Visualizing and teaching evolution through synteny

Embracing the rationalist and empirically-based perspective of science is not easy. Modern science generates disconcerting ideas that can be difficult to accept and often upsetting to philosophical or religious views of what gives meaning to existence [link]. In the context of evolutionary mechanisms within biology, the fact that variation is generated by random (stochastic) events, unpredictable at the level of the individual or within small populations, led to the rejection of Darwinian principles by many working scientists around the turn of the 20th century (see Bowler’s The Eclipse of Darwinism + link).  Educational research studies, such as our own “Understanding randomness and its impact on student learning“, reinforce the fact that ideas involving stochastic processes are relevant to evolutionary, as well as cellular and molecular, biology and are inherently difficult for people to accept (see also: Why being human makes evolution hard to understand). Yet there is no escape from the science-based conclusion that stochastic events provide the raw material upon which evolutionary mechanisms act, as well as playing a key role in a wide range of molecular and cellular level processes, including the origin of various diseases, particularly cancer [Cancer is partly caused by bad luck](1).

All of which leaves the critical question, at least for educators, of how to best teach students about evolutionary mechanisms and outcomes. The problem becomes all the more urgent given the anti-science posturing of politicians and public “intellectuals”, on both the right and the left, together with various overt and covert attacks on the integrity of science education, such as a new Florida law that lets “anyone in Florida challenge what’s taught in schools”.

Just to be clear, we are not looking for students to simply “believe” in the role of evolutionary processes in generating the diversity of life on Earth, but rather that they develop an understanding of how such processes work and how they make a wide range of observations scientifically intelligible. Of course the end result, unless you are prepared to abandon science altogether, is that you will find yourself forced to seriously consider the implications of unescapable scientific conclusions, no matter how weird and disconcerting they may be.

There are a number of educational strategies, in part depending upon one’s disciplinary perspective, on how to approach teaching evolutionary processes. Here I consider just one, based on my background in cell and molecular biology.  Genomicus is a web tool that “enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversely across different species, and chronologically along evolutionary time.”  It is one of a number of recently developed web-based resources that make it possible to use the avalanche of DNA (gene and genomic) sequence data being generated by the scientific community. For example, the ExAC Browser enables one to examine genetic variation in over 60,000 unrelated people. Such tools supplement and extend a range of tools accessible through the U.S. National Library of Medicine / NIH / National Center for Biotechnology Information (NCBI) web portal (PubMed).

In the biofundamentals© / coreBio course (with an evolving text available here), we originally used the observation that members of our subfamily of primates,  the Haplorhini or dry nose primates, are, unlike most mammals, dependent on the presence of vitamin C (ascorbic acid) in their diet; without vitamin C we develop scurvy, a potentially lethal condition. While there may be positive reasons for vitamin C dependence, in biofundamentals© we present this observation in the context of small population size and a forgiving environment. A plausible scenario is that the ancestral population of the Haplorhini lost the L-gulonolactone oxidase (GULO) gene (see OMIM) needed for vitamin C synthesis. The remains of the GULO gene found in humans and other Haplorhini genomes is mutated and non-functional, resulting in our requirement for dietary vitamin C.

How, you might ask, can we be so sure? Because we can transfer a functional mouse GULO gene into human cells; the result is that vitamin C dependent human cells become vitamin C independent (see: Functional rescue of vitamin C synthesis deficiency in human cells). This is yet another experimental result, similar to the ability of bacteria to accurately decode a human insulin gene), that supports the explanatory power of an evolutionary perspective (2),


In an environment in which vitamin C is plentiful in a population’s diet, the mutational loss of the GULO gene would be benign, that is, not selected against. In a small population, the stochastic effects of genetic drift can lead to the loss of genetic variants that are not strongly selected for. More to the point, once a gene’s function has been lost due to mutation, it is unlikely, although not impossible, that a subsequent mutation will lead to the repair of the gene. Why? Because there are many more ways to break a molecular machine, such as the GULO enzyme, but only a few ways to repair it. As the ancestor of the Haplorhini diverged from the ancestor of the vitamin C independent Strepsirrhini (wet-nose) group of primates, an event estimated to have occurred around 65 million years ago, its ancestors had to deal with their dietary dependence on vitamin C either by remaining within their original (vitamin C-rich) environment or by adjusting their diet to include an adequate source of vitamin C.

