\ Visualizing Evolution: June 2008

Monday, June 30, 2008

Microraptor: The Four-Winged Dinosaur

Last Friday my old classmate Julian shared his master's research project, a 3D animation depicting microevolution in the process of antibody affinity maturation. I've already said this in a comment, but I'd like to restate that the animated simulation of evolution in the movie is absolutely stellar, so do give it a look!

I'd also like to point out that the biomedical communications company Julian works for did some animations for a Nova special last February on a feathered dinosaur called Microraptor. The full episode is available on Nova's website, here.

The scenes they animated were the flight tests of the model dinosaur in a wind tunnel,
this CG feather,and a really dynamic 3-D evolutionary tree:
As an illustrator trapped in the 2nd Dimension, I admit to getting Maya envy occasionally, especially when I see stuff like this. In the future I'd like to explore some of the uses for 3D software in visualizing evolution--functional uses beyond simply making things dynamic-looking (not to undermine the importance of making things look dynamic, of course!).

Friday, June 27, 2008

Visualizing Microevolution (link updated)


A bit about me, since I'm the new guy:

I'm a former classmate of Heidi's from Biomedical Communications at U of T. At BMC, I focused on biomedical animation, and now work at a medical animation studio in Toronto. I share Heidi's interest in evolution and visualization (and visualizing evolution). I thought I'd share my master's research project animation, and talk about my approach.

My animation dealt with evolution, but not on the level of the organism, as we often think of (and visualize) the process. The goal was to visualize evolution on the cellular level -- microevolution -- in the process of antibody affinity maturation.

In my animation, I wanted to show some of the cellular and molecular details involved in the process, but more importantly, I wanted to try to visualize the evolutionary changes at the population level (in this case, the change in affinity in the population of centrocytes). To visualize this population-level view of microevolution, I needed to show the distribution of affinity within the variable population, directional change, and the vital role of time in the process. To try to show all this, I created a virtual population of cells, and used scripting and dynamics in Maya (the 3D software) to simulate evolution in this population. The results of the simulation are shown in a cartoony graph.

The first few minutes provide an outline of the process, and then the simulation part starts about two and a half minutes in.
Here's a (new) link:

Antibody-Affinity Maturation

Therizinosaur: Mystery of the Sickle-Claw Dinosaur

I just wanted to share a link to a recent Flagstaff Live article about an exhibit at the Museum of Northern Arizona on the dinosaur Therizinosaur which contains a lot of cool-looking paleoart:
Illustration by Victor O. Leshyk
Leshyk blends a strong fine arts background with studies in anatomy, physical science and natural history. As the current scientific illustrator at the Bilby Research Center at Northern Arizona University, and an educational background in both science and fine arts, he is well versed in detailed drawings by hand, computer-based images, and clay and wire models, all of which were involved in the Therizinosaur exhibit.
Check out those claws. I just love this guy's art. He even has a piece on convergent evolution (it's not part of this particular exhibition but by gosh, I had to show it):
Illustration by Victor O. Leshyk

Nice! So I guess if you live in the Flagstaff, AZ area, go check it out. Me, I'm too far away. : (

Thursday, June 26, 2008

Ventastega curonica

From Science News, a newly described fossil gives evidence of the transition from fish to land-dwelling tetrapods. This is Ventastega curonica, from the late Devonian (365 million years ago) of Latvia, in a recent article in the journal Nature. It's the most primitive Devonian tetrapod, and is intermediate transitional form between Tiktaalik (our favorite early tetrapod) and the later Devonian tetrapods like Acanthostega and Ichthyostega. So I guess it's a fishomander, of sorts?

Alas! One more missing link means two more gaps in the fossil record!

Anyway, to stay on topic, here is the illustration being shown on all the news sites:
Illustration by Philip Renne - click for big

He looks so happy! I had to piece this together since most of the news sites are showing a cropped version sans the bottom-dwelling Bothriolepis in the background, and the only full-version I could find has poor resolution. And Philip Renne doesn't seem to have a website, unless all the media sites are mispelling his name, in which case, Philip, I appologize for my lack of link.

Anyway, I like the painting itself. It's colorful, has a nice balance, looks like it may have been designed for a book cover. But we're missing the most important part of the animal. The innovations of Ventastega are in its legs, and all we get to see here is the big smiley head! Man, that reflection on the eyeball is nice, though. And the angle is so dynamic; I feel like I'm right there in the water with him!

Here's an illustration from Devonian Times showing the nearly complete braincase, shoulder girdle, and partial pelvis:
Illustration by Dennis C. Murphy

Maybe the reason the illustrations don't show details of the foot is we don't have them represented by fossils.

