Showing posts with label book review. Show all posts
Showing posts with label book review. Show all posts

Friday, August 23, 2024

The Song of the Dodo

The Song of the Dodo,
by David Quammem.
One of my favorite science writers is David Quammen. I’ve discussed several of his books in this blog before, such as Breathless, Spillover, and The Tangled Tree. A copy of one of his earlier books—The Song of the Dodo: Island Biogeography in an Age of Extinctions—has sat on my bookshelf for a while, but only recently have I had a chance to read it. I shouldn’t have waited so long. It’s my favorite.

Quammen is not surprised that the central idea of biology, natural selection, was proposed by two scientists who studied islands: Charles Darwin and the Galapagos, and Alfred Russell Wallace and the Malay Archipelago. The book begins by telling Wallace’s story. Quammen calls him “the man who knew islands.” Wallace was the founder of the science of biogeography: the study of how species are distributed throughout the world. For example, Wallace’s line lies between two islands in Indonesia that are only 20 miles apart: Bali (with plants and animals similar to those native to Asia) and Lombok (with flora and fauna more like that found in Australia). Because islands are so isolated, they are excellent laboratories for studying speciation (the creation of new species through evolution) and extinction (the disappearance of existing species).

Quammen is the best writer about evolution since Stephen Jay Gould. I would say that Gould was better at penning essays and Quammen is better at authoring books. Much of The Song of the Dodo deals with the history of science. I would rank it up there with my favorite history of science books: The Making of the Atomic Bomb by Richard Rhodes, The Eighth Day of Creation by Horace Freeland Judson, and The Maxwellians by Bruce Hunt.

Yet, The Song of the Dodo is more than just a history. It’s also an amazing travelogue. Quammen doesn’t merely write about islands. He visits them, crawling through rugged jungles to see firsthand animals such as the Komodo Dragon (a giant man-eating lizard), the Madagascan Indri (a type of lemur), and the Thylacine (a marsupial also known as the Tasmanian tiger). A few parts of The Song of the Dodo are one comic sidekick away from sounding like a travel book Tony Horwitz might have written. Quammen talks with renowned scientists and takes part in their research. He reminds me of George Plimpton, sampling different fields of science instead of trying out various sports.

Although I consider myself a big Quammen fan, he does have one habit that bugs me. He hates math and assumes his readers hate it too. In fact, if Quammen’s wife Betsy wanted to get rid of her husband, she would only need to open Intermediate Physics for Medicine and Biology to a random page and flash its many mathematical equations in front of his face. It would put him into shock, and he probably wouldn’t last the hour. In his book, Quammen only presents one equation and apologizes profusely for it. It’s a power law relationship

S = c An .

This is the same equation that Russ Hobbie and I analyze in Chapter 2 of IPMB, when discussing log-log plots and scaling. How do you determine the dimensionless exponent n for a particular case? As is my wont, I’ll show you in a new homework problem.
Section 2.11

Problem 40½. In island biogeography, the number of species on an island, S, is related to the area of the island, A, by the species-area relationship: S = c An, where c and n are constants. Philip Darlington counted the number of reptile and amphibian species from several islands in the Antilles. He found that when the island area increased by a factor of ten, the number of species doubled. Determine the value of n.
Let me explain to mathaphobes like Quammen how to solve the problem. Assume that on one island there are S0 species and the area is A0. On another island, there are 2S0 species and an area of 10A0. Put these values into the power law to find S0 = cA0n and 2S0 = c(10A0)n. Now divide the second equation by the first (c, S0, and A0 all cancel) to find 2 = 10n. Take the logarithm of both sides, so log(2) = log(10n), or using a property of logarithms log(2) = n log(10). So n = log(2)/log(10) = 0.3. Note that n is positive, as it should be since increasing the area increases the number of species.

When I finished the main text of The Song of the Dodo, I thumbed through the glossary and found an entry for logarithm. “Aww,” I thought, “Quammen was only joking; he likes math after all.” Then I read his definition: “logarithm. A mathematical thing. Never mind.”

About halfway through, the book makes a remarkable leap from island biogeography—interesting for its history and relevance to exotic tropical isles—to mainland ecology, relevant to critical conservation efforts. Natural habitats on the continents are being broken up into patches, a process called fragmentation. The expansion of towns and farms creates small natural reserves surrounded by inhospitable homes and fields. The few remaining native regions tend to be small and isolated, making them similar to islands. A small natural reserve cannot support the species diversity that a large continent can (S = c An). Extinctions inevitably follow.

The Song of the Dodo also provides insight into how science is done. For instance, the species-area relationship was derived by Robert MacArthur and Edward Wilson. While it’s a valuable contribution to island biogeography, scientists disagree on its applicability to fragmented continents, and in particular they argue about its relevance to applied conservation. Is a single large reserve better than several small ones? In the 1970s a scientific battle raged, with Jared Diamond supporting a narrow interpretation of the species-area relationship and Dan Simberloff advocating for a more nuanced and less dogmatic view. As in any science, the key is to get data to test your hypothesis. Thomas Lovejoy performed an experiment in the Amazon to test the species-area relationship. Parts of the rainforest were being cleared for agriculture or other uses, but the Brazilian government insisted on preserving some of the native habitat. Lovejoy obtained permission to create many different protected rainforest reserves, each a different size. His team monitored the reserves before and after they became isolated from adjacent lands, and tracked the number of species supported in each of these “islands” over time. While the results are complicated, there is a correlation between species diversity and reserve size. Area matters.

One theme that runs through the story is extinction. If you read the book, you better have your hanky ready when you reach the part where Quammen imagines the death of the last Dodo bird. Conservation efforts are featured throughout the text, such as the quest to save the Mauritius kestrel.  
 
The Song of the Dodo concludes with a mix of optimism and pessimism. Near the end of the book, when writing about his trip to Aru (an island in eastern Indonesia) to observe a rare Bird of Paradise, Quammen writes
The sad, dire things that have happened elsewhere, in so many parts of the world—biological imperialism, massive habitat destruction, fragmentation, inbreeding depression, loss of adaptability, decline of wild populations to unviable population levels, ecosystem decay, trophic cascades, extinction, extinction, extinction—haven’t yet happened here. Probably they soon will. Meanwhile, though, there’s still time. If time is hope, there’s still hope.

