Sharpies and sea squirts

Virginia Scofield is a colleague, co-author (Lambert et al. 2005), and friend of mine. She makes an extended appearance in this presentation by Sunni Brown, recorded at Duarte Design.



Lots of stuff to consider in this warm, personable presentation!

Reference

Lambert G, Faulkes Z, Lambert CC, Scofield VL. 2005. Ascidians of South Padre Island, Texas, with a key to species. The Texas Journal of Science 57(3): 251-262.

Open Lab 2011 begins! Plus: About the buttons

The indefatigable Bora Zivcovik recently announced that the submissions for Open Lab 2011 are now up! So everybosy start hitting the button!

I’m pleased to have designed the submission buttons again for 2011. I’ve kept the same basic logo from Open Lab 2009, which I wrote about here.

For 2010, Bora said he wanted something intense. I had an image of bubbling lava in mind, and ended up with bright reds and yellows on the botton, which I thought worked well.

This year, my starting point was a post I’d written about over on Better Posters about contrasting colours. Blue and orange is a tried and true pairing for movie posters, so I thought, what the heck – I’ll try it. Steal from the best and all.

I almost used the concentric “pond ripple” background last year, but remembered it for this year. Initially, I was thinking about the ripples in terms of waveforms in physics(!), but in this final design, I liked that the blue ripples evoke cool water. It made a nice contrast to the “heat” I was going for on the 2010 button. The contrast was important, because one of my goals is to make each button very distinct. The new 2011 button needs to be immediately recognizable as being different than the others, because all three buttons up show up on many blogs.

I’m fairly happy with how these have turned out, and it is always very cool it see them on other people’s blogs. But although they have served well for the last three years, I hope that Bora and the Open Lab team will let me retire this design after Open Lab 2011 is published. I’d like to see something fresh for the Open Lab 2012 buttons, whether from me or someone else.

Reimagining the CBC logo

I don’t always listen to movie soundtracks while I’m working. Sometimes, I listen to the CBC Radio 3 podcast. On a recent episode, host Grant Lawrence interviewed Gene Simmons of KISS. Simmons suggested a new Radio 3 logo, which got mocked up like this:

They asked for feedback about the logo, so I sent an email, which got read on this week’s podcast (starts at 23:26). Several other listeners responded much more to the source of the suggestion than the logo itself, methinks.

For the record, I saw the logo above on the podcast, which I like much more than this one on the Radio 3 website:

I think the grays help make the top one a bit more edgy, like street art; the bright colours on the bottom one look a little too cartoony.

You can find a history of CBC logos here. I don’t remember the butterfly...

Open Lab 2010 cover: Dude, where’s my Comic Sans?

Andrea Kuszewski and Jason Goldman both were tantalizing that there would be Comics Sans on the cover. But nooooOOOOooo... the big fibbers.

Unveiled at A Blog Around the Clock.

The secret life of a banner

When Dr. Becca announced that she wanted a new banner for her new blog, my response was simple:

“Designing a banner sure beats working.”

She liked what I did. Hooray! So let me take you through the  design process. The first step was reading the directions. I fired up Corel Photo-Paint, and set the dimensions to a new page to her specifications.

The picture

Almost everything was dictated by the title, “Fumbling towards tenure track.” The key word to me was “fumbling,” which immediately has some possibilities for a graphic interpretation. When I hear the word “fumble,” I think of the most famous fumble in Canadian history.

Robert Stanfield has sometimes been described as the best prime minister Canada never had. On the campaign trail in the 1970s, he was playing a little football with some of the reporters, firing off several nice passes. He dropped the ball once. And guess what picture made the front page of the most widely circulated newspaper in the country the next day? This one:

The picture is credited with harming, if not destroying, Stanfield’s chance of winning a federal election. Read more about this picture here.

To me, no other picture so completely captures the frustration of a fumble. So I wanted to use that in the banner. The shape wasn’t right to use the whole photo, but I was able to crop it to show just the fumble.

