Search This Blog

Thursday 8 September 2016

On global money and markets.

A few trillion of our closest friends.

Yet more inconvenient truths from pre darwinian design.

There's Quality Control Even in the Cell's Trash Pickup
Evolution News & Views

Construction workers get more respect than cleanup crews, but both are equally important. Imagine if all the debris from building your house never got hauled away. You could probably not walk anywhere without stepping over piles of junk. Cells, too, have masterful architects, busily constructing proteins and other molecules from ingredients imported through the cell membrane. The waste products, though, could quickly crowd out the productive workers. Worse, some of the waste is toxic, requiring specially trained haz-mat teams to deal with it.

Several recent papers show how cleanup crews play essential roles in the cell's quality control systems. Here's what three scientists in Germany say about "In vivo aspects of protein folding and quality control" in Science Magazine:

Proteins are synthesized on ribosomes as linear chains of amino acids and must fold into unique three-dimensional structures to fulfill their biological functions. Protein folding is intrinsically error-prone, and how it is accomplished efficiently represents a problem of great biological and medical importance. During folding, the nascent polypeptide must navigate a complex energy landscape. As a result, misfolded molecules may accumulate that expose hydrophobic amino acid residues and thus are in danger of forming potentially toxic aggregates. To ensure efficient folding and prevent aggregation, cells in all domains of life express various classes of proteins called molecular chaperones. These proteins receive the nascent polypeptide chain emerging from the ribosome and guide it along a productive folding pathway. Because proteins are structurally dynamic, constant surveillance of the proteome by an integrated network of chaperones and protein degradation machineries, the proteostasis network (PN), is required to maintain protein homeostasis in a range of external and endogenous stress conditions. [Emphasis added.]
We see here that the cleanup crews work right alongside the construction crews and surveillance crews. "Chaperones are a kind of Technical Inspection Authority for cells," Phys.org explains. "They are proteins that inspect other proteins for quality defects before they are allowed to leave the cell." When molecular chaperones cannot fold a protein properly in time, the surveillance crew must make a go/no-go decision, because some amino acids might clump into toxic aggregates. Figures in the Science paper illustrate the "Proteostasis Network" involving cleanup crews like the proteasome system, autophagy, and the lysosome system.

Similar findings were announced in PLOS ONE:

Protein chaperones are molecular machines which function both during homeostasis and stress conditions in all living organisms. Depending on their specific function, molecular chaperones are involved in a plethora of cellular processes by playing key roles in nascent protein chain folding, transport and quality control. Among stress protein families -- molecules expressed during adverse conditions, infection, and diseases -- chaperones are highly abundant. Their molecular functions range from stabilizing stress-susceptible molecules and membranes to assisting the refolding of stress-damaged proteins, thereby acting as protective barriers against cellular damage.
Another German website describes how the "protein degradation pathway" works to achieve "successful recycling." Aberrant proteins are tagged with ubiquitin, a small protein, by two independent surveillance crews. A shredding machine called the proteasome recognizes the tags and provides docking points for them. These quality-control measures ensure that only the bad proteins are degraded.

A large number of different proteins in a cell have to be degraded -- some 30 percent of all cellular protein structures formed by folding of amino acid chains are faulty. The problem for the cells is that these incorrectly folded proteins do not have a uniform structure, making it difficult to identify all of them correctly. If breakdown of these "useless" proteins goes wrong, they are deposited in the cell and disturb its homeostasis. This can lead to death of the cell and trigger a number of diseases, including neurodegenerative disorders such as Alzheimer's and Parkinson's.
It's been a while since we talked about the proteasome. More has been learned in the past four and a half years. A cell needs just the right number of these trash recyclers. Consequently, their numbers also are regulated for quality control. Nature tells how complicated this molecular machine is.

The proteasome is composed of 33 subunits assembled in two sub-complexes, the 20S core particle (CP), flanked at one or both ends by the 19S regulatory particle (RP) to form the 26S proteasome. Proteasome assembly requires the assistance of proteasome assembly chaperones. Four evolutionarily conserved 19S RACs [regulatory particle assembly chaperones]: Nas2, Nas6, Hsm3 and Rpn14 in yeast, and p27 (also known as PSMD9), p28 (also known as PSMD10), S5b (also known as PSMD5) and Rpn14 (also known as PAAF1) in mammals are needed for regulatory particle assembly. In addition, yeast cells have Adc17, a stress-inducible RAC, which is vital for cells to survive conditions, such as accumulation of misfolded proteins, which overwhelm the proteasome. This suggests that cells have evolved adaptive signalling pathways to adjust proteasome assembly to arising needs, but how this is achieved is unknown.
You get the picture. The proteasome is complex! (We won't concern ourselves with how cells "have evolved" these systems.)

