Portrait of Science and Education Annotated Publications

[1] Ling, MHT. 2016. The Bioinformaticist’s/Computational Biologist’s Laboratory. MOJ Proteomics and Bioinformatics 3(1): 00075. [PDF]

[2] Ling, MHT. 2017. Problem-Based Learning (PBL), an Important Paradigm for Bioinformatics Education. MOJ Proteomics and Bioinformatics 5(4): 00166. [PDF]

[3] Ling, MHT. 2017. A Personal Narrative of 6 Pre-University Research Projects Over 7 Years (2009-2015) Yielding 19 Manuscripts. MOJ Proteomics & Bioinformatics 6(3): 00193.

Acquisition of research skills, including scientific enquiry, is an important requirement in scientific education, after the acquisition of a body of fundamental knowledge. Working on research projects is a direct means to gain research skills, as well as gaining a firsthand experience of the research environment. Here, I shall narrate my experience and learnings as a research mentor involving 22 pre-university students in 6 research and development projects over a period of 7 years, yielding a total of 19 peer-reviewed manuscripts. I have 3 intentions to this narration - (a) to demonstrate that pre-university students can carry out useful research, (b) summarize my learning experience in this journey, and (c) providing some pointers and encouragement to my fellow mentors and intended mentors. I learnt that (1) pre-university students can produce publishable work but (2) the scope of the projects must be well-defined with specific and measurable end-points, (3) the involvement of the mentor is substantial both in project formation and project management, (4) quality work can be achieved when students understand the background and context of their work, (5) enduring working relationship between students and mentors requires time and efforts to build, and (5) the students can pleasantly surprise the mentor with their quality of writing and reasoning. Upon reflection, I feel that I gained as much as the mentees / protégés, if not more, and this encouraged me.

[4] Ling, MHT. 2017. Towards Portrait [(Auto) Ethnography, Narrative, and Action Research] of Bioinformatics. EC Proteomics and Bioinformatics 2(1): 29-35.

A bioinformaticist often interacts with many professionals and work on multiple projects at the same time; hence, highly social. Qualitative portrayal approaches; such as action research, ethnography, and narratives; have been employed in healthcare education and practices but limited in bioinformatics. In this article, I review 12 portraits in healthcare education and practices and argue that there are both intrinsic and extrinsic benefits for bioinformaticist to engage in portrayals of the field. Publication is the main extrinsic benefit. The main intrinsic benefit comes from learning and consolidating past experiences, forming a launch pad into the future. I conclude by listing 6 directions in which a bioinformaticist can embark on.

[5] Chan, OYW, Keng, BMH, Ling, MHT. 2018. Science/Education Portraits I: Identifying Success Factors of Pre-Tertiary Bioinformatics Research Experience from Students’ Perspective. Advances in Biotechnology and Microbiology 8(2): 555734.

Many studies suggest substantial benefits in incorporating research experience into science education, with several studies examining the success factors for undergraduate research experience. It has been known that early research experience has an impact on the career paths of the students. However, little has been known about the success factors of research experience at a high-school level. This study uses a reflective email interview method (2 years post-completion of the research experience) to identify success factors from the perspective of the students on their pre-tertiary bioinformatics research experience. Six success factors emerge from this analysis: (a) student’s intrinsic motivation / interests, and goals, (b) peer pressure, (c) student’s perceived workload, (d) context of project, (e) culture of science and recognition of student’s work, and (f) quality of supervision.

[6] Ling, MHT. 2018. Science/Education Portraits II: Pre-Tertiary and Undergraduate Research Mentors Should Consider Publication as Project Endpoint. MOJ Proteomics & Bioinformatics 7(2):127‒129.

Scholarly publication is a common productivity metric for researchers of all levels. Despite the benefits of publications to pre-undergraduate and undergraduate research students, they tend to be less productive in terms of publication counts than graduate research students. Here, I narrate my personal experiences as an attempt to try to convince fellow pre-tertiary and undergraduate research mentors research mentors to consider publications as a suitable endpoint for any research projects, as they can have lasting mutual benefits to both the student / mentee, and project mentors.

[7] Ling, MHT. 2018. Science/Education Portraits III: Perceived Prevalence of Data Fabrication and/or Falsification in Research. Advances in Biotechnology and Microbiology 11(5):555824.

