Rising Star: My favourite questions

It’s Day 16 and the underground astronauts at Rising Star have managed to “hangout” (virtually, via Google) with classrooms from around the world: with little kids as young as five, to university students! In these classrooms, learners get to ask us questions ranging from the experiences of the excavation, to what we know (or hypothesize) about our strange relative, Homo naledi. I have recently written about how I became a part of the project more generally, but today I want to focus on some of my favourite questions, which many people might be interested in, but may be too shy to ask. I am focusing a bit more on the experience questions (of caving) because I think there will be plenty of opportunity to discuss and flesh out the debate about the small hominin in years to come.

1. What kinds of animals live there?

The farm on which the Rising Star Cave System is found has quite a bit of wildlife. Some of it, like the Nguni cattle (two cows and a bull), the blesbok (three babies were born during our stay!), springbok and impala were recently purchased. But we also see mice and steenbok and other little creatures on the farm. At the mouth of the cave, birds (two fledglings learning to fly through the top of Command Center), porcupines (we use their pointy, but soft quills to excavate out more delicate specimens), dassies and snakes have made a few featured appearances. Deeper into the cave, near Superman Crawl, we have found wandering toads (which Marina has rescued) and spiders (including a long-dead “crystal spider” where the body, on it’s web, was encased in dripping lime). But as we get to Dragon’s Back, the only friends we find are insects and bats. In the Chamber, it is almost only ever us and the occasional bat.

20181115_065444

Angharad Brewer Gillham’s (trainee) excellent drawing of our Blesbok males chasing each other around the farm, featuring Marina Elliott (original), Keneiloe and me (trainees).

2. How small do you have to be to get to the Dinaledi Chamber?

When the original call was made for excavators, it was clear that it would be ideal if individuals chosen were relatively small in order to get through spaces: in particular one 18cm pinch point which occurs somewhere in the chute. This was initially a psychological barrier to me applying. I was small by most human standards, but there was certainly no way I could fit through 18cm! Luckily, this pinchpoint was such that there are multiple ways to manoeuvre around it. Once I arrived at Rising Star, however, it was clear that I wouldn’t be that unusual in dimension: the other astronauts present (in the 2018 expedition) are smaller than I am, but the cavers are pretty tall men, one with a little build. Don’t get me wrong! You cannot be too robust if you hope not to get stuck, but the majority of the problems one is likely to encounter is mental, rather than physical.

3. Did you ever get hurt/stuck?

Yes and yes. In the first week of excavation I climbed out of the chute, traversed Dragon’s Back, climbed down a ladder off of Dragon’s Back and then twisted my ankle… on flat ground… Which just goes to show that flat surfaces are super dangerous! But, after a couple of days of rest, I was right as rain and could continue caving, albeit with a strappy boot for slight ankle support. Safety is emphasized over and over again at Rising Star. Marina Elliott (lead excavator) emphasizes safety at each morning briefing; Lee Berger always says “Stay safe” as we are about to descend; we harness up when climbing the Dragon’s Back and are encouraged to take our journey in and out of the cave slowly and carefully. The safety cavers are on standby both at the front of the cave (at Command Centre) and at the top of the chute (right by the chamber), and any injury in the Chamber itself has a protocol that’s already been detailed. We also have (much needed) safety helmets and overalls. In general, I feel pretty safe, as long as I remain attentive. But the physical nature of the journey in and out of the cave means that each day I leave with fresh new bruises on my legs, sensitive knees and some scratches on my arm.

As for whether we get stuck? Learning to navigate through caves, especially if you are not used to it (as Kenni, one of the other trainees, and I were not), is difficult. You are tempted to tackle spatial problems like you would in a mall. However, this is practically not possible in the three dimensional space of a cave. Learning to twist your body, moving sideways, or crouching and crawling in strange ways is something that takes a little time to become intuitive. During orientation, we were taken through a path that included areas named “Upside-down-turnaround” (the name says it all) and “ballerina’s passage” (where tilting sideways like a ballerina is encouraged), which resulted in a little snag for all of us. But reevaluating the space, taking a deep breath and trying again, ultimately led to success! Every day I go up or down the chute, something snags at my pocket, or my thighs get lodged into a narrow section temporarily. But a good pull up or breath out gets me dislodged quickly enough.

4. How do you pee?

The journey into the cave is only really 200m, but it’s quite a complicated one (through narrow passages, Superman’s Crawl, the climb up Dragon’s Back -harnessed- and a 12m climb down the rocky chute). Then we are down in a pretty confined, humid space. This means that, once we are down in the Dinaledi Chamber (where we excavate), it is a bit of a mission to go to the… uh… bathroom. Apparently in previous excavations a rule needed to be made to take out whatever you made… if you catch my meaning. Our strategy? Hold it in. No-one wants to confuse water and pee bottles.

