Category Archives: biology

biology, Darwin Eats Cake, evolution, Politics, science

Antibiotic resistance and corporate agriculture

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So, over the weekend, Nicholas Kristof wrote a nice piece in the New York Times in which he laid out the basic facts and statistics regarding the cavalier use of antibiotics in agriculture. His column is full of interesting (i.e., depressing) figures, one of the most striking of which is that the agricultural use of antibiotics in the state of North Carolina exceeds the medical use of antibiotics for the entire United States.

Anyway, the basic punchline is this: when someone in your family is hospitalized or killed by some food-borne, antibiotic-resistant pathogen, you can thank the huge agricultural corporations and the millions of lobbyist dollars they have spent blocking food-safety legislation.

Happy eating!

These full-page comics come out badly here on the blog, so to see a more readable version, go to the Darwin Eats Cake website.

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Sørensen SJ, Bailey M, Hansen LH, Kroer N, & Wuertz S (2005). Studying plasmid horizontal transfer in situ: a critical review. Nature reviews. Microbiology, 3 (9), 700-10 PMID: 16138098

biology, Darwin Eats Cake, evolution, evolutionary psychology, science

Traffic, preterm birth, and adaptationism

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So, here’s a thing:

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This relates to a criticism that I made of evolutionary psychology, but which applies to many naive adaptationist arguments: it is easy to come up with a plausible-sounding adaptive explanation of just about anything. In most cases, it is equally easy to come up with an equally plausible-sounding explanation of the exact opposite phenomenon.

Barnett AG, Plonka K, Seow WK, Wilson LA, & Hansen C (2011). Increased traffic exposure and negative birth outcomes: a prospective cohort in Australia. Environmental health : a global access science source, 10 PMID: 21453550

biology, evolution, science, video

1971 Canadian Evolution Video

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So, do you remember 1971? Me neither. As I understand it, everyone was on drugs. And in Canada, they were all on METRIC DRUGS!!

This video is a little on the long side for the 2011 sensibility, but is pretty awesome. There are a couple of the things in particular that I like about it. First, most videos that I have seen illustrate evolution by having organisms transform. You know, like you have the fish who swims to the edge of the land, wriggles out, and grows legs. Unfortunately, I think that can reinforce two surprisingly common misunderstandings about evolution: (1) that it involves organisms changing adaptively during their lifetimes, and (2) that it involves a degree of intentionality.

That’s not so say that those video makers misunderstand the evolutionary process, just that the most common way of presenting the process to a broader audience lends itself to a particular misinterpretation.

In this video, novel forms arise as offspring, often to the noticeable surprise of their parents. Also, some of those novel forms are adaptive, while others are not.

Here’s the second thing. Videos like this always face a challenge: how do you illustrate mating and reproduction without traumatizing the children? This video comes up with some awesome mating procedures, from eyeball things smashing into each other to a system that involves the male blowing into the female’s nose.

Confidential to my wife: I’ve got an idea for later.

biology, culture, evolution, science

More on Nowak et al at the Chronicle

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So, an article has just come out this morning in the Chronicle of Higher Education covering the controversy over the Nowak et al Nature paper attacking kin selection. I’ve written about the paper twice previously, once here, providing an xtranormal video dramatization of the issues, and once here, trying to provide some context to explain why so many people had gotten up in arms about this particular paper (as opposed to the hundreds of scientific papers published every year that are equally wrong).

Unfortunately, the article is behind the Chronicle’s paywall, so you may not be able to read it. (I don’t know if they permit the same sorts of work-arounds that the New York Times does.)

The thing that most strikes me in the article comes at the end:

Right now Mr. Nowak is working to understand the mathematics of cancer; previously, he has outlined the mathematics of viruses. It falls within his career mission to “provide a mathematical description where there is none,” he says, a goal at once modest and lofty. He would also like to write a book on the inter­section of religion and science, a publication that would no doubt further endear him to atheists.

