AI Research Assistant: Use Cases (5/5)

07/2026·
Daniel Ebbert
Daniel Ebbert
· 34 min read
blog

In this post, now that we have our AI assistant setup complete, I will showcase three use cases that are enabled by this specific setup we’ve been working towards. In each case I’ll outline the use case and then give an example based on my work, followed by illustrating how the information and knowledge flowed from our sources in Obsidian and Zotero to the AI assistant and from there into the answer given by the AI assistant. This is not about getting any answers from the AI, it’s about getting answers grounded in your work. After these use cases I will cover some temptations to resist when using such a setup and outline some directions I am considering for future development. All examples in the following were generated using GLM 5.2.

Use Case 1: Claim Verification

The first use case I would like to present is one of academic integrity. In our writing we rely on other sources and every time we cite a source we should be accurately representing the source we’re citing. While that sounds admirable in principle, in practice that is hard to do, given the wide range of sources we often cite. However, such a task is easy for an AI to perform. Let me illustrate this with an example. The fragment I’m using here for this example is from a recent publication of mine. This example is purposefully short as it’s only chosen to illustrate this type of usage.

Prompt to the AI:

I am working on a paragraph for a paper. Check that I am citing each source correctly. This is the text:

A challenge in video-based learning is mind wandering, broadly defined as thoughts unrelated to the current task. Mind wandering is a frequent cognitive phenomenon, with a recent meta-analysis showing that students engage in mind wandering approximately 30% of the time during learning activities (Wong et al., 2022). These frequent episodes of mind wandering have been shown to negatively impact on learning outcomes (Wong et al., 2022).

Following this prompt the AI assistant made some tool calls to access my Zotero database and then provided me with the following answer:

Show AI response (Claim Verification)

I found the source. Here is my verification:

Source identification

The cited source matches the paper in your Zotero library:

  • Title: Task-unrelated thought during educational activities: A meta-analysis of its occurrence and relationship with learning
  • Authors: Wong, A. Y., Smith, S. L., McGrath, C. A., Flynn, L. E., & Mills, C.
  • Year: 2022
  • Journal: Contemporary Educational Psychology, 71, 102098
  • Citekey: @wongTaskunrelatedThoughtEducational2022

Citation format check

“Wong et al., 2022” is correct. With five authors, APA 7 uses “Wong et al.” from the first citation onward. The year is correct.

Content / claim verification

Claim 1: “students engage in mind wandering approximately 30% of the time during learning activities”

This is accurate. The abstract states: “students are off-task about 30% of the time during educationally relevant activities.”

One small terminological note: the paper uses “task-unrelated thought” as its primary term (with mind wandering as a parenthetical gloss). If precision matters for your framing, you could note that the 30% figure specifically pertains to task-unrelated thought in educational contexts. But “mind wandering” is defensible given the paper explicitly equates the two in its title framing.

Claim 2: “These frequent episodes of mind wandering have been shown to negatively impact on learning outcomes”

This requires a correction. The meta-analysis found a negative correlation (r = −0.27, a small-to-medium effect), not evidence of causal impact. “Negatively impact on” implies causation that a meta-analysis of predominantly correlational studies cannot establish. Suggested rewording:

“These frequent episodes of mind wandering are associated with poorer learning outcomes (Wong et al., 2022).”

or, more precisely:

“These frequent episodes of mind wandering share a small-to-medium negative relationship with learning outcomes (Wong et al., 2022).”

This preserves the finding accurately without overclaiming causality.

I know this source I cited quite well and the answer the AI assistant gave me is correct. I could have phrased this better to avoid implying a causal impact. While this example is only with a few sentences and one source, the same type of prompt can be made with whole paragraphs, or even full drafts of manuscripts.

What happened behind the scenes is that the AI assistant searched my Zotero library for the source I cited (Wong et al., 2022). The Zotero MCP performed a semantic search and returned the matching entry, including the full text of the paper. The AI assistant then read the abstract and located the exact figure I cited: “students are off-task about 30% of the time during educationally relevant activities.” From there, it compared my phrasing against the original wording and identified two issues: first, the source uses “task-unrelated thought” rather than “mind wandering” as its primary term, and second, my phrasing implied a causal impact when the meta-analysis reported only a correlational relationship (r = -0.27). The key point here is that the AI assistant did not rely on its training data to verify my claims. It accessed the actual source stored in my Zotero library and checked my text against it.

