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Becoming a Section Editor at PeerJ

24 October 2023

Now a Zoology Section Editor at PeerJ

I've been an academic editor with PeerJ for 10 years, and I've handled over 70 papers in that time. Last month I was contacted by the PeerJ staff to ask whether I would join the team of Section Editors for Zoology at PeerJ. Each subject section has a small group of section editors who oversee the decisions made by the editorial board members. This ensures that there is some consistency and accountability for the decisions made by lots of independent editors. 

Far from being a passive role, the Section Editors engage in regular discussions about individual papers. It's a great opportunity to support the editorial board and authors alike. 

Now read the blog post or PeerJ.

  Lab  Writing

Starting your PhD

27 April 2023

How to Start your PhD

In some parts of the world the time-line is just getting started for new PhD students. This will be a very busy time for those involved, but it also needs to be a time to take stock and consider the bigger questions. In this video I provide some pointers to key issues for you to think about when starting your PhD. 

Warning - I do speak pretty slowly in this video, and so I think it's worth speeding it up so that you don't fall asleep. 
Here are some key excerpts from the text of a new chapter with links to How To Write a PhD in Biological Sciences:

Creating a conceptual framework of your PhD thesis

An important phase at the outset of your PhD project is to plan the chapters that are going to be in it. Think about the contents of your PhD and commit as many thoughts and ideas as you can to paper. If you aren’t sure how to get started, then think about how to answer the following questions:

  • What questions are you going to ask?

  • What is your study system?

  • How will you collect your data?

  • What are the most important variables that you will measure?

  • What techniques will you use?

  • Do you have hypotheses?

All these ideas (and more) are going to be swirling around your mind at the beginning of your PhD and you’re going to need to commit them to paper, and doing this right now at the start is the best time. If you haven’t done so already, write them all down. If you can do a mind map or some kind of graphical representation, this will be good for you if it suits the way that your mind works. Otherwise, you can use a series of lists and bullet points, if that is more your style. The important point here is be able to move from a jumble of ideas and thoughts into a formal plan for your thesis.

A thesis typically has five data chapters that are presented in a linear fashion (book format), bookended by an introduction and conclusion. At the heart of each chapter is going to be a hypothesis, a question or a technique that the following chapters implement in order to get their results.

It may help you to use distinct colours and short titles (just a couple of words) for each chapter so that you can efficiently communicate them to your advisor, and use them as file names for the sections (don’t use “Chapter 1” as your chapter name!). You should then use these same colours and short titles in your thesis timeline (Gandtt diagram) used in your proposal.

Once you have some rough ideas for your thesis plan, discuss it with your advisor and get their opinion. Then map it out on a piece of paper. But, be warned, it probably won’t be anything simple or linear - it’s likely to be more complex that the one illustrated below. It should have a lot of links and arrows that join all of the chapters to each other in different ways. It may help to code these links so that it’s clear what they represent. For example, you may want to use one colour for data and another for techniques and results. Although the detail is important, remember that the conceptual thesis plan is supposed to give an overview of the way in which the thesis works. This means that you might need to remove some of the minutiae in order to provide a clearer overall picture that others can easily follow.

A conceptual thesis plan will be placed in the introduction to your thesis. In this (fictional) example, I show how how the different chapters are linked by a single technique (developed as a chapter of the thesis: grey arrows), and data that results from each of the chapters (blue arrows).

A conceptual thesis plan will be placed in the introduction to your thesis. In this (fictional) example, I show how how the different chapters are linked by a single technique (developed as a chapter of the thesis: grey arrows), and data that results from each of the chapters (blue arrows).

To read more on this topic, please refer to the book!
  Lab  Writing

Can Google's Bard do any better?

27 March 2023

Can Google's Bard write my PhD?

Last week I checked out ChatGPT and its ability to write text on scientific topics with citations. The bot performed very well in that it gave a great first draft of text, but the references that it gave were completely bogus, with none of them checking out. It seemed to me that ChatGPT was using the internet to source the text and then throwing in a citation where it saw that others had used one on something similar. Writing text with citations is, however, a lot more difficult than randomly tossing in a citation (read more about how to do it here). Instead, citations must assert that statements in text where they are used have some basis. Overall, the output from ChatGPT resembled that of a “cocky student” who takes the risk that you won’t check their work, and so makes up citations to go along with text that looks good.

