Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design
by Stephen C. Meyer (2013)
This is Stephen Meyer's sequel to Signature in the Cell (2009). Signature focused on the problem of the origin of genetic information and the case for intelligent design, using some arguments similar to those of Shiller in 5th Option. I found that book to be really well written. The explanations were clear, arguments well structured, lots of good references. This one is no different. It focuses on the mystery of the Cambrian explosion, when numerous new animal forms appeared quite suddenly in the fossil record, seemingly with no transitional ancestors that would explain their unique features according to gradual Darwinian processes. Part 1 examines the first problem posed by the Cambrian explosion: the missing forms and fossils. If Darwinism is true, there should be innumerable transition fossils, but they're wholly missing. Part 2 zeroes in on genetics and the problems it has accounting for the new Cambrian creatures. And Part 3 takes a look at some post-Darwinian theories, including intelligent design. Here's some summary notes I took while reading. Hopefully it covers the main points, but if you want the details, you'll just have to read the book (or ask).
Chapter 1 lays out the problem, which Darwin acknowledged. The fossil record shows an 'explosion' of new body plans in the Cambrian period representing most animal phyla, phyla which weren't present in the pre-Cambrian fossil record. Assuming Darwinism is true, a reliable fossil record should show a progressive, gradual development of animal forms, but the record is discontinuous. Darwin, and his followers, hypothesized that perhaps the fossil record was simply incomplete (i.e., the forms existed, but didn't fossilize, or couldn't, perhaps because they were too small or too soft). Chapter 2 describes the discovery of fossils in the "Burgess Bestiary" and the problems it suggested, for example, the fact that it seemed as if big changes came first, not later, after many small-scale changes, the opposite of Darwin's hypothesis. New phyla seemingly arrived fully formed, without transitional forms between them and their presumed common ancestor. Chapter 3 tackles the explanations proposed in response to this contradiction and shows that they hold no water. Small organisms (single cells) and soft body parts can and do get fossilized, and there IS a fossil record of pre-Cambrian creatures. Chapter 4 further demonstrates that the fossils are not simply missing. The known pre-Cambrian fossils do not represent ancestors for the new phyla that crop up during the Cambrian (at least in the vast majority). In the few comparisons to be made, pre-Cambrian forms are either too dissimilar from later Cambrian forms (compounding the problem of missing fossils showing gradual change) or too differentiated (meaning they can't be common ancestors to various known phyla). The fossil record may not be complete, but it is well enough represented to imply that the picture it presents is largely complete (i.e., discontinuous appearance of new forms). We're just looking at it in the wrong way (i.e., assuming universal descent via only natural selection and random mutation).
Chapter 5 looks at the comparative study of genes supposedly proving a pre-Cambrian common ancestor. But Meyer shows that molecular studies produce widely divergent results, and are based on the assumption of universal common descent. (In other words, to use such studies and their estimated molecular dating to prove common descent is circular reasoning.) The hypothetical dates of a common ancestor vary so widely that they don't prove much at all. Chapter 6 looks at the hypothetical trees of life created based on molecular and anatomical comparison between organisms. Meyer shows that comparisons of different molecules produce totally different trees, comparisons between anatomy and molecules produce different trees, and comparisons of different anatomies also produce different trees. The trees contradict each other and are mutually exclusive. In other words, there's currently no reliable picture of the proposed tree of life.
Chapter 7 looks at Gould and Eldredge's theory of 'punctuated equilibrium' (punk eek), proposed in order to explain the discontinuity in the fossil record and the fact that organisms tend to remain the same for long periods of time. But by proposing the idea that speciation proceeds too rapidly to appear in the fossil record, the theory ran into its own problems. Populations needed to be large enough to produce viable mutations, and then small enough to promote that trait. And the only way to get those mutations in the first place was by the same gradual neo-Darwinian process of random mutations (bottom-up, not top-down, as the fossil record suggests). In other words, 'punk eek' ran into the same problems: more transitional fossils should be in the fossil record from the time when variations cropped up between competing species. The Cambrian explosion was still a mystery.
