Arzakem's Biotopia
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  • Me and my Moto
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    Monday, October 31, 2005

    Slimy Pond Pet

    I was surprised yesterday by my cousin's new pond entity - a common river eel. He took the eel from a river about 22 km from us. Actually he wasn't the one who caught this. He only paid some kids on the area to catch something for him. He was surprised when they came back with the eel. If he hadn't paid for it the eel would surely find its way cooked and eaten by these kids as this is a usual catch for them. Talks of larger eels stimulated our interest into going back to the place again. Let's just see if there's something bigger waiting for us there.

    Eels can live on ponds as long as there is water movement and rocky crevices where it can hide in solace. I've had fire eels in my aquarium 2 years ago and it's fun to watch them pop their heads out to look for food.

    My cousin supplied apple snails to feed it. I doubt it takes that but normal fish pellets could be better alternative.

    eel picture
    This eel is about 18 inches long. A Big-headed slimy pet.

    arzakem posted at 5:21:00 PM 0 joined. Access your PC from anywhere!!!

    I hope you're not serious!

    Got this from unexplained-mysteries.com and it made me laugh.

    arzakem posted at 4:58:00 PM 0 joined. Access your PC from anywhere!!!

    Friday, October 28, 2005

    One Fine Day

    Last night was irritating - imagine a road traffic to hold you for about an hour. And there's that strong rain that soaked me up while I crossed the streets. Moreso, I never had any jacket with me because I thought there won't be any rain since it was about 30 degrees Celsius yesterday morning. When I arrived home, I forgot to bring the DVD I was supposed to watch. "There goes another boring day...", I thought while slowly losing reality in 40 winks.

    Morning arrives and I woke up in one of the best morns I've ever had. Birds chirp, roosters cock, and those turkeys cackle from our neighbor. Immediately I grabbed my phone and took some shots...click...

    morning sun
    Here comes the sun, do-do-dodo, here comes the sun...

    coconut
    I sure hoped that coconut trunk could have grown leaves.

    carps
    These carps are having coffee while that clam is waiting for cookie crumbs to fall over. I thought these clams won't survive but they did. It's a nice addition to my species-rich pond.

    oscar
    This Albino Oscar loves to eat from my hand. He's got a personality and I love it.

    leaves
    I wanted to have a shot with the dew but the camera won't work.

    potatoes
    I always thought potatoes grow underground. This proves me wrong. These potatoes just grew from our backyard and it creeps up these trees and now it's having fruits. What? Potatoes are fruits?


    I can hear this tree shouting, "Free me from this prison!!! Please!!!" It could easily get an Emmy.

    I think I have to rename this blog by the way. I don't get any more dark thoughts with a fine day. And it's nice to have a brighter disposition. :D

    arzakem posted at 9:20:00 AM 0 joined. Access your PC from anywhere!!!

    Thursday, October 27, 2005

    Will you please send me your Pond pics?

    I'm definitely starting on another blog. This time it will be on my long-time interest - garden ponds. I find the hobby time-spending but very much stress-relieving. Somehow, I couldn't find any ponds around town except on some aquaria stores and they're not really that good. I've seen great pond pictures from other pond websites but never on blogs. If you could hand me over some pictures I would be very much delighted. My email is arzakem@gmail.com.

    Perhaps if anyone can send me their own pictures then I could start on posting on my "pond blog" as much as possible and with enough data ;). Please help me on this.

    A garden pond
    Nice setup... shot from a garden shop

    Another garden pond
    Another garden setup... lesser water though

    fairy moss everywhere
    Fairy mosses from my own pond

    fighting fish
    Two bettas after a roundbout. The other one's hidden (red)

    acei
    That bright blue thing is my Yellow-tailed Acei

    arzakem posted at 10:14:00 PM 0 joined. Access your PC from anywhere!!!

    Tuesday, October 25, 2005

    Rosa Parks and equality

    pictures of mrs. rosa parks - credits from yahoo

    My post would be worth giving tribute to a woman who has inevitably brought forth racial equality in the most powerful of nations. A woman of great courage and fair judgment, she will be missed and honored by the world as one of history's most important persons.

    I only hope that what she died promoting would forever be in our minds and that we may never get back to what we were before. I would always consider racism as deeds of barbaric and uncivilized nature. People like Mrs.Parks make us think better and go on living peacefully and beyond wars.

    arzakem posted at 11:40:00 AM 0 joined. Access your PC from anywhere!!!

    Friday, October 21, 2005

    Me and my Moto

    Life has been cruel to me - all I can afford taking pictures is a Motorola e398 and it's not a digital cam. Huh, but that wouldn't stop me from taking pics with everything. And should I tell you that my cat is also named Moto? That's a revelation - I'm promoting Motorola mobiles and cool-named Cats.

    Great week it was... here are proofs:

    This is Moto. And he's looking at me (of course dumbo!)
    picture of my cat

    I should call this "The Mysteries of Creation" (???????)
    picture of clouds

    Raining Friday. I believe this road leads to nowhere but getting wet!
    picture of trees on a rainy day

    What could be ruining a beautiful natural shot?
    picture of rocks from a beach

    A view at the pier after island hopping
    picture of a seaside port view

    Moto on a watchful eye over my tropical fish pond
    picture of a cat overviewing a pond of tropical fishes

    And this is my Flowerhorn fish. Not named yet. Maybe I'll call him Rola.
    picture of a flowerhorn fish


    I'm no professional photographer and I still wear glasses so don't ever judge my picture takes. Send me a digital camera if you won't stop complaining. :)

    arzakem posted at 9:40:00 PM 0 joined. Access your PC from anywhere!!!

    Thursday, October 06, 2005

    Not just a Jedi Mind Trick

    The Star Wars saga is over and the book is closed.