At this point we can start to use Genomicus to examine the results of evolutionary processes (a YouTube video on using Genomicus)(3).  In Genomicus a gene is indicated  by a pointed box  ; for simplicity all genes are drawn as if they are the same size (they are not); different genes get different colors and the direction of the box indicates the direction of RNA synthesis, the first stage of gene expression. Each horizontal line in the diagram below represents a segment of a chromosome from a particular species, while the blue lines to the left represent phylogenic (evolutionary) relationships. If we search for the GULO gene in the mouse, we find it and we discover that its orthologs (closely related genes) can be found in a wide range of eukaryotes, that is, organisms whose cells have a nucleus (humans are eukaryotes).
We find a version of the GULO gene in single-celled eukaryotes, such as baker’s yeast, that appear to have diverged from other eukaryotes about ~1.500,000,000 years ago (1500 million years ago, abbreviated Mya).  Among the mammalian genomes sequenced to date, the genes surrounding the GULO gene are also (largely) the same, a situation known as synteny (mammals are estimated to have shared a common ancestor about 184 Mya). Since genes can move around in a genome without necessarily disrupting their normal function(s), a topic for another day, synteny between distinct organisms is assumed to reflect the organization of genes in their common ancestor. The synteny around the GULO gene, and the presence of a GULO gene in yeast and other distantly related organisms, suggests that the ability to synthesize vitamin C is a trait conserved from the earliest eukaryotic ancestors.

Now a careful examination of this map (↑) reveals the absence of humans (Homo sapiens) and other Haplorhini primates – Whoa!!! what gives?  The explanation is, it turns out, rather simple. Because of mutation, presumably in their common ancestor, there is no functional GULO gene in Haplorhini primates. But the Haplorhini are related to the rest of the mammals, aren’t they?  We can test this assumption (and circumvent the absence of a functional GULO gene) by exploiting synteny – we search for other genes present in the syntenic region (↓). What do we find? We find that this region, with the exception of GULO, is present and conserved in the Haplorhini: the systemic region around the GULO gene lies on human chromosome 8 (highlighted by the red box); the black box indicates the GULO region in the mouse. Similar syntenic regions are found in the homologous (evolutionarily-related) chromosomes of other Haplorhini primates.

The end result of our Genomicus exercise is a set of molecular level observations, unknown to those who built the original anatomy-based classification scheme, that support the evolutionary relationship between the Haplorhini and more broadly among mammals. Based on these observations, we can make a number of unambiguous and readily testable predictions. A newly discovered Haplorhini primate would be predicted to share the same syntenic region and to be missing a functional GULO gene, whereas a newly discovered Strepsirrhini primate (or any mammal that does not require dietary ascorbic acid) should have a functional GULO gene within this syntenic region.  Similarly, we can explain the genomic similarities between those primates closely related to humans, such as the gorilla, gibbon, orangutan, and chimpanzee, as well as to make testable predictions about the genomic organization of extinct relatives, such as Neanderthals and Denisovians, using DNA recovered from fossils [link].

It remains to be seen how best to use these tools in a classroom context and whether having students use such tools influences their working understanding, and more generally, their acceptance of evolutionary mechanisms. That said, this is an approach that enables students to explore real data and to develop  plausible and predictive explanations for a range of genomic discoveries, likely to be relevant both to understanding how humans came to be, and in answering pragmatic questions about the roles of specific mutations and genetic variations in behavior, anatomy, and disease susceptibility.

Some footnotes:

(1) Interested in a magnetic bumper image? visit: http://www.cafepress.com/bioliteracy

(2) An insight completely missing (unpredicted and unexplained) by any creationist / intelligent design approach to biology.

(3) Note, I have no connection that I know of with the Genomicus team, but I thank Tyler Square (soon to be at UC Berkeley) for bringing it to my attention.

In an age of rampant narcissism and social cheating – the importance of teaching social evolutionary mechanisms.

