Darwinism vs. the real world XXIV

   Heat and Temperature -- What's the Difference? 

Howard Glicksman March 23, 2016 12:41 PM 

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.

We live in a world made up of matter. Matter consists of atoms and molecules that follow the laws of nature. Organic life is made up of atoms and molecules that are organized into cells. Our body has trillions of them. Heat and temperature are physical phenomena and, although related to each other, they are not the same thing.

Heat is the transfer of energy from one object to another. When a machine uses energy, it naturally gives off heat. This applies to the body as well. When our cells use oxygen to release energy from glucose, they give off heat. The laws of nature not only cause the release of heat when energy is used, they also cause the transfer of heat from a warmer object to a cooler object when they come in contact with each other. When you touch a hot stove, the transfer of heat from it to your fingers will burn them. Grab an ice cube and the transfer of heat from your hand to it will cause it to melt.

In contrast, temperature is a measure of an object's internal energy, reflected in its amount of random molecular motion. This energy is often derived from heat but can come from other sources, like electrical and nuclear energy. The higher an object's temperature, the more random motion there is among its molecules. Conversely the lower an object's temperature, the less random motion there is among its molecules.

For some molecules, like H2O, the amount of random motion can affect its physical state. If the temperature of H2O is below 32oF (0oC), it is a solid -- ice. And when its temperature is between 32oF-212oF (0oC-100oC), H2O is liquid water. Finally, when the temperature of H2O is greater than 212oF (100oC) it is a gas called water vapor or steam. The effects of heat on an object's temperature, physical state, and functional capacity apply not only to working machines but to the cells of the body as well.

Everybody knows that going outside in the sun during the summer will make you feel hot. And going outside without a coat in the winter will make you feel cold. And most people know that the temperature inside the body (core temperature) is normally higher than on the skin (surface temperature). All you have to do is blow on your hands and feel the heat to figure that out. As humans, we are warm-blooded, while most reptiles, amphibians, fish, and insects, are cold-blooded. But most people do not understand why and how the body follows the rules and keeps its core temperature within a certain range to stay alive. That's what the next few articles in this series will explain.

Just as a machine can malfunction if it is too hot or too cold, so too, the cells that make up the organs of the body can malfunction if the core temperature is too high or too low. The core temperature of the body is a reflection of the amount of random molecular motion within its cells. Most of the enzymes the body uses for its metabolic processes work best within an ideal temperature range. For the human body the normal range for the core temperature is 97o-99oF (36o-37oC).

If the core temperature rises too high or drops too low, it may affect not only the function of the enzymes but also the integrity of the proteins and the plasma membrane. A core temperature greater than 107oF (42oC) usually causes structural and enzymatic protein breakdown, causing impairment of cellular respiration and destabilization of the plasma membrane. This ultimately results in brain malfunction, loss of temperature control, muscle breakdown, and multi-system organ failure. A core temperature below 91oF (33oC) usually causes a significant reduction in enzyme activity and metabolic function, resulting in a marked decrease in energy production. This too leads to brain malfunction, loss of temperature control, impaired muscle function, and multi-system organ failure.

Clearly, it is important for the body to control its core temperature. To understand how thermoregulation is accomplished, you must first understand how the laws of nature affect the body with respect to heat and temperature.

The core temperature of the body is affected mainly by two processes: how much heat the body produces from the energy its cells use to function and how much heat the body gains from, or loses to, its surroundings.

The chemical reactions in the body can either release or use up energy. The sum total of all these chemical reactions is called the metabolism. Chemical reactions that release energy while breaking down complicated molecules, like glucose (C6H12O6), into simpler ones, like carbon dioxide (CO2) and water (H2O), are called catabolic reactions. Chemical reactions that use energy to build more complex molecules, like proteins, from simpler ones, like amino acids, are called anabolic reactions. Both catabolic and anabolic reactions take place side by side in the cell.

The cell is only able to harness about one quarter of the energy that is released from the breakdown of complex molecules like carbohydrates, fats, and proteins. It places this energy in special energy-storage molecules (e.g., ATP). The remaining three-quarters of the energy is released into the body as heat. The energy-storage molecules, like ATP, then transfer their energy within the cell so it can be used for anabolic processes and functional activities. These include things like the synthesis of proteins for cell structure and enzymes that promote vital chemical reactions, ion pumps (like the sodium-potassium pump) for cellular integrity and function, muscle contraction, gland and nerve cell function, and gastrointestinal absorption. All of these processes ultimately result in the release of heat. So most of the energy the body uses eventually results in the release of heat.

