Interactive Cladograms!

Even before people knew of the theory of evolution, we have categorized the living things around us into groups, and groups within groups, and so on. For thousands of years we've understood that all hoofed animals were different from wolves and dogs and other canids, but that together these were mammals that had characteristics different from another group called 'birds,' and that mammals and birds were more similar to each other than to another group that included bugs and spiders.

Once evolution was in the picture, the reasons these groupings exist in the first place became crystal clear: each group contains a common ancestor which 'branched off' in speciation events. A tree-shape is indeed the best visual way to represent this, and has been from the start. This was Darwin's first tree from his notebook:(neat, eh?)

By the way, his handwriting is hard to read, so:

"I think (sketch) Case must be that one generation then should be as many living as now. To do this and to have many species in same genus (as is) requires extinction."

Trees can be ridiculously simple to ridiculously complex (see previous post). But if you want a tree to be a useful database of life in its entirety, there's really only one way to go, and that is a clade that is interactive, with the ability to zoom in on levels of detail from the base of the tree and its major branches to the very ends where individual species exist.

Here are a few very great examples, in no particular order:

Wikispecies - Like Wikipedia, this wiki is an open directory that anyone can contribute too. While this doesn't look like a tree, it indeed is, and navigation up and down the branches is quick and easy (so long as you know where you're going, that is). The great thing about the individual pages is the "taxonavigation" at your fingertips: every grouping from species up is visible and clickable. I should mention that Wikipedia has scientific classification lists as well, but not nearly to the amount of detail as Wikispecies, though they do have more factual information.

UCMP Web Lift to Taxa - This extremely comprehensive tree is the one we used as part of my favorite undergraduate biology course: Systematic Zoology. It's a bit hard to navigate, unfortunately. As you zoom in on the tree, look for the "Systematics" button to move down the branches. Navigation lacks a way to move back down the branch, but the good thing about this site compared to the others is the abundance of pages describing the larger groups (rather than only having individual pages for species at the end of each branches, they have an entire page describing the phylum cnidaria, for example.)

The Tree of Life Web Project - This awesome page is the result of some five hundred contributing scientists. Its organization is similar to that of Wikispecies, but like the UCMP page, it also includes actual trees on each page, much appreciated by visual people such as myself. Aside from that, I also have to say it's just designed better in general and is nicer-looking than the others.

Wolfram Demonstrations Tree of Life Project - I can't comment on this one because I have not downloaded it yet, but the demonstration looks neat and really gives you an idea of what interactive trees could look like in the future. The idea of clicking on branches to move up and down the tree rather than text links is terribly exciting to me.

So where is all of this going? Will we see the day when every species is documented and compiled in a database like this? It will always have to be changing. Placements of groups on the tree of life change, and disputes exist between scientists. Sometimes clades determined by genetic data disagree with those based on phenotype. But the dynamic nature of these interactive databases even allows for the discrepancies to be communicated.

I look back at the sketched tree drawn by Charles Darwin, and I have to wonder what he would think about all of this.

Visual Complexity

Here is an amazing collection of visual complexity in biology. It's like looking at beautiful works of geometric abstract art, except there is rigid scientific meaning behind each one, which only makes them all the more beautiful.

Especially check out the Mammal Supertree and the Tree of Life:

Bolinsky's response to the "Expelled" plagiarism

Update for yesterday's post.

This email, written by XVIVO medical illustrator David Bolinsky and forwarded to Richard Dawkins, explains in more detail the depth of the plagiarism on the part of the makers of the 'Expelled' movie.

It's a must-read.

Plagiarism at its Worst

As a professional illustrator, the one thing that truly gets my blood boiling is plagiarism. What's worse is when pieces of scientific art are plagiarized by anti-science propagandists, often creationists, to construct straw-man arguments.

At last year's annual conference of the Association of Medical Illustrators in Bozeman, Montana, I saw many amazing talks and presentations, but only one received a standing ovation.

XVIVO, a scientific illustration and animation studio in Connecticut, showed their 3D animated movie 'Inner Life of a Cell.' I'm sure you've seen it by now, if not, check it out. Medical illustrator David Bolinsky and Dr. Robert Liu presented the animation, explaining how they found innovative ways to use the features of the 3D software such as duplication and textures, as well as animating certain shots backwards, to create their highly complex sequences.

