The Theory of the Molecular Evolutionary Clock

Dr. Emile Zuckerkandl, 1986.

Dr. Emile Zuckerkandl, 1986.

It thus appears possible that there would be no evolution without molecular disease.”
-Linus Pauling. “Molecular Disease, Evolution and Genic Heterogeneity,” 1962.

In the early 1960s, Linus Pauling and Emile Zuckerkandl, a French postdoctoral fellow who had arrived at Caltech in 1959, began researching the characteristics of hemoglobin extracted from a number of different species of animals. Zuckerkandl used a technique called fingerprinting, a process taught to him by a Caltech graduate student named Richard T. Jones, to create patterns of the amino acid sequences in each hemoglobin molecule.

[In her Master of Science thesis (pdf link), Dr. Melinda Gormley described fingerprinting, which was invented by the English chemist Vernon Ingram, as “a two-step process, [that] utilizes paper electrophoresis and paper chromatography. It produces splotches on paper at various locations; each mark corresponds to a peptide (two or more linked amino acids).”]

Once patterns had been prepared for several species, Pauling and Zuckerkandl compared them two at a time, and it was from the results of these comparisons that the theory of the Molecular Evolutionary Clock was developed.

The Molecular Clock differs from other evolutionary theories in that it tracks the evolution of a molecule rather than the evolution of a species. The theory states that, every so often, a mutation occurs in a given hemoglobin molecule. Generally speaking, this mutation is the source of a molecular disease, but will not cause any significant change to any organism other than its host.

Occasionally, however, a mutation will cause a lasting alteration to the molecule, and as the organism with the altered molecule reproduces, the change becomes permanent. More alterations of this nature can then occur on top of the original modification, thus resulting in even more differences in those hemoglobin molecules that have descended from the mutated original.

It is these differences that Pauling and Zuckerkandl were interested in when they compared the fingerprint patterns of different species, and their research led to an important breakthrough. As the duo compared more and more fingerprint patterns in a wider range of combinations, they observed that the number of differences between fingerprints lessened as the two species became more closely related. Pauling later stated that

[Zuckerkandl] found that in the beta chain of the human and the beta chain of the horse, for example, 20 of the 146 amino acids are different; but with human and gorilla, only one is different. It is the same amount of difference, just one amino acid residue, as between ordinary humans and sickle cell anemia patients, who manufacture sickle-cell-anemia hemoglobin.

From there Pauling and Zuckerkandl proposed that the comparative-fingerprinting method could be used to speculate as to how long ago any two species deviated from a common ancestor. Even more specifically, they reached the conclusion that one amino acid would be substituted every eleven to eighteen million years for any given species.

The evolutionary theory of the Molecular Clock was not readily accepted by scientists because it proposed a constant rate of evolution. However, it’s importance has now been noted and more research has been done on Pauling and Zuckerkandl’s original work. See, for instance, the very thorough examination conducted by Dr. Gregory J. Morgan in his 1998 paper “Emile Zuckerkandl, Linus Pauling, and the Molecular Evolutionary Clock, 1959-1965.” [pdf link], as well as Naoyuki Takahata’s “Molecular Clock: An Anti-neo-Darwinian Legacy,” [Genetics, (May 2007) 176: 1-6; not freely available online] which concludes that “a molecular clock is a most remarkable manifestation and a tribute from nature to anyone who studies evolutionary biology.”

For more information on Pauling’s hemoglobin work, please visit the website It’s in the Blood!  A Documentary History of Linus Pauling, Hemoglobin and Sickle Cell Anemia, and for more on Linus Pauling, check out the Pauling Online portal.

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Carleton Gajdusek, Doug Strain and Richard T. Jones

Before settling completely in to 2009, we would like to take a moment to note the 2008 passing of three men who had, in various ways, inhabited the Pauling orbit.

D. Carleton Gajdusek died on December 12, 2008 at the age of 85.  Gajdusek was a former graduate student of Pauling’s who received international acclaim – culminating in the 1976 Nobel Prize for Medicine –  for his research on a disease called kuru.

Gajdusek built his scientific reputation studying indigenous peoples throughout Asia and South America, in all cases seeking out unique diseases specific to small and isolated populations.  Kuru was a fatal disease that plagued the Fore tribe of New Guinea.  Sufferers of kuru experienced declines into madness before death, and their autopsies revealed that the disease had ravished their brains, shooting it through with holes.  Gajdusek’s breakthrough, and its resulting impact, is summarized nicely by Donald G. McNeil, Jr. in his excellent New York Times obituary of the Nobel laureate:

In 1957, Dr. Gajdusek…realized that the victims had all participated in “mortuary feasts” in the decades before the custom was suppressed in the 1940s by missionaries and the Australian police.

The Fore, who lived as they had in the Stone Age, cooked and ate the bodies of tribe members who had died, and smeared themselves with the brains as a sign of respect for the dead.