The five astronauts (from back to frony: me, Angharad, Keneiloe, Becca and Marina) down in Hill Antechamber all together for the first time.

5. What does it smell like down there?

Kenni had the perfect response to this question: “It smells like the wet.” The Dinaledi Chamber is a consistent 18 degrees Celsius, with 99% humidity. Every rock you touch is slightly damp, as is the sediment we move as we excavate. Just like all excavation sites, there is certainly an earthy smell as well once we start digging (also, our faces are closer to the ground). Think about the smell that you get when you pass an active construction site, where they pile on sand and clay into heaps. I think we settled on wet, muddy clothes as the final “smell” of the Dinaledi Chamber. Not unpleasant, but certainly distinctive.

It’s probably also worth mentioning sound and sight. The Chamber, without our lights and headlamps on, is pitch black: any light is merely your brain trying to make sense of the void. When we do not speak and try not to move, there is no sound at all…

We have been asked so many cool and interesting questions which have made us think more broadly about our experiences and about the science, that it is impossible to address them all. (“When did you know you wanted to be a” -slight pause- “ologist?” was also a great one). I hope you enjoyed these questions as much as I did! And don’t be shy to message or tweet me any more!

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Rising Star: How I got here

Two months ago, I decided to send through my motivation letter and CV to the Lee R Berger Foundation, to become one of the new (trainee) Underground Astronauts for the Rising Star Expedition in the Cradle of Humankind (South Africa). The purpose of the excavation is to retrieve and understand more about the distribution of Homo naledi remains in the Dinaledi Chamber, where the original excavations of this interesting hominin took place, a few years earlier in 2013/2014. The first excavation was unique for many reasons: the high profile nature of the excavation and find (filmed and recorded by National Geographic), the environment of the chamber (30m below the surface, through narrow, difficult to navigate passages), and the international, public call for application to excavation, by Lee Berger. The original six astronauts were made famous overnight, and, with them all being women, this was an important moment in showcasing (badass) women in science. Believe me, I have spent 10 days with two of these women. They are totally badass!

Image may contain: 7 people, including Keneiloe Callisto Molopyane and Marina Elliott, people smiling, outdoor

We are now on Day 10 of the expedition (photo by Marina Elliott), and it both feels like I had only applied yesterday, and it feels like I am comfortably in a place I would call home. Already, in this short time, I have made incredible friends and mentors who I (quite literally) trust with my life, have learned to navigate through incredibly challenging caving environments, and have helped to set up and begin an excavation in the Dinaledi Chamber. This week has been filled with mental and physical challenges. All this while intermittently hanging out with school kids from across the world, via Google hangouts, and spamming my social media with images and quips from the excavation. Oh, and did I mention I sprained my ankle?

I think it is worth explaining how I got here. I intend making alternative posts about my new mentors and friends, and about some of the more intricate adventures which have already taken place. Life at Rising Star is out of a movie: challenging, hopeful, fun and beautiful (in and out of the cave system). But, it is clear, stemming from the Hangouts I have done with the school children, that a lot of people want to know how it is that I am here: what drove me to apply, and, presumably, what they need to do to potentially be a part of something similar. Keneiloe and Angharad (the other two trainees on the expedition, and, you guessed it, badass women) have stories with surprising similarities and differences, and I hope you get to hear theirs soon as well!

Of course, a brief look at my handful of blog posts will hint that I am at least slightly obsessed with Homo naledi: from why it is important to carefully deconstruct how we as scientists make educated assumptions about things like the skin colour of the find, to why the finding of Homo naledi in a second cave system is important in shattering preconceptions about our small-brained relative. The time period of these finds were largely during the course of my PhD, and both my supervisor, Becky Ackermann, and my friend and colleague, Lauren Schroeder, were part of the scientific teams analysing and publishing on the finds. (Two other badass women in science).

It was only recently when I found myself in a situation where I was both minimally constrained with respect to work-load, and physically capable of the work that such an excavation would entail. Archaeological excavations are a lot of work, and, even in good, easy-to-reach conditions, require strength and endurance. The Dinaledi Chamber, in which I currently excavate, is additionally very difficult to reach, and I will undoubtedly write up a short description of the journey in the next few days (and our training day to prepare us)!

This year has also been a largely privileged year for me. Just a few months earlier I was offered a travel scholarship to go to the 2018 European Society for Human Evolution Conference in Portugal. I met some amazing people at this conference, and it became clear that at least a few of them were applying for the Rising Star expedition. To my surprise, many of them did not think they fit the full criteria for the expedition, but did not want to miss out on such an amazing opportunity. Some of them had caving or climbing or curating experience. Some of them had PhDs. Some of them were not terribly small. In general, despite all of the people I am meeting making me feel inadequate as a potential candidate, they too felt inadequate.

