Monday, August 01, 2016

Field Notes Digitzation

Together with another student in the CUNY Graduate Center, I was able to get a grant from the Provost"s Digital Initiatives Grant. This grant allows us to start something exciting, the digitization of the notes taken by scientists in the field.
There's a few jsutifcations for this type of project. On the one hand, field notes are an important part of thproduction of science.  Workers record observations ---actual data--- in their notebooks and use that later on to produce scientific ideas and publications. Nearly everything else we do is heavily computerized and digitized, But taking an iPad out to a field station is very rarely a realistic option. If it's not clear why, field sites are often remote, with no electricity and no connectivity. Field sites are also often harsh, without proper shade; high temperatures; extremely high humidity, all things that can wear on electronics. Despite that however most of us still take our cell phones into the field. But paper and pen, that's a technology that continues to stand up to the field environment.   Field notes are also a pastiche of what in the digital world are multiple types of media: sketches of an outcrop; maps of field sites; tables of data; lists of GPS coordinates; alongside spontaneously recorded blocks of text. Most digital solutions to this mixture of media are simply replications of paper and pen notes on a screen. Digital pens reverse the process of digitization; they insert digitzation into our already existing processess.
But why digitize at all? Digitizating your field notes creates a back up of them. Most of us do this by photocopying and scanning the pages in our notebooks. This is a timeconsuming nuissance that sometimes still produces unreadable sections of our notes. Some people go so far as to cut out the spine outof their notebooks in order to make scanning easier. With a digital pen, the only extra work to produce a visual backup of your notes is turning syncing to your phone or simply turning on your phone and opening an app before writing. This alone makes the digitiation of field notes through smart pens worth investigating.  As long as  pen system can be found that fits into research budgets; that produces accurate renditions of handwritting; and that is manageable and portable, you've got something worth investigating and potentiallyy incorporating.
But I think smart pens offer us a lot more than redundant back ups. They make field notes shareable. Even if you previously had a set of scanned pages from your notebook, sharing them can be difficult. The files tend to be large if they're high quality. You may've scanned to PDF or TIFF,  and that decision may've dependded on the scanner you were using. Whoever you want to send the files too may need you to make the files smaller, or even the email program their campus uses may require that! And if you didn't bundle every page together, that'd mean you have to batch resize every file. A digital pen system should manage your files, it should let you send entire notebooks or ranges of pages in a choice of formats
If another worker, or you yourself, want to search for a particular passage or subject in your notes, digitzation has tremendous potential to aid in that. When I use a notebook, I put a table of contents or index in the first few pages and I add to it over time. That's how most of us make our notes "searchable". Really important things I flag with a post-it type of sticker. Usually I put a header on each page. When I really start getting desperate I'm drawing stars, using highlighers, or anything to make a page stand out; because more often than note when I'm searching through a notebook I'm flipping through the pages quickly and need something jarring to make a page or passage stand out. A digital system should be able to do that and expand beyond it. A digital system should handle indices and tags, but also should make note searchable from the start. When we're evaluating these systems, handwriting recognition and searchability are prime criteria.
Not all field notes are spontaneous. A lot of field notes are very patterned and regular: you're measuring or estimating the size, colors, rock types, strike and dip of beds at an outcrop, thickness of beds, etc. Or you're recording the location, body mass, length, species, and sex of a dozens of living specimens at multiple locations. We're doing that because this data will be used later on. We're building databases from our notes. For most of us this means getting back from the field, to our labs and computerrs, cracking open our notebooks, marveling at the amount of dust they've taken in, and then entering by hand all of the data. Sometimes we're lucky enough to have junior lab workers that can be assigned this tasks, and often we're the more junior worker that get's assigned it. With smart pens we should be able to save time, by writing the notes we should be also be generating text that can then be copied as a whole into a database. In fact we should be able to have that entire process automated. And if we have some connectivity at our field locations, we should practically be able to build databases in real time or nightly. But one thing that should be apparent in academia is that saving time often isn't much of a draw. What does the PI care if a digital process saves a student's time? Well one added benefit of digitization is that it can result in less errors. The data entered into fields can be set to be numbers, text, or a mix of both, just like in a spreadsheet. This prevents the handwriting recognition system from mistaking a "7" for an "h" or something along those lines. Or it can at least throw a flag up for a human to review when it hits a contradiction like that. It also allows for errors to be addressed while there is still someone in the field. Even with a notebook alone, there can be confusion about what's recorded. If it's months later, even the person who took the notes can be unsure of what they were recording and why. Having the people back at the lab able to contact a field worker while on location can clear up errors and make us more confident in our decisions regarding how we've resolved errors.