When the body hasn't eaten for a while and is at total rest, the amount of energy it requires to maintain its cellular integrity and total organ function is called its basal metabolic rate (BMR). Think of the BMR as being like the amount of energy a car uses while idling in traffic. It needs a minimum amount of energy just to keep the engine running before the driver steps on the accelerator. So too, the BMR is a measure of the amount of energy the body uses just to maintain its cellular and organ function while it waits to be put into action. And just like a car, the faster the body moves and the more work it does, the more energy it needs, the more heat it releases, and the higher its internal energy and temperature. So the laws of nature regarding the release of heat when energy is used to do work affects the body's core temperature, not only when it is at complete rest (BMR) but with any level of activity.

Since the body is surrounded by air (or sometimes water) it is always losing heat to, or gaining heat from, its environment. Since most people prefer to stay in surroundings where their core temperature (97o-99oF, 36o-37oC) is higher than the ambient temperature, the body is usually constantly losing heat to its surroundings. In the same way that heat radiates from the sun, much of the heat produced by the body's metabolism is lost through the skin into the surroundings. This accounts for about one-half of the body's heat loss.

Conduction involves the transfer of heat from one object to another by direct contact. If the body comes in contact with something cooler or warmer than itself, as when swimming in a cold river or sitting in a hot sauna, then heat is transferred to or from the body by conduction. Heat loss by conduction usually takes place between the skin and the air surrounding the body and is often aided by convection. Convection is the phenomenon where heated air at the surface of the skin moves away from the body and is replaced by cooler air, which is more effective in taking away heat. This is why a cool breeze against the skin causes more heat loss. Conduction, aided by convection, generally accounts for about one-quarter of the body's heat loss.

Finally, evaporation takes place when water on a surface absorbs heat from it and is released into the air as water vapor. Heat loss by evaporation takes place from the lungs, the mouth, and, most importantly, from perspiration on the surface of the skin. Evaporation accounts for about one-quarter of the total heat lost from the body.

In summary, the laws of nature demand that heat be released when energy is used to do work. The body invariably produces heat from its metabolism, which allows it to live and function normally within its environment. The laws of nature also demand that a warmer object transfer heat energy to a cooler one when they come in contact with each other. Since the body is surrounded by air that is usually cooler than its core temperature, this means that it is usually losing heat to its environment. The body's core temperature is therefore determined by its total production of heat through its metabolism and how much heat it loses to, or gains from, its surroundings.

The molecules that make up the cells and perform the functions of the body work best within a given temperature range. To control its core temperature and stay healthy, the body must take into account these two laws of nature that naturally cause internal heat production and the transfer of heat to, or from, the environment. Next time, we'll look at how the body does it and whether, given this understanding of how life works, the explanations of evolutionary biology are satisfying.

On irreconcilable differences between Darwin and God.

Character and Theology Aside, What About Denis Lamoureux's Science?

David Klinghoffer March 21, 2016 12:43 PM

As Denyse O'Leary points out, it's a good thing Stephen Meyer was thereon stage in Toronto, migraine attack or not. Otherwise, between atheist Lawrence Krauss and theistic evolutionist Denis Lamoureux, there would have been little to debate. Perhaps surprisingly, Lamoureux focused his attack on Meyer, even while proclaiming him his "brother in Christ" and flinging buttery approval at Krauss. Simple humanity, it seems, would have dictated turning your fire away from the stricken man and directing it at your shared opponent.

But I leave it to his fellow Christians to reflect on Dr. Lamoureux's character, and how little daylight there is between his "theistic" position and Krauss's atheism. What, though, about his science?

In defending Darwinism, Lamoureux's signal contribution drew on his expertise in teeth. Evolving them was a snap -- "Teeth emerged. Very easy to do." Paleontologist Günter Bechly, a pretty impressive scientist, begs to differ, on that as well as other points raised by Lamoureux. He blogs about the "Lamoureux delusion." First on the question of dental evolution:

Lamoureux elaborated on the origin of teeth from placoid scales on the jaws of Paleozoic acanthodian "sharks". However, his own diagram showed that these placoid scales already included all crucial morphological features of teeth (upper enamel layer, lower dentine layer, pulp cavity, bony base). That dermal denticle scales on jaws gradually grew larger to form teeth is not a convincing example of macroevolution, but rather just quantitative change through microevolution that is not even denied by Young Earth Creationists. At best, his example is evidence for common descent with modification, which is fully compatible with Intelligent Design and thus cannot be used against it. Finally, the example has no bearing at all on the crucial question, if an unguided Neodarwinian process can explain the pattern of morphological change over time, and therefore it is impotent as an argument against Intelligent Design anyway.

