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  • July 24, 2010
  • 02:22 PM

The great golden digger wasp, the Concorde fallacy, and free will

by Ryan Kitko in Cunabulum

Sphex ichneumoneus, the great golden digger wasp, about to enter her burrow.A few weeks ago, I noticed some alarmingly large insects that resembled wasps outside the front entrance of the biology building at Kenyon College. They would fly a few centimeters above the sandy gravel, no doubt surveying the best landing spot. Only a handful of these solitary wasps were here hovering over at least a dozen wasp-diameter holes in the loamy soils under this protected overhang. Suddenly, one landed and disappeared into her burrow. Ah! Digger wasps! I had read about them but never before observed them in the wild. Well, as wild as a well-manicured college campus is in the relative calm of summer. The wasps were a mixture of brilliant orange contrasted with a deep black color. Almost blue iridescent wings fluttered periodically as they danced around the burrows. After consulting available guides and experts in the natural sciences division at Kenyon, it was confirmed these are indeed the great golden digger wasps (Sphex ichneumoneus). These beautiful solitary wasps emerge in the summer and spend about 6 weeks building multiple burrows that they then provision with paralyzed katydids. When the female - the males do not assist in burrow building or provisioning - is satisfied with her stash, she lays a single egg and closes the burrow, commonly completing this process 10 times before her short adult life is over. This species is common to much of the United States, so it's not a surprise to find them here in Ohio.The sheltered gravel/sand area outside Higley Hall at Kenyon College is the perfect burrow building habitat for the great golden digger wasp.My usual curiosity of the natural world doesn't typically extend beyond plants, but my interest was piqued. When searching for information on species I have not encountered before, I am often disappointed. Indeed, the great many species out there have been described in full maybe once - the original description - and mentioned a handful of other times in other publications as simply being an associate of other species. It's unusual to find such a detailed account of the life history of a single species, but I was pleasantly surprised with Sphex ichneumoneus. This species and its relatives have been observed in great detail and their behavior has made our species ponder the nature of philosophical fallacies and free will. What a creature!Investment and returnOver six breeding seasons in the 1970s, H. Jane Brockmann recorded data of wasp behavior from three sites. Typically, each female will work on her own to dig and provision her burrow, but sometimes two females will begin provisioning the same nest in 5-15% of cases. The interloper takes advantage of the other wasp's spent investment and the two will be bringing katydids into the same nest. But because they spend most of their time away from the nest seeking new prey, it is only a coincidence if the two meet and fight over the nest. Fights last between 2 and 16 minutes and often the loser would leave and never return. Because of this one-on-one interaction where both insects have varying degrees of past interest (their future interests would be identical), the data can be thought of in simple game theory mechanics. The founding wasp took the time to dig the burrow and begin provisioning it, while the joiner risked being discovered and the subsequent fight to cheat and not build her own burrow. When faced with a fight, however, each has the same prize and motivation: a well-provisioned nest is worth fighting for, saving the winner days more of additional digging and hunting to lay a single egg.The "sunk cost fallacy," or Concorde fallacy, so named because the British and American governments continued to fund the faster trans-Atlantic Concorde flights even when there was no longer any economic incentive to do so, refers to decisions based on past investment because of loss aversion instead of on the rational potential future gains. Brockmann, along with Richard Dawkins, asked the question, "Do digger wasps commit the Concorde fallacy?" in their 1980 publication. The available evidence suggested that the wasp with the least prior investment in a burrow would give up first in a fight and abandon her effort. This result was not skewed by size advantage, which wasp visited the burrow most recently, or whether the winner was the founder or the joiner. Put plainly, the winner was usually the one who brought the most katydids to the burrow. As Brockmann and Dawkins say, "It is hard to resist the suspicion that the wasps are behaving as if following the Concorde fallacy." But are they?Number of katydids each fight participant brought. Nine fights were over empty burrows. From Dawkins & Brockmann, 1980.Further, the fight length was strongly dependent on how many katydids the loser brought. Falling into the Concorde fallacy, you might conclude that the loser will fight more vigorously because of greater prior investment in the burrow and less vigorously for those she has barely begun to provision. The losing wasp appears to rationalize: "Fight only as long as is proportional to your individual investment in this burrow." This case study informed the ongoing discussion of whether we humans consider such strategies to be "good" in our assessment relative to their evolutionary stability. The Concordian strategy versus the strict economist (fight based on potential future gain) is fully revealed here in this brilliant case study.Free willJust one more quick interesting note about these creatures. In Daniel Dennett's book Elbow Room, he reproduces an account by Woolridge in 1963 about the deterministic behavior of Sphex ichneumoneus. Woolridge watched the wasps return to their burrows with katydids, leaving them just outside while they went inside to inspect. Normally, the wasp is inside for a few seconds, then reemerges and drags the paralyzed katydid backward down into the burrow. He decided to alter the pattern to see if the wasp's behavior changed. When the wasp entered the burrow, Woolridge would subtly move the katydid a few inches from the burrow threshold. The wasp reemerged to find he prey moved, dragged it back to the threshold, then dove back into the burrow alone to inspect again. Woolridge writes, "On one occasion this procedure was repeated forty times, always with the same result." The wasp appears to be an unwilling participant in a free will experiment. She is not a free agent, but instead is driven by environmental cues: once a katydid is near the threshold, I must inspect the burrow and only then can I bring it inside. This property, an apparent lack of free will, was even given the name sphexishness. Dennett notes that publications on free will are rife with fears of sphexishness. Call it genetic determinism or a behavioral loop. Perhaps, though, we're all a little sphexish.And what of the wasps?I know their short adult lives will be over soon, but I've enjoyed viewing them through the window these past few weeks. Apparently, though, their lives were meant to be shorter than usual. I walked out the door the other day and noted the acrid smell of pesticides on the air. It got stronger as I approached the burrows and each hole was wet, as if it had been sprayed. Sphex ichneumoneus is a solitary wasp that is not inclined to sting anything but katydids. If you approach them or their burrows, they fly away, bothering no one. I was told our department administrative assistant tried to fill the holes in one day and I suspect she alerted the maintenance department to their presence, thus leading to their demise. Perhaps if people took the time to find out more about the supposed threat before eradicating it, they might change their minds about the course of action. That at least one good motivation for effective science education.... Read more »

