Tuesday, August 21, 2012

Why didn't I publish this? Quasi-Repost: Messing around with trees: Ardipithecus ramidus

Hey there, haven't posted anything in a while haven't I? Well this isn't a new post either. I just went through some of my older stuff and stumbled upon this Post I wrote a year ago, which I never published. Probably because I thought it's bad. Well, either I've lost my sense for quality, or I didn't realised this Post was actually quite interesting. Be it as it may, here it is:


A few weeks back when I desperately sought for stuff to waste my time with, I came up with a very nice, but also quite strange Idea: How about ruining some phylogenetic trees?


There are some nice Tools on the Internet which enable you to execute small to middle scale analyses for free and without relying on huge clunky programs. One of them, which I use quite a lot right now, is on the homepage phylogeny.fr (Dereeoer et al. 2008). It’s usually a tool for DNA data, but with some little adjustments you can also use it for basic morphological Datasets.



For my first target, I decided to attack a big fish and therefore the most easiest to attack: Ardipithecus ramidus.

The authors didn’t publish a tree by themselves, but they did publish a nice little table of characters to show how and  good ol’ Ardi is related to other hominids.


White et al. 2009




So my first step was to reconstruct a tree from this table, the results weren’t really surprising:










Now what happens if I change some of the more controversial characters (some characters of the pelvis and some regarding the C/P3 complex) from “derived” to “ancestral” (I refuse to use the word “primitive” in this context)?










Well looks like this didn’t do the trick. Let’s try something more drastic, like deleting all dental characters.






Gotcha!

You see, from the 68 characters that were listed in the initial character table, 34 of them were located on the teeth. And most of the phylogenetic signal which separated Ardi from the other early hominids is located within those 34 characters.

I would’ve loved to deconstruct this tree even further, but I couldn’t find any means without doing completely ridiculous stuff. This is mostly because of the way White et al. (2009) defined their Outgroup Taxa. The Outgroup is one of the most crucial parts in phylogenetic reconstruction because it defines the ancestral state of all characters. Therefore different Outgroups can change the topology of your tree in a huge way. The Outgroup characters in the Table from White et al. consist of inferred character states from a hypothetical last common ancestor. Since we have hardly an Idea how this last common ancestor looked like (I wrote something about this here), there is a huge space for “inference”, others might even call it “speculation” or “guessing”.

Keep in mind that this whole stuff is just the result of me, messing around with this stuff. Nothing of this has any scientific value. However, I still learned some interesting stuff while doing this.

First of all, although discussions about Systematics and phylogenetic trees can become really boring from time to time, they’re sometimes very helpful when you try to get to the core of a certain problem. They also provide nice means to visualise these problems and the effect it has when you change certain parameters.

In the end, when you intend to challenge the initial taxonomic placement of Ardipithecus ramidus there are two things you have to look at.

Try to show that most of the dental characters White et al. (2009) used are redundant and/or false and try to show that their inferred ancestral character states are wrong.




You see, Phylogenetic trees can be good for something and if it only is for stating the obvious...

References:

Dereeper A. et al. (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist Nucleic Acids Research. 1; 36


White, T. D. et al. (2009) Ardipithecus ramidus and the Paleobiology of Early Hominids. Science 326, 64. S 64-86.





Wednesday, April 4, 2012

(Not) always worth mentioning: Bipedalism in fossils

News of potentially bipedal fossils always seem to be interesting. However there are different kinds of bipedalisms and not everyone of them is worth mentioning.

Friday, March 23, 2012

Some random question:

I read a very interesesting paper yesterday which really made think about anumber of things. But instead of sharing all these rather confusing thoughts with you, I'm just going to throw a random question in here, mostly because I'm interesed in the opinions of other people on this topic. Also because I'm rather confused right now and this might help me in overcoming it.
Anyways, the question is as follows:

Where does the causal foundation of (morphologic) characters lay, in ontogeny or in phylogeny?

I hope I was able to formulate it in a proper matter, if not let me know and I try to explain it better. Also let me know what you think the answer to this question is.

And also, if you're interested in the article which caused my confusion, here it is:


Vergara-Sillva, F. (2009). Pattern Cladistics and the Realism-Antirelaism debate in the Philosophy of biology. Acta Biotheor,57. S. 269-294.

