Organizing a large amount of information?

One of the questions I have now that I'm approaching the start of a PhD is about organization. I've written piddly little papers, a few articles, and a larger dissertation, though only 12,000 words. Compared to this a PhD thesis is a huge undertaking!  I'm wondering how people go about organizing their thoughts and work - both for smaller academic papers, and larger projects as well.

I need to organize my cats.  I mean my work.

My mother-in-law is a fiction writer who also has an academic background, so her advice in this has been really useful.  For her writing she uses Scrivener: "Scrivener is aimed at writers of all kinds—novelists, journalists, academics, screenwriters, playwrights—who need to structure a long piece of text while referring to research documents. Scrivener is a ring-binder, a scrapbook, a corkboard, an outliner and text editor all rolled into one."

Sounds good to me!  So I've downloaded a free trial (https://www.literatureandlatte.com/trial.php), which allows you to use it for 30 different days (they don't have to be consecutive).  Afterwards, it's only $40 to buy which sounds quite worth it if I find it's a useful organizing tool!  We'll see how this goes and if it's a good solution.  I can use all the help I can find.

Talk or Poster? Talk or Poster?

It's done!  It's done and finished, a neat 7 page paper related to my proposed PhD topic, ready to be submitted to Evolang X.  But - I'm torn.  Do I want to be considered for a talk or a poster?

I've done 4 posters at conferences now, and I should really start stepping up and getting experience speaking in front of people (and answering terrifying questions at the end).  However, while I like my paper and where I'm going with it, it doesn't really offer all that much original material or any new findings or research results.  So... I'm not really sure it deserves a 20 minute spcheel.

I'm including this picture simply because it's useful.
If you're presenting a poster - how big is it going to actually look?

But!  It is original in that it says 'hey guys, there's this interesting research material that could totally be applied to these other research questions in new and interesting ways'.  And that is relevant and interesting.  But 20 minute talk interesting?

But I would like to do a talk.  And maybe in 6 months I will have more information to speak about.  And maybe it doesn't matter what I think, because it will be decided by a comittee anyways whether or not it will be selected for a talk.

So maybe I will request to be considered for a talk, and then I will know whether or not there's enough in the paper that deserves people's attention that long, all eyes on me, complete with challenging scary questions at the end.

It will be a learning opportunity, whatever happens.

Back from excavation, nursing archaeology wounds

I woke up with morning with a start - I'm late for site, everyone will have left without me!  But no, I'm back at home in England, no longer smelly and dirty, and with marginally less grit from layer 7 still stuck to my face.

I spent the last 6 weeks at Menez Dregan, hands down the most brilliant and interesting Lower Palaeolithic site in all of Brittany.  Many photos and musing are to follow, as it was inspiring and eventful.  More than anything, I want to return next year.

But on my mind today is finding a bandage or support for my hand - trowelling through concrete-like sediment for so long has left my right thumb prone to dislocating if I so much as tie my shoe.  It's probably something I should see the doctor about.  But maybe it will, you know, just go away...

Another archaeology injury I've acquired is very similar to my bookshelf necklace-making craft pain I will call the 'shoulder blade of fire'.  The muscles used to hold arms extended complain in the evening, as if I've been holding cinder blocks at arms length all day.  It does make typing a bit of a pain.

But all this has been so worth the beauty and the learning I got to experience, with my husband, making new friends, eating delicious food, bumbling along in French.

I promise to share my most favourite of these experiences in later posts.  Along with some yummy recipes.

Neanderthal or Neandertal?

Both of these spellings (and pronunciations) are commonly found - is either more correct to use?

In short, nope!

Neanderthals get their name from the Neander Valley (or Neandertal in German), near Dusseldorf in Germany.  This valley is where the first Neanderthal fossils were found, around 150 years ago.

OMG, it's a Neandertal baby!!
Or is it a Neanderthal baby...?

'Thal' is an old form of the word 'valley', so Neandertal (the place) used to be called Neanderthal.  Nowadays 'thal' is spelled as 'tal' after a German spelling reform at the beginning of the 20th century (people loved those back then, didn't they?), which is probably why we see Neandertal in spelling now and again.  It tends to be less
common I get the impression...

Neanderthals' taxon is Homo neanderthaensis, with the 'th', so I guess purists could argue that it's better to spell it with the 'th'.  But what is appropriate in language is defined by what people use (generally), so whichever!

