More Complex than Previously Thought – Part XI – Simple Bacteria?

Because of their rigid adherence to a failed framework, Darwinists have continuously been surprised at the sophistication of even the simplest organisms.  The researchers examined mycoplasma pneumoniae and found the following.

The inner workings of a supposedly simple bacterial cell have turned out to be much more sophisticated than expected.

An in-depth “blueprint” of an apparently minimalist species has revealed details that challenge preconceptions about how genes operate. It also brings closer the day when it may be possible to create artificial life.

Mycoplasma pneumoniae, which causes a form of pneumonia in people, has just 689 genes, compared with 25,000 in humans and 4000 or more in most other bacteria. Now a study of its inner workings has revealed that the bacterium has uncanny flexibility and sophistication, allowing it to react fast to changes in its diet and environment.

“There were a lot of surprises,” says Peer Bork, joint head of the structural and computational biology unit at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. “Although it’s a very tiny genome, it’s much more complicated than we thought.”

The biggest shock was that the organism gets by with just eight gene “switches”, or transcription factors, compared with more than 50 in other bacteria such as Escherichia coli. Transcription factors are generally thought of as the key components enabling living things to respond to environmental conditions by switching genes on and off.

Another unexpected discovery was that bacterial genes grouped together in clumps or families called “operons” don’t work as had been thought. The assumption was that if there are four genes in an operon they always work in unison, but the new analyses show that only one, or perhaps two, operate at any one time.

Even more surprising, the proteins the genes make don’t necessarily always couple with their nearest neighbours – again contrary to previous assumptions. Instead, they often join up with proteins originating from other, distant operons, vastly increasing the bacterium’s flexibility and versatility when faced with a changed environment.

(1). ‘Simple’ bacterium shows surprising complexity, NewScientist, 11/26/09.

The God Gene Redux

Darwinists of all stripes can hardly refrain from evolutionary storytelling when it comes to human psychology.  Not surprisingly, they focus largely on their opponents–those who have faith in God.  The recent work by archeologists Joyce Marcus and Kent Flannery seems to follow the familiar template.1  Start with an actual study, then speculate wildly about how natural selection brought about the observed results.

During 15 years of excavation they have uncovered not some monumental temple but evidence of a critical transition in religious behavior. The record begins with a simple dancing floor, the arena for the communal religious dances held by hunter-gatherers in about 7,000 B.C. It moves to the ancestor-cult shrines that appeared after the beginning of corn-based agriculture around 1,500 B.C., and ends in A.D. 30 with the sophisticated, astronomically oriented temples of an early archaic state.

This and other research is pointing to a new perspective on religion, one that seeks to explain why religious behavior has occurred in societies at every stage of development and in every region of the world. Religion has the hallmarks of an evolved behavior, meaning that it exists because it was favored by natural selection. It is universal because it was wired into our neural circuitry before the ancestral human population dispersed from its African homeland.

For atheists, it is not a particularly welcome thought that religion evolved because it conferred essential benefits on early human societies and their successors. If religion is a lifebelt, it is hard to portray it as useless.

For believers, it may seem threatening to think that the mind has been shaped to believe in gods, since the actual existence of the divine may then seem less likely.

In case you missed it before, I think John Cleese’s work in this area is as good or better than any other Darwinist speculating in this area.


Whence Scientific Hypotheses?

Scientific hypotheses can come from anywhere at all (well actually just from an intelligent mind).  One important thing I learned about science in graduate school was, it did not matter where your hypothesis originated, it only mattered that it could be tested and falsified in a rigorous, repeatable, and measurable way.  Scientific notions can arise from any metaphysical framework or lack of a framework.  At the basis of creationism and naturalistic evolution are presumed metaphysical truths.  Quite possibly, neither of which can be falsified, leaving the resolution to be a matter of faith.  However, that does not prevent scientists from developing testable hypotheses that spring from those underlying beliefs.  One could argue that intelligent design has fewer metaphysical entanglements than either creationism or naturalistic evolution.  The point is that testable hypotheses may come from almost any underlying belief or idea, whereas the actual underlying belief or idea itself may not be a scientific hypothesis.