On Lamoureux and the "oldest bilaterian":

To refute Stephen Meyer's claims in his book "Darwin's Doubt", Lamoureux presented the discovery of alleged 585 million year old traces of early bilaterian animals from the Ediacaran period. This evidence is based on a Science publication byPecoits et al. (2012). However, Lamoureux forgot to mention that the dating and identification of these traces is highly disputed (see here and here). Actually, the most recent publication on this issue by Mángano & Buatois (2014) clearly states that "With respect to the Ediacaran, we agree with more conservative estimations that the oldest bilaterian trace fossils are dated to approximately 560 Ma ... The oldest subdivision (Avalon; 575-560 Ma) does not contain undisputed bilaterian trace fossils, and therefore has not been considered ... An earlier appearance of bilaterian trails (585 Ma) has been recently suggested. However, the age of the trace-fossil-bearing strata is highly contended, probably being Late Palaeozoic".

It is especially noteworthy that large unicellular organisms (protists) can produce traces on the sea floor that are remarkably similar to those of bilaterian animals, as Matz et al. (2008) showed in a study titled "Giant deep-sea protist produces bilaterian-like traces".

On nylonase:

Lamoureux mentioned the discovery of Nylon-eating bacteria as empirical proof that evolution can create new complex specified information and new proteins (nylonase enzyme) within only 40 years of time. This is actually an "old hat" in the creation vs evolution debate (see Wikipedia), and it sounds impressive only when one ignores two facts:

1. Dembski (2001) established in his book "No Free Lunch" a value 500 Bits as complexity threshold for Complex Specified Information (CSI), which could not originate by natural processes given the probabilistic resources of our universe. It has not been established that the new information in nylonase matches this threshold and thus represents CSI at all (see here).
2. Newer research by Negoro et al. (2007) has shown that the nylonase enzyme did not evolve by gene duplication and frameshift mutation as originally assumed, but arose from a pre-existing carboxyesterase enzyme, which already had some capacity to degrade nylon oligomers. In other words: Nylonase is NOT new information (also see here)!

On the "God of the gaps" objection, Bechly agrees that "explaining lightning and thunder with Thor's activity" would be "a God of the Gaps argument." But ID is different, obviously:

As Intelligent Design theorist Stephen C. Meyer explained in the same debate and in his books "Signature in the Cell" and "Darwin's Doubt", Intelligent Design makes an inference to the best explanation, not based on an argument from ignorance (what we do NOT know), but based on what we DO know about causes now in operation that could bring about the effect in question.

These are fighting words:

Indeed it is Theistic Evolution which is a redundant and dispensable concept (see this Forbes article), because it is either Neodarwinism in a cheap tuxedo (which it usually is), or it is a cowardly euphemism for Intelligent Design. In either case it is not a genuine alternative to Neodarwinism or Intelligent Design.

"Neo-Darwinism in a cheap tuxedo" -- I like that. Or maybe in rented clerical attire.

The appearance of evenhandedness?

Larry Moran -- Voice of Reason

Ann Gauger March 21, 2016 1:58 PM

We weren't the only ones to notice Krauss's "shenanigans" duringSaturday's debate with Meyer and Lamoureux. Over at his blogSandwalk, biochemist Larry Moran of the University of Toronto (where the event took place) posted a straightforward commentary, without innuendo or name-calling (aside from his usual label of "intelligent design creationists").

The main point that he picked up from Stephen Meyer's presentation was the argument that ID predicted the functionality of most of the genome, rather than its being mostly junk. ID proponent Richard Sternberg made this claim in the 1990s, and it is being confirmed by ongoing research and the ENCODE project. Moran argues that ENCODE doesn't demonstrate what ID proponents claim, and that the genome still is full of junk. But that's an argument that time and more research will answer.

The really interesting thing is what happened in the comments section after the post. He acknowledged that some ID proponents do science in good faith (in contrast to Krauss's repeated assertions during the debate):

I believe that there are ID proponents who are attempting to perform science in good faith.