The typeface

Again, the word “fumbling” played into the choice. The typeface couldn’t be something rigid. It needed to have a bit of the unfinished, slightly haphazard, hand-drawn look to it. I simply scrolled down through the list I had, and found about three that fit the bill. I settled on Ripe, a free typeface I’d found through this article. It wasn’t hand drawn, but it did have some of the variation in letter shape I wanted. And I liked the roundness of it, which suggested a little of the playfulness implied by a fumble. (It has some problems with descending letters, like g, p, and q, though.)

The colours

Dr. Becca wanted something that matched this:

(Why she has this as her avatar... well, I suppose that’s her story to tell.)

I used a trick Garr Reynold talks about in Presentation Zen Design (which I reviewed here): use the colours in the photo. Corel Photo-Paint calls this tool the “eyedropper,” while others call it a colour picker or something similar. It measures and copies the colour at a point in the image. The text and background match the avatar, because the colours were literally picked from the avatar’s photo.

The dark yellow lifted from Dumbo’s hat highlighted the key word, “fumbling,” which I also emphasized by making the text larger and by jiggering the placement a little. Dark blue from Dumbo’s skin for the rest of the title, and light blue for the background, and, as the French say, “Voila!”

The result:

A virtual camera lucida

Sometimes, the scientific literature sucks at getting information to you.

I was looking at the table of contents of a new issue of The Journal of Crustacean Biology and saw an article about how to photograph soft-bodied crustaceans. Hm, I wonder why photographing soft-bodied crustaceans is difficult, I thought.

And the abstract mentioned software to deal with short focal planes by merging several pictures. The software is Helicon Focus.

Yes, I should be happy that I have found something useful, but... dagnabbit, why didn’t I know about this years ago?

For instance, here’s part of Figure 3 from a paper a few years back (Espinoza et al. 2006) on the left, compared to a new picture processed with Helicon Focus (click to enlarge).

These are neurons stained through a technique called backfilling. The best backfills are really superb, and you can see a lot of detail. But they’re often in thick tissue, and neurons go all over the place through it, making it hard to see all the relevant detail. The way people usually got around this was to get a camera lucida attached to a drawing tube through a microscope, then trace the axons as you focused up and down.

I was actually very pleased with the pictures in Figure 3 as published, which had dark cells against a very clear background. But the one shown here on the left shows the problem of getting all the relevant detail in the shot. The cell bodies on the right are okay, but the ones down a little deeper in the ganglion on the left and their axons are already blurring out.

The processed version on the right is better.

Having played with this a bit, sometimes there are things you can see in the individual frames that do get lost in the processed version. The biggest problem is when there is some detail underneath something else. You can often see it under the scope and in the individual frames, but not so well in the composite image.

This was so startling and so useful to me, I briefly entertained the thought of trying to turn this into a neuroscience methods paper. Then I looked and found short references that it had been used in the invertebrate neurobiology literature a couple of years ago (Scanell et al. 2008) in a journal I read. D’oh! Another shrewd Faulkes scheme bites the dust.

But at least I can spread the word through a blog post. A slightly more recent paper by Berejnov and company (2009) has nothing whatsoever to do with biology, but gives a better example of what you might get from this kind of software.

As I was writing this, I read an interview with Neil Gaiman, where he said this, mostly in relation to book publishing in particular genres:

Information used to be gold: hard to find, expensive, the equivalent of going off into the desert and coming back with a perfect lump of gold. Now, it’s the equivalent of going off into the jungle, in which there is information everywhere and what you are trying to find is the piece that is useful, while ignoring the noise.

I do wish the process of finding useful things was a little less jungle-like.