DAWKINS, R., & BROCKMANN, H. (1980) Do digger wasps commit the concorde fallacy?. Animal Behaviour, 28(3), 892-896. DOI: 10.1016/S0003-3472(80)80149-7  

  • July 24, 2010
  • 12:09 PM

Are most experimental subjects in behavioral science WEIRD?

by Michael Meadon in Ionian Enchantment

My supervisor David Spurrett and I have a commentary on an important paper - "The weirdest people in the world?" (pdf) - in the most recent edition of Behavioral & Brain Sciences. The authors, Canadian psychologists Joseph Henrich, Steven Heine and Ara Norenzayan, argues that most experimental subjects in the behavioral sciences are WEIRD - Western, Educated, Industrialized, Rich, and Democratic - and thus weird - not representative of most human beings. And this, if true, is a very serious problem indeed. Behavioral scientists (anthropologists, psychologists, behavioral economists and so on) are often interested in explaining the brains, minds and behavior of Homo sapiens as a species. (Some scientists, of course, are only interested in understanding specific cultures or what makes us different, but one important goal of the behavioral sciences has long been to explain universal human behavior). As evolutionary psychologists John Tooby and Leda Cosmides have put it, they "seek to characterize the universal, species-typical architecture of [the information-processing mechanisms that generate behavior]".

But... Henrich and his colleagues review a large body of literature that seems to show that, across several domains, Western undergraduates - the workhorses of the behavioral sciences - are extreme outliers. In other words, if they are correct, most of the data behavioral scientists have used to test hypothesis and drive theorizing have been derived from subjects who are possibly the least suited for generalizing about the human race. Take as an example the Müller-Lyer illusion. In the diagram below, the lines labeled "a" and "b" are exactly equal in length, but many subjects perceive "b" as longer than "a".

This finding (which goes back all the way to 1889) has been used to make deductions about how the human visual system works. The Wikipedia article on the illusion, for example, states that one possible explanation for the effect is that "the visual system processes that judge depth and distance assume in general that the 'angles in' configuration corresponds to an object which is closer, and the 'angles out' configuration corresponds to an object which is far away". Plausible enough. Except that for some people - San foragers, for example - the illusion does not exist, and in many other non-WEIRD societies the effect size is significantly smaller. Henrich and his colleagues cite the work of Segall et. al. (1996), who worked out the magnitude of the illusion across 16 societies by varying the relative lengths of "a" and "b" and then asking subjects to indicate when they thought the lines were equal. The percentage by which "a" must be longer than "b" before the lines are adjudged equal - what they call the "point of subjective equality" (PSE) - varies substantially between subjects from different cultures - and, importantly, WEIRD-subjects are extreme outliers. The results are summarized in the following graph:

Both WEIRD adults and children (aged 5-11) require "a" to be 18%+ longer than "b" before they're perceived as equal, but for the San and South African miners, the illusion simply does not exist - their PSEs are not statistically distinguishable from 0. Why this difference arises is unknown, but Segall et. al. claim it is due to WEIRD people's visual systems developing differently because modern environments expose them to ("unnatural") shapes like 'carpeted corners', thus calibrating their visual systems in a way that favors the emergence of the illusion. Whatever the true explanation, however, it is clear that it is not permissible to use the existence of the illusion among WEIRD subjects to make inferences about the visual system. This is especially true since the San subjects were hunter-gatherers, just like all people for the vast majority of human evolutionary history. Given that species-typical features of the visual system would have evolved in this period, it is particularly telling that PSE seems to be positively correlated with the 'modernity' of the societies in question. (Warning: this is an "eyeball" observation; I haven't done a proper statistical analysis. Caveat emptor).

This is one example from an extremely long paper, but it conveys a flavor of the kind of evidence the authors present. (For much more, see "We agree it's WEIRD, but is it WEIRD enough?" over at Neuroanthropology). Having read the article very carefully, and despite some concerns, I think Henrich, Heine and Norenzayan are right: the Western undergraduate is often unrepresentative of humanity, and the behavioral science literature needs a lot of fixing as a result. (Most obviously, we need far more large, highly-powered, globally representative, prospectively designed, cross-cultural studies). Serious as this is, unfortunately, it gets worse... Since David and I worked extremely hard to present our argument clearly and concisely in our commentary (pdf - our piece starts on p. 44 of the pdf, paginated by BBS as p. 104), and I doubt I could improve on it, what follows is a slightly edited - simplified and somewhat de-academicized - version of the meat of our argument. (Note: each issue of BBS consists of a "target article" - in this case, Henrich et. al. - and 20 or so short peer-commentaries).

