عصير كتاب: تصميم الخلية لـ فازل رنا The Cell’s Design By Fazale Rana

Posted: يوليو 9, 2016 in الكون ونشأة الحياة, الكتابات العامة, الإلحاد, تدوينات سريعة, عصير الكتب

بسم الله الرحمن الرحيم

The Cell’s Design

How Chemistry Reveals the Creator’s Artistry

By: Fazale Rana

للتحميل: (PDF) (DOC)

cells-design

نبذة مُختصرة عن الكتاب:

من أهمّ كُتُب «فازل “فضل” رنا» على الإطلاق.

الكتاب يُعتبر أهمّ المؤلَّفات في مجاله بعد كتاب «صندوق داروين الأسود» لـ «مايكل بيهي»، ولو أنَّ كتاب «بيهي» مُهتم أكثر بنقد الدَّاروينية، إلَّا أنَّ كتاب «تصميم الخلية» مُهتم أكثر ببيان أدلَّة التَّصميم في الخلية.

المؤلِّف يعترف بفضل كتاب «مايكل بيهي» في تعميم فكرة «التَّعقيد غير القابل للاختزال»، وأنَّ مثل هذه الأنظمة دليل واضح على أنَّها نِتاج تصميم ذكي، ولكنَّه يقول إنَّ هذه الميزة ليست وحدها الدَّالَّة على التَّصميم الذَّكي، وإنَّما هُناك عشرات الأدلَّة الأخرى على التَّصميم في الخلية.

بسبب احتواء الكتاب على الكثير من التَّفاصيل العلمية الدَّقيقة، فهو أنفع لمن له خلفية علمية في مجاليّ الأحياء والكيمياء، ومع ذلك، فإنَّ عوامّ الباحثين أمثالي يستطيعون تحصيل فوائد جمَّة وكثيرة من الكتاب رغم ثِقَل مادَّته.

المُقدَّمة، مع الفصل الأول والأخير هُم خُلاصة هذا الكتاب، وأنصح على الأقل بقراءة هذه الفُصُول بشكل كامل، مع تصفُّح هذا العصير.

Introduction: A Rare Find

· Theists and atheists alike can see design in biological and biochemical systems. Even the well-known evolutionary biologist Richard Dawkins, an outspoken atheist, acknowledges that “biology is the study of complicated things that give the appearance of having been designed for a purpose.” [Richard Dawkins, The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design (New York: Norton, 1996), 1.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 158-160). Baker Books. Kindle Edition.]

· The late Francis Crick, who shared the Nobel Prize for discovering the structure of DNA, cautioned, “Biologists must constantly keep in mind that what they see was not designed, but rather evolved.”5 So even though life’s chemistry looks as if it’s the product of a Creator, many in the scientific community suppress this obvious intuition. [Francis Crick, What Mad Pursuit (New York: Basic Books, 1988), 138.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 165-167). Baker Books. Kindle Edition.]

· As biochemists learn more about the details of the cell’s chemical systems, the appearance of design becomes increasingly pervasive and profound. Currently, hundreds of scientists who represent a range of scientific disciplines express skepticism about “the ability of random mutation and natural selection to account for the complexity of life.”6 This skepticism largely fuels the recent resurgence of the creation (intelligent design)/evolution controversy in America. [“A Scientific Dissent from Darwinism,” Discovery Institute, February 2007, http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=660.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 172-176). Baker Books. Kindle Edition.]

· According to Behe, irreducible complexity describes “a single system composed of several well-matched interacting parts that contribute to basic function, wherein removal of any one of the parts causes the system to effectively cease functioning.” [Behe, Darwin’s Black Box, 39.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 181-183). Baker Books. Kindle Edition.]

· The case for intelligent design made in Darwin’s Black Box is compelling. Still, Behe’s explanation rises and falls on the perceived validity of the concept of irreducible complexity. Several scientists have leveled significant challenges against this argument.8 And, even though Behe has responded to these critics, many skeptics remain unconvinced.9 [8. For example, Bruce H. Weber, “Biochemical Complexity: Emergence or Design?” Rhetoric & Public Affairs 1 (1998): 611–16; Philip Kitcher, “Born-Again Creationism,” in Intelligent Design Creationism and Its Critics: Philosophical, Theological and Scientific Perspectives, ed. Robert T. Pennock (Cambridge, MA: MIT Press, 2001), 257–87; Matthew J. Brauer and Daniel R. Brumbaugh, “Biology Remystified: The Scientific Claims of the New Creationists,” in Intelligent Design Creationism and Its Critics, 289–334. 9. Michael J. Behe, William A. Dembski, and Stephen C. Meyer, Science and Evidence for Design in the Universe (San Francisco: Ignatius, 2000), 133–49.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 190-192). Baker Books. Kindle Edition.]

· In many respects, Behe pioneered the biochemical case for intelligent design in Darwin’s Black Box. The Cell’s Design continues this exploration and strives to make the biochemical case for a Creator much more compelling. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 208-210). Baker Books. Kindle Edition.]

· In most works of this nature, the authors are quick—perhaps too quick—to declare the inability of evolutionary processes to produce certain features of the biological realm. Their argument goes something like this: “If evolution can’t produce it, then a Creator must have.” The Cell’s Design avoids this negative approach. Instead of focusing on what evolution can or cannot do, this book emphasizes the aspects of biochemical systems that make a positive case for intelligent design. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 217-221). Baker Books. Kindle Edition.]

· The technical terminology that is so much a part of cell biology and biochemistry can feel overwhelming for many people. So, the details have been limited to those necessary to show the Creator’s fingerprints. However, the Creator’s signature style is ultimately most evident in the finer points of the cell’s chemistry. Please keep in mind, that for an Artist’s work to be fully appreciated, one must take the time to study its subtleties and nuances. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 231-234). Baker Books. Kindle Edition.]

1 Masterpiece or Forgery?

· Philosopher Jay Richards and astronomer Guillermo Gonzalez point out in their book The Privileged Planet that most individuals have no idea how they make the distinction between an intelligently designed object and one generated by natural processes. They just intuitively do. [Guillermo Gonzalez and Jay W. Richards, The Privileged Planet: How Our Place in the Cosmos Is Designed for Discovery (Washington, DC: Regnery, 2004), 293–311.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 268-270). Baker Books. Kindle Edition.]

· To properly reason from analogy, several factors must be considered: • The relevance of similarities is critical. The properties being compared must be relevant to the conclusion. • The number of similarities that are part of the analogy impacts the likeliness of the conclusion. The greater the number of similarities the greater the validity of the conclusion. • The number of events, objects, or systems that enter into the comparison influences the conclusion. The greater the number of separate comparisons, the more probable the conclusion. • The diversity of the events, objects, or systems compared has bearing on the conclusion. Greater diversity translates into greater confidence about the conclusion reached through comparison. • Disanalogy is important. In addition to shared similarities—the ways in which the events, objects, or systems differ must be considered. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 392-400). Baker Books. Kindle Edition.]

2 Mapping The Territory

· The same year that Jan Vermeer painted The Artist’s Studio (1665), Robert Hooke discovered cells.4 Following his initial work, a number of biologists reported the existence of cells in plants and animals. These discoveries culminated in the cell theory developed independently by Matthias Schleiden in 1838 and Theodor Schwann in 1839. This theory states that cells are the fundamental units of life and the smallest entities that can be considered “life.” As a corollary, all organisms consist of one or more cells. Most life-forms on Earth are single-celled (bacteria, archaea, and protozoans). Multicellular organisms (plants, animals, and fungi) are made up of specialized cells that carry out the many activities necessary for life. [4. Details about the cell’s structural and chemical makeup can be found in any introductory biology textbook. For this chapter, the book consulted was Karen Arms and Pamela S. Camp, Biology, 3rd ed. (Philadelphia: Saunders College Publishing, 1987).] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 461-466). Baker Books. Kindle Edition.]

· By the mid-1950s, biologists recognized two fundamentally distinct cell types: eukaryotic and prokaryotic. Eukaryotic cells contain a nucleus, organelles, and internal membrane systems. Unicellular protists and multicellular fungi, plants, and animals are examples of eukaryotic organisms. Prokaryotic cells are typically about one micron in diameter. These cells appear to be much simpler than eukaryotic cells. Apart from a cell boundary, prokaryotes lack any visible defining features. They don’t have a nucleus, organelles, or internal membranes. Their genetic material consists of “naked” highly coiled DNA that resides in the cytoplasm. Bacteria and archaea are prokaryotic organisms. Archaea are similar to bacteria in appearance, but fundamentally differ in their biochemical makeup. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 472-478). Baker Books. Kindle Edition.]

4 Such A Clean Machine

· Motors and machines are found not only under the hoods of automobiles. They are also found inside of cells. One of the most remarkable advances in biochemistry during the last part of the twentieth century has been the recognition that many biochemical systems function as molecular-level machines. Remarkably, some of these biomolecular motors bear an eerie resemblance to humanly designed engines. Yet, these biomachines are far superior in construction and operation than their man-made counterparts. Biomachines make a powerful case for biochemical intelligent design and reinvigorate one of history’s most well-known arguments for a Creator’s existence: the Watchmaker argument popularized in the eighteenth century by William Paley, a British theologian. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 984-989). Baker Books. Kindle Edition.]

· The bacterial flagellum has become the “poster child” for Intelligent Design.3 The flagellum looks like a whip and extends from the bacterial cell surface. Some bacteria have only a single flagellum, others possess several. Rotation of the flagellum(a) allows the bacterial cell to navigate its environment in response to various chemical signals. [Michael J. Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution (New York: Free Press, 1996), 69–73.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 997-1000). Baker Books. Kindle Edition.]

· An ensemble of over forty different kinds of proteins makes up the typical bacterial flagellum. These proteins function in concert as a literal rotary motor. The bacterial flagellum’s components stand as direct analogs to the parts of a man-made motor, including a rotor, stator, drive shaft, bushing, universal joint, and propeller.4 The bacterial flagellum is essentially a molecular-sized electrical motor. The flow of positively charged hydrogen ions through the bacterial inner membrane powers the flagellum’s rotation.5 As research continues on the bacterial flagellum, its machinelike character becomes increasingly evident.6 [(October 1995): 489–520. 5. David F. Blair, “Flagellar Movement Driven by Proton Translocation,” FEBS Letters 545 ( June 12, 2003): 86–95; Christopher V. Gabel and Howard C. Berg, “The Speed of the Flagellar Rotary Motor of Escherichia coli Varies Linearly with Protonmotive Force,” Proceedings of the National Academy of Sciences, USA 100 ( July 22, 2003): 8748–51. 6. For example, a cursory survey of the prestigious journal Nature over the last several years turns up the following papers: Scott A. Lloyd et al., “Structure of the C-Terminal Domain of FliG, a Component of the Rotor in the Bacterial Flagellar Motor,” Nature 400 ( July 29, 1999): 472–75; William S. Ryu, Richard M. Berry, and Howard C. Berg, “Torque-Generating Units of the Flagellar Motor of Escherichia coli Have a High Duty Ratio,” Nature 403 ( January 27, 2000): 444–47; Fadel A. Samatey et al., “Structure of the Bacterial Flagellar Hook and Implication for the Molecular Universal Joint Mechanism,” Nature 431 (October 28, 2004): 1062–68; Yoshiyuki Sowa et al., “Direct Observation of Steps in Rotation of the Bacterial Flagellar Motor,” Nature 437 (October 6, 2005): 916–19.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1003-1008). Baker Books. Kindle Edition.]

· The rotary motor, F1–F0 ATPase, plays a central role in harvesting energy for cellular use.7 F1–F0 ATPase associates with cell membranes. The mushroom-shaped F1 portion of the complex extends above the membrane’s surface. The “button of the mushroom” literally corresponds to an engine turbine. [Matti Saraste, “Oxidative Phosphorylation at the Fin de Siècle,” Science 283 (March 5, 1999): 1488–93.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1009-1013). Baker Books. Kindle Edition.]

· The rotary motor F1–F0 ATPase consists of a rotor, cam, turbine, and stator. The F1–F0 ATPase turbine interacts with the part of the complex that looks like a “mushroom stalk.” This stalklike component functions as a rotor.8 The flow of positively charged hydrogen ions (or in some instances sodium ions) through the F0 component embedded in the cell membrane drives the rotation of the rotor.9 A rod-shaped protein structure that also extends above the membrane surface performs as a stator. This protein rod interacts with the turbine holding it stationary as the rotor rotates. [8. Hiroyuki Noji, “The Rotary Enzyme of the Cell: The Rotation of F1-ATPase,” Science 282 (December 4, 1998): 1844–45; William S. Allison, “F1-ATPase: A Molecular Motor that Hydrolyzes ATP with Sequential Opening and Closing of Catalytic Sites Coupled to Rotation of Its ã Subunit,” Accounts of Chemical Research 31 (December 1998): 819–26; Hiroyuki Noji and Masasuke Yoshida, “The Rotary Machine in the Cell, ATP Synthase,” Journal of Biological Chemistry 276 ( January 19, 2001): 1665–68. 9. Vinit K. Rastogi and Mark E. Girvin, “Structural Changes Linked to Proton Translocation by Subunit c of the ATP Synthase,” Nature 402 (November 18, 1999): 263–68; Joachim Weber and Alan E. Senior, “ATP Synthesis Driven by Proton Transport in F1–F0–ATP Synthase,” FEBS Letters 545 ( June 12, 2003): 61–70; Wolfgang Junge and Nathan Nelson, “Nature’s Rotary Electromotors,” Science 308 (April 29, 2005): 642–44.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1016-1022). Baker Books. Kindle Edition.]

