Saturday, August 24, 2013

Minor Spliceosomes as Real Time Sensors In Gene Regulation

More Theoretical Complexity

New research out of the University of Pennsylvania reveals yet another fascinating aspect of gene expression regulation. In the higher species genes are not one continuous DNA segment. Instead there are intervening segments within genes known as introns (intervening regions). Many introns are quite long and some are short. After a gene is copied by the transcription machinery (known as RNA polymerase), resulting in an mRNA transcript, these major and minor introns are spliced out of the mRNA by the major and minor spliceosomes, respectively. The new research shows that the minor spliceosomes can be turned off, thus turning off the expression of that gene.

When introns were first discovered, evolutionist figured they were yet more junk DNA. After all, why should genes have intervening regions which are simply removed from the gene copy? But introns are found throughout the genome. If they were junk why would they be so prevalent? Furthermore, how is it that spliceosomes can edit introns so precisely? If there were no introns then there would be no need for spliceosomes and so they would never evolve. And even if they did evolve there would be nothing for them to do and so evolution would discard them. On the other hand, if introns evolved first, then there would be no spliceosome to remove them. The resulting proteins would not function and the organism would quickly die. Either way, it is yet another conundrum for evolutionists.

In fact spliceosomes are incredibly complicated and perform sophisticated functions. The new research has found another function, and it presents yet another problem for evolution. The research discovered that the abundance of one of the key parts of the minor spliceosome can vary dramatically. Its abundance is controlled by a special protein and its abundance, in turn, controls whether the minor spliceosome is turned on or off. And this, in turn, controls whether or not a large number of very important genes are expressed.

Thus one single action has severe consequences for the cell. It is not a design that is gradually implemented. So not only are separate and independent structures and mechanisms simultaneously required for successful splicing, and not only are those structures and mechanisms incredibly complex, but the design space is highly nonlinear and discontinuous. This is yet another conundrum for evolution, the theory that calls for slow gradual change. Here is how one report described the findings:

The investigators found that a scarce, small RNA, called U6atac, controls the expression of hundreds of genes that have critical functions in cell growth, cell-cycle control, and global control of physiology. … These genes encode proteins that play essential roles in cell physiology such as several transcription regulators, ion channels, signaling proteins, and DNA damage-repair proteins. Their levels in cells are regulated by the activity of the splicing machinery, which acts as a valve to control essential regulators of cell growth and response to external stimuli. Dreyfuss, who studies RNA-binding proteins and their role in such diseases as spinal muscular atrophy and other motor neuron degenerative diseases, describes the findings as “completely unanticipated.”

The theory of evolution attempts to explain how the species arose. With the inexorable march of science, that explanation is becoming increasingly complex.

Thursday, August 22, 2013

Wednesday, August 21, 2013

The Damsel Fish and its Amazing Survival Strategies

Multiplying Entities

When young damsel fish (Pomacentrus amboinensis) are in danger their eyes shrink while they grow false eyespots on their tail to fool their predators. They also undergo other morphological and behavior changes to escape attack. Research out of Australia not only elucidated these tactics but demonstrated that they work, increasing the survival rate of the young fish by an amazing five-fold. And while the researchers had to admit that all of this was “an amazing feat of cunning for a tiny fish,” they nonetheless ignored Occam’s advice and multiplied entities when they added nothing to the science by ascribing it all to random chance (No natural selection does not induce the good mutations to occur, it merely kills off the bad ones—every mutation leading up to the damsel and its “amazing” capabilities must be random with respect to need. Selection doesn’t magically make fantastic designs appear.):

It all goes to show that even a very young, tiny fish a few millimetres long have evolved quite a range of clever strategies for survival which they can deploy when a threatening situation demands.

It all goes to show? In fact, to be a bit more precise, none of it shows the damsel evolved. That’s right, even though the evolutionists claim that “it all goes to show” that the clever strategies evolved, from an empirical science perspective, none of the evidence shows any such thing.

All versus none—that’s quite a gap between evolutionary thought and science. As usual evolution is the contra indicator. It abuses science, turning it upside down to support its preconceived, mandated result.

Sunday, August 18, 2013

Weekend Roundup

Evolution is Making a List

Homing pigeons have always been fascinating but now Nicole Blaser has shown that they have a spatial map and cognitive capabilities. Or as the University of Zurich doctoral student put it, “Pigeons use their heads to fly.” And how did the pigeons obtain their incredible capabilities? Despite intensive research, that is not yet “definitively clear.

Perhaps those capabilities predate birds altogether. As we know with evolution anything can happen, and evolutionists are now having to conclude that flight-ready bird brains were present in dinosaurs, before birds themselves evolved.

And while we’re on the subject of birds and bird brains, Alice Auersperg’s research is showing that Cockatoos can track and predict the emergence of temporally out of sight objects. Their abilities rival those of apes and young children.

