Gungasnake's "Evolution is Bunk" Digression

gungasnake wrote:

Where are the fish with legs?

Gunga, you need to google "Muddskippers"

Einherjar wrote:

gungasnake wrote:

Where are the fish with legs?

Gunga, you need to google "Muddskippers"

This is a mudskipper:



I don't see any legs or feet. I take it you don't have any comment on the other topics I mentioned?

1. How did snakes evolve? Being a snake is actually a sort of a complex deal. You need a very long and narrow body, hearts, lungs and all that sort of stuff have to be differently shaped and packed differently than you find in normal animals, you need to know how to slither, which is a fairly complex skill... Attaining all of that would take many generations.

Consider however that the very first step along such a path (at least according to the theory of evolution) would have to be being born as a quadraplegic (without any arms or legs, due to mutation).

Quote:

I don't see any legs or feet. I take it you don't have any comment on the other topics I mentioned?

The finns have bones with joints in them. they are a precursor to feet.

I'll add that snakes didn't loose their limbs in a single generation, and that lizards evolve to live without legs every once in a while. (we even have the fossils to proove it).

You have mudskippers which live and feed on land, and you have lungfish which breathe air. Why wouldn't fish evolve to live on land? are you seriously proposing that the insects would eat the fish and not the other way around?

How did methamorphosis evolve? I have no problems accepting a gradualistic account.

Paranormal capabilities do not exist. (by definition)

If you want to debate this you will have to axplain what would keep microevolution from becomming macroevolution.

Source .pdf File


INTRODUCTION
A question the biologist frequently hears, and which tends to perplex him because he
does not think along those lines, is What good is this animal, or that plant?' The implication
is that a particular organism was designed and put on the earth in order to be of some
obvious direct or indirect benefit to man; or if it isn't of any such benefit, perhaps it should
be eliminated. The biologist, on the other hand, feels that all organisms exist simply
because they have adapted successfully to their environment, and are thus able to survive ...


... MODIFICATION OF MARINE MAMMALS
The ancestors of the marine mammals at one time lived on land. Close to 100 million
years ago, in some cases, they began evolving into aquatic creatures, resuming life in the
water from which their land ancestors had come originally, but with vastly different
structures. The earliest known fossil whales go back some 60 million years, to the Eocene
epoch ...

''' Cetacean fore-limbs are in the form of flippers. They have the same arm bones as humans, and the same five fingers (except that rorquals lack the thumb). They differ only in having many more bones in the two central digits. A pair of bones embedded in th flesh about where one would expect the hips to be (in the abdominal wall close to the vent) is all that is left of the pelvic girdle. A second pair of bones, present in some species, represents the upper leg bone, and a few species have a third pair, a vestige of one of the lower leg bones. Embryo whales, up to about one inch, show tiny flaps for both fore and hind limbs, possessed by their remote ancestors ...

Cetacean Evolution

Land animals are a reservoir from which some, so long as their have been land animals, have evolved to dwell in the sea. These animals, unlike fish, retain evidence of their exclusively land dwelling ancestors. So it has been with whales (cetaceans) which descended from four-legged mammals.

In Georgia, a 40-million-year-old, yet-to-be-named species of whale with a pelvis like that of a land mammal was found in 1993. Richard C. Hulbert Jr., who described it, suggests that this transitional whale had large hind limbs.

In Egypt, Philip D. Gingerich found, in 1993, a whale that had external legs. The legs were too small to have helped propel the animal on land. Called Basilosaurus, this whale most likely spent all of its time in water. Gingerich speculates that it used its tiny hind limbs to grasp its partner during copulation. In central Pakistan, Gingerich unearthed in 2000, two 47-million-year-old early aquatic whales, about the size of sea lions that he named Artiocetus clavis and Rodhocetus balochistanensis. These are the first of cetaceans ever discovered with intact ankle bones. Since living cetaceans have no vestige of these bones, the discovery of early whales with distinctly artiodactyl ankles provides a "Rosetta stone" to a reading of the descent of whales. The ankle had a unique form that's found only in artiodactyls.