· The molecular motor myosin generates the force that produces muscle contraction and transports organelles throughout the cell. In contrast to the biomotors just discussed, myosin is not a rotary motor. Rather, it’s a linear motor with a rigid lever arm. Myosin also possesses a molecular hinge that functions as a pivot point for the swinging lever arm (see figure 4.7).21 Through genetic engineering and biophysical studies, researchers have directly (and indirectly) observed the swing of myosin’s lever arm and the swiveling of the myosin hinge.22 These measurements of the myosin motor in operation provide convincing proof of the swinging lever arm model for myosin motor function and myosin’s machinelike character. [21. Steven M. Block, “Fifty Ways to Love Your Lever: Myosin Motors,” Cell 87 (October 18, 1996): 151–57; Roger Cooke, “The Actomyosin Engine,” FASEB Journal 9 (May 1995): 636–42. 22. For example, James D. Jontes, Elizabeth M. Wilson-Kubalek, and Ronald A. Milligan, “A 32° Tail Swing in Brush Border Myosin I on ADP Release,” Nature 378 (December 14, 1995): 751–53; Michael Whittaker et al., “A 35-Å Movement of Smooth Muscle Myosin on ADP Release,” Nature 378 (December 14, 1995): 748–51; Jeffery T. Finer, Robert M. Simmons, and James A. Spudich, “Single Myosin Molecule Mechanics: Piconewton Forces and Nanometre Steps,” Nature 368 (March 10, 1994): 113–19; Roberto Dominguez et al., “Crystal Structure of a Vertebrate Smooth Muscle Myosin Motor Domain and Its Complex with Essential Light Chain: Visualization of the Pre-Power Stroke State,” Cell 94 (September 4, 1998): 559–71; A. F. Huxley, “Support for the Lever Arm,” Nature 396 (November 26, 1998): 317–18; Yoshikazu Suzuki et al., “Swing of the Lever Arm of a Myosin Motor at the Isomerization and Phosphate-Release Steps,” Nature 396 (November 26, 1998): 380–83; Ian Dobbie et al., “Elastic Bending and Active Tilting of Myosin Heads During Muscle Contraction,” Nature 396 (November 26, 1998): 383–87; Fumi Kinose et al., “Glycine 699 Is Pivotal for the Motor Activity of Skeletal Muscle Myosin,” Journal of Cell Biology 134, no. 4 (August 1996): 895–909; Thomas P. Burghardt et al., “Tertiary Structural Changes in the Cleft Containing the ATP Sensitive Tryptophan and Reactive Thiol Are Consistent with Pivoting of the Myosin Heavy Chain at Gly699,” Biochemistry 37 ( June 2, 1998): 8035–47; Katalin Ajtai et al., “Trinitrophenylated Reactive Lysine Residue in Myosin Detects Lever Arm Movement during the Consecutive Steps of ATP Hydrolysis,” Biochemistry 38 (May 18, 1999): 6428–40; J. E. T. Corrie et al., “Dynamic Measurement of Myosin Light-Chain-Domain Tilt and Twist in Muscle Contraction,” Nature 400 ( July 29, 1999): 425–30; Josh E. Baker et al., “A Large and Distinct Rotation of the Myosin Light Chain Domain Occurs upon Muscle Contraction,” Proceedings of the National Academy of Sciences, USA 95 (March 17, 1998): 2944–49; Susan Lowey, Guillermina S. Waller, and Kathleen M. Trybus, “Skeletal Muscle Myosin Light Chains Are Essential for Physiological Speeds of Shortening,” Nature 365 (September 30, 1993): 454–56.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1126-1132). Baker Books. Kindle Edition.]

· Dynein is a massive molecular motor that plays a role in generating a wavelike motion in eukaryotic flagella (which possess a fundamentally different structure than bacterial flagella). These motors also move cargo throughout the cell along microtubule tracks that are part of the cell’s cytoskeleton (chapter 2, p. 39). In addition, dynein helps maintain the Golgi apparatus (chapter 2, p. 40) and plays a role in cell division (mitosis). [Stephen M. King, “The Dynein Microtubule Motor,” Biochimica et Biophysica Acta (BBA) / Molecular Cell Research 1496 (March 17, 2000): 60–75.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1133-1136). Baker Books. Kindle Edition.]

· Dynein is a massive molecular motor that moves cargo throughout the cell along microtubule tracks. Dynein’s power stroke alters the angle between the cargo-binding stalk and the stalk that connects the AAA ring to the microtubule. Remarkably, the distance that dynein moves along the microtubule for each power stroke varies with the size of the cargo attached to this molecular motor. As the load increases, the distance that dynein moves per power stroke decreases. It appears that the dynein motor literally shifts gears in response to the load. [R. A. Cross, “Molecular Motors: Dynein’s Gearbox,” Current Biology 14 (May 4, 2004): R355–56; Roop Mallik et al., “Cytoplasmic Dynein Functions as a Gear in Response to Load,” Nature 427 (February 12, 2004): 649–52.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1147-1151). Baker Books. Kindle Edition.]

· Experience teaches that machines and motors don’t just happen. Even the simplest require thoughtful design and manufacture. This common understanding undergirds one of history’s best known arguments for God’s existence. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1174-1175). Baker Books. Kindle Edition.]

· According to the Watchmaker analogy: Watches display design. Watches are the product of a watchmaker. Similarly: Organisms display design. Therefore, organisms are the product of a Creator. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1194-1198). Baker Books. Kindle Edition.]

· Atheist B. C. Johnson underscored Hume’s case by arguing that Paley did not use a strict enough criterion for identifying intelligent design. Paley argued that design is evident when a system contains several parts that work together for a purpose. Johnson, in contrast, says, “We can identify a thing as designed, even when we do not know its purpose, only if it resembles the things we make to express our purposes.”33 Others argued that organisms are not machines, and those who saw them as such took the analogy too far. According to these skeptics, the analogy between machines and living systems was simply an explanatory analogy, an illustration that provided a framework to guide understanding.34 The merit of the Watchmaker argument then rests on the questions: Do living systems resemble man-made machines enough to warrant the analogy? And, if so, how strong is this analogy, and can a conclusion reasonably be drawn from it? [33. B. C. Johnson, The Atheist Debater’s Handbook (Buffalo: Prometheus Books, 1981), 45. 34. David Depew, “Intelligent Design and Irreducible Complexity: A Rejoinder,” Rhetoric and Public Affairs 1, no. 4 (1998): 571–78.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1206-1214). Baker Books. Kindle Edition.]

· The Watchmaker line of reasoning was best articulated by Anglican natural theologian William Paley (1743–1805). In the opening pages of his 1802 work Natural Theology; or, Evidences of the Existence and Attributes of the Deity Collected from the Appearances of Nature, Paley sets forth his famous analogy. In crossing a heath, suppose I pitched my foot against a stone, and were asked how the stone came to be there; I might possibly answer, that, for any thing I knew to the contrary, it had lain there for ever. . . . But suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place; I should hardly think of the answer which I had before given, that, for any thing I knew, the watch might have always been there. Yet why should not this answer serve for the watch as well as for the stone? Why is it not as admissible in the second case, as in the first? For this reason, and for no other, viz. that, when we come to inspect the watch, we perceive (what we could not discover in the stone) that its several parts are framed and put together for a purpose, e.g. that they are so formed and adjusted as to produce motion, and that motion so regulated as to point out the hour of the day; that, if the different parts had been differently shaped from what they are, of a different size from what they are, or placed after any other manner, or in any other order, than that in which they are placed, either no motion at all would have been carried on in the machine, or none which would have answered the use that is now served by it. . . . This mechanism being observed . . . , the inference, we think, is inevitable, that the watch must have had a maker: that there must have existed, at some time, and at some place or other, an artificer or artificers who formed it for the purpose which we find it actually to answer; who comprehended its construction, and designed its use. [William Paley, Natural Theology; or, Evidences of the Existence and Attributes of the Deity Collected from the Appearances of Nature, 12th ed. (1802; Weybridge, Surrey, UK: printed by S. Hamilton, 1809), 1–3.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1176-1190). Baker Books. Kindle Edition.]

· Biomotors and machines are not explanatory analogies. The motors and machines described in this chapter are motors and machines by definition. And, because machines stem from the work of a designer, these molecular-level machines must emanate from the work of an Intelligent Designer. The strong, close, and numerous analogies between biological motors and man-made devices logically compel the conclusion that these biomotors, and consequently life’s chemistry, are the product of intelligent design. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1219-1223). Baker Books. Kindle Edition.]

· The analogy between molecular motors and man-made machinery finds additional strength in cutting-edge work conducted by researchers developing nanodevices.35 These molecular-level devices are comprised of precisely arranged atoms and molecules. With dimensions less than 1,000 nanometers (one-billionth of a meter), nanostructures have applications in manufacturing, electronics, medicine, biotechnology, and agriculture among others. [Robert F. Service, “Borrowing from Biology to Power the Petite,” Science 283 ( January 1, 1999): 27–28.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1224-1227). Baker Books. Kindle Edition.]

· An important breakthrough was announced at the Sixth Foresight Conference on Molecular Nanotechnology (November 1998). Scientists, working separately at Cornell University and at the University of Washington in Seattle, “like molecular mechanics . . . [,] have unbolted the motors from their cellular moorings, remounted them on engineered surfaces and demonstrated that they can perform work.” [Service, “Borrowing from Biology,” 27–28.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1228-1231). Baker Books. Kindle Edition.]

· According to Wang, “The Kai complexes are a rotary clock for phosphorylation, which sets up the destruction pace of the night-dominant Kai complexes and the timely releases of KaiA.” [Jimin Wang, “Recent Cyanobacterial Kai Protein Structures Suggest a Rotary Clock,” Structure 13 (May 2005): 735–41.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1254-1255). Baker Books. Kindle Edition.]

· This work is just the beginning. Even greater support for the Watchmaker argument will likely accrue with future advances in nan-otechnology—particularly as researchers continue to borrow from the superior designs found inside the cell to drive developments in nanotechnology. [Joe Alper, “Chemists Look to Follow Biology Lead,” Science 295 (March 29, 2002): 2396–97; Nadrian C. Seeman and Angela M. Belcher, “Emulating Biology: Building Nanostructures from the Bottom Up,” Proceedings of the National Academy of Sciences, USA 99 (April 30, 2002): 6451–55; George M. Whitesides, “The Once and Future Nanomachine,” Scientific American, September 2001, 78–83.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1275-1277). Baker Books. Kindle Edition.]

· Recent work, described as “science at its very best,” provides insight into the superior intelligence of the Designer responsible for the molecular motors found in nature.44 In the quest to build nanodevices, synthetic chemists have produced molecular switches, gears, valves, shuttles, ratchets, turnstiles, and elevators.45 These molecular-level devices have obvious utility in nanodevices, but their construction holds additional significance. They represent a significant step towards the “holy grail” of nanotechnology: single-molecule rotary motors capable of rotating in a single direction that can power movement in nanodevices.46 [44. Corinna Wu, “Molecular Motors Spin Slowly but Surely,” Science News 156 (September 11, 1999): 165. 45. See, for example, Jovica D. Badjiæ et al., “A Molecular Elevator,” Science 303 (March 19, 2004): 1845–49; David I. Gittins et al., “A Nanometre-Scale Electronic Switch Consisting of a Metal Cluster and Redox-Addressable Groups,” Nature 408 (November 2, 2000): 67–69; Thoi D. Nguyen et al., “A Reversible Molecular Valve,” Proceedings of the National Academy of Sciences, USA 102 ( July 19, 2005): 10029–34; Thomas C. Bedard and Jeffrey S. Moore, “Design and Synthesis of Molecular Turnstiles,” Journal of the American Chemical Society 117 (November 1, 1995): 10622–71; T. Ross Kelly, Imanol Tellitu, and José Pérez Sestelo, “In Search of Molecular Ratchets,” Angewandte Chemie 36 (September 17, 1997): 1866–68; Richard A. Bissell et al., “A Chemically and Electrochemically Switchable Molecular Shuttle,” Nature 369 (May 12, 1994): 133–37; Peter R. Ashton et al., “Acid-Base Controllable Molecular Shuttles,” Journal of the American Chemical Society 120 (November 25, 1998): 11932–42. 46. See, for example, Jonathan Clayden and Jennifer H. Pink, “Concerted Rotation in a Tertiary Aromatic Amide: Towards a Simple Molecular Gear,” Angewandte Chemie 37 (August 3, 1998): 1937–39; Anne Marie Schoevaars et al., “Toward a Switchable Molecular Rotor: Unexpected Dynamic Behavior of Functionalized Overcrowded Alkenes,” Journal of Organic Chemistry 62 ( July 25, 1997): 4943–48.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1278-1283). Baker Books. Kindle Edition.]