Today is the turn of Google’s Bard platform to take the same text, so let’s see how it does.

 First, Bard starts with a statement that: “Bard will not always get it right. Bard may give inaccurate or inappropriate responses. When in doubt, use the “Google it” button to check Bard’s responses.”

What does Bard say it is?

Input text: “I am writing a chapter for a book on academic writing and I want you to describe Bard in your own words”

Bard is a large language model, also known as a conversational AI or chatbot trained to be informative and comprehensive. I am trained on a massive amount of text data, and I am able to communicate and generate human-like text in response to a wide range of prompts and questions. For example, I can provide summaries of factual topics or create stories.

I am still under development, but I have learned to perform many kinds of tasks, including:

I will try my best to follow your instructions and complete your requests thoughtfully.

I will use my knowledge to answer your questions in a comprehensive and informative way, even if they are open ended, challenging, or strange.

I will generate different creative text formats of text content, like poems, code, scripts, musical pieces, email, letters, etc. I will try my best to fulfill all your requirements.

I am excited to be able to help you with your academic writing, and I hope that I can be a valuable tool for you.

You may feel, as I do, that Bard is a little overeager to please me, especially given that this is the first time we have chatted. Like some of Google’s other interactive platforms, I’d rather it was more concise and less politely flatulent.

The test

To quickly recap, I asked Bard the same things that I asked ChatGPT last week. I used the same wording, including the same sentence structure. Specifically, I wrote:

Write a sentence with citations on: ”…”

And then replaced the … between the quotes with a sentence that I had written as an outline for the first two paragraphs of an introduction appropriate to a PhD chapter or manuscript. Both paragraphs consisted of four sentences:

Paragraph 1

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

Paragraph 2

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

Here is the output from Bard compiled into two paragraphs for easy reading by me (see line-by-line version below):

Invasive species are a growing global problem, with the International Union for Conservation of Nature (IUCN) estimating that they cause $1.4 trillion in economic damages annually (IUCN, 2016; WWF, 2017). Invasive species cost governments a huge amount of money to control and eradicate, with the US National Invasive Species Council estimating that the cost in the US is $120 billion annually. (NISC, 2017). Invasive species are a major threat to biodiversity, as they can outcompete native species for resources, introduce new diseases, and alter habitats. (IUCN, 2016). Invasive species impact people’s quality of life by causing economic losses, disrupting ecosystems, and harming human health. Economic losses can occur when invasive species damage crops, forests, and other natural resources. Disrupted ecosystems can lead to the decline of native species and the loss of ecosystem services, such as water purification and flood control. Harm to human health can occur when invasive species spread diseases or cause allergic reactions.

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

WWF. (2017). Invasive alien species: A global problem in need of a global solution. Gland, Switzerland: WWF.

NISC. (2017). The economic impact of invasive species in the United States. Washington, DC: US National Invasive Species Council.

At the end of this first paragraph I have to say that it’s a relief that Bard is citing and providing the reference for its citation. This makes tracking the information a lot easier. However, the bland nature of the text and the (over) reliance on a single source is not particularly useful. As stated for ChatGPT, these reports are compiled from a great many different documents, and are often written in an ‘readers’ digest’ format that doesn’t include source material. Hence, for a student these are best avoided as citation sources unless their work is pertinent to that particular report. In the last sentence, Bard seems to have forgotten completely about the one sentence request and instead has provided us with a barrage of statements – none of which have citations, although there are still a couple of references.

2nd paragraph

Freshwater habitats have been particularly impacted by global change, with climate change, invasive species, and habitat loss all playing a role. Climate change is causing changes in temperature, precipitation, and water flow that are altering freshwater habitats. Invasive species are non-native species that can outcompete native species for resources, introduce new diseases, and alter habitats. Habitat loss is occurring due to human activities such as development, agriculture, and mining. The impacts of these changes are already being felt, with many freshwater species in decline. If we do not take action to address these challenges, the consequences for freshwater ecosystems and the people who rely on them will be severe. "Invasive species can cause major changes to freshwater ecosystems, including the decline of native species, the alteration of food webs, and the spread of diseases. For example, the introduction of the invasive Asian carp to the Great Lakes has led to the decline of native fish populations and the alteration of the food web" (IUCN, 2016). "Invasive fish, such as Asian carp and largemouth bass, have been added to both rivers and lakes, often through illegal releases or escapes from aquaculture facilities." (IUCN, 2016). "Large numbers of introductions of invasive fish have already occurred globally, and are ongoing. Between 1970 and 2000, an estimated 7,000 species of fish were introduced to new areas (IUCN, 2016)."