An interview with David Quammen, by www.authorsroad.com

https://www.youtube.com/watch?v=Quq7PNH1zWM

Friday, August 2, 2024

If I Understood You, Would I Have This Look on My Face?

I’m a big Alan Alda fan. As a teenager, I would watch him each week as Hawkeye Pierce on M*A*S*H. Besides being an actor, Alda also had a second career as a science communicator, hosting the PBS series Scientific American Frontiers.

The cover of If I Understood You, Would I Have This Look on My Face? superimposed on Intermediate Physics for Medicine and Biology.
If I Understood You, Would
I Have This Look on My Face?

by Alan Alda.
After writing this science blog for seventeen years, I’ve decided I should try to figure out what I’m doing. So I read Alda’s book If I Understood You, Would I Have This Look on My Face? My Adventures in the Art and Science of Relating and Communicating. In his introduction, Alda writes
You run a company and you think you are relating to your customers and employees, and that they understand what you’re saying, but they don’t, and both customers and employees are leaving you. You’re a scientist who can’t get funded because the people with the money just can’t figure out what you’re telling them. You’re a doctor who reacts to a needy patient with annoyance; or you love someone who finds you annoying, because they just don’t get what you’re trying to say.

But it doesn’t have to be that way.

For the last twenty years, I’ve been trying to understand why communicating seems so hard—especially when we’re trying to communicate something weighty and complicated. I started with how scientists explain their work to the public: I helped found the Center for Communicating Science at Stony Brook University in New York, and we’ve spread what we learned to universities and medical schools across the country and overseas.

But as we helped scientists be clear to the rest of us, I realized we were teaching something so fundamental to communication that it affects not just how scientists communicate, but the way all of us relate to one another.

We were developing empathy and the ability to be aware of what was happening in the mind of another person.
The first half of the book describes a variety of improvisation techniques that teach how to increase your empathy and your ability connect to others; almost how to read someone’s mind. Alda believes that empathy is the key to communicating: “relating is everything.”

While I find these ideas interesting, improvisation isn’t something I have any experience with and, frankly, have little interest in trying. After all, most of these methods require interpreting facial expressions and body language. What could any of this have to do with the solitary process of writing a blog post?

Then I reached Chapter 15: “Reading the Mind of the Reader.” It starts
I know it sounds odd, but we’ve found that it’s possible to have an inkling of what’s going on in the mind of our audience even when they’re not actually in the room with us—like when we write.
I wish this chapter had been longer. Alda stresses the importance of writing from the reader’s perspective
In his elegant book The Sense of Style, Steven Pinker says that to write as if the reader were looking over your shoulder is probably to not possible. It’s just too difficult to take on the perspective of another person.

I wonder...
He then describes Steven Strogatz’s success in writing about mathematics, and how he “engages the reader as a friend.” Readers of my blog might be familiar with Strogatz, whose work I have discussed before (here, here, here, and here). Alda concludes this chapter about writing with
My guess is that even in writing, respecting the other person’s experience gives us our best shot at being clear and vivid, and our best shot, if not at being loved, at least at being understood.
Another technique to improve a scientist’s writing is to tell stories. The secret is to first introduce the main character and their goal. For a scientist, this may be to test a hypothesis. Then, crucially, comes some obstacle that puts everything in suspense. Finally, some turning point arises and the story resolves. Alda claims that a story is engaging because you get “caught up in someone's struggle to achieve something.”
If we’re looking for a way to bring emotion to someone, a story is the perfect vehicle. We can’t resist stories. We crave them.
I’m going to try to incorporate more empathy and story-telling into these blog posts. An even greater challenge will be to use these techniques in a textbook like Intermediate Physics for Medicine and Biology as we prepare the 6th edition. My years of experience teaching undergraduates based on IPMB should help. I’ll do my best.

I’ll let Alda have the last word.
So, it’s really not that complicated: If your read my face, you’ll see if I understand you. Improv games, and even exercises on your own, can bring you in touch with the inner life of another person—even when you sit by yourself and write.

 

Alan Alda on If I Understood You, Would I Have This Look on My Face?

https://www.youtube.com/watch?v=y8xPr6fJRMs 


Alan Alda on why communication is so important to science.

https://www.youtube.com/watch?v=abr6CqbNdM4

Friday, June 14, 2024

Bernard Leonard Cohen (1924–2012)

The Nuclear Energy Option: An Alternative for the 90s. by Bernard Cohen, superimposed on Intermediate Physics for Medicine and Biology.
The Nuclear Energy Option: An Alternative for the 90s.
by Bernard Cohen.
Today is the one hundredth anniversary of the birth of American nuclear physicist Bernard Cohen. In Intermediate Physics for Medicine and Biology, Russ Hobbie and I discuss Cohen mainly in the context of his work on the risk of low levels of ionizing radiation and his opposition to the linear no threshold model. Today, I will examine another aspect of his work: his advocacy for nuclear power. In particular, I will review his 1990 book The Nuclear Energy Option: An Alternative for the 90s.

Why read a 35-year old book about a rapidly changing technology like energy? I admit, the book is in some ways obsolete. Cohen insists on using rems as his unit of radiation effective dose, rather than the more modern Sievert (Sv). He discusses the problem of greenhouse gases and global warming, although in a rather hypothetical way as just one of the many problems with burning fossil fuels. He was optimistic about the future of nuclear energy, but we know now that in the decades following the book’s publication nuclear power in the United States did not do well (the average age of our nuclear power plants is over 40 years). Yet other features of the book have withstood the test of time. As our world now faces the dire consequences of climate change, the option of nuclear energy is an urgent consideration. Should we reconsider nuclear power as an alternative to coal/oil/natural gas? I suspect Cohen would say yes.

