عصير كتاب: بصمة في الخلية لـ ستيفن ماير Signature in the Cell By Stephen Meyer

Posted: يونيو 9, 2016 in لاهوت طبيعي, الكون ونشأة الحياة, الكتابات العامة, الإلحاد, عصير الكتب

بسم الله الرحمن الرحيم

Signature in the Cell

DNA Evidence for Intelligent Design

By: Stephen C. Meyer

للتحميل: (PDF) (DOC)

signature-cell

نبذة مُختصرة عن الكتاب:

هذا الكتاب من أهمّ الكُتُب التي تتناول موضوع الإحكام والإتقان فيما يخُصّ أصل الحياة.

المؤلِّف هو فيلسوف العُلُوم الأمريكي المشهور جداً «ستيفن ماير»، والذي له كتاب آخر تمّ ترجمته بواسطة مركز براهين بعُنوان شكّ داروين، وهو أيضاً من أهمّ المؤلَّفات التي تنقد نظرية التَّطوُّر الداروينية، وأحدثها أيضاً!

أعتقد – والله أعلم – أنَّ مركز براهين قائمة على ترجمة هذا الكتاب بالفعل: «بصمةٌ في الخلية»، وهو بالفعل كتاب يستحق التَّرجمة، فهو كتاب فريد من نوعه، يُدلِّل على وُجُود التَّصميم والإحكام والإتقان في الكون من خلال وجود المعلومات المُشفَّرة في شريط الحامض النَّووي في الخلية.

الكتاب يُمثِّل سيرة ذاتية لـ «ستيفن ماير»، يستعرض فيها مراحل حياته المُختلفة أثناء دراسته لإشكالية أصل أو نشأة الحياة، قد بيَّن هو نفسه في مُقدِّمة الكتاب أنَّه فضَّل هذا الأسلوب الذي لا أفضله أنا شخصياً كمُحاولة منه لتوصيل كلّ المعلومات للقارئ بشكل تاريخ مُرتَّب، مع كل التَّفاصيل، ليفهم الموضوع من بدايته إلى نهايته!

الكتاب يتناول في البداية التَّعريفات العلمية والفلسفية التي يتمّ التَّعرُّض لها أثناء مُناظرات إثبات التَّصميم الحكيم، بالإضافة إلى سرد تاريخي لكل المواضيع الغامضة المُتعلِّقة بالحمض النَّووي، بداية من المنظور البدائي للخلية، وصولاً إلى كيفية اكتشاف شكل جزيء الحمض النووي الحلزوني! (الفُصُول الثلاثة الأولى).

فيما بعض يتناول المؤلِّف كلّ السيناريوهات الطَّبيعية لتفسير نشأة المعلومات الجينية، ويقوم بتفنيدها وبيان بُطلانها، ثمَّ يقوم بعرض الأسباب التي من أجلها يعتقد أنَّ التَّصميم الذَّكي هو التَّفسير الأفضل لظاهرة المعلومات الجينية، وفي النِّهاية يقوم بالرَّد على كلّ الاعتراضات المُوجَّهة لأنصار التَّصميم الذَّكي.

أثناء قراءتي للكتاب وجدته مُمِلَّاً في كثيرٍ من الأحيان، ولكن لماذا شعرتُ بهذا الملل؟! لأنَّ الكتاب يُحاول توضيح الواضحات، وتوضيح الواضحات والبديهيات من أصعب المُشكلات! فالكتاب يُحاول أن يُبيِّن طريقة تعرُّفنا على التَّصميم فيما هو حولنا، وإذا لم تُفكِّر في المسألة مِن قبل ففكِّر فيها الآن، ما هو الدَّليل العقلي أو المنطقي على أنَّ الذي تعرف أنَّه مُصمَّم ومصنوع بإحكام، بالفعل مُصمَّم ومصنوع بإحكام؟!

لعلَّك لن تعرف الإجابة بشكل مُباشر، هذا لأنَّك بمُجرَّد النَّظر إلى الشيء تستطيع إدراك ما إذا كان مصنوعاً بإحكام أم أنَّه مُجرَّد شيء عشوائي! ما الذي يحدث في عقولنا يجعلنا قادرين على التَّفريق بين ما هو مُصمَّم ومصنوع بإحكام، وبين ما هو غير ذلك؟!

هذا هو مدار الكتاب كلُّه تقريباً، والملل نابع من كون ما يتم توضيحه في الكتاب بالنِّسبة لي على الأقل واضح جداً، فمسألة أنَّ المعلومات الجينية لا يُمكن أن تكون إلَّا نتاج عِلْم أمرٌ واضحٌ وبيِّن، ولكن الكتاب يُحاول إقامة حُجَّة علمية منطقية على أنسان انتكست فطرتهم، وانطمست بصيرتهم، فالله المُستعان!

كلمة أخيرة: بعض المؤلَّفات تدور حولها الأساطير فيما يخُصّ قُوَّتها ومَدَى إحكام حُجَّتها، ولكن عندما تقرأ الكتاب بنفسك قد لا تجد الكتاب كما كنت تتوقّعه. هذا الكتاب بالنِّسبة لي كان كذلك، كنت أظنُّه أقوى من ناحية الكلام العِلْمي عن الخلية، وعن المعلومات الجينية، ولكنَّ المؤلِّف فضَّل أن يهتمّ أكثر بكيفية عرض حُجَّة التَّصميم الذَّكي أكثر من عرض الحُجج العلمية التي على أساسها قال بالتَّصميم الذَّكي! خُصُوصاً أنَّه عَوَّل كثيراً على كتاب «ويليام ديمبسكي» المشهور جداً بعُنوان «استنتاج التَّصميم» (The Design Inference) المُتخصِّص في كيفية اكتشاف التَّصميم واستنتاج وجوده.

الكتاب يستحقّ في رأيي تقدير جيِّد جداً، وما زلت أرجو أن يُترجم إلى اللغة العربية.

Prologue

· The theory of intelligent design is not based on a religious text or document, even if it does have implications that support theistic belief. Instead, intelligent design is an evidence-based scientific theory about life’s origins that challenges strictly materialistic views of evolution. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 103-105). HarperCollins. Kindle Edition.]

· According to modern neo-Darwinists such as Oxford’s Richard Dawkins, living systems “give the appearance of having been designed for a purpose.” But, to Dawkins and other contemporary Darwinists, that appearance of design is entirely illusory, because wholly undirected processes such as natural selection and random mutations can produce the intricate design–like structures in living systems. In their view, natural selection can mimic the powers of a designing intelligence without being guided or directed in any way. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 106-109). HarperCollins. Kindle Edition.]

· In contrast, the theory of intelligent design holds that there are tell-tale features of living systems and the universe that are best explained by an intelligent cause—that is, by the conscious choice of a rational agent—rather than by an undirected process. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 110-111). HarperCollins. Kindle Edition.]

· Meyer, “The Origin of Biological Information and the Higher Taxonomic Categories.” See also Meyer, “The Cambrian Information Explosion”; “DNA and the Origin of Life”; “Evidence of Design in Physics and Biology,” 53–111; “The Scientific Status of Intelligent Design”; “Teleological Evolution”; “DNA by Design”; “The Explanatory Power of Design”; Meyer, Nelson, and Chien, “The Cambrian Explosion.”

· Thus, Signature in the Cell does not just make an argument; it also tells a story, a mystery story and the story of my engagement with it. It tells about the mystery that has surrounded the discovery of the digital code in DNA and how that discovery has confounded repeated attempts to explain the origin of the first life on earth. Throughout the book I will call this mystery “the DNA enigma.” [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 180-183). HarperCollins. Kindle Edition.]

· As evolutionary biologist Francisco Ayala has recently explained, Darwin explained the appearance of design without recourse to an actual designer. He gave us “design without a designer.” [Ayala, “Darwin’s Greatest Discovery.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 202-203). HarperCollins. Kindle Edition.]

1 DNA, Darwin, and the Appearance of Design

· As Newton wrote in his masterpiece The Opticks: “How came the Bodies of Animals to be contrived with so much Art, and for what ends were their several parts? Was the Eye contrived without Skill in Opticks, and the Ear without Knowledge of Sounds? … And these things being rightly dispatch’d, does it not appear from Phænomena that there is a Being incorporeal, living, intelligent…?” [Newton, Opticks, 369–70.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 215-217). HarperCollins. Kindle Edition.]

· As Crick himself put it thirty-five years after he and Watson discerned the structure of DNA, biologists must “constantly keep in mind that what they see was not designed, but rather evolved.” [Crick, What Mad Pursuit, 138.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 222-224). HarperCollins. Kindle Edition.]

· As Richard Dawkins notes, “The machine code of the genes is uncannily computer-like.” Software developer Bill Gates goes further: “DNA is like a computer program but far, far more advanced than any software ever created.” [Dawkins, River out of Eden, 17.] [Gates, The Road Ahead, 188.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 233-235). HarperCollins. Kindle Edition.]

· As origin-of-life researcher Bernd-Olaf Küppers explains, “The problem of the origin of life is clearly basically equivalent to the problem of the origin of biological information.” [Küppers, Information and the Origin of Life, 170–72.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 241-242). HarperCollins. Kindle Edition.]

· After the early 1960s advances in the field of molecular biology made clear that the digital information in DNA was only part of a complex information-processing system, an advanced form of nanotechnology that mirrors and exceeds our own in its complexity, storage density, and logic of design. Over the last fifty years, biology has advanced as scientists have come to understand more about how information in the cell is stored, transferred, edited, and used to construct sophisticated machines and circuits made of proteins. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 257-260). HarperCollins. Kindle Edition.]

· Francis Collins, scientific director of the project, described the genome as a “book,” a repository of “instructions,” and the “book of life.” The Human Genome Project, perhaps more than any discovery since the elucidation of the structure of DNA in 1953, has heightened public awareness of the importance of information to living things. If Watson and Crick’s discovery showed that DNA stores a genetic text, Francis Collins and his team took a huge step toward deciphering its message. [Elizabeth Pennisi, “Finally, the Book of Life.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 265-268). HarperCollins. Kindle Edition.]

· As evolutionary biologist George Williams notes, “You can speak of galaxies and particles of dust in the same terms because they both have mass and charge and length and width. [But] you can’t do that with information and matter.” [Interview with Williams, in Brockman, ed., The Third Culture, 42–43.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 276-277). HarperCollins. Kindle Edition.]

· A blank magnetic tape, for example, weighs just as much as one “loaded” with new software—or with the entire sequence of the human genome. Though these tapes differ in information content (and value), they do not do so because of differences in their material composition or mass. As Williams concludes, “Information doesn’t have mass or charge or length in millimeters. Likewise matter doesn’t have bytes…. This dearth of shared descriptors makes matter and information two separate domains.” [Interview with Williams, in Brockman, ed., The Third Culture, 42–43.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 277-281). HarperCollins. Kindle Edition.]

· When scientists during the late 1940s began to define information, they did not make reference to physical parameters such as mass, charge, or watts. Instead, they defined information by reference to a psychological state—the reduction of uncertainty—which they proposed to measure using the mathematical concept of probability. The more improbable a sequence of characters or signals, the more uncertainty it reduces, and thus the more information it conveys. [Klir and Wierman, Uncertainty-Based Information.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 282-285). HarperCollins. Kindle Edition.]

· We now know that we do not just create information in our own technology; we also find it in our biology—and, indeed, in the cells of every living organism on earth. But how did this information arise? And what does the presence of information in even the simplest living cell imply about life and its origin? Who or what “wrote” the book of life? [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 297-299). HarperCollins. Kindle Edition.]

· As George Williams (himself an evolutionary biologist) notes, “Evolutionary biologists have failed to realize that they work with two more or less incommensurable domains: that of information and that of matter…. The gene is a package of information, not an object. The pattern of base pairs in a DNA molecule specifies the gene. But the DNA molecule is the medium, it’s not the message.” [Williams, Natural Selection, 11.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 307-310). HarperCollins. Kindle Edition.]

· As the information theorist Hubert Yockey observes, the “genetic code is constructed to confront and solve the problems of communication and recording by the same principles found…in modern communication and computer codes.” Yockey notes that “the technology of information theory and coding theory has been in place in biology for at least 3.85 billion years,” or from the time that life first originated on earth. What should we make of this fact? How did the information in life first arise? [Yockey, “Origin of Life on Earth,” 105.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 311-315). HarperCollins. Kindle Edition.]

· Many evolutionary biologists admit, of course, that living organisms “appear to have been carefully and artfully designed,” as Richard Lewontin puts it. As Richard Dawkins states, “Biology is the study of complex things that appear to have been designed for a purpose.” Nevertheless, Lewontin and Dawkins, like evolutionary biologists generally, insist that the appearance of design in life is illusory. Life, they say, looks designed, but was not designed by an actual intelligent or purposive agent. [Lewontin, “Adaptation.”] [Dawkins, The Blind Watchmaker, 1.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 317-321). HarperCollins. Kindle Edition.]

· Evolutionary biologists have a theory that can apparently explain, or explain away, the appearance of design without invoking an actual designer. According to classical Darwinism, and now modern neo-Darwinism, the mechanism of natural selection acting on random variations (or mutations) can mimic the effects of intelligence, even though the mechanism is, of course, entirely blind, impersonal, and undirected. [Mayr, “Darwin: Intellectual Revolutionary.” The effort to explain biological organisms naturalistically was reinforced by a trend in science to provide fully naturalistic accounts for other phenomena such as the precise configuration of the planets in the solar system (Pierre Laplace) and the origin of geological features (Charles Lyell and James Hutton). It was also reinforced (and in large part made possible) by an emerging positivistic tradition in science that increasingly sought to exclude appeals to supernatural or intelligent causes from science by definition (see Gillespie, “Natural History, Natural Theology, and Social Order”). See also Darwin, On the Origin of Species, 481–82.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 323-326). HarperCollins. Kindle Edition.]

· As Darwin explained, “There seems to be no more design in the variability of organic beings, and in the action of natural selection, than in the course which the wind blows.” Or as evolutionary biologist Francisco Ayala explains, “The functional design of organisms and their features would…seem to argue for the existence of a designer. It was Darwin’s greatest accomplishment [however] to show that the directive organization of living beings can be explained as the result of a natural process, natural selection, without any need to resort to a Creator or other external agent.” Thus, Ayala and other Darwinian biologists not only affirm that natural selection can produce “design without a designer,” they also assert that it is “creative without being conscious.” [Darwin, Life and Letters, 1:278–79.] [Ayala, “Darwin’s Greatest Discovery,” in Ruse and Dembski, eds., Debating Design, 58. As the late Harvard evolutionary biologist Ernst Mayr explained, “The real core of Darwinism…is the theory of natural selection. This theory is so important for the Darwinian because it permits the explanation of adaptation, the ‘design’ of the natural theologian, by natural means, instead of by divine intervention” (Foreword, in Ruse, ed., Darwinism Defended).] [Ayala, “Darwin’s Greatest Discovery,” Proceedings of the National Academy of Sciences, 8573.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 341-347). HarperCollins. Kindle Edition.]

