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.

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.

More Complex than Previously Thought – Part VIII – DNA Differences

Previously, it was considered to be axiomatic that all cells in the human body contained the same DNA. However, recent research found differences between the DNA contained in blood cells and other tissue in the body.

This discovery may undercut the rationale behind numerous large-scale genetic studies conducted over the last 15 years, studies which were supposed to isolate the causes of scores of human diseases.

Except for cancer, samples of diseased tissue are difficult or even impossible to take from living patients. Thus, the vast majority of genetic samples used in large-scale studies come in the form of blood. However, if it turns out that blood and tissue cells do not match genetically, these ambitious and expensive genome-wide association studies may prove to have been essentially flawed from the outset.

This discovery sprang from an investigation into the underlying genetic causes of abdominal aortic aneurysms (AAA) led by Dr. Morris Schweitzer, Dr. Bruce Gottlieb, Dr. Lorraine Chalifour and colleagues at McGill University and the affiliated Lady Davis Institute for Medical Research at Montreal’s Jewish General Hospital. The researchers focused on BAK, a gene that controls cell death.

What they found surprised them. AAA is one of the rare vascular diseases where tissue samples are removed as part of patient therapy. When they compared them, the researchers discovered major differences between BAK genes in blood cells and tissue cells coming from the same individuals, with the suspected disease “trigger” residing only in the tissue. Moreover, the same differences were later evident in samples derived from healthy individuals.
“In multi-factorial diseases other than cancer, usually we can only look at the blood,” explained Gottlieb, a geneticist with McGill’s Centre for Translational Research in Cancer. “Traditionally when we have looked for genetic risk factors for, say, heart disease, we have assumed that the blood will tell us what’s happening in the tissue. It now seems this is simply not the case.”

It remains to be seen how many other differences will be discovered. But what is certain, is that a whole other layer of complexity has been added to the enormous complexity of biological systems. Yet we are told that there is “no evidence of design or a Designer.”

Expelled Exposed…Exposed

From the website NCSE Exposed:

Of course critics of ID (like the folks at the NCSE) should have every right to publish their views within academic circles and should have the full protection of academic freedom. But academic freedom doesn’t just mean the freedom to agree with the predominant viewpoint. Academic freedom in science means nothing if it doesn’t include the right to hold legitimate minority scientific viewpoints. ID proponents have published serious scientific research in mainstream, credible academic venues. Many of them have sterling academic qualifications and accomplishments. They have earned the right to freely express their views without fear of intimidation or discrimination.

But free expression of pro-ID views in the academy is exactly what the NCSE doesn’t want. “Expelled Exposed” is now exposed for what it really is: it’s not just a website making the case against ID (which is perfectly fine if that’s what ID critics want to do)—it’s a website attempting to convince people that ID deserves no academic freedom. In other words, “Expelled Exposed” is an effort to encourage the further persecution of ID-proponents.

Ironically, by denying that professionally qualified ID proponents have a right to “a place in academia,” “Expelled Exposed” has justified the central thesis of the documentary Expelled, namely that qualified ID proponents do not receive academic freedom to hold, discuss, and promote their views within the academy.

I like the Discovery Institute more all the time based in part on the rabid hatred that many Darwinists have for this tiny organization. Can such intense fear and hatred come from a defense of “science” or is there something deeper going on?

Evidence as Parable?

In this post, I seek to take a step back from the ID/evolution debate, and consider things from a Christian perspective.  Jesus often spoke in parables, and explained the reason to his disciples:

“The knowledge of the secrets of heaven has been given to you, but not to them. This is why I speak to them in parables, ‘Though seeing, they do not see; though hearing, they do not hear or understand'” (Mat. 13:11,13).

When thinking about design in the universe, it makes one wonder why God created a universe where evidence seems to perpetually point in two possible directions.  In other words, we don’t find a message encoded into DNA that says something akin to “God was here,” written in every known language.  Certainly He could have done that, but it seemed to be part of His purpose that evidence for creation be presented in the same manner as He spoke through Jesus (i.e., in parables).  Unbelievers in the days of Jesus consistently misinterpreted the meaning of His parables, just as the evidence of design is consistently misinterpreted by today’s unbelievers.

