Explorative Synthetic Biology in AI: Criteria of Relevance and a Taxonomy for Synthetic Models of Living and Cognitive Processes

This article tackles the topic of the special issue “Biology in AI: New Frontiers in Hardware, Software and Wetware Modeling of Cognition” in two ways. It addresses the problem of the relevance of hardware, software, and wetware models for the scientific understanding of biological cognition, and it clarifies the contributions that synthetic biology, construed as the synthetic exploration of cognition, can offer to artificial intelligence (AI). The research work proposed in this article is based on the idea that the relevance of hardware, software, and wetware models of biological and cognitive processes—that is, the concrete contribution that these models can make to the scientific understanding of life and cognition—is still unclear, mainly because of the lack of explicit criteria to assess in what ways synthetic models can support the experimental exploration of biological and cognitive phenomena. Our article draws on elements from cybernetic and autopoietic epistemology to define a framework of reference, for the synthetic study of life and cognition, capable of generating a set of assessment criteria and a classification of forms of relevance, for synthetic models, able to overcome the sterile, traditional polarization of their evaluation between mere imitation and full reproduction of the target processes. On the basis of these tools, we tentatively map the forms of relevance characterizing wetware models of living and cognitive processes that synthetic biology can produce and outline a programmatic direction for the development of “organizationally relevant approaches” applying synthetic biology techniques to the investigative field of (embodied) AI

Chemical communication between synthetic and natural cells: a possible experimental design

The bottom-up construction of synthetic cells is one of the most intriguing and interesting research arenas in synthetic biology. Synthetic cells are built by encapsulating biomolecules inside lipid vesicles (liposomes), allowing the synthesis of one or more functional proteins. Thanks to the in situ synthesized proteins, synthetic cells become able to perform several biomolecular functions, which can be exploited for a large variety of applications. This paves the way to several advanced uses of synthetic cells in basic science and biotechnology, thanks to their versatility, modularity, biocompatibility, and programmability. In the previous WIVACE (2012) we presented the state-of-the-art of semi-synthetic minimal cell (SSMC) technology and introduced, for the first time, the idea of chemical communication between synthetic cells and natural cells. The development of a proper synthetic communication protocol should be seen as a tool for the nascent field of bio/chemical-based Information and Communication Technologies (bio-chem-ICTs) and ultimately aimed at building soft-wet-micro-robots. In this contribution (WIVACE, 2013) we present a blueprint for realizing this project, and show some preliminary experimental results. We firstly discuss how our research goal (based on the natural capabilities of biological systems to manipulate chemical signals) finds a proper place in the current scientific and technological contexts. Then, we shortly comment on the experimental approaches from the viewpoints of (i) synthetic cell construction, and (ii) bioengineering of microorganisms, providing up-to-date results from our laboratory. Finally, we shortly discuss how autopoiesis can be used as a theoretical framework for defining synthetic minimal life, minimal cognition, and as bridge between synthetic biology and artificial intelligence.Comment: In Proceedings Wivace 2013, arXiv:1309.712

Editorial: ‘Inter-Identities’ in Life, Mind, and Society

The main funding for this research was received by the Ministry of Economy and Competitiveness (Spain) FFI2014-52173-P Research Project on Inter-Identities (PIs: AE and KR-M). AE and KR-M also acknowledge funding from the Basque Government Research Groups IT 1228-19 to IAS Research on Life, Mind and Society

A Role for Bottom-Up Synthetic Cells in the Internet of Bio-Nano Things?

The potential role of bottom-up Synthetic Cells (SCs) in the Internet of Bio-Nano Things (IoBNT) is discussed. In particular, this perspective paper focuses on the growing interest in networks of biological and/or artificial objects at the micro- and nanoscale (cells and subcellular parts, microelectrodes, microvessels, etc.), whereby communication takes place in an unconventional manner, i.e., via chemical signaling. The resulting "molecular communication" (MC) scenario paves the way to the development of innovative technologies that have the potential to impact biotechnology, nanomedicine, and related fields. The scenario that relies on the interconnection of natural and artificial entities is briefly introduced, highlighting how Synthetic Biology (SB) plays a central role. SB allows the construction of various types of SCs that can be designed, tailored, and programmed according to specific predefined requirements. In particular, "bottom-up" SCs are briefly described by commenting on the principles of their design and fabrication and their features (in particular, the capacity to exchange chemicals with other SCs or with natural biological cells). Although bottom-up SCs still have low complexity and thus basic functionalities, here, we introduce their potential role in the IoBNT. This perspective paper aims to stimulate interest in and discussion on the presented topics. The article also includes commentaries on MC, semantic information, minimal cognition, wetware neuromorphic engineering, and chemical social robotics, with the specific potential they can bring to the IoBNT

