We see that the Darwinian world view must look upon the present sentimental conception of the value of life of the human individual as an overestimate completely hindering the progress of humanity.... The state only has an interest in preserving the more excellent life at the expense of the less excellent.
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Darwinists Refute ID Irreducible Complexity Argument 10/31/2005
The origin of novelty, the development of new arrangements of interlocking parts that some call irreducibly complex, can only be understood in the light of the last 20 years of research in cell biology and development.At first glance this sounds very Lamarckian, so lets examine a book review by another evolutionist who published his remarks in the journal Cell.1 Douglas Erwin of the National Museum of Natural History in Washington DC was not all that impressed with their arguments. In fact, he thinks the authors didnt to their homework researching the abundant literature on the subject. He did, however, appreciate the magnitude of the problem the book tried to address:
The diversity and complexity of life on Earthfrom bacteria and fungi to plants and animalssuggest the generation of remarkable variation upon which natural selection can act. But how do new traitsnew morphological architectures (bodyplans), developmental processes, and behaviorsarise? Did the vertebrate brain and neural crest arise through processes that are different from those that generated new hairs on the legs of the fruit fly? Can major evolutionary transitions in the history of life be explained by random variationvariation that is random with respect to the future needs of the organismfiltered through the process of natural selection? These questions are not new, but the promise of a more mechanistic basis for answering them through comparative developmental biology imbues them with a fresh urgency.Erwin summarizes their argument: animals have evolved to evolve. Variations acted on by natural selection have produced phenotypic plasticity or evolvability they ability to adapt to changing environments (see 08/04/2004 entry on this idea).
In Kirschner and Gerharts view, there are four aspects of gene regulation and development in animals that constrain the direction of heritable variation. These are the extensive conservation across metazoa of certain regulatory patterns; a modular pattern of organismal design; what the authors term weak linkages in gene regulation, caused by, in their view, regulatory interactions that do not specify outcomes; and nondeterministic outcomes of development.To Erwin, what they are saying is, natural selection needs some help. He denies it. Natural selection can get along just fine without random genetic variation that is biased toward viability, functional utility, and relevance to environmental conditions. He thinks that Kirschner and Gerhart dont understand what random means:
This is the first place where the authors get into trouble; for through much of the book they seem to fundamentally misunderstand how evolutionary biologists use the term random. By random mutation, evolutionary biologists mean random with respect to the adaptive needs of the organism, not, as the authors would have it in the early part of the book, completely random in the sense that many nonevolutionary biologists may think of the word random. One of Charles Darwins key insights was that the combination of undirected mutation and natural selection is a powerful positive force for evolutionary creativity (and not, as so many later biologists have suggested, merely a negative force). Evolutionary biologists have long understood that the nature of variation depends critically on what has already evolved. Indeed, there is a rich literature discussing how phylogeny, function, structure, and other features constrain evolutionary variation. Kirschner and Gerhart ignore this uncomfortable fact, dismissing constraint as a minor effect, or trivial, for example, in explaining why mollusks (sic) and echinoderms were less able to evolve wings than vertebrates. They refer to variation as random alterations that can have little positive impact or that lead to catastrophic failure. This results in the appearance of some odd comments as, for example, when the authors claim that evolutionary biologists do not commonly appreciate... that present-day organisms come from previous organisms. Indeed.Want to meet a few? he asks in effect. He accuses them of a limited view of the evolutionary literature on the subject which undercuts most of their own arguments in favor of facilitated variation.
Erwin puts this new book into a new genre of books finding the current model of evolution incomplete. Most other authors, however, have had the good sense not to proclaim a major new scientific theory or an original, far-reaching recasting of evolutionary theory, as these do in their Preface. Erwin mentions several books that do a better job attempting to solve problems of evolutionary innovation that remain unresolved by the Modern Synthesis, the reigning paradigm of evolution developed in the 1940s by Mayr, Simpson, Wright, Haldane, Dozhansky, Fischer, and others. He is not sure, though, that any combination of these books amounts to a revision of the Modern Synthesis.
Looking at the thesis of the book in more detail, Erwin cuts to the chase. He says that Kirschner and Gerhart dont recognize the effect of environment on variation.
Presenting no evidence, they claim that these waves of innovation are not linked to changes in the physical environment. In fact, one of the most exciting areas of current research addresses how the origin and spread of these innovations are linked to a variety of geochemical, climatic, and other changes. These core processesDNA, RNA, and protein synthesis, formation of the cytoskeleton, and limb patterninghave descended relatively unchanged since they first arose.Erwin does agree with them on one point: most evolution within the Animal Kingdom since the Cambrian radiation of metazoans involved the carefully regulated deployment of these core processes, and that environmental conditions can become a rich source of new phenotypes that can become developmentally integrated and viable. For instance, mutations might exhibit exploratory behavior and the most useful will become stabilized:
Kirschner and Gerhart invoke exploratory behavior as a means of avoiding what they view as an otherwise insurmountable difficulty: that novelty appears to require multiple, correlated changes from phenotype to function.Does a bacterial flagellum come to mind here? Erwin also likes their wonderful and most appropriate term for the compartmentalization of network modules: invisible anatomy. Here he praises the book:
The most important part of this book is, in my view, the authors description of the evolutionary significance of the interactions between compartments and the conserved regulatory networks that underlie them via weak linkages [i.e., signals that trigger a response without specifying information about what the response should be]. Although the authors do not emphasize this sufficiently (at least for a paleontologist), this network of relationships imposes a developmental reality to the architectural forms described as body plans and generally characterized within Linnean systematics as phyla and classes. As Kirschner and Gerhart note, this modularity of design often allows relatively independent evolution of different body parts without greatly increasing the coordination among them. The gills, paddles, mouthparts, claws, and walking legs of various arthropods are all modifications of a single ancestral structure. The modularity of arthropod body plans has enabled the rapid adaptation of limbs without inhibiting the workings of the whole animal.Now, to the troubling parts of the book. Erwin is glad they have tackled one of the most challenging issues in evolution, and appreciates their insights as far as they go and as incomplete as their theory is. But he criticizes the lack of justification and depth of detail that leave far too much to the imagination of the reader. The book, therefore, feels more like a vision of where the field should go rather than a thoroughly constructed theory of the origins of phenotypic novelty.
To their credit, Kirschner and Gerhart tackle the problem of phenotypic novelty more forthrightly than other revisionist books like those of the late Stephen Jay Gould. This leads Erwin to list some of the outstanding problems. Some seem strong enough to make one wonder if evolutionary theory has ever really addressed the core questions Charles Darwin set out to solve:
The generation of morphological variants is a critical issue, and several of these book authors have raised important questions and proposed new viewpoints. But the generation of variation is only the beginning of the problem of evolutionary novelty. Novel phenotypes succeed or fail based on their ecological relationships with other organisms and with the physical environment. This ecological dimension is conspicuously lacking in these books, yet we cannot really understand novelty without it. In particular, evolutionary biologists need to address such issues as how phenotypic space expands, how new niches are constructed, and related ecological events.One thing Erwin is sure of: in spite of all these fundamental issues challenging evolutionary theory, no one outside the Darwinian camp need apply:
Is the neo-Darwinian view of evolution in need of reformation? Certainly the diversity of rumblings indicates some degree of unhappiness, but evolutionary biologists have regularly published new models of evolution since the late 19th century (see Bowler, The Eclipse of Darwinism, Johns Hopkins, 1993). Is there reason to think that our view of evolution needs to change? The answer is almost certainly yes, although not, as the purveyors of creationism/intelligent design would have it, because the reality of evolution is under question. Rather, we need to revise our view of evolution to reflect a more detailed understanding of how genetics and development both allow and facilitate phenotypic variation, to take into account the temporal dynamics of changes in the environment, and to incorporate the likelihood that there is selection and feedback at multiple levels (cell, tissue, organism, clade). The central issues that need to be incorporated into evolutionary theory are the origin of phenotypic novelty and the discontinuous patterns of appearance of new phenotypes.Now wait wasnt that EurekAlert said that this book solves, putting to rest the claims of the intelligent design movement? At the end of Erwins book review, is he still at square one? He dismisses The Plausibility of Life as an entertaining read of only introductory value into recent trends in evolutionary theory. In sum, it contains a lot of sound and fury, signifying little: But with its sometimes troubling limitations, the book falls short of the major new theory that the authors promise in their introduction.
1Douglas H. Erwin, A Variable Look at Evolution, Cell, Volume 123, Issue 2, 21 October 2005, Pages 177-179, doi:10.1016/j.cell.2005.10.003.
If you get a kick out of watching villains shoot themselves in the foot, you will rollick with this entry. We provided extended quotes to let you savor the moment. Here is the biggest problem in the history of evolutionary thought: the abrupt appearance of new body plans and complex structures with interrelated parts each necessary for function. The Darwinists realize that the creationists and intelligent design proponents have been hammering them on the fact that they have no answers. And finally, here was the new book that EurekAlert said was going to put those criticisms to rest once for all. And what is it? Blind search! Exploratory behavior is putting feelers out in the dark and seeing if anything sticks. But then what is leading the blind: the blind random variations in the molecules, or the blind random variations in the environment? Can anyone really believe that a succession of blind actions will produce irreducibly complex systems like wings, gills, paddles, mouthparts, claws, legs, and rotating motors of exquisite design and efficiency? If this book had the answer, Erwin would not have left it (the origin of phenotypic novelty) and the discontinuous patterns of appearance (e.g., the Cambrian Explosion), as unsolved problems. Then Erwin did us the favor of pointing out that all the other books dont solve them, either though they have been trying since the 19th century. [Quiz question: in what century did Charles Darwin write his famous book?]Stupid Evolution Quote of the Week: In a detailed article in the journal Cell1 about ATP synthase, the smallest rotary motor that works in both directions with high efficiency and drives the synthesis of up to 40kg of ATP per day in a resting human, Yi Qin Yao, Wei Yang and Martin Karplus only mentioned evolution once. Here it is: Interestingly the conformational changes in the beta subunits have been shown to correspond to their lowest frequency normal modes. This implies that the structure of the protein is designed by evolution such that the motions required for its function can take place with a low energy cost. (Emphasis added).
1Yao et al., A Structure-Based Model for the Synthesis and Hydrolysis of ATP by F1-ATPase, Cell, Volume 123, Issue 2, 21 October 2005, Pages 195-205, doi:10.1016/j.cell.2005.10.001.
Next headline on: Cell Biology Dumb Ideas
Baloney Detecting Exercise: Alan Elsner of Reuters tries to make the
case that the U.S. is becoming hostile to science largely because of its
opposition to evolution (see MSNBC
Replace the word scientists by elitists and the article makes a lot more sense. Conservatives love good science, but they have this thing about leftist liberals in academia (see 12/02/2004) who always seem to take the far-left position on everything and try to cloak it in scientific robes. Will education really suffer if the leftists lose power? Will students be deprived if Darwinist lies are expunged from science textbooks? Will hearing that alternatives to evolutionary theory exist make students bored with science? See non-sequitur in the Baloney Detector.Take Their Word For It: Venus was formed about the same time as Earth, around 4.6 billion years ago, but you wouldnt know from looking at it. Source: Space.com.