He knows that the debate on kin selection is far from over, though he sees the ad hominem attacks as a good sign. “If the argument is now on this level,” he says, “I have won.”

along with this comment from Smayersu

Science is written in the language of mathematics. Why is it that the biologists cry “foul” when the mathematicians and physicists investigate the theory of evolution? The biological community should welcome the help of those who are trained to examine problems from a rigorous mathematical perspective.

Two things.

First, the criticism of Nowak had nothing to do with his providing a mathematical framework. In fact, most of the people who have criticized Nowak are, themselves, mathematical biologists. The issue is that the paper discounts and misrepresents a huge body of mathematical work. In fact, while Nowak has written a number of interesting and original papers, he has also written a number of papers in which he claims to “provide a mathematical description where there is none,” the problem being that in many cases, there actually is a mathematical description. Often quite an old one.

It is as if I were to write a paper that said, “You know who was wrong? Albert Einstein! Because, look, Special Relativity does not work when you incorporate gravity. So I’ve created a new thing that I call “Generalized Relativity.”

Second, it is absolutely true that ad hominem attacks do not constitute legitimate scientific criticism. However, the fact that some of the attacks on Nowak have been ad hominem certainly does not constitute evidence that he is right.

To my mind, the relevance of the ad hominem attacks is this. They reflect a deep sense of frustration on the part of the field towards Nowak and his career success. Nowak has repeatedly violated one of the basic principles of academic scholarship: that you give appropriate credit to previous work. And yet, the academic system has consistently rewarded him over other researchers who put more effort into making sure that they are doing original work and into making sure to credit their colleagues.

It is as if, after publishing my paper on Generalized Relativity, I were to be awarded tens of millions of dollars in grant money and a chair at Harvard, while the legions of physicists pointing out Einstein’s later work were ignored. I’m guessing that I might find myself the subject of some ad hominem attacks, but it would not mean that I was right.

As a colleague of mine commented this morning, “ah, Nowak thinks he’s won because of the ad hominem attacks. by that standard, Donald Trump must be a serious presidential candidate.”

Nowak, M., Tarnita, C., & Wilson, E. (2010). The evolution of eusociality Nature, 466 (7310), 1057-1062 DOI: 10.1038/nature09205

Behavior, biology, neuroscience, science

Study sheds light on coming robot apocalypse

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So, in many of the standard narratives, the robot apocalypse is triggered when the machines figure out that humans are fundamentally flawed, or because their self awareness produces an instinct for self defense.

Well, a new paper just out in Biological Psychiatry describes an experiment in which researchers successfully teach a computer to reproduce aspects of schizophrenia. This raises the possibility of an alternative scenario: the machines just go crazy and start killing people, Loughner-style.

After suffering from paranoid delusions, Skynet sends Vernon Presley back in time to kill his own grandfather, or something.

Actually, the paper reports a study in which a computational (neural network) model is used to examine eight different putative mechanistic causes of a particular set of symptoms often seen in schizophrenia: narrative breakdown, including the confusion of autobiographical and non-autobiographical stories. This models one putative source of self-referential delusions.

The basic setup is that the researchers use an established system of neural networks called DISCERN. The system is trained on a set of 28 stories. Once the system is trained, you can feed it the first part of any one of the stories, and it will regurgitate the rest of the appropriate story.

Half of the stories are autobiographical, everyday stuff like going to the store. The other half are crime stories, featuring police, mafia, etc.

The experiment is to mess with the DISCERN network in one of eight different ways. Each of the eight types of perturbation is meant to instantiate a neural mechanism that has been proposed to cause delusions in schizophrenia. Then, the researchers feed the computer the first line of a story and look at the magnitude and nature of the errors in the output.

Models were evaluated by their ability to reproduce errors seen in an experimental group of subjects diagnosed with schizophrenia. Basically, they are interested in finding perturbations that mix up different stories, so that the “I” of the autobiographical stories becomes associated with the gangsters and police in the non-autobiographical crime stories.