In Chapter 4 of The Nuclear Energy Option Cohen writes
We have seen that we will need more power plants in the near future, and that fueling them with coal, oil, or gas leads to many serious health, environmental, economic, and political problems. From the technological points of view, the obvious way to avoid these problems is to use nuclear fuels. They cause no greenhouse effect, no acid rain, no pollution of the air with sulfur dioxide, nitrogen oxides, or other dangerous chemicals, no oil spills, no strain on our economy from excessive imports, no dependence on unreliable foreign sources, no risk of military ventures. Nuclear power almost completely avoids all the problems associated with fossil fuels. It does have other impacts on our health and environment, which we will discuss in later chapters, but you will see that they are relatively minor.
He then compares the safety and economics of nuclear energy with other options, including solar and coal-powered plants for generating electricity. Some of the conclusions are surprising. For instance, you might think that energy conservation is always good (who roots for waste?). But Cohen writes
Another energy conservation strategy is to seal buildings more tightly to reduce the escape of heat, but this traps unhealthy materials like radon inside. Tightening buildings to reduce air leakage in accordance with government recommendations would give the average American an LLE [loss of life expectancy] of 20 days due to increased radon exposure, making conservation by far the most dangerous energy strategy from the standpoint of radiation exposure!
His Chapter 8 on Understanding Risk is a classic. He begins
One of the worst stumbling blocks in gaining widespread public acceptance of nuclear power is that the great majority of people do not understand and quantify the risks we face. Most of us think and act as though life is largely free of risk. We view taking risks as foolhardy, irrational, and assiduously to be avoided….

Unfortunately, life is not like that. Everything we do involves risk.

He then makes a catalog of risks, in which he converts risk to the average expected loss of life expectancy for each case. This LLE is really just a measure of probability. For instance, if getting a certain disease shortens your life by ten years, but there is only one chance out of a hundred of contracting that disease, it would correspond to an LLE of 0.1 years, or 36 days. In his catalog, the riskiest activity is living in poverty, which has an LLE of 3500 days (almost ten years). Smoking cigarettes results in an LLE of 2300 days. Being 30 pounds overweight is 900 days. Reducing the speed limit on our highways from 65 to 55 miles per hour would reduce traffic accidents and give us an extra 40 days. At the bottom of his list is living near a nuclear reactor, with a risk of only 0.4 days (less than ten hours). He makes a compelling case that nuclear power is extraordinarily safe.

Cohen summarizes these risks in a classic figure, shown below.

Figure 1 from Chapter 8 of The Nuclear Energy Option, superimposed on Intermediate Physics for Medicine and Biology.
Figure 1 from Chapter 8 of The Nuclear Energy Option.

Our poor risk perception causes us (and our government) to spend money foolishly. He translates societies efforts to reduce risk into the cost in dollars to save one life.

The $2.5 billion we spend to save a single life in making nuclear power safer could save many thousands of lives if spent on radon programs, cancer screening, or transportation safety. This means that many thousands of people are dying unnecessarily every year because we are spending this money in the wrong way.
He concludes
The failure of the American public to understand and quantify risk must rate as one of the most serious and tragic problems for our nation.
I agree.

Cohen believes that Americans have a warped view of the risk of nuclear energy.

The public has become irrational over fear of radiation. Its understanding of radiation dangers has virtually lost all contact with the actual dangers as understood by scientists.
Apparently conspiracy theories are a problem we face not only today but also decades ago, when the scientific establishment was accused of hiding the “truth” about radiation risks. Cohen counters
To believe that such highly reputable scientists conspired to practice deceit seems absurd, if for no other reason than that it would be easy to prove that they had done so and the consequences to their scientific careers would be devastating. All of them had such reputations that they could easily obtain a variety of excellent and well-paying academic positions independent of government or industry financing, so they were to vulnerable to economic pressures.

But above all, they are human beings who have chosen careers in a field dedicated to protection of the health of their fellow human beings; in fact, many of them are M.D.’s who have foregone financially lucrative careers in medical practice to become research scientists. To believe that nearly all of these scientists were somehow involved in a sinister plot to deceive the public indeed challenges the imagination.
To me, these words sound as if Cohen were talking now about vaccine hesitancy or climate change denial, rather than opposition to nuclear energy. 

What do I think? I would love to have solar and wind supply all our energy needs. But until they can, I vote for increasing our use of nuclear energy over continuing to burn fossil fuels (especially coal). Global warming is already bad and getting worse. It is a dire threat to us all and to our future generations. We should not rule out nuclear energy as one way to address climate change.

Happy birthday, Bernard Cohen! I think if you had lived to be 100 years old, you would have found so many topics to write about today. How we need your rational approach to risk assessment. 

 Firing Line with William F. Buckley Jr.: The Crisis of Nuclear Energy.

https://www.youtube.com/watch?v=ipOrGaXn-r4&list=RDCMUC9lqW3pQDcUuugXLIpzcUdA&start_radio=1&rv=ipOrGaXn-r4&t=52

Friday, December 8, 2023

One Hot Summer: Dickens, Darwin, Disraeli, and the Great Stink of 1858

One Hot Summer, by Rosemary Ashton, superimposed on Intermediate Physics for Medicine and Biology.
One Hot Summer,
by Rosemary Ashton.
I recently finished Rosemary Ashton’s book One Hot Summer: Dickens, Darwin, Disraeli, and the Great Stink of 1858. Her prologue begins
What was it like to live in London through one of the hottest summers on record, with the Thames emitting a sickening smell as a result of the sewage of over two million inhabitants being discharged into the river? How did people cope with the extraordinary heat leading up to the hottest recorded day, Wednesday, 16 June 1858? What did those living or working near the Thames—including at the Houses of Parliament and the law courts in Westminster Hall—do when they found their circumstances intolerable? What did the newspapers say?
Ashton proposes to examine London for just a few months in the summer of 1858, providing a snapshot of one moment in Victorian England. Such a microhistory provides insight into the life of mid-19th century Britain.
Microhistory, the study in depth and detail of historical phenomena, can uncover hitherto hidden connections, patterns, and structures. Some events and incidents are revealed over time to have been life changing or nation building. Examples from 1858 are the tackling of London’s sewage and the resultant improvement of public health, Brunel’s engineering feats, the initial laying of the Atlantic telegraph cable, the beginnings of a long process of attaining justice and equality in the matter of marriage and divorce, and the transformation of the miscellaneous medical practice into a proper profession.
She focuses on the novelist Charles Dickens, biologist Charles Darwin, and politician Benjamin Disraeli.
A comparatively neglected time in Disraeli’s career can be shown to have been remarkably important in bringing him to prominence. The attention of historians and biographers has focused hitherto on his reckless youth, his racy novels, his controversial journalism, and his late-won success from 1868, when he finally became prime minister. His hard work in the parliamentary session of 1858, particularly in the hectic weeks before the summer break beginning on 2 August, and his success in turning round a hostile press and distrustful colleagues by his efforts, deserve to be acknowledged. In Dickens’s case his painful and self-exposing actions in connection with his failed marriage have been fully discussed, but no detailed account exists of the day-to-day struggles he faced in the long summer which followed his catastrophic error of judgment in advertising his separation from his wife in the early days of June. As for Darwin, though much has been written about his abrupt shock and change of plans on receiving in mid-June Wallace’s letter outlining natural selection, little attention has been paid to the interaction between his family life and scientific work in summer 1858.