Is Darwin or ID the New Halloween Spook? 10/30/2005
If the Darwin costume is scaring the children, acting panicky or hysterical only makes it worse. Which side wants to keep high school students in the dark, and and which side wants to turn on the lights? Which side wants to shield impressionable elementary students from pedagogical tricks, and treat them to the truth? Which side is shrieking and threatening, and which side is calmly asking for an enlightened discussion of the facts? The thing apparently scaring the Darwinists the most is that the morning twilight reveals their long night on Bald Mountain is coming to an end, and that can only mean one thing: Thanksgiving is near.Georgia Tech Bioneers Plagiarize Mother Nature to Advance Science 10/29/2005
Copying the ideas of others is usually frowned upon, but when it comes to the work of Mother Nature, scientists are finding they can use nature as a template. Thats how an interesting press release from Georgia Tech begins (reproduced on EurekAlert) about a new center on campus called the Center for Biologically Inspired Design (CBID). This new multidisciplinary research center (see a similar story about Caltech, 06/25/2005) seeks to explore natural solutions to physical problems and apply them to human engineering projects. This approach is often called biomimetics, or the imitation of nature (for examples, see 07/16/2005 on sharks and beavers, 10/05/2004 on pine cones, 09/21/2004 on termites, 08/27/2002 on geckos, and many others in the Amazing category of Chain Links). A well-known example is the invention of Velcro® by someone who became intrigued by the sticking ability of cockleburs (see Waynes Word for a popular account). The press release describes the origin and purpose of the CBID:
An interdisciplinary group of scientists and engineers at the Georgia Institute of Technology recently formed the Center for Biologically Inspired Design (CBID) with the goal of capitalizing on the rich source of design solutions present in biological processes. The researchers believe nature can inspire design and engineering solutions that are efficient, practical and sustainable and thus have the potential to greatly enhance new technologies, materials and processes.The center has 17 initial members, but expects to grow. One of its goals is to extend its discoveries for public benefit: CBID researchers also want to communicate to government and industry officials that nature can provide unique design solutions to the problems they must address.
The center also reaches beyond to a network of citizens, scientists and entrepreneurs that explores practical solutions adapted from natural systems and native cultures and then applies these solutions to fundamental environmental, economic and social challenges. The name for this network is: Bioneers. An invited talk by the Bioneers Southeast Forum is being held today at the Atlanta campus of Savannah College of Art and Design
Any examples from this new research approach? Sure: learning navigation from honeybees (02/15/2005), studying orienteering in lobsters (01/06/2003), imitating materials manufacture by diatoms 10/01/2004), and studying neuromechanical principles of animals (02/09/2005) to build better robots and prosthetics for a few. The skys the limit. Subjects for investigation abound: the gathering and transporting of energy, remote sensing, locomotion, system organization, and eco-friendly technology. One professor is studying fish ears to build an auditory retina.
Another ancillary benefit will ensue from this approach, according to one of the CBID biology professors: biomimetry even offers inspiration for the way students and faculty learn.
OK, Intelligent Design community, charge again! (See 06/25/2005 commentary.) This is exactly the kind of new infusion of creative energy and practical benefit that a design perspective can bring to science and technology. Despite the humorous reference to Mother Nature, this approach does not need to focus on the identity of the Designer to parlay design detection (a fundamental principle of intelligent design) into fruitful scientific research. This is not to say that knowing the Designer personally would be a hindrance, obviously but it demonstrates that design science can produce a cooperative enterprise among diverse people regardless of their religion. Maybe someday the plagiarism will be rectified by appropriate attribution. For now, though, the ACLU and other religion-hating groups would not be able to get their bony fingers on the CBID, because members only need good observational and engineering skills. Simultaneously, the ability to tell spooky Darwinian stories would drop off the list of qualifications. Are Georgia Tech and Caltechs new multidisciplinary centers for biological design indicating that a major shift in scientific research is underway? Is there a promised land beyond the crumbling, haunted remains of Down House? Bioneers! O Bioneers! The fruitful land, the frontier of discovery and happiness, belongs to you.Charity? Chimps Dont Get It Nor Give It 10/28/2005
The science news media took note of an experiment showing that chimpanzees dont care to share, even when it costs them nothing (see the BBC News and Science Now, Tightwad Primates). Joan Silk and a team at UCLA created an apparatus where a chimp could pull one rope to get a treat for itself, or pull another to both get one and give one to another chimp in an adjacent cage. Even when the neighboring chimp begged for the reward, the chimps tested were no more likely to share than to be selfish. They could see it cost them nothing to pull the rope that shared the treats, but they didnt seem to care; half the time they would pull the selfish rope, whether alone or with the hopeful neighbor. Humans, by contrast, will give to charities or donate blood to help people across the world they will never meet. National Geographic titled their report, Uncaring Chimps May Shed Light on Humans, Study Says.
It may shed light on humans, all right, but not in the way evolution-obsessed National Geographic wants. It underscores the difference between humans and animals. Even though the study was investigating the evolution of primate behavior, they had to admit that altruistic behavior appears to be a uniquely human trait.Its Official: Mangroves Would Have Prevented Most Tsunami Damage 10/28/2005
EurekAlert summarized a paper in Science1 that confirmed an earlier claim (02/10/2005) that intact mangrove forests along the Asian coastlines would have prevented the bulk of damage and death from last years mega-tsunami. A large, diverse research team from seven nations estimated that more than 90% of the damage could have been prevented by the buffer effect of mangrove forests absorbing the wave energy. See also Science News,2 that said that in areas of maximum tsunami intensity, little could have prevented catastrophic destruction; but areas hit by 4- to 5-meter waves were modest enough for vegetation to make a difference.
Mangroves grow naturally in coastline thickets about 30 trees per 100 square meters, but have been drastically reduced by business interests to the point of becoming an endangered species. The cleared coastlines were among the hardest hit by the waves. For instance, two shoreline villages unprotected by mangroves in India were obliterated, whereas three other villages behind a screen of mangroves hundreds of meters thick survived.
The affected nations are now looking again at restoring this natural protection zone, this living dyke, realizing that mangroves will not only provide defense from the next extreme storm surge, but also enrich local fisheries and habitats of many native species.
1Danielson et al., The Asian Tsunami: A Protective Role for Coastal Vegetation, Science, Vol 310, Issue 5748, 643, 28 October 2005, [DOI: 10.1126/science.1118387].
2Ben Harder, Breaking Waves: Mangroves shielded parts of coast from tsunami, Science News, Week of Oct. 29, 2005; Vol. 168, No. 18, p. 276.
Famous last words: Look at this mess of trees blocking our view of the sea. How are we supposed to get our boats on the water through all that tangled up wood in the way? Those mangroves are such a pain. Cut em all down. Ill start a fishery, and Sam, think of all the money you could make with a beach resort hotel over there.Red Blood Cells Are Master Contortionists 10/28/2005
Biophysicists have analyzed why red blood cells are able to squeeze through tight spaces on their journeys through our tissues, reports the UCSD Jacobs School of Engineering. Their membranes contain a network of 33,000 hexagons arranged in a complex geodesic dome formation. Each hexagon vertex is joined with flexible lines to a central maypole-like proto-filament, giving it the ability to twist and contort without breaking. This contortionist ability serves another purpose beyond just enabling the cell to get through tight spaces: it also helps squeeze out the oxygen into the tissues. Despite being twisted, folded, flattened or stretched, the geodesic structure permits the cell to pop back into its familiar biconcave shape.
The press release states, Their paper in Annals of Biomedical Engineering uses aeronautical terms commonly used to describe the changing position of an airplane to explain how the six attached spectrin fibers make a proto-filament swivel and flip. Science Now took note of this study on bendable blood.
The shape of red blood cells is also the optimum for maximizing surface area (for diffusion) without sacrificing volume (for payload). If they were rigid disks, they would get stuck, starving tissues of oxygen and causing death. As you work today, think about those little erythrocyte spelunkers making their rounds, delivering the goods from that last breath of air to every cubic micrometer of your body. The Creator thought of everything.Emperor Penguins Get More Respect 10/27/2005
A handsomely-dressed emperor penguin made the cover of Science News this week. Gerald Kooyman of Scripps Institute is gratified over the success of the documentary March of the Penguins; Ive been telling people theyre remarkable for years, he said. In the article, Susan Milius brought out several additional amazing facts not mentioned in the film.
1Susan Milius, How can emperor penguins live like that?, Science News, Week of Oct. 22, 2005; Vol. 168, No. 17 , p. 26.
Fortunately, Susan Milius did not try to speculate on how the emperor penguin evolved. If you tried to count how many lucky mutations would be needed to evolve from a dinosaur to an early bird to an emperor penguin, what number would you come up with? Hundreds? Thousands? Tens of thousands? Its a total remake. The biochemistry of the cell, the oxygen handling capabilities, the pressure protection and scuba gear, the dive suit, the lungs, the bones, the dietary adaptations, core body heat, timing of the molt, ability to waddle upright, the stiff body and flippers, the incubating patch and tough feet, eyes adapted to deep underwater vision, navigating ability over vast distances on ice and in the sea and these are just some of the physical changes that the ambitious dinosaur would need.Cellular Black Box Reveals Precision Guidance and Control 10/27/2005
Amazing discoveries about the cell are being made each week. Its a shame more people dont hear about them. They are usually written up in obscure journals with incomprehensible jargon, but when explained in plain English, the findings are truly astounding. Not long ago, the cell was a black box, a mechanism of unknown inner workings that somehow survived and reproduced. Only recently have imaging techniques allowed us to peer inside the box at the nanometer scale (one nanometer is a billionth of a meter) and see what is going on. Prepare to be astonished.
A fundamental shift in thinking about cellular processes has occurred since the structure of DNA was elucidated in the 1950s, and has been accelerating ever since. What used to be mere chemistry is now mechanics; what used to be imagined as fluids mixing in a watery balloon is now programmed robotic machinery. Cells dont just perform chemical reactions like we did in high school, pouring mixtures together and seeing if they explode or not. Its more like robotics, and is properly known these days as biophysics. Cells are not just tossing ingredients together, but guiding them into place with motors, pivots, guardrails and inspectors.5 The cell is engaged in precision manufacture with molecular machines and motorized transport. The coolness factor of these molecule-sized gadgets would blow away any competition in Popular Mechanics if they could be appropriately visualized and described. Lets try with some recent examples.
Though the articles valiantly attempt to describe what happens at these submicroscopic levels, the subject matter would greatly benefit from top-notch animation. Microscopic imaging technology keeps improving, though; some day soon, it may be possible for scientists to watch the machinery of the cell at its own nanometer scale in real time.
1Sanbonmatsu et al., Simulating movement of tRNA into the ribosome during decoding, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0503456102, published online before print October 25, 2005.
2Kim et al., Probing the active site tightness of DNA polymerase in subangstrom increments, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0505113102, published online before print October 25, 2005.
3Myong et al., Repetitive shuttling of a motor protein on DNA, Nature 437, 1321-1325 (27 October 2005) | doi: 10.1038/nature04049.
4Eckhard Jankowsky, Biophysics: Helicase snaps back, Nature 437, 1245 (27 October 2005) | doi: 10.1038/4371245a.
5This is not to say that biomolecular machinery looks like human machinery. Straight lines and geometric shapes are rare; tRNA entering a ribosome looks like spaghetti in a blender to an untrained eye. In addition, at the nanometer scale, molecules are subject to the random vibrations of Brownian motion. It has taken decades of careful research to tease out the order and intricacy of the cells moving parts. Nevertheless, the language of motors and machines in the literature is apt and ubiquitous, as is the language of physics (piconewtons of force, thermodynamics, translational motion in nm/s and rotational motion in Hz or rps). Human engineers are trying to emulate some of these machines in the new science of nanotechnology.