Henrich et al. underplay – to the point of missing – that how the behavioural sciences research community itself is constituted introduces biases. That the subject-pool of behavioural science is so shallow is indeed a serious problem, but so is the fact that the majority of behavioural researchers are themselves deeply WEIRD. People in Western countries have, on average, a remarkably homogeneous set of values compared to the full range of worldwide variability (Inglehart & Welzel 2005), and the data Henrich and his colleagues present suggest similarly population-level homogeneity in cognitive styles. Moreover, academics are more uniform than the populations from which they are drawn, so it is likely behavioral scientists are even WEIRDer than their most common subjects. Henrich and his colleagues review a bunch of studies and experiments that did not strike those who designed and conducted them as focused on outliers. Intelligent scientists acting in good faith conducted, peer-reviewed, and published this research, in many cases honestly believing that it threw light on human nature. This forcefully illustrates the power of the biases on the part of researchers themselves. It also suggests that, besides widening the pool of subjects, there are significant gains to be made by broadening the range of inputs to the scientific process, including in the conception, design, and evaluation of empirical and theoretical work. Given that diverse groups are demonstrably better at some kinds of problem solving, as things stand, the WEIRD-dominated literature is robbed of potentially worthwhile perspectives, critiques, and hypotheses that a truly global research community could provide. Clearly, simply increasing the number of behavioural sciences&nbs... Read more »

Henrich, J., Heine, S., & Norenzayan, A. (2010) The weirdest people in the world?. Behavioral and Brain Sciences, 33(2-3), 61-83. DOI: 10.1017/S0140525X0999152X  

  • July 24, 2010
  • 11:57 AM

Adventures with Citizen Science: perspectives of a shark biologist

by WhySharksMatter in Southern Fried Science

Those of you who follow me on Twitter or are friends with me on facebook may have seen that last month, I asked for volunteers to come catch and tag sharks with me here in Charleston. While I was pleased by how excited respondents were for this opportunity, I would be remiss if I didn’t [...]... Read more »

  • July 24, 2010
  • 08:55 AM

Why moss blows smoke rings

by Thomas Kluyver in Thomas' Plant-Related Blog

Science via Youtube today. Let’s start with some smoke rings.  They go an impressively long way—much further than a simple puff of smoke fired with the same force would: So, why might a moss need to do the same thing? It’s all about spores. Mosses spread by spores, a bit like microscopic seeds. For peat [...]... Read more »

  • July 23, 2010
  • 11:47 PM

Jellyfish: Pretty from a Distance

by Kevin Zelnio in Deep Sea News

Photo from Dan Herschman's Flickr Stream (Click on Image).
A link from one of readers (thanks Ashley!) pointed us to a story on MSNBC about a very large Lion’s Mane jellyfish (Cyanea capillata) that broke apart and stung up to 100 people on a New Hampshire beach last Wednesday. Lion’s Manes can get very big, their . . . → Read More: Jellyfish: Pretty from a Distance... Read more »

Nüchter, T., Benoit, M., Engel, U., Özbek, S., & Holstein, T. (2006) Nanosecond-scale kinetics of nematocyst discharge. Current Biology, 16(9). DOI: 10.1016/j.cub.2006.03.089  

  • July 23, 2010
  • 10:54 PM

Viruses are objectively better than bacteria – DotW throwdown

by thomastu in Disease Prone

I am throwing down the gauntlet. James, you sir, have insulted my and my discipline’s honour for the last time. Time for a good ol’ fashion debate. Here and now, let the readers be the judge. Have at you, sirrah! Viruses are better than bacteria. I really shouldn’t have to say this; it is almost [...]... Read more »

Pearson, H. (2008) 'Virophage' suggests viruses are alive. Nature, 454(7205), 677-677. DOI: 10.1038/454677a  

  • July 23, 2010
  • 11:36 AM

When bivalves attack (or: bivalves vs birds, the battle continues)

by Darren Naish in Tetrapod Zoology

Regular readers will, hopefully, have shared my surprise on learning - firstly - that oystercatchers are sometimes 'captured' and killed by bivalves, and - secondly - that someone was clever enough to photograph such an occurrence and publish it (Baldwin 1946). Prior to seeing Baldwin's paper, I might well have imagined that such cases can occur occasionally, but I wasn't aware of anyone recording them.

