CREATIONISM, Intelligent Design (I.D.) and EVOLUTION

CREATIONISM, Intelligent Design (I.D.) & EVOLUTION NEWS 9/30/05
Edited by Edward T. Babinski

WHOLE GENOME DUPLICATION, CREATIONISM AND I.D.
I read last year about the evidence that "whole genome duplication" had taken place not only in plants, but in two very similar but distinct species of zebra fish. Then, recently, I learned that there is now evidence that "whole genome duplication" took place at least twice in the vertebrate line. What's interesting is the evidence that remains in, say, the two species of zebra fish, one species of which has almost twice the amount of genetic material as the other one, with of course many of those duplicated genes without on-off codons, just unused pseudogene duplicates.

Anyway, please do a google search on the topic of "whole genome duplication" or WGD or zebra fish sometime, and let me know what the I.D.ists think of the evidence for this.

Also, if there is a Designer who keeps any sort of close tabs on nature, whole genomes are getting away from Him, just duplicating themselves whole, and leaving many of those duplicates unused, and in fact in the case of the two zebra fish species we know for a fact that the one with the unduplicated smaller genome gets along just fine without duplicating its whole genome as happened in the case of its close cousin.

Another favorite of mine is the evidence of chromosomal fusion seen inside Human Chromosome #2, which still even retains a remnant of the second centromere, and a reversed telomeric region INSIDE the fused chromosome (telomeres are found at the tips of chromosomes not in their MIDDLE, and they have a certain orderly direction to them, pointing outward toward the tips.) Chimps have two shorter chromosomes with a specific banding pattern that aligns quite closely with the banding patterns of the single elongated Human chromosome #2--which as I said, contains internal evidence as well, of once having been two chromosomes. So the evidence of a fusion with the sloppy leftover results still being visible inside human chromosome #2 is not contestable. It's a fact.

The problem for creationists and anyone who thinks that the Designer oversees every little wiggly thingy, is a problem that both creationists and I.D.ists can't seem to face. Though I do recall seeing Berlinski admit on The Daily Show interview two weeks ago, that he accepts evolution and also only pushes I.D. forward as an hypothesis for a FEW things in nature, not everything in nature. So is Berlinski admitting that Darwinism has some force for many things, just not all changes in nature? Looks like the creationists and I.D.ists are backing themselves into a corner. Perhaps?

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23 September 2005
"Insight Into Eye Evolution Deals Blow To Intelligent Design"
How complex and physiologically remarkable structures such as the human eye could evolve has long been a question that has puzzled biologists. But in research reported this week in Current Biology, the evolutionary history of a critical eye protein has revealed a previously unrecognized link between certain components of sophisticated vertebrate eyes - like those found in humans - and those of the primitive light-sensing systems of invertebrates. The findings, from researchers at the University of Oxford, the University of London and Radboud University in The Netherlands, put in place a conceptual framework for understanding how the vertebrate eye, as we know it, has emerged over evolutionary time. Human sight relies on the ability of our eye to form a clear, focused image on the retina. Critical to this function is the eye lens and the physical properties that underlie the transparency of the lens. The eye's ability to precisely refract light is because of high concentrations of special proteins called crystallins found in lens cells.

Vertebrates such as fish, frogs, birds, humans and other mammals all experience image-forming vision because our eyes express crystallins, which helps form the lens that is needed. But our invertebrate relatives, such as sea squirts, have only simple eyes that detect light but are incapable of forming an image.

This lead to the view that the lens evolved within vertebrates early in vertebrate evolution, raising the question: How could a complex organ with such remarkable physical properties have evolved in the first place? Researcher Sebastian Shimeld from Oxford approached this question by examining the evolutionary origin of one crystallin protein family, known as the ß?-crystallins. Focusing on sea squirts, the researchers found that these creatures possess a single crystallin gene, which is expressed in its primitive light-sensing system. The identification of this single crystallin gene strongly suggests that it is the gene from which the more complex vertebrate ß?-crystallins evolved.

