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Hydrophilicity Analysis of Proteins

There are many thousands of scientific publications referencing use of the Hopp and Woods procedure for finding antigenic portions of protein molecules based on their sequences. Research breakthroughs with major pathogens of mankind have been reported. Tom recently added the coronavirus COVID-19 to the list of successful applications of the method.

If you're interested in delving into Tom's long record of hydrophilic/hydrophobic publications, click here for a listing. On the other hand, if you would like to read a little mystery story about the scientific intrigues surrounding the method's origins, read on below.

While most molecular biologists are familiar with both the Hopp and Woods hydrophilicity plotting procedure and the hydropathic plotting procedure of Kyte and Doolittle, they are not necessarily aware that the latter method is a nearly identical copy, published well after Hopp and Woods.

Furthermore, strong evidence suggests Kyte and Doolittle obtained the inspiration for their concept via a backdoor peek into Tom's unpublished studies, provided to them by Richard Lerner, then Director of the Scripps Institute in La Jolla.

While it is unlikely any direct proof exists that Kyte and Doolittle's method was lifted from Tom while he was a postdoc in the New York laboratory of Nobel Prize winner Gerald Edelman, the circumstantial evidence is strong and available in the public domain.

Most notably, a controversy broke out between Lerner and Doolittle, regarding which of the eminent men had truly originated the idea of hydropathic plotting. As was reported in Science Magazine, Lerner insisted that he came up with the idea while strolling in New York's Central Park in May, 1979 and wrote it on a napkin. He claimed he told Doolittle about the idea later while discussing influenza virus antigens. Doolittle claims to have thought up the idea in October, 1978. Neither man claims a date as early as Tom's inspiration in 1975.

And there is another key fact to consider. Richard Lerner was in New York City in 1979 to meet with Tom's boss, Gerald Edelman. Edelman even introduced Lerner and Tom briefly in the hallway on a chance encounter. Although there was no discussion of Tom's method at that moment, it seems all too coincidental that Lerner had his inspiration later that same day.

It doesn't take a rocket scientist (or even a molecular biologist) to put two and two together. The route from Tom's boss, Edelman, to Lerner, to Doolittle is a very short loop. Why would Edelman give away Tom's unpublished work? Perhaps because he never had any enthusiasm for Tom's idea, and never supported its development.

In fact, Tom had originated the idea in his PhD thesis work at Cornell Medical College four years earlier, in 1975, in discussions with his thesis advisor, Kenneth Woods. A primitive version of the method was even described in Tom's PhD thesis published in February of 1977. When Tom joined the Edelman lab and gave a seminar on the hydrophilicity method in March of 1977, it was roundly criticized and all-but shot down. Tom did three years of protein chemistry work for Edelman, then moved on to the New York Blood Center, where he immediately finished his long-neglected hydrophilicity study and published it well ahead of Doolittle.

To their credit, Kyte and Doolittle referenced Tom's paper in a note added in proof at the end of their paper, stating that it was a closely similar method (an understatement considering the methods are virtually identical). However, this afterthought placement of the citation is highly irregular. The common place for such citations is up front in the paper's introduction. If Kyte and Doolittle had cited Tom there, it seems unlikely peer reviewers would have considered the paper sufficiently innovative to warrant publication in a first-line scientific journal.

Tom has continued to contribute to this interesting field of science, writing papers and articles that deepen our understanding of hydrophilic/phobic analysis. His observations regarding membrane proteins and identification of other classes of protein-protein interaction sites can be found among these articles. More.