· Significant steps toward this goal were achieved in 1999 when a team of researchers from Boston College and a collaborative team from the University of Groningen in the Netherlands and Tohuku University in Japan independently designed and synthesized the first single-molecule rotary motors with the capability of spinning in one direction.47 The rotation of the motors is driven by UV radiation and heat or through chemical energy. These synthetic molecular motors are the product of careful design and planning. The light- and heat-driven molecular motor made by the team from the universities of Groningen and Tohuku depends upon the “unique combination of axial chirality and the two chiral centers in the molecule” positioned just right in three-dimensional space.48 Likewise, the molecular motor developed by the team from Boston College is dependent upon molecular chirality, as well as fine-tuning of the molecular substituents.49 It is clear these molecular motors did not happen by accident or as the natural outworking of the laws of chemistry and physics. In fact, the chemically driven molecular motor—comprised of only seventy-eight atoms—took over four years to build.50 [47. T. Ross Kelly, Harshani De Silva, and Richard A. Silva, “Unidirectional Rotary Motion in a Molecular System,” Nature 401 (September 9, 1999): 150–52; Nagatoshi Komura et al., “Light-Driven Monodirectional Molecular Rotor,” Nature 401 (September 9, 1999): 152–55. 48. Komura et al., “Molecular Rotor,” 152–55. 49. Kelly, De Silva, and Silva, “Rotary Motion,” 150–52. 50. Anthony P. Davis, “Synthetic Molecular Motors,” Nature 401 (September 9, 1999): 120–21.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1284-1293). Baker Books. Kindle Edition.]

· Work done in the burgeoning arena of nanoscience and nanotechnology not only highlights the machinelike character of these biomotors, it exposes the elegance and sophistication of their design. The cell’s machinery is vastly superior to anything that the best human designers can conceive or accomplish. As a case in point, bacterial flagella operate near 100 percent efficiency.61 This capability stands in sharp distinction to man-made machines. Electric motors only function at 65 percent efficiency and the best combustion engines only attain a 30 percent efficiency. The superiority of the cell’s molecular machines is consistent with the notion that the intelligent designer is the Creator described in the Bible. It also prompts the question: Is it really reasonable to conclude that these biomotors are the products of blind, undirected physical and chemical processes, when they are far beyond what the best human minds can achieve? Life’s biomolecular motors not only bring to light one of the most remarkable design features inside the cell, they also highlight the Creator’s artistry. The elegance and beauty of the cell’s machinery cannot be overlooked in the midst of making the case for intelligent design. [Kazuhiko Kinosita Jr. et al., “A Rotary Molecular Motor That Can Work at Near 100% Efficiency,” Philosophical Transactions of the Royal Society B 355 (April 29, 2000): 473–89.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1372-1381). Baker Books. Kindle Edition.]

5 Which Came First?

· DNA houses the information the cell needs to make proteins, which play a role in virtually every cell function. Proteins also help build practically every cellular and extracellular structure (see chapter 2, p. 42). Given this importance, the information housed in DNA defines life’s most fundamental operations and structures. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1413-1415). Baker Books. Kindle Edition.]

· Mutual interdependence of DNA and proteins stands as a major stumbling block for evolutionary explanations of life’s origin.4 Origins-of-life researchers even refer to this conundrum as the chicken-and-egg paradox. Because these two molecules are so complex, scientists don’t think DNA and proteins could simultaneously arise from a primordial soup. [Iris Fry, The Emergence of Life on Earth: A Historical and Scientific Overview (New Brunswick, NJ: Rutgers University Press, 2000), 100–101.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1422-1425). Baker Books. Kindle Edition.]

· While the RNA-world hypothesis rescues the origin-of-life paradigm from the chicken-and-egg paradox on paper, in practical terms it appears largely untenable. Numerous problems abound for the RNA-world hypothesis.5 For example, it’s unlikely that the prebiotic chemical reactions identified in the laboratory for the production of ribose and the nucleobases could take place on early Earth. And, even if these compounds did form, it’s unlikely they could assemble into functional RNA molecules. In fact, Leslie Orgel, one of the world’s leading origin-of-life researchers, has said, “It would be a miracle if a strand of RNA ever appeared on the primitive Earth.”6 [5. Fazale Rana and Hugh Ross, Origins of Life: Biblical and Evolutionary Models Face Off (Colorado Springs: NavPress, 2004), 109–21. 6. Leslie Orgel quoted in ibid., 115.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1430-1435). Baker Books. Kindle Edition.]

· The “chicken-and-egg” systems of DNA replication, protein synthesis, and protein folding raise questions about how life’s chemistry came into existence. Molecules that comprise these operations can’t exist apart from one another—unless a Divine Artist created them at the same time. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1528-1530). Baker Books. Kindle Edition.]

6 Inordinateattention to Detail

· The last half-century of research into the structure-function relationships of biochemical systems has consistently demonstrated that the function of biomolecules critically depends on the exact location and spatial orientation of its chemical constituents. In many instances, function is controlled by just a few chemical groups. For example, substituting a single amino acid in some proteins can have dramatic effects on their function. In other cases, the strict spatial arrangement of a suite of amino acids controls the protein’s function. (See the discussion of aquaporins below.) In addition, the interactions between biomolecules often depend on the exacting placement of chemical groups. For example, in many biochemical pathways, proteins bind with each other. These protein-protein interactions are highly specific, occurring only between particular proteins. Recent work, for example, indicates that the specificity of protein binding depends on the exact placement of only a few amino acids located on the three-dimensional surface of the folded protein.4 The number of high-precision biochemical systems is far too numerous to detail. As each week passes, biochemists report on more and more examples of biochemical fine-tuning in the scientific literature.5 Looking at a few examples conveys a sense of the remarkable exactness of biochemical systems. [4. Deepa Rajamani et al., “Anchor Residues in Protein-Protein Interactions,” Proceedings of the National Academy of Sciences, USA 101 (August 3, 2004): 11287–92. 5. Some recently discovered examples of biochemical fine-tuning can be found at http://www.reasons.org/ as part of the Today’s New Reason To Believe (TNRTB) feature. Some examples that have appeared recently under the TNRTB banner include: Won-Ho Cho et al., “CDC7 Kinase Phosphorylates Serine Residues Adjacent to Acidic Amino Acids in Minichromosome Maintenance 2 Protein,” Proceedings of the National Academy of Sciences, USA 103 (August 1, 2006): 11521–26; Daniel F. Jarosz et al., “A Single Amino Acid Governs Enhanced Activity of DinB DNA Polymerases on Damaged Templates,” Science 439 ( January 12, 2006): 225–28; William H. McClain, “Surprising Contribution to Aminoacylation and Translation of Non-Watson-Crick Pairs in tRNA,” Proceedings of the National Academy of Sciences, USA 103 (March 21, 2006): 4570–75; Kobra Haghighi et al., “A Mutation in the Human Phospholamban Gene, Deleting Arginine 14, Results in Lethal, Hereditary Cardiomyopathy,” Proceedings of the National Academy of Sciences, USA 103 ( January 31, 2006): 1388–93; Surajit Ganguly et al., “Melatonin Synthesis: 14-3-3-Dependent Activation and Inhibition of Arylalkylamine N-Acetyltransferase Mediated by Phosphoserine-205,” Proceedings of the National Academy of Sciences, USA 102 ( January 25, 2005): 1222–27; Yohei Kirino et al., “Specific Correlation between the Wobble Modification Deficiency in Mutant tRNAs and the Clinical Features of a Human Mitochondrial Disease,” Proceedings of the National Academy of Sciences, USA 102 (May 17, 2005): 7127–32; Yoshie Hanzawa, Tracy Money, and Desmond Bradley, “A Single Amino Acid Converts a Repressor to an Activator of Flowering,” Proceedings of the National Academy of Sciences, USA 102 (May 24, 2005): 7748–53; Stefan Trobro and Johan Åqvist, “Mechanism of Peptide Bond Synthesis on the Ribosome,” Proceedings of the National Academy of Sciences, USA 102 (August 30, 2005): 12395–400; Tianbing Xia et al., “RNA-Protein Recognition: Single-Residue Ultrafast Dynamical Control of Structural Specificity and Function,” Proceedings of the National Academy of Sciences, USA 102 (September 13, 2005): 13013–18; A. J. Rader et al., “Identification of Core Amino Acids Stabilizing Rhodopsin,” Proceedings of the National Academy of Sciences, USA 101 (May 11, 2004): 7246–51; Rajamani et al., “Anchor Residues,” 11287–92; Lina Salomonsson et al., “A Single-Amino Acid Lid Renders a Gas-Tight Compartment within a Membrane-Bound Transporter,” Proceedings of the National Academy of Sciences, USA 101 (August 10, 2004): 11617–21; Gianguido Coffa and Alan R. Brash, “A Single Active Site Residue Directs Oxygenation Stereospecificity in Lipoxygenases: Stereocontrol Is Linked to the Position of Oxygenation,” Proceedings of the National Academy of Sciences, USA 101 (November 2, 2004): 15579–84; Isabel Martinez-Argudo, Richard Little, and Ray Dixon, “A Crucial Arginine Residue Is Required for a Conformational Switch in NifL to Regulate Nitrogen Fixation in Azotobacter vinelandii,” Proceedings of the National Academy of Sciences, USA 101 (November 16, 2004): 16316–21; Oded Danziger et al., “Conversion of the Allosteric Transition of GroEL from Concerted to Sequential by the Single Mutation Asp-155 ¨ Ala, Proceedings of the National Academy of Sciences, USA 100 (November 25, 2003): 13797802; Hu Pan et al., Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA Recognition through a Combination of Rigid Docking and Induced Fit,” Proceedings of the National Academy of Sciences, USA 100 (October 28, 2003): 12648–53; Yoshimitsu Kuwabara et al., “Unique Amino Acids Cluster for Switching from the Dehydrogenase to Oxidase Form of Xanthine Oxidoreductase,” Proceedings of the National Academy of Sciences, USA 100 ( July 8, 2003): 8170–75. This sampling represents the tip of the iceberg. Countless examples of biochemical fine-tuning are littered throughout the scientific literature.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1563-1573). Baker Books. Kindle Edition.]

· Once a protein is damaged, it’s prone to aggregate with other proteins. These aggregates disrupt cellular activities. Protein degradation and turnover, in many respects, are just as vital to the cell’s operation as protein production. And, as is the case for mRNAs, protein degradation is an exacting, delicately balanced process.20 This complex undertaking begins with ubiquitination. When damaged, proteins misfold, adopting an unnatural three-dimensional shape. Misfolding exposes amino acids in the damaged protein’s interior. These exposed amino acids are recognized by E3 ubiquitin ligase, an enzyme that attaches a small protein molecule (ubiquitin) to the damaged protein.21 Ubiquitin functions as a molecular tag, informing the cell’s machinery that the damaged protein is to be destroyed. Severely damaged proteins receive multiple tags. [20. Michael H. Glickman and Noam Adir, “The Proteasome and the Delicate Balance between Destruction and Rescue,” PLoS Biology 2 ( January 20, 2004): doi:10.1371/journal.pbio.0020013, http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0020013. 21. Stryer, Biochemistry, 794–95.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1705-1712). Baker Books. Kindle Edition.]

· A massive protein complex, a proteasome, destroys damaged ubiquitinated proteins, functioning like the cell’s garbage can. The overall molecular architecture of the proteasome consists of a hollow cylinder topped with a lid that can exist in either an opened or closed conformation. Protein breakdown takes place within the cylinder’s interior. The lid portion of the proteasome controls the entry of ubiquitinated proteins into the cylinder. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1715-1718). Baker Books. Kindle Edition.]

· The molecular precision—pervasive in nearly all aspects of life’s chemical systems—raises questions about the capability of undirected evolutionary processes to achieve such carefully crafted designs (see chapter 14, p. 270). The molecular fine-tuning of biochemical systems is exactly what would be expected if life is the product of a Creator. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1756-1758). Baker Books. Kindle Edition.]

7 The Proper Arrangement of Elements

· The last half-century or so of research has yielded remarkable details about the structure and function of a myriad of proteins. Based on these insights, most biochemists would conclude that proteins are structured in the most advantageous way for their specific biochemical roles. So, too, is DNA. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1785-1787). Baker Books. Kindle Edition.]

· Amino acids (small subunit molecules) link together in a head-to-tail fashion to form the polypeptide chains that constitute proteins (see chapter 2, p. 42). In principle, these molecules can join up in any possible sequence. Some sequences generate useful proteins. Many yield junk polypeptides that lack function. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1788-1790). Baker Books. Kindle Edition.]

· Recent studies indicate that, like proteins, the structural features of DNA are also exceptional. DNA consists of two chainlike molecules (poly-nucleotides) that twist around each other to form the DNA double helix (see chapter 2, p. 48). The cell’s machinery forms polynucleotide chains by linking together four different subunit molecules called nucleotides. The nucleotides used to build DNA chains are adenosine (A), guanosine (G), cytidine (C), and thymidine (T) (see figure 2.7, p. 49). DNA houses the information needed to make all the polypeptides used by the cell. The sequence of nucleotides in DNA strands specifies the sequence of amino acids in polypeptide chains. Scientists refer to this sequence of nucleotides as a gene. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1846-1852). Baker Books. Kindle Edition.]

· There are sixty-four possible codons that can be used to specify the twenty amino acids. Because of the excess number, however, more than one codon can correspond to the same amino acid. In fact, up to six different codons specify some amino acids—others are signified by only one. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1855-1858). Baker Books. Kindle Edition.]

