Posted on 02/20/2005 2:45:33 PM PST by DannyTN
Those assuming the evolution of eukaryotic genomes has progressed upward in complexity may find the following abstract from PNAS1 startling:
We use the pattern of intron conservation in 684 groups of orthologs from seven fully sequenced eukaryotic genomes to provide maximum likelihood estimates of the number of introns present in the same orthologs in various eukaryotic ancestors. We find: (i) intron density in the plant-animal ancestor [sic] was high, perhaps two-thirds that of humans and three times that of Drosophila; and (ii) intron density in the ancestral bilateran [sic] was also high, equaling that of humans and four times that of Drosophila. We further find that modern introns are generally very old, with two-thirds of modern bilateran introns dating to the ancestral bilateran [sic] and two-fifths of modern plant, animal, and fungus introns dating to the plant-animal ancestor [sic]. Intron losses outnumber gains over a large range of eukaryotic lineages. These results show that early eukaryotic gene structures were very complex, and that simplification, not embellishment, has dominated subsequent evolution. (Emphasis added in all quotes.)In their paper, Harvard biologists Scott Roy and Walter Gilbert used the maximum-likelihood phylogenetic method instead of maximum parsimony, and feel it provided a better ancestral tree. In fact, they used the same data as other scientists who used parsimony, and got very different results. They are emphatic about their conclusions:
These results push back the origin of very introndense genome structures over a billion years to the plant-animal split [sic]. Indeed, ancestors at the divergences [sic] between major eukaryotic kingdoms as well as the ancestral bilateran appear to have harbored nearly as many introns as the most intron-dense modern organisms. This is a sharp repudiation of the common assumption that intron-riddled gene structures arose only recently.This bias toward intron loss instead of gain appears to be a general trend among eukaryotes, they conclude. What does this mean? The only way to rescue an evolution toward “improvement” with these results is to suggest that introns are bad, like parasites, and that over time, eukaryotes got better at ridding themselves of them. They reject that and other notions, assuming instead that “It seems much more likely that different selection or mutation regimes for introns along different lineages are driving the observed instances of gene streamlining.” Although intron function and evolution is still largely unknown, they leave only an admission of ignorance of what their results mean – only that geneticists had better re-examine their assumptions:
In addition, our analysis shows that the majority of introns are themselves very old. Two-thirds of bilateran introns were present in the bilateran ancestor [sic]; 40% of opisthokont introns were present in the ophisthokont ancestor; and 40% of plant, animal, and fungal introns were present in the plant–animal ancestor. This is quite different from what is commonly assumed and surprising in light of relatively fast rates of intron turnover observed in nematodes and flies.
These results contradict the assumption that genome complexity has increased through evolution. Instead, species have repeatedly abandoned complex gene structures for simpler ones, questioning the purpose and value of intricate gene structures. These results suggest a reconsideration of the genomics of eukaryotic emergence [sic].
Introns and the complex molecular machines that process them (spliceosomes – see 09/12/2002 and 09/17/2004 entries) are still mysterious, but does anyone see a neat picture of evolution here? Why would some introns be ultra-conserved (see 05/27/2004 entry), and others be removed? Evolutionary theory is not helping explain introns or spliceosomes, and may be missing entirely the picture of what is going on. Why not approach the data from the perspective of intelligent design and entropy? The complexity was apparently present from the start. Where did it come from? The notions of ancestry in this picture are fictional. The assumed trees are filled with gaps. What seems apparent is devolution, not evolution.
Some have suggested that introns provide opportunities to expand the genetic code through alternative splicing, so that more information can be gleaned out of a compact code. Others have pointed to robustness and repair as possible functions. Let a new generation of geneticists approach this problem without fogged-up Darwinian glasses on. They certainly cannot see things any worse than the Darwin Party has done so far.
Creation-Evolution Headlines; misunderstanding science articles that are clearly over their head for....how long have these clowns been in operation?
It's all psycobabble to me. What exactly does this mean in everyday english??
My first question has always been: "What makes you think that evolution is progress?"
That genes started out complex with more information in them than the current genes. That genes have lost information along the way.
It's supportive of the creationist claims that mutations only result in the loss of information, which usually results in the loss of functionality. It's never the other way.
You can't get to the kind of additional information that evolution needs to evolve higher life forms, with the kinds of mutations we see. Mutations are headed the wrong direction. They are weakening the gene pool.
LOL ... what an obvious error... / sarcasm
"Creation Evolution Headlines" - Joe Sixpacks quoting scientific papers with lots o' technical jargon to wow and stupify the audience.
It means my friend Gene has fallen off the wagon.
Well..he always was a fan of entropy.
More science misquoted and taken out of context by nutcase creationists. Why don't you folks give it a rest and post this stuff in the "Religion" section, where it belongs??
When Evo's start posting their speculations in "Religion" where it belongs, we Creationists will do the same.
Tell me, what was misquoted?
