The articles posted on this feed (now only a few per year) have included many accessible updates on the technical literature; commentaries on that literature; and introductions (with links) to major new articles associated with the Biology Worthy of Life project. The content in general has related to the dramatic discoveries re-shaping our understanding of organisms, especially in the field of gene regulation. However, the focus is now shifting toward evolution, and the meaning of organic wholeness. All, or nearly all, articles now being posted are part of an online book titled “Organisms and Their Evolution — Agency and Meaning in the Drama of Life” (formerly called “Evolution As It Was Meant To Be — And the Living Narratives That Tell Its Story”). All articles, notes, and commentaries are by Stephen L. Talbott of The Nature Institute. https://bwo.life/org/comm/news.htm stevet@netfuture.org (Stephen L. Talbott) stevet@netfuture.org (Stephen L. Talbott) holistic biology whole organism biology genetics evolution epigenetics gene regulation> gene expression> holism versus mechanism meaning in biology and evolution Tue, 29 Nov 2022 14:30:00 GMT Tue, 29 Nov 2022 14:30:00 GMT 1440 en-us The history of language gives us a reflection of the evolution of human consciousness. It points to a time before we became aware of our own existence as distinct Selves observing a world “out there” and separate from ourselves. How accurate (or inaccurate) our own experience of a subject-object dualism is can be properly assessed only against the background of the evolution of consciousness, so far as it can be traced. Oddly, though, contemporary evolutionary theory has not had much to say about the evolution of consciousness. This ought to concern us because the evolved character of our own consciousness unavoidably frames and limits our theory of evolution. The ancients read the “face” of what we think of as the outer world rather as we today can still read the face of another human being — that is, they read material phenomena as expressions of inner being. Can we learn anything by setting their experience over against our own alienation from the outer world? This may be the same question as, “Can we overcome the dualistic heritage of the past several centuries?” https://bwo.life/bk/evolconsc.htm https://bwo.life/bk/evolconsc.htm Tue, 29 Nov 2022 14:30:00 GMT epistemology evolution/of consciousness inwardness (intention, idea, meaning) mailto:stevet@netfuture.org The fundamental pathologies of gene-centered thinking in biology arise from the materialist bent of virtually all reputable biologists. This mindset prevents them from acknowledging the organizing ideas that constitute whole cells and whole organisms as what they are. It also forces them to attempt to understand the organism from the bottom up, starting with genes. But when they do this, they inevitably end up attributing to genes the organizing ideas that actually belong to the whole cell and whole organism. https://bwo.life/bk/inherit2.htm https://bwo.life/bk/inherit2.htm Tue, 29 Nov 2022 14:30:00 GMT evolution/and development evolution/inheritance evolution/and mutations explanation/part and whole gene/mutation gene/genocentrism mailto:stevet@netfuture.org A science that has for centuries forsworn qualities as “merely subjective” must regard the idea of a qualitative science as a contradiction in terms. Here I offer three examples of current work illustrating what a qualitative science can be — and how essential it is to any genuine knowledge of the world. This is extremely problematic for an evolutionary theory that has no means for addressing observed qualitative patterns running through taxonomic groups. https://bwo.life/bk/qualsci.htm https://bwo.life/bk/qualsci.htm Thu, 13 Oct 2022 14:30:00 GMT evolution/as mindless process form/organismal holism/as polarity mailto:stevet@netfuture.org We know organisms only as wonderfully integrated wholes, and we know inheritance only as an inheritance of whole cells. This truth was obscured during the era of genes and molecular biology, when biologists came to see genes as substitutes for cells and organisms. But the consequence of this was that biologists lost sight of the central problem