Cell biology

This week’s article at Design Disquisitions is about Perry Marshall’s ‘Evolution 2.0’ thesis and his criticisms of intelligent design. This article responds to some of his recent writings on his blog and his interaction with Stephen Meyer a few weeks back. Bottom line is, his philosophy of science has significant problems and he has some grave misconceptions about what ID is: A few days ago I was listening to an episode of Unbelieveable?, the fantastic radio debate show and podcast at Premier Christian Radio. The episode was a fairly recent one between Stephen Meyer and Perry Marshall. Marshall is the author of Evolution 2.0 and writes at his blog Cosmic Fingerprints. I’ve read some of his work and he makes some Read More ›

From ScienceDaily: New research by scientists at the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA overturns a long-standing paradigm about how axons — thread-like projections that connect cells in the nervous system — grow during embryonic development. The findings of the study, led by Samantha Butler, associate professor of neurobiology, could help scientists replicate or control the way axons grow, which may be applicable for diseases that affect the nervous system, such as diabetes, as well as injuries that sever nerves. … They found that neural progenitors organize axon growth by producing a pathway of netrin1 that directs axons only in their local environment and not over long distances. This pathway of netrin1 Read More ›

From ScienceDaily: The ability to generate oxygen through photosynthesis — that helpful service performed by plants and algae, making life possible for humans and animals on Earth — evolved just once, roughly 2.3 billion years ago, in certain types of cyanobacteria. This planet-changing biological invention has never been duplicated, as far as anyone can tell. Instead, according to endosymbiotic theory, all the “green” oxygen-producing organisms (plants and algae) simply subsumed cyanobacteria as organelles in their cells at some point during their evolution. Endosymbiotic theory (life forms acquire useful units the way corporations acquire businesses) is a favourite in the coffee room around here but it is not up there with gravity. Still, do say on: Fischer and his colleagues found Read More ›

From Diana Kwon at The Scientist: While analyzing genetic material found in a wastewater treatment plant, scientists uncovered the genomes of four new species of related giant viruses. These newly discovered specimens, dubbed Klosneuviruses, challenge the notion that giant viruses evolved from a fourth domain of life, researchers wrote in a study published today (April 6) in Science. … Some scientists believe that rather than having a common ancestor, these giant viruses began as small viruses and gradually accumulated host genes over time. Analysis of the Klosneuvirus genome reveals evidence supporting the latter theory, according to the authors of the present study. More. These viruses have up to 1.57 million base pairs, with many genes encoded for components of translation Read More ›

From Jennifer Frazer at Scientific American: Gemmata obscuriglobis excels at breaking rules. Like the platypus, to whom these bacteria have been compared, they possess a baffling arsenal of oddities. Although it has been controversial, they seem to contain membrane-bound compartments. One of those compartments surrounds their DNA. That would make it, apparently, a nucleus. But bacteria are thought to be devoid of nuclei – hence the terms prokaryote (“pre-kernel”) for bacteria and archaea, and eukaryote (“true kernel”) for all nucleated life (which includes all multicellular organisms). The eye-popping apparent commonalities don’t end there. … If that is the case, it means one of two equally astounding things must be true: either this humble bacterium, isolated from freshwater near the Maroon Read More ›

From ScienceDaily: Researchers have described the 3D structure of the genome in the extremely small bacteria Mycoplasma pneumoniae. They discovered previously unknown arrangements of DNA within this tiny bacteria, which are also found in larger cells. Their findings suggest that this type of organization is a universal feature of living cells. DNA contains the instructions for life, encoded within genes. Within all cells, DNA is organised into very long lengths known as chromosomes. In animal and plant cells these are double-ended, like pieces of string or shoelaces, but in bacteria they are circular. Whether stringy or circular, these long chromosomes must be organised and packaged inside a cell so that the genes can be switched on or off when they Read More ›

From ScienceDaily: When an individual cell needs to move somewhere, it manages just fine on its own. It extends protrusions from its leading edge and retracts the trailing edge to scoot itself along, without having to worry about what the other cells around it are doing. But when cells are joined together in a sheet of tissue, or epithelium, they have to coordinate their movements with their neighbors. It’s like walking by yourself versus navigating a crowded room. To push through the crowd, you have to communicate with others by talking (“Pardon me”) or tapping them on the shoulder. Cells do the same thing, but instead of verbal cues and hand gestures, they use proteins to signal to each other. Read More ›

From ScienceDaily: A subset of protein complexes whose role has long been thought to consist only of chemically degrading and discarding of proteins no longer needed by cells appears to also play a role in sending messages from one nerve cell to another, researchers report. … Paper. (paywall) Together, the researchers say, these findings suggest that the neuronal membrane-bound proteasome is vitally important for cell signaling. Their experiments bring up a host of new questions about what specific proteins this complex is degrading, what compounds it’s expelling and what happens when this system breaks down, Ramachandran says. He and Margolis, he says, are already discovering links between glitches in this system and neurological disease, such as neurodegeneration. “Realistically, understanding the Read More ›

