Prabhupada, Room Conversation with Krishna Tiwari, Molecular Biologist, UCLA, May 25, 1973: So I don’t think your science has reached to the point to find out the measurement of the living entity. But we get information that there is a measurement. kesagra-sata-bhagasya, satamsah sadrsatmakah [Cc. Madhya 19.140] The tip of the hair you divide into one hundred parts, and take that part, again divide into one hundred parts, that is the measurement. That is one ten-thousandth part of the tip of the hair. How far do you agree with this? Full Conversation
Molecular Machines in the Cell
Discovery Institute, June 11, 2010
Long before the advent of modern technology, students of biology compared the workings of life to machines. In recent decades, this comparison has become stronger than ever. As a paper in Nature Reviews Molecular Cell Biology states, “Today biology is revealing the importance of ‘molecular machines’ and of other highly organized molecular structures that carry out the complex physico-chemical processes on which life is based.” Likewise, a paper in Nature Methods observed that “most cellular functions are executed by protein complexes, acting like molecular machines.”
A molecular machine, according to an article in the journal Accounts of Chemical Research, is “an assemblage of parts that transmit forces, motion, or energy from one to another in a predetermined manner.” A 2004 article in Annual Review of Biomedical Engineering asserted that “these machines are generally more efficient than their macroscale counterparts,” further noting that “[c]ountless such machines exist in nature.” Indeed, a single research project in 2006 reported the discovery of over 250 new molecular machines in yeast alone!
Molecular machines have posed a stark challenge to those who seek to understand them in Darwinian terms as the products of an undirected process. In his 1996 book Darwin’s Black Box: The Biochemical Challenge to Evolution, biochemist Michael Behe explained the surprising discovery that life is based upon machines:
Shortly after 1950 science advanced to the point where it could determine the shapes and properties of a few of the molecules that make up living organisms. Slowly, painstakingly, the structures of more and more biological molecules were elucidated, and the way they work inferred from countless experiments. The cumulative results show with piercing clarity that life is based on machines–machines made of molecules!
Molecular machines haul cargo from one place in the cell to another along “highways” made of other molecules, while still others act as cables, ropes, and pulleys to hold the cell in shape. Machines turn cellular switches on and off, sometimes killing the cell or causing it to grow. Solar-powered machines capture the energy of photons and store it in chemicals.
Electrical machines allow current to flow through nerves. Manufacturing machines build other molecular machines, as well as themselves. Cells swim using machines, copy themselves with machinery, ingest food with machinery. In short, highly sophisticated molecular machines control every cellular process. Thus, the details of life are finely calibrated and the machinery of life enormously complex.
Behe then posed the question, “Can all of life be fit into Darwin’s theory of evolution?,” and answered: “The complexity of life’s foundation has paralyzed science’s attempt to account for it; molecular machines raise an as-yet impenetrable barrier to Darwinism’s universal reach.”
Even those who disagree with Behe’s answer to that question have marveled at the complexity of molecular machines. In 1998, former president of the U.S. National Academy of Sciences Bruce Alberts wrote the introductory article to an issue of Cell, one of the world’s top biology journals, celebrating molecular machines. Alberts praised the “speed,” “elegance,” “sophistication,” and “highly organized activity” of “remarkable” and “marvelous” structures inside the cell. He went on to explain what inspired such words:
The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. . . . Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts.
Likewise, in 2000 Marco Piccolini wrote in Nature Reviews Molecular Cell Biology that “extraordinary biological machines realize the dream of the seventeenth- century scientists … that ‘machines will be eventually found not only unknown to us but also unimaginable by our mind.’” He notes that modern biological machines “surpass the expectations of the early life scientists.”
A few years later, a review article in the journal Biological Chemistry demonstrated the difficulty evolutionary scientists have faced when trying to understand molecular machines. Essentially, they must deny their scientific intuitions when trying to grapple with the complexity of the fact that biological structures appear engineered to the schematics of blueprints:
Molecular machines, although it may often seem so, are not made with a blueprint at hand. Yet, biochemists and molecular biologists (and many scientists of other disciplines) are used to thinking as an engineer, more precisely a reverse engineer. But there are no blueprints … ‘Nothing in biology makes sense except in the light of evolution’: we know that Dobzhansky (1973) must be right. But our mind, despite being a product of tinkering itself strangely wants us to think like engineers.
But do molecular machines make sense in the light of undirected Darwinian evolution? Does it make sense to deny the fact that machines show all signs that they were designed? Michael Behe argues that in fact molecular machine meet the very test that Darwin posed to falsify his theory, and indicate intelligent design.
Darwin knew his theory of gradual evolution by natural selection carried a heavy burden:
If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.
… What type of biological system could not be formed by “numerous successive slight modifications”? Well, for starters, a system that is irreducibly complex. By irreducibly complex I mean a single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning.
Molecular machines are highly complex and in many cases we are just beginning to understand their inner workings. As a result, while we know that many complex molecular machines exist, to date only a few have been studied sufficiently by biologists so that they have directly tested for irreducible complexity through genetic knockout experiments or mutational sensitivity tests. What follows is a non-exhaustive list briefly describing 40 molecular machines identified in the scientific literature. The first section will cover molecular machines that scientists have argued show irreducible complexity. The second section will discuss molecular machines that may be irreducibly complex, but have not been studied in enough detail yet by biochemists to make a conclusive argument.
Selected list of molecular machines:
I. Molecular Machines that Scientists Have Argued Show Irreducible Complexity
1. Bacterial Flagellum
2. Eukaryotic Cilium
3. Aminoacyl-tRNA Synthetases (aaRS)
4. Blood clotting cascade
5. Ribosome
6. Antibodies and the Adaptive Immune System
7. Spliceosome
8. F0F1 ATP Synthase
9. Bacteriorhdopsin
10. Myosin
11. Kinesin Motor
12. Tim/Tom Systems
13. Calcium Pump
14. Cytochrome C Oxidase
15. Proteosome
16. Cohesin
17. Condensin
18. ClpX
19. Immunological Synapse
20. Glideosome
21. Kex2
22. Hsp70
23. Hsp60
24. Protein Kinase C
25. SecYEG PreProtein Translocation Channel
26. Hemoglobin
27. T4 DNA Packaging Motor
28. Smc5/Smc6
29. Cytplasmic Dynein
30. Mitotic Spindle Machine
31. DNA Polymerase
32. RNA Polymerase
33. Kinetochore
34. MRX Complex
35. Apoptosome / Caspase
36. Type III Secretory System
37. Type II Secretion Apparatus
38. Helicase/Topoisomerase Machine
39. RNA degradasome
40. Photosynthetic system
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