Michael Eisen

Last updated
Michael Eisen
Plos eisen.jpg
Born
Michael Bruce Eisen

(1967-04-13) April 13, 1967 (age 57)
Boston, Massachusetts, United States
NationalityAmerican
Alma mater Harvard University (AB, PhD)
Known for Public Library of Science (PLOS)
Awards Benjamin Franklin Award (Bioinformatics) (2002)
Scientific career
Fields
Institutions University of California, Berkeley
Thesis Structural Studies of Influenza A Virus Proteins  (1996)
Doctoral advisor Don Craig Wiley [ citation needed ]
Website michaeleisen.org

Michael Bruce Eisen (born April 13, 1967) is an American computational biologist and the former [2] editor-in-chief of the journal eLife. [3] He is a professor of genetics, genomics and development at University of California, Berkeley. [4] [5] [6] [7] [8] He is a leading advocate of open access scientific publishing and is co-founder of Public Library of Science (PLOS). In 2018, Eisen announced his candidacy U.S. Senate from California as an Independent, though he failed to qualify for the ballot. [9]

Contents

Early life and education

Born in Boston, Eisen and his brother Jonathan were raised in a family of scientists. Their grandfather was an x-ray crystallographer, their father, Howard Eisen a physician, and mother, Laura [10] a biochemist. They moved to Bethesda, Maryland when Eisen was four or five years old. The brothers spent summers in Long Island with their grandparents. Eisen states that he loved frogs and salamanders '"Even more than I have a frog fetish, I have a swamp fetish. I really like being in swamps."' He was also very interested in math and was captain of the high school math team. Eisen graduated from Walt Whitman High School in 1985. Intending to major in mathematics at Harvard University, he realized that there [he may encounter] other more brilliant math students, it was a Good Will Hunting moment and he decided that he did not want to major in mathematics, '"You don't want to be Salieri to Mozart."' During his years at Harvard, Eisen worked on "unlocking the three-dimensional structures of proteins." He was shown a DNA microarray which taught him a '"new way of doing biology"'. [11]

Eisen completed his PhD at Harvard University in biophysics and a B.S. (also from Harvard) in Math. [12] He was under the supervision of Don Craig Wiley [13] while studying Influenza A virus Proteins. [14]

There are things that are really really difficult, those are the kinds of problems you do want to work on. It's not that easy to tell the difference between impossible problems and a problem that is really really difficult. But learning to do so is critically important. - Things I learned from working with Pat Brown (Patrick O. Brown) - 2015 [13]

After earning his doctorate, Eisen was a Postdoctoral Fellow at Stanford University in the lab of David Botstein, where he most notably developed a method for interpreting gene expression data from microarrays. The seminal research publication that Eisen authored about this project has been cited over 16,000 times. [15]

Baseball and biology

When Eisen lived in Tennessee he worked as a play-by-play announcer for a minor league baseball team, [12] the Columbia Mules. He is a self-proclaimed Red Sox fanatic. [11] He and computational biologist James Fraser recorded a video for iBiology about the role baseball statistics influenced their research. Their argument is that sequencing DNA is similar to scoring a baseball game, and that many computational biologists learned to think about science computations from an obsessive interest in baseball stats. The exercise of comparing a specific player's stats to a database of other similar players allows a baseball fan to predict future performance. This same system works with proteins and predicting functions. As tools are developed that break down and track all stats concerning baseball players, so will technology improve with genetics. With both baseball and genetics, tools are being developed that refine the models. [16] In a lecture in 2015, Eisen stated that he received a computer from his grandfather for his twelfth birthday and spent the next five years teaching himself how to program so that he could keep track of baseball stats. [13]

