Week 12: Farewell

Dear reader,

After nearly three months of senior projecting, it is time to say farewell. Well, maybe not quite yet – there are still more than two weeks left until senior project presentations, where we, the seniors, will share our findings with and showcase our final products. I’m really excited to see what everyone else has discovered over the past months! With such a diverse array of projects, there will be something to learn from each and every presentation.

My own final product will be the not-so-grand spectacle of… a research paper. My friends’ ideas of compiling a bird photo album or having a live, captive mockingbird demo were much more engaging, and definitely would have made for a more interesting showcase than 15 pages of text- and graph-filled paper. Unfortunately, the first idea wasn’t sufficiently academic, and the second one was impractical (and at least slightly unethical), so I’ll have to settle for a plain old research paper. It’s a work in progress at the moment, but it should be finished up in time for the showcase. Also, if you want to see a less stale version of my project, my presentation will be from 7:30 to 7:45, on Wednesday, May 23rd, at the DoubleTree Hilton Hotel.

Now, back to the specifics of this week, where I conducted the third round of surveys at the four close sites. It was a wonderful, peaceful close to the project, with pleasant temperatures and melodious birdsong.

On Monday, I was feeling lazy, so I walked the loop around my house. This was the only day that could be classified as “chilly,” but the crisp air and breeze perfectly complemented the wispy clouds overhead.

The next day, I surveyed the BASIS site, accompanied by SALT Bot (many thanks for the salty yet helpful company). Unfortunately, no photos from that day to share, but plenty from Wednesday, when I took my final survey trip to Coyote Valley.

Interestingly, 3 out of the 4 local sites happened to have a railroad running through them. Coincidence?

Perhaps the most interesting sighting of the day was a flock of Red-winged Blackbirds going after a raven. After a brief aerial battle, they succeeded in chasing the predatory raven away:

Wednesday also marked the day that I finished analyzing my local recordings. On Thursday, I took a break from surveys, and did analysis of Sierra Foothills data – enough to bring all six sites up to at least two valid individuals (most have more). Here’s what the updated graph looks like:

Not looking good for a difference in mimetic frequency between urban and rural… and a t-Test confirms that there is no statistically significant disparity. So, collecting more data only gave more support for the null hypothesis: any difference in the averages of the two groups is simply due to random variation. Individual variation was super high among mockingbirds not only in the same urban/rural habitat, but even among the birds at any particular site. I’d have to record and analyze hundreds more birds to obtain a statistically significant difference (which may not even exist at all). But for now, with the amount of individuals I have, the answer to one of my primary questions is NO, there is no difference between urban and rural mimetic frequencies.

The other question I had set out to answer was about how the ecological links of model species to mockingbirds differed between rural and urban sites, if at all. This is a question I am still in the process of answering, using the catalogue of all mimicked species. The answer will be found in my paper and presentation!

That’s all for data. Here are some more photos from Friday, the final survey day! It was spent ambling around Alviso, listening to mockingbirds, and playing a seemingly endless game of hat tug-of-war with the wind.

Somehow, I noticed this sign for the first time on the final day of my project, on my way out of Alviso. Welcome, indeed!

 

First piece of advice for next year’s prospective senior projectors… do it! Don’t back out. You won’t regret it – it’ll let you skip three months of school. Kidding – though that might be one reason to participate in the project, the main reason, at least for me, was the potential for independent discovery. On the three month journey, you will learn much not only about the topic you are pursuing, but also about yourself. It won’t always be a smooth ride, but that’s what the external and BASIS advisors are there for: to talk over challenges and find ways for you to overcome them.

Speaking of advisors, I first of all have to thank Mr. Sean Peterson of UC Berkeley’s Beissinger Lab. I probably wouldn’t trust myself with a recording device and give myself access to the lab’s recordings, but Sean did, and for that I am very grateful. Also, without our weekly phone calls and discussions, there’s no way my project could have progressed as it did. Many thanks also go out to Dr. Anuradha Murthy, my BASIS advisor, for all the support and advice. In fact, Dr. Murthy was the one that sent me along the path of a bird-related project at the beginning of the year.

Another piece of advice for the juniors: do what your heart tells you to do! If you have some unconventional passion, then there surely is a way you can translate that passion into a feasible senior project. Go for it!