Let's not quibble over when ID proponents made a prediction and whether it counts as a true predication [sic]. Right now, they are staking the reputation of ID on the claim (= prediction) that most of our genome is functional.

We'll see what happens when they realize the truth.

Then further on, in response to an attack on ID by a poster he says,

Bill says,

But the point is moot. ID is not a scientific endeavor. Never has been. It's a political movement with a social agenda to inject religion into American public schools. Simple as that.

The debate took place in Canada where we allow the teaching of religion in public schools. None of us give a damn about the American Constitution. We're interest[ed] in knowing whether the science is valid or not.

If the Intelligent Design proponents have legitimate complaints about evolution and if they have good scientific arguments in favor of design then those ideas should be taught in Canadian schools in spite of what some judge in Pennsylvania said ten years ago.

Lawrence Krauss tried to show that ID was not science but he did a horrible job. Meyer countered by presenting a lot of science forcing Krauss to deal with the very science that he said ID doesn't do!

Bill, you are being dangerously naive if you think you can simply dismiss the ID movement because it's not science (according to your definition). The general public doesn't care. All they see is serious attacks on evolution that look a lot like science.

Yes, ID is a movement and so are the desires to do something about climate change or GMO's. There are lots of "movements" with social and political agenda[s]. Many of them deal with science in one way [or] another. It's the role of scientists to evaluate the scientific arguments in spite of the agenda. We have to show that the goal of the movement is either compatible or incompatible with the scientific facts.

Yes. That's the level at which the debate should be held.

It doesn't mean that Moran agrees with us. He's just being fair. He even granted Meyer some points in the debate, before expressing his own view:

During the debate, Stephen Meyer emphasized [the] random nature of evolution and its inability -- according to him -- to come up with new protein folds and new information in a reasonable amount of time.

Krauss misunderstood the argument, which was based on the frequency of mutations, and tried to dismiss it by pointing out that evolution is not random -- it's directed and guided by natural selection.

Meyer corrected him by pointing out that the issue was the probability of mutations and not the probability of fixation once the mutation occurred. (This was when he was struggling with a migraine so he didn't do as good a job as he could have.)

Krauss stumbled on for a bit emphasizing natural selection and the fact that evolution is not random.

That was embarrassing. I think Krauss gets most of his information about evolution from Richard Dawkins so he (Krauss) probably doesn't know about random genetic drift or historical contingency or any of the other features of the history of life that make it "random" (in the colloquial sense).

I suspect that Krauss still holds on to the Dawkins view that life has the appearance of design. Truth is, in the big picture, life really doesn't have the appearance of design. Certainly our genome doesn't look designed and my back was not designed for walking upright as it let's me know every morning when I get out of bed.

Designed or not, Professor Larry Moran has distinguished himself as someone even-handed in his assessment of this debate. Thanks for the voice of reason, Dr. Moran.

The salmon vs. Darwin

Another Fine-Tuned Mechanism Gets Salmon Home

Evolution News & Views March

What is carbonic anhydrase and why does it matter? The presence of this enzyme in salmon hearts points to another case of intelligent design in these remarkable fish that were depicted in Illustra Media's film Living Waters. News via the Journal of Experimental Biology explains the challenge salmon face swimming upstream:

Fish plumbing is contrary. As the heart is the last organ that blood passes through before it returns to the gills, and with little direct blood supply to the ceaselessly contracting muscle, there are occasions when it could be on the verge of failure. 'We know this can happen under certain conditions like exhaustive exercise in combination with hypoxia or elevated water temperature', says Sarah Alderman from the University of Guelph, Canada. Added to the challenge of keeping the heart supplied with oxygen, Alderman explains that the haemoglobin that carries oxygen in fish blood is finely tuned to blood pH: the more acidic the red blood cells, the less able haemoglobin is to carry oxygen, which could prevent the red blood cells of exercising fish from picking up oxygen at the gills if they didn't have an effective pump to remove acid from the cells and restore the pH balance. [Emphasis added.]

