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Care for Appetizers? Electric Proteins, Spidey Sense, and More

Welcome to the second day of the New Year! Like tasty sliders, these short news stories should get the juices flowing for big developments in 2020.

Electric Proteins

Dr. Stuart Lindsey at Arizona State University is an expert in single-molecule dynamics in biomolecules. Older methods of observing protein structure, such as X-ray crystallography, only gave single snapshots of the highly dynamic world, he says, where proteins rapidly change conformations and interact in complex ways. Electron transport has been well known in the cases of photosynthesis and metabolism. But a few years ago, his team was astonished to find that a run-of-the-mill protein conducted electricity. The protein was acting like a wire!

Further observations revealed that all proteins conduct electricity — even the ones that had “weren’t designed to do this”—

Until quite recently, proteins were regarded strictly as insulators of electrical current flow. Now, it seems, their unusual physical properties may lead to a condition in which they are sensitively poised between an insulator and a conductor. (A phenomenon known as quantum criticality may be at the heart of their peculiar behavior.) [Emphasis added.]

Lindsay’s team found, furthermore, that conduction occurs only when the protein is bound to its ligand. “The right connector is the very molecule that protein has evolved to recognize,” he says in a video clip. But surely the specificity implies design, not evolution, because of the fine-tuning of active site to substrate. Conduction becomes a signal related to the protein’s function. Since all proteins conduct in this fashion, this discovery opens up new possibilities for protein analysis, sequencing genomes, and biomimetic applications. Once again, observations overcome the lethargy of thinking that there are no more mysteries out there. Fascinating new layers of design keep coming to light with each closer look.

Spidey Sense

The orb webs of spiders are widely known to be made of one of the strongest yet most flexible materials in nature — the envy of materials scientists. Even children know, too, that backyard spiders have a “spidey sense” that can detect when a prey has been caught by the vibrations in the web. They have watched as the spider trots nimbly on its eight legs straight to the target. How many knew that the geometry of the web takes them in the right direction from the signals in the vibrations alone?

Spiders can tell the difference between vibrations from the wind and those of prey. Now, Siam News reports on a new model that shows spiders can also determine the direction and distance of prey from the vibrations alone. Most previous models, they say, were one-dimensional. A new two-dimensional model shows that the vibrations encode additional information.

“By continuously testing the web, the spider acquires the dynamical response of the web approximately on a circle centered at the web’s origin, and with radius significantly small with respect to the web dimensions,” Kawano said. “Numerical simulations show that identification of the prey’s position is rather good, even when the observation is taken on the discrete set of points corresponding to the eight legs of the spider.”

Perhaps more discoveries about animal designs will be made with models that take into account the information encoded in vibrations.

2020 Vision on Cilia

Since cilia were introduced as one of Michael Behe’s first examples of irreducibly complex molecular machines in 1996, much more has been learned about them. A new report from University of North Carolina at Chapel Hill adds another layer of complexity. These cellular “antennae” act as communication beacons that affect electrical wiring in the nerves. And if the cilium’s “signaling hub” isn’t wired correctly, debilitating neural diseases can result.

“Our experiments demonstrate that ciliary signaling facilitates appropriate patterns of axon tract development and connectivity,” said Anton, who is a member of the UNC Neuroscience Center. “Disrupting ciliary signaling can lead to axonal tract malformations in JSRD.” [Joubert syndrome-related disorders.]

Although cilia are found on most cell types, their significance in brain development, has been largely underappreciated, until recently.

Scientists now know that cilia sense the environment around them, and dysfunctional cilia mess up axonal growth and connectivity during fetal development.

Behe’s descriptions related primarily to how cilia are built and how they function. If these UNC scientists seek to understand “precise manipulation of ciliary signaling,” it would be opportune for ID scientists to go beyond anatomy and physiology of cilia, and explore the information content in the signals as well.

Transitional Forms

Behold a transitional form: not in a Darwin tree diagram, but within a single organism: a centipede. Japanese scientists at Tohoku University watched with interest how this creature transitions from walking to swimming. The scientists “decoded the flexible motor control mechanism underlying amphibious locomotion, or the ability to walk on land and to swim in water, in centipedes.” What is being learned in this simple example could be studied in more complex animals that make transitions between media.

The embedded video clip shows the centipede’s smooth transition between land and water without missing a beat, as the legs give way to whole-body undulations in the water. The scientists realized that control systems are required to pull this off. Each limb must be in communication with the brain, to send and receive signals, and to know when to switch modules. A figure caption explains,

Control mechanism suggested from behavioral experiments. Either “walking” or “swimming” mode can be selected at each part. When a “swimming” signal comes from the brain, it is sent posteriorly, and “swimming” mode is selected at each body part. However, it is overridden by “walking” mode at the point where the leg contacts the ground. Then, “walking” signal is sent hereafter.

In Brief…

MicroRNAs (miRNA) are coming of age. How specific are their interactions with messenger RNAs (mRNA), and what roles do they play in gene regulation? Researchers at the Whitehead Institute for Biomedical Research found “surprising individuality of microRNAs” and are seeking to identify targets where miRNAs bind to mRNAs, reports This could represent a coming quantum leap in understanding genetics. “Altogether, these findings paint a much richer picture of miRNA-mediated gene repression,” the article says.

Junk DNA” continues to rise in value. Scientists at the University of Otago are finding active genes in non-coding DNA, reports in another recent article. Finding active modules of enzymes coded for in regions thought to be “non-functional variants” of genes represents “a fundamental discovery,” concludes Professor Barry Scott of Massey University. Another breakthrough is the discovery that “modular enzymes” can generate more than one product. “Scientists in many fields — including medicine — should go back and take a look at previously discarded ‘junk genes’, because some of these may actually produce useful bioactive products,” Scott advises.

Undoing devolution. Could genetic reprogramming overcome deafness? The Massachusetts Eye and Ear Infirmary is experimenting with methods to regrow hair cells in the inner ear, reports Medical Xpress. Good science should bring positive benefits. Sometimes that involves getting the bugs out of programmed modules that have failed. “The most significant aspect of the current study is the fact that fully mature mammalian inner ear still retains the capacity to divide and regenerate if it is sufficiently reprogrammed,” Dr Zheng-Yi Chen comments. If they succeed, similar reprogramming methods might work on the retinas of the blind and the central nervous systems of the paralyzed. As working legs are better than crutches, original designs are better than artificial props — and would be most satisfying to patients. Perhaps science will uncover devolved capacities for regeneration, and find ways to reprogram those, too.

The future looks bright for design-guided science. These are a few ways in which ID advocates could take the lead in 2020.

Photo: Sliders as appetizers, by Prayitno, via Wikimedia Commons.