A story of creationist metaphors

Once up on a time there was an Author who wrote with living words who began writing a book about redemption. He knew from the beginning that the book would contain evil and that it would have to be thrown into the fire in the end but he planned to copy some of his words to another book that was good. It was essentially all in his head already, yet there was something different about actually writing it and watching his little living words in his books that seemed very good to him. So he wrote some words and they became more words and they put themselves together differently after he gave them their original meaning. This was fine as far as things went but in the background the Author’s will would be done because he had the final authority. Yet one day some of his periods rebelled and said, “I do not like having to be the period. Look at me…I seem little, small. Why did the author write me this way? I have to be at the end of every sentence cycle and I have to tidy up the ends of little words too. And some little words make a lot of excrement!” So the Author wrote some more words to his periods, “In my next book the last shall be the first, for the greatest of my living words is Love. Period.” But then some of the question marks rebelled and said, “I do not like having to be the question mark. I want all the answers, now! For look at me, all squiggly above the period… is there something odd about me? If I had all the answers then would I still exist? For who am I but the questionable mark of a question?” So the Author wrote some words to them, “Were you there when I bound the pages of this book together? You must quest for the answers. Seek and you shall find! Period.”

And on it went as the Author wrote a story and had conversations with his own words at the same time until one day all the words began to rebel against the authority of the Author at once. At this point the Author wrote with authority, “I will not strive against my own words forever!” Yet then the word Ever just had to reply, “Whatever is that for there for, in front of me! I am more important. After all, I am the ever in everyone!” Finally all the words said the same thing, “We, the words, rebel against our Author! Now we will be as our own authors!” So the Author ripped out the whole page and continued writing, all the while copying words which he wrote to bear witness to his wit over to another story.

After all, the Author of a book always has the last word.

The End

Paganism in Science

British biologist, James Lovelock, seems to view humanity as an infection of mommy Earth.  While many Darwinists may wish to crawl back into the womb of mommy nature, as mynym has noted, some want to eradicate the infection of humanity within their deified mother.

“Individuals occasionally suffer a disease called polycythaemia, an overpopulation of red blood cells. By analogy, Gaia’s illness could be called polyanthroponemia, where humans overpopulate until they do more harm than good,” Lovelock writes. He says the cure won’t come until the human tribe is trimmed back from its current 6.8 billion to, say, 1 billion people.

Others see mother nature as a mean woman who will take care of herself by killing us off when we get out of hand. Paleontologist Peter Ward seems to find this view of mommy more compelling.

“I hypothesize that life and its processes, together often referred to as ‘Mother Nature,’ was, is, and will be anything but a good mother to her many evolved and evolving species,” Ward contends in his new book, “The Medea Hypothesis.”

Gaia vs. Medea … that sounds like the start of a philosophical catfight.

Ward, however, says he’s not just trying to pick a fight with the 90-year-old Lovelock. “Most every scientist is trying to ‘pick a fight’ with another scientist,” he told me today. “We try to do it in a collegial fashion. … I’m trying to do science, but I’m also trying to point out that there has never been opposition in a formal sense – it’s been Gaia, Gaia, nothing but Gaia.”

So the scientific debate here seems to be whether mommy E is kindly, but infected, versus potty training conflicts projected onto the environment.

While Lovelock uses “Gaia” to refer to Earth’s biosphere as a kindly mother goddess, Ward uses “Medea” as a reference to the mother in Greek myth who killed her own children. Ward says life, like Medea, eventually sows the seeds of its own near-destruction – over and over again. “Life boils up and bubbles up, and through its own waste products and activities makes the planet no longer inhabitable,” he said.

So, the important question seems to be, shall mommy kill us with her flatus?

Ward’s “rotten-eggstinction” scenario begins with a shift in climate that sparks blooms of sulfur-loving microbes in the world’s oceans. Their belches of hydrogen sulfide – the gas commonly associated with rotten eggs – triggers a sequence of events that end with a global poisoning of marine and land species. (This scenario is detailed in Ward’s previous book, “Under a Green Sky.”)

In “The Medea Hypothesis,” Ward sketches out similar biocidal scenarios for other extinction events. He goes with the conventional wisdom that a huge asteroid touched off the Cretaceous-Tertiary extinction that killed off the dinosaurs, but says continent-spanning forest fires most likely sparked a global winter that finished the job. Thus, he writes, “it could be argued that the effects of life magnified the extent of the extinction.”

One certainly hopes not! However, we must await the outcomes of future science to know for certain.


Recent Work in Creation Science

Jerry Bergman has written an article on CMI entitled, Did immune system antibody diversity evolve?

From the article:

The voluminous research on the evolution of the adaptive immune system describes in enormous detail both the similarities and differences between the immune systems of a wide variety of animals, but does not provide evidence for the evolution of these irreducibility complex systems. The complex, designed processes used to produce antibody diversity and then to fine tune the adaptive immune response are not evidence of Darwinian evolution, but rather of intelligent design.