I'd never browsed Devonian Times before; their illustrations have a lovely consistency: black sillouette with red bones. Check out the pages for Tiktaalik, Ventastega, Ichthyostega, and Acanthostega. The site makes it really easy to compare fossil forms. Though I would have put them in chronological and not alphabetical order.

I'm going to try to track down the full Nature article at the library this weekend, so hopefully another update on Ventastega will follow.

Wednesday, June 25, 2008

Darwin's Canopy: Update

The results are in on the Darwin's Canopy art installation, and London's Natural History Museum has chosen Tania Kovat's "Tree":

From the New Scientist: Tania Kovats' TREE has been chosen. It will consist of a cross-section of a 200-year-old oak tree, cut lengthways and running along the full length of the ceiling. It was inspired by Darwin's "tree of life" diagram.
Awesome! That was one of my picks! I'm just relieved they didn't go with one of the more abstract entries. The judges were unanimous in this decision and according to the NHM site, work has already begun on the installation, which is to be unveiled on February 12th, 2009, Darwin's 200th birthday.

More on the artist from NHM:

Tania Kovats is a British artist who works primarily in sculpture and in the exploration of landscape. She is currently exploring Darwin’s voyage while in South America.

'The starting point for this proposal, known as Tree, was Darwin’s iconic branching tree drawing, the first representation of his theory of evolution.'

Tania Kovat’s recent work includes the Museum of the White Horse. Visit the Museum of the White Horse website.

Tuesday, June 24, 2008

Apple Evolution

Related to my post on automotive evolution, here is an image depicting 30 years of evolution of Apple products from designer Edwin Tofslie (who has a lot of neat design work in addition to this):

You'll want to click for big. A lot of familiar machines are depicted here. I was just thinking about our old Apple IIGS the other day from when I was a kid. And there's the bulbous blue iMac we used in undergrad... and there are the Macs we used in graduate school... and there's the G5 I'm using right now! Ah, nostalgia attacks again!

Except for this:
I'm glad this is extinct.

Anyway, look it over, keeping in mind how evolution of technology relates to biological evolution. Look for overall trends and think about the selective pressures (or 'mutations' or 'genetic drift') that drove those adaptations. And perhaps try to imagine what the future Apple will look like.

And here are a couple more computer-related examples. I have no idea what's going on in either of these but what's interesting is the fact that they're represented as cladistic trees!

Saturday, June 21, 2008

More Calvin and Hobbes

Last week's entry in which I included a Calvin and Hobbes comic made me feel nostalgic. And then curious to see if the boy and his tiger had anything to say on the subject of evolution. I found these three online: (And now I am seriously considering picking up a copy of the printed anthology, for a number of reasons!)

Friday, June 20, 2008

Scientists Fix Bugs in Our Understanding of Evolution

From the European Molecular Biology Laboratory (EMBL), an article about a tool which allows a more accurate insight into evolution of DNA and protein sequences.
In the current issue of Science [EMBL researchers] uncover systematic errors in existing methods that compare genetic sequences of different species to learn about their evolutionary relationships. They present a new computational tool that avoids these errors and provides accurate insights into the evolution of DNA and protein sequences. The results challenge our understanding of how evolution happens and suggest that sequence turnover is much more common than assumed.
Wish I could provide more commentary than that, but I'm too tired, so here's a nice visualization from the press release:

Sunday, June 15, 2008

Darwin's Canopy: Art inspired by evolution

The Natural History Museum of London has announced the 10 finalists on the short list for a permanent display called Darwin's Canopy, which will be unveiled on Feb 12th, 2009, Darwin's 200th birthday. You can see a slide-show of the proposals at the New Scientist, here.

I found the majority of the ideas a bit strange and abstract for my taste (can I say "artsy-fartsy"?), but here are three that I really like.

The first is by Tania Kovats, which features the classic branching tree as a representation of natural selection causing speciation.
It appears from the sketch as though it will take up the entirety of the hall's ceiling, and thus have a good impact on those museum visitors who take the time to look up. And the tree is an iconic enough image that I think most viewers would know what it is intended to represent.

This next installation, proposed by Alison Turnbull, is really the only in in my opinion which properly conveys Darwin's idea about natural selection, though I wonder how visible it would be if they used actual moths on ceilings that look rather high, at least in the photographs I've seen of the hall.
'This work, Biston betularia aka The Peppered Moth, was prompted by the numerous and precise references to colour in Darwin's account of the voyage of the Beagle.'
Lastly, I like this idea by Rachel Witeread, a sculptor who has the idea of having a series of panels with the imprinted footprints of humans and animals.
This one is nice because the human element is included in a naturally fair way, as just another set of footprints among those of the other animals.