Once a land animal takes to living in the ocean the ancient mariner problem arises: "Water, water every where/ Nor any drop to drink." When did wales evolve the ability to survive without fresh water as marine cetaceans do today? J. G. M. (Hans) Thewissen reported in 1986 on how fossil whale teeth can help to answer that question: Isotope composition of mammalian teeth is a direct reflection of the isotope composition of the ingested water. This turns out to be so because body temperature is nearly constant in mammals. Modern freshwater cetaceans have tooth phosphate delta18O values at least three permil lower than those of marine cetaceans. Evidently by the Middle Eocene some had evolved an osmoregulatory system to handle the excess salt load of living free of the land. Whale species first appear in the Early Eocene.

Pakicetus is the oldest known whale genus. A well-preserved skull of Pakicetus was unearthed in Pakistan by Thewissen in 1991 and 1992. Extrapolating from younger fossil transitional whales, it would have spent much of its life on land. In 1993, Thewissen found, in Pakistan, a 50-million-year-old fossil whale with legs and feet. He named this transitional whale Ambulocetus natans. How its legs attached to the rest of its skeleton, a critical factor in understanding the animal's locomotion, is as yet unknown as its pelvis was not found. Thewissen suggests that, sea-lion-sized, Ambulocetus led an amphibious lifestyle. It could walk on land, but the shape of its bones suggests it had weak hind limbs. It may have walked by dragging its body as do sea lions.

Pakicetus and Nalacetus ingested fresh water. Their fossils are found only in shallow freshwater deposits. Ambulocetus (Figure d05ii) ingested salt water. Its fossils occur only in littoral (beach) beds. Possibly they lived like pinnipeds (seals, walruses). Indocetus ingested sea water. Its fossils have only been found in marine beds.

So, near the beginning of the Age of Mammals cetaceans were with the shape of large wolves but greatly different being in the clade that does not include those carnivores but includes today the herbivore hoofed animals (artiodactyls) with an even number of toes, which include cows, sheep, goats, pigs, deer, and hippopotamuses, and now we know also cetaceans, which include whales, dolphins, and porpoises.

The mammals that would evolve into whales once roamed the continents but they gave up their dry lifestyle for one under the waves. The oldest transitional land cetacean forms are 55-million-years old (beginning of the Eocene epoch). Among the changes, ancient whales lost their legs and pelvises and developed the characteristic fluked tail that propels the leviathan when it flexes its back up and down. Living whales have no visible hind limbs, but some have internal finger-size bones that are vestiges of hips and legs.

Could Evolution be Falsified, Could Creationism be Falsified?



We have two opposing theories that attempt to account for the origin of species. Evolution, based on a number of sciences, proposes that all life on Earth has evolved from earlier species and that this pattern of evolutionary descent goes all the way back to unicellular creatures some 3.5 billion years ago. Creationism, which is rooted in the Christian-Islamic religious tradition, argues that a perfect being created all of life, presumably from, so to speak, a set of divine blueprints. Being perfect, God is thought of as a non-physical supreme being, an all-powerful, all-knowing and a loving God. Anything less would be imperfect.

We have already addressed the issue of evidence for evolution in other papers, and the evidence is overwhelming. (See, for example, the links in the more advanced sources on evolution section of my web site.) The evidence cited by creationists in support of their belief takes the form of attacks on the alleged insufficiency of evolution to account for complexity of organisms and on the widespread presence of gaps in the fossil record. Both forms of evidence pertain to incompleteness in the evolutionary account. As noted in my critical comments on the Philip Johnson paper, explanatory and data incompleteness, which characterizes all sciences, does not constitute negative evidence against any scientific theory, rather it, to the extent it is actually the case, constitutes theoretical completeness and, in regard to evidence, a lack evidence on some aspects of the theory. Negative evidence, on the other hand, occurs when a theory's predictions are met with contradictory data. No such data exist in regard to evolutionary biology, hence the incompleteness of evolutionary biology does not constitute, in and by itself, evidence against it, let alone evidence in support of divine design. Deficiencies in one theory do not count as evidence for another.

