Darwinism vs. the real world. XXXII

How the Body Controls Its Calcium

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.

When an archaeologist finds what she thinks may be a human artifact, she would ordinarily ask herself about its origin and function. The archaeologist knows that to identify such an artifact, the object must show evidence of having been produced by human intelligence, for a purpose. If she had found some rounded pieces of bronze that looked like they could be fit together to form a helmet, would she think that they had come about only by chance and the laws of nature? Of course not. She would know that bronze is a manmade alloy of copper and tin and that a helmet is used to protect the human skull and the brain within it from injury.

Evolutionary scientists, for their part, find skulls of different animals, which not only protect the brain from injury, but also have openings for the eyes, nose, and mouth. However, without considering what it takes to produce and maintain these structures, they claim that skulls arose unguided by purely natural processes, demonstrating the validity of Darwinian theory.
In the last few articles in this series, I have shown that the production and maintenance of the human skeleton requires multiple coordinated parts and process. It needs cells called osteoblasts and osteoclasts, the movement of calcium back and forth from the blood as the bone acts as a reservoir for the calcium needs of the body through its tissue fluid, and the presence of activated Vitamin D to bring in enough calcium from the gastrointestinal system. In addition, the body must have Ca++ ions in the blood for clotting. It needs calcium pumps in the cells to keep the Ca++ ion concentration of the cytosol ten thousand times less than the blood so it can signal proper nerve, gland, heart, and all other muscle function. When anyone looks at a skeleton, this is what they should know before they try to figure out where it came from.
But even that's not enough when taking into account how the bones relate to the body's calcium metabolism. For when it comes to life, real numbers have real consequences. Clinical experience teaches that not just any Ca++ ion concentration in the blood will do. It has to be the right amount. The normal blood level for calcium is between 8 to 10 units and if it rises above or drops below this range by more than 30 percent, the result is often lethal. So how does the body maintain control of its calcium?
As we've discussed in the past, the first thing you need to take control is a sensor that can detect what needs to be controlled. The cells of the four parathyroid glands that are embedded in the four corners of the thyroid gland have sensors that can detect the level of calcium in the blood.
The second thing you need to take control is something to integrate the data by comparing it to a standard, decide what must be done, and send out a message. When the calcium level in the blood drops, the parathyroid gland cells send out more parathormone (PTH) and when it rises they send out less PTH. Due to being broken down by enzymes, the metabolic effect of a given amount of PTH, like for most other hormones, only lasts several minutes, allowing the body to maintain moment to moment control.
The third thing you need to take control is an effector that can do something about the situation. The calcium blood level is determined by how much calcium moves in and out of the bone, how much is lost through the filtering of blood by the kidneys, and how much is brought into the body through the gastrointestinal system with the help of calcitriol (activated Vitamin D). Vitamin D is activated when the liver adds a hydroxyl group (OH) to its 25th carbon, followed by the kidney adding another one to its first carbon to produce calcitriol. If the kidney adds the OH to its 24th carbon instead, it results in an inactive form of Vitamin D.
PTH travels in the blood and attaches to specific PTH receptors on the bone cells and tells the osteoclasts to breakdown more bone to release more calcium and the osteoblasts to take in less calcium by making less bone. PTH also attaches to specific PTH receptors on the cells of the kidney tubules and tells them to take back more calcium from the urine that is presently in production. Finally, PTH attaches to specific PTH receptors on specialized cells in the kidneys and tells them to put OH on the first carbons of more 25 OH Vitamin D than on its 24th carbon, producing more calcitriol.
The combined effect of PTH is to increase the blood level of calcium by promoting its release from the bone, reuptake by the kidneys, and absorption into the body by the gastrointestinal system by increasing the production of calcitriol. When the blood level of calcium drops, the parathyroid glands send out more PTH to make the level rise back toward normal and when the level rises, they send out less PTH so it drops back toward normal. Due to the absolute need for the body to control its blood level of calcium, the absence of PTH or PTH receptors makes life impossible.
An abnormally high calcium level (hypercalcemia) is usually due to having too much PTH released by one or more of the parathyroid glands or widespread cancer. Since calcium is directly related to the development of bone, hypercalcemia can often result in weakening of the bone with increased pain and even fractures. Calcium also is connected with nerve function and hypercalcemia can cause anxiety, depression, and difficulties with concentration. This can progress to confusion, lethargy, coma, and death. Calcium is also important for heart function and hypercalcemia can cause rhythm disturbances and problems with heart function. However, one of the commonest problems encountered early on with hypercalcemia is the formation of kidney stones, because the increased blood calcium increases the amount of calcium in the urine, which can join with phosphate and come out of solution to form calcium phosphate crystals. This happens particularly when the person with hypercalcemia is dehydrated and is making very concentrated urine. For our earliest ancestors, this would have led to recurrent kidney infections and compromised kidney function.
An abnormally low calcium level (hypocalcemia) is usually due to low parathyroid gland function. This is often related to previous central neck surgery or radiation, severe Vitamin D deficiency, or chronic renal failure. Since calcium plays a major role in nerve and muscle function, the commonest early complaints of hypocalcemia are tingling and numbness of the hands and feet and around the mouth, in addition to muscle twitching and spasm. This can progress to seizures, difficulty breathing, and life-threatening cardiac rhythm problems.
The system the body uses to control its blood level of calcium requires calcium sensors on the parathyroid gland cells, the ability for these cells to produce PTH, properly adjusted release of PTH to the change in the calcium blood level, enzymes to limit the effect of PTH, and specific PTH receptors on the bone cells, tubule, and specialized cells of the kidneys. Without any one of these five components being present and doing what they're supposed to do, the whole system would fail and calcium control would be lost.
But for our earliest ancestors to have survived, like all other living creatures, not only would they have needed this irreducibly complex system but, in addition, it would have had natural survival capacity to make sure the blood level of calcium stayed within the right range. In other words, the systems the body uses must do the right thing at the right time and they must do these well enough to survive under the laws of nature. In any realistic perspective, this casts serious doubt on the idea that life came about by chance and nature's laws alone.

