Sunday, 5 November 2017
The Original artist v. Darwin.
Design in Living Color
Evolution News | @DiscoveryCSC
Evolution News | @DiscoveryCSC
Our colorful world — what a joy it is! Who doesn’t love the beauty of butterflies, the colors of birds and tropical fish, or the colorful eyes of a loved one? Mechanistically speaking, though, color is ‘nothing but’ wavelengths of light reflecting off surfaces or emanating from energy sources within a particular range of frequencies we artificially designate as “visible light.” We respond physically to wavelengths only because our bodies come equipped with highly complex sensory systems. We respond emotionally to the qualia of color — the redness of red, the greenness of green, the beautiful spectrum in a rainbow — because of something deeper in our consciousness.
Blind nature is oblivious to qualia. It has no obligation to invent creatures able to manipulate color, or to perceive it. Least of all is nature obliged to produce artists that use color for purely aesthetic reasons unrelated to survival. Yet the living world is filled with colors in profusion, often with spectacular effect. This fact requires an explanation. One could think of reasons natural selection might favor an ecological system of uniform browns or blacks. Camouflage would be perfect in such a world! What does blind evolution care about color?
To outline evolutionary explanations for color, Science Magazine recently presented “The Biology of Color,” a review article by Innes C. Cuthill with 27 authors from the U.K. and U.S. The editors summarize the goal:
Animals live in a colorful world, but we rarely stop to think about how this color is produced and perceived, or how it evolved. Cuthill et al. review how color is used for social signals between individual animals and how it affects interactions with parasites, predators, and the physical environment. New approaches are elucidating aspects of animal coloration, from the requirements for complex cognition and perception mechanisms to the evolutionary dynamics surrounding its development and diversification.
“Elucidating” means shedding light, which presupposes that science does not only observe light, but produces light in the realm of understanding: i.e., scientific explanation. Since we know from the “rules of science” these days that design explanations must be excluded, it’s fair to say this article summarizes the state of the art in evolutionary explanations for color. Contributors include a broad spectrum (so to speak) of scientific disciplines: “evolutionary biologists, behavioral ecologists, psychologists, optical physicists, visual physiologists, geneticists, and anthropologists” — all committed to evolutionary theory. For curious readers, these experts will map the route to proper Darwinian answers, shedding colorful light along the way:
The interdisciplinary field of animal coloration is growing rapidly, spanning questions about the diverse ways that animals use pigments and structures to generate color, the underlying genetics and epigenetics, the perception of color, how color information is integrated with information from other senses, and general principles underlying color’s evolution and function. People working in the field appreciate linkages between these parallel lines of enquiry, but outsiders need the easily navigable roadmap that we provide here.
Following their roadmap, we proceed down the yellow brick road to the wizard of ahh’s, hoping the promised understanding will be forthcoming. For openers, let’s check the flashlight they provide (the “elucidating” device).
In the past 20 years, the field of animal coloration research has been propelled forward by technological advances that include spectrophotometry, digital imaging, computational neuroscience, innovative laboratory and field studies, and large-scale comparative analyses, which are allowing new questions to be asked. For example, we can now pose questions about the evolution of camouflage based on what a prey’s main predator can see, and we can start to appreciate that gene changes underlying color production have occurred in parallel in unrelated species. Knowledge of the production, perception, and evolutionary function of coloration is poised to make contributions to areas as diverse as medicine, security, clothing, and the military, but we need to take stock before moving forward.
This is some high-tech flashlight! We need to learn how to use it, in other words. How do we use evolution to shed light? It is “daunting to the outsider,” they warn. They outline key questions needing elucidation:
How nanoscale structures are used to manipulate light
How dynamic changes in coloration occur on different time scales
The genetics of coloration (including key innovations and the extent of parallel changes in different lineages)
Alternative perceptions of color by different species (including wavelengths that we cannot see, such as ultraviolet)
How color, pattern, and motion interact
How color works together with other modalities, especially odor
Some of us will prefer carrying our trusty ID flashlights for illumination, but let’s give the Darwinians a chance to show off their brand. First, we listen to the commercial:
From an adaptive standpoint, color can serve several functions, and the resulting patterns frequently represent a trade-off among different evolutionary drivers, some of which are nonvisual (e.g., photoprotection). These trade-offs can vary between individuals within the same population, and color can be altered strategically on different time scales to serve different purposes. Lastly, interspecific differences in coloration, sometimes even observable in the fossil record, give insights into trait evolution. The biology of color is a field that typifies modern research: curiosity-led, technology-driven, multilevel, interdisciplinary, and integrative.