Use Case 2: Internal Coherence

As academics we write a lot over the course of our career and might not always remember which stances we’ve taken or want to be consistent in the points we make across the papers we write. With our publications as part of the vault we can check whether what we’re arguing in a manuscript we’re working on aligns with the trajectory of work that we’ve already published. While it is of course okay to change our minds, to readers familiar with our work, this would need to be explained so they can also understand why we changed our minds. Let me give you an example with a conclusion section from a draft of mine:

I am working on the draft of a manuscript. Check whether this conclusion section I've written aligns with the arguments made in my previous publication, including work that is still under review. The section is:

Even among learners predisposed to reflect on their learning processes, the appraisal of whether a thought is aligned with their goals remains their own. Claiming that we can objectively appraise a learner's thoughts ignores the learners' agency in self-regulating their learning. If the learner is actively regulating their learning, they are the only ones capable of deciding whether a thought is congruent with their current goals or impedes their learning process. This transforms our role from external judges to facilitators who enable learners to make this appraisal.

This problem also extends to the literature on off-task thought detection using objective measures, such as eye-tracking (Kuvar et al., 2023). If these detection technologies were to be transferred to adaptive educational technologies such as the eye-mind reader by Mills et al. (2021), they risk not supporting learners' autonomous self-regulation of learning (Molenaar, 2022). By having a system pre-emptively make the decision for the learner, these technologies may absolve the learner of the need to develop their own meta-awareness and internalised refocusing skills. This could lead the learner to become reliant on the system rather than their own regulatory capacity. Therefore, any further study of mind wandering in a naturalistic setting needs to centralise the learner, normalise their experience of off-task thoughts, and enable a neutral appraisal of whether a thought is helpful to their specific learning trajectory. After all, it is their learning process.

Following from this prompt the AI assistant performed a lot of tool calls to search for and read my previous publications as well as all of my work that is under review and stored in my vault. Additionally, it performed multiple tool calls to access the sources I cited in my Zotero database and then provided me with the following answer:

Show AI response (Internal Coherence)

I’ve now reviewed the draft conclusion against your published and under-review work. Here is my assessment.


Overall Verdict

The conclusion is broadly consistent with the trajectory of your previous work, but it makes several extensions and shifts that need to be flagged. The most significant tension concerns your stance on objective detection measures (eye-tracking), which your thesis and conceptual paper treat as a complementary research tool, while this conclusion frames their deployment in adaptive educational technologies as potentially harmful to learner agency. The shift is defensible, but it is a new argument, not a restatement of prior positions.


1. Points of Strong Alignment

Learner agency and goal-dependent appraisal

The claim that “the appraisal of whether a thought is aligned with their goals remains their own” is well-grounded in your prior work:

  • Thesis conclusion (Ch. 8): “it is not the off-task thoughts that affect how well a learner is learning; it is the learner’s judgment concerning these off-task thoughts that impacts learning.”
  • Thesis (Ch. 8, future research): “the influence of off-task thoughts on learning should not only be studied in relation to goals set by the researcher, but also in relation to goals set by learners.”
  • Conceptual paper (Cognitive Science): The COPES framework positions the Evaluation of thoughts against learner-set Standards as the learner’s own metacognitive act.

The draft’s first paragraph faithfully extends this line of reasoning.

Normalising off-task thoughts

The call to “normalise their experience of off-task thoughts” aligns directly with:

  • Thesis (Final Remarks): “Instead of seeing off-task thought as the bane of successful learning… it is viewed… as something that is outside of the learners control and thus needs to be accepted.”
  • Conceptual paper: “It is normal for learners to experience TUTs, regardless of their self-regulation capabilities.”

Naturalistic setting as a research imperative

The draft’s call for studying mind wandering “in a naturalistic setting” is consistent with a core recommendation from the thesis: “research aiming to determine the relationship between SRL and off-task thoughts should be conducted in a naturalistic setting, as the transferability from experimental to naturalistic settings is not given.” The case study paper (Metacognition and Learning) was itself an argument for this.

Internalised refocusing

The concern about technologies that “absolve the learner of the need to develop their own… internalised refocusing skills” maps onto the thesis discussion of how self-regulated learners may “inherently refocus their thoughts back to the task through an internalised process whereby they are not explicitly aware of their off-task thoughts at all.” You are applying this concept to the technology question, which is a natural extension.


2. Points of Tension or Potential Misalignment

The stance on objective detection measures (eye-tracking)

This is the most significant area of tension. In your thesis and conceptual paper, eye-tracking and objective detection measures are framed positively as a research complement to self-caught thought reports:

  • Thesis (Ch. 8, implications for theory): “Such an approach to measuring off-task thoughts could be achieved by using objective modalities for off-task thought detection (for an overview see @kuvarDetectingWhenMind2023), in combination with self-caught thought reports.”
  • Thesis (Ch. 8, future research): Recommends “self-caught thought reports and objective measures of off-task thoughts [@kuvarDetectingWhenMind2023].”
  • Case study paper (Limitations): “This limitation could be overcome by including an objective measure of off-task thoughts that does not rely on the participants’ self-reports, such as eye-tracking (Kuvar et al., 2023).”