This idea of a microhistory sounds fun, and I thought readers of Intermediate Physics for Medicine and Biology might be interested in learning about events in the summer of 1858 that influenced physics, biology, and medicine. So, in this blog post I augment Ashton’s analysis by adding incidents from the world of science.

Charles Darwin (age 48, all ages are as of summer 1858) had been developing his theory of evolution by natural selection for twenty years, since returning to England in 1836 after his famous voyage on the HMS Beagle. Over the years he had told his friends Joseph Hooker (age 41) and Charles Lyell (age 61) about his ideas, but had never published them. Ashton describes how on June 18, 1858 Darwin received a letter from Alfred Russel Wallace (age 35), containing a draft of a paper describing the same idea of natural selection as the mechanism of biological evolution, written while Wallace was collecting biological specimens in the Malay Archipelago. Hooker and Lyell arranged to have some early private writings of Darwin’s, along with the paper by Wallace, published on July 1 at a meeting of the Linnean Society of London

On the Origin of Species, by Charles Darwin, superimposed on Intermediate Physics for Medicine and Biology.
On the Origin of Species,
by Charles Darwin.
The following year, Darwin published his much more detailed book On the Origin of Species, changing biology forever. One of the most pugnacious of the advocates for natural selection was his young friend Thomas Henry Huxley (age 33), known as “Darwin’s Bulldog.” In 1858 Huxley was the Fullerian Professor of Physiology at London's Royal Institution, and on June 17, 1858 he gave the Royal Society’s annual Croonian Lecture. Darwin’s friend Charles Lyell—winner of the Royal Society’s prestigious Copley Medal in 1858 for his contributions to geology—never completely embraced natural selection.

On June 10, 1858 the botanist Robert Brown died in London, at age 84. In Chapter 4 of IPMB, Russ Hobbie and I write

This movement of microscopic-sized particles, resulting from bombardment by much smaller invisible atoms, was first observed by the English botanist Robert Brown in 1827 and is called Brownian motion.
Brown’s death had an interesting impact on the Darwin/Wallace publications. Ashton writes
By a stroke of luck the death of the former president Robert Brown had induced the [Linnean] society to postpone its summer meeting from 17 June, the day before Darwin received Wallace’s letter, to Thursday, 1 July. This meant that Darwin (and Wallace) would not have to wait until September to have their papers made public.
One of the most famous scientists in England during 1858 was Michael Faraday (age 65). In Chapter 8 of IPMB, Russ and I discuss electromagnetic induction, which underlies transcranial magnetic stimulation of the brain.
In 1831 Michael Faraday discovered that a changing magnetic field causes an electric current to flow in a circuit.
Faraday, Maxwell, and the Electromagnetic Field, by Forbes and Mahon, superimposed on Intermediate Physics for Medicine and Biology.
Faraday, Maxwell, and the
Electromagnetic Field
,
by Forbes and Mahon.

After a long career at the Royal Institution, Faraday moved from his home at the RI to a house at Hampton Court in 1858. In their book Faraday, Maxwell, and the Electromagnetic Field, Nancy Forbes and Basil Mahon write
As Faraday’s health and mental faculties declined, he began to relinquish his various responsibilities at the Royal Institution, finally handing over the directorship to John Tyndall in 1865. The consequent loss of income, and of his flat, would have been a worry, but in 1858 Prince Albert, a great admirer, had asked the queen to put a house at Hampton Court at his disposal. Faraday had refused at first, fearing the high cost of repairs, but the queen said she would pay. He and Sarah [his wife] moved in, and the new house became his last home.
Although his research career was winding down, Faraday was still a great science communicator. On June 12, 1858 he gave a RI lecture “On the relation of gold to light,” about light scattering from gold colloids (nowadays we would call them gold nanoparticles). He was also famous for his Christmas lectures, which he gave annually throughout the 1850s.

Faraday’s work in electricity and magnetism was carried on by the young James Maxwell (age 27), who was married on June 2, 1858 in Aberdeen, Scotland. That year, Maxwell published his paper “On Faraday’s Lines of Force” (although it had been read before the Cambridge Philosophical Society in late 1855 and early 1856). Forbes and Mahon write
In February 1857, [Maxwell] decided to send a copy of his paper “On Faraday’s Lines of Force” to the great man [Faraday]. No doubt, he did so with some trepidation… He needn’t have worried. As we’ve seen, Faraday’s response was grateful, gracious, and charming. The two had at once formed a rare bond.
In the 1860s Maxwell continued his research on electromagnetism, and eventually developed the four Maxwell’s equations that rival Darwin’s theory of evolution as the most significant scientific contribution of the 19th century.