· Biochemists have known for some time that highly repetitive nucleotide sequences are unstable and readily mutate. The most common type of mutation to repetitive sequences is the insertion and/or deletion (indels) of one or more nucleotides. These mutations are devastating. They almost always result in the production of highly defective polypeptide chains. A survey of the genomes from several organisms by researchers at the University of California, San Diego, indicates that codon usage in genes is designed to avoid the type of repetition that leads to unstable sequences.11 Although the details are beyond the scope of this book, other studies similarly indicate that codon usage in genes is also set up to maximize the accuracy of protein synthesis at the ribosome12 (see chapter 2, p. 50). [11. Martin Ackermann and Lin Chao, “DNA Sequences Shaped by Selection for Stability,” PLoS Genetics 2 (February 2006): e22. 12. Hiroshi Akashi, “Synonymous Codon Usage in Drosophila melanogaster: Natural Selection and Translational Accuracy,” Genetics 136 (March 1994): 927–35; Xuhua Xia, “How Optimized Is the Translational Machinery in Escherichia coli, Salmonella typhimurium and Saccharomyces cerevisiae?” Genetics 149 (May 1998): 37–44; Marco Archetti, “Selection on Codon Usage for Error Minimization at the Protein Level,” Journal of Molecular Evolution 59 (September 2004): 400–15; Eduardo P. C. Rocha, “Codon Usage Bias from tRNA’s Point of View: Redundancy, Specialization, and Efficient Decoding for Translation Optimization,” Genome Research 14 (November 2004): 2279–86.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1861-1867). Baker Books. Kindle Edition.]

· For nearly twenty years, biochemists have understood why phosphates are critical to the structures of DNA and RNA.13 This chemical group is perfectly suited to form a stable backbone for the DNA molecule. Phosphates can form bonds with two sugars at the same time (phosphodiester bonds) to bridge two nucleotides, while retaining a negative charge (see figure 7.3). Other compounds can form bonds between two sugars but won’t retain a negative charge. The negative charge on the phosphate group imparts the DNA backbone with stability protecting it from cleavage by reactive water molecules. [F. H. Westheimer, “Why Nature Chose Phosphates,” Science 235 (March 6, 1987): 1173–78.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1880-1884). Baker Books. Kindle Edition.]

· The specific nature of the phosphodiester bonds is also optimized. For example, the phosphodiester linkage that bridges the ribose sugars of RNA could involve the 5’ OH of one ribose molecule with either the 2’ OH or 3’ OH of the adjacent ribose moiety. In nature, RNA exclusively makes use of 5’ to 3’ bonding. A study conducted in the early 1990s explains why life employs these types of bonds. It turns out that 5’ to 3’ linkages impart much greater stability to the RNA molecule than 5’ to 2’ bonds. [Ryszard Kierzek, Liyan He, and Douglas H. Turner, “Association of 2’ –5’ Oligoribonucleotides,” Nucleic Acids Research 20 (April 11, 1992): 1685–90.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1885-1888). Baker Books. Kindle Edition.]

· Numerous recent studies provide insight as to why deoxyribose and ribose were selected as the sugar molecules that make up the backbones of DNA and RNA. Deoxyribose and ribose are five-carbon sugars that form five-membered rings. Researchers have demonstrated that it’s possible to make DNA analogs using a wide range of different sugars that contain four-, five, and six-carbons that can adopt five- and six-membered rings. But they have shown that these DNA variants have undesirable properties compared to DNA and RNA built with deoxyribose and ribose, respectively (see figure 7.4). [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1892-1895). Baker Books. Kindle Edition.]

· For example, some of these DNA analogs don’t form double helices. Others do, but the nucleotide strands interact either too strongly, too weakly, or they display inappropriate selectivity in their associations.15 Additionally, other studies show that DNA analogs made from sugars that form 6-membered rings adopt too many structural conformations.16 This diversity is objectionable. If DNA assumes multiple conformations, then it becomes extremely difficult for the cell’s machinery to properly execute DNA replication and repair, as well as transcription. Also researchers have shown that deoxyribose uniquely provides the necessary space within the backbone region of the DNA double helix to accommodate the large nucleobases. No other sugar fulfills this requirement.17 [15. Albert Eschenmoser, “Chemical Etiology of Nucleic Acid Structure,” Science 284 ( June 25, 1999): 2118–24. 16. Eveline Lescrinier, Matheus Froeyen, and Piet Herdewijn, “Difference in Conformational Diversity between Nucleic Acids with a Six-Membered ‘Sugar’ Unit and Natural ‘Furanose’ Nucleic Acids,” Nucleic Acids Research 31 ( June 15, 2003): 2975–89. 17. Gaspar Banfalvi, “Why Ribose Was Selected as the Sugar Component of Nucleic Acids,” DNA and Cell Biology 25 (March 2006):189–96.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 1898-1905). Baker Books. Kindle Edition.]

8 The Artist’s Handwriting

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· In the Islamic world, calligraphy is more than just writing with a flourish. It’s a form of fine art.1 In fact, many Muslims hold calligraphers in the highest regard. Because of Islam’s taboo on pictorial representation, calligraphy is both the chief vehicle of artistic expression and an important means of teaching the tenets of the faith. Calligraphy often “illustrates” the Qur’an and adorns the walls and ceilings of mosques. Sometimes calligraphy is purely art with the letters so richly stylized that they are practically illegible. On other occasions calligraphy conveys the Qur’an’s declarations. For Muslims, the words of the Qur’an are so treasured that only the best efforts and highest quality are worthy of them. [Wikipedia contributors, “Calligraphy,” Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/wiki/Calligraphy (accessed July 13, 2006); Wikipedia contributors, “Islamic Calligraphy,” Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/wiki/Arabic_calligraphy (accessed July 12, 2007); Wikipedia contributors, “Sheikh Hamdullah,” Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/wiki/Sheikh_Hamdullah (accessed July 12, 2006).] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2017-2022). Baker Books. Kindle Edition.]

· Whether transmitting details for a wedding, or religious ideas, all forms of calligraphy are motivated by a desire to relay highly prized information. Whether an individual reads the Qur’an or receives an invitation, he or she immediately recognizes that someone, somewhere, is responsible for the communication. No matter what form the message takes, the information being conveyed always originates in a mind. Information can’t be separated from the activity of an intelligent agent.2 And this connection makes this property a potent marker for intelligent design. [Peter Kreeft, Fundamentals of the Faith: Essays in Christian Apologetics (San Francisco: Ignatius, 1988), 25–26.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2026-2031). Baker Books. Kindle Edition.]

· Over the last forty years, biochemists have learned that the cell’s systems are, at their essence, information-based. Proteins and DNA are information-rich molecules. And, like the outpouring from a calligrapher’s pen, the structural and functional expressions of molecular-level messages are draped with an artistic elegance and clever logic worthy of an esteemed Writer. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2032-2034). Baker Books. Kindle Edition.]

· Information theorists maintain that the amino acid sequence of a polypeptide constitutes information.3 Just as letters form words, amino acids strung together form the “words” of the cell, polypeptides.4 In language, some letter combinations produce meaningful communication. Others produce gibberish—“words” with no meaning. Amino acid sequences do the same. Some produce functional polypeptides, whereas others produce “junk”—polypeptides that serve no role.5 Treating amino acid sequences as information has been a fruitful approach for researchers attempting to characterize the functional utility of different amino acid sequences and understand the origin of proteins.6 According to information theorist Bernd-Olaf Küppers, the structure of the information found in proteins is identical to the architecture of human language (see table 8.1).7 [3. Bernd-Olaf Küppers, Information and the Origin of Life (Cambridge, MA: MIT Press, 1990), 6–27. 4. See, for example, Michael Denton, Evolution: A Theory in Crisis (Bethesda, MD: Adler & Adler, 1986), 308–25; Walter L. Bradley and Charles B. Thaxton, “Information and the Origin of Life,” in The Creation Hypothesis: Scientific Evidence for an Intelligent Designer, ed. J. P. Moreland (Downers Grove, IL: InterVarsity, 1994), 188–90. 5. Harvey Lodish et al., Molecular Cell Biology, 4th ed. (New York: Freeman, 2000), 257. 6. Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life (New York: Cambridge University Press, 2005); Hubert P. Yockey, Information Theory and Molecular Biology (Cambridge: Cambridge University Press, 1992); Küppers, Information and the Origin of Life. 7. Küppers, Information and the Origin of Life, 24–25.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2037-2044). Baker Books. Kindle Edition.]

· Information theorists assert that DNA, like polypeptides, contains instructions. In fact, DNA’s chief function is information storage. It houses the directions necessary to make all the polypeptides used by the cell. The polynucleotide chains of DNA form when the cell’s machinery links together four different nucleotides: A, G, C, and T (described in chapter 2, p. 48). The sequence of nucleotides in the DNA strands specifies the sequence of amino acids in polypeptide chains. These coded instructions are called genes. Through the use of genes, DNA stores the messages functionally expressed in the amino acid sequences of polypeptide chains. According to Küppers, the structure of human language also yields insight into the informative content of DNA. Nucleotides function as characters that build letters and the genes function like words. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2054-2061). Baker Books. Kindle Edition.]

· The analogical language used by molecular biologists to describe the flow of information in biochemical systems is no accident. According to Küppers, “The analogy between human language and the molecular-genetic language is quite strict. . . . Thus, central problems of the origin of biological information can adequately be illustrated by examples from human language without the sacrifice of exactitude.”8 Biochemical systems are, in fact, information systems. And everyday experience teaches that information only comes from a mind. [Küppers, Information and the Origin of Life, 23.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2072-2076). Baker Books. Kindle Edition.]

· The semantic level of information ascribes meaning to the order of symbols, letters, and so forth. This dimension arises because some sequences have meaning (cat) and others don’t (tca). The pragmatic level of information recognizes that the meaning of the arrangement depends upon agreement between two parties: the sender and the recipient. Their agreement ascribes meaning to some sequences and not to others. It provides the basis for the recipient of information to respond or take action based on the sender’s direction. According to Küppers, The identification of a character as a “symbol” presupposes certain prior knowledge . . . in the form of an agreement between sender and recipient. Moreover, semantic information is unthinkable without pragmatic information, because the recognition of semantics as semantics must cause some kind of reaction from the recipient. [Küppers, Information and the Origin of Life, 32-33.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2082-2090). Baker Books. Kindle Edition.]

· Recent work by a team of chemical engineers and biochemists powerfully highlights the language content and structure of biochemical information.11 These researchers sought an approach to rationally design novel nonnatural peptide antibiotics. In the last decade or so, microbiologists and biochemists have discovered that a number of organisms possess relatively small peptides in their skin, saliva, sweat, and so forth. These peptides display antimicrobial activity and appear to be an important part of the immune system.12 The new antibiotics attract interest because they appear to be active against bacteria that are resistant to the most potent medicines available. [11. Christopher Loose et al., “A Linguistic Model for the Rational Design of Antimicrobial Peptides,” Nature 443 (October 19, 2006): 867–69. 12. Michael Zasloff, “Antimicrobial Peptides of Multicellular Organisms,” Nature 415 ( January 24, 2002): 389–95.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2098-2104). Baker Books. Kindle Edition.]

· While DNA and proteins are typically considered the only information-containing molecules of biochemical systems, recent studies indicate that oligosaccharides house information as well. Oligosaccharides are carbohydrates—a class of biomolecules that consists of compounds composed of carbon, hydrogen, and oxygen in the specific ratio of 1:2:1, respectively. [Biochemists use the general formula CnH2nOn (where n can be any number) to represent carbohydrates.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2115-2118). Baker Books. Kindle Edition.]

· The structural complexity of oligosaccharides gives them the capacity to house much more information per unit length than DNA, RNA, and proteins. The only basis of information for DNA, RNA, and proteins is the sequence of nucleotides and amino acids. For oligosaccharides, information is not limited just to the sugar sequences. It can also be contained in the variety of chemical substituents that bind to the sugars, the multiple types of bonds that form between sugar subunits, and the branching that occurs along the oligosaccharide chain.15 For example, the two amino acids glycine and alanine can be linked in two ways: alanine-glycine or glycine-alanine. Galactose and glucose can be joined together in thirty-six different ways. Each variation represents a unique piece of information. [Mark A. Lehrman, “Oligosaccharide-Based Information in Endoplasmic Reticulum Quality Control and Other Biological Systems,” Journal of Biological Chemistry 276 (March 23, 2001): 8623–26.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2132-2137). Baker Books. Kindle Edition.]

· Information-rich biomolecules (proteins, DNA, RNA, and oligosac-charides) and the information-based biochemical systems—central to life’s most fundamental activities—strongly indicate that a Divine hand penned life at its most basic level. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2145-2146). Baker Books. Kindle Edition.]

· Alternate splicing. The DNA sequences that make up genes in eukaryotes consist of stretches of nucleotides that specify the amino acid sequence of polypeptide chains (exons), interrupted by nucleotide sequences that don’t code for anything (introns). After the gene is copied into an mRNA molecule, the intron sequences are excised and the exons spliced together by a protein-RNA complex known as a spliceosome20 (see figure 5.2, p. 103, for the splicing process, though spliceosome is not shown). Splicing is an extremely precise process. Mistakes in splicing are responsible for some human diseases. Medical disorders result because splicing errors fatally distort or destroy information—temporarily stored in mRNA—necessary to assemble polypeptide chains at ribosomes. And improperly produced polypeptides cannot carry out their functional role in the cell. In his textbook Essentials of Molecular Biology, George Malacinski points out why proper polypeptide production is critical: “A cell cannot, of course, afford to miss any of the splice junctions by even a single nucleotide, because this could result in an interruption of the correct reading frame, leading to a truncated protein.”21 [20. Alan G. Atherly, Jack R. Girton, and John F. McDonald, The Science of Genetics (Fort Worth: Saunders College Publishing, 1999), 321–28. 21. Malacinski, Essentials of Molecular Biology, 261–65.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2201-2209). Baker Books. Kindle Edition.]

