NOTE FROM THE EDITOR

“A doctor can save maybe a few hundred lives in a lifetime. A researcher can save the whole world.” - Craig Venter This annual Special Edition once again combines outstanding papers from two conferences: The 32nd annual conference of the Southern African Institute for Industrial Engineering (SAIIE32) (4-6 October 2021, held in Muldersdrift, South Africa), The 22nd annual international conference of the Rapid Product Development Association of South Africa (RAPDASA) (3-5 November 2021, held in Pretoria, South Africa). After the first on-line conferences in 2020 due to COVID-19 regulations, it was excellent to see a return to some normality in 2021 – both these conferences were physical, and the participants were truly hungry for the physical networking opportunities. The Special Edition, introduced in 2016, continues to showcase the best research presented at these conferences. Papers undergo the same double-blind peer review process using the journal’s criteria; and the choice of those included in this Special Edition was based on rankings provided by the reviewers and on a final check of their quality and suitability by the editors of the journal. It was interesting to notice that, in 2020, both conferences focused on the road ahead after the period of uncertainty, with the following two themes: SAIIE32: Steps, and RAPDASA: Industry 4.0 – Digital manufacturing industrializing Africa. It demonstrates the resilience of humankind, and the drive to move forward. For this very reason, the feature article as selected by the chief editor, was authored by young Industrial Engineers, looking forward at what the future may hold, with the title: “Beyond The Industrial Engineering Frontier: A Few Steps In History And A Giant Leap Into The Future”. Although industrial engineers are a relatively small community of professionals, I am always inspired by the relevant, innovative, and far-reaching impact that we can have on every aspect of our society. As you read through the papers in this Special Edition, I trust that you will be inspired by the exemplary work that represents our discipline of industrial engineering. Teresa Hattingh Guest editor

RFEX: Simple Random Forest Model and Sample Explainer for non-Machine Learning experts

Machine Learning (ML) is becoming an increasingly critical technology in many areas. However, its complexity and its frequent non-transparency create significant challenges, especially in the biomedical and health areas. One of the critical components in addressing the above challenges is the explainability or transparency of ML systems, which refers to the model (related to the whole data) and sample explainability (related to specific samples). Our research focuses on both model and sample explainability of Random Forest (RF) classifiers. Our RF explainer, RFEX, is designed from the ground up with non-ML experts in mind, and with simplicity and familiarity, e.g. providing a one-page tabular output and measures familiar to most users. In this paper we present significant improvement in RFEX Model explainer compared to the version published previously, a new RFEX Sample explainer that provides explanation of how the RF classifies a particular data sample and is designed to directly relate to RFEX Model explainer, and a RFEX Model and Sample explainer case study from our collaboration with the J. Craig Venter Institute (JCVI). We show that our approach offers a simple yet powerful means of explaining RF classification at the model and sample levels, and in some cases even points to areas of new investigation. RFEX is easy to implement using available RF tools and its tabular format offers easy-to-understand representations for non-experts, enabling them to better leverage the RF technology.

Epigenetics Theoretical Limits of Synthetic Genomes: The Cases of Artificials Caulobacter (C. eth-2.0), Mycoplasma Mycoides (JCVI-Syn 1.0, JCVI-Syn 3.0 and JCVI_3A), E-coli and YEAST chr XII

In (Venetz et al., 2019), authors rebuilt the essential genome of Caulobacter crescentus through the process of chemical synthesis rewriting and studied the genetic information content at the level of its essential genes. Then, they reduced the native Caulobacter crescentus native Caulobacter NA1000 genome sequence real genome ( 4042929 bp ) to the 785,701-bp reduced synthetic genome. Here we demonstrate the existence of a palindromic-like mirror structure that exists in real genomes and disappears totally in the synthetic genome. This biomathematic meta-organization is based on characteristic proportions of Fibonacci numbers between DNA single strand nucleotides proportions TC / AG on the one hand and TG / AC on the other hand. In both cases, we suggest that this meta-structure enhances the three-dimensional cohesion of the two DNA strands of the genome. We then generalize this study to the different synthetic genomes and synthetic cells published by the Craig Venter Institute on Mycoplasma Mycoides JCVI-syn1.0 (in 2010), JCVI-syn3.0 (in 2016) and JCVI-syn3A (in 2019). Finally, in the discussion section, we extend this study to synthetic genomes of E-Coli and Yeast chromosome XII.

