Showing posts with label genetics. Show all posts
Showing posts with label genetics. Show all posts

Saturday, March 19, 2022

Lizard tails, gecko toes, and Mission: Impossible

In Mission: Impossible! Ghost Protocol (the fourth installment of the series), a memorable scene has the heroic--and nigh-indestructible--Ethan Hunt (Tom Cruise) climbing the outside of the Burj Khalifa, more than 1700 feet above the ground. Because it's Mission: Impossible, Hunt of course has no harness, rope, or other climbing gear--only a pair of adhesive gloves and some rubber-soled shoes. 

When tech wizard Benji (Simon Pegg) is giving Ethan the demo of how the gloves work, he emphasizes that to un-stick the glove from the window, Ethan needs to use a "rolling-off motion." Ethan, being the super-agent he is, quickly masters this rolling motion and proceeds to use the gloves to pull himself up the sheer glass wall of the skyscraper. 

(It probably goes without saying that, of course, one of the gloves' batteries die once he is past the point of no return, requiring him to finish the climb with only one miracle sticky glove, which manages to catch his entire body weight from a free-fall a short time later.)

As with most action movies, willing suspension of disbelief is required to truly appreciate the stunts that punctuate Ghost Protocol at predictable intervals. But in this case, the physics isn't actually that far-fetched: it's likely that the gloves are biomemetic--technology and engineering inspired by the design and/or function of biological systems. In this case, judging by their appearance and Benji's description of how they work, it's a safe assumption that the gloves are based on the biomechanics and biophysics that help geckos, flies, and other small animals scale walls, dangle from ceilings, and perform other impossible missions. 

The climbing abilities of various lizards have been an object of fascination at least since the time of Aristotle, but it's only within the last century or so that we've been able to start building a detailed understanding of how the structure of their feet enables those abilities. With the advent of advanced microscopy, computer modeling, and incredibly sensitive force detection tools, the mechanism of lizard toe adhesion has become more well understood.

A lizard climbing up a wall or across a ceiling has to have a way to "turn on" and "turn off" the stickiness of its feet. Always "on" and the lizard can't move; always "off" and it's stuck (heh) with the limitations of gravity like we poor bipeds. So how does it work? 

As with many seemingly miraculous everyday occurrences, lizards can thank physics for their selectively sticky feet. Like Benji's magic sticky gloves, lizard feet have a differential stress response: they respond differently to tension than to shear forces. When under tension, the adhesive force is strong; but subject it to a shearing or bending force and it weakens enough to detach. The "rolling motion" Ethan uses to un-stick his hand from the Burj Khalifa's glass produces that shearing force, and lizards create a similar type of motion in their feet when they walk. 

The notion of a material that responds differently to different kinds of force shouldn't be too unfamiliar: rope is strong under tension (pulling) but weak under compression or shear (sideways) forces, whereas many kinds of structural materials (girders etc.) are strong under compression but weaker under shear or tension forces. This is one of the reasons why earthquakes, tidal waves, and other disturbances that produce strong shear forces can cause massive amounts of structural damage, even though they generate less total force than the weight of the building itself pressing downward every day. 

But these are all examples of solid objects demonstrating internal strength or weakness, which is a far cry from adhesion (stickiness) between two different objects--and this is where the physics comes in. As it turns out, gecko feet owe their stickiness to the millions of tiny setae (projections) that make up the bottom surface of each toe--more than 14,000 per square millimeter. Because of their microscopic size, each seta experiences tiny, transient molecular forces known as van der Waals forces when it contacts another surface. 

Although van der Waals forces are among the weakest interactions between molecules, they nonetheless can provide a significant amount of adhesive force when applied to the millions of individual setae on each foot. In one clever study, Autumn et al calculated an adhesive force of more than five atmospheres--more than enough to hold a tiny lizard against the ceiling. 

What's especially fascinating about Autumn et al's results is that they were able to demonstrate that the adhesive forces were primarily the result of the size and shape of the setae, rather than their chemical composition: when they created simulated setae out of rubber and polyester resin, they observed the same adhesive properties as were present in the gecko toes. They were also able to demonstrate that the adhesive force increases significantly as the setae get smaller--which may be part of the reason this type of setal structure has been evolutionarily selected in so many climbing lizards.