I decided that I too had at least some of the criteria Lee Berger and his team was looking for. I was reasonably fit (a new development), was relatively small-bodied (for modern humans, not Homo naledi), had a PhD in Palaeoanthropology, some field experience in relatively extreme environments, and a few accomplishments and interests with respect to Science Communication. I was also South African, and was reasonably certain that there were few of us who could or would apply, despite encouragement for us to do so. The fact that I had no caving or climbing background was a large limitation in my own mind! And every time I head back up the chute, I curse my limited upper body strength and larger thighs (which keep getting lodged)!

Curse You - curse you thighs

All of these criteria seemed to come together at the ideal moment, and many were experiences I had randomly taken up as chance and opportunity would have them, without any particular end goal in mind. I acknowledge that at least a few of these are possible because of privilege, and a small amount because I typically like to try or experience new and unusual things.

If I had to create a checklist of advice I would give to both schoolkids and adults who hope to one day also be lucky enough to have an opportunity like this, it would probably amount to the following:

  • Do things that interest you. I know that this is a very privileged piece of advice. Not everyone has time and money to truly pursue their interests. But if you enjoy something like climbing or running, or even writing or something creative, then even a small amount of consistent practice can make you good enough for taking on an unusual call some time in the future. Doing unusual things, or typical things well enough, can land you unexpected opportunities.
  • Do things that might not interest you. Some of my field experiences were thrust upon me, but can be considered good career moves, and were incredibly beautiful moments in my life. Similarly, even if you find exercise tedious, feeling a little more physically capable than you might have been before can provide a huge mental breakthrough, and add substantially to your confidence. If you plan to apply to Rising Star in the future, I would suggest push-ups.
  • Apply. You might be more qualified, or at least interesting enough to be considered, than you thought.

I hope that this is helpful and encouraging!

AAPA name change

The AAPAs are next week (Yay!), but sadly I will not be going due to having a job, living on the other side of the world and needing to pay for myself (Aww!). To everyone who is going: I hope you have a great time, learning and networking and catching up with old friends. 

Last year I was one of the winners for the 2017 Pollitzer Student Travel Awards, ranked within the top 10 (Yay!), covering the following topic.

In ~750 words or less, make a case either for or against changing the name of the American Association of Physical Anthropologists. If you argue for a name change, what should the new one be?

I was invited to share my opinions to a committee on the Presidential Panel “What’s in a name?” However, this panel discussion has been moved to this year (Aww!) and I thought I’d share my essay with others, hoping it may help stimulate this discussion. To be clear: I think there are already a lot of good arguments for name change, particularly in changing “Physical Anthropology” to “Biological Anthropology”, centered around the disciplines role in racism.

I do hope that panel members additionally consider how having one of the largest conventions for bioanth so essentially (in name and locality) placed in America might be adding to a discipline that is already deeply imperialistic and extractive. I also hope that some of the voices included in this conversation are from the countries from which many of the materials are taken or analysed to help glorify the career of a foreigner.  I also hope that most of those voices are from people representative of their country. i.e. not only racially classified as white.

I only included two references, but was deeply inspired, at the time, by “Darwin’s Hunch” by Christa Kuljian, which I highly recommend. The essay is clunky: I am quite verbose and restricting me to 750 words means joining thoughts were not always an option. But I hope you get the gist.

Image result for darwins hunch

If you also were invited to speak to the panel last year, but can’t make it, please feel free to send me your essay: I am happy to include it, both attributed or anonymously.

 

The essay

“Physical Anthropology” as a term is an interesting one. On one hand it has historically described the discipline of which I am currently a part. On the other, it defines only a narrow bit of this discipline, the history of which I am ashamed. Physical anthropologists of the past were often anatomists interested in human evolution and race. Their approach was certainly a physical one. Every fossil that was found was carefully excavated and measured, and detailed observations and drawings were made. But it was not just fossils. Primates were of great interest to these anthropologists as well. And they were shot and notes were taken and they were measured. But it didn’t stop at animals. In an attempt to place all living things in an evolutionary sequence, humans, too, were observed and measured. Desperate to find the secrets of human evolution, populations (mainly non-European) were seen as “the missing link” between the primordial beings in the fossil record, and the “longer evolved” Europeans. The Khoisan, particularly, have a dismal history within the context of physical anthropology. From the story of Saartjie Baartman, the “living fossil” paraded by Georges Cuvier, to the endless measuring of crania and genitals of the Kalahari San well into the 20th century, physical anthropology was the scientific justification for incredible violations against living people.