It is commonly claimed by creationists that evolution is not really scientific because they claim that all tests of evolution presuppose evolution and it therefore cannot be falsified by any test, i.e., there is no possibility of obtaining evidence that contradicts evolution. Some opponents of creationism claim the same of it. Scientists and philosophers agree that evolution is falsifiable, and most philosophers, including myself, believe that creationism can, in principle, be falsified, providing creationist avoid using ad hoc hypotheses that in turn have no possibility of being tested. This requires that when the data goes against the creationist view, they avoid speculating on God's mysterious ways.

Here are some ways (but not all of the ways) that evolution could be falsified and creationism confirmed, and vice verse.



1) If we found that fossils of all types, from those of simple organisms with primitive skeletal traits to those of more complex organisms with more advanced skeletal traits, were found mixed at all geological levels, this would constitute clear evidence against evolution. Evolution predicts that in ordered geological strata, the remains of organisms with more primitive traits should precede those with more advanced traits since advanced traits evolve from more primitive traits. In contrast, since God created all creatures at the beginning of the Earth, creationism predicts that fossil remains, both primitive and advanced, should be much more mixed (even given the Great Flood). Such a time-wise, geological mixing of primitive and advanced forms would constitute strong evidence that primitive and advanced forms of life were created at the same time, that is, creationism would be confirmed. The actual geological record is massively and clearly in support of evolution.



2) Evolution predicts that there should be at least some transitional forms between ancestral and descendent species and traits (or, if you prefer, between more primitive and more advanced yet similar species or traits), e.g., there should be transitional forms between reptiles and mammals, between ancient apes and humans, between primitive and advanced jaw structures, limb structures, etc. If creationism is true, there is no reason to find fossils of extinct transitional forms, that is, God would not be expected to create intermediate forms. One could argue that a lack of transitional forms would count more strongly against evolution than it would count for divine creation since God, in his inscrutable way, may have created a wealth of intermediate forms. Nonetheless, there is already an abundance of transitional forms in the fossil record, and their number is steadily increasing, so evolution has passed this test.


3) Organisms can be grouped on the basis of some common features, as with mammals, vertebrates and arthropods. Evolution predicts that the traits of the various species within such a grouping, e.g., skeletal structure, should all be modifications of a basic plan characterizing the whole group. Such variations of a basic plan are called homologies, or cross-species patterns. At the evolutionary beginning of the group, an ancestral species would possess the basic trait in a primitive form, and all following members of the group, which descend with modification from the ancestral species, would possess homologous traits. For instance, the number of forelimb bones and how they are jointed should be the same for all mammalian species, and this is what we find, as with the wing of a bat and the arm of a human. Their forelimbs, as with their other body parts, are homologous because bats and humans evolved from a common ancestor in the distant past. It doesn't make sense in terms of biological engineering for an all-powerful God, who designs all species from scratch, to create body parts with the same basic structure when they have such different functions, e.g., forelimbs for flight, forelimbs for ground locomotion, forelimbs for grabbing tree branches and forelimbs for holding things. Aeronautical engineers do not constrain themselves to designing the wings of planes as modifications of the design of deer legs or human arms; so why should God?



4) Vestigial structures and traits are dysfunctional remnants of originally functional structures and traits, e.g., vestigial hips and vestigial second lungs in snakes, vestigial limbs in some whales and vestigial genes in many contemporary species, like the vitamin C pseudogene in primates. Evolution predicts that organisms with vestigial features must have ancestors in which the feature was functional. On the flip side, phylogenetically earlier species would never have vestigial features that are fully functional in later, descendent species, e.g., vestigial nipples should never be found in amphibians or reptiles. The paleontological, anatomical and genetic data bear this out, so evolutionary biology passes this crucial test. In contrast, there is nothing in creationism that plausibly accounts for vestigial features whatever their phylogenetic pattern; why would God waste biological resources on non-functional features?



5) If there were significant disagreements between the pattern of evolutionary relationships derived from multiple, independent lines of inquiry, e.g., from fossils, comparative anatomy, biogeography, molecular genetics and biology (patterns of protein and DNA sequences), then this would count against evolutionary biology. But the record is clear and getting stronger every year - these independent lines of inquiry all lead to essentially the same pattern of evolutionary relationships. Only in some fine details are there differences, and this is due to a paucity of data on those points. If there were significant disagreements, this would not necessarily constitute evidence in support of creationism, but it would constitute evidence against evolution as currently understood.