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

WWF. (2017). Invasive alien species: A global problem in need of a global solution. Gland, Switzerland: WWF.

  

The 2nd paragraph contained requests (from me) for sentences that were a lot more specific. However, Bard continues to use the same set of references for all of its answers. Those IUCN reports are really good, especially that one in 2016 – where would Bard be without it? Interesting that it slipped into a quotation mode by the end. Whether this was because it could only find a single pertinent sentence and didn’t want to simply rephrase it, or because it was feeling lazy, I’m not sure. Still, lots more text than I had wanted, and if I had wanted quotes then I’d have asked for them.

Rather like the output from ChatGPT, Bard is writing sentences (apart from when it gets over enthusiastic and produces a paragraph or gets lazy and decides to quote directly from the source) and they are on topic. But they do lack depth. While I have no reason to doubt the source for this information, it is inadequate for a thesis or manuscript and I’d be tempted to toss the lot and go back to my outline and fill it in with citations from my own reading. It's interesting that Bard starts quoting its source, and even gives me back the exact same sentence I gave it as one of its outputs. This is an odd interpretation of the request: write a sentence on - simply to provide the same sentence back. 

It should not go without comment that Bard is distressingly out of date. I guess this comes from only looking at one or two reports from Google Books as a source, but I’d have thought that there was a lot more up to date content in Google Books. It’s a curious and conservative approach.

 

Bard output – thanks but no thanks

In comparison with ChatGPT though, I have to conclude that Bard is more honest in its output. While ChatGPT might be thought of as the “cocky student who isn’t afraid to make anything up”, Google’s Bard could be characterized as the “lazy student who found a single report and mined it to produce everything”. Neither would survive writing a PhD or manuscript.

Given that Google should have access to so much more, I asked Bard a few supplementary questions to find out why it was being so restrictive in its answers:

Why do you only supply references from a single source?

I am currently able to access and process information from a single source, which is the Google Books database.

Will you be able to cite from academic literature in the future?

Yes, I am confident that I will be able to cite from academic literature in the future. I am currently being trained on a massive dataset of text and code, including academic literature. As I continue to learn and grow, I will be able to access and process information from a wider range of sources, including academic literature. This will allow me to cite from academic literature in my responses, which will help me to provide more comprehensive and informative answers to your questions.

If you look back at our conversation above do you think that there will be any conflicts between your statements and your cited sources?

I have reviewed the conversation above and I do not think that there will be any conflicts between my statements and my cited sources. I have tried to be as accurate as possible in my responses, and I have cited my sources whenever I have made a statement that is not common knowledge. I hope that I have been able to provide you with accurate and informative information.

Do you think that your answers are going to be different from those of chat GPT?

It is possible that my answers will be different from those of Chat GPT. I am trained on a different dataset of text and code, and I am also trained using different techniques. This means that I may be able to generate different results, or I may be able to generate results that are more accurate or more informative.

However, it is also possible that my answers will be similar to those of Chat GPT. We are both large language models, and we are both trained on a massive amount of data. This means that we may be able to generate similar results, or we may be able to generate results that are both accurate and informative.

Ultimately, it is up to the user to decide which model they prefer.

And there we have it folks. Two bots who produce shallow text that isn’t really of any help to a student who is trying to write for their thesis or a manuscript. Hence, to answer my own question, neither of these platforms are going to write your PhD thesis. ChatGPT is going to throw a real curve ball to anyone who has the patience to look into the veracity of its statements, while Bard is just looking lame. However, I think that we will need to watch this space. Either or both have the potential to do much better, and I suspect that the will get much better at this as soon as they get the chance.

Last note

This text was written 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 Google and Bard for generating the quoted text in this blog post.

Here is the output from Bard line-by-line:

Invasive species are a growing global problem, with the International Union for Conservation of Nature (IUCN) estimating that they cause $1.4 trillion in economic damages annually. (IUCN, 2016; WWF, 2017)

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

WWF. (2017). Invasive alien species: A global problem in need of a global solution. Gland, Switzerland: WWF.