Well, there are some limitations: From John Timmer at Ars Technica: Nothing about DNA is 100 percent accurate or even as close to the accuracy we’ve come to expect from our electronic bit storage media. Simply synthesizing DNA of a desired sequence will sometimes result in an error, as will amplifying it or decoding it again. And some specific sequences are especially error prone, like long runs of a single base (like TTTTTTTTTT) or stretches that are a mix of Gs and Cs. So any encoding method has to be robust to these issues. Fortunately, we’ve already developed encoding algorithms that stand up to data loss. The authors went with Fountain codes, which allow packet-based data to be transmitted over Read More ›

Can protein folding complexity be formed by stochastic processes? With 14 intermediate steps?
JILA Team Discovers Many New Twists in Protein Folding

Biophysicists at JILA have measured protein folding in more detail than ever before, revealing behavior that is surprisingly more complex than previously known. . . .
They fold into three-dimensional shapes that determine their function through a series of intermediate states, like origami. Accurately describing the folding process requires identifying all of the intermediate states.
The JILA research revealed many previously unknown states by unfolding an individual protein. For example, the JILA team identified 14 intermediate states—seven times as many as previously observed—in just one part of bacteriorhodopsin, a protein in microbes that converts light to chemical energy and is widely studied in research.
“The increased complexity was stunning,” said project leader Tom Perkins, a National Institute of Standards and Technology (NIST) biophysicist working at JILA, a partnership of NIST and the University of Colorado Boulder. “Better instruments revealed all sorts of hidden dynamics that were obscured over the last 17 years when using conventional technology.”
“If you miss most of the intermediate states, then you don’t really understand the system,” he said.
Knowledge of protein folding is important because proteins must assume the correct 3-D structure to function properly. Misfolding may inactivate a protein or make it toxic. Several neurodegenerative and other diseases are attributed to incorrect folding of certain proteins.

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Laura Geggel interviews virologists at LiveScience, who offer arguments against the idea, for example: “Take a cat, a plant and a rock, and leave them in a room for days,” said Amesh Adalja, an infectious disease physician and an affiliated scholar at the Johns Hopkins Center for Health Security in Baltimore. “Come back, and the cat and the plant will have changed, but the rock will essentially be the same,” he said. Like a rock, most viruses would be fine if they were left indefinitely in a room, Adalja said. In addition, he noted that living beings have self-generated and self-sustaining actions — meaning they can seek out sustenance and behave in self-preserving ways. In other words, “they’re taking actions Read More ›

From science writer Suzan Mazur, author of Paradigm Shifters, continuing her interview at Huffington Post with Swedish deep evolution investigators Charles Kurland and Ajith Harish regarding … their central position on deep evolution, which is that the most recent universal common ancestor (MRUCA) is complex not a simple bacteria and “is the root of eukaryote and akaryote lineages” containing “more than a thousand Superfamilies.” Kurland and Harish think MRUCA represents complex survivors from a now extinct biosphere. On horizontal gene transfer as routine: Charles Kurland: We have to remember there’s only a little background of horizontal gene transfer in bacterial populations. The simple reason is that bacteria eat DNA. So sequences are going in all the time. Most of them get Read More ›

From science writer Suzan Mazur, author of Paradigm Shifters, at Huffington Post: I recently had a three-way phone conversation with Swedish deep evolution investigators Charles Kurland and Ajith Harish about their phylogenomic Tree of Life (ToL) based on protein structure, which shows that we are descended from a “complex” ancestor — MRUCA (most recent universal common ancestor) — not a simple bacteria. Kurland and Harish think a ToL paradigm shift may be in order. What’s more, Kurland and Harish figure that MRUCA was not the first ancestor, but represents complex survivors of a now-extinct biosphere. The findings of Kurland and Harish challenge not only mainstream ToL perspectives, but also those of endosymbiosis hypothesis fans, as well as the “HGT industry” Read More ›

From Kelly Rae Chi at Nature: n 2004, oncologist Gideon Rechavi at Tel Aviv University in Israel and his colleagues compared all the human genomic DNA sequences then available with their corresponding messenger RNAs — the molecules that carry the information needed to make a protein from a gene. They were looking for signs that one of the nucleotide building blocks in the RNA sequence, called adenosine (A), had changed to another building block called inosine (I). This ‘A-to-I editing’ can alter a protein’s coding sequence, and, in humans, is crucial for keeping the innate immune response in check. “It sounds simple, but in real life it was really complicated,” Rechavi recalls. “Several groups had tried it before and failed” Read More ›