· Science often shows that our perceptions of nature do not match reality. A straight pencil appears bent when inserted in a glass of water; the sun appears to circle the earth; and the continents appear immobile. Perhaps, living organisms only appear to be designed. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 350-351). HarperCollins. Kindle Edition.]

· As philosopher of science Michael Ruse notes, biologists ask about “the purpose of the fins on the back of the stegosaurus” or “the function of the bird’s feathers” and discuss whether “the Irish elk’s antlers did or did not exist in order to intimidate rivals.” “It is true,” Ruse continues, “that during the nineteenth century [some physicists] suggested that the moon exists in order to light the way home of lonely travelers, but no physicist would use such language today. In biology, however, especially evolutionary biology, this kind of talk is commonplace.” He concludes, “The world of the evolutionist is drenched in the anthropomorphism of intention.” And yet “paradoxically, even the severest critics” of such intentional language slip into it “for the sake of convenience.” [Ruse, “Teleology in Biology.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 363-368). HarperCollins. Kindle Edition.]

· As Richard Dawkins notes, “Apart from differences in jargon, the pages of a molecular-biology journal might be interchanged with those of a computer-engineering journal.” [Dawkins, River Out of Eden, 17.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 377-379). HarperCollins. Kindle Edition.]

· As if to underscore the point, University of Chicago cell biologist James Shapiro describes the integrated system of proteins that constitutes the mammalian blood-clotting system “as a powerful real-time distributed computing system.” In the same context he notes that many biochemical systems within the cell resemble “the wiring diagram for an electronic circuit.” [Shapiro, review of Darwin’s Black Box, by Michael Behe.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 379-382). HarperCollins. Kindle Edition.]

· As the historian of biology Timothy Lenoir observes, “Teleological thinking has been steadfastly resisted by modern biology. And yet in nearly every area of research, biologists are hard pressed to find language that does not impute purposiveness to living forms.” [Lenoir, The Strategy of Life, ix.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 382-384). HarperCollins. Kindle Edition.]

· What the other scientists did dispute was a controversial new hypothesis that Thaxton and his colleagues had floated in the epilogue of their book in an attempt to explain the DNA enigma. They had suggested that the information in DNA might have originated from an intelligent source or, as they put it, an “intelligent cause.” Since, in our experience, information arises from an intelligent source, and since the information in DNA was, in their words, “mathematically identical” to the information in a written language or computer code, they suggested that the presence of information in DNA pointed to an intelligent cause. The code, in other words, pointed to a programmer. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 456-461). HarperCollins. Kindle Edition.]

2 The Evolution of a Mystery and Why It Matters

· Wöhler dashed off a letter to fellow chemist Jöns Jakob Berzelius: “I can no longer, as it were, hold back my chemical water; and I have to let out that I can make urea without needing a kidney, or even of an animal, whether of man or dog: the ammonium salt of cyanic acid (cyansäures Ammoniak) is urea.” [As quoted in Kauffman and Chooljian, “Friedrich Wöhler (1800–1882), on the Bicentennial of His Birth,” 126.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 561-564). HarperCollins. Kindle Edition.]

· The experiment, eventually replicated in laboratories around the world, showed that the chemical compounds in living organisms could be artificially synthesized. Though chemists before Wöhler had synthesized naturally occurring mineral substances, many assumed it was impossible to synthesize compounds found in organisms, since it was thought that organic matter contained mysterious and immaterial “vital forces.” As Sir Fredrick Gowland Hopkins later suggested, Wöhler’s discovery marked the beginning of a challenge to the “primitive faith in a boundary between the organic and the inorganic which could never be crossed.” For this reason, Wöhler’s work would also exert a profound influence on scientific ideas about the origin of life for over a century and would serve as a starting point for my own investigation of the topic. [Partington, A History of Chemistry.] [Florkin, A History of Biochemistry, 251–52.] [Hopkins, “BAAS Presidential Address,” 382.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 564-571). HarperCollins. Kindle Edition.]

· In the Origin, Darwin did not try to explain the origin of the first life. Instead, he sought to explain the origin of new forms of life from simpler preexisting forms, forms that already possessed the ability to reproduce. His theory assumed rather than explained the origin of the first living thing. Since this limitation of Darwin’s theory was widely recognized, it raised a question: Why were nineteenth-and twentieth-century biologists and philosophers so sure that Darwin had undermined the design argument from biology? If scientists at the time had no detailed explanation for how life had first arisen, how did they know that design—that is, actual intelligent design—played no role in this critically important event? [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 595-600). HarperCollins. Kindle Edition.]

· Since the time of the ancient Greeks, there have been two basic pictures of ultimate reality among Western intellectuals, what the Germans call a Weltanschuung, or worldview. According to one worldview, mind is the primary or ultimate reality. On this view, material reality either issues from a preexisting mind, or it is shaped by a preexistent intelligence, or both. Mind, not matter, is, therefore, the prime or ultimate reality—the entity from which everything else comes, or at least the entity with the capacity to shape the material world. Plato, Aristotle, the Roman Stoics, Jewish philosophers such as Moses Maimonides, and Christian philosophers such as St. Thomas Aquinas each held some version of this perspective. [For a detailed treatment of this perspective in ancient philosophy, see Sedley, Creationism and Its Critics in Antiquity.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 611-616). HarperCollins. Kindle Edition.]

· Many of these early modern scientists thought that their studies of nature confirmed this view by providing evidence, in Sir Isaac Newton’s words, of “an intelligent and powerful Being” behind it all. This view of reality is often called idealism to indicate that ideas come first and matter comes later. Theism is the version of idealism that holds that God is the source of the ideas that gave rise to and shaped the material world. [Newton, General Scholium, Mathematical Principles of Natural Philosophy.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 617-621). HarperCollins. Kindle Edition.]

· The opposite view holds that the physical universe or nature is the ultimate reality. In this view, either matter or energy (or both) are the things from which everything else comes. They are self-existent and do not need to be created or shaped by a mind. Natural interactions between simple material entities governed by natural laws eventually produce chemical elements from elementary particles, then complex molecules from simple chemical elements, then simple life from complex molecules, then more complex life from simpler life, and finally conscious living beings such as ourselves. In this view matter comes first, and conscious mind arrives on the scene much later and only then as a by-product of material processes and undirected evolutionary change. The Greek philosophers who were called atomists, such as Leucippus and Democritus, were perhaps the first Western thinkers to articulate something like this view in writing. [Kirk and Raven, The Presocratic Philosophers.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 621-627). HarperCollins. Kindle Edition.]

· Following the widespread acceptance of Darwin’s theory of evolution in the late nineteenth century, many modern scientists adopted this view. This worldview is called either naturalism or materialism, or sometimes scientific materialism or scientific naturalism, in the latter case because many of the scientists and philosophers who hold this perspective think that scientific evidence supports it. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 628-631). HarperCollins. Kindle Edition.]

· In astronomy, for example, the French mathematician Pierre Laplace offered an ingenious theory known as the “nebular hypothesis” to account for the origin of the solar system as the outcome of purely natural gravitational forces.* In geology, Charles Lyell explained the origin of the earth’s most dramatic topographical features—mountain ranges and canyons—as the result of slow, gradual, and completely naturalistic processes of change such as erosion or sedimentation.* In physics and cosmology, a belief in the infinity of space and time obviated any need to consider the question of the ultimate origin of matter. And, in biology, Darwin’s theory of evolution by natural selection suggested that an undirected process could account for the origin of new forms of life without divine intervention, guidance, or design. Collectively, these theories made it possible to explain all the salient events in natural history from before the origin of the solar system to the emergence of modern forms of life solely by reference to natural processes—unaided and unguided by any designing mind or intelligence. [Laplace, (Vietnamese)Exposition du système du monde.] [Lyell, Principles of Geology.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 645-653). HarperCollins. Kindle Edition.]

· Although Laplace’s nebular hypothesis provided additional support for a materialistic conception of the cosmos, it also complicated attempts to explain life on earth in purely material terms. Laplace’s theory suggested that earth had once been too hot to sustain life, since the environmental conditions needed to support life existed only after the planet had cooled below the boiling point of water. For this reason, the nebular hypothesis implied that life had not existed eternally, but instead appeared at a definite time in earth’s history. [Ernst Haeckel, for instance, in The History of Creation, stated: “We can, therefore, from these general outlines of the inorganic history of the earth’s crust, deduce the important fact that at a certain definite time life had its beginning on earth, and that terrestrial organisms did not exist from eternity” (401).] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 655-658). HarperCollins. Kindle Edition.]

· As Darwin himself noted in 1866, “Though I expect that at some future time the [origin] of life will be rendered intelligible, at present it seems to me beyond the confines of science.” [Darwin, More Letters of Charles Darwin, 273.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 662-663). HarperCollins. Kindle Edition.]

· The problem of the origin of life was, at this time, rendered more acute by the failure of “spontaneous generation,” the idea that life originates continually from the remains of once living matter. This theory suffered a series of setbacks during the 1860s because of the work of Louis Pasteur. In 1860 and 1861, Pasteur demonstrated that micro-organisms or germs exist in the air and can multiply under favorable conditions.* He showed that if air enters sterile vessels, contamination of the vessels with microorganisms occurs. Pasteur argued that the observed “spontaneous generation” of mold or bacterial colonies on rotting food or dead meat, for example, could be explained by the failure of experimenters to prevent contamination with preexisting organisms from the atmosphere.* Pasteur’s work seemed to refute the only naturalistic theory of life’s origin then under experimental scrutiny. [Farley, The Spontaneous Generation Controversy, 103ff.; Lechevalier and Solotorovsky, Three Centuries of Microbiology, 35–37.] [Farley, Spontaneous Generation Controversy, 103–7, 114, 172; Lanham, Origins of Modern Biology, 268.] [Nevertheless, the doctrine of spontaneous generation did not die easily. Even after Pasteur’s work, Henry Bastian continued to find microbial organisms in various substances that had been sealed and “sterilized” at 100 degrees C or higher. Not until the 1870s, when microbiologists like Cohn, Koch, and Tyndall perfected methods of killing heat-resistant spores, were Bastian’s observations discredited. Despite an increasingly critical scientific response to his experimental methods and conclusions, Bastian continued to offer observational evidence for spontaneous generation from inorganic matter for another thirty years. Nevertheless, these and other attempts yielded to a familiar pattern of refutation. Experiments supposedly establishing the spontaneous occurrence of microorganisms remained tenable only as long as sterilization methods were inadequate to kill existing microorganisms or prevent bacterial contamination of experimental vessels from the surrounding environment. When sources of microorganisms were identified and methods of destroying them perfected, observational evidence for spontaneous generation was withdrawn or discredited. In the minds of some scientists, especially after the turn of the century, development seemed to confirm that living matter is too complex to organize itself spontaneously, whether beginning from organic or inorganic precursors. Although Huxley and Haeckel accepted Pasteur’s results, both insisted that his work was not relevant to abiogenesis (life arising from nonliving matter), as his experiments discredited only theories of what Haeckel called “plasmogeny” or what Huxley called “heterogenesis,” i.e., spontaneous generation from once living matter (Haeckel, The Wonders of Life, 115; Kamminga, “Studies in the History of Ideas,” 55, 60).] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 664-671). HarperCollins. Kindle Edition.]

· First, Darwin had established an important precedent. He had shown that there was a plausible means by which organisms could gradually produce new structures and greater complexity by a purely undirected material process. Why couldn’t a similar process explain the origin of life from preexisting chemicals? Darwin’s theory also implied that living species did not possess an essential and immutable nature. Since Aristotle, most biologists had believed that each species or type of organism possessed an unchanging nature or form; many believed that these forms reflected a prior idea in the mind of a designer. But Darwin argued that species can change—or “morph”—over time. Thus, his theory challenged this ancient view of life. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 725-730). HarperCollins. Kindle Edition.]

· If Darwin was right, then it was futile to maintain rigid distinctions in biology based on ideas about unchanging forms or natures. This reinforced the conviction that there was no impassable or unbridgeable divide between inanimate and animate matter. Chemicals could “morph” into cells, just as one species could “morph” into another. [For instance, John Tyndall argued, “There does not exist a barrier possessing the strength of a cobweb to oppose the hypothesis which ascribes the appearance of life to that ‘potency of matter’ which finds expression in natural evolution” (Fragments of Science, 434). As Kamminga explains, Tyndall held that “it was inconsistent to believe in evolution and at the same time reject abiogenesis” (“Studies in the History of Ideas,” 57).] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 732-734). HarperCollins. Kindle Edition.]

· Darwin sketched out a purely naturalistic scenario for the origin of life. He emphasized the role of special environmental conditions and just the right mixture of chemical ingredients as crucial factors in making the origin of life possible: “It is often said that all the conditions for the first production of a living organism are present…. But if (and Oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., that a protein compound was chemically formed ready to undergo still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed.” [Darwin, “Letter to Hooker”; see also Darwin, Life and Letters, 18.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 739-745). HarperCollins. Kindle Edition.]

· In my first year of research, I came across a statement by Russian scientist Aleksandr Oparin. Oparin was the twentieth century’s undisputed pioneer of origin-of-life studies, and his comment helped me to identify another key reason for the Victorian lack of concern about the origin-of-life problem. “The problem of the nature of life and the problem of its origin have become inseparable,” he said. [Oparin, Genesis and Evolutionary Development of Life, 7.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 747-750). HarperCollins. Kindle Edition.]

· To explain how life originated, scientists first have to understand what life is. That understanding, in turn, defines what their theories of the origin of life must explain. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 750-752). HarperCollins. Kindle Edition.]

· Cells were viewed as “homogeneous and structure-less globules of protoplasm,” [Haeckel, The Wonders of Life, 135.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Location 757). HarperCollins. Kindle Edition.]