To break away from this term, however, is not easy. For one, it implies a rejection of the way our science was done in the past, and support of a more nuanced approach to our discipline, both the way it is conducted, and the way it is interpreted. However, this rejection may be seen as dishonest. If the history of the discipline has led us towards the more nuanced approach, then rejecting it may be seen as a rejection of historic truth, and a path that was unavoidable given the socio-historic context.

I have attended the AAPAs for several years. Each time I am in awe of the multiple approaches taken by researchers to look at human variation and evolution. While some still use the methods employed in the past, the questions are almost always those of variation, not typology: itself an incredibly different approach. The approach has become a biological one: one that incorporates genetics, behaviour, variation (Caspari 2003). It is no longer a physical one: of types, of races, of “missing links”. From as early as 1951, Sherwood Washburn, the academic grandfather of many primatologists, termed the “New Physical Anthropology”, stating the foundation of nuance and inter-disciplinary approaches which we all now associate with Biological Anthropology (Mikels-Carrasco 2012).

Two years ago, I attended a student meeting at the AAPAs. Here, I suggested a forum for international students. It was immediately rebuked by another member, who said that it was the American Association. I was quite shocked. As an international student myself, I had always taken the name to be a historic remnant, not a declaration of positionality. I know that because the meetings, the journal and many of the organisers are American, that the majority of people attending will be from the USA (or Canada). And yet, once again, looking at the posters, attending the presentations, very little of the material or data collected and analysed and researched are originally from North America. The imperialistic nature of the discipline that was once “Physical Anthropology” is still there, and is still substantive. It is no longer Georges Cuvier parading Sarah Baartman, but a plethora of wealthy American students attending fieldschools in Kenya or Tanzania, bringing few Africans into the discipline, yet posing for pictures with African workers, Mrs Ples and the Daasanach. This is understandable on many levels: research is an expensive endeavour and development in many parts of Africa, South America and the Middle East is slow.

But one way to bridge this gap and to communicate an intention not only to move away from where our discipline was, but to move towards a place where it is more inclusive and engaging, is through name change. Name change of “the world’s leading professional organization for physical anthropologists”, is an important symbolic start. For these reasons, I propose the name of the American Association of Physical Anthropology be changed to the International Conference for Biological Anthropologists.

Full citations for essay:

Caspari, R. 2003. From Types to Populations: A Century of Race, Physical Anthropology, and the American Anthropological Association. American Anthropologist, Vol. 105, No. 1, Special Issue: Biological Anthropology: Historical Perspectives on Current Issues, Disciplinary Connections, and Future Directions, pp. 65-76

Mikels-Carrasco, J. 2012. Sherwood Washburn’s New Physical Anthropology: Rejecting the “Religion of Taxonomy”. History and Philosophy of the Life Sciences, Vol. 34, No. 1/2, Human EvolutionAcross Disciplines: Through the Looking Glass of History and Epistemology, pp.79-101.

 

 

FouR tRicks for using R in ReseaRch

I promised to do this a long while ago… a year and a half ago… But a lot has happened since then (to me I mean, but also the whole global socio-political situation), and I was busy finishing my PhD and undergoing periods of personal and professional angst. I still am, really, but I’ve learned to grow comfortable with it: like an itch that’s both terrible and immensely satisfying to scratch.

Anyway…

R…

I have used the program for a few years. And I think, for the first time, I am starting to grow comfortable with it. Don’t be dismayed! I did not have a programming background, I was one of the first to use it in my department, I relied on many other programs as well, and I could still use it satisfactorily for a lot longer. But right now I feel like I have a stride that I didn’t have before, and thought that maybe I can write down some (r)evelations which I have found particularly useful, so that you, dear reader, can get in your stride a lot quicker.

R has almost become a buzz package, which many young researchers are using for their data management, statistics and, even, their write-ups. Of course, the cool kids use Python, but I am not a cool kid.

-svgug

In anthropology, where data can come in a variety of forms (intensely qualitative or highly quantitative), R’s flexibility allows us to use a variety of techniques which few other programs can, with minimal processing power. AND It has a strong, supportive, online community! I have used R for geometric morphometrics (3D morphology analyses), for plotting sexy plots and for cleaning up my (and others) dirty dirty data. I have made plenty of mistakes, and have made some highly satisfying discoveries. Instead of keeping them to myself, here are some key points which I have learned:

 

Use those damned (l/s/t)apply functions!

It is very unlikely that you will only need to apply a function once or twice. And it becomes super tedious doing this over and over again manually. In other words, we often need to repeat analyses, either by applying them to different samples or different variables, or by repeating analyses on different versions of re-sampled data.

