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Rethinking biology: What role does physical structure play in the development of cells?

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That’s structuralism, in part. Further to Evelyn Fox Keller’s comment that the landscape of biological thought is being “radically reconfigured,” a cancer geneticist writes to say that a tumor’s physical environment fuels its growth and causes treatment resistance:

The forces of cancer

In vitro experiments showing that cancer cells actively migrate in response to fluid flow have supported the hypothesis that fluid escaping from the boundary of a tumor may guide the invasive migration of cancer cells toward lymphatic or blood vessels, potentially encouraging metastasis. There remains controversy over how the fluid forces induce the migration; the cells may respond to chemical gradients created by the cells and distorted by the flowing fluid,8 or the fluid may activate cell mechanosensors. Because of the potential for new therapeutic interventions, the transduction of mechanical fluid forces into biochemical signals by cell mechanosensors is an active area of investigation. In a more direct manner, the fluid flow can physically carry cancer cells to lymph nodes.

And fluid pressure is just one of the many forces in a tumor that can influence its development and progression. Tumors also develop increased solid pressure, as compared with normal tissue, stemming from the uncontrolled division of cancer cells and from the infiltration and proliferation of stromal and immune cells from the surrounding tissue and circulation. High-molecular-weight polysaccharides known as hydrogels found in the extracellular matrix (ECM) also add pressure on a tumor. The most well-studied of these hydrogels is hyaluronan; when the polysaccharide absorbs water, it swells, pressing on surrounding cells and structural elements of the tissue. More. (The Scientist, April 1, 2016)

and

May the Force be with you

The dissection of how cells sense and propagate physical forces is leading to exciting new tools and discoveries in mechanobiology and mechanomedicine.

Of course, mechanical properties and forces aren’t just important in disease, but in health as well. Almost all living cells and tissues exert and experience physical forces that influence biological function. The magnitudes of those forces vary among different cell and tissue types, as do cells’ sensitivities to changes in magnitudes, frequencies, and durations of the forces. Touch, hearing, proprioception, and certain other senses are well-known examples of specialized force sensors. But force detection and sensing are not limited to these special cases; rather, they are shared by all living cells in all tissues and organs. The underlying mechanisms of force generation and detection are not well understood, however, leaving many open questions about force dynamics; the distance over which a force exerts its impact; and how cells convert mechanical signals into biochemical signals and changes in gene expression (The Scientist, February 1, 2017)More.

We may come to understand evolution better if we see what can and can’t happen in physics terms.

See also: Keller: Landscape of biological thought is being “radically reconfigured”

Comments
Neuromodulators are conserved across insect taxa, but how biogenic amines and their receptors in ancestral solitary forms have been co-opted to control behaviors in derived socially complex species is largely unknown. Synthesizing current findings that reveal potential ancestral roles of monoamines in insects, we identify physiological processes and conserved behaviors under aminergic control, consider how biogenic amines may have evolved to modulate complex social behavior, and present focal research areas that warrant further study.
Origins of Aminergic Regulation of Behavior in Complex Insect Social Systems J. Frances Kamhi,1,* Sara Arganda,2,3 Corrie S. Moreau,4 and James F. A. Traniello Front Syst Neurosci. 2017; 11: 74. doi: 10.3389/fnsys.2017.00074
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January 15, 2018
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[...] our candidate sets of genes for sterility form functional modules within the living bee brain's TRN. Moreover, these same gene sets colocate to a single, albeit large, region of the TRN's topology. This spatially organized and convergent pattern contrasts with a null expectation for functionally unrelated genes to be haphazardly distributed throughout the network. Our meta-genomic analysis therefore provides first evidence for a truly “social transcriptome” that may regulate the conditional expression of honeybee worker sterility.