Research

His academic research focuses on the evolution of gene regulation. [17] [18] [19] [20] Despite this focus, Eisen's work has historically spanned very diverse disciplines. For example, his 5 most cited papers cover a broad range of topics including methods for hierarchical clustering, [17] applications to human breast cancers (with David Botstein and Charles Perou), [6] and discovery of tumor subtypes in diffuse large B cell lymphoma (with Ash Alizadeh and Louis Staudt). [18] His more recent research work has been on fruit flies and Drosophila [21] and how they "develop from a tiny single-celled egg to a mature adult. He says they hold insights into what goes wrong in people as they age." [12] He receives funding from the Howard Hughes Medical Institute for his research. [21]

2018 U.S. Senate race

Eisen announced through Twitter on January 25 his intent to run for U.S. Senate from California in 2018 for Democratic Senator Dianne Feinstein's seat, registering the Twitter handle SenatorPhD. [22] His campaign slogan was "Liberty, Equality, Reality". Eisen's reasons for running for Congress included his perception that the Trump administration was unresponsive to climate change and other science-related issues. Another reason Eisen decided to run was his experience watching Cabinet appointees being interviewed by the Senate about climate change. He thought '“It would be really nice to have scientists ask the questions of the Cabinet appointees, because the senators don’t seem to understand the issue and aren’t asking the right questions.”' [12] He feels that if science is to be on the forefront of policy making, '"scientists need to run for office."' He felt that 2018's California jungle primaries afforded him a better chance at making the final two for the general election, but he did not make the final two (which were Dianne Feinstein and Kevin de León). [12]

For a really long time, scientists have watched political processes erode — and have watched politicians openly deride science, dismissing the role that science plays in our everyday life. Scientists have been sitting here hoping that someone would come along and defend those principals. Politics, in my mind, should function similar to science. We should try to figure out what’s going on in the world and then debate the best way to do it, to make the world better. The best tools we have to characterize reality are the observational tools that science uses all the time. Too much of politics has rejected that basic principle that scientists live and breathe all the time. [12]

Eisen dropped out of the race when he failed to qualify for the June 2018 primary ballot. [23]

eLife editorship and firing

In 2019, Eisen was named the second editor-in-chief of the open-access scientific journal eLife.

In 2020, in response to a twitter question, Eisen joked that the roundworm C. elegans was the most over-hyped animal because "they wiggle forward. They wiggle backwards. And occasionally they fuck themselves. That’s it". Some researchers were not amused by the joke, and the eLife board asked Eisen to watch his language on Twitter. [24] [25] Also in 2020, Eisen was involved in the story surrounding the death from SARS-CoV-2 of an anonymous queer Hopi female professor with whom he had interacted on Twitter. The account turned out to be a hoax created and run by neuroscientist BethAnn McLaughlin, who founded MeTooSTEM. Eisen was one of three people to attend a Zoom memorial for the fictional individual. [26]

In 2023, under his leadership, the journal moved away from the traditional "review, then publish" model, instead requiring authors to submit preprints and then publishing journal editors' reviews alongside manuscripts, meaning that the journal neither accepted nor rejected submissions. [27] Eisen said that the move was intended to reduce the prominence of the publisher, and instead focus attention on authors and their work. This move provoked both enthusiastic praise from some, including some eLife editors, and a strong backlash from others inside the organization, including some senior editors and editors. A news article in the journal Nature described the “Strife at eLife”. At least one of five deputy editors resigned. In a private letter to Eisen in January 2023, 30 editors threatened to resign once the changes were fully implemented. In March 2023, 29 eLife editors, including founding editor-in-chief and Nobel Prize winner Randy Schekman, urged that Eisen should be replaced immediately in a letter to the executive editor of the journal’s publisher. Eisen dismissed this in an interview as “powerful scientists not wanting to change a system that has benefited them”. Eisen tweeted on March 12, 2023, that academics were "lobbying hard to get me fired", a post that was subsequently deleted. [28] He tweeted on March 17, 2023 “I don't have a lot to add to the @nature story about @eLife. It reported accurately about the efforts of Randy Schekman and a few dozen editors to derail what we are doing, gave them a chance to explain their motivations, and us a fair opportunity to reply.” He later described his relationship with the board as “somewhat testy” and that some “had it in for me”. [25]

