Life Masters Physics
Living things, especially cells, have mastered the forces of advanced physics in ingenious ways. This ingenuity sometimes inspires physicists to try to copy it. Here are some recent examples:
- Photosynthesis and quantum mechanics: Nature reported that plants take advantage of quantum mechanics in photosynthesis.1 “The photosynthetic apparatus of cryptophyte algae is odd – its pigments are farther apart than is expected for efficient functioning. A study into how this apparatus works so well finds quantum effects at play.” Grondelle and Novoderezhkin continued, showing that plants exceed humans at this skill:
It is common knowledge that plants, algae and certain bacteria use photosynthesis to convert solar energy into a form that can be used by the organisms to live and reproduce. But what is less well known is that the efficiency of photosynthesis might depend in part on quantum-mechanical processes. On page 644 of this issue, Collini et al.2 report evidence suggesting that a process known as quantum coherence ‘wires’ together distant molecules in the light-harvesting apparatus of marine cryptophyte algae. This is the first time that this phenomenon has been observed in photosynthetic proteins at room temperature, rather than at much lower temperatures, bolstering the idea that quantum coherence influences light harvesting in vivo.
Collini et al appeared surprised by their discovery: “Intriguingly, recent work has documented that light-absorbing molecules in some photosynthetic proteins capture and transfer energy according to quantum-mechanical probability laws instead of classical laws at temperatures up to 180 K,” they said. “This contrasts with the long-held view that long-range quantum coherence between molecules cannot be sustained in complex biological systems, even at low temperatures.” The plants’ ability to use “counter-intuitive design” employ quantum mechanical laws boosts the efficiency of light harvesting. Grondelle and Novoderezhkin titled their article, “Quantum design for a light trap.”
- Smart grid technology: Continuing on the theme of photosynthesis, a commentary in PNAS by David M. Kramer (Washington State U)3 describes how plants and other phototrophs (light-loving organisms) employ a “smart grid” system to dissipate excess energy and prevent damage:
To deal with the Promethean consequences of harvesting light, phototrophs have evolved a photonic “smart grid” that balances the delivery of light energy to its two photosystems—photosystem I (PSI) and photosystem II (PSII)—to prevent overexcitation and subsequent production of reactive oxygen species. Like human-engineered electrical systems, the photonic smart grid can regulate energy transfer at several levels. Unlike its engineered counterparts that have controllable power plants, phototrophs cannot down-regulate the sun. Instead, when light capture exceeds the capacity of the system to process it, it must be dissipated or rerouted to avoid photodamage. Chloroplasts deal with this problem by adjusting the properties of the photosynthetic antennae under photodamaging conditions.
Kramer went on to describe how the power plant has a fail-safe mechanism. The default state of the conformation of molecules in the photosystem is probably in the quenched mode – the safe mode. “In this way, several different stimuli can result in similar down-regulation of the photonic smart grid.”
- Adhesion by cohesion: We know that post-it notes work by creating cohesive forces with tiny droplets on paper. Beetles employ a similar trick to stick to leaves. They are so good at it, they can cling to leaves with a force 100 times their own weight, and then instantly detach themselves. They achieve this by controlling thousands of tiny liquid droplets in their feet. The adhesion created by surface tension in any one drop is small, but the large number of droplet contacts adds up.
Inspired by the success of the beetles, engineers at Cornell, with funding from the National Science Foundation and DARPA, have created a prototype adhesive that works on the same principle. It controls the droplets with electric fields. By reversing the fields, it can detach the device easily. Their main problem is figuring out how to keep the droplets from coalescing, but they are making progress. Science Daily reported that their palm-size device that employs water surface tension might make it possible for future Spider-man mimics to walk on walls.
- Acoustical nanomechanics: “NASA Studies Nanomechanics of Inner Ear,” announced PhysOrg. We often take our balance for granted, but it depends on sophisticated responses of tiny hair cells to the environment (see also a second PhysOrg article on this subject). But how do the hair cells maintain enhanced sensitivity to very small movements without being overwhelmed by large movements? The article describes how the amplifier can be instantly switched on or off by the organism.
The inner ear organs are designed and precisely attuned to changes in the environment: for the hearing organ, a change in the sound pressure, such as caused by a car horn, can deform the ear drum and rapidly lead to the recognition and location of the sound. For the balance organ, movement of the head, such as unexpectedly stepping off the curb, is sensed and rapidly leads to motor reflexes to maintain equilibrium. The more sensitive our ability is to detect these changes, the more acute our sensation. This remarkable tuning and amplification to detect the slightest stimuli, allows us to adjust our posture.