    Somehow, it brings me to some realizations that Lucas' mindpot had been cooked and served to us in terms of character unknowingly. Do not fear! Yes indeed to the padawans of the multitude, Yoda whispers in the wind, "do not fear, fear begets anger, and anger begets aggression". Actually, it's a reference to all religious that classify themselves as "God-fearing". Will fear bring anger? That might be of no sense but if you fly for a bird's-eye view of the current sociological climate, it would seem that anger springs from too much of being "in fear". Afraid of losing power, a politician resort to ordering the massacre of his people; afraid of losing business monopoly, a conglomerate would absorb the few small-scale striving workers; afraid of being sent to a hellish place, a pastor would lead his followers to his personal infallible theories; afraid of losing everything, a man would willingly sacrifice his dearest.

    You see it's all about fear. I was raised in fear and I grew up with it. Perhaps Lucas never really grasped into the oblique reference of his thinkings reflected into the characters of the Star Wars Universe yet he did made up something that made sense. Dividing that Universe into a Dark and Light Side was meant to be like the real world. Though it seems that being a Jedi, sans fear, sans love, sans emotion, is Utopic in nature - it is the very opposite of the Lighter side of reality. Maybe it explains why anger and aggression occurs everywhere. It's just that we were raised to be fearing and recessive that the darkness of hearts are bursting in silence. And who can tell that the Sith represents the aristocratic rule of reality? Was it that Love was associated with being with the darker side? Perhaps deceit occurs as ubiquitous as love and fear precedes them all.

    I have to live without this fear. It shouldn't be a Jedi mind trick only but a better way of life.

    arzakem posted at 7:00:00 PM 0 joined. Access your PC from anywhere!!!

    Monday, October 03, 2005

    In the defense of Evolution

    (The Defender's Guide may be reprinted or distributed, in its entirety, without alteration, but not for profit. All distribution must be made free of charge to the recipients. Anyone displaying a copy of the Defender's Guide at another web site is advised to check back periodically to see whether a new edition is available.)

    Defender's Guide to Science and Creationism: IV: Evolutionary Biology

    Mark I. Vuletic

    [Last updated 17 January 2005]


    Introduction
    While creationists may disagree with one another about the age of the universe and the age of the Earth, they are unanimous in rejecting evolution. Strictly "biological" arguments are dealt with in this section, but arguments related to the fossil record are discussed in section V, and moral, theological, and philosophical objections are treated in sections VI and VII.
    Index of creationist misunderstandings

    4.1: The perfection of structures like the human eye is proof of creation.

    4.2: "Irreducibly complex" things could not have evolved by small steps, and evolutionists have not even tried to show that they have.

    4.3: There is no explanation for how the bacterial flagellum could have evolved.

    4.4: Evolutionists cannot explain how feathers could have evolved.

    4.5: Evolutionists cannot tell us exactly how most organisms and biological structures arose.

    4.6: Evolutionists cannot explain how butterfly metamorphosis could have evolved.

    4.7: The genetic variation exhibited in microevolution was put in deliberately put in place by the creator in advance, and did not arise from mutation.

    4.8: Homologous features do not prove ancestral relationships between any organisms, because all classifications above the species level are man-made and arbitrary.

    4.9: The peppered moth does not demonstrate evolution because no speciation occurs.

    4.10: Mutations are always harmful.

    4.11: Mutations are rarely beneficial, so they cannot drive evolution. Would you want your house built by a carpenter who made 99 bad houses for every good one?

    4.12: Mutations never increase the amount of genetic information.

    4.13: Chromosome numbers cannot change without producing harmful effects.

    4.14: Punctuated equilibrium posits massive mutations which cause an organism to give birth to a radically different organism, like a reptile giving birth to a bird.

    4.15: There are plenty of mutations that cause birth defects, but none that cause "birth improvements."

    4.16: The rate of mutation is too small for mutation to serve as a source of variation.

    4.17: Regardless of mutation rates, the rate of microevolution is too low to account for the macroevolutionary change observed in the fossil record.

    4.18: Macroevolution remains unproved because no one has observed it. In fact, macroevolution is in principle unobservable, so evolution is unscientific.

    4.19: No one has ever seen one species arise from another.

    4.20: If evolution were true, fish would have evolved into amphibians and land animals more than once.

    4.21: Sexual reproduction could not have come about through evolution.

    4.22: There is no evidence for the rapid development of new species in nature.

    4.23: Natural selection is a tautology: the fittest survive, and those who survive are the fittest.

    4.24: Given uniform population growth rates, there could not have been humans before 10,000 years ago.

    4.25: Haldane's Dilemma proves that human could not have evolved over the time span evolutionists say they did.

    4.26: If humans had evolved from apes, there would no longer be any apes around.
    Analysis

    4.1: ASSERTION: The perfection of structures like the human eye is proof of creation.

    RESPONSE: (i) The human eye is actually quite flawed, as evidenced strikingly by the fact that the photoreceptors in the eye are embedded upside-down in the retina. The photoreceptors face away from the lens of the eye, so that their attached blood vessels and bipolar cells (neurons that convey information from the receptors to the brain) rest between the receptors and the lens. This causes deficiencies in human vision, most notably a blind spot in the visual field of each eye caused by the holes where the neurons exit the eye.

    The squid eye, by contrast, does not have this problem: its photoreceptors are wired in the correct way. This raises the question of why a creator whose crowning invention was the human being would make such a grave engineering error in the human eye but not in that of a presumably less important creature. As the title of a Jared Diamond article puts it, "If the creationists are right, God is a squid" (Diamond 1985).

    Imperfect engineering is, of course, apparent in far more than the human eye. Useless and inefficient structures abound in the natural world; for instance, the hollow bones of flightless birds, the clumsy "thumb" of the giant Panda, and the vestigial pelvis of pythons and whales (Futuyma 1983:198-200). If these structures were created, they must have been designed specifically to look like they had evolved.