'Thal' and 'tal' in the German are both pronounced the same, which reflects how some people (like me!) spell Neanderthal but say 'Neander-tal'.  However, pronouncing the 'th' is totally common and often used in the English pronunciation of the species.

In short, say whatever, spell whatever... it's language!  As I said, what is 'appropriate' is all about what people use, and in what situation.  It's all about conventions, and there are conventions of using both :)

Neanderthal Language: did we once have a linguistic cousin?

In a recent paper ("On the antiquity of language: the reinterpretation of Neandertal linguistic capacities and its consequences"), Dan Dediu and Stephen Levinson argue that modern language was a feature of both Neanderthals and modern humans, and therefore of our common ancestor as well.  This takes their date for the origin of language to around 4-500,000 years ago at least, far beyond the common (though what I consider as very conservative!) view that language emerged around 100,000 years ago.

Illustration of hypothesized dates and
communication systems, shown alongside
tool technologies and hominin species 

Whether or not Neanderthals had complex language, or any form of complex communication system such as a protolanguage, has been debated for decades.  More and more though, the evidence seems to bolster the idea that our very close cousins were more similar to us than the classical brutish view, both cognitively as well as behaviourally.

In my previous post "Are we being a bit unfair to Neanderthals?", I discussed the tendency for people to be quite negative when thinking about Neanderthals, to compare their culture to more modern examples of our own, and scorn them as "the other" - languageless, dumb, and trying-to-be-human-but-not-quite-getting-it.  It's an unbalanced view, when humans and Neanderthals had broadly similar behavioural and cultural signature in the record, especially when you look at contemporary examples in the record.

Some might say that the classic image of the Neanderthal has had a makeover - we now know that sometimes, some of them buried their dead.  Sometimes, some of them pierced teeth or shells, and used red ochre and black manganese as colourants.  Often, they made beautiful stone tools with great skill and knowledge of flint working.  Sometimes they interbred with modern humans.

But still, the nul hypothesis for some has remained that Neanderthals are crap versions of humans.  Equally, if you are going to attribute intelligence to a species, don't you also need evidence to attribute them with a lack of intelligence?

Now, with evidence of interbreeding between the species, and the Neanderthal genome sequenced, it's harder to think of Neanderthals so simply as 'the other'.  Dediu and Levinson's article doesn't contain the Neanderthal racism I often find myself complaining about.

Most interesting and unique about their article is the implications for studying language evolution and linguistics, suggesting for example,

the present-day linguistic diversity might better reflect the properties of the design space for language and not just the vagaries of history, and could also contain traces of the languages spoken by other human forms such as the Neandertals.

It's a great article synthesizing lots of relevant information on Neanderthals as well as language origins research, and I recommend it as a good read for anyone with an interest!

Book Launch Tour: The Vesuvius Isotope, by Kristen Elise, Ph.D.

This post is part of a book launch tour for the release of The Vesuvius Isotope, a new book by drug discovery biologist Kristen Elise.  This book might be of interest to those of use that enjoy a thriller with a bit of archaeology thrown in :)  All the posts on Kristen's blog tour are related in some way to the content of her new novel - see below and be intrigued, maybe you've found your next Summer read!

The Crocodile Library of Tebtunis

[F]or some of the Egyptians the crocodiles are sacred animals... and each of these two peoples keeps one crocodile selected from the whole number, which has been trained to tameness, and they put hanging ornaments of molten stone and of gold into the ears of these and anklets round the front feet, and they give them food appointed and victims of sacrifices and treat them as well as possible while they live, and after they are dead they bury them in sacred tombs, embalming them.

-The Histories, Herodotus (ca. 484–425 BCE) 

In the winter of 1899/1900, an expedition into the Fayoum Oasis outside of Cairo, Egypt was initiated. The expedition was led by the University of California at Berkeley and the Hearst Foundation. Its goal was to excavate an ancient site: the ancient city of Tebtunis. The researchers were looking for human mummies; what they found instead were mummified crocodiles.

One of the workers from the expedition was so disgruntled that he took a machete and began hacking at one of the mummified crocodiles. And this was how it was discovered that within some of the crocodiles, an incredibly large collection of papyrus documents had been preserved for two thousand years. Papyri were found both in the crocodiles, where they were sometimes used as part of the mummification process, and within the city itself. More than 30,000 ancient texts were eventually recovered from Tebtunis, comprising the largest collection of ancient papyri that exists in the United States today.