Chapter 8 introduces the second problem posed by the Cambrian explosion. What exactly produced all the new genetic information required for the new cell types and organs seen in the Cambrian phyla? Can this be explained using neo-Darwinian models? Chapter 9 highlights the problem: DNA contains the information for forming proteins, and random changes to specified information (like words in a book) almost inevitably lead to degraded meaning. It becomes gibberish. Wouldn't DNA suffer the same fate, with mutations inevitably producing non-functional proteins? Proteins are typically made of hundreds of amino acids. How many of the astronomical number of possible amino-acid sequences are functional, and how likely is it that random mutation would stumble upon one of those functional sequences? Chapter 10 answers that question, with an in-depth explanation of Doug Axe's work on proteins. While sequences of any length contain many possible functional proteins, compared with the total number of sequences, they are extremely rare. For proteins 150 amino acids in length, the ratio of proteins that fold correctly to those that don't is 1 to 10^74. But the ratio for properly folded proteins that are also functional is 1 to 10^77. Even by generously assuming that one organism can randomly search through these possibilities and come up with a new gene for a new protein in its lifetime, given all the organisms that ever lived in life's 3.8-billion-year history, the probability of reaching a new functional protein is still about 1 in 10^37. In other words, no dice. Such odds are as slim as slim can be. And keep in mind that the Cambrian explosion was mere millions of years long and required the creation of new cell types requiring whole sets of novel genes. Random mutation followed by natural selection CANNOT account for the necessary amount of new genetic information. There simply wasn't enough time for neo-Darwinist processes to do their thing. Chapter 11 deals with the response to Axe's ideas: that known gene-producing processes can explain the production of new genes and proteins. Meyer shows that they cannot. These processes, like exon-shuffling, either presuppose existing genetic information, thus begging the question, or posit 'de novo' creation of genes (i.e., creation out of nothing, new genes with no known precursors). And either way, they don't explain how these processes can solve the problem of searching 'combinatorial space' for the specific functional sequences among way more non-functional ones. Chapter 12 describes experiments showing that genes requiring more than 2 coordinated mutations to produce a new gene are implausible given the entire time and populations available for evolution. In short, neo-Darwinism can't account for the arrival of new genes, new proteins, new traits. The probabilities are too astronomical given the assumed processes at work. Something else is going on. (This has led many researchers to propose new theories for the origin of novel genetic information, which Meyer analyses in Chapters 15 and 16.)
Chapter 13 looks at the origin of body plans and the highly complex processes that go into the growth of embryos to their final form. New forms require new regulatory networks, which switch genes on and off in the right places at the right time in order to differentiate cells, organs, and make sure they're all in the right place in the body. But mutations to these regulatory genes inevitably result in faulty organisms. A new regulatory network requires numerous coordinated mutations, since every part of the system works together, and the system as a whole is hierarchically structured. You can't just change one part of the system to make a new network. Chapter 14 poses perhaps the biggest problem with the development of new forms: epigenetic information, i.e., inherited information that isn't contained in the genes. While genes are necessary for proper development, other things are at work. For example, sea urchin embryos can develop up to 500 cells after their nuclei (which store their DNA) have been removed. How is this possible? It turns out that the pre-existing form of the cell (including its cytoskeleton, centrosome, cell membrane targets, ion channels, and sugar structures that form on the membrane, all of which are essential to the development of an organism's form) is inherited directly from cell to cell. Genes don't code for forms, so new forms require new epigenetic information, wherever and whatever it is. (Random mutation and natural selection can't account for the creation or adaptation of this epigenetic information.)
