There’s an old saying about the leopard not being able to change its spots. But snowshoe hares do it twice a year: replacing a thick white winter coat with a lighter brown summer coat.
Summer-coated snowshoe hare (Image: Walter Siegmund).
European rabbits, which is what Noe is, don’t do this- she does shed twice a year, but her fur is the same color each time.
Winter-coated hare (Image: D. Gordon E. Robertson).
For hares, the timing of the coat replacements is roughly correlated with snowfall, and it’s easy to picture how a white coat helps camouflage them in winter and a brown one in summer. But there’s a problem: climate change means that seasons are shifting, so their white coats come in too soon and stay too long. This is a big problem for the hares: white makes them stand out to predators on a brown (or green) background.
In theory, natural selection will weigh heavily on hares in the years to come: the hares that have coat-changing cycles that more closely match snowfall will survive, while those with the older cycle will probably be eaten. Over time, the hare population will adapt to the new seasons. But there are two big IFs here: this will only happen IF the seasonal changes happen slowly enough so that the hares have time to adapt, and IF all the hares aren’t preyed upon faster than the survivors can have babies.
Because hares breed like…rabbits (sorry, couldn’t resist the cliche), they will probably be okay in the long term. But there are many, many other species for whom rapid climate change will create insurmountable problems in the decades to come.
One of the questions I’m interested in is how changes in the technology available to create science visualizations have affected the final products. While there are obvious differences related to the final display media- like paper and ink vs. monitors and pixels- other “hidden” technologies also play a part in creating visualizations.
Let’s look at the case of visualizations for which you need to do some sort of math in order to create. These include graphs and charts, but also less obviously number-based visualizations, like those showing the relationships among species.
Essentially, we base our understanding of the relationships among species upon how similar they are. Today, this means classifying many traits of different species, creating a table of the different types of traits each species has, and determining what percentage of traits they share in common.* Then we compare the percent similarity among each species, and use that information to construct phylogenetic trees- visualizations of the relationships among the species.
Example of a phylogenetic tree (c) Surachit CC-BY-SA 3.0
Clearly, some mathematical calculations need to be done here. And the more traits and species you are trying to deal with, the more complex the calculations become. Today’s biologists use computers- and even supercomputers- to help them crunch all the numbers they need to be crunched. Once that step is done, other computer programs help them construct the phylogenetic trees.
So, let’s step back in time to the early days of evolutionary biology. In Darwin’s day, this mathematical approach to evolutionary biology didn’t exist. Species were classified in a more qualitative way, but one that was still based upon similarities and differences. This approach relied more on the judgement of the individual scientist in determining which species were most closely related, rather than a compilation of percentages. The visualizations that resulted relied less on math, and more on individual judgment and traditional conventions of design.
But does this mean that early biologists didn’t use math when creating visualizations? Not at all. Most probably used math at least in some amount to help them figure out relationships between species. And (to get a bit off-topic) they also used complex math for other aspects of biology, such as determining population densities. To help them in this task, they actually had a fair array of tools, such as logarithmic tables, Napier’s bones, slide rules, and possibly even mechanical calculators.**
Modern slide rule (c) ArnoldReinhold CC-BY-SA 3.0
But were these tools really widespread among biologists? And did the introduction of more powerful calculating devices help spur the change in biology that led to the number-heavy world of today? I suspect the answer to the latter question is yes.
So, getting at the title of this post, did Darwin use a slide rule? My (admittedly limited, so far) research hasn’t been able to turn up any examples of this. However, I did find an autobiography of his fellow biologist, Alfred Russel Wallace, that talks about using a slide rule as a boy:
“My brother had one of these rules, which we found very useful in testing the areas of fields, which at that time we obtained by calculating the triangles into which each field was divided. To check these calculations we used the slide-rule, which at once showed if there were any error of importance in the result. This interested me, and I became expert in its use, and it also led me to the comprehension of the nature of logarithms, and of their use in various calculations.” (From Wallace, A. R. 1905. My life: A record of events and opinions. London: Chapman and Hall. Volume 1. via Charles Darwin Online)
If Wallace used a slide rule, it’s reasonable to think Darwin might have too. And early visualizations of evolution probably did use tools other than pens, ink, and straight brainpower.