Two of the eight perturbations performed significantly better than the others:

  1. Working memory disconnection: Connections within the neural network that fell below a certain threshold strength were discarded.
  2. Hyperlearning: During the backpropagation part of the neural network training, the learning algorithm overreacts to prediction errors. After DISCERN was trained, hyper-trained for an additional 500 cycles.
These two were then further extended, with the addition of a parameter to each, at which point the modified hyperlearning model outperformed the disconnection model. 
So, what to make of it?  It seems like an interesting piece of work. It is hard to know how much light this sheds on schizophrenia, since the brain is a heck of a lot bigger and more complicated than this model. And, well, sometimes things scale up in the straightforward way, and sometimes they don’t. 
What one hopes will be the outcome of this sort of work is that is will prompt additional research. While we can’t guarantee that results extrapolated from computational systems such as this one will have any predictive value for the brain. But, it should be possible at least to construct predictions. A collaboration involving neuroscientists of various stripes could then potentially come up with some clever experiments, which would be interesting, if for no other reason than that they had a direct connection back to this sort of computational model.
Spot-on commentary. Via, as usual, xkcd.
The other thing we can take away is this. We now know how to train up a schizophrenic neural network. Combine it with this punching robot:
Asimov’s-law-violating robot. Via Geekologie.

Teach it to snort coke, and we’ve got all the makings of a Charlie Sheen bot.

Hoffman RE, Grasemann U, Gueorguieva R, Quinlan D, Lane D, & Miikkulainen R (2011). Using computational patients to evaluate illness mechanisms in schizophrenia. Biological psychiatry, 69 (10), 997-1005 PMID: 21397213

For more on this article, check out 80beats, over at Discover Blogs.

biology, Books, evolution, science

Field Notes on Science and Nature

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So, I wanted to draw your attention to a new book called Field Notes on Science and Nature, just published by Harvard University Press.  The book is the result of several years of work by Michael Canfield, who is not only a personal friend from graduate school, but also a really smart and genuinely nice guy.
The book is an exploration of the similarities and differences in how laboratory and field scientists collect and use notes.  It includes excerpts from the notes of a range of researchers, along with essays about how they use those notes.  I haven’t seen the actual book yet, but the website promises a lot of cool eye candy, like this
and this
Although the book has already been printed, Mike is interested in continuing to explore these issues on the web. He is particularly interested in questions of how current grad students and researchers navigate between pen-and-paper notes and other types of technology.
If you or someone you know (a student, a colleague, a frenemy, etc.) might be willing to share some of your notes and experience, you (or they) should drop Mike an e-mail (canfield@fas.harvard.edu) and join in the conversation.
And finally: congratulations, Mike!  I can’t wait to get my hands on a copy of the book!

biology, culture, science, video

WTF, 1942? Bugs Bunny dons blackface to sell war bonds.

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So, one of the features of studying things like biological species or languages, is that they’re not really things. Or rather, they are things, but in a fuzzy, not-very-thingy kind of way.

What I mean is that it is often difficult to define the exact boundaries of a species or language. Fundamentally, this is a consequence of the fact that we are trying to apply discrete labels (such as “English” or “Moloch horridus“) to populations of things (speakers or individuals) that exhibit a degree of variation (e.g., dialects or subspecies), and that change over time.

For example, I can easily read a newspaper article written in the 1950s. I can read something from the 1700s and understand it, but it might sound weird. I can read Shakespeare and understand it, but I probably make use of a lot of the footnotes. By the time I’m reading Chaucer, some things might look familiar, but I probably require help to correctly understand most of the words. So, while those texts are all, in a sense, English, the gradual process of change means that the English of 800 or 1000 years ago is as foreign to me as contemporary French or German.

The same is true of biological species. In that context, people sometimes refer to “diachronic species,” which is a way of breaking up a single, continuous biological lineage into subsections that can be given different labels. Given enough knowledge of the biology, one could use not-completely-arbitrary criteria to decide whether two individuals in the same lineage (say, where one was a distant ancestor of the other) should be classified as members of the same species. However, defining break points along the lineage to define species is an inherently arbitrary exercise.

