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Researcher asks, Is the cell REALLY a machine?

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He offers a bullet list of his reasons for doubt, then an abstract:

Abstract:It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell’s organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes. – Author Daniel J. Nicholson Is the cell really a machine? Journal of Theoretical Biology, Volume 477, 21 September 2019, Pages 108-126 (paywall) More.

He does not say here how he would prefer to envision the cell.

Some Darwinians are uncomfortable because the machine metaphor implies design, as Jonathan Wells noted in 2014:

According to pro-evolution philosophers Massimo Pigliucci and Maarten Boudry, “creationists and their modern heirs of the Intelligent Design movement have been eager to exploit mechanical metaphors for their own purposes.” So “if we want to keep Intelligent Design out of the classroom, not only do we have to exclude the ‘theory’ from the biology curriculum, but we also have to be weary [sic] of using scientific metaphors that bolster design-like misconceptions about living systems.” Pigliucci and Boudry conclude that since “machine/information metaphors have been grist to the mill of ID creationism, fostering design intuitions and other misconceptions about living systems, we think it is time to dispense with them altogether.”

But there are better reasons to dispense with the machine metaphor (and Pigliucci and Boudry mention some). Although the mechanistic approach has borne some fruit in biological research, the truth is that living things are very different from machines. Jonathan Wells, “Revolutionary Biology” at Evolution News and Science Today

Cells are more than machines but that only makes any form of Darwinism less likely.

One reader wrote to say that the whole thing reminds him of J. Scott Turner’s Purpose and Desire: What Makes Something “Alive” and Why Modern Darwinism Has Failed to Explain It.

A lot of things would, these days.

Hat tip: Pos-darwinista

Before you go: DNA uses “climbers’ ropes method” to keep tangles at bay It all just swished into place among unthinking cells billions of yours ago. Otherwise we wouldn’t be here. Go tell it on the mountain.

DNA as a master of resource recycling

The amazing energy efficiency of cells: A science writer compares the cell to human inventions and finds that it is indeed amazingly energy-efficient.

In addition to DNA, our cells have an instruction language written in sugar Of course it all just tumbled into existence and “natural selection” somehow organized everything. As if.

Cells find optimal solutions. Not just good ones.

Researchers build “public library” to help understand photosynthesis

Wait. “The part of the plant responsible for photosynthesis is like a complex machine made up of many parts, … ” And machines just happen all by themselves, right? There is no information load to account for; it just evolved by natural selection acting on random mutation the way your Android did!

In Nature: Cells have “secret conversations” We say this a lot: That’s a lot of information to have simply come into being by natural selection acting on random mutation (Darwinism). It’s getting not only ridiculous but obviously ridiculous.

Follow UD News at Twitter!

Researchers: Helpful gut microbes send messages to their hosts If the strategy is clearly identified, they should look for non-helpful microbes that have found a way to copy it (horizontal gene transfer?)

Cells and proteins use sugars to talk to one another Cells are like Neanderthal man. They get smarter every time we run into them. And just think, it all just tumbled into existence by natural selection acting on random mutations (Darwinism) too…

Researchers: First animal cell was not simple; it could “transdifferentiate” From the paper: “… these analyses offer no support for the homology of sponge choanocytes and choanoflagellates, nor for the view that the first multicellular animals were simple balls of cells with limited capacity to differentiate.”

“Interspecies communication” strategy between gut bacteria and mammalian hosts’ genes described

Researchers: Cells Have A Repair Crew That Fixes Local Leaks

Researchers: How The Immune System “Thinks”

Follow UD News at Twitter!

Researcher: Mathematics Sheds Light On “Unfathomably Complex” Cellular Thinking

How do cells in the body know where they are supposed to be?