    (ia) Some creationists argue that the bizarre wiring of the human eye is designed to filter out ultraviolet rays, and that the squid has normal wiring because it lives at depths where ultraviolet rays do not penetrate. Frank Zindler responds:
    First of all, what good is it to protect the photoreceptors when the neuronal fibers coming from them are subjected to greater amounts of supposedly damaging UV radiation? (The neuronal fibers run in front of the photoreceptors.) The UV would be just as damaging to the neurons as to the photoreceptors. In fact, the major damage done by UV appears to be to the lens at the front of the eye. Why couldn't god have designed a cornea that reflected all UV, protecting all the internal parts of the eye? Now THAT would be a sign of design!
    Secondly, the tiny difference in thickness between the photoreceptor layer and the anterior surface of the retina is of no significant importance with respect to UV protection.
    Thirdly, and this is probably the most important point: If water absorbs UV so efficiently (and it does), why is it that fishes -- like all vertebrates -- have THEIR retinas on backwards also? (Zindler 1998)

    (ii) But could biological structures as complex as the human eye, even admitting its imperfections, arise via evolution? Naturally, no one has observed the evolution of the eye in a laboratory because of the timescale involved, but one can look to the gradations in the present world for clues. In fact, nature displays progressions of simple to complex visual structures (Ecker 1990:65-66), such that one can see how the eye could have gradually developed.

    (iii) Paul R. Gross explains how a model by Dan Nilsson and Sussanne Pelger has bolstered the case for the natural evolution of the eye by small steps:
    In a 1994 theoretical paper, Nilsson and Pelger modeled one possible evolutionary pathway to the geometry of a fish-like eye from a patch of photo-responsive cells. There were already such cells -- among the oldest organisms on Earth -- a billion years before there were eyes. Nilsson and Pelger used pessimistic estimates of the relevant parameters (such as the intensity of selection) for their number-crunching. The point was to determine how many plausible, populational micro-steps of variation would be needed, under minimal assumptions, for very weak selection to yield a fish-like eye -- and then under reasonable assumptions to convert micro-steps into generations and years. The order of magnitude answer was 350,000 -- a geological blink of the eye. (Gross 2003)

    There has been a strange controversy about the fact that popular writings by Richard Dawkins have incorrectly described Nilsson's and Pelger's work as a computer simulation, when it is in fact a mathematical model. Creationists appear to be very worked up about this, but as Nilsson himself explains:
    I have not considered this to be very serious, because a simulation would be a mere automation of the logic in our paper. A complete simulation is thus of moderate scientific interest, although it would be useful from an educational point of view.
    The Nilsson and Pelger (1994) paper remains scientifically sound, and it has not been challenged in any scientific journal with a peer review system. (Nilsson 2003)

    4.2: ASSERTION: "Irreducibly complex" things could not have evolved by small steps, and evolutionists have not even tried to show that they have.

    RESPONSE: According to creationist Michael Behe, who coined the term "irreducible complexity," an irreducibly complex system is "a single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning" (Behe 1997). However, there is no reason at all why such systems could not evolve. Allen Orr explains:
    An irreducibly complex system can be built gradually by adding parts that, while initially just advantageous, become -- because of later changes -- essential. The logic is very simple. Some part (A) initially does some job (not very well, perhaps). Another part (B) later gets added because it helps A. This new part isn't essential, it merely improves things. But later on, A (or something else) may change in such a way that B now becomes indispensable. (Orr 1998)

    As Orr notes, gene duplication often provides the route by which irreducibly complex processes arise:
    Molecular evolutionists have shown that some genes are duplications of others. In other words, at some point in time an extra copy of a gene got made. The copy wasn't essential -- the organism obviously got along fine without it. But through time this copy changed, picking up a new, and often related, function. After further evolution, this duplicate gene will have become essential. (Orr 1998)

    Not only are there mechanisms whereby irreducibly complex systems can be gradually evolved, but Russell Doolittle (who was unfairly criticized in Behe's book) also describes experimental proof that one of Behe's favorite examples of an irreducibly complex system (the blood-clotting process) is not even irreducibly complex to begin with:
    Recently the gene for plasminogen was knocked out of mice, and, predictably, those mice had thrombotic complications because fibrin clots could not be cleared away. Not long after that, the same workers knocked out the gene for fibrinogen in another line of mice. Again, predictably, these mice were ailing, although in this case hemorrhage was the problem. And what do you think happened when these two lines of mice were crossed? For all practical purposes, the mice lacking both genes were normal! [A footnote here refers to Bugge et al. 1996.] Contrary to claims about irreducible complexity, the entire ensemble of proteins is not needed. (Doolittle 1998)

    As for the claim that evolutionists have not even tried to posit and research mechanisms whereby allegedly irreducibly complex systems could have evolved, John Catalano (2004) gives short shrift to that claim.

    For extensive links to articles by and on Michael Behe and his cavalcade of irreducible complexity, see John Catalano's "Behe's Empty Box" at www.world-of-dawkins.com/Catalano/box/behe.htm. For a beautifully illustrated critique of Behe along the same lines as Orr, see Keith Robison's "Darwin's Black Box: Irreducible Complexity or Irreproducible Irreducibility?" at www.talkorigins.org/faqs/behe/review.html

    4.3: ASSERTION: There is no explanation for how the bacterial flagellum could have evolved.

    RESPONSE: I refer the reader to an article by Ian Musgrave on the evolution of the bacterial flagellum, at www.health.adelaide.edu.au/Pharm/Musgrave/essays/flagella.htm.

    4.4: ASSERTION: Evolutionists cannot explain how feathers evolved.

    RESPONSE: (i) The standard view is that feathers evolved from reptilian scales. One can see how this might have happened when one looks at gradations in the present world, where there seem to be intermediates between scales and feathers, often on the same bird. Christopher McGowan explains:
    If we examine the wing of a penguin, we see a wide range of covering structures, from small structures that look like scales at the leading edge, to structures that are obviously feathers at the trailing edge. There are all shades in between. (McGowan 1984:119)

    McGowan goes on to point out that
    feathers and scales are essentially just variations on a theme; both are formed of a horny protein called keratin, and they both develop along similar embryonic pathways. (McGowan 1984:120)

    4.5: ASSERTION: Evolutionists cannot tell us exactly how most organisms and biological structures arose.

