Asked at the Journal of Theoretical Biology: Is the cell REALLY a machine?

_{Denyse O'Leary

August 11, 2021

Cell biology, Intelligent Design}

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Highlights
•Self-organization plays a key role in specifying the cellular architecture.
•Most proteins are functionally promiscuous and interact opportunistically.
•Directed movement occurs in the absence of design by generating order out of chaos.
•The non-genetic heterogeneity of cell populations implies that every cell is unique.
•Physics, not engineering, proves most helpful in understanding cellular complexity.
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.
Daniel J. Nicholson, “Is the cell really a machine?” at Journal of Theoretical Biology Volume 477, 21 September 2019, Pages 108-126

The paper is closed access.

“Machine” is at best an analogy to certain aspects of cells. Readers write to say that, unlike machines, cells seek their own good (inherent teleology).

Comments

The cell has clear molecular nanotech machines in itkairosfocus_{August 14, 2021
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As to, "Is The Cell REALLY A Machine?" The cell is similar to a machine, yet it is also profoundly different from a machine. Profoundly different in a way that makes the inference to Intelligent Design exponentially stronger, not weaker. As David Klinghoffer noted in an article entitled "Problems with the Metaphor of a Cell as "Machine", "Too often, we envision the cell as a "factory" containing a fixed complement of "machinery" operating according to "instructions" (or "software" or "blueprints") contained in the genome and spitting out the "gene products" (proteins) that sustain life. Many things are wrong with this picture, but one of the problems that needs to be discussed more openly is the fact that in this "factory," many if not most of the "machines" are themselves constantly turning over -- being assembled when and where they are needed, and disassembled afterwards. The mitotic spindle...is one of the best-known examples, but there are many others. Funny sort of "factory" that, with the "machinery" itself popping in and out of existence as needed!,,,"
Problems with the Metaphor of a Cell as "Machine" - David Klinghoffer July 2012 Excerpt: Too often, we envision the cell as a "factory" containing a fixed complement of "machinery" operating according to "instructions" (or "software" or "blueprints") contained in the genome and spitting out the "gene products" (proteins) that sustain life. Many things are wrong with this picture, but one of the problems that needs to be discussed more openly is the fact that in this "factory," many if not most of the "machines" are themselves constantly turning over -- being assembled when and where they are needed, and disassembled afterwards. The mitotic spindle...is one of the best-known examples, but there are many others. Funny sort of "factory" that, with the "machinery" itself popping in and out of existence as needed!,,, http://www.evolutionnews.org/2012/07/problems_with_t062691.html
And as Jonathan Wells explains in an article entitled, "Why the Design in Living Things Goes Far Beyond Machinery", "If a laptop computer were a plant or animal, it would start out as a protocomputer consisting of perhaps a few transistors, a little memory with some software, and a battery on a small circuit board. Then it would obtain materials from its surroundings to fabricate other components, and it would make its circuit board larger and more complex. Along the way, it would find ways to recharge its own battery. It would also write more programs. After reaching maturity, the laptop would run its programs by itself—imagine keys on the keyboard going up and down as though pressed by some unseen finger. If components were damaged, the computer could repair or replace them while continuing to operate. Eventually, the computer would fabricate one or more protocomputers, each capable of developing into other laptops just like it. A lot of design goes into laptop computers. How much more design would have to go into making a laptop computer that could do all the things listed above? No one knows. But such a computer would certainly require more design, not less."
Greater Than the Sum - Why the Design in Living Things Goes Far Beyond Machinery by Jonathan Wells – Summer 2016 Excerpt: An organism, however, in contrast to an isolated structure, rearranges its parts over time. An organism imposes organization on the materials it comprises, and its organization changes throughout its life cycle. To see how remarkable this is, imagine a machine familiar to most of us: a laptop computer. If a laptop computer were a plant or animal, it would start out as a protocomputer consisting of perhaps a few transistors, a little memory with some software, and a battery on a small circuit board. Then it would obtain materials from its surroundings to fabricate other components, and it would make its circuit board larger and more complex. Along the way, it would find ways to recharge its own battery. It would also write more programs. After reaching maturity, the laptop would run its programs by itself—imagine keys on the keyboard going up and down as though pressed by some unseen finger. If components were damaged, the computer could repair or replace them while continuing to operate. Eventually, the computer would fabricate one or more protocomputers, each capable of developing into other laptops just like it. A lot of design goes into laptop computers. How much more design would have to go into making a laptop computer that could do all the things listed above? No one knows. But such a computer would certainly require more design, not less. And the design would be radically different from human design, because, after the origin of the protocomputer, the design would be intrinsic rather than extrinsic. So the inference to design from molecular machines is robust, but it's only the beginning. There is design in living things that far transcends the machine metaphor—and it should inspire awe. http://www.salvomag.com/new/articles/salvo37/greater-than-the-sum.php
The level of engineering and 'intelligent design' required to explain how such complexity is even remotely possible is simply many orders of magnitude beyond any machine that man has ever designed. As James Shapiro (of "The Third Way") himself stated, "No human contrivance operates with either the degree of complexity, the precision, or the efficiency of living cells."
"No human contrivance operates with either the degree of complexity, the precision, or the efficiency of living cells." James A. Shapiro, "21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering," Gene, Vol. 345: 91-100 (2005) http://www.evolutionnews.org/2013/04/are_we_right_to071511.html
The denial by Darwinists that life is the product of design,, (especially in this day and age of having a better grasp of just how complex a cell actually is at the molecular level), is simply inexcusable.
"It is not enough to say that design is a more likely scenario to explain a world full of well-designed things. Once you allow the intellect to consider that an elaborate organism with trillions of microscopic interactive components can be an accident...you have essentially lost your mind." Jay Homnick - senior editor of The American Spectator - 2005 Psalm 139:13-14 For You formed my inmost being; You knit me together in my mother’s womb. I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well.
bornagain77_{August 13, 2021
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This seems more like a discussion in semantics or meanings of words applied outside their usual contexts. Consider: biophysics is using science to discover or explain aspects of physics applied to living organisms. Bioengineering is using known aspects of living systems to make changes to get something different. Both can work at the cell level. Therefore both physics and engineering can be applied biologically. Engineering can also be used to understand cell organization and operation at the systems level. As for :"is the cell a machine?" I prefer to say the cell is like an automated factory, using nanomachines and various supplied materials to produce needed products. No two factories are identical, having different machines, inventories, workers, schedules, priorities, etc. However, the machines in the factories may be identical just as the nanomachines inside cells may be identical - at least in cells of the same species. I believe this distinction from "machine" to "factory" resolves the author's concerns about calling a cell a machine.Fasteddious_{August 12, 2021
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from the article:
Physics, not engineering, proves most helpful in understanding cellular complexity.
just another Darwinian very absurd non-sense .... these guys are so desperate ... why Darwinists don't demonstrate that physics in their fancy labs and create a simple cell ?martin_r_{August 11, 2021
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Is The Cell REALLY A Machine?
i as an engineer would rather call it "a technology"...martin_r_{August 11, 2021
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