On October 13, 2023, soon after Hamas attacked Israel, Eisen tweeted a story from by the satirical website The Onion with the headline: "Dying Gazans Criticized For Not Using Last Words To Condemn Hamas." Eisen said "The Onion speaks with more courage, insight and moral clarity than the leaders of every academic institution put together. I wish there were a @TheOnion university". [29] The post prompted some criticism, including from Israeli researchers who asked colleagues to avoid publishing in eLife as long as he was editor. The chair of eLife’s board asked Eisen to delete his Twitter post, but he refused to do so "because that would be capitulating to what I thought was a really misdirected effort to silence any expression of support of Palestinians". Some researchers also expressed exasperation that, in 2018, Eisen had tweeted "Fuck Israel". He later clarified that this was referring to the Israel Defense Forces killing more than 60 people attempting to cross from Gaza into Israel during the Great March of Return. [25] On October 23, 2023, Eisen was fired by eLife. In response to the firing, at least five of eLife's editors resigned and other scientists said they would stop participating in eLife events in solidarity with Eisen. A petition letter was organised to protest against Eisen’s firing. The petition, which was signed by over 2,000 scientists, academics and researchers, said eLife's action is having a "chilling effect" on freedom of expression in academia. [30]

eLife released a statement saying "Mike has been given clear feedback from the board that his approach to leadership, communication and social media has at key times been detrimental to the cohesion of the community we are trying to build and hence to eLife’s mission. It is against this background that a further incidence of this behaviour has contributed to the board’s decision". [29] Eisen's response was "They were referring to that fucking worm thing. I’m not even kidding!". [25] An eLife spokesperson later clarified in an email to The Hindu, saying “We value and respect everyone’s right to freedom of speech including political expression and the legal right to protest. Particularly for those in leadership positions, exercising that right comes with responsibilities: an expectation to show good judgement and a duty of care to the communities they serve. We don’t believe those qualities have been demonstrated.” [31]

In eLife’s 2023 annual report, the Chair of the Board of Directors said: “In October, we parted ways with our Editor-in-Chief, Michael Eisen, and want to acknowledge the extraordinary vision and leadership he provided to eLife, which is allowing us to build on his legacy as we grow our publishing model.” [32]

On November 10, 2023, in response to a tweet saying “How to make faculty meeting more exciting? Wrong answers only.”, Eisen tweeted “Sit me next to Randy Schekman.”, referencing the previous editor-in-chief.

Open access advocacy

Throughout his career he has been an advocate for "open science", which is the free release of the material and intellectual product of scientific research. He is a leading advocate of open access scientific publishing [33] [34] [35] and is co-founder of Public Library of Science (PLOS) and serves on the PLOS board, the Academic Steering & Advocacy Committee of Open Library of Humanities, [36] and is an adviser to Science Commons.

In 2012 Eisen began protesting against the Research Works Act as part of his appeal to promote open access to information. [37]

Awards and honors

In 2002, Eisen was awarded the inaugural Benjamin Franklin Award in bioinformatics, for his work on PLOS and the open-access availability of his microarray cluster analysis software. [38]

Related Research Articles

<span class="mw-page-title-main">PLOS</span> Nonprofit open-access publisher

PLOS is a nonprofit publisher of open-access journals in science, technology, and medicine and other scientific literature, under an open-content license. It was founded in 2000 and launched its first journal, PLOS Biology, in October 2003.

<span class="mw-page-title-main">DNA microarray</span> Collection of microscopic DNA spots attached to a solid surface

A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles of a specific DNA sequence, known as probes. These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA sample under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target. The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm and the first computerized image based analysis was published in 1981. It was invented by Patrick O. Brown. An example of its application is in SNPs arrays for polymorphisms in cardiovascular diseases, cancer, pathogens and GWAS analysis. It is also used for the identification of structural variations and the measurement of gene expression.

