Thursday, April 21, 2022

Anything but the line-up

You all know I’m always pondering how progressive thinking sneaks into how we talk about evolution.  And how if we could break some of these habits, we might begin to dismantle the ladder-of-life, which is so deeply engrained. Here is a common thing I see in lots of science communication that I think is one of these (relatively) easy to break habits – lining up some organisms when you talk about how some *trait* evolves. Let’s say you were talking about the evolution of multicellularity and went with a diagram like this:

 Evolution of Multicellularity

Show this and the audience is likely to walk away with any number of ladder-y misconceptions. Or feel that any ladder-y notions they came with are totally fine. Like humans evolved from 'simple' things like bacteria. Like being unicellular is less ‘advanced’. Like humans are the most complex, really impressive, best species so evolution has stopped. We could go on, but what would be some ways to dismantle any of these and still talk about what we wanted talk about? Here’s an easy one – refocus on the character states!

Now this is still feeling pretty progressive, but perhaps the notions that some living taxa are ancestors of other living taxa are disrupted a little? I also suspect that labeling these states might trigger us to wonder about the evolutionary complexities here. How many times have these kinds of transitions happened? Is evolution really so directional or can lineages revert to being unicellular? Are these states fairly thought about as bins or is it more of a continuum? Now this, this is really thinking about evolution. Understanding such character transformations was a primary motivation for developing phylogenetic methods in the first place!

And in fact we have plenty of information to suggest that the stepwise directional path above is not right. We know that there have been evolutionary transitions to and from multicellularity. There are plenty of lineages where we have a heck of a time trying to classify them because the cells sometimes stick together and sometimes go their own ways. So if we are going to be fair, it’s probably more like a spectrum or even something non-linear altogether. What’s for sure is that we will never understand the diversity of life forms, nor how and why this diversity came to be, if we enter with the ladder-of-life mindset at the top.

My broader point here is to say we do our field no favors by playing on misconceptions. I get it, we want to make things simple, draw on ideas that will ‘click’ with audiences. But we are selling evolution so short when we do it.  I am convinced that any talk or paper can be just as compelling, if not more, by stepping away from the linear narrative. I know we can handle breaking the norms and our audiences can too.

Sunday, April 8, 2018

Tree responsibly: Part 2

In part 2 of this series, I want to talk about how we can draw trees that promote tree thinking instead of undermining it. But first let’s consider whether we can or should worm our way out of this possibly time-consuming task. You might say, well, I just draw the trees – it’s the viewer’s job to interpret them correctly.* However, it is well established that the many members of any audience (whether students or practicing scientists) are not trained in tree-thinking and will come to incorrect conclusions about what a tree is meant to convey. 

The other option is to warn the audience that the way the tree is drawn is likely to evoke some misconceptions. Indeed, this is essentially the approach taken on the evogeneao website, which has an interactive tree of life and other teaching resources. This page has a long section about distortions and limitations that explains that their tree is drawn to tell the human’s story and thus makes it look like evolution is goal-oriented (with the goal being humans). I'm glad they included this section and it may provide its own learning goal (leading the reader to say, how does this tree make me think that? How could it be drawn not to make me think that?). But I remain nervous that readers won’t scroll and dig into what may be viewed as details, details. So my opinion is that if we want readers to interpret trees correctly, we should actually draw them in ways that dispel misconceptions and encourage correct interpretation.  Here are some of my suggestions and related thoughts:

First, those of us that spend a lot of time wandering the phylogenetics literature know that trees more often look like what’s on the left than what’s on the right.

Tree on the left adapted from here.  

And what’s on the right looks a lot more like what’s in textbooks, review articles, and popular science.  So guess what’s in the middle?  People making choices about which taxa to show, how to draw the tree, and what story they want to tell with the tree.  Given that, let’s talk choices.

Ladder-y versus ultrametric

Both of the trees above have the same topology (implying the same set of relationships), but the one on the left is much more likely to trigger ladder-thinking because some of the tips are higher and others are lower.  The easy fix is to make the tree ultrametric, as on the right, helping to communicate that all taxa are extant (as they are in this pretend example) and that all have continued to evolve towards the present. 

We also choose which taxa to include, and by simply choosing those which make our trees a little more balanced, we can make it harder to view any tip as ‘basal’. Berkeley's Understanding Evolution site has a quite a few other nice tips for making trees that are less prone to misinterpretation.