References

Berejnov, V., Sinton, D., & Djilali, N. (2010). Structure of porous electrodes in polymer electrolyte membrane fuel cells: An optical reconstruction technique Journal of Power Sources 195 (7), 1936-1939. DOI: 10.1016/j.jpowsour.2009.10.050

Espinoza SY, Breen L, Varghese N, Faulkes Z. 2006. Loss of escape-related giant neurons in a spiny lobster, Panulirus argus. The Biological Bulletin 211: 223-231. http://www.biolbull.org/cgi/content/abstract/211/3/223

Hegna, T. (2010). Photography of Soft-Bodied Crustaceans via Drying, Whitening, and Splicing Journal of Crustacean Biology 30(3): 351-356. DOI: 10.1651/09-3253.1

Scannell, E., Dell'Ova, C., Quinlan, E., Murphy, A., & Kleckner, N. (2008). Pharmacology of ionotropic and metabotropic glutamate receptors on neurons involved in feeding behavior in the pond snail, Helisoma trivolvis Journal of Experimental Biology 211(5): 824-833. DOI: 10.1242/jeb.011866

Data underload: Correlation of mood and precipitation, according to Garbage

For those who don’t get the reference...

Shameless cross-promotion

I normally don’t cross-promote my other blogs. But I was pretty pleased with how the Better Posters checklist came out, and thought it might be worth mentioning here, in case a few of you missed it over the new year. There’s a PDF version here.

I was also pleasantly surprised to get a very positive response to yesterday’s post on the “arm’s length” test. So you might want to check that out, too.

Mention map

MentionMap is a fun little application that visualizes comments to other Twitter users. Fun to click around on, and maybe a good way to discover some folks you’d find interesting.

Hat tip to Flowing Data.

Valley life explained graphically

This morning I found a site called TrendsMap that breaks Twitter trends out by region.

Poor physics...

This graphic shows what people respond when they hear the word “science” in free association tests. From Dr. Kiki’s blog, The Bird Brain.

Happy to see biology looming so prominently, but have no idea why. Odd that physics doesn’t make it on the board.

Buttonman

My design for the Open Laboratory 2009 submission buttons is being used this year. Go me!


Clickable now! So if you see something you like here, there, or anywhere, nominate it!

Open Laboratory 2009 candidate logo design

A Blog Around the Clock asked for graphics for buttons to encourage people to submit nominations for the next Open Laboratory anthology of science blogging. The one above is my take.

The goal here is not to get people to vote for me, just to explain a little bit of the thought process behind the design. For comparison, here is last year’s logo:


Basically, I wanted to make my design to be 180° away from last year’s. So I started with the idea of a greenish hue for the background. Similarly, I looked for a font that was distinct from the heavy font used in last year’s logo. I wanted to play with the idea of expressing the feeling of “openness” in the type, so the letters are set very far apart.

The space at the top is deliberately unfilled here. The idea is that this space can be used to put in different things like “Nominate for,” “Judge for,” “Featured in,” and so on.

Win, lose, or draw, it was worth the bit of time I put in, because I learned a few new tricks in Corel Photo-Paint doing this.

Check out the other fine button designs by Daniel Brown (who blogs at Biochemical Soul) at A Blog Around the Clock, and leave a vote in the comments.

Reassessing a font

My interest in graphics lead me to be very curious about Eco-font when I read about it on the TED blog late last year. Ecofont is designed to cut ink use; the main website claims it can be 20% less.

When I first downloaded and tried it, I was disappointed. It renders very badly on a computer screen, and looks relentlessly washed out and gray. I recently changed my mind, however, when I saw it actually printed. Using a standard inkjet printer and regular font sizes (11 or 12 point), it is quite readable, much more so than on the screen. At larger sizes, however, the ink-saving holes become more visible and legibility starts to become an issue again.

I’m not using it for things that will probably remain digital (manuscripts that will be sent by email, etc.). I do plan on using it for forms and things that I have to print.

In praise of evolutionary trees: a personal gallery

Charles Darwin's On the Origin of Species By Means of Natural Selection contains exactly one picture (here).

