Hello everybody, thank you for so many responses and thousands of reads of my posts. Three months ago today, I first started blogging my story. We are now at Part 7! This part was supposed to be about what happened after I reported my experiences to Berkeley Lab in early 2016, but I am taking a quick detour with two blogposts: this Part and this post. I would like to mention some recent updates and my interaction with journal editor of 3D Printing and Additive Manufacturing (3DP+) regarding an Ahead of Print article of RZ, titled “Skeletides: A Modular, Simplified Physical Model of Protein Secondary Structure”, which I believe is a clear derivation of my previous work. Over the last one month, I requested the editor to modify abstract/introduction to specify that the authors’ new work is based on my existing work, and also to cite my arxiv publications that lay out the path forward for this field and this kind of future publications.
I first want to thank all of you since there has been so much support and so many of you have reached out to me. Thank you so much, and thanks for telling your stories. I am disheartened by some of your experiences. I am also not very surprised that these issues are affecting many of you.
Problem with crediting, and the associated bullying & silencing, is a taboo topic that nobody speaks about. All these terrible issues in academia are just hushed up and wiped away, which further fuels and motivates bullies and harassers. This bro-culture affects many people whose life and career get ruined.
I am proud that I raised my voice and highlighted few of these problems in academia hoping that some of you will benefit from my experience and will not repeat the same mistakes that I did – ironically – by just keeping my head down and working hard. I am hoping that you will be able to catch the signs of bullying, credit-shifting and manipulation early on, and will be able to act accordingly.
One thing that I have learned in the last couple of months is that the people who have the power or the voice to really do something about these issues in general – by raising voices, stopping such behavior, implementing policies, holding perpetrators accountable – do hesitate to act. May be it is easier to stay silent and keep doing philanthropic empty lip-services.
I have heard that my posts have been read by many people within Berkeley Lab, UC Berkeley and other campuses. Thank you! People have been reading out passages of my posts to each other. Some people have found comfort. I am glad it helped ease/identify your sufferings at some level. This is my reward for writing almost a book-length story.
Within days of my posting, Berkeley Lab’s new Chief Diversity Officer had reached out to me asking for an in-person meeting. I have invited them to come have the conversation on Twitter.
Now about that publication …
Because of a consistent support by Berkeley Lab (and funding by Department of Energy), RZ is now publishing a journal paper that is essentially a simplified version of my work. This paper was published online as Ahead of Print on Jan 21, and is now awaiting publication in the next issue of the journal 3D Printing and Additive Manufacturing (3DP+). The paper is titled, “Skeletides: A Modular, Simplified Physical Model of Protein Secondary Structure,” which the authors say is “a new, simplified molecular protein model made from modular building blocks.”
I somehow got notified about it since I think the concept looks the same.
There is an overarching similarity of language and methodology that suggests a strong inspiration from my work. Let’s just say that RZ is amply inspired by my work – and words – and forgets to mention that in this paper.
I have added a more detailed list of similarities in a separate post here.
I had reached out to the journal Editor-in-Chief, Skylar Tibbits, at the end of January, and later sent him a detailed document explicitly showing how this paper is just a derivative work, and that the authors need to properly credit me.
Tibbits said that he is cooperating to help resolve the issue. What I just learned after they looked at it for about a month is that the journal will not do anything.
Tibbits has known my work for a long while too. Years – as far back as 2012. He came to my symposium as a speaker in AAAS’15, I visited his lab at MIT in 2014, we discussed further collaboration in 2015. In short, he has known me and my work for a really long time.
The paper has really two parts: (1) a model (Skeletide) that is a simplified version of my models, and (2) self-assembly that I was planning to do and had talked about it with RZ. I had also talked about it with Tibbits back in 2015, as a collaboration effort with his lab at MIT and myself, in an email titled “Collaboration ideas” where I explicitly said to him: “The first thing to try would be to study how the model behaves through various circulations in a tank of water (or any liquid).” in response to his email to brainstorm.
RZ’s entire paper has sentences that suggest strong inspiration from my work and writings, but there is absolutely no mention of that. I also explained some of those ideas in Arxiv papers, and PeppyChain is a similar model with higher precision to make model making simpler. There is a total absence of proper crediting of me. My work has been cited as degrading, derogatory, problematic as just “another example” having a problem of: “hard to manipulate longer chains” – the reason they provide as why they are working on the “new” “simplified” one. Good thing!