Structure and function of gene regulatory networks associated with worker sterility in honeybees Julia A. Sobotka, Mark Daley, Sriram Chandrasekaran, Benjamin D. Rubin, Graham J. Thompson DOI: 10.1002/ece3.1997 Ecology and Evolution http://onlinelibrary.wiley.com/doi/10.1002/ece3.1997/epdf
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 15, 2018
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Cascades of transcriptional regulation are the common source of the forward drive in all developmental systems. Increases in complexity and specificity of gene expression at successive stages are based on the collaboration of varied combinations of transcription factors already expressed in the cells to turn on new genes, and the logical relationships between the transcription factors acting and becoming newly expressed from stage to stage are best visualized as gene regulatory networks. However, gene regulatory networks used in different developmental contexts underlie processes that actually operate through different sets of rules, which affect the kinetics, synchronicity, and logical properties of individual network nodes. Contrasting early embryonic development in flies and sea urchins with adult mammalian hematopoietic development from stem cells, major differences are seen in transcription factor dosage dependence, the silencing or damping impacts of repression, and the impact of cellular regulatory history on the parts of the genome that are accessible to transcription factor action in a given cell type. These different features not only affect the kinds of models that can illuminate developmental mechanisms in the respective biological systems, but also reflect the evolutionary needs of these biological systems to optimize different aspects of development.
Rothenberg, E.V. HPLS (2017) 39: 37. https://doi.org/10.1007/s40656-017-0164-z
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January 14, 2018
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This paper presents “optimal identification,” a framework for using experimental data to identify the optimality conditions associated with the feedback control law implemented in the measurements. The technique compares closed loop trajectory measurements against a reduced order model of the open loop dynamics, and uses linear matrix inequalities to solve an inverse optimal control problem as a convex optimization that estimates the controller optimality conditions. In this study, the optimal identification technique is applied to two examples, that of a millimeter-scale micro-quadrotor with an engineered controller on board, and the example of a population of freely flying Drosophila hydei maneuvering about forward flight. The micro-quadrotor results show that the performance indices used to design an optimal flight control law for a micro-quadrotor may be recovered from the closed loop simulated flight trajectories, and the Drosophila results indicate that the combined effect of the insect longitudinal flight control sensing and feedback acts principally to regulate pitch rate.
Faruque, I.A., Muijres, F.T., Macfarlane, K.M. et al. Biol Cybern (2018). https://doi.org/10.1007/s00422-017-0742-x
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 14, 2018
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The rich experiences of an intentional, goal-oriented life emerge, in an unpredictable fashion, from the basic laws of physics. Here I argue that this unpredictability is no mirage: there are true gaps between life and non-life, mind and mindlessness, and even between functional societies and groups of Hobbesian individuals. These gaps, I suggest, emerge from the mathematics of self-reference, and the logical barriers to prediction that self-referring systems present. Still, a mathematical truth does not imply a physical one: the universe need not have made self-reference possible. It did, and the question then is how. In the second half of this essay, I show how a basic move in physics, known as renormalization, transforms the "forgetful" second-order equations of fundamental physics into a rich, self-referential world that makes possible the major transitions we care so much about. While the universe runs in assembly code, the coarse-grained version runs in LISP, and it is from that the world of aim and intention grows.
Origin Gaps and the Eternal Sunshine of the Second-Order Pendulum Simon DeDeo https://scirate.com/arxiv/1712.03113
Parole, parole, parole... Where's the beef? The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 13, 2018
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It is an exciting time for research into life's origins. Both the origins of life and the search for life on other worlds will benefit from re-conceptualizing the nature of life, leading to new approaches and new progress on long-standing questions. [...] it will be up to an emerging community of scholars to develop these approaches into new frameworks, merging theory and experiment, to solve the problem of the origins of life and start the next chapter on one of the great open questions in science.