And well… Confession time. I love my “for loops”: a technique which incorporates curly brackets and empty vectors which you ultimately intend to fill with useful numbers. But this technique is slow compared to R’s base functions. The apply functions allow you to repeat analyses multiple times, across the length of your dataframe, and/or with re-sampling, while saving outputs in multiple different formats. They are “built in”, so to speak, making the code highly efficient.

And I wish that my sample sizes were so positively large that I would feel the time difference it would take to run a “for loop” versus using R’s base functions. While the R community is the best, sharing code with a “for loop” is totally embarrassing. Don’t do what I did. If you don’t know what a “for loop” is, you have a chance to be saved. But, if you don’t care about traumatizing your fellow R-users, you can learn how to loop analyses here. I’d rather you “for loop” under responsible supervision.

 

Understand ggplotting

Probably one of the most iconic packages in R is ggplot2. The graphs are incredibly flexible, with the potential to be sexy and slick. But a lot of people struggle with the package, and find it far easier to use the base function for simple graphs. The trick with ggplot2 is to see it almost like a GIS: where you are able to manipulate the various layers, and where you can easily slap more on at a later point.

  • Just like a GIS, the first bit of code tells you where your are (I am wanting a map of this data frame, show-casing these columns in the data frame). The “aes” function is essential, and it is also possible to add colour in this part of the code as well, stipulating the variable it should draw from.

My_plot <- ggplot(Dataframe, aes(x=Var1, y=Var2, fill = Var3))

  • The next bit tells R how you would like to plot it (geom_line() for lines, geom_point() for scatter, etc.). You don’t even have to fill in the brackets! R already knows… I think this bit confuses people the most. The base functions automatically presume what graph you want based on the kinds of variables you select. But it is here where you are able to overlay multiple different kinds of graphs, which would be far more complicated using plot(). Anyway, at this point you already have a graph! Hooray! If you save this as an object, you can just tack on everything else afterwards.

My_plot <- My_plot + geom_boxplot()

  • Just like GIS, it’s the following functions (layers) which make it sexy. Some built-in or downloadable themes are already quite attractive, such as theme_bw() or theme_classic(). These have standard fonts for axes and legends, background/font/point colors and shapes. But you are still able to manipulate or change these further. You very likely will want to change the legends, or axes labels, or add a title to your graph. Once again, you can do this separately, or tack it on to your already saved graph.
  • You can add additional statistics to the graph: adding the mean to a boxplot, for instance, or an ellipse to a scatter.

I highly recommend this tutorial, where you can go through the basics, putting it all together to make a sexy sexy final graph.

 

Tidy up your data (using tidyr, ddply)

I discovered these embarrassingly late in my R usage, and don’t really know how I did much without them. The biggest problem with R is not learning how to use it for statistics (when it comes to stats, coding is the least of your worries), but wrangling your data into manageable, clean formats, without toggling a thousand times between R and excel. While trying to keep your data as clean as possible is essential, life often throws you nice juicy lemons of messy data from which you need to make some sweet stats-lemonade. (I need to work on my metaphors). But there are plenty of very useful packages designed to make your data nice and clean and easy to use.

MessyDesk

My personal opinion is to try get everything related to each other into a single dataframe. I hate toggling between multiple datasets looking for a single variable (such as weight or color), or trying to find all the variables related to a single individual.

Next, you want to ensure that everything is of an appropriate class. 90% of the time people ask me why their code is not working, it’s because their numbers are classified as factors and not numerically (LPT: use as.numeric()). One problem that can creep in is if you have missing, or have added inappropriate, values. Make sure that there are no “i’s” instead of “1’s”, or that all the “NAs” are acknowledged by R.

 

Find useful packages (tied up with strings)

The really great thing about R is that no matter what you need, there is likely a package (or five) that will suit you. Since a lot of my research revolves around 3D morphological comparisons, the geomorph package was particularly useful, and the authors host workshops around the world! It is also possible to contribute to (or stalk) developing packages through the github repository. This is an amazing opportunity to throw yourself into the R community, and one which I wish I had taken greater advantage of earlier in my R usage.

One immensely useful package, which I have not needed to use (but I almost wish I could!), is lubridate, for working with dates and times.

Possibly one of the most useful packages for beginners is swirl. It allows you to learn R in R, with a variety of courses, using prompts.

 

I hope you found this (and/or the numerous links) useful. What do you use R for? Have you found it difficult to get started?

 

Homo naledi: Why the new finds are a big deal

Almost every time we find some bones of a new human ancestor or cousin, scientists freak out. They argue about whether it deserves it’s own species status, whether it is directly ancestral to us, why or whether it’s important, and what all this means. With the human (or, more accurate, hominin) fossil record so sparse, almost every time we find something, it reaffirms or rejects current hypotheses and assumptions about our evolution. So why all the fuss about Homo naledi?