Chapter 15 looks at the post-neo-Darwinist theory of 'self-organization' that has been proposed to account for some deficits of neo-Darwinism. However, Meyer shows that these theories, too, presuppose genetic information (like gene regulatory networks) and do not explain how epigenetic information self-organizes. It cannot. The shape and location of morphogenic cell features are inherited directly and not determined by their chemical properties. They, too, are a form of pre-existing information that must be presupposed in order for the theory to work. Chapter 16 looks at some other modern theories (like James Shapiro's 'natural genetic engineering', neo-Lamarckism, evo-devo), and shows that they run into similar problems (presupposing large amounts of pre-existing information). Chapters 17, 18, and 19 focus on intelligent design. Meyer argues that it is a valid scientific theory that uses abductive reasoning, like much historical science, and is the best and only explanation for all the problematic features of the Cambrian (rapid top-down appearance, hierarchical genes and gene networks, new animal forms and later variations on those forms that stick to the basic body plan, modular genes, novel information, etc.). He argues that there is no rational reason for denying its status as 'science.'
My only beef with the book is a relatively small one. Meyer seems to think there is only one definition of 'naturalism' (other than methodological naturalism): materialism. Funny that the last footnote is a quote from Alfred Whitehead, who developed a naturalistic philosophy that makes room for mind AND a cosmic mind (God, perhaps). Yet Meyer doesn't raise this possibility that materialism is just one form of naturalism, which would go a long way to reconciling scientific methodology and even some of its core philosophical assumptions with the subject matter of religion (values, questions of the ultimate, soul, free will, etc.). David Ray Griffin has written many good books arguing for an expanded naturalism, showing that one doesn't have to believe the only options are materialistic naturalism and supernaturalism (i.e., God creating the world out of nothing and intervening in it whenever he wants), which has its own serious philosophical problems. So while Darwin's Doubt if a great argument for intelligent design, I think it should be rounded out with a read of some of Griffin's books, like Religion and Scientific Naturalism or Reenchantment without Supernaturalism. But that's a minor point, as so little of the book has to do with theology. The focus is pretty tight on the science and Meyer does a good job despite what I see as one minor weakness in what is really an inessential part of his argument (relegated to the final chapter or two).
by Stephen C. Meyer (2013)
This is Stephen Meyer's sequel to Signature in the Cell (2009). Signature focused on the problem of the origin of genetic information and the case for intelligent design, using some arguments similar to those of Shiller in 5th Option. I found that book to be really well written. The explanations were clear, arguments well structured, lots of good references. This one is no different. It focuses on the mystery of the Cambrian explosion, when numerous new animal forms appeared quite suddenly in the fossil record, seemingly with no transitional ancestors that would explain their unique features according to gradual Darwinian processes. Part 1 examines the first problem posed by the Cambrian explosion: the missing forms and fossils. If Darwinism is true, there should be innumerable transition fossils, but they're wholly missing. Part 2 zeroes in on genetics and the problems it has accounting for the new Cambrian creatures. And Part 3 takes a look at some post-Darwinian theories, including intelligent design. Here's some summary notes I took while reading. Hopefully it covers the main points, but if you want the details, you'll just have to read the book (or ask).
Chapter 1 lays out the problem, which Darwin acknowledged. The fossil record shows an 'explosion' of new body plans in the Cambrian period representing most animal phyla, phyla which weren't present in the pre-Cambrian fossil record. Assuming Darwinism is true, a reliable fossil record should show a progressive, gradual development of animal forms, but the record is discontinuous. Darwin, and his followers, hypothesized that perhaps the fossil record was simply incomplete (i.e., the forms existed, but didn't fossilize, or couldn't, perhaps because they were too small or too soft). Chapter 2 describes the discovery of fossils in the "Burgess Bestiary" and the problems it suggested, for example, the fact that it seemed as if big changes came first, not later, after many small-scale changes, the opposite of Darwin's hypothesis. New phyla seemingly arrived fully formed, without transitional forms between them and their presumed common ancestor. Chapter 3 tackles the explanations proposed in response to this contradiction and shows that they hold no water. Small organisms (single cells) and soft body parts can and do get fossilized, and there IS a fossil record of pre-Cambrian creatures. Chapter 4 further demonstrates that the fossils are not simply missing. The known pre-Cambrian fossils do not represent ancestors for the new phyla that crop up during the Cambrian (at least in the vast majority). In the few comparisons to be made, pre-Cambrian forms are either too dissimilar from later Cambrian forms (compounding the problem of missing fossils showing gradual change) or too differentiated (meaning they can't be common ancestors to various known phyla). The fossil record may not be complete, but it is well enough represented to imply that the picture it presents is largely complete (i.e., discontinuous appearance of new forms). We're just looking at it in the wrong way (i.e., assuming universal descent via only natural selection and random mutation).