Researchers A Kill Cancer Code Is Embedded in Every Cell

Comments
Engineers harness the materials, dynamics and forces of nature, to design and effect useful functional structures.kairosfocus
July 15, 2019
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EugeneS @36: "the word ‘harnessing’ in the comments above reminded me of Michael Polanyi’s view on life as boundary conditions harnessing the laws of nature without being reducible to them." Interesting observation.PeterA
July 14, 2019
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GPuccio, I have been away for a long time for various reasons. Nice to be back and watching out for your contributions. Your focusing on the word 'harnessing' in the comments above reminded me of Michael Polanyi's view on life as boundary conditions harnessing the laws of nature without being reducible to them.EugeneS
July 14, 2019
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I'm sympathetic to Dionisio creating a fake dialogue like that, although it is embarrassing at the same time. He and others of us here find absurd statements in scientific papers like the one quoted. Researchers blithely make their claims with inaccurate or false statements. It gives a clear insight into the mental-bias at work. So, OLV posts these little clips, showing all manner of stupidity from the authors of peer-reviewed papers, and then nobody comments on them. We can't get the author to join us for an open dialogue (although one did recently). So, instead of losing the moment, he created an imaginary dialogue and impersonated the scholar. We do something similar when we comment "evolutionists would say …" and it is something like impersonating them.Silver Asiatic
July 4, 2019
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Mimus
I think the PavelU account is pretty obviously run by the same person that posts under Jawa/OLV, PaoloV, PeterA and probably a bunch more. This one being his idea of a pro-evolutionary poster…
Ok, thanks. I've only recently returned here and started to notice the similarity among those identities. I think the previous name was Dionisio. Well, I took the bait in this case. I'm glad it will not lead to a dialogue.Silver Asiatic
July 4, 2019
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AaronS1968
I can’t handle this I’m have an identity crisis.
Wait until ET tells you about all the people I am supposed to be. If it were true, I would have no time to actually work for a living. :)Brother Brian
July 3, 2019
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I can’t handle this I’m have an identity crisisAaronS1978
July 3, 2019
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Mimus, next you are going to tell us that ET is really Joe, Joey, Virgil, Frankie, Sharon, etc. :)Brother Brian
July 3, 2019
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Well that would be awkward and really bad if you are right, im not gonna lie I’ve had that thought a couple of times in generalAaronS1978
July 3, 2019
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I think the PavelU account is pretty obviously run by the same person that posts under Jawa/OLV, PaoloV, PeterA and probably a bunch more. This one being his idea of a pro-evolutionary poster...Mimus
July 3, 2019
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“evolution has chosen NuMA as a strategic molecule” Evolution acts with foresight and does a great job in choosing just the right molecules for strategic actions. ???? Like a master planner or builder, evolution actively sorts through options and picks what will work best for future generations. ???Silver Asiatic
July 3, 2019
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PavelU, “evolution has chosen NuMA as a strategic molecule” Do you know of any literature that explains how that could have happened? That’s an unsupported claim. Total nonsense. Not even wrong. That shows how little seriousness that text reflects. What a shame! That’s not real science.jawa
July 3, 2019
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OLV, You didn’t quote important parts of paper @25. Did you read the paper carefully or just picked a few things here and there? It looks like the latter. For example, did you miss this scientific statement intentionally or by accident because you didn’t notice it? This is definitely a serious scientific affirmation at the end of section 3: “evolution has chosen NuMA as a strategic molecule” It seems like you avoided mentioning it because it destroys your ID fantasies. Would you dare to argue against the above quoted statement? I doubt it.PavelU
July 2, 2019
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Shouldn’t unscientific terms like “orchestrating, choreographing, coordinating, in concert,...” be banned from scientific literature? :) Perhaps authors should think twice before using those politically incorrect terms. :) Here’s an example of apparent abuse and misuse of such terms: Mechanisms of Spindle Positioning: Lessons from Worms and Mammalian Cells Sachin Kotak Biomolecules. 2019 Feb; 9(2): 80. doi: 10.3390/biom9020080 Proper positioning of the mitotic spindle is fundamental for specifying the site for cleavage furrow, and thus regulates the appropriate sizes and accurate distribution of the cell fate determinants in the resulting daughter cells during development and in the stem cells. The past couple of years have witnessed tremendous work accomplished in the area of spindle positioning, and this has led to the emergence of a working model unravelling in-depth mechanistic insight of the underlying process orchestrating spindle positioning. In this review, I will mainly discuss how the abovementioned components precisely and spatiotemporally regulate spindle positioning by sensing the physicochemical environment for execution of flawless mitosis. To efficiently grow and divide, all cells undergo a series of tightly regulated events known as the cell cycle. In eukaryotes, the cell cycle comprises Interphase and M-phase. M-phase is further divided into