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Biophysics Miscellany

“Bees … by virtue of a certain geometrical forethought … know that the hexagon is greater than the square and the triangle and will hold more honey for the same expenditure of material.” – Pappus of Alexandria (first half of the 4th Century AD)

Here’s a bunch of stuff about bees … just because they’re cool.

Last week in describing the search for extraterrestrial life I recounted the celebration in the Eagle pub of the discovery of the structure of DNA, as told by James Watson in The Double Helix. I got a couple of lines in response from Raynor Smith that put it in perspective. I posted it above my desk and now share with you: “These great men did indeed discover the secret of life. The secret is to gather with friends in a warm pub, and raise your glass to celebrate your accomplishments, and likewise those of your friends, whether large and earthshaking or small and humble.”

From the old blog WHAT’S NEW by Robert L. Park – Friday, November 19, 2010

Tizard told a salutary story of Rutherford, when he was presiding over a meeting of the [Royal] Society, and had been listening for half-an-hour to a young biologist reading a paper. When the paper was finished Rutherford said, “Before I invite discussion on this paper there is one remark I would like to make. I have listened to you, sir, for half-an-hour, and although I believe I am considered to be a fairly intelligent man I have not understood a word you said. Now, would you mind getting up again, and telling us in five minutes what you did, why you did it, and what results you got?”

From the Editorial by R. V. Jones in Notes and Records of the Royal Society, 27 (1972).

What is Biophysics?

Medical physics and and biotechnology: highlights of 2023

Of course the central question is, ” What is biophysics?” (from the Biophysics Journal, March, 2016). In our usual humble way physicists proclaim that Life is Physics (January, 2019) as well as Life: modern physics can’t explain it – but our new theory, which says time is fundamental, might (April, 2023 – [arXiv article]), The laws of life (March, 2017), The physics of life (January, 2016), (see rebuttal of this at Starlings’ patterns are not spontaneous – March, 2016), Physical Models of Living Systems (January, 2015) – see author interview Questions and answers with Philip Nelson (January, 2015) – Does cell biology need physicists? (January, 2011), and Physics and the cell (October, 2010). More recently there is ‘Breakthrough’ could explain why life molecules are left- or right-handed (June, 2023), A New Idea for How to Assemble Life (May, 2023), Actin assembly is a physics problem (February, 2023) and Starfish Whisperer Develops a Physical Language of Life (January, 2023). We have literally been at it forever or, at least if your definition of forever is “quite a while”, then consider that the book “Mathematical Biophysics: Physico-Mathematical Foundations of Biology” by Nicolas Rashevsky was published in 1938! We do also try to be useful to humanity as in Physics techniques line up to advance medical care (December, 2019) and more specifically to my subfield of physics –  Dynamic nuclear polarization: how a technique from particle physics is transforming medical imaging (May, 2023) and Using particle physics to foster medical innovation (September, 2020).

Perhaps the most acclaimed (or derided) book by a physicist on the essential human question is What is Life? (Cambridge University Press, 1944) by Erwin Schrodinger. This classic was still garnering attention more than seventy years later as evidenced in the August, 2018 review of the book Schrodinger’s cat among biology’s pigeons: 75 years of What Is Life?. (See a more modern and slightly different take in the article in quanta magazine, What is Life?, July, 2022). The ideas put forward by Schrodinger, in particular the combination of physical laws and information theory, are a riff on Maxwell’s Demon and are further elaborated on in a modern context in How Maxwell’s Demon Continues to Startle Scientists (April, 2021), Quantum coherence turns up the heat on Maxwell’s demon (October, 2020), and Does new physics lurk inside living matter? (August, 2020). Also, there is the unsolved problem of how a bunch of molecules become alive. Have a look at The conceptual framework for measuring the emergence of life (March, 2014) for one take on it. On top of that there is The surprising physics of babies: how we’re improving our understanding of human reproduction (February, 2023).