· Miller’s experiment received widespread coverage in popular publications such as Time magazine and gave chemical evolutionary theory the status of textbook orthodoxy almost overnight. As science writer William Day reflected, “It was an experiment that broke the logjam. The simplicity of the experiment, the high yields of the products and the specific biological compounds…produced by the reaction were enough to show the first step in the origin of life was not a chance event, but was inevitable.” [Shapiro, Origins, 98.] [William Day, Genesis on Planet Earth, 5.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 930-934). HarperCollins. Kindle Edition.]

3 The Double Helix

· Harmke Kamminga puts it this way: “At the heart of the problem of the origin of life lies a fundamental question: What is it exactly that we are trying to explain the origin of?” [Kamminga, “Protoplasm and the Gene,” 1.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 972-974). HarperCollins. Kindle Edition.]

· As Watson and Crick later explained: “The phosphate-sugar backbone of our model is completely regular, but any sequence of the pairs of bases can fit into the structure. It follows that in a long molecule, many different permutations are possible, and it therefore seems likely that the precise sequence of the bases is the code which carries the genetic information.” [Watson and Crick, “Genetical Implications,” 965.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1318-1321). HarperCollins. Kindle Edition.]

· Watson and Crick’s discovery would forever change our understanding of the nature of life. At the close of the nineteenth century, most biologists thought life consisted solely of matter and energy. But after Watson and Crick, biologists came to recognize the importance of a third fundamental entity in living things: information. And this discovery would redefine, from that point forward, what theories about the origin of life would need to explain. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1322-1325). HarperCollins. Kindle Edition.]

4 Signature in the Cell

· In Darwin’s time few, if any, biologists talked about biological or genetic information, but today they routinely refer to DNA, RNA, and proteins as carriers or repositories of information. Biologists tell us that DNA stores and transmits “genetic information,” that it expresses a “genetic message,” that it stores “assembly instructions,” a “genetic blueprint,” or “digital code.” [Watson and Crick, “A Structure for Deoxyribose Nucleic Acid”; “Genetical Implications,” esp. 964; Schneider, “Information Content of Individual Genetic Sequences”; Loewenstein, The Touchstone of Life. Hood and Galas, “The Digital Code of DNA.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1327-1330). HarperCollins. Kindle Edition.]

· Shannon’s theory of information was based upon a fundamental intuition: information and uncertainty are inversely related. The more informative a statement is, the more uncertainty it reduces. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1373-1374). HarperCollins. Kindle Edition.]

· Shannon’s theory cannot distinguish functional or message-bearing sequences from random or useless ones. It can only measure the improbability of the sequence as a whole. It can quantify the amount of functional or meaningful information that might be present in a given sequence of symbols or characters, but it cannot determine whether the sequence in question “produces a specific effect.” [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1426-1429). HarperCollins. Kindle Edition.]

· All this suggested to me that there are important distinctions to be made when talking about information in DNA. In the first place, it’s important to distinguish information defined as “a piece of knowledge known by a person” from information defined as “a sequence of characters or arrangements of something that produce a specific effect.” Whereas the first of these two definitions of information doesn’t apply to DNA, the second does. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1432-1435). HarperCollins. Kindle Edition.]

· Proteins are specified in two ways. First, proteins display a specificity of shape. The strangely irregular shapes of proteins that Kendrew and others discovered turned out to be essential to the function of the proteins. In particular, the three-dimensional shape of a protein gives it a hand-in-glove fit with other equally specified and complex molecules or with simpler substrates, enabling it to catalyze specific chemical reactions or to build specific structures within the cell. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1505-1508). HarperCollins. Kindle Edition.]

· The sequence hypothesis suggested that the nucleotide bases in DNA functioned just like alphabetic letters in an English text or binary digits in software or a machine code. According to Crick’s hypothesis, it is the precise arrangement or sequence of these bases that determines the arrangement of amino acids—which, in turn, determines protein folding and structure. In other words, the sequence specificity of amino acids in proteins derives from a prior specificity of arrangement in the nucleotide bases on the DNA molecule. [Judson, The Eighth Day of Creation, 332–35.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1573-1577). HarperCollins. Kindle Edition.]

· Gene expression begins as long chains of nucleotide bases are copied during a process known as “transcription.” During this process, the genetic assembly instructions stored on a strand of DNA are reproduced on another molecule called “messenger RNA” (or mRNA). The resulting single-stranded copy or “transcript” contains a sequence of RNA bases precisely matching the sequence of bases on the original DNA strand. (RNA also uses chemicals called bases to store genetic information, but it uses a slightly different chemical alphabet than DNA. RNA substitutes a base called uracil for the base thymine used in the DNA.) [Alberts, et al., Molecular Biology of the Cell, 106–8; Wolfe, Molecular and Cellular Biology, 48.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1609-1613). HarperCollins. Kindle Edition.]

· After it is produced, the messenger-RNA molecule travels to the ribosome, a molecular machine that helps translate the mRNA assembly instructions. These instructions consist of a series of three-letter genetic “words” called “codons.” Each codon consists of three bases and directs the cell to attach a specific amino acid to a growing chain of other amino acids. For example, the mRNA word UUA directs the ribosome to attach the amino acid leucine, whereas AGA specifies the amino acid arginine. Other codons direct the ribosome to start or stop building proteins. This translation process occurs with the aid of specific adapter molecules (called transfer RNAs, or tRNAs) and specific enzymes (called aminoacyl-tRNA synthetases). [Alberts, et al., Molecular Biology of the Cell, 108.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1613-1618). HarperCollins. Kindle Edition.]

· So what kind of information does DNA contain, Shannon information or specified information? Mere complexity or specified complexity? The answer is—both. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1672-1673). HarperCollins. Kindle Edition.]

· Thus, in addition to a quantifiable amount of Shannon information (or complexity), DNA also contains information in the sense of Webster’s second definition: it contains “alternative sequences or arrangements of something that produce a specific effect.” Although DNA does not convey information that is received, understood, or used by a conscious mind, it does have information that is received and used by the cell’s machinery to build the structures critical to the maintenance of life. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1706-1709). HarperCollins. Kindle Edition.]

· As the origin-of-life biochemist Leslie Orgel observes: “Living organisms are distinguished by their specified complexity. Crystals…fail to qualify as living because they lack complexity; mixtures of random polymers fail to qualify because they lack specificity.” [Orgel, The Origins of Life, 189.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1714-1716). HarperCollins. Kindle Edition.]

· To quote the information scientist Hubert Yockey again, “The genetic code is constructed to confront and solve the problems of communication and recording by the same principles found…in modern communication and computer codes.” [Yockey, “Origin of Life on Earth,” esp. 105.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1721-1723). HarperCollins. Kindle Edition.]

5 The Molecular Labyrinth

· Molecular biologists describe the process of protein synthesis, or “gene expression,” as a two-stage process of information transfer involving many smaller discrete steps and many molecular machines. This process proceeds as long chains of nucleotide triplets (the genetic message) are first copied during a process known as “transcription” and then transported (by the molecular messenger mRNA) to a complex organelle called a ribosome. At the ribosome site, the genetic message is then “translated” with the aid of a suite of adapter molecules called transfer RNAs to produce growing amino-acid chains—chains that fold into the functional proteins the cell needs to survive. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1893-1898). HarperCollins. Kindle Edition.]

· The first stage in the process of protein synthesis is called transcription. During transcription, a copy, or transcript, of the DNA text is made by a large protein complex, known as RNA polymerase, that moves down the DNA chain and “reads” the original DNA text. As RNA polymerase proceeds, it makes an identical copy of the DNA transcript in an RNA format. (Like DNA, RNA contains four chemical bases, called nucleotide bases. These bases are the same as those in DNA with one exception: RNA uses a base called uracil instead of thymine.) The resulting single-stranded RNA copy, or transcript, then moves from the chromosomes to the ribosome in the outer cytoplasm to begin translation, the next step in the processing of genetic information. [Watson, et al., Molecular Biology of the Gene, vol. 1:360–81.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1899-1904). HarperCollins. Kindle Edition.]

· Transcription can be thus described in a few simple sentences. Yet any such description conceals an impressive complexity. In the first place, RNA polymerase is an extraordinarily complex protein machine of great specificity. The RNA polymerases present in the simplest bacteria (Mycoplasma) comprise several separate protein subunits with (collectively) thousands of specifically sequenced amino acids. [Fraser, et al., “The Minimal Gene Complement.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1904-1907). HarperCollins. Kindle Edition.]

· RNA polymerase performs several discrete functions in the process of transcription. First, it recognizes (and binds to) specific regions of the DNA that mark the beginning of genes. Second, it unwinds (or helps unwind) the DNA text, exposing the strand that will serve as the template for making the RNA copy. Third, it sequesters and positions RNA bases (A, U, G, C) with their complementary partners on the DNA template (T, A, C, G, respectively). Fourth, it polymerizes or links together the separate RNA nucleotides, thus forming a long message-bearing ribbon of mRNA. As molecular biologist Stephen Wolfe explains: “The structure of the RNA polymerases reflects the complexity of their activities in RNA transcription. The enzymes have sites that recognize promoters, react with initiation, elongation and termination factors, recognize DNA bases for correct pairing, bind and hydrolyze RNA nucleotides, form phospho-diester linkages, terminate transcription and perhaps unwind and rewind DNA.” [Watson, et al., Molecular Biology of the Gene, vol. 1:368–80.] [Wolfe, Molecular and Cellular Biology, 580–81, 639–48.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1908-1915). HarperCollins. Kindle Edition.]

· Yet for all its complexity and specificity, RNA polymerase alone does not ensure accurate transcription. The process involves several other complex and functionally integrated parts and steps. For example, for RNA polymerase to access the genetic text, the DNA double helix must unwind and expose the nucleotide bases. Further, to initiate transcription, the RNA polymerase must bind to the correct part of the DNA sequence in order to begin transcribing at the beginning of a genetic message, rather than in the middle or at the end. For its part, the DNA text provides a promoter sequence or signal upstream of the actual coding sequence to facilitate recognition of the correct location by the RNA polymerase. Yet the RNA polymerase cannot, on its own, find this site with any reliability. In prokaryotes (cells without nuclei), a protein known as sigma factor combines with the core RNA polymerase enzyme (itself a composite of enzymes) to form a larger “holoenzyme.” The addition of this sigma-factor protein increases the accuracy of RNA polymerase–DNA binding by roughly a million times, making recognition of promoter sequences and thus accurate transcription possible. [Wolfe, Molecular and Cellular Biology, 639, 731.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1918-1926). HarperCollins. Kindle Edition.]

· The next step in gene expression, called translation, exhibits even greater integrated complexity. Whereas transcription makes a single-stranded copy—a transcript—of DNA in an RNA format, translation uses that information to build a protein. Since many biologists think of protein molecules themselves as information-rich molecules constructed from a twenty-character amino-acid alphabet, they think of the process of protein synthesis as a process of translating information from the four-character alphabets of DNA and RNA into the twenty-character amino-acid alphabet; hence the name “translation.” [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1957-1961). HarperCollins. Kindle Edition.]

· Even in the simplest prokaryotic cells, the process of translation utilizes many dozens of separate proteins or protein machines, each one of which is produced during translation. [Fraser, et al., “Minimal Gene Complement,” 399.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1961-1962). HarperCollins. Kindle Edition.]

· The process of translation begins as the ribosome subunits dissociate and the messenger RNA (mRNA) binds to the smaller of the two subunits (see Fig. 5.7). Auxiliary proteins known as initiation factors catalyze this disassociation and temporarily stabilize the second subunit in its disassociated state. At the same time, a group of three RNA bases on a transfer-RNA (tRNA) molecule binds to the first triplet of RNA bases on the mRNA molecule as it docks in the ribosome. The groups of three bases on mRNA are called codons or triplets. The groups of three bases to which they bind on the tRNA are called anticodons. The sequence AUG constitutes the “initiator codon” at the head of the mRNA transcript. [Watson, et al., Molecular Biology of the Gene, vol. 1:443.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 1965-1970). HarperCollins. Kindle Edition.]

· As Richard Lewontin notes, “No living molecule [i.e., biomolecule] is self-reproducing. Only whole cells may contain all the necessary machinery for self-reproduction…. Not only is DNA incapable of making copies of itself, aided or unaided, but it is incapable of ‘making’ anything else…. The proteins of the cell are made from other proteins, and without that protein-forming machinery nothing can be made.” [Lewontin, “The Dream of the Human Genome.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2031-2034). HarperCollins. Kindle Edition.]

· Biochemist David Goodsell describes the problem, “The key molecular process that makes modern life possible is protein synthesis, since proteins are used in nearly every aspect of living. The synthesis of proteins requires a tightly integrated sequence of reactions, most of which are themselves performed by proteins.” [Goodsell, The Machinery of Life, 45.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2045-2047). HarperCollins. Kindle Edition.]

· Jacques Monod noted in 1971: “The code is meaningless unless translated. The modern cell’s translating machinery consists of at least fifty macromolecular components which are themselves coded in DNA: the code cannot be translated otherwise than by products of translation.” (Scientists now know that translation actually requires more than a hundred proteins.) [Monod, Chance and Necessity, 143.] [Bult, et al., “Complete Genome Sequence”; Glass, et al., “Essential Genes of a Minimal Bacterium.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2048-2051). HarperCollins. Kindle Edition.]

· As Lewontin asks, “What makes the proteins that are necessary to make the protein?” As David Goodsell puts it, this “is one of the unanswered riddles of biochemistry: which came first, proteins or protein synthesis? If proteins are needed to make proteins, how did the whole thing get started?” The end result of protein synthesis is required before it can begin. [Lewontin, “The Dream of the Human Genome,” esp. 33.] [Goodsell, The Machinery of Life, 45.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2052-2055). HarperCollins. Kindle Edition.]

· The cell needs proteins to process and express the information in DNA in order to build proteins. But the construction of DNA molecules (during the process of DNA replication) also requires proteins. So which came first, the chicken (nucleic acids) or the egg (proteins)? If proteins must have arisen first, then how did they do so, since all extant cells construct proteins from the assembly instructions in DNA. How did either arise without the other? [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2056-2059). HarperCollins. Kindle Edition.]

· As the late British philosopher Sir Karl Popper mused, “What makes the origin of life and the genetic code a disturbing riddle is this: the code cannot be translated except by using certain products of its translation. This constitutes a really baffling circle: a vicious circle it seems, for any attempt to form a model, or a theory, of the genesis of the genetic code.” [Popper, “Scientific Reduction.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2060-2062). HarperCollins. Kindle Edition.]