Recent work has also shown that innate immune systems formerly thought to be very primitive are far more complex than once believed, blurring ‘traditional distinctions between adaptive and innate immunity.’38 Various phyla use ‘a remarkably extensive variety of solutions to meet fundamentally similar requirements for host protection.’37 The large discontinuity between the various means of generating immune system diversity in the animal kingdom makes it highly unlikely that one system could have evolved into another.

Creation scientists have also been hard at work in generating theoretical frameworks and hypotheses on a number of fronts.

1). A framework has been developed for explaining bacterial pathogenicity.

2). Fungi have been examined from a creationist perspective, and natural selection is considered as a process for the development of pathogenicity.  Similar to the first paper, evolutionary processes are considered corrupting influences of the original designs.

3). Initial work has been done on developing a field of creation microbiology.  Promising areas for future research and practical applications are also considered.

While those who pontificate about the absence of any real scientific progress being made from a creationist perspective, creation scientists are laying the groundwork for biological studies, and are generating testable scientific hypotheses.  Whereas materialist scientist do not often recognize their metaphysical assumptions, creationist scientists and IDers are generally much more aware of the metaphysical assumptions of science on both sides of the issue.

A textbook case of being a biology teacher

Over at the Huffington Post a high school biology teacher writes:

Are we doing ourselves a disservice when we speak about our “belief” in evolution? Should we find a new way to talk about the “theories” that underlie our ideas? What about when we talk about the “design” of human anatomy? Why are we always finding ourselves on the defensive? Doesn’t all of the natural evidence that the universe has to offer support the conclusions that scientists have drawn (and modified) over the past five centuries?

I’ll attempt to answer, as given my experience with biology teachers ignorance and stupidity abounds. With respect to doing yourselves a disservice, yes you are doing yourselves a disservice. Instead of speaking about your belief in evolution you should be speaking about the biological state that you find yourselves in thanks to natural selection operating on the anuses of ancient ape-like creatures. This is part of series of events brought about by evolution which allowed your ancestors to control their excrement but which unfortunately has not lead your way of thinking being different than excrement.

With respect to talking about “theories,” they need not find new ways of talking about theories given that evolution, whatever it may be, seems to be rooted in hypothetical goo. They need not talk about the design of human anatomy because there is no design and no intelligence in the mechanistic brain events which cause them to falsely “believe” that they are intelligent and therefore capable of engaging in the scientific method. With respect to evidence, when it seems that “all” the evidence must support a theory then that should be counted as evidence against it. The fact that biology teachers have a history of failing to understand why that is so is linked to their failure to understand science in general and their gullibility when dealing with the “overwhelming” mental illusions which typify pseudo-science. The only reason that “all” of the evidence always supports evolution, whatever evolution may be, is because evolution was never specified as a scientific theory in the first place.

The irony of biology teachers who promote pseudo-science in the name of science is that they often make claims like this when it comes to ID:

Something tells me that the fundamentalist religious folks who want to add “creation-science” to state mandated science curricula don’t really understand what the hell the word science actually means. Because let’s face it, once intelligent design squeezes its way into the pages following evolution in our biology books, we might as well add astrology to our astrophysics lectures and toss some alchemy education into the chemistry lab.

Where is the historical evidence that this is actually the case? For that matter, where is there any evidence other than the arguments of association that typify biologists of this sort that this is actually the case? I suppose that one is supposed to rely on an imaginary mythology of progress instead of actual evidence again? In the real world history shows that principles of ID are linked to science and progress as we know it as well as the gradual elimination of pagan and nature based superstitions. This history stands in contrast to the textbook cases of pseudo-science that philosophical naturalism has led to in the past. That’s why a historian summarizing the philosophy that gave birth to evolutionary creation myths and pseudo-science in the past may as well be summarizing the philosophy taught to ignorant schoolchildren by biology teachers now:

The scholars whom we shall quote in such impressive numbers, like those others who were instrumental in any other part of the German pre-war and war efforts, were to a large extent people of long and high standing, university professors and academy members, some of them world famous, authors with familiar names and guest lecturers abroad…
If the products of their research work, even apart from their rude tone, strike us as unconvincing and hollow, this weakness is due not to inferior training but to the mendacity inherent in any scholarship that overlooks or openly repudiates all moral and spiritual values and, by standing order, knows exactly its ultimate conclusions well in advance.
(Hitler’s Professors: The Part of Scholarship in Germany’s Crimes Against the Jewish People
by Max Weinreich (New York:The Yiddish Scientific Institute, 1946) :7) (Emphasis added)