of inheritance — how an organism’s unified character and entire way of being are passed on to its offspring. We will need to recover our sight of that problem before we can make fundamental progress in understanding evolution. https://bwo.life/bk/inherit1.htm https://bwo.life/bk/inherit1.htm Thu, 28 Oct 2021 14:30:00 GMT evolution/and development evolution/inheritance evolution/and mutations gene/as difference-maker holism mailto:stevet@netfuture.org We cannot explain the purposiveness of organisms by referring to natural selection or cybernetic devices. We must reckon with the organism’s interiority, which includes the play of thinking through the organism, whether consciously or unconsciously. In humans, our conscious intentions are seamlessly continuous with the unconscious realization of those intentions at the cellular (including genomic) level. All our physiological processes are inherently purposive whether consciously or otherwise https://bwo.life/news/linnean/talk_notes.htm https://bwo.life/news/linnean/talk_notes.htm Wed, 21 Jul 2021 14:30:00 GMT inwardness (intention, idea, meaning) mailto:stevet@netfuture.org The question of the directiveness of evolution turns out to be almost trivially simple, with an unproblematic answer: evolutionary “development” must be at least as directive (purposive in an organic sense, or “telos-realizing”) as the development of an individual organism. Unfortunately, however, evolutionary biologists have bypassed this conclusion because they are rigorously trained to ignore in their theoretical work what they know very well in their direct acquaintance with organisms. https://bwo.life/bk/devo_l.htm https://bwo.life/bk/devo_l.htm Tue, 15 Jun 2021 14:30:00 GMT development (ontogeny) evolution evolution/and development mailto:stevet@netfuture.org The world of the cell and its molecules is so different from what we can readily picture to ourselves that it remains virtually unknown to us. It is a real question whether we can speak at all of “things” at that scale, as opposed to forces or potentials. https://bwo.life/bk/microworld.htm https://bwo.life/bk/microworld.htm Thu, 15 Apr 2021 14:30:00 GMT machine-idea mailto:stevet@netfuture.org Given the modern-day, almost fetish-like preoccupaton with genes, it is a remarkable fact that almost no one in our society is aware of the dramatic story about how our genes enter into our lives. Here is presented an overview of that story. https://bwo.life/bk/epigene2.htm https://bwo.life/bk/epigene2.htm Thu, 21 Jan 2021 14:30:00 GMT chromosome/chromatin holism plasticity/genome transcription transcription/transcription factors mailto:stevet@netfuture.org Biologists reject the idea of teleology, or purposiveness, in evolution because they have refused to acknowledge it theoretically even where they cannot help recognizing it in practice — namely in the development of individual organisms. Mice embryos consistently coordinate all their growth and activity along a path toward adulthood. Attempts to explain this purposively directed development by appealing to natural selection are blatantly circular, while also importing human purposiveness “under the table” through the appeal to machine models in biology. https://bwo.life/bk/evotelos.htm https://bwo.life/bk/evotelos.htm Tue, 10 Nov 2020 14:30:00 GMT development (ontogeny) evolution/and development inwardness (intention, idea, meaning) machine-idea mailto:stevet@netfuture.org Is the form of an organism something that needs to be explained? Or does our our subtle tracing of biological form and transformation already give us the explanation and understanding we seek — because through this tracing we apprehend the thinking that is the intelligible principle of the organism’s form? https://bwo.life/bk/form2.htm https://bwo.life/bk/form2.htm Tue, 23 Jun 2020 14:30:00 GMT development (ontogeny) form holism machine-idea mailto:stevet@netfuture.org How does the yet-unrealized form of a mature animal become the ‘goal’ of the animal’s embryological development? How can we understand future-directed causation and top-down causation in biology? https://bwo.life/bk/form1.htm https://bwo.life/bk/form1.htm Thu, 28 May 2020 14:30:00 GMT development (ontogeny) form holism