6 The Origin of Science and the Possibility of Design

· Charles Darwin also did little experimental science. He did make several descriptive studies of barnacles and worms and some experimental studies about how species spread through seed dispersal and other processes. Yet his masterpiece, On the Origin of Species by Means of Natural Selection, contains neither a single mathematical equation nor any report of original experimental research. Yet he formulated a great scientific theory. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2135-2138). HarperCollins. Kindle Edition.]

· As many historians of science have noted, the founders of modern science needed to assume that if they studied nature carefully, it would reveal its secrets. Their confidence in this assumption was grounded in the Greek and Judeo-Christian idea that the universe is an orderly system—a cosmos, not a chaos. As the British philosopher Alfred North Whitehead explained, “There can be no living science unless there is a widespread instinctive conviction in the existence of an Order of Things. And, in particular, of an Order of Nature.” Whitehead argued that confidence in this proposition was especially inspired by the “medieval insistence upon the rationality of God.” [Whitehead, Science and the Modern World, 2–4, 13.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2188-2193). HarperCollins. Kindle Edition.]

· As sociologist of science Steve Fuller notes, Western science is grounded in “the belief that the natural order is the product of a single intelligence from which our own intelligence descends.” This foundational assumption gave rise to the idea that nature was “intelligible,” that it had been designed in accord with discernable laws that could be understood by those who subjected nature to careful scrutiny. Or as the astronomer Johannes Kepler said, scientists have the job of “thinking God’s thoughts after him.” [Fuller, Science vs. Religion? 15. See also: Crombie, Augustine to Galileo; Jaki, “Science: Western or What?”; Butterfield, The Origins of Modern Science; Hooykaas, Religion and the Rise of Modern Science.] [As cited in Holton, Thematic Origins of Scientific Thought, 86.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2196-2200). HarperCollins. Kindle Edition.]

· As the Oxford physicist and historian of science Peter Hodgson observes: “According to Judeo-Christian beliefs the world is the free creation of God from nothing. The structure of the world cannot therefore be deduced from first principles; we have to look at it, to make observations and experiments to find out how God made it. This reinforces the Aristotelian principle that all knowledge comes through the senses, but requires that it be situated within a wider set of beliefs concerning the nature of the world that is implicit in the doctrine of creation.” Hodgson notes that early scientists assumed that the world was both rational—because it was created by a Mind—and contingent—because that Mind had acted freely. These assumptions led to “a fresh style of scientific thinking,” one that “was made possible by the Judeo-Christian vision of the world.” [Hodgson, “The Christian Origin of Science,” 145; 142.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2223-2229). HarperCollins. Kindle Edition.]

· As I studied the history of science, I soon discovered, however, that many of these scientists did not just assume or assert by faith that the universe had been designed; they also argued for this hypothesis based on discoveries in their disciplines. Johannes Kepler perceived intelligent design in the mathematical precision of planetary motion and the three laws he discovered that describe that motion. Other scientists perceived design in many of the structures or features of the natural world upon which the laws of nature operated. Louis Agassiz, the leading American naturalist of the nineteenth century, for whom the Agassiz Chair is named at Harvard, believed that the patterns of appearance in the fossil record pointed unmistakably to design.* Carl Linnaeus argued for design based upon the ease with which plants and animals fell into an orderly groups-within-groups system of classification.* Robert Boyle insisted that the intricate clocklike regularity of many physical mechanisms suggested the activity of “a most intelligent and designing agent.” [Agassiz, Essay on Classification; see also Rieppel, “Louis Agassiz (1807–1873) and the Reality of Natural Groups,” 34.] [“Rational inquiry must inevitably, in Linné’s [Linnaeus] opinion, lead, not to skepticism or disbelief, but to the acknowledgment of and respect for an omniscient and omnipotent Creator” (Larson, Reason and Experience, 151).] [The full passage reads: “For the characters and impressions of wisdom that are conspicuous in the curious fabric and orderly train of things can with no probability be referred to blind chance, but must be ascribed to a most intelligent and designing agent” (Boyle, A Free Enquiry, 101). See also Lennox, “Robert Boyle’s Defense of Teleological Inference.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2238-2246). HarperCollins. Kindle Edition.]

· As he explained: “Though these bodies may, indeed, persevere in their orbits by the mere laws of gravity, yet they could by no means have, at first, derived the regular position of the orbits themselves from those laws…. [Thus] this most beautiful system of the sun, planets, and comets could only proceed from the counsel and dominion of an intelligent and powerful being.” [Newton, General Scholium, Mathematical Principles of Natural Philosophy (1969).] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2252-2255). HarperCollins. Kindle Edition.]

7 Of Clues to Causes

· Stephen Jay Gould, the Harvard paleontologist and historian of science, insisted that the “historical sciences” such as geology, evolutionary biology, and paleontology used different methods than did “experimental sciences” such as chemistry and physics. Interestingly, he also argued that understanding how historical sciences differed from experimental sciences helped to legitimate evolutionary theory in the face of challenges to its scientific rigor by those who questioned its testability. Gould argued that historical scientific theories were testable, but not necessarily by experiments under controlled laboratory conditions. Instead, he emphasized that historical scientists tested their theories by evaluating their explanatory power. [Gould, “Evolution and the Triumph of Homology.” Following the nineteenth-century philosopher of science William Whewell, Gould describes the process of testing in the historical sciences as seeking “consilience.” “Consilience” occurs when many facts can be explained well by a single proposition or theory. Gould also notes that despite the differences between historical and experimental sciences, both share “nomothetic undertones,” meaning, in the case of the historical sciences, that they depend upon knowledge of the laws (Greek nomos) of nature to make inferences about the past (see esp. 64–65). Cleland, “Methodological and Epistemic Differences”; “Historical Science, Experimental Science, and the Scientific Method.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2309-2314). HarperCollins. Kindle Edition.]

· But there was a problem with this kind of reasoning, one that Lipton and many philosophers of science had noted. Many regarded “inference to the best explanation” as little more than a slogan, because no one could say exactly what made an explanation best. “Sure,” many argued, “we often infer hypotheses that, if true, best explain the evidence, but what does it mean to explain something and to explain it best?” [Lipton summarized the problem this way: “One reason ‘Inference to the Best Explanation’ has been so little developed, in spite of its popularity, is clear. The model is an attempt to account for inference in terms of explanation, but our understanding of explanation is so patchy that the model seems to account for the obscure in terms of the equally obscure” (Inference to the Best Explanation, 2).] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2417-2420). HarperCollins. Kindle Edition.]

· Darwin thought that when explaining past events, scientists should seek to identify established causes—causes known to produce the effect in question. Darwin appealed to this principle to argue that presently observed microevolutionary processes of change could be used to explain the origin of new forms of life in the past. Since the observed process of natural selection can produce a small amount of change in a short time, Darwin argued that it was capable of producing a large amount of change over a long period of time. In that sense, natural selection was “causally adequate.” [Darwin, On the Origin of Species, 80–130.] [Darwin also argued that the process of descent with modification was a vera causa of certain kinds of patterns found among living organisms. He noted that diverse organisms share many common features. He called these “homologous” and noted that we know from experience that descendants, although they differ from their ancestors, also resemble them in many ways, usually more closely than others who are more distantly related. So he proposed descent with modification as a vera causa (a known cause) for homologous structures. That is, he argued that our uniform experience shows that the process of descent with modification from a common ancestor is “causally adequate” or capable of producing homologous features (On the Origin of Species, 131–70; esp. 159, where Darwin refers to the “community of descent” as a “vera causa” of homologies among plant species). See also Meyer, “Of Clues and Causes,” 112–36; Kavalovski, “The Vera Causa Principle,” 104–29; Hodge, “Darwin’s Theory and Darwin’s Argument”; Recker, “Causal Efficacy”; Kitcher, “Darwin’s Achievement”; Hull, The Philosophy of Biological Science, 50–51.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2485-2489). HarperCollins. Kindle Edition.]

· According to Scriven, in order to establish the cause of a past event, historical scientists must first show that any candidate cause “has on other occasions clearly demonstrated its capacity to produce an effect of the sort here under study.” As Scriven put it, historical scientists must show that “independent evidence supports the claim that it [the cause] can produce this effect.” [Scriven, “Causes, Connections and Conditions in History,” 250; “Explanation and Prediction in Evolutionary Theory,” 481. As Hodge explains: “One should invoke only causes whose…competence to produce such an effect can be known independently of their putative responsibility for that phenomenon” (“The Structure and Strategy of Darwin’s ‘Long Argument,’” 239).] [Scriven, “Explanation and Prediction in Evolutionary Theory,” 481. See also Hodge, “The Structure and Strategy of Darwin’s ‘Long Argument,’” 239; Meyer, “Of Clues and Causes,” 79–111; see esp. 108–10 for a discussion comparing Scriven’s “retrospective causal analysis” and the vera causa principle.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2493-2496). HarperCollins. Kindle Edition.]

· Michael Scriven, for example, points out that historical scientists can make inferences about the past with confidence when they encounter evidence or a condition for which there is only one known cause. When historical scientists know that there is only one known cause of a given effect, they can infer the cause from the occurrence of its effect. When scientists can infer a uniquely plausible cause, they can avoid the fallacy of affirming the consequent—the error of ignoring other possible causes with the power to produce the same effect. [See the discussion of Sober below. See also Scriven, “Explanation and Prediction in Evolutionary Theory,” 480; “The Temporal Asymmetry of Explanations and Predictions.”] [Meyer, “Of Clues and Causes,” 96–108.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2500-2504). HarperCollins. Kindle Edition.]

· In his book Reconstructing the Past, Elliott Sober shows that the tasks of inferring the past may be easy or difficult (or even impossible) depending upon whether there are many causes that produce the effect in question or just one. He suggests that the severity of the problem confronting historical scientists will depend on whether the processes linking the present and past are “information preserving” or “information destroying.” To Sober, an information-preserving process is one that maps a present state to a single past state, whereas an information-destroying process is one that maps a present state to a multiplicity of possible past states. [Sober, Reconstructing the Past, 1–5.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2504-2509). HarperCollins. Kindle Edition.]

· Whether reconstructing the past is easy or difficult depends upon whether there is a single cause or condition that gives rise to a given present state or whether there are many possible past causes or conditions that give rise to a given present state. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2518-2520). HarperCollins. Kindle Edition.]

· Even so, Michael Scriven describes the historical method of “retrospective causal analysis” as a simple three-part method of evaluating proposed causal explanations. Many historical scientists find it helpful to think of it this way. According to Scriven, in order to establish a causal claim, the historical scientist needs: (1) “evidence that his candidate [cause] was present” and (2) evidence that “it has on other occasions clearly demonstrated its capacity to produce an effect of the sort here under study.” Additionally, the historical scientist needs to establish that there is (3) an “absence of evidence (despite a thorough search)…of…other possible causes.” [Scriven, “Causes, Connections and Conditions in History,” 249–50.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2625-2630). HarperCollins. Kindle Edition.]

· As he explained in a letter to Asa Gray: “I…test this hypothesis [universal common descent] by comparison with as many general and pretty well-established propositions [facts] as I can find…. And it seems to me that, supposing that such a hypothesis were to explain such general propositions, we ought, in accordance with the common way of following all sciences, to admit it till some better hypothesis be found out.” [Darwin, Life and Letters, 1:437.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2636-2639). HarperCollins. Kindle Edition.]

· When I first noticed the subtitle of Lyell’s book, “By Reference to Causes Now in Operation,” a light came on for me. I immediately asked myself: What causes now in operation produce digital code or specified information? Is there a known cause—a vera causa—of the origin of such information? What does our uniform experience tell us? As I thought about this further, it occurred to me that by Lyell and Darwin’s own rule of reasoning and by their test of a sound scientific explanation, intelligent design must qualify as, at least, a possible scientific explanation for the origin of biological information. Why? Because we have independent evidence—“uniform experience”—that intelligent agents are capable of producing specified information. Intelligent activity is known to produce the effect in question. The “creation of new information is habitually associated with conscious activity.” [Quastler, The Emergence of Biological Organization, 16.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2676-2682). HarperCollins. Kindle Edition.]

· But is intelligent design the “only known cause” of the origin of specified information? I was now more than intrigued with this possibility, especially given the implications for the status of the design argument in biology. If intelligent design turned out to be the only known or adequate cause of the origin of specified information, then the past action of a designing intelligence could be established on the basis of the strongest and most logically compelling form of historical inference—an inference from the effect in question (specified information) to a single necessary cause of that effect (intelligent activity). Moreover, if intelligent design were shown to be the only known cause, if it were shown to be a uniquely adequate cause, then intelligent design would also automatically meet the causal-existence criterion of a best explanation as well. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2683-2689). HarperCollins. Kindle Edition.]

· Is intelligent design in fact the best explanation for the origin of life? I knew that the central question facing scientists trying to explain the origin of the first life was precisely: How did the sequence-specific digital information necessary to building the first cell arise? [Küppers, Information and the Origin of Life, 170–72.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2689-2691). HarperCollins. Kindle Edition.]

8 Chance Elimination and Pattern Recognition

· By the time I finished my Ph.D. studies, in 1990, I was familiar with most of the main theories then current for explaining the origin of life. These theories exemplified a few basic strategies of explanation. Some relied heavily on chance—that is, on random processes or events. Some invoked lawlike processes—deterministic chemical reactions or forces of attraction. Other models combined these two approaches. In this respect, research on the origin of life followed a well-established pattern in the sciences, one explicitly recommended by the leading scientists of our time. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2703-2707). HarperCollins. Kindle Edition.]

· In Monod’s shorthand, “chance” referred to events or processes that produce a range of possible outcomes, each with some probability of occurring. The term “necessity,” on the other hand, referred to processes or forces that produce a specific outcome with perfect regularity, so that the outcome is “necessary” or inevitable once some prior conditions have been established. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2711-2714). HarperCollins. Kindle Edition.]

· What does it mean to say that something happened by chance? When is it reasonable to invoke chance in an explanation? And what justifies excluding such an explanation from consideration? [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2732-2733). HarperCollins. Kindle Edition.]

· The case of the investigating engineers, however, is different. They did not specify an underlying process capable of producing bridge failure as a possible outcome. They cited chance purely to conceal what they did not know about the cause of the bridge failure. Any official receiving this answer would have correctly regarded it as an admission of ignorance, a fancy way of saying, “We don’t know what happened” or “We can’t explain it.” [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2749-2752). HarperCollins. Kindle Edition.]

· There’s a second aspect to this, however. When scientists say that something happened by chance, they do not usually mean to deny that something caused the event in question. (Some interpretations of quantum physics would stand as an exception.) Instead, they usually mean that the event in question occurred because of a combination of factors so complex that it would have been impossible to determine the exact ones responsible for what happened or to have predicted it. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2752-2755). HarperCollins. Kindle Edition.]