A Thread Across the Ocean, by John Steele Gordon, superimposed on Intermediate Physics for Medicine and Biology.
A Thread Across the Ocean,
by John Steele Gordon.
Besides Faraday and Maxwell, a third great Victorian physicist was William Thomson (age 34), who was one of the main scientists involved in developing the transatlantic telegraph. As part of that effort, in February of 1858 Thomson patented the mirror galvanometer, which is an instrument to measure electrical current. In his book A Thread Across the Ocean, John Steele Gordon describes this device.
In a long submarine cable, immersed in a conducting medium—saltwater—the current if often very low, sometimes no more than ten mircoamperes. (The current in a standard incandescent lightbulb is about 100,000 times as great.) The standard galvanometers then available were often inadequate to detect a signal coming through a cable that would be two thousand miles long. So Thomson—half Einstein, half Edison—developed a much better one. He took a very small magnet and attached a tiny mirror to it. Both together weighed no more than a grain. He suspended the magnet from a silk thread and set it in the middle of the coil of very thin insulated copper wire.

When the faint current flowing through the cable was allowed to flow through the copper coil, it created a magnetic field. This caused the magnet, with its attached mirror, to deflect. Thomson simply directed a beam of light from a shaded lamp onto the mirror and allowed it reflection to hit a graduated scale.

In June of 1858 two ships—the Agamemnon and the Niagara—attempted to meet in the middle of the Atlantic Ocean, splice together the two halves of the cable, and then each pay out the cable as they sailed toward shore: the Niagara toward Newfoundland and the Agamemnon toward Ireland. However, a terrible storm struck the North Atlantic that month, nearly capsizing the Agamemnon with Thomson on board and aborting the mission.

On Sunday, June 20, the storm unleashed a fury such as few sailors ever see and even fewer live to tell about. The caption feared that the coil on the deck, working against its restraints, might break lose and smash through the side, undoubtedly causing the ship to founder.

A second try several weeks later proved more successful. On August 16, the first transatlantic telegraph message was sent between Queen Victoria in England and President James Buchanan in the United States. Unfortunately, the cable soon failed, and it was not until some years later that reliable telegraph service was established across the Atlantic.

Based on his basic research discoveries and his contributions to the telegraph, Thomson became a scientific hero. Gordon writes

In 1892, William Thomson became the first British scientist to be raised to the peerage, when Queen Victoria created him Lord Kelvin of Largs. He has been known ever since as Lord Kelvin. In 1908, the year after he died, the Kelvin temperature scale, devised by him in the 1850s, was named in his honor.

The absolute temperature scale, with Kelvin’s name attached to the unit of temperature, appears throughout IPMB.

Still another notable Victorian physicist was George Stokes (age 36), who at that time was the Lucasian Professor at Cambridge University (a position held earlier by Isaac Newton and later by Stephen Hawking). IPMB often uses Stokes’ law for the viscous force of a small sphere in a fluid. Stokes and Thomson were close friends, and their many letters are preserved. I provide a few excerpts from these letters during late 1857 and 1858.

2 College, Glasgow

Dec. 23, 1857

My Dear Stokes

That principle, in the hydrodynamics of a “perfect liquid”, which I first learned from you, is something that I have always valued as one of the great things of science, simple as it is, and I now see more than ever its importance. One conclusion from it is that instability, or a tendency to run to eddies, or any kind of dissipation of energy, is impossible in a perfect liquid (a fluid with neither viscosity nor compressibility)... [several pages follow with many equations]...Some of the simplest applications of the theory are very interesting: for instance the... case of a circular disc or oblate spheroid, moving... in a perfect [liquid]...

As to Faraday’s magneto-optic experiment, I think my argument that it must depend on a peculiar state of motion induced by magnetic influence (Proceedings R. S. June or July 1856) is unanswerable. Have you considered it?...

It seems like old times for me to be writing you so long a letter, and I am afraid you will be less disposed to be so bored. Your redress simply be not to read it.

With best wishes for a “Merry Christmas” of which there can be no doubt now, I remain

Yours always truly

William Thomson

Stokes responded,

69 Albert Street Regent's Park London N.W.

Feb. 12, 1858

My Dear Thomson,

I have been so very busy of late that your letter has remained for a long time unanswered. I now set to answer it, though I have still got plenty of work before me...

Without having a decided opinion either way I have always inclined to the belief that the motion of a perfect incompressible liquid, primitively at rest, about a solid which continually progressed, was unstable... [pages of math...]

In speculating a good while ago (in fact no great time after Faraday’s discovery) as to the cause of magnetic rotation I naturally tried rotations of the luminiferous ether as suggested by Ampere’s theory...

Yours very truly

G. G. Stokes

Finally, late in 1858, Stokes wrote

The Athenaeum

Oct 5/58

My Dear Thomson,

... It is a great pity to see the [transatlantic] cable in its present state after apparently so successful a laying down. Still the thing has been done and even if this should be utterly lost the matter will not I presume rest there.

I did not go to Leeds this meeting [The British Science Association met in Leeds in 1858]. On the morning of the 27th my wife was safely delivered of a fine boy. She is going on very well but I am afraid her complete recovery will be slow.

Yours very truly

G. G. Stokes

James Joule (age 39) was yet another English physicist of the Victorian era. His name appears repeatedly in IPMB because the unit of energy is named after him. In the 1840s Joule had done pioneering work on the mechanical equivalent of heat and the conservation of energy, and in the 1850s had collaborated to explain the Joule-Thomson effect. In 1858 he was in a train wreck while traveling home from London. Although unhurt, the accident made him reluctant to travel, somewhat isolating him from the scientific community.

Gray’s Anatomy, below Intermediate Physics for Medicine and Biology.
Gray’s Anatomy.

 A major event in medicine occurred during the summer of 1858: the publication of the first edition of Gray’s Anatomy. In his article “Happy Birthday, Gray’s Anatomy,” Adrian Flatt (Proc. Bayl. Med. Cent., 22:342–345, 2009) writes

Anatomy Descriptive and Applied was first published in London in the summer of 1858 by two young demonstrators of anatomy in St. George’s Hospital at Hyde Park Corner… These two young men were very different. Henry Gray [age 31] wrote the text; he was 4 years older than Henry Vandyke Carter [age 27], who drew all the illustrations…
The print number of 2000 books had been decided, page size was fixed, and all the paper purchased. Considerable adjustments were successfully made and by mid May 1857, the work was going well but was to be interrupted by the absence of Gray. He had received an invitation to “attend” the Duke of Sutherland on his private yacht sailing around England and Scotland and at the estate at Dunrobin Castle for the next 6 months, from June to November 1857. This was manna from heaven for Gray; service for such an aristocrat would be of enormous help to his practice. Carter continued work on the book, of which the final proof corrections were done in late June or early July 1858, in time for the book to be available for students arriving in September.
Gray died at age 34, just three years after publication of his textbook, of smallpox. Apparently the relationship between Gray and Carter was strained. Flatt states that
Gray never gave Carter one penny from all the royalties the early editions of the book earned.
Diagram of the causes of mortality in the army in the East (1858)
Diagram of the causes of mortality
in the army in the East (1858).