Re-conceptualizing the origins of life Sara I. Walker, N. Packard, G. D. Cody DOI: 10.1098/rsta.2016.0337 http://rsta.royalsocietypublishing.org/content/375/2109/20160337.full.pdf
Parole, parole, parole... Where's the beef? The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 13, 2018
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The origin of life is widely regarded as one of the most important open problems in science. It is also notorious for being one of the most difficult. [...] researchers have been able to generate nearly all components of living cells under different plausible scenarios for prebiotic environments. But, these ‘bottom-up’ approaches have not yet generated anything nearly as complex as a living cell. At most we are lucky to generate short polypeptides or polynucleotides or simple vesicles—a far cry from the complexity of anything living.
Re-conceptualizing the origins of life Sara I. Walker, N. Packard, G. D. Cody DOI: 10.1098/rsta.2016.0337 http://rsta.royalsocietypublishing.org/content/375/2109/20160337.full.pdf
Parole, parole, parole... Where's the beef? The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 13, 2018
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Over the last several hundred years of scientific progress, we have arrived at a deep understanding of the non-living world. We have not yet achieved an analogous, deep understanding of the living world. The origins of life is our best chance at discovering scientific laws governing life, because it marks the point of departure from the predictable physical and chemical world to the novel, history-dependent living world. This theme issue aims to explore ways to build a deeper understanding of the nature of biology, by modelling the origins of life on a sufficiently abstract level, starting from prebiotic conditions on Earth and possibly on other planets and bridging quantitative frameworks approaching universal aspects of life. The aim of the editors is to stimulate new directions for solving the origins of life. The present introduction represents the point of view of the editors on some of the most promising future directions.
Re-conceptualizing the origins of life Sara I. Walker, N. Packard, G. D. Cody DOI: 10.1098/rsta.2016.0337 http://rsta.royalsocietypublishing.org/content/375/2109/20160337.full.pdf
Parole, parole, parole... Where's the beef? The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 13, 2018
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Downward causation is the controversial idea that ‘higher’ levels of organization can causally influence behaviour at ‘lower’ levels of organization.
Coarse-graining as a downward causation mechanism Jessica C. Flack Phil. Trans. R. Soc. A375: 20160338. http://dx.doi.org/10.1098/rsta.2016.0338 http://rsta.royalsocietypublishing.org/content/375/2109/20160338.full.pdf
Parole, parole, parole... Where's the beef? The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 13, 2018
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[...] downward causation describes how information might cascade from higher-level components through lower levels. “The kind of computation performed and resultant output, and hence the detailed switching of transistors at the micro level, depends on the kind of programme loaded into the computer (word processor, music, or graphics for example) – a high level concept.” - (Ellis, 2008) [...] we can analyse our “system” of interest in three major levels (Marr, 1982): 1. Computational: what does the system do and why? 2. Algorithmic: how does the system is doing it? 3. Implementation: what is the structure of the system [...] mapping the structure of a system e.g., brain may not be the best option we have to understand its function. Computational neuroscience tries to work primarily not in the structural level but the algorithmic level.
Causality in Neuroscience, an Essay Kayson Fakhar DOI: 10.13140/RG.2.2.10215.55205 Biological Psychology Lab, Department of Psychology, European Medical School, Carl von Ossietzky University, Oldenburg, Germany, In Progress, https://www.researchgate.net/profile/Kayson_Fakhar2/publication/319987272_Causality_in_Neuroscience_an_Essay/links/59c51c68aca272c71bb8d58c/Causality-in-Neuroscience-an-Essay.pdf
Parole, parole, parole... Where's the beef? The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 13, 2018
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Origin of behaviours is one of the most puzzling issues in religions, philosophy and science. Complex systems cannot or hardly can be described and investigated as a unified single scale phenomenon. [...] the brain is a complex system, which can be investigated thoroughly in many levels of organization [...] components of each level have their own properties. These components interact [with] each other via various mechanisms and thus influencing other levels’ output. [...] there are differences between “levels of organisation” and the “levels of investigation”. The same categorisation is relevant for scientists, as a biochemist, one might be only interested in the interaction between molecules and measures the behaviour of a cell culture as a part of the brain. A problem of communication may arise here between scientists who are working on the same subject e.g., the brain.