Today I'm very pleased to report that I'm now aware of numerous additional such occurrences: I owe a huge debt of thanks to Tet Zoo regular Dartian, who went ferreting through the ornithological literature on my behalf. As you'll see, he turned up some real gems. We can now say that sea- and wading birds of many different kinds are known to have been 'captured', disabled or even killed by bivalves on occasion. These occurrences are still comparatively rare, but they're far more numerous than I would previously had thought. Read the rest of this post... | Read the comments on this post...... Read more »

Tsipoura, N., & Burger, J. (1999) Shorebirds and Surf Clams: An Unusual Interaction. Waterbirds: The International Journal of Waterbird Biology, 22(1), 140. DOI: 10.2307/1522003  

  • July 23, 2010
  • 11:32 AM

Protein Function: how do we know that we know what we know?

by Iddo Friedberg in Byte Size Biology

The trouble with genomic sequencing, is that it is too cheap. Anyone that has a bit of extra cash laying around, you can scrape the bugs off your windshield, sequence them, and write a paper. Seriously?

Yes, seriously now: as we sequence more and more genomes, our annotation tools cannot keep up with them. It’s like unearthing thousands of books at some vast archaeological dig of an ancient library, but being able to read only a few pages here and there. Simply put: what do all these genes do? The gap between what we do know and what we do not know is constantly growing. We are unearthing more and more books (genomes) at an ever-increasing pace, but we cannot keep up with the influx of new and strange words (genes) of this ancient language. Many genes are being tested for their function experimentally in laboratories. But the number of genes whose function we are determining using experiments is but a drop in the ocean compared to the number of genes we have sequenced and whose whose function is not known We may be sitting on the next drug target for cancer or Alzheimer’s disease, but those proteins are labeled as “unknown function” in the databases.... Read more »

Godzik, A., Jambon, M., & Friedberg, I. (2007) Computational protein function prediction: Are we making progress?. Cellular and Molecular Life Sciences, 64(19-20), 2505-2511. DOI: 10.1007/s00018-007-7211-y  

  • July 23, 2010
  • 11:13 AM

Methods Fail: Testing the pre-menopausal cougar hypothesis.

by EcoPhysioMichelle in C6-H12-O6 (old)

ScienceDaily has an article from earlier this month, Ticking Biological Clock Increases Women's Libido, New Research Shows, that claims that women who are approaching menopause become "more willing to engage in a variety of sexual activities to capitalize on their remaining childbearing years" and that they are more prone to one night stands and "adventurous bedroom behavior" than their younger counterparts.... Read more »

  • July 23, 2010
  • 10:53 AM

The will and its freedom: biological evidence from invertebrates

by Björn Brembs in

A few weeks ago, Lars Chittka invited me to write an article "about free will in insects" for a Proceedings of the Royal Society B (Biological Sciences) Special Feature on 'Information processing in miniature brains' that he is editing. Given our work on spontaneity in flies and my mentor being Martin Heisenberg, how could I decline?I think I will first give a very brief overview of what people used to call "free will" and why it was such a controversy. I hope to get the gist across in about two paragraphs. Much of this info will be distilled from Bob Doyle's website and his article in William James Studies. Bob also published a letter to Nature in response to Martin Heisenberg's article there. Is it just coincidence that it was Heisenberg's father Werner Heisenberg who discovered the uncertainty principle?Then I plan to go on to argue that today the old, metaphysical free will of course does not exist in the almost 'spiritual' sense and that no prominent scholar has entertained that idea at least since Popper and Eccles' book "The self and its brain" in 1977. Instead, I will try and make the case that the term "free will" should be recast in biological terms, as a trait that evolved and keeps evolving to different degrees in different animals. I plan to use evidence from flies, leeches and other invertebrate animals to emphasize that even so-called 'simple' brains possess the capacity to behave unpredictably, i.e., freely. Any difference in freedom between animals is merely gradual.I probably should also spend a paragraph or so elaborating on the selection pressures leading to spontaneous behaviors and behavioral variability.Once the capacity for freedom has been shown, it will take less work convincing the readers of the capacity to 'will'.All of this should be couched in the notion that the dichotomy between indeterminism and determinism is a false dichotomy, because brains operate in the gray area between the two. This may be the most difficult concept to grasp, that indeterminism and determinism are not mutually exclusive, but delineate a spectrum of what one may call 'probabilism'. I may try and refer to evolution as also using both concepts of mutation (indeterminate) and selection (determinate) in a probabilistic process. I may even try and refer to Bayesian Statistics, although I know little more than the basic idea behind it. The main task of this section will be to argue that what we call freedom is more than just chance. Chance, or randomness is a prerequisite for freedom, a necessary component but it's not sufficient. Let me quote from our press release at the time: [co-author George Sugihara]"This nonlinear signature eliminates the two alternative explanations of spontaneous turning behavior in flies that would run counter to free will, namely complete randomness and pure determinism. These represent opposite and extreme endpoints in discussions of brain functioning which mirror the free will debate." To that, I'd only add that our subjective notion of 'Free Will' is essentially an oxymoron: we would not consider it 'will' if it were completely random and we would not consider it 'free' if it were entirely determined. Nobody would attribute any responsibility to our action if it had happened entirely coincidental. On the other hand, if our action was completely determined by external factors such that there was no alternative, again the person would not be held responsible. So if there is anything remotely close to free will, it must exist somewhere between chance and necessity - which is exactly where fly behavior comes to lie. George again finds the right words: "Our results address the middle ground between simple determinism and randomness that is currently not well understood or characterized. We speculate that if free will exists, it is in this middle ground." This leads me to believe that the question of whether or not we have free will appears to be posed the wrong way. Instead, if we ask 'where between chance and necessity are we located?' one finds that this is precisely where humans and animals differ. Humans may not have free will in the philosophical sense, but even flies have a number of behavioral options they need to decide between. Humans are less determined than flies and possess even more options. With this small reformulation, the topic of free will becomes the new biological research area of studying spontaneous behavior and can thus be discerned from the philosophical question.If after all that there's still room in the article, I'll review some of the data on the human default mode network and what they might contribute to the debate.Let's see, if enough people express interest in the comments, I may put a draft version online for comments and review. All commenters will at least be mentioned in the acknowledgements, of course.Heisenberg, M. (2009). Is free will an illusion? Nature, 459 (7244), 164-165 DOI: 10.1038/459164aDoyle, R. (2009). Free will: it's a normal biological property, not a gift or a mystery Nature, 459 (7250), 1052-1052 DOI: 10.1038/4591052cBriggman, K. (2005). Optical Imaging of Neuronal Populations During Decision-Making Science, 307 (5711), 896-901 DOI: 10.1126/science.1103736... Read more »

