The Next Chapter

After three years in Brownsville, Texas studying Black-Spotted Newts, I am finally done. UTRGV holds little sway over me now, thankfully. But now I am just 2 weeks away from beginning my PhD studies. Not much time to rest, but life never really follows a steady path.

Earlier this year I had listed six different PhD positions I had an interest in applying for. Well this project is none of those, although it is with one of the same labs. It was actually a rather quick turn around from first interview to acceptance. Roughly two weeks after the first interview I get an email back asking about this position and I jumped on it.

I will be studying unisexual salamanders on an island in the middle of Lake Erie. Within the Ambystoma genus  there is a lineage of populations that are entirely female. This isn't all too unique as there are actually some lizards and at least one species of lizard that are entirely female. What makes this lineage so fascinating is that it can 'breed' with at least five different species!

Morphologically this unisexual clade can't be consistently distinguished from the population host species (afterall, they're hybrids in a sense). Instead there is a heavy reliance on genetic data to identify individuals in the unisexual group with mitochondrial DNA unique to this complex.

When doing some preliminary reading for the study I kept running across the term 'genomotype', which I thought was a Canadian spelling for genotype. I was wrong. After a bit I came to realise that it was actually in reference to the coding system used to signify the species genomes within the individual. Each individual of the unisexual complex can have anywhere between 2 and 5 sets of chromosomes, which can be from different species. As an example, an individual with an n of 3 (3 sets of chromosomes) could be identified as LLT (2 sets from A. laterale (L) and one from A. texanum (T)). Other species it has been known to hybridize with are A. barbouri (B), A. jeffersonianum (J), and A. tigirinum (Ti). It's an amazing system and makes for an amazing adaptive capacity for the lineage.

While my study won't be specifically on the genetics, I want to incorporate the genetics to some degree.

I still have some newt work to finish up, but I think I'm going to try and keep in contact with my replacements to hear about the progress.

Understudies

Twice now I've played the role of adviser for new grad students. Each time has been an exciting experience, getting to know someone new but also getting to teach them the ropes. For both students I've gotten to show them environmental DNA techniques and field surveying.

My problem though is that I've held them up a bit too much at times. The first student was definitely able to pick it up quicker, but both have been slow to really push their own research agenda. In each case they've just tagged along when I did field work, which isn't bad, I'd just like them to pick up the reins for themselves. The thing is, I know I've held them up in that process to some extent, especially for my current partner.

The problem is that I've been the one to really pioneer eDNA for the entire University, so I'm the one that has had to be the teacher and show them the methods and come up with the procedures, etc. It's been a lot of fun, but eDNA isn't going to be my project, it's theirs. So I've found myself explaining my ideas and my concerns and how they should plan their study - at one point I even laid out around 9 different projects or assessments that the current student should do. Pointing them in the right direction is one thing, but straight up telling them how to do it all has deprived them of the experience to figure it out themselves.

It's a tough trick to nail down, but I think part of it is also hampered by the fact that I'm not their actual adviser. If it were my lab, I might not feel as bad about it, but as it is I may have been giving them advice or telling them to do things that our adviser doesn't actually want to do.

This all came to a head for me today when my current 'student' actually told me to join her in the field. I was excited to find she had taken the lead on it, to later hear that our adviser pushed her to do it. My solution was to try and get her thinking about what all would be needed, so that way she would have a bit more experience with planning a field outing. "What else do you need for this? Did you contact the field manager? How will you do this thing once we're out there?" I had to make sure she asked herself these questions, and it turns out there were some things she forgot to grab. It seemed like it was her first time doing so, not a problem, we all go through that learning phase. I hope it helped get her more comfortable with the process though. (I also forgot where I put something, showing her that even a more experienced individual forgets things).

All in all, this is still something I need to get better at doing - giving them space to do their own work, while providing a gentle nudge in the right direction.

My Last MS Conferences?

In February I have three things to focus on writing: my thesis, and two conference presentations. Luckily, both of the presentations will be on the same material, so I just have to make one poster.

The first conference will be the trial run: a presentation at the Graduate Research Conference for UTRGV. Last year I presented on the success of the borescope and actually won first place poster presentation for biology. So really, I have a reputation to uphold. More importantly though, this year 1st place has a 1000$ prize - a bit more useful. I really enjoy making presentations, and this one is no different. I think it came out well.

The second conference will be more meaningful: the Texas Chapter of the Wildlife Society Conference. My presentation is going to be on the distribution modeling that I worked on last semester. It came out really well and has some major impact on for future conservation practices and status determination.