Causality in Neuroscience, an Essay Kayson Fakhar DOI: 10.13140/RG.2.2.10215.55205 Biological Psychology Lab, Department of Psychology, European Medical School, Carl von Ossietzky University, Oldenburg, Germany, In Progress, https://www.researchgate.net/profile/Kayson_Fakhar2/publication/319987272_Causality_in_Neuroscience_an_Essay/links/59c51c68aca272c71bb8d58c/Causality-in-Neuroscience-an-Essay.pdf
Parole, parole, parole... Where's the beef? The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 13, 2018
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A reliable understanding of the nature or causation is the core feature of science. [...] top-down causation changes the nature of the lower elements. There is not just a situation of invariant lower level elements obeying physical laws; rather we have the nature of lower level elements being changed by context. Often the way this occurs ensures that the way the lower level elements obey physical laws fulfils higher level purposes. This is then an aspect of adaptive selection.
ON THE NATURE OF CAUSATION IN COMPLEX SYSTEMS George F R Ellis http://www.newdualism.org/papers/G.Ellis/RSSA2008.pdf
Where's the beef? The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 13, 2018
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UD is publicly presented as an ID website, hence ID topics should be discussed. And these days I think the main ID topic is biology research, where real complex functionally specified informational complexity is increasingly being revealed by dedicated scientists using more sophisticated technologies that allow the wet lab researchers to peek deeper within the biological systems “in vivo”, dumping an avalanche of data on the cloud servers for many dry lab researchers to process it using better computer systems and algorithms. Multilayered controls within marvelously designed biological systems are leaving researchers speechless. Multidisciplinary research teams are working hard in many scientific institutions trying to understand all that functional complexity. As outstanding questions get answered, new ones are raised. It’s beyond fantastic. But we ain’t seen nothing yet. The most fascinating discoveries are still ahead. The noise we’re hearing is just the cacophony produced by the orchestra musicians tuning their individual instruments separately. That’s why we read so many times expressions like “surprisingly” and “unexpectedly” in the research papers. That’s the result of their narrow-minded reductionist bottom-up research approach. But that’s most of the information available to us today, so we have to use it in our studies. We haven’t heard the orchestra playing the most wonderful symphony yet. The curtains are not quite open. The beautiful biological ballet choreography hasn’t been displayed with all its splendor. All that is still ahead. We should encourage more young students who like science to consider pursuing biology-related research careers. Then they’ll enjoy seeing true wonders beyond anything they ever imagined.Dionisio
January 12, 2018
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It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering.
Top-down models in biology: explanation and control of complex living systems above the molecular level Giovanni Pezzulo, Michael Levin J. R. Soc. Interface 2016 13 20160555; DOI: 10.1098/rsif.2016.0555 http://rsif.royalsocietypublishing.org/content/13/124/20160555
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 11, 2018
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[...] the consequence of altered Hippo signaling in specific tissues on whole-body physiology, and the effect of such changes upon disease progression remains unexplored. Future studies aimed at understanding the integrative nature of the Hippo pathway on human physiology will be required to reveal the extent that this pathway influences biological function and the implications of targeting this pathway for clinical benefit.
Watt KI, Harvey KF and Gregorevic P (2017) Regulation of Tissue Growth by the Mammalian Hippo Signaling Pathway. Front. Physiol. 8:942. doi: 10.3389/fphys.2017.00942
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 11, 2018
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Genetic elements compete for transmission through meiosis, when haploid gametes are created from a diploid parent. Selfish elements can enhance their transmission through a process known as meiotic drive. In female meiosis, selfish elements drive by preferentially attaching to the egg side of the spindle. This implies some asymmetry between the two sides of the spindle, but the molecular mechanisms underlying spindle asymmetry are unknown. Here we found that CDC42 signaling from the cell cortex regulated microtubule tyrosination to induce spindle asymmetry and that non-Mendelian segregation depended on this asymmetry. Cortical CDC42 depends on polarization directed by chromosomes, which are positioned near the cortex to allow the asymmetric cell division. Thus, selfish meiotic drivers exploit the asymmetry inherent in female meiosis to bias their transmission.
