Pauling, Zuckerkandl and the Molecular Clock

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Dr. Emile Zuckerkandl, 1986.

In 1963, a year after first publishing their ideas on the study of molecules as indicators of evolutionary patterns, Emile Zuckerkandl and Linus Pauling continued to explore what they felt to be a very promising thread of inquiry.

Specifically, the two joined in arguing that the molecular clock method – as they had since termed it – might be used to derive phylogenies (or evolutionary trees) from essentially any form of molecular information. This position was further explicated in “Molecules as Documents of Evolutionary History,” an article published in Problems of Evolutionary and Industrial Biochemistry, a volume compiled in 1964 on the occasion of Soviet biochemist Alexander Oparin’s 70th birthday.

Zuckerkandl and Pauling’s most influential work on this subject was first put forth that same year, in a paper that they presented together at the symposium “Evolving Genes and Proteins,” held at the Rutgers University Institute of Microbiology. The talk, formally published a year later and titled, “Evolutionary Divergence and Convergence at the Level of Informational Macromolecules,” classified molecules that occur in living matter into three groups. Each of these groups was identified according to new terms that the pair had developed that were based on the degree to which specific information contained in an organism was reflected in different molecules. These three categories were:

1.Semantophoretic Molecules (or Semantides), which carry genetic information or a transcript of it. DNA, for example, was considered to be composed of primary semantides.

2. Episemantic Molecules, which are synthesized under control of tertiary semantides. All molecules built by enzymes were considered episemantic.

3. Asemantic Molecules, which are not produced by the organism and do not express (directly or indirectly) any of the information that the organism contains. In their discussion, Zuckerkandl and Pauling were quick to point out that certain asemantic molecules may shift form. Viruses, for example, can change form when integrated into the genome of the host; so too can vitamins when used and modified anabolically.

Semantides were considered most relevant to evolutionary history, but the term never caught on in biology, paleontology, or other allied fields relevant to the study of evolution. Nonetheless, whatever the nomenclature, the “semantides” that Zuckerkandl and Pauling wanted to investigate – DNA, RNA, and polypeptides – proved indeed to be precisely the treasure trove of information on evolutionary history that the duo had hoped would be the case.


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A figure from the French translation of Zuckerkandl and Pauling’s 1964 paper.

Fundamentally, Zuckerkandl and Pauling aimed to elucidate how one might gain information about the evolutionary history of organisms through comparison of homologous polypeptide chains. In examining these substances, the researchers sought specifically to uncover the approximate point in time at which the last common ancestor between two species disappeared. In essence, it is this approach that we speak of when we use the terms “molecular clock” or “evolutionary clock.”

Zuckerkandl and Pauling argued that, by assessing the overall differences between homologous polypeptide chains and comparing individual amino acid residues at homologous molecular sites, biologists and paleontologists would be better equipped to evaluate the minimum number of mutational events that separated two chains.

With this information in hand, researchers would thus be empowered to exhume the details of evolutionary history between species, as inscribed in the base sequences of nucleic acids. This set of data, they believed, would hold even more useful information than would corresponding polypeptide chain amino acid sequences, since not all substitutions in the nucleotides would be expressed by differences in amino acid sequence.


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A table from Zuckerkandl and Pauling’s 1965 Bruges paper.

As their work moved forward, Pauling and Zuckerkandl published another paper, 1965’s “Evolutionary Divergence and Convergence in Proteins.” This publication appeared in Evolving Genes and Proteins, a volume that emerged from a conference that the two had attended in Bruges, Belgium.

By this point, the duo’s idea of the molecular clock, or “chemical paleogenetics,” had elicited opposition from organismal evolutionists and taxonomists, as well as some biochemists. Now referring to their “semantides” simply as informational macromolecules, Zuckerkandl and Pauling used the 1965 meeting to argue strongly against their skeptics. Zuckerkandl chided

Certainly we cannot subscribe to the statement made at this meeting by a renowned biochemist that comparative structural studies of polypeptides can teach us nothing about evolution that we don’t already know.

Pauling likewise added that

Taxonomy tends, ideally, not toward just any type of convenient classification of living forms (in spite of a statement to the contrary made at this meeting).

Directly challenging those present who were attempting to discredit the idea of the molecular clock, the pair insisted that taxonomy tended toward a phyletic classification based on evolutionary history. Since the comparison of the structure of homologous informational macromolecules allowed for the establishment of phylogenetic relationships, the Zuckerkandl-Pauling studies of chemical paleogenetics therefore had earned a place within the study of taxonomy. This, they argued, was true both as a method of reinforcing existing phyletic classifications and also of increasing their accuracy. Specifically, the two claimed that

The evaluation of the amount of differences between two organisms as derived from sequences in structural genes or in their polypeptide translation is likely to lead to quantities different from those obtained on the basis of observations made at any other higher level of biological integration. On the one hand, some differences in the structural genes will not be reflected elsewhere in the organism, and on the other hand some difference noted by the organismal biologist may not be reflected in structural genes.