* I’m oversimplifying this a bit, because another important thing to consider is whether the traits are based on shared ancestry, rather than convergent evolution, and some other factors. Because of these factors, some of the traits in your table are more important than others, so are “weighted” more heavily in your calculations.
** Charles Babbage of Difference Engine fame was a contemporary of Darwin’s, and they even corresponded about his calculating devices.
The fall semester has started this week, and the last few weeks leading up to it have been a whirlwind of getting set up for teaching, putting in conference proposals, and continuing to chip away on my visualization project. As a consequence of the latter, I am learning much more about birds than I thought I would. (Did you know that there is an Indonesian bird called the Satanic Nightjar? Now you do.)
All together, it has been a busy time. So, in an effort to at least keep posting occasionally on this blog, here are three recent bird-related links of interest:
First, a pretty cool story about a woman who built an outdoor run/play area for her cats, so that they would not kill songbirds, get hit by cars, mauled by dogs, or have to deal with other outdoor hazards. Cats- both feral and domestic- are actually quite a large threat to bird populations: the USFWS estimates that domestic outdoor cats kill upwards of 39 million birds a year! So this is a creative solution, and I have to say looks pretty fun for the cats.
Next, the Cornell Lab of Ornithology is building bird-recognition software that will ultimately be used to create a “smart” ID/advice system for people who need help IDing a bird. They’re asking for help from the public to help build the software by taking a “color challenge” that matches a color to a bird. The results will be used to help figure out how we see color when looking at birds. If you’ve maxed out your levels on Angry Birds, this might be a good substitute 🙂
Finally, a research blogging post on a study looking at the relationships between songbirds and parrots. The researchers studied retroposons (“jumping genes”) in several different types of birds, and confirmed another study a few years back that surprised people when it suggested that songbirds, parrots, and falcons were all closely related. The post gives you a good breakdown of the study and its importance.
Metaphors in science can be powerful things- they can provide unifying frameworks for thinking about the world, suggest exciting new insights, or at times color our interpretations so that what we see is what we expect to see. Science is communicated to non-scientists largely through metaphors. Sometimes these communication strategies work, and at other times they don’t.
One of the key metaphors used to describe the pattern of descent with modification or evolution over time is the image of a branching tree. I’ve discussed some of the limitations of the tree metaphor in a previous post; essentially, it’s difficult for us to discard the misleading aspects of the tree metaphor while using other associations to communicate about the pattern of evolution. A current PLoS Biology paper by David Penny points out the problems of conflating a branching pattern of evolution in general with cultural associations of a “tree of life” (an image found in varying forms in several cultures), and points out that the tree metaphor only gives us part of the picture.
But do we have to use a tree metaphor at all? Certainly, the tree does a good job of illustrating common descent, and an okay job of showing the formation of new species (species can form through mechanisms like hybridization that the tree isn’t good at depicting). But no metaphor is perfect. Biologists have used other visual metaphors in the past, such as complex systems of symmetry-based relationships, or maps based on ecological affinities of species, but these have their problems as well.
In my graduate work, I’m using digital tools to expand the range of metaphors we have to communicate about evolution, by creating a dynamic evolutionary map. I’m focusing on avian evolution and the pattern of diversification of bird orders over time. I’ll be writing more about this project in the upcoming months, but in this post I want to share the basic draft pattern of the visualization.
