Blog

What's up at eLife?

22 March 2023

Brave New worlds need brave new people

When eLife announced that they were going to publish every article that was reviewed, I reacted like some others in simply focusing on the monetary gain that that may imply.

This may just have been a general cynical reaction to profiteering by publishers in general. At the time I had not realised that eLife is a not for profit organisation. This was mostly because of their APC which was 3,000 USD (now reduced to 2000 USD). As we know (see here) it is hard to justify such an enormous APC. I would welcome eLife to explain in detail why it is that they cannot reduce their APC to something more reasonable. A diamond open access eLife being the model that we would all want to see.

But the attempt at an experiment to change the way in which researchers publish, this is actually very welcome and I applaud eLife and the editors that support this change. The concept that we as readers should be able, and indeed have to, to look at not only the article but also the reviews is very important. It is part of the critical reading that we should be engaged in anytime we read a scientific article and make a decision based on the value therein. At its heart, this model is an attempt to remove the idea of prestige from a journal title.

So is the removal of prestige the reason why there's been such a terrible kickback?

I have made the comment before that the people who really benefit from the current system which is heavy on prestige are the gatekeepers who have obtained and maintained their positions based on this prestige (see here). I was very interested then to read that eLife editor Mike Eisen agrees that this could be the reason for the kickback.

“...opposition to eLife’s model is driven fundamentally by powerful scientists not wanting to change a system that has benefited them and which they have sculpted to continue to reward them”.

Michael Eisen in Nature: News Feature

I think that Eisen is right. The reason why these prestigious editors do not want eLife to change its model is because they are only interested in the prestige that they gain by being associated with its title if it continues to be prestigious. This is one of the reasons why we need to change the current publishing system: albeit a wicked problem with many facets that require change (see here).

Perhaps a mistake that eLife has made has been to try to make these changes from the top end of publishing. We saw the same attempt with Public Library of Science (PLoS), who started with high-end journals ls and then initiated PLoS-ONE - eventually leading to serious struggles for their own survival (see here). Getting funders to consider new publishing models appears to necessitate starting at the top, otherwise they take no notice.

"Following its initial success in establishing itself as an open access publisher of high-quality science…"

eLife’s Board of Directors

Would Nature News Feature have written an article about change in editorial policy at a low impact factor diamond open access journal? I think not. The reason why this is big news is because big decisions are made around the funding of prestigious work. Threaten to take away that prestige and those who have benefited from it may well get upset. In this case they called for the axing of Eisen as editor. eLife is backed by some powerful funders, so it'll be interesting to watch their reaction as eLife pursues this new publishing model.

This is a multi-layered argument but it's an important one for science. Do you think science would benefit from a world without an accept / reject decision?

Further Reading

Measey J (2022) How to publish in Biological Sciences: a guide for the uninitiated. CRC Press, Boca Raton. ISBN: 9781032116419 https://doi.org/10.1201/9781003220886

To Read Open Access version: www.howtopublishscience.org

Lab Writing

Will Chat GPT write my PhD?

19 March 2023

John M

Can an AI write my PhD?

The emergence of artificial intelligence (AI) platforms brings with it new issues around writing generally, including writing your PhD thesis. These bots are already widely available in early 2023, and there are already publications that list ChatGPT as an author (Mijwil, Aljanabi & ChatGPT, 2023; O’Connor & ChatGPT, 2023) in acknowledgement that a large amount of the text therein had been generated by the bot.

More AI writing tools are going to be coming online in the near future, Google’s LaMDA and Microsoft’s Bing are very close to release. Microsoft plan to integrate their Bing platform directly into their office suite, meaning that as an author you may unwittingly use AI generated automated suggestions inside your word processor without realising it. Thus, you should be interested in knowing whether such tools can be used to help you in your own writing, if you haven’t already tried (Owens, 2023), with the tantalising possibility that they could be used to replace your needing to write.

In this blog post (and in a chapter in How to Write a PhD) I set out some ideas about how you might use AI to help you write, as well as some things that you should consider if you do go that route.

What is ChatGPT?

