A blog to chronicle the adventures of Cally Dee in her pursuit of figuring out what she wants to be as a fully fledged adultish person.


So I’m about a week from being down human anatomy and physiology I. Part II starts on the 6th. And then I have physics II in the fall (since I didn’t realized astrophysics doesn’t count) and maybe another chem course (since I didn’t take a sequence… I took gen I and then orgo I, which was how my school worked).

In other news, I have started a month of insanity (except last night because I just kind of died after class) with my friend.

And I got this book in the mail:

which is interesting so far. It compares different systems animals have that “prevent” them from having a lot of our human diseases. Like how birds have drastically higher glucose levels but don’t get diabetes, etc.

Other than that, work is going well. It’s getting a bit easier each day and I’m only working part time since I still have classes.

My last tangential new thought is that I really want to try to do a volunteer physical therapy program in a different country, like maybe through VACorps or something of that nature next summer before I actually end up going into PT school (which I’ll start to apply for this fall after I take my GRE).

oh and i forgot to mention… I had an interview today for a new physical therapy aide job (at home since I’ve graduated and moved home)…

and I GOT IT!! I now will be starting part time working at Schrier Physical Therapy.

arggg i want to be an intern for hopkins!!

I’m going to be gutsy and email to inquiry whether they need underling summer interns or anything. wish me luck!

on their site for the Elisseeff Lab:

Orthopedic reconstruction  

Cartilage tissue was one of the initial targets for tissue repair in the lab.  We studied cartilage tissue growth in hydrogel materials to understand basic cell-material interactions and developed enabling technologies to translate the tissue engineering approaches.  One hydrogel technology was translated to clinical testing via a startup (Cartilix, acquired by Biomet in 2009) and continues development.  As a result of that clinical translation we realized the complexity of joint disease and are now pursuing a multi-targeted approach to the problem that includes lubrication and inflammation in addition to structural repair.

To address structural tissue repair in orthopedic tissues we are developing next generation biomaterial technologies based on our first clinical experience with cartilage repair.  Specifically, we have simplified the surgical procedure for implantation of our materials, created a one step implant process with a new biosynthetic hydrogel.  We are developing new materials that can work with intra-operative biologics (bone marrow, platelets, etc) and composite materials.

Inflammation is another critical aspect in joint disease.  Inflammation can occur after trauma (even surgical trauma) and disease processes and will impact tissue repair.  To address the challenge of inflammation in the joint we partnered with the Yarema Lab that generated a new molecule based on short chain fatty acid hexosamines.  Some of these molecules reduce expression of inflammatory markers such as those found in osteoarthritic cells.  Furthermore, new cartilage production is increased in the OA cells treated with the new small molecules that reduce inflammation.  As these small molecules are not protein growth factors we expect a simpler translation process to testing in the joint and more efficient delivery.

Finally, we have looked at improving lubrication in the joint.  Currently, injections of hyaluronic acid into the joint are quite popular clinically.  HA is purported to be a lubricant but is not retained in the joint for very long.  Taking cues from other industries such as the auto industry where engine surfaces are designed to interact with engine oil, we developed a technology to modify the cartilage surface to interact specifically with HA to retain the molecule in the joint long term.  This technology is also biomimetic in that it replicates the natural function of lubricin in the joint.

Taken together, addressing these three research areas will provide a comprehensive approach to solve the complex clinical challenge of joint dysfunction.”

biomechanics project

So in lieu of graduating, I seem to be finding a lot of things I should be posting that pertain to what I am interested in for the future. This is the abstract from my partner’s and my final paper of our research project.

Cutting losses: tail autotomy reduces swimming efficiency in the green anole (Anolis carolinensis)

Iris Fang, Cally Deppen and Gabriel Rivera

Swarthmore College, Swarthmore, PA, 19081, USA


Locomotion is essential to the survival of many vertebrates. In addition to the “fight-or-flight” escape response, some species including the green anole lizard (Anolis carolinensis) have evolved the ability to autotomize varying lengths of their tails in response to predation to aid escape. While a previous study has been conducted on how tail autotomy affects jumping ability in these arboreal lizards (Gillis et al. 2008), how this defense mechanism affects the lizards’ swimming ability has not yet been studied. In this experiment, we examined changes in swimming mechanics after tail autotomization and found that tail loss resulted in less efficient swimming, as exemplified by significant reductions in wavelengths,  amplitudes, and velocities of the snout, pectoral girdle and pelvic girdle, though not the snout amplitude.

(and here’s a screenshot of the digitizing portion of one of our lizards for good measure): image

(if you are interested in seeing the rest of our paper, notify me using the chat with cally dee option on my page).

My old quiz from the paper about Clingfish by Adam Summers

 Quiz 3

1. Adam Summers and company investigated an organism called Gobiesox maeandricus, or the north clingfish (colloquially called a goby) to see how it is able to adhere to various surfaces as well as how it is able to produce such large suction force as to be able to attach 200 (80 - 210) times its body weight. They hypothesized that the clingfish’s ability to adhere so well must be due to some kind of biological part structuring, for example the clingfishs’ microvilli papillae like structures allowing them to latch so tightly based onto surfaces of varying roughness.