As socioeconomic inequality grows,  the publicly acknowledged importance of traits such as honesty, loyalty, self-sacrifice, and reciprocity appears to have fallen out of favor with some of our socio-economic and political elites. How many people condeHutton quotemn a person as dishonest one day and embrace them the next? Dishonesty and selfishness no longer appear to be taboo, or a source of shame that needs to be expurgated (perhaps my Roman Catholic upbringing is bubbling to the surface here).  A disavowal of shame and guilt and the lack of serious social censure appears to be on the rise, particularly within the excessively wealthy and privileged, as if the society from which they extracted their wealth and fame does not deserve their active participation and support [link: Hutton, 2009].  They have embraced a “winning takes all” strategy.

birds in a flockIf an understanding of evolutionary mechanisms is weak within the general population [link], the situation is likely to be much worse when it comes to an understanding of the role and outcomes of social evolutionary mechanisms. Yet, the evolutionary origins of social systems, and the mechanisms by which such systems are maintained against the effects of what are known as “social cheaters”, are critical to understanding and defending, human social behaviors  such as honesty, cooperation, loyalty, self-sacrifice, self-restraint, mutual respect, responsibility and kindness.

While evolutionary processes are often caricatured as favoring selfish behaviors, the facts tell a more complex, organism-specific story [link: Aktipis 2016]. Cooperation between organisms underlies a wide range of behaviors, from sexual reproduction and the formation of multicellular organisms (animals, plants, and people) to social systems, ranging from microbial films to bee colonies and construction companies [see Bourke, 2011: Principles of Social Evolution] [Wikipedia link].

One of the best studied of social systems involves the cellular slime mold Dictyostelium discoideum [Wikipedia link].  When life is good, that is when the world is moist and bacteria, the food of these organisms, are plentiful, D. discoideum live and reproduce happily as single celled amoeba-like individuals in soil.  Given their small size (~5 μm diameter), they cannot travel far, but that does not matter as long as their environment is hospitable.  When the environment turns hostile, however, an important survival strategy is to migrate to a new location – but what is a little guy to do?  The answer in this species is to cooperate.  Individual amoeba begin to secrete a chemical that acts to attract others; eventually thousands of individuals aggregate to form a multicellular “slug”; slugs migrate around to 1066px-Dicty_Life_Cycle_H01.svgfind a hospitable place and then differentiate into a fruiting body that stands ~1mm (20x the size of an individual amoeba) above the ground.  To form the stalk that lifts the “fruiting body” into the air, a subset of cells (once independent individuals) change shape. These stalk cells die, while the rest of the cells form the fruiting body, which consists of spores – cells specialized to survive dehydration.  Spores are released into the air where they float and are dispersed over a wide range.  Those spores that land in a happy place (moist and verdant), revert to the amoeboid life style, eat, grow, divide and generate a new (clonal) population of amoeboid cells: they have escaped from a hostile environment to inhabit a new world, a migration made possible by the sacrifice of the cells that became the stalk (and died in the process).  Similar types of behavior occur in a wide range of macroscopic organisms [Scrambling to the top: link].  Normally, who becomes a stalk cell and who becomes a spore is a stochastic process [see previous PLoS blog post on stochastics and biology education].

Cheaters in the slime mold system are individuals who take part in the aggregation process (they respond to the migration signal and become part of the slug), but have altered their behavior to avoid becoming a stalk cell – no self-sacrifice for them. Instead they become spores.  In the short run, such a strategy can be beneficial to the individual, after all it has a better chance of survival if it can escape a hostile environment.  But imagine a population made up only of cheaters – no self-sacrifice, no stalk, no survival advantage = death [see link: Strassmann & Queller, 2009].

A classic example of social cheating with immediate relevance to the human situation is cancer.  Within a sexually reproducing multicellular organism, reproduction is strictly restricted to the cells of the germ line – eggs and sperm.  The other cells of the organism, known collectively as somatic cells, have ceded their reproductive rights to the organism as a whole.  While somatic cells can divide, they divide in a controlled and strictly regulated (unselfish) way.  Somatic cells do not survive the death of the organism – only germ line cells (sperm and eggs) are able to produce a new organism.  In the end cellular cooperation has been a productive strategy, as witness the number of different types of multicellular organisms, including humans.  If a somatic cell breaks the social contract and cheats, that is, begins to divide (asexually) in an independent manner, it can lead to the formation of a  tumor and later, if the cells of the tumor start to migrate within the organism, to metastatic cancer.  More rarely (apparently) such cells can migrate between organisms, as in the case of transmissible cancers in dogs, Tasmanian Devils, and clams [see links: Murchison 2009 and Ujvari et al 2016).  The growth and evolution of the tumor cell leads to the death of the organism and the cancer cells’ own extinction, another example of the myopic nature of evolutionary processes.