The draft conclusion, by contrast, frames the transfer of detection technologies to adaptive educational technologies as a risk to autonomous self-regulation. This is not a contradiction per se: your prior work discusses eye-tracking as a measurement tool for research, while the draft discusses its deployment in real-time intervention systems. However, a reader familiar with your thesis would notice that you previously advocated for objective measures and are now raising concerns about their application. The distinction between measurement for research and real-time intervention in adaptive systems should be made explicit in the manuscript to avoid the appearance of inconsistency.

The eye-mind reader (Mills et al., 2021) as a cautionary example

The draft cites the eye-mind reader as an example of a technology that risks undermining autonomous self-regulation. However, the literature note for this paper (@millsEyeMindReaderIntelligent2021) describes it positively: the system “promotes long-term comprehension by detecting and responding to mind wandering” and “led to an improved delayed learning outcome.” The system prompts self-explanation upon detection, which is itself a generative learning activity.

There is a tension here: the eye-mind reader does not simply “make the decision for the learner.” It detects mind wandering and then prompts the learner to engage in a self-explanation, which is a metacognitive activity. The system does not pre-emptively decide whether the thought was congruent with the learner’s goals; it intervenes after detection. Your critique would be more precisely targeted at systems that classify thoughts as detrimental or beneficial on the learner’s behalf without involving the learner in that appraisal. The eye-mind reader, as described, actually engages the learner in a response. You may want to either sharpen the critique or choose a different example.

“Neutral appraisal” language

The draft calls for enabling “a neutral appraisal of whether a thought is helpful to their specific learning trajectory.” The word “neutral” is slightly at odds with your COPES-based framing, in which the appraisal is inherently subjective: the learner evaluates thoughts against their own Standards. “Neutral” might be read as implying an objective stance, which is the very thing you are arguing against. Consider whether “learner-centred appraisal” or “self-directed appraisal” would be more consistent with the theoretical framework you have been building.


3. New Claims That Extend but Do Not Contradict Prior Work

These arguments are new in your oeuvre. They are logical extensions but have not been substantiated in your prior publications:

  1. “This transforms our role from external judges to facilitators” — The thesis discusses implications for practice in terms of scaffolding SRL skills and teaching reaction tactics, but does not frame the researcher’s or educator’s role as “facilitator” versus “external judge.” This is a new rhetorical positioning.

  2. “These technologies may absolve the learner of the need to develop their own meta-awareness” — This is a novel claim. Your prior work discusses meta-awareness as a skill that learners develop through metacognitive monitoring cycles, but you have not previously argued that external detection systems could displace the development of this skill. The Molenaar (2022) HHAIR concept supports this argument (ALTs “take over (offload) regulation from learners”), but you are applying it to mind wandering detection specifically, which Molenaar does not address.

  3. “This could lead the learner to become reliant on the system rather than their own regulatory capacity” — This is a dependency argument that is not made in your prior work. It is plausible and consistent with the HHAIR framework, but it is an empirical claim that would benefit from being framed as a hypothesis rather than a stated consequence.


4. Citation and Reference Concerns

  • Molenaar (2022): This refers to “The concept of hybrid human-AI regulation” (Computers and Education: Artificial Intelligence, Vol. 3, 100070). It is in your Zotero library but has no literature note in the vault. The citation is appropriate for the argument about autonomous self-regulation, as Molenaar explicitly argues that ALTs offload regulation from learners. However, note that Molenaar’s concept is about gradual transfer of regulation from AI to human, not about abandoning AI support entirely. Your draft’s argument is stronger than Molenaar’s position: where she advocates for hybrid regulation with gradual transfer, you seem to caution against the system making the decision at all. Make sure you are not overextending Molenaar’s claim.

  • Mills et al. (2021): As noted above, the eye-mind reader prompts self-explanation rather than making a pre-emptive decision for the learner. The characterisation in your draft may misrepresent the system’s actual function.

  • Kuvar et al. (2023): This is correctly cited as a systematic review of mind wandering detection methods, consistent with how it is cited in your thesis and conceptual paper.


Summary of Recommendations

  1. Clarify the measurement vs. intervention distinction. Your prior work endorses eye-tracking as a research measurement tool. The draft critiques its deployment in adaptive intervention systems. Make this distinction explicit so readers do not perceive inconsistency with your thesis.