Indeed, it was these early observations, coupled with additional work conducted by those scientists who took their ideas seriously, that allowed for the development of a successful measure of rates of evolutionary change over time. Without these data, modern paleontologists, physical anthropologists, and geneticists would not be able to accurately determine evolutionary histories. Today, this technique has been systematized and specialized in the field of bioinformatics, which is now foundational to many studies in both biology and medicine.

The taxonomic purpose of the molecular clock, however, was only a byproduct of Zuckerkandl and Pauling’s main ambitions in studying paleogenetics: to better understand the modes of macromolecular transformations retained by evolution; to elucidate the types of changes discernible in information content; and – most importantly for Pauling – to identify the consequences of these changes for a given organism.


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Linus Pauling, 1992.

Despite its considerable potential, the work of Zuckerkandl and Pauling, though conducted at such a critical juncture in a nascent field, was largely forgotten as recently as the early 1990s. In fact, in Allan Wilson and Rebecca Cann’s 1992 article, “The Recent African Genesis of Humans,” it was implied that the concept of the molecular or evolutionary clock was first developed and employed by a Berkeley anthropologist, Vincent Sarich. Sarich had collaborated with Wilson in 1967 to estimate the divergence between humans and apes as occurring between four to five millions years ago.

Pauling was still alive in 1992, and seeing this article he duly wrote to the editor of its publisher, Scientific American, pointing out that that, in fact, he and Zuckerkandl had, in 1962, issued their own estimate of the disappearance of the last common ancestor of gorilla and man. Zuckerkandl and Pauling’s calculations had yielded a divergence at about 7.6 million years before present, which Pauling pointed out was much closer than Sarich’s figure to the more recent estimates of divergence determined by Sibley and Ahlquist in 1984 and 1987. Notably, Pauling and Zuckerkandl’s estimate continues to remain closer to more contemporary notions of 8 to 10 million years.

Today, Emile Zuckerkandl and Linus Pauling are remembered as having first championed the notion of the molecular clock, even if many of the details now deemed as fundamental still needed to be ironed out by an array of scientists who followed. Regardless, as in so many other areas of science, Pauling proved once more to be on the ground floor of a new discipline. This was an academic venture that continued also to serve the younger Zuckerkandl well, as he continued on through a prolific career in science that concluded with his passing in 2013.

Peter Pauling and the Discovery of the Double Helix, 1952-1953

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Peter Pauling, 1954.

[The life of Peter Pauling: Part 4 of 9]

With Winter break coming fast and Linus Pauling having apparently solved the structure of DNA, Jim Watson and Francis Crick extinguished any hope of modeling their own structure. Eager to take advantage of a few days off, their Cavendish office mate, Peter Pauling, headed for the continent in the company of a friend whom he described as “a mad Rhodes scholar” who had “wooed” him with his “insane plan” for exploring Europe.

On this trip, which was indeed ambitious, Peter visited Munich, Vienna, Linz, Brussels, Frankfurt, and Bavaria, hitchhiking his way from location to location. Crossing Germany, Peter saw neighborhoods still littered with the rubble of the Second World War, alongside industrious people struggling to rebuild. His mode of travel, he confessed to his mother in a letter, had seemed a better idea when its low cost was his only consideration. In person, however, spending several hours standing in or walking through the snow had a way of changing one’s priorities.

Nonetheless, the whole escapade proved a romantic adventure for the young Peter Pauling. He spent Christmas Eve in a gas house belonging to the director of an iron company somewhere in Leoben, Austria. Resting there and watching the snow fall, he wrote again to his mother:

I look out the window to the lovely white mountains. It is grand. Considering the possibilities, Christmas and your birthday [Ava Helen was born on December 24, 1903] could hardly have been spent in a nicer place. Considering impossibilities, I can think of places where I would much prefer to be. Sometimes it is sad to grow up.


 

[Triple Helix animation and narration created by Cold Springs Harbor Laboratory]

With the arrival of the new year, the Cavendish researchers put their skis away, shook the snow from their coats, and resumed their work.  It wasn’t long into the term before Peter learned, from two letters received in February, that his father was, in fact, having difficulty with some of the van der Waals distances hypothesized to be near the center of his DNA model. In response – and almost as an afterthought – Peter casually asked his father for a manuscript of the DNA proposal, mentioning that his coworkers in Max Perutz’ unit would like to give it a read. Upon receiving the paper, Peter promptly revealed to Watson and Crick that the Pauling-Corey model was a triple helix, a concept similar to one that Watson and Crick had developed themselves – and rejected – back in 1951.

This moment was a major turning point for Watson and Crick, who only then realized that they still had a chance to discover the structure before Linus Pauling. That said, what followed may not have been quite the race as it was made out to be after the fact. At least, Peter Pauling did not see it that way, and the casual manner in which his father interacted with him (and with others at the Cavendish) seems also to belie such a dramatization.


 

[Jim Watson recalls learning of the Pauling-Corey triple helical model. Video created by Cold Springs Harbor Laboratory.]

