Publishing Speculative Papers

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Shirafune

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  1. Medical Student
I'm currently a junior majoring in genetics and genomics at a large public California school. I am pursuing an independent scientific writing project with one of my genetics professors on the potential clinical applications of genome editing. I am specifically proposing applications of CRISPR/Cas9 systems in possible treatments/preventative measures of aggressive prostate cancer alongside a review of the relevant literature. The professor thinks I could work on it a little bit more and send it to a journal for publication. She mentioned that there are journals that publish "speculative" papers, but the meeting ended short so I didn't really get a chance to ask more about that.

So I'm wondering what journals these are. Any help will be really great. Thanks!
 
What you are suggesting is worthless unless you have some unique insight into a particular application (say, you are a professor who is writing a review article on your own field & then pontificating on a recent finding). Unless what you are suggesting is a groundbreaking idea (it's not) that no-one has considered (they have) and now that they considered it, they will try it (they won't), then this is worthless.

Yeah, you could write something and maybe get it published in a throwaway journal. Maybe the experience will be worthwhile to you. But what you are proposing is not respectable.
 
What you are suggesting is worthless unless you have some unique insight into a particular application (say, you are a professor who is writing a review article on your own field & then pontificating on a recent finding). Unless what you are suggesting is a groundbreaking idea (it's not) that no-one has considered (they have) and now that they considered it, they will try it (they won't), then this is worthless.

Yeah, you could write something and maybe get it published in a throwaway journal. Maybe the experience will be worthwhile to you. But what you are proposing is not respectable.
Calm yourself...I think you are being a bit ridiculous and harsh. You've been a young student yourself and didn't start out knowing everything. Most papers published are not groundbreaking...not even close. And the rest of those comments aren't even relevant so i won't bother with why they are ridiculous.


@Shirafune...You need to be very precise with your PI and what they want. A short meeting to discuss a proposal/publication is not good. It takes a lot of effort and time to publish anything of quality and a review can certainly be high quality. I'm all about PI's encouraging their students but i think the real message is often lost in what is actually going to happen or what is wanted. You want to write up a proposal... The PI (may want to recruit you to the lab) wants you to learn more about the project you are proposing so you are also required to write a review. They encourage you with enticements of a publication...this is classic tactic. For you, I think the real goal here is to do a phenomenal job on the review bc at the end of the day it will not only help your proposal but you'll gain valuable insights and it will hopefully impress your PI. Furthermore, that review could easily go out for publication and the proposal could go out for review (funding!). Just a PhD's 2 cents.
 
There's nothing inherently disreputable about a review. There are too many of them out there in comparison to the number of data papers available (often my searches will pull up 3-4 reviews for every data paper on a given topic) but they definitely have their uses and (unfortunately) tend to get cited more heavily than data papers as well.

The OP is working with a professor who presumably is an expert in the field. Certainly a reasonable review would be a huge project for an undergraduate, but with the appropriate guidance and sufficient time available it should be possible to produce an informative and publishable paper.
 
Calm yourself...I think you are being a bit ridiculous and harsh. You've been a young student yourself and didn't start out knowing everything. Most papers published are not groundbreaking...not even close. And the rest of those comments aren't even relevant so i won't bother with why they are ridiculous.


@Shirafune...You need to be very precise with your PI and what they want. A short meeting to discuss a proposal/publication is not good. It takes a lot of effort and time to publish anything of quality and a review can certainly be high quality. I'm all about PI's encouraging their students but i think the real message is often lost in what is actually going to happen or what is wanted. You want to write up a proposal... The PI (may want to recruit you to the lab) wants you to learn more about the project you are proposing so you are also required to write a review. They encourage you with enticements of a publication...this is classic tactic. For you, I think the real goal here is to do a phenomenal job on the review bc at the end of the day it will not only help your proposal but you'll gain valuable insights and it will hopefully impress your PI. Furthermore, that review could easily go out for publication and the proposal could go out for review (funding!). Just a PhD's 2 cents.

