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Researcher asks, Is the cell REALLY a machine?

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Cell biology
Intelligent Design
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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
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
June 28, 2019
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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
June 28, 2019
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Gpuccio @5: Excellent insightful commentary. Looking forward to reading the continuation of your comment. Thanks.OLV
June 28, 2019
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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
June 28, 2019
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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://uncommondescent.com/intelligent-design/researchers-evolution-is-random-just-like-the-stock-market/#comment-679576 and this? https://uncommondescent.com/evolution/a-new-bug-for-darwins-finches-mating-disrupted-by-parasite/#comment-679515 and this? https://uncommondescent.com/intelligent-design/why-describing-dna-as-software-doesnt-really-work/#comment-678913OLV
June 28, 2019
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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
June 27, 2019
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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
June 27, 2019
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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
June 27, 2019
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