6) Cladistics, a major tool in comparative anatomy and paleontology, is a statistical analytic method for establishing the evolutionary relationships among species. It makes use of correlations of independent traits. If evolutionary biology were false, there should be no difference in the phylogenetic patterns based on correlations of independent traits and based on dependent traits. Such a failure would not clearly constitute evidence in support of creationism, but it would provide clear negative evidence against evolution. Needless to say, there is a big difference in the phylogenetic patterns based on correlations of independent and dependent traits. Evolution has passed this test.


7) If all forms of life were created by a perfect God, which also then has to be a loving God, we would not expect to find fundamental aspects of the world and of the nature of life that impose great suffering on life's various creatures. We would not expect to find numerous instances of suboptimal design in organisms. (Of course, there's always God's inscrutable ways.) In contrast, if life arose by impersonal, mechanistic physico-chemical means and developed via random genetic mutations, the struggle for existence and hence natural selection, we would expect to find widespread suffering and suboptimal design. Here's a section from my Argument from Design dealing with this test:



(1) There is a lot of random activity, destruction and suffering in the universe. Many natural processes like earthquakes, volcanic eruptions and floods are well suited to the destruction of our homes. Pestilence is well adapted to wiping out our crops and inducing famine, and so on. Disease and predator-prey relations impose suffering and death on all life forms. If this is evidence of design, perhaps the designer has a sadistic side. Or perhaps all this is the result of uncaring physics and evolution. Let's take a closer look at the design of our world, starting with how viruses and microorganisms are well adapted to inflict suffering and death upon their victims.

A. The bacteria Mycobacterium leprae is well adapted to the infection of our body. It enters the body silently and infiltrates the skin and nerves. It multiplies for years and ultimately destroys the nerves, resulting in paralysis, mutilation and disfigurement.

B. The parasite Leishmania is an exquisitely adapted and deadly parasite. It is carried about by sand flies, and when transported to a mammalian victim, it bores through the victim's sinuses and eats out the victim's brain.

C. The bot fly infests humans and many other mammals, especially cattle. They catch female mosquitoes and lay their tiny larvae on the mosquito's abdomen. When the mosquito bites a mammal, a larvae crawls into the wound and begins to grow. The wound begins as an itchy sore on the skin that develops into a large, painful and oozing lesion. After 10 weeks, an inch long maggot crawls out and eventually becomes another fly.

D. The hookworm, which infects 1.3 billion people worldwide, sinks its teeth into the host's intestinal wall and sucks blood from the wound.

E. The blood fluke, Schistosoma, infects some 200 million people worldwide. It swims in ponds until it comes into contact with its primary host, humans. It then releases skin-softening chemicals and drills into the ankles of its human host, Once inside, it infects its host by traveling throughout the circulatory system.

F. The microscopic crustacean Sacculina infects crabs and turns them into castrated, mindless slaves that serve the needs of the parasite instead of themselves.

G. Another, finger-sized parasite crustacean devours the tongue of its fish host and replaces it with itself, thereby getting first shot at any incoming food.

The list goes on, through hundreds of such examples of parasitic adaptations; indeed, most biologists consider parasites among the most successful organisms on our planet.



(2) Most animal species exist in and are highly specialized to rather violent predator-prey relations.

A) The digger wasp is well adapted to carefully sting and paralyze caterpillars and lay their eggs inside the caterpillar's still alive and hence preserved body. The wasp's larva are designed to hatch and slowly eat the alive but paralyzed caterpillar from the inside out, devouring the non-vital organs first so as to keep the caterpillar alive as long as possible. (This parasitic behavior is quite common. Another example is phorid flies, which inject their eggs into the bodies of leaf-cutter ants. When the eggs hatch in the still alive ant, the fly larva chew their way through the ant's innards, finishing with the brain to leave an empty, headless corpse.)

