Mystery at the heart of life

_{Denyse O'Leary

December 21, 2014

Cell biology, Intelligent Design, News}

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By Biologic Institute’s Ann Gauger, at Christianity Today’s Behemoth, the secret life of cells:

Our bodies are made up of some 100 trillion cells. We tend to think of cells as static, because that’s how they were presented to us in textbooks. In fact, the cell is like the most antic, madcap, crowded (yet fantastically efficient) city you can picture. And at its heart lies a mystery—or I should say, several mysteries—involving three special kinds of molecules: DNA, RNA, and proteins.

These molecules are assembled into long chains called polymers, and are uniquely suited for the roles they play. More importantly, life absolutely depends upon them. We have to have DNA, RNA, and protein all present and active at the same time for a living organism to live.

How they work together so optimally and efficiently is not merely amazing, but also a great enigma, a mystery that lies at the heart of life itself. More. Paywall soon after. May be worth it.

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Comments

The ability to recognize close kin confers survival benefits on single-celled microbes that live in complex and changing environments. Microbial kinship detection relies on perceptible cues that reflect relatedness between individuals, although the mechanisms underlying recognition in natural populations remain poorly understood. We hypothesize that the malleable property of TraA has allowed it to evolve and create social barriers between myxobacterial populations and in turn avoid adverse interactions with relatives.
Self-identity reprogrammed by a single residue switch in a cell surface receptor of a social bacterium. Cao P, Wall D Proc Natl Acad Sci U S A. 114(14):3732-3737. doi: 10.1073/pnas.1700315114.

Where's the beef? complex complexity.Dionisio_{July 3, 2017
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[...] we speculate that the maintenance of background biophotonic emissions may play a role in biophotonic energy storage in particular molecules such as proteins that may be involved in biophotonic signal transmission and encoding (action biophotons).
Reply to Salari et al.: Toward understanding the deep mechanisms regarding the biophotons related to human intelligence. Dai J1, Wang Z2, Li Z2, Xiao F3. Proc Natl Acad Sci U S A. 113(38):E5542-3. doi: 10.1073/pnas.1613416113.

Did somebody say "speculate"? :) Isn't that what Darwin did many years ago? Well, apparently he did worse than just speculating, because he grossly extrapolated the built-in variability framework seen in the biological systems and made up the so-called "evo theory" which is just a bunch of archaic pseudoscientific nonsensical daydreams worth much less than the ink that has been wasted to print it. complex complexity.Dionisio_{July 1, 2017
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We would like to thank Salari et al. for their interest in our paper (1) and to give a response to their concerns on the causation of spectral redshift of biophotons related to human intelligence (2). First, it is inappropriate to consider a brain slice (or whole brain) as a single light source to calculate the coherence length because a brain slice contains different types of neurons.
Reply to Salari et al.: Toward understanding the deep mechanisms regarding the biophotons related to human intelligence. Dai J1, Wang Z2, Li Z2, Xiao F3. Proc Natl Acad Sci U S A. 113(38):E5542-3. doi: 10.1073/pnas.1613416113.

OK, but please don't argue. Be nice to each other. :) complex complexity.Dionisio_{July 1, 2017
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[...] we believe that the experimental results presented do not directly support their conclusion. [...] the observed correlation does not reflect a causal relationship but rather an accidental coincidence. [...] the claim that the inhibition of PP2A induces the hyperphosphorylation of MAP tau and interferes with the function of microtubules is highly speculative.
Relationship between intelligence and spectral characteristics of brain biophoton emission: Correlation does not automatically imply causation Vahid Salari,a,b István Bókkon,c,d Roohollah Ghobadi,b,e,f Felix Scholkmann,g,h and Jack A. Tuszynski Proc Natl Acad Sci U S A. 113(38): E5540–E5541. doi: 10.1073/pnas.1612646113