The visualization spans a time period from the Cretaceous (in which we see the hypothesized origin of birds) to the present. This series of gifs is the draft version of the evolution of bird orders over time; each dot represents an order (with some exceptions). When the project is finished, viewers will be able to animate the orders forward in time, as well as examine relationships among orders and the evidence for shared descent. I’m already planning some changes near the beginning of the sequence, based on recent molecular studies. The numbers and cross-hairs will also not be in the final version (I’ve been using them to help me keep track of all the orders as I animate it). You should be able to get a sense for how the animation progresses by clicking through this slideshow:
Birds: so many reasons they are cool, but here’s another one- they’re the only modern surviving dinosaurs. Yes, really.
Crocodiles, turtles, Komodo dragons- all related to dinosaurs, but not descended from dinosaurs. In fact, recent paleontological work has uncovered many new dinosaur species that share features we think of as “birdy.” Things like feathers, specialized bird-like lungs, and bipedalism. These features are found in a group of dinosaurs called maniraptorans, which are in turn cousins to the dinosaur group that includes Tyrannosaurus rex.
Artist's interpretation of a Scansoriopteryx hatchling, a "birdlike" maniraptoran dinosaur. (Image: Matt Martyniuk, azhdarcho.com)
Most of the time when we think of birds, we think of the things that make them birds, and not the things that make them dinosaurs. But that is because we often have the relationship between dinosaurs and birds reversed in our little primate minds; Much of what is bird-like is not exclusive to birds, but rather, to a larger group of dinosaurs. Birds have taken these particular traits in novel directions, but these traits existed independently of all the birdiness we usually attribute to our feathered, flying, bipedal friends, long ago, before the Great Extinction.
Check out his entire post- it’s worth reading.
And here’s a mediocre photo of an excellent museum display, from the American Museum of Natural History’s dinosaur fossil halls. It’s a 3-D cladogram (somewhat like a family tree) of dinosaur relationships. If you look at the upper right corner of the photo, you should be able to just make out the words “ALIVE TODAY.” This is where modern birds fit into the picture: our living dinosaurs.
Dinosaur cladogram from the AMNH. (Image: S. Stephens)
Every year around the US, creationists try to pass bills in state Legislatures either limiting discussion of evolution in classrooms or promoting a strategy called “teaching the controversy.” The latter approach essentially requires science teachers to teach students about both the scientific evidence for evolution and religiously-based philosophy that claims that evolution does not exist (or, alternatively, that some aspects of evolution have occurred, but not others).
Evolution is a fact, backed up by copious amounts of evidence. Natural selection, the modern theory describing how evolution happens, is probably about as well-supported as other scientific theories you may have heard about, such as the theory of gravity or cell theory. Some details of the theory of natural selection are currently being fleshed-out by scientists- a normal and healthy part of the scientific process. There is no debate, however, that natural selection is the best explanation we have today to explain the evidence for evolution that we see all around us. Philosophy and religion can offer no better, evidence-based, explanation of how evolution occurs.
This year, Florida Senate Bill 1854 would require “a thorough presentation and critical analysis of the scientific theory of evolution.” Sounds reasonable, right? Well, Florida State Science standards already require critical discussion in the science classroom. It turns out that the sponsor of this bill, Senator Stephen Wise, sponsored a bill in 2009 that advocated a “teach the controversy” approach to evolution. That bill failed, so he’s apparently trying to sneak religion into science classrooms again this year.
What does Sen. Wise suggest is a good “critical” alternative to evolution? He won’t say. In interviews by reporters, he calls it “non-evolution” or a “theory of whatever.” (In 2009, he called for teaching “intelligent design,” a Christianity-based philosophy which has legally been ruled religion, not science.) If this bill passes, Florida will be opened up to lawsuits similar to those that have cost other states quite a bit of money. It will also presumably have a chilling effect on the state’s efforts to attract high-tech businesses, such as medical research. Perhaps most importantly, it will teach our students something that just isn’t true. Evolution has occurred, and is occurring, and natural selection is the best explanation we have based on the evidence we have.
Floridians! If the prospect of poor science education, revenue-draining lawsuits, and general philosophical confusion bothers you, then you can sign this petition! One useful feature is that this petition sends an e-mail to your state legislatures when you sign, which helps make a greater impact. Non-Floridians can sign too, but the signatures of FL residents will have greater impact. I also urge you to add comments, as well as just signing. And, pass this on!