Besides Schrodinger, many well-known physicists were attracted to biological problems. The book Origins of Life (1999) by famed theoretical physicist Freeman Dyson is another attempt to put a physics spin on life’s origins. Perhaps less well known was the interest shown in biological problems by Albert Einstein. There is the recently found (May, 2021) Long-lost letter from Einstein discusses link between physics and biology – 70 years before evidence emerges (see also Einstein letter reveals interest in animal navigation). The letter was to Karl von Frisch who won the 1973 Nobel Prize in Physiology or Medicine for the discovery of how bees communicate a route to nectar through the waggle dance. Test your german by checking out the original article Die Sprache der Bienen und ihre Nutzanwendung in der Landwirtschaft or you can get a sense of the excitement this generated from the 1949 article in Nature. Actually, physicists have won the Nobel Prize for Physiology or Medicine a number of times as described in Breaking boundaries: how physicists won the Nobel Prize for Physiology or Medicine (September, 2022).

Richard Feynman held a deep interest in biological problems as evidenced by:

There also those physicists who don’t dabble but go into biophysics, although there does seem to be somewhat of a gender divide as discussed in Why does biophysics attract a disproportionate number of women? (June, 2021). A number of physicists do make the transition into medical physics (November, 2019) – see also Studying physics to improve healthcare systems (January, 2022), A focus on cutting-edge medical physics research (July, 2021) and Changing research field from astrophysics to neuroscience (July, 2021). Finally, there is also the question of the biophysics curriculum at various institutions. There has been a lot of discussion of this including Revamping graduate biophysics education (June, 2021).

One of the things you’d think we’d have figured out by now is water. I mean, humans have been studying it for … well, forever. As far back as the 6th century BC the philosopher Thales proclaimed that water is the Primary Principle. And it cannot be stated forcefully enough how important water is to life, all the way from trees:

to the cell:

So perhaps you’d be surprised to see such articles as Water isn’t normal (March, 2024), Water is weird. A new type of ice could help us understand why (February, 2023) or Freshwater ice can melt into scallops and spikes (February, 2022) whose first line is “Water’s wacky density leads to strange effects that researchers are still uncovering” or Controversy Continues Over Whether Hot Water Freezes Faster Than Cold (June, 2022) or Water transforms into gold-coloured metallic solution (August, 2021) and Water as a metal! (July, 2021) or Direct evidence emerges for the existence of two forms of liquid water (February, 2022) and Fast x-ray scattering reveals water’s two liquid phases (November, 2020). In Second critical point appears in two models of water (August, 2020) it is written, “The central role of water in life as we know it makes it easy to forget just how unusual it is. Unlike most other liquids, water is denser at ambient pressure than the ice it forms when it freezes. It also exhibits negative thermal expansion (meaning that it expands on cooling, rather than contracting), becomes less viscous when compressed and boasts no fewer than 17 crystalline phases.” To back up this point there’s also:

where it appears that water is much more complicated than we’d naively thought.

For more articles on research of and about water (with some stuff about fluids in general) have a look at Stuff About Water.

Speaking of water in its frozen form (weren’t we?), check out icicles where I’ve gathered some articles about the “Ice Atlas” put together by my old buddy at the University of Toronto, Professor Stephen Morris. The Ice Atlas contains some 230,000 images of icicles in various states of evolution. This is a serious subject of research since little is known about icicle formation. For a technical discussion see On the origin and evolution of icicle ripples by A.S. Chen and S.W. Morris (September, 2013) or more recently there’s Here’s why icicles made from pure water don’t form ripples (February, 2023) and Icicle Structure Reveals Growth Dynamics (November, 2022).

Some years ago I got interested in work being done to clarify how the eye works. Have a look at Biophysics Approach to the Eye where I collected a number of articles on this topic which “caught my eye” (… sigh).

Our very own Prof. Christopher Bergevin was co-organizer of a conference on the Mechanics of Hearing which was held on June 19-24, 2017, at Brock University. Sounds like it was fun (pun intended, again). Here are some biophysicsy-type articles on hearing that I’ve collected over the years. An intriguing recent (June, 2022) article is Hearing the Quantum Difference. A whole bunch more can be found on Prof. Bergevin’s homepage. Check out York University Biophysics for more information about the biophysics program at York University and Biological Physics Folk for information on the research interests of those doing biological physics (aka biophysics) at York.

The American Physical Society has a number of publications including research journals like Physical Review and physics outreach magazines like Physics Today. In APS News they have a regular feature called This Month in Physics History. Here are a few relevant to biophysics:

Okay, it was patently ridiculous that Rutherford won the Nobel prize for chemistry and not physics but the trend continues as, it seems to me, both the 2017 Nobel Prize for Chemistry and the 2014 Nobel Prize for Chemistry were for what has been described here as biophysics.

