More Complex than Previously Thought – Part XII – Cellular Movement

Research out of Brown University has found that cells move in ways that are much more complex than previously thought.  It’s yet another example of the complexity of life’s design that consistently surprises biologists.

“We’ve learned that cells move in much more complex ways than previously believed,” said Christian Franck, assistant professor in engineering at Brown and the co-lead author of the study published online in the Proceedings of the National Academy of Sciences. “Now, we can start to really put numbers on how much cells push and pull on their environment and how much cells stick to tissues as they move around and interact.”

In the study, Franck and co-lead author Stacey Maskarinec, who both conducted the experiments while graduate students at the California Institute of Technology, placed cells on top of a 50-micron-thick water-based gel designed to mimic human tissue. They added into the gel spheres about a half-micron in diameter that lit up when jostled by the cells’ actions. By combining two techniques — laser scanning confocal microscopy and digital volume correlation — the scientists tracked the cells’ movement by quantifying exactly how the environment changed each time the cell moved. The team recorded results every 35 minutes over a 24-hour period.

What they found was cells move in intriguing ways. In one experiment, a cell is clearly shown operating in three dimensions by extending feelers into the gel, probing at depth, as if thrusting a leg downward in a pool. The Brown and Caltech scientists also found that as a cell moves, it engages in a host of push-pull actions: It redistributes its weight, it coils and elongates its body, and it varies the force with which it “grips,” or adheres, to a surface. Combined, the actions help the cell generate momentum and create a “rolling motion,” as Franck described it, that is more like walking than shuffling, as many scientists had previously characterized the movement.

“The motion itself is in three dimensions,” Franck said.

Brown University (2009, December 17). Cells move in mysterious ways, experiments reveal. ScienceDaily. Retrieved December 17, 2009.

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 X – Internal Organization of Bacteria

A recent paper finds that organization within bacteria is more complex than previously thought:

Simple visual inspection of bacteria indicated that, at least in some otherwise symmetric cells, structures such as flagella were often seen at a single pole. Because these structures are composed of proteins, it was not clear how to reconcile these observations of morphological asymmetry with the widely held view of bacteria as unstructured “bags of enzymes.” However, over the last decade, numerous GFP tagged proteins have been found at specific intracellular locations such as the poles of the cells, indicating that bacteria have a high degree of intracellular organization. Here we will explore the role of chromosomal asymmetry and the presence of “new” and “old” poles that result from the cytokinesis of rod-shaped cells in establishing bipolar and monopolar protein localization patterns. This article is intended to be illustrative, not exhaustive, so we have focused on examples drawn largely from Caulobacter crescentus and Bacillus subtilis, two bacteria that undergo dramatic morphological transformation. We will highlight how breaking monopolar symmetry is essential for the correct development of these organisms.1

1). Dworkin, J. (2009). Cellular Polarity in Prokaryotic Organisms.

More Complex than Previously Thought – Part IX – The Ribosome

The ribosome is a nanomolecular factory that uses genetic instructions and amino acids to build proteins.  If the previous understanding of the functions of the ribosome were not enough evidence for design, new technology has enabled researchers capture nanoscale movements inside the structure and found that the functioning of the ribosome was complicated than previously thought.1

In the protein manufacturing process, the genetic code – or instruction manual – for making proteins lies inside a cell’s double-stranded DNA. When the cell needs to produce more proteins, the DNA unzips into two separate strands, exposing the protein code so it can be duplicated by single-stranded messenger RNA (mRNA). The mRNA dutifully delivers that code to the ribosome, which somehow reads the instructions, or “data tape,” as each amino acid is added to a growing protein chain.

At the same time, other RNA molecules, called transfer RNA (tRNA), bring to the ribosome amino acids, the raw building blocks needed for protein construction.

To help elucidate the ribosome’s movements as it interacts with mRNA and tRNA, the researchers used X-ray crystallography to obtain a highly detailed picture of the ribosome – a mere 21 nanometers wide – from an Escherichia coli bacterium. In addition to revealing atomic level detail, the technique allowed the researchers to capture the ribosome mid-action, a challenge because it acts fast, adding 20 new amino acids to a protein chain every second.

“Scientists used to think that the ribosome made a simple two-stage ratcheting motion by rotating back and forth as it interacts with mRNA and tRNA,” said Cate, who is also a member of the California Institute for Quantitative Biomedical Research (QB3) at UC Berkeley. “What we captured were images of the ribosome in intermediate stages between the rotations, showing that there are at least four steps in this ratcheting mechanism.”

“We suspect that the ribosome changes its conformation in so many steps to allow it to interact with relatively big tRNAs while keeping the two segments of the ribosome from flying apart,” said Cate. “It’s much more complicated than the simple ratcheting mechanism in a socket wrench.”

Cate said that while this study marked a major accomplishment in cracking open the “black box” of ribosomal function, there are far more details yet to be revealed. Advances in imaging techniques over the next decade should allow researchers to go beyond the snapshots taken in this study to high-resolution movies of a ribosome’s movements, he said. (emphasis mine)

1 New Images Capture Cell’s Ribosomes At Work, ScienceDaily, 8/23/09

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?