6Nicastro et al., 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography, Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0508274102, published online before print October 24, 2005.
These are just a few of the reasons students should be allowed to hear about intelligent design. Darwin? He was just an old Victorian who didnt know anything about this. If he had, he might have decided to stick with his training to become a country parson after all. This is the 21st century, folks: the age of nanomachinery and biophysics. Enjoy!Darwinian Fitness/Selection Studies Lack Real-World Experimental Verification, Produce Contradictory Results 10/26/2005
Evolution: Do Bad Husbands Make Good Fathers? is the provocative title of an article in Current Biology1 that conceals the real subject. The first paragraph of the article by David J. Hosken and Tom Tregenza explains the title:
Males sometimes harm their mates as they seek to maximise the number of offspring they sire. But are females really suffering or do the benefits of having sons that inherit their fathers manipulative traits make up for the costs? Three recent studies provide the first hard data addressing this issue, but they differ in their conclusions. (Emphasis added in all quotes.)The article is deeper than a discussion of bad dudes; it is an analysis of the idea of sexual selection what to Darwin was the second most effective agent of evolutionary change after natural selection. (The harmful males under investigation, by the way, are fruit flies, so not to worry, ladies.) Their critique of sexual selection experiments, however, applies equally well to natural selection experiments.
Hosken and Tregenza are not even sure that harmful males could drive the evolutionary process. They listed three reasons why the direct costs probably outweigh any indirect benefits.2 (Evolutionary benefits, after all, must persist in the grandchildren.) The question most interesting in this article is: has sexual selection theory ever been convincingly demonstrated in the wild? Theory is all very well, they say, but as critics have repeatedly pointed out what we really need are good data. The question implies a deficit in that regard even when including the three recent studies that provided the first hard data.
That remark in the article begins a series of doubts over whether experimenters really know anything about selection natural or sexual. Worse, the authors throw doubt on the validity of measuring fitness, arguably the most important parameter in all of Darwinian theory. In mentioning three studies (the ones that differ in their conclusions) they note in passing that one of them sidesteps many of the problems associated with measuring fitness. None of the three studies seems to succeed. The first tries to see if the harm caused by the males is compensated in other ways; the second tries to measure total fitness in a laboratory setting. These two studies produced opposite findings. So what are we to conclude, they ask? Watch out: Perhaps, the main lesson is just how difficult it is to measure something as slippery as fitness.
They turned to the third study, which supposedly sidestepped many of the problems. It found a possibility that the fitness cost of harmful males might be compensated for by indirect benefits. But this study had other problems. It was conducted in a very artificial laboratory environment not out in the real world. They question whether scientists have ever rigorously determined how sexual selection might operate where it counts in nature:
The population was established over 300 generations ago and has been maintained continuously at high population size to retain genetic diversity. The authors claim that this approach means that the flies have had time to become adapted to the laboratory. Although this may be true in the sense that alleles present at low frequencies in the wild population that are beneficial in the lab can be expected to have raced to fixation, it cannot be true in the broader sense of gradual evolution through new mutations. A small glass tube in which males and females are forced into close proximity and walk around on a sea of food bears little resemblance to the varied natural environments where D. melanogaster are found, and it is safe to assume that there will be a continual stream of new mutations that prove beneficial on this laboratory island. Indeed, recent work documents on-going evolution in fly populations maintained in the lab for over a 1000 generations. This constant adaptation to the lab may mean that naturally selected differences between individuals are much more important than sexually selected differences, but whether this is the case in the wild is a point of contention. A second issue is that the lab is particularly unusual in relation to conflicts over mating because of the high-density housing conditions and females cannot escape from males since they are robbed of their major natural defence, which is to simply fly away....One begins to wonder if all this talk about mean-old males, for instance, is an artifact of the lab setup. After all, how would humans get along after being packed shoulder-to-shoulder in prison for 1,000 generations? That question aside, Hosken and Tregenza now hit home and hard. Sexual selection theories need more scientific rigor, and their ending paragraph indicates that convincing experiments have never yet been done.
But we still have no clear idea what the relative magnitude of direct and indirect effects are generally.2 If we are really going to move this debate forward and out of the lab, incorporating the full gamut of costs and benefits of sexual selection, then systems are needed where trans-generational fitness can be measured in nature. Tellingly, in one of the few long-term studies of organisms in the wild, sexual selection is reported to have no fitness consequences, which suggests either the equilibrium situation Fisher envisaged (where the benefits of choice are balanced by natural selection costs), or perhaps that the costs and benefits of sexual selection alone are balanced. If this is the case, and costs generated through sexual conflict are balanced by benefits through traditional sexual selection mechanisms, then we may not expect sexual selection to drive rapid evolutionary change. Determining how commonly males impose serious costs on females without compensatory benefits in nature is the next major challenge in the study of sexual conflict.One interesting footnote. Want to know what they were referring to in one of the few long-term studies of organisms in the wild? Check the references: it was Peter and Mary Grants 2002 study of the Galapagos finch populations, entitled, Unpredictable evolution in a 30-year study of Darwins finches.
1David J. Hosken and Tom Tregenza, Evolution: Do Bad Husbands Make Good Fathers? Current Biology, Volume 15, Issue 20, 25 October 2005, Pages R836-R838.
2For information on the impact of indirect genetic effects on natural selection (i.e., slippage on the treadmill), see these entries: 03/17/2003, 07/23/2003, 10/19/2004.
It is said that those who respect the law and love sausage should never watch either being made. The same could be said of Darwinian theory. Its packaged in the textbooks nice and neat, but inside it is full of baloney, fat, and filler, the composition of which you would not want to know.Dispute Over Hobbit Man Intensifies with New Bones 10/25/2005
The debate over the status of Homo florensiensis has not calmed down (see 09/28/2005), even with the discovery of more bones in the Ling Bua cave on the island of Flores as announced in Nature (437, 1012-1017 (13 October 2005) | doi: 10.1038/nature04022). Michael J. Morwood and colleagues are still sticking with their identification of it as a new species, and are even claiming the little humans had affinities with the Australopithecines. This would mean that they evolved into a species of Homo independently, developing human-like characteristics and even learning to use stone tools by convergent evolution.
H. floresiensis diminutive stature, long arms, and nearly chimp-size brain resemble body proportions of australopithecines, Morwood says. That group of human ancestors lived more than 2 million years ago. The Flores population may have directly evolved into a Homo species from an unknown Asian australopithecine, Morwood speculates. (Emphasis added.)Bruce Bower in Science News, however, stressed that the young dates of the bones 12,000 years, by radiocarbon dating indicate this population survived much longer than originally believed. (The new arm bone dates at 15,000 years, while the new jaw dates to 12,000 years; the original find was dated at 18,000 years, with some bones thought to be as old as 95,000 years.)
Other scientists claim Morwood et al. misidentified them as a new species, and argue, instead, that the skull represents a true Homo sapiens with microcephaly. Robert D. Martin (Field Museum, Chicago) said that a small-brained non-human creature could not have made the sophisticated stone tools found among the remains. Robert B. Eckhardt (Penn State) agreed, claiming that Morwood had underestimated the brain and body size of the population. He said, Im absolutely, totally confident that H. floresiensis will not last.
When Homo florensiensis gets renamed as Homo sapiens that lived in modern times, remember the fanfare and chutzpah displayed by the evolutionary paleoanthropologists over this discovery. Nature and other Darwin foghorns were cocky they had another missing link with which to hammer the creationists. Remember also the incredible leap of imagination that Morwood et al. asked us to believe, that a population of Lucys children moved to Indonesia and evolved into tool-making modern humans independently. The date of 12,000 years for some of the bones must have been a staggering disappointment to the Darwinists. The true date is most likely much less than that. Maybe a living Hobbit will sneak up behind them on Oct. 31 and scare the living daylights out of them or rather, into them.Extraterrestrials Likely to Be Unicellular 10/25/2005
An AP story printed at HeraldNet jokes that extraterrestrial life probably wont look like the negligee-clad Number 6 from [Battlestar] Galactica, the television series that features a genocidal war between humans and their robot creations. Instead, according to the authors of a new book about extraterrestrial life, you would need a microscope to see it. Seth Shostak of SETI Institute, however, only partly agrees. Most worlds would be sterile, and most with life would have unicellular life but with hundreds of billions of planets in our galaxy, he is confident some will have aliens able to carry on a conversation. Dirk Schulze-Makuch and Louis N. Irwin, authors of Life in the Universe, suggest Titan as a good bet for alien life of the microbe kind.
This article has all the usual airy SETI fluff. It is pathetic to see these aimless wanderings in speculation space get associated with science. Life in the Universe was inspired by Star Trek, not chemistry, physics, biology or mathematics. No other religion than secular materialism could get away with scientific carelessness at this level. It could be termed rigor mortis.Intelligent Design War Rages 10/24/2005
Because of the high-profile Intelligent Design trial in Dover, Pennsylvania, the news media and scientific societies are all discussing Darwin vs Design with fervor.
Something is strangely missing in all these reports. No Darwinists seem to be defending any evidence that humans have bacteria ancestors. It seems to be all about power. (Social Constructivists, dont get any ideas.) The ACLU may silence a Behe, but if intelligent design is built into the fabric of the universe, 7,000 Darwinists cannot fight it any more than they can stop a glacier. Same advice still applies: watch for flying baloney, keep away from the heat, know history, re-read If by Kipling, have a deep and abiding respect for brute facts, and fear not the wroth of the people of froth.Archaeopteryx Meets Its Younger Grandpa, and Other Flights of Fancy 10/24/2005
Science Now said that a slightly embarrassing gap in the fossil record has been filled by a find in Wyoming. The oldest known bird, Archaeopteryx was older than its presumed ancestors, the Maniraptorans, its closest dinosaurian relatives. A team near Thermopolis, Wyoming found a maniraptoran dating from about the same time as Archaeopteryx. This new fossil begins to fill the time gap between bird fossils and their closest dinosaur relatives. The team feels this supports the idea that flight evolved from the ground up.
Another team thinks they have figured out the foot feathers on the strange Chinese fossil Microraptor gui (see 05/19/2003). MSNBC News reported that a Texas Tech team believes the foot feathers formed another flight surface, making the animal fly like a biplane. EurekAlert says the Wright Brothers have been upstaged. Sankar Chatterjee of the Texas Tech group remarked that The biplane wing configuration was probably a very first experiment in nature, paralleling the human design of flight. It is intriguing to contemplate that perhaps avian flight, like aircraft evolution, went through a biplane stage before the monoplane was introduced, said Chatterjee. It seems likely that Microraptor invented the biplane 125 million years before the Wright 1903 Flyer.
These researchers feel it was unlikely Microraptor could have run along the ground with its foot feathers, and must have taken off from high branches. The team feels this supports the idea that flight evolved from the trees down.
We dont think that Wilbur and Orville would be flattered by the suggestion that their invention was the product of blind, unguided processes of evolution. Whatever Microraptor gui was, or how it lived, it was not an experiment. Chance does not do experiments. Humans sometimes do, but they more often stumble around in their own imaginations.Listen to Yourself Evolve 10/23/2005
A pretty gene is like a melody, decided Mary Anne Clark at Texas Wesleyan University, so she gave life to musicliterally. She translated the structure of proteins into musical notes so that she could hear protein songs, reported National Geographic News.