Thanks for the input, but I want to clarify things. She is not my PI. I work in a lab focused on bone physiology and its genetic regulation. It just so happens that a major issue of aggressive prostate cancer is osteoblastic bone lesions, so the project I'm working on is kind of an aside. The genetics professor I mention here is teaching one of my classes. As a requirement of my university's honors program, I need to do an "honors contract" with a professor I am taking a course with. She suggested that I write a review paper of CRISPR/Cas9 clinical applications in the context of prostate cancer because I explained my interests and my current research progress. And to be clear, she is in a totally different line of research (fly genetics) than what I have experience in and want to work in (molecular characterization of human disease and gene therapy). She is an amazing person genuinely interested in helping our her students. She has said that I have very good scientific writing skills and that I could just work on this mini project a bit more for submission.

Now, as far as I know, ZFNs are the only ones being used in clinical trials (maybe even TALENs?), but I have yet to read anything on CRISPR/Cas systems, so the basic premise of this review/paper was to (1) review advances in genome engineering, specifically CRISPR/Cas and (2) analyze the future of the field by doing a speculative case study on aggressive prostate cancer. Currently I have ~25 references (3-5 reviews, and the rest data papers). The main point I wanted to get at was where can I actually publish a paper that has "experimental proposal elements" in it. What I'm working on really isn't a proposal or a review in a binary sense.

Thanks again!
 
The main point I wanted to get at was where can I actually publish a paper that has "experimental proposal elements" in it. What I'm working on really isn't a proposal or a review in a binary sense.

Do the experiments then write the paper. It doesn't work the other way around.
 
Well, I could be wrong as i was way off with my first thoughts on the situation. But if i now understand correctly, the OP isn't interested in doing the experiments... Which explains why the OP is searching for a journal to publish this "review with proposal elements". If i have yet again misinterpreted the OP and the OP does intend to do the experiments then as suggested above do the work then worry about where to publish. You could even potentially do a technical piece or brief publication and then include those results in your review...2 papers same effort.

OP-I don't believe i can help you. First, my field of expertise isn't in cancer so the journal's that i frequent would be of no use to you. Second, i only write grants, reviews, and data papers... I wouldn't publish a review with proposal elements bc others could potentially then take those ideas and get them out there faster than i could.
 
Well, I could be wrong as i was way off with my first thoughts on the situation.

If you are going to call me out and state that my comments are not relevant, explain why they are not relevant. Afterwards, I will respond to you. Generally, if Neuronix supports a post, it contains a valid point. An undergraduate without adequate supervision that is writing an article on a field in which they are not an expert about a hypothesis that is not tested is by my definition worthless. Science is hypothesis-driven, not speculation-driven. An untested hypothesis is worthless in the experimental/life sciences.
 
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If you are going to call me out and state that my comments are not relevant, explain why they are not relevant. Afterwards, I will respond to you. Generally, if Neuronix supports a post, it contains a valid point. An undergraduate without adequate supervision that is writing an article on a field in which they are not an expert about a hypothesis that is not tested is by my definition worthless. Science is hypothesis-driven, not speculation-driven.
? You were being a jerk...my dislike of your attitude doesn't require a response. But if you are asking me to point out the flaws in your comments to the OP then okay. A "like" on your comment (regardless of who) isn't validation of its worth. At the same time i fully acknowledge a dislike (by me in this case) isn't validation of its worth either. I don't know Neuronix or you and you don't know me either. This is the interwebs...for all I know Neuronix could be one sexy gamer living in his mom's basement.

The OP has supervision...and won't get far without it.

First...the rudeness of your message to the OP was completely unnecessary. Why be so rude? What did the OP do to you?
Young students don't know what is publishable and what isn't or the effort necessary to do the job justice. Jeez...some PhDs have yet to figure this out (have you read some of the articles out there?) Being rude to the OP isn't going to enlighten them. And it's certainly not going to gain their respect/they are more likely just to ignore your comments thus making them completely unhelpful/useless.

Getting excited about your first paper or the idea of one (which is how i perceived it) and going overboard/not knowing what you're doing is on par for the course. The OP is just getting started (whether that means 1 or 2 years, most likely less) and has no idea what's up and i wouldn't expect them to. A quick pubmed search tells me there are 182 papers that employ the CRISPR/cas system, one of which was a review article that came out just this year. But the OP hasn't gotten that far, i can't be sure they even know about ncbi and pubmed. Just having an idea for a proposal to go on is quite the accomplishment for a junior in college...even if it's not all that new or exciting. Let's encourage the OP to continue developing.