In the case of cancer the organism’s defenses against social cheaters comes in two forms, intrinsic to the individual cheater cells, in the form of cell suicide (known through a number of technical terms including apoptosis, anoikis and necroptosis)[link: Su et al., 2015] and extrinsic and organismic processes, such as the ability of the organism’s immune system to identify and kill cancer cells – a phenomena with therapeutically relevant implications [link: Ledford, 2014].  We can think of these two processes as guilt + shame (leading to cellular suicide) and policing + punishment (leading to immune system killing).  For a cell to escape growth control and to evolve to produce metastatic disease, it needs to inactivate or ignore intrinsic cell death systems and to evade the immune system.

To consider another example, social systems are based on cooperation, often involving the sharing of resources with those in need.  A recent example is the sharing of food (blood) between vampire bats [see link: Carter & Wilkinson, 2013].  The rules, as noted by Aktipis, are simple, 1) ask only when in need and 2) give when asked and able.  In this context, we can identify two types of social cheaters – those who ask when they do not need and those you fail to give when asked and able.  People who refuse to work even when they can and when jobs are available fall into the first group, the rich who avoid taxes and fail to donate significant funds to charities the other.  It is an interesting question of how to characterize those who borrow money and fail to repay it.  Bankruptcy laws that protect the wealth of the borrower while leading to losses to the lender might be seen as acting to undermine the social contract (clearly philosophers’ and economists’ comments here would be relevant).

Given that social systems at all levels are based on potentially costly traits, such as honesty, loyalty, self-sacrifice, and reciprocity, the evolutionary origins of social systems must lie in their ability to increase reproductive success, either directly or through effects on relatives, a phenomena known as inclusive fitness [Wikipedia link]. Evolutionary processes also render social systems vulnerable to cheating and so have driven the development of a range of defenses against various forms of social cheaters (see above).  But recent political and cultural events appear to be acting to erode and/or ignore society’s defenses.

So what to do?  Revolution? From a PLoS Science education perspective, one strategy suggests itself:  to encourage (require) that students and the broader public be introduced to effective instruction on social evolutionary mechanisms, the traits they can generate (various forms of altruism and cooperation), the reality and pernicious effects of social cheaters, and the importance of defenses against them.  In this light, it appears that social evolutionary processes are missing from the Next Generation Science Standards [NGSS link]. Understanding the biology, together with effective courses in civics [see link: Teaching Civics in the Year of The Donald] might serve to bolster the defense of civil society.

Thursday, December 22, 2016 – Mike Klymkowsky

Featured image is used with permission from Matthew Lutz (Princeton University).

Army ants’ ‘living’ bridges span collective intelligence, ‘swarm’ robotics (PNAS)

 

Creation vs Evolution: Why science communication is doomed

Last Tuesday night, Bill Nye the Science Guy had a debate with Ken Ham over creationism vs evolution. I watched part of the debate, and have conflicted feelings on it. I’m going to start by saying I think it was a brilliant marketing move. For one, it suddenly brought the Creation Museum into the forefront of society for next to nothing. While before only a handful had heard of it, now it has risen to national prominence, and I’m sure the number of visits they have will reflect that in the near future.

As for the substance itself, I don’t think this is a very good topic for a debate. Any time you bring religion into a discussion, it turns into an “us vs them” argument where neither party is willing to change their view. Even the advertising and marketing billed it as a debate of “creationism vs evolution” – effectively presupposing the view that one can believe in both (which I’ll come back to). At best, it’s snarky and offhanded, and at worst, antagonistic and ad hominem. I should point out though that this is on both sides – neither side is willing to reconcile.

