Thursday, 8 September 2016
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.
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.
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.
Sunday, 4 September 2016
Broken genes?Says who?
BioLogos, Broken Genes, and Urate Oxidase
The Bigger They Come, The Harder They Fall
Arguments for evolution, the theory that the biological world arose strictly by chance and natural law, are at a high level. The details of how microbes, fish, amphibians, reptiles, birds and the rest actually were created by random mutations are hard to come by. But, evolutionists explain, the species look like they evolved. Don’t the comparisons of their anatomy, geographical locations, and so forth, make evolution the obvious explanation for their origin? One of the strongest such evidences, according to evolutionists such as Dennis Venema, are the so-called shared-errors. Meaningless or, better yet, harmful mutations found in allied species seem to be obvious signs of a common ancestor. For we would never expect such harmful mutations to have arisen independently. They must derive from a common ancestor. This argument has many problems and seems to be another example of how the stronger that an argument is for evolution, the more deeply it is flawed.
One of the problems with this argument is that it contains two suspicious, unspoken, assumptions.
First, the argument assumes that these mutations are meaningless or harmful. That assumption may well be true but, as any historian of evolutionary thought knows, it is a dangerous. The history of evolutionary thought is full of claims of bad, inefficient, useless designs which, upon further research were found to be, in fact, quite useful.
Second, the argument assumes that these mutations are random. In other words, it assumes there cannot be any common mechanisms, properly operating or otherwise, which could tend toward certain designs and mutations.
In fact convergence is ubiquitous and rampant in biology. Repeated designs appear in species so distant that, according to evolutionary theory, their common ancestor could not have had that design. So even evolutionists must agree that common designs must have arisen independently. And this must have occurred many times over, at both the morphological and molecular levels.
In other instances, such “convergence” must have occurred even in allied species. In fact this is true even for the so-called harmful mutations. For instance, evolutionists believe the urate oxidase enzyme, which catalyzes the oxidation of uric acid, was inactivated in humans and the great apes by harmful random mutations. But the different versions of the gene, in the different species, do not easily align with the expected evolutionary pattern. In fact, even evolutionists have to agree that several of the various inferred mutations, in these similar species, could not have arisen from a common ancestor. Instead, they must have arisen independently:
One exceptional change is a duplicated segment of GGGATGCC in intron 4 which is shared by the gorilla and the orangutan. However, because this change is phylogenetically incompatible with any of the three possible sister-relationships among the closely related trio of the human, the chimpanzee, and the gorilla, it might result from two independent duplications. Alternatively, though less likely, a single duplication occurred in the ancestral species of the great apes and had been polymorphic for a sufficiently long time to permit fixation of the duplicated form in the orangutan and the gorilla on one hand and loss in the human and the chimpanzee on the other hand.
The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation.
In contrast, the exon 3 mutation is not shared by H. syndactylus but by the gorilla and the orangutan. The origin of this mutation is therefore multiple and relatively recent in the gibbon lineage.
In other words, when common mutations found in different species cannot easily be explained by common descent, evolutionists do not hesitate to explain them as a consequent of multiple, independent events. This means that, even according evolutionists, similar mutations in allied species do not imply or require common descent. This contradicts the shared-error argument that is supposed to be one of the most powerful evidences for evolution. Unfortunately evolutionists do not include this information in their presentations of the shared-error argument.
The stronger that an argument is for evolution, the more deeply it is flawed.
h/t: DC
Posted by Cornelius Hunter
The Bigger They Come, The Harder They Fall
Arguments for evolution, the theory that the biological world arose strictly by chance and natural law, are at a high level. The details of how microbes, fish, amphibians, reptiles, birds and the rest actually were created by random mutations are hard to come by. But, evolutionists explain, the species look like they evolved. Don’t the comparisons of their anatomy, geographical locations, and so forth, make evolution the obvious explanation for their origin? One of the strongest such evidences, according to evolutionists such as Dennis Venema, are the so-called shared-errors. Meaningless or, better yet, harmful mutations found in allied species seem to be obvious signs of a common ancestor. For we would never expect such harmful mutations to have arisen independently. They must derive from a common ancestor. This argument has many problems and seems to be another example of how the stronger that an argument is for evolution, the more deeply it is flawed.
One of the problems with this argument is that it contains two suspicious, unspoken, assumptions.
First, the argument assumes that these mutations are meaningless or harmful. That assumption may well be true but, as any historian of evolutionary thought knows, it is a dangerous. The history of evolutionary thought is full of claims of bad, inefficient, useless designs which, upon further research were found to be, in fact, quite useful.
Second, the argument assumes that these mutations are random. In other words, it assumes there cannot be any common mechanisms, properly operating or otherwise, which could tend toward certain designs and mutations.
In fact convergence is ubiquitous and rampant in biology. Repeated designs appear in species so distant that, according to evolutionary theory, their common ancestor could not have had that design. So even evolutionists must agree that common designs must have arisen independently. And this must have occurred many times over, at both the morphological and molecular levels.
In other instances, such “convergence” must have occurred even in allied species. In fact this is true even for the so-called harmful mutations. For instance, evolutionists believe the urate oxidase enzyme, which catalyzes the oxidation of uric acid, was inactivated in humans and the great apes by harmful random mutations. But the different versions of the gene, in the different species, do not easily align with the expected evolutionary pattern. In fact, even evolutionists have to agree that several of the various inferred mutations, in these similar species, could not have arisen from a common ancestor. Instead, they must have arisen independently:
One exceptional change is a duplicated segment of GGGATGCC in intron 4 which is shared by the gorilla and the orangutan. However, because this change is phylogenetically incompatible with any of the three possible sister-relationships among the closely related trio of the human, the chimpanzee, and the gorilla, it might result from two independent duplications. Alternatively, though less likely, a single duplication occurred in the ancestral species of the great apes and had been polymorphic for a sufficiently long time to permit fixation of the duplicated form in the orangutan and the gorilla on one hand and loss in the human and the chimpanzee on the other hand.
The nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation.
In contrast, the exon 3 mutation is not shared by H. syndactylus but by the gorilla and the orangutan. The origin of this mutation is therefore multiple and relatively recent in the gibbon lineage.
In other words, when common mutations found in different species cannot easily be explained by common descent, evolutionists do not hesitate to explain them as a consequent of multiple, independent events. This means that, even according evolutionists, similar mutations in allied species do not imply or require common descent. This contradicts the shared-error argument that is supposed to be one of the most powerful evidences for evolution. Unfortunately evolutionists do not include this information in their presentations of the shared-error argument.
The stronger that an argument is for evolution, the more deeply it is flawed.
h/t: DC
Posted by Cornelius Hunter
Trying to eat their cake and yet have it.
The Supposed Dual (Double) Nature of Christ
Was Jesus a Spirit or Wasn't He?
by Hal Flemings
In their zeal to discredit Jehovah’s Witnesses, many writers inadvertently create irreconcilable difficulties for themselves.
Mainstream Trinitarians believe that when Jesus Christ was on the earth in the First Century of our Common Era that he was totally man and totally god. Everyone seems to agree with Jesus at John 4:24 where he stated, "God is a Spirit: and they that worship him must worship him in spirit and in truth." (King James Version) Because God is a spirit and Trinitarians are certain that Jesus is God, they argue that while on earth Jesus was God incarnate, that is, a spirit being enclosed with flesh. Because Jehovah's Witnesses reject this view, literally volumes of books, magazines, tracts, cassette tapes, etc., have been produced to challenge them on the doctrine of the Trinity and the nature of Christ.
....
This paper is not concerned with defending the Witness stand on the nature of Christ at his resurrection or the question of Christ being the Almighty God or not; those matters have been effectively addressed elsewhere.What we are considering here is a serious contradiction.
That contradiction is as follows: these antagonists go to great lengths to establish that while on earth Jesus was God incarnate - a spirit clothed in flesh - but then deny that he was a spirit at all at his resurrection. Either he was a spirit or he was not a spirit. If he was God in the flesh - experiencing two natures simultaneously - then he was a spirit at his resurrection since God is a spirit. On the other hand, if indeed he was, in reality, not a spirit but a "glorified body", then he was not a God-man in the sense Trinitarians understand it, since a God-man is a spirit clothed in flesh. They cannot have it both ways. One of the attacks on the Witnesses has to be abandoned.
Was Jesus a Spirit or Wasn't He?
by Hal Flemings
In their zeal to discredit Jehovah’s Witnesses, many writers inadvertently create irreconcilable difficulties for themselves.
Mainstream Trinitarians believe that when Jesus Christ was on the earth in the First Century of our Common Era that he was totally man and totally god. Everyone seems to agree with Jesus at John 4:24 where he stated, "God is a Spirit: and they that worship him must worship him in spirit and in truth." (King James Version) Because God is a spirit and Trinitarians are certain that Jesus is God, they argue that while on earth Jesus was God incarnate, that is, a spirit being enclosed with flesh. Because Jehovah's Witnesses reject this view, literally volumes of books, magazines, tracts, cassette tapes, etc., have been produced to challenge them on the doctrine of the Trinity and the nature of Christ.
....
This paper is not concerned with defending the Witness stand on the nature of Christ at his resurrection or the question of Christ being the Almighty God or not; those matters have been effectively addressed elsewhere.What we are considering here is a serious contradiction.
That contradiction is as follows: these antagonists go to great lengths to establish that while on earth Jesus was God incarnate - a spirit clothed in flesh - but then deny that he was a spirit at all at his resurrection. Either he was a spirit or he was not a spirit. If he was God in the flesh - experiencing two natures simultaneously - then he was a spirit at his resurrection since God is a spirit. On the other hand, if indeed he was, in reality, not a spirit but a "glorified body", then he was not a God-man in the sense Trinitarians understand it, since a God-man is a spirit clothed in flesh. They cannot have it both ways. One of the attacks on the Witnesses has to be abandoned.
Saturday, 3 September 2016
Darwinism:It's his story and he's sticking to it.
Professor B Supports Evolution
In this age of specialization we look to the experts to tell us what to think. And when it comes to origins, the experts tell us that life evolved. Random mutations, surprisingly enough, are sufficient to create the species. As if we needed another example of this, we now have “Professor B,” who wishes to remain anonymous but can’t help to explain that skeptics of this modern day Epicureanism are “almost certainly wrong” to doubt that proteins can spontaneously arise because it would require something like 10^74 attempts. After all, that figure was “based on a very small sample.” Small sample? If the professor understood statistics he would know small sample sizes do not invalidate results—not to the level he requires. In fact, as we have discussed many times, several studies have arrived at this type of astronomical figure.
When presented with that inconvenient fact, our Professor B switched strategies. Now, it seems that, according to the professor, “a very large number of different amino acid sequences were capable of performing the same biological function.” Therefore it is not a big problem for evolution to create these incredible molecular machines.
That is an absurd misrepresentation of molecular biology. While it certainly is true that a large number of different sequences can perform the same function, we are nowhere close to 10^74. “Very large” in this context is astronomically smaller than 10^74.
As if sensing a problem, Professor B switched to yet another tactic, claiming that evolution is capable of creating astronomical numbers of proteins anyway. It seems, according to the professor, that evolution can rip through 10^42 different proteins in search of what works.
Not that this helps much, as 10^42 is still dozens of orders of magnitude smaller than the needed 10^74. But even the estimate of 10^42 is, itself, absurd. It comes from a paper that assumes the pre existence of bacteria and, yes, proteins. In fact, the evolutionists assumed the earth was covered with bacteria, and each bacteria was full of proteins. That of course is not an appropriate assumption for the question of how proteins could have evolved in the first place. In fact, it is circular. Good thing the professor remained anonymous.
Religion drives science, and it matters.