Besides my two advisors, I also want to thank Ms. Belcher for undertaking the difficult task of organizing and coordinating our projects (yes, including all the pesky deadlines we had to meet). Additionally, my conversations with my family were a great help in determining what to do next, so I have to thank them for that. Also, my friends made me view my passion (craziness?) for birds in a new light, which I really appreciate. And last, but most certainly not least, I must thank the birds! This project wouldn’t have even existed without them.

To any readers, if there’s one thing I hope you will take away from this blog, it’s that nature is awesome, and it’s everywhere! So go outside, experience it, let it give you fun and fascination, strength and solace. Or, simply open your window on a summer afternoon, and listen for a minute or two. Soon enough, you’ll hear the rich, bubbling song of a mockingbird!

 

THE

 

Week 11: Mockingbirds Singing, 24/7

Dear reader,

In the past few blog posts, I’ve mentioned several times the lengths to which mockingbirds go to create difficulties for me. Obtaining recordings over the past three or so weeks went slower than I had hoped. This week, when I was in desperate need of finishing up recordings, I was really hoping for some mockingbird mercy. Luckily, my wish came true, and the birds took pity on me.

In a final salvo of song, the mockingbirds from the BASIS and Coyote Valley sites bid me farewell, and brought my recording sessions to a close. With each site having at least three individuals with over 100 songs, I can now definitively say that there are sufficient individuals to create the final graph for mimetic frequency. Of course, that won’t happen until I analyze this week’s recordings, which has partly taken place already, and partly will take place over the weekend and the final week.

At times during recordings this week, it really did seem like the mockingbird experienced a sort of revival. Individuals that had been quiet during the previous weeks were now bursting into wonderful, easily record-able song. Everywhere I seemed to go, even without the recording device, mockingbirds were singing. From the darkness of 5 am, to dusk, their songs filled the neighborhoods of San Jose. Overall, it was a very enjoyable week, and here are some photos.

On Monday, I recorded at the BASIS site, primarily hoping to add at least 9 songs to a bird that already had 91. As soon as I heard it singing in the distance, I bolted down the street towards it. Although the bird was out of sight, it sang for about a minute: enough to bring it to 100 songs, and to add it to the individual count! Views of the palm-lined streets were nice as well:

The next day, I visited a couple locations in Coyote Valley, and the mockingbirds there didn’t disappoint, singing loudly and clearly from the tops of trees and telephone poles.

The lush landscape of green grass and bright yellow mustard flowers, however, was rapidly fading away into the brown, dry landscape of summer.

On Wednesday, an overcast day, I was back at BASIS, “stalking” the streets for mockingbirds. Apparently, one of the residents walking his dog didn’t take too kindly to this, and I completely understand why. It’s totally natural to be concerned when someone is walking around at a snail’s pace, with a camera, while occasionally glancing at what appears to be people’s rooftops. When I noticed this guy following me even after he had left his dog at home, I decided it was best to come clear and explain myself to avoid any further suspicion. I showed him the recording device and told him that I was watching birds, not people. After that, he relaxed, and half-jokingly remarked that I should wear a hat that said, “I’m just recording birds.” In hindsight, a shirt with “Just your friendly neighborhood birdwatcher” printed in large letters might not have been such a bad idea…

After this incident, I was able to get another individual up to 100 songs, and called it a day: the final recording day. To add to the ongoing “Mockingbird on a Citrus Tree” collection, here’s a mockingbird on an orange tree:

And here’s the last mockingbird I recorded for the project, sitting right overhead on a wire:

You may have noticed that this blog post came on a Thursday, instead of the customary Friday. No, that isn’t because I suddenly became more responsible, or less of a procrastinator. Rather, it was more of a necessity – I will be away at an admit weekend for the next few days, so I wouldn’t have been able to post during those days.

Next week, I’ll be doing surveys and analysis. Many more photos and hopefully nice graphs to come!