Earlier this week, I attended a conference of the National Association of Research in Science Teaching. I wasn’t presenting anything (missed the submission deadline), but it turned out to be fairly worthwhile. I ended up only attending two days of the conference, and focusing primarily on the digital tools/informal science sessions. I did get the chance to chat with a few people about my work and make some connections, which is always nice.
Here are just a few impressions from the conference.
The digital media tools used for science education seemed to mainly fall into two categories: simulations for teaching science concepts, and simulations for assessment purposes. (This is probably not a very profound observation.) The former seems to be the more ‘traditional’ tools, e.g., using racing games or pinball-esque scenarios to teach about physics. The latter are newer to me, at least, and are significant in that they represent an attempt to get away from multiple-choice tests for testing inquiry. There were some neat ideas from both these general categories.
The digital tools for informal learning were more wide-ranging, which you’d expect. There were some cool demos here; two I found interesting were FoldIt (which turns protein-folding problems into crowdsourced puzzle games) and Dancing the Earth (which uses a mixed-reality simulation to teach astronomy concepts).
The session that was probably most useful for me immediately was one on problems in teaching evolution. Some of the bigger conceptual issues raised here were: the challenge of linking evolutionary processes at different scales (e.g., population dynamics & speciation), teaching students to differentiate between useful and non-useful types of evidence, and difficulties with reading phylogenetic trees.
I also went to a session on philosophy of science, objectivity, and teaching about pseudoscience. Some of the ideas from this session would be useful if I ever did teach science again, since it was more geared toward educators. One presentation in particular stands out, on the subject of teaching science in communities which place a high level of emphasis on traditional ecological knowledge. The presenter tried to lay out a strategy that charts a middle course between immediate rejection or fuzzy acceptance of TEK, by focusing on talking about cultural technologies, rather than immediately comparing philosophies. The idea seems to be to focus on areas where there’s common ground (i.e., observation, testing, and building technologies in both traditional cultures and science), rather than immediately alienating students by dismissing their culture or dismissing science as a specialized way of understanding the world. This is an interesting idea to think about.
Finally, trying to present via Skype is just asking for trouble. I attended one session (a digital media session, naturally) in which two presenters were going to present via Skype. Even though everything was clearly set up and working during the break before the session, when it came time to present, something went wrong with the sound on someone’s end. The two presenters ended up being able to give their talks, after much technical tweaking, but this did not go smoothly.
One version of the tree of life, by Ernst Haeckel (Wikipedia)
The evolutionary “tree of life” is a well-known metaphor for the broad scope and branching pattern of evolution over time. This metaphor was first developed by Charles Darwin in On the Origin of Species, as a way to help shape his ideas about evolution by natural selection.
Darwin used several of different metaphors in Origin, but the tree of life is key in that it presents his central organizing vision of shared descent, the idea that all species are related and ultimately evolved from a common ancestor in the distant past. From a single starting point in this image, genetic changes in different populations send species down different evolutionary paths. Some of these “branches” survive, and split in turn to end off new branches. Other branches wither, and species become extinct. The species we see today are represented on the tree by new budding twigs, and those species that have become extinct are represented by the woody branches.
The idea that all species are related by common descent from a single ancestor is quite a profound difference between Darwin’s ideas about evolution and other ideas about evolution that had come before. This is probably the aspect of his theory that has been resisted the most by the general public. If all life is related by common descent, what does this imply about humanity and our place in the world? In Darwin’s view of nature, humans are an integral part of the natural environment, rather than in a separate, special position. Because Western religious traditions emphasize a separation between humans and the rest of nature, Darwin’s ideas were (and have remained) controversial.