By listening to the songs, scientists and students alike can hear the structure of a protein. And when the songs of the same protein from different species are played together, their similarities and differences are apparent to the ear. (Emphasis added in all quotes.)That leads us to the Stupid Evolution Quote of the Week: Therefore, Clark said, by playing the beta globin song for a human and tuatara, an ancient three-eyed lizard, people can hear the process of evolutiona variation on a theme that was present before mammals split from reptiles some 200 million years ago.
Need we remind Clark that Theme and Variations is a musical form created by intelligent composers?Evolution Runs in Reverse 10/22/2005
A commercial for Guinness Beer shows devolution: evolution running in reverse. Its called, The history of life in :50 seconds flat. Is beer drinking a slippery slope to the primordial ooze?
This commercial is really funny to watch, and very clever, but it demonstrates the pervasive influence of Darwinism on our culture. We like the intelligent design commercial by Honda better (see 03/01/2005).Spider Evolution: A Theory in Crisis 10/21/2005
Sea spiders look so similar to land spiders, everyone would have thought they were related. They differ, however, in several significant ways, said Graham Budd and Maximilian Telford in Nature:1 Their bodies are so slender that the digestive systems and gonads are squeezed into their limbs; they possess a forward-pointing proboscis with a terminal mouth; and the males brood the eggs. Now, additional observations are bound to provoke controversy in an already acrimonious field, the field of spider evolution. Organs called chelifores near the proboscis of sea spiders are not related to the chelicerae of land spiders, reported Maxmen, Browne et al. in the same issue,2 because they originate from different parts of the head. The association of chelifores and chelicerae with different parts of the brain implies that the two types of limb are not equivalent, but are derived from different segments, Budd and Telford said. These observations will shake up the field of arthropod evolution.
A check under the hood shows there is more trouble in the engine of arthropod evolution.
This result cuts across previous results based on adult structure, and to see the wider implications we need some historical background. The composition of the arthropod head is one of the bitterest and longest-running problems in animal evolution. Unresolved after more than a century of debate, this sorry tale is (in)famously known as the endless dispute. (Emphasis added in all quotes.)The only way to salvage the evolutionary model is to assume that sea spiders are extraordinary living fossils, retaining an organization of their head that all other living arthropods lost hundreds of millions of years ago, Budd and Telford suggested. The caption of a phylogenetic chart explains how both possible interpretations are distasteful:
a, If pycnogonids branched off before the appearance of insects, crustaceans, myriapods and arachnids, we can interpret their protocerebral chelifores (red) as equivalent to the supposedly anterior great appendage of fossil groups such as Anomalocaris. The labrum (green) would have evolved in the common ancestor indicated with a star. b, But if pycnogonids are related to arachnids, then either their protocerebral chelifores could be an atavistic re-evolution of the great appendage, or the labrum must have evolved independently in arachnids and the other three taxa. Both of these latter hypotheses are contentious, and could raise doubts about the conclusions of Maxmen and colleagues.The former interpretation, taken by Maxmen et al., is that the chelifores are examples of convergent evolution. Pycnogonid chelifores and chelicerate chelicerae are convergent structures, they decided, innervated from different segmental neuromeres. Budd and Telford dont seem ready to swallow that line. They ended their analysis with more bitter words:
The conclusions of Maxmen et al. overturn entrenched ideas about the body plan of the sea spiders and, furthermore, lend support to some controversial theories of arthropod evolution. Unlike their terrestrial analogues, sea spiders lack a poisonous bite, but this paper is bound to inject venom into what is already one of the most controversial of all zoological topics.
1Graham Budd and Maximilian Telford, Evolution: Along came a sea spider, Nature 437, 1099-1102 (20 October 2005) | doi: 10.1038/4371099a.
2Maxmen et al., Neuroanatomy of sea spiders implies an appendicular origin of the protocerebral segment, Nature 437, 1144-1148 (20 October 2005) | doi: 10.1038/nature03984.
You probably didnt even know that the Darwinists had this problem. Behind the scenes, they have been injecting each other with venom and battling each other for over a century about where arthropods fit in the evolutionary tree, all the while telling the rest of us evolution is a fact. Should we feel sorry for them? Do you feel sorry for someone who builds a sand castle on a fault line?Planets and Moons Suddenly Got Much Younger 10/20/2005
A planet or moon covered with craters just looks old, doesnt it? Planetary geologists have long relied on crater counts to estimate the absolute ages of surfaces, such as on the moon, Mars, Europa, and every other solid body. Lots of craters meant old. Few craters meant young. Presumably, impacting bodies came in like clockwork and left their marks over the eons. An uncomfortable fact has come to light that disturbs this simple picture like a bolide: most of the craters are secondary impacts.
Picture a big meteor hitting Mars. Did you know that it could toss up enough debris to create 10 million more craters all from a single event? Thats one of several shocking facts presented by Clark R. Chapman and two colleagues in a Letter to Nature.1 (see also summary on Space.com). Believe it or not, they calculate that some 95% of small craters (1 km in diameter and under) are secondaries, and many of the moderate size craters probably are, too. This means that only a few impactors could quickly saturate a body with craters. It also means that estimating surface ages via crater counts is a lost art, because it just lost its credibility:
Surface ages can be derived from the spatial density of craters, but this association presumes that the craters are made by interplanetary impactors, arriving randomly in time and location across the surface. Secondary craters cause confusion because they contaminate the primary cratering record by emplacing large numbers of craters, episodically, in random and non-random locations on the surface. The number and spatial extent of secondary craters generated by a primary impact has been a significant research issue. If many or most small craters on a surface are secondaries, but are mistakenly identified as primaries, derived surface ages or characteristics of the impacting population size-frequency distribution (SFD) will be in error. (Emphasis added in all quotes.)Their mathematical analysis yielded the 95% figure for secondaries. The production of secondary craters on Europa, they found, was unexpectedly efficient. Although secondary crater formation on icy bodies was so, they feel that similar secondary crater production occurs on rocky bodies like the Moon and Mars, and granted that, has a ripple effect casting the entire method into doubt:
Our work raises doubts regarding methods that use the lunar small-crater distribution to calibrate other inner Solar System surface ages (for example, Mars). If, as on Europa, lunar and martian secondaries are 95% of the small crater (less than a few kilometres) population, the error bars (and thus derived surface ages) on any residual primary crater population become large (uncertainties are 20 times the measured density value). This uncertainty applies to both the measured population on a martian surface unit and the lunar SFD that supposedly represents absolute age. We emphasize that traditional age-dating analyses still derive robust ages when using large craters (greater than a few kilometres diameter), which are less likely to be secondaries. However, the technique becomes increasingly unreliable when applied to dating tiny geographical units using small craters, which may be mostly secondaries.As a result, they conclude that any attempt to age-date surfaces or characterize the population of impactors may suffer a significant and perhaps uncorrectable bias due to the contribution from secondaries. They ended with that case of the single Martian impact that generated 10 million secondaries from 10 to 100 meters in diameter.
Speaking of Mars, the Mars Global Surveyor recently took a sharp image captioned secondary craters. Click here for a look.
1Bierhaus, Chapman and Merline, Secondary craters on Europa and implications for cratered surfaces, Nature 437, 1125-1127 (20 October 2005) | doi: 10.1038/nature04069.
Things are not always what they seem. This announcement must hurt like a rock to Darwinists, who really need those long periods of uniformitarian processes. Imagine ten million craters forming in one day! If crater counts say nothing about age, why could not all the observed cratering have occurred quickly, in relatively recent times?Princess Dione: Check out the color picture of Saturns moon Dione just released by the Cassini team. Raw images from the October 11 flyby from 310 miles above the surface of Dione have been posted by the imaging team and at the Cassini website (also, close-ups of the little moon Telesto that leads Dione at its L4 langrangian point). Dione appears crisscrossed by wavy cracks and bright cliffs (example), some over three miles high.
Genes Are Not Telling the Whole Story
Protein evolution has traditionally been emphasized as a key facet of genome evolution and the evolution of new species, says Andolfatto. The degree of protein sequence similarity between humans and chimpanzees, and other closely-related but morphologically distinct taxa, has prompted several researchers to speculate that most adaptive differences between taxa are due to changes in gene regulation and not protein evolution. My results lend support to this view by demonstrating that regulatory changes have been of great importance in the evolution of new Drosophila species. (Emphasis added in all quotes.)Andolfatto et al. found that about 50% of the non-coding DNA appeared to be under negative selection (i.e., evolutionary conservation), and other parts appeared to be under positive selection (although determining this is a statistical comparison of nucleotide substitutions to polymorphisms, not a linking of variations to actual fitness benefits). This appears to be a double whammy against Kimuras neutral theory of evolution, said Alexey S. Kondrashov, in the same issue of Nature,2 who said about this study, Fruitfly genome is not junk. He began his analysis with a fairy tale that has been debunked:
Once upon a time, the world seemed simple when viewed through the eyes of evolutionary biologists. All genomes were tightly controlled by various forms of natural selection. DNA encoded functional genes, and most mutations that occurred were rejected through negative selection. Those exceptional mutations that were beneficial substituted for the original gene variant (allele) and spread through the evolving populations by positive selection. And polymorphisms where several alleles coexist within a population were maintained by yet another, balancing, form of selection.Though Kondrashov is not ready to conclude that higher vertebrates are lacking in junk DNA and neutral mutations, or that Kimuras neutral theory has been debunked outside of fruit flies, he draws one important conclusion from the new study: It is truly amazing how little we know quantitatively about mutation and selection in the genomes of even the most well-studied organisms. See also Science Daily summary of this story.
(2) A separate study closer to us humans also found a big surprise in our DNA. Ten years ago researchers were talking about the human genome as if there were a commonly-shared genetic code among us all. While that is still largely true, scientists have been stunned by the amount of individual variation. Erika Check, writing in Nature,3 explained:
Exactly one year ago this week, scientists announced that they had finished the Book of Life. The complete sequence of the human genome had been painstakingly reduced to an ordered list of letters representing the four bases of DNA. This text was believed to be virtually identical for every person on Earth and the major differences between individuals, such as hair colour, were said to be the equivalent of typographical errors, no longer than a single letter. The next major task for scientists was to find out which of these tiny differences can cause disease.These discoveries of major individual genetic differences, which began to surface in 2002 and 2003, have grown. Scientists were freaked out to find different numbers of copies of genes in different people, and then to find whole sections missing or written backwards in normal-looking people was almost unbelievable. So far these seem to affect 3.5% of the genome a bigger portion than the oft-alleged differences between humans and chimpanzees. (Those differences have grown, also, in the realization that non-coding elements and regulatory processes play a much more significant role than previously thought.) Some of the differences may be matters of life or death susceptibility to disease, or ability to adapt to certain environments, but many of them seem to provide no obvious phenotypic advantage or disadvantage, and all humans are clearly interfertile still. What all this means is a matter of intense debate. Erika Check concludes, For now, the realization that we are all reading from individual texts has already altered scientists understanding of humanity and of the library of unique volumes that makes up the human race.
1Peter Andolfatto, Adaptive evolution of non-coding DNA in Drosophila, Nature 437, 1149-1152 (20 October 2005) | doi: 10.1038/nature04107.
2Alexey S. Kondrashov, Evolutionary biology: Fruitfly genome is not junk, Nature 437, 1106 (20 October 2005) | doi: 10.1038/4371106a.
3Erika Check, Human genome: Patchwork people, Nature 437, 1084-1086 (20 October 2005) | doi: 10.1038/4371084a.