Perhaps even more remarkable is the finding that expression of the sea squirt crystallin gene is controlled by genetic elements that also respond to the factors that control lens development in vertebrates. This was demonstrated when regulatory regions of the sea squirt gene were transferred to frog embryos where they drove gene expression in the tadpoles' own visual system, including the lens.

The researchers say this suggests that prior to the evolution of the lens, there was a regulatory link between two tiers of genes, those that would later become responsible for controlling lens development, and those that would help give the lens its special physical properties. This combination of genes appears to have then been selected in an early vertebrate during the evolution of its visual system, giving rise to the lens.

The new findings deal a serious blow to the Intelligent Design movement which has long contended that the lack of an apparent evolutionary pathway for complex eye development indicated the presence of a supreme designer.
Ref: Current Biology, Vol. 15, pages 1684-1689, September 20, 2005. DOI 10.1016/j.cub.2005.08.046

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New evidence in favor of cetacean evolution, based on the evolutionary trees of the parasites that different cetacean species carry on their bodies!

Whales have "lice" whose evolutionary antecedents include crabs and shrimp and other arthropods! And the relationships of those parasites to one another also parallel the evolutionary relationships of the different cetacean species to one another!

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And speaking of sea-going parasites, here's a remarkable new discovery, you've got to see the photos!

Tongue-eating parasite

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MORE NEWS

Personal Stories of Creation/Evolution

Ken MacLeod's Story
By Ken MacLeod, 2003

Ed Brayton's Story
By Ed Brayton

Steve Robertson's Story: A Case History of What Happens to a Young-earth Advocate who works in Geology
A graduate of Christian Heritage College

Steve Smith's Testimony
By Steve Smith, 1998

Wendy Wendel's Story
By Wendy Wendel

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Stories of former creationists (who remained Christians after they became evolutionists)

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My friend Ed Babinski communicated a note to me that you [Dr. Colling is writing this to a Wall Street Journal reporter] might be interested in talking about the difficulty that Christians have moving away from creationism and toward a more realistic view of the world.

I routinely encounter this tension myself, and while working with students at a Christian college. All their lives, the students are taught one truth. (Six day literal creation), and are told by well-meaning parents and pastors that rejection of evolution is essential to the Christian faith.

But then these same young people go to college (even a Christian college)and discover an entirely different truth, one that seems on the surface to be diametrically opposed what they have been taught by those people they most trust. Alas, as a result of this dilemma, the students often experience intense personal pain in relationships with their loved ones, and profound confusion regarding their faith.

For me personally, the greatest task of teaching at a Christian college is not to convince or persuade creationists that evolution is true: The reality of evolution is apparent to anyone who cares to take a serious look. (Unfortunately, most don't look!)
Rather, the greatest challenge is to dismantle the flawed premise that says that understanding in science and belief in God are mutually exclusive, and to provide students with a learning environment where students can effectively learn how life truly functions without feeling that they must discard their faith.

I am not sure what direction you are considering with this Gautam, but if you need some help, I will help. We need to do a better job of communicating a message of integration, not continuing the same old "us vs. them" story that seems to get the headlines most of the time. Science and faith are fully compatible.

On a different, but related note, I have another idea for an article.

Does a potential solution to the entire creation/evolution, science/faith, public school teaching controversy sound interesting?

It is Random Design, and comes from the book, Random Designer - Created from Chaos to Connect with the Creator. Sharon Begley (from your WSJ) wrote about it last December from the perspective of teaching evolution at a Christian college, but no one from the national media has yet written about the concept itself. If you have interest, I can help you understand the concept and would be interested in talking with you further.

In my view, the only solution to science/faith, creation/evolution controveries that has a prayer (sorry) of bringing people together is one that acknowledges the world as it really is, while providing a permanent place at the table for the existence of a Creator.
Over 25 years in biology education at a Christian college, Random Design is the only mechanism I see that accomplishes this objective effectively.