machine-idea mailto:stevet@netfuture.org All science is experienced-based. We have a conflicted attitude toward this truth, believing as we do that science must be empirical (based on experience), while at the same time we denigrate experience as merely subjective. Freeing ourselves from this contradiction is a radical step, and delivers biology from the bonds of materialism and reductionism. We also realize that experience gives us the real world because the real world is, by nature, ‘made of experience’. https://bwo.life/bk/epist1.htm https://bwo.life/bk/epist1.htm Thu, 16 Apr 2020 14:30:00 GMT explanation inwardness (intention, idea, meaning) mailto:stevet@netfuture.org There are three central themes in the book, “Organisms and Their Evolution — Agency and Meaning in the Drama of Life”: 1) every organism possesses a narrative agency and does not consist merely of chemical interactions; 2) every animal’s life narrative is an outward expression of interior meaning; and 3) biologists suffer from a kind of blindsight through which they are unable to incorporate much of what they actually know about organisms into their scientific explanations. The book also rests on a fundamental conviction that the world, by nature, manifests itself in thought. https://bwo.life/bk/keys.htm https://bwo.life/bk/keys.htm Tue, 17 Dec 2019 14:30:00 GMT explanation/biological inwardness (intention, idea, meaning) mailto:stevet@netfuture.org When we look at organic development, we see powers of directed change in the only place where they ever appear — in living organisms. These powers can hardly be irrelevant to evolution. https://bwo.life/bk/evo_s.htm https://bwo.life/bk/evo_s.htm Wed, 04 Dec 2019 14:30:00 GMT development evolution/and development mailto:stevet@netfuture.org Causes and effects are never neatly separable in organisms. Over and above physical causation, we discover a story-like coordination of causes. Biologists widely recognize this, but nevertheless try to describe biological processes as if they were nothing but a succession of physical causes and effects. The resulting descriptions are highly self-contradictory. https://bwo.life/bk/cause.htm https://bwo.life/bk/cause.htm Thu, 14 Nov 2019 14:30:00 GMT explanation/and causation holism/contextual mailto:stevet@netfuture.org In living beings, structure arises from movement, not the other way around. Movement and transformation are primary. This is particularly evident in recent discoveries about the functioning of disordered proteins and about the importance of phase transitions in the cytoplasm and nucleoplasm. https://bwo.life/bk/stream.htm https://bwo.life/bk/stream.htm Tue, 27 Aug 2019 14:30:00 GMT holism protein/disordered form/molecular mailto:stevet@netfuture.org The key ideas of natural selection are commonly presented in the form of a core logic, or algorithm, that leads, with absolute certainty, to meaningful evolution. In reality, this logic is empty, and all the meaning depends upon what organism-agents actually do. By itself, the logic of natural selection does not tell us whether there will be any evolutionary change at all. https://bwo.life/bk/ns1.htm https://bwo.life/bk/ns1.htm Fri, 19 Jul 2019 14:30:00 GMT evolution mailto:stevet@netfuture.org RNA splicing and, in some organisms, the reconstruction of shattered genomes (and, in all organisms, the processes of DNA damage repair) illustrate the coherent, holistic, end-directed, epigenetic performance of living narratives. https://bwo.life/bk/coherence.htm https://bwo.life/bk/coherence.htm Sun, 19 May 2019 14:30:00 GMT epigenetics gene regulation holism/contextual RNA mailto:stevet@netfuture.org Every organism, and indeed every significant biological entity from a cell on up, is a governing context that informs and disciplines its own parts, while also participating in larger contexts; and the governance is established by the interwoven ideas that make the context what it is. https://bwo.life/bk/context.htm https://bwo.life/bk/context.htm Tue, 07 May 2019 14:30:00 GMT explanation/part and whole holism/contextual inwardness (intention, idea, meaning) mailto:stevet@netfuture.org The cytoskeleton and cellular membranes illustrate both the integral unity of the cell