Near the end of February 1953, while wishing his father a happy birthday, Peter noted that his office still felt that Linus’ structure required sodium to be located somewhere near the oxygens, whose negative charges would have to cancel out to hold the molecule together. “We agree that everything is a little tight,” he said, referring to the small atomic distances between Pauling’s three polynucleotide chains with phosphate groups in the middle.

As communicated in an earlier letter to his son, Linus Pauling had already identified these structural arrangements as a weakness of the model, and he was in the midst of attempting to correct the issue. Peter confided to his father that, at that time, the Cambridge office had nothing better to offer. He added simply that “We were all excited about the nucleic acid structure,” and concluded with his many thanks for the paper.

In response, Linus Pauling asked for updates on any progress that Watson and Crick were making with their own model, and casually requested that Peter also remind Watson that he should arrive for a scheduled protein conference at Caltech by September 20th. Peter clarified only that the Cavendish group had successfully built the Pauling-Corey model and that Watson and Crick had then discarded it, becoming very involved in their own efforts and “losing objectivity.” It would be up to them, Peter said, to communicate the details of their structure. Shortly thereafter, Watson and Crick sent a letter to Linus Pauling, outlining their structure and including the short article that they had submitted for publication in Nature.


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Crystallographic photo of Sodium Thymonucleate, Type B. “Photo 51.” Taken by Rosalind Franklin, May 1952.

It has been well-established that Pauling and Corey made basic errors in their own modeling  of the structure of DNA. But in March 1953, having no knowledge of the x-ray crystallographic photographs of DNA that had been taken by Rosalind Franklin at Kings College, Pauling felt bewildered by the certainty with which Watson and Crick had rejected his triple helical model. Upon learning its details, Pauling agreed that the double helix model was at least as likely, and he considered it to be a beautiful molecular structure, but he could not understand why his own structure was being ruled out entirely.

At the heart of his confusion lay the fact that he did not believe that any x-ray evidence existed that proved that the phosphate groups might somehow be located on the outside, rather than in the core, of the DNA molecule. Pauling did not believe that this evidence existed because he hadn’t seen it yet; crucially, Watson and Crick had. Indeed, from the point of their realization that Pauling had modeled the structure incorrectly, Watson and Crick worked fervently to once again convince Maurice Wilkins to provide them with Rosalind Franklin’s data.

(On one occasion, they met with Wilkins for lunch at the Crick home, where Peter could often be found for brunch on the weekends. On certain of these earlier brunch occasions, while in the home’s basement dining room, Watson and Crick discussed the feasibility of redoubling their efforts to model DNA while Peter, casually eating biscuits and sipping tea at the table, offered that if they didn’t do it soon, his father would take another shot at it. After the embarrassment of a failed attempt, he assured them, Linus Pauling was a strong bet to get it right the second time around.)

Within a month’s time, and with Rosalind Franklin having left his lab, Wilkins finally consented to providing Watson and Crick with all of the relevant data that he had requested. This proved to be the final piece that the duo needed in building their correct structural model of DNA.


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Pauling en route to Europe, 1953.

While all of this went on, Linus himself was seemingly unconcerned by any “race” for the structure of DNA. In fact, the only racing on his mind was a jaunt across Western Europe in a new sports car.

While Watson and Crick frantically worked to unravel the secrets of DNA before Linus Pauling beat them to it, Linus Pauling himself was debating the virtues of British, German, and Italian motor vehicles. Preparing for multiple trips overseas and in the market for some new wheels, Pauling’s plan was to select a car while in Europe during the Spring for the Solvay Conference, and then to actually pick it up in August, when he and Ava Helen would return to Europe for the International Congress of Pure and Applied Chemistry in Stockholm and Uppsala. The couple would then tour the continent in style before returning to the United States on a Scandinavian freighter and driving across the country from either New York or New Orleans to their California home.

While Peter advised his father that a Jaguar Mark VII was absolutely the best buy of the season, Linus expressed a preference for the slightly more modest convertible Sunbeam-Talbot. Peter countered with the possibility of an Austin A-40 Sports 4-Seater, and Linus finally agreed to have Peter look into purchasing the car on his behalf and scheduling a delivery of sorts. Seeing that his father was finally taking the bait, Peter attempted to spring a trap: “Might you be in need of a chauffeur, mechanic, linguist, travelling companion, navigator, break repairer, tire changer, witty conversationalist etc. on your trip next summer?” he wondered. “I know just the fellow. Good friend of mine.”


 

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A segment of the original Watson and Crick DNA model. 1953.

As the end of March rolled around and the Solvay Conference approached, Linus Pauling alerted his son to the fact that he had not made hotel reservations or, really, any plans for his visit to Cambridge. This responsibility he delegated wholly to Peter, who was somewhat distracted at the time, writing to his father about the blue sky and sun that had finally begun to break up the English winter gloom, and announcing with pride that he had gone to two balls in one week, getting along quite well with the Scandinavian girls. “As a sensible young American, I stand out in this town of pansy Englishmen,” he declared with impunity.