    RESPONSE: Evolutionists can account for many biological structures with considerable ease, as long as they are not held to the unreasonable standard of absolutely exact knowledge. For instance, as Douglas J. Futuyma writes,
    One of the most amazing aspects of evolution is how easy it is to account for major transformations through rather simple changes in developmental processes. Most of the differences among different kinds of mammals are quite simply accounted for by changes in the relative rates of growth of different parts of the body. Speed up the elongation of fingers to get a bat wing; slow down the development of teeth or legs to reduce or eliminate them in whales; slow down the growth of the lateral toes and increase that of the middle one to get a horse's hoof. (Futuyma 1982:63-64)

    4.6: ASSERTION: Evolutionists cannot explain how buttefly metamorphosis could have evolved.

    RESPONSE: The evolution of butterfly metamorphosis is not especially well understood, but this is hardly damning evidence against evolution, since butterfly metamorphosis itself is not especially well understood. It is unfair to criticize evolutionists for not having an evolutionary explanation for a process, when the mechanisms underlying the process have not yet been detailed. Since evolution accounts so well for other processes and structures, it seems that the burden of proof in the meantime must be on creationists to demonstrate that butterfly evolution is not possible, which they have no hope of doing at this time, since they do not know the mechanisms underlying butterfly metamorphosis either.

    4.7: ASSERTION: The genetic variation exhibited in microevolution was put in deliberately put in place by the creator in advance, and did not arise from mutation.

    RESPONSE: (i) Since the kinds of creationists who tend to make this claim also tend to be Biblical literalists, it is worth pointing out that the claim cannot be true if the story of Noah's Flood is true. According to the Flood story, only two of each kind of creature (or at least of most kinds: there is disagreement between certain verses of Genesis) were taken onto Noah's boat, while God sent the rest to a watery grave. Since individual organisms can have at most two alleles for each gene locus (we are excluding plants and assuming that Noah did not have Klinefelter syndrome), this means that each surviving kind of organism could have at most four alleles after the Flood, regardless of how many alleles were created by God in the beginning. But we now see far more alleles per locus for many loci in the populations of most organisms, which means they could only have come into existence by mutation.

    In fact, the creationist claim is even incompatible with the story of Adam and Eve. Adam and Eve could at best hold four alleles per locus in their combined genome. But, as a typical example, locus HLA-DRB1 (one of the genes in the human leukocyte antigen complex) has 59 alleles (Ayala et al. 1993:78), which must have come from mutation.

    (ii) More importantly from a scientific standpoint, experimentation with bacteria has shown that antibiotic resistance can and does arise from beneficial mutation, rather than being already present in the bacteria. Douglas Futuyma explains:
    Joshua Lederberg did an experiment in which he grew thousands of colonies of genetically identical bacteria from a single bacterial cell that was unable to survive in the presence of streptomycin. He divided each colony of cells in two, and grew one half with and one half without streptomycin. A few of the colonies survived on streptomycin, because they carried new mutations for streptomycin resistance. (Futuyma 1983:137)

    Since the bacterium from which the resistant colonies evolved was not itself streptomycin resistant, Lederberg's experiment proves that resistance is generated by a mutation, and is not a quality that needs to be present in bacteria from the start.

    4.8: ASSERTION: Homologous features do not prove ancestral relationships between any organisms, because all classifications above the species level are man-made and arbitrary.

    RESPONSE: Where taxa with fine differences are concerned, the classification of a given species may be a bit contrived (as is the case with transitional forms, which usually could be filed as easily under one class as another), but there are clear major differences between most taxa from genus to kingdom level. Still, the homologies persist across taxa, so either they were made by a deceitful creator who wanted to deceive everyone into believing evolution occurred, or else they constitute real evidence of the ancestral relationships between various kinds of organisms. While classification is a human endeavor, the similarities and differences between various organisms caused by their degree of relatedness constitute a reality independent of the choices we make in our classification system. (Ruse 1982:309-310)

    4.9: ASSERTION: The peppered moth does not demonstrate evolution because no speciation occurs.

    RESPONSE: Industrial melanism in the peppered moth was never intended as an example of speciation in the first place, bur rather as an example of microevolution through natural selection. If the standard account of the peppered moth is correct, then industrial melanism does in fact constitute an example of evolution -- one must simply be clear about exactly what is being claimed.

    I should comment briefly on the recent flap surrounding the peppered moth experiments. A few respectable scientists argued relatively recently that the original peppered moth experiments were flawed. In typical fashion, a number of disreputable creationists seized upon this and blew it all out of proportion, claiming that the experiments had been hoaxes, or that they did not demonstrate natural selection at all. One should read the following letter by Bruce Grant, one of the reputable scientists in question, who rebuts the charge that fraud was involved in the peppered moth experiment, and affirms that the original experiment does indeed demonstrate natural selection quite clearly, at www.pratttribune.com/archives/index.inn?loc=detail&doc=/2000/December/13-653-news92.txt. Ken Miller also privides a very readable presentation of the whole matter at www.millerandlevine.com/km/evol/Moths/moths.html

    4.10: ASSERTION: Mutations are always harmful.

    RESPONSE: On the contrary, some mutations have been shown to be extraordinarily beneficial. For instance, consider the following report by George Bakken:
    Microorganisms have acquired new enzymes that allow them to metabolize toxic industrial wastes never occurring in nature (e.g. chlorinated and flourinated hydrocarbons), and are an increasingly important method of pollution control (Ghosal et al., Science 228: 135-142, 1985). Susumi Ohno (Proc. Natl. Acad. Sci. 81:2421-2425, 1984) found that one such new enzyme, nylon linear oligomer hydrolase, resulted from a frame-shift mutation. Frame-shift mutations scramble the entire structure of a protein, and so the enzyme is a random construct! As would be expected, this new enzyme is imperfect and has only 1% the efficiency of typical enzymes, bu the important thing is that it works (Bakken, n.d.)