  • July 23, 2010
  • 09:36 AM

Acid Test

by Journal Watch Online in Journal Watch Online

Twenty years after the United States moved to take the sting out of acid rain, researchers are getting a clearer picture of how the pollution affected life in sensitive waters. A detailed new survey of lakes in the Adirondack mountains of New York State finds that acidification has caused species losses in every link of […] Read More »... Read more »

Nierzwicki-Bauer, S., Boylen, C., Eichler, L., Harrison, J., Sutherland, J., Shaw, W., Daniels, R., Charles, D., Acker, F., Sullivan, T.... (2010) Acidification in the Adirondacks: Defining the Biota in Trophic Levels of 30 Chemically Diverse Acid-Impacted Lakes. Environmental Science , 2147483647. DOI: 10.1021/es1005626  

  • July 23, 2010
  • 07:02 AM

Sunday Protist - Farming forams: a case of protistan agriculture

by Psi Wavefunction in Skeptic Wonder

"WTF, it's Friday already!" Friday? What Friday? You saw nothing.My previous two Sunday Protist attempts got derailed. With the first one, noticed there was quite a bit to say about them, and decided to postpone it for later as it was a big topic (and unrelated to my current work). Then I picked something relevant to my day job, y'know, two birds one stone, etc. And somehow that led me to paleontology. A warzone in paleontology. Complete and total clusterfuck. With potential inaccuracies here and there that I now need to sort out. Whilst we wait, I'll just do something quick: a case of a foraminiferan apparently growing bacteria and then eating them in perhaps one of the most non-human farming enterprises ever! (leafcutter ants are pretty much human at that phylogenetic distance...)Textularia blocki lives on seagrass. Many forams have interesting associations with seaweeds, ranging from internal parasitism to epiphytic attachment, usually via secretions of sulfated mucopolysaccharides, a fairly common material in the extracellular matrix. T.blocki, however, is a freely motile foram. It leaves peculiar 'grazing traces' as it crawls along the seagrass, without damaging the tissue beneath it:Left: T.blocki with grazing traces on blade of seagrass. Right: (Langer & Gehring 1993 J Foram Res)As made evident in the diagram, the traces consist of two parallel 'walls', consisting of pale whitish adhesive material, presumably containing mucopolysaccharides, devoid of sand grains or other contaminants. Curiously, some forams carried sand grains along, without depositing them. These secretions are formed by pseudopodia, or the 'business' part of the foram: an intricate network of reticulated feet with amazing cytoskeletal properties. When these secretions are left alone in seawater for 48h, a lush garden of bacteria sprung up specifically along the secretion traces:Bacterial gardens along the foraminiferan secretion traces. Note the relatively clean surface of the leaf outside the secretions, supporting that it is the adhesive mucous that attracts bacterial accumulation (Langer & Gehring 1993 J Foram Res)When released back into the medium containing the seagrass lined with traces, the forams approach the nearest trace and follow along it, suggesting they use some form of chemical sensing to determine where the secretions are and how they are oriented. The speed is then reduced, suggesting the foram is then busy grazing on their bacterial harvest.Thus, a 'mere' single celled organism can produce organised tracks of nutritious material, wait for their bacterial crop to grow, and subsequently harvest it. We like to think we invented agriculture. The more biologically-oriented among us point out leafcutter ant fungus gardens and aphid farming. Yet, agriculture has also evolved on the unicellular scale in a small humble foraminiferan living among blades of seagrass. Humbling, isn't it?Interestingly, a similar behaviour has been described gastropods like slugs and limpets, as their mucous also attracts bacterial growth. Convergence: when a good thing is chanced upon multiple times, it will likely be kept by several lineages independently. This applies to language and cultural evolution as well as that of biological organisms.We tend to have a deep conviction that cells are dumb blobs of goo, incapable of any sort of behaviour besides basic phototaxis or whatever. We think cells are just simple chemical response machines – which is true. But ultimately, so are we. There is no fundamental distinction between human social dynamics and the adventures of a crawling amoeba. The difference is all in the quantity and complexity of interactions – the higher the complexity, the more random (stochastic) the system appears (and to an extent, is). While I must concede that in terms of the number of components and pathways involved, human or ant behaviours are more complex than that of an amoeba, that does not mean the proverbial amoeba 'lacks' behaviour entirely.I've mentioned the cellular behaviour stuff before, probably too often for regular readers. Apparently, that idea needs restating though. Also, as a cell biologist, I find it quite...well, pleasing. It's nice that, ultimately, my subjects are no more or less machine-like than humans or plants. Furthermore, where I was heading with this originally, I think part of our notion of cells being 'stupid' comes from the obsession with our own cells. Animal cells are, in fact, quite simple and developmentally retarded. The cause is cell specialisation driven by multicellularity. Eg. an epithelial cell can now afford to lose the ability to hunt around for prey, it no longer needs to coordinate movement in any sophisticated manner, the life cycle can be simplified to terminal differentiation.Curiously, a similar problem plagues modern science and engineering: overspecialisation means that one must no longer have the same level of foundational education to survive, and thus we end up arguably knowing more about less, or perhaps knowing the same about less. I can suck at math or chemistry and get away with it. In the old days, people had to actually have a broader base just to function. Conversely, there was also less information floating around. Which is more efficient? Just as multicellularity vs. unicellularity, each system has its merits and drawbacks. So it's hard to tell.A while back I found a paper on cellular complexity in multicellular vs. unicellular organisms that needs to be discussed in greater detail eventually...---Random Link---ChrisM over at the wonderful Echinoblog (about the cooler deuterostomes; ok, hemichordates and ascidians are cool too) wrote about sperm-eating ciliates infesting starfish.Lots of things like sperm. For example, Monocystis is a gregarine with a penchant for earthworm sperm – infection rates are so high that if you slice up a worm from your backyard and smear the contents of its seminal vesicles on a slide, the chances are pretty good that you'll find some. And by 'some', I mean, LOTS. So if you're ever in the mood for some apicomplexans, all you need is an earthworm, a blade and a scope. There are parasites in pretty much anything and everything, so if you go around examining various animals, you may well find loads of cool protistan denizens in them. Many of which could be undescribed and, perhaps, new to science.Reference... Read more »