Before we rush to buy this amazing flashlight on Amazon, let’s see how well it works. We should be concerned about “evolutionary drivers”, since they are blind, and blindness entails color blindness. How can a blind process understand a trade-off? One thing we learn from the article is that questions about color evolution are producing a flurry of activity among evolutionists:
The study of animal coloration has a venerable history. During the 19th century, early evolutionary biologists set out to explain the diversity of colors that they observed as products of natural selection. The 20th century saw color phenotypes adopted as genetic markers contributing to our understanding of development, genetics, and evolutionary theory.
Before proceeding, we should ask why there is anything else to learn. Didn’t the 19th and 20th century evolutionists figure it out? Apparently not.
In the past two decades, the field has again witnessed explosive growth. Coloration provides exceptional access to phenotypic diversity because we can quantify how color is perceived by the visual systems of diverse species, and humans are visual animals. Contemporary technologies enable biologists to investigate nanoscale and cellular mechanisms producing color; the sensory, neural, and cognitive bases of color perception; and the adaptive implications of external appearances. Progress in each area is rapid, making animal coloration an exciting interdisciplinary field, but one with which it is difficult to keep pace.
Let’s catch our breath in this frenetic race down the yellow brick road, and assess what it is we are looking for. Explanation is not merely description. It’s good to know what gene turns on what color. It’s helpful to find out which colors a predator can perceive. We can even be pleased to learn that a bird of a certain color might have better camouflage. None of these details explain animal coloration. The job of the Darwinians is to tell us how a color-blind process (that doesn’t care whether a creature lives or dies) ended up with a Ladybird beetle’s brilliant reds or a ruby-throated hummingbird’s shimmering throat feathers. It’s not enough to say, “It exists, therefore it evolved.” Nor can they say, “It’s useful, therefore it is adaptive, and natural selection would favor it.” Do you see the circular reasoning inherent in such statements? We seek evidence that evolution did occur, not restatements of what evolutionists believe occurred.
Across animals, coloration serves as a dynamic form of information (Fig. 1). Colorful body parts are moved in behavior, and both pigments and structural colors change at various temporal resolutions. Cephalopods are perhaps the most well-known example, but mobilization of pigments and nanostructures to change coloration is taxonomically widespread. Considerable opportunities exist for dissecting color pigment movements and manipulating their hormonal or neural control. Dynamically changing structural coloration can also manipulate the polarization of light. There is high potential for discoveries regarding how animals perceive polarization and integrate it with color information.
What is “information” to a blind, unguided process? Information fits in well with design theory (e.g., Dembski’s book Being as Communion), but we can’t let scientific materialists employ undefined terms nor import them from a worldview they don’t believe. Information doubles the challenge for evolution, because it requires a transmitter and a recipient that agree on the meaning of the communication.
So far, all we have seen are descriptions, not explanations. Body parts are moved. Animals perceive polarization of light. Animals integrate color information. Great, but how? Why?
We anticipate answers in the subsection, “Genetics of color and evolutionary change.” But careful reading reveals only tricks of the evolutionary trade: co-option, convergence, and similarity. Underneath these superficial narratives, evolutionists need to deal with the origin of complex genetic information, molecular machines, and developmental processes of exquisite order. They try:
For instance, a ketolase enzyme that evolved to modify carotenoid pigments in the retina of birds paved the way for the expression of red pigments in bills and plumage; similarly, the ALX3 transcription factor has come to regulate the expression of melanocyte differentiation in striped rodents.
Saying that something evolved does not mean it did. Can a bird reason, “Oh, now I have this ketolase enzyme. I think I’ll color my beak with it.”? Can a rodent think, “Now that I have ALX3, I can put racing stripes on my back and look really cool.”? Obviously not; the materialist cannot ascribe desires or powers to organisms nor to the molecules involved. We cannot stress enough that evolution is blind and color-blind! It is not personal. It is not a force. It could not care less what happens.
Genes underlying color variation offer insight into the predictability of evolution. Convergent phenotypes commonly arise in parallel; the accurate characterization of color phenotypes has revealed independent changes in similar genetic mechanisms, leading to phenotypic similarity between species.
Predictability is certainly a good quality to have in a theory, but did they predict any of this? No; it is all description after the fact, combined with circular reasoning: “It exists, therefore it evolved.” To have the same accidents occur in independent lineages should amount to falsification of the theory. It certainly does not qualify as an explanation.