and also the temptation to isolate parts in our thought as ‘controlling’ causes. In reality, we discover in every cell the power of the whole to express itself through its parts. https://bwo.life/bk/cell.htm https://bwo.life/bk/cell.htm Tue, 07 May 2019 14:30:00 GMT explanation/and causation holism mailto:stevet@netfuture.org The idea of DNA as an informational sequence encoding a genetic program is giving way to a much more dynamic idea involving three-dimensional chromosomes that actively gesture their meanings https://bwo.life/bk/genes.htm https://bwo.life/bk/genes.htm Tue, 07 May 2019 14:30:00 GMT chromosome/dynamics chromosome/in 3D space gene regulation genome/organization mailto:stevet@netfuture.org The fact of purposive activity — the obvious play of active agency, the coordination of means toward the realization of relatively stable ends, and the undeniable evidence that animals perceive a world and interpret their perceptions according to their own way of life — we can sum up all this by saying that every organism is narrating a meaningful life story. This is not something that a rock, say, loosened by ice and tumbling down the steep slope of a mountain ravine, does in anything like the same manner. The pattern of physical events in the organism is raised by its peculiar sort of coherence toward something like a biography whose “logic” unfolds on an entirely different level from the logic of inanimate physical causation. When we tell a story, the narrative threads convey meanings — for example, motives, needs, and intentions — and these are never a matter of mere physical cause and consequence. https://bwo.life/bk/story_36.htm https://bwo.life/bk/story_36.htm Wed, 30 Jan 2019 14:30:00 GMT explanation/biological explanation/part and whole holism/contextual inwardness (intention, idea, meaning) mailto:stevet@netfuture.org We in the twenty-first century have inherited a rich and extensive library of descriptive literature about living things, their habitats, and their mutual relations, bequeathed to us over the centuries by dedicated naturalists. Unfortunately, in this age of molecular biology and genetic preoccupation, the community of naturalists — or, at least, academically connected ones — has largely died out. It is a shame that biologists today can easily pass through their schooling and into a pristine laboratory without ever having read descriptions such as the following, let alone having observed and investigated these phenomena for themselves. The vignettes in this article, culled from various sources, afford only fragmentary glimpses of the larger panorama of life on earth. But they are enough to remind us of the “miracle” that life can so easily appear to be. The reminder is a useful one, and may stimulate us toward efforts of understanding that are not cramped by prevailing dogmas. https://bwo.life/org/comm/ar/2018/scenes_35.htm https://bwo.life/org/comm/ar/2018/scenes_35.htm Thu, 29 Nov 2018 17:30:00 GMT inwardness (intention, idea, meaning) mailto:stevet@netfuture.org We have all heard about the insignificance of human existence in a cosmos that is indifferent, if not alien, to us. But history and language suggest that the cosmos has a different story to tell. https://bwo.life/org/comm/ar/2018/meaning_33.htm https://bwo.life/org/comm/ar/2018/meaning_33.htm Tue, 15 May 2018 12:30:00 GMT inwardness (intention, idea, meaning) evolution/of consciousness mailto:stevet@netfuture.org Few biologists are reticent about their conviction that organisms are machine-like and have been “tinkered” with throughout evolutionary history by a designer capable of producing intelligent results — all without any intelligent aid from organisms themselves. The designer they have in mind, of course, is natural selection, which has famously been likened to a blind watchmaker and is almost universally referred to as an agent capable of intelligent activity. Not many biologists, whether ID proponents or otherwise, seem particularly interested in confronting the reality of intelligent agency where we observe it directly — in living beings — as opposed to taking the organism merely as evidence for the real guiding intelligence of their preferred Designer. This indifference toward