Maximally unbalanced versus more balanced (oh and I rotated it at one node)

So now a suggestion that is possibly more painful, which is that those of us that estimate phylogenies take on more of the burden of creating education-friendly, misconception-fighting, biology-celebrating tree diagrams. Work on flatworms? Awesome! Make a lively worm-y phylogeny for your homepage that can be freely downloaded and shared. Put it on your lab t-shirt! Put it in the corner of your lab posters! Take it to outreach events! I know that most of us phylogeneticists are not graphic designers, but I think the dividends to come from one glorious, engaging figure are worth the time (and/or monetary investment). And we have such a long way to go to outnumber the 'march of progress' type images that dominate the representation of evolution.

And my last thought is just that I wish that some kind programmer would make a truly easy piece of software to draw trees for educational purposes. Because if you are wondering what I do to make tree figures for teaching (and blogging), I create a pretend dataset in Mesquite and manipulate the tree to fit my purposes. Which sometimes require tinkering in Illustrator. Most teachers don’t have the time to learn Mesquite solely for this purpose, much less the funding for Illustrator licenses. Please feel free to reply to this blog if there are programs you think meet this need.**

In closing, thanks (I guess) to Matt Hahn for trolling me with tree figures to provoke me into writing about this.


*And a few years ago that was more or less my view. We can’t ‘protect’ everyone from seeing trees that foster misconceptions, so it’s better that we teach them how to read trees. We certainly do need to do the latter, but it’s not enough. People who are experts in this area also think so.

**I am aware of FigTree and TreeEdit, but I still think these are probably too fiddly as they require a user to start with a tree file. I’m picturing more like the user says, "I need X tips" and then they move the branches, annotate branches with words, change formats, etc. Mesquite can do most of theses things, but having taught with it, I don’t think it’s reasonable to expect a teacher to wander through the menus just to make a vertebrate phylogeny that’s less ladder-y than what is in the textbook. I also don't think it would be fair to put all the burden on Mesquite, which already serves many needs in the systematics community and does so beautifully. Maybe someone who is good at Java could make a MesquiteLite to pull out and adapt the drawing tools. Even better if it could be an interactive website that students could use! But I'm getting ahead of myself...

Tree responsibly: Part 1

A few years ago I was at a talk that opened with an evolutionary context for the study and had a tree that looked about like this:

I thought ruh-roh, I feel some basal-ancient-ladderness coming on.  And sure enough it was primitive [living] taxa from there on out. This got me thinking about the relationship between tree drawing and tree thinking. This relationship is well established in the science education literature, which has demonstrated that certain tree formats are more likely to trigger misconceptions about evolution (e.g., Novick et al. 2011). Viewers are likely to see the tips that are literally 'lower' on a tree like the one above as being evolutionarily lower*.  Moreover, they are likely to interpret this diagram not as a branching history but as a replacement series with a progressive evolutionary story.  Heck, it is almost begging readers to view evolution as a timeline. If you let it keep slipping, that’s right where you end up.

Going, going, gone.

It is then a very short hop for viewers to interpret that ‘tree’ as something like this.

As I have argued before, this terrible depiction of evolution and its many off-shoots (like this) are not only misleading but downright dangerous. Not to beat a dead horse, but none of the other extant apes (e.g., gorillas, chimps, bonobos) are our ancestors, as implied by this figure (see this great blog by Fabio Mendes for a more complete discussion). In fact, we can’t even be very sure which of the many extinct hominins actually sits on the lineage that gave rise to Homo sapiens (i.e., actually could be correctly referred to as an ancestor).

In exploring the relationship between tree diagrams and tree-thinking in science ed research, there has been a strong emphasis on diagonal trees versus rectangular trees, which often go by “tree” and “ladder” format, respectively. I prefer to stick with diagonal (as in the top diagram) and rectangular (below), because let’s be honest, a rectangular tree can be made to look just as ladder-y as a diagonal tree.

                                                       My Ladder-y Rectangular Tree

What is scary to me is the ladder-y trees seems to be exploding, faster than stick-in-the-muds like me can complain about how they trigger evolutionary misconceptions and make the jobs of evolutionary biologists even harder. Worse yet, these ladder-y trees are often presented the context of trying to expand access to information about phylogenies and evolution. I won’t enumerate them here, but let’s just say that I’ve got sort of a mental burn-book of phylogeny figures that fall in this more-harm-than-good zone**. In part II of this blog entry, I’ll talk about how I think we can improve the state of affairs.

*This is not a thing. Calling a group of organisms 'lower' is just as nails-on-a-chalkboard to me as basal.

*(I realize that I'm making tons of weird hyphenated adjectives today.  That's why it's just a blog.