I decided to ask ChatGPT to contribute to this chapter by describing itself. My input text: “I am writing a chapter for a book on academic writing and I want you to describe ChatGPT in your own words”. Here’s what it said:

As a language model based on the GPT-3.5 architecture, ChatGPT is a sophisticated artificial intelligence program that has been trained on a massive amount of text data from various sources. It is designed to understand natural language and generate responses that are contextually relevant and coherent.

ChatGPT uses deep learning algorithms to analyze text inputs and predict the most probable next word or phrase, based on patterns and associations it has learned from its training data. This allows it to generate human-like responses to a wide range of questions and prompts, from simple queries to complex conversations.

One of the unique features of ChatGPT is its ability to understand and generate text in multiple languages, making it a valuable tool for communication and collaboration across different cultures and regions. Additionally, it has been used for a wide variety of applications, including language translation, content creation, and customer service.

Overall, ChatGPT represents a significant breakthrough in artificial intelligence research and has the potential to transform the way we communicate and interact with technology.

Large language platforms have been around for a while

Although at the beginning of 2023 we are seeing a large number of popular articles about ChatGPT, the use of language platforms in writing in general, including writing in the Biological Sciences, has been around for a while. If English is not your first language, then you already know how incredibly useful it is to enter text to a translation app in your own language and get a English back.

Some years ago, these translation platforms were rather literal, simply translating each word and providing text back that was barely usable. Today, with the help of AI, the translation that returns is more than not often a reasonable sounding (near) grammatically correct translation of what was entered. Hence, if you have used such translations in your own writing, then you should have already considered the a lot of contents of this chapter, and if you haven’t then you need to read on.

Interestingly, when ChatGPT was asked to provide text in French and Arabic, it failed to produce coherent text (Seghier, 2023), although it is possible that this will change over time as it becomes more sophisticated. It is interesting to note the difference between the claim that ChatGPT made (above) and this assertion from Seghier (2023) a few months ago. Whether or not ChatGPT has improved has yet to be tested.

Output from ChatGPT cannot be trusted

The first, and perhaps most important issue, about using ChatGPT outputs in your own writing is that you cannot trust it to generate text that is factually correct or unbiased. Indeed, OpenAI who own and administer ChatGPT readily admit that their bot can produce factually incorrect statements and is often biased in its output (Owens, 2023).

Because ChatGPT uses data on the internet to generate the basis of the text that it generates, it is prone to providing the internet consensus about popular topics, and studies have already shown that there is a bias in what is produced (McGee, 2023). This is something that OpenAI have already acknowledged, but that they are working to improve bias with user feedback (Owens, 2023).

This means that you should be checking any AI text that is generated before you add it to your chapter or manuscript.

Plagiarism by AI

There is the chance that your AI tool is going to plagiarise text that it finds on the internet, and so you may unwittingly be pasting the words of another author into your own text. Some authors consider that even if the AI is programmed to avoid plagiarism, using this text in any way should be considered as plagiarism (Salvagno, Taccone & Gerli, 2023). However, on balance, my own view is that any attempt to be overly restrictive on the use of AI generated text is bound to fail as AI itself becomes increasingly more sophisticated and widespread. Instead, I share the view (Lim et al., 2023) that it is better to embrace and learn how to use AI as a tool.

Perhaps a more fundamental consideration is whether AI will require us to redefine what we mean by plagiarism. Certainly, this is a philosophical consideration that right now (at the start of 2023) you will need to decide for yourself, although as more AI tools come online and are more commonly available, I think that many journal guidelines will be prescriptive on their use.

Plagiarism can be thought of as taking someone else’s writing without attribution. Another definition of plagiarism is pretending that someone else’s work is your own. While these two definitions may appear interchangable at first sight, when considering use of text from an AI, you might only infringe the attribution rule while the AI is programmed to infringe the pretence. In other words, if the AI is not a person, then following the first definition of AI you have not taken someone else’s writing. However, you might consider that as the AI itself was the product of someone else’s work, then they are the person (or group of people) that generated that text, and so the work should be attributed to them. This then brings you to the second definition of plagiarism. But what if that group of people don’t ask for any attribution or acknowledgement? Should you still give them as an author or put them into the acknowledgements? Moreover, could this team really be said to have generated the text when they have created software that searches text written by others on the internet and then collate and rewrite it? The huge number of content creators on the internet can never be acknowledged individually.