Work in progress... stay tuned. :) complex complexity.Dionisio_{July 1, 2017
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Despite enormous efforts, any correlation between “intelligence” and cognitive or physiological/anatomical properties of animal brains is still poorly understood because intelligence depends on multiple factors in parallel and not a single determinant [...]
Relationship between intelligence and spectral characteristics of brain biophoton emission: Correlation does not automatically imply causation Vahid Salari,a,b István Bókkon,c,d Roohollah Ghobadi,b,e,f Felix Scholkmann,g,h and Jack A. Tuszynski Proc Natl Acad Sci U S A. 113(38): E5540–E5541. doi: 10.1073/pnas.1612646113

complex complexity.Dionisio_{July 1, 2017
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If optical communication along myelinated axons is indeed a reality, this would reveal a whole new aspect of the brain, with potential impacts on many fundamental questions in neuroscience.
Possible existence of optical communication channels in the brain Sourabh Kumar,1 Kristine Boone,1 Jack Tuszy?ski,2,3 Paul Barclay,1,4 and Christoph Simon Sci Rep. 6: 36508. doi: 10.1038/srep36508

complex complexity.Dionisio_{June 29, 2017
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[...] many fundamental questions in neuroscience are still open [...] The human brain is a dynamic physical system of unparalleled complexity. [...] many fundamental questions are still unanswered, including the processes underlying memory formation, the working principle of anesthesia, and–most fundamentally–the generation of conscious experience.
Possible existence of optical communication channels in the brain Sourabh Kumar,1 Kristine Boone,1 Jack Tuszy?ski,2,3 Paul Barclay,1,4 and Christoph Simon Sci Rep. 6: 36508. doi: 10.1038/srep36508

complex complexity.Dionisio_{June 27, 2017
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Cis-regulatory elements, such as promoters, enhancers and silencers, are involved in determining the spatio-temporal patterns of gene expression. [...] it could be hypothesized that the binding site in ICR3 likely represents a holder platform for a Fox pioneer factor inducing both early specific neurogenic activation and later expression maintenance.
An Intronic cis-Regulatory Element Is Crucial for the Alpha Tubulin Pl-Tuba1a Gene Activation in the Ciliary Band and Animal Pole Neurogenic Domains during Sea Urchin Development Salvatore Costa,#1 Aldo Nicosia,#2 Angela Cuttitta,2 Fabrizio Gianguzza,1 and Maria Antonietta Ragusa PLoS One. 12(1): e0170969. doi: 10.1371/journal.pone.0170969

complex complexity.Dionisio_{June 25, 2017
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For many years it was thought that [...] This study, as well as recent studies [...] challenge this idea.
An anterior signaling center patterns and sizes the anterior neuroectoderm of the sea urchin embryo. Range RC, Wei Z Development. 143(9):1523-33. doi: 10.1242/dev.128165.

we've seen that happen before, haven't we? complex complexity.Dionisio_{June 22, 2017
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[...] sFRP1/5 and Dkk3 diffuse extracellularly in an anterior-to-posterior gradient and Wnt1 and Wnt8 in a posterior-to-anterior gradient and both gradients work in concert to restrict the ANE around the anterior pole.
An anterior signaling center patterns and sizes the anterior neuroectoderm of the sea urchin embryo. Range RC, Wei Z Development. 143(9):1523-33. doi: 10.1242/dev.128165.

how is such a spatiotemporal mechanism established and activated? complex complexity.Dionisio_{June 22, 2017
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The exact mechanism by which sFRP1/5 either promotes or antagonizes Fzl5/8-JNK signaling is unclear.
An anterior signaling center patterns and sizes the anterior neuroectoderm of the sea urchin embryo. Range RC, Wei Z Development. 143(9):1523-33. doi: 10.1242/dev.128165.

exact mechanism? Oops! they used the same 'tricky' word 'exact' that the Canadian biochemistry professor didn't notice in a question I asked a couple of years ago. Apparently that tricky word made my question dishonest. Should we say that the above quoted statement is also dishonest? :) complex complexity.Dionisio_{June 22, 2017
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[...] the signaling pathways that mediate ANE positioning depend on positive inputs from both primary poles of the embryo.
An anterior signaling center patterns and sizes the anterior neuroectoderm of the sea urchin embryo. Range RC, Wei Z Development. 143(9):1523-33. doi: 10.1242/dev.128165.

hmm... that seems like an 'AND' logic gate, doesn't it? complex complexity.Dionisio_{June 22, 2017
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Taken together, these studies make it tempting to speculate that signaling centers that are active around the opposite pole to that of high Wnt/?-catenin signaling along the primary axis might be an ancient developmental mechanism essential for eumetazoan (cnidarians and bilaterians) body axis specification and patterning.
An anterior signaling center patterns and sizes the anterior neuroectoderm of the sea urchin embryo. Range RC, Wei Z Development. 143(9):1523-33. doi: 10.1242/dev.128165.