The original Naledi finds

In order to place this in context, it’s important to rewind to when the first of the Naledi finds were published. Homo naledi, was introduced formally in 2015, several years after the announcement that “something strange” was found in the base of the long, treacherous Dinaledi Chamber at the Cradle of Humankind in South Africa. Homo naledi truly was something strange. The head was shaped like a better-known hominin, Homo erectus, but unusually small. The body, however, was unlike that seen before: some evidence for climbing, some for walking like we do.

 

naledi_hand-foot
The hand and feet of Homo naledi show a complex mix of locomotion.

 

More unusually, these finds were not accompanied by the bones of many other animals, and certainly no large animals, and were found at the base of a cave that did not appear to have any other entrance. How did these hominins get there? Why were there no other animals? Was it possible that they could have travelled so deep into a cave? If so, why? An individual getting lost in a cave system is one thing, but the carnage was of over a dozen individuals, ranging in age. Was this possibly a burial site, even though burials in the fossil record are often contentious to prove, even for big-brained hominins?

The small brain

Let’s back track even further, to when another find was announced, from Indonesia. In 2004, Homo floresiensis, also called the Hobbit, was described, and dated to around the time that modern humans  like us had already evolved (but presumably not living in the same area). This, too, was a small-brained hominin, living at a time when we did not expect small-brained hominins to live. What is more: these hominins were found with tools that were more sophisticated than what we would expect given the brain size.

 

naledi_hobbit
Hobbit (left) and Naledi (right) skulls. Both are small-brained hominins living in the times of large-brained hominins.

 

So why all the fuss about Naledi?

The finds are from a second cave which the researchers have called the Lesedi Chamber (“Lesedi” meaning “light” in Setswana). And the Lesedi-Naledi finds are astounding for three reasons.

The first is the date. 335-256 thousand years ago may seem like a long time ago, but the vast majority of hominins found at this time have large heads. We were presumed to be well on the way to getting to, what many researchers would consider, a very human likeness in the fossil record. Much more human-like hominins dominate the fossil record from even earlier than this date (or so we thought). The fact that small-headed Homo naledi, and the Hobbits, persist is incredible. However, it is unlikely all researchers are surprised that it was younger than others expected. After all, it was well-known that the initial Naledi finds were only somewhat fossilized (or turned to rock), a process that can take time.

The second reason the new finds are astonishing is because they were found in another cave nearby the original Dinaledi Chamber, under what seems as the exact circumstances (supporting hypotheses that these are likely burials). Large heads mean big brains. Surely, in order to be the social, tool-using, interactive super-predators humans are, big brains are essential? They cost a lot of energy, and, in order to be beneficial, must provide us with an added advantage. If small-brained Naledi is doing something as incredibly social as burying their dead (something we almost always only associate with modern humans), then does that mean big brains are not necessarily what gives us human-like characteristics?

The third reason is: we have a face! The naledi skeleton called Neo (Sesotho for “a gift”), is one of the most complete hominin fossils ever found. This has profound implications in understanding what H. naledi looks like.

Along with the Hobbit, the Naledi finds truly throw in our faces the already scanty collection of features we once thought was preserved only for our lineage of hominins, and certainly only for large-brained hominins.

 

 

Sources:

https://elife.elifesciences.org/content/6/e24231

https://elife.elifesciences.org/content/4/e09560

 

 

The ecosystem of YOU: the good, the bad and the ugly

You are never truly alone. You are very important to the countless numbers of microorganisms that live in your digestive system, in the pores of your skin and on it’s surface. This serves as an (incomplete) summary of some of the organisms that live with you.

The Good

While bacteria are often either dreaded or ignored, many are also incredibly important in keeping you healthy. Some bacteria that live in your gut aid digestion and help make certain vitamins. Others out-compete “bad” bacteria which may make you sick. Mutually beneficial relationships such as those between humans and “good bacteria” are known as symbiotic and a high diversity of such organisms helps keep individuals highly adaptable to changing environments and diets.

Studies on hunter gatherers and non-WEIRD (western, educated, industrialized, rich and democratic) human populations, suggest that westerners have a reduced gut biodiversity, no doubt fueled by antibiotics and our obsession with cleanliness. This may be one explanation for higher levels of food intolerances in recent years. Different microbiome diversities has also been associated with both physical and mental health, as well as stress levels. Similarly, increasing (and repeating) cases of vaginal yeast infections may be explained by lower levels of biodiversity in the vagina, leading to “drying”, or the outcompeting of good bacteria by bad.