And why should they? Both view their side as being right, and weigh the information they have differently. So all that this accomplishes is that both sides become further polarized and further entrenched, and any chance of meaningful dialogue between both sides becomes less and less likely with every angry jab back and forth. It turns into a 21st century war of angry op-eds, vindictive tweets and increasingly hostile and belligerent Facebook posts shared back and forth. This isn’t just limited to religion though – many discussions end this way with people being forced to take sides in an issue that is more complicated than simply being black/white. Rather than discuss the details and come to an understanding of what we agree and disagree on, we’re immediately placed into teams that are at loggerheads with each other.

What is most interesting is what happens to extreme viewpoints when they are criticized. Rather than taking in new information and evaluating it based on its merits, criticism actually results in the consolidation of those perspectives. In lay language, if you have an extreme viewpoint, you dig in your heels, build a trench and get ready to defend yourself against all attackers. This isn’t entirely surprising – when someone attacks you, and in particular attacks you *personally*, why wouldn’t you get defensive. Studies of this have look at this from a political perspective, comparing extreme conservatives to extreme liberals. To quote Psychology Today:

Extreme conservatives believed that their views about three topics were more superior: (1) the need to require voters to show identification when voting; (2) taxes, and (3) and affirmative action. Extreme liberals, on the other hand, believed that their views were superior on (1) government aid for the needy; (2) the use of torture on terrorists, and (3) not basing laws on religion.

But wait! Aren’t these just fringe opinions being heard in the media? The good news is yes. The bad news is that the extremes are what people hear. If you imagine everyone existing on a normal distribution – with extreme opinions on the edges – then the vast majority of the people exist in the gulf between those people. However, those extremes are what people hear. In fact, this is what led to Popular Science shutting down their comments, based on findings by Brossard and Scheufele. What they did was ask people to read a study, and while the article remained the same, one group was exposed to civil comments, and the other to uncivil comments. What they found was striking:

In the civil group, those who initially did or did not support the technology — whom we identified with preliminary survey questions — continued to feel the same way after reading the comments. Those exposed to rude comments, however, ended up with a much more polarized understanding of the risks connected with the technology.

So seeing negative comments not only made people more skeptical of the article, it made them more skeptical of the science itself! That’s a huge concern for us, and how science is written about and discussed. Seeing negative comments, no matter how poorly written or ill-informed they are, makes people fundamentally view the science as being of lower quality. And that resulted in Popular Science closing their commenting section.

So to bring it all full circle, the “debate” was a microcosm of science and the public. Scientists sit back, do their work, and then turn around and say “Hey! You should do this” and then wonder why no one listens to them and why people fight them. We saw this with the New York soda ban, we’re seeing this in other spheres as well, and unless we change how we approach these hot button issues, we’ll lose the support of the fringe opinions (which we have already lost), but also the support of the moderates (which we can still get). I was having this discussion with my friend Steve Mann, who is one of the smartest men I know, and he sums it up best:

“It’s easier to poke fun at people with whom you disagree, particularly if you can imply that they are childish, old-fashioned, religious, or uneducated, than to honestly examine whether there is any merit to what they’re saying, and I think that’s a shame.”

I’m not taking sides – that wasn’t the aim of this piece. The aim of this piece is to tell you to listen with a open mind, discuss issues with others, and at all costs avoid ad hominem and personal attacks. If we want to bring people together, we have to avoid using language that drives us apart. If we want to promote science, we have to discourage hate. And if we want to educate others, we first have to start by understanding others.

Reference:
K. Toner, M. R. Leary, M. W. Asher, K. P. Jongman-Sereno. Feeling Superior Is a Bipartisan Issue: Extremity (Not Direction) of Political Views Predicts Perceived Belief Superiority. Psychological Science, 2013; DOI: 10.1177/0956797613494848

Learning to read the tree of life

From March 22nd to March 24th, 2013, a working group of scientists, science writers, and other experts met at the National Evolutionary Synthesis Center in Raleigh, North Carolina to discuss the state of science in the media and how to improve communication between scientists and journalists.