· A special relationship exists between the nucleotide sequences of the two DNA strands and consequently between the sense and antisense sequences associated with genes. When the DNA strands align, the adenine (A) side chains of one strand always pair with thymine (T) side chains from the other strand. Likewise, guanine (G) always pairs with cytosine (C). Biochemists refer to these relationships as base-pairing rules (see figure 2.7, p. 49). As a consequence, if biochemists know the sequence of one DNA strand, they can readily determine the sequence of the other strand. The DNA sequences of the two strands are complementary. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2333-2338). Baker Books. Kindle Edition.]

· Biochemists have long wondered why the nucleobases adenine (A), guanine (G), thymine/uracil (T/U), and cytosine (C) were chosen to be part of DNA’s and RNA’s structural makeup. At least sixteen other nucleobases could have been selected. For example, experiments designed to simulate the conditions of prebiotic Earth have produced diaminopurine, xanthine, hypoxanthine, and diaminopyrimidine in addition to A, G, T/U, and C.31 From an evolutionary perspective, any of them could have found their way into DNA’s structure. [Stanley L. Miller, “The Endogenous Synthesis of Organic Compounds,” in The Molecular Origins of Life: Assembling Pieces of the Puzzle, ed. André Brack (New York: Cambridge University Press, 1998), 59–85.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2350-2353). Baker Books. Kindle Edition.]

· Recent work by a chemist from Trinity University (Dublin, Ireland) shines new light on this question.32 When adenine, guanine, thymine, and cytosine are incorporated into DNA, they impart the double helix with a unique structural property that causes the information to behave like a parity code. Computer scientists and engineers use parity codes to minimize errors in the transfer of information (see “Parity Codes,” p. 159). None of the other nucleobases give DNA this special quality—only the specific combination of A, G, T, and C. [Dónall A. Mac Dónaill, “A Parity Code Interpretation of Nucleotide Alphabet Composition,” Chemical Communications, no. 18 (September 21, 2002): 2062–63; Dónall A. Mac Dónaill, “Why Nature Chose A, C, G and U/T: An Error-Coding Perspective of Nucleotide Alphabet Composition,” Origins of Life and Evolution of the Biosphere 33 (October 2003): 433–55.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2354-2357). Baker Books. Kindle Edition.]

· Computers usually use either a 7-bit or 8-bit code to represent characters.33 These 7- or 8-bit sequences are called data units. To detect errors that arise during transmission an additional bit, called a parity bit, is added to the data units. The value of the parity bit is assigned either a 1 or a 0 depending on if the error-detection scheme is an even or odd parity code. If even, then the value of the parity bit is chosen so the sum of the “on” (1) bits equals an even number. If an odd parity code is employed then the value of the parity bit is selected so that the sum of the “on” bits equals an odd number (see table 8.2). Errors can occur during data transmission if a 1 is received as a 0, or vice versa. Mistakes can also occur if a bit is lost or dropped. When either problem happens, the sum of “on” bits yields an odd number for an even parity code, and an even number for an odd parity code. When an unexpected sum of “on” bits is tabulated, the transmission’s recipient immediately knows an error has occurred. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2370-2379). Baker Books. Kindle Edition.]

· This extraordinary structural property of DNA suggests that a Mind carefully developed the cell’s information systems. The even parity code found in DNA is identical to those used in computer hardware and software systems to check for errors when data is transmitted. It’s as if an Intelligent Agent hand-selected the nucleobases A, G, T/U, and C to optimize DNA’s structure so errors can be readily detected and minimized when any information is transmitted. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2415-2419). Baker Books. Kindle Edition.]

· Rhetorician David Depew questions if evolutionary biologists Richard Dawkins and Daniel Dennet: “would be happy with [the] assumption that genes “contain” information in the same sense that modern computers do, or with the implication that organisms are merely their readouts? This analogy guided the formation of molecular biology. Like many analogies, it generated some good science, and more recently, a biotechnological revolution. But in singling out genes for causal efficacy at the expense of other epigenetic processes it created a scientific myth.” [David Depew, “Intelligent Design and Irreducible Complexity: A Rejoinder,” Rhetoric & Public Affairs 1 (1998): 571–78.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2426-2431). Baker Books. Kindle Edition.]

· According to these skeptics, application of information theory to problems in molecular biology is predicated on an analogy (albeit a useful one) between biochemical systems, human language, and information schemes. If taken too far, however, this analogy breaks down to the detriment of science and, in this case, the biochemical intelligent design analogy. But exciting new nano- and biotechnologies—such as DNA computing, DNA encryption, and DNA bar coding—provide justification for the biochemical intelligence argument. These emerging technologies reinforce the notion that biochemical information is indeed information. Their applications make use of data housed in DNA in much the same way that humans would handle information. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2431-2436). Baker Books. Kindle Edition.]

· DNA computing had its birth when computer scientist Leonard Adleman recognized that the proteins responsible for DNA replication, repair, and transcription operated as Turing machines.35 This process treats the nucleotide sequences of DNA as input and output strings. The different chemical, biochemical, and physical processes used to manipulate DNA in the laboratory correspond to the finite control and are used to transform the input DNA sequences into output sequences.36 Complex operations can be accomplished by linking together simple laboratory operations performed on DNA with the output of one laboratory operation serving as input for the next. [Leonard M. Adleman, “Computing with DNA,” Scientific American, August 1998, 54–61.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2444-2448). Baker Books. Kindle Edition.]

· Researchers recognize several advantages to DNA computers.38 One is the ability to perform a massive number of operations at the same time (in parallel) as opposed to one at a time (serially) which is typically much slower. Second, DNA has the capacity to store an enormous quantity of information. Theoretically one gram of DNA can house as much information as nearly one trillion CDs. And DNA computers operate, in principle, near theoretical capacities with regard to energy efficiency. The current limitations of DNA computers stem from the chemical nature of the process, namely the inherent incompleteness of chemical reactions and the error prone nature of the biomolecules that operate on DNA.39 (As discussed in chapter 10, biochemical processes inside test tubes are error prone. Inside the cell, however, “quality control” pathways correct most of these errors when they occur.) Much of the current research effort in DNA computing focuses on overcoming its limitations.40 [38. Paun, Rozenberg, and Salomaa, DNA Computing, 1–6; Adleman, “Computing with DNA,” 54–61. 39. Ivars Peterson, “Computing with DNA: Getting DNA-Based Computers Off the Drawing Board and Into the Wet Lab,” Science News 150 ( July 13, 1996): 26–27. 40. Charles Seife, “Molecular Computing: RNA Works Out Knight Moves,” Science 287 (February 18, 2000): 1182–83; Dirk Faulhammer et al., “Molecular Computation: RNA Solutions to Chess Problems,” Proceedings of the National Academy of Sciences, USA 97 (February 15, 2000): 1385–89; Anthony G. Frutos et al., “Demonstration of a Word Design Strategy for DNA Computing on Surfaces,” Nucleic Acids Research 25 (December 1, 1997): 4748–57; Anthony G. Frutos, Lloyd M. Smith, and Robert M. Corn, “Enzymatic Ligation Reactions of DNA ‘Words’ on Surfaces for DNA Computing,” Journal of the American Chemical Society 120 (October 14, 1998): 10277–82; Adrian Cho, “DNA Computing: Hairpins Trigger an Automatic Solution,” Science 288 (May 19, 2000): 1152–53; Kensaku Sakamoto et al., “Molecular Computation by DNA Hairpin Formation,” Science 288 (May 19, 2000): 1223–26.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2451-2459). Baker Books. Kindle Edition.]

· Scientists are currently exploring the bar code concept as a way to identify and track species. DNA bar codes consist of relatively short standardized segments of DNA within the genome unique to a particular species or subspecies in some cases. Biologists have successfully demonstrated that DNA bar codes can be used to identify butterfly, fly, bird, plant, and fungus species.46 Other applications have been suggested. One proposal suggests using short synthetic pieces of DNA incorporated into genes as a bar code that allows them to be quickly identified in laboratory experiments.47 This application differs from species identification. While DNA bar codes used to identify species are naturally part of an organism’s genome, scientists use other types of bar codes to track genes. These man-made bar codes are intentionally incorporated into genes by researchers. These synthetic bar codes are much more like the ones used to price items at a supermarket checkout. The use of DNA as bar codes, again, underscores the informational content of these molecules. DNA computing, steganography, and bar coding all make it clear that treating biochemical information as information goes well beyond a helpful analogy. It is indeed information. [46. Paul D. N. Hebert et al., “Ten Species in One: DNA Barcoding Reveals Cryptic Species in the Neotropical Skipper Butterfly Astraptes fulgerator,” Proceedings of the National Academy of Sciences, USA 101 (October 12, 2004): 14812–17; Paul D. N. Herbert et al., “Identification of Birds through DNA Barcodes,” PLoS Biology 2 (October 2004): e312; W. John Kress et al., “Use of DNA Barcodes to Identify Flowering Plants,” Proceedings of the National Academy of Sciences, USA 102 ( June 7, 2005): 8369–74; M. Alex Smith et al., “DNA Barcodes Reveal Cryptic Host-Specificity within the Presumed Polyphagous Members of a Genus of Parasitoid Flies (Diptera: Tachinidae),” Proceedings of the National Academy of Sciences, USA 103 (March 7, 2006): 3657–62; Mehrdad Hajibabaei et al., “DNA Barcodes Distinguish Species of Tropical Lepidoptera,” Proceedings of the National Academy of Sciences, USA 103 ( January 24, 2006): 968–71; Keith A. Seifert et al., “Prospects for Fungus Identification Using CO1 DNA Barcodes, with Penicillium as a Test Case,” Proceedings of the National Academy of Sciences, USA 104 (March 6, 2007): 3901–6. 47. Robert G. Eason et al., “Characterization of Synthetic DNA Bar Codes in Saccharomyces cerevi–siae Gene-Deletion Strains,” Proceedings of the National Academy of Sciences, USA 101 ( July 27, 2004): 11046–51.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2490-2499). Baker Books. Kindle Edition.]

9 Cellular Symbolism

· Biochemical machinery is, at essence, information-based. And, the chemical information in the cell is encoded using symbols. By itself, this information offers powerful evidence for an Intelligent Designer. But, recent discoveries go one step further. Molecular biologists studying the genetic code’s origin have unwittingly stumbled across a “grass hut” in what may be the most profound evidence for intelligent activity—a type of fine-tuning in the code’s rules. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2573-2577). Baker Books. Kindle Edition.]

· The genetic code’s carefully crafted rules supply it with a surprising capacity to minimize errors. These error-minimization properties allow the cell’s biochemical information systems to make mistakes and still communicate critical information with high fidelity. It’s as if the stranded island inhabitant could arrange the rocks in any three letter combination and still communicate his desperate plight. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2578-2581). Baker Books. Kindle Edition.]

· Interestingly, some codons (stop or nonsense codons) don’t specify any amino acids. They always occur at the end of the gene informing the protein manufacturing machinery where the polypeptide chain ends. Stop codons serve as a form of “punctuation” for the cell’s information system. (For example, UGA is a stop codon.) [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2599-2601). Baker Books. Kindle Edition.]

· The structure of rules for the genetic code reveals even further evidence that it stems from a Creator. A capacity to resist the errors that naturally occur as a cell uses or transmits information from one generation to the next is built into the code. Recent studies employing methods to quantify the genetic code’s error-minimization properties indicate that the genetic code’s rules have been carefully chosen and finely tuned. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2608-2611). Baker Books. Kindle Edition.]

· Why does the genetic code’s error-minimization capacity provide such a powerful indicator for intelligent design? Translating the stored information of DNA into the functional information of proteins is the code’s chief function. Error minimization, therefore, measures the capability of the genetic code to execute its function. The failure of the genetic code to transmit and translate information with high fidelity can be devastating to the cell. A brief explanation of the effect mutations have on the cell shows the problem. A mutation refers to any change that takes place in the DNA nucleotide sequence. [Lubert Stryer, Biochemistry, 3rd ed. (New York: Freeman, 1988), 675–76.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2612-2617). Baker Books. Kindle Edition.]