mitosis (or meiosis in germ cells) and cytokinesis. During mitosis, all animal cells establish an elegant diamond-shaped microtubule-based structure known as a mitotic spindle that is critical for ensuring error-free partitioning of the genomic, as well as intracellular contents (for details, please refer to [1,2]). In addition to this, the accurate positioning of the mitotic spindle is critical for the correct placement of the cleavage furrow, relative sizes and spatial organization of the daughter cells, and faithful segregation of the cell fate determinants during asymmetric cell divisions including in the stem cells several recent reports have highlighted the involvement of numerous actin-associated proteins in choreographing the localization/activity of the ternary complex. it also appears that the link between the components of the ternary components and actin/E-Cadherin function on spindle positioning would be relevant in the context of a tissue, where cells need an extrinsic mechanism to communicate with each other for maintaining proper tissue architecture. cells keep the memory of the interphase cell shape that guide spindle positioning in mitosis. How external forces regulated by retraction fibers polarize the cells for proper spindle positioning remain incompletely understood. Intriguingly, external forces governed by retraction fibers rely on internal astral microtubules to accurately position the mitotic spindle, suggesting external information is getting relayed inside the cells the ternary complex components are also involved in sensing the external mechanical forces. NuMA/dynein pathway work in combination with the actin cloud/myosin pathway in orchestrating mitotic spindle behavior in HeLa cells. the identity of the central molecule/s of the ternary complex that senses the external force, and more importantly what is the relationship between intracellular actin cloud, ERM proteins, and the ternary complex components remain incompletely understood. Interestingly, a relatively recent study by Sugioka and Bowerman has challenged the unifying theme of the involvement of the ternary complex components and dynein in orchestrating spindle positioning in the C. elegans embryos. They have uncovered an entirely new paradigm for controlling spindle positioning. How does cell contact-mediated information regulate spindle positioning in the AB cell? it would be important to investigate the molecular mechanisms by which physical inputs instruct myosin flow to control spindle dynamics. positioning of the centrosomes and asymmetric division of the EMS cell require signaling from the posterior P2 blastomere Wnt-pathway not only induces LIN-5/dynein-dependent spindle positioning in the EMS cell, but also inhibits cortical actomyosin to orchestrate the division axis in the EMS cell either the ternary complex components are asymmetrically activated in such a cellular system or could act in concert with other components of the Wnt signaling to control spindle positioning in EMS cell. it would be quite fascinating to explore how Wnt signaling mechanistically controls the cytoskeleton to direct proper positioning of the mitotic spindle. Taken together, it is becoming increasingly apparent that various cellular systems use multiple mechanisms whereby force generating machinery coordinate with the physical and chemical cues to position the mitotic spindle. These mechanisms may work in concert, or perhaps in an antagonistic way to modulate the spindle dynamics in time and space. it is necessary that the regulators of spindle positioning are tightly and dynamically regulated during mitosis. other than kinases, phosphatases could play a substantial role in fine-tuning the localization of the components of the ternary complex for proper spindle positioning In the last few years we have learned the existence of multiple players that regulate correct positioning of the mitotic spindle in time and space. However, despite the discovery of several sophisticated building blocks that organize and spatiotemporally control spindle positioning, our understanding how these individual pieces collectively communicate to regulate spindle positioning is still far from clear. exciting time lie ahead of us where we can expect novel insights in the theme of spatial and temporal regulation of spindle positioning for error-free cell division.OLV
July 2, 2019
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Perhaps biological cells shouldn’t be compared to machines? At least the few papers cited here show that apparently machine is not the right term. Don’t they? :) BTW, the paper cited @22 is on a very important topic that GP has written extensively about. To those who are interested in seriously clear scientific explanations I strongly suggest reading what GP has written about that and other important topics in this website. I’m sure you’ll enjoy it. The Summa Cum Laude Alumnae from Scott Adams’ online college should stay away from GP’s serious discussions.OLV
July 2, 2019
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Asymmetric recruitment and actin-dependent cortical flows drive the neuroblast polarity cycle Chet Huan Oon and Kenneth E Prehoda eLife. 2019; 8: e45815. doi: 10.7554/eLife.45815 During the asymmetric divisions of Drosophila neuroblasts, the Par polarity complex cycles between the cytoplasm and an apical cortical domain that restricts differentiation factors to the basal cortex. Initially, the Par proteins aPKC and Bazooka form discrete foci at the apical cortex. Foci grow into patches that together comprise a discontinuous, unorganized structure. Coordinated cortical flows that begin near metaphase and are dependent on the actin cytoskeleton rapidly transform the patches into a highly organized apical cap. At anaphase onset, the cap disassembles as the cortical flow reverses direction toward the emerging cleavage furrow. Following division, cortical patches dissipate into the cytoplasm allowing the neuroblast polarity cycle to begin again. neuroblast polarity results not from a single process, but from the stepwise activity of two very different cellular processes: asymmetric targeting and actin- dependent cortical flow.OLV