Cartoon of Darwin as an ape-man, with a tree in the background. (Wikipedia)
In fact, Darwin’s metaphor of the tree of life was so influential in his lifetime that caricatures mocking his idea of common descent generally feature a tree somewhere in the image (while the other common motif is Darwin himself pictured as an ape-man).
What type of tree do you picture when you think about the tree of life?
While the tree of life does a good job of illustrating common descent, this metaphor, like all metaphors, has a few limitations. For one, the tree in the metaphor is often depicted as a temperate tree like an oak, with a thick central trunk. This thick, woody trunk doesn’t map well to what we know about early evolution- for example, we now know that there were probably many instances of gene transfer among different groups of organisms early in the history of life. Some biologists have suggested replacing the traditional oak tree with an image of a mangrove, with many interconnected branches and roots near its base, in recognition of this early complexity in the history of life.
While modern research gives insights into the evolutionary history of life that Darwin could only have dreamed of, his broad metaphor of a tree still seems to be going strong. Regardless of its ultimate shape, the tree of life seems poised to remain with us for a long time to come. However, this does not mean that there aren’t alternative ways to picture evolution. Could an alternative metaphor to the tree of life help us make mental connections about evolution in different ways? This is a question I hope to answer in my own research.
References:
Gruber, Howard E. “Darwin’s ‘Tree of Nature’ and Other Images of Wide Scope.” inHoward E. Gruber and Katja Bodeker (eds.) Creativity, Psychology and the History of Science, pp 241-257.New York: Springer, 2005.
Gruber, Howard E. “Ensembles of Metaphors in Creative Scientific Thinking.” inHoward E. Gruber and Katja Bodeker (eds.) Creativity, Psychology and the History of Science, pp 259-270.New York: Springer, 2005.
Larson, Barbara, and Fae Brauer. The Art of Evolution: Darwin, Darwinisms, and Visual Culture. Hanover, NH: Dartmouth CP, 2009.
Stevens, Peter F. “Pattern and Process: Phylogenetic Reconstruction in Botany.” in Henry M. Hoenigswald and Linda F. Weiner (eds.) Biological Metaphor and Cladistic Classification. pp. 155-179. Philadelphia: U of Pennsylvania, 1987.
Metaphor plays a number of roles in the scientific process, from facilitating exploration of newly-recognized phenomena, to grounding predictive models that aid in analysis, to transporting ideas among different scientific fields, and perhaps finally to public communication. When Charles Darwin wrote On the Origin of Species, metaphor had a central role in shaping his ideas about evolution by natural selection. He also was explicit about using metaphor to describe his theory.
Artificial selection apparent in dogs (Ellen Levy Finch).
Darwin used a number of different metaphors in his book for different aspects of his theory. Some of these metaphors took years to develop, and became central organizing ideas of his work. He used others more to ‘translate’ his ideas for the public consciousness. Howard Gruber lists five main metaphors in the Origin: artificial selection, wedges, war, a tree, and a tangled bank. Of these, the tree of life and warfare metaphors seem to be the two that are most widely referenced today.
Darwin used artificial selection– plant and animal breeding- to relate natural selection to a familiar process. In both types of selection, a population of organisms starts with genetic variation. In natural selection, limited resources and competition mean that only some of the organisms will survive to reproduce. In artificial selection, people pick organisms with desired traits to reproduce. This metaphor illustrates that selection can result in large changes in a population over time. One problem with this metaphor is that “selection” implies a “selector,” and natural selection happens largely via chance.
Action of a wedge (Wikipedia).
The wedge metaphor made it into the first edition of the Origin, but Darwin removed it from the second- so most people haven’t seen it. He says: “The face of Nature may be compared to a yielding surface, with ten thousand sharp wedges packed close together and driven inwards with incessant blows, sometimes one wedge being struck, and then another with greater force.” Wedges that stay in the yielding surface are species that survive, but to stick into the surface they presumably have to pop other wedges out.