Plural Embodiment(s) of Mind. Genealogy and Guidelines for a Radically Embodied Approach to Mind and Consciousness

This article focuses on a scientific approach to the study of cognition that Warren McCulloch introduced in the era of cybernetics as “experimental epistemology.” In line with recent attempts to highlight its contribution to cognitive science and AI, our article intends to draw attention to its unexplored influence on contemporary embodied approaches to the investigation of mind and consciousness. To this end, we will survey a series of models of cognitive systems genealogically related to the McCulloch-Pitts networks-based modeling approach, i.e., von Foerster’s model of the biological computer, the Maturana-Varela model of the autopoietic system, and Varela’s model of emergent selves. Based on examination of the relevant aspects of these models, we will argue that they offered the McCulloch-Pitts “cybernetic of networks” a coherent methodological and theoretical line of development, complementary to the well-known computationalist one. As we will show, this alternative evolutionary line empowered the biological orientation of McCulloch’s experimental epistemology, laying foundations for contemporary “radically embodied” approaches to mind and consciousness – in particular the Thompson-Varela approach. We will identify the heritage of this tradition of inquiry for future research in cognitive science and AI by proposing guidelines that synthetize how its methodological and theoretical insights suggest taking into account the role(s) played by the biological body in cognitive processes – consciousness included

Modulation of hepatic lipid metabolism by olive oil and its phenols in nonalcoholic fatty liver disease

Nonalcoholic fatty liver disease (NAFLD) represents the most common chronic liver disease in western countries, being considered the hepatic manifestation of metabolic syndrome. Cumulative lines of evidence suggest that olive oil, used as primary source of fat by Mediterranean populations, may play a key role in the observed health benefits on NAFLD. In this review, we summarize the state of the art of the knowledge on the protective role of both major and minor components of olive oil on lipid metabolism during NAFLD. In particular, the biochemical mechanisms responsible for the increase or decrease in hepatic lipid content are critically analyzed, taking into account that several studies have often provided different and/or conflicting results in animal models fed on olive oil-enriched diet. In addition, new findings that highlight the hypolipidemic and the antisteatotic actions of olive oil phenols are presented. As mitochondrial dysfunction plays a key role in the pathogenesis of NAFLD, the targeting of these organelles with olive oil phenols as a powerful therapeutic approach is also discussed

Hydroxyapatite–Silicon Scaffold Promotes Osteogenic Differentiation of CGF Primary Cells s

Simple Summary: The aim of this study was to identify new and innovative strategies to improve the tissue-regeneration process. Concentrated growth factor (CGF) is an autologous biomaterial rich in growth factors and multipotent stem cells. The purpose of our study was to evaluate the osteogenic differentiation of CGF primary cells in the presence of a hydroxyapatite–silicon scaffold, which represents a very interesting material in the field of bone reconstructive surgery. Our findings showed that the hydroxyapatite–silicon scaffold provided support to primary CGF cells by enhancing osteogenic differentiation. These data suggest interesting perspectives in the use of CGF together with scaffolds in the field of regenerative medicine. Abstract: The application of scaffolding materials together with stem cell technologies plays a key role in tissue regeneration. Therefore, in this study, CGF (concentrated growth factor), which represents an autologous and biocompatible blood-derived product rich in growth factors and multipotent stem cells, was used together with a hydroxyapatite and silicon (HA-Si) scaffold, which represents a very interesting material in the field of bone reconstructive surgery. The aim of this work was to evaluate the potential osteogenic differentiation of CGF primary cells induced by HASi scaffolds. The cellular viability of CGF primary cells cultured on HA-Si scaffolds and their structural characterization were performed by MTT assay and SEM analysis, respectively. Moreover, the matrix mineralization of CGF primary cells on the HA-Si scaffold was evaluated through Alizarin red staining. The expression of osteogenic differentiation markers was investigated through mRNA quantification by real-time PCR. We found that the HA-Si scaffold was not cytotoxic for CGF primary cells, allowing their growth and proliferation. Furthermore, the HASi scaffold was able to induce increased levels of osteogenic markers, decreased levels of stemness markers in these cells, and the formation of a mineralized matrix. In conclusion, our results suggest that HA-Si scaffolds can be used as a biomaterial support for CGF application in the field of tissue regeneration