· Thus, when scientists say that something happened by chance, they do not usually mean that some entity called “chance” caused something to happen. Instead, they mean that there is a process in play that produces a range of outcomes each of which has a chance or probability of occurring, including the outcome in question. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2759-2761). HarperCollins. Kindle Edition.]

· When scientists attribute an event to chance, they also usually mean there is no good reason to think the event happened either by design or because of a known physical process that must, of necessity, generate only one possible outcome. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2763-2764). HarperCollins. Kindle Edition.]

· Successful appeals to chance must be justified, including their implicit negations of design and necessity. So how do statisticians and scientists test substantive (rather than vacuous) chance hypotheses? How do they decide when to accept and when to reject chance as an explanation? [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2780-2782). HarperCollins. Kindle Edition.]

· Thus, Dembski realized that when we use a statistical plot to track the frequency of some event occurring, we are implicitly looking for a kind of pattern, a pattern of events that suggests something other than chance alone. A pattern of events may present itself as interesting because some physical state of affairs occurs repeatedly. Or a pattern of events may appear interesting because it has some independent functional significance apart from the physical features of the events. Rejection regions sometimes identify repeating patterns; other times they correspond to what I call “functionally significant patterns.” [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2909-2913). HarperCollins. Kindle Edition.]

· But this raises another question. How improbable does an event have to be to justify the elimination of a chance hypothesis? If we begin to detect a pattern in an improbable sequence of events, at what point should our doubts about the chance hypothesis lead us to reject it as untenable or unreasonable? [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2984-2986). HarperCollins. Kindle Edition.]

· As Christian de Duve, a Nobel Prize–winning biochemist who has written several books about the origin of life, explains, “What counts [in assessing the probability of a chance hypothesis] is the number of opportunities provided for a given event to happen, relative to the event’s probability.” [De Duve, Singularities, 233.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 2994-2996). HarperCollins. Kindle Edition.]

9 Ends and Odds

· Earlier, in 1954, biochemist George Wald argued for the causal efficacy of chance in conjunction with vast expanses of time. As he explained, “Time is in fact the hero of the plot…. Given so much time, the impossible becomes possible, the possible probable, and the probable virtually certain.” [Wald, “The Origin of Life,” 48; Shapiro, Origins, 121.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3068-3071). HarperCollins. Kindle Edition.]

· But does chance provide an adequate explanation for the origin of biological information? Or does it merely conceal ignorance of what actually happened? Do chance-based theories cite processes that are known to generate information-rich structures with some known or regular frequency? Or are there good reasons to reject chance as the best explanation for the origin of the information necessary to life? [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3091-3094). HarperCollins. Kindle Edition.]

· Many origin-of-life scientists have similarly recognized how difficult it is to generate specified biological information by chance alone in the time available on the early earth (or even in the time available since the beginning of the universe). As one leading biochemist, Alexander Cairns-Smith, wrote in 1971: “Blind chance…is very limited. Low levels of cooperation he [blind chance] can produce exceedingly easily (the equivalent of letters and small words), but he becomes very quickly incompetent as the amount of organization [information] increases. Very soon indeed long waiting periods and massive material resources become irrelevant.” [Cairns-Smith, The Life Puzzle, 95.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3127-3132). HarperCollins. Kindle Edition.]

· Christian de Duve has devised an illustration that underscores the importance of pattern recognition (and the recognition of functional specificity) in our reasoning about chance hypotheses. He points out: “A single, freak, highly improbable event can conceivably happen. Many highly improbable events—drawing a winning lottery number or the distribution of playing cards in a hand of bridge—happen all the time. But a string of [such] improbable events—drawing the same lottery number twice, or the same bridge hand twice in a row—does not happen naturally.” [De Duve, “The Beginnings of Life on Earth,” 437.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3137-3141). HarperCollins. Kindle Edition.]

· The simplest extant cell, Mycoplasma genitalium—a tiny bacterium that inhabits the human urinary tract—requires “only” 482 proteins to perform its necessary functions and 562,000 bases of DNA (just under 1,200 base pairs per gene) to assemble those proteins. In minimal-complexity experiments scientists attempt to locate unnecessary genes or proteins in such simple life-forms. Scientists use various experimental techniques to “knock out” certain genes and then examine the effect on the bacterial cell to see if it can survive without the protein products of the disabled genes. Based upon minimal-complexity experiments, some scientists speculate (but have not demonstrated) that a simple one-celled organism might have been able to survive with as few as 250–400 genes. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3177-3182). HarperCollins. Kindle Edition.]

· The integrated complexity of even a “minimally complex cell” has made it difficult to calculate the odds of all the necessary components of such a system arising in close association with one another by chance alone. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3201-3203). HarperCollins. Kindle Edition.]

· The skeptics at Wistar argued that it is extremely difficult to assemble a new gene or protein by chance because of the sheer number of possible base or amino-acid sequences. For every combination of amino acids that produces a functional protein there exists a vast number of other possible combinations that do not. And as the length of the required protein grows, the number of possible amino-acid sequence combinations of that length grows exponentially, so that the odds of finding a functional sequence—that is, a working protein—diminish precipitously. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3241-3245). HarperCollins. Kindle Edition.]

· in nature every amino acid found in proteins (with one exception) has a distinct mirror image of itself; there is one left-handed version, or L-form, and one right-handed version, or D-form. These mirror-image forms are called optical isomers (see Fig. 9.2). Functioning proteins tolerate only left-handed amino acids, yet in abiotic amino-acid production the right-handed and left-handed isomers are produced with roughly equal frequency. Taking this into consideration further compounds the improbability of attaining a biologically functioning protein. The probability of attaining, at random, only L–amino acids in a hypothetical peptide chain 150 amino acids long is (1/2)150, or again roughly 1 chance in 1045. Starting from mixtures of D-forms and L-forms, the probability of building a 150-amino-acid chain at random in which all bonds are peptide bonds and all amino acids are L-form is, therefore, roughly 1 chance in 1090. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3265-3272). HarperCollins. Kindle Edition.]

· Functioning proteins have a third independent requirement, the most important of all: their amino acids, like letters in a meaningful sentence, must link up in functionally specified sequential arrangements. In some cases, changing even one amino acid at a given site results in the loss of protein function. Moreover, because there are 20 biologically occurring amino acids, the probability of getting a specific amino acid at a given site is small—1/20. (Actually the probability is even lower because, in nature, there are also many nonprotein-forming amino acids.) On the assumption that each site in a protein chain requires a particular amino acid, the probability of attaining a particular protein 150 amino acids long would be (1/20)150, or roughly 1 chance in 10195. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3275-3280). HarperCollins. Kindle Edition.]

· Their most clear-cut experiments seemed to indicate that, even taking the possibility of variance into account, the probability of achieving a functional sequence of amino acids in several known (roughly 100 amino acid) proteins at random is still “exceedingly small,” about 1 chance in 1063 (to put this in perspective, there are 1065 atoms in our galaxy). Using a variety of mutagenesis techniques, they and other scientists showed that proteins (and thus the genes that produce them) are highly specified relative to biological function. Earlier studies indicated that amino-acid residues at many sites cannot vary without functional loss. [Reidhaar-Olson and Sauer, “Functionally Acceptable Substitutions”; Bowie and Sauer, “Identifying the Determinants of Folding and Activity.”] [Oddly, Sauer’s descriptions of his team’s results often downplay the rarity of functional sequences within sequence space. Instead, he often emphasizes the tolerance for different amino acids that is allowable at each site. For example, the abstract of the paper reporting the figure of 1 in 1063 makes no mention of that figure or its potential significance, stating instead that their results “reveal the high level of degeneracy in the information that specifies a particular protein fold” (Reidhaar-Olson and Sauer, “Functionally Acceptable Substitutions”).] [Bowie and Sauer, “Identifying the Determinants of Folding and Activity”; Reidhaar-Olson and Sauer, “Functionally Acceptable Substitutions”; Chothia, Gelfand, and Kister, “Structural Determinants in the Sequences of Immunoglobulin Variable Domain”; Axe, “Extreme Functional Sensitivity”; Taylor, et al., “Searching Sequence Space for Protein Catalysts.”] [See, e.g., Perutz and Lehmann, “Molecular Pathology of Human Hemoglobin.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3296-3302). HarperCollins. Kindle Edition.]

· How rare, or common, are the amino-acid sequences that produce the stable folds that make it possible for proteins to perform their biological functions? [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3310-3311). HarperCollins. Kindle Edition.]

· The results of a paper he published in 2004 were particularly telling. Axe performed a mutagenesis experiment using his refined method on a functionally significant 150-amino-acid section of a protein called beta-lactamase, an enzyme that confers antibiotic resistance upon bacteria. On the basis of his experiments, Axe was able to make a careful estimate of the ratio of (a) the number of 150-amino-acid sequences that can perform that particular function to (b) the whole set of possible amino-acid sequences of this length. Axe estimated this ratio to be 1 to 1077. [Axe, “Estimating the Prevalence of Protein Sequences.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3320-3324). HarperCollins. Kindle Edition.]

· Fortunately, Axe’s work provided this number as well. Axe knew that in nature proteins perform many specific functions. He also knew that in order to perform these functions their amino-acid chains must first fold into stable three-dimensional structures. Thus, before he estimated the frequency of sequences performing a specific (beta-lactamase) function, he first performed experiments that enabled him to estimate the frequency of sequences that will produce stable folds. On the basis of his experimental results, he calculated the ratio of (a) the number of 150-amino-acid sequences capable of folding into stable “function-ready” structures to (b) the whole set of possible amino-acid sequences of that length. He determined that ratio to be 1 to 1074. [Axe, “Estimating the Prevalence of Protein Sequences.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3329-3334). HarperCollins. Kindle Edition.]

· Axe’s improved estimate of how rare functional proteins are within “sequence space” has now made it possible to calculate the probability that a 150-amino-acid compound assembled by random interactions in a prebiotic soup would be a functional protein. This calculation can be made by multiplying the three independent probabilities by one another: the probability of incorporating only peptide bonds (1 in 1045), the probability of incorporating only left-handed amino acids (1 in 1045), and the probability of achieving correct amino-acid sequencing (using Axe’s 1 in 1074 estimate). Making that calculation (multiplying the separate probabilities by adding their exponents: 1045 + 45 + 74) gives a dramatic answer. The odds of getting even one functional protein of modest length (150 amino acids) by chance from a prebiotic soup is no better than 1 chance in 10164. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3355-3362). HarperCollins. Kindle Edition.]

10 Beyond the Reach of Chance

· Here again Bill Dembski’s work gave me a way to answer this question. Dembski had calculated the maximum number of events that could actually have taken place during the history of the observable universe. He did this to establish an upper boundary on the probabilistic resources that might be available to produce any event by chance. [The number of possible ways to combine elementary particles (and thus the number of combinatorial possible events) is actually much greater than the number of different events that could have taken place in the history of the universe. Why? Because the occurrence of each individual event precludes the occurrence of many other possible events within the larger combinatorial space. The number of combinatorial possible events represents the number of different events that might have occurred before the universe actually unfolded in the way that it did. Dembski correctly identifies the maximum number of events that could actually occur in any given history of the universe as the number that determines the probabilistic resources of the universe. This smaller number determines how many opportunities the universe has to produce a particular outcome by chance. As Dembski explains, it is not the total number of combinatorial possible events (or elementary particles) in the universe that determines the available probabilistic resources, but how many opportunities there are to “individuate” actual events. See Dembski, The Design Inference, chap. 6; see also 209, n.15.] [For Dembski’s treatment of probabilistic resources at the scale of the known universe, see Dembski, The Design Inference, chap. 6.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3411-3414). HarperCollins. Kindle Edition.]

· Dembski’s calculation was elegantly simple and yet made a powerful point. He noted that there were about 1080 elementary particles in the observable universe. (Because there is an upper limit on the speed of light, only those parts of the universe that are observable to us can affect events on earth. Thus, the observable universe is the only part of the universe with probabilistic resources relevant to explaining events on earth.) Dembski also noted that there had been roughly 1016 seconds since the big bang. (A few more have transpired since he made the calculation, but not enough to make a difference!) [The elementary particles enumerated in this calculation include only protons, neutrons, and electrons (fermions), because only these particles have what physicists call “half-integral spin,” which allows them to form material structures. This calculation does not count bosons, which cannot form material structures, but instead only transmit energy. Nor does this calculation count the quarks out of which protons and neutrons are made, because quarks are necessarily bound together within these particles. Even if quarks were counted, however, the total number of elementary particles would change by less than one order of magnitude because there are only three quarks per proton or neutron.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3415-3420). HarperCollins. Kindle Edition.]

· Knowing this, Dembski was able to calculate the largest number of opportunities that any material event had to occur in the observable universe since the big bang. Physically speaking, an event occurs when an elementary particle does something or interacts with other elementary particles. But since elementary particles can interact with each other only so many times per second (at most 1043 times), since there are a limited number (1080) of elementary particles, and since there has been a limited amount of time since the big bang (1016 seconds), there are a limited number of opportunities for any given event to occur in the entire history of the universe. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3427-3432). HarperCollins. Kindle Edition.]

· Dembski was able to calculate this number by simply multiplying the three relevant factors together: the number of elementary particles (1080) times the number of seconds since the big bang (1016) times the number of possible interactions per second (1043). His calculation fixed the total number of events that could have taken place in the observable universe since the origin of the universe at 10139.4 This then provided a measure of the probabilistic resources of the entire observable universe. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3432-3437). HarperCollins. Kindle Edition.]

· Cryptographers, for instance, have established 1 chance in 1094 as a universal limit. They interpret that improbability to mean that if it requires more than 1094 computational steps to decrypt a cryptosystem, then it is more likely than not that the system won’t be cracked because of the limited probabilistic resources of the universe itself.

· MIT computer scientist Seth Lloyd has calculated that the most bit operations the universe could have performed in its history (assuming the entire universe were given over to this single-minded task) is 10120, meaning that a specific bit operation with an improbability significantly greater than 1 chance in 10120 will likely never occur by chance. [Dam and Lin, eds., Cryptography’s Role in Securing the Information Society, 380, n. 17; Lloyd, “Computational Capacity of the Universe”; see also Kauffman, Investigations, 144.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3442-3445). HarperCollins. Kindle Edition.]

