ohio helping my mom provide at home hospice-care for him for almost two months! Although it was horrible watching my dad suffer, as well as knowing what was to come, I am so glad I was able to be there with him and my family during his last months.

How many other jobs would let someone take off two months and work remotely? Not many I bet. I also had a ton of support from colleagues and my research mentors which makes you realize that most academics are amazing humans and care about each other’s well being.


So, given that academics have a soul-fulfilling job (ideally), and have the flexibility and potential to have a decent balance….

How do you ensure a work-life balance to where you make time for friends, family hobbies and a healthy life-style?

Below are some of my tips that I have implemented myself. *Disclaimer- I do not have kids.. so the below tips could likely very well change or be different for those that do have kids.


1. *MAKE* THE TIME FOR THINGS IMPORTANT TO YOU

Aka- Don’t try to ‘find’ the time… Just ‘Make’ the time and stop making excuses.

Example- if exercising is more important to you than the postdoc or faculty happy hour.. then go exercise! Better yet if you can find a colleague or friend to exercise with.

This theme is incorporated in all of the other tips below.


2. BE PRESENT IN WHAT YOU ARE DOING AT THE MOMENT

Whether you are working or relaxing/having fun- try to be present in the moment. 

This advice goes hand in hand with #3 below.

There is no point in taking time off of work if you are thinking about work- so face the fact that in that moment you are not supposed to be working and just enjoy the time. In contrast- if you are working- don’t go on facebook or do other non-work activities. Try to keep to the task at hand.

phd101215s


3. USE YOUR TIME WISELY

I’m sure you have heard that ‘Being Busy is Different than Being Productive‘. Sometimes the hours that you spent working in a day don’t always equate to ‘productive’ hours.

By this, I am not discrediting the creative process or troubleshooting projects, which can sometimes feel unproductive.

However, just be aware of your time spent ‘working’ and how productive you are actually being while away from your other activities/spending time with family/friends. 

For instance- I find that I am mentally most alert, creative and productive in the mornings. So I try to do my writing, data analysis and brainstorming in the mornings, and then save meetings and lab work for the late afternoon and evenings. Everyone likely has times of the day where they are more productive at different types of tasks.

Try to find out when you are most productive with different types of tasks, and then schedule your work day and free time accordingly.


4. INCORPORATE PRODUCTIVE HOBBIES and ACHIEVE YOUR LIFE GOALS

Since I tend to feel guilty unless I feel that I am being productive- (a feeling that I think many academics share) -I have gained an affinity for hobbies that make me feel productive and achieve life goals I have outside of work.

If you feel ‘productive’ when you are doing things outside of work.. chances are that you will decrease that guilty voice in the back of your head that keeps reminding you about ‘work’.  Note that your individual definition of ‘productive’ may vary from mine or someone else’s .

For instance, my mind (aka the guilty conscious) rewards me for several categories: 1) exercise/staying ninja-fit, 2) cooking up awesome meals for friends and family, 3) spending time and staying in touch with friends/family, 4) learning (including improving upon a new skill/language) 5) producing a product (artwork counts), 6) getting enough sleep, and 7) having enough alone time.

If you ‘feed your productivity meter’.. you can actually have fun and put that ‘I should be working” thought to rest.  Again – being productive can include going for a swim or rollerblading (exercise points!), creating a new art piece (you needed to make something for mother’s day anyhow!), cooking with a friend (after all you need to eat -don’t you?), exercising with a friend, learning a new language (e.g. practicing spanish for that upcoming Cuba trip!), learning how to flip off of a wall, or learning a new aerial silks or capoeira move, or becoming a *certified personal fitness trainer.

*I became a NASM certified personal trainer after graduating with my PhD since I was concerned about back-up plans if I didn’t get my current postdoc…so now I have a constant plan B to make ends meet for those academic transitional periods (check out my hardly-ever updated fitness blog here, or my 10 min ab video here).

There are of course a couple of hobbies that you might have to tinker with in order to ease your guilty consciousI admit- it’s still hard for me to curl up with a good fiction book… I’m not perfect. There is that thought in the back of my head that says ‘If you are going to be spending time reading-you should be learning something’. So instead- I curl up with a National Geographic issue or a good non-fiction book (I love Mary Roach’s books!)- since those are both relaxing and ‘productive’, thereby putting my mind at ease.


5. PLAN ACTIVITIES 

My main balance tactic is to plan fun activities, with friends and family and for most of these activities to revolve around some form of physical activity (that way you have fun, socialize and exercise at the same time!).