Another leading figure of Victorian health care was Florence Nightingale (age 38), the founder of modern nursing. In 1858 Nightingale published Notes on Matters Affecting the Health, Efficiency, and Hospital Administration of the British Army. Founded Chiefly on the Experience of the Late War. Presented by Request to the Secretary of State for War. This work contained a color statistical illustration called “Diagram of the Causes of Mortality in the Army of the East” that showed that epidemic disease—which caused more British deaths during the Crimean War than battlefield wounds—could be controlled by nutrition, ventilation, and shelter. The infographic became known as Nightingale’s “coxcomb.” Her achievements in statistics were so remarkable that in 1858 she was selected as the first woman fellow of the Royal Statistical Society. Two years later she established her nursing school at Saint Thomas’ Hospital in London.

Another noteworthy happening in medicine was the death of John Snow (age 45) on June 16, 1858 (London’s hottest day of that steamy summer). Snow was best known for figuring out the source of the Broad Street cholera outbreak in 1854, when he demonstrated that cholera was being spread through contaminated water from one specific pump. He also studied using ether as an anesthesia during surgery. 

The Ghost Map, by Steven Johnson, superimposed on Intermediate Physics for Medicine and Biology.
The Ghost Map,
by Steven Johnson.
In his fascinating book The Ghost MapSteven Johnson writes about the prevailing belief that miasma (bad air) caused disease.

In June 1858, a relentless early-summer heat wave produced a stench of epic proportions along the banks of the polluted Thames. The press quickly dubbed it the “Great Stink”... [Yet] the rates of death from epidemic disease proved to be entirely normal. Somehow the most notorious cloud of miasmatic air in the history of London had failed to produce even the slightest uptick in disease mortality... It's easy to imagine John Snow taking great delight in [this] puzzling data... But he never got the opportunity. He had suffered a stroke in his office on June 10... and died six days later, just as the Great Stink was reaching its peak above the foul waters of the Thames.

Joseph Lister (age 31) was in Edinburgh in 1858, studying the coagulation of blood and inflammation. In the 1860s he developed antiseptic surgery, and later relocated to London. In their article “Joseph Lister: Father of Modern Surgery” (Can. J. Surg., 55:E8–E9, 2012), Dennis Pitt and Jean-Michel Aubin claim that 

it was Lister’s application of germ theory to the care of surgical patients that laid the foundation for what surgeons do now. He directed the minds of physicians and surgeons to the vital necessity of keeping wounds clean and free of contamination.

Finally, in 1858 Elizabeth Garrett Anderson (age 22) was a young woman dreaming of making a career in medicine. She eventually became the first female doctor in the United Kingdom.

Ashton believes that microhistory provides valuable insight into Victorian England. Near the end of her Prologue she concludes

Intense scrutiny of the lives of these men [Dickens, Darwin, and Disraeli, plus Brown, Faraday, Maxwell, Thomson, Stokes, Joule, Gray, Nightingale, Snow, and others] over a short period of a few months allows us to make fresh threads of connection between each of them and the larger society in which they lived, all at a time of public events which provided to be of lasting national importance.

Friday, December 1, 2023

Louis Pasteur, Biological Physicist

Louis Pasteur (1822–1895)
One recurring theme in this blog is how scientists make the transition from working in the physical sciences to studying the biological sciences. Indeed, this theme is intimately related to Intermediate Physics for Medicine and Biology. Recently, I decided to consider a case study of how a prominent scientist straddled physics, biology, and medicine. So, I searched for someone famous who illustrates how one trained in physics can end up contributing to the life sciences. I selected Louis Pasteur.

Louis Pasteur, by Patrice Debré.

I base this study on the biography Louis Pasteur by Patrice Debré (translated from French to English by Elborg Forster). As I read this book, I focused on the key events in Pasteur’s education and early research when he made this transition. 

Pasteur began his career as a physical scientist studying at the École normale supérieure in Paris.

For his doctorate, Pasteur had to submit two theses, one in physics and one in chemistry. The physics thesis brought together several studies concerning the use of the polarimeter… Pasteur’s first studies showed, or rather confirmed, that two isomorphic substances rotate polarized light to the same degree.
Polarization was a new topic in physics at that time. Étienne-Louis Malus, a fellow Frenchman, discovered the Law of Malus, governing how much light passes through two polarizers, in 1808, just 14 years before Pasteur’s birth. Pasteur’s friend and mentor Jean-Baptiste Biot first showed that polarized light could be rotated when passed through certain crystals. Pasteur’s contribution was to prove that crystals formed from tartaric acid could rotate polarized light either clockwise or counterclockwise, depending on the chirality of the crystal (this acid is asymmetric, having two forms that are mirror images of each other, like the left hand and the right hand). In a famous experiment, he inspected the structure of each crystal under a microscope and determined if it was left or right handed. When he then separated the two types of crystals he could obtain rotation in either direction, although a mixture of the two crystals did not rotate light. This discovery, made in 1848, at first appears to arise from physics and chemistry alone, but its relation to biology is that most biological molecules exist in only one version. Handedness matters in biology. Debré writes
In discovering the principles of molecular asymmetry, Pasteur had done nothing less than to forge a key—and this key has unlocked the door to the whole of modern biology… When Pasteur considered asymmetry on a cosmic scale, he went beyond the confines of physics and chemistry to confront the fundamental questions about life.
Pasteur’s next step toward biology came when he was a young professor at the University of Lille.
At the beginning of the academic year 1856, an industrialist of Lille, M. Bigo, whose son Emile was taking Pasteur’s course at the Faculty of Sciences, came to see him. Many manufacturers of beet root alcohol, he said, were having problems with their production…
This led to Pasteur’s research on fermentation, when a microorganism such as yeast brings about a change to a food or beverage, such as producing alcohol. Fermentation and light polarization do not appear to have much in common, but they do.
The findings Pasteur presented to the Academy of Sciences of Lille, and subsequently that of Paris, seemed very different from the studies he had undertaken previously. He was known as a specialist on crystals, and now he had become a theoretician of fermentation. Ranging from polarized planes of light to culture media, his reagents had little in common. Yet the preoccupations that guided Pasteur’s thinking at that period were not really different from those that had haunted him for a long time: he wanted to understand the relationship between life and molecular asymmetry.
The idea that a living microscopic organism was responsible for fermentation was one of Pasteur’s key insights. In fact, there were two types of yeast involved in beet root fermentation. The desirable one produced alcohol. The undesirable one, that led to all the problems, produced lactic acid. Debré concludes
A few years after the request of industrialist Bigo, Pasteur had thus established beyond a doubt that the lactic acid in the vats in the rue d’Esquermes came from an unfortunate contamination with this yeast. He even suggested the means to get rid of this contamination… Pasteur’s research on fermentation created microbiology.
Pasteur’s work on fermentation led to the related question of spontaneous generation. Many scientists at the time thought that living organisms could spontaneously arise in dead and decaying tissue, but Pasteur showed that such decay was always due to germs that entered the tissue from the air.