The slight, but significant health differences between babies delivered by C-section and those by vaginal birth has also been associated with differences in gut biodiversity. Babies born by vaginal birth are said to be more exposed to the bacteria around the mothers vagina and anus, enhancing the babies own microbiome. Such an association implies that the health benefits of vaginal birth may be easily gained by babies born by C-section. In babies, a healthy gut microbiome has shown to influence growth as well. However, stress and stool consisitency have shown stronger correlations with gut diversity.

The Bad

That’s not to say put away the antibiotics and soap just yet. While maintaining high bacterial diversity is key for living a healthful life, it’s important to remain cautious if you live in areas with high population densities, where disease can manifest and spread at phenomenal speed. Bad bacteria which enter the Blood Brain Barrier, infecting your brain and causing meningitis, will result in death if left untreated, and yet can be survived with antibiotics.

But even horrible disease-causing buggies are at least interesting in terms of how they shaped our evolution, and what they tell us about the past (and may help us prevent in the future). Plague (a bacterium, Yersinia pestis) is most famous for causing the Black Death which killed off between 30% and 60% of Europe’s population in  Medieval Times. This deadly bacterium has also been attributed to the eventual falling of the Byzantine (East Roman) Empire, and failure to unite East and West Rome, centuries earlier, in the 6th Century AD.

Nicolas Poussin, The Plague of Ashdod, 1630

Another scourge of humanity, the dreaded mosquito, is a potential vector for one of the diseases that has killed more humans throughout history than any other: malaria. The disease is so deadly, that certain populations have inherited genetic trade-offs which have increased their overall chances of survival. Sickle cell anaemia is the homozygous (inherited by both parents) condition for one of these trade-offs. The haemoglobin molecules (which carry oxygen) affected by this condition cause red blood cells to sickle in shape when dehydrated or affected by malaria. The red blood cells are therefore less flexible and unable to pass through narrow spaces, thereby not sending oxygen to where it may be needed in the body. This condition, left untreated, is not associated with long life span. Yet the heterozygous condition (inherited by one parent only), in regions heavily affected by malaria, is associated with greater survival, adding to the evolutionary success of these individuals.

Another scourge that has remained with us for thousands of years is the bacterium, tuberculosis (TB): Well known in the 19th century as the deadly “consumption”, is even documented by the ancient Greeks. TB can be a slow disease which may also infect other organs, and, as such, it leaves marks on the bones. This makes it very interesting from an archaeological point of view, since we can document the history of the disease, the earliest known archaeological case is in Italy, from 4000BC (and possibly earlier). Initially archaeologists thought TB were transferred to humans from cattle, when living closely with cattle after domestication. Genetic studies have since shown this is not the case. Ancient human remains found in Peru, dating to long before European contact in the region, showed signs of TB. Ancient DNA showed that the strains of TB found in the Peruvian remains came from seals, which, in turn, may have acquired TB from other seals, which got TB from people or animals in Africa. It is still the leading cause of death, and is especially concerning in individuals who have both TB and an immuno-compromised condition such as HIV/AIDS.

The Ugly

There are also not-so-microscopic organisms which may be a part of your ecosystem, many of which are parasitic, not all necessarily harmful. The eyelash or facial mite, Demodex, is harmless, if largely unattractive. We also know of ill-inducing parasites such as tapeworms, which live in the gut, and roundworms, which feast off of our blood, and may bock lymph drainage, causing shocking conditions such as elephantiasis, or swelling in the limbs. But one parasite in particular has proven useful in helping us decipher our own evolutionary history.

Demodex: These little critters live on your eyelashes.

Lice are insect parasites which live in the fur, feathers and hair of numerous warm-blooded animals. In humans they are considered bad, not least because they feast on our blood. They are also vectors for diseases such as typhus and plague. Humans have three different types of louse (the head, body and pubic louse): the phylogenetics of which are particularly interesting. While body and head lice are more closely related to chimpanzee lice, it looks as though we contracted pubic lice from gorillas approximately 3 mya. We will have to leave it up to our imaginations to determine what scenario allowed us to contract these lice from gorillas, but we can potentially say that in order for the clear distinction between the head/body and pubic lice and their respective areas, it is likely that it was around this time when our body hair became more reduced. Hairlessness was no doubt an evolutionary advantage: allowing us to better control our body temperature through sweating.

Determining a divergence date between head and body louse was also incredibly important for finding out when we first started wearing clothing. Body lice are especially adapted to living on fairly hairless bodies under the condition these bodies are clothed. Estimated divergence dates between body and head lice therefore indicate that humans were wearing clothes from about 170-70 kya.