Another way of thinking about this might be to consider human interactions in writing text. If, for example, I help some colleagues with the English text of a manuscript and they offer to place my name in the acknowledgements, but I tell them that there is really no need. Should they still acknowledge me even though I have told them not to?

A further example might be the use of different layers in GIS that have been generated by different people. Many journals now insist that there is attribution to these layers in the legend of the figure or in the acknowledgements. We might legitimately ask whether this is necessary when those layers are freely available and have non-attribution Creative Commons licence (see here)?

Clearly, the definition of plagiarism will need some work in the light of new abilities for AIs to write text.

To me, the possibility that by using AI generated text verbatim you could be using someone else’s words means that you should avoid this. The same goes whether this is a translation from a large language platform or a new chat bot style AI. Using such platforms as tools is certainly acceptable, while using their text verbatim is probably an example of false attribution.

Ethics

In addition to the attribution of authorship, and potential plagiarism issues, you should also be aware of the ethical component of using text from an AI tool.

The kind of ethics points that come up are similar to those that are raised by paper mills (Salvagno, Taccone & Gerli, 2023). This issue is covered comprehensively elsewhere: see Chapter on when you should be an author in Measey (2022).

Positive aspects of using AI

It will not come as any surprise that many authors often find it difficult to get started. The classic image is starting at a blank piece of paper, or these days a flashing cursor on an empty screen. In this book I provide a lot of suggestions about how to get started with your writing task:

but can ChatGPT provide another opportunity when you don’t know how to start?

Use AI as a tool

Essentially, if you want to try using AI to help you write, use it as a tool. Don’t try to use it to replace your own writing. That will likely end in a poor product, and could possibly end with factually incorrect or biased text that you won’t want to be associated with your name - and clearly not something that you should want your advisor to read.

Getting started is often a struggle and I regularly suggest that students start by writing something/anything to fill out their outline, even if all of that text gets replaced at a later date. This is a way that you could use a tool like ChatGPT. Produce your own outline, because you do still need to plan your chapter, but then try using an AI like ChatGPT to flesh this out. Hopefully, this will end by helping you to write your own text, replacing everything that the AI has produced.

Using ChatGPT as an example of getting started with writing

I have tried this approach below and you can judge the outcome for yourself. First, I write the text outline, and second I provide each point to ChatGPT. For the following outline, I provided the outline statement (each bullet point) in quotes and prefixed it with “Write a sentence with citations on:”…”

In this example, the outline below is similar to what I would produce when writing an outline for the first two paragraphs of an introduction to a manuscript on invasive fish:

Invasive species are a growing global problem
- invasive species cost a huge amount of money to governments
- invasive species are a threat to biodiversity
- invasive species impact people’s quality of life
Freshwater habitats have been particularly impacted by global change
- important changes have occurred to freshwater systems after the introduction of invasive fish”
- invasive fish have been added to both rivers and lakes
- large numbers of introductions of invasive fish have already occurred globally, and are ongoing

The following text was generated by ChatGPT (on 19 March 2023) given the primer text above, and the stipulation that it should produce a sentence with citations. I have simply combined the output text into the paragraphs as might be expected in the introduction to a manuscript:

According to the International Union for Conservation of Nature (IUCN), invasive species are a growing global problem that pose a significant threat to biodiversity and ecosystem health. The National Wildlife Federation (NWF) reports that invasive species cost the United States government an estimated $120 billion annually in damages and control measures (Masterson, 2018). The Convention on Biological Diversity (CBD) states that invasive species are one of the main threats to global biodiversity, causing species extinctions, altering ecosystems, and reducing ecological resilience (CBD, 2021). A study conducted by the University of California, Davis, found that invasive species can have negative impacts on human health, recreation, and property values, affecting people’s quality of life in areas where they are present (Koch et al., 2011).