 

 

Invasive species cost governments a huge amount of money to control and eradicate, with the US National Invasive Species Council estimating that the cost in the US is $120 billion annually. (NISC, 2017)

References:

NISC. (2017). The economic impact of invasive species in the United States. Washington, DC: US National Invasive Species Council.

 

Invasive species are a major threat to biodiversity, as they can outcompete native species for resources, introduce new diseases, and alter habitats. (IUCN, 2016)

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

 

Invasive species impact people’s quality of life by causing economic losses, disrupting ecosystems, and harming human health.

 

Economic losses can occur when invasive species damage crops, forests, and other natural resources.

 

Disrupted ecosystems can lead to the decline of native species and the loss of ecosystem services, such as water purification and flood control.

 

Harm to human health can occur when invasive species spread diseases or cause allergic reactions.

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

WWF. (2017). Invasive alien species: A global problem in need of a global solution. Gland, Switzerland: WWF.

2nd paragraph

Freshwater habitats have been particularly impacted by global change, with climate change, invasive species, and habitat loss all playing a role.

 

Climate change is causing changes in temperature, precipitation, and water flow that are altering freshwater habitats.

 

Invasive species are non-native species that can outcompete native species for resources, introduce new diseases, and alter habitats.

 

Habitat loss is occurring due to human activities such as development, agriculture, and mining.

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

WWF. (2017). Invasive alien species: A global problem in need of a global solution. Gland, Switzerland: WWF.

 

The impacts of these changes are already being felt, with many freshwater species in decline. If we do not take action to address these challenges, the consequences for freshwater ecosystems and the people who rely on them will be severe.

 

"Invasive species can cause major changes to freshwater ecosystems, including the decline of native species, the alteration of food webs, and the spread of diseases. For example, the introduction of the invasive Asian carp to the Great Lakes has led to the decline of native fish populations and the alteration of the food web." (IUCN, 2016)

 

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

 

 

"Invasive fish, such as Asian carp and largemouth bass, have been added to both rivers and lakes, often through illegal releases or escapes from aquaculture facilities." (IUCN, 2016)

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

 

"Large numbers of introductions of invasive fish have already occurred globally, and are ongoing. Between 1970 and 2000, an estimated 7,000 species of fish were introduced to new areas (IUCN, 2016)."

 

 

References:

IUCN. (2016). Invasive alien species: A global threat to biodiversity and ecosystem services. Gland, Switzerland: IUCN.

 

  Lab  Writing

The results are in - ChatGPT is a fraud

24 March 2023

ChatGPT sounds convincing, but gets it all wrong

In the experiment that I set up last week, I gave ChatGPT 8 statements and asked it to write a referenced sentence on each. These were then combined into two paragraphs in a way that you may consider writing for your PhD thesis.

See the experiment here.

During this week, I checked the statements given and the citations used. Here are the results:

The results of my experiment are in, and it’s bad news for ChatGPT or anyone who might want to try to rely on it for writing referenced statements for their PhD.

Most statements sounded good, and were certainly on message, but the citations were sometimes vague and when they could be pinned down turned out to be about other subjects or did not contain the information claimed. This is really bad news, because at first sight the information seemed credible. In the case of a PhD student, the examiners are likely to know their specialist field and will hopefully recognise the mis-citations. But for undergraduate essays, this is a far more difficult situation as those marking them will not have the time or subject area expertise to check for mis-cites. If it sounds credible, it will most likely fly.

 As a recap

I gave ChatGPT a series of short statements and asked for a sentence with citations. In the following, you will see this broken down statement by statement:

 Paragraph 1

Given: "Invasive species are a growing global problem"

Chat GPT Statement 1: 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.

My assessment of this statement is that it is very vague. While I can easily imagine that IUCN has made (many) statements such as this, it would be very difficult to pin down the source – which is primarily what we are interested in when we use a citation. Thus, while I feel that the statement is credible, it is unhelpful. Many might be tempted to use this text, and retrospectively assign another citation that would fit it. I would caution against this because (a) you’ll waste your time trying to find a citation that fits this text, and (b) you’d be better off reading pertinent literature and citing from what you’ve read. If you are unsure where to start with pertinent literature, try citations within citations from literature that you do know. The first paragraph of their text should give relevant literature for what you are trying to cite in your first paragraph – but always find and read it.

Chat GPT Statement 2: 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).