Mummified crocodile, Naples Archeological Museum

The majority of the texts date to the second century BC, although others hail from the first or second centuries AD. This is the same era that produced the Villa dei Papiri at Herculaneum, offering an Egyptian counterpart to the Roman resource that is still mostly buried beneath the ash from Mount Vesuvius. And, like the texts from the Villa dei Papiri, the ancient papyri of the Tebtunis excavation are still legible to this day.

Mummified baby crocodile, Naples Archeological Museum

Within the library were more than a dozen fragments of Homer's Odyssey and Iliad. Also found were birth, death, and tax certificates, and petitions to Queen Cleopatra from her subjects. It is unfortunate that no texts have ever been found - either in this database or any other - that were actually written in the hand of Egypt's enigmatic last pharaoh.

Also excavated at Tebtunis were several scientific and medical texts, including at least one example of an illustrated treatise on the medicinal properties of plants. Contrasting with these are a number of astrology and magic texts. The juxtaposition between magic and medicine in the same era underscores a critical transition that was underway at that time - the transition from superstition to true science.

Tebtunis illustrated medical text

It is interesting to note that the Tebtunis papyri are written in both Egyptian and Greek - sometimes within a single document. The demotic Egyptian language was common among earlier pharaohs but rarely used in the later years of the first milleneum BC. A gradual replacement of Egyptian with Greek evolved with the Ptolemaic Dynasty, and the Roman conquest of Egypt brought with it an increase in the use of Latin.

Cleopatra, the last ruler of the Ptolemaic Dynasty, was the only one to speak all three languages.

For more information about the Tebtunis Papyri, visit the Center for the Tebtunis Papyri.

This blog post explores a non-fictional theme or locale that is incorporated in The Vesuvius Isotope, a novel by Kristen Elise, Ph.D. Order your copy at www.kristenelisephd.com.

Kristen Elise, Ph.D. is a drug discovery biologist and the author of The Vesuvius Isotope. She lives in San Diego,  California, with her husband, stepson, and three canine children. Please visit her websites at  ww.kristenelisephd.com and www.murderlab.com. The Vesuvius Isotope is available in both print  www.kristenelisephd.com and www.amazon.com) and e-book formats (www.amazon.com for Kindle, www.barnesandnoble.com for Nook, www.kobo.com for Kobo reader.) 

The Vesuvius Isotope:
When her Nobel laureate husband is murdered, biologist Katrina Stone can no longer ignore the 

secrecy that increasingly pervaded his behavior in recent weeks. Her search for answers leads to 

a two-thousand-year-old medical mystery and the esoteric life of one of history’s most enigmatic 

women. Following the trail forged by her late husband, Katrina must separate truth from legend 

as she chases medicine from ancient Italy and Egypt to a clandestine modern-day war. Her quest 

will reveal a legacy of greed and murder and resurrect an ancient plague, introducing it into the 

twenty-first century.

Exavation en France à Menez Dregan!

This August I will be off to beautiful Brittany in France, to dig at a Lower Palaeolithic site called Menez Dregan for 6 weeks. 

C'est un éclat!

The site has layers rich in stone tools dated to between 350,000 and 500,000 years BP.  It also has some of the earliest evidence of controlled use of fire.

I've never dug at a Lower Palaeolithic site before, which makes it exciting, but I'm also excited for working outside in some (hopefully) good weather, and getting to practice my French.  And eating French food.  Lots of it.

I've made a list of a bunch of French words that one might come across in an archaeological situation, that I'm trying to remember.  Here's a sample:

• Pierre (stone)
• Caillou, galet (pebble)
• Feu (fire)
• Ancien (ancient/old)
• Niveaux (levels)
• Charbon de bois (charcoal)
• Silex (flint)
• L'industrie lithique (lithic industry)
• éclat (flake)
• Chantier (site)
• Fouille (excavation)

Another exciting aspect of this trip is that I (and my husband who will be there too) will effectively be homeless - we finish the contract on our flat days before we leave, so everything's going into storage, and then we're off!  We have a place secured for when we return, but not until a few weeks after... so there might be some couch surfing!  

Online courses related to human evolution

There is a great resource that some of you might have heard of, called Coursera.  It is a website with a collection of online classes offered from top universities around the world that you can take for free.  Sound good?  It's great!