Evolution education is entering an exciting time: scientists are working on the Open Tree of Life — the first comprehensive tree charting the evolutionary relationships of all named species — and many U.S. classrooms are preparing for state adoption of the Next Generation Science Standards (NGSS), in which evolution and common ancestry are central. However, in order to capitalize on these developments, students will need to become competent in the surprisingly tricky skill of “tree thinking.”

Lone tree. Photo by Daveybot on Flickr (CC-BY-NC-SA).
Lone tree. Photo by Daveybot on Flickr (CC-BY-NC-SA).

Trees are one of the most powerful metaphors in art and science. For biologists, the “tree of life” stands for both the unity and diversity of life. But are students and non-scientists accurately interpreting its branches? As I’ve discussed here before, misconceptions about the mechanism of natural selection — often referred to as microevolution — are rampant. However, understanding macroevolution — the big picture of biological evolution, including the common ancestry of life and the relationships among groups of living things — may be even more difficult.

Troubles with trees

Science education researchers have been documenting students’ troubles with trees for many years. Textbooks, museum exhibits, and other learning resources are filled with a variety of tree-inspired diagrams that often represent different types of information from each other. Different diagrams may show different levels of taxa (for example, species, genera, or orders). Some may be oriented horizontally and others vertically. And they may or may not include shared traits, shared ancestors, or time. Some researchers have argued that diagrams that are not cladograms — which use a simple branching system to depict clades, or groups that share a common ancestor — are less useful and only serve to confuse. Yet even cladograms themselves are notoriously easy to misinterpret.

Image by Alexei Kouprianov (CC-BY-SA).
Two styles of cladogram depicting identical relationships. Branches can rotate around nodes without altering the meaning of the diagram. Image by Alexei Kouprianov (CC-BY-SA).

Common misinterpretations of cladograms result from reading from top to bottom (horizontally oriented cladograms) or from left to right (vertically oriented ones) and inferring either an increase in “complexity” (likely reinforced by highly problematic “march of progress” diagrams) or passage of time. Similarly, instead of following the nodes back to a most recent common ancestor, many students focus on the tips (the parts marked with taxa names) and infer that spatial closeness implies a closer evolutionary relationship.

When describing what is represented in cladograms, students focus on perceived “similarities” rather than ancestry. For the most part, the more recently two taxa shared a common ancestor, the more similarities they will have. But because of confounding factors like convergent evolution (when distantly related taxa evolve similar traits in response to similar environmental pressures) perceived similarity can be highly inaccurate, and is not what is represented in a cladogram. For a full summary of the pitfalls with an abundance of clarifying diagram examples, see evolutionary biologist T. Ryan Gregory’s review article (pdf).

The National Evolutionary Synthesis Center (NESCent) recently held a meeting to address some of the challenges in evolution communication. In response to scientists outlining the misinterpretations of trees, paleontology writer Brian Switek tweeted:

If reading across the tips of a cladogram/phylogeny is misleading, we need new imagery for #evocomm to the public.

This suggestion dovetails well with the expectations for science practices set forward in the NRC’s A Framework for K-12 Science Education (from which the NGSS were developed):

By grade 12, students should be able to:
Represent and explain phenomena with multiple types of models—for example, represent molecules with 3-D models or with bond diagrams—and move flexibly between model types when different ones are most useful for different purposes.

Perhaps if students were given a totally different kind of visual model for common ancestry to use alongside the traditional tree metaphor, they could overcome some of the difficulties and learn something about the nature of scientific modeling in the process.

A change of perspective

I met Sonia Stephens a little over a year ago at the NARST (National Association for Research in Science Teaching) annual meeting and was immediately excited by her work. As part of her dissertation in science communication, she had responded to all the conceptual difficulties that trees seem to cause by creating a digital dynamic evolutionary map (DEM).

In her paper in Evolution: Education & Outreach, Sonia explains that the map is essentially a top-down cross-section of a phylogenetic tree. Multiple cross-sections, which animate in sequence, represent different points in time. Taxa appear as dots whose relative spatial distances are determined by phylogenetic relatedness. When reading a cladogram, the intuitive impulse to infer relatedness from spatial distance between branch tips inevitably leads to error. The DEM works with this intuition, rather than against it.

Visualization by Sonia Stephens (CC-BY-NC-SA).
The Dynamic Evolutionary Map showing the present day. Visualization by Sonia Stephens (CC-BY-NC-SA).