  • July 23, 2010
  • 04:50 AM

One principal component to rule them all?

by Razib Khan in Gene Expression

Despite the reality that I’ve cautioned against taking PCA plots too literally as Truth, unvarnished and without any interpretive juice needed, papers which rely on them are almost magnetically attractive to me. They transform complex patterns of variation which you are not privy to via your gestalt psychology into a two or at most three [...]... Read more »

  • July 23, 2010
  • 04:15 AM

Looking for leimotifs in the early history of wheat and rice

by Jeremy in Agricultural Biodiversity Weblog

There are two papers out just now which review in detail archaeobotanical and genetic data to elucidate the early history of crops. Dorian Fuller and numerous co-authors do it for Asian rice (Oryza sativa), Hakan Özkan and others do it for emmer wheat (Triticum dicoccoides). And Fuller actually also comments on the emmer paper on [...]... Read more »

Fuller, D., Sato, Y., Castillo, C., Qin, L., Weisskopf, A., Kingwell-Banham, E., Song, J., Ahn, S., & Etten, J. (2010) Consilience of genetics and archaeobotany in the entangled history of rice. Archaeological and Anthropological Sciences, 2(2), 115-131. DOI: 10.1007/s12520-010-0035-y  

  • July 23, 2010
  • 01:01 AM

Neuromuscular Dynamics of Octopus Arm Movements

by Mike Mike in Cephalove

I was planning on writing an article about cephalopod statocysts (and I still am; I've just had trouble deciding which pieces of research I want to cover and which I want to leave out) to continue on the theme of cephalopod sensory systems.  I've stumbled upon a line research that I just had to blog about, though, so I'm putting off the statocyst post even further.  The research in question is a series of studies by The Octopus Group at the Hebrew University of Jerusalem on the biomechanics and neural control of reaching movements of octopuses.  I read this research some months ago (before I was blogging,) and I was reminded of it while watching Twister (the resident E. dofleini at the Niagara Falls Aquarium) groping about in his enclosure.  I noticed that, as he moved his arms about, the movements almost always started with a bend near the base of the arm, which traveled out to the tip, becoming sharper and moving faster as it proceeded.  It looked for all the world like the way a wave travels through water (or, more geek-ily, the way one imagines spontaneous activity propagating in a spatially extended nervous system.)  The series of studies I will talk about here shows that this is generally the case, and characterizes the way that this happens with some detail, although we still do not know this system in nearly as fine detail as we know the vertebrate neuro-muscular system.  I'm getting ahead of myself, though.Why do we care about the details of how octopuses move their arms?  First, it's just plain cool - who, upon looking at an octopus moving, hasn't wondered how it can possibly keep track of all those arms?  Second, the octopus arm provides a unique model nervous system for a few reasons.  It is a muscular hydrostat - that it, having no bones, it is a system of muscles that run perpendicularly to each other that maintain a roughly constant total volume; this property of an octopus arm allows it to function like a very flexible vertebrate limb because the muscles can pull against each other to form temporary, semi-rigid structures that allow the arms to bear weight.  As such, it is a novel motor system (in terms of research, that is,) with most of the well-characterized motor systems we know of (ie. human, primate, reptile, etc.) are composed of skeletal muscles, which pull against bones.  Besides this, the task of coordinating the movement of eight almost infinitely flexible arms is a herculean task in terms of neural processing, and it would be very informative (as well as a triumph of systems neuroscience) to understand how this is done.  It has been thought, since the early days of octopus neuroanatomy, that much of the movement of the octopus's arms (and probably those of other cephalopods) is encoded in the nervous system of the arms rather than in the central nervous system (Graziadei, 1971).  This is evidenced by the fact that there is no straightforward representation of the arms in the brain of the octopus, as there is in humans and most other vertebrates, as far as we know, and so it is unlikely that fine motor control comes from the central nervous system.  Supporting the importance of the distributed nervous system of the arms is its incredible scale: the nervous system of the arms is much larger than the central nervous system of octopus, containing around 2/3 of all of the neurons in the animal.  The octopus arm, then, is a unique example of a highly complex, distributed motor system that stands in contrast to the centrally controlled motor systems we are most familiar with.  As with almost every topic in comparative neuroscience (I'm a big sucker for it), I think that the octopus motor system is important because by understanding it, we will understand more about vertebrate nervous systems; that is, we will (pretending for a moment that we could actually solve both systems) understand which features of them are critically related to the specifics of vertebrate and invertebrate neural functioning, physiology, development, and ecology.  