Authors mention several times about their work being a simpler version … but they never explain “simpler” to what? Or “simplifications” from what? “Simplified” form of what? That information is missing throughout the paper, a gross oversight of the foundational prior work they have built upon (my body of work). Some examples:
- “The simplified model consists of amino acid units, which can be linked together …”
- “To focus on these model elements, we made inherent simplifications with regard to …”
- “We realized that there is a need for a new, simplified molecular protein model …”
- “… and to simplify construction.”
- “Here, we set out to develop a new, simplified protein model that …”
I just wanted them to give me proper credit by:
- adding this note at the beginning of Introduction:
- “In this paper we are building upon the concepts laid down by Chakraborty’s work on Peppytides, PeppyChains and Physical Biomodeling that constitute a body of novel work, creating a whole new field of study. Chakraborty’s work laid the foundation for how actual physical parameters of scaled, dynamic models for protein folding could be designed, analyzed, and folded into alpha-helix, beta-sheet and beta-turn structures, among other motifs. In this paper, we follow the same path and describe a simplified rendering of polypeptide chains inspired by Peppytide and PeppyChain models, to allow the work to focus on secondary structures of folded proteins, where we are using the same methods and materials for design, computation and analysis.”
- adding this to Abstract:
- “However, it is a challenge to represent all the relevant features of proteins in a single physical model due to their sheer structural complexity. Hence, Chakraborty’s models (Peppytide & PeppyChain) and their expansions into the concepts of a new field of study (Physical Biomodeling) is a pioneering work that shows us how to explore problem solving of this challenge. Here, we have built upon this body of work and made a simplified version where we describe a modular protein model that focuses only on representation of the secondary structure—the underlying structural skeleton.”
- Instead of this:
- “However, it is a challenge to represent all the relevant features of proteins in a single physical model due to their sheer structural complexity. Here, we describe a modular protein model that focuses only on representation of the secondary structure—the underlying structural skeleton.”
The layout of their paper has been taken from my paper, including all section names and layouts. The naming of the model (Skeletide) sounds similar to (and rhymes with) my model name (Peppytide). Both end-rhyme and internal-rhyme! We can write poems now.
Another paper (in Nature Scientific Reports) that was cited here has been termed “pioneer”, but that paper seemed to have cited me and mentioned that they have built on top of my work (Thank you authors!).
Some of you just pointed out to me that there is a term, Shell Game, defined as the effort to hide an original source of work by covering it up with something else. Is this really what is going on? If that is true, next paper will be improvement of Skeletide, and that will eventually become Peppytide with a different name.
Reference list in RZ’s paper looks inspired by my bibliographies. It might be a complete coincidence, but similar to my paper, the citation list starts with Dill and ends with Tibbits. This is quite amusing.
Scientifically speaking, as an expert, I have reservations about the merits of this paper and the way self assembly has been implemented (this is not a correct direction for proteins). But I was not a reviewer, so I will refrain from providing an expert opinion on how off-track the paper is.
Today editor Tibbits got back saying that he is going to publish the paper without any correction. He said “similarities are to be expected.” – Tibbits is giving me the PI “research group” and “team” treatment – which you all know how RZ has misused over the years in silencing me and making me invisible. Tibbits accepts that this paper builds on top of my work, but determines that proper crediting was done already.
Tibbits said that he has made this decision today to reject my request for a correction, in discussions with Berkeley Lab over the last two weeks, and the journal’s ethics team. The email looks to me more like it was in consult with the legal team rather than with any ethics team. He added that if I have further complaints, I should take it to Berkeley Lab (who has already helped him make this decision). I would love to know WHO in Berkeley Lab supports RZ’s behavior. Reversibly Berkeley Lab had said in their 2016 letter to me, where they mentioned Tibbits, that I should not expect to be included in my work as I am a nobody not in the league of these luminaries. (I have been working on this idea long before I came to Berkeley Lab, see my blog post about its history.) Excerpts from Lab’s letter:
I have heard for far too long that this is the standard practice in academia. If that is so, then Holy Moly! This issue needs strong action at a grand scale – which brings me back to what happened when I reported in 2016, the post that was supposed to be Part 7. I am posting that in the next part soon, sorry you all had to wait so long while I tackled the situation.
RZ kept saying to me that my work is not science and I am not at all competent scientifically. So: My work is not science, and their work is science. But … but … but … as they also say, Similarities are to be expected!
I didn’t get due recognition (and opportunity) and probably never will. But the fact is that senior scientists would go to any length to get inspired by my work. That is what I consider to be an award of highest order. So today, I celebrate.
Link to Notes on Similarity blogpost
Link to Part 8 (to be added)