    Since the mutation documented by Ohno allows the microorganisms in question to consume short nylon oligomers as a primary food source, it certainly qualifies as a beneficial mutation. It is interesting to note that the acquisition of this new metabolic activity has been duplicated in the laboratory (although it is not clear whether it involved the same kinds of microorganisms, the same frame-shift mutation, or the same enzyme). Richard Harter reports:
    In the experiments, non-nylon-metabolizing strains of Pseudomonas were grown with nylon oligomers available as the primary food source. Within a relatively small number of generations, they developed these enzyme activities. (Harter 1999)

    Another example comes from researchers working with the nematode Caenorhabditis elegans, who have identified "four genes, that, when mutated, can make these worms use energy more efficiently, feed and swim at a slower pace -- and live many times their normal life-span. Some of the experimental nematodes lived for almost 2 months, far longer than their expected 9 days" (Pennisi 1996:949; see also Lakowski 1996:1010-1013).

    Yet another example, pertaining to humans and AIDS resistance:
    Population geneticist Stephen O'Brien of the National Cancer Institute, his NCI colleagues Michael Dean and Mary Carrington, and their collaborators provide strong confirmatory evidence that people who have two mutant copies of the gene for CCRS (also known as CKRS), the chemokine receptor that HIV uses when it initially infects white cells, are highly resistant to HIV infection. Another, entirely new, finding is that people who get infected with HIV, but have one mutant copy of the CCRS gene, progress to AIDS more slowly than do people without the mutation. (Cohen 1996:1797)

    Even some of the most seemingly deleterious mutations can have great adaptive value in certain environments. For instance, mutations that cause stunted wing growth in Drosophila increase the fly's ability to survive on islands where high winds are present (Ruse 1982:92). This explains why decades of irradiating Drosophila in the laboratory produced only less fit mutants: in a population's normal environment, virtually all mutations must be neutral or deleterious, because the population is already extremely well adapted to its environment (Moore 1983:11-13). But the same mutations that are deleterious in the organism's normal environment may become beneficial on the geographical fringes of a population, or in the event of environmental change throughout the entire geographical range of the population (a hurricane might wipe out all of the winged Drosophila on an island). It also offers a partial explanation why evolution should be expected to proceed in a punctuated manner on the geological time scale.

    Finally, even certain classes of macromutations can be neutral or beneficial. Richard Dawkins presents an example with snake vertebrae:
    The number of vertebrae in different species of snakes varies from 200 to 350. Since all snakes are cousins of each other, and since vertebrae cannot come in halves or quarters, this must mean that, from time to time, a snake is born with at least one more, or one fewer, vertebra than its parents. These mutations deserve to be called macro-mutations, and they have evidently been incorporated in evolution because all these snakes exist. (Dawkins 1996:103)

    (iii) The young-earth creationist organization Answers in Genesis has declared this an argument that "should definitely not be used" by creationists. They advise using the argument critiqued in 4.12 instead.

    4.11: ASSERTION: Mutations cannot be responsible for evolution, since they are usually deleterious. Would you want your house built by a carpenter who made 99 bad houses for every good one?

    RESPONSE: This kind of criticism simply rests on a bad analogy, something like saying that since you stand little chance of winning the lottery with one ticket, therefore you stand little chance of winning the lottery with 10 million tickets. Here is a better analogy for the way mutation and natural selection work to improve things:

    Suppose your house is able to reproduce itself at no cost to you. You allow it to reproduce until you have 100 new houses. Then you ask the carpenter to work on each of the houses, trying to improve them. If the creationist is right, the carpenter will damage 99 of the houses, but will improve one of them. So you throw away the 99 damaged ones, and keep the improved one. That one then reproduces itself 100 times. The carpenter goes to work on the 100 copies of the improved house. He damages 99 of them, but improves one of them further. It is simply enough to see that if the reproduction is fast enough, you will soon end up with a mansion.

    The problem with the creationists' analogy is that it assumes that there is only one chance for mutation to produce a good result. Naturally, if God offers to mutate your DNA, you should refuse, because you are liable to end up worse. However, you can be pretty sure that if God mutates the DNA of every person on earth, someone is bound to end up better than he or she was before. It probably will not be you, but again, evolution does not require everyone to become improved, since even a single improvement will spread as organisms reproduce and compete with one another.

    4.12: ASSERTION: Mutations never increase the amount of genetic information.

    RESPONSE: It is unclear how to evaluate this claim without a definition of "genetic information." If the term simply refers to any functional sequence of DNA, then mutations that duplicate functional sequences of DNA obviously can very easily increase the amount of genetic information in a genome. If novelty is also required, then it is worth noting that point mutations to the duplicate sequences can generate novel functions without impairing the original function. This is, in fact, how hemoglobin evolved.

    4.13: ASSERTION: Chromosome numbers cannot change without producing harmful effects.

    RESPONSE: The first thing to note is that chromosomal aberrations are not universally harmful. As William Klug and Michael Cummings point out, there is normally diversity in chromosomal structure within single species:
    While the chromosome number is commonly regarded as invariant for a given species, the arrangement of chromosomal material is often polymorphic through chromosomal inversions and translocations. These chromosomal aberrations usually have little direct effect on the phenotype because gene content is rearranged but not altered. (Klug and Cummings 1983:528)

    Likewise, chromosome number can change without altering gene content through the fusion or fragmentation of chromosomes. The second edition of Colin Patterson's book Evolution contains a striking pictorial example, showing how the chromosomal patterns of Drosophila pseudoobscura and D. melanogaster can each be derived from the chromosomal pattern of D. subobscura by chromosome fusion: D. pseudoobscura by one fusion, and D. melanogaster by two (Patterson 1999:33)

    4.14: ASSERTION: Punctuated equilibrium posits massive mutations which cause an organism to give birth to a radically different organism, e.g. a reptile giving birth to a bird.

    RESPONSE: This is simply false. Punctuated equilibrium does not require macromutations (or "saltations"). It requires only that evolution proceed rapidly on the geological scale, with long intermittent periods of stasis. This is entirely consistent with ordinary rates and mechanisms of speciation, since "rapid" on the geological scale and "gradual" on the biological scale, are compatible.