See you then,

Sergey

Week 10: Analysis Again

Dear reader,

This is going to be a rather dull, nearly photo-less update post for the past two weeks, nine and ten. If I could sum up these weeks in one word, it would be “analysis.” Still, despite spending time each day analyzing Sierra Foothills data and finishing up all of the existing recordings for the four close sites, there’s a long way to go. Right now, the individual counts (number of birds with over 100 recorded songs) for each site stand as follows:

South San Jose – 4

BASIS – 1

Alviso – 6

Coyote Valley – 1

Sierra Foothills 1 – 2

Sierra Foothills 2 – 1

Since my first practice presentation is on Monday (yikes!), to obtain some preliminary results and visuals, I did stats on all of the data I had already collected (analysis of analysis). The end product was this graph:

Here, the reddish-brown bars represents the three urban sites, and the green bars represent the three rural sites. From this graph, it seems that the urban sites have a higher average mimicry frequency than the rural sites. Indeed, the average frequency for all urban individuals was 10.14%, and the average frequency for rural individuals was 6.41%. However, upon performing a t-Test on the two groups, the obtained P-value was 0.067 — greater than 0.05. This tells us that the difference between the urban and rural individuals is not statistically significant. That’s definitely not a conclusion I want to have moving into the final weeks of the project…*

*While re-reading the post I noticed this previous sentence, and wanted to make a correction. There being no statistically significant difference between urban and rural sites may not be a conclusion I want to have, but I can’t make it my job to try to prove that there is a difference. Operating under the assumption that there is a difference is dangerous, because I might subconsciously attempt to confirm my biases, and this could lead to an incorrect conclusion. If there is no statistically significant difference between the sites, so be it.

Also, as you can see, only three of the sites have standard error bars – this is because the remaining three sites had only one individual when the graph was made. To remedy these many statistical woes, I can either lower the threshold for the number of recorded songs an individual has to have to be included in the calculations for mimetic frequency, or go out and record more songs. Both of these will result in more data points, and potentially make the difference statistically significant (or again affirm that it is not significant).

At the moment, the second option – recording – is preferable, since there are quite a few individuals for these sites that have nearly 100 songs. It should only take an additional day or so of recordings at each of the sites to significantly boost their individual counts. That’s what next week will be dedicated to: completing recordings, and final analysis of these recordings.

Though I did do some recordings this week, the mockingbirds were uncooperative, especially at the BASIS site. On Friday, I walked around for about two hours, with a measly return of only a minute or so of recordings. Maybe it was hot and the birds had exhausted their singing early in the morning, maybe I was just unlucky, or maybe the mockingbirds wanted to have a bit of a laugh at my misfortunes. In any case, adding more recordings will have to happen next week. Unfortunately, I have no photos of mockingbirds to share, but here are some (surprisingly nice) views of the urban BASIS site from a breezy pedestrian bridge over Highway 280:

To be honest, this has been one of my favorite aspects of my project: finding beauty all throughout the Silicon Valley – at both the urban and rural sites. Nature is everywhere, one simply has to look.

Till next week,

Sergey

 

 

 

Week Eight: An Alarming Rate

Dear reader,

It feels like every single week now, I start off the post by mentioning how many weeks there are left, saying that time flies, etc. Though a couple posts back this might have been premature, now it’s actually becoming relevant: the end of the project is approaching at an alarming rate.

In order to draw conclusions from data in time for the presentation in May, I’ll really have to ramp up analysis in the next two weeks. In our weekly phone call on Thursday, my mentor and I discussed the possibility of dropping the two distant rural Sierra Foothills sites from the project, and instead focusing entirely on the local rural Coyote Valley site. We considered this since the lab’s recordings for these sites didn’t specifically target mockingbirds, and contained model species whose calls/songs I wasn’t very familiar with. For now, I’ll try to keep analyzing all three rural sites, but spend more time on Coyote Valley recordings, which should have more familiar species. This should maximize my chances of finishing on time, but if things get rough, I’ll resort to dropping the Sierra Foothills sites.

OK, enough with the depressing musings about time. Things aren’t nearly as bad as I just made them seem, and the situation is far from dire: a couple weeks of solid analysis should get me back on track. For now, let’s get into daily updates, with some interesting photos from the week!

On Monday, I did recordings in South San Jose. The mockingbirds were out and about, but unfortunately did their best to prevent me from getting too many satisfactory recordings. At the moment, the strategy is to cover each local site with the greatest breadth possible, in order to record as many individuals as possible. Every individual with over 100 recorded songs will be included in final calculations.