Chapter 5 looks at the comparative study of genes supposedly proving a pre-Cambrian common ancestor. But Meyer shows that molecular studies produce widely divergent results, and are based on the assumption of universal common descent. (In other words, to use such studies and their estimated molecular dating to prove common descent is circular reasoning.) The hypothetical dates of a common ancestor vary so widely that they don't prove much at all. Chapter 6 looks at the hypothetical trees of life created based on molecular and anatomical comparison between organisms. Meyer shows that comparisons of different molecules produce totally different trees, comparisons between anatomy and molecules produce different trees, and comparisons of different anatomies also produce different trees. The trees contradict each other and are mutually exclusive. In other words, there's currently no reliable picture of the proposed tree of life.
Chapter 7 looks at Gould and Eldredge's theory of 'punctuated equilibrium' (punk eek), proposed in order to explain the discontinuity in the fossil record and the fact that organisms tend to remain the same for long periods of time. But by proposing the idea that speciation proceeds too rapidly to appear in the fossil record, the theory ran into its own problems. Populations needed to be large enough to produce viable mutations, and then small enough to promote that trait. And the only way to get those mutations in the first place was by the same gradual neo-Darwinian process of random mutations (bottom-up, not top-down, as the fossil record suggests). In other words, 'punk eek' ran into the same problems: more transitional fossils should be in the fossil record from the time when variations cropped up between competing species. The Cambrian explosion was still a mystery.
Chapter 8 introduces the second problem posed by the Cambrian explosion. What exactly produced all the new genetic information required for the new cell types and organs seen in the Cambrian phyla? Can this be explained using neo-Darwinian models? Chapter 9 highlights the problem: DNA contains the information for forming proteins, and random changes to specified information (like words in a book) almost inevitably lead to degraded meaning. It becomes gibberish. Wouldn't DNA suffer the same fate, with mutations inevitably producing non-functional proteins? Proteins are typically made of hundreds of amino acids. How many of the astronomical number of possible amino-acid sequences are functional, and how likely is it that random mutation would stumble upon one of those functional sequences? Chapter 10 answers that question, with an in-depth explanation of Doug Axe's work on proteins. While sequences of any length contain many possible functional proteins, compared with the total number of sequences, they are extremely rare. For proteins 150 amino acids in length, the ratio of proteins that fold correctly to those that don't is 1 to 10^74. But the ratio for properly folded proteins that are also functional is 1 to 10^77. Even by generously assuming that one organism can randomly search through these possibilities and come up with a new gene for a new protein in its lifetime, given all the organisms that ever lived in life's 3.8-billion-year history, the probability of reaching a new functional protein is still about 1 in 10^37. In other words, no dice. Such odds are as slim as slim can be. And keep in mind that the Cambrian explosion was mere millions of years long and required the creation of new cell types requiring whole sets of novel genes. Random mutation followed by natural selection CANNOT account for the necessary amount of new genetic information. There simply wasn't enough time for neo-Darwinist processes to do their thing. Chapter 11 deals with the response to Axe's ideas: that known gene-producing processes can explain the production of new genes and proteins. Meyer shows that they cannot. These processes, like exon-shuffling, either presuppose existing genetic information, thus begging the question, or posit 'de novo' creation of genes (i.e., creation out of nothing, new genes with no known precursors). And either way, they don't explain how these processes can solve the problem of searching 'combinatorial space' for the specific functional sequences among way more non-functional ones. Chapter 12 describes experiments showing that genes requiring more than 2 coordinated mutations to produce a new gene are implausible given the entire time and populations available for evolution. In short, neo-Darwinism can't account for the arrival of new genes, new proteins, new traits. The probabilities are too astronomical given the assumed processes at work. Something else is going on. (This has led many researchers to propose new theories for the origin of novel genetic information, which Meyer analyses in Chapters 15 and 16.)