Posted by Cornelius Hunter
In this age of specialization we look to the experts to tell us what to think. And when it comes to origins, the experts tell us that life evolved. Random mutations, surprisingly enough, are sufficient to create the species. As if we needed another example of this, we now have “Professor B,” who wishes to remain anonymous but can’t help to explain that skeptics of this modern day Epicureanism are “almost certainly wrong” to doubt that proteins can spontaneously arise because it would require something like 10^74 attempts. After all, that figure was “based on a very small sample.” Small sample? If the professor understood statistics he would know small sample sizes do not invalidate results—not to the level he requires. In fact, as we have discussed many times, several studies have arrived at this type of astronomical figure.
When presented with that inconvenient fact, our Professor B switched strategies. Now, it seems that, according to the professor, “a very large number of different amino acid sequences were capable of performing the same biological function.” Therefore it is not a big problem for evolution to create these incredible molecular machines.
That is an absurd misrepresentation of molecular biology. While it certainly is true that a large number of different sequences can perform the same function, we are nowhere close to 10^74. “Very large” in this context is astronomically smaller than 10^74.
As if sensing a problem, Professor B switched to yet another tactic, claiming that evolution is capable of creating astronomical numbers of proteins anyway. It seems, according to the professor, that evolution can rip through 10^42 different proteins in search of what works.
Not that this helps much, as 10^42 is still dozens of orders of magnitude smaller than the needed 10^74. But even the estimate of 10^42 is, itself, absurd. It comes from a paper that assumes the pre existence of bacteria and, yes, proteins. In fact, the evolutionists assumed the earth was covered with bacteria, and each bacteria was full of proteins. That of course is not an appropriate assumption for the question of how proteins could have evolved in the first place. In fact, it is circular. Good thing the professor remained anonymous.
Religion drives science, and it matters.
Posted by Cornelius Hunter
Watchtower society's commentary on the earth's place in the divine agenda
EARTH:
The fifth-largest planet of the solar system and the third in order of position from the sun. It is an oblate spheroid, being slightly flattened at the poles. Satellite observations have indicated other slight irregularities in the shape of the earth. Its mass is approximately 5.98 × 1024 kg (13.18 × 1024 lb). Its area is about 510,000,000 sq km (197,000,000 sq mi). Earth’s measurements are (approximately): circumference at the equator, just over 40,000 km (24,900 mi); diameter at the equator, 12,750 km (7,920 mi). Oceans and seas cover approximately 71 percent of its surface, leaving about 149,000,000 sq km (57,500,000 sq mi) of land surface.
The earth rotates on its axis, bringing about day and night. (Ge 1:4, 5) A solar day or an apparent day is a period of 24 hours, the time taken for an observer at any one point on the earth to be again in the same position relative to the sun. The tropical year, which concerns the return of the seasons, the interval between two consecutive returns of the sun to the vernal equinox, is 365 days, 5 hours, 48 minutes, and 46 seconds, on the average. This figure is the one used in solar-year calendar reckoning, and its fractional nature has caused much difficulty in accurate calendar making.
The axis of the earth tilts 23° 27ʹ away from a perpendicular to the earth’s orbit. The gyroscopic effect of rotation holds the earth’s axis in basically the same direction relative to the stars regardless of its location in its orbit around the sun. This tilt of the axis brings about the seasons.
The earth’s atmosphere, composed principally of nitrogen, oxygen, water vapor, and other gases, extends over 960 km (600 mi) above the earth’s surface. Beyond this is what is termed “outer space.”
Bible Terms and Significance. In the Hebrew Scriptures, the word used for earth as a planet is ʼeʹrets. ʼEʹrets refers to (1) earth, as opposed to heaven, or sky (Ge 1:2); (2) land, country, territory (Ge 10:10); (3) ground, surface of the ground (Ge 1:26); (4) people of all the globe (Ge 18:25).
The word ʼadha·mahʹ is translated “ground,” “soil,” or “land.” ʼAdha·mahʹ refers to (1) ground as tilled, yielding sustenance (Ge 3:23); (2) piece of ground, landed property (Ge 47:18); (3) earth as material substance, soil, dirt (Jer 14:4; 1Sa 4:12); (4) ground as earth’s visible surface (Ge 1:25); (5) land, territory, country (Le 20:24); (6) whole earth, inhabited earth (Ge 12:3). ʼAdha·mahʹ seems to be related etymologically to the word ʼa·dhamʹ, the first man Adam having been made from the dust of the ground.—Ge 2:7.
In the Greek Scriptures, ge denotes earth as arable land or soil. (Mt 13:5, 8) It is used to designate the material from which Adam was made, the earth (1Co 15:47); the earthly globe (Mt 5:18, 35; 6:19); earth as a habitation for human creatures and animals (Lu 21:35; Ac 1:8; 8:33; 10:12; 11:6; 17:26); land, country, territory (Lu 4:25; Joh 3:22); ground (Mt 10:29; Mr 4:26); land, shore, as contrasted with seas or waters. (Joh 21:8, 9, 11; Mr 4:1).
Oi·kou·meʹne, translated “world” in the King James Version, denotes “inhabited earth.”—Mt 24:14; Lu 2:1; Ac 17:6; Re 12:9.
In each case of all the above senses in which these words are used, the form of the word in the original language, and more particularly the setting or context, determine which sense is meant.
The Hebrews divided the earth into four quarters or regions corresponding to the four points of the compass. In the Hebrew Scriptures the words “before” and “in front of” designate and are translated “east” (Ge 12:8); “behind” may mean “west” (Isa 9:12); “the right side” may denote “south” (1Sa 23:24); and “the left” may be translated “north” (Job 23:8, 9; compare Ro). East was also (in Heb.) sometimes called the sunrising, as for example, at Joshua 4:19. West (in Heb.) was the setting of the sun. (2Ch 32:30) Also, physical characteristics were used. Being almost the total western boundary of Palestine, the “Sea” (the Mediterranean) was sometimes used for west.—Nu 34:6.
Creation. The planet’s coming into existence is recounted in the Bible with the simple statement: “In the beginning God created the heavens and the earth.” (Ge 1:1) Just how long ago the starry heavens and the earth were created is not stated in the Bible. Therefore, there is no basis for Bible scholars to take issue with scientific calculations of the age of the planet. Scientists estimate the age of some rocks as being three and a half billion years, and the earth itself as being about four to four and a half billion or more years.
As to time, the Scriptures are more definite about the six creative days of the Genesis account. These days have to do, not with the creation of earth’s matter or material, but with the arranging and preparing of it for man’s habitation.
The Bible does not reveal whether God created life on any of the other planets in the universe. However, astronomers today have not found proof that life exists on any of these planets and, in fact, know of no planet besides the earth that is at present capable of supporting the life of fleshly creatures.
Purpose. Like all other created things, the earth was brought into existence because of Jehovah’s will (“pleasure,” KJ). (Re 4:11) It was created to remain forever. (Ps 78:69; 104:5; 119:90; Ec 1:4) God speaks of himself as a God of purpose and declares that his purposes are certain to come to fruition. (Isa 46:10; 55:11) He made his purpose for the earth very clear when he said to the first human pair: “Be fruitful and become many and fill the earth and subdue it, and have in subjection the fish of the sea and the flying creatures of the heavens and every living creature that is moving upon the earth.” (Ge 1:28) There were no flaws in earth or the things on it. Having created all necessary things, Jehovah saw that they were “very good” and “proceeded to rest” or desist from other earthly creative works.—Ge 1:31–2:2.
Man’s habitation on earth is also permanent. When God gave man the law regarding the tree of the knowledge of good and bad, he implied that man could live on earth forever. (Ge 2:17) We are assured by Jehovah’s own words that “all the days the earth continues, seed sowing and harvest, and cold and heat, and summer and winter, and day and night, will never cease” (Ge 8:22) and that he will never destroy all flesh again by a flood. (Ge 9:12-16) Jehovah says that he did not make the earth for nothing but, rather, that he has given it to men as a home and that death will eventually be done away with. God’s purpose, therefore, is for the earth to be the habitation of man in perfection and happiness with eternal life.—Ps 37:11; 115:16; Isa 45:18; Re 21:3, 4.
That this is the purpose of Jehovah God, sacred to him and not to be thwarted, is indicated when the Bible says: “And by the seventh day God came to the completion of his work that he had made . . . And God proceeded to bless the seventh day and make it sacred, because on it he has been resting from all his work that God has created for the purpose of making.” (Ge 2:2, 3) The seventh, or rest, day is not shown in the Genesis account as ending, as in the case of the other six days. The apostle Paul explained that the rest day of God had been continuous right through Israelite history down to his own time and had not yet ended. (Heb 3:7-11; 4:3-9) God says the seventh day was set aside as sacred to him. He would carry out his purpose toward the earth; it would be fully accomplished during that day, with no necessity of further creative works toward the earth during that time.
The Bible’s Harmony With Scientific Facts. The Bible, at Job 26:7, speaks of God as “hanging the earth upon nothing.” Science says that the earth remains in its orbit in space primarily because of the interaction of gravity and centrifugal force. These forces, of course, are invisible. Therefore the earth, like other heavenly bodies, is suspended in space as if hanging on nothing. Speaking from Jehovah’s viewpoint, the prophet Isaiah wrote under inspiration: “There is One who is dwelling above the circle of the earth, the dwellers in which are as grasshoppers.” (Isa 40:22) The Bible says: “He [God] has described a circle upon the face of the waters.” (Job 26:10) The waters are limited by his decree to their proper place. They do not come up and inundate the land; neither do they fly off into space. (Job 38:8-11) From the viewpoint of Jehovah, the earth’s face, or the surface of the waters, would, of course, have a circular form, just as the edge of the moon presents a circular appearance to us. Before land surfaces appeared, the surface of the entire globe was one circular (spherical) mass of surging waters.—Ge 1:2.
Bible writers often speak from the standpoint of the observer on the earth, or from his particular position geographically, as we often naturally do today. For example, the Bible mentions “the sunrising.” (Nu 2:3; 34:15) Some have seized upon this as an opportunity to discredit the Bible as scientifically inaccurate, claiming that the Hebrews viewed earth as the center of things, with the sun revolving around it. But the Bible writers nowhere expressed such a belief. These same critics overlook the fact that they themselves use the identical expression and that it is in all of their almanacs. It is common to hear someone say, ‘it is sunrise,’ or ‘the sun has set,’ or ‘the sun traveled across the sky.’ The Bible also speaks of “the extremity of the earth” (Ps 46:9), “the ends of the earth” (Ps 22:27), “the four extremities of the earth” (Isa 11:12), “the four corners of the earth,” and “the four winds of the earth” (Re 7:1). These expressions cannot be taken to prove that the Hebrews understood the earth to be square. The number four is often used to denote that which is fully rounded out, as it were, just as we have four directions and sometimes employ the expressions “to the ends of the earth,” “to the four corners of the earth,” in the sense of embracing all the earth.—Compare Eze 1:15-17; Lu 13:29.
Figurative and Symbolic Expressions. The earth is spoken of figuratively in several instances. It is likened to a building, at Job 38:4-6, when Jehovah asks Job questions concerning earth’s creation and Jehovah’s management of it that Job obviously cannot answer. Jehovah also uses a figurative expression describing the result of earth’s rotation. He says: “[The earth] transforms itself like clay under a seal.” (Job 38:14) In Bible times some seals for “signing” documents were in the form of a roller engraved with the writer’s emblem. It was rolled over the soft clay document or clay envelope, leaving behind it an impression in the clay. In similar manner, at the arrival of dawn, the portion of the earth coming from the blackness of night begins to show itself to have form and color as the sunlight moves progressively across its face. The heavens, the location of Jehovah’s throne, being higher than the earth, the earth is, figuratively, his footstool. (Ps 103:11; Isa 55:9; 66:1; Mt 5:35; Ac 7:49) Those who are in Sheol, or Hades, the common grave of mankind, are regarded as being under the earth.—Re 5:3.