That’s why I don’t ever expect ID theorists or creation scientists to find a “smoking gun,” that absolutely proves design in nature.  That would remove the necessity of faith.  Likewise, I don’t expect a smoking gun from the side of naturalism that proves that matter and energy are the only things that exist.

As a result, I’m skeptical whenever I hear claims that it has been proven that the mind is either completely material or immaterial, that it has been shown that there is no evidence for design, that there is no evidence for materialism, and so forth.  In other words, by design, there will always be evidence pointing in both directions.  However, when it comes down to an individual’s decision about whether to believe in God, there is enough evidence for each person to decide where they will place their faith in order to fulfill the following verses:

Psalms 19:1 The heavens declare the glory of God; and the firmament sheweth his handywork.

Romans 1:20 For the invisible things of him from the creation of the world are clearly seen, being understood by the things that are made, even his eternal power and Godhead; so that they are without excuse.

That said, ID is an important scientific endeavor that seeks to uncover the evidence for design, which is evident in nature.  For Christians thinking about the issue who might be confused, it is helpful  to remember that the evidence will never be bulletproof, but it will be sufficient for your decision of faith.  Furthermore, the evidence is strong enough so that we are without excuse.

Roddy Bullock: "Of Pots and People"

Roddy Bullock has a good new essay up on ARN:

Of Pots and People

Archeologist with simple piece of pottery: Look what I discovered; I wonder who created it.
Scientist: Wow! What a cool pot; who do you think made it?

Biologist with complex piece of DNA code: Look what I discovered; I wonder who created it.
Scientist: Wow! What a crackpot; why does he think someone made it?

It’s a good thing the Bible doesn’t say God made clay pots. If it did, design-minded archeologists would be out of a job. With little to say about each new find that cannot be turned into a “religious” question, design-inferring archeologists would be relegated to the fate of their like-minded brethren in biology–the realm of “science cannot infer design because design might mean God and science and religion cannot mix.” Archeologists be glad; you get to freely infer intelligent design for objects of obvious design but unknown origin without facing the “might mean God” barrier to truth-seeking. In other words, you get to be scientists and logically infer intelligent design–a luxury not to be taken for granted.

Actually, archeologists are not the exception; they are the rule. Scientists of many stripes infer design to explain phenomena of unknown (and unknowable) origin all the time. Forensic scientists, faced with a dead body and no witnesses look for evidence to piece together a historical narrative to explain a past event: was the death accidental (unintelligent causes) or murder (intelligent causation)? Simple. And what about the good folks over at SETI (Search for Extraterrestrial Intelligence)? Their name says it all. Although embarrassed at being rightly compared to their like-minded biologist counterparts, these scientists regularly collect evidence in the form of radio signals to determine if the signals are the result of background radiation in space (unintelligent causes), or extraterrestrial intelligence (intelligent causes). Easy. A child can do it.

And biologists? Well, there’s the exception to one rule and the imposition of another. Biologists must suppress entertaining any lingering thoughts spurred by logical inferences of design because such thoughts automatically and necessarily lead to “religion” and, unless it’s a God-denying religion, that’s a bad thing. After all, a respectable scientist having “religious” thoughts hasn’t happened since the days of Newton, Boyle, Kepler, Bacon, Pascal, Herschel, Faraday, Joule and, well, you get the idea. It’s been a long time since the natural wonder of the beauty of intelligent design in nature could be scientifically expressed without professional and personal recriminations.

The savvy Darwinist will quickly jump in here with a smug smile and reply that the analogy to archeology does not hold. It happens, he says with the certainty of one-sided thinking, that in our human experience we know that humans can, and have, made pottery for generations. And because we can explain the kind of potter with some certainty, archeology never approaches the “might mean God” line. Living systems, on the other hand, are not known to be made by human intelligence, so we have no basis to infer human design, and any suitable intelligence must mean God, and science and religion cannot mix. You see? The inherent “who” problem in origins science is not to be found in archeology, so there is no inconsistency in letting archeology be respectable science and letting intelligent design be respectable religion (if there is such a thing).

Read more here.

Signature in the Cell

Stephen Meyer discusses his new book Signature in the Cell: DNA Evidence for Intelligent Design.