    4.15: ASSERTION: There are plenty of mutations that cause birth defects, but none that cause "birth improvements."

    RESPONSE: As Edward E. Max writes:
    Does the fact that we know many human detrimental mutations but essentially no clear ones mean that there have been no beneficial mutations in human history? Not at all, since there is a clear bias in what medical scientists have studied. The human mutations we know most about are detrimental because medical scientists preferentially study illnesses that cause significant morbidity and mortality. Consider the theoretical possibility that a beneficial mutation has occurred in a particular human gene; even if this mutation were identified by a comparison of the mutated gene in a child versus the unmutated version of the same gene in both parents, there is no way that this mutation would ever be recognized as beneficial. If the mutation increased intelligence, strength, longevity or specific disease resistance, this would never be apparent without long-term breeding experiments that could obviously never be done on humans. Therefore, since such beneficial mutations in humans could never be recognized in humans, our ignorance of examples cannot be taken as evidence that they don't exist. However, the experiments necessary to demonstrate a beneficial mutation can be done with laboratory organisms that multiply rapidly, and indeed such experiments have shown that rare beneficial mutations can occur. (Max 1999)

    The situation is in fact somewhat better than Max describes, as there are known beneficial mutations in humans. For instance, as pointed out in 4.10, one mutation in the gene for CCRS causes one to progress slower from HIV to AIDS, and two mutations in the same gene increases one's resistance to infection by HIV in the first place (Cohen 1996:1797).

    4.16: ASSERTION: The rate of mutation is too small for mutation to serve as a source of variation.

    RESPONSE: According to Philip Kitcher:
    The charge that mutations are rare depends on confusing the mutation rate per locus (on the order of 1 mutation per 100,000 loci) with the rate per zygote (of the order of 1 mutation per zygote) or the rate per population (of the order of 1 billion per population). From an evolutionary perspective, it is the last of these rates that is important. Hence, although [it] is right to claim that mutations are rare (in one sense), [it] is quite wrong to think that this spells trouble for evolutionary theory. Indeed, neo-Darwinian evolutionary theory insists on the rarity of mutation at any individual locus, claiming, for this reason, that natural selection is a more powerful force than mutation (if mutation were extremely frequent, then selection would play a less crucial role). (Kitcher 1982:97)

    Although mutation without natural selection is not expected to substantially transform a population (though it certainly can have an impact), natural selection causes beneficial mutations to spread quickly through a population. Moreover, if a mutant allele is only detrimental in homozygous form, it will take many generations to eliminate it from the gene pool, even if the homozygous form is lethal (Ruse 1982:79-84). This, as well as the common phenomenon of heterozygote fitness (cases in which the heterozygous form has an advantage neither homozygous form has, as with the malaria resistance conferred by a single sickle-cell allele), helps to keep populations supplied with a reservoir of mutant genes, some of which will have an advantage over the "normal" alleles in the event of environmental change. Populations do not have to wait around for lucky mutations to occur after the environment changes - the mutant genes, now beneficial, are already in the gene pool.

    4.17: ASSERTION: Regardless of mutation rates, the rate of microevolution is too low to account for the macroevolutionary change observed in the fossil record.

    RESPONSE: Philip D. Gingerich makes a few observations about this point, using the "darwin" (d) as a factor of change (1 d = change by a factor of e per million years, e being the base of the natural logarithm: see Gingerich 1983:159):
    [R]ates [of evolution] on the order of 400 d probably characterize speciation and radiation in new adaptive zones...Microevolutionary rates measured on the scale of tens or hundreds of years are much higher than phyletic rates derived from fossils. A microevolutionary rate of 400 d is sufficient to change a mouse into an elephant in 10,000 years...Evolution on a microevolutionary scale is invisible in the fossil record, but this does not preclude microevolutionary processes operating over geological time from producing macroevolutionary change on the longer time scale. Microevolution and macroevolution are different manifestations of a common underlying process. (Gingerich 1983:161).

    4.18: ASSERTION: Macroevolution remains unproved because no one has observed it. In fact, macroevolution is in principle unobservable, so evolution is unscientific.

    RESPONSE: Although information in experimental science is acquired through observation, the observation of a great amount of indirect evidence of a process makes as good a scientific case as the direct observation of a process. As Michael Ruse asks, "[t]he evidence that I have a heart is all indirect, neither I nor anyone else ever seen it, but does anyone really believe that it is not a fact that I have a heart?" (Ruse 1982:58). In the same way, there is sufficient evidence for macroevolution that it can safely be considered a fact without direct observation of the process occurring in our time. We need not, as many unsophisticated creationists put it, observe cats changing into dogs right before our eyes, in order to have a good case for macroevolution.

    4.19: ASSERTION: No one has ever seen one species arise from another.

    RESPONSE: As one example, in 1964, Dr. D. J. Reish removed 5 or 6 polychaetes (Nereis acuminata) from Los Angeles/Long Beach Harbor, and grew his sample to a size of thousands. in 1986, four pairs from this group were brought to Woods Hole Oceanographic Institution; the population at Woods Hole thus had gone through two bottlenecks, which are supposed to help drive evolution through genetic drift. In 1977-1978, two new cultures of N. acuminata were gathered from nearby Long Beach and Newport Beach, and grown under the same conditions as the Woods Hole sample. The three populations were later crossed, and it was found that the only crosses that would not produce viable offspring were the crosses involving the Woods Hole culture and the two new cultures. This signifies nothing less than speciation, and all in the laboratory as well. (Weinberg et al. 1992)

    (iii) The young-earth creationist organization Answers in Genesis has has declared this an argument that "should definitely not be used" by creationists.

    4.20: ASSERTION: If evolution were true, then fish would have evolved into amphibians and land animals more than once.