The apostle Peter compares the literal heavens and earth (2Pe 3:5) with the symbolic heavens and earth (2Pe 3:7). “The heavens” of verse 7 do not mean Jehovah’s own dwelling place, the place of his throne in the heavens. Jehovah’s heavens cannot be shaken. Neither is “the earth” in the same verse the literal planet earth, for Jehovah says that he has established the earth firmly. (Ps 78:69; 119:90) Yet, God says that he will shake both the heavens and the earth (Hag 2:21; Heb 12:26), that the heavens and earth will flee away before him, and that new heavens and a new earth will be established. (2Pe 3:13; Re 20:11; 21:1) It is evident that “heavens” is symbolic and that “earth” here has symbolic reference to a society of people living on the earth, just as at Psalm 96:1.—See HEAVEN (New heavens and new earth).
Earth is also symbolically used to denote the firmer, more stable elements of mankind. The restless, unstable elements of mankind are illustrated by the characteristic restlessness of the sea.—Isa 57:20; Jas 1:6; Jude 13; compare Re 12:16; 20:11; 21:1.
John 3:31 contrasts one that comes from above as being higher than one who comes from the earth (ge). The Greek word e·piʹgei·os, “earthly,” is used to denote earthly, physical things, especially as contrasted with heavenly things, and as being lower and of coarser material. Man is made of earth’s material. (2Co 5:1; compare 1Co 15:46-49.) Nevertheless, he can please God by living a “spiritual” life, a life directed by God’s Word and spirit. (1Co 2:12, 15, 16; Heb 12:9) Because of mankind’s fall into sin and their tendency toward material things to the neglect or exclusion of spiritual things (Ge 8:21; 1Co 2:14), “earthly” can have an undesirable connotation, meaning “corrupt,” or “in opposition to the spirit.”—Php 3:19; Jas 3:15.
The fifth-largest planet of the solar system and the third in order of position from the sun. It is an oblate spheroid, being slightly flattened at the poles. Satellite observations have indicated other slight irregularities in the shape of the earth. Its mass is approximately 5.98 × 1024 kg (13.18 × 1024 lb). Its area is about 510,000,000 sq km (197,000,000 sq mi). Earth’s measurements are (approximately): circumference at the equator, just over 40,000 km (24,900 mi); diameter at the equator, 12,750 km (7,920 mi). Oceans and seas cover approximately 71 percent of its surface, leaving about 149,000,000 sq km (57,500,000 sq mi) of land surface.
The earth rotates on its axis, bringing about day and night. (Ge 1:4, 5) A solar day or an apparent day is a period of 24 hours, the time taken for an observer at any one point on the earth to be again in the same position relative to the sun. The tropical year, which concerns the return of the seasons, the interval between two consecutive returns of the sun to the vernal equinox, is 365 days, 5 hours, 48 minutes, and 46 seconds, on the average. This figure is the one used in solar-year calendar reckoning, and its fractional nature has caused much difficulty in accurate calendar making.
The axis of the earth tilts 23° 27ʹ away from a perpendicular to the earth’s orbit. The gyroscopic effect of rotation holds the earth’s axis in basically the same direction relative to the stars regardless of its location in its orbit around the sun. This tilt of the axis brings about the seasons.
The earth’s atmosphere, composed principally of nitrogen, oxygen, water vapor, and other gases, extends over 960 km (600 mi) above the earth’s surface. Beyond this is what is termed “outer space.”
Bible Terms and Significance. In the Hebrew Scriptures, the word used for earth as a planet is ʼeʹrets. ʼEʹrets refers to (1) earth, as opposed to heaven, or sky (Ge 1:2); (2) land, country, territory (Ge 10:10); (3) ground, surface of the ground (Ge 1:26); (4) people of all the globe (Ge 18:25).
The word ʼadha·mahʹ is translated “ground,” “soil,” or “land.” ʼAdha·mahʹ refers to (1) ground as tilled, yielding sustenance (Ge 3:23); (2) piece of ground, landed property (Ge 47:18); (3) earth as material substance, soil, dirt (Jer 14:4; 1Sa 4:12); (4) ground as earth’s visible surface (Ge 1:25); (5) land, territory, country (Le 20:24); (6) whole earth, inhabited earth (Ge 12:3). ʼAdha·mahʹ seems to be related etymologically to the word ʼa·dhamʹ, the first man Adam having been made from the dust of the ground.—Ge 2:7.
In the Greek Scriptures, ge denotes earth as arable land or soil. (Mt 13:5, 8) It is used to designate the material from which Adam was made, the earth (1Co 15:47); the earthly globe (Mt 5:18, 35; 6:19); earth as a habitation for human creatures and animals (Lu 21:35; Ac 1:8; 8:33; 10:12; 11:6; 17:26); land, country, territory (Lu 4:25; Joh 3:22); ground (Mt 10:29; Mr 4:26); land, shore, as contrasted with seas or waters. (Joh 21:8, 9, 11; Mr 4:1).
Oi·kou·meʹne, translated “world” in the King James Version, denotes “inhabited earth.”—Mt 24:14; Lu 2:1; Ac 17:6; Re 12:9.
In each case of all the above senses in which these words are used, the form of the word in the original language, and more particularly the setting or context, determine which sense is meant.
The Hebrews divided the earth into four quarters or regions corresponding to the four points of the compass. In the Hebrew Scriptures the words “before” and “in front of” designate and are translated “east” (Ge 12:8); “behind” may mean “west” (Isa 9:12); “the right side” may denote “south” (1Sa 23:24); and “the left” may be translated “north” (Job 23:8, 9; compare Ro). East was also (in Heb.) sometimes called the sunrising, as for example, at Joshua 4:19. West (in Heb.) was the setting of the sun. (2Ch 32:30) Also, physical characteristics were used. Being almost the total western boundary of Palestine, the “Sea” (the Mediterranean) was sometimes used for west.—Nu 34:6.
Creation. The planet’s coming into existence is recounted in the Bible with the simple statement: “In the beginning God created the heavens and the earth.” (Ge 1:1) Just how long ago the starry heavens and the earth were created is not stated in the Bible. Therefore, there is no basis for Bible scholars to take issue with scientific calculations of the age of the planet. Scientists estimate the age of some rocks as being three and a half billion years, and the earth itself as being about four to four and a half billion or more years.
As to time, the Scriptures are more definite about the six creative days of the Genesis account. These days have to do, not with the creation of earth’s matter or material, but with the arranging and preparing of it for man’s habitation.
The Bible does not reveal whether God created life on any of the other planets in the universe. However, astronomers today have not found proof that life exists on any of these planets and, in fact, know of no planet besides the earth that is at present capable of supporting the life of fleshly creatures.
Purpose. Like all other created things, the earth was brought into existence because of Jehovah’s will (“pleasure,” KJ). (Re 4:11) It was created to remain forever. (Ps 78:69; 104:5; 119:90; Ec 1:4) God speaks of himself as a God of purpose and declares that his purposes are certain to come to fruition. (Isa 46:10; 55:11) He made his purpose for the earth very clear when he said to the first human pair: “Be fruitful and become many and fill the earth and subdue it, and have in subjection the fish of the sea and the flying creatures of the heavens and every living creature that is moving upon the earth.” (Ge 1:28) There were no flaws in earth or the things on it. Having created all necessary things, Jehovah saw that they were “very good” and “proceeded to rest” or desist from other earthly creative works.—Ge 1:31–2:2.
Man’s habitation on earth is also permanent. When God gave man the law regarding the tree of the knowledge of good and bad, he implied that man could live on earth forever. (Ge 2:17) We are assured by Jehovah’s own words that “all the days the earth continues, seed sowing and harvest, and cold and heat, and summer and winter, and day and night, will never cease” (Ge 8:22) and that he will never destroy all flesh again by a flood. (Ge 9:12-16) Jehovah says that he did not make the earth for nothing but, rather, that he has given it to men as a home and that death will eventually be done away with. God’s purpose, therefore, is for the earth to be the habitation of man in perfection and happiness with eternal life.—Ps 37:11; 115:16; Isa 45:18; Re 21:3, 4.
That this is the purpose of Jehovah God, sacred to him and not to be thwarted, is indicated when the Bible says: “And by the seventh day God came to the completion of his work that he had made . . . And God proceeded to bless the seventh day and make it sacred, because on it he has been resting from all his work that God has created for the purpose of making.” (Ge 2:2, 3) The seventh, or rest, day is not shown in the Genesis account as ending, as in the case of the other six days. The apostle Paul explained that the rest day of God had been continuous right through Israelite history down to his own time and had not yet ended. (Heb 3:7-11; 4:3-9) God says the seventh day was set aside as sacred to him. He would carry out his purpose toward the earth; it would be fully accomplished during that day, with no necessity of further creative works toward the earth during that time.
The Bible’s Harmony With Scientific Facts. The Bible, at Job 26:7, speaks of God as “hanging the earth upon nothing.” Science says that the earth remains in its orbit in space primarily because of the interaction of gravity and centrifugal force. These forces, of course, are invisible. Therefore the earth, like other heavenly bodies, is suspended in space as if hanging on nothing. Speaking from Jehovah’s viewpoint, the prophet Isaiah wrote under inspiration: “There is One who is dwelling above the circle of the earth, the dwellers in which are as grasshoppers.” (Isa 40:22) The Bible says: “He [God] has described a circle upon the face of the waters.” (Job 26:10) The waters are limited by his decree to their proper place. They do not come up and inundate the land; neither do they fly off into space. (Job 38:8-11) From the viewpoint of Jehovah, the earth’s face, or the surface of the waters, would, of course, have a circular form, just as the edge of the moon presents a circular appearance to us. Before land surfaces appeared, the surface of the entire globe was one circular (spherical) mass of surging waters.—Ge 1:2.
Bible writers often speak from the standpoint of the observer on the earth, or from his particular position geographically, as we often naturally do today. For example, the Bible mentions “the sunrising.” (Nu 2:3; 34:15) Some have seized upon this as an opportunity to discredit the Bible as scientifically inaccurate, claiming that the Hebrews viewed earth as the center of things, with the sun revolving around it. But the Bible writers nowhere expressed such a belief. These same critics overlook the fact that they themselves use the identical expression and that it is in all of their almanacs. It is common to hear someone say, ‘it is sunrise,’ or ‘the sun has set,’ or ‘the sun traveled across the sky.’ The Bible also speaks of “the extremity of the earth” (Ps 46:9), “the ends of the earth” (Ps 22:27), “the four extremities of the earth” (Isa 11:12), “the four corners of the earth,” and “the four winds of the earth” (Re 7:1). These expressions cannot be taken to prove that the Hebrews understood the earth to be square. The number four is often used to denote that which is fully rounded out, as it were, just as we have four directions and sometimes employ the expressions “to the ends of the earth,” “to the four corners of the earth,” in the sense of embracing all the earth.—Compare Eze 1:15-17; Lu 13:29.
Figurative and Symbolic Expressions. The earth is spoken of figuratively in several instances. It is likened to a building, at Job 38:4-6, when Jehovah asks Job questions concerning earth’s creation and Jehovah’s management of it that Job obviously cannot answer. Jehovah also uses a figurative expression describing the result of earth’s rotation. He says: “[The earth] transforms itself like clay under a seal.” (Job 38:14) In Bible times some seals for “signing” documents were in the form of a roller engraved with the writer’s emblem. It was rolled over the soft clay document or clay envelope, leaving behind it an impression in the clay. In similar manner, at the arrival of dawn, the portion of the earth coming from the blackness of night begins to show itself to have form and color as the sunlight moves progressively across its face. The heavens, the location of Jehovah’s throne, being higher than the earth, the earth is, figuratively, his footstool. (Ps 103:11; Isa 55:9; 66:1; Mt 5:35; Ac 7:49) Those who are in Sheol, or Hades, the common grave of mankind, are regarded as being under the earth.—Re 5:3.