The 2017 Nobel was for “developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution”. In February, 2020, it was stated that Revolutionary cryo-EM is taking over structural biology while as recently as June, 2020, it was proclaimed that it “opens up a whole new universe” – see Revolutionary microscopy technique sees individual atoms for first time. This is starting to be realized as discussed in The secret lives of cells as never seen before (October, 2021). This was all foretold in The revolution will not be crystallized: a new method sweeps through structural biology (September, 2015).

The 2014 Nobel was for an improved microscopic technique that allows for viewing viruses and even single molecules without destroying them. This allowed for the collection of information about subcellular systems for the first time. See The Nobel Prize in Chemistry: Life in Sharp Focus, Nobel Prize in Chemistry: Celebrating optical nanoscopy, 2014 chemistry Nobel Laureates broke barriers in light microscopy, and Nobel Prize For Chemistry 2014: Eric Betzig, Stefan W. Hell And William E. Moerner Honored For Development Of Super-Resolved Fluorescence Microscopy, Nobel Prize – Seeing Single Molecules, Chemistry Nobel awarded for super-resolution microscopy. There are many articles about the use of “nanoscopy”. One example is Fluorescence nanoscopy in cell biology (September, 2017).

The central question is Optical microscopy – how small can it go? (October, 2020) although now (July, 2021) someone has built a high-resolution microscope using LEGO blocks!

Check out microscopy, spectroscopy, and biophysics for more related articles.

“Classical” physics – like fluid mechanics, thermodynamics (e.g.,Thermodynamics of Evolution), and electromagnetism – is crucial in the description of a number of biological systems. More recently interest has centred around whether quantum phenomena play a role at the macroscopic level of, say, DNA (e.g., Does quantum entanglement in DNA synchronize the catalytic centers of type II restriction endonucleases?) or the cell. In fact, some claim that Quantum Biology May Help Solve Some of Life’s Greatest Mysteries (June, 2019)! At the very least, It’s Time to Take Quantum Biology Research Seriously (May, 2023).

For a recent survey check out the video Quantum effects in biological systems (January, 2021) as well as peruse Articles on Quantum Effects in Biophysics where some possible applications of the quantum to biological systems are described.

One of the most intriguing possible applications of quantum physics in a biological process involves photosynthesis, as discussed in Is photosynthesis quantum-ish? (April, 2018). In June of 2023 it was reported that One photon is all it takes to kick off photosynthesis. Even outside the quantum regime, in October, 2017, Scientists were Rewriting the History of Photosynthesis. Physicists took an early interest in photosynthesis as evidenced by the letter to Nature History: Photosynthesis and the Nobel physicist. This is further discussed in Experiment demonstrates quantum mechanical effects from biological systems (December, 2017), Two-dimensional electronic spectroscopy for the quantum-optics enthusiast (July, 2013) and Does electronic coherence in pigment-proteins facilitate energy transfer in photosynthesis?. The answer given on January 9, 2014 was “yes”, at least according to the authors of Quantum mechanics explains efficiency of photosynthesis! (see also When is Biology Quantum?, February, 2015, and Quantized vibrations are essential to photosynthesis, say physicists, January 22, 2014). There was a talk at the March, 2014 American Physical Society Meeting by the above-mentioned Seth Lloyd entitled Quantum Life: How photosynthetic organisms use quantum coherence to enhance the efficiency of energy transport. There is also What does “quantum coherence ” mean in photosynthesis?. A number of articles over the past few years have delved into the matter. These papers describe how quantum coherence links molecules within light-harvesting proteins and that these links improve the efficiency of energy transfer. This idea that photosynthesis expoits quantum entanglement is not without controversy, however. A May, 2011 story exclaims Photosynthesis disentangled?. The main argument against it is reasonable in that it seems difficult to imagine that coherence can be maintained over such long distances (relatively speaking) or, conversely, over long times, as is discussed in Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer (February, 2017). This seems in conflict with Quantum illumination (May, 2013) where they say that the “information-carrying benefits of entanglement can survive in a lossy environment – even if the entanglement itself does not” and is given further credence in Entanglement gets hot and messy (June, 2020). Clearly the answer to this is still up in the air.