· Some researchers have challenged the optimality of the genetic code.9 But, the scientists who discovered the remarkable error-minimization capacity of the genetic code have concluded that the rules of the genetic code cannot be accidental.10 A genetic code assembled through random biochemical events could not possess near ideal error-minimization properties. Researchers argue that a force shaped the genetic code. Instead of looking to an intentional Programmer, these scientists appeal to natural selection. That is, they believe random events operated on by the forces of natural selection over and over again produced the genetic code’s error-minimization capacity.11 [9. Massimo Di Giulio, “The Origin of the Genetic Code,” Trends in Biochemical Sciences 25 (February 1, 2000): 44; Massimo Di Giulio and Mario Medugno, “The Level and Landscape of Optimization in the Origin of the Genetic Code,” Journal of Molecular Evolution 52 (April 2001): 372–82; Massimo Di Giulio, “A Blind Empiricism against the Coevolution Theory of the Origin of the Genetic Code,” Journal of Molecular Evolution 53 (December 2001): 724–32. 10. J. Gregory Caporaso, Michael Yarus, and Robin D. Knight, “Error Minimization and Coding Triplet/Binding Site Associations Are Independent Features of the Canonical Genetic Code,” Journal of Molecular Evolution 61 (November 2005): 597–607; Stephen J. Freeland, Tao Wu, and Nick Keul-mann, “The Case for an Error Minimizing Standard Genetic Code,” Origin of Life and Evolution of the Biosphere 33 (October 2003): 457–77; Stephen J. Freeland, Robin D. Knight, and Laura F. Landweber, “Measuring Adaptation within the Genetic Code,” Trends in Biochemical Sciences 25 (February 1, 2000): 44–45; Stephen J. Freeland and Laurence D. Hurst, “Load Minimization of the Genetic Code: History Does Not Explain the Pattern,” Proceedings of the Royal Society of London B 265 (November 7, 1998): 2111–19; Terres A. Ronneberg, Laura F. Landweber, and Stephen J. Freeland, “Testing a Biosynthetic Theory of the Genetic Code: Fact or Artifact?” Proceedings of the National Academy of Sciences, USA 97 (December 5, 2000): 13690–95; Ramin Amirnovin, “An Analysis of the Metabolic Theory of the Origin of the Genetic Code,” Journal of Molecular Evolution 44 (May 1997): 473–76. 11. Robin D. Knight, Stephen J. Freeland, and Laura F. Landweber, “Selection, History and Chemistry: The Three Faces of the Genetic Code,” Trends in Biochemical Sciences 24 ( June 1, 1999): 241–47.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2649-2655). Baker Books. Kindle Edition.]

· Even though some researchers think natural selection shaped the genetic code, other scientific work questions the likelihood that the genetic code could evolve. In 1968, Nobel laureate Francis Crick argued that the genetic code could not undergo significant evolution. [F. H. C. Crick, “The Origin of the Genetic Code,” Journal of Molecular Biology 38 (December 1968): 367–79.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2660-2662). Baker Books. Kindle Edition.]

· As with the genetic code, the histone-positioning code suggests the work of an Intelligent Programmer. A code must be deliberately designed. Even more remarkable is the requirement for the genetic and the histone-positioning codes to work in concert with one another. The histone-positioning code overlays the genetic code. These two codes must establish the relationship between the nucleotide sequences of DNA and the amino acid sequences of proteins. At the same time they must precisely position nucleosomes to ensure the proper expression of the information defined by the genetic code. Foresight and careful planning (the work of an Intelligent Agent) are necessary to get these two codes to work together. If haphazardly constructed, they could easily conflict, disrupting key processes within the cell. Remarkably, the universal genetic code is constructed to harbor overlapping or parallel codes better than the vast majority of other possible genetic codes. [Shalev Itzkovitz and Uri Alon, “The Genetic Code Is Nearly Optimal for Allowing Additional Information within Protein-Coding Sequences,” Genome Research 17 (April 2007): 405–12.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2736-2743). Baker Books. Kindle Edition.]

· The recent recognition that the genetic code possesses a unique capacity to resist errors caused by mutation imparts the biochemical intelligent design argument with an entirely new level of credibility. Like a giant SOS shaped with letters ablaze, the optimal nature of the genetic code signals that an Intelligent Agent used those rules to start and sustain life. The fine-tuning that minimizes the likelihood of error indicates that the genetic code cannot be just an accident—happened upon by random biochemical events—nor is it likely the product of undirected evolutionary processes. Genetic code evolution would be catastrophic for the cell. Remarkably, the genetic code originated at the time when life first appeared on Earth. And, it must have been deliberately programmed. No matter how much time there might have been, the code’s complexity makes it virtually impossible that natural selection could have stumbled upon it by accident. Such elaborate rules require forethought and painstaking effort. The message they carry adds an important piece to the analogy that logically compels a Creator’s existence and role in life’s origin and history. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 2749-2757). Baker Books. Kindle Edition.]

11 A style All His Own

· Identical Accidents? While repeated occurrences of biochemical designs logically point to a Creator, that’s not the case for evolutionary processes. If biochemical systems are the product of evolution, then the same biochemical designs should not recur throughout nature. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3095-3097). Baker Books. Kindle Edition.]

· Chance, “the assumed impersonal purposeless determiner of unaccountable happenings,”4 governs biological and biochemical evolution at its most fundamental level. Evolutionary pathways consist of a historical sequence of chance genetic changes operated on by natural selection, which also consists of chance components. The consequences are profound. If evolutionary events could be repeated, the outcome would be dramatically different every time. The inability of evolutionary processes to retrace the same path makes it highly unlikely that the same biological and biochemical designs should be repeated throughout nature. [4. “Chance,” Merriam-Webster’s Collegiate Dictionary, 11th ed., Merriam-Webster, 2007, http://unabridged.merriam-webster.com/ (accessed November 9, 2007).] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3098-3102). Baker Books. Kindle Edition.]

· This concept of historical contingency is the theme of evolutionary biologist Stephen J. Gould’s book Wonderful Life. According to Gould: No finale can be specified at the start, none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages. Alter any early event, ever so slightly, and without apparent importance at the time, and evolution cascades into a radically different channel.5 To help clarify the idea of historical contingency, Gould used the metaphor of “replaying life’s tape.” If one could push the rewind button and erase life’s history, then let the tape run again, the results would be completely different each time.6 The very essence of the evolutionary process renders its outcomes nonrepeatable. [5. Stephen J. Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: Norton, 1989), 51. 6. Ibid., 48.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3102-3109). Baker Books. Kindle Edition.]

· If life results exclusively from evolutionary processes, then shouldn’t scientists expect to see few, if any, cases in which evolution has repeated itself ?7 However, if life is the product of a Creator, then the same designs should repeatedly appear in biochemical systems. [John Cafferky, Evolution’s Hand: Searching for the Creator in Contemporary Science (Toronto: eastendbooks, 1997), 66–69.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3114-3116). Baker Books. Kindle Edition.]

· Over the last decade or so, scientists exploring the origin of biochemical systems have made a series of remarkable discoveries. When viewed from an evolutionary perspective, a number of life’s molecules and processes, though virtually identical, appear to have originated independently, multiple times.8 Evolutionary biologists refer to this independent origin of identical biomolecules and biochemical systems as molecular convergence. According to this concept, these molecules and processes arose separately when different evolutionary pathways converged on the same structure or system. [See, for example, Russell F. Doolittle, “Convergent Evolution: The Need to Be Explicit,” Trends in Biochemical Sciences 19 ( January 1994): 15–18; Eugene V. Koonin, L. Aravind, and Alexy S. Kondrashov, “The Impact of Comparative Genomics on Our Understanding of Evolution,” Cell 101 ( June 9, 2000): 573–76; Harold H. Zakon, “Convergent Evolution on the Molecular Level,” Brain, Behavior and Evolution 59, nos. 5–6 (2002): 250–61.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3117-3121). Baker Books. Kindle Edition.]

· Evolutionary biologists recognize five different types of molecular convergence:11 1. Functional convergence describes the independent origin of biochemical functionality on more than one occasion. 2. Mechanistic convergence refers to the multiple independent emergences of biochemical processes that use the same chemical mechanisms. 3. Structural convergence results when two or more biomolecules independently adopt the same three-dimensional structure. 4. Sequence convergence occurs when either proteins or regions of DNA arise separately but have identical amino acid or nucleotide sequences, respectively. 5. Systemic convergence is the most remarkable of all. This type of molecular convergence describes the independent emergence of identical biochemical systems. [Doolittle, “Convergent Evolution,” 15–18.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3129-3136). Baker Books. Kindle Edition.]

· Table 11.1 lists one hundred recently discovered examples of molecular convergence. This table is neither comprehensive nor exhaustive. It simply calls attention to the pervasiveness of molecular convergence. (Remember, as is true when looking at a particular group of paintings in any gallery, it is fine to skim through them or move on to the next section whenever you’re ready.) [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3137-3139). Baker Books. Kindle Edition.]

· Currently recognized examples of molecular convergence are likely just the tip of the iceberg. For instance, researchers from Cambridge University (United Kingdom) examined the amino acid sequences of over six hundred peptidase enzymes. (Peptidases are proteins that break down other proteins by cleaving bonds between amino acids.) When viewed from an evolutionary standpoint, these workers discovered that there appear to have been over sixty separate origin events for peptidases. This result stands in sharp contrast to what the researchers expected to find: a handful of peptidase families with separate origins. In many cases, the peptidases appeared to converge on the same enzyme mechanisms and reaction specificities. [Neil D. Rawlings and Alan J. Barrett, “Evolutionary Families of Peptidases,” Biochemical Journal 290 (February 15, 1993): 205–18.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3423-3428). Baker Books. Kindle Edition.]

· Researchers from the National Institutes of Health recently made a similar discovery. These scientists systematically examined protein sequences from 1,709 EC (enzyme commission) classes and discovered that 105 of them consisted of proteins that catalyzed the same reaction, but must have had separate evolutionary origins. [Galperin, Walker, and Koonin, “Analogous Enzymes,” 779–90.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3428-3431). Baker Books. Kindle Edition.]

· The common features of DNA replication include 1. semiconservative replication, 2. initiation at a defined origin by an origin-replication complex, 3. bidirectional movement of the replication fork, 4. continuous (leading strand) replication for one DNA strand and discontinuous (lagging strand) replication for the other DNA strand, 5. use of RNA primers, and 6. the use of nucleases, polymerases, and ligases to replace RNA primer with DNA. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3449-3455). Baker Books. Kindle Edition.]

· Considering the complexity of life’s chemical systems, pervasive molecular convergence fits uncomfortably within an evolutionary framework. Paleontologist J. William Schopf, one of the world’s leading authorities on Earth’s early life says, Because biochemical systems comprise many intricately interlinked pieces, any particular full-blown system can only arise once. . . . Since any complete biochemical system is far too elaborate to have evolved more than once in the history of life, it is safe to assume that microbes of the primal LCA [last common ancestor] cell line had the same traits that characterize all its present-day descendents. [J. William Schopf, “When Did Life Begin?” in Life’s Origin: The Beginnings of Biological Evolution, ed. J. William Schopf (Berkeley: University of California Press, 2002), 163.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3535-3540). Baker Books. Kindle Edition.]

12 An Elaborate Mosaic

· The structure of cell membranes stands in sharp contrast to the behavior of bilayers made from pure phospholipids. Purified phospholipids spontaneously form bilayers in water environments. Instead of forming unilamellar bilayers, however, phospholipids assemble into stacks of bilayers (multilamellar bilayers), or alternatively, they form spherical structures that consist of multiple bilayer sheets.9 (These structures resemble an onion, with each layer corresponding to one of the bilayers in the stack.) These aggregates only superficially resemble the cell membrane’s structure that consists of a single bilayer, not bilayer stacks (see figure 12.1). Phospholipids can be manipulated by researchers to form structures composed of only a single bilayer. These particular aggregates arrange into a hollow spherical structure called liposomes or unilamellar vesicles. However, they are considered physically unstable and last only for a limited lifetime.10 Liposomes readily fuse with one another and revert to multilamellar sheets or vesicles.11 In other words, apart from cell membranes, phospholipids spontaneously assemble into multibilayer sheets. So how can cell membranes consist of a single bilayer phase? National Institutes of Health researcher Norman Gershfeld explained that single bilayer phases, similar to those that constitute cell membranes, can be permanently stable but only under unique conditions.12 (Chemists refer to phenomena that occur under a unique set of conditions as critical phenomena.) [9. Danilo D. Lasic, “The Mechanism of Vesicle Formation,” Biochemical Journal 256 (November 15, 1988): 1–11. 10. Ibid. 11. See, for example, Barry L. Lentz, Tamra J. Carpenter, and Dennis R. Alford, “Spontaneous Fusion of Phosphatidylcholine Small Unilamellar Vesicles in the Fluid Phase,” Biochemistry 26 (August 25, 1987): 5389–97. 12. Norman L. Gershfeld, “The Critical Unilamellar Lipid State: A Perspective for Membrane Bilayer Assembly,” Biochimica et Biosphysica Acta 988 (December 6, 1989): 335–50.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3620-3632). Baker Books. Kindle Edition.]

· Protein asymmetry consists of the specific orientation of integral proteins that span the bilayer and differences in the composition of peripheral proteins in the inner and outer monolayers. This asymmetry allows cell membranes to 1. transport materials in a single direction, 2. detect changes in the environment outside the cell, 3. perform specific chemical operations inside the cell, and 4. stabilize the cell membranes through interactions between the cytoskeletal proteins and the interior surface of the bilayer. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3727-3733). Baker Books. Kindle Edition.]

· Finely-tuned phospholipid compositions, an extensive molecular-level organization, and the likelihood that cell membranes harbor information beg the question, Can the biochemical marvel of cell membranes be accounted for apart from a Creator? For most biochemical systems and characteristics, a fundamental lack of knowledge and insight prevent a rigorous assessment of proposed evolutionary explanations. In other words, it’s not possible to say whether evolutionary processes can generate specific aspects of life’s chemistry. But, this limitation is not a consideration for assessing the origin of cell membranes. Origin-of-life researchers have focused enough attention on the problem of membrane origins to permit vigorous evaluation of the likelihood that unguided evolutionary pathways produced them. The origin of cell membranes has to be one of the first steps in life’s emergence. Researchers assume, for the most part, that once membrane components form or appear on early Earth, they readily self-assembled to form the first cell membranes. [Geoffrey Zubay, Origins of Life on the Earth and in the Cosmos, 2nd ed. (San Diego: Academic Press, 2000), 371–76.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3756-3764). Baker Books. Kindle Edition.]