The apostle Peter compares the literal heavens and earth (2Pe 3:5) with the symbolic heavens and earth (2Pe 3:7). “The heavens” of verse 7 do not mean Jehovah’s own dwelling place, the place of his throne in the heavens. Jehovah’s heavens cannot be shaken. Neither is “the earth” in the same verse the literal planet earth, for Jehovah says that he has established the earth firmly. (Ps 78:69; 119:90) Yet, God says that he will shake both the heavens and the earth (Hag 2:21; Heb 12:26), that the heavens and earth will flee away before him, and that new heavens and a new earth will be established. (2Pe 3:13; Re 20:11; 21:1) It is evident that “heavens” is symbolic and that “earth” here has symbolic reference to a society of people living on the earth, just as at Psalm 96:1.—See HEAVEN (New heavens and new earth).
Earth is also symbolically used to denote the firmer, more stable elements of mankind. The restless, unstable elements of mankind are illustrated by the characteristic restlessness of the sea.—Isa 57:20; Jas 1:6; Jude 13; compare Re 12:16; 20:11; 21:1.
John 3:31 contrasts one that comes from above as being higher than one who comes from the earth (ge). The Greek word e·piʹgei·os, “earthly,” is used to denote earthly, physical things, especially as contrasted with heavenly things, and as being lower and of coarser material. Man is made of earth’s material. (2Co 5:1; compare 1Co 15:46-49.) Nevertheless, he can please God by living a “spiritual” life, a life directed by God’s Word and spirit. (1Co 2:12, 15, 16; Heb 12:9) Because of mankind’s fall into sin and their tendency toward material things to the neglect or exclusion of spiritual things (Ge 8:21; 1Co 2:14), “earthly” can have an undesirable connotation, meaning “corrupt,” or “in opposition to the spirit.”—Php 3:19; Jas 3:15.
Slaves of Christ.
Are Jehovah’s Witnesses Christians?
Yes. We are Christians for the following reasons:
We try to follow closely the teachings and behavior of Jesus Christ.—1 Peter 2:21.
We believe that Jesus is the key to salvation, that “there is not another name under heaven that has been given among men by which we must get saved.”—Acts 4:12.
When people become Jehovah’s Witnesses, they are baptized in the name of Jesus.—Matthew 28:18, 19.
We offer our prayers in Jesus’ name.—John 15:16.
We believe that Jesus is the Head, or the one appointed to have authority, over every man.—1 Corinthians 11:3.
However, in a number of ways, we are different from other religious groups that are called Christian. For example, we believe that the Bible teaches that Jesus is the Son of God, not part of a Trinity. (Mark 12:29) We do not believe that the soul is immortal, that there is any basis in Scripture for saying that God tortures people in an everlasting hell, or that those who take the lead in religious activities should have titles that elevate them above others.—Ecclesiastes 9:5; Ezekiel 18:4; Matthew 23:8-10.
Yes. We are Christians for the following reasons:
We try to follow closely the teachings and behavior of Jesus Christ.—1 Peter 2:21.
We believe that Jesus is the key to salvation, that “there is not another name under heaven that has been given among men by which we must get saved.”—Acts 4:12.
When people become Jehovah’s Witnesses, they are baptized in the name of Jesus.—Matthew 28:18, 19.
We offer our prayers in Jesus’ name.—John 15:16.
We believe that Jesus is the Head, or the one appointed to have authority, over every man.—1 Corinthians 11:3.
However, in a number of ways, we are different from other religious groups that are called Christian. For example, we believe that the Bible teaches that Jesus is the Son of God, not part of a Trinity. (Mark 12:29) We do not believe that the soul is immortal, that there is any basis in Scripture for saying that God tortures people in an everlasting hell, or that those who take the lead in religious activities should have titles that elevate them above others.—Ecclesiastes 9:5; Ezekiel 18:4; Matthew 23:8-10.
The mark of the beast.
Forced Reeducation for MDs Who Don't Want to Kill
Wesley J. Smith
Yesterday I commented on a bioethics "Consensus Statement" published by Oxford University that advocates eviscerating medical conscience rights of doctors with religious or moral objections to procedures such as abortion and euthanasia.
Looking more closely at the authoritarian document, I see that the bioethicists would require dissenting doctors to perform community service for their thought crime and to attend reeducation classes about the harm their beliefs cause.
From the "Consensus Statement" (my emphasis):
Healthcare practitioners who are exempted from performing certain medical procedures on conscientious grounds should be required to compensate society and the health system for their failure to fulfill their professional obligations by providing public-benefitting services.
Medical students should not be exempted from learning how to perform basic medical procedures they consider to be morally wrong. Even if they become conscientious objectors, they will still be required to perform the procedure to which they object in emergency situations or when referral is not possible or poses too great a burden on patients or on the healthcare system...
Healthcare practitioners should also be educated to reflect on the influence of cognitive bias in their objections.
Bottom line: Refuse to commit or be complicit in what your religion considers a terrible sin, or your conscience believes to be a terrible wrong, and you will be made to pay! If you are pro-life and want to become an MD, forget about it: You are not welcome in the healthcare professions.
Revelation13:17NIV "so that they could not buy or sell unless they had the mark, which is the name of the beast or the number of its name."
Wesley J. Smith
Yesterday I commented on a bioethics "Consensus Statement" published by Oxford University that advocates eviscerating medical conscience rights of doctors with religious or moral objections to procedures such as abortion and euthanasia.
Looking more closely at the authoritarian document, I see that the bioethicists would require dissenting doctors to perform community service for their thought crime and to attend reeducation classes about the harm their beliefs cause.
From the "Consensus Statement" (my emphasis):
Healthcare practitioners who are exempted from performing certain medical procedures on conscientious grounds should be required to compensate society and the health system for their failure to fulfill their professional obligations by providing public-benefitting services.
Medical students should not be exempted from learning how to perform basic medical procedures they consider to be morally wrong. Even if they become conscientious objectors, they will still be required to perform the procedure to which they object in emergency situations or when referral is not possible or poses too great a burden on patients or on the healthcare system...
Healthcare practitioners should also be educated to reflect on the influence of cognitive bias in their objections.
Bottom line: Refuse to commit or be complicit in what your religion considers a terrible sin, or your conscience believes to be a terrible wrong, and you will be made to pay! If you are pro-life and want to become an MD, forget about it: You are not welcome in the healthcare professions.
Revelation13:17NIV "so that they could not buy or sell unless they had the mark, which is the name of the beast or the number of its name."
Friday, 2 September 2016
A zombie argument struck down (again).
This Sounds Familiar: Theistic Evolutionist Recycles Anti-ID Argument Refuted Years Ago
Evolution News & Views
In a post for the theistic evolutionary group BioLogos, Canadian biology professor Dennis Venema writes affectionately, with only a mild touch of disdain, about the intelligent design movement. Their (meaning our) hearts are in the right place, he tells readers. Like him, advocates of ID want to build an "apologetic" against materialism. They're just going about it in the wrong way. And their science is wrong.
Venema readily concedes that living cells use "highly intricate" processes to manage genetic information. However, is it really "information"? And is the genetic code really a "code"? The quote marks in both cases are Venema's. He uses them in the evident hope of weakening the commonly held intuition that both must be designed. If there is a natural pathway to the genetic code, he argues, then it only looks like a code in hindsight. It only looks like information after evolution improved it.
Venema's argument rests on two premises, one empirical and one philosophical. The empirical premise is that a natural pathway to the genetic code is known, though admittedly many questions remain. The philosophical premise is that finding a "natural" explanation is superior to "interventionism" (the approach of looking for "supernatural" acts of God requiring "miracles"). We should learn from history, he says, and prefer the natural pathway:
As an aside, as a Christian biologist I would be perfectly fine with the answer being either "natural" or "supernatural". Both natural and supernatural means are part of the providence of God, and the distinction is not a biblical one in any case. Perhaps God set up the cosmos in a way to allow for abiogenesis to take place. Perhaps he created the first life directly -- though, as we will see, there are lines of evidence that I think are suggestive of the former rather than the latter. Similarly, I would have been fine with God supernaturally sustaining the flames of the sun for our benefit, as English apologist John Edwards claimed long ago. I do happen to think that solar fusion is an elegant way to "solve" this problem, and as a person of faith I think it evinces a deeper, more satisfying design than some sort of miraculous interventionist approach for keeping the sun going. I recognize, however, that seeing design in the natural process of solar fusion -- or abiogenesis -- is not the sort of argument that some Christian apologists are looking for. [Emphasis added.]
What's notable is the language of faith. Who is making a religious argument here? In this one paragraph, Venema uses the words God, supernatural, providence, biblical, faith, miraculous, and Christian. Such language is tellingly absent from most intelligent design literature, which as a matter of science and of principle avoids questions about the identity of the designer, instead ascribing effects to causes that can be demonstrated scientifically to be necessary and sufficient. The design argument is a purely scientific one, as Michael Behe states in Unlocking the Mystery of Life: "It might have religious implications, but it does not depend on religious premises."
Indeed, ID emphatically isn't an "apologetic" strategy. It is a scientific theory of origins, which may be right or wrong, yet must be judged as science and only as science.
From there, Venema addresses biological matters. In particular, he attempts to refute Stephen Meyer's contention that the genetic code is arbitrary, therefore designed. Well before Stephen Meyer wrote Signature in the Cell (2009), Venema argues, Meyer should have known of the work of Michael Yarus, who as far back as the 1980s was showing that chemical affinities between RNA and amino acids could have led to the genetic code naturally. From simple beginnings -- entirely natural -- today's complex interactions between messenger RNA (mRNA) and transfer RNA (tRNA) could have evolved by a process of "Direct RNA Templating," or DRT:
I recall reading Meyer's argument for an arbitrary code when Signature first came out in 2009, and being surprised by it. The reason for my surprise was simple: in 2009 there was already a detailed body of scientific work that demonstrated exactly what Meyer claimed had never been shown.[1] Though Meyer claimed that "molecular biologists have failed to find any significant chemical interaction between the codons on mRNA (or the anticodons on tRNA) and the amino acids on the acceptor arm of tRNA to which the codons correspond" this was simply not the case.
Overall, Venema's tone is respectful and non-confrontational. That's good. But now it is our turn to be surprised, because another "detailed body of scientific work" has already rebutted his argument. In fact, Dr. Meyer, along with Paul Nelson, addressed DRT in a paper in BIO-Complexity in August 2011, responding specifically to the claims of Michael Yarus (see Ann Gauger's summary here at Evolution News). Not only that, Meyer responded to Venema directly when he brought up the same argument in his critical view of Signature in December 2010 (PDF here; see Meyer's rebuttal and Venema's response).
Other authors have responded to DRT in our pages: Jonathan M. (August 2011), Evolution News (September 2011), and Casey Luskin (December 2011). That's at least six who have replied to Venema's sole empirical support for his argument. In each case, they did so with scientific evidence, not religious arguments or appeals to "apologetic" concerns. Why, then, is Dr. Venema resurrecting DRT as if it is something new? In his article there is not a single reference to any of our post-Signature writings, including the direct dialogue he had with Meyer in 2011 on this very point. How curious. That seems a missed opportunity for engagement.
His omission is doubly regrettable when you consider that the DRT argument fails to address the very issue Venema claims it does: the origin of the genetic code. Chemical affinity is the wrong kind of process to explain biological information. Real information (without the scare quotes) is characterized by aperiodic sequences of building blocks, not the regular, repetitive sequences produced by chemical attraction. That's clear from this sentence, as from Venema's own writing. It's clear from DNA itself. His sole empirical support, therefore, falls away.
The fact that several amino acids do in fact bind their codons or anticodons is strong evidence that at least part of the code was formed through chemical interactions -- and, contra Meyer, is not an arbitrary code. The code we have -- or at least for those amino acids for which direct binding was possible -- was indeed a chemically favored code. And if it was chemically favored, then it is quite likely that it had a chemical origin, even if we do not yet understand all the details of how it came to be.