IF you plan something, then it is easier to turn off the ‘I have to do work’ part of your mind since you already scheduled the non-work activity. 

If I don’t plan something, my default for the weekend tends to be work and exercise (currently working on a 10 year streak of not missing a day of exercise…).I’ve learned from this personality disorder (blame it on my PhD!) and I try to plan at least one thing with my husband or friends every weekend so that I don’t just work away my weekend.

Some of my favorite activities to do with friends/family include:  hiking/backpacking, capoeira (Afro-Brazilian martial arts), aerial silks, and surfing- all great workouts also!

For example, one of my best friends (shown below in the photo) is my former lab manager during my PhD program and we did a duo aerial silks performance together a couple years ago. We would meet at the gym, train together and have fun, and then go out to eat or cook together after. Here is our show we did a couple years back, we performed for both the Athletic Playground and for Tourettes without Regrets: Aerial Silks Show Duo

Me and Cristina performing our Aerial Duo
Me and Cristina performing our Aerial Duo

And with my husband- we push each other to be our better selves (mentally, physically, spiritually, etc.).  Some of our favorite activities together revolve around exercise- whether it be backpacking (see picture below of us climbing half dome), capoeira, or trying out for American Ninja Warrior.

Gerid_Julie_yosemiteIn the end we both got on American Ninja Warrior back in 2011 and 2012 when I was doing my PhD. Here is one of my audition clips that my husband helped me make: ANW 2011 audition and here is my actual run on the obstacle course: American Ninja Warrior 2012 Venice Beach, CA


6. SET A STRUCTURED WORK-SCHEDULE AND WEEKLY ROUTINE

*Disclaimer: I have not yet conquered # 6 here yet…

I tend to still have an unstructured work schedule- where I start work at variable times throughout the week- sometimes as early as 9am and as late as 11am. This of course means that if I start at 11am, and bike to and from the lab that sometimes I don’t get home until 8 or 9pm. This sets me on a bad repetitive schedule where I get off work late, go to sleep late, wake up late.. and repeat the cycle.. ugh. It also means that if I take half a day off to deal with life stuff (DMV, go to a store/bank, etc)- that then I need to work on the weekend when everyone else is having fun…

I still have mixed thoughts about this #6, since a structured work routine would probably allow me to take more time off in the evenings and the weekends. However- it also means I would have to go to bed at a structured time, wake up early and start work early. So the jury is out on # 5 for now… but I have a feeling that once kids come along… # 6 is going to be key.


7. ANY OTHER TIPS FOR ACHIEVING WORK-LIFE BALANCE? FEEL FREE TO COMMENT!


And with that, I will be away for a bit on my honeymoon in Cuba! Whoop! And no I’m not going to do work while I’m on vacation. There’s no wifi where we are staying anyhow! (Side note..Yes I will end up working several weekends when I get back.. but that’s a cool price to pay!).

e81ec13e6d92beb0d5e50425b6588d35--phd-comics-funny-things


 

Reviewing Manuscripts for Peer-Reviewed Journals: How-to guide

So- you’ve been asked to peer-review a manuscript for a journal?

First off..make sure that the request is from a credible source (aka a credible Journal). There are many scam/fake peer-review open access journals out there, all with names that sound very similar to credible journals and all in the name of profit. You don’t want to contribute to these fake-journals. Here is an article on this issue, and another website listing some of the potential scam-journals (although there are more being added everyday!).

If it is a reputable peer-review journal- Congratulations! This means that you have been selected based on your experience, reputation and scientific merit!

Second: How do you start? What do you write? 

phd111214s

These were my questions when I was first asked to write a review for a manuscript in 2012. I was still a graduate student, slightly in disbelief that the journal had chosen me -little me- to review the manuscript for them!

Of course my go-to person for advice at that time was my amazing PhD advisor – (Dr. Nicholas Mills, UC Berkeley). He gave me a great outline and starting point- which I will share my rendition of below (disclaimer:  I have edited his original outline and so if you disagree with anything then just blame me!)

Feel free to leave a comment on any points I might be missing!

My guide to reviewing a manuscript (by section):

  1. Summary of study (2-3 sentences): a) what the objective of the study is, b) how the study was approached and c) what the main conclusions from the study are.
  2. Overall Edits/Comments: – Is the MS is well written and presented? (Ie- Could the flow of the manuscript be improved? Is there clear topic sentences in each paragraph?  Are there run-on sentences or fragments? Does the manuscript have reasonable English/grammar if non English-speaking authors? Are there any consistent mistakes presented throughout the manuscript (i.e. is the word ‘the’ missing frequently?) *Note, you can also comment on whether the manuscript is suitable for the Journal aim and scope, but usually the editor has already done this before sending off to the reviewers.

