2023-24 El Niño?

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Several diagnostic conditions point towards a brewing El Niño event in the Pacific Ocean for the upcoming months of this year; however, this one, like many other instances of brewing El Niños in the recent past, seems somewhat unique. For one, the eastern Pacific Ocean is already warm close to the equator:

Surface ocean temperature over the last twelve weeks. Source: https://www.cpc.ncep.noaa.gov/products/analysis_monitoring/enso_update/sstanim.shtml

Temperature (top) and temperature anomalies at the ocean's surface in the Pacific sector point towards a potential brewing El Niño event in the latter half of 2023; anomaly here refers to the difference between the actual temperature for that week versus the long-term average. Source: https://www.cpc.ncep.noaa.gov/products/analysis_monitoring/enso_update/sstanim.shtml

Here is how the subsurface ocean looks:

So, is this event potentially evolving from the eastern Pacific? Well, at the same time, the development of low-level westerlies over the Western Pacific Warm Pool seems to be underway as well:

Low-level wind anomalies in the Pacific Basin. Source: https://www.cpc.ncep.noaa.gov/products/analysis_monitoring/enso_update/uv850-30d.gif

It is interesting to note the hemispheric symmetry in position between the wind anomalies in the western Pacific and the warm anomaly in the eastern Pacific.

Strong ingredients, strong El Niño? Time will tell.

A voyage to the northern Gulf of Mexico

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A successful sediment trap recovery!

A successful sediment trap recovery!

Early in February (what now seems like eons ago!), during less infectious times, we went out to sea in the Gulf of Mexico. I’ve written before about our sediment trap project and the papers stemming from it. Unfortunately, however, this trip was the last one under the current funding regime, and our job was to ensure that both our traps came back up to the surface (which they did); we would not be redeploying them. Womp womp. However, we are working towards getting more funding so we can continue monitoring Gulf of Mexico sedimentation (and foraminifera!)

The Gulf of Mexico is an important oceanic body of water for the United States and Mexico for several reasons; climatically, it is an essential moisture source. Sea-surface temperatures in the Gulf can have a significant influence on rainfall and atmospheric circulation over a large swath of North America. It also serves as the ultimate sink for the Mississippi and other large river systems of the US and Mexico. Naturally, you can imagine that the record of sediments preserved in the Gulf of Mexico holds many crucial histories of North American climate change and the myriad of interrelated tales concerning paleoecology, paleoanthropology, archaeology, etc. Of course, some of these secrets have already been unearthed: stories that detail the extent of Laurentide Ice-sheet meltwater routing, mysteries of abrupt climate change, oceanographic implications of cometary impacts, Little Ice Age hydroclimate, and so on... but there are many others in the making and indeed, many more yet to see daylight.

An animation depicting daily sea-surface temperature variability in the Gulf of Mexico from 2012-2013. Notice that the structure of the Loop Current is visible in the temperatures! If you pay attention, you can also see an eddy pinching off. This an…

An animation depicting daily sea-surface temperature variability in the Gulf of Mexico from 2012-2013. Notice that the structure of the Loop Current is visible in the temperatures! If you pay attention, you can also see an eddy pinching off. This animation was taken from the Naval Oceanographic Office website.

But the paleoclimate tales yet-to-be extracted from the Gulf of Mexico are not limited to histories of terrestrial climate change. Oceanographically speaking, the Gulf is highly dynamic - featuring the Loop Current and its energetic (and enigmatic!) process of shedding “eddies”. The Loop Current transports warm and salty waters from the Caribbean Sea through the Yucatán Straits into the Gulf and “loops” eastward, exiting outward through the Florida Straits. While doing so, at times, giant (multiple-kilometer-wide) swirling masses of Loop Current waters (eddies) “pinch off” the primary current and flow westward into the northwestern Gulf of Mexico. These warmer waters have unique parameters (oxygen, salinity, etc.) and contrast with cooler, fresher coastal waters. These eddies are very important for the wellbeing of marine ecosystems in the Gulf. They can also act as heat engines for hurricanes that pass over them (as in Katrina). There’s a lot of debate about the future of the Loop Current and its eddy-shedding system with ongoing anthropogenic warming. I’d argue that paleoceanography is hugely important to this endeavor as reliable observations of these processes are highly limited.

Foraminiferal shells housed in the Gulf of Mexico have the potential to tell these stories. Through their species distribution as well as several chemical signatures stored in their calcite shells, “forams” are important indicators of past oceanic processes. This time around, we were interested in collecting specimens of Globorotalia truncatulinoides. We think this is an ideal species for reconstructing winter climate conditions and wanted to see if we could culture some individuals. Towards this, we dragged a plankton net at a water depth of ~80 m (the truncs live in the sub-surface ocean) and collected many planktic species. Overall, I think we were quite successful, and many of those collected individuals are still alive today (well over a month from the time of collection!)