 

Inside Venezuela's mini apocalypse.

The fourth horseman rides on.

Why the talking primate is not just another ape.

Talk to the Animals? Yeah, Right
Tom Bethell 

We are frequently told that humans, mentally, are continuous with the apes. But it has always been an axiom, devoid of facts. Contrary evidence continues to grow. The latest case for a sharp division between us and the animal world was made by Alison Gopnik in her "Mind and Matter" column in the Wall Street Journal ("Adventures in Experimenting on Toddlers").

She illustrated it by posing this "small IQ test" for newspaper readers:

Suppose you see an experimenter put two orange blocks on a machine, and it lights up. She then puts a green one and a blue one on the same machine, but nothing happens. Two red ones work, a black and white combination doesn't. Now you have to make the machine light up yourself. You can choose two purple blocks or a yellow one and a brown one.

You figured it out, right? It's not any particular block that does the trick. Both have to be the same color.

"This simple problem actually requires some very abstract thinking," Gopnik adds. Toddlers as young as 18-to-24-months old "got it right, with just two examples." But other animals had "a very hard time" understanding it. "Chimpanzees can get hundreds of examples and still not get it, even with delicious bananas as a treat." (Chimps do have color vision, in case you were wondering.)

Conventional wisdom has been that toddlers can't learn this kind of abstract logical principle. Child psychologists such as Jean Piaget "believed that young children's thinking was concrete and superficial." Gopnik and her assistant now correct that, saying you have to watch what they do, instead of relying on what they say. Gopnik's article has now been published by the journal Psychological Science.

Ever since Darwin, the idea that there is nothing exceptional about humans has been an axiom of evolutionist thought.

Darwin wrote: "Man in his arrogance thinks himself a great work, worthy the interposition of a deity, more humble & I believe true to consider him created from animals." (See James Rachels, Created from Animals.)

Darwin's loyal followers, from T.H. Huxley to S.J. Gould and continuing today, have toed that line: We have all been deceived by our pride!

"Chimps and gorillas have long been the battleground of our search for uniqueness," Gould wrote in Ever Since Darwin. He went on:

For if we could establish an unambiguous distinction -- of kind rather than of degree -- between ourselves and our closest relatives, we might gain the justification long-sought for our cosmic arrogance. The battle shifted long ago from a simple debate about evolution: educated people now accept the evolutionary continuity between humans and apes. But we are so tied to our philosophical and religious heritage that we still seek a criterion for strict division between our abilities and those of chimpanzees.

The main evidence for an unbridgeable mental gulf between humans and animals comes from language. Children of a certain age (not too old!) can learn a new language practically overnight if they are moved to a foreign country. No one knows how it happens.

Numerous attempts to get young chimps to learn the language that small children easily learn have all failed. A detailed account could read like a comedy, but it would be irreverent -- to Darwinians -- so I shall refrain.

One chimp, Washoe, supposedly learned American Sign Language, but it may have been "confirmation bias." The feat could not be replicated by Nim Chimpsky. Watch the movie Project Nim, about the newborn chimp raised with humans. Nim Chimpsky was defiantly named after Noam Chomsky, the MIT professor who concluded that only humans have the ability to learn languages. Nim couldn't.

David Berlinski once heard Noam Chomsky say:

Every native speaker of a natural language is capable of producing and understanding infinitely many sentences that he has never heard or spoken before.

Chimps on the other hand, have never been able to speak a single sentence. We would never stop hearing about it if one had.

An expert on linguistics argued in 1975 that until man evolved a bent vocal tract he couldn't have produced vowel contrasts and therefore he didn't speak.

This was thought profound, another linguist (Noel Rude) added, "until somebody pointed out that parrots do quite well with just a beak."

The latest craze, with materialism our ruling dogma, has been to turn toward neuroscience. Chimp brains are so similar to human brains, that must be significant, right? Not really. It's the old homology argument, taken out for a new walk.

The claim of evolutionary continuity, made by Darwin, Gould and others -- based on our alleged vanity -- is not so much an argument as an accusation. In fact it is an assault on reason, for all along there has been strong evidence that humans are separated from animals not by a mutation but by a chasm.


Alison Gopnik's fascinating experiment only reinforces that.

Civil War VI

On the art of procastination.

On the global 1%

On origin of life science's and Darwinism's reproducibility issues

ASCB Addresses Problem of False Science

The Most Important Recommendation of All

The American Society for Cell Biology (ASCB) task force on reproducibility in life science research has issued an undated white paper on scientific rigor. The problem is, as we discussed here and here, life science research has been found to lack reproducibility. John Ioannidis is a bit more blunt as he explains that “most published research findings are false,” and that “claimed research findings may often be simply accurate measures of the prevailing bias.” The ASCB white paper is no doubt a step in the right direction. It offers 13 recommendations to encourage more rigor in training, publishing, and standards. But the most important recommendation of all continues to be ignored.

Daniel Sarewitz has noted not only the problem of bias in scientific research but also the causes. Note his final thought in this quote:

All involved benefit from positive results, and from the appearance of progress. Scientists are rewarded both intellectually and professionally, science administrators are empowered and the public desire for a better world is answered. The lack of incentives to report negative results, replicate experiments or recognize inconsistencies, ambiguities and uncertainties is widely appreciated — but the necessary cultural change is incredibly difficult to achieve.

And so it is that science’s much touted self-correcting, feedback loop which ensures science converges on the truth (after all, that’s what Mr. Wells told us in seventh grade science class) is sometimes a little slow to act.

And if the ASCB is still needing to remind scientists to clean their beakers and use checklists, imagine the difficulty in achieving more fundamental change?

This brings us to the recommendation that ASCB did not make—the most important of all. And that is for science to free itself of the excessive metaphysics. Unfortunately, progress on that front is glacial. As Sarewitz notes, one reason bias persists, and is so harmful, is that in the moment it is not perceived as bias. Asking an evolutionist to stop with the metaphysics goes nowhere because it isn’t recognized as metaphysics. Deep philosophy is a part of their “science” as much as red meat is a part of hamburgers.