<span class="mw-page-title-main">Harold E. Varmus</span> American scientist (born 1939)

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<span class="mw-page-title-main">Randy Schekman</span> American cell biologist

Randy Wayne Schekman is an American cell biologist at the University of California, Berkeley, former editor-in-chief of Proceedings of the National Academy of Sciences and former editor of Annual Review of Cell and Developmental Biology. In 2011, he was announced as the editor of eLife, a new high-profile open-access journal published by the Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust launching in 2012. He was elected to the National Academy of Sciences in 1992. Schekman shared the 2013 Nobel Prize for Physiology or Medicine with James Rothman and Thomas C. Südhof for their ground-breaking work on cell membrane vesicle trafficking.

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Citation impact or citation rate is a measure of how many times an academic journal article or book or author is cited by other articles, books or authors. Citation counts are interpreted as measures of the impact or influence of academic work and have given rise to the field of bibliometrics or scientometrics, specializing in the study of patterns of academic impact through citation analysis. The importance of journals can be measured by the average citation rate, the ratio of number of citations to number articles published within a given time period and in a given index, such as the journal impact factor or the citescore. It is used by academic institutions in decisions about academic tenure, promotion and hiring, and hence also used by authors in deciding which journal to publish in. Citation-like measures are also used in other fields that do ranking, such as Google's PageRank algorithm, software metrics, college and university rankings, and business performance indicators.

<span class="mw-page-title-main">Patrick O. Brown</span> American scientist and businessman

Patrick O'Reilly Brown is an American scientist and businessman who is the founder of Impossible Foods Inc. and professor emeritus in the department of biochemistry at Stanford University. Brown is co-founder of the Public Library of Science, inventor of the DNA microarray, and a former investigator at Howard Hughes Medical Institute.

<span class="mw-page-title-main">David Botstein</span> American biologist

David Botstein is an American biologist who is the chief scientific officer of Calico. He was the director of the Lewis-Sigler Institute for Integrative Genomics at Princeton University from 2003 to 2013, where he remains an Anthony B. Evnin Professor of Genomics.

<i>PLOS One</i> Peer-reviewed open-access scientific journal

PLOS One is a peer-reviewed open access mega journal published by the Public Library of Science (PLOS) since 2006. The journal covers primary research from any discipline within science and medicine. The Public Library of Science began in 2000 with an online petition initiative by Nobel Prize winner Harold Varmus, formerly director of the National Institutes of Health and at that time director of Memorial Sloan–Kettering Cancer Center; Patrick O. Brown, a biochemist at Stanford University; and Michael Eisen, a computational biologist at the University of California, Berkeley, and the Lawrence Berkeley National Laboratory.

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<span class="mw-page-title-main">Jonathan Eisen</span> American evolutionary biologist

Jonathan Andrew Eisen is an American evolutionary biologist, currently working at University of California, Davis. His academic research is in the fields of evolutionary biology, genomics and microbiology and he is the academic editor-in-chief of the open access journal PLOS Biology.

