Ideas in theoretical biology

The potential and realized impact of Bohm's views on biology are briefly discussed.     

An essay on the evolution of cognition: Constructing a theoretical conceptual framework

In this essay we provide an interdisciplinary approach to the problem of the evolution of human cognition and suggest the theoretical framework of genetic system theory (GST) for organizing the relevant content of several disciplines. This bio-social-cultural theory is based on the assumption that organisms are dynamic systems which interact with one another and their environment and are themselves composed of dynamic internal relations at several levels. Special emphasis will be placed upon these internal cellular and molecular mechanisms underlying the physiological mechanisms of learning and memory. The human individual organism is emphasized because in its experiential activity over time it is the site of integration for social, and cultural stimuli and because of its unique properties among living things. The primary disciplines for our discussion are drawn from the biological, social, and humanistic sciences and several concrete examples are given from each science.     

意识与麻醉

<正>意识可以定义为"个体觉察自我与环境存在的脑功能状态"也就是说,意识是脑对"存在"的觉察,感知"存在"就是对真实自我和环境的觉察、发生在清醒状态下,对"存在"的觉察是脑的基本功能,也是注意、学习、认知、思维等功能的前提.国际上许多实验室,研究麻醉导致的意识丧失以及麻醉后意识的重启动,来揭示意识的神经基础.最近,Solovey等(J Neurosci,2015,35(30):10866)发现,不同麻醉药物诱导的脑活动模式不同,如果忽略那些具体活动的特征,意识丧失与     

A mean field Ising model for cortical rotation in amphibian one-cell stage embryos

We propose a new physical mechanism of cortical rotation generation in one-cell embryos of amphibians based on a phase transition in the ensemble of microtubules localized to the cortical region of the cell interior. Microtubules, protein polymers formed from tubulin heterodimers, are highly negatively charged, which results in strong electrostatic interactions over tens of nanometers, even in the presence of counterions that partially screen electrostatic interactions. A simplified model that offers a plausible representation of these effects is based on the Ising Hamiltonian, which has been robustly applied to explain a wide range of order-disorder transitions in physics, chemistry and other sciences. An Ising model phase transition, especially with the supercooperative flow alignment effect of global rotation of the cortex, provides an alternative to models of cortical rotation based on microtubule polymerization or motor molecules. Insofar as there is any reality to the concept that microtubules are involved in consciousness, we propose that cortical rotation in the one-cell embryo is a better place to look for the purported microtubule entanglement or coherence properties than the adult brain.     

Multi-scale lines and edges in V1 and beyond: Brightness,object categorization and recognition,and consciousness

In this paper we present an improved model for line and edge detection in cortical area V1. This model is based on responses of simple and complex cells, and it is multi-scale with no free parameters. We illustrate the use of the multi-scale line/edge representation in different processes: visual reconstruction or brightness perception, automatic scale selection and object segregation. A two-level object categorization scenario is tested in which pre-categorization is based on coarse scales only and final categorization on coarse plus fine scales. We also present a multi-scale object and face recognition model. Processing schemes are discussed in the framework of a complete cortical architecture. The fact that brightness perception and object recognition may be based on the same symbolic image representation is an indication that the entire (visual) cortex is involved in consciousness.     

民族院校生物工程专业微生物实验教学体系的构建与实践

微生物学实验是当代生命学科中的一门重要专业必修课。针对民族院校的学生特点和我院生物工程专业的培养特色,阐述将微生物学实验教学体系分为基础验证型、提高设计型和综合研究型3个层次,贯彻"以学生自主实验为主,教师指导为辅"的实验课程教学方针,充分发挥学生在实验教学中的主体作用。在规范基本实验操作的基础上,锻炼学生的自学能力,激发创新意识,培养应用能力。     

Viewing brain processes as Critical State Transitions across levels of organization: Neural events in Cognition and Consciousness,and general principles

In this theoretical and speculative essay, I propose that insights into certain aspects of neural system functions can be gained from viewing brain function in terms of the branch of Statistical Mechanics currently referred to as “Modern Critical Theory” [Stanley, H.E., 1987. Introduction to Phase Transitions and Critical Phenomena. Oxford University Press; Marro, J., Dickman, R., 1999. Nonequilibrium Phase Transitions in Lattice Models. Cambridge University Press, Cambridge, UK]. The application of this framework is here explored in two stages: in the first place, its principles are applied to state transitions in global brain dynamics, with benchmarks of Cognitive Neuroscience providing the relevant empirical reference points. The second stage generalizes to suggest in more detail how the same principles could also apply to the relation between other levels of the structural-functional hierarchy of the nervous system and between neural assemblies. In this view, state transitions resulting from the processing at one level are the input to the next, in the image of a ‘bucket brigade’, with the content of each bucket being passed on along the chain, after having undergone a state transition. The unique features of a process of this kind will be discussed and illustrated.     

Theoretical approaches to holistic biological features: Pattern formation,neural networks and the brain-mind relation

The topic of this article is the relation between bottom-up and top-down, reductionist and “holistic” approaches to the solution of basic biological problems. While there is no doubt that the laws of physics apply to all events in space and time, including the domains of life, understanding biology depends not only on elucidating the role of the molecules involved, but, to an increasing extent, on systems theoretical approaches in diverse fields of the life sciences. Examples discussed in this article are the generation of spatial patterns in development by the interplay of autocatalysis and lateral inhibition; the evolution of integrating capabilities of the human brain, such as cognition-based empathy; and both neurobiological and epistemological aspects of scientific theories of consciousness and the mind.     

Dualism revisited

The problem of consciousness should eventually receive a scientific solution, but there are a number of scientific and philosophical obstacles along the way. I offer solutions to the philosophical problems and proposals for approaching the scientific problems.     

Using topographic networks to build a representation of consciousness

The subject of consciousness has intrigued both psychologists and neuroscientists for many years. Recently, following many recent advances in the emerging field of cognitive neuroscience, there is the possibility that this fundamental process may soon be explained. In particular, there have been dramatic insights gained into the mechanisms of attention, cognition and perception in recent decades. Here, simple network models are proposed which are used to create a representation of consciousness. The models are inspired by the structure of the thalamus and all incorporate topographic layers in their structure. Operation of the models allows filtering of the information reaching the representation according to (1) modality and/or (2) sub-modality, in addition several of the models allowing filtering at the topographic level. The models presented have different structures and employ different integrative mechanisms to produce gating or amplification at different levels; the resultant representations of consciousness are discussed.