Even if the ASCB task force members wanted to address this fundamental problem, they wouldn’t for the backlash would be overwhelming and their professional reputations would be ruined.

So while the pipettes will be sterilized and results double checked to the third decimal point, ASCB will continue to publish junk science driven by the Epicurean mandate that the world must have arisen spontaneously. Unfortunately, the ASCB task force has missed the most important recommendation of all.

Posted by Cornelius Hunter 

File under 'well said" XXVIII

Yesterday is ashes; tomorrow wood. Only today does the fire burn brightly. - 
 Inuit folk wisdom.

A clash of titans XX

It's design all the way down.

Organizer of body axes: 600 million years old molecular principles
Source:
University of Vienna

In humans and in animals, the correct position of tissues, organs and appendages is essential. Two body axes (the head-tail and the back-belly axes) usually define this position by generating a coordinate system, which supplies each cell in the body with its precise address. Thus, for example, the vertebrate central nervous system is always located on the back, and the intestinal tract on the belly of the animal.

In vertebrate early development, an "organizer" forms in the region of the primitive mouth (the blastopore) of the embryo. This organizer is responsible for guiding axis formation of the organism. Its discovery won Hans Spemann a Nobel Prize in 1935. The organizer tissue instructs the surrounding cells to take part in body axes development, enforcing a certain developmental fate on them. Without an organizer, the embryo would not know where the head, the tail, the back and the belly should be. Mistakes in the regulation of body axes can lead to severe developmental defects, for example to the formation of Siamese twins.

In the last 25 years, the researchers largely elucidated the genetic underpinnings of this very particular part of the vertebrate embryo. The widespread assumption was that the organizer was a specific vertebrate feature, since it was not readily observable in insect or worm embryos.

The team of Grigory Genikhovich and Ulrich Technau from the Department of Molecular Evolution and Development of the University of Vienna now demonstrated that not only the principle of the organizer but also its molecular underpinnings are much older than previously supposed. "By performing transplantation experiments and molecular analyses we have found a blastoporal organizer in the embryos of the sea anemone Nematostella vectensis. For inducing axes, it uses the same class of signaling molecules as the vertebrate organizer," explains Technau. "We conclude that this principle of the regulation of the embryonic axes existed already in the common ancestor of vertebrates and sea anemones more than 600 million years ago."

The lake of fire:The Watchtower Society's commentary II

LAKE OF FIRE

This expression occurs only in the book of Revelation and is clearly symbolic. The Bible gives its own explanation and definition of the symbol by stating: “This means the second death, the lake of fire.”—Re 20:14; 21:8.

The symbolic quality of the lake of fire is further evident from the context of references to it in the book of Revelation. Death is said to be hurled into this lake of fire. (Re 19:20; 20:14) Death obviously cannot be literally burned. Moreover, the Devil, an invisible spirit creature, is thrown into the lake. Being spirit, he cannot be hurt by literal fire.—Re 20:10; compare Ex 3:2 and Jg 13:20.

Since the lake of fire represents “the second death” and since Revelation 20:14 says that both “death and Hades” are to be cast into it, it is evident that the lake cannot represent the death man has inherited from Adam (Ro 5:12), nor does it refer to Hades (Sheol). It must, therefore, be symbolic of another kind of death, one that is without reversal, for the record nowhere speaks of the “lake” as giving up those in it, as do Adamic death and Hades (Sheol). (Re 20:13) Thus, those not found written in “the book of life,” unrepentant opposers of God’s sovereignty, are hurled into the lake of fire, meaning eternal destruction, or the second death.—Re 20:15.

While the foregoing texts make evident the symbolic quality of the lake of fire, it has been used by some persons to support belief in a literal place of fire and torment. Revelation 20:10 has been appealed to, because it speaks of the Devil, the wild beast, and the false prophet as being “tormented day and night forever and ever” in the lake of fire. However, this cannot refer to actual conscious torment. Those thrown into the lake of fire undergo “the second death.” (Re 20:14) In death there is no consciousness and, hence, no feeling of pain or suffering.—Ec 9:5.

In the Scriptures fiery torment is associated with destruction and death. For example, in the Greek Septuagint translation of the Hebrew Scriptures the word for torment (baʹsa·nos) is several times used with reference to punishment by death. (Eze 3:20; 32:24, 30) Similarly, concerning Babylon the Great, the book of Revelation says, “the kings of the earth . . . will weep and beat themselves in grief over her, when they look at the smoke from the burning of her, while they stand at a distance because of their fear of her torment [Gr., ba·sa·ni·smouʹ].” (Re 18:9, 10) As to the meaning of the torment, an angel later explains: “Thus with a swift pitch will Babylon the great city be hurled down, and she will never be found again.” (Re 18:21) So, fiery torment here is parallel with destruction, and in the case of Babylon the Great, it is everlasting destruction.—Compare Re 17:16; 18:8, 15-17, 19.


Therefore, those who are ‘tormented forever’ (from Gr., ba·sa·niʹzo) in the lake of fire undergo “second death” from which there is no resurrection. The related Greek word ba·sa·ni·stesʹ is translated ‘jailer’ in Matthew 18:34. (RS, NW, ED; compare vs 30.) Thus those hurled into the lake of fire will be held under restraint, or “jailed,” in death throughout eternity.—

Jesus v.the Pharisees re:ceremonial purity the Watchtower Society's commentary.

Why was handwashing an issue for Jesus’ antagonists?

This was just one of many issues in which Jesus’ enemies found fault with him and his disciples. The Mosaic Law included a number of commands on ceremonial purity regarding such matters as bodily discharges, leprosy, and dealing with human and animal corpses. It also gave instructions on how impurities could be removed. This could be done by sacrifice, washing, or sprinkling.—Lev., chaps. 11-15; Num., chap. 19.

The Jewish rabbis expounded on every detail of these laws. One source says that each cause for impurity would be subjected “to questioning concerning the circumstances in which it may be contracted, how and to what extent it may be transmitted to others, the utensils and objects capable and incapable of becoming unclean, and finally, the means and rituals required for purification.”