Neo-Darwinism was built on a pre-genomic, simplistic view of inheritance. It, and its successors, can no longer pretend to account for the new complexities of genetics that are coming to light.Stem Cell Breakthroughs: No More Ethical Concerns? 10/19/2005
Several science news sites have been reporting two new techniques for creating embryonic stem cells that do not involve the creation of viable embryos (see, for instance, New Scientist, Science Now, and Nature news, 437, 1065 (20 October 2005) | doi: 10.1038/4371065a).
There is no consensus yet, however, whether these methods overcome all the ethical objections to embryonic stem cell research. The ethical impact of one of the methods, alternate nuclear transfer (ANT), hinges on the definition of when life begins. Every bit helps, reported Nature, but
It remains to be seen if either method can do anything to resolve the political impasse over human embryonic stem-cell research....In the same issue of Nature (437, 1076-1077 (20 October 2005) | doi: 10.1038/4371072b), Carina Dennis and Erika Check made it clear where the ethical pressure was coming from: Religious and ethical concerns are forcing researchers using human embryonic stem cells to seek ways to sidestep these issues. The question dogging researchers is what is the definition of an embryo, if it is not viable and could not be implanted. Some critics are not convinced; one says the ANT product is indistinguishable from a natural embryo; another said, You do an engineering step to essentially destroy the embryo so that you can then use it.
Natures editorial writers make no bones about their desire to accelerate stem-cell research, and view these new techniques with cautious optimism the caution deriving from what ethicists will think. Other references in the journal encourage Germany to get rid of its ban on stem-cell research, and the Bush administration to loosen restrictions. And the prior week, Erika Check had reported in Nature about how US progressives fight for a voice in bioethics. She pointed to one incident that illustrates the difference between progressives and conservatives: [Arthur] Caplan [ethicist, U of Pennsylvania] and others were outraged when Republican leaders fought to keep Schiavo on life support against her husbands wishes. Nothing could make clearer the difference between progressive and conservative bioethics, says Caplan. Erika Check reported on steps progressives are taking to organize and combat the influence of conservative bioethicists.
These articles illustrate once again that mad scientists would go berserk with what they could do, if it were not for people with an ethical conscience, often derived from religion, putting the brakes on their reckless (and funding-motivated) enthusiasm. It would be good to read again some of the moral issues and potential horrors of unregulated genetic engineering we listed in our 08/24/2003 commentary (see bullet item Right to Life lobby). Keep the pressure on. We would have no qualms over stem cell research that passes the most rigorous tests of informed ethicists, particularly those who understand Christian principles of compassion, like not grinding up some lives to help others. But be careful. Darwinism has bequeathed to us an unprincipled lot of opportunists and glory-seekers. Their appeals couched in terms of compassion leave ample room for skepticism, when the mouth vocalizing altruistic rhetoric is accompanied with dollar signs in the eyes.Dover I.D. Trial Calls Star Witness 10/18/2005
Michael Irreducible Complexity Behe, the Lehigh biochemist famous for flagella, mousetraps and black boxes, took the stand in the Dover, Pennsylvania trial Monday Oct. 17. This was widely reported, such as in New Scientist, MSNBC News and the Washington Post. For an ID-friendly report with more detail of the actual proceedings, see EvolutionNews.
Behe snowed some of the listeners with technical jargon, but otherwise maintained his position that evidence for intelligent design in biology is overwhelming, based on positive evidence, not admissions of ignorance. He also took swipes at the ability of Darwinian mechanisms to explain molecular machines.
Other school boards are watching this trial with both interest and trepidation. The Washington Post said,
More school boards are considering mandating mention of intelligent design. Randy Tomasacci, a school board member from Shickshinny, north of Harrisburg, said his board is debating whether to require teachers to spend a few days on intelligent design. Were thinking about it, he said. But we dont want to get sued out of existence.For Behes part, he is safe. Though Lehigh University, where he teaches, has repudiated intelligent design, Behe has tenure and (unlike some other ID supporters) cannot be terminated for his views. Reporters and critics, meanwhile, seemed fixated on Behes Catholicism and on whether he believed the Designer is God.
Cant the reporters get fixated on the evidence instead? Maybe they would learn something about science instead of the secret motivations of their caricatured foes. At least anti-ID reporter Alan Boyle is working his way through Lee Strobels book The Case for a Creator among his stack of pro-evolution books and websites (see MSNBC), perhaps after being sufficiently hammered by emails from readers about his bias. MSNBC also printed a story about a parent worried that his daughter might not be accepted by other students if she doesnt agree with ID. No worries. Christians dont believe in doing unto others as they did unto us.Darwin on Offense I: Museums 10/17/2005
Whats the solution to decreasing belief in evolution? More evolution. Thats the message of an article by Lisa Anderson from the Chicago Tribune published online by Yahoo News, Museums take up evolution challenge.
Natural history museums around the country are mounting new exhibits they hope will succeed where high school biology classes have faltered: convincing Americans that Charles Darwins theory of evolution is a rigorously tested cornerstone of modern science. (Emphasis added in all quotes.)Museum curators have not been incognizant of public opinion polls that, for two decades, have shown that high percentages of the public that do not buy Darwins theory of human descent from ape-like ancestors. New exhibits, like Explore Evolution and Darwin are no longer pussyfooting around the E word, calling it change through time or other euphemisms, but putting it out there in bold print and making it exciting.
The article portrays science as necessarily secular, and the opposition as inherently religious:
The majority of scientists deny there is any credible challenge to evolution. They emphasize that scientific theory is not a wild guess, but a hypothesis subjected to careful testing and observation over time. They point to a thoroughly documented geological and radiometric dating of the Earths age and to almost daily developments in genetics and molecular and cell biology that affirm aspects of Darwins 1859 The Origin of Species.The article links antievolutionism to the loss of interest in science among students, and the decline of American scientific leadership, and indirectly uses the word magic to describe religious faith or doubts about Darwinism.
Evolving Planet will use the popular dinosaur exhibits as a draw, but intends to give viewers the whole spiel from chemical evolution to man. John McCarter, Field Museum CEO and president, said that this time were using the dinosaurs as kind of the marquee to draw them in and saying, this is a very complicated story, which youve got to dig into over a long period of time. (See also the 09/22/2005 entry about other museum strategies to combat antievolutionism.)
See Reader Responses to this story.
1By contrast, the entire budget of the new Creation Museum being built by Answers in Genesis (scheduled to open in 2007), with all its exhibits, buildings, life-size dinosaur models, offices, stores, parking lot, hiking trails and property, is $25 million, and is taking five years to complete.
When riding a dead horse, the Sioux strategy is to dismount. The Darwinists have tried this strategy continuing to ride the hobby horse of one-sided propaganda for over a century. They have tried Disney movies. They have tried PBS documentaries. They have flooded the media with specials from National Geographic, the Discovery Channel, and the Science Channel. They have published childrens books, cartoon books, textbooks, magazines, pamphlets and newspapers. They have dominated the national parks and museums with their material. They have taken over the public schools and controlled the science curriculum. Why hasnt it worked? Why do so many Americans still fail to get it? Heres the problem: people sense they are being propagandized. Every one of these attempts to teach evolution is one-sided. Each portrayal assumes evolution is a fact, and uses evidence merely as a prop for a play whose script is already written in stone. Worse, many of them ridicule anyone who disagrees, and fail to give any criticism an honest portrayal.Darwin on Offense II: Strategy Sessions 10/17/2005
The Geological Society of America, normally concerned with technical details of rocks and how many millions or billions of years old they are, devoted two expansive sessions at its annual meeting Oct 16-17, with 24 separate presentations dealing with strategies to oppose intelligent design (ID). Their press release portrays ID advocates as trained attackers, using the word attack four times as if their views and tactics are a frontal assault on science, using spurious arguments and devious methods. Its time for a counterattack, the GSA advises. Donald Wise, one of the four speakers, has made his strategy public: the best defense is a good offense.
So how does a scientist or teacher defend evolution against trained attackers? Dont, suggests geoscientist Donald Wise from the University of Massachusetts. Instead, go after the deep flaws in ID. Take the human body, for instance, he says in his GSA presentation. Its a great argument against ID. Anyone who has ever had back pain or clogged sinuses can testify to this. Our evolutionarily recent upright posture explains our terrible back problems better than ID, and our squished, very poorly designed sinuses dont function at all well and are easily explained by the evolutionarily rapid enlargement of our brains.Eugenie Scott is one of the four speakers at the conference, with a talk on Multiple levels of antievolutionism. The GSA also posted a complete resource kit with abstracts of most of the presentations and links to further information. One of the presentations, seemingly out of place for a geological society, is called Modern Biblical Scholarship as a Resource for Teachers of Evolution.
See Reader Responses to this story.
Irrefutable facts careful testing observation great. When do they begin? It would be harder to find a better illustration of Darwin Party hypocrisy. These rockhounds have the gall to accuse their critics of propaganda tactics and logical fallacies when those are the Darwin Partys stock in trade. For plenty of examples, just look in the chain links here in five years of reporting on evolutionary theory: start here with entry #652 and work back.Grown Man in the Stellar Crib: Now What? 10/14/2005
The cover of Science News has a strange cartoon explained on the inside in an article by Ron Cowen:
Imagine peering into a nursery and seeing, among the cooing babies, a few that look like grown men. Thats the startling situation that astronomers have stumbled upon as theyve looked deep into space and thus back to a time when newborn galaxies filled the cosmos. Some of these babies have turned out to be nearly as massive as the Milky Way and other galactic geezers that have taken billions of years to form. Despite being only about 800 million years old, some of the infants are chock-full of old stars. (Emphasis added in all quotes.)So that explains the star with the face of Jimmy Durante cuddled with infant starlets with their blankies in the maternity ward. Astronomers, though, arent laughing. Finding galactic geezers in the stellar nursery is throwing their cosmological models out of whack:
These chunky babies may be pointing to a cosmic crisis. They dont seem to fit the leading theory of galaxy formation, which cosmologists have relied on for more than 2 decades to explain an assortment of puzzling features of the universe. The theory posits that a pervasive, slow-moving, invisible type of matter vastly outweighs the observable matter in the universe. Under the gravitational influence of this unseen material, known as cold dark matter (SN: 4/23/05, p. 264), galaxies start out as small, starry fragments that merge to become much bigger objects. Thats usually a gradual process, according to the theory.Cowen said that astronomers might tolerate a few exceptions, but most of the anomalous findings are relatively recent. But over the past 18 months, several teams have found so many massive galaxies from this early epoch that the theory is being stretched to its breaking point, he stated as the feeling among astronomers. These disturbing findings have a ripple effect:
Even if the theory of cold dark matter survives this onslaught, the new observations of big galaxies in the most ancient of times have important implications. The findings suggest that the earliest galaxies formed stars in a great hurry, much more rapidly than galaxies that were born even a billion years later did. Whats more, that first generation of stars might have been rife with heavyweights much more massive, on average, than stars from any later epoch.An example in Cowens article was also reported by Robert Roy Britt in Space.Com. They both spoke of a galaxy in the Hubble Ultra Deep Field (03/09/2004) that bulked up amazingly quickly if understood in the context of leading theory (09/29/2005). Proponents of the cold dark matter theory are not yet ready to admit defeat, but are concerned if more and more mature galaxies with mature stars in them will continue to show up in surveys from earliest epochs of the universe. One astronomer admitted, There could be a problem with the theory. Another feared, the theory wont be salvaged with just a small bit of tinkering.