We would come closer to understanding why each system evolved the way it evolved.  Finally, we would exercise our tools of modeling neural computation in a way that would allow us to figure out how generalizable they are.  My final verdict: this is a good thing to study.So now you're bored.  You want to hear about some research!  Well, I won't disappoint; at least, I hope I won't.  We'll start with Gutfreund et al. (1998), one of the early papers out of this research group, which kicked off this line of research by examining the neuromuscular dynamics of octopus reaching movements.  I should note that (presumably for simplicity,) this group generally only studies reaching movements in a single arm - it is not know exactly how their findings might relate to more complicated movements, including those involving multiple arms.  As a disclaimer I am going to leave out description of a large portion of their study, which I encourage you to read in full, for my own convenience, and only present the results that I think are most relevant to the topic at hand.This authors in this study used electromyography (a method of measuring the electrical activity of muscles) in O. vulgaris to determine how arm muscles are activated in sequence to produce octopus reaching movements.  Briefly, they put electrodes through two points in a single arm of their (anesthetized) test animals, then allowed the animals to wake up and elicited reaching movements by tempting the octopus with either a crab or a target that was associated with food.  They videotaped the reaching movement, which allowed them to compare the electromyogram to the behavior of the octopus.  Reproduced below is their first figure, showing the gross cross-sectional anatomy of the octopus arm, as well as their electrode placement:The white arrows indicate the position of the electrode, which is the white line running through the muscle.  The striated outer portions of the arm are the muscle, and the round shape in the middle is the nerve cord of the arm.They found that reaching arm movements usually start with a sharp bend near the base of the arm, which travels outwards until it reaches the tip, accelerating somewhat throughout the extention and then slowing as the arm reaches its target.  Here's a series of images showing the behavior: The authors found that this type of arm extension occurs virtue of a propagating wave of muscle contraction traveling down the arm, from the base to the tip.  Shown here are examples of the type of data they used to confirm this:The left panel shows two electromyograms from a single trial, the top one from the electrode nearer to the arm tip, and the bottom one nearer to the base of the arm.  The arrows indicate when the bend in the arm reached each electrode.  As is apparent, neuromuscular activity at the proximal site started earlier than that at the distal site, coinciding approximately with the timing of the movement of the bend in the octopuses arm.  The graph shows the correlation between the lag in the electromyogram record between the two sites and the time it took for the bend in the arm to move between the two sites.  It's clear that the propagation of the wave of electrical activity down the arm is highly correlated with the motion of the arm.  The authors continue on to characterize some of the properties of these arm movements in more detail and propose a mathematical model for the movement of the octopus arm, but I'll leave those results out, here.  I recommend this article for it's methodological clarity - too seldom do authors take such pains to make their method so clear and so thoroughly address their research question.Moving on, the same reearch group (with a different first author) published a paper in Science describing their experiments with isolated arm preparations (Sumbre et al. 2001).  This is where it gets really interesting to me, because this experiment really gets at the distinction between central and peripheral motor control.  The authors made their preparations by either denervating one arm of an octopus that had already been decerebrated (a procedure somewhat akin to an octopus lobotomy) by severing its connection to the brain, or by severing an arm completely.  ... Read more »

Gutfreund Y, Flash T, Fiorito G, & Hochner B. (1998) Patterns of arm muscle activation involved in octopus reaching movements. The Journal of neuroscience : the official journal of the Society for Neuroscience, 18(15), 5976-87. PMID: 9671683  

  • July 22, 2010
  • 09:00 PM

The virus and the virion

by Vincent Racaniello in virology blog

The illustration at left depicts a virion – the infectious particle that is designed for transmission of the nucleic acid genome among hosts or host cells. A virion is not the same as a virus. I define virus as a distinct biological entity with five distinct characteristics. Others believe that the virus is actually the infected host cell.... Read more »