The idea that large numbers of setae may have a survival advantage in some species is supported by the genomic work of Liu et al, who used genetic data to construct phylogenetic trees showing the evolution of a number of different lizard species. Their results showed that Gekko japonicus, the Schlegel's Japanese gecko, contain more copies of genes for the proteins that form setae than do other lizard species who have fewer setae per unit area. 

In other words, the species that have lots of very tiny setae have more copies of the gene than the species with fewer, larger setae or no setae at all, and the density of setae is closely related to the species' habit: G. japonicus is a typical gecko, with sticky feet that it uses to climb trees and walls and catch prey, and it has the most copies of the gene and the largest setal density; Anolis carolinensis, the green anole, has fewer copies of the gene and a lower setal density, but still demonstrates some wall-climbing ability; and Alligator sinensis, the Yangtze alligator, has only two copies of the gene and no setae--it lives primarily in water and does not climb. These patterns, together with the inferred timing of the genetic differentiation between the species, support the hypothesis that selection pressure drove the increase in the number of setae (and correspondingly stickier feet).  

Liu et al also investigated the evolutionary history of another well-known trait of many lizard species: caudal autotomy, or the ability to "shed" a still-wriggling tail to distract predators and buy time for an escape. Species that have this ability, such as G. japonicus and An. carolinensis, show positive selection pressure for genes associated with wound healing and cell growth, whereas species that don't shed their tails lack those positively selected genes. 

And now we come full-circle, because it turns out that there are a lot of similarities between the physics of gecko toes and the physics of tail autotomy: both rely on the characteristic strong-under-tension-but-weak-under-shear strain responses associated with the microscopic interfaces between surfaces. 

Just as a gecko's foot is covered in millions of tiny setae, which generate adhesive forces, the point at which its tail connects to its body also contains large numbers of tiny pillars of muscle that hold the tail in place but also allow for its quick release. At the point where it detaches during autotomy, the tail contains a roughly conical arrangement of tiny, mushroom-shaped pillars. The "cone" shape at the end of the tail interfaces with a corresponding "socket" shape on the lizard's body--in other words, the tail attaches to the body the way a phone cable attaches to its charging socket. 

Unlike a charging cable, though, the lizard's tail attachment is quite strong under tension--it won't detach if it's pulled straight backward away from its body. This helps prevent the tail from falling off under regular lizard behavior. But if the lizard moves its tail in just the right type of side-to-side motion, its tail separates from its body. 

Baban et al used a biomemetic fracture model to elucidate how this works in detail. They demonstrated that the geometry of the tail-body attachment, along with the specific type of motion the lizard uses to initiate detachment, allows a "fracture plane" to propagate through the tail attachment surface. As the plane propagates, the tail muscles detach from their corresponding partners in the lizard's body, and eventually the entire tail has detached.

By creating silicon-based models of the tail and its attachment socket, Baban et al were able to demonstrate that the arrangement of the micropillars contributes to the tail's behavior under different kinds of stress. In most situations, the flexibility and nanoscale adhesion between the micropillars and their corresponding sockets helps to stop any incipient fractures from propagating. As Ghatak describes in a summary of the Baban article, the flexibility ensures the stresses never build up enough to cause the tail to detach completely.

It's probably unlikely that Ethan Hunt will ever dangle from the Tokyo Skytree by a detachable rope-tail...but one never knows. 


Autumn, Kellar, Metin Sitti, Yiching A. Lang, Anne M. Peattie, Wendy R. Hansen, Simon Sponberg, Thomas W. Kenny, Ronald Fearing, Jacob N. Israelachvili, and Robert J. Full. 2002. "Evidence for van der Waals adhesion in gecko setae." Proc. Natl. Acad. Sci. 99 (19): 12252-12256. https://doi.org/10.1073/pnas.192252799.