For more technical discussions you can peruse Photosynthesis Articles. As well, there is the another twist on the use of entanglement to study biological systems as in, for example, Quantum microscope uses entanglement to reveal biological structures (June, 2021). Finally, also have a look at Robust entanglement-based magnetic field sensor beyond the standard quantum limit (December, 2014).

The understanding of the mechanism of photosynthesis was aided through results of the optical experiments described in The Quantum Dimension Of Photosynthesis and Laser Captures Photosynthesis in Action. This all reminds me of the words of Milton – “… thou Celestial light / Shine inward, and the mind through all her powers / Irradiate, there plant eyes, all mist from thence / Purge and disperse, that I may see and tell / Of things invisible to mortal sight.“

Scientists have in recent years been looking at using photosynthesis to make fuel or boost the efficiency of solar cells – see, for example, Artificial photosynthesis: A pathway to solar fuels (December, 2023) or Hydrogen-producing solar cells mimic photosynthesis (February, 2023). Solar cell improvement using photosynthetic compounds is discussed in Cyanobacteria and nanomaterials give solar cell a boost (June, 2020). The articles Artificial leaf jumps developmental hurdle (February, 2014) and Artificial leaves make fuel from sunlight (July, 2011) talk of how researchers in the US took important steps towards the creation of a commercially viable “artificial leaf” – a hypothetical device that can turn sunlight into electrical energy or fuel by mimicking some aspects of photosynthesis. More recently (September, 2022) Floating artificial leaves could produce solar-generated fuel. Also see articles on artificial photosynthesis. This is underlying theme of the novel Solar by Ian McEwan which I quite enjoyed. In a similar vein their has been recent (April, 2022) work on “quantum batteries” – Quantum batteries harvest energy from light.

“Quantum coherence” may also play a role in other biological systems as discussed in Quantum biology: Do weird physics effects abound in nature? (January, 2013). Some specific examples (I don’t think they’re weird!) include Clearer Quantum Vision (January, 2014) and Light-gathering insects (November, 2012).

Another really fascinating example of quantum mechanics and biology involves how birds use the Earth’s magnetic field to figure out which direction to go when migrating. New insights into this are described in Unravelling the enigma of bird magnetoreception (see also New Study Fuels Debate About Source of Birds’ Magnetic Sense and Quantum chemical reaction behind birds’ internal compass – June, 2021) while This is for the Birds is a collection of articles on bird migration and quantum effects.

I have worked at a number of high-energy particle accelerators (also look at A primer on particle accelerators – July, 2016 – as well as Ten things you might not know about particle accelerators – April, 2014) and over the course of the years there has been found a number of unexpected applications for them like Five ways particle accelerators have changed the world (without a Higgs boson in sight) (February, 2016). Articles like What have particle accelerators ever done for us? (August, 2019), Klystrons for industry (March, 2014), Primed: The smashing science behind particle accelerators (August, 2013) and Accelerating Particles Accelerates Science – With Big Benefits for Society (March, 2013) show that accelerator research feeds into more than just the biomedical industry.

Before continuing on you may want to check out Seven things you may not know about X-rays (November, 2013) and for an interesting take on the early history of X-rays and medical imaging see Naked to the Bone: Medical Imaging in the Twentieth Century (1997). There is a lot of interesting biophysical research happening at Synchrotron Light Sources like the Canadian Light Source, the PETRA III X-ray source, the National Synchrotron Light Source II at Brookhaven National Laboratory (see Brilliant new x-ray source is up and running at Brookhaven (January, 2015) and Brookhaven ushers in a new bright era – April, 2015), Swedish synchrotron promises to open up new avenues for researchers (August, 2015) and the Linac Coherent Light Source at SLAC National Accelerator Laboratory (see also First light beckons at SLAC’s LCLS-II, September, 2022, World’s most powerful X-ray laser beam refined to scalpel precision, August, 2012 and New X-ray tool proves timing is everything, February, 2013). In May of 2009 a synchrotron in China joined the fray. There are two May, 2011 articles on synchrotron light sources; a dedicated issue of Physics in Canada on the Canadian Light Source and Shedding light from Symmetry magazine. See also X-ray pulses on demand from electron storage rings (May, 2014) and The Purest X-Ray Beam (September, 2011). Mind you, you can make X-rays yourself just using Scotch tape and Baking a LINAC (May, 2020)! See Particle Accelerators for Dummies? for a cute piece on how to survive working at a synchrotron. There is now research (July, 2013) on How to make zeptosecond X-ray pulses. There are also advances being made on so-called “free-electron” lasers. See for example A national x-ray free-electron laser facility for rapid, massive biomedical advance (February, 2015) and The first optically synchronised free-electron laser (January, 2015). See also Bright light, big mirror: Precision X-ray focusing at NSLS-II (August, 2013)