Pasteur’s transition to biology became complete after Jean-Baptiste Dumas asked him to investigate a disease that was destroying the silkworm industry in France. To address this issue, he needed to learn more biology.
Pasteur came from crystals. Owing to his scant knowledge of animal biology, he was somewhat apprehensive about experiments on animals. As soon as he accepted Dumas’s assignment, he therefore went, along with his assistant Emile Duclaux, to the physiology course taught by Claude Bernard at the Sorbonne. There he took notes and humbly relived his years of training in the halls of the university. But he found it difficult to learn a whole new field; and indeed, since he had neither the time nor the patience to do this, he soon preferred to form his own ideas on the problem at hand.
Once again, Pasteur was successful in addressing a biological problem; this time bacteria infecting silkworms (they are not really a worm, but a caterpillar).
The caterpillar of Alés led Pasteur from microbiology to veterinary science to medicine… When Pasteur revolutionized the science of his era by discovering the germs and their role, it was only natural that he should become interested in medicine and hygiene.
At this point, Pasteur had essentially completed his transition from physics to biology and medicine. I won’t discuss his later work on the use of antiseptics in surgery, pasteurization, anthrax infection in sheep, or the development of a rabies vaccine. Debré summarizes,
In his last studies, Pasteur recalled that he had started out as a chemist. First in the laboratory of the rue d’Ulm and then in his Institute, his ultimate experiments indicate that he was trying to understand how the same microbe can either kill a person or stimulate his or her resistance. This is where bacteriology merged into immunology. Pasteur brought these neighboring disciplines together. Understanding the role of the molecules, the toxins, and the antitoxins involved both chemistry and biology.
So what do I conclude about Pasteur’s transition from the physical to the biological sciences? It wasn’t part of a long-range plan. Nor was it primarily motivated by the desire to help the sick, at least initially. I see two key points. First, the rotation of polarized light when passed through an organic substance led him naturally from physics to biology; scientific problems don’t always respect academic boundaries. Second, requests to address industrial problems further accelerated this transition, and those problems happened to be biological in nature. There seems to be a lot of chance involved in this transition (I think there often is for many scientists). But, as Pasteur famously said, chance favors the prepared mind
 
 
https://www.youtube.com/watch?v=OXdbQ1JkX7c
 

 https://www.youtube.com/watch?v=1lLNZQVPpQA

Friday, November 24, 2023

The Deadly Rise of Anti-Science

The Deadly Rise of Anti-Science, by Peter Hotez, superimposed on Intermediate Physics for Medicine and Biology.
The Deadly Rise of Anti-Science,
by Peter Hotez.
This week I read The Deadly Rise of Anti-Science: A Scientist’s Warning, by Peter Hotez. Every American should read this book. In his introductory chapter, Hotez writes
This is a dark and tragic story of how a significant segment of the population of the United States suddenly, defiantly, and without precedent turned against biomedical science and scientists. I detail how anti-science became a dominant force in the United States, resulting in the deaths of thousands of Americans in 2021 and into 2022, and why this situation presents a national emergency. I explain why anti-science aggression will not end with the COVID-19 pandemic. I believe we must counteract it now, before something irreparable happens to set the country on a course of inexorable decline…

The consequences are shocking: as I will detail, more than 200,000 Americans needlessly lost their lives because they refused a COVID-19 vaccine and succumbed to the virus. Their lives could have been saved had they accepted the overwhelming scientific evidence for the effectiveness and safety of COVID-19 immunization or the warnings from the community of biomedical scientists and public health experts about the dangers of remaining unvaccinated. Ultimately, this such public defiance of science became a leading killer of middle-aged and older Americans, more than gun violence, terrorism, nuclear proliferation, cyberattacks or other major societal threats.
Where did this 200,000 number come from? On page 2 of Intermediate Physics for Medicine and Biology, Russ Hobbie and I claim that
One valuable skill in physics is the ability to make order-of-magnitude estimates, meaning to calculate something approximately right.

Hotez gives a classic example of estimation when deriving the 200,000 number. First, he notes that 245,000 Americans died of covid between May 1 and December 31, 2021. Covid arrived in the United States in early 2020, but vaccines did not become widely available until mid 2021. Actually, the vaccines were ready in early 2021 (I had my first dose on March 20), but May 1 was the date when the vaccine was available to everyone. During the second half of 2021, about 80% of Americans who died of covid were unvaccinated. So, Hotez multiplies 245,000 by 0.8 to get 196,000 unvaccinated deaths. After rounding this off to one significant figure, this is where he gets the number 200,000.