Multidisciplinary research into the workings of coloration, from genotype to phenotype, and from development to adult, is certainly valuable. We might compare it to discovering an alien spacecraft and figuring out how it works. Such research cannot explain how it emerged by blind, unguided processes. So while we celebrate the progress in understanding coloration, we don’t see in this paper any explanation for it that does not presuppose the success of evolutionary theory.
Whenever they try to link accidents with functions, they run into problems and have to admit ignorance. For instance, Darwin’s sexual selection theory provides a shiny-object narrative at a superficial level, but not at the genetic level:
Genomic insights will prove valuable in investigations of mechanisms by which colorful traits honestly signal individual quality. It is widely accepted that a sexual ornament can reveal quality, because of the challenges associated with producing or bearing such traits, but we remain largely ignorant of the mechanisms that underlie gene-environment interactions causing condition-dependent signaling. Epigenetic studies at the genome scale may offer insight into this question.
Even worse is accounting for structural color. This kind of coloration, seen in birds and insects, relies on precise placement of geometrical molecules at the nanoscale rather than on pigments. How can evolution even approach such masterpieces of “apparent” design?
Knowledge of genetic mechanisms underlying the creation and transport of pigments, such as melanin and carotenoids, has advanced considerably in the past 15 years, but outstanding questions about structural coloration remain. Understanding the genetic control of size and shape dispersion is important because these properties ultimately control optical structures. An appreciation of the genetics of nanostructural color production could also be important for biotechnological applications — for example, the creation of sensors and reporting mechanisms.
The applications mentioned are matters of intelligent design by humans. How could natural selection invent genes that, by accident, are capable of placing molecules in precise positions at the nanoscale that enable them to refract certain wavelengths of light? Then, how does it position them in second-order artistic patterns like those on butterfly wings? Evolutionists admit they don’t know. They sure have their work cut out for them!
The challenge grows as they try to account for “Receptor processing and cognition” in the next section. It grows even more as they try to integrate colors with patterns and motion. We’ve given enough of a taste of their mode of explanation, we trust, to show that evolution is not an explanation; it is belief masquerading as explanation. Like Tom Bethell discussed in Darwin’s House of Cards, evolutionary explanation is a deduction from a pre-ordained worldview that asserts: It is, therefore it evolved. The public deserves better. The public would receive better were alternatives to neo-Darwinism permitted into the discussion. When you only allow one contender in the race, guess who is going to win?
Design detection is science except when it's not?
Mysterious Structures in Arabian Desert: All We Know Is that They Were Designed
Evolution News | @DiscoveryCSC
Evolution News | @DiscoveryCSC
The news media were swept up in a mystery recently, when an Australian archaeologist told how he used Google Earth to discover mysterious rock structures in the Arabian desert. He and his team want to investigate and figure them out. “As of now, researchers have more questions than answers regarding what these structures were used for, who built them, how old are they, and their meaning,” says an article at Forbes.
You can see a gallery of the so-called “gates” in Live Science. You can even find them on Google Earth yourself, if you want to do a little armchair archaeology, by searching for “Harrat Khaybar” and scouting around, trying to match landforms to the photos. We’ve reported finds like this before (here and here). The article at The Express UK says:
David Kennedy, a professor at the University of Western Australia, who helped to discover the gates through satellite imagery, said they “are stone-built, the walls roughly made and low.”
He adds that they “appear to be the oldest man-made structures in the landscape,” and that “no obvious explanation of their purpose can be discerned”.
Only one piece of evidence is helping to nail down the age of the structures. A few of the structures are partly covered by lava flows. That means that they had to be built before the most recent eruptions in this lava field, which could be as recent as 1,300 years ago, or up to 7,000 years ago. Kennedy wants to radiocarbon date the remains if he can launch an expedition. Knowing the date of the oldest structures can help identify what humans lived in that area at the time. Forbes says,
The team will soon publish their research in the journal Arabian Archaeology and Epigraphy. However, this is just the tip of the iceberg, as the saying goes. The next steps will be to lead an archaeological survey of the area, allowing the research team to collect samples and inspect the gates more closely. They will be able to carbon age date the lava fields and potentially the stone walls to determine the timing of construction. In addition, they may find more examples of what these strange people were like in this remote region of Saudi Arabia.