Data fabrication or falsification are considered as “deadly sins” with high impact, above plagiarism, on scientific truth and public confidence. What is the estimated prevalence of data fabrication or falsification? A meta-survey published a decade ago estimated 14.12% of respondents having knowledge of a colleague who fabricated or falsified research data, or who altered or modified research data. This mini-review updates this meta-survey by examining surveys from 2009 to 2018. Results suggests that 17.7% of responses indicated knowledge of fellow scientist’s acts of data fabrication or data falsification. This is consistent with that of a decade ago, which suggests a critical need to address the worst type of research misconduct – data fabrication and falsification.

[8] Ling, MHT. 2019. Science/Education Portraits IV: Experiences from a Decade as Informal Career Counsellor can be Summarized as Personopreneurship. Acta Scientific Medical Sciences 3(3): 151-156.

A teacher is an informal career counsellor; yet, teachers are often the counselee. This essay summarizes the career guidance received and a decade as informal career counsellor as personopreneurship – each of us is our business and the general manager of this business. This is consistent with the view that our curriculum vitae/resume is likened to a marketing document or product brochure. I consolidated the six key themes of personopreneurship as [a] sufficient skills utilization, [b] work that matches a calling and concordant with beliefs and faith, [c] sufficient workload, [d] good working environment, [e] support by superiors, peers, and subordinates; including availability of mentoring, autonomy and freedom to operate/manoeuvre, and [f] sufficient and stable income. Each of these themes will be reviewed based on current literature.

[9] Ling, MHT. 2019. Science/Education Portraits V: The Scientific Tertiary Education that I had Envisioned. Acta Scientific Medical Sciences 2(8): 75-79.

Current tertiary education system has been criticized as being outmoded and inadequate to address modern day needs. Incorporating the concept of stackable credentials, I propose a framework of seminar series and apprenticeship within the 4-year tertiary education system for science. Seminar series can replace teaching while apprenticeship can address the needs of education. Given that a typical undergraduate degree amounts to 2,000 hours, I demonstrate that a combination of seminar and apprenticeship can amount to 1,860 seminar hours and 1,000 apprenticeship hours, which is equivalent to 6 months of full-time employment. This can allow the student room to develop a competency-based portfolio.

[10] Wang, VCC, Ling, MHT. 2020. Science/Education Portraits VI: Anecdotes of Life in Singapore During COVID-19 (February 2020 to September 2020). EC Clinical and Medical Case Reports 3(11): 98-111.

No doubt that the world in 2020 looks very different from that of 2019, due to COVID-19 pandemic, which is the single most impactful event since World War II. This triggered a call to document this event for future ethnographical studies. Many authors from various countries had responded to this call. In this article, we respond with collection of 25 ad-hoc anecdotal portraits of life in Singapore between February to September 2020, to add to the collective documentation for this momentous time in this century. Several of our experiences echo that of other reports from other countries. We iterate the need to document this period. However, we also see anecdotal evidence of benefits from this crisis.

[11] Kim, KD, Chua, SCH, Ling, MHT. 2021. Science/Education Portraits VII: Statistical Methods Used in 1081 Papers Published in Year 2020 Across 12 Life Science Journals Under BioMed Central. Acta Scientific Nutritional Health 5(3): 06-12.

Statistics is an integral part of biology and is required for all undergraduate life science curriculum. However, are biology students trained in statistical skills required in the field? Despite studies listing various commonly statistical methods used in specialised branches of life sciences; such as, immunology and tropical biology; there is a lack of study on the common statistical methods used in life science in general. Here, we examine 1081 articles across 12 life sciences journals under BioMed Central, published in 2020, to elucidate the common statistical methods used in current life science research, as a basis to recommend an updated syllabus to all institutions that educate biologists. 72.7% of the examined articles contains identifiable statistical methods and a total of 2431 instances were identified. Our findings show that the first 3 out of 15 categories of methods; parametric comparison of means (25.38% of instances), correlation/regression (18.88%), and post-hoc test (10.32%); accounts for 54.59% of the instances. In terms of individual methods, the top 8 methods account for 52.04% of the instances – (a) t-test (13.00%), (b) ANOVA (12.26%), (c) unspecified (likely to be Pearson’s correlation) and Pearson’s correlation (9.79%), (d) Benjamini and Hochberg’s False Discovery Rate (FDR) (4.77%), (e) Tukey's HSD (4.36%), (f) Kruskal-Wallis Test (2.96%), (g) Mann-Whitney U Test (2.80%), and (h) Chi Square Test (2.10%). These findings may have an impact on future curriculum design.