Personally, I hope they go with the moths. Some of the other ideas are just too artistically abstract. For example, Richard Wentworth's proposal involves mounting lots of small round mirrors of different sizes to the ceiling:
'The ceiling is dedicated in equal measure to Darwin’s peripheral vision, his capacity for negotiating distractions and his ability to make his own luck.'
Mirrors? This one bothers me, because I find it impossible to imagine the average visitor of the museum looking up, seeing lots of little round mirrors, and instantly being reminded of Darwin's peripheral vision and capacity for negotiating distraction. I also happen to have an extremely strong aversion to snooty-sounding artist statements. Sorry, Richard Wentworth.

Another, and I have to say rather creepy, idea is by Christine Borland and is a sculptural piece of a large tree based on Darwin's original tree of life sketch, but with the addition of human limbs with coin slots, (coin slots?):
'The public are invited to insert coins into the branches of the tree and its human limbs, in the tradition of wishing trees.'
This makes me wish I'd had the chance to propose an idea. These two works just won't help the viewer to understand that they represent evolution, and they don't reflect Darwin's ideas in any concrete way.

The moths, in contrast, bring instantly to mind the idea of slow genetic change over many generations. "Look! See how they go from light to dark? They evolved a darker color to adapt to their changing environment." But anyway, now that you know how I feel, check out the 10 finalists for yourself. And if you're lucky enough to live close, go check out the exhibition. It will be on display until September 14th.

Finally, my thoughts on Artist's Statements, as summed up in a classic Calvin and Hobbes comic:

Wednesday, June 11, 2008

Automotive Evolution: a metaphor for biology?

There are no end-points in evolution. It's not a goal-oriented process leading to some perfected peak design, once reached thus ending the process of change. It's continuous; things are constantly revising their shape over and over again. This is true in biology as well as our own man-made industries.

That's what I thought of when I saw this video of the new BMW GINA Light Visionary Model... a car with a fabric 'skin.'

Be sure to watch to the end... the headlights are the best part. The car BLINKS. Not in a retractable-headlight way but in a fleshy closing of the eyelids way. And whether this is awesome or creepy, I have yet to decide. It's like a switch from a car with an exoskeleton to a vertebrate animal with moving hard parts inside a flexible skin!

Personally I find the evolution of automobiles to be a fantastic metaphor for biological evolution. But for teaching, I'm not sure. Because there are many out there still who don't understand how Natural Selection works without an intelligent hand to guide it. Car evolution is guided by consumer choice, studies on safety, advancements in technology, and the artistic flair of the automotive designer:

horses 'evolve'... do cars?

But the evolution of living things is guided by the blind, selective processes of nature. Unfortunately this leads biologically-ignorant people into thinking the entire process is 'random!' Case in point, a ridiculous blog entry from the Discovery Institute called Do Car Engineers Turn to Darwinian Evolution or Intelligent Design? But wait! To save your brain cells and sanity, I'd recommend going straight to the SGU criticism on the most recent Skeptic's Guide 5x5 podcast. The ID blog entry is based on the premise that automotive designers refer to the 'intelligent design' of their cars rather than the 'evolution' of them. (And I guess the implications are that therefore biological evolution is false?)... even if that premise were true, which it isn't, automotive designers DO refer to their changing designs as 'evolution,' and rightly so!

Logos evolve, too.
Though their design has nothing to do with functionality and everything to do with consumer choice. The actual car is a much better model of what happens in biology.

Thursday, June 5, 2008

A little rant about the caduceus

This may be a bit off-topic, but I must share this little pet-peeve of mine, which is categorized in my brain somewhere between the phrase "a whole nother" and people who type "RU" instead of "are you" in instant messages.

This is a caduceus:
a.k.a. the Wand of Hermes. It's a staff spiralled by two snakes and there's a couple of wings at the top. This is the symbol of commerce, not medicine. What are news reports saying about medicine when they put a caduceus on the screen when talking about doctors or health insurance?

This is the Rod of Aslepius, the symbol of medicine. One rod, one snake, no wings.
As seen on ambulances and other EMT supplies in the Star of Life:
And now that you know that, you'll be seeing caduceuses being used wrong everywhere you look. You're welcome.

Tuesday, June 3, 2008

Is Paleoart Scientific?

After my Paleoartist of the Month post, I received an interesting email from the writer of Bloggasm (great name), who just interviewed James Gurney: Pencil journalism: An artist's attempt to depolarize the proselytizers. The interview covered the same post by Gurney that was featured last week on Pharyngula, where he shared his experience of inviting two Jehovah's Witnesses to sit down and allow him to sketch one of them.