The reader can decide what is "strong evidence" or "quite likely." Are we to conclude that the English language emerged by unguided natural processes because "crisps" and "chips" can refer to the same thing, as he argues? In DNA, the sequence AUG leads to adding methionine to a protein, not because of any chemical attraction, but because it has meaning in a code. It refers to a separate entity that a programmed system knows how to decode. Some amino acids can be coded by multiple DNA triplets (serine has six), but this is another design feature (see Casey Luskin's article here).
What motivates this desire to prefer natural causes? Certainly a fear of "God-of-the-gaps" looms large. Venema adduces "what science will learn some day":
As such, building an apologetic on the presumed future failings of abiogenesis research, when current research already undercuts one's thesis, seems to me as problematic for Meyer in 2009 as it did for Edwards in 1696. Do unanswered questions remain? Of course. Should we bank on them never being answered? Or would it be more wise to frame our apologetics on what we know, rather than what we don't know?
But that's the point. ID argues that we should infer intelligent causes -- when justified through the Design Filter -- because of what we do know, not what we don't know. We do know of a cause that can build information-rich structures with meaning and reference. We do know of a cause that can encode, decode, and translate things into functional hierarchies. That cause is intelligence. We never see natural processes building such things.
Is this "interventionist" thinking? The real appeal to miracles is hoping for unguided natural processes to accomplish, at some unspecified future date, what is demonstrably physically impossible (see Douglas Axe's book Undeniable for the math on that). John Edwards did not use the Design Filter. He speculated, and used theological arguments in so doing. There is no comparison. The real "gaps" argument lies in hoping that science will someday find a natural chemical affinity leading to the genetic code. That is like expecting that someday scientists will find that the molecules in a DVD can organize themselves into a movie that will play in a DVD player. The best explanation appeals to causes known to be in operation that can account for the phenomenon under study: for DVDs and for the genetic code that far surpasses DVDs in functional information. In our universal experience, intelligence is not only the best explanation; it is the only explanation.
Venema promises more posts in a series rebutting Meyer's claim that "evolution is incapable of generating significant amounts of new information." Of course, he is welcome to his own opinion, but not to his own science. To ignore a large body of past dialogue on the very issue under consideration does a disservice to his readers and misinforms them about our position, as if we were the ones unaware of the science. Dr. Venema is warmly encouraged to try again: start with a literature search, provide references, and address an opponent's position as it is, not a caricature of it.
Evolution News & Views
In a post for the theistic evolutionary group BioLogos, Canadian biology professor Dennis Venema writes affectionately, with only a mild touch of disdain, about the intelligent design movement. Their (meaning our) hearts are in the right place, he tells readers. Like him, advocates of ID want to build an "apologetic" against materialism. They're just going about it in the wrong way. And their science is wrong.
Venema readily concedes that living cells use "highly intricate" processes to manage genetic information. However, is it really "information"? And is the genetic code really a "code"? The quote marks in both cases are Venema's. He uses them in the evident hope of weakening the commonly held intuition that both must be designed. If there is a natural pathway to the genetic code, he argues, then it only looks like a code in hindsight. It only looks like information after evolution improved it.
Venema's argument rests on two premises, one empirical and one philosophical. The empirical premise is that a natural pathway to the genetic code is known, though admittedly many questions remain. The philosophical premise is that finding a "natural" explanation is superior to "interventionism" (the approach of looking for "supernatural" acts of God requiring "miracles"). We should learn from history, he says, and prefer the natural pathway:
As an aside, as a Christian biologist I would be perfectly fine with the answer being either "natural" or "supernatural". Both natural and supernatural means are part of the providence of God, and the distinction is not a biblical one in any case. Perhaps God set up the cosmos in a way to allow for abiogenesis to take place. Perhaps he created the first life directly -- though, as we will see, there are lines of evidence that I think are suggestive of the former rather than the latter. Similarly, I would have been fine with God supernaturally sustaining the flames of the sun for our benefit, as English apologist John Edwards claimed long ago. I do happen to think that solar fusion is an elegant way to "solve" this problem, and as a person of faith I think it evinces a deeper, more satisfying design than some sort of miraculous interventionist approach for keeping the sun going. I recognize, however, that seeing design in the natural process of solar fusion -- or abiogenesis -- is not the sort of argument that some Christian apologists are looking for. [Emphasis added.]
What's notable is the language of faith. Who is making a religious argument here? In this one paragraph, Venema uses the words God, supernatural, providence, biblical, faith, miraculous, and Christian. Such language is tellingly absent from most intelligent design literature, which as a matter of science and of principle avoids questions about the identity of the designer, instead ascribing effects to causes that can be demonstrated scientifically to be necessary and sufficient. The design argument is a purely scientific one, as Michael Behe states in Unlocking the Mystery of Life: "It might have religious implications, but it does not depend on religious premises."
Indeed, ID emphatically isn't an "apologetic" strategy. It is a scientific theory of origins, which may be right or wrong, yet must be judged as science and only as science.
From there, Venema addresses biological matters. In particular, he attempts to refute Stephen Meyer's contention that the genetic code is arbitrary, therefore designed. Well before Stephen Meyer wrote Signature in the Cell (2009), Venema argues, Meyer should have known of the work of Michael Yarus, who as far back as the 1980s was showing that chemical affinities between RNA and amino acids could have led to the genetic code naturally. From simple beginnings -- entirely natural -- today's complex interactions between messenger RNA (mRNA) and transfer RNA (tRNA) could have evolved by a process of "Direct RNA Templating," or DRT:
I recall reading Meyer's argument for an arbitrary code when Signature first came out in 2009, and being surprised by it. The reason for my surprise was simple: in 2009 there was already a detailed body of scientific work that demonstrated exactly what Meyer claimed had never been shown.[1] Though Meyer claimed that "molecular biologists have failed to find any significant chemical interaction between the codons on mRNA (or the anticodons on tRNA) and the amino acids on the acceptor arm of tRNA to which the codons correspond" this was simply not the case.
Overall, Venema's tone is respectful and non-confrontational. That's good. But now it is our turn to be surprised, because another "detailed body of scientific work" has already rebutted his argument. In fact, Dr. Meyer, along with Paul Nelson, addressed DRT in a paper in BIO-Complexity in August 2011, responding specifically to the claims of Michael Yarus (see Ann Gauger's summary here at Evolution News). Not only that, Meyer responded to Venema directly when he brought up the same argument in his critical view of Signature in December 2010 (PDF here; see Meyer's rebuttal and Venema's response).
Other authors have responded to DRT in our pages: Jonathan M. (August 2011), Evolution News (September 2011), and Casey Luskin (December 2011). That's at least six who have replied to Venema's sole empirical support for his argument. In each case, they did so with scientific evidence, not religious arguments or appeals to "apologetic" concerns. Why, then, is Dr. Venema resurrecting DRT as if it is something new? In his article there is not a single reference to any of our post-Signature writings, including the direct dialogue he had with Meyer in 2011 on this very point. How curious. That seems a missed opportunity for engagement.
His omission is doubly regrettable when you consider that the DRT argument fails to address the very issue Venema claims it does: the origin of the genetic code. Chemical affinity is the wrong kind of process to explain biological information. Real information (without the scare quotes) is characterized by aperiodic sequences of building blocks, not the regular, repetitive sequences produced by chemical attraction. That's clear from this sentence, as from Venema's own writing. It's clear from DNA itself. His sole empirical support, therefore, falls away.
The fact that several amino acids do in fact bind their codons or anticodons is strong evidence that at least part of the code was formed through chemical interactions -- and, contra Meyer, is not an arbitrary code. The code we have -- or at least for those amino acids for which direct binding was possible -- was indeed a chemically favored code. And if it was chemically favored, then it is quite likely that it had a chemical origin, even if we do not yet understand all the details of how it came to be.
The reader can decide what is "strong evidence" or "quite likely." Are we to conclude that the English language emerged by unguided natural processes because "crisps" and "chips" can refer to the same thing, as he argues? In DNA, the sequence AUG leads to adding methionine to a protein, not because of any chemical attraction, but because it has meaning in a code. It refers to a separate entity that a programmed system knows how to decode. Some amino acids can be coded by multiple DNA triplets (serine has six), but this is another design feature (see Casey Luskin's article here).
What motivates this desire to prefer natural causes? Certainly a fear of "God-of-the-gaps" looms large. Venema adduces "what science will learn some day":
As such, building an apologetic on the presumed future failings of abiogenesis research, when current research already undercuts one's thesis, seems to me as problematic for Meyer in 2009 as it did for Edwards in 1696. Do unanswered questions remain? Of course. Should we bank on them never being answered? Or would it be more wise to frame our apologetics on what we know, rather than what we don't know?
But that's the point. ID argues that we should infer intelligent causes -- when justified through the Design Filter -- because of what we do know, not what we don't know. We do know of a cause that can build information-rich structures with meaning and reference. We do know of a cause that can encode, decode, and translate things into functional hierarchies. That cause is intelligence. We never see natural processes building such things.
Is this "interventionist" thinking? The real appeal to miracles is hoping for unguided natural processes to accomplish, at some unspecified future date, what is demonstrably physically impossible (see Douglas Axe's book Undeniable for the math on that). John Edwards did not use the Design Filter. He speculated, and used theological arguments in so doing. There is no comparison. The real "gaps" argument lies in hoping that science will someday find a natural chemical affinity leading to the genetic code. That is like expecting that someday scientists will find that the molecules in a DVD can organize themselves into a movie that will play in a DVD player. The best explanation appeals to causes known to be in operation that can account for the phenomenon under study: for DVDs and for the genetic code that far surpasses DVDs in functional information. In our universal experience, intelligence is not only the best explanation; it is the only explanation.
Venema promises more posts in a series rebutting Meyer's claim that "evolution is incapable of generating significant amounts of new information." Of course, he is welcome to his own opinion, but not to his own science. To ignore a large body of past dialogue on the very issue under consideration does a disservice to his readers and misinforms them about our position, as if we were the ones unaware of the science. Dr. Venema is warmly encouraged to try again: start with a literature search, provide references, and address an opponent's position as it is, not a caricature of it.
Wednesday, 31 August 2016
File under "well said" XXXIV
Success consists of going from failure to failure without loss of enthusiasm.
Winston Churchill
Winston Churchill
The talking ape continues to testify against Darwinism
In The Kingdom of Speech, Tom Wolfe Tells the Story of Evolution's Epic Tumble.
David Klinghoffer
Darwinian evolution explains biological trivia -- variable finch beaks and the like -- but stumbles when it comes to the major innovations in the long history of life. No innovation could be more revolutionary than how homo sapiens, as Discovery Institute biologist Michael Denton puts it, "slipped suddenly into being on the rich, game-laden African grasslands of the late Pleistocene."The most distinctive thing about man is of course his gift for language. On that, the great Tom Wolfe masterfully explains in a new book out today, Darwinism takes an epic tumble. Evolution cannot explain the very thing that preeminently makes us human. "To say that animals evolved into man," writes Wolfe on the last page of The Kingdom of Speech, "is like saying that Carrara marble evolved into Michelangelo's David."
The analogy is heavy with significance. An artist shapes his medium as an act of deliberate design. Wolfe, one of the most treasured writers alive today, hasn't come out for intelligent design, at least not directly. In previous statements he has shown sympathy for ID, comparing the persecution of ID scientists to the "Spanish Inquisition." Here too he refers to the "Neo-Darwinist Inquisition." But his focus is on the story of how evolution, from Darwin to Chomsky, came up short in explaining speech. He lets the implications of this speak for themselves.
The significance of speech goes beyond merely expressing our exceptional status as humans -- the "cardinal distinction between man and animal." As Wolfe points out, it grants us rule over the earth and its creatures, and even more than that.
In short, speech, and only speech, has enabled us human beasts to conquer every square inch of land in the world, subjugate every creature big enough to lay eyes on, and eat up half the population of the sea.
And this, the power to conquer the entire planet for our own species, is the minor achievement of speech's great might. The great achievement has been the creation of an internal self, an ego.