What you are suggesting is worthless - writing a proposal and/or a review has great worth whether it comes to fruition or not, i don't think one needs to be particularly bright to see the worth in such an undertaking

unless you have some unique insight into a particular application (say, you are a professor who is writing a review article on your own field & then pontificating on a recent finding) - You've never written a review then...or read one? Most are not unique and as stated earlier there are too many. But it is a learning exercise whether the OP understands that or not and thus has meaning and who knows...maybe after such an undertaking the OP will gain unique insights. Having a newbie write a review is usually done in the hopes they'll learn a great deal, start coming up with ideas or expand upon ones they already have and thus improving their future works. The "expert" is there over the shoulder ensuring the necessary elements are in it.

Unless what you are suggesting is a groundbreaking idea (it's not) - you are fully aware of the OPs ideas? Should we assume your first idea for a proposal was groundbreaking? Initial proposals regardless of how genius one thinks they are are rarely if ever groundbreaking. And yet they move forward. At some point you realize how bad it was and then you're that much better on the next one/you start fixing the mediocre parts of it and it develops into something worthwhile...this is how science works/how you learn.

that no-one has considered (they have) - Again, we don't know the specifics...the review will hopefully show what hasn't been considered and revisions to the proposal can be made

and now that they considered it, they will try it (they won't), - who knows... You don't need letters behind your name to come up with something worthwhile. Steve Jobs anyone?

then this is worthless. - i hope you can figure out why it's not

Yeah, you could write something and maybe get it published in a throwaway journal. Maybe the experience will be worthwhile to you. But what you are proposing is not respectable. - what's not respectable?

You are coming across as a graduate student with a chip on their shoulder who has recently been disillusioned by what it really means to do science. My guess..2nd or 3rd year.

This was so long i wasn't sure it was going to post...haha my apologies. Being succinct isn't my strong suit.
 
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what's not respectable?
Neuronix could be one sexy gamer living in his mom's basement.

You're funny. Welcome to the forum. If you knew me you would call me blunt/straightforward, but not rude. I don't sugarcoat things. To each her own. I have already earned my PhD but it has not been officially conferred. You can easily search for my past advice to others on this forum. I intend to continue bench research in some capacity in the future in the field of oncology. My PhD has gone absolutely swimmingly (due to hard work and an excellent, hands-off, supportive mentor). Ain't got no chip- just respond to people how I wished people would have with me- with blunt facts. And I believe I said that the experience itself would be worthwhile for the OP in that he would gain experience reading and writing science.

re: Respectable; a scientific publication that was written by someone with key insight that will be influential for a field. Not everyone wants their name associated with throwaway publications, and you shouldn't either. Speculative papers are of no value (or near no value) in oncology; they are rarely if ever written (I've never seen one) and they are not cited (which I can say from reading >1000 papers). So... worthless to the field. A review is a different matter, but that is not what the OP suggested. Speculation occurs at the end of a paper after the "Results" are displayed- not in the absence of any data.

Hopefully that addresses your concerns. And purchase a mirror.
 
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Whoa...i'm outraged!! (/s). Never implied that i'd want to be associated with something lack luster or disreputable. And the OP doesn't know what's publishable, i think we've established that. Doesn't make their goals of publishing something disreputable. A mirror...why i absolutely have one, how else could i admire myself? And, as already stated, I have a PhD if you were implying i was a 2nd or 3rd year student 😉.

And congrats! Definitely a huge accomplishment! But there's already enough ego in the field lets try to keep it down a bit or at least remember we aren't perfect and starting out is always rocky.
 
Well, the exchange has been slightly toxic. OP, you can get stuff published in journals like Theoretical Biology, but again your best bet is to either take your ideas as a proposal and rework it into a grant application. Having a paper with some good ideas and no data to back them up isn't suddenly going to give you primacy in coming up with those ideas. That's because they will end up in an obscure journal that no one reads. If someone else comes along and tests those ideas and provides strong evidence supporting/refuting them in a highly cited high profile journal, they - not you - will get the credit. So, in a way, it doesn't help you in any substantive way and could hurt you by giving out free ideas that competitors can run with. If you have some interesting ideas, your best bet is to either work them into a grant application (although those, too, often require significant data) or to record them in a personal log and sit on them until you're working in a lab where you can actually test those ideas and can publish the results of the experiments.
 
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