tempting to speculate? hmm... complex complexity.Dionisio_{June 22, 2017
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[...] FoxQ2 initiates an anterior patterning center that implements correct size and positions of ANE structures. [...] the sea urchin embryo uses an ancient anterior patterning system that was present in the common ambulacrarian/chordate ancestor.
An anterior signaling center patterns and sizes the anterior neuroectoderm of the sea urchin embryo. Range RC, Wei Z Development. 143(9):1523-33. doi: 10.1242/dev.128165.

how does FoxQ2 initiate an anterior patterning center? how does the anterior patterning center implement correct size and positions of ANE structures? how did this "patterning system" appear in the common ambulacrarian/chordate ancestor? complex complexity.Dionisio_{June 22, 2017
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[...] researchers within systems biology reintroduce the quest for design principles through mathematical and computational modeling of biological ‘big data’. I have argued for a unifying role of general principles, exemplified through case studies in systems biology where researchers identify design principles. Design principles signify general dependency relations between biological structures and functions through formally defined constraints. General principles address a different type of question. Biologists may ask which network designs can possibly afford the type of robustness observed in biological systems, or why some logically possible phenotypic patterns are not realized in any real-world biological system.
Node-based differential network analysis in genomics Xiao-Fei Zhang, Le Ou-Yang, Hong Yanc DOI: 10.1016/j.compbiolchem.2017.03.010 Computational biology and chemistry

Did somebody say "design"? Complex complexity.Dionisio_{June 20, 2017
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[...] EMFs form a distinct subgroup of multifunctional proteins exhibiting characteristics that distinguish them from hubs, classical multifunctional proteins and the network in general and can pave the way towards a better understanding of protein moonlighting.
Extreme multifunctional proteins identified from a human protein interaction network Charles E. Chapple,1,2 Benoit Robisson,1,2 Lionel Spinelli,1,2,3,4,5 Céline Guien,1,2,* Emmanuelle Becker,1,2,† and Christine Bruna Nat Commun. 6: 7412. doi: 10.1038/ncomms8412

Complex complexity.Dionisio_{June 19, 2017
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Protein multifunctionality may be one of the ways a cell makes more with less. That ELMs (i) can bind competitively or sequentially to different interaction partners in a context-dependant manner, (ii) provide a large panoply of conditional regulatory types through interactions19 and (iii) are more numerous in EMFs, provides a possible molecular explanation of the functional versatility of these proteins. This clearly calls for further studies.
Extreme multifunctional proteins identified from a human protein interaction network Charles E. Chapple,1,2 Benoit Robisson,1,2 Lionel Spinelli,1,2,3,4,5 Céline Guien,1,2,* Emmanuelle Becker,1,2,† and Christine Bruna Nat Commun. 6: 7412. doi: 10.1038/ncomms8412

Complex complexity.Dionisio_{June 18, 2017
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Revisiting generality in biology: systems biology and the quest for design principles Biology and Philosophy 30(5) DOI: 10.1007/s10539-015-9496-9 Sara GreenDionisio_{June 11, 2017
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Error in author's name @3450: The correct name is Sara GreenDionisio_{June 11, 2017
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one can easily tell they're struggling with the issue: Extracting Phenomena, Integrating Explanations, and Styling Representations: Some Frontiers for Philosophizing About Biology Nicholaos Jones Chapter · December 2017 DOI: 10.1007/978-3-319-47000-9_14 In book: Philosophy of Systems Biology, pp.147-156Dionisio_{June 11, 2017
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A common reductionist assumption is that macro-scale behaviors can be described “bottom-up” if only sufficient details about lower-scale processes are available. The view that an “ideal” or “fundamental” physics would be sufficient to explain all macro-scale phenomena has been met with criticism from philosophers of biology. Specifically, scholars have pointed to the impossibility of deducing biological explanations from physical ones, and to the irreducible nature of distinctively biological processes such as gene regulation and evolution. This paper takes a step back in asking whether bottom-up modeling is feasible even when modeling simple physical systems across scales. By comparing examples of multi-scale modeling in physics and biology, we argue that the “tyranny of scales” problem presents a challenge to reductive explanations in both physics and biology. The problem refers to the scale-dependency of physical and biological behaviors that forces researchers to combine different models relying on different scale-specific mathematical strategies and boundary conditions. Analyzing the ways in which different models are combined in multi-scale modeling also has implications for the relation between physics and biology. Contrary to the assumption that physical science approaches provide reductive explanations in biology, we exemplify how inputs from physics often reveal the importance of macro-scale models and explanations. We illustrate this through an examination of the role of biomechanical modeling in developmental biology. In such contexts, the relation between models at different scales and from different disciplines is neither reductive nor completely autonomous, but interdependent.
Biology meets physics: Reductionism and multi-scale modeling of morphogenesis Sara Greena, Robert Batterman https://doi.org/10.1016/j.shpsc.2016.12.003 Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences Volume 61, February 2017, Pages 20–34