2. They tested this hypothesis by first collecting the clingfish on the intertidal of San Juan, Washington, euthanizing and weighing them and took photos to measure the length and suction disc area. They analyzed the fish in detail using electron microscopy. Their interest was in three factors, the surface roughness of the substrate the clingfish would attach to, the force the clingfish exerted to stay on that substrate, and the tensile stress the clingfishs’ suction would be under due to its force created versus its area. This stress would be synonymous with the pressure being produced on the outside the suction cup. They then used 8 different surfaces, each one with a different roughness that they had created, accounting for all factors that were not adhesion-based on surface texture. They then put the clingfish on these various surfaces and pulled them off, measuring the force of the pull using a MTS Synergie 100 materials testing machine at a constant speed. If the fish came off at too quick a rate (less than 30 seconds), they were disregarded (a consideration made given that they were using dead fish rather than live). They took measurements to account for water pressure and other factors as well. To determine if the fish mucus was allowing for better adhesion, they put a viscous fluid into the manmade cups and tested with adhesion accordingly. Lastly to account for viscosity on adhesion they used to different liquids of varying viscosities (one around 20 centipoise and one around 1400 centipoise).


3. Their findings proved their hypothesis to be somewhat invalid in that they identified correctly what structure was involved but not so much how it was producing the effects. It was not so much that the papillae were affecting tremendous adhesion abilities, but rather that the papillae microvillae increased the frictional force, which in turn explained why the clingfish have trouble adhering to glass, a substrate with low frictional coefficients. They also did comparative studies and found that the suction ability fails in manmade suction cups because of slippage of the edges of the cup. The slippage causes a compressive force that results in buckling and allows fluid to flow in, but with clingfish there is no compression because the fish’s papillae grab onto the rough surfaces and latch on instead of letting in leakage as the manmade cups do. In regards to the mucus, the man-made cups did not adhere better with a viscous fluid, however, they did decide that the fish mucus may help the edges of the clingfish’s suction conform to surface irregularities. Their main result was that clingfish are able to adhere to a range of surface roughness, the rougher the better, and that their mucus would allow for better suction, but was not very advantageous in making viscous solutions for the manmade suctions.


4. With this understanding of how the clingfish is able to hold onto rough surfaces so well, it might be advantageous to look also into octopus suction force on smooth surfaces. Octopi suckers work in that the radial area of the inner muscles contract causing the inner walls to become thinner requiring the circumference of the cup to enlarge, making the suction cups volume increase. So because octopi work by altering area (van der Waals?) rather than frictional force, it would be interesting to test clingfish versus octopi on dry surfaces, to try and gain a better understanding of how their different systems work in regards to air densities (assuming the resources would be available to test drier environments in comparison to wetter ones and if it is at all somehow feasible to use these aquatic organisms for air testing, a big “if”). If so, one would assume that clingfish suction would be more useful for both dry and wet grip because of the mechanics using friction, however octopi would probably still reign in suction on smooth surfaces that are wet as well as dry (because the frictional force would still be low on smooth surfaces). The reason to test these different suction techniques in non-aquatic settings would be that it could help further understanding from things as simple as how to get window/shower/car props to stay on (e.g. dashboard GPS/phone holders), to more complicated advances like in robotics and trying to develop stronger grips, stability in walking, etc. The contrast in the two different types of suctions at different water densities in the air would provide a more valuable look at different situations, both worldwide and to account for such factors and the greenhouse affect and humidity becoming more rampant in some areas while other becoming drier.


5. This experiment would be a bit more complex in that there are more factors at work and so there will be more data overall. The first major difference, due to the morphological differences in octopi/clingfish suction, it probably would be necessary to use live organisms. I admit I’m not sure if dead octopi can retain suction, but I doubt it considering they are using muscular contractions… so unless there was access to electrical stimuli, and even then decaying would be a problem, so live octopi would be preferable. It makes sense to then use live clingfish as well to eliminate other variance; though I’m not sure live clingfish could be used well. I understand that live clingfish, being fish, would need to be in water longer, so the parameters of time would need to be altered. It would be more important to measure how just the force needed to pull the fish off surfaces rather than any semblance of time so standards of exclusion (the minimum 30 seconds adhesion for the clingfish in the previous study) would definitely have to be adjusted or removed entirely. The scientists would test at various surfaces of roughness starting with very smooth surfaces such as glass, to the rougher surface previously tested with clingfish in the aforementioned study in just a normal room with standard atmospheric conditions (37 degrees centigrade, standard water vapor, etc) as a baseline. The mechanics would be virtually the same, sticking the organisms (or in the case of the octopi, a sucker rather than all of them) to the surface and see how long each sucker was able to hold onto the surface. They would proceed through each surfaces recording that data for both organisms and then go back and modify the air, to simulate all various climates. The temperature needs to be maintained to have less confounding factors. The results most important to take note of would be how much force each type of suction can produce on dry to wet surfaces, comparing each level of wetness and using variations of surface roughness to allow for better comparison.