  2. Sharpen or replace the eye-mind reader example. The system prompts self-explanation, which engages the learner. If your critique targets systems that pre-emptively classify thoughts without learner involvement, the eye-mind reader is not the strongest example. Alternatively, reframe the critique to acknowledge that the eye-mind reader engages the learner but still bypasses the learner’s own detection of the thought.

  3. Reconsider “neutral appraisal.” Your COPES framework positions appraisal as the learner’s subjective evaluation against their own Standards. “Neutral” may undercut this.

  4. Flag the new claims as hypotheses, not established consequences. The arguments about absolving learners of meta-awareness development and creating system dependency are extensions of your prior work, not substantiated by it. Framing them as risks or hypotheses would be more consistent with the calibrated hedging in your other publications.

  5. Consider creating a literature note for Molenaar (2022) in the vault, given that you are now citing it in manuscript drafts.

This answer is a good example of how the PKM enabled the AI assistant to give a useful answer. I stored the full text of all my work in my vault and, therefore, the AI was able to access these and use them to inform its answer to me. For example, when we look at section 1 of its answer on points of strong alignment we can see how it is pulling from a chapter of my PhD thesis as well as a paper of mine that was recently published to then conclude that the reasoning in the section I gave it aligns with the reasoning in my thesis and the recent paper. Not only that, it also correctly identifies that there are points of tension where my thinking has evolved in regard to automated mind wandering detection technologies. While I don’t necessarily agree with all of the content of the AI’s answer, it clearly shows that this answer is strongly informed by the data sources provided to it and the points it makes give me something to think about that might result in me changing something in my writing.

Separately from the quality of the answer, this is also a good example of AI not always strictly following instructions. In the prompt I had asked it to check this section against my previous publications and works that are still under review but already stored in my vault. Further, as previously shown, in my agent definition I’m instructing the AI assistant to not be proactive and to closely stick to the instructions given. But, despite all of that, we can see that the AI assistant still ran checks for each source I am citing if the source supports the claim I am making, even though I did not instruct it to do so and did not want it to be proactive. This is a constant point of frustration, but there is only so much we can do to control the AI assistant’s behaviour.

Use Case 3: Learning from Reviews

The last use case I would like to present here is related to paper submissions and reviews. When we submit a paper to a journal that usually gets reviewed by some of our peers and only if our peers and the editor deem it good enough will it be published. As part of each review we get peer-review reports or feedback. I store every single review I’ve gotten since I started my PhD in my vault and that presents a learning opportunity, but once again, we as humans forget. However, an AI with access to all of these reviews can read a draft before we submit it to a journal and then go over the reviews and determine which points previous reviewers made might also apply to the current draft I am working on. As with the previous two use cases, let me give you an example. As the draft for this example I’m using the preprint of a manuscript that I’ve written that is currently under review.

I am working on a draft of a paper. Check this draft located in the vault at "Publications/Experiment Interpolated Testing vs Self-Explanation/Meta-Awareness of Mind Wandering (JCAL)" against all previous peer-reviews I've received and determine which critiques from previous peer-reviews might also apply to this work along with a suggestion for how I could improve this work to avoid getting the same critique.

After the AI assistant read my draft and my previous peer-reviews, the answer I got was:

Show AI response (Learning from Reviews)

I now have a comprehensive picture of all peer reviews Daniel has received across his publications and the current JCAL v2 draft. Let me compile the analysis.


Cross-Review Analysis: Recurring Critiques Applied to the JCAL v2 Draft

I have reviewed the v2 draft against all peer reviews you have received across the following submissions:

  • Mind Wandering Reactions Case Study (LAK25, then Metacognition and Learning, rounds 1 and 2)
  • SRL and Mind Wandering Conceptual Paper (Metacognition and Learning, then Cognitive Science)
  • TRI Meta-Analysis (Review of Educational Research rounds 1 and 2, Psychonomic Bulletin & Review, Contemporary Educational Psychology)
  • SmartQuiz Experiment (AIED 2026)
  • ECTEL 2024 Doctoral Consortium
  • LAK 2024 Doctoral Consortium
  • HERGA 2023 Poster

Below are the critiques from these previous reviews that also apply to the current JCAL v2 draft, ordered by severity (likelihood of recurrence and impact). Each entry identifies the source review(s), the specific issue in the v2 draft, and a concrete suggestion.


1. Theoretical model-measurement misalignment (COPES vs. self-report SRL-O)

Source reviews: LAK25 meta-review (Reviewer 1 + meta-reviewer); Metacognition and Learning Reviewer 2 (Comment 10).

Previous critique: The COPES model (Winne) conceptualises SRL as a series of dynamic, task-level events. Winne has advocated for decades for trace-based measures. Using a self-report aptitude questionnaire (SRL-O) to operationalise COPES constructs is a fundamental theory-measurement mismatch. The LAK25 meta-reviewer stated explicitly that this cannot be resolved by arguing self-reports are acceptable for meta-awareness; the entire theoretical model would need to be changed (e.g., to Zimmerman’s) or the measurement approach changed to traces.