Spindle asymmetry drives non-Mendelian chromosome segregation Takashi Akera1, Lukáš Chmátal1, Emily Trimm1, Karren Yang1, Chanat Aonbangkhen2, David M. Chenoweth2, Carsten Janke3,4, Richard M. Schultz1, Michael A. Lampson Science 03 Nov 2017: Vol. 358, Issue 6363, pp. 668-672 DOI: 10.1126/science.aan0092
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 11, 2018
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The vast majority of eukaryotes have two copies of each chromosome and reproduce sexually. Meiosis is a vital process that produces gametes (eggs and sperm) by reducing the number of chromosome copies to one; fertilization between egg and sperm restores the chromosome copy number to two. During female meiosis, one set of chromosomes is expelled into a tiny cell called a polar body, whereas the other is segregated into the egg. It is a fundamental tenet of genetics that there is a random, 50% chance for any particular chromosome to be segregated into the egg versus the polar body. However, cases in which one copy of a chromosome is inherited with greater than 50% frequency have been reported in many species (1), but the molecular mechanism of this preferential inheritance has remained obscure. Recent work has indicated that centromeres, the chromosomal regions that form attachments to microtubules that mediate chromosome segregation during meiosis, compete with each other for inheritance during female meiosis (2). Thus, the essential DNA sequences that mediate accurate chromosome segregation are actually “selfish” (or parasitic) genetic elements that have invaded our genome. On page 668 of this issue, Akera et al. (3) provide the most detailed molecular mechanism to date that explains how a parasitic DNA sequence has used the asymmetry of oocyte meiosis to ensure its own inheritance and therefore its spread through populations. http://www.sciencemag.org/about/science-licenses-journal-article-reuse
Competing chromosomes explain junk DNA Francis J. McNally Science 03 Nov 2017: Vol. 358, Issue 6363, pp. 594-595 DOI: 10.1126/science.aaq0200
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 11, 2018
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Guided by biological curiosity, exploratory bioinformatics analysis of the single-cell RNA-seq and related data yields many actionable insights. One of the surprising observations is that genes with similar expression patterns in early embryogenesis share specific transposons in their promoters. During ZGA, while LTRs are linked to transient, forceful and early induction of several hundred genes, SINE elements are associated with the upregulation of thousands of essential genes. The machinery that transcribes retro-transposons may also be used to establish the expression landscape of early embryos.
Exploratory bioinformatics investigation reveals importance of “junk” DNA in early embryo development Steven Xijin Ge BMC Genomics 2017 18:200 https://doi.org/10.1186/s12864-017-3566-0
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 11, 2018
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Data from the literature suggest that lncRNA, often via interaction with proteins, functions in specific genomic loci or use their own transcription loci for regulatory activity. In this review, we summarize recent findings supporting the importance of DNA loci in lncRNA function and the underlying molecular mechanisms via cis or trans regulation, and discuss their implications in cancer. In addition, we use the 8q24 genomic locus, a region containing interactive SNPs, DNA regulatory elements and lncRNAs, as an example to illustrate how single-nucleotide polymorphism (SNP) located within lncRNAs may be functionally associated with the individual’s susceptibility to cancer.
Junk DNA and the long non-coding RNA twist in cancer genetics H Ling, K Vincent, M Pichler, R Fodde, I Berindan-Neagoe, F J Slack & G A Calin Oncogene 34, 5003–5011 doi:10.1038/onc.2014.456
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 11, 2018
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The central dogma of molecular biology states that the flow of genetic information moves from DNA to RNA to protein. However, in the last decade this dogma has been challenged by new findings on non-coding RNAs (ncRNAs) such as microRNAs (miRNAs). More recently, long non-coding RNAs (lncRNAs) have attracted much attention due to their large number and biological significance. Many lncRNAs have been identified as mapping to regulatory elements including gene promoters and enhancers, ultraconserved regions and intergenic regions of protein-coding genes. Yet, the biological function and molecular mechanisms of lncRNA in human diseases in general and cancer in particular remain largely unknown.