(ALSO: if you want to read an article talking more about Summers’ findings: http://news.yahoo.com/secret-clingfish-suction-power-found-182608876.html)

Professor Adam Summers

A while back we had a lecture from Adam Summers of the University of Washington and I took some notes to the extent of:


Sticky fish, sand swimmers and sharks- adventures in biomechanics

-       Adam Summers

Is there a limit on the size a shark can be? – 8 lineages of sharks have developed gigantism and sharks are larger on average: about a meter (1000 species of sharks)

So why are the sharks so large?

                  Forces balanced on shark (thrust v drag on horizontal, lift and static sinking force on vertical axis)

                   Static sinking force driven by skeleton

                   Lift driven by .5 x density x velocity^2 x constant x lifting area

                                     Lifting area is the most important factor

                                     Lift proportion to length^2

                                     The cartilage (sinking force proportional to length^3 eventually surpasses the curve of lift/length^2 but bony fish reach this point first, aka bony fish are shorter when they reach their max size for lift)

                   So cartilage releases a constraint
                   NOTE: that sharks had bones evolutionarily in the past

Sharks have routine cyclic loads with huge cycles
                   8x10^6 tail beats
                   2x10^9 tail beats in a lifetime

Cyclic loading leads to fatigue – tiny cracks that elongate and cause more cracks over time

                   NOTE: cartilage does not heal

                   fatigue by decreasing number of cycles
                   strain by overbuilding things to hundred times the load you expect the object to experience BUT cartilage is not overbuilt…

Periometer – a machine that tests the direct measure of damping

                   Can be used in vitro and in vivo

Things with high coefficients are bad at damping (like rubber). Apparently shark cartilage and rubber are almost identical in dampening ability

                   Stiffness inversely proportional to damping à this relationship can’t be broken unless the material is broken into composites

                    Tesserae tied together with peri…

Cartilage cannot be tested dry or it if fundamentally different from when it is wet

The central core of the cartilage (mineralized tesserae is just as stiff as compact bone)

                   Shark has high modulus material overlaid on a high damping material (like bulletproof vest – works once but then if you get hit in the same place twice, there is no protective value again)

                   Bioinspired material improvement – make the system a multishot deal

Solid/solid interactions (mediated by water) – ie. the burrowing fish

                   Burrowing, aggressive interactions, prey reduction, and adhesion

WATER MAKES A DIFFERENCE – presence of capillary adhesion disappears, other things appear

Pacific Sandlance

                   Everything eats it, it is widely distributed, and it burrows

What makes a burrowing skull? Ie. A sicilian

                   Compactness, highly mineralized

So how does a sandlance burrow considering it does not have a highly mineralized skull?
Do they mix up the sand to go through it via fluidizing? No

And they can burrow into everything (all sediments). But do they have a preference in grain size of the sediments?  - yes, clear preference for .5mm grain size. But why?

                   looked at the fish scale, not normal, scales go from dorsal to ventral, fused at .5mm

                                     There are critical friction points

Suction cups from the sea

                   Gobies have mucus all around edge of suction area, and edge covered in lumps

                    And all these lumps packed tightly in columns, are covered in hair (also seen in geckos and spiders)
                   and these hairs are sticky, but not when you look at a larger scale

                   They can attach up to 200x body weight

                   Found that as roughness of substrate goes up, ability to suck stays the same. The only outlier is glass.
                                     so the papillae are not affecting adhesion but increasing friction (hence why they don’t work on glass)
                   2-5% of disk width is can still stick on to

Failure of suction is when edges slip in and create a compressive force that causes buckling and allows fluid to flow in

 No compression with the fish because the papillae grab onto the rough surface and latch on rather than allow leakage like manmade suction cups


(I remember being particularly fascinated by the idea of harnessing the qualities of shark cartilage to apply to future bulletproof vest ideas)


So I graduated from Swarthmore this past Sunday and now have a B.A. in biology!

Even before graduating I had started taking summer classes at a community college near home. I’m taking human anatomy and physiology part one, and will be taking the second part this summer as well.

In more exciting news, I just got an interview for a physical therapy practice near by my home. It’s on Friday, wish me luck!!

Lastly, I’m trying to do a summer volunteer internship at a hospital nearby to experience acute and/or rehabilitation therapy settings. That and maybe volunteer at an acute pediatric facility on weekends if possible.

I’ve also gotten in contact with one of the few alums from my now alma mater that became a physical therapist and he’s steering me along with helpful hints and advice to get where I want to be. I might get to visit him in the nearby future.

I will soon be trying to get a certification in personal training and work my way up to other ACSM certificates.

I am also going to be working on finally getting my yoga teaching certification by continuing yoga immersions (I’ve got my eye on one that does about a weekend a month from this September until next June).

And last but not least, I have finally made a list of a few physical therapy schools I am interested in and have been looking up requirements and whatnot.

General update (yes it’s been quite a while). New semester, taking a biomechanics course (or I was) and now I’m just doing research projects until I graduate. One entails our cute little lizard friends and watching their motions and how they change after tail loss. The other is on turtles and symmetry. Poster presentations and the like coming up.