Here are a couple of photographs from our plankton tow:

Globorotalia truncatulinoides - the species we were after!

Globorotalia menardii - another sub-surface dwelling foraminifera.

Pulleniatina obliquiloculata - a juvenile specimen

Globigerinella calida

Orbulina universa - this was a spectacular specimen of O. universa (amidst copepods) where you can see through the spherical final chamber and observe the secondary whorl of chambers.

And remember things can get rather rocky when you are out to sea and looking under a microscope!

Transitioning from Papers 3 to Bookends: Part 2 - The How

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After making the radical decision to uproot my reference management system, I decided to take the plunge with Bookends ($73.99 for MacOS+iOS version with an additional $9.99 per year Pro features on iOS). I now had the seemingly formidable task of moving all my PDFs and their attached references from Papers into Bookends. Spoiler: I managed to do this with relative ease.

Here are the steps I followed for my transition from Papers to Bookends (including the associated setbacks and successes):

0. Trying out Bookends

Before moving your entire database(s) to Bookends, I suggest you try out some simple functionality by dragging and dropping (or searching for) a PDF of a paper and check whether an accurate reference is retrieved. You also have the option of autocompleting an entry (Refs → Autocomplete Paper or Cmd+Shift+C). Try editing a reference manually and get familiar with the Bookends interface. I strongly recommend reading the official website’s FAQ, tutorials, support as well as the provided documentation.

1. “Import References from Papers”

Bookends has a handy built-in option to import references from Papers (or Sente or EndNote): File → Import References

Outcome: All the references move into Bookends but not the PDFs (or attachments, in Bookends’ parlance).

Potential Problems: If you receive a “no references exported from Papers” error, try restarting Bookends (while keeping Papers open).

2. Set up a preferred PDF naming structure

Explore writing your own reference and citation formats

Bookends can automatically rename an imported PDF based on the reference that it eventually retrieves. For example, Bookends can make s2-342439.pdf into Thirumalai-2011-Journal-Geol.pdf after crawling through the text. If you’d like to, you can customize this structure by first making (or choosing) a format in the manager: Biblio → Formats Manager.

Outcome: You will be able to choose your preferred naming structure in the preferences.

3. Optional: Set yourself up for iOS usage

Designate the format for renaming PDFs in Bookends and assign the attachments’ folder to the one in your iCloud drive

If you intend on using Bookends on iOS, make sure you go ahead and download the app now. Follow instructions here to import a PDF through a search engine. Ensure that sync has been enabled; now, a ‘Bookends’ folder will be created in your iCloud directory.

On the desktop version, open up preferences and in the drag-down list, choose iCloud Folder for iOS Sync as your attachments folder. The default, inside Documents, does not jive if you want to have an iCloud-synced iOS version, so you might as well follow the above steps even if you don’t want to use the iOS version (the free app supports this as well).

Outcome: You have a folder titled “Bookends” under iCloud Drive.

4. Find all your Papers' PDFs:

Find and consolidate all the PDFs stored in Papers’ virtual library.

Since you’ve already imported references from Papers, Bookends will be populated, but they will not have PDFs attached to them. If imported correctly, it will yield an error that the PDF (with a long, machine-readable string name) cannot be found. This problem stems from Papers’ opaque Virtual Library and file handling system. But this also poses an advantage: now we simply need to gather all the PDFs wherever Papers stores them (with intact names!) and paste them into the Bookends’ folder (inside the iCloud drive).

Go to your Papers’ virtual library/database location in Finder to start this procedure. In this overarching structure, search for .pdf and then ‘add’ a search where you filter by PDF kinds.

Outcome: You are able to select all the originally-named Papers PDFs under one search.

5. Move the PDFs to your Bookends Folder

Before you move anything, make sure that Bookends on your desktop is closed.

Depending on the number of PDFs you have, I would recommend moving in segments. For context, I copied ~1500 PDFs (of ~5000) from the Papers’ search folder and pasted into the Bookends folder (in iCloud Drive) first before doing the rest. The time for the overall transition including the wait for iCloud to upload all these files (make sure there are no small ‘uploading’ clouds visible in Finder!) was about ~20 mins.

Outcome: You have all your Papers’ PDFs in the Bookends Folder.

6. Allow Bookends to do its thing

Batch Edit: rename all your attachments

Open up Bookends, and if the attachment folder has been set to the one under the iCloud drive appropriately, all your references ought to have PDFs attached to them! Scroll through the references and make sure that PDFs are attached.

Now, since nobody likes those cruddy long, undecipherable names that Papers provides, let’s rename the PDFs based on our chosen format. Refs → Global Change → Rename Attachments. This took about ~35 minutes for me.

And - that’s it!

Outcome: All your Papers’ references are in Bookends, with PDFs intact, AND the PDFs are all inside the Bookends folder, named based on the structure you chose! Voila!

If you followed these steps, you ought to be able to open up Bookends on iOS and slowly wait for the iCloud sync to weave its magic.