Jesus’ opponents asked him: “Why do your disciples not observe the tradition of the men of former times, but they eat their meal with defiled hands?” (Mark 7:5) Those religious enemies were not referring to the taking of sanitary measures. As a ritual, the rabbis required that water be poured over their hands prior to eating. The above-quoted source adds: “It is also debated which vessels are to be used for the pouring, which kind of water is suitable, who should pour, and how much of the hands should be covered with water.”


Jesus’ reaction to all these man-made laws was simple. He told the first-century Jewish religious leaders: “Isaiah aptly prophesied about you hypocrites, as it is written, ‘This people honor me with their lips, but their hearts are far removed from me [Jehovah]. It is in vain that they keep worshipping me, for they teach commands of men as doctrines.’ You let go of the commandment of God and cling to the tradition of men.”—Mark 7:6-8.

For adult stem cell research:The hits just keep on coming!

In Reversing Stroke Damage, a Stunning Success for "Anti-Science"?

Wesley J. Smith

Once again the damned-with-faint-praise field of adult stem cell research seems headed toward significant treatment breakthroughs. This time the target is stroke.

The Washington Post announces, "Stanford researchers 'stunned' by stem cell experiment that helped stroke patient walk":

Stanford researchers studying the effect of stem cells injected directly into the brains of stroke patients said Thursday that they were "stunned" by the extent to which the experimental treatment restored motor function in some of the patients.

While the research involved only 18 patients and was designed primarily to look at the safety of such a procedure and not its effectiveness, it is creating significant buzz in the neuroscience community because the results appear to contradict a core belief about brain damage -- that it is permanent and irreversible.

The results, published in the journalStroke, could have implications for our understanding of an array of disorders including traumatic brain injury, spinal cord injury and Alzheimer's if confirmed in larger-scale testing.

The stem cells involved came from bone marrow, not destroyed embryos.

Grain of salt. Grain of salt. Grain of salt. Sometimes early studies such as this come to naught.

Still, not bad for a field that just 15 years go was denigrated as not nearly as hopeful as embryonic by "the scientists" seeking the almighty funding buck. Meanwhile adult stem cell advocates were branded as "anti-science" for expressing significant ethical concerns and scientific doubts about the embryonic approach.

How many embryonic studies this hopeful with human research, formerly touted widely as the "only hope"? That would be a big fat zero.

Darwinism vs..the real world. XXXI

Forming Strong Bones Is an Irreducibly Complex Process

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.

Visit a museum of natural history and you are likely to encounter a human skeleton or two. Next to them you might find an exhibit showing a famous paleontologist unearthing human bones from antiquity along with a commentary that confirms evolutionary biologists' claim that life came about by chance and the laws of nature alone.

What you will not find is an explanation of the cellular and molecular basis for the bones you are looking at nor how they related to the calcium metabolism of the body in which they were housed. It would be like visiting the Kennedy Space Center and seeing all the different rockets there without an explanation of the ingenuity it took to build and launch them into space.

In the last two articles in this series, I showed that although bone is a solid tissue, it nevertheless has a dynamic metabolism in which cells called osteoblasts deposit calcium into the protein meshwork they lay down and others called osteoclasts remove it. Ninety-nine percent of the body's calcium content is located in bone and 99 percent of that is in crystalline form. The remaining 1 percent of bone calcium is dissolved as Ca++ ions in the tissue fluid surrounding the bone cells. This bone tissue fluid is in direct contact with the circulation through the capillaries. This means that bones act as reservoirs for the calcium metabolism of the body.

As important as calcium is in helping to form the bones to protect the organs and provide attachment for muscles so we can breathe, move around, and handle things, it also works in the blood to help clotting and acts as a chemical signal within cells to bring about nerve, gland, heart, and all other muscle function. To accomplish the job of cell signaling, the Ca++ ion concentration in the cytosol must be in the order of ten thousand times less than it is in the fluid outside the cell. Just as the cell uses the sodium-potassium pump to maintain its proper chemical content, it uses the calcium pump to push Ca++ ions out to maintain this ten thousand-fold difference.

Now, don't you think natural history museums should provide this sort of information about how life actually works and not just how it looks? After all, it isn't rocket science.

So far we have seen how calcium can move in and out of the bone and other cells. In addition, since there are Ca++ ions dissolved within the blood, this means that they are filtered out of the body through the kidneys. What still needs to be explained is how the body gets the calcium it needs in the first place. Nobody ever tells us to be sure we take in enough sugar or salt. In fact, we're usually told to be careful not to take in too much or else we'll get fat and develop diabetes or high blood pressure. The gastrointestinal system readily absorbs all the sugar and salt we take in and deals with it later through various hormones and the kidneys. But that's not the case for calcium. Without some sort of chemical assistance, the intestine can only absorb about 10 percent of the calcium it encounters, which is why we have to make sure we take in enough calcium to have strong bones. So what does the body need to help the gastrointestinal system bring in enough calcium so it can survive within the laws of nature.

Calcium is a mineral that is naturally present in foods like milk products, eggs, nuts, fruits, and green leafy vegetables. However, without Vitamin D, our earliest ancestors wouldn't have been able to absorb enough calcium to build up their bones and survive within the laws of nature. Vitamins are essential chemicals that the body generally does not produce but are needed for certain metabolic reactions and must therefore be obtained from the diet or supplements. The body can make its own Vitamin D when exposed to sunlight. However, since Vitamin D deficiency can lead to significant debility and even death, we generally increase our intake through supplements and fortified foods such as milk, orange juice, and cereals. However, the Vitamin D we make ourselves and bring in from our diet does not help in the absorption of calcium from the gastrointestinal system until it becomes activated by the body.