organisms follows rather naturally when you have conceived organisms as machines, which always require an external designer. But we will take the alternative path, turning toward the organism’s inherent life. https://bwo.life/org/comm/ar/2017/id_32.htm https://bwo.life/org/comm/ar/2017/id_32.htm Thu, 14 Dec 2017 12:30:00 GMT evolution/intelligent design explanation/biological inwardness (intention, idea, meaning) machine-idea mailto:stevet@netfuture.org Does evolutionary theory explain the origin and reality of purposiveness in the life of organisms? Or does the reality of purposiveness point us toward severe and disabling inadequacies in the reigning versions of the theory? This is a large and ambitious article — the first (and more preparatory) part of a two-part effort to reconceptualize evolution in an unexpectedly fundamental way. The second (forthcoming) part is tentatively entitled, “Is Directed Evolution a Necessary Assumption in Biology?” NOTE: the current article is a major expansion and recasting of an earlier article, “Can Darwinian Evolutionary Theory Be Taken Seriously?” It covers extensive new territory and is far more adequate to the topic. Little of the earlier piece remains. http://thenewatlantis.com/publications/evolution-and-the-purposes-of-life http://thenewatlantis.com/publications/evolution-and-the-purposes-of-life Fri, 31 Mar 2017 12:30:00 GMT evolution evolution/as mindless process evolution/intelligent design inwardness (intention, idea, meaning) machine-idea mailto:stevet@netfuture.org Molecular biologists have spent several decades trying to identify how “one thing causing another” explains the organism. It is a simplistic and decontextualized way of looking that ends up in radical falsehood. The study of genes and their expression shows us that the organism is a living, intentional activity coordinating its parts in relation to the needs of the whole. Here I try to offer a glimpse of this whole at the molecular level. https://bwo.life/org/comm/ar/2015/genes_29.htm https://bwo.life/org/comm/ar/2015/genes_29.htm Tue, 10 Nov 2015 14:30:00 GMT chromosome/chromatin chromosome/dynamics DNA epigenetics gene/indefinability gene regulation genome/organization genome/remodeling machine-idea plasticity rna transcription mailto:stevet@netfuture.org It makes little sense to try to explain how intelligence arises in organisms, given that we see nothing but intelligence there — for example, in the processes producing the brain. The really interesting challenge is to distinguish the intelligence at work in our bodies from the intelligence we possess as our own conscious activity. https://bwo.life/org/comm/ar/2015/bodily-wisdom3_28.htm https://bwo.life/org/comm/ar/2015/bodily-wisdom3_28.htm Wed, 29 Apr 2015 14:30:00 GMT explanation/biological inwardness (intention, idea, meaning) mailto:stevet@netfuture.org Confusion over the meaning of “epigenetics” reflects fundamental confusion about the nature of organisms and biological causation. Epigenetics really points us to the intentional activity of the whole organism — an activity in which DNA is caught up. The organism is making use of its DNA, not being governed by it. https://bwo.life/org/comm/ar/2015/unthinking_epigenetics_27.htm https://bwo.life/org/comm/ar/2015/unthinking_epigenetics_27.htm Thu, 26 Mar 2015 14:30:00 GMT chromosome/chromatin DNA/noncoding epigenetics explanation/and causation gene/genocentrism gene regulation holism/contextual inwardness (intention, idea, meaning) mailto:stevet@netfuture.org Both the history of research on induced pluripotency and the current discoveries regarding the microbiome testify to the decisive importance of context, relationship, and interaction in the life of the organism. https://bwo.life/org/comm/ar/2015/lit-notes3_26.htm https://bwo.life/org/comm/ar/2015/lit-notes3_26.htm Thu, 08 Jan 2015 14:30:00 GMT development explanation/biological explanation/and causation holism/contextual pluripotency/induced explanation/part and whole microbiome mailto:stevet@netfuture.org You’ll have a hard time believing how the invisible microbes within us function as part of our own life. And perhaps not so hard a time believing how biologists are tempted immediately to regard particular