Seeing that I'm nearing the end of my MS, these may be the last conferences I go to for black-spotted newt research. I'm looking to add a few more over summer and go back to IHS and ASIH, but that may not be so easy once I'm no longer a student at UTRGV. Part of the reason though is that I have some more plans to work on before I leave Texas, and presenting on one of those ideas would be a huge boost for me and the research.

Chapter Changes

Today was a far better day than yesterday.

I went in today with my mind set on doing work, specifically pop gen stuff. With deadlines closing in, I've really needed to get on this bit. It shouldn't take long thankfully, but it has to start to actually end. In order to do this properly, the genome basically needs to be cleansed. Mitochondrial DNA is usually fairly clean, but there are still some chunks that aren't coding and some alignments will have voids in them due to the mapping to reference process. Once everything is cleaned up and properly arranged, each set of genes for each specimen goes through a partitioning procedure that takes a few hours identifying the best evolutionary model for each gene. The whole thing is fairly tedious as a lot of this has to be done manually, and in my case it's being done twice for two different analyses (whole mito genome and partial genome with more samples).

Human mtDNA. Unlike nuclear DNA, mtDNA is circular
- a remnant of its origin as an endosymbiotic bacteria

That will be the last new thing I actually need to do apparently.

While cleaning out the genome, my adviser comes, and in his lackadaisical manner just points at it and says, "That's the last you'll need for your thesis!"

Shocked, I turn to ask him about the eDNA. I was expecting my third chapter to be eDNA. Lo and behold though, my last chapter was changed... without my knowledge...

My adviser has a habit of doing this, and everyone in the lab has experienced it multiple times. I was just under the impression that my thesis was set. Turns out, my third chapter will now be a broader discussion of the novel survey methods I pioneered and developed for newts. This includes three main components: eDNA, borescope, and artificial burrows.

Previously, I had already been able to show that our eDNA primers are effective, working even in low concentration samples. I was expecting to do a few more trials to get a good set of data for some stats. I guess that's going to my lab partner now. All the same, this is some fairly exciting work because we were able to use standard procedures and nested primers to identify newt DNA in some rather murky water from our local resacas (similar to oxbow lakes, but some key differences). Over the next few months I'm sure I'll still get around to doing those trials, but now they just won't be a part of my thesis. No big.

The other two novelties are my own making. Prior work with black-spotted newts had found them buried underground. With the implementation of a borescope, I was able to do the same thing, but without ripping up the ground and still get data on how deep they were. In addition, the borescope technology can take photos or video of the entire process so that we can document other cohabitants of these microhabitats. In the past I've been able to document tarantulas, centipedes, snakes, and even a full grown neotoma rat! I'm really excited about this development because there are actually a lot of practical uses for borescopes in the field. Consider the standard flip board. Snakes love 'em. Try flipping one without a stick though, and there's a good risk of getting bit. In addition, just the act of lifting the board exposes the ground underneath, breaking the humidity barrier that made it so enticing. By using a borescope to look underneath, there's a reduced risk of snake bite, the humidity barrier wouldn't be broken, and everything there would remained relatively undisturbed.

But the other addition I made to surveys was the use of artificial burrows. I feel like they were probably considered before, but they were impractical because they would have to be destroyed to find whatever was in them. With the inclusion of the borescope, that is no longer a problem. Artificial burrows have a dual practicality to them. 1. It's a very passive form of trap - anything can crawl in or out at it's own leisure. 2. When a creature is found, we can quickly see just how deep it is underground. Subterranean lifestyles are hard to study, but are incredibly important, especially for something that lives in, effectively, a desert. Soil characteristics, humidity, water table level, temperature - all are potentially important variables when considering an ecological niche, and by knowing how deep something goes we actually have an idea of where to measure! Of course this won't replace the utility of coverboards, but it adds another handy tool that can provide guidance on how to collect a wealth of other data, broadening our scope of research potential.

While upset that I didn't get much of a say in this change, I am actually really glad that I'll have the chance to provide a deep discussion on the utility of each. It's not a typical research paper in that we don't have much data to analyze. But we have enough to confirm that things work. I'm hopful that my adviser will expand on these in the future, I know I plan on it.

This was a lot more off-the-cuff than I had original intended.

PhD Prospects

This may be a bit premature, but it's been a really exciting time as I look around for PhD projects. So far I've looked at around 6 different labs, and may have already gotten accepted by one! So here I just want to lay out the different options that I have so far, and which ones I'm most excited about.

1. The first project that really caught my eye was working with Dr. Urban at UConn studying the impact of climate change on salamanders. Anthropogenic climate change is a fact, and there is already an abundance of evidence of ecological impacts, including impacts towards salamanders. This was my top choice, but I wasn't fortunate enough to get it. So it goes. The email he sent me indicated that there were other applicants that complimented his current lab, which I suppose is fair enough. A friend of mine from UConn suggested that he just didn't get the funding for it. Which also makes a lot of sense. I have seen and heard of many projects this past year that got either defunded or completely screwed over due to the current administrations views on science. Just a lesson to you all - have backups!