We can relate to Kennedy’s immediate sense that these structures were man-made, because we are human and know what humans do. And readers of Evolution News, as intelligent design advocates, could run our handy-dandy Design Filters and decide that these structures pass the test: they are not products of chance or natural law, and they contain specified information. But we would want to apply sufficient rigor, because a look at the surroundings with Google Earth shows some parallel lines that could be “natural.” Some of the perfect circles we see are clearly volcanic vents, also not candidates for design. Then there is the issue of distinguishing the ancient “mysterious” structures from a few modern roads and buildings out there.
Assuming our results concur with Kennedy’s, we can also relate to his enthusiasm to find an “explanation for their purpose”. But we know that intelligent design theory does not need to know the purpose of an artifact; it is sufficient to deduce that some purpose or intent was involved. Intelligent design stops when we try to figure out the who and the why. For instance, in cases where we have good reason to think a cosmic designer made something, we go too far in ID to specify it was God, or to presume to know what God’s purpose was. Those questions are better addressed by theologians after the design inference is made.
But we must also clear up another issue as well: what do we mean by purpose or intent? If not careful, we attribute intent to honeybees who build elaborate honeycombs for the purpose of laying their eggs. The living world is rich with complex patterns exhibiting function that result from animal behaviors: bird nests, termite mounds and ant hills, and this striking example produced by a puffer fish as part of its mating dance (see this BBC video). Are we to locate the intention in the tiny brains of bees and ants?
We might argue that the Arabian ‘gates’ show design because they go beyond mere survival needs. But even then, we can’t easily dismiss animal behaviors with that argument, because some animals seem to make artworks of gratuitous beauty. The elegant glass houses of diatoms, for instance, don’t seem to require such elegant geometrical perfection to be functional. Nor do the Golden Ratios of plants that we talked about recently seem necessary for survival.
Evolutionists, in their reductive mindset, are likely to lump human designs into the same basket as termite mounds. Building things is just something the human animal does. Rock structures in the desert are mere consequences of large human brains and evolved behaviors, they might say. In this view, intent and purpose get swallowed up by the all-encompassing blob of natural selection. How do we escape that line of argument? How do we defend true intention for intelligent design?
Nancy Pearcey, a Discovery Institute Fellow and a contributor to these pages, has shown one sure-fire strategy. In her latest book Finding Truth, she argues that if Darwinians want to reduce human purposes to natural selection, then we need to show them that their explanation points both ways. What’s good for the goose is good for the gander: if natural selection produced humans who built the Arabian structures, then it also produced academic professors who write journal papers attributing everything to natural selection. Obviously, such an argument implodes in on itself. The only way to argue for evolution is to plagiarize theistic positions, which take truth and purpose seriously. Without believing in truth and intent, a Darwinian commits intellectual suicide.
Having established that truth and intention cannot be artifacts of chance and natural law, we can employ them to re-examine cases of animal designs. Instead of attributing intent to honeybees, plants, or birds, we can locate the intent in something higher. Our own programmed systems (robots, computer networks, and so on) were intended to function using parts that we arranged for that purpose; the parts would never do those things without our guidance. This distinguishes the ‘human animal’ from the rest of nature without diminishing our physical attributes and commonalities with primates. Bodies enable our human minds to choose to design things.
Since in our uniform experience every system exhibiting functional coherence (to use Doug Axe’s term in Undeniable) — wherein we witnessed the system coming into being — was the product of human intelligent design, we can use the principle of uniformity to infer that a mind was behind the functionally-coherent systems we did not witness coming into being (provided they pass the Design Filter). The designing mind, additionally, must have the ability to apprehend truth and intention as genuine qualities of personhood. (Without that, all explanation comes crashing down.) Any scientist proposing to offer a scientific explanation, therefore, must necessarily presuppose that truth and intention are fundamental properties of intelligent agents.
Looking back at those stone structures decaying in the desert over thousands of years, we can feel some kinship to the makers, even if we don’t know them. Like us, those human beings had minds. Like us, they had purposes. For whatever reason, their intelligent, designing minds set them to work building large rows of stones, some of them almost 1,700 feet long, for reasons we can only guess at. What’s not in doubt is that they had a plan.
Darwinian apologists well behind on their homework
This is embarrassing: “Darwin’s Doubt” debunker is 14 years behind the times
Posted by vjtorley under Intelligent Design
Posted by vjtorley under Intelligent Design
Over at The Skeptical Zone, Mikkel “Rumraket” Rasmussen has written a post critical of Dr. Stephen Meyer, titled, Beating a dead horse (Darwin’s Doubt), which is basically a rehash of comments he made on a thread on Larry Moran’s Sandwalk blog last year. The author’s aim is to expose Dr. Stephen Meyer’s “extremely shoddy scholarship,” but as we’ll see, Rasmussen’s own research skills leave a lot to be desired.