What is synthetic genomics anyway?

You may have heard of synthetic genomics. This headline-grabbing, high-profile, big science topic is starting to emerge catalysed by the pioneering work of famous names in synthetic biology and biotechnology like George Church and Craig Venter. But what is synthetic genomics and what is it being used for? As a prominent researcher at a recent UK meeting said: “Is it just synthetic biology with bigger bits of DNA?” Well no, not quite…

Bioética y nuevas fronteras de la genética, Manuel Ruiz de Chávez y Raúl Jiménez Piña (coordinadores), México: Fontamara-Conbioética, 2018.

La historia de la genética es relativamente reciente, pero es una historia de cambios acelerados que han obligado a que a cada paso nos cuestionemos sobre las opciones éticas que se nos presentan. Aunque se hicieron avances en genética desde que Mendel inauguró la disciplina, podemos situar el inicio de la genética contemporánea —la genética molecular— con el descubrimiento de la estructura del ADN por Watson y Crick en 1953. En los siguientes años, la genética verá el desarrollo de técnicas para secuenciar el código genético humano. En la década de 1960 el eje central de la investigación en genética fue la regulación de la expresión de los genes, que ya en los años 70 se pudo controlar y manipular. Pasamos entonces a la era de la genómica, que sin duda tiene su momento estelar en 2003 cuando Craig Venter y Francis Collins anunciaron que habían completado la secuencia del genoma humano. La genética ha seguido avanzando desde entonces en la dirección de la edición genética, es decir, en la capacidad de modificar el código genético para que un organismo presente rasgos genéticos específicos. Todo esto, particularmente la edición genética, nos ha dado un poder inmenso para modificar el mundo natural —finalmente, todos los seres vivos compartimos la misma estructura genética básica, el ADN, y todos nuestros genes son susceptibles de ser modificados—. Así, por un lado, nos ha dado el poder de modificar plantas y animales y de crear organismos genéticamente modificados o transgénicos; por otro lado, el poder de prevenir y tratar enfermedades, de influir sobre la reproducción, así como de modificar y mejorar rasgos genéticos de un ser humano. Aquí dejaré de lado el asunto de la modificación genética de plantas y animales y me centraré en las aplicaciones de la genética para la salud humana.

Venter, J. Craig (1946–)

J. Craig Venter is an entrepreneurial scientist who has made international headlines for his work sequencing the human genome, discovering new microorganisms and genes in the ocean, and, more recently, engineering synthetic life. Patents on his discoveries caused international concern and speculation about intellectual property rights relating to DNA.

Drama on the I-270 Tech Corridor

This chapter focuses upon one particular geographic region in suburban Washington, DC, which serves as a microcosm for the challenges and opportunities of the larger drug development enterprise. Our story begins with the efforts to sequence the human genome, an ambitious project that led to an increasingly bitter and highly publicized rivalry between the personalities of Craig Venter and Francis Collins from the private and public sectors, respectively. This same initiative gave rise to the dramatic growth in a cadre of biotechnology companies in suburban Maryland dedicated to exploiting the commercial opportunities associated with the human genome. The bubble would ultimately be burst as a result of various legal and executive decisions and in doing so, obliterated billions of dollars in wealth and effectively shudder an entire sector. All the while, another upstart biotechnology company, MedImmune, continued on a lower profile but ultimately more successful path to introduce innovative new medicines. However, this company would itself suffer a series of setbacks of its own making that resulted from the failed commercial launch of an improved influenza vaccine.