While the wedge metaphor implies that competition is necessary for survival, the warfare metaphor makes this more explicit. For example, seedlings need to overcome “enemy” seedlings in a competition for space, and males compete for females in sexual selection. Today, the warfare metaphor is largely known by the phrase “survival of the fittest” (which didn’t actually appear in the first edition of Origin).
Darwin’s tree metaphor is probably his central organizing vision of evolution over time. From a single starting point, genetic changes in different populations send species down different evolutionary paths. Some of these “branches” survive, and split in turn to end off new branches. Other branches wither, and species become extinct. Over time, the single starting species gives rise to a multitude of different species, some persisting and some passing away. The metaphor of the “tree of life” is one that Darwin worked on for years and was never entirely satisfied with, but it’s a metaphor that still has a lot of resonance today.
Another "tangled bank": a coral reef (Richard Ling, Wikipedia).
While the tree of life represents the grand scope of evolution over time, the tangled bank illustrates the diversity of life that we can see all around us: “It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us.” He uses the diverse “tangled bank” to illustrate how complexity can arise from the interaction of a few simple rules for natural selection. This is actually the final grand metaphor in the Origin, and in it he tries to provide readers with a vision of life’s diversity, underpinned by the common relationships of species.
References:
Darwin, Charles, and James T. Costa. The Annotated Origin: A Facsimile of the First Edition of On the Origin of Species. Cambridge, MA: Harvard, 2009. Print.
Gruber, Howard E. “Diverse Relations Between Psychology and Evolutionary Thought.” inHoward E. Gruber and Katja Bodeker (eds.) Creativity, Psychology and the History of Science, pp 167-191.New York: Springer, 2005. Print.
This semester, I worked on a small science visualization research project, partly for a course, and partly as a pilot study related to my possible ultimate dissertation research. I’ll probably break up my discussion of this project into a few posts.
I was interested in looking at whether interactivity affects people’s understanding of phylogenetic trees. Phylogenetic trees are one of the key tools used in the field of evolutionary biology to represent hypothesized evolutionary relationships among species or other biological groups. They let us both explore relationships among living species and make inferences about the history of life.
However, interpreting tree diagrams often presents a challenge to students. On trees, the nodes (branch points) symbolize the last common ancestor between the species represented by the branch tips. Inexperienced readers tend to “read” relationships along branch tips, rather than by nodes, which can lead to misconceptions like inferring that species on the tips gave rise to other species (e.g., frogs to snakes to birds). The correct way to read phylogenies is to think of the nodes as focal points that connect related species.
One of the diagrams from the project introduction.
My experiment was designed to test whether making a phylogenetic tree diagram interactive, in such a way as to emphasize the importance of branch-point connections, would help people recall relationships more accurately when drawing the tree from memory. Cognitive theory suggests that interactive science visualizations could be useful for building understanding, because as we manipulate a visualization, we are able to generate slightly different viewpoints of it. We then put these points of view together into a mental model. A number of groups (e.g., here, here) have experimented with interactive trees, but in most of these projects, viewers interact with the tree by selecting branch tips in a higher-level tree, which takes them to a screen with a lower-level tree. With this type of navigation, the viewer effectively zooms in on a specific region of the tree, and the overall context for the tree is lost.
For this project, I created a tree of Florida bird families, based on the information on the Tree of Life website. To help people with unfamiliar families, there was a thumbnail photo of a representative species and a short fact about each family on the tree.
Viewers could click on a node to "open up" a branch.
Viewers were presented with a complete tree (so they didn’t lose the overview of the entire tree), and had the ability to select one node with its connected species to highlight at one time (thus maintaining the importance of reading by nodes).
Example of an "open" branch.The overall non-interactive tree. All photos open-source from Wikipedia.
My experiment worked like this: 1) viewers read a description of how to read a phylogenetic tree, 2) they either interacted with a dynamic tree or viewed a static tree, 3) were asked to draw the tree from memory, and 4) answered some questions about themselves and the tree. They weren’t told ahead of time that they would have to draw the tree from memory. In my next post, I’ll talk about what actually happened…