Complex complexity.Dionisio_{June 10, 2017
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It would be interesting to investigate whether decreased CDK1/Cyclin A coordinates this switch in attachment stability at the prometaphase to metaphase transition with the re-activation of PP1 and consequently with SAC silencing. This could explain how PP1 switches off the SAC despite elevated Cyclin B levels in early metaphase.
Protein Phosphatase 1 inactivates Mps1 to ensure efficient Spindle Assembly Checkpoint silencing Margarida Moura,1,2,† Mariana Osswald,1,2,† Nelson Leça,1,2 João Barbosa,1,2 António J Pereira,1,2 Helder Maiato,1,2,3 Claudio E Sunkel,1,2,4,* and Carlos Condi eLife. 2017; 6: e25366. doi: 10.7554/eLife.25366

Complex complexityDionisio_{June 10, 2017
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Despite the rekindled interest in this century-old idea, the concept of cell assembly still remains ill-defined and its operational principle is poorly understood.
Theory of Connectivity: Nature and Nurture of Cell Assemblies and Cognitive Computation. Li M1, Liu J2, Tsien JZ Front Neural Circuits. 10:34. doi: 10.3389/fncir.2016.00034.

Complex complexity.Dionisio_{June 4, 2017
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Further testing of this power-of-two-based logic in additional neural circuits and animal species will be highly desirable, and exploring its applications in general artificial intelligence systems can also be informative. Collectively, such efforts will likely lead to a better understanding of how the brain’s logic is organized in specific circuits and how various other rules and properties might be integrated [...]
Brain Computation Is Organized via Power-of-Two-Based Permutation Logic Kun Xie,1,2,† Grace E. Fox,1,† Jun Liu,1,2,† Cheng Lyu,3,4,† Jason C. Lee,1,† Hui Kuang,1,† Stephanie Jacobs,1 Meng Li,1,2 Tianming Liu,3 Sen Song,5 and Joe Z. Tsien Front Syst Neurosci. 10: 95. doi: 10.3389/fnsys.2016.00095

Unfortunately this otherwise good paper does contain some text that is archaic pseudoscientific hogwash. Work in progress... stay tuned. Complex complexity.Dionisio_{June 4, 2017
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Perhaps it will be best approached by studying in simpler organisms (drosophila larvae) in which structural connectivity and functional imaging can be better analyzed [...] [...] further testing in the koniocortex and motor cortex, which have six-layered cortices, will be necessary. It will also be crucial to examine whether and how this logic operates [...] [...] it will be of considerable interest to examine how environmental and emotional contexts (including habituation vs. novelty) might affect cell-assembly response patterns in neural circuits.
Brain Computation Is Organized via Power-of-Two-Based Permutation Logic Kun Xie,1,2,† Grace E. Fox,1,† Jun Liu,1,2,† Cheng Lyu,3,4,† Jason C. Lee,1,† Hui Kuang,1,† Stephanie Jacobs,1 Meng Li,1,2 Tianming Liu,3 Sen Song,5 and Joe Z. Tsien Front Syst Neurosci. 10: 95. doi: 10.3389/fnsys.2016.00095