What was taken out of context?
We interpreted the results differently than they did, but it seems to me the quotes accurately representative of what was concluded.
Great Post!
Does this just substantiate the fact that genes are
evolving downward through time as we all knew?
Or, is this just a petty attempt to alleviate one's own
doubts about faith by disparaging others' beliefs?
I agree... Creationists are the only proof of their claims.
All physics textbooks should include this warning label:
"This textbook contains material on Gravity. Universal Gravity is a theory,
not a fact, regarding the natural law of attraction. This material should be
approached with an open mind, studied carefully, and critically considered."
The Universal Theory of Gravity is often taught in schools as a fact, when
in fact it is not even a good theory.
First of all, no one has measured gravity for every atom and every star. It
is simply a religious belief that it is "universal".
Secondly, school textbooks routinely make false statements. For example,
"the moon goes around the earth." If the theory of gravity were true, it
would show that the sun's gravitational force on the moon is much stronger
than the earth's gravitational force on the moon, so the moon would go
around the sun. Anybody can look up at night and see the obvious gaps in
gravity theory.
The existence of tides is often taken as a proof of gravity, but this is
logically flawed. Because if the moon's "gravity" were responsible for a
bulge underneath it, then how can anyone explain a high tide on the opposite
side of the earth at the same time? Anyone can observe that there are 2–not
1–high tides every day. It is far more likely that tides were given us by
an Intelligent Creator long ago and they have been with us ever since. In
any case, two high tides falsifies gravity.
There are numerous other flaws. For example, astronomers, who seem to have
a fetish for gravity, tell us that the moon rotates on its axis but at the
same time it always presents the same face to the earth. This is patently
absurd. Moreover, if gravity were working on the early earth, then earth
would have been bombarded out of existence by falling asteroids, meteors,
comets, and other space junk. Furthermore, gravity theory suggests that the
planets have been moving in orderly orbits for millions and millions of
years, which wholly contradicts the Second Law of Thermodynamics. Since
everything in the Universe tends to disorder according to the 2nd Law,
orderly orbits are impossible. This cannot be resolved by pointing to the
huge outpouring of energy from the sun. In fact, it is known that the flux
of photons from the sun and the "solar wind" actually tends to push earth
away.
There are numerous alternative theories that should be taught on an equal
basis. For example, the observed behavior of the earth revolving around the
sun can be perfectly explained if the sun has a net positive charge and the
planets have a net negative charge, since opposite charges attract and the
force is an inverse-square law, exactly as the increasingly discredited
Theory of Gravity. Physics and chemistry texts emphasize that this is the
explanation for electrons going around the nucleus, so if it works for
atoms, why not for the solar system? The answer is simple: scientific
orthodoxy.
The US Patent Office has never issued a patent for anti-gravity. Why is
this? According to natural law and homeopathy, everything exists in
opposites: good-evil; grace-sin; positive charges-negative charges; north
poles-south poles; good vibes-bad vibes; etc. We know there are
anti-evolutionists, so why not anti-gravitationalists? It is clearly a
matter of the scientific establishment elite protecting their own.
Anti-gravity papers are routinely rejected from peer-reviewed journals, and
scientists who propose anti-gravity quickly lose their funding. Universal
gravity theory is just a way to keep the grant money flowing.
Even Isaac Newton, said to be the discoverer of gravity, knew there were
problems with the theory. He claims to have invented the idea early in his
life, but he knew that no mathematician of his day would approve his theory,
so he invented a whole new branch of mathematics, called fluxions, just to
"prove" his theory. This became calculus, a deeply flawed branch having
to do with so-called "infinitesimals" which have never been observed. Then
when Einstein invented a new theory of gravity, he, too, used an obscure bit
of mathematics called tensors. It seems that every time there is a theory of
gravity, it is mixed up with fringe mathematics. Newton, by the way, was
far from a secular scientist, and the bulk of his writings is actually on
theology and Christianity. His dabbling in gravity, alchemy, and calculus
was a mere sideline, perhaps an aberration best left forgotten in describing
his career and faith in a Creator.
To make matters worse, proponents of gravity theory hypothesize about
mysterious things called gravitons and gravity waves. These have never been
observed, and when some accounts of detecting gravity waves were published,
the physicists involved had to quickly retract them. Every account of
anti-gravity and gravity waves quickly turns to laughter. This is not a
theory suitable for children. And even children can see how ridiculous it is to
imagine that people in Australia are upside down with respect to us, as gravity
theory would have it. If this is an example of the predictive power of the theory
of gravity, we can see that at the core there is no foundation.
Gravity totally fails to explain why Saturn has rings and Jupiter does not.
It utterly fails to account for obesity. In fact, what it does "explain" is
far out-weighed by what it does not explain.