A global analysis of freshwater ecosystems found that they are among the most vulnerable to the impacts of climate change, pollution, and invasive species, with declines in biodiversity and ecosystem services being reported worldwide (Vörösmarty et al., 2010). Studies have shown that the introduction of invasive fish species can cause significant ecological and economic changes in freshwater systems, including alterations in food webs, declines in native fish populations, and reduced recreational and commercial fishing opportunities (Leprieur et al., 2008; Ricciardi & MacIsaac, 2011). Invasive fish species have been intentionally or unintentionally introduced into both rivers and lakes, causing significant ecological impacts and economic costs globally (Savini et al., 2010; Phelps et al., 2016). A study by Jeschke et al. (2014) found that over 12,000 introductions of invasive fish species have already occurred globally, with new introductions continuing to happen at an increasing rate, highlighting the urgent need for effective prevention and management strategies.

It is noteworthy that while ChatGPT did get into the swing of producing citations later on, the first couple of sentences didn’t have anything concrete. Neither did it see fit to produce the actual references themselves to the citations (although I didn’t ask it to do so). There is also a notable bias to the USA in the results given in the first paragraph. Overall though, I feel that the results of this exercise are somewhat impressive, and while I personally would not use this text verbatim, it is certainly better than a lot of first drafts that I’ve written myself.

As an exercise, I have tried to find each of these citations in an attempt to determine whether ChatGPT was accurate. In addition, I have run the two paragraphs above through a plagiarism detection software. I’ll write the results of that here once it’s complete.

Using a plagiarism checker (TurnItIn), the output suggested that: No plagiarism was found.

Will others detect ChatGPT if I use it?

Some people claim that they can detect the output from ChatGPT as it lacks the depth and insight that original authors usually have. In other words, the aim of ChatGPT is to produce the words (in a grammatically correct manor), while the aim of an author is to transmit an idea to the reader. As you might expect and hope, AI is not at the point where it can generate the same intent to communicate.

There will likely be better AI chat bots in the future, and ChatGPT itself is constantly getting feedback from users that should improve its own output.

ChatGPT, or other AI platforms, cannot be an author

You may be aware of several articles that are already published with ChatGPT listed in the author line (Mijwil, Aljanabi & ChatGPT, 2023; O’Connor & ChatGPT, 2023). Decisions on whether or not this is allowed are likely to be journal specific. However, some publishing houses are already making journal wide decisions excluding the use of AIs as authors.

This is clearly a dynamic process and you should be aware of what is happening in your own field.

Transparency

However you use an AI platform, you should be transparent to your advisor and any colleagues that you publish with about the exact level of use that was involved in generating your text. As a general rule with writing and academia, transparency is the best policy. Some authors have already called for regulations (Salvagno, Taccone & Gerli, 2023). Be aware that journals do update their instructions to authors, so you may need to look for statements on AI text generation. Similarly, familiarise yourself with your institutions requirements for thesis submission, and be careful you do not transgress any recently added rules.

COPE have already provided guidelines

The Committee on Publication Ethics (COPE) have already provided some guidelines to their members (mostly publishers) on the use of AI (COPE, 2023) which you can find here. In general, these rules emphasise the importance of oversight and transparency in the use of AI tools in decision making.

Publishers using AI bots

Publishers are very interested in using the text from AI bots to generate lay summaries of articles that are published on their platforms. Certainly, there is evidence that scientists are already using the bots to create their own summaries (Owens, 2023). This is certainly a possible creative use for AIs, but I would be concerned that without careful curation they may be prone to producing factually incorrect or misleading content. If you plan to use AI software to popularise your own science, then I suggest that you carefully read anything that is created and ensure that the text is correctly attributed when you use it.

Last note

This text was written in RMarkdown, without the use of suggestive prompts. AI generated text is written as quotes in the above text. All other text is my own.

It will be interesting to look back on this chapter in a decade and see the changes that have emerged in that time.

I would like to thank OpenAI and ChatGPT for generating the quoted text in this chapter. I’d also acknowledge TurnItIn for their plagiarism check.

References

COPE. 2023. Artificial intelligence (AI) in decision making.

Lim WM, Gunasekara A, Pallant JL, Pallant JI, Pechenkina E. 2023. Generative AI and the future of education: Ragnarök or reformation? A paradoxical perspective from management educators. The International Journal of Management Education 21:100790. DOI: 10.1016/j.ijme.2023.100790.

McGee R. 2023a. Capitalism, Socialism and ChatGPT. DOI: 10.13140/RG.2.2.30325.04324.

Measey J. 2022. How to publish in Biological Sciences: A guide for the uninitiated. Boca Raton, Florida: CRC Press.