Unfortunately this otherwise good paper does contain some text that is archaic pseudoscientific hogwash. Work in progress... stay tuned. Complex complexity.Dionisio_{June 4, 2017
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Extending the similar multi-categorical investigations to other modulatory neuron types (such as serotonin, adrenergic or cholinergic neurons) will be necessary and informative. It will be of great interest to examine how neural ontogeny and circuit development lead to such a remarkably deterministic blueprint [...] It is widely believed that functional selectivity reflects the underlying structural connectivity. Although the specific-to-general coding patterns suggest their underlying wiring logic, the direct evidence for such wiring patterns awaits future demonstration.
Brain Computation Is Organized via Power-of-Two-Based Permutation Logic Kun Xie,1,2,† Grace E. Fox,1,† Jun Liu,1,2,† Cheng Lyu,3,4,† Jason C. Lee,1,† Hui Kuang,1,† Stephanie Jacobs,1 Meng Li,1,2 Tianming Liu,3 Sen Song,5 and Joe Z. Tsien Front Syst Neurosci. 10: 95. doi: 10.3389/fnsys.2016.00095

Work in progress... stay tuned. Complex complexity.Dionisio_{June 4, 2017
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[...] it has long been recognized that there is a need to establish the basic computational frameworks that may underlie the brain’s functions [...] The human brain is estimated to have approximately 86 billion neurons [...] and each neuron has tens of thousands of synapses [...] leading to over one hundred trillion synaptic connections. On top of this astronomical complexity, one needs to map each connection or neuron to a given stimulus, yet possible numbers of stimuli that can be used are infinite given the complex, ever-changing nature of the world we live in. Adding yet another layer of complexity to this seemingly hopeless situation are the well-known variations in the number of neurons, axonal/dendritic branches and synapses—not only over the course of development and aging, but also across individual brains and animal species.
Brain Computation Is Organized via Power-of-Two-Based Permutation Logic Kun Xie,1,2,† Grace E. Fox,1,† Jun Liu,1,2,† Cheng Lyu,3,4,† Jason C. Lee,1,† Hui Kuang,1,† Stephanie Jacobs,1 Meng Li,1,2 Tianming Liu,3 Sen Song,5 and Joe Z. Tsien Front Syst Neurosci. 10: 95. doi: 10.3389/fnsys.2016.00095

Complex complexity.Dionisio_{June 3, 2017
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This same paper has been referenced @523 & 1412-1413: Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications Karl J. Niklas, Sarah E. Bondos, A. Keith Dunker and Stuart A. Newman Front. Cell Dev. Biol., http://dx.doi.org/10.3389/fcell.2015.00008 http://journal.frontiersin.org/article/10.3389/fcell.2015.00008/full#h1Dionisio_{June 1, 2017
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Two approaches have been shown to decrease inter-sister kinetochore distances in old oocytes: first, increasing the oocyte levels of Mps1 to strengthen the SAC during MI exit and secondly, restoring the levels of securin to enhance separase inhibition in MII oocytes. [...] restoring securin levels or overexpressing Mps1 partially reverses the inter-sister kinetochore distance and decreases the frequency of premature sister chromatid separation (PSCS). These approaches both improve cohesion but they target the same pathway so are unlikely to be additive. However, combining one of these approaches with increasing Sgo2 to increase protection of centromeric cohesin may provide a highly effective combinatorial approach to improving the fidelity of chromosome number of oocytes in cases of advanced maternal age.
Maternal age-dependent APC/C-mediated decrease in securin causes premature sister chromatid separation in meiosis II Ibtissem Nabti, Rosanna Grimes, Hema Sarna, Petros Marangos & John Carroll Nature Communications 8, Article number: 15346 (2017) doi:10.1038/ncomms15346 https://www.nature.com/articles/ncomms15346

Had we stayed in Eden, none of this would have been an issue. Complex complexity.Dionisio_{May 30, 2017
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Sister chromatid attachment during meiosis II (MII) is maintained by securin-mediated inhibition of separase. In maternal ageing, oocytes show increased inter-sister kinetochore distance and premature sister chromatid separation (PSCS), suggesting aberrant separase activity. [...] maternal ageing compromises the oocyte SAC–APC/C axis leading to a decrease in securin that ultimately causes sister chromatid cohesion loss. Manipulating this axis and/or increasing securin may provide novel therapeutic approaches to alleviating the risk of oocyte aneuploidy in maternal ageing.
Maternal age-dependent APC/C-mediated decrease in securin causes premature sister chromatid separation in meiosis II Ibtissem Nabti, Rosanna Grimes, Hema Sarna, Petros Marangos & John Carroll Nature Communications 8, Article number: 15346 (2017) doi:10.1038/ncomms15346 https://www.nature.com/articles/ncomms15346

Had we stayed in Eden, none of this would have been an issue. Complex complexity.Dionisio_{May 30, 2017
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