Baban, Navajit S., Ajymurat Orozaliev, Sebastian Kirchhof, Christopher J. Stubbs, and Yong-Ak Song. 2022. "Biomimetic fracture model of lizard tail autotomy." Science 375 (6582): 770-774. https://doi.org/10.1126/science.abh1614.  

Ghatak, Animangsu. 2022. "How does a lizard shed its tail?" Science 375 (6582): 721-722. https://doi.org/10.1126/science.abn4949.

Liu, Yan, Qian Zhou, Yonjun Wang, Longhai Luo, Jian Yang, Linfeng Yang, Mei Liu, Yingrui Li, Tianmei Qian, Yuan Zheng, et. al. 2015. "Gekko japonicus genome reveals evolution of adhesive toe pads and tail regeneration." Nature Communications 6, 10033. https://doi.org/10.1038/ncomms10033.

Monday, February 15, 2010

Links for the week of 2/8/2010

Physical sciences:
Scientists from the Weizmann Institute of Science in Rehovot, Israel figure out how to get water to freeze at different temperatures by modifying the electric charge on the surface it is sitting on. (ScienceNews)

Plastic water? misc.ience describes how scientists are able to make hydrogels that retain their shape, but are made almost entirely out of water.

Biology:
Researchers at the University of Maryland shed light on how Egyptian bats track their prey. Rather than firing sound waves directly at it, they shoot to either side. This makes them less likely to locate prey, but once they have found it, they can follow it more accurately. (EcoTone)

Beware mussels bearing "gifts": Neuroskeptic describes a study of amnesia caused by toxins in shellfish.

It's now fairly common knowledge that bees dance to tell other bees where to find food. But a recent study in Current Biology shows that they also use short buzzes to tell each other not to go to a dangerous location. Ed Yong at Not Exactly Rocket Science describes the study.

Female crickets can apparently warn their young of environmental dangers: baby crickets born to mothers hunted by wolf spiders are more likely to freeze and hide when they detect the spiders. (Not Exactly Rocket Science)

Sociology/human psychology:
Also from Neuroskeptic: A study of whether antipsychotic medication can reduce psychotic experiences in marijuana users.

If you want to encourage altruism, lead by example...and cleaning that bathroom might not hurt, either. A recent study suggests that watching other people perform good deeds increases the observer's altruistic tendencies. Interestingly, smells associated with cleaning also seem to increase altruism. (Psych Central; Not Exactly Rocket Science)

Daniel Hawes at Ingenious Monkey-20 two 5 has an excellent pair of posts on factors affecting girls' success in math.

A number of bloggers have written about Inuk, an ancient Greenlander whose entire genome was recently sequenced. Gene Expression describes the genetic relationships between Inuk's people (which anthropologists call the Saqqaq) and other human groups. Ed Yong describes what we know about his appearance, and how we know it.

John Tierney of The New York Times describes a sociological study conducted using the Times' own records. As it turns out, articles that inspire awe and those that deal with complex topics are the most likely to be forwarded on. (I wonder if there might be selection bias--perhaps readers of The New York Times are more likely to be interested in complex or awesome topics?)

Is religion necessary for morality? A common belief (for lack of a better word) is that religions originally developed to provide a basis for morality--i.e., to give the members of the society rules to follow to keep the society functioning. A recent analysis of studies in moral psychology, however, suggest that religious training and beliefs do not affect how people make moral decisions. Instead, the authors suggest, religion may have filled other needs in early society, such as the need to feel in control of one's surroundings. (björn brembs blog)

Friday, February 5, 2010

Links for the week of 2/1/2010

Since I don't seem able to put together a daily links post, maybe weekly will be more manageable. Within each group, links are posted in approximately reverse chronological order (most recent first). (Yes, I know some of these are from before Feb. 1. I never said what the error bars were on that date.)