    RESPONSE: First of all, many populations of fish are in fact continuing to evolve. One should not, however, expect them to again evolve fully into amphibians, because the niche they would be exploiting is already occupied by amphibians. D. H. Patent explains:
    Many animals of today appear to be in transition between like in the water and life on land. These organisms can survive at least for limited periods of time in either environment. But we cannot say what the future holds for them. We do not know if they are "on the way" to a terrestrial existence. The chances are, in fact, that they are not really evolving away from an acquatic existence. A species cannot take over a niche that is already occupied by another unless it is in some way better adapted to that niche. Since present land animals have been evolving for millions of years, they have become about as well adapted to land living as possible; a newcomer which is trying to "fit in" is not likely to displace them. (Patent 1977:58-59)

    4.21: ASSERTION: Sexual reproduction could not have come about through evolution.

    RESPONSE: I will leave this question to Don Lindsay, who takes it up at www.cs.colorado.edu/~lindsay/creation/sex.html.

    4.22: ASSERTION: There is no evidence for the rapid development of new species in nature.

    RESPONSE: Here are two examples: (i) 3,500 years ago, a small lake was separated from Lake Victoria by a sandbar. There are now five species endemic to the new lake; they have evolved from the original species in a geological instant (McGowan 1984:29). (ii) A population of Nereis acuminata isolated in 1964 was no longer able to interbreed with its ancestors by 1992 (Weinberg et al. 1992).

    4.23: ASSERTION: Natural selection is a tautology: the fittest survive, and those who survive are the fittest.

    RESPONSE: (i) Fitness is never defined in terms of an organism's ability to survive; rather, it is defined in terms of the organism's reproductive success.

    (ii) Robert Pennock explains a second problem:
    Consider the formula: May the best man win. It seems harmless, but the creationist now points out that we determine which team is best by seeing which wins. If that is what it means to be "best," then the expressed wish seems to reduce to "May the team that wins be the team that wins." It is thus vacuous dogma, objects the creationist, to subsequently explain who won in terms of one team's being "better" than the other. However, we sports fans are not fooled into abandoning the game by such arguments. Of course we do determine which is the best team by looking at its record of wins , and we would certainly explain why it won the trophy by noting its superior record over its rivals. But we understand that this is not the end of the story...even though we do judge on the basis of record, we do not doubt that it is the physical traits of a team, its superior characteristics and playing ability, that make it better than the others. Understanding this, we also understand that it is possible that the best team might not win...This parallels the distinction that biologists make between evolution by natural selection and evolution by natural drift, and the mere fact that we recognize such distinctions is by itself sufficient to show that the tautology objection does not hold in either sports or evolutionary theory. (Pennock 1999:101)

    Pennock is pointing out what Mills and Beatty explicitly state: that fitness is better described in terms of an organism's propensity to leave offspring, than in terms of the actual number of offspring that organism leaves. Quantitatively, fitness (relative to an environment) should be understood as the expected number of descendants to be left: "the weighted sum of [possible numbers of descendants], where the appropriate weights are the probabilites of [leaving that number of descendants]" (Mills and Beatty 1979:11). Since the idea of fitness as propensity to leave offspring does not entail that an organism will in fact leave any offspring at all, the idea is thus not tautologous.

    To put it yet another way, alleles that increase in frequency in a population do not necessarily do so because they confer greater fitness upon their hosts - some alleles increase in frequency because of genetic drift and bottleneck effects. Organisms that reproduce more than their peers due to sheer luck and happenstance are not automatically fitter, even though they are the survivors.

    (ii) The young-earth creationist organization Answers in Genesis has declared the argument that natural selection is tautologous "doubtful, hence inadvisable to use" by creationists.

    4.24: ASSERTION: Given uniform population growth rates, there could not have been humans before 10,000 years ago.

    RESPONSE: Population growth rates are not uniform. Robert Pennock elaborates:
    While application of the principle of uniformity makes good sense when speaking of radioactive decay or random mutation, it does not work so simply given what we know of the history of human population size...Data on other animal species in nature reveal that population size is typically highly variable, with cycles of increase and decrease that average a growth rate of zero, which is what scientists believe held for most of the early history of the human species as well. It was only the advent of agricultural production, the development of permanent settlements and cities, and the introduction of mechanization that allowed the rate of human population growth to depart significantly from this norm to achieve exponential increase. (Pennock 1999:225)

    4.25: ASSERTION: Haldane's Dilemma proves that human could not have evolved over the time span evolutionists say they did.

    RESPONSE: I have not been able to assess this claim myself, so I refer the reader to two other sites that discuss it:
    Robert William's very technical response at www.gate.net/~rwms/haldane1.html.
    Mark L. Bakke's comparatively non-technical response at http://www.bakkster.com/r_crea18.htm.

    4.26: ASSERTION: If humans had evolved from apes, there would no longer be any apes around.

    RESPONSE: (i) Nothing in evolutionary biology says that humans evolved from apes. Rather, humans and apes both evolved from a common ancestor which (as it so happens) is not around anymore.

    (ii) Even if evolutionists did claim that humans evolved from apes (because there are instances when evolutionists claim that a species is descended from another species still in existence today; apes and humans are just not one of these instances), to say that such evolution is impossible because there are still apes around today would be like arguing that an American cannot have Japanese ancestry since there are still Japanese people around.

    (iii) The young-earth creationist organization Answers in Genesis has disavowed this argument as an argument that "should definitely not be used" by creationists.
    References

    F. J. Ayala et al. 1993. MHC polymorphism and human origins. Scientific American 269(6):78-83.

    G. S. Bakken. [n.d.] Creation or Evolution? Berkeley: National Center for Science Education. [Pamphlet]

    M. Behe. 1997. Molecular machines: experimental support for the design inference. www.arn.org/docs/behe/mb_mm92496.htm.

    J. Catalano. 2004. Publish or perish: some published works on biochemical evolution. www.talkorigins.org/faqs/behe/publish.html.