Thursday, March 15, 2012

The road towards madness: Thesis Devlog part 2: I actually did something last month

A lot of stuff happened in during the last month, and most of it was quite positive.
I was able to clear out most of the obstruction that were preventing me from getting started on my thesis. In fact, I spent the last two weeks in the Senckenberg-Museum in Frankfurt, acquiring my first Data for my Thesis, so technically I already started working on it.
I’ve never visited a collection before so I was really excited to take a look “behind the scenes” of a museum, especially the Senckenberg. I was born in the Area around Frankfurt, and I visited the Senckenberg quite a lot when I was a child and I still have very fond memories of those visits, Funnily enough most parts of the upper floors of the museum haven’t changed a bit since I was a kid. This place also partially responsible for getting interested me in Paleoanthropology a few years back. Well it was a lecture of Bernard Wood which I visited, but it was hosted by the Senckenberg.
Anyways, as I said I never visited a collection before that, so I was really excited to get this opportunity. I just love old stuff and Collections are always a great place for that. I had skulls on my desk which were acquired during the 1840s, a time when nobody besides Darwin and some other few people ever thought about natural selection, where the first Neanderthal was still to be discovered and where people could become respectable biologists by simply walking through the jungle with a Rifle in their hand, occasionally shooting in the trees and collecting all the dead stuff which fell in front of their feet.
I often stopped my work wondering who also might have held this object in their hand and what they might’ve done with it.

I also stopped my work from time to time to wonder what I was looking for. I wasn’t really trained to this kind of work I’m supposed to do right now. Sure I know to navigate myself on a human skull and I know how a primate skull basically looks like. But identifying smaller structures on skulls of non-adult primates? That’s quite difficult. So the first few days where mostly spent with me trying to navigate myself around this stuff. Funnily enough, large portions of the more challenging parts of this thesis will involve me having to learn the appropriate skills while doing the actual work, which is quite interesting.

I learned a lot of stuff in the last few weeks and I also regained huge parts of my motivation for science in general. There were quite a few things which got me down in the past few months, most of them dealt with the more ‘administrative’ parts of science and less with the actual work. I was even thinking about whether or not I’m suited for this kind of work. Honestly I still don’t know if I really am, but what I’m sure about is that I don’t care about that. Either I will be able to do things the way I want, or I won’t do it. If I would wanted to get an easy job, I would’ve gone into engineering and not Anthropology in the first place.

At some point I might write about this in more detail, but what I will promise right now is that, as soon as I’m allowed to, I will simply put my Thesis somewhere up where everybody will have access to it. If my time allows it, I will even try and translate the whole thing into English. I want to do this, because I think that, even if this thing is a complete mess, someone else might find something of value in it. And be it as an example of what you should never do while writing a Thesis. The alternative was either putting this thing in my shelf and letting it gather dust, or publishing my results in some obscure Journal which no one is ever going to read anyway. Ideas are the forces that drive scientific innovation and I strongly believe that the more Ideas you have to discuss the better you’re able to really get some kind of scientific progress.

Wednesday, February 1, 2012

The road towards madness: Thesis Devlog part 1: "Get started fool!"

(In the vague hope of creating some kind of regularity in my writing, as well as to give myself some space where I could organise my thought, I decided to start a “Development-Blog” (or “Devlog” as it is called among us cool people) for my Thesis. I intend to write this once per month and I will present you what I have done so far and what I want to accomplish in the next few weeks. Watch as I make dumb mistake after dumb mistake and how the stress of this work will make me go insane as the year porgresses).


I’m sitting at my Thesis for quite some time by now. Well, “sitting” isn’t really the appropriate term. I circling around it, like a dog who isn’t sure if he should really lay down on the carpet or not. It goes without saying that this isn’t a really satisfying state of affairs, for three reasons:


1. This is the last thing I need to do to graduate from University.


2. I don’t have anything better to do.


3. I only have time until January 2013 to graduate before I have to re-do my Psychology-finals, which I already took in 2010.


So despite being more or less unprepared for the work that lies ahead of me, I decided to simply jump into the fray and hope for the best.
But before I start to tell you what kind of stuff I need to do, let me quickly tell you what exactly my Thesis is about.
The goal of my Thesis is to compare phylogenetic trees of the relationships between great Apes and Humans from different ontogenetic stages with each other. I want to do this mostly because it’s interesting to see how certain Traits are affected by ontogenetic processes and how those traits effect phylogenetic trees. Also this was the first Idea where none of my Professors told me that it is too big, too expensive, or just stupid.

So far my plans are to do this study with the following taxa:


Papio


Pongo


Pan


Homo


You probably have noticed that there are no Gorillas in my species sample. That’s because my advisor told that it would probably be better for my results if I exclude them. As I tried to show a few months ago, there are some problems when it comes to the reliability of phylogenetic trees who try to resolve the relationships between Gorillas, Chimpanzees and Humans. Excluding the Gorillas from my sample helps me to avoid that this “trichotomy-problem” is somehow effecting my results.
I’m not very happy about this, since it also limits my possibilities of drawing more wider ranging conclusions from my thesis.
But fortunately, nobody is expecting me to make some kind of ground breaking work. all I have to make sure is that my study is well executed on a technical level and that I don’t make any factual mistakes.