How it applies to the JCAL v2: Section 2.6 draws on the COPES model as the theoretical framework, and Section 4.4 uses the SRL-O self-report questionnaire to measure SRL aptitude. The same mismatch exists. The JCAL v2 does not address or even acknowledge this tension. A reviewer familiar with Winne’s work (or the LAK25 meta-reviewer, if they review for JCAL) would flag this immediately.

Suggestion: Add an explicit justification for why a self-report aptitude measure is acceptable within the COPES framework for this specific research question. The argument should be that RQ2 examines the relationship between SRL aptitude (a trait-like characteristic) and meta-awareness frequency (also trait-adjacent), not SRL events. Alternatively, reframe the theoretical framework to use a model that is more compatible with aptitude measures (e.g., Zimmerman’s three-phase model or Pintrich’s framework), or acknowledge the mismatch in the limitations section. Do not leave it unaddressed; the LAK25 meta-reviewer considered this a fatal flaw.


2. No reliability estimates reported for SRL-O subscales in the current sample

Source review: Metacognition and Learning Reviewer 3 (Comment 23).

Previous critique: The reviewer noted that the manuscript reported external Cronbach’s alpha benchmarks (0.76-0.88 from prior studies) but placed the current sample’s reliability estimates in a supplementary table. The reviewer called this “methodologically problematic” because reliability is sample-dependent and external benchmarks should not substitute for transparent reporting in the present dataset.

How it applies to the JCAL v2: The v2 draft (Section 4.4) describes the SRL-O subscales used and cites Broadbent et al. (2022) but does not report Cronbach’s alpha (or equivalent) for the Metacognition, Online Effort Regulation, or Online Task Strategies subscales in the current sample of 138 participants. This is exactly the same omission that was previously flagged.

Suggestion: Report internal consistency estimates (Cronbach’s alpha or McDonald’s omega) for each SRL-O subscale in the current sample, either in the Procedure section or in a table. This is a straightforward addition that pre-empts the critique entirely.


3. Causal language for correlational findings

Source reviews: Metacognition and Learning Reviewer 3 (Comment 25: “conflates correlation with causation and overgeneralizes from the findings”); RER Reviewer 1 (Comment 15: “causal language is not warranted given the non-experimental nature of the data”); Psychonomic Bulletin & Review Reviewer 3 (Point 4: “educational implications overgeneralize from lab studies”).

How it applies to the JCAL v2: Several passages use directional or causal language for correlational findings:

  • Abstract: “indicating that meta-aware learners perform better on subsequent knowledge tests” implies that meta-awareness causes better performance.
  • Lay summary: “Students who reported being better at self-regulating their learning reported fewer unrelated thoughts” (this one is correctly hedged).
  • Conclusion: “only if learners are unaware of their off-task thoughts does it negatively affect learning” implies causation from a correlational result.
  • Discussion (Section 6): “an increase on the scale corresponded to a decrease in the number of thought reports” is acceptable, but “meta-aware learners perform better” is not.

RQ2 and RQ3 are correlational/exploratory, not experimental. RQ1 is experimental but produced null results. The positive correlation between thought reports and knowledge gain (tau = .15) is a weak effect and should not be interpreted as evidence that meta-awareness improves learning.

Suggestion: Audit the abstract, discussion, and conclusion for causal language. Replace “meta-aware learners perform better” with “meta-awareness was positively associated with knowledge test performance.” Replace “only if learners are unaware… does it negatively affect learning” with “the negative association between off-task thoughts and learning may be limited to instances where learners lack meta-awareness.” Add a sentence in the discussion explicitly noting the correlational nature of RQ2 and RQ3 findings and that no causal claims can be made.


4. “So what” / practical implications underdeveloped

Source reviews: JCAL Reviewer 2 (Comment 16: “biggest weakness is the lack of clear answers to the ‘so what’ question”); Cognitive Science Reviewer 1 (Comment 4: “insufficient discussion of how educators might leverage this understanding”); RER Reviewer 1 (Comment 16: “I’d like to see more recommendations for practice, and not just future research”).

How it applies to the JCAL v2: The practical implications paragraph in Section 7 is brief and essentially says: these approaches do not work for short videos, so consider video length, and encourage note-taking. The conclusion focuses on theoretical implications but the practical takeaway is thin. The main novel finding (positive correlation between thought reports and learning) is not translated into a concrete actionable recommendation. The lay summary says “Teaching students awareness of unrelated thoughts could result in more efficient learning sessions” but this is not elaborated in the discussion.