Did Dr. Meyer fail to document his sources?
Rasmussen focuses his attack on chapter 10 of Dr. Meyer’s book, “Darwin’s Doubt.” He writes:
Having read the book, a recurring phenomenon is that Meyer time and again makes claims without providing any references for them. Take for instance the claim that the Cambrian explosion requires lots of new protein folds, from Chapter 10 The Origin of Genes and Proteins:
(Rasmussen proceeds to quote from Meyer’s book, on which he comments below – VJT.)
In the whole section Meyer dedicates to the origin of novel folds, he makes zero references that actually substantiate [his assertion] that the [C]ambrian diversification, or indeed any kind of speciation, or the [appearance of] new cells types or organs, require[d] new protein folds. ZERO. Not one single reference that supports these claims. At first it reads like what I quote[d] above, lots of claims, no references. Later on he eventually cites the work of Douglas Axe that atte[m]pts to address how hard it is to evolve new folds (and that work has its own set of problems, but never mind that). Axe makes the same claim in his ID-journal Bio-complexity papers (which eventually Meyers cites), but in Axe’s papers, that claim is not supported by any reference either. It’s simply asserted as fact. In other words, Meyer makes a claim, then cites Axe making the same claim. Neither of them give a reference.
(N.B. For ease of readability, I have used square brackets to correct Rasmussen’s spelling and punctuation errors, and I have also inserted four extra words, without which his meaning would have been obscure to readers, in the preceding paragraph – VJT.)
Rasmussen repeats his accusation that Dr. Meyer frequently makes claims in his book without providing any references for them, at the very end of his post:
Later Meyer gets a ID-complexitygasm when he asserts, again without any support, that:
“The Cambrian animals exhibit structures that would have required many new types of cells, each requiring many novel proteins to perform their specialized functions. But new cell types require not just one or two new proteins, but coordinated systems of proteins to perform their distinctive cellular functions.”
Where does he get this? His ass, that’s where.
Do new cell types require new kinds of proteins?
I find it quite astonishing that Rasmussen would require documentation for Dr. Meyer’s claim that new cell types would require new types of proteins, for three reasons. First, it’s a well-known fact that each different cell type has different cluster of differentiation proteins. Bojidar Kojouharov, a Ph.D. Student in Cancer Immunology, describes these proteins as follows:
Clusters of Differentiation (CD) are cell surface proteins used to differentiate one cell type from another. Each CD marker is a different surface protein from the others. As such, it will likely have different functions and may be expressed on different cells. Technically, different CD markers don’t really have to have anything in common, other than the fact that they are on the cell’s surface. Usually, it’s safe to assume any Clusters of Differentiation is a protein.
Second, it is widely admitted by authors in the field that the complex organisms which appeared in the Cambrian would have required a host of new cell types. Here, for instance, is what P. V. Sukumaran, of the Geological Society of India, says in his paper, Cambrian Explosion of Life: the Big Bang in Metazoan Evolution (RESONANCE, September 2004, pp. 38-50):
Yet another feature of the Cambrian explosion is the quantum jump in biological complexity. The early Cambrian animals had roughly 50 cell types while the sponges that appeared a little earlier had only 5… (p. 44, sidebar)
Unicellular life is relatively simple; there is little division of labour and the single cell performs all functions of life. Obviously the genetic information content of unicellular organisms is relatively meagre. Multicellular life, on the other hand, requires more genetic information to carry out myriads of cellular functions as their cells are differentiated into different cell types, tissues and organs. But new cell types themselves require specialised proteins, and novel proteins arise from novel gene sequences, that is new genetic information. As the organisms that appeared in the Cambrian explosion had many more novel and specialised cell types than their prokaryotic ancestors, the amount of new genetic information that arose in the Cambrian explosion represents a large increase in biological information. (p. 47)
Third, it turns out that Dr. Meyer provided the very references that Rasmussen chides him for failing to supply, over 14 years ago, in his 2001 paper, The Cambrian Explosion: Biology’s Big Bang, which he co-authored with Paul Nelson and Paul Chien, which is listed on page 471 of the bibliography of Dr. Meyer’s book, Darwin’s Doubt. (Actually, the bibliography cites a later and slightly more polished 2003 version of the same paper.) Allow me to quote from pages 32-33 of the 2001 paper (emphases mine – VJT):
As noted, the new animals of the Cambrian explosion would have required many new cell types and, with them, many new types of proteins acting in close coordination. It follows, therefore, that if the neo-Darwinian mechanism cannot explain the origin of new cell types (and the systems of proteins they require), it cannot explain the origin of the Cambrian animals. Yet given the number of novel proteins required by even the most basic evolutionary transformations, this now seems to be precisely the case.