· The instability of primitive bilayers in salt is perhaps most problematic. It is difficult to imagine any aqueous location on early Earth free of salt. In fact, primitive bilayer stability would have been compromised at salt levels far less than those found in Earth’s oceans today. And, early Earth’s oceans were one and a half to two times more salty.53 That condition makes the emergence of primitive membranes even less likely. The exacting requirements for primitive bilayer assembly also make it unlikely these structures could encapsulate a self-replicator via dehydration-hydration cycles. Once dehydrated, unless the “just-right” conditions existed upon rehydration, the bilayers could not reform. In fact, a recent survey of the scientific literature shows that every step in the proposed pathway from prebiotic amphiphilic compounds to contemporary cell membranes strictly depends on exacting compositional and environmental factors.54 These stringent requirements make it unlikely that cell membranes could have emerged under the conditions of early Earth. [53. Kaplan, “Fresh Start,” 7. 54. Jacquelyn A. Thomas and F. R. Rana, “The Influence of Environmental Conditions, Lipid Composition, and Phase Behavior on the Origin of Cell Membranes,” Origins of Life and Evolution of Biospheres 37 ( June 2007): 267–85.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3837-3846). Baker Books. Kindle Edition.]

13 Coloring Outside The Lines

· Most scientists acknowledge the appearance of design in biochemical systems but argue that it’s not true design. Rather, they claim this characteristic is an artifact of evolutionary processes that stems from natural selection operating repeatedly on random inheritable variations over vast periods of time to produce and fine-tune biochemical systems. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3883-3885). Baker Books. Kindle Edition.]

· Like a small child coloring outside the lines of a picture—blind, undirected, chance processes of evolution are just as likely to produce “jury-rigged” structures as they are to produce fine-tuned structures. The likelihood of these makeshift outcomes led the late evolutionary biologist Stephen Jay Gould to argue in his classic essay The Panda’s Thumb that biological imperfections would “win no prize in an engineering derby.”2 Instead, they make a compelling case for evolution. From an evolutionary standpoint, if a “design” somehow works—even imperfectly—there is no impetus for it to further evolve. [Stephen Jay Gould, The Panda’s Thumb: More Reflections in Natural History (New York: Morton, 1980), 24.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3886-3890). Baker Books. Kindle Edition.]

· For Gould, “odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce.”3 In other words, even though biochemical systems are replete with elegant design features, the assortment of imperfections in life’s chemistry undermines the case for biochemical intelligent design. From an evolutionist viewpoint, an all-powerful, all-knowing Designer would never scribble so haphazardly. [Stephen Jay Gould, The Panda’s Thumb: More Reflections in Natural History (New York: Morton, 1980), 20-21.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3890-3894). Baker Books. Kindle Edition.]

· Careful consideration suggests that imperfections may not be as big a problem for the biochemical intelligent design analogy as they appear at first glance. Perhaps a Creator’s intentional activity can explain suboptimal biochemical systems. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3895-3897). Baker Books. Kindle Edition.]

· Mutations. Chemical and physical insults to DNA inevitably cause abnormalities. So do errors made by the cell’s machinery during DNA replication. The cell possesses machinery that can repair this damage, but sometimes errors occur and the repair is not completely effective. Then the nucleotide sequence of DNA becomes permanently altered. [Roderic D. M. Page and Edward C. Holmes, Molecular Evolution: A Phylogenetic Approach (Malden, MA: Blackwell Science, 1998), 63–65; Wen-Hsiung Li, Molecular Evolution (Sunderland, MA: Sinauer Associates, 1997), 23–30.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3901-3904). Baker Books. Kindle Edition.]

· Less than peak performance. Nonuniversal genetic codes (discussed in chapter 9, p. 177) supply an excellent example of how mutations and other natural processes degrade optimal systems—in this case, the universal genetic code that is optimized to withstand errors caused by substitution mutations. Deviants of the universal genetic code, nonuniversal genetic codes arise when changes occur in tRNA molecules in such a way that the assignments of stop codons or low frequency codons are altered (see chapter 10, p. 187). [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3912-3915). Baker Books. Kindle Edition.]

· Even though the second law of thermodynamics causes systems to tend toward disorder, its operation is absolutely necessary for life to be possible. The effects of entropy leads to the “downhill” flow of energy that makes it possible for cells to carry out all of their metabolic abilities. Entropy also drives the formation of cell membranes, the precise folding of proteins, and the assembly of the DNA double helix. From an intelligent design perspective, the second law of thermodynamics reflects the providential care of the Creator. The decay associated with the second law appears to be an unavoidable trade-off. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3921-3925). Baker Books. Kindle Edition.]

· Engineers who invent complex systems often face trade-offs and must purposely design some components to be suboptimal in order to achieve the maximum overall performance. In fact, if a system consists of finite resources and must accomplish numerous objectives, then the system must represent a compromise. Inevitably its objectives will compete with one another. Any attempt to maximize performance in one area will degrade performance in others. When confronted with trade-offs, the engineer carefully manages them in such a way as to achieve optimal performance for the system as a whole. And this overall efficiency can be accomplished only by intentionally suboptimizing individual aspects of the system’s design. [Private correspondence with Dr. Mark Wharton, November 28, 2005. Dr. Wharton holds a PhD in aerospace engineering from the Georgia Institute of Technology and has worked for the NASA Marshall Space Flight Center since 1990. He is an internationally recognized expert in the control of structures and is the principal investigator of the International Space Station experiment.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3926-3931). Baker Books. Kindle Edition.]

· Life’s chemistry is complex. Biochemists lack detailed understanding of the structure and functional behavior of most biochemical systems, even those that have been the subject of focused investigation. Rarely do biochemists understand how a specific process interacts with others inside the cell, let alone globally throughout the organism. When evolutionary biologists label a biochemical system “imperfect,” they do so largely from ignorance. Any claim that a certain aspect of life’s chemistry exemplifies poor design is largely based on a scientist’s authority, not a comprehensive understanding of that system and its interrelationship to other biomolecular processes. All too often biochemists gain new insight into the operation of a so-called imperfect biochemical system only to discover another marvelous illustration of the elegant designs that define life’s chemistry. Based on current knowledge, however, some systems truly appear to be poorly designed. Limited knowledge about these systems doesn’t permit the case for biochemical intelligent design to be made. These seemingly faulty designs, however, provide an opportunity to scientifically test the biochemical intelligent design hypothesis. If life is indeed the product of a Creator, then new discoveries should yield insights that transform these biochemical aberrations into remarkable works of art. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3937-3947). Baker Books. Kindle Edition.]

· A few representative examples such as glycolysis, bilirubin production, uric acid metabolism, junk DNA, and genetic redundancy show how time can produce the kind of scientific advance that rehabilitates the image of biochemical systems that at one time or other acquired the reputation as bad designs. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 3948-3950). Baker Books. Kindle Edition.]

· Many evolutionary biologists regard “junk” DNA as one of the most potent pieces of evidence for biological evolution.21 According to this view, junk DNA results when undirected biochemical processes and random molecular and physical events transform a functional DNA segment into a useless molecular artifact. This segment remains part of an organism’s genome solely because of its attachment to functional DNA. Junk DNA persists from generation to generation.22 The amount varies from organism to organism, ranging from 30 percent to nearly 100 percent of an organism’s genome.23 [21. Edward E. Max, “Plagiarized Errors and Molecular Genetics: Another Argument in the Evolution-Creation Controversy,” TalkOrigins Archive, May 5, 2003, http://www.talkorigins.org/faqs/molgen/ (accessed August 12, 2003). 22. Li, Molecular Evolution, 395–99. 23. Ibid., 379–84.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4050-4055). Baker Books. Kindle Edition.]

· Making a difference. Junk DNA at one time represented an insurmountable challenge to the biochemical intelligent design argument and appeared to make an ironclad case for evolution. Now, recent advances suggest otherwise. Much to the surprise of scientists, junk DNA has function. Based on the characteristics possessed by pseudogenes, few molecular biologists would have ever thought junk DNA plays any role in the cell’s operation. However, several recent studies unexpectedly identified functions for both duplicated and processed pseudogenes. Some duplicated pseudogenes help regulate the expression of their corresponding genes.35 And, many processed pseudogenes code for functional proteins.36 The scientific community is also well on its way to establishing functional roles for endogenous retroviruses and their compositional elements. Recent advances indicate that this class of noncoding DNA regulates gene expression and helps the cell ward off retroviral infections by disrupting the assembly of retroviruses after they take over the cell’s machinery.37 [35. See, for example, Sergei A. Korneev, Ji-Ho Park, and Michael O’Shea, “Neuronal Expression of Neural Nitric Oxide Synthase (nNOS) Protein Is Supressed by an Antisense RNA Transcribed from an NOS Pseudogene,” Journal of Neuroscience 19 (September 15, 1999): 7711–20; Shinji Hirotsune et al., “An Expressed Pseudogene Regulates the Messenger-RNA Stability of Its Homologous Coding Gene,” Nature 423 (May 1, 2003): 91–96; Evgeniy S. Balakirev and Francisco J. Ayala, “Pseudogenes: Are They ‘Junk’ or Functional DNA?” Annual Review of Genetics 37 (December 2003): 123–51; Shinji Hirotsune et al., “Addendum: An Expressed Pseudogene Regulates the Messenger-RNA Stability of Its Homologous Coding Gene,” Nature 426 (November 6, 2003): 100. 36. Esther Betrán et al., “Evolution of the Phosphoglycerate mutase Processed Gene in Human and Chimpanzee Revealing the Origin of a New Primate Gene,” Molecular Biology and Evolution 19 (May 2002): 654–63; Örjan Svensson, Lars Arvestad, and Jens Lagergren, “Genome-Wide Survey for Biologically Functional Pseudogenes,” PLoS Computational Biology 2 (May 5, 2006): e46; Nicolas Vinckenbosch, Isabelle Dupanloup, and Henrik Kaessmann, “Evolutionary Fate of Retroposed Gene Copies in the Human Genome,” Proceedings of the National Academy of Sciences, USA 103 (February 28, 2006): 3220–25. 37. Jerzy Jurka, “Subfamily Structure and Evolution of the Human L1 Family of Repetitive Sequences,” Journal of Molecular Evolution 29 (December 1989): 496–503; Atherly, Girton, and McDonald, Science of Genetics, 597–608; for example, Greg Towers et al., “A Conserved Mechanism of Retrovirus Restriction in Mammals,” Proceedings of the National Academy of Sciences, USA 97 (October 24, 2000): 12295–99; Jonathan P. Stoye, “An Intracellular Block to Primate Lentivirus Replication,” Proceedings of the National Academy of Sciences, USA 99 (September 3, 2002): 11549–51; Caroline Besnier, Yasuhiro Takeuchi, and Greg Towers, “Restriction of Lentivirus in Monkeys,” Proceedings of the National Academy of Sciences, USA 99 (September 3, 2002): 11920–25; Theodora Hatziioannou et al., “Restriction of Multiple Divergent Retroviruses by Lv1 and Ref1,” EMBO Journal 22 (February 3, 2003): 385–94; Clare Lynch and Michael Tristem, “A Co-Opted gypsy-Type LTR-Retrotransposon Is Conserved in the Genomes of Humans, Sheep, Mice, and Rats,” Current Biology 13 (September 2, 2003): 1518–23; Vera Schramke and Robin Allshire, “Hairpin RNAs and Retrotransposon LTRs Effect RNAi and Chromatin-Based Gene Silencing,” Science 301 (August 22, 2003): 1069–74; Wenhu Pi et al., “The LTR Enhancer of ERV-9 Human Endogenous Retrovirus Is Active in Oocytes and Progenitor Cells in Transgenic Zebrafish and Humans,” Proceedings of the National Academy of Sciences, USA 101 ( January 20, 2004): 805–10; Catherine A. Dunn, Patrik Medstrand, and Dixie L. Mager, “An Endogenous Retroviral Long Terminal Repeat Is the Dominant Promoter for Human â1,3–Galactosyltransferase 5 in the Colon,” Proceedings of the National Academy of Sciences, USA 100 (October 28, 2003): 12841–46; François Mallet et al., “The Endogenous Retroviral Locus ERVWE1 Is a Bona Fide Gene Involved in Hominoid Placental Physiology,” Proceedings of the National Academy of Sciences, USA 101 (February 10, 2004): 1731–36.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4102-4111). Baker Books. Kindle Edition.]

· As with pseudogenes and endogenous retroviruses, molecular biologists now recognize that the SINE DNA found in the genomes of a wide range of organisms plays an important part in regulating gene expression and offers protection when the cell becomes distressed.38 Researchers have also identified another potential function for SINEs—regulation of gene expression during the course of development. [Wen-Man Liu et al., “Cell Stress and Translational Inhibitors Transiently Increase the Abundance of Mammalian SINE Transcripts,” Nucleic Acids Research 23 (May 25, 1995): 1758–65; Tzu-Huey Li et al., “Physiological Stresses Increase Mouse Short Interspersed Element (SINE) RNA Expression In Vivo,” Gene 239 (November 1, 1999): 367–72; Richard H. Kimura, Prabhakara V. Choudary, and Carl W. Schmid, “Silk Worm Bm1 SINE RNA Increases Following Cellular Insults,” Nucleic Acids Research 27 (August 15, 1999): 3380–87; Wen-Ming Chu et al., “Potential Alu Function: Regulation of the Activity of Double-Stranded RNA-Activated Kinase PKR,” Molecular and Cellular Biology 18 ( January 1998): 58–68.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4111-4114). Baker Books. Kindle Edition.]