Here we see a double challenge the salmon faces. It has to avoid excess acid so that the hemoglobin can carry oxygen, and it has to get the oxygen all the way from the gills through its entire body to the heart. Here's where carbonic anhydrase comes to the rescue:

But Alderman and her colleagues, Till Harter, Tony Farrell and Colin Brauner from the University of British Columbia, Canada, also knew that fish can take advantage of a sudden drop in red blood cell pH to release oxygen rapidly at tissues -- such as red muscle and the retina -- when required urgently. An enzyme called carbonic anhydrase -- which combines CO2 and water to produce bicarbonate and acidic protons, and vice versa -- lies at the heart of this mechanism. Normally there is no carbonic anhydrase in blood plasma; however, the enzyme has been found in salmon red muscle capillaries, where it facilitates the reaction of protons -- that have been extruded from the red blood cell -- with bicarbonate to produce CO2, which then diffuses back into the red blood cell. The CO2 is then converted back into bicarbonate and protons in the blood cell, causing the pH to plummet and release a burst of O2 from the haemoglobin. Could salmon take advantage of this mechanism to boost oxygen supplies to the heart when the animals are working full out? Possibly, but only if carbonic anhydrase was accessible to blood passing through the heart.What is carbonic anhydrase and why does it matter? The presence of this enzyme in salmon hearts points to another case of intelligent design in these remarkable fish that were depicted in Illustra Media's film Living Waters. News via the Journal of Experimental Biology explains the challenge salmon face swimming upstream:

Fish plumbing is contrary. As the heart is the last organ that blood passes through before it returns to the gills, and with little direct blood supply to the ceaselessly contracting muscle, there are occasions when it could be on the verge of failure. 'We know this can happen under certain conditions like exhaustive exercise in combination with hypoxia or elevated water temperature', says Sarah Alderman from the University of Guelph, Canada. Added to the challenge of keeping the heart supplied with oxygen, Alderman explains that the haemoglobin that carries oxygen in fish blood is finely tuned to blood pH: the more acidic the red blood cells, the less able haemoglobin is to carry oxygen, which could prevent the red blood cells of exercising fish from picking up oxygen at the gills if they didn't have an effective pump to remove acid from the cells and restore the pH balance. [Emphasis added.]

Here we see a double challenge the salmon faces. It has to avoid excess acid so that the hemoglobin can carry oxygen, and it has to get the oxygen all the way from the gills through its entire body to the heart. Here's where carbonic anhydrase comes to the rescue:

But Alderman and her colleagues, Till Harter, Tony Farrell and Colin Brauner from the University of British Columbia, Canada, also knew that fish can take advantage of a sudden drop in red blood cell pH to release oxygen rapidly at tissues -- such as red muscle and the retina -- when required urgently. An enzyme called carbonic anhydrase -- which combines CO2 and water to produce bicarbonate and acidic protons, and vice versa -- lies at the heart of this mechanism. Normally there is no carbonic anhydrase in blood plasma; however, the enzyme has been found in salmon red muscle capillaries, where it facilitates the reaction of protons -- that have been extruded from the red blood cell -- with bicarbonate to produce CO2, which then diffuses back into the red blood cell. The CO2 is then converted back into bicarbonate and protons in the blood cell, causing the pH to plummet and release a burst of O2 from the haemoglobin. Could salmon take advantage of this mechanism to boost oxygen supplies to the heart when the animals are working full out? Possibly, but only if carbonic anhydrase was accessible to blood passing through the heart.

Well, what do you know! That's what Alderman's team found: the enzyme is present on the surface of the heart chambers. Using the heart itself as their "reaction vessel," they were able to see the pH plummet as the enzymes went into gear. 

Working closely together, the duo painstakingly developed a technique where they could measure the pH in the beating heart with pH probes that were thinner than a human hair. Eventually, the duo's persistence paid off and the pH in the heart plummeted as they fed CO2 into the pulsating chambers. And when they added a carbonic anhydrase inhibitor (produced by Claudia Supuran) to the fluid, the pH fall slowed dramatically. Carbonic anhydrase was responsible for the drop in pH.

The Protein Data Bank 101 website shows pictures of this enzyme and describes its mode of action. 

An enzyme present in red blood cells, carbonic anhydrase, aids in the conversion of carbon dioxide to carbonic acid and bicarbonate ions. When red blood cells reach the lungs, the same enzyme helps to convert the bicarbonate ions back to carbon dioxide, which we breathe out. Although these reactions can occur even without the enzyme, carbonic anhydrase can increase the rate of these conversions up to a million fold.

There's an evolutionary conundrum about this enzyme: functional equivalence without sequence similarity:

This ancient enzyme has three distinct classes (called alpha, beta and gamma carbonic anhydrase). Members of these different classes share very little sequence or structural similarity, yet they all perform the same function and require a zinc ion at the active site. Carbonic anhydrase from mammals belong to the alpha class, the plant enzymes belong to the beta class, while the enzyme from methane-producing bacteria that grow in hot springs forms the gamma class. Thus it is apparent that these enzyme classes have evolved independently to create a similar enzyme active site.