It's an evolutionary tree, a visual depiction of relationships between organisms. Such a relationship is now known a phylogeny, a word that Darwin coined. The point Darwin is trying to make with it is not the one that most people associate with evolutionary trees; Darwin was trying to emphasize what he called his Principle of Divergence. Nevertheless, trees have become more broadly representative of the entire evolutionary enterprise.

In that vein, and because variation is a key theme of evolution, I thought I would present the trees I've published in my research papers, with some commentary, for Darwin Day. I don't pretend that my trees are anywhere near as impressive as, say, David Hillis's massive, beautiful supertrees, but I present them here nonetheless.

There are two scientific stories being told here. One is about digging (figures 1, 2, 3, 4 and 6), and the other is about escape responses (figures 5, 7, and 8). I've grouped them in chronological order, however.

Figure 1.


This figure represents, well, bafflement. Not on my part, but on the part of the taxonomists. At the time, carcinologist Fred Schram memorably described the phylogeny of this group (Reptantia) as a "morass." Nobody had much of an idea of who was related to what, so instead of nice two way splits... a five way free-for-all. Original dissertation here (be warned, it's big!).

Figure 2.


This tree is nice and simple, and lends itself to using diagonal lines. Original paper here.

Figure 3.


This tree is considerably more complex. I'm trying not only to show the taxonomic groupings, but key features. The angle of the diagonal lines isn't terribly aesthetically pleasing to me, but I was trying to make the figure as compact as possible. Original paper here.

Figure 4.


Getting featured on the cover is always a nice ego boost. On this one, there's an ancestor nestled at the bottom of the tree, the earliest known decapod crustacean. Original paper here.

When I showed this figure to the editor, Glenn Northcutt, when he was visiting our campus, he asked, "Why are the animals pointing to the right?" He explained that in vertebrate anatomy, there was a long tradition of the anterior always being to the left. I'm pleased he published the figure anyway. Still...

Figure 5.


You'll notice everything facing left from here on in.

This one has even more species, with various traits in the branches. It was just easier to make straight lines instead of diagonals. Original paper here.

Figure 6.


That this one is back to diagonals is indicative of how long that paper sat waiting for me to revise and put it into the hands of editors! It was actually created well before the one above. Original paper here.

Figure 7.


Similar to the one before last, I think this one offers a few improvements in presentation. More of the taxa names are properly aligned, for starters. This and the cover are probably my two best looking trees. Original paper here.

Figure 8.


These two trees were the most complicated I've had to make yet. I was trying to show more groups of animals and more features. The size of this thing meant that I had to "chop the tree down" and show it horizontally, and that I couldn't show little icons of the animals, as I had done before. I really like putting in the pictures, because in some of my papers, they're about the only indication of what the organism looks like! But there was no possibility to do that and have any hope that the thing would fit on the page.

The other thing I like about this is that it shows that a tree is really an hypothesis. There are two trees, because there are two major competing hypotheses. There are similarities between them, and it turns out that both of them give the same "punch line" for my story anyway, which is multiple, repeated losses of certain neurons. Original paper here.

One thing I'm rather pleased with is that I've never re-used a tree. I've always redrawn them, always trying to look at each one afresh and make decisions appropriate for that tree. I hope these trees give a glimpse of the importance of evolutionary thinking in the research that I do.

Charles Darwin's first evolutionary tree (pictured) was not the first -- that honour lies with Jean-Baptiste Lamarck. nor was he the first to make the creation of trees rigorous and following explicit, testable rules -- that distinction lies with Willi Hennig. Nevertheless, I think we should celebrate evolutionary trees as part of Darwin Day because they represent one of the most important elements that Darwin brought to biology: history. Or maybe "deep time" is a better term.

Organisms have a past, and that past matters. That ancestry helps explain features of organisms that may otherwise be inexplicable, and it gives us a way to make predictions about organisms that we have not yet studied.