Vitamin D, like iron and thyroid hormone, does not dissolve well in the blood and must attach to a specific carrier protein made in the liver to be transported throughout the body. The liver begins the activation process of Vitamin D by adding a hydroxyl (OH) group to its 25th carbon. Then it is transported to the kidneys, where another OH group is added. Depending on the calcium needs of the body, the OH is added to either the 24th carbon, keeping it relatively inactive or to the 1st carbon which activates it to become calcitriol. Calcitriol is activated Vitamin Dwhich then attaches to specific Vitamin D receptors in the nucleus of the intestinal cells and signals them to absorb more calcium. In a normal diet, this can increase the calcium absorption from 10 to 30 percent and in ones with very low calcium up to 90 percent.

It is clear that the body's ability to form strong bones and have the right amount of calcium inside and outside its cells is an irreducibly complex process, requiring several different properly working components. If you are comparing human and other animal bones to confirm the validity of Darwinism, shouldn't you educate people about this as well?

But we aren't finished yet! Even though we have explained how the calcium pump works to keep the Ca++ ion level low in the cell, how Vitamin D becomes activated and allows the gastrointestinal system to absorb enough calcium, and how the bone cells take calcium from or deposit it into its tissue fluid, we have not explained how the body controls its blood level of calcium. For it is a matter of life and death. That's what we'll look at next time.

All in the family?

Recent Genetic Research Shows Chimps More Distant From Humans, Neanderthals Closer
Casey Luskin 

Research published in Nature over the past few months is showing a much greater genetic distance between humans and chimps than previously thought, while revealing a closer one between humans and Neanderthals.


A Nature paper from January, 2010 titled, ""Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content,"" found that Y chromosomes in humans and chimps "differ radically in sequence structure and gene content," showing "extraordinary divergence" where "wholesale renovation is the paramount theme." Of course, the paper attributes these dramatic genetic changes to "rapid evolution during the past 6 million years."
One of the scientists behind the study was quoted in a Nature news article stating, "It looks like there's been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages." The news article states that "many of the stark changes between the chimp and human Y chromosomes are due to gene loss in the chimp and gene gain in the human" since "the chimp Y chromosome has only two-thirds as many distinct genes or gene families as the human Y chromosome and only 47% as many protein-coding elements as humans." According to the news piece, "Even more striking than the gene loss is the rearrangement of large portions of the chromosome. More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome, and vice versa, whereas this is true for less than 2% of the remainder of the genome."
But not wishing to offend the "the "myth of 1%"", the Nature news article carefully adds, "The remainder of the chimp and human genomes are thought to differ in gene number by less than 1%."
While this research takes us genetically further from apes, a more recent report in Nature news takes us genetically much closer to Neanderthals. Titled, "Neanderthals may have interbred with humans," the article explains that "A genetic analysis of nearly 2,000 people from around the world indicates that such extinct species interbred with the ancestors of modern humans twice, leaving their genes within the DNA of people today." According to this new article:[I]t may help explain the fate of the Neanderthals, who vanished from the fossil record about 30,000 years ago. "It means Neanderthals didn't completely disappear," says Jeffrey Long, a genetic anthropologist at the University of New Mexico, whose group conducted the analysis. There is a little bit of Neanderthal leftover in almost all humans, he says.
Given the high degree of skeletal similarity between humans and Neanderthals, the notion that we interbred is nothing new. They have been  called  a possible "race" of our own species, as  studies have found  their body shape is highly similar to that of modern human variation. Indeed, discovery of "morphological mosaics" indicates that they likely interbred with modern humans. The  finding of a modern-humanlike hyoid bone in a Neanderthal implies that they may have had language capabilities.


Textbooks often depict Neanderthals as primitive, bungling brutes with a vaguely human-like form (see above)--an attempt to instill the ape-to-human icon in students. But as Time Magazine  reported in 1999, there's increasing evidence showing that this evolutionary interpretation was wrong, and Neanderthals were essentially "all just people":
The real message, [a Washington University paleoanthropologist Erik] Trinkaus believes, is that to people living in the Stone Age, Neanderthals were just another tribe. "They may have had heavier brows or broader noses or stockier builds, but behaviorally, socially and reproductively they were all just people."
(Michael D. Lemonick, "A Bit of Neanderthal in Us All?," Time Magazine (April 25, 1999).)


Some ID proponents might disagree with me on this particular point, but it's my view that Neanderthals were a race of human beings that ultimately went extinct. Either way, it's becoming increasingly clear that Neanderthals do nothing to bolster the case that humans evolved from more primitive hominids.

Neanderthals:Ancient mariners?

Neanderthals beat modern humans to the seas by 50,000 years, say scientists
By TED THORNHILL 

We like to think we were superior to Neanderthals, but when it came to seafaring, they were way ahead of modern humans, according to a new study.
George Ferentinos, of the University of Patras in Greece, believes that our extinct cousins were sailing the seas about 50,000 years before us.
Modern humans took to the seas 50,000 years ago, having first appeared between 100,000 and 300,000 years ago.
However, stone Neanderthal tools dating back at least 100,000 years have been found on the Greek mainland and on the Greek islands of Lefkada, Kefalonia and Zakynthos, which means they must have been travelling in boats.
Some have theorised that the tools ended up in these locations because when the Neanderthals lived in the Mediterranean, the islands were physically connected to the mainland.
However, as New Scientist reports, Ferentinos has compiled data that shows the length of time the islands have been surrounded by water matches the age of the tools found on them.
He has determined that sea levels 100,000 years ago used to be 120 metres (390 feet) lower than they are today because of Earth’s much larger ice caps.
But there still would have been around 180 metres of water around Greece because the seabed sinks to 300 metres.
The journey to the islands is between three and seven miles and Ferentinos is convinced that Neanderthals made regular trips on the water. 
It’s feasible, some say, that the Neanderthals merely swam to the islands, but Thomas Strasser of Providence College in Rhode Island backs Ferentinos’s theory, having found Neanderthal tools on Crete, which is far too far to swim with tools – being 25 miles from its nearest neighbour.
Neanderthals were by no means the first hominins to use boats. As Nature magazine has reported, one million-year-old stone tools have been found on the Indonesian island of Flores. 
Neanderthals appeared around 700,000 years later.
They had thick set features and heavy foreheads. They were around six inches shorter on average than modern people, but their brains were 20 per cent bigger.
They were excellent hunters. They supplemented their diet of deer, bison, boar and bear with seal, fish, shellfish, nuts, grains and plants.