Further complicating the picture, there are different forms of the enzymes depending on the tissue or cellular compartment they are located in. These allow fine tuning of the enzyme's activity: "Thus isozymes found in some muscle fibers have low enzyme activity compared to that secreted by salivary glands," in the case of mammals.Carbonic anhydrase (CA) was the first enzyme found to contain zinc, abiochemistry textbook says; now, hundreds are known. Zinc and other metals are often essential for function in metalloenzymes. The PDB-101 article explains,

Zinc is the key to this enzyme reaction. The water bound to the zinc ion is actually broken down to a proton and hydroxyl ion. Since zinc is a positively charged ion, it stabilizes the negatively charged hydroxyl ion so that it is ready to attack the carbon dioxide.

It's not surprising that this enzyme is present in the salmon, since it exists in all three domains of life. What's amazing is that the salmon's heart is studded with these enzymes that are "at the ready" when the large fish is fighting with all its might to leap above cascades and waterfalls, facing daunting challenges without the benefit of food. (Living Waters says, "The sockeye are so focused on their objective that after leaving the ocean, they do not eat again.")

If the pH dropped too early as the blood travels through the salmon's body, it would be less able to carry its precious oxygen cargo. But right when it is needed during that Olympic high jump over a waterfall or away from a hungry bear, the fish uses its CA enzymes in its heart to drop the pH and release the oxygen it needs. The spent blood then travels to the gills to load up with more oxygen. In the original paper in the Journal of Experimental Biology, the authors summarize what they found:

Combined, these results support our hypothesis of thepresence of an enhanced oxygen delivery system in the lumen of a salmonid heart, which could help support oxygen delivery when the oxygen content of venous blood becomes greatly reduced, such as after burst exercise and duringenvironmental hypoxia.

How many independent systems do we see at work in the remarkable migration of the salmon? The fish has a built-in map of its destination. It has the ability to memorize waypoints by smell. It can navigate by the earth's magnetic field. It has a sixth sense, the lateral line. It can distinguish odors by parts per trillion. Each of its body systems contain thousands of molecular machines like carbonic anhydrase that are located just where they need to be, doing what they need to do to support the whole organism.

If any one of these systems is a testament to intelligent design, how much more the composite? The only fish story here is the notion that all this came together by unguided natural processes -- sheer dumb luck.

On taking on big science's gatekeepers.

Is There a Scientific Establishment?

David Klinghoffer March 15, 2016 4:30 PM

The term "Establishment" is controversial. It invariably implies a critical stance, suggesting a system, a power structure, in need of a shakeup or worse. It's not a description anyone would welcome having applied to himself. Nobody wants to be seen as defending entrenched privilege. Depending on the context, some deny the existence of such an entity to begin with.

What about in the world of science, and specifically biology? Is it fair to speak of an Establishment there, primed to be updated by "rogue" outside forces? It seems so. Or perhaps "rigidly calcified mindset" is the better phrase. Today in the New York Times, Amy Harmon reports on hints of decalcification, a modest but significant move in science research publishing toward "preprints." That is, publishing directly online without first submitting your work to the official gatekeepers: peer-reviewed journals.

Don't worry -- it's not as if this research then goes unreviewed or uncriticized. Instead the review process happens immediately and organically. Those interested enough to read your work can tell anyone and everyone what they think. Minus the online aspect, it's the way Charles Darwin published his ideas:

On Feb. 29, Carol Greider of Johns Hopkins University became the third Nobel Prize laureate biologist in a month to do something long considered taboo among biomedical researchers: She posted a report of her recent discoveries to a publicly accessible website, bioRxiv, before submitting it to a scholarly journal to review for "official'' publication.

It was a small act of information age defiance, and perhaps also a bit of a throwback, somewhat analogous to Stephen King's 2000 self-publishing an e-book or Radiohead's 2007 release of a download-only record without a label. To commemorate it, she tweeted the website's confirmation under the hashtag #ASAPbio, a newly coined rallying cry of a cadre of biologists who say they want to speed science by making a key change in the way it is published.

Such postings are known as "preprints'' to signify their early-stage status, and the 2,048 deposited on three-year-old bioRxiv over the last year represent a barely detectable fraction of the million or so research papers published annually in traditional biomedical journals.