NASA wants to understand these mechanisms so as to help astronauts avoid vertigo in space. They are studying the hair cells in toadfish. “Fossil evidence, dating from at least the Devonian Period 400 million years ago, shows that the elaborate sensory structures used to sense the organism’s movement are remarkably conserved among vertebrata. The results demonstrate an active process in the hair cells of an ancient bony fish, thus suggesting that the mechanism is ancestral, and may underlie the broad appearance of active hair cell processes in amphibians, reptiles, birds, and mammals, including humans.” For a picture of one of the hair cells, see Science Daily.
- Cilia got rhythm: A paper in Nature last month tackled the problem of how cilia and flagella beat with regular oscillations.4 To understand it, the researchers came up with a mathematical model that employed “opposed motors and springs.” In particular, they studied the oscillation of the flagellum in sperm cells to come up with a “sperm equation.” This excerpt sounds like something out of an engineering textbook:
Any oscillation can be described as a sum of sinusoidal oscillations of increasing frequency, called Fourier modes; sideways oscillations can be described by the temporal Fourier modes of tangent angles. Power-spectrum analysis showed that experimentally observed oscillations in tangent angles were well approximated using only the first (fundamental) Fourier mode, so the sperm equation could be analytically solved using values of this mode. Tangent angles quantify the curvature of the axoneme at a given position, and the curvature is geometrically related to the sliding distance between doublets at that position. The sperm equation thus relates time-dependent angular movement at each position to the extent and rate of inter-doublet sliding at that position, and to the local forces that either oppose or promote further sliding.
The model contains two adjustable parameters – stiffness and friction of the active material inside the axoneme that deforms and exerts force during bending. It also contains several fixed parameters that J�licher and colleagues independently measured and fed into the equation. These include the hydrodynamic drag of the moving flagellum and its ordinary stiffness, both of which oppose active deformation, and the beat frequency. The authors obtained an excellent fit to the data, with both internal stiffness and friction taking the negative values expected for an active material. Importantly, a microscopic model of dynein behaviour, incorporating the force-dependent detachment concept illustrated in Figure 2, predicted negative values for stiffness and friction similar to those obtained by fitting the sperm equation.
The authors went on to describe physics concepts like beat frequency, force-detachment relationships, piston-like movement of doublets at the base of the cilia, and sliding friction. Your life depended on a sperm cell understanding the physics of beating its way to an egg cell – and still depends on trillions of other cilia and flagella being good physicists in the cells of your body today.
- Bacterial flagellar switch: A paper in Science discussed how the flagella of a bacteria can cooperate by using a stochastic switch.5 Several of the authors work in the Department of Physics at Oxford – not just the biology department. “The elements of protein signaling networks are often complexes that change their activity in response to binding specific ligands,” their paper began. “Multisubunit protein complexes often show cooperativity, with either binding or activity showing a switchlike sigmoidal dependence upon ligand concentration.”
The authors introduced the concept of “conformational spread” to explain the switching behavior between clockwise (CW) and counterclockwise (CCW) rotation. The description went on to discuss physical properties of the system: elasticity, a two-state Poisson process, stochastic coupling, and more. The fact that these cellular machines can be described with the tools of mechanics not only emphasizes the physics in biophysics, but shows how human engineers envy the techniques that living things have mastered.
- Thermodynamics: Maxwell’s demon found: The 19th-century physicist James Clerk Maxwell knew that entropy must increase in a system, but envisioned a way to overcome it: putting an intelligent selector in the system. A “demon” could, in principle, isolate hot and cold molecules into different compartments, for instance. PNAS reported that bacteria could be employed to harness random Brownian motion to turn gears.6
The laws of thermodynamics prohibit extraction of useful work from the Brownian motion of molecules or particles in systems at equilibrium (nonexistence of a perpetuum mobile of the second kind or Maxwell demon). When, however, such randomly moving objects interact with certain types of time-varying external potentials or with asymmetric geometrical obstacles under nonequilibrium conditions, their motions can be “rectified” and made directional. This phenomenon, first considered by Smoluchowski and then analyzed in detail by Feynman, underlies the operation of so-called Brownian ratchets and motors. The examples of biological “Brownian motors” include kinesin and myosin proteins converting chemical energy into directed motion on microtubules, and bacteria propelling themselves in viscous fluid owing to the “asymmetry”/chirality of flagellar rotation.
The authors suggest that human engineers could employee flagella as Maxwell demons to turn nanoscopic gears. It should be noted that all the instances they listed of Brownian ratchets are found in living systems or were produced by human engineers.
- Network engineering: To build a better distribution network, make like a leaf. PhysOrg announced that “Leaf veins inspire a new model for distribution networks.”
Following the straight and narrow may be good moral advice, but it’s not a great design principle for a distribution network. In new research, a team of biophysicists describe a complex netting of interconnected looping veins that evolution devised to distribute water in leaves. The work, which bucks decades of thinking, may compel engineers to revisit some common assumptions that have informed the building of many human-built distribution networks.