The disease confounded explanation because the mashed brains of the victims, injected into chimpanzees’ brains, produced no symptoms. All known disease-causing bacteria, viruses and parasites produced symptoms within days or weeks. But when the chimps developed kuru two years later, Dr. Gajdusek theorized that a slow-acting virus was at work, somehow not producing the expected immune reactions.

One of his assistants found “scrapie-affiliated particles” — fibrils resembling those in the brains of sheep with scrapie. But it was Stanley B. Prusiner who identified them as tangles of normal proteins that had misfolded and clumped, “teaching” other proteins to follow; he named them prions. They are now recognized as the cause of kuru, scrapie, human Creutzfeldt-Jakob disease and bovine spongiform encephalopathy, better known as mad cow disease. Dr. Prusiner won his own Nobel in medicine for that work in 1997.

McNeil’s obituary also describes Gajdusek as “difficult and eccentric,” in no small part because he was an admitted pedophile, convicted in 1997 of molesting one of the at least-fifty indigenous children that he adopted, raised and financially-supported over the course of his life.  Much more on this component of Gajdusek’s biography is spelled out by Thomas H. Maugh II in his Los Angeles Times obituary.

Pauling and Gajdusek were decades-long friends.  It is uncertain, though in our opinion unlikely, that Pauling was aware of Gajdusek’s personal proclivities.  On the contrary, the final communication from Pauling to Gajdusek that is contained in our files – dated December 28, 1993 –  indicates that Pauling hoped to appoint Gajdusek for five years as a staff member at the Linus Pauling Institute of Science and Medicine.  Likewise, the FBI’s investigation and subsequent arrest of Gajdusek did not take place until 1996, two years after Pauling’s death.

Letter from Linus Pauling to Carleton Gadjusek, December 28, 1993.

Letter from Linus Pauling to Carleton Gadjusek, December 28, 1993.


Douglas C. Strain passed away on November 15, 2008, at the age of 89.  A Caltech undergraduate who had occasion to take classes from Pauling, Strain went on to found Electro Scientific Industries, Inc., a pioneer of Oregon’s now-thriving technology sector.

Strain was raised in the Quaker tradition.  A conscientious objector during World War II, he was sympathetic to Linus and Ava Helen Pauling’s perspective on issues of peace and civil liberties. (This older post of ours, titled “An Outspoken Man,” relies heavily on Strain’s recounting of Pauling’s response to the anti-Japanese hysteria that arose in the immediate aftermath of the Pearl Harbor attack.)

A success in business, Strain was also an accomplished philanthropist who generously supported education at a number of institutions in both Oregon and California.  Strain’s intersecting interests in Pauling and in education culminated in his support of the OSU Libraries Special Collections — our reading room is named in his honor.

Though their contacts were limited following Doug’s graduation from Caltech, Strain remained a keen observer of Linus Pauling’s life and career.  In a 1995 oral history interview, Strain offered these perceptive thoughts on Pauling’s talents and multi-facted persona.

He was always off on his own ideas.  He was not a team player.  He would not, I don’t think, work well in a scientific team.  He was really an original guy and you either went along with Pauling or you weren’t there, that sort of thing.  But he was very stimulating because he was so openly enthusiastic about his ideas and always tried to be very intellectually honest about what he believed.  I mean, a lot of experimentation, a lot of proof.  He expected everybody else to do the same.  He was a very tough taskmaster for his graduate students.  I know for a fact.

The Oregonian has published an obituary of Doug Strain and also covered his memorial service.


Richard T. Jones was an Oregon Health Sciences University biochemist who passed away on February 26, 2008, aged 78.  Jones was both a Caltech undergraduate as well as a graduate student of Pauling’s in the late-1950s and early-1960s, who contributed to Caltech’s sprawling program of hemoglobin research.  One important component of Jones’s hemoglobin work was his introduction to the group of a technique called “molecular fingerprinting,” which Pauling and a third colleague, Emile Zuckerkandl, used to develop their influential theory of the molecular evolutionary clock.

Pauling was frequently asked to provide recommendations of his students for various positions around the world, and he had no trouble in relaying brutally-honest opinions, some of them rather starkly negative.  It is clear, however, that Pauling was a fan of Jones’s work.

Letter of recommendation for Richard T. Jones, written by Linus Pauling, December 12, 1959.

Letter of recommendation for Richard T. Jones, written by Linus Pauling, December 12, 1959.

Following his tenure at Caltech, Jones went on to chair the biochemistry department at the University of Oregon before relocating to OHSU, where he worked for thirty years, including a short term as acting University President.  Interestingly, one of Jones’s primary research interests during his time in Oregon was the study of blood substitutes, to some degree echoing Pauling’s work on oxypolygelatin during World War II.

One month before his death, OHSU honored Jones by renaming its Basic Science Building in his honor.