· None of these probabilistic resources is sufficient to render the chance hypothesis plausible. Dembski’s calculation is the most conservative and gives chance its “best chance” to succeed. But even his calculation confirms the implausibility of the chance hypothesis, whether chance is invoked to explain the information necessary to build a single protein or the information necessary to build the suite of proteins needed to service a minimally complex cell. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3445-3448). HarperCollins. Kindle Edition.]

· The paper was written by P. T. Mora, a senior research biologist at the National Institutes of Health. Here’s what he wrote: To invoke statistical concepts, probability and complexity to account for the origin and the continuance of life is not felicitous or sufficient. As the complexity of a molecular aggregate increases, and indeed very complex arrangements and interrelationships of molecules are necessary for the simplest living unit, the probability of its existence under the disruptive and random influence of physico-chemical forces decreases; the probability that it will continue to function in a certain way, for example, to absorb and to repair, will be even lower; and the probability that it will reproduce, still lower. Statistical considerations, probability, complexity, etc., followed to their logical implications suggest that the origin and continuance of life is not controlled by such principles. An admission of this is the use of a period of practically infinite time to obtain the derived result. Using such logic, however, we can prove anything…. When in statistical processes, the probability is so low that for practical purposes infinite time must elapse for the occurrence of an event, statistical explanation is not helpful. [Mora, “Urge and Molecular Biology,” 215.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3558-3566). HarperCollins. Kindle Edition.]

· In the words of Brooks: “The nitrogen content of early Pre-Cambrian organic matter is relatively low (less than .015%). From this we can be reasonably certain that: there never was any substantial amount of ‘primitive soup’ on earth when Pre-Cambrian sediments were formed; if such a soup ever existed it was only for a brief period of time.” [Brooks, The Origins of Life, 118.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3596-3599). HarperCollins. Kindle Edition.]

· Christian de Duve expresses the reasoning of researchers who favor this approach: “A string of improbable events—drawing the same lottery number twice, or the same bridge hand twice in a row—does not happen naturally. All of which lead me to conclude that life is an obligatory manifestation of matter, bound to arise where conditions are appropriate.” [De Duve, “The Beginnings of Life on Earth,” 437.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3629-3632). HarperCollins. Kindle Edition.]

11 Self-Organization and Biochemical Predestination

· Among them was a young biophysicist at San Francisco State University named Dean Kenyon. As he wrote a year later: “It is sometimes argued in speculative papers on the origin of life that highly improbable events (such as the spontaneous formation of a molecule of DNA and a molecule of DNA polymerase in the same region of space at the same time) become virtually inevitable over the vast stretches of geological time. No serious quantitative arguments, however, are given in support of such conclusions.” Instead, he argued, “such hypotheses are contrary to most of the available evidence.” To emphasize the point Kenyon noted: “If the association of amino acids were a completely random event…there would not be enough mass in the entire earth, assuming it was composed exclusively of amino acids, to make even one molecule of every possible sequence of…a low-molecular-weight protein.” [Kenyon and Steinman, Biochemical Predestination, 31; 206.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3654-3661). HarperCollins. Kindle Edition.]

· What accounts for the difference between a chunk of marble and a great sculpture? What explains the difference between a cloud and a message created from steam by a skywriter? What accounts for the difference between a functioning cell and the various molecules that jointly constitute it? These questions raise the classical philosophical issue of reductionism. Does the whole reduce to the sum of its parts? Or conversely, do the properties of the parts explain the structure and organization of the whole? As with many such questions, the best answer is, “It depends.” [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3681-3685). HarperCollins. Kindle Edition.]

· As Polanyi concluded, “Whatever may be the origin of a DNA configuration, it can function as a code only if its order is not due to the forces of potential energy. It must be as physically indeterminate as the sequence of words is on a printed page.” [Polanyi, “Life’s Irreducible Structure,” 1309.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3843-3845). HarperCollins. Kindle Edition.]

· I realized that explaining DNA’s information-rich sequences by appealing to differential bonding affinities meant that there had to be chemical bonds of differing strength between the different bases along the information-bearing axis of the DNA molecule. Yet, as it turns out, there are no differential bonding affinities there. Indeed, there is not just an absence of differing bonding affinities; there are no bonds at all between the critical information-bearing bases in DNA. In the lecture hall the point suddenly struck me as embarrassingly simple: there are neither bonds nor bonding affinities—differing in strength or otherwise—that can explain the origin of the base sequencing that constitutes the information in the DNA molecule. A force has to exist before it can cause something. And the relevant kind of force in this case (differing chemical attractions between nucleotide bases) does not exist within the DNA molecule. [The bases do participate in weak van der Waals and hydrophobic interactions, but these chemical affinities are so slight and nonspecific as to be incapable of determining the specific sequential arrangements of the bases in the DNA molecule.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3876-3883). HarperCollins. Kindle Edition.]

· Later I found that the noted origin-of-life biochemist Bernd-Olaf Küppers had concluded much the same thing. As he explained, “The properties of nucleic acids indicate that all the combinatorially possible nucleotide patterns of a DNA are, from a chemical point of view, equivalent.” In sum, two features of DNA ensure that “self-organizing” bonding affinities cannot explain the specific arrangement of nucleotide bases in the molecule: (1) there are no bonds between bases along the information-bearing axis of the molecule and (2) there are no differential affinities between the backbone and the specific bases that could account for variations in sequence. [Küppers, “On the Prior Probability of the Existence of Life,” 364.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3891-3896). HarperCollins. Kindle Edition.]

· To demonstrate this to my students, I would bring a small magnetic “chalkboard” to class with a message spelled on it, such as “Biology Rocks!” using the same kind of plastic letters that my kids used at home. I would point out that the magnetic forces between the letters and the metallic surface of the chalkboard explain why the letters stick to the board, just as forces of chemical attraction explain why the nucleotides stick to the sugar-phosphate backbone of the DNA. But I would also point out that there are no significant forces of attraction between the individual letters that determine their arrangement, just as there are no significant forces of attraction between the bases in the information-bearing axis of the DNA molecule. Instead, the magnetic forces between the letters and the chalkboard allow numerous possible letter combinations, some of which convey functional or meaningful information and most of which do not. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3901-3907). HarperCollins. Kindle Edition.]

· Suppose that every time adenine (A) occurred in a growing genetic sequence, it attracted cytosine (C) to it,26 which attracted guanine (G), which attracted thymine (T), which attracted adenine (A), and so on. If this were the case, the longitudinal axis of DNA would be peppered with repetitive sequences of ACGT. Rather than being a genetic molecule capable of virtually unlimited novelty and characterized by unpredictable and aperiodic sequences, DNA would contain sequences awash in repetition or redundancy—much like the arrangement of atoms in crystals. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 3987-3991). HarperCollins. Kindle Edition.]

12 Thinking Outside the Bonds

· The astrophysicist Fred Hoyle had a similar way of making the same point. He famously compared the problem of getting life to arise spontaneously from its constituent parts to the problem of getting a 747 airplane to come together from a tornado swirling through a junk yard. An undifferentiated external force is simply too blunt an instrument to accomplish such a task. Energy might scatter parts around randomly. Energy might sweep parts into an orderly structure such as a vortex or funnel cloud. But energy alone will not assemble a group of parts into a highly differentiated or functionally specified system such an airplane or cell (or into the informational sequences necessary to build one). [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4097-4102). HarperCollins. Kindle Edition.]

· Thus, as Yockey notes: “Attempts to relate the idea of order…with biological organization or specificity must be regarded as a play on words that cannot stand careful scrutiny. Informational macromolecules can code genetic messages and therefore can carry information because the sequence of bases or residues is affected very little, if at all, by [self-organizing] physicochemical factors.” [Yockey, “A Calculation of the Probability of Spontaneous Biogenesis,” esp. 380.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4112-4115). HarperCollins. Kindle Edition.]

· Sometimes when I’ve used these illustrations I’ve been asked: “But couldn’t we discover a very particular configuration of initial conditions that generates biological information? If we can’t hope to find a law that produces information, isn’t it still possible to find a very particular set of initial conditions that generates information in a predictable law-like way?” But this objection just restates the basic self-organizational proposal in new words. It also again begs the question of the ultimate origin of information, since “a very particular set of initial conditions” sounds precisely like an information-rich—a highly complex and specified—state. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4142-4146). HarperCollins. Kindle Edition.]

· As I reflected on the failure of these models, my interest in the design hypothesis increased. But the reason for this was not just that self-organizational scenarios had failed. Instead, it was that self-organizational theories failed in a way that exposed the need for an intelligent cause to explain the relevant phenomena. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4301-4303). HarperCollins. Kindle Edition.]

13 Chance and Necessity, or The Cat in the Hat Comes Back

· As Christian de Duve explains, theories of prebiotic natural selection necessarily fail because they “need information which implies they have to presuppose what is to be explained in the first place.” [De Duve, Blueprint for a Cell, 187.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4400-4402). HarperCollins. Kindle Edition.]

· In the same way, the concept of prebiotic natural selection begs the question of how nature generated the sequence-specific information-rich DNA and proteins that are needed to make self-replication, and thus natural selection, possible. Indeed, for this reason, Theodosius Dobzhansky, one of the leading evolutionary biologists of the twentieth century, insisted in 1968 that “Prebiological natural selection is a contradiction in terms.” [Dobzhansky, “Discussion of G. Schramm’s Paper,” 310.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4406-4409). HarperCollins. Kindle Edition.]

14 The RNA World

· By the mid-1980s many researchers concluded that both DNA-first and protein-first origin-of-life models were beset with many difficulties. As a result, they sought a third way to explain the mystery of life’s origin. Instead of proposing that the first informational molecules were proteins or DNA, these scientists argued that the earliest stages of abiogenesis unfolded in a chemical environment dominated by RNA molecules. The first scientist to propose this idea was Carl Woese, a microbiologist at the University of Illinois. Walter Gilbert, a Harvard biophysicist, later developed the proposal and coined the term by which it is now popularly known, the “RNA world.” [Gilbert, “Origin of Life.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4756-4761). HarperCollins. Kindle Edition.]

· RNA-first advocates proposed an early stage in the development of life in which RNA performed both the enzymatic functions of modern proteins and the information-storage function of modern DNA, thus sidestepping the need for an interdependent system of DNA and proteins in the earliest living system. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4785-4787). HarperCollins. Kindle Edition.]

· As Gilbert and others envision it, a molecule of RNA capable of copying itself (or copying a copy of itself) first arose by the chance association of nucleotide bases, sugars, and phosphates in a prebiotic soup (see Fig. 14.2). Then because that RNA enzyme could self-replicate, natural selection ensued, making possible a gradual increase in the complexity of the primitive self-replicating RNA system, eventually resulting in a cell with the features we observe today. Along the way, a simple membrane, itself capable of self-reproduction, enclosed the initial RNA enzymes along with some amino acids from the prebiotic soup. [Szostak, Bartel, and Luisi, “Synthesizing Life,” esp. 387–88.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4788-4792). HarperCollins. Kindle Edition.]

· The RNA World Scenario in Seven Steps. Step 1: The building blocks of RNA arise on the early earth. Step 2: RNA building blocks link up to form RNA oligonucleotide chains. Step 3: An RNA replicase arises by chance and selective pressures ensue favoring more complex forms of molecular organization. Step 4: RNA enzymes begin to synthesize proteins from RNA templates. Step 5: Protein-based protein synthesis replaces RNA-based protein synthesis. Step 6: Reverse transcriptase transfers genetic information from RNA molecules into DNA molecules. Step 7: The modern gene expression system arises within a proto-membrane. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4801-4806). HarperCollins. Kindle Edition.]

· Problem 1: RNA Building Blocks Are Hard to Synthesize and Easy to Destroy: Before the first RNA molecule could have come together, smaller constituent molecules needed to arise on the primitive earth. These include a sugar known as ribose, phosphate molecules, and the four RNA nucleotide bases (adenine, cytosine, guanine, and uracil). It turns out, however, that both synthesizing and maintaining these essential RNA building blocks, particularly ribose (the sugar incorporated into nucleotides) and the nucleotide bases, has proven either extremely difficult or impossible to do under realistic prebiotic conditions. [Shapiro, “Prebiotic Cytosine Synthesis”; Waldrop, “Did Life Really Start Out in an RNA World?”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4817-4821). HarperCollins. Kindle Edition.]

· As Dean Kenyon explains, “The chemical conditions proposed for the prebiotic synthesis of purines and pyrimidines [the bases] are sharply incompatible with those proposed for the synthesis of ribose.” Or as Shapiro concludes: “The evidence that is currently available does not support the availability of ribose on the prebiotic earth, except perhaps for brief periods of time, in low concentration as part of a complex mixture, and under conditions unsuitable for nucleoside synthesis.” [Kenyon and Mills, “The RNA World.”] [Shapiro, “Prebiotic Ribose Synthesis,” 71.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4853-4857). HarperCollins. Kindle Edition.]

· Problem 2: Ribozymes Are Poor Substitutes for Proteins: Another major problem with the RNA world is that naturally occurring RNA molecules possess very few of the specific enzymatic properties of proteins. To date, scientists have shown that ribozymes can perform a small handful of the thousands of functions performed by modern proteins. Scientists have shown that some RNA molecules can cleave other RNA molecules (at the phosphodiester bond) in a process known as hydrolysis. Biochemists also have found RNAs that can link (ligate) separate strands of RNA (by catalyzing the formation of phosphodiester bonds). Other studies have shown that the RNA in ribosomes (rRNA) promotes peptide-bond formation within the ribosome* and can promote peptide bonding outside the ribosome, though only in association with an additional chemical catalyst.* Beyond that, RNA can perform only a few minor functional roles and then usually as the result of scientists intentionally “engineering” or “directing” the RNA catalyst (or ribozyme) in question. [Noller, Hoffarth, and Zimniak, “Unusual Resistance of Peptidyl Transferase.”] [Zhang and Cech, “Peptide Bond Formation.”] [Illangasekare, et al., “Aminoacyl-RNA Synthesis Catalyzed by an RNA.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4864-4872). HarperCollins. Kindle Edition.]

· Problem 3: An RNA-based Translation and Coding System Is Implausible: The inability of RNA molecules to perform many of the functions of protein enzymes raises a third and related concern about the plausibility of the RNA world. RNA-world advocates offer no plausible explanation for how primitive self-replicating RNA molecules might have evolved into modern cells that rely on a variety of proteins to process genetic information and regulate metabolism. [Joyce, “RNA Evolution and the Origins of Life.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4878-4882). HarperCollins. Kindle Edition.]