Suggestion: Expand the practical implications to address: (a) what should educators do given that neither interpolated testing nor self-explanation improved outcomes for short videos? (b) what does the positive correlation between meta-awareness and learning suggest for instructional design? (c) what specific strategies could be used to foster meta-awareness (e.g., brief reflection prompts, awareness training)? Connect these to the Randall et al. (2022) reference already cited, which studied self-regulatory strategies to reduce mind wandering.


5. Inter-rater reliability (kappa = 0.47) is moderate and could be questioned

Source reviews: RER Reviewer 1 (Comment 10: “Cohen’s Kappa values were not particularly high”); RER Reviewer 2 (Comment 3: “low inter-rater-reliability has implications for the overall reliability of the screening process”).

How it applies to the JCAL v2: Section 4.5 reports an initial Cohen’s kappa of 0.47, which is moderate agreement. The draft states that all disagreements were discussed until 100% agreement was reached. However, a reviewer could question whether the initial moderate agreement indicates that the coding scheme itself is ambiguous, and whether the resolution process (discussion to consensus) introduced coder drift or bias. This is especially relevant because the thought type categories (TUT, TRI, ED, on-task) involve subjective judgment.

Suggestion: Add a brief justification for the moderate kappa, noting that thought report coding involves inherent subjectivity in interpreting free-text responses. Report the number of thought reports coded and the number of disagreements. Consider reporting kappa after the first round of discussion (not just the initial value) to show improvement. If possible, report a final kappa on a held-out subset to demonstrate post-consensus reliability.


6. TRI category conflates metacognitive monitoring with interference

Source reviews: RER Reviewer 2 (Comment 1: “TRI definition has a large overlap with metacognition”); Psychonomic Bulletin & Review Reviewer 3 (Point 1: “the distinction between TRI vs. metacognition seems blurred”); Contemporary Educational Psychology Reviewer 1 (Major Concern 1: “Labeling such processes as ‘interference’ is problematic. It conflates potentially beneficial cognitive activities with genuinely distracting thoughts”).

How it applies to the JCAL v2: Section 4.5 defines TRI as “a thought about the task that represented an interruption in the flow of the task (e.g., thinking about the task’s difficulty, questioning understanding).” “Questioning understanding” is a metacognitive monitoring judgement, not interference. This is the exact conflation that was flagged across three separate submissions of the TRI meta-analysis. A reviewer who has encountered this critique before (or who is familiar with the metacognition literature) would flag it.

Suggestion: Refine the TRI coding definition to distinguish between metacognitive monitoring (which is on-task and beneficial) and genuine task-related interference (thoughts that interrupt the flow without contributing to learning). Consider whether “questioning understanding” should be coded as on-task rather than TRI. Add a sentence acknowledging the conceptual overlap and explaining the coding decision.


7. Data exclusion and outlier handling

Source reviews: AIED 2026 (Review 2 and 4: “excluding participants based on outcome variables risks introducing bias”; “exclusions appear uneven across conditions”); RER Reviewer 1 (Comment 12: “more information on outlier criteria”); Contemporary Educational Psychology Reviewer 2 (Point 5: “outlier detection should be based on the model, not descriptive evaluation”).

How it applies to the JCAL v2: Section 4.7 excludes 42 participants for incomplete data, then applies outlier detection using “the standard deviation method, a cutoff of two standard deviations, and the interquartile range method” simultaneously, excluding all identified outliers. The resulting group sizes are uneven (47, 51, 40). The use of multiple simultaneous outlier criteria is unusually conservative and the rationale is not provided. The uneven group distribution after exclusion could introduce bias.

Suggestion: Justify the use of multiple outlier detection methods. Report how many participants were identified as outliers by each method and how many were excluded in total due to outliers (as distinct from the 42 who did not complete the study). Consider reporting sensitivity analyses with and without outliers to show robustness. Address the uneven group sizes in the limitations.


8. No figures for results presentation

Source reviews: Metacognition and Learning Reviewer 1 (Comment 8: “provide at least 1 or 2 figures for your primary results rather than 10+ large tables of stats”); Psychonomic Bulletin & Review Reviewer 1 (Point 4: “forest plots should be in main text, not supplementary”).

How it applies to the JCAL v2: The results section (Section 5) presents all findings in tables (Tables 1-5). Figure 1 is a procedure diagram. There are no figures visualising the primary results (e.g., group comparisons, SRL-thought report relationships, correlation scatter plots). This was previously flagged as a readability issue.