First, DINOSAURS!:
Fossil Feather Colors Really ARE Written in Stone (Living the Scientific Life)
The renaissance of technicolour dinosaurs continues (and the gloves come off...) (Not Exactly Rocket Science)
Oldest feathered dino shows its colors (Science News)
Newly Described Bird-Like Dinosaur Predates Archaeopteryx by 15-20 Million Years (Living the Scientific Life)

Next: Running...ur doin it rong...(maybe):
Evo. Anthro. Study Suggests You Might Be Running Wrong (Laelaps)
New Nature Magazine Cover Story Shines More Light on Barefootin' (Runner's World Peak Performance)

How to not be annoying at the gym, courtesy of Peter at Obesity Panacea:
Appropriate Gym Etiquette
Annoying Gym Personalities
What to Wear


And finally, assorted other interesting things:
Seven habits of highly successful toads (Not Exactly Rocket Science)
Friday Weird Science: Preserving the Species (Neurotopia)
Un-Natural Disasters (In Terra Veritas)
Backyard Chickens: An Art, A Science, A Social Movement (Food Politics)
Dave Munger (formerly of the Cognitive Daily) has launched a new blog, The Daily Monthly. It's awesome.
Bees can learn to discriminate human faces (Arthropoda)
Playing to Learn (NYTimes Op/Ed)
Looking inside the structure of the Yellowstone caldera (Eruptions)
Power source for a light saber (Dot Physics)

Thursday, January 21, 2010

New NSF-funded site on science education

I just got this update from a friend (via LinkedIn):

A new NSF-funded site has just launched. According to the release:

"[The site is] dedicated to cataloging best practices in media-based science education and getting the word out about--and discussing--innovative new media-based science education programs and concepts (where media includes both traditional and new media). The site is located at:

http://www.mediasciencelearning.com/

To celebrate its launch (and help get its discussion areas quickly up to critical mass), the grantees (at their own expense, not NSF's) are giving away Zingerman's gift certificates to the best (and most prolific) contributors to the site's case discussions, located at:

http://www.mediasciencelearning.com/CaseStudies

Related to this, if you know of any great media-based science education programs that ought to be highlighted by this site (or you run one yourself and are looking for feedback, publicity, collaborators, or funders), you can submit it at:

http://www.mediasciencelearning.com/addacase/
"

Sunday, January 17, 2010

Some more useful science online resources

Scivee--share your science online!

SciNet--a new social network for scientists of all stripes, from AAAS.

Periodic Table
--interactive periodic table. h/t Staten Island Academy student in ScienceOnline session. (Play with the temperature slider and see how the states of different elements change!)

Miss Baker's Biology Class--some really amazing student projects, blogs, etc.

Staten Island Academy's blog community
--a great role model for student blogging.

Saturday, January 16, 2010

Some cool science and education web sites, courtesy of ScienceOnline2010

FieldTripEarth--free data, plus info from real, live research programs going on all over the world.

NESCent--the National Evolutionary Synthesis Center. More (lots more) free data, plus educational materials on cutting-edge evolution research. (I think when the speaker demonstrated this, half the room started drooling at the data that are available...)

EduWeb--a source for online/digital, educational games on science, technology, history, and art.

Dryad--another open access data depository.

PRI's The World Science--weekly science podcasts, news stories, etc.

Scitopia--a peer-reviewed-research search engine.

Fold.it--play computer games for SCIENCE!

Spot.us--donate to journalists needing funding to cover their stories.

Science for Citizens--find research projects looking for volunteers.

Pandemic II (game)
--play the bad guy. Design germs, infect people, get points!

Science Cheerleaders
--learn basic science facts, find citizen science projects, and take a brain makeover quiz!

Friday, January 16, 2009

Self-catalytic RNA enzymes

GumbyTheCat recently posted about a study in which researchers created self-replicated RNA enzymes. There was a bit of discussion in the comments about what those enzymes are all about and whether they are, indeed, "true" enzymes (i.e., proteins).

As I have access to Science magazine online, I was able to read the actual article (Gumby's post was based only on the abstract, I think), and so I can now answer the question of what, exactly, an RNA enzyme is, and how the research group got it to replicate itself.