· SINEs possess regions that the cell’s machinery methylates (attaches the methyl chemical functional group). This process turns genes off. Depending on the tissue type, SINEs display varying patterns of DNA methylation. These diverse patterns implicate SINEs in the differential gene expression that occurs during development.39 [Wen-Man Liu et al., “Alu Transcripts: Cytoplasmic Localisation and Regulation by DNA Methyl–ation,” Nucleic Acids Research 22 (March 25, 1994): 1087–95; Wen-Man Liu and Carl W. Schmid, “Proposed Roles for DNA Methylation in Alu Transcriptional Repression and Mutational Inactivation,” Nucleic Acid Research 21 (March 25, 1993): 1351–59; Carol M. Rubin et al., “Alu Repeated DNAs Are Differentially Methylated in Primate Germ Cells,” Nucleic Acids Research 22 (November 25, 1994): 5121–27; Igor N. Chesnokov and Carl W. Schmid, “Specific Alu Binding Protein from Human Sperm Chromatin Prevents DNA Methylation,” Journal of Biological Chemistry 270 (August 4, 1995): 18539–42; Utha Hellmann-Blumberg et al., “Developmental Differences in Methylation of Human Alu Repeats,” Molecular and Cellular Biology 13 (August 1993): 4523–30.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4114-4117). Baker Books. Kindle Edition.]

· Much in the same way the scientific community acknowledges function for SINE DNA, molecular biologists now recognize that LINEs critically regulate gene expression. For example, researchers have identified a central role for LINE DNA in X chromosome inactivation.40 [Jeffrey A. Bailey et al., “Molecular Evidence for a Relationship Between LINE-1 Elements and X Chromosome Inactivation: The Lyon Repeat Hypothesis,” Proceedings of the National Academy of Sciences, USA 97 ( June 6, 2000): 6634–39; Christine Moulton Clemson et al., “The X Chromosome Is Organized into a Gene-Rich Outer Rim and an Internal Core Containing Silenced Nongenic Sequences,” Proceedings of the National Academy of Sciences, USA 103 (May 16, 2006): 7688–93.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4117-4119). Baker Books. Kindle Edition.]

· Highly inefficient. Researchers have recently come to recognize that cells employ a wasteful process when producing proteins. Roughly 30 percent of all proteins synthesized must be degraded by the cell because they are improperly made.47 Anyone with experience in manufacturing would agree that a production process with a 30 percent defect rate needs much improvement. These problems challenge the notion that a Creator produced life’s chemistry. However, the seemingly wasteful process of protein synthesis actually plays a critical role in the ability of the immune system to respond rapidly to viral infections. After proteins outlive their usefulness to the cell or become damaged in the process of carrying out their cellular function, they are degraded. Their breakdown occurs in a highly orchestrated fashion catalyzed by a large protein complex called a proteasome.48 Degradation releases the protein’s amino acids and makes them available for use in the production of new proteins. [47. Ulrich Schubert et al., “Rapid Degradation of a Large Fraction of Newly Synthesized Proteins by Proteasomes,” Nature 404 (April 13, 2000): 770–74. 48. Michael Gross, Travels to the Nanoworld: Miniature Machinery in Nature and Technology (New York: Plenum Trade, 1999), 86–90.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4153-4161). Baker Books. Kindle Edition.]

14 The Masterpiece Authenticated

· The sheer beauty and artistry of life’s chemical systems is undeniable. So, too, is the appearance of design. For those who regard this glorious treasure as the handiwork of a Creator, the page-by-page details supplied by researchers provide a rare and intimate glimpse into the art and thoughts of the Divine Master. Even scientists who maintain that undirected processes (natural selection operating iteratively on random genetic change) produced the elegant chemical systems in the living realm find this appearance of biochemical design awe-inspiring. [See, for example, Ursula Goodenough, The Sacred Depths of Nature (New York: Oxford University Press, 1998).] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4266-4271). Baker Books. Kindle Edition.]

· Speculation has the first flagellum arising from the merger of the type III secretion apparatus and a filamentous protein system. Presumably, both structures provided the microbe with prior services, neither of which had anything to do with motility. These evolutionary explanations have not gone unchallenged, however. Evolution’s critics point out that these explanations seem plausible, but only on the surface. In essence, they are no more than evolutionary “just-so” stories.6 Invariably, the naturalistic scenarios proposed to account for the origin of irreducibly complex systems are highly speculative and lack any type of detailed mechanistic undergirding. This problem is clearly the case for all the evolutionary explanations offered to account for the emergence of the bacterial flagellum. [The phrase “just-so” refers to Rudyard Kipling’s Just-So Stories. This book, first published in 1902, contains mythical accounts of how various natural phenomena came about like “How the Whale Got His Throat,” “How the Leopard Got His Spots,” and “How the Camel Got His Hump,” to name a few. This phrase is also an academic term used to describe ad hoc, unverifiable, unfalsifiable narrative accounts of how some organism or biological trait came into existence.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4295-4301). Baker Books. Kindle Edition.]

· Biologists Mark Pallen and Nicholas Matzke state that: the flagellar research community has scarcely begun to consider how these systems have evolved. This neglect probably stems from a reluctance to engage in the “armchair speculation” inherent in building evolutionary models. [Pallen and Matzke, “Origin of Species to the Origin of Bacterial Flagella,” 784–90.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4301-4304). Baker Books. Kindle Edition.]

· The proposed evolutionary explanations for fine-tuning and optimization of biochemical systems in no way invalidate the case for biochemical intelligent design. These two elegant design features of biochemical systems are precisely what can be expected if life is the product of a Creator. According to the late evolutionary biologist Stephen Jay Gould, “Textbooks like to illustrate evolution with examples of optimal design. . . . But ideal design is a lousy argument for evolution, for it mimics the postulated action of an omnipotent creator.” [Stephen Jay Gould, The Panda’s Thumb: More Reflections in Natural History (New York: Norton, 1980), 20.] [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4346-4350). Baker Books. Kindle Edition.]

· The Weight of Evidence The examples discussed throughout this book reveal some of the defining features of life’s chemical systems that correspond to the distinctive characteristics of systems designed by humans. A summary of the features from these systems tips the scales in favor of creation authenticating the masterpiece. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4443-4446). Baker Books. Kindle Edition.]

· Irreducible complexity. As highlighted in Behe’s Darwin’s Black Box, biochemical systems typically are irreducibly complex. They are composed of numerous components, all of which must be present for the system to have any function at all. Many man-made systems are also irreducibly complex; therefore, this feature indicates intelligent design. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4446-4449). Baker Books. Kindle Edition.]

· Chicken-and-egg systems. Which came first? Many biochemical systems are made up of components that mutually require each other for all the components to be produced. For example, ribosomes make proteins, yet, in turn, are formed from proteins. So proteins can’t be made without ribosomes, and ribosomes can’t be made without proteins. The mutual interdependence of the components of many biochemical systems signifies intelligent design. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4449-4452). Baker Books. Kindle Edition.]

· Fine-tuning. Many biochemical structures and activities depend on the precise location and orientation of atoms in three-dimensional space. Man-made systems often require a high-degree of precision to function. Fine-tuning reflects intelligent design. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4453-4454). Baker Books. Kindle Edition.]

· Optimization. Many biochemical structures and activities are designed to carry out a specific activity while operating at peak performance. Manmade systems often are planned in the same way. Optimization demonstrates the work of an Intelligent Agent. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4455-4456). Baker Books. Kindle Edition.]

· Biochemical information systems. Information comes from intelligence. At their essence, the cell’s biochemical systems are information-based. The presence of information in the cell, therefore, must emanate from an Intelligent Designer. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4457-4458). Baker Books. Kindle Edition.]

· Structure of biochemical information. The evidence for intelligent design goes beyond the mere existence of information-based biochemical systems. Biochemical information displays provocative structural features, such as language structure and the organization and regulation of genes, that also point to the work of a Creator. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4459-4461). Baker Books. Kindle Edition.]

· Biochemical codes. The information-based biochemical systems of the cell employ encoded information. The genetic code, the histone code, and even the parity code of DNA are three examples. The encoded information of the cell requires an Intelligent Designer to generate it. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4461-4463). Baker Books. Kindle Edition.]

· Genetic code fine-tuning. The rules that comprise the genetic code are better designed than any conceivable alternative code to resist errors that occur as the genetic code translates stored information into functional information. This fine-tuning strongly indicates that a superior Intelligence designed the genetic code. The universal genetic code also has been optimized to house multiple parallel codes. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4464-4467). Baker Books. Kindle Edition.]

· Quality control. Designed processes incorporate quality control systems to ensure the efficient and reproducible production of quality product. Many biochemical systems employ sophisticated quality control processes and consequently reflect the work of an Intelligent Designer. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4467-4469). Baker Books. Kindle Edition.]

· Molecular convergence. Several biochemical systems and/or biomolecules isolated from different organisms are structurally, functionally, and mechanistically identical. These biochemical systems have independent origins. Given these systems’ complexity, it is unwarranted to conclude that blind random natural processes independently produced them. Rather, molecular convergence reflects the work of a single Creator that employs a common blueprint to bring these systems into existence. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4469-4473). Baker Books. Kindle Edition.]

· Strategic redundancy. Engineers frequently design systems with redundancy, particularly for those components that play a critical role in the operation of the system. When engineers incorporate duplicate parts into their designs, the redundant components form a responsive backup circuit. Many duplicated genes in genomes operate as a responsive backup circuit, reflecting the work of a Creator. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4473-4476). Baker Books. Kindle Edition.]

· Trade-offs and intentional suboptimization. When engineers design complex systems, they often face trade-offs and must purposely design components in the system to be suboptimal in order to achieve overall optimal performance. Many biochemical systems display evidence of intentional suboptimization to balance trade-offs pointing to the work of a Divine Engineer. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4476-4479). Baker Books. Kindle Edition.]

· In light of these criteria, it is significant that so many disparate characteristics of life’s chemistry bear an uncanny resemblance to human designs. And for each category that is part of the biochemical intelligent design analogy, numerous examples abound in cells—far more than could be described in this work. In a sense, the information presented grossly understates the case for biochemical intelligent design. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4479-4482). Baker Books. Kindle Edition.]

· Life’s minimum complexity. Life in its bare minimal form is remarkably complex. Minimal life seems irreducibly complex. There appears to be a lower bound of several hundred genes, below which life cannot be pushed and still be recognized as “life.” In Darwin’s Black Box, Behe demonstrated that individual biochemical systems are irreducibly complex. In its totality, life appears that way as well. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4485-4488). Baker Books. Kindle Edition.]

· Molecular-level organization of simplest life. Over the last decade or so, microbiologists have come to recognize that prokaryotes (the simplest life-forms) display an exquisite spatial and temporal organization at the molecular level. Common experience teaches that it takes thought and intentional effort to carefully organize a space for functional use. By analogy, the surprising internal organization of prokaryotic cells bespeaks of intelligent design. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4488-4492). Baker Books. Kindle Edition.]

· Exquisite molecular logic. Often, the design and operation of biochemical systems are remarkably clever. Many aspects of life’s chemistry display an eerie though appealing molecular logic that indicates a Creator’s wisdom. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4492-4494). Baker Books. Kindle Edition.]

· Preplanning. Planning ahead indicates purpose and reflects design. Many biochemical processes, like the assembly of the bacterial flagellum, consist of a sequence of molecular events and chemical reactions. Often the initial steps or initial structures of the pathways elegantly anticipate the pathway’s final steps. Biochemical preplanning points to divine intentionality in life’s chemistry. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4494-4497). Baker Books. Kindle Edition.]

· Molecular motors. Individual proteins and protein complexes literally are direct structural and functional analogs to machines made by humans. These molecular motors revitalize the Watchmaker argument for a Creator’s existence. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4497-4499). Baker Books. Kindle Edition.]

· Cell membranes. These structures, which establish the cell’s external and internal boundaries, require precise chemical compositions to form stable structures. Cell membranes also display exquisite organization that includes asymmetric inner and outer surfaces, dynamic structural and functional domains, and many specialized embedded machines. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4499-4501). Baker Books. Kindle Edition.]

· The designs of biochemical systems inspire human designs. Some of the most important advances in nanoscience and nanotechnology come from insight gained from life’s chemical operations. Apart from this insight, researchers struggle to discover, let alone implement, the principles needed to build molecular devices. The fact that biochemical systems can inspire human design indicates that life’s chemistry was produced by the One who made humankind. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4502-4505). Baker Books. Kindle Edition.]

· Man can’t do it better. Frequently, humans fail in their attempts to duplicate the cell’s complex and elegant chemical processes in the laboratory. When humans mimic biochemical processes, they find that their best efforts are cumbersome and lead to crude and inefficient systems. It doesn’t seem reasonable to believe that blind random processes can account for the elegance of life’s chemistry when the best researchers utilizing state-of-the-art technology can’t produce even remotely comparable systems. [Fazale Rana: The Cell’s Design (How Chemistry Reveals the Creator’s Artistry) (Kindle Locations 4505-4509). Baker Books. Kindle Edition.]

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