Uncommon Descent Serving The Intelligent Design Community

Researcher asks, Is the cell REALLY a machine?


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.

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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”

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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

Engineers harness the materials, dynamics and forces of nature, to design and effect useful functional structures. kairosfocus
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
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
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
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
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
I can’t handle this I’m have an identity crisis AaronS1978
Mimus, next you are going to tell us that ET is really Joe, Joey, Virgil, Frankie, Sharon, etc. :) Brother Brian
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 general AaronS1978
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
“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
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
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
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
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
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
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
“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.180243 OLV
  Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D OLV
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
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
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
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
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
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
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
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
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
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
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
OLV and others (continued): 5) The paper, like much of the post-post-neo-darwinian thought, proposes nothing really scientific about its declared "new ideas". OK, let's say the cell is not only a machine. As said, I can fully agree with that. But then, what is it? Here comes the magic. The language in the paper becomes as vague and ambiguous as possible. So, what are the new principles that should help us understand what the "non-machine" cell really is? a) Self-organization. Wow! This is really something. We learn that cellular structure, that were thought to arise by self-assembly, in reality originate by self-organization. IOWs, they arise in spite of stocastic events, and they arise as fluid structures far from equilibrium. OK. Still, they arise. Now the problem is: self assembly is quite easy. You just need well designed parts, and everything comes together nicely- But self-organization... Well self-organization is clearly magic! Do you remember the scene in Mary Poppins, where the room gets ordered by itself? Well, something like that. In self-organization form and structure and function do arise, like in self assembly. But they arise dynamically, against all possible stocastic noise, and, of course. far from equilibrium, and requiring a lot of dissipative energy balance. Piece of cake, of course. So, self-assemby certainly requires good design. And self-organization? Probably, just magic. But, of course, self-organization, whatever it is, does require extra good design. And probably much more. Not magic, but extremely good science, a science so good that we still don't understand it at all. b) And then comes the ambiguity about stocastic systems, Brownian motion, and so on. 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". For example: "intracellular transport is deemed to result from the harnessing of Brownian motion" "In this way, by stochastically switching between two distinct conformational states as a result of repeated cycles of ATP hydrolysis, the motor protein is able to harness the perturbations of Brownian motion to move in a specific direction along a cytoskeletal track " Now, what does "harnessing" mean? harness: a set of straps and fittings by which a horse or other draught animal is fastened to a cart, plough, etc. and is controlled by its driver. to harness: put a harness on (a horse or other draught animal). Control and make use of (natural resources), especially to produce energy. The key word is: control. If I am swimming in the sea, I can try to harness the energy of the waves to go where I want to go. To use random events to get a functional results, we need one of two things: 1) An intelligent agent 2) A machine designed and built by an intelligent agent. There is no other way. Unless, of course, I create a new post-post-neo-darwinian term. What about "self-harnessing"? :) gpuccio
OLV, i am from Europe, i apologize for my bad English, it is not my first language. you wrote: "CRISPR - Many people could thing that scientists made that up from scratch." i debated lots of people, from very stupid to very smart atheists, however, from my experience, 99% of atheists (don't matter how smart they are) have no idea in what they actually believe, what the ET actually claims ... they are familiar with some general stuff like ATB resistance, vestigial organs, 'bad' design of human eye, but that is it .... when they get teached they usually drop the conversation or attack me... When i do my study, i am usually focused on so called 'convergent' evolution (repeated evolution). When i first came across repeated evolution stuff, i thought, these biologists guys must be joking... 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. OLV, i would need someone native speaking, to make small grammar corrections (from time-to-time). Thank you. p.s. the UD-URLs you have mentioned, yes, i am following lots of things, but like i said, i am totally focused on convergent evolution stuff. martin_r
Gpuccio @5: Excellent insightful commentary. Looking forward to reading the continuation of your comment. Thanks. OLV
OLV and others: I have given a quick (and incomplete) look at the paper. It is at the same time interesting and frustrating. It is interesting because it highlights a few important concepts that, while absolutely obvious for all those who have some true understanding of modern biology, may not be really clear to all. The main idea is that the cell is not a machine (well, at least not a traditional machine I would say), but rather: " cells, unlike machines, are self-organizing, fluid systems that maintain themselves in a steady state far from thermodynamic equilibrium by continuously exchanging energy and matter with their surroundings." The second main idea is that: " by virtue of their microscopic size, cells (and their molecular constituents, even more so) are subject to very different physical conditions compared to macroscopic objects, like machines." Those "different physical conditions" are essentially stocastic factors, like Brownian motion. The paper analyzes in particular four aspects of the cell, to emphasize those points:
As we will see, according to this alternative view, the cellular architecture is regarded as a fluid, self-organizing process; protein complexes are conceived as transient, pleomorphic ensembles; intracellular transport is deemed to result from the harnessing of Brownian motion; and cellular behaviour is viewed as a probabilistic affair, subject to stochastic fluctuations.