From that "internal self," endowed with curiosity and longing, flows the riches of civilization -- art, religion, philosophy, literature, science, and so much more. How impressive, really, is a theory of origins if it can shed no light on the origin of any of that?
Wolfe frames his story in terms of two pairs of rivals or doppelgängers -- Charles Darwin and Alfred Russel Wallace, on one hand, and linguists Noam Chomsky and Daniel Everett on the other. As in every other book of his that I've read, Wolfe is sharply attuned to matters of status, rank, class -- which explain so much not only in fashion or politics but in the history of ideas. In both of these pairs of scientists, one is the established figure, the man of rank and prestige (Darwin, Chomsky), while he was overtaken and nearly knocked from his pedestal by a field researcher of lesser cachet (Wallace, Everett), a "flycatcher" in Wolfe's phrase.
In 1858, Wallace panicked Darwin into going public with his theory, which Wallace had thought up independently while in a malarial swoon on the other side of the world. The co-discoverer of evolution by natural selection came later to reject the comprehensive explanatory power of his and Darwin's theory.
Wallace showed, writes Wolfe, that "natural selection can expand a creature's powers only to the point where it has an advantage over the competition in the struggle for existence." What's more, "natural selection can't produce any 'specially developed organ' that is useless to a creature...or of so little use that it is not until thousands and thousands of years down the line that the creature can take advantage of the organ's full power."
Speech is the most obvious example of a power inexplicable in terms of natural selection. Only a designer could look ahead that way, using foresight and working out a plan, which led Wallace to his proto-intelligent design view, arguing for "the agency of some other power," "a superior intelligence," a "controlling intelligence," at work in guiding evolution. Darwin, meanwhile, was left to speculate absurdly about speech being an extension of bird song.
And there the matter was left until Chomsky came on the scene in the 1950s with his own notion of an evolved language "organ," hidden somewhere, as yet undetected, in the brain. Known as much for this theory as for his "Radical Chic" (Wolfe's famous phrase) politics, Chomsky intimidated his field and looked askance at "flycatchers" who left the air-conditioned department building to investigate obscure languages in obscure, inconvenient, and unhygienic parts of the world.
Chomsky's theory reigned supreme until 2008 when a flycatcher, Daniel Everett, revealed a primitive language, that of the Pirahã, a people of the Amazon, that lacked a key linguistic feature (recursion) that Chomsky held to be universal. It must be universal if a shared, evolved "organ" was responsible for all human speech. The conclusion of Everett's research was that speech, not a product of evolution, was in truth an "artifact" of human devising.
The study of linguistics was thrown into chaos. Chomsky himself, even as he all but denied the existence of his rival, was compelled to admit that after decades of his labor, "The evolution of the faculty of language largely remains an enigma":
[I]n thirty years, Chomsky had advanced from "specific neural structures, though their nature is not well understood" to "some rather obscure system of thought that we know is there but we don't know much about it."
We hardly understand language today, what it is, any better today than Aristotle, who explained it as a system of "mnemonics," an aid to memory.
The Kingdom of Speech is a brief, wonderfully written book, often hilarious. The bits about Darwin's dog and Chomsky's "visiting Martian" (a fixture of his lectures), for example, are delicious. The role of social prestige, not science, in accounting for a failed idea's persistence is a theme that nobody is better suited to explore than Tom Wolfe. He tells how in Darwin's own day, "people began to judge one another socially according to their belief, or not, in Darwin's great discovery." How little has changed!
Wolfe, it's true, does not pull the obvious trigger. He fairly begs to be introduced to Michael Denton. If speech is an artifact, how did man acquire the capacity to devise and use it? As Dr. Denton writes in his recent book, Evolution: Still a Theory in Crisis, the exalted intellectual capacities shared by men and women of all races, and accessed only through language, probably were not much use in hunting mammoths. He writes:
One of the most curious features of human evolution, and one that poses at the outset an intriguing and still unanswered challenge to the Darwinian and functionalist narrative, is the fact that all modern humans share the same higher intellectual capabilities. This means, incredible though it may seem, a brain capable of the intellectual feats of an Einstein, a Newton, or a Mozart must have already emerged in our last common ancestors more than 200,000 years ago. Such intellectual abilities seem absurdly powerful, beyond any conceivable utility for hunter-gatherers on that ancient savanna, and hence beyond any functionalist explanation.
Language, Denton writes, the "Type-defining homolog," is "consistent with a saltational origin." In other words, it appears to have sprung into existence, "slipped suddenly into being," from no primitive or animal model before it.
Alfred Wallace, as ever, pointed the way. Such a power, coming into existence when it could not possibly serve an evolutionary purpose, can only be accounted for as the product of design. Wolfe prefers to let us pull that trigger for ourselves.
David Klinghoffer
Darwinian evolution explains biological trivia -- variable finch beaks and the like -- but stumbles when it comes to the major innovations in the long history of life. No innovation could be more revolutionary than how homo sapiens, as Discovery Institute biologist Michael Denton puts it, "slipped suddenly into being on the rich, game-laden African grasslands of the late Pleistocene."The most distinctive thing about man is of course his gift for language. On that, the great Tom Wolfe masterfully explains in a new book out today, Darwinism takes an epic tumble. Evolution cannot explain the very thing that preeminently makes us human. "To say that animals evolved into man," writes Wolfe on the last page of The Kingdom of Speech, "is like saying that Carrara marble evolved into Michelangelo's David."
The analogy is heavy with significance. An artist shapes his medium as an act of deliberate design. Wolfe, one of the most treasured writers alive today, hasn't come out for intelligent design, at least not directly. In previous statements he has shown sympathy for ID, comparing the persecution of ID scientists to the "Spanish Inquisition." Here too he refers to the "Neo-Darwinist Inquisition." But his focus is on the story of how evolution, from Darwin to Chomsky, came up short in explaining speech. He lets the implications of this speak for themselves.
The significance of speech goes beyond merely expressing our exceptional status as humans -- the "cardinal distinction between man and animal." As Wolfe points out, it grants us rule over the earth and its creatures, and even more than that.
In short, speech, and only speech, has enabled us human beasts to conquer every square inch of land in the world, subjugate every creature big enough to lay eyes on, and eat up half the population of the sea.
And this, the power to conquer the entire planet for our own species, is the minor achievement of speech's great might. The great achievement has been the creation of an internal self, an ego.
From that "internal self," endowed with curiosity and longing, flows the riches of civilization -- art, religion, philosophy, literature, science, and so much more. How impressive, really, is a theory of origins if it can shed no light on the origin of any of that?
Wolfe frames his story in terms of two pairs of rivals or doppelgängers -- Charles Darwin and Alfred Russel Wallace, on one hand, and linguists Noam Chomsky and Daniel Everett on the other. As in every other book of his that I've read, Wolfe is sharply attuned to matters of status, rank, class -- which explain so much not only in fashion or politics but in the history of ideas. In both of these pairs of scientists, one is the established figure, the man of rank and prestige (Darwin, Chomsky), while he was overtaken and nearly knocked from his pedestal by a field researcher of lesser cachet (Wallace, Everett), a "flycatcher" in Wolfe's phrase.
In 1858, Wallace panicked Darwin into going public with his theory, which Wallace had thought up independently while in a malarial swoon on the other side of the world. The co-discoverer of evolution by natural selection came later to reject the comprehensive explanatory power of his and Darwin's theory.
Wallace showed, writes Wolfe, that "natural selection can expand a creature's powers only to the point where it has an advantage over the competition in the struggle for existence." What's more, "natural selection can't produce any 'specially developed organ' that is useless to a creature...or of so little use that it is not until thousands and thousands of years down the line that the creature can take advantage of the organ's full power."
Speech is the most obvious example of a power inexplicable in terms of natural selection. Only a designer could look ahead that way, using foresight and working out a plan, which led Wallace to his proto-intelligent design view, arguing for "the agency of some other power," "a superior intelligence," a "controlling intelligence," at work in guiding evolution. Darwin, meanwhile, was left to speculate absurdly about speech being an extension of bird song.
And there the matter was left until Chomsky came on the scene in the 1950s with his own notion of an evolved language "organ," hidden somewhere, as yet undetected, in the brain. Known as much for this theory as for his "Radical Chic" (Wolfe's famous phrase) politics, Chomsky intimidated his field and looked askance at "flycatchers" who left the air-conditioned department building to investigate obscure languages in obscure, inconvenient, and unhygienic parts of the world.
Chomsky's theory reigned supreme until 2008 when a flycatcher, Daniel Everett, revealed a primitive language, that of the Pirahã, a people of the Amazon, that lacked a key linguistic feature (recursion) that Chomsky held to be universal. It must be universal if a shared, evolved "organ" was responsible for all human speech. The conclusion of Everett's research was that speech, not a product of evolution, was in truth an "artifact" of human devising.
The study of linguistics was thrown into chaos. Chomsky himself, even as he all but denied the existence of his rival, was compelled to admit that after decades of his labor, "The evolution of the faculty of language largely remains an enigma":
[I]n thirty years, Chomsky had advanced from "specific neural structures, though their nature is not well understood" to "some rather obscure system of thought that we know is there but we don't know much about it."
We hardly understand language today, what it is, any better today than Aristotle, who explained it as a system of "mnemonics," an aid to memory.
The Kingdom of Speech is a brief, wonderfully written book, often hilarious. The bits about Darwin's dog and Chomsky's "visiting Martian" (a fixture of his lectures), for example, are delicious. The role of social prestige, not science, in accounting for a failed idea's persistence is a theme that nobody is better suited to explore than Tom Wolfe. He tells how in Darwin's own day, "people began to judge one another socially according to their belief, or not, in Darwin's great discovery." How little has changed!
Wolfe, it's true, does not pull the obvious trigger. He fairly begs to be introduced to Michael Denton. If speech is an artifact, how did man acquire the capacity to devise and use it? As Dr. Denton writes in his recent book, Evolution: Still a Theory in Crisis, the exalted intellectual capacities shared by men and women of all races, and accessed only through language, probably were not much use in hunting mammoths. He writes:
One of the most curious features of human evolution, and one that poses at the outset an intriguing and still unanswered challenge to the Darwinian and functionalist narrative, is the fact that all modern humans share the same higher intellectual capabilities. This means, incredible though it may seem, a brain capable of the intellectual feats of an Einstein, a Newton, or a Mozart must have already emerged in our last common ancestors more than 200,000 years ago. Such intellectual abilities seem absurdly powerful, beyond any conceivable utility for hunter-gatherers on that ancient savanna, and hence beyond any functionalist explanation.
Language, Denton writes, the "Type-defining homolog," is "consistent with a saltational origin." In other words, it appears to have sprung into existence, "slipped suddenly into being," from no primitive or animal model before it.
Alfred Wallace, as ever, pointed the way. Such a power, coming into existence when it could not possibly serve an evolutionary purpose, can only be accounted for as the product of design. Wolfe prefers to let us pull that trigger for ourselves.
Speaking up in behalf of speaking out.
University of Chicago President Decries "Efforts to Suppress Discussion of Charles Darwin's Work"
Sarah Chaffee
Attempts to limit free speech on college campuses are many -- for example, at Yale, students berated professor Nicholas Christakis after he suggested that the school shouldn't regulate Halloween costumes that were not culturally sensitive.
Someone finally decided to stand up and defend freedom of speech as a defining principle of education. This summer, the University of Chicago's Dean of Students, John Ellison, sent a letter to all incoming freshman, stating:
Once here you will discover that one of the University of Chicago's defining characteristics is our commitment to freedom of inquiry and expression. This is captured in the University's faculty report on freedom of expression. Members of our community are encouraged to speak, write, listen, challenge, and learn, without fear of censorship. Civility and mutual respect are vital to all of us, and freedom of expression does not mean the freedom to harass or threaten others. You will find that we expect members of our community to be engaged in rigorous debate, discussion, and even disagreement. At times this may challenge you and even cause discomfort.