B) God designed the cheetah with teeth, claws, eyes, nose, leg muscles, backbone and brain specialized to the efficient killing of gazelles. The gazelle in turn is specialized to out maneuver the cheetah and to run longer than it, thereby starving the cheetah and its offspring. So we have evidence of design for both the survival of cheetahs and the violent consumption of gazelles and the survival of gazelles and the starvation of cheetahs. Actually, this looks more like designs of competing gods, or of a sadistic god who enjoys spectator blood sports (sort of a divine Roman circus for competing animal species).

C) In Lake Victoria, there is a species of Cichlid fish that has acquired an unusual way to protect its young from the many predators of the lake: its stores its eggs in its mouth and even keeps its young in there after hatching until they grow too large for such safe keeping. However, in the competition between fishes of the lake, a species of cat fish has evolved an insidious response: it lays its eggs right where the cichlid does so that the cichlid mother fish will take the cat fish's eggs into its mouth along with its own eggs. Unfortunately for the cichlid, the eggs of the cat fish hatch before those of the cichlid, and they eat the young cichlids as they hatch, all in the mouth of the protective cichlid mother fish. And the cicklid mother fish, not knowing the young predatory cat fish are not her own, continues to house them in her protective mouth while they grow larger and devour her own.



(3) Even relations within a species can be violent. Here are just a couple of examples.

A. The red-back spider was designed with the female many times larger than the male and their behavior fine tuned to a most gruesome mating ritual. During copulation in a "69"
position, the male offers its abdomen to the fangs of the female for consumption. This gains the male time for further insemination. To be a father and pass on his genes, he has to be a meal. Another example of familial cannibalism is the Stegodyphus spider, whose young eat their mother before leaving their maternal web.

B. The male gender of the bug Xylocaris Maculipennis mates with a female and then seals her shut with a chemical mating plug. The plug prevents sexual access by competing males. Over time, the males of this species adapted to this constraint with a stabbing rape technique where they by-pass the mating plug by non-fatally impaling the female next to the plug and inseminating her there. Males then further adapted with homosexual stabbing rape, in which they impale a male and inject their genes into the competitor's bloodstream. The rape victim then passes on those genes when it impales a female. This is a clever design by which the rapist conceives by proxy.



(4) At the biological level, all species have redundancy and significant and sub-optimal anatomical and physiological "design" that reveal the opportunistic compromises of evolution. In the struggle for survival, evolution has to make use of whatever resources it has for adaptation, and these come down to the genes and physiology inherited by various creatures and whatever random genetic mutations these creatures receive. This means that evolution proceeds by trial and error, and a creature's design is constrained by traits already in place. New traits must necessarily be modifications of previously existing traits. This is called historical constraint. While evolution can modify already existing traits, evolution is extremely limited in its ability to undo them and start anew. The design of all creatures is thus a compromise between legacy hardware and conflicting needs. Here are some examples.

A. The African locust evolved from a non-flying ancestor. When, as a function of a small number of homeotic gene mutations, they acquired wings on their thorax, nerve cells in the abdomen, which is further down the body, were co-opted to control the wings. This resulted in a long nerve signal path from the head down past the thorax to the abdomen and then back up to the wings at the thorax. This inefficiency is typical of evolution. An intelligent designer would have produced a more direct connection from the brain to the wings.

B. Flowering plants normally require the help of pollinating insects for fertilization. Some flowering plants, like dandelions, became self-pollinating and hence have no need for flowers to attract pollinating insects. They still expend the energy to grow them because the genes for producing them are still functional. This is an example of a legacy trait that has lost its function.

C. Baleen whales, which do not have teeth, evolved from terrestrial mammals that had teeth. The genetic record of this evolutionary past reveals itself in the appearance (and then disappearance) of embryonic teeth during the fetal whale's development in the womb. The embryonic teeth are, of course, never used and hence are a waste of developmental resources.

D. A similar example is that of the appearance of cartilage gill bars in all terrestrial vertebrates, including humans, that appear early in embryonic development. These precursors of gills are produced by genes inherited from our distant marine ancestors. Gene activations later in embryonic development shape these gill bars into jaw and throat structures.

E. Whales with vestigial limbs. The vestigial limbs are not functional but are merely shrunken remnants of limbs inherited from their Eocene, legged cetacean ancestors.