Animal rights above human needs?Pros and Cons.

Peer review demythified.

1,500 scientists lift the lid on reproducibility
Monya Baker

More than 70% of researchers have tried and failed to reproduce another scientist's experiments, and more than half have failed to reproduce their own experiments. Those are some of the telling figures that emerged from Nature's survey of 1,576 researchers who took a brief online questionnaire on reproducibility in research.

The data reveal sometimes-contradictory attitudes towards reproducibility. Although 52% of those surveyed agree that there is a significant 'crisis' of reproducibility, less than 31% think that failure to reproduce published results means that the result is probably wrong, and most say that they still trust the published literature.
Data on how much of the scientific literature is reproducible are rare and generally bleak. The best-known analyses, from psychology1 and cancer biology2, found rates of around 40% and 10%, respectively. Our survey respondents were more optimistic: 73% said that they think that at least half of the papers in their field can be trusted, with physicists and chemists generally showing the most confidence.


The results capture a confusing snapshot of attitudes around these issues, says Arturo Casadevall, a microbiologist at the Johns Hopkins Bloomberg School of Public Health in Baltimore, Maryland. “At the current time there is no consensus on what reproducibility is or should be.” But just recognizing that is a step forward, he says. “The next step may be identifying what is the problem and to get a consensus.”Failing to reproduce results is a rite of passage, says Marcus Munafo, a biological psychologist at the University of Bristol, UK, who has a long-standing interest in scientific reproducibility. When he was a student, he says, “I tried to replicate what looked simple from the literature, and wasn't able to. Then I had a crisis of confidence, and then I learned that my experience wasn't uncommon.”
The challenge is not to eliminate problems with reproducibility in published work. Being at the cutting edge of science means that sometimes results will not be robust, says Munafo. “We want to be discovering new things but not generating too many false leads.”
  The scale of reproducibility
But sorting discoveries from false leads can be discomfiting. Although the vast majority of researchers in our survey had failed to reproduce an experiment, less than 20% of respondents said that they had ever been contacted by another researcher unable to reproduce their work. Our results are strikingly similar to another online survey of nearly 900 members of the American Society for Cell Biology (see go.nature.com/kbzs2b). That may be because such conversations are difficult. If experimenters reach out to the original researchers for help, they risk appearing incompetent or accusatory, or revealing too much about their own projects.A minority of respondents reported ever having tried to publish a replication study. When work does not reproduce, researchers often assume there is a perfectly valid (and probably boring) reason. What's more, incentives to publish positive replications are low and journals can be reluctant to publish negative findings. In fact, several respondents who had published a failed replication said that editors and reviewers demanded that they play down comparisons with the original study.

Nevertheless, 24% said that they had been able to publish a successful replication and 13% had published a failed replication. Acceptance was more common than persistent rejection: only 12% reported being unable to publish successful attempts to reproduce others' work; 10% reported being unable to publish unsuccessful attempts.Survey respondent Abraham Al-Ahmad at the Texas Tech University Health Sciences Center in Amarillo expected a “cold and dry rejection” when he submitted a manuscript explaining why a stem-cell technique had stopped working in his hands. He was pleasantly surprised when the paper was accepted3. The reason, he thinks, is because it offered a workaround for the problem.Others place the ability to publish replication attempts down to a combination of luck, persistence and editors' inclinations. Survey respondent Michael Adams, a drug-development consultant, says that work showing severe flaws in an animal model of diabetes has been rejected six times, in part because it does not reveal a new drug target. By contrast, he says, work refuting the efficacy of a compound to treat Chagas disease was quickly accepted4.The corrective measures
One-third of respondents said that their labs had taken concrete steps to improve reproducibility within the past five years. Rates ranged from a high of 41% in medicine to a low of 24% in physics and engineering. Free-text responses suggested that redoing the work or asking someone else within a lab to repeat the work is the most common practice. Also common are efforts to beef up the documentation and standardization of experimental methods.

Any of these can be a major undertaking. A biochemistry graduate student in the United Kingdom, who asked not to be named, says that efforts to reproduce work for her lab's projects doubles the time and materials used — in addition to the time taken to troubleshoot when some things invariably don't work. Although replication does boost confidence in results, she says, the costs mean that she performs checks only for innovative projects or unexpected results.
Consolidating methods is a project unto itself, says Laura Shankman, a postdoc studying smooth muscle cells at the University of Virginia, Charlottesville. After several postdocs and graduate students left her lab within a short time, remaining members had trouble getting consistent results in their experiments. The lab decided to take some time off from new questions to repeat published work, and this revealed that lab protocols had gradually diverged. She thinks that the lab saved money overall by getting synchronized
 instead of troubleshooting failed experiments piecemeal, but that it was a long-term investment.
  Irakli Loladze, a mathematical biologist at Bryan College of Health Sciences in Lincoln, Nebraska, estimates that efforts to ensure reproducibility can increase the time spent on a project by 30%, even for his theoretical work. He checks that all steps from raw data to the final figure can be retraced. But those tasks quickly become just part of the job. “Reproducibility is like brushing your teeth,” he says. “It is good for you, but it takes time and effort. Once you learn it, it becomes a habit.”
  One of the best-publicized approaches to boosting reproducibility is pre-registration, where scientists submit hypotheses and plans for data analysis to a third party before performing experiments, to prevent cherry-picking statistically significant results later. Fewer than a dozen people mentioned this strategy. One who did was Hanne Watkins, a graduate student studying moral decision-making at the University of Melbourne in Australia. Going back to her original questions after collecting data, she says, kept her from going down a rabbit hole. And the process, although time consuming, was no more arduous than getting ethical approval or formatting survey questions. “If it's built in right from the start,” she says, “it's just part of the routine of doing a study.”

The cause
The survey asked scientists what led to problems in reproducibility. More than 60% of respondents said that each of two factors — pressure to publish and selective reporting — always or often contributed. More than half pointed to insufficient replication in the lab, poor oversight or low statistical power. A smaller proportion pointed to obstacles such as variability in reagents or the use of specialized techniques that are difficult to repeat.