microorganisms as opportunities for exerting neat control over everything from liver cancer to autism. https://bwo.life/org/comm/ar/2014/microbiome_25.htm https://bwo.life/org/comm/ar/2014/microbiome_25.htm Tue, 09 Dec 2014 14:30:00 GMT explanation/and causation explanation/biological explanation/part and whole holism/contextual mailto:stevet@netfuture.org A study of plant form reveals that organic form is a causal principle; in a very real sense, it is form that brings about its own physical embodiment, not physical interactions that bring about form. A realization of this truth would radically transform biological thinking. https://bwo.life/org/comm/ar/2014/brady_24.htm https://bwo.life/org/comm/ar/2014/brady_24.htm Tue, 11 Nov 2014 14:30:00 GMT development (ontogeny) evolution/intelligent design explanation/biological explanation/and causation form/organismal holism/contextual holism/versus mysticism and vitalism inwardness (intention, idea, meaning) mailto:stevet@netfuture.org Excerpt: “How many molecular biologists today would feel such freedom — the kind of freedom Richard Conn Henry knew within the physics community? I mean, for example, the freedom to wonder aloud whether intention and agency, so difficult to banish from biological description, might be at least as fundamental to our understanding of local molecular interactions as those interactions are to our understanding of intention and agency.” https://bwo.life/org/comm/ar/2014/mental_cell_23.htm https://bwo.life/org/comm/ar/2014/mental_cell_23.htm Tue, 09 Sep 2014 14:30:00 GMT explanation/biological inwardness (intention, idea, meaning) mailto:stevet@netfuture.org A late 19th-century work by the Russian philosopher, Vladimir Solovyov, convincingly demonstrates that "sexual love", culminating in human romantic love, cannot be understood merely as a means for propagating the species; it explains the evolutionary process more than being explained by it. Solovyov’s book is a useful counterpoint to twenty-first century sociobiology. https://bwo.life/org/comm/ar/2014/love_22.htm https://bwo.life/org/comm/ar/2014/love_22.htm Fri, 01 Aug 2014 14:30:00 GMT evolution/sociobiology explanation/part and whole inwardness (intention, idea, meaning) mailto:stevet@netfuture.org Contents: “Viruses, cytoplasmic DNA, and the web of life”; “The (molecular) days of our lives”; “DNA and RNA brought to life”; “Functional vs. nonfunctional DNA binding”. https://bwo.life/org/comm/ar/2014/lit-notes2_21.htm https://bwo.life/org/comm/ar/2014/lit-notes2_21.htm Thu, 03 Jul 2014 14:30:00 GMT chromosome/chromatin DNA explanation/causation gene/genocentrism gene regulation machine idea plasticity/genome transcription/transcription factors mailto:stevet@netfuture.org There is no rigid, psyche/soma, inner/outer or mind/matter dichotomy in the human being or in any other organism. There is no rigid, psyche/soma, inner/outer or mind/matter dichotomy in the human being or in any other organism. From the body as a whole to its various parts, from the macro scale to the micro, from conscious activity to unconscious processes, from human speech to the communication of the cell, we see bodily gesturing that at the same time expresses an inner or psychic content — expresses, for example, intention and judicious choice as part of a life story. In short, we see something like speech in its broadest sense — a word- or logos-activity. There seems to be an unbroken continuity from the most intensely conscious thought and speech down to fully unconscious expressions. https://bwo.life/org/comm/ar/2014/bodily-wisdom2_20.htm https://bwo.life/org/comm/ar/2014/bodily-wisdom2_20.htm Tue, 10 Jun 2014 14:30:00 GMT explanation/biological inwardness (intention, idea, meaning) mailto:stevet@netfuture.org When intelligent design theorists emphasize “machine-design” in the organism as evidence of the past activity of an intelligent designer, they do an injustice both to the organism and to their own interests. If they want to combat the dominant materialistic commitments of contemporary science, they could begin by recognizing that the organism itself manifests, in every aspect of its life, a presently acting wisdom. It does not contain machine-like devices, and does