Consider, for example, the transition from a prokaryotic cell to a eukaryotic cell. This transition would have produced the first appearance of a novel cell type in the history of life. Compared to prokaryotes, eukaryotes have a more complex structure including a nucleus, a nuclear membrane, organelles (such as mitocondria, the endoplasmic recticulum, and the golgi apparatus), a complex cytoskeloton (with microtubulues, actin microfilaments117 and intermediate filaments) and motor molecules.118 Each of these features requires new proteins to build or service, and thus, as a consequence, more genetic information. (For example, the spooled chromosome in a modern eukaryotic yeast [Saccharomyces] cell has about 12.5 million base pairs, compared to about 580,000 base pairs in the prokaryote Mycoplasma.)119 The need for more genetic information in eukaryotic cells in turn requires a more efficient means of storing genetic information. Thus, unlike prokaryotic cells which store their genetic information on relatively simple circular chromosomes, the much more complex eukaryotic cells store information via a sophisticated spooling mechanism.120 Yet this single requirement — the need for a more efficient means of storing information — necessitates a host of other functional changes each of which requires new specialized proteins (and yet more genetic information) to maintain the integrity of the eukaryotic cellular system.
For example, nucleosome spooling requires a complex of specialized histones proteins (with multiple recognition and initiation factors) to form the spool around which the double stranded DNA can wind.121 Spooled eukaryotic DNA in turn uses “intron spacers,” (dedicated sections of non-coding DNA), in part to ensure a tight electrostatic fit between the nucleosome spool and the cords of DNA.122 This different means of storing DNA in turn requires a new type of DNA polymerase to help access, “read,” and copy genetic information during DNA replication. (Indeed, recent sequence comparisons show that prokaryotic and eukaryotic polymerases exhibit stark differences).123 Further, eukaryotes also require a different type of RNA polymerase to facilitate transcription. They also require a massive complex of five jointly necessary enzymes to facilitate recognition of the promoter sequence on the spooled DNA molecule.124 The presence of intron spacers in turn requires editing enzymes (including endonucleases, exonucleases and splicesomes) to remove the non-coding sections of the genetic text and to reconnect coding regions during gene expression.125 Spooling also requires a special method of capping or extending the end of the DNA text in order to prevent degradation of the text on linear (non-circular) eukaryotic chromosomes.126 The system used by eukaryotes to accomplish this end also requires a complex and uniquely specialized enzyme called a telomerase.127
Thus, one of the “simplest” evolutionary transitions, that from one type of single-celled organism to another, requires the origin of many tens of specialized novel proteins, many of which (such as the polymerases) alone represent massively complex, and improbably specified molecules.128 Moreover, many, if not most, of these novel proteins play functionally necessary roles in the eukaryotic system as a whole. Without specialized polymerases cell division and protein synthesis will shut down. Yet polymerases have many protein subunits containing many thousands of precisely sequenced amino acids. Without editing enzymes, the cell would produce many nonfunctional polypeptides, wasting vital ATP energy and clogging the tight spaces within the cytoplasm with many large useless molecules. Without tubulin and actin the eukaryotic cytoskeloton would collapse (or would never have formed). Indeed, without the cytoskeleton the eukaryotic cell can not maintain its shape, divide, or transport vital materials (such as enzymes, nutrients, signal molecules, or structural proteins).129 Without telomerases the genetic text on a linear spooled chromosome would degrade, again, preventing accurate DNA replication and eventually causing the parent cell to die.130
Even a rudimentary analysis of eukaryotic cells suggests the need for, not just one, but many novel proteins acting in close coordination to maintain (or establish) the functional integrity of the eukaryotic system. Indeed, the most basic structural changes necessary to a eukaryotic cell produce a kind of cascade of functional necessity entailing many other innovations of design, each of which necessitates specialized proteins. Yet the functional integration of the proteins parts in the eukaryotic cell poses a severe set of probabilistic obstacles to the neo-Darwinian mechanism, since the suite of proteins necessary to eukaryotic function must, by definition, arise before natural selection can act to select them.