· Why RNA Catalysts Can’t Do What True Enzymes Can: There is a fundamental chemical reason for the limited functionality of RNA catalysts—one that casts still further doubt on the RNA-world hypothesis and specifically on its account of the origin of the translation system. Because of the inherent limitations of RNA chemistry,* single RNA molecules do not catalyze the coordinated multistep reactions that enzymes, such as synthetases, catalyze. [The twenty protein-forming amino acids are capable of a much wider range of chemical interactions than are the four nucleotide bases. The four bases are exclusively hydrophilic (water-attracting) molecules, and they form mainly hydrogen bonds with each other. On the other hand, some amino acids are hydrophilic; some are hydrophobic; some are acidic; and some are basic. This diversity of properties among its constitutive chemical groups allows proteins to attain more complex three-dimensional geometries than do the simple pairing interactions between bases in RNA molecules. As a result, proteins play functional roles that RNA does not and, in many cases, probably cannot.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4950-4953). HarperCollins. Kindle Edition.]

· Problem 4: The RNA World Doesn’t Explain the Origin of Genetic Information: As I sifted through the primary scientific literature on the RNA-world hypothesis, it did not take me long to realize that the hypothesis faced significant problems quite apart from the central sequencing problem that most interested me. Yet I also realized that it did not resolve the mystery of the origin of biological information—which I had, heretofore, called the DNA enigma. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 4981-4985). HarperCollins. Kindle Edition.]

· As Orgel and Joyce explain, “Without evolution [i.e., prebiotic natural selection] it appears unlikely that a self-replicating ribozyme could arise, but without some form of self-replication there is no way to conduct an evolutionary search for the first primitive self-replicating ribozyme.” [Joyce and Orgel, “Prospects for Understanding the Origin of the RNA World,” 35.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5054-5057). HarperCollins. Kindle Edition.]

· Robert Shapiro has resorted to one of my old standbys—Scrabble letters—to illustrate why neither chance, nor chance and natural selection combined, can solve the sequencing problem in the RNA world. While speaking in 2007 at a private conference on the origin of life, he asked an elite scientific audience to imagine an enormous pile of Scrabble letters. Then he said, “If you scooped into that heap [of letters], and you flung them on the lawn there, and the letters fell into a line which contained the words, ‘To be or not to be, that is the question,’ that is roughly the odds of an RNA molecule, given no feedback [natural selection]—and there would be no feedback, because it [the RNA molecule] wouldn’t be functional until it attained a certain length and could copy itself—appearing on earth.” [Shapiro, as quoted in Brockman, ed., Life: What a Concept!, 90.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5057-5063). HarperCollins. Kindle Edition.]

· Problem 5: Ribozyme Engineering Does Not Simulate Undirected Chemical Evolution: These ribozyme-engineering experiments typically deploy one of two approaches: the “rational design” approach or the “directed evolution” approach. In both approaches, biologists try to generate either more efficient versions of existing ribozymes or altogether new ribozymes capable of performing some of the other functions of proteins. In the rational-design approach, the chemists do this by directly modifying the sequences of naturally occurring RNA catalysts. In the directed-evolution (or “irrational design”) approach, scientists seek to simulate a form of prebiotic natural selection in the process of producing ribozymes with enhanced functional capacities. To manage this they screen pools of RNA molecules using chemical traps to isolate molecules that perform particular functions. After they have selected these molecules out of the pool, they generate variant versions of these molecules by randomly altering (mutating) some part of the sequence of the original molecule. Then they select the most functional molecules in this new crop and repeat the process several times until a discernible increase in the desired function has been produced. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5077-5085). HarperCollins. Kindle Edition.]

· In 1980, Francis Crick lamented, “An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going.” [Crick, Life Itself, 88.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5133-5136). HarperCollins. Kindle Edition.]

· In 1988, the German biochemist and origin-of-life researcher Klaus Dose followed suit with an equally critical assessment of the state of the field. Dose explained that research efforts to date had “led to a better perception of the immensity of the problem of the origin of life on earth rather than to its solution. At present, all discussions on principle theories and experiments in the field either end in a stalemate or a confession of ignorance.” [Dose, “The Origin of Life.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5136-5139). HarperCollins. Kindle Edition.]

15 The Best Explanation

· Contemporary biology has shown that cells are a repository of information, and that the information they contain is essential for even minimal biological function. Consequently, origin-of-life researchers have realized that if they were to explain the origin of the first life, they would need to explain how the information in DNA or some other alternative molecular precursor arose. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5213-5215). HarperCollins. Kindle Edition.]

· Reason 1: No Other Causally Adequate Explanations: Despite the “thorough search” described in Chapters 8–14, I found no other causally adequate explanations for the DNA enigma. In my search, I examined the main theories of the origin of life (and/or biological information) exemplifying each of three mutually exhaustive categories of explanation: chance, necessity, and the combination of the two. [Monod, Chance and Necessity. Chance-based theories invoke processes that produce particular outcomes with a low probability. Theories of necessity invoke processes that produce specific outcomes with a high probability, typically with a probability of one. For this reason, these two general categories of explanation plus explanations combining them are generally considered to represent a logically exhaustive set of possible explanatory approaches, at least from within a materialistic framework.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5277-5280). HarperCollins. Kindle Edition.]

· Reason 2: Experimental Evidence Confirms Causal Adequacy of ID: If attempts to solve the information problem only relocated it, and if neither chance, nor physical-chemical necessity, nor the two acting in combination explains the ultimate origin of specified biological information, what does? Do we know of any entity that has the causal powers to create large amounts of specified information? [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5324-5326). HarperCollins. Kindle Edition.]

· Assume for the moment that the reducing gases used by Stanley Miller did actually simulate the conditions on the early earth. Would his experimental results establish the plausibility of an undirected process of chemical evolution? Not necessarily. Prebiotic simulation experiments invariably generate biologically irrelevant substances as well as desirable building blocks such as nucleotide bases, sugars, and amino acids. But without investigator intervention, these undesirable by-products react with desirable building blocks to form inert compounds, such as a tar called melanoidin, the curse of the prebiotic chemist. Simulation experiments have repeatedly shown that such destructive chemical processes would have predominated in any realistic prebiotic chemical environment. [Thaxton, Bradley, and Olsen, The Mystery of Life’s Origin, vi.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5344-5350). HarperCollins. Kindle Edition.]

· To prevent such “interfering cross-reactions,” chemists must intervene using various traps and other techniques to isolate and remove chemicals* that alter desirable building blocks. For example, as I noted in Chapter 14, the formose reaction that produces ribose sugar also produces many other undesirable chemical by-products that, absent the intervention of a chemist, will react destructively with ribose. [Thaxton, Bradley, and Olsen, The Mystery of Life’s Origin, 102.] [Shapiro, “Prebiotic Ribose Synthesis.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5350-5353). HarperCollins. Kindle Edition.]

· Investigators also artificially manipulate the initial conditions in their experiments. In so doing, they take into account information about—knowledge of—the properties of their reagents. For example, prebiotic chemists typically choose to radiate their chemical mixtures with short-wavelength ultraviolet light because they know that longer-wavelength light degrades the amino acids they are trying to produce.* In these and many other ways, investigators must routinely manipulate chemical conditions both before and after performing “simulation” experiments in order to protect them from destructive naturally occurring processes. These manipulations constitute “profoundly informative intervention[s].”* Every choice the investigator makes to actualize one condition and exclude another—to remove one by-product and not another—imparts information into the system. Therefore, whatever “success” these experiments have achieved in producing biologically relevant compounds occurs as a direct result of the activity of the experimentalist—a conscious, intelligent, deliberative mind—performing the experiments. [Thaxton, Bradley, and Olsen, The Mystery of Life’s Origin, 184.] [Polanyi, “Life Transcending Physics and Chemistry,” esp. 64.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5353-5362). HarperCollins. Kindle Edition.]

· Ribozyme Engineering Demonstrates the Causal Adequacy of ID: Conscious intelligence plays the same essential role in ribozyme engineering. Recall that ribozyme engineers attempt to enhance the capacity of RNA catalysts in order to demonstrate the plausibility of the RNA world. In particular, ribozyme engineers want to show that linking enzymes called RNA ligases can acquire true polymerase function, making possible template-directed self-replication. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5405-5408). HarperCollins. Kindle Edition.]

· Reason 3: ID Is the Only Known Cause of Specified Information: The inability of genetic algorithms, ribozyme engineering, and prebiotic simulations to generate information without intelligence reinforced what I had discovered in my study of other origin-of-life theories.* Undirected materialistic causes have not demonstrated the capacity to generate significant amounts of specified information. At the same time, conscious intelligence has repeatedly shown itself capable of producing such information. It follows that mind—conscious, rational intelligent agency—what philosophers call “agent causation,” now stands as the only cause known to be capable of generating large amounts* of specified information starting from a nonliving state. [Dose, “The Origin of Life”; Yockey, Information Theory and Molecular Biology, 259–93; Thaxton, Bradley and Olsen, The Mystery of Life’s Origin, 42–172; Thaxton and Bradley, “Information and the Origin of Life”; Shapiro, Origins.] [Of course, the phrase “large amounts of specified information” again begs a quantitative question, namely, “How much specified information or complexity would the minimally complex cell have to have before it implied design?” Recall that Dembski has calculated a universal probability bound of 1 out of 10139 (which he now rounds to 1 chance in 10150) corresponding to the probabilistic/specificational resources of the known universe. Recall further that probability is inversely related to information by a logarithmic function. Thus, the universal small probability bound of 1 out of 10150 translates into roughly 500 bits of information. Thus, chance alone does not constitute a sufficient explanation for the de novo origin of any specified sequence or system containing more than 500 bits of (specified) information. Further, since systems characterized by complexity (a lack of redundant order) defy explanation by self-organizational laws, and since appeals to prebiotic natural selection presuppose, but do not explain, the origin of the specified information necessary to a minimally complex self-replicating system, intelligent design best explains the origin of the more than 500 bits of specified information required to produce the first minimally complex living system. Thus, assuming a nonbiological starting point (see Chapter 13, section headed “The Conservation of Information”), the de novo emergence of 500 or more bits of specified information will reliably indicate design.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5469-5474). HarperCollins. Kindle Edition.]

16 Another Road to Rome

· Dembski’s work on elucidating the forms of reasoning by which we infer design goes back to a seminal paper he wrote on the nature of randomness, “Randomness by Design.” It was this and another paper that first brought Dembski to my attention and led to our initial collaboration. In it he shows that randomness cannot properly be understood except with reference to patterns that random objects systematically violate—once a pattern is matched, randomness dissolves. From studying the nature of the patterns used to defeat randomness, Dembski came upon the design inference. He presented an outline of the design inference in 1993 in Seattle in a paper, “Theoretical Basis for the Design Inference.” He developed these ideas into a doctoral dissertation about the foundations of probability theory (1996) and then went on to publish that dissertation in 1998: The Design Inference. He expanded on this work in his 2002 sequel, No Free Lunch. His idea of specification, which sits at the heart of the design inference, is subtle and requires some technical sophistication to elucidate in full, though the essence of the idea can be illustrated clearly with examples of the kind used in this chapter. Dembski’s most current formulation of specification appears in his article “Specification,” available at http://www. designinference.com/documents/ 2005.06.Specification.pdf. The most user-friendly treatment of his work on design inferences, with an application to biology, appears in Dembski and Wells, The Design of Life, chap. 7.

· Dembski notes that we invariably attribute events, systems, or sequences that have the joint properties of “complexity” (or small probability) and “specification” to intelligent causes—to design—not to chance or physical-chemical necessity. [Dembski, The Design Inference, 1–35, 136–223.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5633-5635). HarperCollins. Kindle Edition.]

· A specification is a match or correspondence between an observed event and a pattern or set of functional requirements that we know independently of the event in question. Events or objects are “specified” if they exhibit a pattern that matches another pattern that we know independently. I will return to this idea below. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5636-5638). HarperCollins. Kindle Edition.]

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· A specification is a match or correspondence between an observed event and a pattern or set of functional requirements that we know independently of the event in question. Events or objects are “specified” if they exhibit a pattern that matches another pattern that we know independently. I will return to this idea below. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5636-5638). HarperCollins. Kindle Edition.]

· Two Types of Specifications: Since specifications come in two closely related forms, we detect design in two closely related ways. First, we can detect design when we recognize that a complex pattern of events matches or conforms to a pattern that we know from something else we have witnessed. Tourists at Mt. Rushmore recognize patterns etched in the rock that exactly match patterns that they know from seeing faces of presidents on money or in paintings. Because the shapes carved into the mountain are also highly complex, they correctly infer that they are the product of intelligent activity, rather than undirected processes. Second, we can detect design when we recognize that a complex pattern of events has a functional significance because of some operational knowledge that we possess about, for example, the functional requirements or conventions of a system. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5756-5763). HarperCollins. Kindle Edition.]

17 But Does It Explain?

· Argument from Ignorance? Over the years, I have participated in many debates about the theory of intelligent design at scientific conferences, on university campuses, and on television and radio programs. In nearly every debate, my debate partner has claimed that the case for intelligent design constitutes an argument from ignorance. Arguments from ignorance occur when evidence against a proposition is offered as the sole (and conclusive) grounds for accepting some alternative proposition. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 5999-6003). HarperCollins. Kindle Edition.]

18 But Is It Science?

· To say that an idea, theory, concept, inference, or explanation is or isn’t scientific requires a particular definition of science. Yet if different scientists and philosophers of science could not agree about what the scientific method is, how could they decide what did and did not qualify as science? And how could I argue that the theory of intelligent design is scientific, if I could not say what I meant by “science”? Conversely, how could critics of intelligent design assert that intelligent design is not science without articulating the standard by which they made this judgment? How could any headway in this debate be made without an agreed-upon definition? [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 6454-6458). HarperCollins. Kindle Edition.]

· Such an approach allows science to be defined more broadly as, for instance, “a systematic way of studying nature involving observation, experimentation, and/or reasoning about physical phenomena.” So far, so good. The difficulty has come when scholars tried to equate science with a particular systematic method of studying nature to the exclusion of other such methods. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 6460-6463). HarperCollins. Kindle Edition.]

· Reason 1: The Case for ID Is Based on Empirical Evidence: The case for intelligent design, like other scientific theories, is based upon empirical evidence, not religious dogma. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 6473-6475). HarperCollins. Kindle Edition.]