For more articles on Synchrotron Light Sources and X-rays have a look at Synchrotrons and You.

And don’t forget about neutron beams – Neutron scattering for structural biology (June, 2020) and Neutron beams reveal how two potential pieces of Parkinson’s puzzle fit (January, 2015).

A major problem for biomedical applications is that accelerator facilities are just too big. But there have been advances in making compact accelerators which could be useful in medical applications. See, for example, Microchip accelerators (August, 2021). For information on recent advances in accelerators check out Accelerator Advances.

Finally, for some different angles on the use of accelerators have a look at the story Autos to accelerators about how some in old auto towns like Lansing Michigan are using the skills still in the town to make accelerators as well as Accelerator-treated bandages create healing environment and Accelerator-powered carbon dating (January, 2015).

Accelerators produce particle beams for cancer therapy. The question asked in December, 2022, wass, “Photons, protons or electrons: which will bring FLASH radiotherapy to the clinic?“

As mentioned above, for biomedical research there is so-called proton therapy (also known as hadrontherapy) which is driving both accelerator and detector physics – see, for example Physics drives ongoing developments in proton therapy (December, 2019). The idea of using a proton beam for cancer therapy came from the physicist Robert Wilson in 1946 – see Particle accelerators take up the fight against cancer from the December, 2006, issue of the CERN Courier as well as Hadron therapy: collaborating for the future from the November, 2011, CERN Courier. For a review of Hadrontherapy circa 2010 check out Scientific and Technological Development of Hadrontherapy. Further articles include CERN congratulates CNAO on a world’s first proton treatment of a cardiac pathology (February, 2020), Dual-energy CT for proton therapy planning reaches the clinic (May, 2019), Proton therapy enters precision phase (October, 2016), Accelerating the fight against cancer (October, 2014), Particle Beam Cancer Therapy: The Promise and Challenges (March, 2014), Particle accelerators join fight against brain cancer (January, 2014), and Advancements in proton therapy cause for celebration (October, 2011). Even the engineers agreed that Particle therapy comes of age (December, 2010). For a bit of the history of hadrotherapy check out A lifetime in biophysics (August 26, 2014) which chronicles the life of Eleanor Blakely.

For recent articles on hadrontherapy check out Stuff about Hadrontherapy.

One shouldn’t forget about (or not learn about) how the natural world includes many sources (including you!) of radiation. And it could have huge implications like – Radioactivity May Fuel Life Deep Underground and Inside Other Worlds (May, 2021). But first, let’s get out of the way, The Difference Between Radioactivity and Radiation. The basics about natural radioactivity are given in: The particle physics of you (November, 2015), This radioactive life (February, 2016), and Everything Emits Radiation (February, 2007). And then there’s bananas. Yes, bananas, as discussed in Go Figure: What bananas tell us about radiation (October, 2011) and Antimatter from bananas (July, 2009). It’s also true that we are still learning about the effects of even small radiation doses as discussed in Chernobyl’s legacy and why assessing radiation risk is so difficult (July, 2019) and Fukushima may have scattered plutonium widely (July, 2020).

There’s a long history of medical uses of radioactive isotopes as described in a Special Physics is Canada issue on medical isotopes (January, 2010). The shutdown of several nuclear reactors around the world in 2009 (including Canada’s Chalk River facility) that were used predominantly to produce medical isotopes was called The medical testing crisis (December, 2013). This was still true as of 2020 as described in Shortages expected as McMaster becomes the world’s only supplier of medical isotope used to treat prostate cancer (January, 2020). The consequences of this crisis led physicists to consider other methods for medical isotope production. If you want to get into the game yourself then there is always The Do-it-Yourself Cyclotron. Good luck. There are efforts to make desktop sized cyclotrons for medical isotope production as discussed in Medical-isotope cyclotron designs go full circle (March, 2012). See also Terbium: a new “Swiss army knife” for nuclear medicine for other nuclear medicine advances.