What happens when the trash system itself gets trashy? Researchers at Massachusetts General Hospital have been figuring out "proteasome dysfunction" and its health consequences. Even little bitty worms in the soil know about how bad that can be. They monitor their trash cans!

Maintaining appropriate levels of proteins within cells largely relies on a cellular component called the proteasome, which degrades unneeded or defective proteins to recycle the components for the eventual assembly of new proteins. Deficient proteasome function can lead to a buildup of unneeded and potentially toxic proteins, so cells usually respond to proteasome dysfunction by increasing production of its component parts. Now two Massachusetts General Hospital (MGH) investigators have identified key molecules in the pathway by which cells in the C. elegans roundworm sense proteasome dysfunction, findings that may have application to treatment of several human diseases.
When the trash system goes wrong, the cell goes wrong. Cancer and neurodegenerative diseases can result.

Autophagy ("self-eating") is another important cleanup pathway that degrades and recycles waste. It can act on just parts of the cell or the whole cell. Researchers from the University of Missouri found an unexpected place where autophagy plays a vital role. You may have heard that mitochondrial genes are inherited from the mother. After an egg cell is fertilized, the sperm cell's mitochondria need to be digested to prevent a condition called heteroplasmy. The paper in the Proceedings of the National Academy of Sciences shows how two cleanup crews work together to prevent this condition:

Maternal inheritance of mitochondria and mitochondrial genes is a major developmental paradigm in mammals. Propagation of paternal, sperm-contributed mitochondrial genes, resulting in heteroplasmy, is seldom observed in mammals, due to postfertilization targeting and degradation of sperm mitochondria, referred to as "sperm mitophagy." Our and others' recent results suggest that postfertilization sperm mitophagy is mediated by the ubiquitin-proteasome system, the major protein-turnover pathway that degrades proteins and the autophagic pathway.... Our findings provide the mechanisms guiding sperm mitochondrion recognition and disposal during preimplantation embryo development, which prevents a potentially detrimental effect of heteroplasmy.

This brief survey of cell cleanup provides glimpses into a wondrous array of networks of complex molecular machines that know just what to do to keep cells humming. When evolution is mentioned at all, the main thing said is that the machines are "evolutionarily conserved." In other words, they have not evolved. It's important that we look at the details inside the cell occasionally. That's where the evidence for design often shines the brightest.

Darwinism Vs. the real world. XXXIII

How the Body Deals with Gravity
Howard Glicksman 





Editor's note: Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that's because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body. With that in mind, Evolution News is delighted to offer this series, "The Designed Body." For the complete series, see here. Dr. Glicksman practices palliative medicine for a hospice organization.


Our muscles, under the control of our nerves, allow us to breathe, swallow, move around and handle things. The peripheral nerves send sensory information about what is going on outside and inside the body to the spinal cord and the brain and from them send back motor instructions to the muscles to tell them what to do. In a previous article in this series, I described some of the sensors that as transducers convert phenomena into information the body can use. Pressure is detected by sensors in the skin; body motion, particularly of the head, is detected by the vestibular apparatus within the inner ear; and the proprioceptors provide information on the status of the muscles, tendons, and joints.

My last article described some of the reflexes (involuntary pre-programmed automatic motor responses without conscious direction from the brain) the body uses to avoid serious injury and maintain its position. Now let's look at how the body deals with the law of gravity and what it takes to keep its balance. Remember that when evolutionary biologists tell us about life and the mechanism by which it must have come about, they only deal with how it looks and not how it must actually work within the laws of nature. Ask yourself which is a more plausible explanation for how life arose: chance and the laws of nature alone, or intelligent design?

An object's center of gravity is a theoretical point about which its weight is evenly distributed. For an object that has a uniform density with a regular and symmetrical shape, such as a square piece of solid wood, the center of gravity is at its geometric center. Place a square solid wooden block on a table and push it more and more off the edge. It will fall to the ground when its center of gravity is no longer on the table.