Speaking of apes and humans, research out of Japan continues to reveal the importance of epigenetic differences. Their research suggests that DNA methylation changes “contribute to transcriptional and phenotypic diversification in hominid evolution.” In other words, evolution occurred via incredibly complex molecular “bar code” mechanisms which, themselves, must have been created by evolution. So evolution must have created the mechanisms which cause evolution to occur. That is what philosophers call a self-referential theory. (Other people just call it wrong).

But epigenetics is only one of many. Another conundrum is the genetic networks which, as McGill University’s Leon Glass explains, are so complex that researchers have been slow to unravel them. Yet everyone is certain they evolved.

One sure sign that a problem is not solved (and therefore not a fact) is when the answer continues to switch between alternatives. For origin of life researchers, those alternatives have included a warm little pond (as Darwin put it), deep sea hydrothermal vents, and outer space. Last year the ball went back into the warm little pond court, but now NASA’s Mike Russell just hit it back into the deep sea hydrothermal vent court. So what’s next? Look for a new comet soon that puts the ball back into outer space.

Of course none of these problems are very serious since it is certain that evolution is true. In fact, not only did evolution create all things, it also supplies right and wrong and the proper punishment to go along with it. As evolutionists at Michigan State University now explain, “We found evolution will punish you if you’re selfish and mean.” So evolution is not only true, it is also good. It’s making a list and checking it twice; it’s gonna find out who’s naughty and nice.

Saturday, August 17, 2013

Resistance To Change In Early Fly Experiments

The Eyes Have It

When Charles Darwin first proposed his theory of evolution it was well understood that evolution does not come easily. Breeders knew that they could induce only limited biological change in a population. These limitations were described in the Law of Compensation, discussed by such luminaries as Johann Goethe, which explained that there were constraints on how much a species could vary. In the 150 years since Darwin this problem for evolution has only become worse. Not only do species resist change, but the change we do observe is brought about not by simple perturbing forces such as random mutations, but by profoundly complex processes that function as adaptation machines. None of this ever raised any doubts for evolutionists, however, because in their view evolution must be true.

Evolutionists have always been nonplussed by the evidence for complex adaptation in biology. In the 20th century evolutionists tried to show that random mutations could bring about evolutionary change. Not only did they spectacularly fail, but in the process they stumbled upon evidence for profound adaptation. Here is how evolutionist Julian Huxley described one example in his 1953 book Evolution in Action:

Finally, we have the curious fact that the harmful effects of mutant genes may automatically be selected back toward normality. For instance, the so called the eyeless mutant of the famous fruit fly, Drosophila, at its first appearance had no or small eyes and was less healthy and in general less capable of survival than normal wild-type of flies. But after a pure eyeless strain had been bred for eight or ten generations, both its health and vigor and it’s eyes were almost normal. Any odd mutant genes already present in small numbers in the strain, which reduced the harmful effects of the eyeless mutation, automatically multiplied at the expense of those which did not. Natural selection, in fact, provided a genetic servo-mechanism to regulate the mutant back toward normality in its effect. [40]

Yes it was a curious fact. And it could have been used to learn more about adaptation. But under evolution it was viewed as just another product of natural selection. It is another example of how evolution is not vulnerable to scientific findings.

Podcast: Aristotelianism is Dead, Long Live Aristotelianism

The Three T’s

Thursday, August 15, 2013

Undeniable Proof of Evolutionists

This is Not a Hoax

Are there really people who believe everything came from nothing? Yes, and to prove it we now have this rare, never before seen, footage of real evolutionists. There are many skeptics who don’t believe there are any evolutionists left, but in fact there are many enclaves yet to be studied. We predict that soon anthropologists will bring us a much greater understanding of this bizarre phenomenon.

Sunday, August 4, 2013

Evolutionist: We do not promote any “spiritual ideologies.”

But Evolution is a Scientific Fact

After our recent reporting on new research out of John Mattick’s lab on how RNA structure conservation suggests that, even according to evolution, yet more of the mammalian genome is functional, lead author Martin Smith informed us that we had it all wrong:

Hello bloggers. I am the lead author from that paper. I would simply like to point out that the study looks at evolutionary data to make the findings. By promoting our research to support intelligent design, you are intrinsically admitting that evolution is a fact and that it is central to biology and the natural world.

We explicitly measured genetic mutations across 35 mammalian species. We made predictions against a null hypothesis that uses a phylogenetic tree calculated from these mutations. Phylogenetic trees are how Darwin illustrated his theory of evolution (which is a scientific fact). We show that at least 13.6% of all mammalian genomes have evidence of common RNA structural components, but these structural components vary between each individual species consistently with their common ancestry.

In summary, the work shows that at least 14% of our genome (likely over 30%) displays explicit evolutionary evidence of function through RNA secondary structure alone. Our work should find common ground between the ENCODE findings and its critiques, as it is focused on evolutionary evidences. It does not promote any spiritual ideologies and was performed in a scientifically objective manner. 