When I asked her about what people would need to understand in order to use the map, she said:

I assumed a basic knowledge of biology, having seen (though not necessarily knowing all the nuances of) phylogenetic trees, and familiarity with at least some terminology, e.g. evolution, genes, species, etc. In order to integrate the DEM into a classroom setting, you’d want to provide more context for these concepts.

The DEM is free to use (under creative commons license CC-BY-NC-SA) and Sonia is always interested to hear from possible collaborators.

Another digital innovation on evolutionary tree diagrams, the amazing OneZoom Tree of Life Explorer, will be visualizing the Open Tree of Life. As detailed in an article on the PLOS community pages, OneZoom’s tree breaks the static, paper-bound mold — and it includes three different fractal shape options, which may prevent some types of misinterpretation. However, unlike the DEM all versions retain the branching metaphor.

Rosindell & Harmon 2012
Users can toggle between three different tree shapes in the OneZoom Tree of Life Explorer. (Rosindell & Harmon 2012).

The flexibility of digital visualization has the potential to overcome many of the obstacles to “tree thinking.” I’m looking forward to seeing research evaluating the affordances of these new tools and the development of appropriate educational supports.

References

Gregory, T. R. (2008). Understanding evolutionary trees. Evolution: Education and Outreach, 1(2), 121-137.

Stephens, S. (2012). From Tree to Map: Using Cognitive Learning Theory to Suggest Alternative Ways to Visualize Macroevolution. Evolution: Education and Outreach, 5(4), 603-618.

Communicating about evolution: the danger of shortcuts

When we talk about evolution and education, our first thoughts usually race to evangelical churches, school boards, and states like Kansas and Tennessee. While cultural battles over “belief” in evolution and its place in public schools are certainly important, a lesser-known issue is that acceptance and understanding are not the same thing, and  many people who enthusiastically “believe” in evolution don’t actually understand the basics of how it works. This may not be a problem if our only concern is that the public votes to keep non-science out of the public science classroom. But an understanding of evolution impacts more than just one hot-button issue at a time. It is necessary to understand issues surrounding antibiotic and pesticide resistance, overfishing, potential effects of climate change, the relevance of animal models in medical research, and it is the conceptual framework through which all other biological fields can be best understood.

A wide variety of evolution misconceptions have been documented in the science education research literature at all levels from elementary students through college students, museum visitors, and the general public.  The recently open-access [1] journal Evolution: Education and Outreach is an excellent resource for those looking for insights into communicating with non-experts about evolution. Evolutionary biologist T. Ryan Gregory contributed a review article (pdf) in 2009 that nicely summarizes the most prevalent misconceptions about natural selection. Others have documented learning difficulties associated with macroevolution, the relatedness of species, and interpreting tree diagrams. U.C. Berkeley’s Understanding Evolution website has a good starting list of common misconceptions related to all aspects of evolution.

Experts who do understand evolution by natural selection often use shortcuts and metaphors that are mostly harmless among those in the know. However, these same shortcuts can reinforce and even cause many misconceptions among students and members of the public without strong evolution backgrounds. Increased awareness of the science education research on evolution among teachers, informal educators, exhibit designers, documentary filmmakers, and journalists could go a long way toward preventing further entrenchment of these misconceptions.

I’ll attempt to outline some of the major misconceptions and learning difficulties related to the mechanism of natural selection and discuss some common ways of talking about evolutionary processes that can reinforce these misconceptions.

Darwin's Finches
Darwin’s finches or Galapagos finches. Charles Darwin, 1845. U.S. public domain.

Fitness and “survival of the fittest”

To evolutionary biologists, fitness has a very specific meaning: the number of offspring left by individuals of a species having a certain genetic makeup compared to other individuals with different genetic makeups. A recent “daily explainer” on i09, “Why ‘survival of the fittest’ is wrong,” tackled some of the issues wrapped up in this word. The colloquial usage of “fit” as “big, strong and healthy” [2] makes the phrase misleading. And evolution isn’t really about survival at all. It’s entirely about reproduction. Often living longer can mean more chances to mate, but survival only contributes to evolutionary fitness inasmuch as it enables an increase in successful reproduction events. An organism that lives to the upper limit of its lifespan — but never successfully reproduces — contributes exactly nothing to the next generation.