Suggestion: Add at least one figure visualising the primary result of interest. For RQ1, a bar plot of thought reports by group with error bars. For RQ2, a coefficient plot showing the GLM estimates for each SRL-O subscale. For RQ3, a scatter plot of thought reports vs. knowledge gain. This improves readability for a journal audience and pre-empts the critique.


9. Terminology density / jargon in abstract and introduction

Source reviews: Metacognition and Learning Reviewer 1 (Comment 1: “results discussed in the abstract were quite jargony”); Metacognition and Learning Reviewer 3 (Comment 20: “presupposes reader familiarity with domain-specific terminology”); ECTEL 2024 DC Reviewer 2: “significant overlap of complex SRL terms, but they are not all well-addressed.”

How it applies to the JCAL v2: The abstract uses terms like “interpolated testing,” “self-caught thought reports,” “meta-awareness,” “metacognitive monitoring,” and “online task strategies subscales” without definition. The lay summary is more accessible, but the structured abstract itself remains jargon-heavy. JCAL has an interdisciplinary audience (education + technology), not all of whom will be familiar with mind wandering terminology.

Suggestion: Add brief parenthetical definitions for key terms in the abstract (e.g., “self-caught thought reports (participants self-report off-task thoughts as they notice them)”). Ensure that the first use of each acronym in the introduction is accompanied by a definition. The lay summary already helps here, but the structured abstract should be independently accessible.


10. Individual differences in meta-awareness ability not addressed

Source review: Cognitive Science Reviewer 1 (Comment 2: “the model assumes relatively uniform ability to detect TUTs; needs to address how working memory capacity, executive function, and attention control might moderate the SRL-TUT relationship”).

How it applies to the JCAL v2: The JCAL draft assumes that all participants have equivalent capacity to become meta-aware of their off-task thoughts. The finding that Metacognition subscale scores negatively predict thought reports (the opposite direction of what the scale ostensibly measures) could partly be explained by individual differences in meta-awareness ability. The draft discusses this in terms of “metacognition without awareness” (Reder, 1996) but does not address stable individual differences in the capacity for meta-awareness.

Suggestion: Add a brief discussion in the limitations or discussion section noting that individuals vary in their capacity for meta-awareness (citing Grabman & Dodson, 2024, which is already in the Cognitive Science version). Acknowledge that this variability could partly explain the unexpected direction of the Metacognition subscale results. This is a low-effort addition that pre-empts a critique you have already received.


11. Video duration and ecological validity

Source reviews: JCAL Reviewer 2 (Comment 11: “intervention was very brief… inappropriate to expect these skills to change”); Psychonomic Bulletin & Review Reviewer 3 (Point 4: “educational implications overgeneralize from lab studies”); JCAL Reviewer 1: “more control of variables such as video content.”

How it applies to the JCAL v2: This was already raised by JCAL’s own Reviewer 2 in round 1 and is partially addressed in the limitations (Section 7). However, the practical implications paragraph still generalises from a single 8-minute video to recommendations for educators. The null findings for RQ1 could be entirely attributable to the video being too short for mind wandering to accumulate, which undermines the practical recommendation that interpolated testing and self-explanation are ineffective.

Suggestion: More carefully qualify the practical recommendations to specify that they apply to short videos only. State explicitly that the 8-minute video limits the generalisability of the null RQ1 findings and that the effectiveness of these interventions may differ for longer videos. This is already partially present but should be tightened.


Summary Table

#CritiqueSource Review(s)Severity
1COPES-measurement misalignmentLAK25, M&L R2Critical
2No reliability estimates for SRL-OM&L R3High
3Causal language for correlationsM&L R3, RER R1, PBR R3High
4“So what” / practical implicationsJCAL R2, CogSci R1, RER R1High
5Moderate inter-rater kappaRER R1, RER R2Medium
6TRI/metacognition conflationRER R2, PBR R3, CEP R1Medium
7Data exclusion / outlier handlingAIED 2026, RER R1, CEP R2Medium
8No results figuresM&L R1, PBR R1Medium
9Jargon in abstractM&L R1, M&L R3, ECTEL DCLow-Medium
10Individual differences not addressedCogSci R1Low-Medium
11Video duration / ecological validityJCAL R2, PBR R3, JCAL R1Low (partially addressed)

The most critical item is #1 (COPES-measurement misalignment). This was considered a fatal flaw by the LAK25 meta-reviewer and it remains unaddressed in the JCAL v2. I would prioritise addressing this before the next review round, as a reviewer familiar with Winne’s work will almost certainly raise it again.

After reading this review, we can clearly see that the AI assistant systematically processed the entire manuscript I gave it (about 9000 words), then went through each peer-review I’ve gotten and outlined in detail with reference to the original review how the point made by previous reviewers would apply to the current manuscript I’m working on and how I could address it preemptively. While I might not agree with every point raised or think that some other points are not as severe as the AI makes them out to be, these do give me valuable feedback on what I can address in my manuscript to improve my work and increase my chances of acceptance.