After the initial summary, it is best to address any issues in the below sections one by one referring to Page or Line number of the text.

As an example- you could write “P5, L13 – This sentence doesn’t make sense and needs to be clarified and rewritten”. Although this example is a bit vague, and its always good to include as many helpful details as possible to the author.

It is also useful to point out spelling mistakes or grammatical errors as a list of minor points again referred to by page and line number.

  1. Abstract: Does the Abstract accurately represent what was studied and found in the manuscript? Is the Abstract stand-alone in content? (ie- can you understand everything in the Abstract without having read the full manuscript?) Are all acronyms and species defined in Abstract (no abbreviations should be used here)
  2. Introduction: Does the introduction give a thorough background of what is already known and include the relevant literature?  (Make suggestions of any omissions here). Does the end of the Intro have a set of hypotheses or objectives that will be addressed by the study?
  3. Methods: Is the method’s section is clear?  Would you be able to repeat every step of the process yourself from the information provided? (ie- a lot of manuscripts are often unclear in this section). Point out any steps that that need greater clarification and make sure that the study includes sufficient replication. Do the stated replicates in the methods match the degrees of freedom (N -1) in the results section? Lastly- are the methods valid? (ie- are there appropriate controls and treatments? Is there appropriate replication and randomization? Were all of the experiments performed under the same conditions or at the same time? If not, how did they account for the variability?)
  4. Data analysis: Is there a data analysis section (there should be one!) Does the statistical approach appear solid? Can you tell exactly how the data was handled (i.e. how the measurements taken translate to variables used in the stats models)? (This often an area where clarification is needed). Again-do the degrees of freedom match the number of replicates? Is there any evidence of pseudoreplication? (If there is pseudoreplication- suggest using blocks and random effects via mixed models).  Was transformation of the data necessary? Were correct error distributions used for the type of data?
  5. Results: Are the results clearly presented with full statistical details (F, df, P rather than just P)? Does the layout of the Results match the sequence of observations presented in the Methods? Do any Tables or Figures contain too little information that could be better presented just as text? Do the Fig and Table legends, axis legends make sense and tell you what you need to know? (Figure and Table legends should be ‘stand-alone’, and should have all species names and acronyms spelled out and descriptions of the treatments.)
  6. Discussion: Does the Discussion follow the same order/sequence as the methods and results? Does the Discussion stay on track and address the Objectives and Results? Is the Discussion too long? Could the Discussion be reduced in places? Does the Discussion address the hypotheses or objectives presented at the end of the Intro? Are all of the statements/conclusions justified by the Results obtained?  Are the limitations of the study appropriately discussed?
  7. References: Are all of the in-text references in the bibliography? Are all of the references consistent in capitalization (only nouns and first words should be capitalized)? Are all species names italicized? Are all journal names presented consistently? Do all references follow the preferred journal citation style?
  8. Acknowledgements: Are there any conflicting funding sources that might affect the results in the study?

Good luck! You can do it (especially with a cup of coffee)!

I will be joining you in spirit this weekend while I write my own review for a recent request I received.

phd100107s.gif

Hot off the Press!

My newest publication on the current state of biological control of water hyacinth in the Sacramento-San Joaquin River Delta is hot off the press! (Journal of Biological Control)

 

Here is the link to the publication, and you can read it and download it free of access for 50 days! (after that just shoot me an email and I’ll send you a copy if you are interested).

This manuscript is a product from some of my work, and collaborations, from the past year that I described a bit in an earlier blog post .

I could not have done this without the help and mentorship of many folks at the USDA, including Kent McCue, Patrick Moran, and Paul Pratt, USDA Research Leader and a specialist in the biological control of aquatic weeds. There were also some very amazing technicians at USDA including Matt Perryman, Caroline Nunn, Anna Beauchemin, Ethan Grossman, and Clayton Sodergren who put a lot of work into this research as well.

Below is a figure (ArcGIS work by Clayton Sodergren) highlighting the spatial variation in peak weevil densities (Aug-Nov. 2015) in the Delta, as well as demonstrating the variation in the abundance and distribution of the two weevil species (Neochetina bruchi and N. eichhorniae).

AnnualReport_Hopper_Fig.1

Mentoring, and Delta Science Fellows Early Career Leadership Workshop April 25-27

Woooooshhhh… that’s what the past two weeks have felt like!