[12] Ling, MHT. 2023. ChatGPT (Feb 13 Version) is a Chinese Room. Novel Research in Sciences 14(2): NRS.000832.

ChatGPT has gained both positive and negative publicity after reports suggesting that it is able to pass various professional and licensing examinations. This suggests that ChatGPT may pass Turing Test in the near future. However, a computer program that passing Turing Test can either mean that it is a Chinese Room or artificially conscious. Hence, the question of whether the current state of ChatGPT is more of a Chinese Room or approaching artificial consciousness remains. Here, I demonstrate that the current version of ChatGPT (Feb 13 version) is a Chinese Room. Despite potential evidence of cognitive connections, ChatGPT exhibits critical errors in causal reasoning. At the same time, I demonstrate that ChatGPT can generate all possible categorical responses to the same question and response with erroneous examples; thus, questioning its utility as a learning tool. I also show that ChatGPT is capable of artificial hallucination, which is defined as generating confidently wrong replies. It is likely that errors in causal reasoning leads to hallucinations. More critically, ChatGPT generates false references to mimic real publications. Therefore, its utility is cautioned.

[13] Shin, AW, Yan, LZW, Poh, KSH, Ling, MHT. 2023. Science/Education Portraits VIII: Duoethnography of First-Generation Bioscience Undergraduates in a Private Education Institute in Singapore. Acta Scientific Microbiology 6(6): 24-35.

It has been well-recognized that first-generation undergraduate faces unique challenges. This is made worse by being a first-generation undergraduate in a private education institution (PEI), commonly characterized by lesser resources as compared to public education institution, during COVID-19 associated social restrictions. Currently, there is no study to on first-generation university undergraduates pursuing their undergraduate education via a PEI in Singapore during this COVID-19 pandemic. In this article, we document the journey, challenges, and triumphs of three first-generation bioscience undergraduates in Singapore pursuing their bachelor’s degree in a PEI during the pandemic using duoethnographical approach. Our analysis suggests that challenges faced by first-generation undergraduate in a PEI in Singapore during COVID-19 associated restrictions can be seen as sum of challenges faced by first-generation undergraduate and challenges faced by in the education sector during COVID-19 associated restrictions; but the resourcefulness, resilience, and adaptability of first-generation undergraduate are also evident.

[14] Işık, EB, Brazas, MD, Schwartz, R, Gaeta, B, Palagi, PM, van Gelder, CWG, Suravajhala, P, Singh, H, Morgan, SL, Zahroh, H, Ling, M, Satagopam, VP, McGrath, A, Nakai, K, Tan, TW, Gao, G, Mulder, N, Schönbach, C, Zheng, Y. De Las Rivas, J, Khan, AM. 2023. Grand Challenges in Bioinformatics Education and Training. Nature Biotechnology 41: 1171–1174.

[15] Hon, RYH, Ling, MHT. 2024. Science/Education Portraits IX – Reproducibility and Transparency of Systematic Reviews. Medicon Medical Sciences 7(2): 36-40.

The main advantage of systematic review (SR) over other review types, such as narrative review, is its transparent and rigorous approach to minimize bias and ensure future replicability. Reproducibility, comprehensiveness, and transparency are the 3 keys to minimize bias. Reproducibility and transparency are deemed more important than comprehensiveness as missing literature may be identifiable from a reproducible and transparent SR lacking comprehensiveness but missing literature cannot be identified from a comprehensive SR lacking reproducibility and/or transparency. Hence, a SR lacking reproducibility and/or transparency is a narrative review. Several studies on published SRs report poor reproducibility and transparency. Here, we examine a sample of 100 SRs published in 2023 and indexed within PubMed for reproducibility and transparency on 10 criteria – 7 for reproducibility and 3 for transparency. In terms of reproducibility, our results show that only 31 SRs gave sufficient information for reconstructed searches in PubMed to yield search results within 10% of the hits reported. In terms of transparency, none of the SRs provided the full list of search results and only 5 SRs provided sufficient information to determine which study is excluded by which exclusion criterion. Hence, our results support previous studies reporting poor reproducibility and transparency in SRs. We propose that search URLs should be given whenever possible, and the full list of search results with inclusion / exclusion analysis should be given in all cases.