Monday, July 3, 2017

Moving the needle

[Note, this post is not about phylogenies]

I’ve sensed some ‘what’s-the-big-deal’-ness in response to recent discussion about inappropriate behavior at the recent Evolution meetings, so I want to explain why I take this so seriously. I think you should care too, assuming you are interested in making science more diverse and inclusive.  I’ll speak from my own experience here, making this a perhaps uncommonly personal post.  First, I should say that I have been lucky throughout my career to have exceptional mentors (both men and women) who strongly encouraged my interest in science and always made me feel supported.  But early on, it became apparent to me (and my female peers) that being a woman in science was going to present extra challenges. None of my experiences are unique and I have colleagues who had a much harder time*. One thing it seems like we all discovered was the amount of caution that was needed in interacting with male scientists, especially senior ones.  Being friendly was sometimes taken as openness to flirtation, which could escalate to unwanted touching or worse. So as young woman in science, I learned how to tread carefully and how to be friendly but divert conversations when there were red flags. I learned what the flags are (“looks like you’ve been working out!” or “why is someone like you single?”**). I learned to avoid places and situations where inappropriate behavior is likely to happen, even if it meant sometimes missing out on networking***, and I found friends with whom I could safely discuss these issues. Friends who understood that it’s not as simple as ‘not putting up’ with bad behavior, especially from senior scientists in a community that is so tightly woven through letters of recommendation, reviews, grant panels, and committees.

For me, these social acrobatics became part of the fabric of interacting with other scientists. Another skill like presenting posters, or making aesthetically appealing slides.  It wasn’t until a few years ago that I realized how much mental and emotional energy I wasted on these acrobatics as a younger scientist. Energy that I could have devoted to science or something else! Energy that some of my peers never had to spend****. Now that I am a faculty member, inappropriate behavior towards me has become less common, but I worry for my students and other young scientists. I wish I could prevent unprofessional behavior from clouding their experiences. I wish I could save them from the wasted energy of handling those who behave inappropriately. I wish I could keep them from ever having to become social acrobats themselves. They shouldn’t have to. But it doesn’t seem like things have changed that much in the 16 years I’ve been in this field. For my mentees, I try to prepare them, let them know that I know it happens, welcome them to come talk with me about their concerns, and ask them to brainstorm with me on how to make things better.  With regard to the Evolution meetings, the Society for Systematic Biology has called for suggestions. I’m hoping that together we’ll come up with ideas that could actually move the needle.

*To get a sense, peruse the nearly 900 responses to Gina Baucom’s post about crappy things said to or about women in academia.

**I know that these may seem incredibly obvious but when it’s someone senior, someone you respect, and someone that you would never imagine would hit on you, it takes a while (at least for me) to realize what it is.  I have learned now to look past rank and listen to my gut.

***If we want access to science for everyone, no one should have to make these choices.

****These are my experiences but I imagine the same goes for other underrepresented groups in STEM.

Monday, May 15, 2017

Back to the future

One of the most pervasive carryovers from ladder-of-life thinking is that some living species are older than others.  These are often thought of as sitting on the lower rungs of the ladder.  Of course, tree-thinking rejects this notion as all living species have evolved the same amount of time from their shared common ancestor at the base.  Nonetheless I hear so many phrases that reflect the continuing influence of ladder-thinking, even among evolutionary biologists.  So here's a good one - 'That trait goes all the way back to echinoderms' [or insert any taxon perceived to be old]. The speaker almost certainly wanted to communicate that the trait was present in the common ancestor of echinoderms and vertebrates.  So what's the problem with using the shorthand 'back to echinoderms'?  Well, it suggests that an echinoderm was the common ancestor of echinoderms and vertebrates (not true even if that ancestor *looked* more like an echinoderm) and/or that echinoderms haven't been evolving since their split with other deuterostomes.  This is particularly dangerous as it often leads to poor experimental design --  using living species perceived to be old or primitive as stand-ins for ancestors.  Certainly studying echinoderms can help us make inferences about that common ancestor, but so would studying any other descendant.

So in summary:

p.s.  I think it would be a little better to say 'out to echinoderms' -- if your listener assumes humans are starting point, then going 'out' to echinoderms spans the clade that captures both humans and echinoderms, which maps to a particular ancestral node.  But why not just use a couple more words and say the trait was present in the common ancestor of deuterostomes.