What enabled the AI assistant to do this was the way my reviews are stored in the vault. Each review is stored as a note with the metadata type: peer-review and filed in the same folder as the publication it relates to. That means the AI assistant could filter for all notes with that metadata type and then read through them alongside the current draft. For example, when the AI assistant flagged the COPES-measurement misalignment as the most critical issue (point 1 in its output), it was pulling from the LAK25 meta-review stored in my vault, which had explicitly called this a fatal flaw. It then matched that critique against my current draft, in which I use the COPES model as a theoretical framework. The same applies to point 3 (causal language for correlations), which traces back to critiques I received from three separate reviewers across three different submissions, all stored in the vault. The AI assistant was able to cross-reference all of these against the current draft in a single pass. Without the reviews being stored in a structured, machine-readable way, this kind of cross-referencing would not have been possible.

Based on these use cases and examples I hope you can now understand why I consider this specific setup so powerful and how helpful it can be.

Temptations to Resist

Beyond these practical applications, there are broader considerations worth addressing. Now that you’ve gotten a glimpse of the type of usage this type of system can be put to, it is time to address the elephant in the room called responsible usage of AI. Morality is relative and what is considered responsible or acceptable use of AI will differ based on who is asked and what the AI is being used for in which context. It is a wide range between asking an AI to explain something, which most people would be fine with, to asking an AI to generate a full paper for you, which I think most people would object to.

I am firmly of the position that human oversight of AI-generated content is essential, which is also reflected in the language used in these posts as I refer to an AI assistant. To stick with the metaphor, an assistant does not do work by themselves; an assistant assists you, as the word itself suggests. That means you are in charge and responsible. I of course realise that this boundary is all too easy to cross and any technology can be appropriated and used for a different purpose, but it also comes with an intent, and the intent of this specific combination of technology I’ve been writing about is only to assist you, and I trust your moral judgement to draw the line between using the AI to assist you and the AI doing the work for you.

A helpful guideline is to not use the AI for tasks that you couldn’t do yourself. If you couldn’t do the task yourself, you’re lacking the skills and knowledge to assess the AI’s output and thus shouldn’t be using it for this case. Furthermore, another helpful guideline is to consider the distribution of intellectual labour between yourself and the AI. The intellectual contribution of the work should be yours, and that is exactly the point being objected to when someone uses AI to generate a full paper. But, what if the AI is generating something based on your work, as this setup enables, and under your instruction and revision? This is a fine line and a judgement call you will have to make for yourself.

Next Steps

Now that we’ve covered my entire current setup along with some use cases it is time for you to get to work on your own setup. I recommend you start by analysing which software you’re already using as part of your workflow and which state the sources of information and knowledge you rely on are in. Let’s say you already have an Obsidian vault but it doesn’t contain your publications in full text then a next step could be to convert those to markdown and import them, or you might already have both Obsidian and Zotero in place and have the information in those highly organised, then the next step would be to set up the MCPs and get started on using this system. The starting point will be very individual but hopefully the explanations given in this series have enabled you to make an informed decision about how to set up a system that works for you. One practical note: for the MCPs to work, both Zotero and Obsidian need to be running when you use the AI assistant, as the MCPs connect to them via their local APIs.

Future Development

While my current setup is already very useful to me, there always are things that could be improved. A few things that I’m considering to try are things like agentmemory (a library that gives agents persistent memory across sessions). Currently each session starts from scratch, or in other words, the AI assistant does not retain information between sessions. Enabling some sort of memory across sessions would get rid of this limitation and potentially prove useful down the line. Other avenues worth exploring are to make the setup multimodal. Currently it is primarily text based, simply because most of my work is text based, but sometimes being able to generate images would be useful, for this something like the MCP for openrouter (which enables image generation through the same router you are already using) could be useful. Another potentially useful addition would be to enable the creation of office documents like Word files or PowerPoint presentations, and while there are skills for that purpose, I am not sure if they are needed if presentation slides can also be created in Markdown. When considering the next steps in this journey something like the OpenHuman project (an open-source framework for building personal AI assistants) is useful inspiration, although I will likely build my own system as I want to continue to be able to exchange each part, as explained in this series, when needed.

Closing Note

As a final note, I should mention that I used the AI assistant described in this series to refine these posts. From checking internal coherence to verifying that claims are supported and terminology is used consistently, the system fed information about itself into posts about it.

If you’ve followed along this whole series of post and think it would be useful to attend a workshop on how to build your own AI research assistant please contact me, I will gladly give such a workshop.