Frontiers of (Doing) Science

An update from one of my former colleagues (Steve Suhr), by way of the Lansing (MI) State Journal. Steve and Marie-Claude Senut (his wife, who is also a molecular biologist/Neuroscientist) decided to open their own scientific business (Biomilab LLC) after their soft-money (grant-dependent) positions ended at Michigan State University. As research grants have become both more scarce and more competitive, their options were to either uproot their lives yet again or strike out on their own. Having moved around the country extensively in the name of doing science, this was more of a rational lifestyle choice than a risk-taking venture.

Mom-and-pop entrepreneurship in the name of science. In this case, "shop" could be replaced by "collaborate". I don't suppose that they will limit their collaborations to the "local", however.

Described by Steve as a "Mom-and-Pop biotech company", Biomilab's business revolves around contracting with academic labs to do protocols and analyses involving specialized equipment or expeertise that the contracting lab does not have immediate access to. Steve specializes in genetic engineering (the creation of transgenic constructs), while Marie-Claude specializes in neurogenesis and neural differentiation. Good luck Steve and Marie-Claude!

Steven T. Suhr, at the edge of a new frontier. COURTESY: Lansing State Journal.

Freely-associated Earth Day and Outdoor Adventure-related Content

This is being cross-posted to my micro-blog, Tumbld Thoughts.

Here is a recent story on how 70,000 ladybugs have been released in the Mall of America to combat aphid infestations of the interior foliage. At 4.2 million square feet, the Mall of America has developed an incipient ecosystem [1]. The dynamics of this ecosystem will interesting to observe, particularly in light of the work that has been done in the field of biospherics (e.g. Biosphere 2, which is sponsored by the University of Arizona) [2]. Speaking of self-sustaining ecosystems.......

Nice ecosystem animation for Earth Day, courtesy of Google Doodle. Surf the web to find the true meaning of Earth Day, I guess. Speaking of surfing.....

Why it pays to Surf Michigan. No, really! There is a thriving (albeit obscure) surf culture in the US state of Michigan [3]. Lake Michigan surfing (inset on the left, picture from the St. Joseph Pier on Lake Michigan) has been going on for years, usually in the Fall and Spring when gales present waves large enough for surfing on.

When there is significant rainfall (such as during the past few weeks) or Spring snowmelt, the inland rivers (inset on the right, picture from the Red Cedar River in front of the Administration Building at Michigan State University) allow for interesting surf conditions.

Rincon Beach Park, Santa Barbara County, CA. There is also beachfront right across the street from the UCSB campus.

Surfing at Michigan State is a bit like a cold UC Santa Barbara with ducks on a river (odd mental image, I'm sure). Speaking of academically-oriented surfing [4], here is a profile on the "Physics of Surfing" class offered at UC San Diego [5]. Happy outdoor adventuring!

Scenes from the "Physics of Surfing" class, which combines lessons in instrumentation, oceanography, and of course surfing.

NOTES:

[1] this has parallels to ecosystems that emerge due to climatic changes such as the retreat of glaciers.

[2] Allen, J.   People Challenges in Biospheric Systems for Long-Term Habitation in Remote Areas, Space Stations, Moon, and Mars Expeditions. Life Support and Biosphere Science, 8, 67-70 (2002).

[3] Pictures of wetsuit adventurers in interesting conditions courtesy of Matuli Surf Company (Matulis brothers, Midland, MI).

[4] Here is a list of the top 10 surf colleges from Surfer magazine. Michigan State (nor any other Michigan University) is on it. The only odd duck here is NYU, which offers you the opportunity to surf Long Island (and perhaps the sewers). I might add Florida Atlantic University (FAU) to the list, at least during hurricane season.

[5] A few more links about those skeptical of the academic value of studying surfing: 1) a video on the physics of surfing by Kevin Stahl and friends, 2) a white paper called "The Physics of Ocean Waves" by Michael Twardos (courtesy of Snake Gabrielson's Surflibrary.org), 3) a story by John Jeka at the University of Maryland in the "Neuromorphic Engineer" called "Light touch-contact: not just for surfers". The article profiles the role of touch (e.g. somatosensory information) in helping people and other animals keep their balance when moving across a surface.

Richard Gordon, Transmogrifying from Virtual to Physical, Brought us Bits of Embryogenesis

I was honored to be able to bring Dr. Richard (Dick) Gordon to the Michigan State campus for a seminar on April 9 (see video on Vimeo). Currently at the Gulf Specimen Marine Laboratory (and retired from the University of Manitoba), Dick is a theoretical development biologist of the highest caliber [1]. He gave a talk entitled "Cause and Effect in the Interaction between Embryogenesis and the Genome" [2]. He even brought toys [3] to illustrate his theory of cellular differentiation.