There are a few other possibilities and abilities that digitzed notes offer beyond handwritten notes. By having searchable text, the frequency and co-occurence of words can be tabulated and studied. This potentially can tell us something about how a worker learns about their field site. Perhaps there are differences in word occurence between people new to the location and others who are experts about the field site? Perhaps there's a difference, or similarity, between expert scientists and expert non-scientists about the site. Those are more distant possibilities for this project. At the moment, we're just trying to figure out what digital processes and practices work best for a variety of scientific fields.

Wednesday, May 18, 2016

Dangerous Fieldwork

We've known for a long time that scientific fieldwork can be dangerous. Roy Chapman Andrews was attacked by bandits for example. And for women, it's been publicly known for a few years now that there is massive harassment, by their scientific colleagues, in the field (and the lab, and the classroom, and the rest of academia. Yikes.).

But the foreign government allowing the research in the first place? They're not supposed to represent much of a physical danger. Yet here we have a researcher,  28 year-old Cambridge PhD student Giulio Regeni, who was apparently tortured and killed by the security apparatus of "President" Sisi in Egypt. Sisi came to power in what amounted to a counter-democratic coup. The longtime Egyptian dictator Hosni Mubarak resigned after public protests over his reign, and Mohammed Morsi, a member of the Muslim Brotherhood political party, was elected afterwards. The Egyptian military ultimately balked at this, initiated a coup, and used a tremendous amount of violence (killing more than 800 people in one instance) to suppress not only the Muslim Brotherhood but any dissent.

So perhaps it shouldn't be surprising to learn that they kidnapped him, burnt and tortured him, and ultimately killed him. In addition to the plain old evilness of this regime, it shows that the Sisi government is not really thinking about researchers in Egypt. It should be obvious that there's a tremendous amount of field and other research going on in the land of the Pharaohs & Fatimids. Also recall that the dinosaur Spinosaurus aegypticus was first discovered there, and that the Fayum is an amazing and important primate fossil site. There's a huge number of researchers there, in fact there's entire field schools that operate under this same government and security apparatus.

Tuesday, May 17, 2016

Luwians the Trojan War and wannabe Schliemanns

Schliemann was the famous discoverer of Troy, who made the possibility of it's fabled Trojan War seem a little more realistic. He bucked the authorities and the prevailing knowledge of his time.

http://www.dw.com/image/0,,18934757_304,00.jpg
Also a straight up pimp?
So, ever since his discovery, people have tried to emulate him. In fact this isn't really something that was brought about by Schliemann's success; people certainly claimed to be rebel scientists before even Galileo was around. Schliemann particularly comes up here because of this article interesting and highly critical article from Jason Colavito:

http://www.jasoncolavito.com/blog/swiss-geoarchaeologist-claims-lost-luwian-civilization-caused-the-bronze-age-collapse-and-the-trojan-war

There Colavito discusses Eberhard Zangger's idea that Troy, and it's fall, is the ground-source for the Atlantis mythos. Zangger ties this Atlantis-via-Troy idea up with 'secret and suppressed history' and ancient lines of kinds. So Aeneas meets the Davinci Code I guess.

The Luwians did it?


Here's Zangger's site promoting the idea. The other thing that gets distorted here is that the Luwian language---a real thing---is blown up into 'the Luwian people' These Luwians are part and parcel of the fall of Troy. Except they didn't exist.  It's a language, but not a people, not like, say, German or Hittite, which were both languages and peoples.
This is an odd thing that lots of people seem to do, assuming a language group also represents an ethnic people and a culture. This isn't the case now, you don't need to be an Anglo practising the English culture just because you speak English. More people today speak English as a second language than as a primary language too. In the past this sort of thing would've also happened. So lots of people could be Luwian speakers without being 'the Luwians'.

So the Luwians, apparently, didn't do it.

GIS or Lidar experience?

Got an undergrad degree in Geology?
Have at least a year's worth of grad coursework in GPS (and didn't end up in a lake?) and/or LIDAR and the like? 

Then apply for this USGS job in California. The work involves GIS and mapping in a science center.
The listing closes in about a week.


https://www.usajobs.gov/GetJob/ViewDetails/437878400/