If you need some input for your story idea, and/or if you have interest in pursuing this second direction, please let me know. I have written opinion editorials for the Chicago Sun Times and York Dispatch (Dover, Pa. Intelligent Design court case), been interviewed by NPR and Christian Networks Journal. I am currently working on writing additional articles for the Christian audiences, the national science education crowd (to address the intelligent (or not so intelligent) design issue), and would also like to communicate with general audiences such as those of the WSJ as well. I will also be writing the feature book article for Science and Theology News that will go to press in December.

The Random Designer web site

All best,
Richard G. Colling

Richard G. Colling Ph.D.
Professor of Biology
Olivet Nazarene University

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J. Scott tried setting up a pro-creationist answer but instead wound up leaving the creationist fold, here is his story

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Luke Wenke lwenke/hotmail.com was a young-earth creationist in college and had created a website to battle evolution. Below is Luke's letter to Answers in Genesis in which he mentioned my name and the influence that a packet of geologist's reports I sent him on the Green River formation, had upon him. Sarfati of Answers in Genesis wrote Luke a long letter urging him to reconsider the fact that what had been sent to him in that packet of materials was from an "apostate," and should not be heeded, only the word of God should be heeded. But Luke was not convinced by the arguments of Jonathan Sarfati of Answers in Genesis.

"Dear Answers in Genesis, I see you have a link to my creation-evolution website, 'Dirt or Slime?' on your 'Noah's Ark Site Chronology' page. I just killed that site today, so you should take that link off, because my pages no longer exist. About 2 months ago I became convinced that the earth is millions of years old by the Green River formation. I was sent material from a former young-earther (Ed Babinski) which included responses from creationists. Your article in Creation magazine raises no further evidence. Except that a hurricane left 6 inches of deposits. The formation is several hundred feet! It has dark and light layers and there are even layers with animal tracks and thin volcanic ash layers. There are 6 million layers and I think that means a layer every second or so, across many miles, if the Flood was true, etc. An old earth makes a lot more sense..."

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Robert A. Moore, former young-earth creationist [his personal story about leaving the fold is in Leaving the Fold: Testimonies of Former Fundamentalists], wrote a little booklet chock full of arguments against the literal interpretation of Noah's Flood. His arguments remain a thorn in the side of modern day creationists like Woodmorappe who go to great pains to try and sloth them off, to little avail.

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Interesting also is the fairly recent story of a biology prof. hired by Wheaton College (Billy Graham's alma mater, and the "Harvard" of Evangelicalism), whose contract was apparently not renewed at Wheaton because he was too strongly pro-evolution, and didn't pay enough respect to the "modified dirt" hypothesis of the creation of man as relayed in the Bible. His case was mentioned in an article in the Chronicle of Higher Education. I can send his name and other info on request.

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DR. TERRY GRAY
Terry Gray (biochemist, tried for heresy in a very conservative denomination for writing that God used evolution). Material on Terry Gray's trial.

Evolution in Bacteria

ETB Response on Theology Web

By Sylas July 21, 2005

If you thought evolution was slow and gradual, think again. You may even be helping it along, says Bob Holmes.

So begins one of the main cover stories in the July 9 edition of New Scientist. This is my second thread based on this issue; there will be at least two more.

This article is about exceptionally rapid evolution, especially in response to a changing environment. The initial example is fish. Every fisherman knows that you should throw back the tiddlers. By doing this, you deliberately limit your catch so as to ensure the next generation of fish will survive and go on to repopulate stocks for the next fishing season. Commercial fisheries often work to the same principle, using wide meshed nets that allow baby fish to escape for another day.

Unfortunately, this well intentioned strategy has backfired. By sparing the smaller fish, fisherfolk are not only letting the fingerlings get away; they are changing the selective pressures on the population. Evolutionary change in response can reshape a whole species in a very short space of time. Fifteen years of commercial fishing off the Atlantic coast of Canada has resulted in a reduction in the average size of mature fish by almost half.