It's nice that the post is getting him lots of attention, but personally I remain much more interested in the entries about art and technique and dinosaurs.

On that note, on May 27, Laelaps featured an interview with Paleoartist Michael Skrepnick, someone I already have in mind for a future PAotM. Skrepnick discusses how he became a paleoartist, as well as some of the challenges of reconstructing extinct animals, the techniques he uses, and the scientific validity of paleoart.

The interview reminded me of an interesting and slightly annoying conversation I had last year. In graduate school, I asked the professor of my Vertebrate Paleontology class, "Why are Parasaurolophus so often depicted with a fan of skin stretched under their head-crest?" Like so:
(painting by Rich Penney)

With a smirk, my professor said it was "because dinosaur artists need to make money." I was taken aback! So, of course, I had to bring up the subject the next time we were in the fossil lab together. I asked what he thought of reconstructions. He didn't like them! It's one thing to draw the bones, but once you start adding flesh and environment, you're bound to make mistakes, he asserted. I wish I could remember his exact words, but his point was that these types of illustrations are just artworks, not science.

Well, to an extent, I dissagree. Even something like this:
(from the Natural History Museum, if you can't tell)

...makes certain assumptions about the animal that future research could show to be wrong... placement of bones, posture, etc...(Actually I'm not sure how old this drawing is, but it looks painfully quadrupedal, doesn't it?)

And what's more, mistakes that have been made in the past, such as the idea that the Parasaurolophus crest was an air chamber or some kind of snorkel:
(from a very, very old book called "All About Dinosaurs")

... also existed in the literature. It wasn't a fanciful idea drawn up willy-nilly by a carried-away artist, but was rather illustrated based on what was believed by scientists about the fossil at the time.

I'll admit, as an artist who is partial to this kind of work, I'm probably biased. So I'll quote Michael Skrepnick from the above linked article:
Throughout the history of paleontology, paleo art has provided a reliable visual record, and essentially a "mirror" of progress within the science. Greater advances in technology, related disciplines, sheer volume of specimens and research, all reinforce an increasingly accurate assessment of ancient life on earth.
I'll admit Skrepnick might be biased, too, but I couldn't have said it better than that. Indeed we can confidently assume that the more we learn, the more accurate the art becomes. He continues:

Not so very long ago, snarling, upright theropods stalked slow, lumbering, swamp dwelling sauropods, incapable of walking unsupported on dry land. At the time, it was accepted, "cutting edge" science, today we have a much revised understanding of diversity and extremes in dinosaur evolution. Barriers have been broken, sauropods twice the size walk freely on land, tyrannosaurs have "tipped" forward, small theropods have feathers, psittacosaurs have "quills", etc. . .

Is our understanding now refined enough to offer a realistic vision of lost worlds ?

What I wonder, will today's " cutting edge " look like, in 2108 ? . . .

So what is the worth of paleoart? Yes it is fluid, and dynamic, and changes with scientific views and is bound to continue to change. But I think its real value lies in the way it captures the imagination of the general audience. Think especially of young people, whose early interest in science often begins with reading about fantastic prehistoric creatures. We owe it to them to make biological history exciting, to give it life and color and generally just more badass and cool. Here, have some more James Gurney to prove my point:


Sunday, June 1, 2008

Paleoartist of the Month

It's the first of June, which means it's time for Paleoartist of the Month! Each month I'll feature a favorite paleoartist based on some merits that I haven't decided yet. Right now, it's pretty random. Please feel free to submit ideas for July!

June's Paleoartist is James Gurney, who we all know as the artist behind Dinotopia:
The reason I chose Gurney for this month is because I just learned through Pharyngula that he has a blog which he updates almost daily. (Hey, he uses blogspot, too!) It's full of such useful information about illustration, color, light, form, style, that I've linked it on my own sidebar and will be checking it daily from now on. He even has a series of entries on Dino Art Tips!
I wish I would have discovered this site months ago. Reading it has been a delight, and he shares his ideas and methods on a number of techniques. It always makes me happy to see people with amazing talent openly sharing what they do and how they do it. It's going to take me weeks to read through all the back entries!
What I particularly love about Gurney's work is how genuinely animal-like his dinosaurs appear. Even when they stand along side humans in the utopian cities of his Dinotopia books, their behavior and mannerisms are believable as fellow creatures who really did once live on this earth, and not monsters dreamed up in some fantasy.
And of course, to bring it all home, good paleoart (even when it's not strictly scientific) allows our imagination to flourish, and to feel the existence of these long-gone beings who once inhabited this very planet, losing out to natural selection in the long run but definitely leaving their mark.