After all the applause, the two animators did have some tough questions to answer, though. The animation is aesthetically gorgeous, and precisely demonstrates inner workings of organelles and molecules in the cell, at multiple scales from cellular to molecular. However, the problem they admitted having was in simplifying these processes so much. They explained this was necessary; in order to see anything at all, certain elements just had to be left out.

For example, in the scene showing transcription of proteins, amino acids seem to fly into the ribosome as if directed by an unseen hand, ushered in one by one in the correct order. In reality, they explained, a sea of amino acids exists in the region of the ribosome, and they automatically fit in place in their correct order as the protein is transcribed. To show the process in real time (which is unbelievably fast), they simply couldn't show that level of complexity.

And herein lies the problem with the video when viewed without narration or explanation. It looks like a constructed machine, but not only that; it looks like every movement is being controlled by some intelligence. I think we all saw what was coming, but I didn't imagine to what extent!

The creationist responses to the YouTube video, where it showed up after the convention, were immediate. I suppose it's difficult for someone with no science background to understand that these 3D models are representations of what's going on in a cell. It's not as if the scientists shrunk themselves down and crawled in there "Fantastic Voyage" style with a nanobot video camera. (Some day, though... some day...)

But here's the really amusing/annoying part. This is a very, VERY well known animation in science illustration and animation circles. It's about the last piece of visualization you want to rip off and not get caught. Maybe it would be slightly more risky to rip off the introductory credits sequence to 'House M.D.' but that's beside the point.

Ripping it off is apparently what the makers of the anti-evolution movie 'Expelled: No Intelligence Allowed' have done.

Check out Pharyngula to read the letter from their lawyer. (By the way, PZ Myer's blog is just about the best evolution blog there is!)

The highlight of the letter:

This letter will also serve as notice to you that XVIVO intends to vigorously and promptly pursue its legal remedies for your copyright infringement, unless and until Premise Media, Rampant Films, and their officers, employees, and agents comply with the following demands:

1. That Premise Media, Rampant Films, and its officers, employees, and agents remove the infringing segment from all copies of the "Expelled" film prior to its scheduled commercial release on or before April 18, 2008;
2. That all copies of the "Inner Life" video in your possession or under your control be returned to XVIVO;
3. That Premise Media notify XVIVO, on or before April 18, 2008, of its compliance with the above demands.

XVIVO, I love you even more than I did. Which was already a lot. It's always great to see the artists standing up for themselves!

Now, they didn't take the animation directly. They were at least smart enough (I guess) to change the colors of the structures.

'Expelled' screenshot on the left. XVIVO's on the right. (Thanks to PZ Myers for the screenshots, wherever you got them!)

As much as I'm debating whether to even watch this documentary on YouTube when and if it becomes available, I am looking forward to seeing what, if any, commentary is provided when showing this animation. Beyond the classic argument from ignorance of "look at how complicated this is! How could this form by chance alone?" I don't expect much at all.

It will be a happy day when XVIVO wins this fight.

First Post - An Introduction

The origins of this blog go back to a train ride. An agonizingly long (27 hour) train ride home to visit my family. I'd brought a small sketch book with me and was spending a lot of my time doodling. As a professional (I can say that now that I'm finally out of school) scientific illustrator, I tend to spend a lot of time doing that.

For some reason, I started to doodle trees. Evolutionary trees--also called clades. I was playing with all the different ways I knew of to represent species relations using clades, and since I had a lot of time on my hands, I started to sketch out other ways of representing evolutionary history. I ended up filling most of the book, and rather surprised myself by the depth of the subject

There are many, many ways to visualize evolution. Just a few that I thought of on my long journey were:

• Cladistics
• Line of descent drawings
• Shared character / vestigial character illustrations
• Development (embryo comparison)
• Animations

I am hoping with this blog that I, along with the other contributors, can explore these and other topics, as well as how to best use them to educate both scientists and lay people on the topic of evolutionary biology.

Have an idea or wish to contribute? Please send me an email!