Junk DNA and the long non-coding RNA twist in cancer genetics H Ling, K Vincent, M Pichler, R Fodde, I Berindan-Neagoe, F J Slack & G A Calin Oncogene 34, 5003–5011 doi:10.1038/onc.2014.456
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 11, 2018
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Many regions of the genome replicate asynchronously and are expressed monoallelically. It is thought that asynchronous replication may be involved in choosing one allele over the other, but little is known about how these patterns are established during development. We show that, unlike somatic cells, which replicate in a clonal manner, embryonic and adult stem cells are programmed to undergo switching, such that daughter cells with an early-replicating paternal allele are derived from mother cells that have a late-replicating paternal allele. Furthermore, using ground-state embryonic stem (ES) cells, we demonstrate that in the initial transition to asynchronous replication, it is always the paternal allele that is chosen to replicate early, suggesting that primary allelic choice is directed by preset gametic DNA markers. Taken together, these studies help define a basic general strategy for establishing allelic discrimination and generating allelic diversity throughout the organism.
Programming asynchronous replication in stem cells Hagit Masika, Marganit Farago, Merav Hecht, Reba Condiotti, Kirill Makedonski, Yosef Buganim, Tal Burstyn-Cohen, Yehudit Bergman & Howard Cedar Nature Structural & Molecular Biology 24, 1132–1138 (2017) doi:10.1038/nsmb.3503
embryonic and adult stem cells are programmed to undergo switching are programmed? how? The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 11, 2018
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Assembly of the small ribosomal subunit from an RNA strand and 33 proteins is an intricate and dynamic process. Two cryo-EM studies now provide insight into a complicated complex of at least 51 trans-factors that act on the preribosomal small subunit to sequentially fold it into a 3D molecular machine.
Ribosome origami Joanna Rorbach, Shintaro Aibara & Alexey Amunts Cryoelectron microscopy, Ribosome, RNA folding Nature Structural & Molecular Biology 24, 879–881 (2017) doi:10.1038/nsmb.3497
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January 11, 2018
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Deadenylation of mRNAs is generally associated with translational inhibition and mRNA decay. A study now reports that, unexpectedly, highly expressed genes tend to have shorter poly(A) tails and suggests that poly(A) tails can be 'pruned', generating a 30-nucleotide-biased phased distribution, likely due to protection by poly(A)-binding proteins.
Poly(A) tails: longer is not always better Luciana A Castellano & Ariel A Bazzini Nature Structural & Molecular Biology 24, 1010–1011 (2017) doi:10.1038/nsmb.3509
unexpectedly? The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 11, 2018
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The helicase intrinsic to DNA polymerase ? (Pol?), the versatile mediator of microhomology-based repair of DNA double-strand breaks and stalled replication forks, is now revealed to be a member of an elite group of proteins known as annealing helicases. This small family of enzymes remodels DNA intermediates in multiple repair processes that are crucial to preserving genome stability and warding off cancer and aging.
Pol? helicase: drive or reverse Judith L Campbell & Hongzhi Li Nature Structural & Molecular Biology 24, 1007–1008 (2017) doi:10.1038/nsmb.3510
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 11, 2018
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During protein synthesis, mRNA and tRNAs must be moved rapidly through the ribosome while maintaining the translational reading frame. This process is coupled to large- and small-scale conformational rearrangements in the ribosome, mainly in its rRNA. The free energy from peptide-bond formation and GTP hydrolysis is probably used to impose directionality on those movements. We propose that the free energy is coupled to two pawls, namely tRNA and EF-G, which enable two ratchet mechanisms to act separately and sequentially on the two ribosomal subunits.