An RNA enzyme, it turns out, is not a true enzyme. That is, it isn't a protein made up of amino acids. It's actually a strand of RNA. The particular RNA enzymes this group made look kind of like a capital T with one side of the crossbar a lot longer than the other. Like all RNA, they're made up of nucleotides (a nucleotide is a molecule consisting of a sugar molecule--ribose, in the case of RNA--a phosphate group, and a nitrogenous base). (I am forced to conclude that the "RNA" in "RNA enzyme" is an adjectival form, rather than a description of what the enzyme catalyzes.)

To understand how the enzyme works, you first need to know a bit about bonding in nucleic acids (DNA and RNA). What follows is a brief discussion; details can be found in any introductory biology textbook.

A single strand of a nucleic acid is a polymer (a really big molecule made up of a lot of similar, smaller subunits called monomers). As mentioned above, the monomers in nucleic acids are nucleotides. When nucleotides join together to form a nucleic acid, the sugars and phosphates bond together to form a "backbone." The nitrogenous bases stick off one side of the backbone. There are five nitrogenous bases that can form nucleotides: thymine, adenine, uracil, guanine, and cytosine. They are abbreviated T, A, U, G, and C, respectively. A, T, G, and C are found in DNA; RNA contains A, U, G, and C. So, a single strand of RNA looks kind of like half a ladder; the rungs are A, U, C, and G molecules. A double-stranded nucleotide (such as DNA) looks like a full ladder; the base in each "rung" is bonded to another base on a rung on the other side of the ladder. The bonded bases form a full rung. (Of course, a DNA molecule really looks like a twisted ladder, but the physics of why it twists isn't important for our purposes here.)

These bases aren't just any random molecules, though. As it turns out, their molecular structures force them to bond together in specific ways: A can bind only with T or U, and G can bind only with C (and vice versa, in each case). In a double-stranded nucleotide, therefore, each rung is made up of either a C-G pair or an A-T (or A-U if it's RNA) pair. You can probably see the beauty of this arrangement: it means that if you have one half of a double strand of RNA or DNA, you can construct the other half.

As I mentioned before, the RNA enzymes in this study look like lopsided Ts. The stem of the T is actually a double strand of RNA: part of the RNA molecule has bonded to itself. (A similar structure is found in some kinds of RNA that take part in transcription and translation in eukaryotic cells.) The crossbars of the T are single strands of RNA.

Each enzyme forms from two smaller pieces of RNA: a straight piece (called "B") and a piece that looks like a regular (i.e., not lopsided) T (called "A"). The straight piece binds to one of the crossbars of the T-shaped piece to form the lopsided T (which the researchers refer to as "E", for enzyme).

Each enzyme (and each sub-enzyme piece) actually exists in two "mirror-image" forms (i.e., E and E', A and A', and B and B'). The mirror-image forms can bind to each other because of the way the bases pair. However, A doesn't bind to A', or B to B'. Instead, A binds to B', and B bonds to A'. The A-B' combination forms E; the A'-B combination forms E'. [EDIT: the previous sentences should read "Instead, A binds to B, and B' binds to A'. The A-B combination forms E; the A'-B' combination forms E'."] The drawing below shows my lame attempt to summarize.

Essentially, when the researchers put some E into a mixture of A, B, A', and B', the A' and B' pieces bonded to the E to form molecules of E'. Once there was some E' in the mixture, the A and B molecules could bond to it to form new E molecules, and Presto! self-replicating RNA.

Of course, it wasn't really that simple. And actually, the not-simple part is kind of cool: The original E that the researchers used wasn't very efficient at catalyzing its own formation. So, basically, the researchers evolved it. They generated new A and B with mutations--variations in the sequences of bases on the backbone--and selected the ones that formed E that could replicate itself most quickly.

Because they have groovy tools (such as polymerase chain reaction machines) and computer to do the analysis, they were able to try a whole lot of different combinations in order to find the set of A and B that produced the most efficient E.

All in all, a really groovy little study!

Lincoln, Tracey A., and Gerald F. Joyce, 2009. "Self-sustained replication of an RNA enzyme." Sciencexpress. published online 8 January 2009; 10.1126/science.1167856.