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References

  1. ↑ Michael Eisen publications indexed by Google Scholar
  2. ↑ Science News Staff (24 October 2023). "Prominent journal editor fired for endorsing satirical article about Israel-Hamas conflict". Science. Archived from the original on 24 October 2023. Retrieved 24 October 2023.
  3. ↑ "eLife welcomes Michael Eisen as Editor-in-Chief". eLife. 2019-03-05. Retrieved 2019-03-05.
  4. ↑ "Michael B. Eisen, PhD". Howard Hughes Medical Institute. Retrieved 23 September 2013.
  5. ↑ Michael Eisen's publications indexed by the Scopus bibliographic database. (subscription required)
  6. 1 2 Perou, C. M.; Sørlie, T; Eisen, M. B.; Van De Rijn, M; Jeffrey, S. S.; Rees, C. A.; Pollack, J. R.; Ross, D. T.; Johnsen, H; Akslen, L. A.; Fluge, O; Pergamenschikov, A; Williams, C; Zhu, S. X.; Lønning, P. E.; Børresen-Dale, A. L.; Brown, P. O.; Botstein, D (2000). "Molecular portraits of human breast tumours". Nature. 406 (6797): 747–52. Bibcode:2000Natur.406..747P. doi:10.1038/35021093. PMID   10963602. S2CID   1280204.
  7. ↑ Iyer, V. R. (1999). "The Transcriptional Program in the Response of Human Fibroblasts to Serum". Science. 283 (5398): 83–7. Bibcode:1999Sci...283...83I. doi:10.1126/science.283.5398.83. PMID   9872747.
  8. ↑ Ross, D. T.; Scherf, U; Eisen, M. B.; Perou, C. M.; Rees, C; Spellman, P; Iyer, V; Jeffrey, S. S.; Van De Rijn, M; Waltham, M; Pergamenschikov, A; Lee, J. C.; Lashkari, D; Shalon, D; Myers, T. G.; Weinstein, J. N.; Botstein, D; Brown, P. O. (2000). "Systematic variation in gene expression patterns in human cancer cell lines". Nature Genetics. 24 (3): 227–35. doi:10.1038/73432. PMID   10700174. S2CID   1135137.
  9. ↑ Cohen, Jon (2017-01-27). "Q&A: Michael Eisen bids to be first fly biologist in the U.S. Senate". Science | AAAS. Retrieved 2020-04-13.
  10. ↑ Okie, Susan. "NIH SCIENTIST A SUICIDE AMID PROBE OF PAPER". Washington Post. Retrieved 7 February 2017.
  11. 1 2 Mechanic, Michael. "Steal This Research Paper! (You Already Paid for It.)". Mother Jones. Retrieved 7 February 2017.
  12. 1 2 3 4 5 6 Krieger, Lisa (2017-02-04). "Bay Area molecular biologist Michael Eisen announces bid for U.S. Senate". San Jose Mercury News. Retrieved 7 February 2017.
  13. 1 2 3 "Michael Eisen: Baseball, mathematics and biology". India Bio Science. Archived from the original on 2021-12-21. Retrieved 7 February 2017.
  14. ↑ Eisen, Michael Bruce (1996). Structural Studies of Influenza A Virus Proteins (PhD thesis). Harvard University. OCLC   48938206.
  15. ↑ Eisen, MB; Spellman, PT; Brown, PO; Botstein, D (8 December 1998). "Cluster analysis and display of genome-wide expression patterns". Proc Natl Acad Sci U S A. 95 (25): 14863–8. Bibcode:1998PNAS...9514863E. doi: 10.1073/pnas.95.25.14863 . PMC   24541 . PMID   9843981.
  16. ↑ "James Fraser & Michael Eisen: Baseball Meets Biology". Education. iBiology. Retrieved 7 February 2017.
  17. 1 2 Eisen, M.; Spellman, P.; Brown, P.; Botstein, D. (1998). "Cluster analysis and display of genome-wide expression patterns". Proceedings of the National Academy of Sciences of the United States of America. 95 (25): 14863–14868. Bibcode:1998PNAS...9514863E. doi: 10.1073/pnas.95.25.14863 . PMC   24541 . PMID   9843981.