The ribosome moves: RNA mechanics and translocation Harry F Noller, Laura Lancaster, Jie Zhou & Srividya Mohan Nature Structural & Molecular Biology 24, 1021–1027 (2017) doi:10.1038/nsmb.3505
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 11, 2018
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So we conclude chemotaxis of myxomycetes represents a clear comparative example of how certain fundamental capabilities for the origin of cognition may arise in the minimum living systems, and how this is possible only through the action of regulatory mechanisms. It is only in the presence of regulation that specific disturbances acquire a meaning for the system. This becomes, thus, a biosemiotic foundation of the basics of cognitive minimum principles by which emerging regulatory system factors acquire those minimum principles offered in cognitive biology [...] [...] slime mould provides an insightful example of a biosemiotic entity able to perform cognitive tasks and to explain the first steps from mechanistic automation to decision, as well as of coordination and cooperation, and also an ideal testbed for consciousness as a minimal conscious biological organism. [...] the slime mould perceives its world in parallel, process the information perceived concurrently, makes decisions in a decentralised manner and represents the decision, or results of the computation, in spatially distributed configuration of its protoplasmic tubes; the tubes configuration per se might act a program, [...]
Slime mould: the fundamental mechanisms of biological cognition Jordi Vallverd´ua, Oscar Castroa, Richard Maynec, Max Talanovb, Michael Levinf, Frantisek Balu?skae, Yukio Gunjid, Audrey Dussutourg, Hector Zenilh, Andrew Adamatzkyc https://www.researchgate.net/publication/321488794 December 2017 DOI: 10.13140/RG.2.2.14221.84969
Where's the beef? The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
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One of the long-standing mysteries of evolutionary genomics is the source of the wide phylogenetic diversity in genome nucleotide composition (G?+?C versus A?+?T), which must be a consequence of interspecific differences in mutation bias, the efficiency of selection for different nucleotides or a combination of the two. [...] although genomic G?+?C composition is strongly driven by mutation bias, it is also substantially modified by direct selection and/or as a by-product of biased gene conversion. Moreover, G?+?C composition at fourfold redundant sites is consistently elevated above the neutral expectation—more so than for any other class of sites.
Evolutionary determinants of genome-wide nucleotide composition Hongan Long, Way Sung, Sibel Kucukyildirim, Emily Williams, Samuel F. Miller, Wanfeng Guo, Caitlyn Patterson, Colin Gregory, Chloe Strauss, Casey Stone, Cécile Berne, David Kysela, William R. Shoemaker, Mario E. Muscarella, Haiwei Luo, Jay T. Lennon, Yves V. Brun & Michael Lynch Nature Ecology & Evolution (2018) doi:10.1038/s41559-017-0425-y
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 11, 2018
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Despite much progress, many questions remain. Elucidating the components and operation of the transcriptional networks continues and, for many tissues, the relative importance of the spatial or temporal component of gradients needs to be determined. How opposing gradients cross-talk and are integrated into networks is poorly understood.
Morphogen rules: design principles of gradient-mediated embryo patterning James Briscoe, Stephen Small Development 2015 142: 3996-4009; doi: 10.1242/dev.129452 http://dev.biologists.org/content/142/23/3996.full.pdf
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 9, 2018
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Further investigations will be necessary to gain a better molecular understanding of the various mechanisms and the contributions that they make in each tissue. [...] positional information is not a static measure but a process that arises from the dynamics of interactions within the network. [...] boundary precision and size scaling are built into the system. The system is robust to fluctuations in the morphogen signal and provides an effective memory when morphogen signal declines [...]
Morphogen rules: design principles of gradient-mediated embryo patterning James Briscoe, Stephen Small Development 2015 142: 3996-4009; doi: 10.1242/dev.129452 http://dev.biologists.org/content/142/23/3996.full.pdf
The known -not the unknown- clearly points to complex functionally specified informational complexityDionisio
January 9, 2018
January
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2018
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