    J. Cohen. 1996. Receptor mutations help slow disease progression. Science 273(5283):1797-1798.

    R. Dawkins. 1996. Climbing Mount Improbable. New York: W. W. Norton & Co.

    J. Diamond. 1985. If the creationists are right, God is a squid. Discover 6(6):91.

    R. F. Doolittle. 1998. A delicate balance. bostonreview.mit.edu/br22.1/doolittle.html.

    R. L. Ecker. 1990. Dictionary of Science and Creationism. Buffalo: Prometheus.

    D. J. Futuyma. 1983. Science on Trial: The Case for Evolution. New York: Pantheon.

    P. D. Gingerich. 1983. Rates of evolution: effects of time and temporal scaling. Science 222:159-161.

    P. R. Gross. 2003. A scientific scandal. www.talkreason.org/articles/blurred.cfm#scandal.

    R. Harter. 1999. Are mutations harmful? www.talkorigins.org/faqs/mutations.html.

    P. Kicther. 1982. Abusing Science: The Case Against Creationism. Cambridge: MIT Press.

    W. S. Klug and M. R. Cummings. 1983. Concepts of Genetics. Columbus: Charles E. Merrill.

    B. Lakowski and S. Hekimi. 1996. Determination of life-span in Caenorhabditis elegans by four clock genes. Science 272(5264):1010-1013.

    E. E. Max. 1999. The evolution of improved fitness by random mutation plus selection. http://www.talkorigins.org/faqs/fitness.html.

    C. McGowan. 1984. In the Beginning...: A Scientist Shows Why the Creationists are Wrong. Buffalo: Prometheus.

    S. K. Mills and J. H. Beatty. 1979. The propensity interpretation of fitness. In Sober 1994:3-23.

    J. A. Moore. 1983. Evolution, education, and the nature of science and scientific inquiry. In Zetterberg 1983:3-17.

    D.-E. Nilsson. 2003. Beware of Pseudo-science: a response to David Berlinski's attack on my calculation of how long it takes for an eye to evolve. www.talkreason.org/articles/blurred.cfm#lund.

    A. H. Orr. 1998. Darwin v intelligent design (again). bostonreview.mit.edu/br21.6/orr.html.

    D. H. Patent. 1977. Evolution Goes on Every Day. New York: Holiday House.

    C. Patterson. 1999. Evolution: Second Edition. London: The Natural History Museum.

    E. Pennisi. 1996. Worm genes imply a master clock. Science 272(5264);949-950.

    R. T. Pennock. 1999. Tower of Babel: The Evidence Against the New Creationism. Cambridge, Mass: MIT Press.

    M. Ruse. 1982. Darwinism Defended: A Gudie to the Evolution Controversies. London: Addison-Wesley.

    E. Sober (ed.). 1994. Conceptual Issues in Evolutionary Biology: Second Edition. Cambridge, Mass: MIT Press.

    J. R. Weinberg et al. 1992. Evidence for rapid speciation following a founder event in the laboratory. Science 46(4):1214-1220.

    J. P. Zetterberg (ed.). 1983. Evolution versus Creationism: The Public Education Controversy. Phoenix: Oryx Press.

    F. Zindler. 1998. www.2think.org/hii/message15.shtml.

    Copyright © 2005, Mark I. Vuletic. All rights reserved.

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    Sunday, October 02, 2005

    FFVII: Advent Children (Warning - Spoilers Ahead!)

    Cloud overseeing Zak's BladeCloud & Aerith
    When I've watched FF: Spirits Within years ago, I was a little desperate - this ain't the Final Fantasy movie in my mind. But seeing FFVII: Advent Children is a masterpiece and this might be the one final fantasy we've been waiting for!

    The movie itself captures my nostalgic moments of playing it in the good ol' PSX reminiscing my casual irks defeating Final Weapon. It was like being into the world off FF7 again - seeing familiar faces, places, summons, and even ubiquituous moogles. When Kadaj, the lead antagonist character, summoned Bahamut and seemingly would want to summon another, I admit I had wished it was Leviathan. Anyway, the excellent piece is movie-long and wouldn't leave you longing for more. But I still wished there were more and it was longer, like a 3-CD set game.

    For a list of familiar appearances, I have listed it below. And if you're someone who grew up playing the game and living up to defeat and finish Sephiroth off, here's your final fantasy to see that you never buried him deeper than one foot in the ground. The story happens almost about 2 years since the playstation game.

    One thing - no chocobos were seen in the game.

    VincentCloud vs Sephiroth
    **Familiar Characters who appeared:
    Cloud Strife
    Tifa
    Aerith
    Zak
    Sephiroth
    Barret
    Marlene
    Vincent
    Yuffie
    Red XIII
    Cait Sith
    Cid
    The Orphans and Denver
    Rufus (he's alive really)
    Rude & Reno
    Shion & Elena
    Jenova (never in the flesh)


    **Familiar Places:
    Midgar
    Shinra
    The Slums
    Frozen Crater
    Outskirts of Midgar
    Ajit and the Forgotten Capital
    Zak's home
    The ruined Church where Aerith's flowers grow

    **Familiar Things worth noticing:
    a moogle (?)
    materias
    Cloud's sword collection
    Shinra motorcycles (cool!!!)
    Tifa's store and exact surroundings
    Cloud & Tifa's limit breaks
    Cid's Sierra


    Kadaj and his boysCloud in battle aura
    And here are the 8 battle scenes (that's right - EIGHT) I've counted. These battles would make the Matrix look like an old Chinese DragonballZ movie.

    1. Cloud vs Kadaj's boys outside Midgar
    2. Tifa vs Loj inside the ruined church
    3. Cloud & Vincent vs Kadaj and his boys at the Forgotten Capital
    4. Rude & Reno vs. Kadaj's boys at the Midgar Plaza
    5. Cloud and his allies vs Bahamut at Midgar
    6. Cloud vs Kadaj's boys off a motorcycle fight
    7. Cloud vs Kadaj
    8 Cloud vs Sephiroth (yeah!!!!)

    To all FFVII fans, never ever miss this movie/DVD. It's a helluva dream come true.

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