Check out Medical Isotopes for articles on advances in generating medical isotopes.

There have been a number of applications of particle physics (also called high energy physics) to medicine. This is outlined in Particle physics: a valuable driver of innovation in medicine (2012). One of the more well known medical diagnostics is Positron Emission Tomography (PET) (2005). PET makes use of the concept of antimatter-matter annihilations (specifically positron-electron annihilations) and subsequent high-speed techniques for the detecting the resultant gamma ray photons. One needs a cyclotron (like that at the TRIUMF laboratory in Vancouver) to create the beta+ emmiters. There were 34 publicly funded PET facilities in Canada as of 2015. One also needs photon detectors where ultrafast detection is ultra-good (June, 2020).

The PET method continues to be tweaked and improved as evidenced by, for example, Ultrafast photon detectors enable reconstruction-free medical imaging (November, 2021) and Timing the life of antimatter particles may lead to better cancer treatment (October, 2020). For further articles on the uses and advances in PET scan technology see PET.

The positrons emitted during a PET scan don’t necessarily annihilate immediately. Sometimes they form a bound state with the electron called positronium. The first positronium image was recorded during a PET scan in October of 2021. This is a really interesting development.

There has also been, for obvious reasons, a great deal of interest in The Physics of Cancer (April, 2019). There is a dedicated conference series Physics of Cancer out of Leipzig that have been happening since 2010 and there was a American Institute of Physics Advances Physics of Cancer conference in 2012. As well there is a series of books by Claudia Tanja Mierke:

For more on this topic check out Physics of Cancer.

The fundamental units are crucial in allowing for quantitative descriptions of nature. It has even been argued that A co-ordinated measurement system is one of humanity’s greatest achievements – we must stick with it (May, 2023). They have been updated and redefined. This was announced in 2016 – The new system of units (January, 2016), A New Era for the Ampere (December, 2016) and further refined with Electrical resistance standard could get a revised quantum definition (February, 2022). This was implemented as discussed in Living with the New SI (March, 2019) and New definition of the kilogram comes into force (May, 2019) which leads to new defined exact values for the Planck constant (h), the elementary electric charge (e), the Boltzmann constant (kB), and the Avogadro constant (NA) which further leads to redefinitions in terms of these constants of the kilogram, ampere, kelvin, and mole. For an overview of the whole program see Special Issue: The Revised SI: Fundamental Constants, Basic Physics and Units – Annalen der Phyik, Volume 531, Issue 5, May, 2019. You can learn about the 26th meeting of the General Conference on Weights and Measures (where this was voted on) which took place at Palais des Congres in Versailles in November, 2018 in As of Today, the Fundamental Constants of Physics (c, h, e, k, NA) Are Finally … Constant!. You can also view the presentations at the meeting:

  1. “The Quantum Hall Effect and the Revised SI,” by Klaus von Klitzing
  2. “The Role of the Planck Constant in Physics,” by Jean-Philippe Uzan
  3. “Optical Atomic Clocks: Opening New Perspectives on the Quantum World,” by Jun Ye
  4. “Measuring with Fundamental Constants: How the Revised SI Will Work,” by Bill Phillips

at Open Session to consider the revision of the SI. With respect specifically to temperature, apparently various primary thermometers, based on a wide range of different physics, had uncovered errors in the International Temperature Scale of 1990 which set the stage for rethinking the kelvin. These methods are discussed in Advances in thermometry.

So-called “tweezers”, either optical, magnetic, or acoustic, are used to manipulate macroscopic sized objects like cells, among other things.

Here are some articles on biophysics from the popular press to the scientific journals with an extremely biased selection criteria – namely, do I find them interesting or remotely relevant!

Generally more technical papers can be downloaded from the arXiv e-print archive on Biological Physics and Medical Physics. There is also the Quantitative Biology arXiv and bioRXiv. [Be warned that these are NOT refereed papers (though some “replace” the original submission with the refereed journal version when it appears) so some of the conclusions reached here could be, and probably are, utter nonsense.]