July 2, 2019
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E3 Ubiquitin Ligase TRIM Proteins, Cell Cycle and Mitosis Santina Venuto and Giuseppe Merla Cells. 2019 May; 8(5): 510. doi: 10.3390/cells8050510 The cell cycle is a series of events by which cellular components are accurately segregated into daughter cells, principally controlled by the oscillating activities of cyclin-dependent kinases (CDKs) and their co-activators. In eukaryotes, DNA replication is confined to a discrete synthesis phase while chromosome segregation occurs during mitosis. During mitosis, the chromosomes are pulled into each of the two daughter cells by the coordination of spindle microtubules, kinetochores, centromeres, and chromatin. These four functional units tie chromosomes to the microtubules, send signals to the cells when the attachment is completed and the division can proceed, and withstand the force generated by pulling the chromosomes to either daughter cell. Protein ubiquitination is a post-translational modification that plays a central role in cellular homeostasis. E3 ubiquitin ligases mediate the transfer of ubiquitin to substrate proteins determining their fate. One of the largest subfamilies of E3 ubiquitin ligases is the family of the tripartite motif (TRIM) proteins, whose dysregulation is associated with a variety of cellular processes and directly involved in human diseases and cancer. During mitosis TRIMs superfamily has been shown to exert important roles in the regulation of the main components of the mitotic spindle machinery, including kinetochores, centrosomes and midbodies that are important elements for ensuring chromosomes orientation and segregation to be performed correctly.OLV
July 2, 2019
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“Once thought an immediate and automatic step“? Why did they think so? Functional complexity of the complex functionality in biological systems: Precise specification of cell fate or identity within stem cell lineages is critical for ensuring correct stem cell lineage progression and tissue homeostasis. Failure to specify cell fate or identity in a timely and robust manner can result in developmental abnormalities and diseases such as cancer. However, the molecular basis of timely cell fate/identity specification is only beginning to be understood. Cell fate decision-making in stem cell lineages is often binary: that is, newly born sibling cells ultimately rest in two discrete, steady and switch-like equilibrium states Once thought an immediate and automatic step, cell fate/identity specification has recently been found to be a progressive and tightly regulated process. Strategies that accelerate the transition from cell fate/identity decision to commitment must be in place to ensure timely and robust fate/identity specification. Future work using powerful model systems such as fly stem cell lineages and naturally occurring lineage reprogramming promise to unveil new regulatory principles underlying timely fate/identity determination. Advanced time-lapse live imaging technique precisely monitoring gene transcription and 3D chromatin dynamics in vivo will certainly be helpful in extending and deepening our understanding of the rapid cell fate/identity commitment process. Faster, higher, stronger: timely and robust cell fate/identity commitment in stem cell lineages Kun Liu, Ke Xu, and Yan Song Open Biol. 2019 Feb; 9(2): 180243. doi: 10.1098/rsob.180243OLV
July 2, 2019
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  Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3DOLV
June 30, 2019
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Gpuccio @8: “The concept should be simple enough: Random events do not generate function.” “Design generates function. And, of course, good design can certainly intelligently use random events to do that.” “It’s interesting how the paper itself uses, more than once, the word “harnessing”. “ I couldn’t agree more. Also, very interesting papers on robustness that you cited @11 & 12. Thanks.OLV
June 29, 2019
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GP @12: “ next time some earnest post-post-neo-darwinist tries to hypnotize you with the concept of stochasticity, just neutralize him with this simple magic word: Robustness!” Excellent. Thanks.OLV
June 28, 2019
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John_a_designer @13: “it more analogous to a factory which can automatically replicate itself by replicating all its machines. Furthermore, it can only do this because it is pre-programmed to do this.” Good point.OLV
June 28, 2019
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Silver Asiatic @14: “Just focusing on the absurdities of repeated evolutionary scenarios alone can fill your blog for years. News of such things may never come to an end.” Agree. :)OLV
June 28, 2019
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Martin_r @7: I’m bookmarking your new website and will look into it and contact you when I see it’s ready. Thanks. You may want to follow GPuccio’s insightful posts in this UD website. His clear biology-related explanations could help you to add value to your new blog. They’re available only here in UD. BTW, what’s your first language? Just curious.OLV
June 28, 2019
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Martin_R
When i first came across repeated evolution stuff, i thought, these biologists guys must be joking…
I had the same reaction when I first encountered convergent evolution. It's the most ridiculous concept - beyond belief.
I was collecting CE/RE-articles for years, now i am ready to start a blog… I just purchased a domain name and web-hosting, i paid 5 years upfront. https://Stuffhappens.info Please bookmark the URL, and get back to me (Contact us) when it is finished, this is a very ‘working’ version, most of the posts are still hidden. Again, the blog is not official yet.