The human body is made of muscles, organs, fat, and bone, each with a different density. Although the physical outline of the body is symmetrical from side to side, its shape is very irregular. The center of gravity for most people while standing or lying with their arms at their sides is in the midline, near their belly button (umbilicus). To stay standing, the body's center of gravity must remain between its two feet, both from side to side and back to front, otherwise it falls. Movement of the arms or legs away from the body or bending the spine in any direction changes the body's center of gravity. Carrying an object, especially at a distance from the body, will also change its center of gravity. For our earliest ancestors to survive within the laws of nature, they not only had to stay balanced while standing, but also walking, with only one foot, and running, with neither foot, in contact with the ground. In other words, the human body is an inherently unstable object that needs to take control to stay balanced.

The neuromuscular system keeps the body in position while balancing itself in relation to gravity. Although the spinal cord provides reflexes that help it maintain its posture, it is largely the brain (particularly the brainstem and the cerebellum) that provides the coordinated motor patterns needed to maintain balance. To make ongoing adjustments, the brain receives sensory data from mainly four different sources: the pressure receptors in the feet, the proprioceptors (particularly of the neck and the rest of the spinal column), the vestibular apparatus within the inner ear, and vision.

The pressure sensors in the feet inform the brain of the body's weight distribution relative to its center of gravity. Stand up and lean from side to side, and back and forth. Notice the difference in the pressure sensations felt from each foot with these movements, the feeling of imbalance, and the immediate adjustments that must be made to stay standing.

The proprioceptors of the neck and the rest of the spinal column provide the brain with information about the relative position of the head and the rest of the body. Bend your neck forward and backward and then bend from your waist in any direction. Wherever your neck and spinal column go so goes your head and the rest of your body. Notice the feeling of imbalance as your center of gravity moves away from being between your feet and how you quickly have to adjust to avoid falling.

The vestibular apparatus contributes sensory information about the speed and direction of head and neck angular motion and linear and vertical body movement. In addition, it helps to stabilize the retinal image. Look in a mirror, focusing on your eyes, and move your head slowly up and down and from side to side. Notice that your eyes automatically move in the opposite direction, allowing them to remain in focus. You are seeing the effects of the vestibulo-ocular reflex.

Now, continue to focus on your eyes and move your head up and down and from side to side as fast as you can. You cannot consciously control your eyes fast enough to compensate for these movements. It takes place automatically because of your decision to focus on your eyes (or any other object) while your head and body are in motion. Notice also how you felt a bit dizzy and off balance. This is caused by the strong alternating nerve impulses being sent from the vestibular apparatus on each side of the head to the brain due to the speed of your head movements.

The eyes provide the brain with an image of the environment in which the body is located. Clinical experience teaches that with concentration, training, and slow movement, vision can often help maintain the body's equilibrium without information from the pressure sensors, the proprioceptors, and the vestibular apparatus. Close your eyes and begin to walk, progressively increasing your speed. Notice how difficult it is to maintain your balance. Closing your eyes makes you totally dependent on the pressure sensors in the feet, the proprioceptors of the spine and limbs, and the vestibular apparatus, throwing you slightly off balance. Now do this exercise again, but this time with your eyes open. It is apparent that visual cues greatly contribute to being able to maintain your balance.

One of the first indications that a person may have a problem with their balance is when they inadvertently fall in the shower. While taking a shower, most people close their eyes to shampoo their hair and then quickly turn their head and neck, and often their whole body, to rinse it off. Moving this way with their eyes closed means their brain can no longer use visual cues to maintain their balance. If a person has condition like a sensory neuropathy (common in diabetics), which limits the reception of the sensory data from the feet, or Multiple Sclerosis, which slows the nerve impulse velocity in the brainstem, or degeneration of the cerebellum, which causes poor coordination, then they will come to realize how important their vision is. Without it, it becomes difficult or impossible for them to maintain balance.

All clinical experience teaches that for our earliest ancestors (and the theoretical intermediate organisms that led up to them) to maintain their balance, they would have needed to have an irreducibly complex system with a natural survival capacity similar to our own. This would have had to include different sensors located in strategic places to provide information on the body's position in space and relationship with gravity, a central nervous system to receive and analyze it, and the ability to access automatic motor reflexes and send voluntary motor messages fast enough to prevent a fall. For the force of gravity waits for no man and is an equal opportunity leveller, of sorts.


Just because similar organisms have similar mechanisms to maintain their balance does not, in and of itself, explain where those mechanisms and their ability to react properly and quickly came from in the first place. Evolutionary biology, as I said, is very good at describing how life looks, but has no capacity to explain how it must work within the laws of nature to survive. My next article will look at how we are able to accomplish purposeful movements and perform goal-directed activities. As everything else in this series has shown, it's not as simple as evolutionary biologists would have us believe.