Meanwhile, another pair of astronomers is saying, Cold dark matter who needs it? Cooperstock and Tieu published a paper on ArXiv that demonstrates how galaxy rotation curves could be understood without invoking massive, unseen halos of dark matter. Britt also took note of that proposal on Space.com. Their model, which uses ordinary general relativity instead of dark matter, was tested initially with individual galaxies. Next, they want to test it with clusters of galaxies.
Instant galaxies and stars with appearance of age that sounds like creation, not evolution. If God stretched out the heavens in the beginning, as it says multiple places in the Bible, it could have done weird things to space and time, such as making things look older than they really are. But abrupt appearance would be the rule, just like it is in the fossil record of life on earth.Debate Sampler 10/13/2005
The debate between Darwinism and Intelligent Design (ID) continues unabated. Here are samples of recent reasonings, harangues and actions in the news:
In spite of the occasional lies and rhetorical fluff, its good to see these ideas being debated. Darwinists can no longer assume their position is unassailable. A well-tuned Baloney Detector is your best defense against the People of Froth (see 09/26/2005 commentary).Early Dino: Early Bird? 10/12/2005
Is it a bird or a dinosaur? The cover of Nature Oct. 13, 2005 shows a creature with feathery fuzz and feather-like structures on its arms, but the article inside1 describes only the bones of a new dromeosaurid theropod fossil found in Argentina. Theropods are the group the contained Velociraptor and other species often portrayed as skilled and voracious hunters. The cover art shows this new chicken-sized species, named Buitreraptor, with a lizard in its snout or beak whatever it is; the picture blurs the distinction between dinosaurs and birds. But was there a relationship?
Popular reports on this discovery (see The Scotsman, EurekAlert) reproduce the artwork but emphasize the revolutionary nature of this fossil. A 90-million-year-old dinosaur with striking bird-like features may force scientists to rewrite part of the family tree of the extinct reptiles, reported The Scotsman, suggesting that flight evolved in two separate evolutionary paths. The problem relates to the dating and the location. The ancestor of this species, with its ostensibly bird-like attributes, would have had to live before the Pangaea supercontinent broke up, because its similar-looking descendants in China, North America and now South American bore striking similarities. That means that flight would have had to evolve twice on different continents. The report on EurekAlert explains:
Results of an analysis of evolutionary relationships of advanced theropods undertaken as part of this research indicate that the Gondwanan dromaeosaurs and Rahonavis, an animal previously considered to be a very primitive bird, actually constitute a separate branch of the dromaeosaurid family tree. This branch is distinct from Velociraptor and other Laurasian dromaeosaurids, including some of the famous feathered dinosaurs from China. [See 10/10/2005 entry]. and with flight, presumably feathers. The scientific paper in Nature mentions neither feathers, skin, fuzz or integumentary structures, but the cover art shows the creature covered in them. Probably based on the artwork alone, The Scotsman said that it probably sported short feathers. Yet the association of Buitreraptor to birds, feathers or flight is not at all clear. Study of more specimens will, according to one of the discoverers, provide information that may be useful to understanding the changes in body proportions that led to the origin of birds and flight.
Sidelight: Speaking of Velociraptor, the deadly villains of Jurassic Park may not have been as vicious as thought. The BBC News reported on Dr. Phil Manning (U of Manchester), who built an artificial Velociraptor claw to study its mechanics. His team concluded it was too fragile to slash into the flesh of a live animal, and instead of disemboweling the prey, must have been used simply to hold onto it while biting. At most, the claws could only produce small, rounded punctures and would not have endangered vital organs. While not dismissing the reputation of Velociraptor as a predator, Mannings study considers it exaggerated.
1Makovicky et al., The earliest dromaeosaurid theropod from South America, Nature 437, 1007-1011 (13 October 2005) | doi: 10.1038/nature03996.
No sooner had we recounted how Nature had bluffed around the problems with bird evolution by printing cover art of feathered dinosaurs (10/10/2005), when they did it again! At least last time there was some indication on the fossils of fuzz or flayed skin, but this time, the artist took liberties with complete absence of evidence.Molecular Machine Updates 10/11/2005
Scientists continue to make headway understanding the detailed workings of molecular motors. The two most famous rotary motors yielded additional secrets recently:
1Xing, Liao and Oster, Making ATP, Proceedings of the National Academy of Sciences USA, published online before print October 10, 2005, 10.1073/pnas.0507207102.
2Sowa et al., Direct observation of steps in rotation of the bacterial flagellar motor, Nature 437, 916-919 (6 October 2005) | doi: 10.1038/nature04003.
3Akeda and Galan, Chaperone release and unfolding of substrates in type III secretion, Nature 437, 911-915 (6 October 2005) | doi: 10.1038/nature03992. See also the News and Views section by Blaylock and Schneewind, Microbiology: Loading the type III cannon, Nature 437, 821 (6 October 2005) | doi: 10.1038/437821a.
Some evolutionists have identified similarities between the TTSS and the bacterial flagellum, and suggested that the flagellum evolved from the TTSS by co-option. There are many problems with this suggestion, not the least of which is that most of the protein structural parts of the flagellum are unique. The authors of the TTSS paper did not mention this suggestion or anything about evolution. In fact, evolutionary theory was useless for all three papers. Describing the machines in terms of their design was perfectly appropriate, illustrating again the utility of scientific research from a design perspective. The two brief mentions of evolution in the ATP synthase paper were useless appendages, like vestigial organs of a less-evolved philosophy (sarcasm intended).Have We Been Sold a Bill of Goods About Feathered Dinosaurs and Bird Evolution? 10/10/2005
Most people remember the poignant moment at the end of Jurassic Park when the professor, on a flight away from his harrowing experiences on the island of dinosaurs run amok, sees a flock of modern birds and ponders their peaceful existence as descendants of the velociraptors and tyrannosaurs that nearly killed him and his friends. The story of birds evolving from dinosaurs has taken on the status of confirmed truth in the minds of many. This has been reinforced by repeated announcements of alleged feathered dinosaur fossils being uncovered in China. Yet Alan Feduccia, a paleontologist at University of North Carolina at Chapel Hill, has long contested this view. He and his colleagues have just come out swinging against his fellow evolutionists, accusing them of easy-believism and wish-fulfillment in spite of the evidence. According the U of NC press release:
The theory that birds are the equivalent of living dinosaurs and that dinosaurs were feathered is so full of holes that the creationists have jumped all over it, using the evolutionary nonsense of dinosaurian science as evidence against the theory of evolution, he said. To paraphrase one such individual, This isnt science . . . This is comic relief. (Emphasis added in all quotes.)Feduccia has published 150 papers and six major books, including one The Age of Birds (Harvard, 1980) and The Origin and Evolution of Birds (Yale, 1996). He and his colleagues have published these attacks on bird-from-dinosaur evolution in the Journal of Morphology. His views were also reported by EurekAlert that asked, Did feathered dinosaurs exist?
Although Feduccia believes birds and dinosaurs had a common reptilian ancestor, he argued, to say dinosaurs were the ancestors of the modern birds we see flying around outside today because we would like them to be is a big mistake. His team, using powerful microscopes, compared the skin of reptiles, the effects of skin decomposition, and the alleged protofeathers on fossils.
Here are some of the reasons in the press release for doubting the dino-to-bird evolution story:
Feduccia said the publication and promotion of feathered dinosaurs by the popular press and by prestigious journals and magazines, including National Geographic, Nature and Science, have made it difficult for opposing views to get a proper hearing.So what does Feduccia himself believe about the evolution of birds? It is now clear that the origin of birds is a much more complicated question than has been previously thought, he said.
Is it possible that the leading scientific journals in the world, including Nature and Science both of which highlighted artwork of feathered dinosaurs on their covers were capable of falling for and promoting a delusional fantasy? Does this mean that major museums, like the Natural History Museum of Washington DC and many others, with their Birds are Dinosaurs displays, are promoting falsehoods based on flawed evidence? Does this mean the traveling museum exhibit of feathered dinosaurs is a fraud? Is it possible that evolutionary paleontology is imploding from the credibility gap caused by this lapse of rigor? Does this raise the possibility that Darwinists are wrong about other claims? You heard it right here from an evolutionist chagrined at the fact that these wishful hopes touted as fact have given ammunition to the creationists. We hope you enjoyed the comic relief. Relief from comedy posing as science would be better.Ancient Reptiles Exceed Textbook Explanations 10/07/2005
Each new fossil from Chinas Liaoning province seems to force a rewrite of the textbooks. National Geographic News reported on fossils of pterosaurs with much higher diversity... than one could possibly expect. Two species found in the Jehol area (02/21/2003) had long beaks with sharp teeth, and wingspans up to 8 feet. It was once thought that pterosaurs glided instead of flapping their wings, Stefan Lovgren reported. However, researchers have now established that all but the largest pterosaurs could sustain powered flight. See also LiveScience. The paper in Nature1 says that, surprisingly, bird fossils show more diversity than the pterosaurs. 40 pterosaur remains (16 species) and 1,000 birds (21 species) have been found in the deposits. The closest relatives of the two new pterosaur species are from Europe, the discoverers said, also with apparent surprise. This unexpected mixture of different pterosaur groups in these Chinese deposits, they wrote, indicates a very complex evolutionary history of pterosaurs in general, which is just beginning to be deciphered.
Under the sea, another group of extinct reptiles are changing the textbooks. Scientists from University of Newcastle in Australia found plesiosaurs that apparently munched on clams, snails and crabs instead of fish, as previously assumed. Discoverers found stomach stones (gastroliths) for grinding up prey. The report in Science1 states, These finds point to a wider niche than has previously been supposed for these seemingly specialized predators and may also influence long-running controversy over the question of gastrolith function in plesiosaurs.
1Wang et al., Pterosaur diversity and faunal turnover in Cretaceous terrestrial ecosystems in China, Nature 437, 875-879 (6 October 2005) | doi: 10.1038/nature03982.
2McHenry et al., Bottom-Feeding Plesiosaurs, Science, Vol 310, Issue 5745, 75, 7 October 2005, [DOI: 10.1126/science.1117241].
One interesting thing about the new pterosaurs is that their habits and physical characteristics overlapped those of birds in many striking ways; some of them almost looked like pelicans. The scientists had to presume that the pterosaurs occupied the shore niche and the birds occupied the land niche. These flying reptiles are being seen more and more as skilled pilots (09/09/2005), not just dumb gliders manipulating the webbing between their fingers. To imagine one kind of creature mastering flight by an evolutionary process is tough enough for a Darwinist, but four independent groups (pterosaurs, insects, birds, bats)? Throwing around phrases like convergent evolution is not going to solve the problems.Science Writer Advocates Debate with Creationists 10/06/2005
The Darwinist monopoly on science has backfired, suggested Michael Balter in the Los Angeles Times in a Sunday commentary. A human evolution writer for Science magazine (e.g., 09/09/2005, 03/04/2005, 11/12/2004, 02/27/2004, 02/15/2002), Balter advocated engagement with the opposition. A national debate over how best to explain the complexity of living organisms would better serve our children, and adults too.
Balter is confident that science (evolution) would win such a contest, but cited several reasons why a national debate is necessary. Most scientists dont want any debate, he wrote. To them, evolution has already won, and deserves a monopoly in science classrooms. The success of the Discovery Institute in finding hundreds of scientists unconvinced of Darwinian evolution, added to the consistent findings of polls that the majority of Americans do not accept evolution, Balter argues, suggests that scientists have won few converts during at least the last two decades despite a 1987 U.S. Supreme Court decision banning the teaching of creationism in the classroom.