But after several dozen biologists vowed to rally around preprints at an "ASAPbio'' meeting last month, the site has had a small surge, and not just from scientists whose august stature protects them from risk. On Twitter, preprint insurgents are celebrating one another's postings and jockeying for revolutionary credibility.

One diagnostic of a genuine Establishment would be that its members maintain that the system, for everyone's good, couldn't be much different from how it is. In this case, there's nothing necessary about the traditional manner in which biologists publish their work. Physics, as Harmon notes, has had preprints for decades, and the field is healthier for it:

Unlike physicists, for whom preprints became a default method of communicating discoveries in the 1990s, biomedical researchers typically wait more than six monthsto disseminate their work while they submit it -- on an exclusive basis -- to the most prestigious journal they think might accept it for publication. If, as is often the case, it is rejected, they try another journal. As a result, it can sometimes take years to publish a paper, which is then typically available for a time only to colleagues at major academic institutions whose libraries pay for subscriptions. And because science is in many ways a relay, with one scientist building on the published work of another, the communication delays almost certainly slow scientific progress.

True, it's not that preprints are intended to replace traditional publishing. Those interviewed for the article are careful to say they aren't rejecting the big journals. You wouldn't want to offend the Establishment!

Many have taken pains to reiterate their wish not to disrupt the journal system, only to enhance it. With enough scientists pushing to legitimize preprints, they hope journals will allow the systems to coexist.

"It's not beer or tacos," as James Fraser, an assistant professor at the University of California, San Francisco put itat last month's conference, "it's beer AND tacos."

Still, this sounds exactly like a revolt, if mild, seeking to slip out from under some of the bonds of a burdensome hierarchy -- one that up till now has controlled the flow of ideas and artificially constrained debate through access and credentialing, with an eye to maintaining its own power and prestige. What will it mean for insurgent scientific ideas like intelligent design and the critique of Darwinism? Time will tell, but the development seems like a hopeful one.

Yet more on pre evolutionary design.

Collective Motion: A New Level of Design Found in Proteins

Evolution News & Views March 15, 2016 3:06 AM

A "previously unidentified mechanism for modulating protein affinity" has come to light. A team of scientists at the Max Planck Institute for Biochemical Chemistry, publishing in the Proceedings of the National Academy of Sciences, has identified new functional roles for collective motions within protein molecules. These motions, referred to as allostery, allow one end of the protein to affect a distant part through what is termed "allosteric communication."

Intermolecular interactions are one of the key mechanismsby which proteins mediate their biological functions. For many proteins, these interactions are enhanced or suppressed by allosteric networks that couple distant regions together. The mechanisms by which these networks function are just starting to be understood, and many of the important details have yet to be uncovered. In particular, the role of intrinsic protein motion and kinetics remains particularly poorly characterized. [Emphasis added.]

This is cutting-edge research. The team studied a common protein named ubiquitin which, as the name implies, is ubiquitous in the cell. It serves as a molecular "tag" on other molecules slated for degradation by the proteasome. As such, it needs to form connections with the proteasome and with a variety of other proteins. What they found is that distant parts of the molecule could affect binding affinity of other parts through motions transmitted throughout the entire molecule.

To determine how this collective motion influences bindingand other functions of ubiquitin (e.g., presence of different covalent linkages), we performed an extensive structural bioinformatics survey of known ubiquitin crystal structures. Because the peptide bond conformation was the most recognizable feature of the collective mode, we used its conformation as a "marker" for structural discrimination. Themost significant relationship we found was the universal association between the NH-in state and binding to the ubiquitin-specific protease (USP) family of deubiquitinases (Fig. S11). This association has been previously noted and issurprising because the peptide bond is at least 6.8 Å from any USP (Fig. 3A).

By comparing mutants with wild-type forms, the team found several kinds of motion that involve twisting, rocking and stretching. Mutations on a peptide bond between two specific amino acid residues, in particular, had a surprising effect, reducing binding affinity by a factor of 10 (or abolishing it altogether). This suggests low tolerance for mutation.

They found "strong allosteric coupling between opposite sides of the protein" in some cases. "Given the relative subtlety of the expansion and contraction" of allosteric interactions, they found it "surprising" again that two different states could produce large effects. It implies that ubiquitin and its ligand "appear to adapt their conformations mutually to establish a complementary binding interaction" for best fit at the appropriate times.