Perhaps more importantly, trees remind us that life is ancient. Organisms have been engaged in the struggle for existence on this planet a long, long time. Even the two centuries since Darwin's birth is a paltry handful of heartbeats in evolutionary time.

Before I go, I have one last tree. I did not create this one; I am grateful to Neurotree for this information. Since today is Darwin Day, an event that bills itself as a celebration of science and humanity, let me add in some personal connections. It's a reminder that the scientific community is, from a certain point of view, very small.

Figure 9.

8 Steps:

Zen Faulkes (The University of Texas-Pan American)
was a post-doc for

|

David L. Macmillan (University of Melbourne)
who was a grad student for

|

Graham Hoyle (University of Oregon)
who was a research assistant for

|

Bernard Katz (University College London)
who was a post-doc for

|

John Carew Eccles (Australian National University)
who was a grad student for

|

Charles Scott Sherrington (University of Oxford)
who was a post-doc for

|

Michael Foster (University of Cambridge)
who was a grad student for

|

Thomas Henry Huxley
who was a collaborator, friend and colleague of

|

Charles Robert Darwin (Independent)

Darwin created the foundation for evolutionary biology; Huxley created the biological curriculum for universities of his day; Michael Foster was a pioneer in physiology; Sherrington stood at the precipice between general physiology and neurobiology; Eccles, then Katz, strode into neurobiology; Hoyle stepped into the realm of invertebrate neuroethology using insects; Macmillan, while still a neuroethologist, preferred crustaceans as subjects; and I try to follow as best I can.

Descent with modification, indeed.

Vestigial icons

Quick! What's the icon circled in red mean?

"Save," right?

Now, what does that icon depict?

It's a 3½" floppy disk.

When was the last time you used a 3½" floppy disk?

I'm guessing it's been about 5 years since most people have touched one.

So why is that still showing up as an icon for "save"?


I wonder how long it'll be before that 3½" floppy fades as a symbol for "save." What will replace it? Will it be a flash drive icon, or perhaps something less computer centered, like a bank vault?. I wonder if there are computer users now how recognize that it means "save," but not why it means save.

Beautiful tree

This is a phylogeny of most known dinosaur species. While I appreciate the scientific information it contains, I also enjoy it just as a piece of graphic design. I'm tempted to make it one of my "Classic graphics" columns, but maybe that will be for another time.

Here's the article in New Scientist about it.

A word is needed for an inability to think graphically

Illiteracy is the inability to read with any proficiency. The use of the word goes back to the 1600s.

Innumeracy is an inability to use mathematics with any proficiency. This word was coined in the 1980s.

I know of no similar word to describe an inability to read, create, and understand information graphically.

I am thinking about this now because I am awake very late at night working on a graph to help out a student. The images are the graphical equivalent of a student handing in a written assignment in LOLspeak.

I wonder how many people can't make head or tails of a simple X/Y scatterplot?

Voice of fire, shrimp style

I was working on some images for a poster this afternoon, and I liked this one, so I thought I'd share it. It's a shrimp antenna magnified 50 times under a dissecting microscope. The title of the post is a reference to a well-known Barnett Newman abstract painting.

This is a nice object lesson in the lure of photomanipulation, though, as the previous post mentioned.

The top image has been rotated, the out of focus dots in the background removed by a little cloning, and the overall image sharpened. The original raw image is shown at right. I would say the top one is more attractive, but is it equally honest?

The line between beautifying and falsifying

The Chronicle of Higher Education has an article about the problems of digital image manipulation. It's a very tough thing. I've had several pictures that are clear through the microscope, but the subtleties are hard to capture on film. A little contrast enhancement makes it more visible, but have you changed the data in a way that changes the interpretation?

I'm going to have to think about whether and how to talk about his in my biological writing class this fall.

If you want to see professional retouching in a way that will make you look twice at images for a while, try looking at this professional retoucher's web page.