When Linus finally arrived at Cambridge in April, however, he found his son’s sensibilities to be somewhat lacking. Peter had in fact not made the requested hotel reservations, and while campus accommodations were fine for the son, they were not so wonderful for the elder Pauling. Watson later joked that, “the presence of foreign girls at breakfast did not compensate for the lack of hot water in his room.”

When the moment of truth finally came, Peter and his father strode into the Cavendish offices to see the model that Watson and Crick had constructed. Upon inspection, Linus reiterated the interpretation that he had given to his son earlier: the structure was certainly possible, but to be certain, Pauling would first need to see the quantitative measurements that Wilkins had provided. By way of response, Watson and Crick produced “Photo 51,” Rosalind Franklin’s now-famous image that enabled crucial measurements concerning the structure of the B-form of DNA.

Presented with this evidence, Linus Pauling quickly conceded that Watson and Crick had solved the problem. Later that night, the Paulings, together with Watson, had dinner with the Cricks at their home at Portugal Place to celebrate. To quote Watson, each “drank their share of burgundy.”


 

So was it a race? And if so, what was Peter Pauling’s role? Was he a double agent or an informant? Or merely an unwitting accomplice, ignorant of the full implications of his actions?

In trying to answer these questions, it is important to emphasize that, for Peter, the “race for DNA” had never been a race at all. His father, he believed, was only interested in the nucleic acids as an interesting chemical compound. Linus Pauling clearly didn’t attack the structure with the same tenacity as Watson, in particular, who regarded the genetic material as the holy grail of biology, the secret of life. As Peter would write two decades later in New Scientist 

The only person who could conceivably have been racing was Jim Watson. Maurice Wilkins has never raced anyone anywhere. Francis Crick likes to pitch his brains against difficult problems… For Jim, however…the gene was the only thing in life worth bothering about and the structure of DNA was the only real problem worth solving.

In 1966, Jim Watson, then in the process of writing his book on the discovery of DNA, The Double Helix, sent Peter Pauling an early draft. His concern, he explained, was that he accurately portray Peter’s role in the entire affair; that, and he didn’t want Peter to sue him for defamation.

Peter laughed and told his old office mate that he thought it was a very good book; certainly very exciting. However, he pointed out that Watson should ask Linus Pauling for an agreement not to sue him, too. After all, Peter said, “He has more experience than I do.”

Peter Pauling: The Race that Wasn’t, 1952

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Peter Pauling with his parents, ca. 1950s.

[The life story of Peter Pauling. Part 3 of 9]

“This tub moves steadily but slowly along.” So wrote Peter Pauling in a letter to his mother, Ava Helen Pauling, riding somewhere in the Atlantic in the hull of a cargo ship that had been built in 1926. “It took us two and a half days to reach the open sea.”

Having said goodbye to the nightlife of Montreal, and having entrusted his brother Crellin with the needle to his old turntable, Peter took to the sea without much to his name save a bottle of duty free Canadian Rye Whiskey; which, he lamented, did not keep him as warm onboard the cold ship as a good overcoat might have done. (Ava Helen, ever concerned for her son’s well-being, would see to it that he would have money to pick up some warmer clothes once he had arrived in Cambridge, paid for in matured war bonds.) Onboard the ship, Peter shared his cramped cabin space with three roommates: a Scot, a “very pleasant and hard-working” Englishman, and an 18 year old “pipsqueak” just out of rugby. Ever the charismatic socialite, Peter must have been excited to spend his days at sea with such an assortment of characters.

Arriving in England in the fall of 1952, Peter began his studies at Cambridge University, working under John Kendrew, a Peterhouse Fellow in Max Perutz’ Molecular Biology Unit at the Cavendish laboratory for physics. Although the Cavendish traditionally had not extended its focus beyond physics and physical chemistry to questions of biology, Sir Lawrence Bragg – director of the Cavendish and chair of the university’s Physics department – had recently supported an expansion of the lab’s scope to include the mapping of biological molecular structures.

This new Molecular Biology Unit would spearhead several important discoveries, among them Kendrew’s and Perutz’ work on the atomic structure of proteins, the program of research that Peter was brought on to support and an accomplishment significant enough to garner the 1962 Nobel Prize in Chemistry. That same year, two other former Cavendish researchers – James Watson and Francis Crick – would receive their shared Nobel Prize in Physiology or Medicine for their discovery of the double helical structure of DNA, a breakthrough that Peter Pauling certainly observed from a front row seat, and even, perhaps, helped to make possible.


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Francis Crick and James Watson, walking along the the Backs, Cambridge, England. 1953. (Image Credit: The James D. Watson Collection, Cold Springs Harbor Laboratory Archives.)