Chapter 13 looks at the origin of body plans and the highly complex processes that go into the growth of embryos to their final form. New forms require new regulatory networks, which switch genes on and off in the right places at the right time in order to differentiate cells, organs, and make sure they're all in the right place in the body. But mutations to these regulatory genes inevitably result in faulty organisms. A new regulatory network requires numerous coordinated mutations, since every part of the system works together, and the system as a whole is hierarchically structured. You can't just change one part of the system to make a new network. Chapter 14 poses perhaps the biggest problem with the development of new forms: epigenetic information, i.e., inherited information that isn't contained in the genes. While genes are necessary for proper development, other things are at work. For example, sea urchin embryos can develop up to 500 cells after their nuclei (which store their DNA) have been removed. How is this possible? It turns out that the pre-existing form of the cell (including its cytoskeleton, centrosome, cell membrane targets, ion channels, and sugar structures that form on the membrane, all of which are essential to the development of an organism's form) is inherited directly from cell to cell. Genes don't code for forms, so new forms require new epigenetic information, wherever and whatever it is. (Random mutation and natural selection can't account for the creation or adaptation of this epigenetic information.)
Chapter 15 looks at the post-neo-Darwinist theory of 'self-organization' that has been proposed to account for some deficits of neo-Darwinism. However, Meyer shows that these theories, too, presuppose genetic information (like gene regulatory networks) and do not explain how epigenetic information self-organizes. It cannot. The shape and location of morphogenic cell features are inherited directly and not determined by their chemical properties. They, too, are a form of pre-existing information that must be presupposed in order for the theory to work. Chapter 16 looks at some other modern theories (like James Shapiro's 'natural genetic engineering', neo-Lamarckism, evo-devo), and shows that they run into similar problems (presupposing large amounts of pre-existing information). Chapters 17, 18, and 19 focus on intelligent design. Meyer argues that it is a valid scientific theory that uses abductive reasoning, like much historical science, and is the best and only explanation for all the problematic features of the Cambrian (rapid top-down appearance, hierarchical genes and gene networks, new animal forms and later variations on those forms that stick to the basic body plan, modular genes, novel information, etc.). He argues that there is no rational reason for denying its status as 'science.'
My only beef with the book is a relatively small one. Meyer seems to think there is only one definition of 'naturalism' (other than methodological naturalism): materialism. Funny that the last footnote is a quote from Alfred Whitehead, who developed a naturalistic philosophy that makes room for mind AND a cosmic mind (God, perhaps). Yet Meyer doesn't raise this possibility that materialism is just one form of naturalism, which would go a long way to reconciling scientific methodology and even some of its core philosophical assumptions with the subject matter of religion (values, questions of the ultimate, soul, free will, etc.). David Ray Griffin has written many good books arguing for an expanded naturalism, showing that one doesn't have to believe the only options are materialistic naturalism and supernaturalism (i.e., God creating the world out of nothing and intervening in it whenever he wants), which has its own serious philosophical problems. So while Darwin's Doubt if a great argument for intelligent design, I think it should be rounded out with a read of some of Griffin's books, like Religion and Scientific Naturalism or Reenchantment without Supernaturalism. But that's a minor point, as so little of the book has to do with theology. The focus is pretty tight on the science and Meyer does a good job despite what I see as one minor weakness in what is really an inessential part of his argument (relegated to the final chapter or two).
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