But all these factors are exacerbated by common forces, says Judith Kimble, a developmental biologist at the University of Wisconsin–Madison: competition for grants and positions, and a growing burden of bureaucracy that takes away from time spent doing and designing research. “Everyone is stretched thinner these days,” she says. And the cost extends beyond any particular research project. If graduate students train in labs where senior members have little time for their juniors, they may go on to establish their own labs without having a model of how training and mentoring should work. “They will go off and make it worse,” Kimble says.What can be done?
Respondents were asked to rate 11 different approaches to improving reproducibility in science, and all got ringing endorsements. Nearly 90% — more than 1,000 people — ticked “More robust experimental design” “better statistics” and “better mentorship”. Those ranked higher than the option of providing incentives (such as funding or credit towards tenure) for reproducibility-enhancing practices. But even the lowest-ranked item — journal checklists — won a whopping 69% endorsement.The survey — which was e-mailed to Nature readers and advertised on affiliated websites and social-media outlets as being 'about reproducibility' — probably selected for respondents who are more receptive to and aware of concerns about reproducibility. Nevertheless, the results suggest that journals, funders and research institutions that advance policies to address the issue would probably find cooperation, says John Ioannidis, who studies scientific robustness at Stanford University in California. “People would probably welcome such initiatives.” About 80% of respondents thought that funders and publishers should do more to improve reproducibility.

“It's healthy that people are aware of the issues and open to a range of straightforward ways to improve them,” says Munafo. And given that these ideas are being widely discussed, even in mainstream media, tackling the initiative now may be crucial. “If we don't act on this, then the moment will pass, and people will get tired of being told that they need to do something.”

When scientism trumps actual science.

On that South Dakota Academic Freedom Bill, Here's More Bad Journalism -- and Science Censorship -- from Patrick Anderson

Casey Luskin 

 

 

 

I have already noted the grossly inaccurate reporting by Patrick Anderson with the Argus Leader in South Dakota, who falsely claimed that the academic freedom bill in that state would bring intelligent design into public schools. Now I've discovered another article by Mr. Anderson, "S.D. plan allows evolution critique in class," which is even more inaccurate.

It opens with the statement that "Creationism would be easier to teach in South Dakota classrooms if a bill in the state Senate becomes law, according to a California-based nonprofit." Of course that innocuous-sounding California-based outfit is the National Center for Science Education, whose mission is focused on censorship. They constantly relabel credible scientific viewpoints as "creationism" and other forms of "religion," in hopes of using the law to censor those ideas and keep them hidden from students in public schools. Anderson, as we'll see, is following their lead and becoming a science censor himself.

He quotes NCSE deputy director Glenn Branch. But does he quote the language of the bill itself, which clearly excludes religious advocacy from protection under its provisions? Take a wild guess. The answer is no.

To Anderson's credit, he did talk to us here at Discovery Institute as well, and wrote:

But the model bill and South Dakota's do not advance intelligent design or creationism, said Casey Luskin, research coordinator for the Institute.
"If a teacher were to teach creationism in a state that has an academic freedom bill, they would not be protected by that bill in any way, shape or form," Luskin said. "We actually do not support teaching or pushing intelligent design in public schools."
Debating evolution doesn't mean invoking religion, Luskin said. His group's model legislation offers protection to teachers who question the science of evolution, so they don't have to worry about losing their job, Luskin said.
If something is written into curriculum, such as climate change or evolution, an academic freedom bill allows teachers to, in the case of South Dakota, "understand, analyze, critique, or review" without being stopped by school officials.

"Schools should teach the evidence for and against evolution," Luskin said.

But that last comment merely serves Anderson as a foil, as he immediately thereafter cites the president of the South Dakota Teachers Association, Julie Olson, who could hardly be more dogmatic:

Evolutionary principles are central to science, not just biology, and they're not up for debate, Olson said....
"I don't know what their arguments would be," Olson said. "What's the proof?"

Olson is candid in stating her view that students should be prevented from debating and questioning Darwinian evolution. She claims ignorance about what the scientific challenges to Darwin's theory might be, and I wouldn't be surprised if she really is unaware of those challenges.

 

But the reporter, Patrick Anderson, is aware of them. I know that because I sent him the very answer to Olson's objection in an e-mail -- information that he apparently did not see fit to print in his article. Here's what I wrote (the numbers in parentheses refer to PDFs of papers from the mainstream technical literature that I also sent to Anderson):

Per our conversation I wanted to send you some mainstream scientific papers that discuss scientific challenges to core tenets of neo-Darwinian evolution, especially as they're taught in textbooks. Please note that many of these authors are neo-Darwinian evolutionists. But they all nonetheless recognize scientific weaknesses in neo-Darwinian theory that challenge common textbook claims about the evidence for evolution, including:
(1) Major conflicts in the tree of life (011; 274b). It's not religion to note that genome sequence data does not fit the treelike pattern seen in textbook diagrams.
(2) Problems with textbook discussions of vertebrate embryos (064; 300). It's not religion to note that vertebrate embryos start off development differently, contradicting textbook diagrams.
(3) Non-speciation and limited change in "Darwin's finches" (015, Speciation Undone). It's not religion to point out that Darwin's finches can still interbreed and only exhibit small-scale oscillating selection which does not show the evolution of fundamentally new types of organisms.
(4) The lack of importance of evolutionary theory for doing good biology research (020). It's not religion to point out that you don't need neo-Darwinian evolution to figure out how molecular machines like ATP synthase work.
(5) Challenges to the adequacy or primacy of natural selection and random mutation for causing evolution (023, 373). It's not religion to point out that living organisms contain features which would require multiple mutations to arise before giving any advantage, and that population genetics models shows that evolving these structures by mutation and selection would be infeasible given normal population sizes and timescales.
This is just a small smattering of what's out there in the peer-reviewed literature as far as challenges go to the evidence that's cited for the mainstream neo-Darwinian viewpoint.