One mutant showed a two-fold weaker affinity for its particular USP. "Although this change may seem like a moderate effect," they note, "it isactually surprisingly large and highly significant when one considers that it is allosterically triggered by the simple rotation of a solvent-exposed peptide bond on a distal side of the protein."

These motions are so rapid -- on the order of microseconds -- they were not really considered significant until recently. Other motions they mention, like "pincer time" and "tumbling time," occur on different time scales, the former being quicker, the latter being much slower. This may suggest a kind of timing code for different functions.

Their conclusions reveal a significant new area of study: switch-controlled "allosteric communication" in protein molecules:

This study revealed an allosteric switch affecting protein-protein binding through collective protein motion at the microsecond time scale.... Whereas most known microsecond to millisecond time-scale motions involve excursions to excited, lowly populated states, this motion occurs between two ground state ensembles with nearly equal populations (NH-in and NHout). Strikingly, the peptide bond conformation is allosterically coupled through a diverse set of interactions that triggers contraction/ expansion of the entire domain. This type of global domain motion reveals apreviously unidentified mechanism for modulating protein affinity. The presence of this allosteric network suggeststhere may be heretofore undiscovered ways in which macromolecular assemblies and covalent linkages regulate ubiquitin binding. More broadly, this study demonstrates how relatively modest changes in hydrogen bond networks and the protein backbone can bring about distant changes in protein conformation and binding affinity.

We encounter, therefore, a whole new level of specificity in protein architecture. It's not the old picture of an active site surrounded by haphazard amino acid residues. Any change could affect the allosteric communication of the whole protein. Clearly, mutants were less able to take advantage of the benefits of collective motion.

How did an unguided process arrive at a molecular machine that not only grips its substrate and catalyzes a reaction efficiently, but moves with intrinsic twists and stretches to improve the grip? The design specs for proteins just shot up a notch, and along with them, the challenges to Darwinian evolution.

On Charles Darwin and Rube Goldberg

My Debate with Michael Ruse -- Evolution as a Rube Goldberg Machine

Cornelius Hunter March 17, 2016 3:32 AM 

Editor's note: Evolution News is delighted to welcome back Dr. Hunter as a contributor. He is a Fellow with the Center for Science & Culture, Adjunct Professor at Biola University, and author of the award-winning Darwin's God: Evolution and the Problem of Evil. He blogs at Darwin's God

It was great to see Professor Michael Ruse again last week in Northern California for our debate on the question, "Is Evolution Compelling?" He was in good spirits as usual, and his jokes were much better than mine. But I had one big advantage over my erudite opponent: I was not defending the age-old idea that the world of life arose by chance. The main problem, as I explained at the outset, is that the scientific evidence contradicts unguided evolution. That is a very simple point, but it opens new worlds of thought.

I used my time to discuss a range of scientific evidence from biology. On that evidence, unguided evolution simply makes no sense. But I almost hesitate to show you my list simply because there is nothing special about it. One of the difficulties in explaining the problems with evolution to an audience is the plethora of examples from which to choose. I had a long list of fascinating biological designs that refute evolutionary thought. I like every one of them, because they all add a different angle on why evolution fails. But there are far too many to fit into an evening's presentation. I was changing my mind right up to the last day, but as difficult as it is, one must pare back the list to fit the time constraint.

I began with one of my favorites, micro RNA. I then discussed the failure of evolution's nested hierarchy. Later I had fun with echolocation and the DNA code, and I finished with directed adaptation. The obvious and unavoidable truth is that evolution is believed to be a fact not because of the science, but despite the science.

I also punctuated my scientific examples with some philosophy of science concerns. One of them is the problem of parsimony. I explained Occam's Razor, and how a sure sign of a failing theory is if it becomes overly complicated. The appeal of heliocentrism over geocentrism was not that of an improvement in accuracy, but in simplicity. Like heliocentrism, Copernicus' geocentrism had epicycles. So why make the move? Because Copernicus was able to use fewer epicycles. That is how important simplicity is in science.

Theory complexity is the enemy in science, and it would require volumes to explain all the details in today's theory of evolution. The reason why evolution is so complicated is that with each scientific failure, the theory is adjusted yet again. Today it resembles one of Rube Goldberg's wonderful machines.

For this theory, there is no ray of hope. I think I left the audience convinced that evolution is an utterly failed attempt. That's not because of any rhetorical skills on my part, but simply because I took the side of science. This isn't at all complicated. What is complicated is the question of why people believe in evolution to begin with. But that's another story.