not require an engineer-designer who at various times in the past acted externally upon already given materials as human engineers do. https://bwo.life/org/comm/ar/2014/id-questions_19.htm https://bwo.life/org/comm/ar/2014/id-questions_19.htm Thu, 15 May 2014 14:30:00 GMT evolution/intelligent design machine-idea inwardness (intention, idea, meaning) mailto:stevet@netfuture.org The idea that the organism is a machine or consists of machine-like parts is a distortion of the truth so extreme and so contrary to what is immediately evident that we can only see it as a kind of collective aberration of the scientific mind https://bwo.life/org/comm/ar/2014/machines_18.htm https://bwo.life/org/comm/ar/2014/machines_18.htm Thu, 24 Apr 2014 14:30:00 GMT machine-idea machine-idea/code form/molecular mailto:stevet@netfuture.org Hox genes, often cited as "controllers" of organismal form, turn out to be dependent for their expression on the various factors that control THEIR spatial form in the nucleus. In a second paper, metabolism is proposed as a replacement for DNA at the head of important causal chains in the organism. And a special issue of the journal “Cell” looks for the unifying threads that make sense of the tidal waves of isolated data available to biologists today. Where can those threads be found, if not in the whole organism, as a unity, and not in any particular parts? In sum, as the feverish obsession with DNA as First Cause continues to lose its force, we may be seeing a long-delayed effort to understand the whole organism. https://bwo.life/org/comm/ar/2014/lit-notes1_17.htm https://bwo.life/org/comm/ar/2014/lit-notes1_17.htm Mon, 31 Mar 2014 14:30:00 GMT chromosome/dynamics gene/regulation form/organismal holism/contextual mailto:stevet@netfuture.org The remarkable discovery and investigation of “competing endogenous RNAs”, or ceRNAs, durings the past three years or so illustrates the challenge of biological explanation. If we are faithful to observation, we recognize that in the organism the larger pattern, or context, should, in the proper sense, be seen as the cause of the the part-processes through which the pattern comes to manifestation. This is the stumbling block for conventional scientists of a materialistic bent. Yet it turns out to be a truth that they implicitly accept and work with all the time. https://bwo.life/org/comm/ar/2014/rna-partners_16.htm https://bwo.life/org/comm/ar/2014/rna-partners_16.htm Tue, 11 Feb 2014 14:30:00 GMT RNA explanation/biological explanation/part and whole form/organismal holism inwardness (intention, idea, meaning) gene regulation evolution/as mindless process mailto:stevet@netfuture.org The way in which a cell’s identity depends on the micro-niche in which it is found raises questions of identity and context, organism and environment, self and world — fundamental questions arising throughout all of biology. Among these questions: When biologists speak of the organism’s activity, who exactly do they mean to say is performing that activity? When they acknowledge that something in the organism is context-dependent, what in fact is it dependent upon — what agency, or unified sphere of activity, or principle, or lawfulness, or other reality of any sort are they appealing to? They cannot be pointing merely to a particular collection of objects, because the collection can be endlessly varied or perturbed, and yet the context remains more or less coherent, and the organism more or less maintains its character. What is coherent? What has this character? https://bwo.life/org/comm/ar/2014/who-are-we_15.htm https://bwo.life/org/comm/ar/2014/who-are-we_15.htm Thu, 16 Jan 2014 14:30:00 GMT explanation/part and whole holism/contextual plasticity mailto:stevet@netfuture.org Organisms, from the bacterium to the human being, are, in one sense or another, reasoning agents; they pursue intentions and purposes, which may or may not be conscious. Reckoning with the distinction between conscious human intentions and the intentions at work in our bodies or in lower organisms is key to avoiding illegitimate use of psyche-related terms in biology. https://bwo.life/org/comm/ar/2013/bodily-wisdom-to-knowing-self_14.htm