The failure of evolutionists to win converts is only partly a reflection of the continuing influence of religion, he said. Yet it also implies that scientists have not been persuasive enough, even when buttressed by strong scientific evidence that natural selection alone can account for lifes complexity. Part of their lack of persuasiveness has been their very reluctance to engage their opponents. Its time for a change, Balter argues:
Pro-evolution scientists have little to lose and everything to gain from a nationwide debate. Lets put the leading proponents of intelligent design and our sharpest evolutionary biologists on a national television panel and let them take their best shots. If biblical literalists want to join in, let them. Lets encourage teachers to stage debates in their classrooms or in assemblies. Students can be assigned to one or the other side, and guest speakers can be invited. Among other things, students would learn that science, when properly done, reaches conclusions via experimentation, evidence and argument, not through majority view. (Emphasis added in all quotes.)To those who worry about injecting religion in science class, Balter said its too late. Religious faith and thinking are already in the classroom, as the opinion polls strongly suggest, he wrote. And the courts should stay out of it because educators would not be required nor allowed to advocate a religious point of view.
Balter spoke of a long history of bitter debates between religion and science, and claimed that after Darwin seemed to have refuted the arguments of William Paley, Darwins theories were rigorously tested and criticized before they won over the majority of scientists.
For these reasons, todays evolutionists should not break tradition, but engage the critics. The best way to teach the theory of evolution is to teach this contentious history. The most effective way to convince students that the theory is correct is to confront, not avoid, continuing challenges to it.
Balters surprising declaration of support for teaching the controversy, a policy the intelligent design movement has long advocated, goes against the grain of positions taken by scientific institutions like Nature (see 04/27/2004). He argues, though, that evolutionists should engage the debate with gusto: Bring it on.
Anyone watching the controversy over evolution should see this as a major shift in strategy by someone pretty high up in the Science establishment. Its good that Balter wants this to be a debate in the open marketplace of ideas rather than the courts, and if the Darwinists are really willing to put their best arguments toe-to-toe with those of intelligent design, that would be a refreshing change.Make Your Own Privileged Planet 10/06/2005
NASA-Ames Research Center has produced an online simulation game called AstroVenture that allows kids to try to design a habitable planet. After they pick half a dozen parameters, the game tells them whether humans could live there or not.
This is a cute feature that, with caveats, could be useful for parents and teachers. The main problem is that it is too simplistic. The planet-construction dialog asks what kind of star you want to put your planet around, how close to the star, how big it is, whether it has water and a few other things. These are fine and good, but not enough. It doesnt discuss many other factors that could be show-stoppers: crustal composition, type of atmosphere, place in the galaxy, eccentricity of the orbit, size and distance of moon, and much more. Still, kids may be surprised to find how few of their choices actually work.Creation-Evolution Contest in Grand Canyon: New York Times Prints Eyewitness Report 10/06/2005
New York Times reporter Jodi Wilgoren explored parallel universes along the Colorado River this summer (here for multimedia version). She rode a raft with a creationist group led by Tom Vail for several days, then rode with another party led by evolutionist Eugenie Scott. Her experiences with these two groups illustrated the stark contrast between the worldviews at conflict in American society. Two groups examining the same evidence, she remarked. Traveling nearly identical itineraries, snoozing under the same stars and bathing in the same chocolate-colored river. Yet, standing at opposite ends of the growing creation-evolution debate, they seemed to speak in different tongues.
Wilgoren mentioned several scientific evidences that Tom Vail discussed as support for his Genesis Flood interpretation. One, the smooth perpendicular folds in Carbon Canyon, he explained as evidence the material had to be soft when bent. The long-age view is that pressure over time could give the rocks plasticity; Thats just a theory, Vail replied. He also discussed evidence for a mass kill event covering 5,700 square miles. He pointed to a vertically-oriented nautiloid that could not have remained in its position for tens of thousands of years while it was being buried slowly. On the evolution groups raft, a geologist who had been questioned about it only responded that scientists had not documented the billions of nautiloids creationists cite and had found no stunning pattern in their orientation.
Although Wilgoren asserted the correctness of the scientific view of the ages of the rocks and the canyon, her anecdotes about the behavior of the people of the parties seemed as contrasting as that of the differing interpretation of the canyon. She portrayed creationists in the group praying for one another and expressing their joy and thankfulness to God over the beauty surrounding them. The evolutionists, on the other hand, she portrayed as flippant and disrespectful about religion. Perhaps that was best illustrated in the music. Creationists sang hymns of praise accompanied by flute and guitar. Eugenie Scott, on the other hand, taught her group this ditty about a fishlike invertebrate evolutionists claim is one of our ancestors: Its a long way from amphioxus / Its a long way to us. / Its a long way from amphioxus to the meanest human cuss. / Goodbye fins and gill slits / Hello lungs and hair! / Its a long, long way from amphioxus, / But we come from there.
Another observation Jodi Wilgoren made was that all on the creationist raft had voted for George Bush, and all but two on the evolutionist raft for John Kerry. She also pointed out polls that show a third of the American public believe the Bible should be taken literally and that nearly half believe humans were created in nearly their present form within the last 10,000 years.
The article was peppered with the usual claims and counter-claims about science and religion, facts and faith. But Wilgoren gave surprisingly good press to Tom Vail, who used to teach the evolutionary view before becoming a Christian, and whose book Grand Canyon: A Different View has ranked 17th out of 800 products in the national park bookstores. It has sold 40,000 copies, she said, despite science organizations protests of its sale in park shops. She gave Vail the last word: We can read Gods word and we know what were supposed to do. Its real clear up here what were supposed to do.
Considering the disdain with which creationists are usually treated, Jodi Wilgoren gave a pretty fair and balanced presentation. The only flaws are the assumptions that evolutionists have the better science. Some of her words assume that evolutionary geologists have science on their side. We will suggest changes to the underlined words.Stupid Evolution Quote of the Week: Network Evolution Trumps ID 10/05/2005
This entry will make more sense after reading yesterdays story on the evolution of modular networks (10/04/2005). A reader sent in a reference to a very similar article from scientists at Johns Hopkins published in PLoS Biology.1 It must be Network Evolution Week. Before awarding the SEQOTW prize, some background is necessary.
Like the Weizmann team, the Johns Hopkins team sought to explain biological network organization in terms of material mechanisms of mutation and natural selection. They reasoned that constraints (the environment) dictate the dynamic character of network motifs and their interrelationships. By awarding a structural stability score (SSS) to biological motifs in fruit flies and worms based on their ability to recover from perturbations, they found stable motifs cluster in a non-random way that determine the overall network structure. They suggested, with apparent trepidation, that the environment therefore constrains biological networks to take a predictable form through pure mechanistic forces
Do common driving forces underlie the organization of biological networks? It seems fantastic to suggest that such forces could exist, considering that the biological entities involved are as diverse as genes, enzymes, and whole cells. Nevertheless, even functionally unrelated systems may have evolved under fundamental constraints. The analysis presented here suggests that the dynamic properties of small network motifs contribute to the structural organization of biological networks. In particular, robustness of small regulatory motifs to small perturbations is highly correlated with the non-random organization of these networks. (Emphasis added in all quotes.)That their explanatory toolkit is limited to material causes is clear in a subsequent paragraph:
An evolutionary argument may help explain the overrepresentation of structurally stable motifs in real networks compared to random graphs. Evolutionary pressure may select for network innovations that are structurally stable because these configurations are robust to variations in the strength of the connections. A high SSS indicates that it is likely that randomly assigned connection strengths and signs will result in a stable equilibrium, while a low SSS indicates that stability is possible although it requires precisely weighted connection strengths. Easily parameterized network designs that are predisposed to dynamical stability can be advantageous considering the evolutionary mechanisms of random mutation and natural selection. Of course, stability to small perturbations is by no means the only functional constraint on network performance and structure. For instance, in the developmental transcriptional regulation network in Drosophila [fruit fly] considered here, irreversible switching of transcriptional circuits involving feedback regulation is an important determinant of irreversibility of the developmental progress, which might lead to selection of relatively unstable network motifs with feedbacks. The C. elegans [roundworm] neuron network, which strays the furthest from structural stability in our analysis, may also have functional constraints leading to overrepresentation of oscillators and memory switches. Nevertheless, the correlation between network motif overrepresentation and the SSS suggests that stability of small functional circuits may be a basic constraint common to all networks, which along with other functional requirements can significantly bias the likelihood that a given motif is selected for.Functional constraints, in their context, can only come from the environment not from design. This was made clear in an earlier statement: Regulation of gene expression is dependent on the particular demands of a cell with respect to its environment. In their experiments, environmental perturbations governed the structural stability score awarded the network motifs. The reader is referred to yesterdays discussion (10/04/2005) about whether the environment can generate robust, modular network design.
Now to the Stupid Evolution Quote of the Week. Liza Gross, commenting on this paper in the same issue of PLoS Biology,2 used this paper to flaunt the superiority of Darwinian evolution over intelligent design:
While intelligent-design proponents enjoy their 15 minutes of fame denying the role of evolutionary forces in generating complex networks in nature, scientists are probing the organizing principles that govern these networks. Traditional models of complex networks assumed that connections between unitssuch as genes, proteins, neurons, or speciesoccur randomly. These notions changed as studies of protein interaction networks and other biological systems revealed small world featurescharacterized by short paths between nodes and highly clustered connectionsand varying levels of organization, with certain patterns of local connections occurring more frequently in complex networks than in random networks. What determines the abundance of these so-called network motifs in specific networks is not known....In short, whos on the net? Certainly not a designer. Networks are things that just happen from time to time. Maybe some day, after we have studied the networks in more detail, we can test that idea.
The Runner-Up prize could go to another paper in the same issue of PLoS Biology.3 Skerker et al. marveled at the abilities of cells to process information and execute programs. They didnt try to explain how the systems evolved. They just declared that they did:
Cells have the remarkable ability to sense, respond to, and adapt to their internal and external environments in order to maximize survival or accurately execute a developmental program. Such behavior requires the ability to process information, and cells have evolved complex regulatory and signaling systems capable of sophisticated information-processing tasks.
1Prill, Iglesias and Levchenko, Dynamic Properties of Network Motifs Contribute to Biological Network Organization, Public Library of Science Biology, Volume 3, Issue 11, November 2005 (published 10/04/2005), DOI: 10.1371/journal.pbio.0030343.
2Liza Gross, Charting the Interplay between Structure and Dynamics in Complex Networks, Public Library of Science Biology, Volume 3, Issue 11, November 2005 (published 10/04/2005), DOI: 10.1371/journal.pbio.0030369.
3Skerker et al., Two-Component Signal Transduction Pathways Regulating Growth and Cell Cycle Progression in a Bacterium: A System-Level Analysis, Public Library of Science Biology, Volume 3, Issue 11, November 2005 (published 10/04/2005), open access article.
Prill et al. subscribe to the same goofy theory as the 10/04/2005 attempt, and the same comments apply. Friends, Romans, and First Corinthians, and all reasonable, thinking people, let us understand two principles that undermine the whole premise of this claim and others like it:University of Idaho President Announces Evolution-Only Policy 10/05/2005
Timothy P. White, President of the University of Idaho, just issued a letter to faculty, staff and students to articulate the University of Idahos position with respect to evolution: This is the only curriculum that is appropriate to be taught in our bio-physical sciences. The Discovery Institute calls this naked viewpoint discrimination.