This change process is also true of other (non-linguistic) aspects of culture. There is clearly a continuum of American culture stretching back from the present into the past. And each additional year that we move back, the more the culture seems foreign to me. But how far back is far enough to where you would actually call it a different culture? Again, there is an inherent arbitrariness here that means there is no real answer to the question. I suspect that if you were to take a survey, people’s answers would depend a lot on how old they are.

However, I want to make a pitch for World War II being the natural break point in American culture, if for no other reason than that it would provide a psychological distance that would assuage my discomfort with this video from 1942.

Now, I don’t know what came up for you, but at the time of posting, the related videos that pop up at the end include classics such as “Nazi Duck” and “Bugs Bunny Nips the Nips.”

Also, what’s up with the 1942-era shape of Elmer Fudd’s head?

biology, Darwin Eats Cake, evolution, religion, science

As opposed to the light of what?

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So, most biologists are familiar with the quotation by Theodosius Dobzhansky, “Nothing in biology makes sense except in the light of evolution.” In fact, in my experience, if you go to a biology conference, there’s about a 50% chance that at least one of the speakers will introduce their talk with this line. What is typically not made explicit in these talks is, as opposed to what other light?

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I have most often heard this quotation used when the speaker is talking to an audience of ecologists or molecular / cell biologists. While both of those fields are clearly tied into evolutionary ideas, explicit thought about evolution is often secondary to other considerations, such as accurately describing the behavior of these very complicated systems on much shorter timescales (months or years in ecology, perhaps down to milliseconds in molecular biology). My sense has always been that people pull out this quotation when they get excited about an evolutionary question in their work, but somehow they feel some anxiety about how their colleagues will react. In a practical sense, then, people seem to quote Dobzhansky when they want to ask a why question. The “as opposed to what” part would be the more descriptive what, where, when, and how questions that constitutes the bulk of the work in biology.

Since this is one of those quotations that just floats around the community, what people may not know is that this was actually the title of one of Dobzhansky’s papers. The paper, published in 1973, was written as a critique of anti-evolutionist arguments by creationists. The “as opposed to what” part, then, was originally divine intervention and intelligent design.

Theodosius Dobzhansky circa 1966. Photo via Wikipedia.

The interesting thing about this paper is that it is written from the perspective of a religious man, and the arguments are more theological than scientific or sociological in nature. Dobzhansky himself was a committed member of the Eastern Orthodox Church. He argues that life is God’s creation, but that natural selection is the mechanism that God has chosen.

It is wrong to hold creation and evolution as mutually exclusive alternatives. I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation. Creation is not an event that happened in 4004 B. C.; it is a process that began some 10 billion years ago and is still under way.

Dobzhansky then continues with many of the now-familiar arguments for the overwhelming empirical evidence supporting the fact of evolution – in the fossil record, in the patterns of diversity of life, and in the molecular similarities among all species. What strikes me as particularly interesting in the article is the argument that he invokes to defend against claims that God deliberately created patterns that resemble those that would result from an evolutionary process – for example, the claim that God created dinosaur fossils, when no dinosaurs ever existed, or that God made dinosaur fossils appear to be much older than they actually are.

He says that to claim that God arranged things in this way is blasphemous, as it accuses Him of “systematic deceitfulness.” This, in fact, seems to be the core of Dobzhansky’s argument. The evidence is so strong that it admits only two possible explanations: either evolution is true, or God is deceitful. He rejects the latter on the grounds that such a claim would be “as revolting as it is uncalled for.”

Finally, Dobzhansky winds up with a quotation from Pierre Teilhard de Chardin:

Is evolution a theory, a system, or a hypothesis? It is much more – it is a general postulate to which all theories, all hypotheses, all systems must henceforward bow and which they must satisfy in order to be thinkable and true. Evolution is a light which illuminates all facts, a trajectory which all lines of thought must follow – this is what evolution is.

He notes that Teilhard (a Jesuit priest and paleontologist) was a deeply religious man, and that his faith was not at all in conflict with a belief in evolution and natural selection. I reproduce the quote here because it kicks ass.

Theodosius Dobzhansky (1973). Nothing in Biology Makes Sense Except in the Light of Evolution The American Biology Teacher, 35 (3), 125-129