· In this book, to name just one example, I have developed an argument for intelligent design based on the discovery of digital information in the cell. In addition, other scientists now see evidence of intelligent design in the “irreducible complexity” of molecular machines and circuits in the cell,* the pattern of appearance of the major groups of organisms in the fossil record,* the fine-tuning of the laws and constants of physics,* the fine-tuning of our terrestrial environment,* the information-processing system of the cell, and even in the phenomenon known as “homology” (evidence previously thought to provide unequivocal support for neo-Darwinism). [Behe, Darwin’s Black Box.] [Meyer, et al., “The Cambrian Explosion.”] [See, generally, Craig, “God, Creation and Mr. Davies,” 163; “Barrow and Tipler on the Anthropic Principle vs. Divine Design,” 389.] [Gonzalez and Richards, The Privileged Planet.] [See Nelson and Wells, “Homology in Biology.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 6476-6482). HarperCollins. Kindle Edition.]

· Reason 2: Advocates of ID Use Established Scientific Methods: The case for intelligent design follows from the application of not one, but two separate systematic methods of scientific reasoning—methods that establish criteria for determining when observed evidence supports a hypothesis. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 6486-6488). HarperCollins. Kindle Edition.]

· Reason 3: ID Is a Testable: Theory Most scientists and philosophers of science think that the ability to subject theories to empirical tests constitutes an important aspect of any scientific method of study. But for a theory to be testable, there must be some evidential grounds by which it could be shown to be incorrect or inadequate. And, contrary to the repeated claims of its detractors, the theory of intelligent design is testable. In fact, it is testable in several interrelated ways. [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 6498-6502). HarperCollins. Kindle Edition.]

· As Michael Shermer argues, “Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragmented copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution.” Or as Ken Miller argues: “The critics of evolution like to say that the complexity of the genome makes it clear that it was designed…. But there’s a problem with that analysis, and it’s a serious one. The problem is the genome itself: it’s not perfect. In fact, it’s riddled with useless information, mistakes, and broken genes…. Molecular biologists actually call some of these regions ‘gene deserts,’ reflecting their barren nature.” Or as philosopher of science Philip Kitcher puts it, “If you were designing the genomes of organisms, you would not fill them up with junk.” [Shermer, Why Darwin Matters, 75.] [Miller, Only a Theory, 37, 96–97.] [See also Kitcher, Living with Darwin, 57.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 6535-6541). HarperCollins. Kindle Edition.]

· ID advocates advance a different view of nonprotein-coding DNA. [Some advocates of intelligent design think that an intelligent cause is directly responsible for only the information present in the first living organisms; other ID advocates think intelligent design is responsible for the information necessary to produce subsequent forms of life as well. Those who hold the latter view predict that the nonprotein-coding DNA in both eukaryotes and prokaryotes should perform functional roles. Those who hold the former view predict that only the noncoding DNA in prokaryotes should perform functional roles. The discovery that noncoding DNA plays an important functional role in both prokaryotic and eukaryotic organisms confirms the prediction of the more expansive ID hypothesis. I hold this latter view. See Meyer, “The Origin of Biological Information.” In this book, however, I have argued only for intelligent design as the best explanation of the origin of the information necessary to build the first living cell.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Location 6542). HarperCollins. Kindle Edition.]

· As William Dembski explained and predicted in 1998: “On an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function.” [Dembski, “Intelligent Science and Design.” Here’s what Dembski writes about junk DNA: “[Intelligent] design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term ‘junk DNA.’ Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 6545-6547). HarperCollins. Kindle Edition.]

· Contrary to their claims, recent scientific discoveries have shown that the nonprotein-coding regions of the genome direct the production of RNA molecules that regulate the use of the protein-coding regions of DNA. Cell and genome biologists have also discovered that these supposedly “useless” nonprotein-coding regions of the genome: (1) regulate DNA replication,* (2) regulate transcription,* (3) mark sites for programmed rearrangements of genetic material,* (4) influence the proper folding and maintenance of chromosomes,* (5) control the interactions of chromosomes with the nuclear membrane (and matrix),* (6) control RNA processing, editing, and splicing,* (7) modulate translation,* (8) regulate embryological development,* (9) repair DNA,* and (10) aid in immunodefense or fighting disease* among other functions. In some cases, “junk” DNA has even been found to code functional genes.* Overall, the nonprotein-coding regions of the genome function much like an operating system in a computer that can direct multiple operations simultaneously. [Von Sternberg and Shapiro, “How Repeated Retroelements Format Genome Function.”] [Han, Szak, and Boeke, “Transcriptional Disruption by the L1 Retrotransposon”; Bethany Janowski, et al., “Inhibiting Gene Expression at Transcription Start Sites”; Goodrich and Kugel, “Non-coding-RNA Regulators of RNA Polymerase II Transcription”; Li, et al., “Small dsRNAs Induce Transcriptional Activation in Human Cells”; Pagano, et al., “New Small Nuclear RNA Gene-like Transcriptional Units”; Van de Lagemaat, et al., “Transposable Elements in Mammals”; Donnelly, Hawkins, and Moss, “A Conserved Nuclear Element”; Dunn, Medstrand, and Mager, “An Endogenous Retroviral Long Terminal Repeat”; Burgess-Beusse, et al., “The Insulation of Genes”; Medstrand, Landry, and Mager, “Long Terminal Repeats Are Used as Alternative Promoters”; Mariño-Ramírez, et al., “Transposable Elements Donate Lineage-Specific Regulatory Sequences to Host Genomes.”] [Green, “The Role of Translocation and Selection”; Figueiredo, et al., “A Central Role for Plasmodium Falciparum Subtelomeric Regions.”] [Henikoff, Ahmad, and Malik, “The Centromere Paradox”; Bell, West, and Felsenfeld, “Insulators and Boundaries”; Pardue and DeBaryshe, “Drosophila Telomeres”; Henikoff, “Heterochromatin Function in Complex Genomes”; Figueiredo, et al., “A Central Role for Plasmodium Falciparum”; Schueler, et al., “Genomic and Genetic Definition of a Functional Human Centromere.”] [ Jordan, et al., “Origin of a Substantial Fraction”; Henikoff, Ahmad, and Malik, “The Centromere Paradox”; Schueler, et al., “Genomic and Genetic Definition of a Functional Human Centromere.”] [Chen, DeCerbo, and Carmichael, “Alu Element-Mediated Gene Silencing”; Jurka, “Evolutionary Impact of Human Alu Repetitive Elements.”; Lev-Maor, et al., “The Birth of an Alternatively Spliced Exon”; Kondo-Iida, et al., “Novel Mutations and Genotype–Phenotype Relationships”; Mattick and Makunin, “Non-coding RNA.”] [McKenzie and Brennan, “The Two Small Introns of the Drosophila Affinidisjuncta Adh Gene”; Arnaud, et al., “SINE Retroposons Can Be Used In Vivo”; Rubin, Kimura, and Schmid, “Selective Stimulation of Translational Expression”; Bartel, “MicroRNAs”; Mattick and Makunin, “Small Regulatory RNAs in Mammals.”] [Dunlap, et al., “Endogenous Retroviruses”; Hyslop, et al., “Downregulation of NANOG Induces Differentiation”; Peaston, et al., “Retrotransposons Regulate Host Genes.”] [Morrish, et al., “DNA Repair Mediated”; Tremblay, Jasin, and Chartrand, “A Double-Strand Break in a Chromosomal LINE Element”; Grawunder, et al., “Activity of DNA Ligase IV”; Wilson, Grawunder, and Liebe, “Yeast DNA Ligase IV.”] [Mura, et al., “Late Viral Interference Induced”; Kandouz, et al., “Connexin43 Pseudogene Is Expressed.”] [Goh, et al., “A Newly Discovered Human Alpha Globin Gene”; Kandouz, et al., “Connexin43 Pseudogene Is Expressed”; Tam, et al., “Pseudogene-Derived Small Interfering RNAs”; Watanabe, et al., “Endogenous siRNAs from Naturally Formed dsRNAs”; Piehler, et al., “The Human ABC Transporter Pseudogene Family.”] [Mattick and Gagen, “The Evolution of Controlled Multitasked Gene Networks”; Von Sternberg and Shapiro, “How Repeated Retroelements Format Genome Function.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 6550-6561). HarperCollins. Kindle Edition.]

· Reason 5: ID Addresses a Specific Question in Evolutionary Biology There is another closely related reason to regard intelligent design as a scientific theory. It addresses a key question that has long been part of historical and evolutionary biology: How did the appearance of design in living systems arise? As noted in Chapter 1, both Darwin and contemporary evolutionary biologists such as Francisco Ayala, Richard Dawkins, and Richard Lewontin acknowledge that biological organisms appear to have been designed.* Nevertheless, for most evolutionary theorists, the appearance of design is considered illusory, because they are convinced that the mechanism of natural selection acting on random variations (and/or other similarly unguided mechanisms) can fully account for the appearance of design in living organisms. [Dawkins, The Blind Watchmaker, 1.] [Ayala, “Darwin’s Revolution.”] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 6606-6612). HarperCollins. Kindle Edition.]

· Reason 6: ID Is Supported by Peer-Reviewed Scientific Literature Critics of the theory of intelligent design often claim that its advocates have failed to publish their work in peer-reviewed scientific publications. For this reason, they say the theory of intelligent design does not qualify as a scientific theory.* According to these critics, science is what scientists do. Since ID scientists don’t do what other scientists do—namely, publish in peer-reviewed journals—they are not real scientists and their theory isn’t scientific either. [For example, Judge Jones asserted in his decision: “We find that ID is not science and cannot be adjudged a valid, accepted scientific theory as it has failed to publish in peer-reviewed journals” (Kitzmiller et al. v. Dover Area School District, 400 F.Supp.2d).] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 6625-6629). HarperCollins. Kindle Edition.]

19 Sauce for the Goose

· Many scientific theories infer or postulate unobservable entities, causes, and events. Theories of chemical evolution invoke past events as part of the scenarios they use to explain how the modern cell arose. Insofar as these events occurred millions of years ago, they are clearly not observable today. Darwinian biologists, for their part, have long defended the putatively unfalsifiable nature of their claims by reminding critics that many of the creative processes to which they refer occur at rates too slow to observe in the present and too fast to have been recorded in the fossil record. Further, the existence of many transitional intermediate forms of life, the forms represented by the nodes on Darwin’s famous branching tree diagram, are also unobservable.* Instead, unobservable transitional forms of life are postulated to explain observable biological evidence—as Darwin himself explained. But how is this different from postulating the past activity of an unobservable designing intelligence to explain observable features of the living cell? [Meyer, “Of Clues and Causes,” 120; Darwin, On the Origin of Species, 398; Hull, Darwin and His Critics, 45.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 6839-6846). HarperCollins. Kindle Edition.]

· Robert Pennock, one of the witnesses in the Dover trial, argued that the unobservable character of a designing intelligence precludes the possibility of testing intelligent design scientifically because, as he explained, “science operates by empirical principles of observational testing; hypotheses must be confirmed or disconfirmed by reference to…accessible empirical data.” [Pennock, Expert Witness Report.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 6879-6882). HarperCollins. Kindle Edition.]

20 Why It Matters

· As George Gaylord Simpson, the leading neo-Darwinist a generation ago, stated: “Man is the result of a purposeless and materialistic process that did not have him in mind. He was not planned.” [Simpson, The Meaning of Evolution, 344.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 7202-7203). HarperCollins. Kindle Edition.]

· In light of this, Simpson and a host of prominent Darwinian scientists—from Douglas Futuyma to William Provine to Stephen Jay Gould to Richard Dawkins—have insisted that Darwinism (and the broader blind-watchmaker thesis) has made a materialistic worldview more plausible. [Futuyma, Evolutionary Biology, 5.] [“The implications of modern evolutionary biology are inescapable…. Evolutionary biology undermines the fundamental assumptions underlying ethical systems in almost all cultures, Western civilization in particular” (Provine, “Evolution and the Foundation of Ethics”).] [Gould, Ever Since Darwin, 33.] [Dawkins, The Blind Watchmaker, 6.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 7204-7207). HarperCollins. Kindle Edition.]

· As Dawkins stated, “Darwin made it possible to become an intellectually fulfilled atheist.”* Or as the late Harvard paleontologist Stephen J. Gould argued, Darwin formulated “an evolutionary theory based on chance variation and natural selection…a rigidly materialistic (and basically atheistic) version of evolution.” Or as Gould explained elsewhere, “Before Darwin, we thought that a benevolent God had created us,” but after Darwin, “biology took away our status as paragons created in the image of God.” [Dawkins, The Blind Watchmaker, 6.] [Gould, Ever Since Darwin, 33, 147, 267.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 7208-7212). HarperCollins. Kindle Edition.]

· Similarly, many major biology texts present evolution as a process in which a purposeful intelligence (such as God) plays no detectable role. As Kenneth Miller and Joseph Levine explained in the fourth edition of their popular textbook, Biology, the evolutionary process is “random and undirected” and occurs “without plan or purpose.”* Or as W. H. Purvis, G. H. Orians, and H. C. Heller tell students in Life: The Science of Biology, “The living world is constantly evolving without any goals. Evolutionary change is not directed.” [Miller and Levine, Biology, 658. A later edition of the textbook deleted this language.] [Purvis, Orians, and Heller, Life, 14.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 7212-7216). HarperCollins. Kindle Edition.]

· As Douglas Futuyma’s biology text puts it, “By coupling undirected, purposeless variation to the blind, uncaring process of natural selection, Darwin made theological or spiritual explanations of the life processes superfluous.” [Futuyma, Evolutionary Biology, 5.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 7217-7219). HarperCollins. Kindle Edition.]

· The British analytical philosopher Bertrand Russell understood the connection between the denial of design (or what he called “prevision”) and humankind’s existential predicament. As he explained in 1918: That Man is the product of causes which had no prevision of the end they were achieving; that his origin, his growth, his hopes and fears, his loves and his beliefs, are but the outcome of accidental collocations of atoms; that no fire, no heroism, no intensity of thought and feeling, can preserve an individual life beyond the grave; that all the labours of the ages, all the devotion, all the inspiration, all the noonday brightness of human genius, are destined to extinction in the vast death of the solar system, and that the whole temple of Man’s achievement must inevitably be buried beneath the debris of a universe in ruins—all these things, if not quite beyond dispute, are yet so nearly certain, that no philosophy which rejects them can hope to stand. [Russell, Mysticism and Logic, Including a Free Man’s Worship, 10–11.] [Stephen C. Meyer: Signature in the Cell (DNA Evidence for Intelligent Design), (Kindle Locations 7283-7290). HarperCollins. Kindle Edition.]

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