Great job and a great resource. I wish you a lot of success with it. Just focusing on the absurdities of repeated evolutionary scenarios alone can fill your blog for years. News of such things may never come to an end.Silver Asiatic
June 28, 2019
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There is no doubt that at some level organic molecules have the innate ability to self-organize. I don’t know of any prominent ID’ist who would dispute that. So the fact of self-organization is hardly a disproof of design and it’s hardly proof that the nano-machines, we have discovered in the cell, aren’t really machines. It is also a fact that basic life forms don’t spontaneously self-organize or “generate”. I learned that in my H.S. biology class back in the 1960’s. Louis Pasteur, I was taught, carried out experiments in the 19th century which showed there was no such thing as spontaneous generation. Yeah, I also know there is no such thing as absolute proof but “the burden of proof” certainly shifts to those who believe otherwise. If that is what you believe, where is the evidence for spontaneous generation? On the other hand, it may correct to say that the cell is not a machine because it is not a single machine but composed of many nano-machines operating and cooperating in a systematic integrated way. In other words, it more analogous to a factory which can automatically replicate itself by replicating all its machines. Furthermore, it can only do this because it is pre-programmed to do this. Who or what did the pre-programming? Only an intelligence-- a very advanced intelligence-- has that kind of capability.john_a_designer
June 28, 2019
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OLV and others: And here is another one, about the best studied animal model: C. elegans: Developmental robustness in the Caenorhabditis elegans embryo https://onlinelibrary.wiley.com/doi/full/10.1002/mrd.22582
SUMMARY: Developmental robustness is the ability of an embryo to develop normally despite many sources of variation, from differences in the environment to stochastic cell?to?cell differences in gene expression. The nematode Caenorhabditis elegans exhibits an additional level of robustness: Unlike most other animals, the embryonic pattern of cell divisions is nearly identical from animal to animal. The endoderm (gut) lineage is an ideal model for studying such robustness as the juvenile gut has a simple anatomy, consisting of 20 cells that are derived from a single cell, E, and the gene regulatory network that controls E specification shares features with developmental regulatory networks in many other systems, including genetic redundancy, parallel pathways, and feed?forward loops. Early studies were initially concerned with identifying the genes in the network, whereas recent work has focused on understanding how the endoderm produces a robust developmental output in the face of many sources of variation. Genetic control exists at three levels of endoderm development: Progenitor specification, cell divisions within the developing gut, and maintenance of gut differentiation. Recent findings show that specification genes regulate all three of these aspects of gut development, and that mutant embryos can experience a “partial” specification state in which some, but not all, E descendants adopt a gut fate. Ongoing studies using newer quantitative and genome?wide methods promise further insights into how developmental gene regulatory networks buffer variation.
Again, emphasis mine. So, next time some earnest post-post-neo-darwinist tries to hypnotize you with the concept of stochasticity, just neutralize him with this simple magic word: Robustness!gpuccio
June 28, 2019
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OLV and others: This is a paper about the problems I have tried to discuss: Superstability of the yeast cell-cycle dynamics: ensuring causality in the presence of biochemical stochasticity. https://www.sciencedirect.com/science/article/pii/S0022519306005509?via%3Dihub
Abstract: Gene regulatory dynamics are governed by molecular processes and therefore exhibits an inherent stochasticity. However, for the survival of an organism it is a strict necessity that this intrinsic noise does not prevent robust functioning of the system. It is still an open question how dynamical stability is achieved in biological systems despite the omnipresent fluctuations. In this paper we investigate the cell cycle of the budding yeast Saccharomyces cerevisiae as an example of a well-studied organism. We study a genetic network model of 11 genes that coordinate the cell-cycle dynamics using a modeling framework which generalizes the concept of discrete threshold dynamics. By allowing for fluctuations in the process times, we introduce noise into the model, accounting for the effects of biochemical stochasticity. We study the dynamical attractor of the cell cycle and find a remarkable robustness against fluctuations of this kind. We identify mechanisms that ensure reliability in spite of fluctuations: ‘Catcher states’ and persistence of activity levels contribute significantly to the stability of the yeast cell cycle despite the inherent stochasticity.
Emphasis mine.gpuccio
June 28, 2019
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GP @5: “stocastic decisional systems in the cell” That seems like a whole topic in itself deserving a separate discussion. Perhaps a new OP by GP? :)OLV
June 28, 2019
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Gpuccio @5 & @8: You made me laugh out loud. You wrote those two insightful comments after what you called “a quick (and incomplete) look at the paper“. Had you reviewed the paper thoroughly and completely then you could have written a whole book. Well done, doctor! Thanks again for delighting us with your serious commentaries and OPs, including the ones that you write after “quick (and incomplete) looks at papers” :)OLV
June 28, 2019
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