Wow, that is quite a slam. Like Marshall McLuhan upbraiding the Columbia University professor (click above), Smith gets right to the point and informs us not only that his work reveals evolution but that evolution is a fact.

There’s only one problem: none of this makes any sense.

It is always good to hear from evolutionists for it provides yet more insight into the world of those who believe evolution is a fact. Smith claims that by promoting the research to support intelligent design, we are intrinsically admitting that evolution is a fact and that it is central to biology and the natural world.

But we made no reference whatsoever to intelligent design. Smith and co-workers used evolutionary theory and found evidence of functional DNA. In other words, if evolution is true, then we have yet more evidence of function for yet more of the genome. Those results do not comport well with Dan Graur’s view that most of the genome must be junk. None of this makes evolution a fact, much less “central to biology and the natural world.”

Next Smith confuses theory with data and states that they “explicitly measured genetic mutations across 35 mammalian species.” Actually they did no such thing, explicitly or otherwise. What they did do was to compare the genomes of 35 different species. Since they believe those species somehow all evolved from a common ancestor, they inferred that the differences were due to mutations.

That is an interpretation of the data according to a theory. It is not a measurement.

And just in case there was any doubt, Smith repeats again the metaphysical claim that evolution is a scientific fact. He then says they do not promote any “spiritual ideologies.” That is precisely what they are doing.

Saturday, August 3, 2013

More Functions For “Junk” DNA

Introns Can Regulate Gene Expression

In the aftermath of Dan Graur’s claim that either our genome is mostly junk or evolution is false, new research is finding yet more ways that the so-called junk DNA is, in fact, functional. This time it is the introns which have been found to help with regulation of gene expression. As one of the researchers explained:

This discovery, involving what was previously referred to as "junk," opens up a new level of gene expression control that could also play a role in the development of many other tissue types. Our observations were quite surprising and they open entirely new avenues for potential treatments in diverse diseases including cancers and leukemias.

But as we explained, not only does Graur’s claim vastly underestimate the malleability of evolutionary theory—evolutionists could easily accommodate a largely functional genome—it will never even be tested.

For evolutionists will never allow the genome to be viewed as functional or mostly functional, no matter what the evidence. Instead, any and all functions—and there will be many—for “junk” DNA will never alter its status of junk but merely will be viewed as lucky function which the “junk” DNA happened to stumble upon.

As with the so-called vestigial structures—another evolutionary construct—function is, ultimately, irrelevant. A structure is “vestigial,” or DNA is “junk,” not by virtue of any objective criterion dealing with function, but because evolutionists say so.

Evolutionary conclusions are driven by evolutionary assumptions, not by the evidence. Junk DNA does not support the claims of evolution; rather, evolution supports the claims of junk.

Religion drives science and it matters.

Friday, August 2, 2013

Bell’s Number, the Interactome, and a Peek at a Monumental Problem for Evolution

Oh my

If you ever wondered how the biological world could have arisen from random events and a few simple natural laws then you might be interested in a recent paper introducing some basic, fundamental problems confronting evolutionary theory. For whereas man-made machines may have a great number of components, such machines are specifically designed to limit the number of interactions. The components only interact with a small number of other components and a matrix describing these interactions would be very sparse. Not so for many biological systems. The paper shows that the magnitude of the interactome—the sum total of all interactions in systems such as the nervous system—is on the order of Bell’s number, which scales faster than exponentially. Indeed, for n discrete components, the logarithm of Bell’s number is n[log(n) – 1].

This means that even if we believe, with Moore, that compute power doubles every 18 months or so, it nonetheless will be impossible to analyze even a single synapse for another few millennia. And the visual cortex of a mouse? That will take about 10 million years to analyze.

But what if even Moore was pessimistic? Or what if only a tiny fraction of the interactions actually need to be characterized, say 0.001%? Such luck would not appreciably change the answer.

Technological advances and modeling simplifications do little in the face of the curse of dimensionality and researchers now use the term “complexity brake” to describe the resistance of biological systems to computer analysis. In fact, this brake is only going to become worse, for the more we learn about biological systems, the more complexity we discover:

Improved technologies for observing and probing biological systems has only led to discoveries of further levels of complexity that need to be dealt with. This process has not yet run its course. We are far away from understanding cell biology, genomes, or brains, and turning this understanding into practical knowledge. The complexity break is very apparent in the figure (shown above).

All of this not only means that the analysis of such biological systems is impossible, it also means that the evolution of such biological systems is impossible, or at least scientifically unlikely. For the problems in analyzing these systems also apply to evolving these systems.

Not only is there a large number of interactions but, unlike a bottle filled with a gas which can be characterized by averages and distributions, in biological systems the specific, individual interactions matter.

It would be serendipity on steroids to say that evolution, with its limited experimental powers, designed and created a few basic components which then, as luck would have it, combined in such a way to produce far greater complexity and emergent behaviors.

And that, here in the twenty first century, is increasingly what evolutionary theory is all about: serendipity.