Oleic Acid and Hydroxytyrosol Inhibit Cholesterol and Fatty Acid Synthesis in C6 Glioma Cells

Recently, the discovery of natural compounds capable of modulating nervous system function has revealed new perspectives for a healthier brain. Here, we investigated the effects of oleic acid (OA) and hydroxytyrosol (HTyr), two important extra virgin olive oil compounds, on lipid synthesis in C6 glioma cells. OA and HTyr inhibited both de novo fatty acid and cholesterol syntheses without affecting cell viability. The inhibitory effect of the individual compounds was more pronounced if OA and HTyr were administered in combination. A reduction of polar lipid biosynthesis was also detected, while triglyceride synthesis was marginally affected. To clarify the lipid-lowering mechanism of these compounds, their effects on the activity of key enzymes of fatty acid biosynthesis (acetyl-CoA carboxylase-ACC and fatty acid synthase-FAS) and cholesterologenesis (3-hydroxy-3-methylglutaryl-CoA reductase-HMGCR) were investigated in situ by using digitonin-permeabilized C6 cells. ACC and HMGCR activities were especially reduced after 4 h of 25 μM OA and HTyr treatment. No change in FAS activity was observed. Inhibition of ACC and HMGCR activities is corroborated by the decrease of their mRNA abundance and protein level. Our results indicate a direct and rapid downregulatory effect of the two olive oil compounds on lipid synthesis in C6 cells

Coffee Bioactive N-Methylpyridinium Attenuates Tumor Necrosis Factor (TNF)-α-Mediated Insulin Resistance and Inflammation in Human Adipocytes

Although coffee consumption has been historically associated with negative health outcomes, recent evidence suggests a lower risk of metabolic syndrome, obesity and diabetes among regular coffee drinkers. Among the plethora of minor organic compounds assessed as potential mediators of coffee health benefits, trigonelline and its pyrolysis product N-methylpyridinium (NMP) were preliminary shown to promote glucose uptake and exert anti-adipogenic properties. Against this background, we aimed at characterizing the effects of trigonelline and NMP in inflamed and dysfunctional human adipocytes. Human Simpson-Golabi-Behmel syndrome (SGBS) adipocytes were treated with NMP or, for comparison, trigonelline, for 5 h before stimulation with tumor necrosis factor (TNF)-α. NMP at concentrations as low as 1 µmol/L reduced the stimulated expression of several pro-inflammatory mediators, including C-C Motif chemokine ligand (CCL)-2, C-X-C Motif chemokine ligand (CXCL)-10, and intercellular adhesion Molecule (ICAM)-1, but left the induction of prostaglandin G/H synthase (PTGS)2, interleukin (IL)-1β, and colony stimulating factor (CSF)1 unaffected. Furthermore, NMP restored the downregulated expression of adiponectin (ADIPOQ). These effects were functionally associated with downregulation of the adhesion of monocytes to inflamed adipocytes. Under the same conditions, NMP also reversed the TNF-α-mediated suppression of insulin-stimulated Ser473 Akt phosphorylation and attenuated the induction of TNF-α-stimulated lipolysis restoring cell fat content. In an attempt to preliminarily explore the underlying mechanisms of its action, we show that NMP restores the expression of the master regulator of adipocyte differentiation peroxisome proliferator-activated receptor (PPAR)γ and downregulates activation of the pro-inflammatory mitogen-activated protein jun N-terminal kinase (JNK). In conclusion, NMP reduces adipose dysfunction in pro-inflammatory activated adipocytes. These data suggest that bioactive NMP in coffee may improve the inflammatory and dysmetabolic milieu associated with obesity