Showing posts with label Academic publishing. Show all posts
Showing posts with label Academic publishing. Show all posts

Friday, July 25, 2025

Catch-22 in Biomedicine: Where Innovation Goes to Die

Welcome to the biomedical field, where the real disease is the system, and the only approved cure is being part of the club.

Let’s start with a fun little circle, a biomedical version of a hamster wheel — Catch-22 with a white coat and a PubMed badge. Here’s how it works:  

  1. To Be Read, You Must Be Indexed.
    No matter how groundbreaking, disruptive, or life-saving your research is, it won’t exist in the eyes of the AI models and policymakers, unless it’s indexed in PubMed. That’s the velvet rope to the scientific VIP lounge.

  2. To Be Indexed, You Must Be Published in a Journal That’s... You Know, PubMed-Worthy.
    And to get into one of those? You need money. Either:

    • Pay the journal a small fortune (ranging from $2,000 to “you’re gonna need a second mortgage”), or

    • Be part of The Club™ - that elite group of insiders who don’t need to pay because they’ve been publishing in the same journals since Watson and Crick shared a sandwich.

  3. Oh, You Did Something Novel? Sorry, That’s Not on the Approved Menu.
    Maybe you developed a cost-saving, patient-driven clinical trial. Fantastic! But if it wasn’t:

    • Funded by Big Pharma, or

    • Backed by the NIH and conducted by a prestige university with ivy-covered walls,
      …then guess what? It doesn’t count. Reviewers will call it “methodologically unsound,” Editors will say "it's not interesting to our readers", which is code for “you didn’t buy the right ticket.”

  4. Citations: The Scientific Echo Chamber
    “You cite me, I cite you, we all cite the same five people we've known since grad school.”
    If your work isn’t already blessed by the existing canon, if it dares to question current paradigms, or (God forbid) it talks about a topic not discussed by the establishment, it’s tossed into the "Thanks but no thanks" pile.

    Citations are the currency of academia. But like real currency, they tend to trickle upward.


Exhibit A: The Case of PATM

Ever heard of People Are Allergic to Me (PATM)? No? Neither has most of PubMed, and certainly not your favorite dermatology AI (that will also tell you it's all in your head).

There was a peer-reviewed paper in JMIR Dermatology showing a microbial connection to PATM. It should’ve led to more interest in this condition. 
But alas, JMIR Derm isn’t indexed in PubMed - a technicality that renders the findings invisible (unless the work was funded by NIH). Not because they’re invalid. Just… you know… they weren’t invited to the club gala.

Now you might think, “But what about establishment research?” Surely that gets through, right?

Monell Center — a well-regarded sensory science institute — published a genetic study on TMAU, another condition ignored for decades. Even they faced an uphill battle. The research showed genetic heterogeneity, meaning the story isn’t as simple as the textbooks would like. Ten years to publish (DNA of 130 subjects that contacted Monnell in 1999 to 2007; the paper was published in 2017). Ten. Because journals prefer tidy answers like “it’s just gene X” over complex truths like “it’s complicated and we don't fully understand it yet.”


Meanwhile, In the Land of AI

Your health chatbot? Your AI diagnostic assistant? It only reads what’s been indexed. It’s like a well-read librarian who refuses to touch any book without a barcode.

Which means all those brilliant papers:

  • From underfunded startups,

  • Crowdfunded patient trials,

  • Off-mainstream yet rigorous researchers...

Are off the radar. So AI, policy, and public knowledge stay blissfully ignorant — not due to a lack of evidence, but a lack of access.


So Why Does This Matter?

Because if you're a poor patient, or a researcher without connections, or someone who just wants to challenge bad assumptions, the system isn't just hard - it's set up to make you invisible.

Innovation doesn't fail here because it’s wrong.
It fails because it wasn’t published in the right place, by the right people, citing the right authorities.


The Streetlight Effect in Science

We’re all looking for the cure under the scientific streetlight - not because it’s there, but because that’s where the funding, indexing, and citations shine.

Meanwhile, in the dark, the real solutions — weird, messy, complex, human solutions - are waiting. But who’s going to look there?

Nobody. Unless someone with the right credentials takes a flashlight.


REFERENCES

Gabashvili IS. Cutaneous bacteria in the gut microbiome as biomarkers of systemic malodor and People Are Allergic to Me (PATM) conditions: insights from a virtually conducted clinical trial. JMIR Dermatology. 2020 Nov 4;3(1):e10508. doi: 10.2196/10508

Guo Y, Hwang LD, Li J, Eades J, Yu CW, Mansfield C, Burdick-Will A, Chang X, Chen Y, Duke FF, Zhang J, Fakharzadeh S, Fennessey P, Keating BJ, Jiang H, Hakonarson H, Reed DR, Preti G. Genetic analysis of impaired trimethylamine metabolism using whole exome sequencing. BMC Med Genet. 2017 Feb 15;18(1):11. doi: 10.1186/s12881-017-0369-8. PMID: 28196478; PMCID: PMC5310055.

Monday, July 24, 2023

The Past, Present, and Future of AI-Powered Medicine

In this era of rapidly advancing technology, Artificial Intelligence (AI) is spearheading transformative changes, particularly within the healthcare sector. A prime example is ChatGPT, a game-changer that is fast becoming an influential player in the biomedical field. Its potential to catalyze innovation and revolutionize medical research is profound. 

A MedrXiv paper posted today is a systematic review of AI in biomedical literature. The scope of this review is broad, encompassing preprints, peer-reviewed articles, case reports, patents, clinical trials, and even FDA approvals. The paper talks about impact of AI, including ChatGPT, across all medical specialties and subsets of publications, finding overrepresented domains within each subset, highlighting potential research gaps, biases, or areas of excessive focus. 

The pace at which the biomedical literature is growing is staggering, with two new papers being added every minute, around the clock. The MedrXiv paper also brings to light the limitations of current medical publishing models. 

The human author collaborated with ChatGPT, Bing, Claude, and Bard, and used SciSpace Copilot to review hundreds of systematic reviews and thousands of unique records across various databases. It aimed to comprehensively map out past achievements, current developments, and potential future directions in AI-based medical research. The paper represents the latest brainchild of an open science collaboration project, which welcomes participation from others at https://osf.io/87u6q/

The study reveals that as ChatGPT matures, it's finding applications across diverse medical specialties demanding cross-disciplinary collaboration. A fascinating trend shows a transition from theoretical to clinical applications in the AI literature, mirroring developments within the ChatGPT space.

Despite challenges such as ensuring the quality of training data and managing ethical concerns, ChatGPT is fostering the adoption of AI tools within medical areas that have been historically underrepresented in AI application.

If you have an interest in the future of medicine and the role AI technologies like ChatGPT play in shaping it, check out this project. It offers a compelling glimpse into what the future of healthcare might look like. 


REFERENCES

Gabashvili I.S. Artificial Intelligence in Biomedicine: Systematic Review. medRxiv 2023.07.23.23292672; doi: https://doi.org/10.1101/2023.07.23.23292672

Gabashvili I.S. The impact and applications of ChatGPT: a systematic review of literature reviews. arXiv:2305.18086 [cs.CY] https://doi.org/10.48550/arXiv.2305.18086

Gabashvili IS. ChatGPT in Dermatology: A Comprehensive Systematic Review JMIR Preprints. 02/06/2023:48979. medRxiv 2023.06.11.23291252; https://doi.org/10.1101/2023.06.11.23291252

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