Tuesday, I visited Alviso. Spring here was in full force, as witnessed by the arrival of one of Silicon Valley’s most prominent urban migrants: the Hooded Oriole. These beautiful, black and orange birds are in the Icteridae (blackbird) family, and nest in fan palm trees all across the Bay Area. If you have palm trees by your house, look up and listen for their harsh chatter or whistled “wheet” call – there’s a good chance they’re up there!

Hooded Orioles are also excellent model species for mockingbirds, with both their chatter and “wheet” calls imitated in mockingbird song. After enjoying watching the orioles building nests, I walked through the more heavily populated area of Alviso. My binoculars and recording device ended up arousing the suspicion of a curious middle-aged guy, who originally thought I was out to kill birds! Surprisingly, eight weeks into the project was the first time I had to explain to someone what the heck I was doing roaming the streets with binoculars and a paper bag containing a white cardboard case. Still, the guy was friendly, and told me that his wife often sees mockingbirds and bluebirds on the next street down. Following his advice was a good idea: I soon stumbled upon two different singing male mockingbirds, and managed to get abundant recordings from both!

Also, this isn’t a very small mockingbird, but rather a very big lemon.

On Wednesday, I stayed home to do analysis, and was able to finish a decent chunk of the Alviso recordings from previous weeks.

Thursday was my birthday, or, as I prefer, bird-day. Sadly, on the morning recordings-walk around BASIS that morning, I was able to get a prolonged recording of only one mockingbird singing, so this will definitely be the site I focus on visiting next week and the week after next. As if to make up for the lack of birds, though, I was greeted by a giant army of caterpillars on a park bench – thousands upon thousands of squirming insects!

Not a very pleasant birthday surprise, but it would have been much worse if I had sat down on the bench without happening to glance down. As it turns out, these are tussock moth caterpillars: if their blood gets onto skin, it will burn, and cause blisters and boils to pop up! An adaptation, by the way, to defend against predatory birds…

On Friday, I spent some time analyzing Sierra Foothills recordings. A more difficult process than analyzing local recordings, but one that I’ll have to come to terms with in the upcoming weeks.

Sorry that the post this week wasn’t very mockingbirdy. Next week, I’m hoping to have done enough analysis to actually begin sharing some important mockingbird-related data to the blog post.

Till then,

Sergey

 

 

 

Week Seven: Mockingbird Heaven

Dear reader,

Seven weeks down, five weeks to go. It’s hard to believe that the senior project is now more than half over. If time were a bird, it would be a Peregrine Falcon.

This seventh week was a combo of conducting surveys at the four local sites, and carrying out analysis at home. Analysis is moving along slowly but steadily, emphasis on slowly. From now on, if I want to finish on time, every week will have to be an analysis week, and almost every day will have to be an analysis day. Right now, I’m shooting for a minimum of one hour of recording time per site – or six hours total. Analysis for six hours should fit into the remaining time, but to get six hours of recordings will take some more work.

Luckily, finding singing mockingbirds in the coming weeks shouldn’t present a problem. Though I did no recordings this week, mockingbirds were ubiquitous at the survey locations, and were singing more actively than a couple weeks ago, when I first did recordings. At Alviso, Coyote Valley, and South San Jose, it seemed that as soon as I got out of earshot of one singing mockingbird, another one’s song would drift towards me from a distant bush or fence post. Alviso, especially, was heaven for mockingbirds – it seemed that every second house had a mockingbird perched on its weather vane.

Here’s a quick rundown of how surveys went, with some photos.

On Monday, I was joined by SALT Bot on a survey walk around the four corners of the BASIS site. Many thanks to him for the company and for writing down a ton of bird names in the notepad. Unfortunately, this was by far the least productive of the four surveys. No new birds were added to the site list obtained in February, but abundance data for the existing list got updated.

On Tuesday, I did surveys at Alviso, a neighborhood of San Jose by the SF Bay. Despite the neighborhood’s fascinating history (former site of a steamboat port and fish cannery), it’s not a tourist attraction – “ghost town” would be a more apt description. Though some people do continue to live here, many of the cars and houses look neglected. I preferred to focus my attention on the nature – the plentiful singing mockingbirds and the expansive salt marshes stretching towards the bay:

Also, several sets of freight and passenger train tracks run through the town.