References:
117 Russell F. Doolittle, “The Origins and Evolution of Eukaryotic Proteins,” Philosophical Transactions of the Royal Society of London B 349 (1995): 235-40.
118 Stephen L. Wolfe, Molecular and Cellular Biology (Belmont, CA: Wadsworth, 1993), pp. 3, 6-19.
119 Rebecca A. Clayton, Owen White, Karen A. Ketchum, and J. Craig Ventner, “The First Genome from the Third Domain of Life,” Nature 387 (1997): 4459-62.
120 Stephen L. Wolfe, Molecular and Cellular Biology, pp. 546-50.
121 Ibid.
122 H. Lodish, D. Baltimore, et. al., Molecular Cell Biology (New York: W.H. Freeman, 1994), pp. 347-48. Stephen L. Wolfe, Molecular and Cellular Biology, pp. 546-47.
123 Edgell and Russell Doolittle, “Archaebacterial genomics: the complete genome sequence of Methanococcus jannaschii,” BioEssays 19 (no. 1, 1997): 1-4. Michael Y. Galperin, D. Roland Walker, and Eugene V. Coonin, “Analogous Enzymes: Independent Inventions in Enzyme Evolution,” Genome Research 8 (1998): 779-90.
124 Stephen L. Wolfe, Molecular and Cellular Biology, pp. 580-81, 597.
125 Ibid., pp. 581-82, 598-600, 894-96.
126 Ibid., p. 975.
127 Ibid., pp. 955-975.
128 Ibid., p. 580.
129 Ibid., pp. 17-19.
130 Ibid., pp. 955-975.
And here’s a highly pertinent quote from pages 5-6 of the paper:
Each new cell type requires many new and specialized proteins. New proteins in turn require new genetic information encoded in DNA. Thus, an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information. For example, molecular biologists have recently estimated that a minimally complex cell would require between 318 to 562 kilobase pairs of DNA to produce the proteins necessary to maintain life.20 Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require an amount of DNA greater by several orders of magnitude (e.g., the genome size of the worm Caenorhabditis elegans is approximately 97 million base pairs21 while that of the fly Drosophila melanogaster (an arthropod), is approximately 120 million base pairs.22 For this reason, transitions from a single cell to colonies of cells to complex animals represent significant (and in principle measurable) increases in complexity and information content. Even C. elegans, a tiny worm about one millimeter long, comprises several highly specialized cells organized into unique tissues and organs with functions as diverse as gathering, processing and digesting food, eliminating waste, external protection, internal absorption and integration, circulation of fluids, perception, locomotion and reproduction. The functions corresponding to these specialized cells in turn require many specialized proteins, genes and cellular regulatory systems, representing an enormous increase in specified biological complexity. Figure 5 shows the complexity increase involved as one moves upward from cellular grade to tissue grade to organ grade life forms. Note the jump in complexity required to build complex Cambrian animals starting from, say, sponges in the late Precambrian. As Figure 5 shows Cambrian animals required 50 or more different cell types to function, whereas sponges required only 5 cell types.
(Note: Figure 5 can be viewed in this later version of the paper, where it is labeled as Figure 10 – VJT.)
References:
20 Mitsuhiro Itaya, “An estimation of the minimal genome size required for life,” FEBS Letters 362
(1995): 257-60. Claire Fraser, Jeannine D. Gocayne, Owen White, et. al., “The Minimal Gene Complement of Mycoplasma genitalium,” Science 270 (1995): 397-403. Arcady R. Mushegian and Eugene V. Koonin, “A minimal gene set for cellular life derived by comparison of complete bacterial genomes,” Proceedings of the National Academy of Sciences USA 93 (1996): 10268-73.
21 The C. elegans Sequencing Consortium, “Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology,” Science 282 (1998): 2012-18.
22 John Gerhart and Marc Kirschner, Cells, Embryos, and Evolution (London: Blackwell Science, 1997), p.
121
Did Dr. Meyer distort the words of geneticist Susumu Ohno?
Rasmussen also accuses Dr. Meyer of distorting the words of Susumu Ohno, a geneticist and evolutionary biologist whose work he discussed in chapter 10 of his book, Darwin’s Doubt:
It gets much worse, turns out Meyer is making assertions diametrically opposite to what his very very few references say. Remember what Meyer wrote above?
“The late geneticist and evolutionary biologist Susumu Ohno noted that Cambrian animals required complex new proteins such as, for example, lysyl oxidase in order to support their stout body structures.”