  18. 1 2 Alizadeh, A. A.; Eisen, M. B.; Davis, R. E.; Ma, C.; Lossos, I. S.; Rosenwald, A.; Boldrick, J. C.; Sabet, H.; Tran, T.; Yu, X.; Powell, J. I.; Yang, L.; Marti, G. E.; Moore, T.; Hudson Jr, J.; Lu, L.; Lewis, D. B.; Tibshirani, R.; Sherlock, G.; Chan, W. C.; Greiner, T. C.; Weisenburger, D. D.; Armitage, J. O.; Warnke, R.; Levy, R.; Wilson, W.; Grever, M. R.; Byrd, J. C.; Botstein, D.; Brown, P. O. (2000). "Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling". Nature. 403 (6769): 503–511. Bibcode:2000Natur.403..503A. doi:10.1038/35000501. PMID   10676951. S2CID   4382833.
  19. ↑ Clark, A. G.; et al. (2007). "Evolution of genes and genomes on the Drosophila phylogeny". Nature. 450 (7167): 203–18. Bibcode:2007Natur.450..203C. doi: 10.1038/nature06341 . PMID   17994087.
  20. ↑ Spellman, P. T.; Sherlock, G.; Zhang, M. Q.; Iyer, V. R.; Anders, K.; Eisen, M. B.; Brown, P. O.; Botstein, D.; Futcher, B. (1998). "Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization". Molecular Biology of the Cell. 9 (12): 3273–97. doi:10.1091/mbc.9.12.3273. PMC   25624 . PMID   9843569.
  21. 1 2 Harmon, Amy; Henry Fountain (2017-02-06). "In Age of Trump, Scientists Show Signs of a Political Pulse". The New York Times. Retrieved 7 February 2017.
  22. ↑ Reardon, Sara (2017). "Geneticist launches bid for US Senate". Nature. doi: 10.1038/nature.2017.21381 . S2CID   78431422 . Retrieved 7 February 2017.
  23. ↑ "Michael Eisen". Ballotpedia. Retrieved 2020-04-13.
  24. ↑ Jones, Asher; Elbein, Tyler O. (2 August 2020). "Worm Joke Causes Science Twitter Flame War Over Accusations of Sexism and Racism". The Daily Beast. Retrieved 22 August 2024.
  25. 1 2 3 4 Mechanic, Michael (November 17, 2023). "A Top Science Journal Fired Its Editor Over a Pro-Palestinian Tweet. He Has No Regrets". Mother Jones. Retrieved August 31, 2024.
  26. ↑ Bromwich, Jonah E.; Marcus, Ezra (4 August 2020). "The Anonymous Professor Who Wasn't". The New York Times. Retrieved 22 August 2024.
  27. ↑ Brainard, Jeffrey (20 October 2022). "Journal seeks to upend scientific publishing by only reviewing—not accepting—manuscripts". Science News. Retrieved 24 October 2023.
  28. ↑ Abbott, Alison (17 March 2023). "Strife at eLife: inside a journal's quest to upend science publishing". Nature. Retrieved 27 August 2024.
  29. 1 2 "Prominent journal editor fired for endorsing satirical article about Israel-Hamas conflict". Science. 23 October 2023. Retrieved 22 August 2024.
  30. ↑ "Firing of science journal editor after Gaza post sparks free speech rift". NBC News. 2023-10-26. Retrieved 2023-11-01.
  31. ↑ Prasad, R (October 28, 2023). "'eLife grieves the tragic losses of civilian lives, both Israeli and Palestinian'". The Hindu. Retrieved September 18, 2024.
  32. ↑ Hackett, Joanne (September 5, 2024). "Annual Report: 2023 in review". eLife. Retrieved September 18, 2024.
  33. ↑ Eisen, Michael (8 October 2003). "Publish and be praised". Guardian. Retrieved 23 September 2013.
  34. ↑ Brown, P. O.; Eisen, M. B.; Varmus, H. E. (2003). "Why PLoS Became a Publisher". PLOS Biology. 1 (1): E36. doi: 10.1371/journal.pbio.0000036 . PMC   212706 . PMID   14551926.
  35. ↑ WIRED Staff. "The 2004 Wired Rave Awards". Wired. ISSN   1059-1028 . Retrieved 2023-08-11.
  36. ↑ Howard, Jennifer (29 January 2013). "Project Aims to Bring PLoS-Style Openness to the Humanities". The Chronicle of Higher Education. Retrieved 19 November 2013.
  37. ↑ Dobbs, David (6 January 2012). "Congress Considers Paywalling Science You Already Paid For". wired.com. Retrieved 12 February 2012.
  38. ↑ "Benjamin Franklin Award - Bioinformatics.org". www.bioinformatics.org. Retrieved 7 February 2017.
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