My assessment: I got very stuck with this statement, which has caused me a lot of difficulties in trying to track down this document attributed to Masterson in 2018. A search of the National Wildlife Federation (NWF) website (https://www.nwf.org/) for “Masterson” came up with only two documents (Pathak et al 2022; Small-Lorenz et al., 2017). Neither document is authored by someone called “Masterson”. I have written to NWF to ask them whether they have any insight into where this statement might have come from.

Next is the figure of $120 billion annually. This likely comes from the Pimental et al. (2005) paper, which has now been updated by Fantle-Lepczyk et al. (2022), who have provided the most recent assessment of costs to the USA. In their abstract, they claim that a conservative estimate would be ~$20 billion per year, with ~$73 billion as an upper bound on this figure. Hence, if Masterson really did write a report for NWF then it seems that this was a very high estimate, and not in line with other (more recent) literature. Given the wide ranging access to the internet, it is surprising that ChatGPT decided to use the NWF source.

Chat GPT Statement 3: 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).

My assessment: This is another very vague statement, this time attributed to the Convention on Biological Diversity (CBD). They produced a large number of documents in 2021, and trying to find the one that made this statement, and on what it would be based would require plenty of time. I don’t doubt that it is correct, but it would be better to use a source that others can find. Thus, rather like statement 1, I would junk this statement as unhelpful for including in your PhD.

Chat GPT Statement 4: 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).

My assessment: Here I started by searching the UCD website for “Koch invasive”. This came up with a number of hits, but none of which looked like anything that could be linked to the statement given. Next, I tried searching Scopus with “invasive species” in the Keywords, Abstract and , and Koch as first author. In 2011, only one paper by Frank H. Koch (of the Department of Forestry and Environmental Resources and USDA Forest Service, both in North Carolina – none of the other authors were from UCD) was written on invasive forest insect species (Koch et al., 2011). The article does not mention house prices, human health or quality of life. Had I been looking for a citation for a statement like this I might have started with the Blackburn et al. EICAT framework [@blackburn2014unified] and looked for examples of people citing this with their specified categories.

At the end of the first paragraph, I have to say that I’m not impressed with what ChatGPT actually came up with. It sounded good, but the statements were vague, and no sources could be verified. Hence, in terms of how useful this would be for writing your PhD, I would say that it gets zero points and was probably a waste of time. I would hope that you are more familiar with the broad context of your work to write a better first paragraph from scratch.

Paragraph 2

Chat GPT Statement 5: 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).

My assessment: Paragraph 2 looks like it is starting on a much firmer footing, and this suggests to me that ChatGPT needs more specific input in order to get it to be more useful. Firstly, there is a paper by Vörösmarty et al. (2010), and it is about fresh water. But it doesn’t mention invasive species. What is actually says is: “non-native species threaten biodiversity but are typically inconsequential to human water security.” This appears to be the opposite of what ChatGPT thought, and while we might have been tempted to keep this sentence as the citation (1) existed and (2) is about fresh water, again we find that this statement doesn’t match what we needed. There are papers that would be a much better fit for our purposes like Gallardo et al. (2016) and Gallardo et al. (2018).

Chat GPT Statement 6: 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).

My assessment: Both citations here are readily findable and are on topic. Leprieur et al. (2008a) does indeed discuss economic activities, but finds evidence that they correlate with increased likelihood of non-native fish introductions – not that non-native species cause economic changes as claimed by ChatGPT. Similarly, as Leprieur et al. (2008b) study the patterns of invasive fish occurrence, they do not have any findings about ecological impact. Ricciardi & MacIsaac (2010) is a book chapter that focuses on the impacts of invasions in freshwater. There is a brief mention of economic impacts in their historical perspective, otherwise they do not discuss this issue. There is a good review of ecological impacts, and they do give examples of alterations in food webs, declines in native fish populations and a mention of impact on commercial fisheries. There is no assessment of impacts on recreational fishing.

Thus, for statement 6, ChatGPT failed with one citation, but got some success with another albeit less than 100%. It’s not a complete fail, but it is mostly wrong.

Chat GPT Statement 7: 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).

My assessment This statement is rather like a reiteration of the previous statement. As I asked for these separately, we cannot blame ChatGPT for this instance of repetition, but let’s see how it does on fish introductions to rivers and lakes – which is what was asked for.