Our commitment to academic freedom means that we do not support so-called "trigger warnings," we do not cancel invited speakers because their topics might prove controversial, and we do not condone the creation of intellectual "safe spaces" where individuals can retreat from ideas and perspectives at odds with their own.
Fostering the free exchange of ideas reinforces a related University priority -- building a campus that welcomes people of all backgrounds. Diversity of opinion and background is a fundamental strength of our community. The members of our community must have the freedom to espouse and explore a wide range of ideas.
(Note that the University has clarified that this does not ban the use of trigger warnings or setting up safe spaces.) The letter has received national attention and generated controversy. Professors from the school and from different schools across the country, and the Foundation for Individual Rights in Education (FIRE), among others, rightly commend the university on its stance. FIRE notes that it "hopes that students, faculty, and administrators nationwide take a cue from UC and recommit to freedom of speech on their own campuses."
The letter follows a report generated by a specially-organized university group on freedom of expression.
Robert J. Zimmer, President of the University of Chicago, followed the letter with an op-ed in the Wall Street Journal, "Free Speech Is the Basis of a True Education." After discussing the intellectual skills students need for successful lives, including recognizing cultural differences, identifying complexity, and engaging in critical thinking about evidence, Zimmer states:
One word summarizes the process by which universities impart these skills: questioning. Productive and informed questioning involves challenging assumptions, arguments and conclusions. It calls for multiple and diverse perspectives and listening to the views of others. It requires understanding the power and limitations of arguments. More fundamentally, the process of questioning demands an ability to rethink one's own assumptions, often the most difficult task of all.
Essential to this process is an environment that promotes free expression and the open exchange of ideas, ensuring that difficult questions are asked and that diverse and challenging perspectives are considered. This underscores the importance of diversity among students, faculty and visitors--diversity of background, belief and experience. Without this, students' experience becomes a weak imitation of a true education, and the value of that education is seriously diminished.
One could not ask for a more thorough endorsement of free speech in universities. The concept of freedom of expression is crucial for many areas, not least in debate over Darwinism. Although he is almost certainly referencing it historically, note Zimmer's mention of evolution:
... Some assert that universities should be refuges from intellectual discomfort and that their own discomfort with conflicting and challenging views should override the value of free and open discourse.
We have seen efforts to suppress discussion of Charles Darwin's work, to insist upon particular political perspectives during the McCarthy era, to impose exclusionary acts of racial and religious discrimination, and to demand compliance with various forms of "moral" behavior.
The silencing being advocated today is equally problematic. Every attempt to legitimize silencing creates justification for others to restrain speech that they do not like in the future. [Emphasis added.]
Wow. Today the situation is reversed: those who question Darwin's work face discrimination. But the University of Chicago's position, at least in principle, would support free debate about neo-Darwinism and intelligent design, along with all other issues.
If only intelligent design proponents routinely faced this perspective. Perhaps Eric Hedin, physicist at Ball State University, would still be teaching his interdisciplinary honors course, "Boundaries of Science," which included some material on intelligent design. Perhaps the Michael Polanyi Center at Baylor University would still exist, with Dembski at its head.
Zimmer proclaims that violations of liberty pave the way for future restrictions. And professor Geoffrey Stone, chair of UC's Committee on Freedom of Expression, in an article quoted by FIRE, notes that academic freedom is key because first, "bitter experience has taught that even the ideas we hold to be most certain often turn out to be wrong," second, silencing some speech leads to more silencing, and third:
[A] central precept of free expression is the possibility of a chilling effect.... The potential costs of speaking courageously, of taking controversial positions, of taking risks, is greater than ever. Indeed, according to a recent survey, about half of American college students now say that it is unsafe for them to express unpopular views. Many faculty members clearly share that sentiment.
Stone's points hits home: intolerance of dissent from Darwinism has sparked all three of these issues.
Even though UC's position does not address intelligent design specifically, any step towards academic freedom on campus is beneficial. Freedom of speech staves off a downward spiral of viewpoint discrimination, allowing new (and sometimes more accurate) ideas to come forward.
After all, as Zimmer noted:
Universities cannot be viewed as a sanctuary for comfort but rather as a crucible for confronting ideas and thereby learning to make informed judgments in complex environments. Having one's assumptions challenged and experiencing the discomfort that sometimes accompanies this process are intrinsic parts of an excellent education. Only then will students develop the skills necessary to build their own futures and contribute to society.
It's high time for universities to extend protections to those who question neo-Darwinism. Perhaps Chicago's ringing endorsement of academic freedom will open more doors for evolution skeptics. We commend Robert Zimmer, John Ellison, and UC's Committee on Freedom of Expression for their courage.
Sarah Chaffee
Attempts to limit free speech on college campuses are many -- for example, at Yale, students berated professor Nicholas Christakis after he suggested that the school shouldn't regulate Halloween costumes that were not culturally sensitive.
Someone finally decided to stand up and defend freedom of speech as a defining principle of education. This summer, the University of Chicago's Dean of Students, John Ellison, sent a letter to all incoming freshman, stating:
Once here you will discover that one of the University of Chicago's defining characteristics is our commitment to freedom of inquiry and expression. This is captured in the University's faculty report on freedom of expression. Members of our community are encouraged to speak, write, listen, challenge, and learn, without fear of censorship. Civility and mutual respect are vital to all of us, and freedom of expression does not mean the freedom to harass or threaten others. You will find that we expect members of our community to be engaged in rigorous debate, discussion, and even disagreement. At times this may challenge you and even cause discomfort.
Our commitment to academic freedom means that we do not support so-called "trigger warnings," we do not cancel invited speakers because their topics might prove controversial, and we do not condone the creation of intellectual "safe spaces" where individuals can retreat from ideas and perspectives at odds with their own.
Fostering the free exchange of ideas reinforces a related University priority -- building a campus that welcomes people of all backgrounds. Diversity of opinion and background is a fundamental strength of our community. The members of our community must have the freedom to espouse and explore a wide range of ideas.
(Note that the University has clarified that this does not ban the use of trigger warnings or setting up safe spaces.) The letter has received national attention and generated controversy. Professors from the school and from different schools across the country, and the Foundation for Individual Rights in Education (FIRE), among others, rightly commend the university on its stance. FIRE notes that it "hopes that students, faculty, and administrators nationwide take a cue from UC and recommit to freedom of speech on their own campuses."
The letter follows a report generated by a specially-organized university group on freedom of expression.
Robert J. Zimmer, President of the University of Chicago, followed the letter with an op-ed in the Wall Street Journal, "Free Speech Is the Basis of a True Education." After discussing the intellectual skills students need for successful lives, including recognizing cultural differences, identifying complexity, and engaging in critical thinking about evidence, Zimmer states:
One word summarizes the process by which universities impart these skills: questioning. Productive and informed questioning involves challenging assumptions, arguments and conclusions. It calls for multiple and diverse perspectives and listening to the views of others. It requires understanding the power and limitations of arguments. More fundamentally, the process of questioning demands an ability to rethink one's own assumptions, often the most difficult task of all.
Essential to this process is an environment that promotes free expression and the open exchange of ideas, ensuring that difficult questions are asked and that diverse and challenging perspectives are considered. This underscores the importance of diversity among students, faculty and visitors--diversity of background, belief and experience. Without this, students' experience becomes a weak imitation of a true education, and the value of that education is seriously diminished.
One could not ask for a more thorough endorsement of free speech in universities. The concept of freedom of expression is crucial for many areas, not least in debate over Darwinism. Although he is almost certainly referencing it historically, note Zimmer's mention of evolution:
... Some assert that universities should be refuges from intellectual discomfort and that their own discomfort with conflicting and challenging views should override the value of free and open discourse.
We have seen efforts to suppress discussion of Charles Darwin's work, to insist upon particular political perspectives during the McCarthy era, to impose exclusionary acts of racial and religious discrimination, and to demand compliance with various forms of "moral" behavior.
The silencing being advocated today is equally problematic. Every attempt to legitimize silencing creates justification for others to restrain speech that they do not like in the future. [Emphasis added.]
Wow. Today the situation is reversed: those who question Darwin's work face discrimination. But the University of Chicago's position, at least in principle, would support free debate about neo-Darwinism and intelligent design, along with all other issues.
If only intelligent design proponents routinely faced this perspective. Perhaps Eric Hedin, physicist at Ball State University, would still be teaching his interdisciplinary honors course, "Boundaries of Science," which included some material on intelligent design. Perhaps the Michael Polanyi Center at Baylor University would still exist, with Dembski at its head.
Zimmer proclaims that violations of liberty pave the way for future restrictions. And professor Geoffrey Stone, chair of UC's Committee on Freedom of Expression, in an article quoted by FIRE, notes that academic freedom is key because first, "bitter experience has taught that even the ideas we hold to be most certain often turn out to be wrong," second, silencing some speech leads to more silencing, and third:
[A] central precept of free expression is the possibility of a chilling effect.... The potential costs of speaking courageously, of taking controversial positions, of taking risks, is greater than ever. Indeed, according to a recent survey, about half of American college students now say that it is unsafe for them to express unpopular views. Many faculty members clearly share that sentiment.
Stone's points hits home: intolerance of dissent from Darwinism has sparked all three of these issues.
Even though UC's position does not address intelligent design specifically, any step towards academic freedom on campus is beneficial. Freedom of speech staves off a downward spiral of viewpoint discrimination, allowing new (and sometimes more accurate) ideas to come forward.
After all, as Zimmer noted:
Universities cannot be viewed as a sanctuary for comfort but rather as a crucible for confronting ideas and thereby learning to make informed judgments in complex environments. Having one's assumptions challenged and experiencing the discomfort that sometimes accompanies this process are intrinsic parts of an excellent education. Only then will students develop the skills necessary to build their own futures and contribute to society.
It's high time for universities to extend protections to those who question neo-Darwinism. Perhaps Chicago's ringing endorsement of academic freedom will open more doors for evolution skeptics. We commend Robert Zimmer, John Ellison, and UC's Committee on Freedom of Expression for their courage.
Why Dawinism continues to go to seed.
How a Dry Seed Can Live a Thousand Years
Evolution News & Views
Maybe you have some in your garage: old seed packets that never made it into your gardening project years ago. Would they sprout if you planted them now? It's likely some would. Seeds can last for decades, sometimes centuries. In 2005, a date palm seed that survived dry conditions at Masada for 2,000 years germinated and remains on display in Israel, nicknamed Methuselah. The oldest carbon-dated seeds that have grown into viable plants are flowers that were buried under Siberian permafrost for 32,000 years, according to National Geographic.
What does it take to keep a seed viable for many years of slumber? At a basic level, we can envision some requirements. The seed must be able to shut down all non-critical operations. It must protect its vital parts, like its genetic information. And it must remain watchful for conditions that would allow it to wake up and carry out its growth program. The details, however, are truly astonishing. Some of them are described in an open-access paper in the Proceedings of the National Academy of Sciences, "Regulatory network analysis reveals novel regulators of seed desiccation tolerance in Arabidopsis thaliana." Seven geneticists in Mexico looked into this "remarkable" operation:
Desiccation tolerance (DT) is a remarkable process that allows seeds in the dry state to remain viable for long periods of time that in some instances exceed 1,000 y. It has been postulated that seed DT evolved by rewiring the regulatory and signaling networks that controlled vegetative DT, which itself emerged as a crucial adaptive trait of early land plants. Understanding the networks that regulate seed desiccation tolerance in model plant systems would provide the tools to understand an evolutionary process that played a crucial role in the diversification of flowering plants. In this work, we used an integrated approach that included genomics, bioinformatics, metabolomics, and molecular genetics to identify and validate molecular networks that control the acquisition of DT in Arabidopsis seeds. [Emphasis added.]