F. Most pythons have vestigial pelvises that are not even attached to the vertebrae. The growth of such non-functional parts during embryonic development costs resources, but they're there as legacy traits.

G. Snakes evolved from reptiles with two lungs, but because of the narrowness of the snake body, snakes today have only one functioning lung along with a non-functional vestigial lung. All such vestigial traits retained in the adult organisms are a waste biological resources.

H. Birds evolved from small, dinosaur-like reptiles with teeth. All living birds are toothless, yet they still have genes inherited from their reptilian ancestors that can be turned on to produce teeth.

I. Flounder fish live on the sea bottom and have flat bodies whose eyes are side by side on the same, up-side of their head. Flounder evolved from normal shaped fish whose eyes are on opposite sides of the head, and this evolutionary background is reflected in their embryonic form where the eyes are initially on opposite sides of their head and then one eye moves to the other side. If God designed flounder, why didn't he have them develop from the get-go with their eyes on opposite sides of their head? This would certainly make more efficient use of developmental resources.

J. The human body has many such design inefficiencies and compromises. For example, the optic nerve that connects the light-sensing retina of our eyes to our brain emerges as a bundle of nerve fibers from a point behind the retina and then spread out over the retina. Light, of course, must pass through this mesh of nerve fibers before it can reach the light sensitive retinal cells. This organization results in a blind spot, a reduction of resolution and a structural weakness that promotes detached retinas. The squid eye, in contrast, is free from these flaws because its optic nerve attaches to the back side of the retina, which avoids a blind spot and anchors the retina. Our eyes have their organizational shortcoming because the basic design of the human eye has been inherited from our distant mammalian ancestors. Hundreds of millions of years ago, as a matter of chance mutations, the layer of cells that happened to become light sensitive were located differently than the corresponding layer in ancestors of squids. Both designs evolved along separate tracks, and for the human eye there is no going back.

K. The organization of the prostate in males is so bad that if it were designed by an engineer it would be an indication of outright incompetence. The urethra tube, which channels urine from the kidney to the penis, passes through the prostate gland. As the prostate enlarges with age, it squeezes the urethra tube, obstructing the flow of urine and even causes death in extreme cases. A simple fix would be to have the urethra tube run along the outside of the prostate.

L. A related design flaw is the development of male testes. During embryonic development, the testes appear inside the abdomen. To get down to the scrotum, they have to pass through the abdominal wall, and this leaves a weak spot in the abdominal wall called the inguinal canal. This weak spot can herniate and thereby damage the intestines and restrict blood flow to the testes.

M. A nice example of evolutionary opportunism and compromise in humans is the design of our spinal column. As a species, we are especially prone to lower back problems. The reason for this is that we are a bipedal species, and standing and walking upright requires that all of the body's weight above the legs be supported by the spinal column and balanced at the pivot points where the backbone meets the hips, resulting in a great deal of stress on the lower backbone. Part of the problem here is a conflict between structural support and the need of the human female's birth canal to pass a large brained infant at birth. The other part of the problem is that the human backbone-hip design is a modification of the basic quadrupedal design. Our distant vertebrate ancestors walked on all fours, and in this quadrapedal context, the skeletal design is quite efficient.



There are many other examples (our immune system, our rib cage, which is to short to fully enclose and protect most vital organs, and so on), but the point has been made. The nature of life is what we would expect if its development is under the control of impersonal, trail-and-error, full-of-compromises evolution. It is not what we would expect if life was created by a perfect God. (If you're interested in additional material on this topic, you could take a look at The Scars of Evolution: What Our Bodies Tell Us About Human Origins by Elaine Morgan, The Panda's Thumb: More Reflections on Natural History and Hen's Teeth and Horses Toes, both by Stephen Jay Gould, and The Blind Watchmaker: Why The Evidence Of Evolution Reveals A Universe Without Design by Richard Dawkins.)



Conclusion: there are ways to falsify evolutionary biology and ways to falsify creationism. In terms of passing such just these 6 crucial tests, the score is evolution 6, creationism 0.

Einherjar wrote:

gungasnake wrote:

Where are the fish with legs?