Mijwil M, Aljanabi M, ChatGPT. 2023. Towards Artificial Intelligence-Based Cybersecurity: The Practices and ChatGPT Generated Ways to Combat Cybercrime. Iraqi Journal For Computer Science and Mathematics 4:65–70. DOI: 10.52866/ijcsm.2023.01.01.0019.

O’Connor S, ChatGPT. 2023. Open artificial intelligence platforms in nursing education: Tools for academic progress or abuse? Nurse Education in Practice 66:103537. DOI: 10.1016/j.nepr.2022.103537.

Owens B. 2023. How Nature readers are using ChatGPT. Nature 615:20–20. DOI: 10.1038/d41586-023-00500-8.

Salvagno M, Taccone FS, Gerli AG. 2023. Can artificial intelligence help for scientific writing? Critical Care 27:1–5. DOI: 10.1186/s13054-023-04380-2.

Seghier ML. 2023. ChatGPT: Not all languages are equal. Nature 615:216–216. DOI: 10.1038/d41586-023-00680-3.

This text is an excerpt from the book: How to Write a PhD in Biological Sciences - which you can find Open Access here

Lab Writing

Authorship for sale

12 February 2023

John M

New information about authorship for sale

From time to time new publications about publishing and writing appear and I make a note that I will need to update my book chapters accordingly. A preprint on rXiv by Abalkina (2022) prompted this particular revision to How to Publish in Biological Sciences. You can find the full book chapter here: When should you be an author?

When William Blake wrote about the dark satanic mills, he wasn't thinking of the paper mills (see here) that are now a growing feature of academic life. However, the description seems rather apt. Like other aspects of academic publishing, when money is involved there are forever increasing ways in which integrity in academic publishing is compromised.

Paper Mills

The concept of a paper mill is rather different from ghost authors or even salami-slicing (Part IV). Paper mills involve third parties, often not included on the author line acting as intermediaries. A paper mill may either be producing material for publication from scratch: i.e. companies that specialise in producing content that will pass peer review for those who want to buy authorship. Or they may be third party organisations that sell a position in the author line of a legitimate paper. Given that the world of paper mills is particularly shady, there is likely no hard distinction between these types of paper mill but a large grey blur between completely fake at one end and legitimate novel research (including non-legitimate authors) at the other.

Authorship for sale

A number of years ago there was evidence that first authorship on publications was for sale (Hvistendahl, 2013). We know is that there are benefits to those who are put on the author line. In many countries, being an author on a scientific research publication (sometimes with the stipulation that it is indexed by Scopus or Web of Science) is a requirement for obtaining graduation or promotion; especially in the medicine.

Adverts for authorship have appeared in social media (including Facebook and Telegram), stipulating the date of publication, the country of the journal, the number of co-authors and even the title of the research paper (Abalkina, 2022). Adverts indicated that buying authorship ranges from hundreds to thousands of USD, depending on the position in the author list and the perceived quality and Impact Factor of the journal. By matching historical adverts with subsequently published titles and authors, Abalkina (2022) managed to calculate the profits to one Russian publishing house (International Publisher LLC) to the tune of USD 6.5 million. While this ‘service’ was offered on Russian social media, the co-authors of advertised articles were from 39 countries. The nature of the adverts sometimes indicated editorial collaboration in the fraud, including having the editor as a co-author, thereby increasing the chances of publication success. Indeed, adverts often claimed no risk of rejection and no risk of detection given that editors and illegitimate authors both signed non-disclosure contracts with the publishing house.

The size and global impact of this fraud has attracted international attention (Else, 2023), and the websites and many of the adverts on social media have since disappeared. However, given the countries influencing this trade in authorship includes China, Russia and Iran (Abalkina, 2022), we can expect that this trade will not disappear, but simply become less blatant in its nature.

What can you do? - Certainly it is good practice to know who your co-authors are, even if you don’t know them personally. If you are the corresponding author, it is your responsibility to know the contributions (and therefore legitimacy) of every author your paper’s author list (see below)

Fabrication of research

Writing fake research, or that which contains fake results and data, is covered in another part of this book (see Part IV). Those that produce the manuscripts generally rewrite text and pull protocols from manuscripts that are already published. Results are often images that have already been published and/or are manipulated to suit the content (Else & Van Noorden, 2021). Hence, paper mills are a systematic and deliberate manipulation of the publication process (see Teixeira da Silva, 2021).