When Peter Pauling first moved into the office that he shared with James Watson, Francis Crick, and Jerry Donahue, Watson noted that Peter was “more interested in the structure of Nina, Perutz’s Danish au pair girl, than in the structure of myoglobin.” Crick, too, felt that the young Pauling was “slightly wild,” but still the office mates hit it off immediately. According to Watson, Peter’s presence meant that, “whenever more science was pointless, the conversation could dwell on the comparative virtues of girls from England, the Continent, and California.” Watson and the young Pauling even made a point of visiting The Rex art house cinema together to watch the 1933 romantic film Ecstasy, which Watson referred to affectionately as, “Hedy Lemarr’s romps in the nude.”

Women aside, Peter was most concerned by the day-to-day troubles that were typical of English life in the early 1950s. He wrote to his mother about the lack of a bathtub in the small, cold, damp room that he now inhabited, and complained about the space’s perpetual lack of sunlight. He did praise his fortune at having scoured London and finding a suitable teapot, and he requested that Ava Helen kindly make him a pair of curtains for his window (which she happily obliged).

In letters to his father, Peter preferred to talk about cars, or his recent dinners with the Braggs and their daughter Margaret, rather than his own research pursuits. Linus, on the other hand, was immediately curious about the intellectual climate at the Cavendish and was especially interested in the work of Francis Crick, who a year earlier had been part of a collaborative effort to develop a theory of mathematical representation for x-ray diffraction that was fast becoming a standard in the field.


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Linus Pauling and Robert Corey examining models of protein structure molecules. approx. 1951. (Image credit: The Archives, California Institute of Technology)

The previous year, 1951, Linus Pauling had bested Bragg and the physical chemists at Cambridge in becoming the first to publish the alpha helical structure of many proteins. Despite the desire prevailing at the Cavendish to eventually beat Linus Pauling at his own game, Watson and Crick had been warned to keep away from the study of DNA by the head of the lab. Bragg knew that Maurice Wilkins and Rosalind Franklin, of King’s College London, were already working on the problem using Franklin’s photos and crystallographic calculations of the A and B forms (low and high hydration levels, respectively) of DNA.

Wilkins’ and Franklin’s work was proceeding slowly, however, and Peter Pauling and Jerry Donahue – another Caltech graduate now stationed overseas as a post-doc – were both in regular communication with Linus Pauling. These contacts provided Watson and Crick with insight into what was going on in Pasadena. In his correspondence, Peter joked about the mounting competition between Caltech and the researchers at the Cavendish and King’s College. “I was told a story today,” he said to his father. “You know how children are threatened ‘You had better be good or the bad ogre will come get you?’ Well, for more than a year, Francis and others have been saying to the nucleic acid people at King’s, ‘You had better work hard or Pauling will get interested in nucleic acids.'”

While Watson and Crick urged Wilkins to provide them with Franklin’s images and calculations so that they might model the structure themselves, Peter stoked the fires of their urgency, assuring them that his father was no doubt only moments away from solving the problem. Donahue was equally convinced: for him, Linus Pauling was the only scientist likely to produce the right structure.

By December, the fate that Jerry Donahue and Peter Pauling had been predicting seemed to come true: a letter from Linus to his son claimed that he had indeed determined the structure of DNA. The letter gave no details, simply confirming for Watson and Crick that Pauling and his Caltech partner Robert Corey had somehow solved the problem. Watson later recounted his colleague’s distress in hearing this news, recalling that Crick “began pacing up and down the room thinking aloud, hoping that in a great intellectual fervor he could reconstruct what Linus might have done.” But it seemed to be too late. Pauling’s DNA paper was set to appear in the February 1953 issue of Proceedings of the National Academy of Sciences. In all likelihood, it would be time to move on to new projects.

Alexander Rich, 1924-2015

Alexander Rich. Photo by Donna Coveney.

Alexander Rich. Photo by Donna Coveney.

Today we remember Dr. Alexander Rich, a student and colleague of Linus Pauling who passed away in April at the age of 90. Rich and Pauling were among the group of scientists who embarked on one of the most exciting scientific quests of the 20th century – the so-called “race for DNA.” Rich’s friends and colleagues also remember him for his endless desire to know more about the processes propelling life, a trait that is evident in his career as a biochemist. According to Pauling, this holistic interest in and understanding of science allowed Rich to make invaluable contributions to multiple disciplines.

Nucleic acids – the carriers of genetic information within a cell’s nucleus – were first identified in 1868 when Friedrich Miescher isolated the DNA compound for the first time. For some eighty-five years, however, the structure of DNA remained undescribed. In the 1940s and 1950s, scientists around the world began to focus more on the problem, working to build an accurate model of the DNA molecule in hopes of fully understanding its role in the process of gene expression.

In 1953, using Rosalind Franklin’s experimental data, James Watson and Francis Crick published their proposal of a double helical structure for the DNA molecule, and quickly became scientific celebrities once their model was deemed correct. Like Rosalind Franklin and, indeed, Linus Pauling, Alexander Rich was among the many researchers whose work and contributions to the understanding of proteins and nucleic acids abetted Watson and Crick’s discovery of the DNA molecule’s structure.