2. Hellbenders at Virginia Tech. This is now my current top choice. A large component of this project appears to be outreach. I love this idea because there are a lot of private citizens that just don't know much about amphibians and reptiles, resulting in a fear. In my current position I've had to describe salamanders as "water-lizards" and reassure one woman that they weren't bacteria. In the future, I want to be part of an outreach group, both to disseminate general science knowledge, but also to inform the public about the benefits of herps and why they aren't to be afraid of. This project really plays to that desire of mine, and the fact that it's with hellbenders, the largest North American salamanders, really suits me! Still waiting to hear back from this project, but should come around the end of the month.


3. Alligator outreach at Clemson University. To be honest, I didn't really know about Clemson University before this. Apparently they have a good football team? Similar to the hellbender work, this has a big outreach component. I think a lot of people have a general misgiving around alligators, but they don't take much mind of people generally. One of my current field sites has alligators that I can see almost every time I go out. This is some exciting work though, if for no other reason than to say, "My PhD work was on alligators".

4. Mojave Desert Tortoises and the military. This project I think I already have the go ahead for, so that's rather exciting. Every since undergrad, I had wanted to work with Mojave tortoises - it was a rather common listing for summer internships, but I never got one. I remember one of the most frustrating aspects of those callouts though was that they asked for prior experience with Mojave tortoises. These are federally endangered animals that only have this one study working on the,, so I'm not sure how I could've gotten such previous experience!! Whatever. Now it looks like they want me. The interview was actually a lot of fun because I got to describe my experience being self-taught with R and ArcGIS.

5.  Terrapins in Alabama.I like turtles. This project sounds like a rather standard ecological study of terrapins with the inclusion of genetic variability. The idea being that I would investigate the link between natural or sexual selection on population structure and trait variation. Certainly sounds like a fun project.

6. Amphibian behavior plasticity OR Chytrid study. This lab was the most recent find, and I'm currently writing my cover letter for it. The behavior plasticity study is highly attractive to me. Around the end of my undergrad, I conducted a behavior study on tadpoles to identify plasticity in anti-predator behaviors when a possible unpalatable model (toad tadpole) was present. My results were actually really good (p = 0.53), but not at the significant level. Since then, I've really wanted another chance at conducting this project, or something facsimile. This position sounds like exactly what I was looking for. Also it's in Canada, so that's almost reason enough.

So far, these are the projects I've really taken a good look at with intent of applying. I won't stop looking until I have something locked down that really suits me. In addition, I'm looking to apply to UConn and Texas A&M in general - UConn because there are just so many salamanders up there, and A&M because it may give me a chance to continue working with black-spotted newts (they've really grown on me, and at this point I'm basically the foremost expert on them).

Restarting

Ha ha... look at that. Over a year without anything! I am freaking amazing at this!

But really though, I do want to try and get into the habit of doing this more. So I'm going to try and do a hardcore stance. As I think I had mentioned in a previous post, I used to have a blog under a different name long ago during undergrad. I'll be reviving that space as my general blog space, used for dream recounts, random thinkings, fun stories, things of that sort. The old posts on there will still remain, despite a few of them displaying some serious drama regarding roommates of the time, because I don't want to seem as if I'm hiding anything - just be aware that I'm not proud of some of those and look back on them with embarrassment (though not all of them). This blog space will be specific for my research and position updates. Now that I'm having a hard look into Ph.D. positions, I'll be gushing about those for some of the first few.

Lastly, if you're more interested in deeper discussions, I'm planning to try and do long posts regarding specific topics where I look into actual data and form arguments from that. This last group will be very slow to come out due to my own real-life schedule and the difficulty in finding and analyzing the data. I already have a few planned out, and in the future these will be categorized more broadly. For example I already have two climate change related topics I want to discuss, specifically the environmental impact of wind turbines and the green tech advances taking place in China.

So more concisely:

My old blog "General Bearings" (used to be "Ramblings of a Young Biologist") will be for random thoughts, dream reminiscing, fun stories, etc. Can be found here.

This blog space will be for my more professional life: current research updates, job opportunities, etc.

The new blag space "Hox Talks" will be for the long-form, in-depth, discussions. Many of these will likely touch on politics, as so many things do, providing policy suggestions based on the data and my own values (I will try to point this out when appropriate). This space can be found here.

Let's see if I can actually keep to any of this, as I have such a long history of doing so.