You can take many of them in real time and follow along with a class, with weekly lectures and assignments, and you even get a certificate of completion at the end.  Or, you can look into the archive for a class that has already happened, and use the material at your own pace.

The courses cover loads of topics and disciplines, from medicine to computer science to nutrition, but I thought I'd share some links to ones that might be interesting for students of human evolution:

(already started): Archaeology's Dirty Little Secret, Brown University
Beginning July 7th: A Brief History of Humankind, University of Jerusalem
Beginning August 19th: Animal Behaviour, University of Melbourne
Beginning January 3rd 2014: Introduction to Genetics and Evolution, Duke University
Beginning January 21st 2014: Human Evolution: Past and Future, University of Wisconsin-Madison

I've been perusing a course on Writing in the Sciences, which has video lectures of powerpoint presentations, led by an instructor, and I'm finding it really useful.  I'm sure this course, Introduction to Public Speaking, might be useful for the student as well!

I've signed up for Human Evolution: Past and Future, which is being run by the lovely John Hawks of John Hawks' Weblog.  You can read his posts about MOOCs, or 'Massive Open Online Courses" here: http://johnhawks.net/taxonomy/term/1380. 

Preparing a paper is hard; and other difficulties

I feel a bit like this... 3 years old and lost in a maze!

I've been trying my hardest to put together a full paper to submit to the 10th International Conference on the Evolution of Language (Evolang X).  It's the perfect motivation to dive into some related research before I start my PhD this Autumn.  It forces me to read and think about my project, and I'm hoping it means I'll have a good head start on getting to grips with the material.

But - and here's a news flash - preparing a paper is really hard!

It makes me wonder about the process researchers go through when submitting a paper.  Why did they choose that topic?  How did they decide what journal to submit to?  Is it a stipulation of a research team you're a part of that you need to produce a certain amount of publications?  Or is it entirely on the onus of a researcher to decide whether they want to publish a certain aspect of their work or not?

I'm full of lovely naieve questions like this.  Hopefully I'll come to understand this strange world more as I enter into it more seriously.

But back to the difficulty of writing this paper.

I guess I started out with 'wanting to write a paper for this conference' instead of 'having a piece of research and wanting to publish it' first.  It's a sort of top down rather than bottom up approach.  Is that a weakness in my research?  Like, I sat down with a blank page and wondered what question I could address, rather than having some original research I had been working on already, which I then decided to share.  Wrong approach?  Perfectly fine?  Who knows!

The piece is really pointing out a correlation between two cognitive abilities, and bringing together the research from the one discipline and offering it as something to apply to questions we have in another.  Is that reasonable?  Useful?  Warrented?  Interesting?

I have a project proposal that I submitted for my PhD, which I am treating as a roadmap for what areas of research I should further familiarize myself with, before creating a more robust project idea that really will end up shaping something that can confidently be called a PhD project.  At the moment I'm aware it's more 'grand proposals' and less 'coherent plans' at this stage, but I really want to get to grips with what I will be addressing and how I will address it over the next three years.

And the first step I have decided is to write this paper.  It will be a small piece of research that will (hopefully) be the first contribution to the form and shape of my PhD.  Will it come together as something useful?  I hope so.

No PhD funding... hunger imminent but still happy

I received the unfortunate news that I wasn't successful in being awarded any funding for my PhD to start this Autumn.  Sigh.

I've saved an scrimped for the last 3.5 years, so I'll manage through the first one alright before things get perilously dangerous, and there are more opportunities to apply for funding in the second year of a PhD.

It's a sad realization - but still, I've reminded myself that a PhD without funding for some people is an impossibility, as it was for me for the last three years.  Now (thanks to a suprise success online jewellery business - see right hand side of blog), I'll hopefully be able to bumble through with flexible part time work.

Another cheer up tactic is that Southampton is a great university, I love the project I want to study, and Clive Gamble is an amazing academic that I have the opportunity to study with.  No funding is the icing on the cake - and while cake without icing can be a bit dry and hard to swallow, it still tastes good!  And I definitely wont be fat at the end of eating my whole cake.  This analogy has to stop now.

But it is that time of year - are you, dear reader, waiting to hear about funding decisions?  Have you been given the good/bad news?  What are our thoughts about PhD funding in general?