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Born in Hartford, Connecticut in 1924, Alexander Rich served in the U.S. Navy during World War II, then went on to Harvard University, where he received a bachelor’s degree in biochemical sciences in 1947 and graduated from Harvard Medical School in 1949. Soon after receiving his medical degree, he moved to Pasadena, where he worked as a research fellow in Linus Pauling’s lab at the California Institute of Technology, and where he lived with future Nobel laureate Martin Karplus, a fellow student of Pauling’s.

Blessed with a nimble mind, Rich was able to jump back and forth between chemistry and biology as his research interests progressed, all the while paying close attention to the broader implications of his research for the field of medicine. Rich became particularly well-known for his work on the structure and chemistry of fiber compounds, research which quickly became useful to the study of nucleic acids. By isolating strands of nucleic acids within fibrous compounds, Rich was able to produce images of their structure.

Though his pictures were not as clear or impactful as those captured by Rosalind Franklin, many have since posited that his work could have been of equal significance to Franklin’s had Caltech housed more fine-focus x-ray equipment.  Regardless, Rich was held in high esteem by Watson and Crick who, before publishing their DNA structure, asked that Rich review their work and corroborate their ideas.

Collagen model built by Alexander Rich and Francis Crick. September 1955.

In the wake of Watson and Crick’s triumph, the structure of nucleic acids continued to intrigue Rich. This time around however, it was RNA that caught his attention. Like DNA, RNA carries genetic material and is vital to the formation of proteins. It is thus necessary to understand the structure and function of RNA to fully comprehend DNA’s role in protein formation.

Rich began research in this area during James Watson’s brief stay at Caltech, and some now speculate that Rich’s interest in RNA images led Watson to focus entirely on RNA. While in Pasadena, Rich and Watson collected different images of RNA in an attempt to understand its physical structure, but the x-ray crystallographic photographs available at the time were not sufficient enough to discern a conclusive model.

Rich’s stint at Caltech came to an end in 1954 and he subsequently moved into his own laboratory at the National Institute of Mental Health (NIMH). While there he continued to delve into questions regarding the structure and composition of RNA. At the NIMH Rich was, at long last, successful in creating an image of RNA that provided hints about its structure. Rich concluded that RNA consists of a single-stranded nucleic acid that binds with complementary strands of RNA to form a temporary double helix – a process he described as molecular hybridization. Many were skeptical that a single-stranded nucleic acid could temporarily form a double helix, but Rich was able to show that this is made possible by the shedding of water molecules that comes about when the two strands bind.

Not only did this finding contribute enormously to the understanding of RNA’s structure and function, but Rich’s contributions to the understanding of molecular hybridization in nucleic acids has opened up many more possibilities. For example, polymerase chain reaction, a process used to identify genes, is based on the principle of hybridization. Today, methods of this sort are fundamental to all sorts of work in biotechnology and to the analysis of DNA.

Alexander Rich with Linus Pauling, among others, at a scientific meeting in the Soviet Union.  Image Source: Alexander Rich Collection.

Alexander Rich with Linus Pauling, among others, at a scientific meeting in the Soviet Union. Image Source: Alexander Rich Collection.

Following his tenure at the NIMH, Rich became a professor of Biophysics at the Massachusetts Institute of Technology, beginning in 1958 and lasting until his death. His investigations there included the discovery of Z-DNA, which is a type of DNA molecule that takes a zigzag form and follows a left-handed wind rather than the more common right-handed wind. His work at MIT also showed that protein synthesis occurs in a polysome – the name given to a cluster of Ribosomes that work together.

Alexander Rich received high honors for his contributions, including election to the National Academy of Sciences and receipt of the 1995 National Medal of Science – the highest scientific honor bestowed by the U.S. government.  It is no wonder then that Linus Pauling recalled his former pupil with great pride. “Of the several men with MD degrees who have worked with me,” he once noted, “I think that Dr. Rich may well be the one with the broadest grasp of science as a whole.”

Dr. Pnina Abir-Am, Resident Scholar

Pnina Abir-Am

Dr. Pnina Abir-Am, historian of science at Brandeis University’s Women’s Studies Research Center, is the first individual to complete a term as Resident Scholar in the OSU Libraries for the 2012-13 school year.  An accomplished scholar, Abir-Am has authored and edited a number of noteworthy publications, including the influential book Uneasy Careers and Intimate Lives: Women in Science, 1789-1989 (Rutgers University Press, 1987, 1989) co-edited with Dorinda Outram.

Abir-Am traveled across the country to conduct research in support of another book, DNA at 50: A Revisionist History of the Discovery of DNA Structure, scheduled for publication in 2013.  Delving into the Pauling Papers, the Jack Dunitz Papers, the David and Clara Shoemaker Papers and the History of Science Oral History Collection, Abir-Am sought “to better explain Pauling’s failure with solving the structure of DNA by examining in greater detail his deployment of a group known as ‘Pauling’s boys.'”