Furthermore, changes persist even after a moratorium of fishing was announced. The mean size of fish does start to increase again, but it is not a simple reversal to restore the previous equilibrium. The response of populations to new circumstances brings about more change than simple size. The smaller fish tend to produce fewer eggs, and this inhibits recovery. Also (though this is not mentioned explicitly) changes in fish populations have follow-on effects for other organisms, and after fishing is removed the resulting environment is not the same as originally.

There are now sufficiently many examples of this to show that rapid evolution is not an exception, but a normal part of our dynamic world. Other instances of change discussed include substantial reduction in tusk length for elephants in response to poaching; in the size of bighorn sheep and the size of their horns in response to trophy hunting, experimental simulation of selective fishing in controlled fish populations, changes in the beaks of Darwin's finches on the Galapagos islands in response to climate cycles, cyclic changes in the relative proportions of three mating strategies of the "side-blotched lizard" in south west USA due to an unstable equilibrium, and changes in breeding cycles of squirrels in response to increase temperatures in recent years. Sometimes change is chaotic; as for the finches where the pressures alternate from year to year. Sometimes there is a sudden development of a new consistent trend in response to some new effect, as in the size of fish.

It is also hard to predict exactly what effects will be; but appreciating the potential for rapid evolutionary change does allow some planning for how we manage the environment. For example, in fishing, the article suggests we should consider throwing back both the largest and smallest fish, and keeping only a mid range. This would tend to select for rapid growth, with the "fittest" fish being those spending the least amount of time at the intermediate fishable size. But we don't know what other changes would be attendant upon that. Another strategy is simply to have some strict no fish zones; from which no fish are taken at all, which should blunt selective effects.

The article also notes that microbes are champions at rapid evolution, and that new genes can jump between lineages, breaking the simple pattern of inheritance and allowing new genes and new proteins to sweep across a range of organisms. For example, chemists have developed new compounds, ever seen on earth before; weedkillers like atrazine and 2,4-D, or nitrotoluenes such as TNT. Yet in just a few decades new enzymes have evolved that are able break these chemicals down and even use them for food. Once they have evolved these genes can jump lineages and spread through diverse populations. This may be a useful tool for finding new ways to clean up toxic waste problems.

The article points out that a common response to environmental change is also extinction. Some species just do not adapt to new circumstances, and die out.

One of the serious implications of rapid evolution is for conservationists. Attempts to "preserve" endangered species with captive breeding programs and habitat management is placing them in new situations entirely from those in which they first evolved; and what is preserved may be a lineage undergoing rapid evolution away from the starting point we sought to conserve.
Cheers -- Sylas

Dee Dee Warren (FOUNDER OF TWEB): I don't think any of this is news. Nor would I call it "evolution" either.

POSTED IN RESPONSE BY EDWARD T. BABINSKI
Why not call it evolution, Dee Dee? As Sylas pointed out bacteria have evolved means to digest chemical substances that human beings have only recently made in labs, substances not found in nature. So do you believe that the gene(s) necessary for bacteria to digest the manufactured explosive chemical, TNT, were:

a) created "in the beginning" and hidden inside bacteria and only became activated recently after TNT was invented by human chemists? Think of what an infinite number of genes it would be necessary to hide inside all the world's bacteria, because they are amazingly adaptable little critters.
b) a Designer steps in and deliberates mutates or hands out new genes to bacteria all the time?
c) the bacterial species itself "evolved" something new?

Speaking of those wiley bacteria, they were even caught digesting nylon, a substance that didn't exist until 1935 (they had reduced some nylon in a discard bin to a gooey substance, which is how the little culpits were caught in the act). A study of their genomes, compared with their non-nylon eating cousins', demonstrated that a simple frame shift mutation was responsible for their amazing new digestive ability. Though they were still at least 50X away from fully digesting the nylon, and hence still couldn't extract more than a fraction of the possible energy that might be extracted from the breakdown process.
[For details and responses to creationist objectors, see Dave Thomas's article].
Futher mutational shuffling of genes might enable some of those bacteria to more fully digest nylon, in which case, Victoria's Secrets might be out of business.

