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.

Reference:
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.

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

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 I

I’ve written before about how Ocam’s razor consistently slices the wrong way in biology…meaning that there is a continuous trend of discovering that the machinery of life is more complex than previously thought. 

Scientists have recently discovered,(1) that ribosomes have a “proofreading step,” which is said to recognize errors shortly after making them and has an analog to a computer’s delete button. 

It turns out, the Johns Hopkins researchers say, that the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products which, as workhorses of the cell, carry out the very business of life.

“What we now know is that in the event of miscoding, the ribosome cuts the bond and aborts the protein-in-progress, end of story,” says Rachel Green, a Howard Hughes Medical Institute investigator and professor of molecular biology and genetics in the Johns Hopkins University School of Medicine. “There’s no second chance.” Previously, Green says, molecular biologists thought the ribosome tightly managed its actions only prior to the actual incorporation of the next building block by being super-selective about which chemical ingredients it allows to enter the process.

Joey Campana discusses this subject (more complex than previously thought) in detail(2):

“More complex than once thought”

 

 

A revealing reason that Darwinian thought has not been helpful is that it tends to see biology in simplis-tic terms that are, well, too simple. When searching Google for phrases such as “more complex than pre-viously thought,” over a million-and-a-half hits cur-rently result. Some things that were “more complex than thought” from the first few pages include re-search findings in the following areas:

  1. communication among cells
  2. the oldest animal genomes
  3. bird flight orientation
  4. genes
  5. patterns of neuronal migration during cortical development
  6. the relationship between evolution and embry-onic development
  7. p53 ubiquitination and degradation
  8. human memory
  9. the fetal immune system
  10. the mouse genome
  11. visual processing in the brain
  12. regulation of neuronal survival in the retina
  13. COX enzymes
  14. the human genome
  15. the female human body
  16. cerebellar circuitry and learned behaviors
  17. estrogen receptors
  18. neural induction (list truncated)

 ….

Currently, “less complex than once thought” only returns two hits. The data coming out of the labs would suggest that we begin to expect that things are more complex. We would stand a greater chance of being correct.

So, the science of biology would be well served by a paradigm shift focusing on design analogs and assuming design rather than assuming chance. When an information recording and trascription system is involved in biology, scientists should first start with all they know about information recording and transcription systems. Error detection and correction is an integral part of these types of systems designed by humans, and engineers can also benefit from the analysis of the machines of life.

(1). The Ribosome: Perfectionist Protein Maker Trashes Errors
(2). http://www.arn.org/docs/article_the_design_isomorph_and_isomorphic_complexity.pdf