Sunday, May 7, 2017

Naming nodes

A friend texted me today to share a ‘crazy’ biology fact – that ‘a slug is not a critter but a fungus’.  Of course, I had to protest immediately.  A slug is not a fungus, it is a mollusk! (Which I guess would colloquially be a critter?)  This interchange made me think about how that kind of statement translates for an evolutionary biologist.  When we say, a [species] is a [taxonomic group], we are saying, that species belongs to a clade, a branch of the tree of life, that we have given a name.  So it’s really a statement about evolutionary history.  A slug does not belong to the clade that we call fungi.  A slug is in the mollusk clade, which is a branch of lophotrochozoans, which is a branch of animals, which is a branch of eukaryotes, etc.  So a slug *is* all of those. The limit on the number of these statements is only the number of nodes (and corresponding clades) which we have assigned names.  Since all species share common ancestors back in time, at some point, the slug’s history will intersect with the fungus; that is, we will eventually arrive at a node which sits along both of their evolutionary histories.  Currently, this node is the opisthokonts, whose descendants are eukaryotes with a single posterior flagellum.  Naming these nodes give us a handy way to remember traits that the species belonging to that clade possess (although some may have subsequently lost those synapomorphies).  So then you might wonder, how do we decide which nodes to name?  Anyone who publishes a phylogeny is free to name any node they wish, although typically only nodes that are well-supported by various sources of evidence would be named.  Among those with good support, authors often pick those that correspond to some previously named group (like a genus) in order to carry that information (whatever characteristics originally resulted in the group's description as a separate genus). Many nodes however don’t contain members that had a traditional name (pre-phylogenetics), but nonetheless correspond to a group with some distinctive features, like the Opisthokonts.  Thus, taxonomy and classification return to the same principles that have long guided the field – that names function to convey information about organisms – about their evolutionary history (their relatedness to other organisms) and their traits.  In this sense, naming is a choice -- about which information we think is interesting or important to communicate. I always think if bacteria were doing the taxonomy instead of humans we would have many fewer named nodes within the animal clade and many more along branches in their part of the tree.

P.S. The title 'naming nodes' will only be entertaining to those of you who are also fans of Best in Show.  Taxonomy is a far more valuable endeavor than naming nuts, but certainly less funny.

Friday, December 2, 2016

The phylogenetics of equality

In previous articles (here and here*), I have argued that understanding phylogenetic trees is a core part of understanding evolution, and thus biology as a whole.  My last blogpost emphasized that using terms like basal and early-diverging to refer to taxa misrepresents what phylogenies communicate, and therefore leads to misunderstanding about how evolution works. I would guess that at least some readers thought, "Well is that so bad?  So what if I casually talk about a group of species as basal, and some in the audience incorrectly take this to mean less evolved? I just mean to say that they have retained some ancestral character states that I am interested in, and saying 'basal' as a shorthand is convenient."

Here I'd like to stress that contributing to ladder-of-life thinking** with sloppy tree-speaking has real tangible consequences, that we should take seriously, not just as biologists, but as citizens. Today Dan Lowe, friend in political philosophy sent me this article, written by a group of political scientists. They conducted a survey in which they asked 2000 participants (who were all white) to rank how 'evolved' they believe blacks and whites to be using a 0-100 scale placed below a popular depiction of the "ascent of man", an image which undoubtedly stirs up ladder-of-life thinking.***

Thirty-eight percent of the respondents rated blacks less evolved, with rationales including being more 'closer to' or 'like animals'.  The researchers report being surprised by these results, but I am not at all surprised.  Not just because we know that racism is prevalent in our country, but also because the public understanding of evolution, and particularly common ancestry, is depressingly low. 

Anyone who has been taught evolution (including tree thinking) should protest, no humans could ever be considered less 'evolved' than any other! All humans are more closely related to each other than to any other species, so none of us is 'closer to animals'! Anyway, all of us are animals. We belong to a branch of the tree that we call animals, and we are all equally related to other animals. Moreover, it is meaningless and biologically incorrect to consider any group of living organisms primitive or 'less evolved'. The real danger of any suggestion otherwise is that there is some biological or evolutionary rationale for racism.  We must be emphatic that there is not. 

Right now, many of us are thinking, what can we do to celebrate diversity and support inclusiveness? Here's one thing.  We can teach evolutionary biology and teach it well.  We can make a point to state that humans are part of evolutionary history just like everything else on the planet and the same principles that apply to other living organisms apply to us, too.  Just as we, as humans, are not more 'evolved' than a fern, none of the populations of humans are any more evolved than any other.

p.s. Thanks to Scott Taylor for comments.

p.p.s. Hateful comments in response to this post will be deleted.

*full text versions available from my website

**ladder-of-life thinking = thinking that promotes the idea that some species are more primitive (less 'evolved') than others; is associated with the ladder-of-life or the great chain of being (scala naturae), in which species are ranked from least to most evolved.  The ladder-of-life is not consistent with the tree-like structure of evolution. Although it has been rejected since Darwin, the vestiges of progressive thinking remain and are the source of many misconceptions regarding phylogenies. 

***I think I am going to have to write a post just about this depiction, and probably I'll make a new version, with a tree and all rotated around, that would have the opposite effect, i.e. stimulate tree-thinking instead of ladder-thinking.