The end of April was filled with presentations, meetings, field trips, manuscript revisions,  free food (I love free food…) and lots of mentoring.

The action started on April 23rd, as I proudly watched my undergraduate student, Vincent Spadone, present his undergraduate thesis work on ‘Interactions of the Biological Control Agents on the Invasive Water Hyacinth”.

IMG_6632
My undergraduate student-Vincent Spadone- presenting his thesis research on the ‘Interactions of the Biological Control Agents on the Invasive Water Hyacinth’

Vince, a senior and Environmental Science Major at UC Berkeley, has been helping me with some of my research since the Summer of 2016. I have also been mentoring him on his senior thesis project exploring the inter-and intraspecific species interactions among the weevil, Neochetina bruchi, and the plant hopper, Megamelus scutellaris. These two herbivores have both been released in the Sacramento-San Joaquin River Delta and the associated Tributaries for control of water hyacinth. Thus it was in Vince and my interests to explore the potential interactions between these two species and whether these interactions hinder or benefit the biological control of water hyacinth.

So far the results of his laboratory experiments are preliminary but it appears that the planthopper avoids contact with the weevil, and potentially has lower survivorship in the presence of the weevil. However, when both species are present- they appear to cause more damage on water hyacinth compared to when these species are on separate plants. However, more replication is needed to reach more accurate conclusions.


The next day on April 24th, I zipped to UC Davis to present my research to the lab (Ted Grosholz’s lab at UC Davis). Then,  I loaded up with research supplies from the UC storeroom and headed to Sacramento to get ready for the Delta Science Fellows Early Career Leadership Workshop (April 25-27). I had been looking forward to this workshop for quite some time now and I even had to purchase my first business suit ever to properly present my work to the Delta Stewardship Council on April 27th.

Below is my business outfit I finally settled on, and one that actually fit my muscular shoulders (thank you gymnastics and aerial arts for making shopping difficult).

Julie Hopper, ready for Business!
Ready to present my work!

We stayed at the Holiday Inn in Sacramento, so I had some time before the Welcome Dinner to run around the riverfront. I was shocked to see how high the water level was, even after all of the flooding we received. See for yourselves below!!

Sacramento Flooded River Front.jpg
The Flooded Sacramento River Front

After arriving, the two days zipped by, starting with a welcome dinner where the 2016 Delta Science Fellows and mentors got to meet the 2017 Fellows and their mentors. Then the next day was packed with presentations on the Delta, and lots of science communication and career advice. We also practiced our elevator pitches for presenting to the Delta Stewardship Council, and I think we did pretty well! You can see the video of us presenting below. I’m speaking at 24:09 (I was pretty nervous!): Delta Stewardship Council Presentations.

After, we were rewarded by a guided field trip to Putah Creek by Dr. Peter Moyle. Here are some pictures from our trip, including a group photo of the 2016 and 2017 fellows. Of course the trip was also accompanied by really good sandwich wraps and cookies!

March For Science, San Francisco, 2017

Wow- yesterday was a fantastic turn out for the Science March in San Francisco! There were thousands of scientists, science lovers and science allies that met at Justin Herman Plaza pre 11am for a rally with some great speeches, and great company, with the march setting off at 12:30 to the Civic Center where the Earth Day Festival merged with a science fair.

Below is my husband and fellow scientist-Gerid Ollison- holding up our sign at the SF Rally, and a snapshot of the march through SF. See my husband’s blog on his work as an evolutionary molecular biologist and bioinformatician here: http://www.theolligist.com

And below my mom (the short one of course) doing her part with her fellow friends and scientists in Washington DC- marching despite the poor weather!

photo 1

I saw some awesome posters that made me laugh. My favorites included “It’s so bad that even introverts are here!”, “Got Plague? Me Neither.. Thank Science”, “Heard of Polio? No? Thank Science”, “Make America Smart Again” and lastly- this ‘alternative cat’ below.

Alternative Cat San Francisco Science March

So.. what do we do from here?

Well in my opinion- we need to stay politically active and engaged in our local communities. Outreach is super important as more pro-science politicians will be elected if the general public understands the application and importance of science!

Also in order to increase and maintain funding for our science, we need to diversify the funding for our research (as mentioned by Jim Sanchirico at the Science Communication workshop that I blogged about last week).

All in all- I think this march was a good start in promoting the importance of science and creating awareness about the dangers of climate change denial, the defunding of science agencies, and silencing scientists.