The netted patterns seen in leaves may not only be the most efficient way to get cargo from here to there; it may also provide the best safety net. The “tree network” most commonly deployed lacks the redundancy of leaf networks. “By contrast, in the leaves of most complex plants, evolution has devised a system to distribute water that is more supple in at least two key ways,” responding to fluctuating demand and re-routing around damaged parts of the network. Videos in the article show how water is distributed in different kinds of leaves. The article also pointed out that the loopy network design is also found in corals and insect wings. “These findings could seriously shake things up,” a researcher said. “People will have to take another look at how they design these kinds of systems.” One of the researchers is further studying how the design handles fluctuating loads, “guided by nature’s own solution in the leaf.”
The last entry talked about evolution numerous times: e.g., “evolution has devised a system” to do this or that, personifying evolution as some kind of engineer directing mutations toward a goal – an invalid notion in evolutionary theory. As evidence, the article pointed to the ginkgo tree as a “primitive” (less evolved) plant with a simpler distribution of veins. The article did not point explain, though, if its leaves were primitive, why it survived as a “living fossil” from ancient times all the way to the present, nor why corals, more ancient than ginkgo, already were outfitted with the more-advanced loop network design.
1. Grondelle and Novoderezhkin, “Photosynthesis: Quantum design for a light trap,” Nature 463, 614-615 (4 February 2010); doi:10.1038/463614a.
2. Collini et al, “Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature,” Nature 463, 644-647 (4 February 2010); doi:10.1038/nature08811.
3. David M. Kramer, “The photonic ‘smart grid’ of the chloroplast in action,” Proceedings of the National Academy of Sciences, online February 5, 2010, doi: 10.1073/pnas.0914429107. 4. T. J. Mitchison and H. M. Mitchison, “Cell biology: How cilia beat,” Nature 463, 308-309 (21 January 2010); doi:10.1038/463308a.
5. Bai, Branch et al, “Conformational Spread as a Mechanism for Cooperativity in the Bacterial Flagellar Switch,” Science, 5 February 2010: Vol. 327. no. 5966, pp. 685-689, DOI: 10.1126/science.1182105. 6. Sokolov et al, “Swimming bacteria power microscopic gears,” Proceedings of the National Academy of Sciences, January 19, 2010 vol. 107 no. 3 969-974, 10.1073/pnas.0913015107.
Don’t you get sick of the constant credit evolution gets for engineering design? It’s sickening because it is nonsensical. Evolution is not an engineer. It is not a person. It cannot organize parts for a goal; it is completely a random, instantaneous response to immediate circumstances. Evolutionists commit two fallacies with sickening frequency. For one, they use evolution as an active verb, saying, for instance, that hearts evolved to pump blood. That phrase evolved to is the fallacy: it implies goal-directed behavior. Only intelligent agents direct things toward functional goals. Matter in motion does not – nor do non-sentient living things. The apparent goal-directed behavior of bacteria toward a chemical gradient or moths toward a light is an artifact of their design. The organisms are not “deciding” to set goals and work toward achieving them. When you see evolved to, or find design and evolution in the same sentence, red flags should go up. The science and philosophy referees need to call a foul.
The second fallacy evolutionists commit is kind of like the anthropic principle in cosmology: “If the universe were not finely tuned for life, we wouldn’t be here to worry about the question.” That’s a dodge, not an explanation. It doesn’t explain why the universe is designed or how it got that way; it is an appeal to a counterfactual. Similarly, natural selection theory implies that if the bird did not evolve a wing, it wouldn’t be flying; if the plant did not employ quantum mechanical light traps, it wouldn’t be harvesting light. It does not follow that the bird did evolve the wing. That would be the logical consequence only if evolution is assumed a priori to be the only option. But it is not. One cannot assume what needs to be proved (circular reasoning). Since our uniform experience is that intelligent agents do engineering, intelligent design should be the default inference to the best explanation for wings, hearts and photosynthetic systems.
The item about Maxwell’s demon (#7 above) is noteworthy. As the Second Law of Thermodynamics is sometimes defined, all natural systems increase in entropy. We know that humans can overcome the law of increasing entropy (locally and temporarily) by exerting goal-directed work, such as in harnessing the chemical energy of gasoline (from sunlight) in a well-designed piston engine. Is that natural? If humans are natural products of evolution, then everything they do should be defined as natural. That would mean, however, that decreasing entropy is also natural – a contradiction with the Second Law of Thermodynamics, a law of nature if there ever was one. And what about the real-world Maxwell demons like ATP synthase motors, flagella and other Brownian ratchets that harness random thermal energy to perform useful work? Are they natural? It is only by making the word natural a self-contradictory concept, or by abandoning the universality of laws of nature, that a materialist can deny intelligent causes are at work in the universe and played a role in its origin.