Conclusion

You truly are an ecosystem of weird and wonderful little bugs, which help you thrive, feed off of your bodily fluids, and may kill you off. When thinking about our own evolution, it is essential to consider how these organisms have played their part.

 

 

 

 

The fascinating and frustrating tale of Eugene Dubois

In her excellent biography, The Man who Found the Missing Link, Pat Shipman is a lot more nuanced and sympathetic to Eugene Dubois than I am, and if you wish for a less biased and more detailed account of his life, I highly recommend the well-researched book, written with incredible dedication from a talented author.

Eugene Dubois himself was an interesting character. He was thoroughly intrigued by Darwin’s Theory of Evolution, and determined to find the missing link between humans and apes.

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The Man Who Found the Missing Link by Pat Shipman, about the life of Eugene Dubois.

In the 1880’s, two hypotheses regarding the whereabouts of human origins prevailed. Darwin thought that it was likely humans evolved in Africa, which he proposed in The Descent of Man. Ernst Haeckel, a comparative anatomist who championed evolution, believed human origins likely in Asia. The answer, for Dubois, lay on the premise of which ape species we most closely resembled. African apes (chimpanzees and gorillas) are large-bodied; but gibbons (or “lessor apes”, as they are now known), have a lower limb locomotion that, to him, did not appear so different from bipedalism (the upright walk of humans) despite their long arms. Gibbons also do not appear to have the high levels of sexual dimorphism of great apes: males and females look very similar to each other relative to, say, gorillas, where males are almost twice the size of females.

By that time, British naturalist, Richard Lydekker, had found a fossilized ape in northern India. The origins were probably not in Europe. Neanderthals, which had already been found in several locations Europe, were not wholly considered “non-human”. For instance, many opponents to Neanderthals as ancestral to modern humans argued that the Neanderthal morphology of heavy, “surprised” brow ridges and rugged, thick bones, was of pathology. Still others explained that Neanderthals, while different from modern human “types” (ah, the days of rampant typological thinking…) were more primitive, but still “human”.  They therefore did not prove a link to apes, and were thus not considered “missing links”.

Dubois wanted to find the missing link, not an ape, and not a proto-human which could be mistaken as pathological. He agreed with Haeckel that human evolution was catalysed in Asia, particularly south east Asia, where gibbons and orangutans currently survive. And, like your average stereotypical mad scientist, gave up his prospects of a comfortable position in Amsterdam as an anatomy professor, to be a military surgeon in the Indonesian colonies; all with the hope he could run mass excavations on the side in order to find his treasure…

One thing that may have contributed to Dubois leaving his otherwise comfortable anatomy position was an incredible fascination and dedication to evolutionary understanding and science. Dubois, however, also comes across as… difficult. And a sincere mistrust of his adviser does not appear to help him with his ambitions to stay within the confines of the university. And that’s where I feel particular frustration. Not necessarily for the man alone, but for the discipline of palaeoanthropology as a whole. His life seems an often repeated tale, a groundhog life, if you will, of the natural scientist. He spends so much time in his early career fighting for recognition, fighting for funding (for who would fund such an eccentric ambition?), fighting against the unsupported paradigms enforced by the old guard (who are still sceptical about human evolution) to come to an end.

Then he finally achieves what he sets out to achieve: he finds the missing link! He finds a skullcap, teeth and femur (upper leg) of Homo erectus: the first of our genus (of which we currently know) to spread across the old world, into Asia and Europe. The skullcap is large: far larger than an ape of even gargantuan size, which indicates it must be human-ish, yet with a shape that is flatter and more “pinched” behind the brows, like an ape. Despite the initial (and usual) criticisms of the skull being that of a pathological individual, or of a proto-proto human (but not quite apelike enough to deserve “missing link” status), Dubois status as a palaeontologist was quickly affirmed. He had found the ape-man.

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Homo erectus, Neanderthal and modern human skulls (left to right). Proto-proto-human, proto-human and human?

Homo erectus, like the Neanderthals, have been redeemed within the scientific literature as far more sophisticated than earlier researchers gave them credit, some even questioning their separate species status. Also, since then, fossil hominins (human relatives) have been found in Africa, with even earlier dates and with far more “ape-like” characteristics. But it was Dubois which inspired further study on human evolution.

And then he became “it”. He became the researcher who refused to shift paradigms, refused to fully acknowledge others finds (for instance, that similar skullcaps found in China, were as old, or contemporary with his own), and hogged up is own finds: refusing others access to study the fossils, and becoming deeply suspicious of those that did.

It is both a sad and glorious story. It is of a man who gave up everything to find a scientific treasure, and succeeded. But it also highlights the treachery of mistrust, which academia (even over a century later) can inspire.