And bacteria aren't the only living things to come up with new mutations to handle new man-made substances. There's also mosquitoes, cottom budworms, and houseflies that have undergone some ingenious mutations since the advent of DDT (another man-made chemical ending in T):
"Mosquitoes that are resistant to DDT have evolved multiple copies of the esterase genes that enable them to detoxify it; the cotton budworm has altered the target of the poison, and houseflies have altered the proteins that transport the poison. [So there is a variety of _possible_ mutations that can reduce the killing effects of the same pesticide, in this case, DDT, on an organism. This increases the odds that such resistance could occur via the same random mutations that naturally occur in every organism during meiotic divisions of its germ cells.-- E.T.B.] The insecticides select for those resistant phenotypes, and the genes that confer this
resistance are transmitted to the next generation."
From Random Mutations and Intelligent Design

If you believe that nature can only Devolve and never Evolve, and that mutations must be viewed as harmful, the truth is that mutations are not all harmful, and nature certainly isn't simply devolving.
DROSOPHILIDS FLY IN THE FACE OF DE-EVOLUTION, INSTEAD THEY HAVE EVOLVED!
We see species of flies in Hawaii found no place else on earth. Presumably the drosophilid fly (commonly called the "fruit fly," but that's not all it eats, not in Hawaii) was among the first insects to reach those islands soon after they started to form (about 8 million years ago), and proceeded to fill a variety of niches that drosophilid flies do not fill elsewhere around the world.
Check out the classic article, titled, "Nothing in Biology Makes Sense Except in the Light of Evolution," written by an Orthodox Christian who was also a world class evolutionary scientist, Dobzhansky--scroll down to the part that reads "Adaptive Radiation: Hawaii’s Flies"

Pics of different fruit flies found only on the Hawaiian islands

Add to this a creationist comment (!) about how Hawaiian fruit flies are larger and more brightly colored compared with the rest of the fruit flies on earth, and have even evolved a type of "song" that the mainland fruit flies never evolved. (!) Obviously, some new morphologies and behaviors peculiar to certain species of fruit flies have evolved on the Hawaiian islands:
www.creationmoments.com/radio/transcript.asp?track_id=94

About 25% of all the drosophila species on earth are found only on those tiny Hawaiian islands. While it is the fruit flies that are the best known, many other insect groups have diversified also. Hawaii boasts a carnivorous caterpillar, the happy face spider and a whole host of other fascinating endemic arthropods, many of which are brilliantly illustrated in the book, Hawaiian Insects and Their Kin by Francis Howarth and William Mull. Lush, and also in the book, Remains of a Rainbow; Rare Plants and Animals of Hawai'i by David Liittschwager & Susan Middleton.
Doesn't sound like devolution to me. Sounds like evolutionary adaptations.
How about species of blind cave fish and blind salamanders that lose their eyes? Is it just a case of degeneration? No, because they gained more sense glands in their tongues and their movement-sensing organs known as lateral line canals (that lay alongside their bodies) grew larger and more sensative. These changes were pro-adaptive ones, so pro-adaptive mutations occur.

In fact evidence that whole genome duplication took place in the past without killing organisms has been gathered from comparing the chromosomes and genomes of closely related species of plants, as well as in cases of closely related species of animals (zebra fish). Yet the organisms didn't die, not even from chromosomes doublings or whole genome duplication.