OK. It is well known that cell structures are dynamic, that they exist, like the cell itself, far from equilibrium. It is also well known that all main cellular events include the "harnessing" of stocastic components. I have discussed in some detail those aspects in my OPs here, for example about the ubiquitin system, or the structure of chromatin. I could not agree more. And even some superficial review of what is known about "decisions" about symmetric or asymmetric mytosis in stem cell compartments would yeld a lot of information about stocastic decisional systems in the cell. So, what's the problem with the paer? Indeed, there are many of them: 1) The concept and definition of "machine" used in the paper is certainly too restrictive. While it can apply to something like a watch or a car, it certainly does not correspong to modern informational systems. And yet, modern informational systems, including complex computers and computer networks, are machines. And what about quantum computers? The idea the authors have of a machine seems to be rather old fashioned. 2) The authors concede very generously (so much so that I am a little surprised that their work has been accepted for publication) that machines are based on design, and can be understood in terms of design. OK. But that seems to imply that cells are not designed, given that they "are not machines". I strongly disagree. 3) The point is: cells are probably (certainly, IMO) not only machines. But they are machines just the same, at many levels. And very complex machines indeed. That "machine" aspect could never be achoieved withoput complex engineering, and screams design. 4) Just to be more clear, let's consider macroscopic structures in multicellular beings. In a sense, we know that many of them "resemble" similar microscopic structures in the individual cell, at least in terms of function. So, for example, we have in the cell skeletal and contracting components, just as we have bones and muscles at the macroscopic level. Now, can we deny that bones and muscles realize a machine-like organization? What about the single cell? OK, it is true: celllar structures are microscopic, are much more dynamic, and exist far from equilibrium. True. We would not usually say that, literally, of a bone (even if at some levels the bone, too, is that way). But microtubules and microfilaments have to control cell shape and motion, just as bones and muscle controll the motion of the body. It is true, of course, that the cellular components are more dynamic. More in next post. gpuccio
Martin_r, “make your own CRISPR dna editing tool… don’t steal it from our Creator !” Good point. Many people could thing that scientists made that up from scratch. Glad we’re on the same page, I like good company. :) PS. BTW, did you see this? https://uncommondesc.wpengine.com/intelligent-design/researchers-evolution-is-random-just-like-the-stock-market/#comment-679576 and this? https://uncommondesc.wpengine.com/evolution/a-new-bug-for-darwins-finches-mating-disrupted-by-parasite/#comment-679515 and this? https://uncommondesc.wpengine.com/intelligent-design/why-describing-dna-as-software-doesnt-really-work/#comment-678913 OLV
Who are these guys ? How they dare? from the paper: " ... accumulation of data that are inconsistent with an engineering view of the cell." again, who are these guys? Biologists, go, and create your own cell ! GO .. DO IT ! GO .. DO IT ! sooner, you are not allowed to talk about what is engineered and what is not… what is a bad design and what is not… BIOLOGISTS, WHO ARE ??? HOW YOU EVEN DARE ? IN WHAT WAY ARE YOU QUALIFIED TO REVIEW ANY KIND OF DESIGN? GO GO GO.... and make your own CRISPR dna editing tool… don’t steal it from our Creator ! p.s. OLV, i just noticed your first comment, i see, we are on the same page. martin_r
MAPK cascades are responsible for protein phosphorylation and signal transduction events associated with plant hormone signaling and therefore they play an essential role in the regulation of development, senescence, stress signaling and acclimation. Many cases of MAPK involvement in AUX, ABA, JA, SA, ET, and BR signaling have been identified and these demonstrate the complex structure, extensive crosstalk and dynamics of the signaling network. The molecular mechanisms that regulate MAPK assembly, activity (both activation and inactivation) and substrate binding require further elucidation. The specificity of the MAPK module is achieved by coordinated expression of its components, by protein complex assembly and by subcellular localization not only MAPKKK18 activity but also the concentration of the protein is tightly controlled within the target compartment. The activation of a typical MAPK module is rapid but transient. Subsequently, MAPK inactivation is achieved via dephosphorylation by dedicated protein phosphatases that function as part of a negative feedback loop to control the hormonal response. MAPKKK18 downregulation by UPS is a significant factor in determining the nature of the MAPK signal output. A consistent feature of MAPK function in hormone signaling is the existence of central MAPK-dependent hubs allowing extensive crosstalk between hormonal pathways, which leads to precisely regulated cellular functions. In principle, these MAPKs may use more sophisticated mechanisms to diversify signal outputs determined by different stimuli, such as tissue distribution and the formation of acontext-specific signalosome. The very complexity of MAPK cascades means that it is often difficult to define them in detail and to assign them a specific role in a particular biological process. Thus, to date, no MAPK cascade, together with its downstream substrates, has been defined in its entirety in any plant system. many questions remain, Which cellular elements function as molecular switches to support precise crosstalk and interaction outcomes between MAPK cascades? How do plants discriminate between hormone signaling pathways? How do MAPK cascades maintain specificity? • What governs MAPK distribution within the cell? What post-transcriptional and translational mechanisms are employed to regulate this distribution? • Which signaling systems are responsible for MAPK inactivation? How do these work? Which ligands target MAPK pathways to regulate their activity? We believe that the answers to these questions will provide exciting discoveries and establish further the crucial role of MAPKs in plants. MAPK cascades, like other signaling networks, display a wide range of regulatory properties and the extension of MAPK research to all economically important crops is particularly relevant for ensuring sustainable food production globally. Mitogen-Activated Protein Kinase Cascades in Plant Hormone Signaling Front Plant Sci. 2018; 9: 1387. doi: 10.3389/fpls.2018.01387 Przemys?aw Jagodzik,1 Ma?gorzata Tajdel-Zielinska,2 Agata Ciesla,2 Ma?gorzata Marczak,2 and Agnieszka Ludwikow2,* OLV
The day humans will design something that at least remotely could resemble a biological cell, specially a eukaryotic cell, they will uncork all the champagne bottles in the world and celebrate their super achievement, all night long,... Yeah, right... until they wake up from their wishful dreaming. :) OLV

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