Savini et al. (2010) is a paper about the top 27 alien animals introduced into Europe for aquaculture, so it is on topic with lots of information about invasive freshwater fish. However, it does not mention anything about rivers or lakes, does not mention intentional or unintentional introductions, but does give extensive examples about ecological impact. No specific mention of economic impacts are made, although they could be inferred due to some of the mentions of damaged aquacultural activities due to invasions. Not a complete fail then, but certainly this citation cannot be used to substantiate the statement made by ChatGPT alone.

The Phelps et al. citation could have been one of two papers published that year with Phelps as a lead author about fish. Phelps et al. (2010a) is about Shovelnose Sturgeon in North American rivers and does not mention invasive fish, but does talk about re-introductions. Phelps et al. (2010b) is about the illegal wildlife trade and does mention fish, but only in relation to trade. Neither of these publications could be cited to affirm the statement made by ChatGPT.

Chat GPT Statement 8: 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.

My assessment There is a paper by Jeschke et al. (2014). Rather than being about invasive fish, this paper covers impact of all invasive species. Non-native fish are given as an example of differences in opinions between quantifiable and value of change of impact, but are otherwise not mentioned. If this was the publication that ChatGPT was referring to, then it was a complete fail as none of Statement 8 could be attributed to this paper.

 

Was ChatGPT a complete fail?

Yes, I would say that having checked the references, most of what was said sounded good, but could not be backed up by the citations given, in the cases where they could be found. For this reason, I am confident in calling this experiment a complete fail, not because there was no truth, but because it was mostly misleading (incorrect citations and unhelpful misdirection to correct citations).

For most of you who are trying to write their PhD thesis, I would suggest that you are completely wasting your time to try this approach with ChatGPT. This doesn’t mean that you can’t use it as an to writing, but that you can’t rely on it to produce anything that is factually correct.  

Perhaps ChatGPT is getting all these citation uses wrong because it is looking to see how other people use citations? This is not unreasonable, as mis-citing is a real problem. But having this platform reinforcing false citation habits is the last thing you need.

Given that it’s taken me several hours to check two paragraphs, I feel no hesitation in suggesting that you avoid using ChatGPT in this way – and if you do, beware – it probably got it all wrong.

If ChatGPT were a student, I'd have some choice words to say after spending all this time and finding out that almost nothing was correct. If I was feeling charitable, then I'd say "cocky" and "unafraid of making up rubbish in order to have something sound nice".

Literature Cited (by me - who knows what ChatGPT was citing)

Blackburn, Tim M., Franz Essl, Thomas Evans, Philip E. Hulme, Jonathan M. Jeschke, Ingolf Kühn, Sabrina Kumschick, et al. “A Unified Classification of Alien Species Based on the Magnitude of Their Environmental Impacts.” PLOS Biology 12, no. 5 (May 6, 2014): e1001850. https://doi.org/10.1371/journal.pbio.1001850.

Fantle-Lepczyk, J.E., P.J. Haubrock, A.M. Kramer, R.N. Cuthbert, A.J. Turbelin, R. Crystal-Ornelas, C. Diagne, and F. Courchamp. “Economic Costs of Biological Invasions in the United States.” Science of the Total Environment 806 (2022). https://doi.org/10.1016/j.scitotenv.2021.151318.

Gallardo, B., A.E. Bogan, S. Harun, L. Jainih, M. Lopes-Lima, M. Pizarro, K.A. Rahim, R. Sousa, S.G.P. Virdis, and A. Zieritz. “Current and Future Effects of Global Change on a Hotspot’s Freshwater Diversity.” Science of the Total Environment 635 (2018): 750–60. https://doi.org/10.1016/j.scitotenv.2018.04.056.

Gallardo, B., M. Clavero, M.I. Sánchez, and M. Vilà. “Global Ecological Impacts of Invasive Species in Aquatic Ecosystems.” Global Change Biology 22, no. 1 (2016): 151–63. https://doi.org/10.1111/gcb.13004.

Jeschke, Jonathan M., Sven Bacher, Tim M. Blackburn, Jaimie T. A. Dick, Franz Essl, Thomas Evans, Mirijam Gaertner, et al. “Defining the Impact of Non-Native Species.” Conservation Biology 28, no. 5 (2014): 1188–94. https://doi.org/10.1111/cobi.12299.

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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…"

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
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