Forterre, P. (2010) Defining Life: The Virus Viewpoint. Origins of Life and Evolution of Biospheres, 40(2), 151-160. DOI: 10.1007/s11084-010-9194-1  

  • July 22, 2010
  • 06:00 PM

Scientific Ethics and the Myth of Stalin's Ape-Man Superwarriors

by Eric Michael Johnson in The Primate Diaries

Why the Soviets would fund a human-chimp hybridization program in the first place and what can be learned from this sordid tale of ethical misconduct is an important topic and fascinating in its own right. Il'ya Ivanov represents a scientist, widely respected in his field, whose dedication to find out if something could be done blinded him to ask whether it should be done. It also reminds us of the role that politics can play in the development of scientific research even if the scientists directly involved are not political themselves.... Read more »

  • July 22, 2010
  • 05:34 PM

Chubbier Climate

by Journal Watch Online in Journal Watch Online

Climate change is a good deal if you’re a marmot living on a mountainside in Colorado – so far, at least. Warmer temperatures are enabling the burrowing mammals to get fatter and have more babies, researchers report in today’s issue of Nature. The finding – drawn from a field study that’s run for nearly 50 […] Read More »... Read more »

Ozgul, A., Childs, D., Oli, M., Armitage, K., Blumstein, D., Olson, L., Tuljapurkar, S., & Coulson, T. (2010) Coupled dynamics of body mass and population growth in response to environmental change. Nature, 466(7305), 482-485. DOI: 10.1038/nature09210  

  • July 22, 2010
  • 04:10 PM

Recruitment variation and the benthos - connected or not?

by John Carroll in Chronicles of Zostera

For years, the "supply-side" ecology has been a common theme describing mechanisms for benthic species distributions and densities. In general terms, the amount and extent of a particular organism is driven by the supply of larvae to a given area. This larval supply can thus be seen as driving benthic community structure, especially for marine invertebrates - as their life cycles contain a planktonic larval stage which allows for dispersal over relatively long distances. Thus, many of these populations are considered "open" and their continuation is dependent on some large supply of larvae. This makes sense, and it has been demonstrated many times in the literature. However, this has often been demonstrated on hard bottom communities. Soft bottom benthos don't always display similar patterns. A recent paper by Dr. Megan Dethier from the Friday Harbor Laboratory at the University of Washington, details an experiment conducted investigated very small, post set, infaunal recruits. Sampling these habitats is often difficult due to the 3-D nature of soft sediments. She was able to demonstrate that for a number of taxa she was working with, the strongest recruitment was not in areas where the largest adult populations existed. This suggests that for many of the soft bottom benthos she studied, the supply of larvae is not limiting the adult populations, but rather some post-settlement processes, such as predation, competition or abiotic stressors.LEWIN, R. (1986). Supply-Side Ecology: Existing models of population structure and dynamics of ecological communities have tended to ignore the effect of the influx of new members into the communities Science, 234 (4772), 25-27 DOI: 10.1126/science.234.4772.25Dethier, M. (2010). Variation in recruitment does not drive the cline in diversity along an estuarine gradient Marine Ecology Progress Series, 410, 43-54 DOI: 10.3354/meps08636This is a particularly interesting article, because "supply-side" ecology doesn't always hold true in soft bottom benthos. I have observed this first hand with the scallop restoration work on Long Island. Over 6 years, we have monitored larval supply of scallop spat at a number of different locations, and then each winter and spring, we conduct benthic surveys for juvenile densities. There isn't always a match between sites where we had the highest numbers of post-set and the highest juvenile densities. The main causes for this mismatch is likely to be predation or physical factors.On another project, I am investigating scallop settlement on artificial seagrass units. I design collectors to mimic seagrass, each collector has 10 artificial seagrass shoots. Half of the collector (5 shoots) is enclosed in a mesh bag (just under 1mm) and the other half exposed to predation. There is an order of magnitude difference between the number of available settlers (those inside the bags) when compared to those actual "recruits" (those scallops outside the bags). This low pattern of surviving recruits holds up regardless of location within the grass mats (either on small or large mats, at the center or the edge). This indicates to me that predation is a major contributing factor structuring the scallop populations, at least in the estuary in which I work, Hallock Bay, Long Island.... Read more »

  • July 22, 2010
  • 01:21 PM

Y Chromosome III: Evolutionary Strata!

by Kele in Kele's Science Blog

The primary model for Y-chromosome degeneration is a decrease in X-Y recombination. Because and X and Y chromosomes are not kept the same by swapping DNA segments with each other, but the X can still recombine with itself in females, the Y chromosome is allowed to degenerate. We will discuss how this all works next [...]... Read more »

Lahn BT, & Page DC. (1999) Four evolutionary strata on the human X chromosome. Science (New York, N.Y.), 286(5441), 964-7. PMID: 10542153  

Ross, M.T., D.V. Grafham, A.J. Coffey, R.A. Gibbs, S. Beck, J. Rogers, D.R. Bentley, & et al. (2005) The DNA sequence of the human X chromosome. Nature, 325-337. info:/10.1038/nature03440

Skaletsky H, Kuroda-Kawaguchi T, Repping S, Wilson RK, Rozen S, Page DC, & et al. (2003) The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature, 423(6942), 825-37. PMID: 12815422  

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