https://bwo.life/org/comm/ar/2013/bodily-wisdom-to-knowing-self_14.htm Thu, 05 Dec 2013 14:30:00 GMT explanation/biological inwardness (intention, idea, meaning) mailto:stevet@netfuture.org Transitions between different phases of matter (for example, from solid to semi-liquid to liquid, or from liquid to gel) are now being explored as fundamental organizing principles of the cell and as factors in the regulation of gene expression. Moreover, water, which plays a central role in so many phase transitions as well as in molecular binding, has been called a “biomolecule” — with good reason. https://bwo.life/org/comm/ar/2013/phases-of-life_13.htm https://bwo.life/org/comm/ar/2013/phases-of-life_13.htm Thu, 14 Nov 2013 14:30:00 GMT form/molecular gene regulation holism/organism as a “formed stream” machine idea/code protein mailto:stevet@netfuture.org The genetic code was supposed to carry the meaning of DNA. Of the many lines of emerging evidence showing that “code” is a misnomer, perhaps the least attention has been (at least until recently) been given to synonymous codons. They were supposed to be more or less equivalent, but they are now testifying in a loud voice about the inadequacies of the code idea. https://bwo.life/org/comm/ar/2013/genetic-synonyms-are-not-synonymous_12.htm https://bwo.life/org/comm/ar/2013/genetic-synonyms-are-not-synonymous_12.htm Thu, 24 Oct 2013 14:30:00 GMT DNA DNA/junk form/molecular gene regulation machine idea/code translation mailto:stevet@netfuture.org Among all its other personas, DNA is now showing signs of being used by the organism as an intercellular signaling molecule. Small DNA fragments can be moved from donor cells through the bloodstream and into recipient cells, where they can be incorporated into chromosomes and employed in the production of proteins — all with physiological consequences. https://bwo.life/org/comm/ar/2013/yet-another-face-of-dna_11.htm https://bwo.life/org/comm/ar/2013/yet-another-face-of-dna_11.htm Sun, 29 Sep 2013 14:30:00 GMT DNA signaling mailto:stevet@netfuture.org Both the proponents of intelligent design and the most antagonistic conventional biologists hold a remarkably similar set of assumptions. It is these that frame their disputes, and it is the letting go of the faulty assumptions that could lead to an overcoming of the disputes. https://bwo.life/org/comm/ar/2013/sectarian-quarrel_10.htm https://bwo.life/org/comm/ar/2013/sectarian-quarrel_10.htm Thu, 12 Sep 2013 14:30:00 GMT evolution/intelligent design evolution/as mindless process mailto:stevet@netfuture.org Human beings, it appears, often are genomic mosaics, with different cell populations having variously modified DNA. And the early embryo is a veritable incubator of sometimes drastically modified genomes. This points to yet another way the organism manages its own genome. https://bwo.life/org/comm/ar/2013/real-walter-gilbert_9.htm https://bwo.life/org/comm/ar/2013/real-walter-gilbert_9.htm Thu, 22 Aug 2013 14:30:00 GMT development genome/remodeling mailto:stevet@netfuture.org A one-celled organism that can patch back together its own genome even when it has been fragmented by radiation into a thousand pieces tells us a great deal about the functioning of living creatures in general. https://bwo.life/org/comm/ar/2013/shattering-the-genome_8.htm https://bwo.life/org/comm/ar/2013/shattering-the-genome_8.htm Fri, 02 Aug 2013 14:30:00 GMT gene/genocentrism genome/remodeling holism machine-idea mailto:stevet@netfuture.org Introduction to a collection of notes on gene regulation culled from the technical literature. Warning: you may find their impact overwhelming. https://bwo.life/org/comm/ar/2013/thousand-stranded-tapestry_7.htm https://bwo.life/org/comm/ar/2013/thousand-stranded-tapestry_7.htm Fri, 19 Jul 2013 14:30:00 GMT epigenetics gene regulation holism transcription mailto:stevet@netfuture.org Here is where you can access all previous articles from the Rediscovering Life service. https://bwo.life/org/comm/news.htm#archive https://bwo.life/org/comm/news.htm#archive Thu, 24 Apr 2014 14:30:00 GMT holistic biology whole organism biology genetics evolution epigenetics gene regulation> gene expression> holism versus mechanism meaning in biology and evolution mailto:stevet@netfuture.org