Wednesday, I took a pleasant survey walk around my neighborhood, made slightly unpleasant towards the end by the sun’s heat. Gathering survey and recording data in the morning will be important, not only because the birds are most active then, but also because I would prefer not to burn to a crisp in the afternoon sun.

Also, an important discovery was that plastic owls can appear very realistic:

Thursday was the final survey day, at Coyote Valley. The mustard flowers were in full bloom, stretching out like a green and yellow carpet towards the hills in the distance.

This site in particular seemed to have the most perceptible change in mockingbird abundance and activity from three weeks ago. Mockingbirds were scattered all across the valley, singing from the tops of bushes, trees, fences, and houses. Hopefully a sign of good things to come next week, when I’ll be doing recordings here.

I’ll end this post with a video of a mockingbird singing from Coyote Valley. Sorry for the shaky video – I wish I had a tripod handy at the moment. Still, what matters is that the mockingbird was singing loud and clear. Enjoy!

See you next week,

Sergey

 

 

 

Week Six: No Quick Fix

Dear reader,

Last week, I talked a bit about the analysis process, which is pretty subjective. Listening through recordings and then classifying songs based on their song type means introducing a ton of biases. These biases include my experience (or, more often, inexperience) listening to birds in the field and any classification tendencies I might have. For example, I might count a repeated, two-note vocalization as a single song type, while others might count each note in the vocalization as belonging to separate song types.

This week, I’ll discuss some examples of difficulties that have arisen in analysis so far. There’s really no quick fix for these difficulties: each one has to be sorted out in its own way, and this greatly lengthens the analysis process. It all depends on how the bird is singing. If it’s taking time between songs, and making them clear cut, it can take half a minute to breeze through a minute-long recording. Other times, a five second fragment might take five minutes to analyze, not counting the mandatory break at the end to clear my mind of all the green lines, dots, and curves on the screen.

First off, the subjectivity is hopefully not as big of an issue as it may seem. Though it’s true that a different researcher would classify songs differently, there’s only one person doing analysis for this project. If the work was split in half with someone else, comparing mimicry frequencies would be problematic. As long as I do my best to apply the same analysis standard to every single recording, the calculated mimicry frequencies should be statistically comparable.

The primary difficulty is identifying what bird the mockingbird is mimicking, if it’s even mimicking at all. Mockingbirds have such a diversity of original songs that many of them end up being acoustically similar to other birds’ songs and calls. Differentiating between mimicry and original songs hasn’t been as easy as I hoped it would be. Then, there’s also the potential problem of imperfect mimicry. Mockingbirds are known to introduce variation into other bird’s songs, making their vocalization a hybrid of their original song and another bird’s song. For example, in this fragment, the middle five vocalizations sound similar to California Scrub-Jay calls in their rise in pitch, but have a less raspy and more whistly tone than actual calls would. The question is, count them as a mimicry event? Give the mockingbird 0.5 of the event and the scrub-jay 0.5 of the event, as other researchers have done? Or count all the calls as mockingbird vocalizations that simply happen to sound like scrub-jay calls?

In addition to this, I’m not even close to knowing every single song and call out there. Resources that let me compare recordings to sonograms and other recordings, such as Xeno-canto and Cornell’s All About Birds, have been a great help. Still, even if it’s obvious that a song is not a mockingbird original, it can take a lot of work to pinpoint which exact bird is being imitated.

The next problem is a bit embarrassing to admit to having. It involves background singing – other species of birds singing during the recorded mockingbird’s song. This makes it possible to mistake background singing for mimicry. In some cases, background singing is easy to sort out since the frequency and beginning of the phrase is completely off from what is expected for the mockingbird song. For example, here is an Oak Titmouse calling in the background (top vocalizations) of a Northern Mockingbird song (bottom).

Other times, it’s much harder to tell which bird the sound belongs to. For example, when listening to the fragment below in the field, the third vocalization sounded like a Western Tanager’s call. It would be quite surprising, but not impossible, for a mockingbird to mimic a tanager (which is uncommon in suburban habitats), so at home I took a closer look at the sonogram.

It reveals that there are two separate vocalizations: one upslurred and the other downslurred. It would be impossible for a mockingbird to produce both sounds simultaneously, so the conclusion is that there was an actual, real-life Western Tanager calling somewhere in the background. Which is pretty strange, since tanagers usually don’t migrate into the Silicon Valley until April, though some do overwinter here. But strange is more likely than impossible, so tanager it is!

