Twisted Tree of Life Award: NPR on the Evolution of Crying

Well, normally I really like NPR science stories. But this one dug into my anti adaptationism feelings. Adaptationism is, in essence, the practice of saying something must be adaptive (i.e., beneficial), simply because it is there in an organism. Such cases are also referred to as "just so stories" - a play on the old Kipling "Just So Stories".  That is, in essence, people who claim something is adaptive just because it is there are in essence telling you something is this way because it is just so.   I am actually not sure of the whole history of using the just-so analogy to refer to adaptationist stories - I know Stephen Jay Gould discussed this a lot in his books and lectures, but not sure who first did it. 

Anyway - NPR has an adaptationistic doozy from Morning Edition: 

Teary-Eyed Evolution: Crying Serves A Purpose : NPR

Basically, it seems the gist of the argument here is the following line:

Scientists who study evolution say crying probably conferred some benefit and did something to advance our species — because it's stayed with us.

Wow - that is like straight out of the adaptationist playbook.  The problem with this argument is that many things exist and persist in organisms even when they are not adaptive.  There are many reasons why this can happen from constraints (e.g., if bones were not adaptive in humans it would be pretty hard to get rid of them) to  invisibility to selection (e.g., some features that only show up after reproductive age may not really influence fitness) and so on.

In essence the NPR story is one of the worst examples of adaptationism in the good science press I have seen in a while.  Sure this shows up all over the place.  But rarely this bad at NPR.  The story ends with an even worse line than the rest

Maybe that's another reason evolution kept humans weeping: Tears help reveal the truth. And that's because along with the tears, we've evolved a very sophisticated ability to interpret them.

Yes that is right.  Crying has been maintained in humans because we also evolved another adaptive feature - the ability to interpret tears.  So the logic here is that crying is adaptive because it is needed for another adaptive trait for which there is no evidence it is adaptive.

So for their story on crying and for in essence inventing some just so stories to explain why they think it is adaptive, NPR is the recipient of my Twisted Tree of Life Award.  Previous recipients are

• Twisted tree of life award #6: Scientific American Origins piece for dissing microbes
• Twisted tree of life award #5: Nicholas Wade & use of higher, lower, ladders, etc
• Twisted Tree of Life Award #4: Hoxful Monsters Blog on "Primitive" Animals
• Twisted Tree of Life Award #3: The Columbus Dispatch on Ancient Bacteria
• Twisted Tree of Life Award #2: Science Friday on the Five Kingdoms
• Twisted Tree of Life Award #1: Salk Institute Press Release on Kinases

See also these things for some stuff on evolution of crying:

• Darwin in the Crib - oldie but goodie from Carl Zimmer in 2005
• Zimmer's NY Times article related to the above. 
• A Critique of the Adaptationist Programme from Larry Moran at Sandwalk
• My Evolution textbook has some discussion of 

Story behind the science: #PLoS Genetics "Evolutionary mirages" paper

So there is this cool new paper out in PLoS Genetics: Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers. and I have wanted to write about it for a week or so. You see, the paper is about something I have been interested in for most of my career - how the particular processes by which mutations occur can sometimes be biased (i.e., some types of mutations are more common than others) and that these biases can create highly ordered patterns in genomes and in turn that observation of these ordered patters can sometimes be misinterpreted as being the result of adaptation. Mistaken claims of adaptation in genomics are a favorite topic of mine - and let me to create (with tongue in cheek) a new omics word - Adaptationomics.

Anyway - so I really really like this paper. But there is a week bit of a problem in writing about it. You see, it is by my brother, Michael Eisen, a Prof. at UC Berkeley (and a student in his lab Richard Lusk). And, well, I don't want to say anything wrong or stupid about the paper since, well, my brother will be pissed off. And so I have not written about it yet. But then I realized the best way to write about this one is to simply ask my brother for the "Story behind the science" for the paper, as I have been doing for some other recent papers.

If you want a summary of the paper, here it is in their own words:

Authors summary: Because mutation is a random process, most biologists assume that apparently non-random features of genome sequences must be the result of natural selection acting to create and preserve them. Where this is true, genome sequences provide a powerful means to infer aspects of molecular, cellular, and organismal biology from the signatures of selection they have left behind. However, recent analyses have shown that many aspects of genome structure and organization that have traditionally been attributed to selection can often arise from random processes. Several groups—including ours—studying the sequences that specify when and where genes should be produced have identified common, seemingly conserved, architectural features, based on which we have proposed new models for the activity of the complex molecular machines that regulate gene expression. However, in the work described here we simulate the evolution of these regulatory sequences and show that many of the features that we and others have identified can arise as a byproduct of random mutational processes and selection for other properties. This calls into question many conclusions of comparative genome analysis, and more generally highlights what Michael Lynch has called the “frailty of adaptive hypotheses” for the origins of complex genomic structures.

Conclusions: Lynch has eloquently argued that biologists are often too quick to assume that organismal and genomic complexity must arise from selection for complex structures and too slow to adopt non-adaptive hypotheses. Our results lend additional support to this view, and extend it to show that indirect and non-adaptive forces can not only produce structure, but also create an illusion that this structure is being conserved. We do not doubt that many aspects of transcriptional regulation constrain the location of transcription factor binding sites within enhancers. Indeed a large body of experimental evidence supports this notion, and we remain committed to identifying and characterizing these constraints. But if this process is to be fueled by comparative sequence analysis, as we believe it must be, it is essential that we give careful consideration to the neutral and indirect forces that we now know can produce evolutionary mirages of structure and function.

I must say I love the title lead in "Evolutionary mirages" which is another but much better way of saying "Adaptationism is a bad thing".

Anyway, before I get in any more trouble, here are some words about the paper from the Senior Author, Michael Eisen, my brother. Questions by me (I know, not very creative ones - but they will have to do):

Kudos to New Scientist's "24 myths and misconceptions" about evolution

New Scientist has a pretty good article on myths and misconceptions about evolution (see Evolution: 24 myths and misconceptions).

They really hit on many of my pet peeves on evolution. Among my favorites:

• Everything is an adaptation produced by natural selection
• Natural selection leads to ever-greater complexity
• The bacterial flagellum is irreducibly complex
• Darwin is the ultimate authority on evolution

Many of these fit in well with my Adaptationomics Award which I will start giving out again soon ....

Forget McCain - the Real Problem in the New York Times - Adaptationism

Unlike McCain and his followers, generally, I really like the New York Times, especially the Science articles. But they do continuously irk me in one area - they repeatedly include lame adaptationistic evolutionary arguments. Now I am not the only person in the bloggersphere railing against people who say something MUST be adaptive simply because it is there (Larry Moran is the most persistent and interesting critic of adaptationism out there).

This week the Times has a doozy in the article on "Play" from the Sunday Magazine. In the article, Robin Henig writes

"If play is an extravagance, why has it persisted? It must have some adaptive function, or at least a benefit that outweighs its cost, or it would have been winnowed out by the forces of natural selection."

This is nearly a PERFECT adaptationistic line. And more importantly, it is simply not true. Some things persist in biological systems even when they have a cost that outweighs the benefit. And other things persist when they are neutral. Now I am not saying one way or another whether play has a benefit (the article is interesting and reasonably sound in many ways). But such statements as the one quoted above show a common misunderstanding of evolution. Evolution is NOT only about beneficial things persisting and detrimental ones going away. It is much more complex and interesting in fact. If you want to learn more about the perils of adaptationism, go to Larry Moran's blog. He really has some good stuff on it. Or go to the great gurus themselves - Gould and Lewontin.