Well, much later in the same chapter, Meyer finally references Ohno:
“Third, building new animal forms requires generating far more than just one protein of modest length. New Cambrian animals would have required proteins much longer than 150 amino acids to perform necessary, specialized functions.21″
What is reference 21? It’s “21. Ohno, “The Notion of the Cambrian Pananimalia Genome.””
What does that reference say? Let’s look:
“Reasons for Invoking the Presence of the Cambrian Pananimalia Genome.
Assuming the spontaneous mutation rate to be generous 10^-9 per base pair per year and also assuming no negative interference by natural selection, it still takes 10 million years to undergo 1% change in DNA base sequences. It follows that 6-10 million years in the evolutionary time scale is but a blink of an eye. The Cambrian explosion denoting the almost simultaneous emergence of nearly all the extant phyla of the kingdom Animalia within the time span of 6-10 million years can’t possibly be explained by mutational divergence of individual gene functions. Rather, it is more likely that all the animals involved in the Cambrian explosion were endowed with nearly the identical genome, with enormous morphological diversities displayed by multitudes of animal phyla being due to differential usages of the identical set of genes. This is the very reason for my proposal of the Cambrian pananimalia genome. This genome must have necessarily been related to those of Ediacarian predecessors, representing the phyla Porifera and Coelenterata, and possibly Annelida. Being related to the genome – possessed by the first set of multicellular organisms to emerge on this earth, it had to be rather modest in size. It should be recalled that the genome of modern day tunicates, representing subphylum Urochordata, is made of 1.8 x 10^8 DNA base pairs, which amounts to only 6% of the mammalian genome (9). The following are the more pertinent of the genes that were certain to have been included in the Cambrian pananimalia genome.”
The bold is my emphasis. I trust you can see the problem here. So, Meyer makes a single goddamn reference to support the claim that the Cambrian explosion required a lot of innovation of new proteins, folds, cell-types and so on. What do we find in that references? That Ohno is suggesting the direct opposite, that he is in fact supporting the standard evo-devo view that few regulatory changes were what happened, that the genes and proteins were already present and had long preceding evolutionary histories.
Once again, Rasmussen hasn’t done his homework. A little digging on my part revealed that Dr. Meyer had previously discussed the Dr. Ohno’s claims at considerable length and responded to those claims, in his 2001 paper, The Cambrian Explosion: Biology’s Big Bang, which he co-authored with Paul Nelson and Paul Chien (bolding mine – VJT):
Ironically, even attempts to avoid the difficulty posed by the Cambrian explosion often presuppose the need for such foresight. As noted, Susumo Uno, the originator of the hypothesis of macroevolution by gene duplication, has argued that mutation rates of extant genes are not sufficiently rapid to account for the amount of genetic information that arose suddenly in the Cambrian.114 Hence he posits the existence of a prior “pananimalian genome” that would have contained all the genetic information necessary to build every protein needed to build the Cambrian animals. His hypothesis envisions this genome arising in a hypothetical common ancestor well before the Cambrian explosion began. On this hypothesis, the differing expression of separate genes on the same master genome would explain the great variety of new animal forms found in the Cambrian strata.
While Ohno’s hypothesis does preserve the core evolutionary commitment to common descent (or monophyly), it nevertheless has a curious feature from the standpoint of neo-Darwinism. In particular, it envisions the pananimalian genome arising well before its expression in individual animals.115 Specific genes would have arisen well before they were used, needed or functionally advantageous. Hence, the individual genes within the pananimalian genome would have arisen in a way that, again, would have made them imperceptible to natural selection. This not only creates a problem for the neo-Darwinian mechanism, but it also seems to suggest, as Simon Conway Morris has recently intimated,116 the need for foresight or teleology to explain the Cambrian explosion. Indeed, the origin of a massive, unexpressed pre-Cambrian genome containing all the information necessary to build the proteins required by not-yet-existent Cambrian animals, would strongly suggest intelligent foresight or design at work in whatever process gave rise to the pananimalian genome. (pp. 31-32)
In short: Dr. Meyer was not only aware that Dr. Ohno had proposed the existence of a pananimalian genome; he also explicitly referred to it in his 2001 paper, in order to demonstrate that Intelligent Design would be the best explanation of such a genome.
I’ll leave it to my readers to decide whether it is Dr. Meyer or Rasmussen who is guilty of “extremely shoddy scholarship.” Let me conclude by recalling an old saying: “People who live in glass houses shouldn’t throw stones.”
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