In her Resident Scholar presentation, Abir-Am argued – as have many others – that Pauling was ideally positioned to solve the DNA structure, given his great successes in protein research from 1936-1951 and culminating in his elucidation of the alpha-helix.  The question then, is why did he fail to discover the double helix?  Why did he lose the “race” to James Watson and Francis Crick?

The reasons for the failure are manifold, and Abir-Am acknowledges many that have been pointed out by other researchers.  For one, Pauling was very casual in his approach, believing protein structures to be of more importance than DNA.  He also underestimated the research being conducted by certain of his peers, including Erwin Chargaff, J.T. Randall and Rosalind Franklin.

In particular, Abir-Am argues that Pauling disregarded the work being conducted at Kings College, London, believing that physicists like J.T. Randall and Maurice Wilkins could not be expected to solve a complex biological structure like DNA, as their training left them ill-equipped for the task.  By the time Pauling did get serious about the DNA structure, he was too far behind the competition, using poor quality data and rushing a structure to print. Indeed, in the end, Pauling’s attitude toward DNA could be summed up as “too little too late,” a situation further reinforced by the political problems – culminating in the revoking of his passport – that he faced throughout 1952.

Abir-Am sheds new perspective by focusing on the social structure surrounding Pauling at Caltech during the early 1950s. In examining the story from this perspective, Abir-Am wonders what “Pauling’s boys” – understudies, peers and other colleagues including Alexander Rich, Robert Corey, Eddie Hughes, Verner Schomaker, Jerry Donohue, David Harker and Pauling’s second-born son, Peter – could have done to render Pauling’s attempt at DNA more successful.

Abir-Am posits that “the boys” could have done plenty: collect x-ray crystallographic data, collaborate on model building, make calculations, serve as delegates at conferences and even collect intelligence on rivals.  To some extent all of this did occur, but never to the point where Pauling shied away from his manifestly wrong triple-helical structure.

In thinking about what could have gone differently, Abir-Am offers three possible conjectures as to why “the boys,” all hugely talented, didn’t steer Pauling down a more productive path:

  1. They did voice their objections but Pauling ignored them since, after the success of the alpha-helix, he was no longer seeking advice;
  2. Long accustomed to accepting Pauling’s ways, “the boys” lost the ability to criticize his work;
  3. Pauling did not inform “the boys” of his interest in DNA because he wanted to surprise them.

By the conclusion of her stay, Abir-Am was still wrestling with these questions and evaluating her conjectures.  An entire chapter of her DNA book will be devoted to Pauling’s failed structure – we’ll be very excited to read it!

The OSU Libraries Resident Scholar Program offers stipends of up to $2,500 per month to support research using the collections of the Special Collections & Archives Research Center.  For more on the program, check out its homepage. And to read of the work done by past Resident Scholars, see this link.

Update

After seeing this post, Dr. Abir-Am asked that we add some comments of her own, which are included here.

My initial reaction to OSU-SCARC’s (Oregon State University, Special Collections and Archive Research Center) Paulingblog’s entry of 11-21-12, reporting on my lecture “‘Pauling’s Boys’ and the Mystery of DNA Sructure” was “Wow, they did a better job than I might have done on my own!” Indeed, OSU-SCARC’s Program for Resident Scholars is a scholar’s paradise: a spacious reading room flooded by sunlight provides a superb “room with a view” of gorgeous Oregon trees. State of the art equipment scans archival documents straight into your flash drive. Rare, as well as recent, books that scholars might need to complement one’s ongoing archival research, line the reading room’s walls forming tasteful panels. The entrance is flanked by two glass cases for archival exhibits that rotate periodically and give the foyer a museum look.

But above all, SCARC is a paradise because of its angelic people, all eager to help resident scholars make the best of their precious stay. I was amazed at how readily the SCARC personnel not only guided me through the maze of archival documents in their care, but also helped me in preparing essential visuals. By displaying photomontages of Pauling and his associates, I was better able to convey his enigmatic predicament, as a leading molecular structurist who missed the solution of DNA structure, even though he was surrounded by many gifted and loyal associates, or “boys” in his era’s jargon. Along these lines, a slide of attendees at the Pasadena international conference on “Protein and Nucleic Acid Structure” which Pauling organized in September 1953, captured by photo 2 above, (click for enlargement) distinguished between “boys” from rival groups by color circles around their heads. These graphical devices were critical for my new argument that the outcome of competition over DNA structure was a matter of group rather than individual action.

Having spent considerable time in many archives on both sides of the Atlantic ocean, I have to conclude that OSU-SCARC, situated in the remote splendor of the Pacific Northwest, provides greater scholar-friendly opportunities than anything I have seen, including my prior favorite CCAC. (Churchill College Archive Center in Cambridge, UK) I now count SCARC scholars among my cherished colleagues and consider their work to be a valuable resource for my own chapter on Pauling & Co.’s effort with DNA structure. Last but not least, SCARC’s interest in this chapter, as well as in my forthcoming book DNA at 50 proved invigorating in propelling me toward a speedier revision of both chapter and book.