The papers I sent him provide strong documentation of the scientific criticisms, found in the mainstream scientific literature, of core neo-Darwinian claims, especially as they are taught in textbooks. Here are the full citations of the papers that the numbers refer to:

• 011: Trisha Gura, "Bones, Molecules or Both?," Nature, 406 (July 20, 2000): 230-233.
• 274b: Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist, 2692 (January 21, 2009).
• 064: Michael K. Richardson, James Hanken, Mayoni L. Gooneratne, Claude Pieau, Albert Raynaud, Lynne Selwood, and Glenda M. Wright, "There is No Highly Conserved Embryonic Stage in the Vertebrates: Implications for Current Theories of Evolution and Development," Anatomy and Embryology, 196 (1997): 91-106
• 300: Elizabeth Pennisi, "Haeckel's Embryos: Fraud Rediscovered," Science, 277 (September 5, 1997): 1435.
• 015: Peter R. Grant and B. Rosemary Grant, "Unpredictable Evolution in a 30-Year Study of Darwin's Finches," Science, 296 (April 26, 2002): 707-711
• Speciation Undone: Peter R. Grant and B. Rosemary Grant, "Speciation undone," Nature, 507 (March 13, 2014): 178-179.
• 020: Philip S. Skell, "Why do we invoke Darwin?," The Scientist, 19 (August 29, 2005): 10.
• 023: Michael J. Behe and David W. Snoke, "Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues," Protein Science, 13 (2004): 2651-2664.
• 373: Eugene V. Koonin, "The Origin at 150: is a new evolutionary synthesis in sight?," Trends in Genetics, 25 (2009): 473-475.

So the reporter was informed that there are serious scientific criticisms of neo-Darwinian theory -- especially as it is taught in textbooks. Yet he makes no mention of any of it. Instead, he tries to rebut me by quoting a teacher who frankly admits her own lack awareness of the relevant data, and who leaves readers with the impression that there are no legitimate scientific criticisms of Darwinian evolution that could possibly be introduced in schools.

This makes Patrick Anderson not only an inaccurate reporter, but a censor. He withholds from readers crucial facts in his possession that are directly relevant to the story.

That's exactly how media censorship works in the evolution debate. You're seeing it right here before your very eyes. I've seen before, literally hundreds of times.

Neither enough monkeys nor keyboards

Essential Prediction of Darwinian Theory of Macroevolution Falsified by Information Degradation


Kirk Durston

I was struck, but not surprised, by a statement made a few days ago by Neil Turok, Director of the Perimeter Institute for Theoretical Physics here in Waterloo, Ontario. Speaking of the apparent collapse of evidence for a critical component of the Big Bang theory, he responded, ‘even though hundreds or thousands of people are working on an idea, it may still be wrong.’

His statement is a harbinger of a much greater collapse looming on the scientific horizon, also involving thousands of scientists. There is mounting evidence that most, if not all the key predictions of the neo-Darwinian theory of macroevolution are being consistently falsified by advances in science, several of which I will discuss in later posts. Here, we look at a fundamental prediction Darwinism makes regarding the increase of genetic information.

Computer information is digitally encoded using just two symbols (‘1’ and ‘0’). We now know that the instructions for the full diversity of life, are digitally encoded in the DNA of all living things using a four-symbol alphabet. In  more technical terms, this is referred to as functional information.

In the neo-Darwinian scenario for the origin and diversity of life, the digital functional information for life would have had to begin at zero, increase over time to eventually encode the first simple life form, and continue to increase via natural processes to encode the digital information for the full diversity of life.

An essential, falsifiable prediction of Darwinian theory, therefore, is that functional information must, on average, increase over time.

Interestingly enough, a prediction of intelligent design science is quite the opposite. Since information always degrades over time for any storage media and replication system, intelligent design science postulates that the digital information of life was initially downloaded into the genomes of life. It predicts that, on average, genetic information is steadily being corrupted by natural processes. The beauty of these two mutually incompatible predictions in science is that the falsification of one entails verification of the other. So, which prediction does science falsify, and which one does science verify?

Ask any computer programmer what effect ongoing random changes in the code would do for the integrity of a program, and they will universally agree that it degrades the software. This is precisely the first problem for neo-Darwinian theory. Mutations produce random changes in the digital information of life. It is generally agreed that the rate of deleterious mutations is much greater than the rate of beneficial mutations. My own work with 35 protein families suggests that the rate of destruction is, at minimum, 8 times the rate of neutral or beneficial mutations. Simply put, the digital information of life is being destroyed much faster than it can be repaired or improved. New functions may evolve, but the overall loss of functional information in other areas of the genome will, on average, be significantly greater. The net result is that the digital information of life is running down.

The second series of falsifying observations is indicated by actual organisms we have studied most closely. First, the digital information for the bacterial world is slowly eroding away due to a net deletional bias in mutations involving insertions and deletions. A second example is the fruit fly, one of the most studied life forms in evolutionary biology. It, too, is showing an ongoing, genome-wide loss of DNA across the entire genus. Finally, humans are not exempt. As pointed out in this PNAS paper, "a consideration of the long-term consequences of current human behaviour for deleterious-mutation accumulation leads to the conclusion that a substantial reduction in human fitness can be expected over the next few centuries in industrialized societies unless novel means of genetic intervention are developed". 

We continue to discover more examples of DNA loss, suggesting that the biological world is slowly running down. Microevolution is good at fine-tuning existing forms within their information limits and occasionally getting something right, but the steady accumulation of deleterious mutations on the larger scale suggests that mutation-driven evolution is actually destroying biological life, not creating it.

In conclusion, the digital information of life appears to be steadily degrading rather than increasing, falsifying an essential prediction of neo-Darwinian theory, and verifying a prediction of intelligent design science. This is hardly a surprise, as every other area of science, except for evolutionary biology, grants that natural processes degrade information, regardless of the storage media and copying process. For neo-Darwinian macroevolution to work, it requires something that is in flat-out contradiction to the real world.

(Edited for clarity, 11:46 EDT, June 26, 2015)