Populations and generations

The mechanism of natural selection is based in population thinking. To an expert, a population is a group of organisms of the same species that interbreed and that live in the same geographic area. Importantly, it is not an equivalent term to species. However, most non-experts do not think in terms of populations. They think in terms of individuals, species, or ecosystems. This translates to mistaken assumptions about what evolution acts on. Many people think that evolution happens to one individual during its lifetime, or that entire species (including all the individuals) gradually change into new species. Again, shortcuts such as “over time, the finches gained bigger beaks” can reinforce the idea that all members of the species grew bigger beaks. A better statement would have been “over many generations, finches with large beaks had more offspring than finches with smaller beaks, until nearly the whole population had large beaks.”

Adaptation

Adaptation is nearly ubiquitous as a “vocab” word for elementary-age students, before they understand anything about genetics. Students are expected to learn that an adaptation is something along the lines of “a trait of an organism that helps it survive in its environment.” This often devolves into “just-so story” explanations about how beavers have big teeth because they chew on trees all the time, or giraffes have long necks because they are always reaching high into the trees for food. It doesn’t help that journalists, teachers, and lecturers often use colorful metaphorical shortcuts to talk about adaptation. While their intention may be to create a lively article or talk, an expert’s metaphor is often a non-expert’s reality.

In his review article, Gregory highlights some of the problematic language used to describe adaptation:

Thus, adaptations in any taxon may be described as “innovations,” “inventions,” or “solutions” (sometimes “ingenious” ones, no less). Even the evolution of antibiotic resistance is characterized as a process whereby bacteria “learn” to “outsmart” antibiotics with frustrating regularity.

Human tendency to anthropomorphize everything from animals to inanimate objects and natural processes is well known, and tough to combat. (See Heider and Simmel’s 1944 experiment in which people assign intentions, emotions and even genders to moving geometric shapes.) In the context of evolution anthropomorphic descriptions can lead to the misconception that individual organisms try to modify themselves to better fit the environment, and then pass down those acquired traits to their offspring. A shaky understanding of genetics also underpins this idea, but sloppy communications can reinforce it.

A focus on adaptation from the early grades forward can also lead to the idea that each organism is perfectly adapted for its particular environment and niche, and that every feature of an organism has an adaptive purpose. Evolutionary biologists know this simply isn’t the case. Most traits that we call adaptations are simply “good enough.” They were a little more useful in a given circumstance than other traits — they weren’t designed from the ground up for the current situation. Learning about adaptation — and developing misconceptions about it — before grasping the genetic, generational mechanism of natural selection can put students at a disadvantage when they get to middle and high school biology classes.

Unity and diversity: a two-step process

As Gregory emphasized in his review article, evolution by natural selection is a two-step process: (1) new variation arises by random mutation and recombination, and (2) individuals with certain variants have more offspring than other individuals with different variants. Focusing on either mutation alone or selection alone can lead to the following misconceptions, respectively: that evolution is completely random, and that evolution results in perfectly optimized organisms. When communicating about evolution with non-experts, it is important never to refer to one without referencing the importance of the other.

Evolution is tricky. For those of us who understand it, its power to make everything else in biology crystal clear is deceptive. Most of us had naive ideas about evolution as children or students. As we progressed in our studies of science these were replaced with more accurate mental models. But we are the exceptions — most people don’t go on to major in science or think about it for a living. Yet as citizens they are often called upon to make decisions that require an understanding of evolution. And as humans, an understanding of evolution can contribute to a deeper appreciation of nature. Shortcuts are catchy — droning on about populations and generations can get tedious and wordy. It takes talent to communicate about evolution both accurately and compellingly, but experts and science writers and educators have a responsibility to get it right.

[1] Evolution: Education and Outreach used to be open-access, then it was toll-access, and now everything from January 2013 onward is open-access, but you’ll still have trouble getting the older issues.
[2] Amusingly, the British meaning of “attractive” for “fit” is actually a little more accurate in cases of sexual selection — though we’d still have to change it to “Reproduction of the Fittest.”