Dick's virtual world avatar (Paleo Darwin) is seated in the middle picture.

Dick Gordon, master collaborator.

The theoretical model he presented suggests that differentiation waves [4] pulse through the embryo during development, which set up spatially-restricted gene expression and differentiation into distinct cellular types. According to this view, each cell's differentiation is a binary and recursive process (e.g. one "decision" point building upon another), and is contingent upon the cell's position and environment. In this sense, higher-level organization (e.g. modules) are not caused by gene expression. Rather, gene expression changes that lead to observable phenotypic modules [5] and other patterns are caused by the extracellular environment of a developing organism.

An example of a Wurfel toy, taken from a slide in his talk. A fine example of Canadian innovation.

There were many profound moments in this lecture. An overarching theme of the talk was how candidate ideas (e.g. hypotheses) are tested, implemented, and critically examined in the course of doing science. One of these was the "organizer" experiments of Hans Spemann [6], in which a piece of tissue transplanted to an embryo can induce the formation of a second animal. Subsequent experiments have shown that while transplanted tissue accomplishes this, other transplanted materials (even some which are non-organic) can induce this response as well. Perhaps the effect is not due to the tissue itself, but the hydrophobicity or hydrophilicity of the materials transplanted. This might be characterized as a special case of Type I error due to incomplete experimental information [7].

Picture of Hans Spemann (inducers).

Another candidate idea presented was Alan Turing's notion of "morphogens". Morphogens are hypothetical molecules proposed by Turing to drive pattern formation in a developing organism [8]. According to the talk, morphogens are not the causal factor for morphogenesis, nor are genetic regulatory cascades. Instead, they are both driven by expansion and contraction waves that course through the embryo. These waves (which have been observed) also trigger the mechanisms of differentiation (e.g. signaling molecules and gene expression changes) in cells. A good example of the problems related to establishing causality in a complex systems.

Picture of Alan Turing (morphogens).

Time-course (and illustration) of differentiation waves moving across an embryo from the talk.

After the talk, Dick and I discussed the possible role of differentiation wave-like activity in the process of in vitro (or perhaps even in vivo) cellular reprogramming (the controlled phenotypic transformation of a cell from one phenotype to another). Interesting stuff, and as always, you are welcome to participate in the Embryo Physics course [9], which is made possible by a fine group of people. Please contact myself or Dick if you are interested in presenting.

The scene of the crime, so to speak. Some quiet moments before my virtual lecture (Scenes from a Graphical, Parallel Biological World) given in April, 2012.

NOTES:

[1] He was originally trained in chemical physics at the University of Oregon (home of the Oregonator). See his Google Scholar profile for more information. According to their records, he has a h-index of 32 (which is quite impressive). He also has an Erdos number of 2i (long story).

Animation of the Oregonator (activator/inhibitor system). COURTESY: Scholarpedia.

[2] Here is a link to the version of this talk (.pdf slides) presented in the Embryo Physics course on March 20, 2012.

[3] One of these was a Wurfel, which is a bunch of wooden blocks joined together with an elastic string. I own one of these, and before this lecture I had no idea as to its name!

The Wurfel was used to demonstrate the configurational constraints and opportunities afforded to the genome due to a cell's biophysical and epigenetic context. For more fun (and combinatorics) with puzzles, please see the following blog post: Puzzle Cube. Paleotechnologist blog, August 31 (2011).

[4] According to his talk, these may either be calcium waves or something functionally similar. For an introduction to embryonic calcium waves (and how to image them), please see:

Gillot, I. and Whittaker, M.   Imaging Calcium Waves in Eggs and Embryos. Journal of Experimental Biology, 184, 213–219 (1993).

[5] Here is a video from Jeff Clune (University of Wyoming) demonstrating how modularity might have evolved using the software platform HyperNEAT (evolutionary neural networks). Based on the following paper:

Clune, J., Mouret, J-B., and Lipson, H.   The evolutionary origins of modularity. Proceedings of the Royal Society B, 280, 2012-2863 (2013).

[5] Here is a YouTube video that explains Spemann's organizer experiments in more detail.

[6] This fits very much within the scope of the Hard-to-define-Events (HTDE) approach. For more information, please see the HTDE 2012 workshop website.

[7] Here are some examples of morphogenesis (sensu Turing) the morphogen concept modeled using the Gro programming language (from the Klavins Lab, University of Washington).