The presidents next sentence says, we affirm scientific principles that are testable and anchored in evidence. Darwinism will have a hard time with that policy (see next entry).Can Networks Design Themselves? 10/04/2005
A molecular biologist and a physicist at the Weizmann Institute of Science in Israel (see also 09/26/2003) wrote a paper in PNAS1 with an intriguing title: Spontaneous evolution of modularity and network motifs. Can a network arise spontaneously?
Biologists increasingly speak of the interaction of genes, proteins and metabolic processes in terms of networks (e.g., 12/20/2004, 03/22/2004, 01/28/2004, 01/27/2003, 01/10/2003). The networks with which most of us are familiar, like the power grid or internet, came about with intensive programming and intentional engineering. After the network architecture and the rules of interaction were defined, however, many unforeseen and spectacular patterns emerged. It could be argued that each emergent property of the internet had its roots in intelligent causes, however, since only sentient beings humans use the internet, and they do so with purpose and intent. In biological system there are also characteristic network-like patterns. Could these have arisen without purpose and intent? For Kashtan and Alon to prove this, they need to establish that networking behavior can be an emergent property of the molecules of the cell, without any programming.
In the history of computer software design, one important revolution was the invention of modular programming. Early programmers got tangled in their own spaghetti code, writing routines that jumped to other routines in such complex ways that the entire system became one single point of failure. Programmers realized that certain functions could be modularized, or segregated into independent routines that, though part of the big system, focused only on their own task. A module for addition, for instance, might take two undefined inputs, and have the function: add these two inputs together. The next module up the chain can call this module and give it any two numbers, and be assured the sum will be faithfully returned. Computer systems and networks built with a modular design were found to be much easier to maintain, and became much more robust against perturbations. A module could be upgraded or replaced without requiring a rewrite of the entire system. Biological networks also appear to work in modular fashion. Kashtan and Alon believe that they have found purely natural reasons for why this is so:
Biological networks have an inherent simplicity: they are modular with a design that can be separated into units that perform almost independently. Furthermore, they show reuse of recurring patterns termed network motifs. Little is known about the evolutionary origin of these properties. Current models of biological evolution typically produce networks that are highly nonmodular and lack understandable motifs. Here, we suggest a possible explanation for the origin of modularity and network motifs in biology. We use standard evolutionary algorithms to evolve networks. A key feature in this study is evolution under an environment (evolutionary goal) that changes in a modular fashion. That is, we repeatedly switch between several goals, each made of a different combination of subgoals. We find that such modularly varying goals lead to the spontaneous evolution of modular network structure and network motifs. The resulting networks rapidly evolve to satisfy each of the different goals. Such switching between related goals may represent biological evolution in a changing environment that requires different combinations of a set of basic biological functions. The present study may shed light on the evolutionary forces that promote structural simplicity in biological networks and offers ways to improve the evolutionary design of engineered systems. (Emphasis added in all quotes.)In short, if the environment is modular, the network will become modular. This has been the problem, they reason, with computer models of evolution. Modelers used to give the computer a fixed goal and let the evolutionary algorithm figure out the way to reach it, by rewarding each routines fitness as it got warmer. These two researchers, instead, tried routinely switching the goal during the run. The networks that won out in the end were the modular ones:
The networks evolved under modularly varying goals were able to adapt to nearly perfect solutions for each new goal, within about three generations after the goal was switched. This evolvability was caused by the fact that the evolved networks for the different goals differed only slightly. For example, in many cases they differed in the threshold value of a single neuron, allowing switching between the networks with a single mutation....So the winners evolved not only to be modular, but to be evolvable. This, they think, is the secret of how biological networks became so robust in spite of changing circumstances. Once a module for chemotaxis arose, for instance, a bacterium could reuse it with just a few rewiring changes if the chemical attractant changed. But who is doing the discovering? The subject of their sentence was, Networks that evolve... discover... The language of intent continues in another sentence in the ending discussion. Watch the subject:
In such cases [evolution with fixed goals], when the goal changes, the networks take a relatively long time to adapt to the new goal, as if it starts evolution from scratch. Under modularly varying goals, in contrast, adaptation to the new goal is greatly speeded up by the presence of the existing modules that were useful for the previous goal.That last sentence used a passive voice verb: adaptation... is greatly speeded up. This hides the implication that the modules are seeking to adapt with goal-directed behavior. The authors are clearly not intentionally attributing intrinsic purpose to the modules. Their discussion of fitness landscapes in the subsequent paragraph treats the modules as pinballs on a bumpy landscape. Shifting goals keeps the landscape undulating so that the pinballs dont get trapped on local fitness maxima. So is goal-effective modularity a true emergent property, as pointless and aimless as water running down a slope and seeking the least obstructed path? They actually experimented more to clarify this possibility. Notice the words information processing and useful:
One possible explanation for the origin of the motifs in the evolved networks is that modular networks are locally denser than nonmodular networks of the same size and connectivity. This local density tends to increase the number of subgraphs (42). To test this possibility, we evolved networks to reach the same modularity measure Q as the networks evolved under modularly varying goals, but with no information-processing goal (see Supporting Text). We find that these modular networks have no significant network motifs (Fig. 9). They show relatively abundant feedback loops that are antimotifs in the networks evolved under modularly varying goals. It therefore seems that the specific network motifs found in the evolved networks are not merely caused by local density, but may be useful building blocks for information processing.In other words, unless information processing was programmed in as a goal, mere environment-shifting produced anti-motifs a backward step. That is why their only success came with emphasis on achieving useful building blocks for information processing. But what is useful to a network? Why would a non-sentient network seek to process information? If not the network, is there an outside agent that cares about such things? Like the tree in the woods falling without a sound, can there be information without a mind to conceive of it?
At this point, they compared their computer models to actual biological networks. Here, they could not escape portraying the genes and cells as if they were tiny sentient beings:
How is evolution under modularly varying goals related to actual biological evolution? One may suggest that organisms evolve in environments that require a certain set of basic biological functions....They threw in a bonus that their study might help engineers evolve improved networks. But understanding biology was clearly the intent of the paper. How to get biological design without a designer that quest was evident in their last two sentences. In summary, they said, this study presents a possible mechanism for spontaneous evolution of modularity and network motifs. It will be important to extend this study to understand how evolution could generate additional design features of biological systems.
1Nadav Kashtan and Uri Alon, Spontaneous evolution of modularity and network motifs, Proceedings of the National Academy of Sciences USA, published online before print September 20, 2005, 10.1073/pnas.0503610102.
Foul, time out, game over. They just violated the No Free Lunch Principle. You just caught them in the act. This is the persistent sin of evolutionists, engraved with an iron stylus on their stony hearts. They only get away with this evil because no preacher is allowed past the walls of the Darwin Party fortress to call them to repentance. Naturalists cannot attribute will, purpose, intent and information processing to mindless entities. This violates their core assumptions as philosophical naturalists (materialists), whose goal was to rid natural explanations of teleology (purpose, final causes).Muscle Motor Observed in Action 10/03/2005
Myosin proteins have been heavily studied in recent years since they are critical to many cellular and tissue functions, including muscle. According to EurekAlert Scientists from the Burnham Institute for Medical Research and the University of Vermont have captured the first 3-dimensional (3D) atomic-resolution images of the motor protein myosin V as it walks along trackways made of actin:
Myosins are a large family of motor proteins that interact with actin filaments for motor movement and muscle contraction. Myosin V is the workhorse of the myosin protein family. It exists to ferry a cargo of proteins needed in a specific place at a specific time. Fueled by hydrolysis -- the process of converting the molecule adenosine triphosphate (ATP) into energy -- myosin V travels in one direction using actin as a track to deliver its payload of cell vesicles and organelles. Myosin V is also involved in transporting proteins that signal and communicate with other cells.Using 3D electron cryo-microscopy, the Burnham team took snapshots of the action to put together a sequence that allowed them to visualize myosin in its natural state. They were able to see structural changes in the myosin and the actin, including movement of the lever arm, the scientists said.
The tight specs of this molecular machinery were underscored in the press release. The precise characterization of this myosin-actin interface is critical, it stated, evident by the way a single amino acid change in myosin leads to familial hypertrophic cardiomyopathy (FHC), an undetectable condition resulting in death by sudden cardiac arrest in otherwise healthy young adults.
Pictures say a thousand words, and in this press release the pictures and the words are all about design and nothing about evolution. A key point here is that myosin V is useless without the actin trackway. Considering the horrible impact from even one mutation, this appears to represent an irreducibly complex system similar to the classic illustration by Michael Behe of a mousetrap, where if a single part is removed, it can no longer function. Suppose a cell was producing thousands of specialized proteins and they had no place to go, or no way to get there. In cells, everything must work together: the cargo, the delivery system, and the recipients.Darwinian Phylogenetic Tools Are Mathematically Flawed 10/01/2005
Many evolutionists use software tools to construct evolutionary trees from genetic data. Two mathematicians have just reported in Science1 that several popular tree-building algorithms can give misleading results:
Markov chain Monte Carlo (MCMC) algorithms play a critical role in the Bayesian approach to phylogenetic inference. We present a theoretical analysis of the rate of convergence of many of the widely used Markov chains. For N characters generated from a uniform mixture of two trees, we prove that the Markov chains take an exponentially long (in N) number of iterations to converge to the posterior distribution. Nevertheless, the likelihood plots for sample runs of the Markov chains deceivingly suggest that the chains converge rapidly to a unique tree. Our results rely on novel mathematical understanding of the log-likelihood function on the space of phylogenetic trees. The practical implications of our work are that Bayesian MCMC methods can be misleading when the data are generated from a mixture of trees. Thus, in cases of data containing potentially conflicting phylogenetic signals, phylogenetic reconstruction should be performed separately on each signal. (Emphasis added in all quotes.)Will this workaround cure all problems, though? Only for small data sets maybe. The more data, the more impossible the task becomes:
For small trees one can hope to overcome the slow convergence by using multiple starting states. However, mixtures coming from large trees may contain multiple species subsets where one tree has T1 as an induced subtree and the other has T2. If there are k such subsets, then about 15k random starting points will be needed. Thus if there are 10 disagreement subsets, then 1510 random starting points will be needed in order to sample from the posterior distribution.Thats over 576 billion. Most tree-building programs try to take shortcuts around the computational hurdles, but these mathematicians are not sure that the heuristic algorithms used are successful in avoiding assumptions that could bias the results. Their paper has proven one way the results can be misleading. Are there others?
In our setting, BMCMC [Bayesian Markov-Chain Monte Carlo] methods fail in a clearly demonstrable manner. We expect that there is a more general class of mixtures where BMCMC methods fail in more subtle ways. These subtle failures may occur for many real-world examples where the Markov chains quickly converge to some distribution other than the desired posterior distribution. Users of BMCMC methods should ideally avoid mixture distributions that are known to produce degenerate behavior in various phylogenetic settings. A good practice is to decompose the data into nonconflicting signals and perform phylogenetic reconstruction separately on each signal. Our work highlights important unresolved questions: how to verify homogeneity of genomic data and what phylogenetic methods can efficiently deal with mixtures.Thus, they leave some potential gaping loopholes unexplored.
1Mossel and Vigoda, Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees, Science, Vol 309, Issue 5744, 2207-2209, 30 September 2005, [DOI: 10.1126/science.1115493].
What this seems to say is that the method might work on closely-related organisms, like species of snails, but the more you mix different types of organisms into a tree of common ancestry, the more the results of these popular methods will give misleading results. Even with the closely-related trees, though, how can one be sure that the answers might fail in more subtle ways? And how do we know that once the smaller trees are assembled, the algorithms wont mislead horrendously in the final mix?