Professor emeritus earns national honor from AAAS


December 10, 2020

By Mike Killeen

Like any good grandfather, Henry Jakubowski has one important role in retirement.

“I’m helping take care of my new granddaughter, who will soon be 5 months old,” Jakubowski said.

But the professor emeritus of chemistry, who retired June 30 after a 32-year teaching career at the College of Saint Benedict and Saint John’s University, also continues to work within the field. And, he was recently named a Fellow of the American Association for the Advancement of Science (AAAS).

Jakubowski was one of 489 members honored by the AAAS “because of their efforts toward advancing science applications that are deemed scientifically or socially distinguished.”

His citation notes Jakubowski’s “distinguished contributions to molecular modeling chemistry education and for faculty development in molecular visualization” in the Education section.

A virtual induction ceremony for all the Fellows will be held Feb. 13, 2021.

“The Chemistry Department is delighted to congratulate Henry on being named a Fellow by the American Association for the Advancement of Science,” said Alicia Peterson, associate professor and chair of the department at CSB and SJU. “This well-deserved honor recognizes his contributions and dedication to the field.”

Jakubowski believes he was honored, in part, for the online work he developed.

“Ever since I came to CSB/SJU, I’ve been promoting computer visualization of molecules for education and research, mostly for biomacromolecules and their complexes,” Jakubowski said. “We received a National Science Foundation (NSF) grant around 1990 to purchase Silicon Graphics workstations and software to analyze molecules. 

“As I became more adept at biomolecular visualization, I would develop lots of images showing the properties of biomolecules like proteins and nucleic acids. I started putting them online and writing detailed legends to accompany them,” Jakubowki continued.

“At Tom Creed’s suggestion (a former psychology professor at CSB/SJU), I assembled it all into a book and used it as the sole text for my biochemistry course,” Jakubowski said. “I decided to put it on the web for free after spending time in China and realizing that the book could be used anywhere, at any time, but more importantly in places that lacked educational resources.”

Initially, Jakubowski’s students would use expensive commercial modeling software and then make videos describing the structure and function of the biomacromolecules from the computer output for a final project. With the help of a student, Dan Farraro (’00), he started using free web modeling software. Jakubowski then uploaded the student tutorials into his online book to add interactivity to the book. 

“Around 2006 I put a hit counter on just the table of contents page. That page alone has had about 450,000 hits from all over the world. I think the accessibility, broad usage and interactive nature of the book was clearly a factor in my selection as an AAAS Fellow.”

Since 2010, Jakubowski has greatly expanded his activity in biomolecular visualization with an education focus as well as research focused on experimental drug design. He is leading a team of biochemists to write a brand new online biochemistry text that would cover a traditional full-year sequence of biochemistry. 

That project is part of the LibreText project developed by Delmar Larsen, Ph.D., from the University of California-Davis, to create free online chemistry texts for an entire four-year curriculum. Jakubowski is working with IT staff at UC-Davis and software developers at the National Center for Biotechnology Information to use a molecular modeling program that can be directly imbedded into the online biochemistry textbook.

“I will be working on this book for another two years – at least,” Jakubowski said.

Having always been a champion of online books, Jakubowki was asked about the advantages of the format.

“An online textbook can become ‘alive’ in ways that classical print textbook can’t,” he said. “This happens through interactive molecular models and mathematical graphs as well as smart figures and problems.

“Then there’s the cost of classical textbooks, which are increasingly prohibitive and unfair to those who can’t afford it and more generally to under-resourced communities globally,” Jakubowski said. “Online text can be updated immediately to incorporate the latest research findings making them more relevant and exciting for students.

“For example, I included a section on CRISPR/Cas 9 gene editing for which the Nobel Prize in Chemistry was just awarded before it was in any printed text. I just included a section based on an October 2020 article on the possible non-biological origins of chemical reactions that are found in a ubiquitous biological pathway called the Kreb’s Cycle. Likewise, relevant new findings on COVID-19 can be added as they appear,” he added.

“Henry was passionate about involving students in a variety of successful laboratory research projects.  He’s also a great advocate for online textbooks, both due to their lower cost and their ability to bring graphics alive on the screen with 3D modeling. Even though he is retired from teaching, he is actively writing for LibreTexts,” Peterson said.

In addition to his book, Jakubowski is part of two different collaborative groups with faculty from around the country who are interested in biomolecular visualization. 

In 2016, one group was awarded a one-year seed NSF grant to assess and promote biomolecular visualization literacy. That seed grant has turned into new four-year NSF grant to continue and expand the project. 

“Before the pandemic, we traveled around the country, giving workshops for faculty and post-docs on biomolecular visualization to increase the use of interactive, visual models to enhance student learning. Now we do them remotely by Zoom,” Jakubowski said. 

He is also a member of yet another grant team based at the Protein Data Bank at Rutgers University. This year, that team was awarded a five-year NSF grant to develop case-studies at the interface of biology and chemistry. The case studies center on selected structures of key protein and nucleic acids that affect health and disease. 

Jakubowski believes that these collaborations and new grants played a significant role in his AAAS award. He feels “honored to have been recognized for these decades of work,” but he’s far from done.

“Paradoxically, I am working on more grants simultaneously now than ever before,” Jakubowski said. “I work on them most days. In addition, I’m still active promoting policies to address climate change. Through my work with the Citizens’ Climate Lobby, I’ve met with U.S. House and Senate members or their staff in this pursuit.”

But even that work comes back to his granddaughter.

“She’ll be 80 in 2100, and I am moved to do everything I can now to enable her to grow and thrive in a livable climate,” Jakubowski said.

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