Geneticists recently compared the genomes of two closely related species of Zebra fish, one of which they knew had far more genetic material than the other. But a full genome comparison revealed even more. It revealed that the species with the far greater amount of genetic material probably got it as the result of a massive mutation in the past in which the entire genome had been duplicated, because they found that many duplications of genes existed, while some of the duplicate genes have apparently been weeded out, and others of the dups now lay in non-utilized portions of the genome, and stills others of the dup had undergone some minor mutations making them near-dups, and they were in utilized portions of the genome--hence it appears like those new active genes came about as the result of a massive whole genome duplication and subsequent whittling down of duplicate genes. Yet the organism didn't die in the process, both species of Zebra fish exist today.

That reminds me, have you heard about human chromosome #2? It still contains remnants of its origin from a different kind of mutation, a mutation in which two previous chromosomes fused into a single chromosome. Geneticists point out that human chromosome #2 still contains the remnants of a SECOND centromere (the little button in the middle of chromosomes) and also contains reversed telomeric regions (in the midst of the chromosome, instead of at its ends where teleomeric regions are normally found), that together provide evidence that human chromosome #2 is the result of a fusion of two chromosomes.
Keep in mind that chimp and human chromosomes are very near in number (chimps have one extra chromosome) and even more telling, the chromosomes of both chimp and human are nearly identical in length and even have distinctive chromosomal bands that line up when homologous chimp and human chromosomes are lined up beside each other. But the chimp has one extra chromosome, while human chromosome #2 contains visible evidence of being the result of a fusion of two chromosomes that are both found in the chimp. (And that explains why chimps have one extra chromosome than humans, it's not an extra chromosome in chimps, but in humans two chromosomes fused into one, most probably from a common primate ancestor of both chimp and human).

BIG EVOLUTIONARY CHANGES
If a creationist seeks evidence of really BIG changes, and complains that bacteria are still bacteria and flies are still flies on Hawaii, and fish are still fish (blind or not), then it's only necessary to point out to them that the BIG changes all started out small and long ago, like when the first bacteria became eukaryotes (bigger single cells with distinct nuclei) and the first eukaryotes became aggregated together to form the first colonial multi-cellular ogranisms, etc. So, all big things start out small. Or like when the first vertebrates evolved in the Cambrian from previous simple bi-lateral species that existed, those first vertebrates didn't look like species with vertebral columns do today with their amazing variety from fish to amphibians to reptiles to mammals, monkeys and man. Instead the earliest vertebrates back in the Cambrian consisted of only a tiny species without a jaw, no boney spine, a thin almost worm-like critter with merely a notocord for "spine" and a slightly darkened eye spot at one end of the notocord. The BIG change from that little critter in the Cambrian to today's vertebrates would take several hundred million years.

Also keep in mind that once a line of evolution is moving along it keeps diverging, so you wouldn't expect a fruit fly to evolve into a vertebrate, it's already an insect and already of a certain variety of fly, it's not likely that it will evolve into even another kind of insect because evolution doesn't work backwards toward common ancestors. Neither would one expect a vertebrate like a camel to evolve backward till it became one of those simple little species of the earliest common ancestors of all vertebrates we saw in the Cambrian. "It is easier for a camel to go through the eye of a needle" than for such a thing to happen. Actually it's easier for the earliest common ancestor of all vertebrates to squiggle through the eye of a needle than for a camel with its boney vertebrae to do so.

Nor would we expected a wild dog in Africa to one day grow gills and take to the ocean, barking and chasing catfish in the sea. Though if a modern land mammal DID return to the sea, we WOULD expect it to retain the mammalian features it had previously evolved and not simply jettison it's mammalian four chamber heart and lung for a fish's heart and gills, i.e., not simply revert back to literally being a fish! Take for example the evolution of whales, vertebrates that returned to the sea: "Whales have hearts like ventricles and auricles like mammals, they are warm-blooded, have lungs, nurse their young--just like mammals on land. They even have eyelids that move... [the Right Whale even still has a pelvis, femur and tibia inside its body!] Darwin viewed the similarities as signs that whales (including porpoises and dolphins) descended from mammals that lived on land." [Carl Zimmer, Evolution]
Whales Hind Limb Rudiments