What I need to organise right now is where I get my sample from, where I’m going to get my measuring tools from and how I’m going to pay for this stuff.


The first question fortunately is quite easy to answer, since there are some rather big collections at several museums in the german-speaking area. So far I plan to go to the Senckenberg-Museum in Frankfurt (which is right around the corner), the Museum of the Institute of anthropology of the University of Z├╝rich and the Museum of natural history in Berlin.
I hope that I’m able to collect all my data until June, but this means that I need to make sure I get access to those collections within the next few months.


The next point bothers me a little bit. I need to collect some osteometric data for my Thesis but funnily enough my Institute doesn’t seem to own the appropriate tools for these kind of work anymore. This strange because we still have rooms full of old skeletons where nobody knows where they’re from, but no means of analysing them in a proper manner.
Fortunately I think I know where I could get those tools from, but those things are fairly expensive, which brings me to the last problem.


Spending several weeks in different towns to have a look at primate skulls is a fun thing to do, but it costs money. I still need a place to sleep and something to eat from time to time. My initial plan was to apply for a grant which our biology department offers for students who are about to graduate. Unfortunately I needed a letter of recommendation from my advisor for this, something he refused to do because he wanted to see other projects to be supported. This grant would have been enough for me to ravel to each and every museum I desired without having to worry about how I’m going to pay my bills. I still get mad about this, although there’s really nothing a can do about this. Instead I decided to apply for a different grant, which doesn’t need the approval of my advisor, I still need to the application for this and I hope I’m able to do this by the end of this week. As an alternative route I took a side very boring side job and try to save as much money as I can. Luckily enough, my Institute will still pay for the stuff I directly need to do my work e.g. those expensive measuring tools, computer programs etc.


Essentially I was able to sort out most of the aforementioned points, the only thing I need to do right now, is to get going. The most important thing right now is to fix the time when I have to visit the different collections as well as to find out if there are really no tools in this Institute. I also try to get my application for this grant ready and I hope I can give you some more information on that sometime later this week.
I think that’s it for now, let’s just hope things will go as planned (which they probably won’t).

Tuesday, November 22, 2011

Apes (and other primates) on the internet -The digital morphology museum

I’m a huge fan of Internet Databases, such as the Nespos Database, where you can get access to CT-Scans of original fossils as well as recent specimens for your work.. However what always bothers me is that all those databases aren’t completely open to the public. For example to get access to the Nespos Database, you need to explain why you need access to it, you need to be a member of an academic institution and you need to pay for a membership.
These things make it rather difficult, if for example biology teachers want to use these materials during their courses (which would be a really great thing).
This is why I was really excited, when I read on Lawn Chair Anthropology about the “Digital morphology museum” of the university of Kyoto. Here you can take a look at their whole stock of CT and MRT-Scans of a bunch of different Primate specimens and, after a small registration process, you can even download these Scans for free.


Right now I’m thinking about something for which I can use this Database. Perhaps some kind of online course? I don’t know but I’ll come up with something.


If you want to take a look for yourself, you can do it right here.



Wednesday, November 16, 2011

A lot of trees here...

Those few and lucky people who read this blog on a more regular basis probably have realised that  a lot of the stuff I wrote recently dealt in some manner with phylogenetic trees.
On one hand this does not seem to be very suprising since taxonomic questions always were some kind of focus of this blog. However the other reason for this is because I finally found a suitable topic for my M.A. Thesis (yaaaay!). I won't write about the exact topic as of yet simply because I still need to write it down properly, but if you're interested, just look at the comments under this Post, it's mentioned in one of them.

I plan on covering the whole process of me writing the thesis, analysing my data and whatever else I need to do on this Blog. This is going to be my first real scientific work so it might be interesting to see what kind of stupid mistakes I make and in what kind of pitfalls and Problem I might run into. Also, I want to use this blog as a Plattform where I can write down some of the ideas I get while working on my thesis. In fact this is why I wrote my last post and there's another one coming soon.

In other news: This week I'm in Frankfurt at the Senckenberg-Museum to attend a congress about the ecology and organisms of the eocene. Since I'm mostly interested in primates and I don't have that much knowledge about fossil invertebrates and I also have to prepare my Thesis (yaaaay!), I will probably visit the conference only on Friday, since this is the "primate day".
Of course, good ol' "Ida" will be a big topic on this day and from what I can tell from the abstracts, I'm pretty sure the discussions are going to be very "interesting".