When the planet Pluto was discovered in 1930 by Clyde Tombaugh, he relied on
“gravitational calculations”. But Tombaugh was a Unitarian, a liberal
religious group that supports the Theory of Gravity. The modern-day
Unitarian-Universalists continue to rely on liberal notions and dismiss
ideas of anti-gravity as heretical. Tombaugh never even attempted to
justify his "gravitational calculations" on the basis of Scripture, and he
went on to be a founding member of the liberal Unitarian Fellowship of Las
Cruces, New Mexico.
It is safe to say that without the Theory of Gravity, there would be no talk
about a "Big Bang", and important limitations in such sports as basketball
would be lifted. This would greatly benefit the games and enhance revenue
as is proper in a faith-based, free-enterprise society.
The theory of gravity violates common sense in many ways. Adherents have a
hard time explaining, for instance, why airplanes do not fall. Since
anti-gravity is rejected by the scientific establishment, they resort to
lots of hand-waving. The theory, if taken seriously, implies that the
default position for all airplanes is on the ground. While this is obviously
true for Northwest airplanes (relying on "A Wing and a Prayer"), it appears
that Jet Blue and Southwest have a superior theory that effectively
harnesses forces that overcome so-called gravity.
It is unlikely that the Law of Gravity will be repealed given the present
geo-political climate, but there is no need to teach unfounded theories in
the public schools. There is, indeed, evidence that the Theory of Gravity
is having a grave effect on morality. Activist judges and left-leaning
teachers often use the phrase "what goes up must come down" as a way of
describing gravity, and relativists have been quick to apply this to moral
standards and common decency.
It is not even clear why we need a theory of gravity---there is not a single
mention in the Bible, and the patriotic founding fathers never referred to
it.
Finally, the mere name “Universal Theory of Gravity” or “Theory of Universal
Gravity” (the secularists like to use confusing language) has a distinctly
socialist ring to it. The core idea of "to each according to his weight,
from each according to his mass" is communist. There is no reason that
gravity should apply to the just and the unjust equally, and the saved
should have relief from such "universalism." If we have Universal Gravity
now, then Universal health care will be sure to follow. It is this kind of
Universalism that saps a nation's moral fiber.
Overall, The Theory of Universal Gravity is just not an attractive theory.
It is based on borderline evidence, has many serious gaps in what it claims
to explain, is clearly wrong in important respects, and has social and moral
deficiencies. If taught in the public schools, by mis-directed "educators",
it has to be balanced with alternative, more attractive theories with
genuine gravamen and spiritual gravitas.
Author: Ellery Schempp
My genes aren't missing. They're right in my dresser where I left them.
But have they shrunk?
In fact, they used the same data as other scientists who used parsimony, and got very different results.
In other words, the conclusions do not follow from the data, but rather from the assumptions made in interpreting the data. Other scientists use an assumption they call "parsinomy"; the current authors use one they call "maximum likelihood".
I went and read the paper - it's online, just follow the links - and here is my short analysis.
We have two critters - A and B - presumed descended from a common ancestor, X. Where the genomes of A and B are identical, we assume those bits inherited from X. But what of the differences? Let's say that A has a feature F (specifically in the paper, an intron - look it up to find out why this is important), and B does not. There are two possibilities.
(1) X had the feature F, A inherited it, but B lost it.
(2) X did not have F, B duly did not inherit it, and A gained it.
Clearly, assumption (1) leads to the conclusion that features are gradually lost, which means genomes are becoming simpler over time. And assumptionm (2) leads to the exact opposite conclusion.
Well, which is right?
I don't know, and neither it seems do the experts, but what I do know is probability theory, and the key section of the paper, which is all about probability theory, is flat wrong. Here is my analysis.
Once two lines of descent have split - as X split into A and B - their subsequent histories are independent. This leads the authors to suppose that the probability that A will gain an intron (F) is independent of the probability B will gain one, and vice versa. That is dubious, but since they don't use this assumption it doesn't matter. (To see why it's dubious, would you agree that chickens and ducks have completely independent susceptibilities to bird flu? I hope not)
But the assumption they do make is even more dubious, namely that the probabilities A or B will lose introns are independent. This is the basis of their initial probability equations, which are based on the assumption of independent probabilities of intron retension, and hence of their entire conclusion.
But that assumption cannot be true. If we investigate A, say, and find F, we assume A has "retained" F. But when we now investigate B, and find it lacks F, our interpretation of the data must take into account what we know about A. In other words, what would be the probability B has lost F, given that A has retained it. That is proper Bayesian reasoning, and it dramatically affects our interpretation of the evidence. In particular, if an intron has been retained by A, this greatly increases the posterior probability it would also have been retained by B, and hence casts serious doubt on the prior assumption of retention.
To cut to the chase: the author's assumption of independent probabilities gives a much greater likelihood for the assumption of retention rather than acquisition, and hence a much larger estimate for the complexity of the early genome.
The author's conclusion is a consequence of their assumptions, and in my opinion the dramatic nature of the conclusion is entirely an artifact of error in those assumptions.
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