For now, we won't quibble about the evolution lingo, knowing that it's par for the course in journals these days (but maybe not for long, Doug Axe speculates in Chapter 12 of his new book Undeniable: How Biology Confirms Our Intuition That Life Is Designed). What's important to notice are the evidences of functional coherence that he shows are the hallmarks of invention, especially when arranged in a hierarchical manner for a high-level function. Here, the paper dazzles us with glimpses at astonishing complexity. "DT organisms orchestrate a complex number of responses to protect cellular structures and prevent damage to proteins and nucleic acids," they say in the introduction. Lest we overwhelm you with detail, let's get just a taste of what goes on in the plant preparing its seeds for long periods of dormancy:
As predicted, desiccation-intolerant (DI)-specific down-regulated genes were enriched (FDR < 0.05) in the following Gene Ontology (GO) categories: molecular function: oxidoreductase activity and nutrient reservoir; and biological process: lipid and carbohydrate biosynthesis, seed development, and ABA and stress responses such as water, oxidation, and temperature... A more detailed analysis of the same set of genes ... showed enrichment in processes such as abiotic stress, LEA protein synthesis, and metabolic pathways including raffinose, stachyose, and trehalose biosynthesis....
Enough said? We'll stick to layman terms from now on. Clearly, preparation for DT is no simple matter! To find out what genes and transcription factors are involved, they compared wild-type plants with mutants unable to prepare for desiccation. In their words, "The finding that genes that are not activated in desiccation-intolerant mutants during seed maturation belong to water stress and cell protection mechanisms confirmed that desiccation-intolerant mutants fail to activate mechanisms required to acquire DT in the seed."
The genes that prepare a seed for dryness cooperate in regulatory networks. Stephen Meyer shows in Chapter 13 of Darwin's Doubt that one does not just tweak developmental gene regulatory networks (dGRNs) willy-nilly and expect to get a new function (that was Charles Marshall's story for the Cambrian explosion, remember? See Debating Darwin's Doubt, Chapters 10-11). For one thing, GRNs "do not tolerate random perturbations to their basic control logic," all available evidence shows (p. 130). For another, it would require just as much information to rewire a GRN for a novel function as it would to evolve new genes, so that's no solution at all (p. 134). But enough about origins; let's get back to the mechanics of DT.
You can well imagine conditions in the soil that would attack a seed's genetic information. When the plant is growing, numerous processes survey and repair DNA. But what happens when the seed goes to sleep? Counter-intuitively, water can be one of the night stalkers.
One of the most intriguing questions about how seeds in the desiccated state can remain viable for periods of time that can exceed centuries is particularly how the integrity of DNA is preserved to prevent permanent damage making the seed unviable. Three types of DNA damage under physiological conditions have been reported: hydrolysis of the N-glycosyl bond, hydrolytic deamination of cytosine to form uracil, and DNA damage by oxidation. The first two types of DNA damage are catalyzed by water, and therefore the last layers of water that interact with DNA need to be removed or decreased to prevent damage, and the third is mediated mainly by reactive oxygen species (ROS).
The plant uses a clever trick to protect its DNA from attack by water. It replaces water molecules with sugars. Hydroxyl groups (OH) of certain sugars can provide the necessary bonds to stabilize proteins, DNA and membranes from these kinds of damage. The team found that biosynthesis of three particular sugars is up-regulated during the final stages of seed preparation, in agreement with this mechanism. They also found genes were increased for five kinds of enzymes involved in protection from reactive oxygen species (ROS).
Therefore, accumulation of antioxidant components during the late maturation stage contributes to controlling their storage potential, and helps to prevent damage from accumulated ROS during seed maturation. Accumulation of RFOs [the raffinose family of oligosaccharides, one of the types of protective sugars] and activation of mechanisms that prevent damage by ROS allow maximum metabolism reduction to decrease the production of toxic compounds and to prevent membrane, DNA, RNA, and protein damage.
All these genes are accompanied by transcription factors that switch them on and off. The authors speak about not only regulatory networks, but regulatory subnetworks. One, for instance, downregulates proteins involved in germination, to prevent early sprouting. Another is involved in stress tolerance. They identified at least four such subnetworks. Some of the subnetworks themselves involve hundreds of genes!
The researchers spoke mainly about preparation for desiccation. They didn't get into other equally fascinating questions: What activities continue during the decades or centuries of slumber? (We know from our own sleep that our hearts must still beat, we must continue breathing, and much more.) How are genes repaired by cosmic ray damage and other contingencies? And what re-activates growth processes when conditions are right for sprouting? How does a blind seed, buried in the dark soil, know when it's time to wake up? What are the first steps it takes to germinate?
This brief glimpse at desiccation tolerance in one model plant ensures is that the answers to those questions will likely be just as complicated -- and fascinating. Like so many things in the biosphere, the apparently simple process of a seed preparing for sleep is anything but simple. Evolution stories often trade in generalities. Intelligent design evidences are best seen in the details. Like Doug Axe says, biology with a design perspective becomes like a great geocaching game. "What makes finding a well-conceived geocache so delightful," he explains, "is not just the sense of having found something that was hard to find -- though that's part of it -- but the sense of having found something that was meant to be found and cleverly made hard to find" (Undeniable, p. 248). It appears we just found a good prize right under our feet.
Evolution News & Views
Maybe you have some in your garage: old seed packets that never made it into your gardening project years ago. Would they sprout if you planted them now? It's likely some would. Seeds can last for decades, sometimes centuries. In 2005, a date palm seed that survived dry conditions at Masada for 2,000 years germinated and remains on display in Israel, nicknamed Methuselah. The oldest carbon-dated seeds that have grown into viable plants are flowers that were buried under Siberian permafrost for 32,000 years, according to National Geographic.
What does it take to keep a seed viable for many years of slumber? At a basic level, we can envision some requirements. The seed must be able to shut down all non-critical operations. It must protect its vital parts, like its genetic information. And it must remain watchful for conditions that would allow it to wake up and carry out its growth program. The details, however, are truly astonishing. Some of them are described in an open-access paper in the Proceedings of the National Academy of Sciences, "Regulatory network analysis reveals novel regulators of seed desiccation tolerance in Arabidopsis thaliana." Seven geneticists in Mexico looked into this "remarkable" operation:
Desiccation tolerance (DT) is a remarkable process that allows seeds in the dry state to remain viable for long periods of time that in some instances exceed 1,000 y. It has been postulated that seed DT evolved by rewiring the regulatory and signaling networks that controlled vegetative DT, which itself emerged as a crucial adaptive trait of early land plants. Understanding the networks that regulate seed desiccation tolerance in model plant systems would provide the tools to understand an evolutionary process that played a crucial role in the diversification of flowering plants. In this work, we used an integrated approach that included genomics, bioinformatics, metabolomics, and molecular genetics to identify and validate molecular networks that control the acquisition of DT in Arabidopsis seeds. [Emphasis added.]
For now, we won't quibble about the evolution lingo, knowing that it's par for the course in journals these days (but maybe not for long, Doug Axe speculates in Chapter 12 of his new book Undeniable: How Biology Confirms Our Intuition That Life Is Designed). What's important to notice are the evidences of functional coherence that he shows are the hallmarks of invention, especially when arranged in a hierarchical manner for a high-level function. Here, the paper dazzles us with glimpses at astonishing complexity. "DT organisms orchestrate a complex number of responses to protect cellular structures and prevent damage to proteins and nucleic acids," they say in the introduction. Lest we overwhelm you with detail, let's get just a taste of what goes on in the plant preparing its seeds for long periods of dormancy:
As predicted, desiccation-intolerant (DI)-specific down-regulated genes were enriched (FDR < 0.05) in the following Gene Ontology (GO) categories: molecular function: oxidoreductase activity and nutrient reservoir; and biological process: lipid and carbohydrate biosynthesis, seed development, and ABA and stress responses such as water, oxidation, and temperature... A more detailed analysis of the same set of genes ... showed enrichment in processes such as abiotic stress, LEA protein synthesis, and metabolic pathways including raffinose, stachyose, and trehalose biosynthesis....
Enough said? We'll stick to layman terms from now on. Clearly, preparation for DT is no simple matter! To find out what genes and transcription factors are involved, they compared wild-type plants with mutants unable to prepare for desiccation. In their words, "The finding that genes that are not activated in desiccation-intolerant mutants during seed maturation belong to water stress and cell protection mechanisms confirmed that desiccation-intolerant mutants fail to activate mechanisms required to acquire DT in the seed."
The genes that prepare a seed for dryness cooperate in regulatory networks. Stephen Meyer shows in Chapter 13 of Darwin's Doubt that one does not just tweak developmental gene regulatory networks (dGRNs) willy-nilly and expect to get a new function (that was Charles Marshall's story for the Cambrian explosion, remember? See Debating Darwin's Doubt, Chapters 10-11). For one thing, GRNs "do not tolerate random perturbations to their basic control logic," all available evidence shows (p. 130). For another, it would require just as much information to rewire a GRN for a novel function as it would to evolve new genes, so that's no solution at all (p. 134). But enough about origins; let's get back to the mechanics of DT.
You can well imagine conditions in the soil that would attack a seed's genetic information. When the plant is growing, numerous processes survey and repair DNA. But what happens when the seed goes to sleep? Counter-intuitively, water can be one of the night stalkers.
One of the most intriguing questions about how seeds in the desiccated state can remain viable for periods of time that can exceed centuries is particularly how the integrity of DNA is preserved to prevent permanent damage making the seed unviable. Three types of DNA damage under physiological conditions have been reported: hydrolysis of the N-glycosyl bond, hydrolytic deamination of cytosine to form uracil, and DNA damage by oxidation. The first two types of DNA damage are catalyzed by water, and therefore the last layers of water that interact with DNA need to be removed or decreased to prevent damage, and the third is mediated mainly by reactive oxygen species (ROS).
The plant uses a clever trick to protect its DNA from attack by water. It replaces water molecules with sugars. Hydroxyl groups (OH) of certain sugars can provide the necessary bonds to stabilize proteins, DNA and membranes from these kinds of damage. The team found that biosynthesis of three particular sugars is up-regulated during the final stages of seed preparation, in agreement with this mechanism. They also found genes were increased for five kinds of enzymes involved in protection from reactive oxygen species (ROS).
Therefore, accumulation of antioxidant components during the late maturation stage contributes to controlling their storage potential, and helps to prevent damage from accumulated ROS during seed maturation. Accumulation of RFOs [the raffinose family of oligosaccharides, one of the types of protective sugars] and activation of mechanisms that prevent damage by ROS allow maximum metabolism reduction to decrease the production of toxic compounds and to prevent membrane, DNA, RNA, and protein damage.
All these genes are accompanied by transcription factors that switch them on and off. The authors speak about not only regulatory networks, but regulatory subnetworks. One, for instance, downregulates proteins involved in germination, to prevent early sprouting. Another is involved in stress tolerance. They identified at least four such subnetworks. Some of the subnetworks themselves involve hundreds of genes!
The researchers spoke mainly about preparation for desiccation. They didn't get into other equally fascinating questions: What activities continue during the decades or centuries of slumber? (We know from our own sleep that our hearts must still beat, we must continue breathing, and much more.) How are genes repaired by cosmic ray damage and other contingencies? And what re-activates growth processes when conditions are right for sprouting? How does a blind seed, buried in the dark soil, know when it's time to wake up? What are the first steps it takes to germinate?
This brief glimpse at desiccation tolerance in one model plant ensures is that the answers to those questions will likely be just as complicated -- and fascinating. Like so many things in the biosphere, the apparently simple process of a seed preparing for sleep is anything but simple. Evolution stories often trade in generalities. Intelligent design evidences are best seen in the details. Like Doug Axe says, biology with a design perspective becomes like a great geocaching game. "What makes finding a well-conceived geocache so delightful," he explains, "is not just the sense of having found something that was hard to find -- though that's part of it -- but the sense of having found something that was meant to be found and cleverly made hard to find" (Undeniable, p. 248). It appears we just found a good prize right under our feet.
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