In addition to background singing, there’s also other ambient noise.

https://staceynaitoblog.com/2015/12/24/the-grinchs-medical-maladies/

Cars, trains, planes, humans talking, dogs barking, you name it. All of these make a recording much harder to analyze, since their sounds essentially mask the lower frequencies of the mockingbird song. Large portions of some recordings pretty much had to be discarded because of this background noise.

That’s all for this week. Next week will consist of surveys in the morning, and more analysis in the afternoon. Fun!

Till then,

Sergey

 

Week Five: Staying Alive

Dear reader,

Well, that title is definitely an exaggeration: at no point in the week was my life in peril. But, truth be told, I was quite sick for the first half of this week, and wasn’t able to do much work on either analysis or recordings. Also, the title rhymes nicely, so that’s what it’s gonna be.

I tried to make up for lost time during the latter half of the week, but didn’t get quite as much analysis done as I’d hoped for. Unlike every single previous post, this one won’t contain a single photo of birds, or even nature. Instead, this time around I’ll talk a bit about what I really mean by “analysis.”

It might sound fancy, but in reality, “analysis” is basically listening to a recording made in the field, and then classifying mockingbird vocalizations in the recording by song type. Song type has two broad categories for mockingbird song: original mockingbird song, or song obtained by imitating another bird’s song or call. Originally, I was planning to classify by time: count the seconds of original song, count the seconds of mimicked song for every different mimicked species, and calculate mimicry frequency for each of the six sites by taking (total mimicry time)/(total singing time).

Over the past few weeks and on the sick days this week, I read a few papers from mockingbird researchers. It turns out that no ornithologist (bird scientist) actually uses the time method while studying mockingbird song. Instead, they define a song type as an “acoustically distinct sound that is normally repeated by an individual” (Gammon 2014, Farnsworth et al. 2011). A stretch of repeated song types is designated as a “song,” or “bout.” Bouts might contain anywhere from one vocalization to more than 10, but the key is that the vocalizations are all of the same song type. Each bout is then classified by song type (original or mimetic), and mimicry frequency is calculated as (mimicry events)/(total songs). To clarify a bit, here’s a screenshot of one of the recordings labeled with the lingo:

This right here is basically a dream scenario to analyze, with the help of Kaleidoscope’s features. Kaleidoscope viewer allows each recording to be viewed as a sonogram, plotting frequency on the y-axis and time on the x-axis. It also lets the user play the fragment of the recording shown on the screen (only 5 seconds here). In this particular recording, each song type is super clear cut, and can be easily told apart from the others both visually (on the sonogram) and audibly (by simply hearing the different sounds as the recording plays). This fragment of recording doesn’t have any mimicry (mimicry frequency would be 0, since none of the five song types are mimicked) but the different Northern Mockingbird (NOMO) song types are easily distinguishable here. This isn’t always the case. Mockingbirds love to transition between song types over a few vocalizations, leading to some amount of subjectivity in analyzing the recordings. For example:

The mockingbird starts off by nearly perfectly imitating a California Scrub-Jay call three times for Song #1. Then, it loses the higher frequencies, so that the vocalization still sounds similar to a CASJ call, but not enough to be classified as an accurate imitation. It repeats this five times for Song #2. Then, the song type becomes sufficiently distinct from Song #2’s song type, and describes the two vocalizations in Song #3, which are also specific to a NOMO. This is all pretty subjective, and an experienced researcher might well have classified this fragment differently. However, as classified by me, the mimicry frequency in this fragment would be (1 mimicked bout)/(3 total) = 0.33. Now, instead of doing this for a five second screen fragment, imagine repeating the process while scrolling through a five minute recording – that is analysis.

Also, this is officially the first week I’ve spent more time sitting in a chair than watching/recording birds (I was thinking of starting a counter for each one in the blog sidebar). From here on out, expect even more of the former, but also some more of the latter. There are still several recording weeks and two survey weeks left, so I’ll try to get some non-screenshot photos up on the posts as well. Unfortunately, WordPress requires a paid premium account to post video and audio, but one day I’ll film a mockingbird singing and link to the video externally.

Well, that’s all for now. Next time around, I’ll talk about some other difficulties that have come up during analysis.

Till then,

Sergey