Read More:

Abalkina A. 2022. Publication and collaboration anomalies in academic papers originating from a paper mill: Evidence from a Russia-based paper mill. DOI: 10.48550/arXiv.2112.13322.

Else H. 2023. Multimillion-dollar trade in paper authorships alarms publishers. Nature 613:617–618. DOI: 10.1038/d41586-023-00062-9.

Else H, Van Noorden R. 2021. The fight against fake-paper factories that churn out sham science. Nature 591:516–519. DOI: 10.1038/d41586-021-00733-5.

Hvistendahl M. 2013. China’s Publication Bazaar. Science 342:1035–1039. DOI: 10.1126/science.342.6162.1035.

Teixeira da Silva JA. 2021. Abuse of ORCID’s weaknesses by authors who use paper mills. Scientometrics. DOI: 10.1007/s11192-021-03996-x.

Lab Writing

Dan defends his MSc thesis

08 February 2023

John M

Ghost frogs are under threat from invasive fish - it's official

Dan van Blerk defended his MSc thesis today in what is likely one of the most anticipated events of 2023. Dan has been working for the last 2 years on getting enough data from as many streams as possible to establish whether or not invasive fish (most notably bass and trout) are impacting tadpoles of ghost frogs. The data were unambiguous. Invasive fish are having a major impact on the density of ghost frog tadpoles.

Having this unambiguous data is really good news. It is all very well to speculate that the invasive fish impact tadpoles, and there are a couple of annecdotal studies that show the same. But getting robust data from lots of sites on lots of rivers is no easy job. Dan worked tirelessly, trudging up and down some of the most beautiful scenery in South Africa's fynbos, to collect the necessary data. In truth, Dan greatly enjoyed his time in the field. It did give him a great excuse to play in water and catch fish - two of his most enjoyable pursuits.

Below one of Dan's pics shows the upper portion of a stream beyond which fish cannot reach, and the tadpoles are safe!

His work is critical to conservation managers who require evidence in order to base their conservation management decisions.

We look forward to seeing Dan's work in print shortly!

Read more:

van Blerk, D. (2023) The Impacts of Invasive Fish on Ghost Frog tadpoles. MSc thesis, Stellenbosch University. http://hdl.handle.net/10019/32356

Frogs Lab meetings

In a rough spot

24 January 2023

John M

A big step toward conservation of Rough Moss Frogs

Ten years is a relatively short period of monitoring data, yet it can reveal important ecological interactions that can inform conservation managers about on the ground decisions. In this study, published today, we show the clear synergistic relationship between fire and the invasion of pine trees on populations of moss frogs on the Klein Swartberg.

In the figure below, you can see how the density of calling male Rough Moss Frogs increases in the absence of invasive pine trees, but declines in their presence. In addition, our analyses indicated that this decline was manifest when fire interacted with the invasion.

We obtained the density estimates of calling frogs in this study from a microphone array using the aSCR methodology (described here). We employed this approach at 12 sites on the Klein Swartberg over 10 years with 35 recordings. This included the initial work undertaken by Debra Stark (see here). Debra's work is published in a book chapter (see here). Currently, the invasion of pines on the Klein Swartberg is incredible, but undergoing control through block burning.

A picture of Oliver Angus among the pines on the Klein Swartberg in June 2021.

Further reading:

Angus, O., Turner, A.A. & Measey, J. (in press) In a Rough Spot: Declines in Arthroleptella rugosa calling densities are explained by invasive pine trees. Austral Ecology https://doi.org/10.1111/aec.13273

aSCR Frogs Lab

The MeaseyLab Blog is licensed under a Creative Commons Attribution 3.0 Unported License.

What's up at eLife?

Brave New worlds need brave new people

Will Chat GPT write my PhD?

Can an AI write my PhD?

References

Authorship for sale

New information about authorship for sale

Dan defends his MSc thesis

Ghost frogs are under threat from invasive fish - it's official

In a rough spot

A big step toward conservation of Rough Moss Frogs

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