There are a few caveats. On the one hand, our estimate may be too high. The vaccine is not perfect. If all of the 200,000 unvaccinated people who died would have gotten the vaccine, some of them would still have perished from covid. If we take the vaccine as being 90% effective against death, we would multiple 196,000 times 0.9 to get 176,400. On the other hand, our estimate may be too low. Covid did not end on January 1, 2022. In fact, the omicron variant swept the country that winter and at its peak over 2000 people died of covid each day. So, the total covid deaths since the vaccine became available—the starting point of our calculation—is certainly higher than 245,000.

As Hotez points out, other researchers have also estimated the number of unnecessary covid deaths, using slightly different assumptions, and all the results are roughly consistent, around 200,000. (Hotez’s book appears to have been written in mid-to-late 2022; I suspect the long tail of covid deaths since then would not make much difference to this estimation, but I’m not sure.) 

In the spirit of an order-of-magnitude estimate, one should not place too great an emphasis on the precise number. It was certainly more than twenty thousand and it was without a doubt less than two million. I doubt we’ll ever know if the “true” amount is 187,000 or 224,000 or any other specific value. But we can say with confidence that about a couple hundred thousand Americans died unnecessarily because people were not vaccinated. Hotez concludes

That 200,000 unvaccinated Americans gave up their lives needlessly through shunning COVID-19 vaccines can and should haunt our nation for a long time to come.

Infectious disease scientists such as Peter Hotez, Tony Fauci, and others are true American heroes. That far-right politicians and journalists vilify these researchers is despicable and disgusting. We all owe these scientists so much. Last Monday was “Public Health Thank You Day” and yesterday was Thanksgiving. I can think of no one more deserving of our thanks than the scientists who led the effort to vaccinate America against covid. 

Why Science Isn’t Up for Debate, with Peter Hotez.

https://www.youtube.com/watch?v=PbGfeksduGE

Friday, May 19, 2023

Breathless

Breathless: The Scientific Race to Defeat a Deadly Virus, by David Quammen, superimposed on Intermediate Physics for Medicine and Biology.
Breathless,
by David Quammen.
Whenever David Quammen has a new book, I put it on my “to read” list. Recently I finished his latest: Breathless: The Scientific Race to Defeat a Deadly Virus. Here’s the opening paragraph:
To some people it wasn’t surprising, the advent of this pandemic, merely shocking in the way a grim inevitability can shock. Those unsurprised people were infectious disease scientists. They had for decades seen such an event coming, like a small, dark dot on the horizon of western Nebraska, rumbling toward us at indeterminable speed and with indeterminable force, like a runaway chicken truck or an eighteen-wheeler loaded with rolled steel. The agent of the next catastrophe, they knew, would almost certainly be a virus. Not a bacterium as with bubonic plague, not some brain-eating fungus, not an elaborate protozoan of the sort that cause malaria. No, a virus—and, more specifically, it would be a “novel” virus, meaning not new to the world but newly recognized as infecting humans.
Quammen—a national treasure—is writing about covid (or, to use its official name, SARS-CoV-2). The coronavirus pandemic did not startle him; he almost predicted it in his earlier book Spillover. Quammen’s book Breathless is to tracing the origins and variants of covid as Walter Isaacson’s book The Code Breaker is to developing a vaccine for covid: required reading to understand what we’ve all been through the last three years. (And what I went through last month with my first case of covid, but I’m healthy now and feeling fine.)

Breathless describes the scientists who developed amazing software to analyze the virus’s genome, such as Áine O’Toole’s genomic pipeline PANGOLIN. Intermediate Physics for Medicine and Biology doesn’t discuss computational genomics, but at the heart of IPMB is the idea that you can combine a hard science like computer programming with a biological science like genomics to gain more information about, and insight into, biology and medicine. Quammen interviewed O’Toole about her experience writing the PANGOLIN program (“O’Toole stayed up late one night, and the next morning, there it was.”). But he didn’t interview just her. He talked to 96 heroic scientists and medical doctors who sought to understand covid, from those I’ve never heard of such as O’Toole to those we all are familiar with such as the brilliant Anthony Fauci. These interviews give the book credibility, especially given all the covid conspiracy theories and anti-vaccine nonsense that floats around the internet these days.

For anyone who may doubt the reality of evolution, I challenge you to try making sense of covid variants without it. Quammen takes us through the list: Alpha, Beta, Gamma, and the frightening Delta.
And after Delta, we knew, would come something else. The Greek alphabet contains twenty-four letters; at that point, the WHO [World Health Organization] list of variants only went up to mu. A virus will always and continually mutate, as I’ve noted, and the more individuals it infects, the more mutations it will produce. The more mutations, the more chances to improve its Darwinian success. Natural selection will act on it, eliminating waste, eliminating ineptitude, carving variation like a block of Carrara marble at the hands of Michelangelo, finding beautiful shapes, preserving the fittest. Evolution will happen. That’s not a variable, it’s a constant.
The latest variant, Omicron, seems to have appeared just as Quammen was finishing his book.
Omicron’s panoply of mutations reflects a period of active, extensive evolution—because the mutations not only occurred but they were preserved, within the lineage, suggesting they offered adaptive value.
One of the most interesting questions addressed in Breathless is the source of covid. Was it a lab accident, a spillover from an animal host (called a zoonotic event), or a malevolent attempt at biological warfare? Quammen doesn’t provide a definitive answer, but he favors the conclusions reached in a review article written by a group of prominent virologists led by Eddie Holmes.
Yes, Holmes and his coauthors agreed, the possibility of a lab accident can’t be entirely dismissed. Furthermore, that hypothesis may be nearly impossible to disprove. But it’s “highly unlikely,” they judged, “relative to the numerous and repeated human-animal contacts that occur routinely in the wildlife trade.” Failure to investigate that zoonotic dimension, with collaborative studies, crossing borders between countries and boundaries between species, would leave this pandemic festering and the world still very vulnerable to the next one.
Run, do not walk, to your library or bookstore and get Breathless. You need to read this book. Take special heed of Quammen’s alarming, disturbing, terrifying last sentence.
There are many more fearsome viruses where SARS-CoV-2 came from, wherever that was.

 A conversation with author and journalist David Quammen.

https://www.youtube.com/watch?v=jsREp6XI0nY