Confirmation Bias with Search Engines

A short preface: the rest of this post is not mean't as a political statement. While I am a US citizen, I do not have many positive feelings about any of our presidential hopefuls - they all have their faults.

This morning I got a bit of a disappointing message. An acquaintance of mine posted a photo of three search engines (Google, Bing, and Yahoo) filling in the statement "Hillary Clinton is ". Both Yahoo and Bing came out with some very negative comments against Clinton, which is not too surprising. Then there was the Google search. Google was purported to have only good things to say. This individual then took this to indicate that Google may be in the pockets of HRC, or are just trying to bias their own results in favor of her. I simply cannot let this slide.

I responded with a decently long comment thread with images of each of these search engines responding to the same phrase, but I also replaced Hillary Clinton with the names of each of the other three main contenders for office: Donald Trump, Gary Johnson, and Jill Stein. The results were hardly shocking.

I'll start with Google. To be fair, I was using Google Chrome web browser which maybe was giving me different results, but I have my doubts. In each case the results were mixed. Clinton was indeed called 'awesome', and is suspected of winning according to Google. However at the same time she was referred to as a 'robot' and suspected of losing. The last result is just a statement of fact, because she is indeed running for president. A similar ratio is there for Trump, 2 positive ('awesome' and 'going to win'), 1 negative ('dead'), and 1 statement of face ('orange'). I will not comment on the 'not a conservative' because that could be seen as positive or negative depending on your personal leanings. Of the four, only Gary Johnson has fillings that are somewhat policy related, and then poor Jill Stein doesn't even get a full fill-in ('Jill Stein is from'). In my opinion, Google's search seems to actually force a neutrality bias because as we will soon get to, the other two engines have very clear impressions of our presidential candidates.

On to Yahoo, the little engine that could. Yahoo seems to favor giving far more results than Google which gives us an opportunity to get a larger perspective on the situation. As it turns out, my acquaintances post is more or less accurate. Most accusations appear, just in a different order. So is Yahoo in the pockets of Trump? Well clearly no. Heck Yahoo called him Hitler, falling for Godwin's law. None of those fill-ins sound positive to me either. Gary Johnson and Jill Stein get similar treatments, but more of the questioning variety. Is Johnson a libertarian, liberal, or republican - taking all bets. At least Stein has some facts associated with her: she is indeed an option for president. So perhaps this means that Yahoo is in the pockets of the candidate that has the least support nation wide and has the least money - that definitely makes sense.

Finally we get to Bing, the Google wanna-be. Again Hillary gets no love as noted in the picture above. My search didn't come out with 'murderer', but hey being a witch is close enough, right? Oh, but what's this. A little Trump love from Bing? Trump is apparently 'going to win' and is 'America's last hope'. Sounds to me like Trump has Bing's number... Oh wait, there's Hitler references again. Good ol' Godwin strikes back. Johnson, again, brings up actual policy debate (vaccines and borders). Finally, Stein just get's hit by the synonym monster twice ('not anti-vaccination' and 'not an anti-vaxxer'; 'wacko' and 'loon'). With more positive findings from Trump and Stein, it looks like Bing is clearly against Johnson and Clinton.

But really no. The problem with basing assertions on what search engines fill in for you is that you completely misunderstand human psychology and search engines. First of all, humans love to complain, we just do. Any student that has ever used RateMyProfessor.com knows this. You could have the best professor, but there are just too many people that hold grudges because they couldn't figure out a simple due date and they want you to know about it. The point being, it's far easier and more entertaining to write something negative than it is to write something positive. Negativity just makes us more 'colorful' with our words and is ironically fun to express. As a result, a majority of articles (especially when dealing with politics) are going to be negative. Hell, this entire post is based off my own disdain towards a topic and I wrote it in about 15 minutes. Secondly, with so much negativity going around search engines are going to pick up on that because search engines are predominately based on what is the most frequently found and what is searched. Having actually written an 'n-gram' code in the past, I'm well aware of this limitation. Lastly, as mentioned before, people like to read negativity, especially when it agrees with them. Thus, more searches are likely going to be negative searches. This is called 'confirmation bias'. You want something negative, so you search for something negative that agrees with you. It's no wonder that these searches are predominately negative then.

As my last point, I just want to refer back to the original image. The Google search shown only brought up 2 fill-in's for Clinton, but mine had 5. The only one's shown were the same two positives that I had gotten as well. Simple answer: it's the fucking internet, don't believe everything it spouts. In 5 minutes with Powerpoint I was able to make Bing a total Trump whore. It's a bit sloppy, but I hope it gets the point across: don't trust everything you read. I encourage you, as potential voters, go and do these same searches for yourselves, because for all you know, I'm lying too!