The morphogen concept was some of Turing's later work. Even though Turing was a computing pioneer, his coupled reaction-diffusion model of chemical morphogenesis have become a prevailing view of how developmental morphogenesis proceeds. However, these ideas are also useful in the computational modeling of textures. See Turing's classic paper for more information:

Turing, A.M.   The Chemical Basis of Morphogenesis. Philosophical Transactions of the Royal Society of London, 237 (641), 37–72 (1952).

[8] While not formally a MOOC, the Embryo Physics course is an example of distributed learning. For more information, watch for the forthcoming paper:

Gordon, R.   The Second Life Embryo Physics Course. Systems Biology in Reproductive Medicine, x(x), xxx-xxx (2013).

Clearly I need to tag these...

Ah, the foibles/joys of pattern recognition........ Pictures from the ground at Oval Beach (Saugatuck), Lake Michigan. But apparently, there is a face in the sand.



Hopefully in the future Facebook can fare better than the illusion of Cydonia.

1976, low resolution.

2001, high resolution.

UPDATE: April 9, 2014.

With the new pattern recognition algorithm DeepFace [1], perhaps Facebook faces will be more distinguishable from Facebook visual interesting patterns from now on.

[1] Taigman, Y., Yang, M., Ranzato, M.A., and Wolf, L.   DeepFace: Closing the Gap to Human-Level Performance in Face Verification. Conference on Computer Vision and Pattern Recognition (CVPR), 2014

Dawkins talk, Michigan State University, 3/2/09

I attended the Richard Dawkins talk at MSU the other night. This was part of their WorldView lecture series. This was the first event in the series for which the Wharton Center was sold out (about 1200 or so seats). I have now attended lectures from four great minds in evolution: Richard Dawkins and E.O. Wilson (at Michigan State) and Ernst Mayr and Steven Jay Gould (at the University of Florida). Dawkins is good for
his combination of scientific and religious skepticism with evolutionary biology, which was in full form the other night.

The Dawkins talk was called "The Purpose of Purpose", and was a good general audience talk. I noticed how self-promoting the whole Dawkins enterprise was: his website looks like its part e-commerce website, part self-help guru website. This is a good model for aspiring intellectual brokers (e.g people who want to become rich and famous in exchange for 10 years of higher education). Anyways, the talk was about how not everything in the world around us has "purpose" (e.g. got there via a designer or is there for our utilization), and how things that look like they have purpose and things that DO have conscious purpose (such as art or human artifacts).

Our hosts for the evening. LEFT: Dr. Fred Dyer (MSU Zoology), RIGHT: Dr. Richard Dawkins (Oxford). COURTESY: Dr. Wesley Elsberry.

To accomplish this, he broke down purpose into two different types: archipurpose and neopurpose. Archipurpose involves things that are causal but not neccessarily purposeful (like a bird's wings or stars in the universe). When pre-scientific peoples looked up into the sky, they assumed that the stars were put there by God for our pleasure. They then built monuments and sacrified virgins accordingly. On the other hand, neopurpose is the direct byproduct of conscious intervention, and its products generally serve a definable purpose. This is not to be confused with the purpose of a bird's wing -- wings are there so that the bird can fly, but got there via natural selection rather than by a master
designer.

There were parts of the talk where he seemed a bit sluggish (perhaps it was just my imagination). The old Dawkins chestnut that our bodies are the vessels for our genes (and thus serve an archipurpose) was used as an example. while I understand what he is saying, I think that specific argument is a bit shortsighted. He also contrasted domesticated species, whose evolution is governed by neopurpose (artificial selection by human breeders) with wild, naturally-selected species. I thought this was an excellent way to drive this point home, and wished he had spent a bit more time exploring this theme. But overall, it was an outstanding talk.

Fred Dyer, the chair of our Zoology Department, fielded questions from the audience. At WorldView, questions are solicited from the audience and the moderator fields the best of the crop. This works well, since giving the mike to audience members in a first come, first serve fashion can lead to really bad questions. Dawkins revealed that he was not dogmatic about his atheism and skepticism: he would gladly change his mind in a heartbeat if he saw convincing scientific evidence of God. He also has no time for homeopathic medicine, which reminds me of a great quote from the Futurama episode "Crimes of the Hot":

Robot: Calling all scientists......

Human: I have a degree in homeopathic medicine!

Robot: You have a degree in boloney!

Dawkins is currently on a barnstorming tour across the USA. If you can catch one of his speaking engagements, I highly recommend it.