Gunga, you need to google "Muddskippers"

This is a mudskipper:



I don't see any legs or feet. I take it you don't have any comment on the other topics I mentioned?

His alternative is poofism.

I've never heard of anybody using mudskippers as any sort of a proof of evolution before; some sort of a prototype amphibean possibly.

There IS evidence of change in our biosphere and, if you let evolutionists get away with claiming that all evidence of change is evidence of EVOLUTIONARY change, then they win, no question. I simply don't believe in letting them get by with that.

What the evidence DOES show is that the engineering and re-engineering of complex life forms was an ongoing concern of some sort in past ages, but that it is no longer going on and hasn't been during recorded history.

Thus the evidence of vestigial legs in whales despite there being at least two features of whales which could not plausibly or even possibly evolve, i.e. sonar and baleen. For that matter, the first whales or proto-whales were carnivores, and hippos aren't, which, if there is anything to the idea of whales arising from hippos, also says bio-engineering and not evolution.

Ghost in the machine[/size]


03/05/2003


By Graeme O'neill


An Australian biologist has shocked the scientific community with the revelation that non-coding 'junk' DNA that forms most of the human genome is actually the main source of human individuality. Graeme O'Neill reports.

Occasionally, science gets it spectacularly wrong, only to experience one of those forehead-slapping, Homer Simpson-type "D'oh!" moments of revelation years later. Such a moment happened at an international conference on protein structure and function in the south-west Victorian seaside resort of Lorne two weeks ago when Brisbane molecular biologist John Mattick blew away 26 years of cobwebs, and his audience, by heralding the birth of a new branch of genetics.

Mattick, director of the Institute for Molecular Bioscience at the University of Queensland, explained why, after the first primitive bacterial cells appeared in what Charles Darwin described as a "small, warm pond", it took another 3.5 billion years for the first multicellular organisms to evolve. He also explained why it takes a mere 30,000-odd genes to make a human, and why some 98% of the human genome consists of so-called "junk" DNA that does not code for proteins.

It's not junk at all, Mattick told his audience. Rather, it's the ghost in the machine. All that genetic gibberish contains the instructions for assembling and operating the complex cellular machinery of higher organisms, be they human, shrew, whale, eagle or Californian redwood.

In 1977, Mattick was a young post-doctoral researcher at the Baylor College of Medicine in Houston, Texas, when British biologist Richard Roberts and American Phillip Sharp made the discovery that ultimately won them a Nobel prize for medicine in 1993. Roberts and Sharp found that the genes of the higher organisms, known as eukaryotes, are interspersed with extensive tracts of non-coding DNA, dubbed "introns".

Bacteria, the Earth's original prokaryotic life forms," lack introns. Their genes are uninterrupted and are arrayed neatly end-to-end. Eukaryotic genes, in contrast, form lonely islands or archipelagos in an ocean of "junk" DNA.
Long before researchers delivered the first draft of the Human Genome Project in 2001, it was clear that genes would account for less than 2% of the 3.5 billion "letters" of DNA code that it takes to make and operate a human.

"The discovery of introns was the biggest surprise in the history of molecular biology," Mattick says. "Nobody anticipated that the genes of higher organisms would be split into mosaics of protein-coding information separated by vast tracts of apparently useless information."

A gene is essentially a DNA-coded recipe for a protein. Before the protein can be produced, all the "useless infor­mation" has to be edited out. When a gene is activated, enzymes copy its entire DNA code, introns and all, into RNA, a single-strand molecule of genetic code similar to DNA. The introns are then excised and the protein-coding modules are assembled into an uninterrupted "recipe" for the protein.

"It was assumed that because genes code for proteins, the non-coding sequences must be non-functional," Mattick says. "Without a shred of evidence, most geneticists concluded non-coding sequences were ancient evolutionary junk."

Along with introns, and the long stretches of non-coding DNA genes, there are also numerous faded genes called pseudogenes, with no apparent function, plus a huge community of ancient retroviruses. Mattick describes retroviruses as parasitic "hobos" that have infiltrated genomes over hundreds of millions of years to become permanent residents and active citizens.