The Paulingblog’s Photo 2 conveys the civilized environment of OSU Libraries’ Willamette Lecture Room. For the sake of completeness, I wish to remind future applicants that the environment outside OSU’s library can also become a much cherished memory, especially the wild rapids of the McKenzie River which we survived during the Labor Day weekend preceding my 9-5-12 talk. Hopefully, the treasures I left untouched, whether in the archive or in the nearby Oregonian wild nature (e.g. Upper Klamath – I signed a petition to open it for rafting – Crater Lake, Sunset Bay) will soon cheer additional beneficiaries of SCARC’s Program for Resident Scholars.

Rafting on the McKenzie River, Labor Day weekend, 2012.

Rafting on the McKenzie River, Labor Day weekend, 2012.

Pauling Predicts the Process of Gene Replication

A segment of the original Watson and Crick DNA model. 1953.

“…I realized that I myself might discover something new about the nature of the world, have some new ideas that contributed to better understanding of the universe. For seventy years the motive to obtain greater understanding has dominated my life.”

-Linus Pauling. “The Nature of Life, Including My Life. Chapter 1 – How I developed an Interest in the Question of the Nature of Life.” May 5, 1992.

On May 28, 1948, Linus Pauling gave the 21st Sir Jesse Boot Foundation Lecture at the University of Nottingham. His talk, “Molecular Architecture and the Processes of Life,” presented many interesting examples of the important roles that certain molecules play in the human body. In so doing, Pauling discussed topics such as respiration, genetics and the immune system, and in typical Pauling fashion, displayed a knack for providing simple yet fascinating explanations of complicated subject matter. Although the entirety of his speech is interesting, Pauling’s comments concerning the gene were clearly well ahead of his time, and that is the focus of today’s post.

By 1948 it had already been suggested, through experimentation by Oswald Avery, that DNA was the genetic material. However most major scientists, including Pauling, still thought it more likely that proteins, being more complex and versatile substances than DNA, would carry the building blocks of heredity. As a result, DNA didn’t gain much importance until James Watson and Francis Crick discovered its structure in 1953. But scientists concerned themselves with trying to understand the gene long before they were aware of its place in the DNA molecule.

Pauling and two colleagues in Glasgow, Scotland, April 1948.

Included among these interested researchers was Pauling, who in his Boot Lecture predicted both the basic manner in which genes act as templates for proteins as well as the means by which gene replication might occur.

 I believe that the same process of molding of plastic materials into a configuration complementary to that of another molecule, which serves as a template, is responsible for biological specificity. I believe that genes serve as the templates on which are molded the enzymes that are responsible for the chemical characters of the organisms, and that they also serve as templates for the production of replicas of themselves.

As it turned out, Pauling’s simple statement had outlined the basics of the now familiar mechanism for the transcription of a protein from an RNA molecule. At the time of his talk, he may not have known the specific elements of the procedure, but the bulk of his prediction was more or less spot-on.

So an impressive start, but Pauling wasn’t done there. Continuing, he commented on how he imagined the gene might replicate itself.

The detailed mechanism by means of which a gene or a virus molecule produces replicas of itself is not yet known. In general the use of a gene or virus as a template would lead to the formation of a molecule not with identical structure but with complementary structure. It might happen, of course, that a molecule could be at the same time identical with and complementary to the template on which it is molded. However, this case seems to me to be too unlikely to be valid in general, except in the following way. If the structure that serves as a template (the gene or virus molecule) consists of, say, two parts, which are themselves complementary in structure, then each of these parts can serve as the mold for the production of a replica of the other part, and a complex of two complementary parts thus can serve as the mold for the production of duplicates of itself.

Again, Pauling hit the nail right on the head. We are now aware that DNA replication occurs precisely in this manner, and the fact that he was able to logically deduce the essentials of the mechanism without knowing the site or the structure of the gene is rather remarkable.

To read Pauling’s entire speech, click this link. For more information on Linus Pauling ranging from his attempts at elucidating the structure of DNA to his prolific peace work, please visit the Linus Pauling Online portal.

The Triple Helix

We have seen Paulings paper on Nucleic Acid. Have you? It contains several very bad mistakes. In addition, we suspect he has chosen the wrong type of model.

-James Watson, letter to Max Delbrück, February 20, 1953.

We were very interested to see that a model of the Pauling-Corey “triple helix” structure of DNA has been built by Farooq Hussain.  As Hussain notes on his website, the model was constructed based on drawings published by Linus Pauling and Robert Corey in their paper detailing the incorrect structure.

The proposed triple helix structure of DNA. Model by Farooq Hussain.

Hussain’s representation of the triple helix is striking; especially so when compared with Watson and Crick’s far more elegant and intuitive double helix, surely the most famous molecule in history.

Double helix model, courtesy of P. Shing Ho.

Indeed, Watson was well within his right to feel confident in his February letter to Delbrück.  As he noted before closing, “Today I am very optimistic since I believe I have a very pretty model, which is so pretty I am surprised no one has thought of it before.”

For more on the triple helix, see our write-up on the subject, published in April 2009.