To Mattick, the dogma that all that non-coding DNA was the accumulated detritus of hundreds of millions of years of evolution made little sense. After all, eukaryotes had inherited a basic complement of genes from their bacterial ancestors, yet bacteria had accumulated no junk DNA in 4 billion years. It seemed much more likely that the supposedly ancient "junk" was a relatively recent innovation, and that it had a function.

As gene sequencing sped up in the 1980s, researchers began comparing corresponding genes in different organisms and it became clear that introns have been conserved over hundreds of millions of years. The DNA code, and the number and position of introns in genes, are uncannily similar in organisms related as distantly as mammals, insects, and plants.

If "junk" DNA has no function, why would natural selection replicate it with such fidelity across such enormous time scales? "I started to suspect that there was something else going on here, something that we did not expect," Mattick says. "If these sequences are faithfully reproduced, but don't code for proteins, maybe they were transmitting genetic information in another form, as RNA molecules produced in parallel with ­protein-coding information.

"If this were true, then we were looking at a massive parallel processing system producing secondary signals that integrate and regulate the activity of genes and proteins. In effect, they co-ordinate complex programs involved in the ­development of complex organisms."

Working for CSIRO in the mid-1980s and then later at the University of Queensland, Mattick scoured the scientific literature for evidence to support, or scotch, his radical hypothesis. "The big leap I made was to entertain the idea that non-coding DNA might actually be the very basis of complexity in higher organisms."

In 1993, Mattick took six months sabbatical leave in the laboratory of eminent British molecular geneticist Peter Goodfellow at Cambridge University. "Rather than do something conventional, I spent the time scratching my intellectual itch about introns," he says. The pieces began to come together.

Before returning home, Mattick gave a seminar to a packed house in Cambridge. He proposed that introns were the remains of molecular parasites, similar to retroviruses, that had invaded the first eukaryotic cells, inserting themselves into genes and dividing them into "modules".

A bacterial gene codes for only one protein. But the intron-divided modules of genes in higher organisms can be mixed and recombined during RNA ­editing to create multiple proteins with different functions. Even more important, says Mattick, the same editing process produces multiple RNA signals. Mattick has evidence that RNA molecules wield ultimate control over when and where genes switch on and off. By switching integrated networks of genes on, and switching others off, RNAs control cell identity. They sculpt the myriad specialised cells of the immune and blood systems, make heart cells for hearts, nerve cells for brains, and liver cells for livers. RNAs also co-ordinate the miraculous development process of growth and differentiation that builds a perfect human baby from a few anonymous embryonic cells.

"It's an amazingly robust and predictable process, self-organising and exquisitely accurate," he says. "People simplistically assumed there is sufficient information just in the combination of proteins and regulatory factors to roll out the embryonic program. It's like expecting all the transistors, screws, rivets and other bits of a Boeing 747 to just assemble themselves."

If Mattick is right, and his evidence persuades a growing number of colleagues that he is, the descendants of his DNA-parasitic "hobos" are the "gnomes of the genome", toiling away unnoticed in the city of the cell, organising and running the whole, wondrous shebang.

He thinks it likely that the "Rnome", as he calls it, is the major source of human individuality, not just the genes. And non-coding DNA offers a barn-door target for mutation relative to the tiny amount of DNA devoted to genes. Disturbances in the RNA networks, affecting how genes respond to environmental cues, may explain complex geneticdisorders such as auto-immune diseases that do not obviously involve mutant genes.

Mattick expects that as the science of Rnomics evolves, it will enormously increase the precision and power of genetic engineering of higher organisms.

Roberts and Sharp won a Nobel prize for discovering introns. A quarter of a century later, an Australian biologist has finally offered a coherent explanation of what introns, and all that "junk", actually do.

Other than that, you've not tried to answer the second part of that one, i.e. if evolving feet and legs is such an easy thing, why don't we ever see the first sign of it in the millions of fish we haul in every year? The law of averages says we'd have to, if it was possible.

You'd HAVE TO lose your legs and feet all at once since nothing could survive any sort of a process of losing them gradually. In fact, that sort of thing is what evolutionists usually claim, i.e. that you get some sort of fairly large change via mutation, and then the mutated creature adapts.