Exaptation:Darwinian code for spin?

Darwinism's tree of life examined

It's Design all the way down VIII

It's design all the way down VII

UT Southwestern physiologists uncover a new code at the heart of biology
UT SOUTHWESTERN MEDICAL CENTER

DALLAS - Sept. 23, 2015 - UT Southwestern physiologists trying to understand the genetic code have found a previously unknown code that helps explain which protein should be created to form a particular type of cell.

The human body is made up of tens of trillions of cells. Each cell contains thousands of proteins, which determine how the cell should form and what functions it needs to perform. Proteins, in turn, are made up of hundreds of amino acids. The blueprint for each protein is specified by genetic codons, which are triplets of nucleotides that can make 20 different types of amino acids. The way in which amino acids are linked together then determines which proteins are eventually produced, and in turn, what functions the cell will have.

What researchers found was that not only does the sequence of the amino acids matter, but so does the speed of the process in which the amino acids are put together into a functional protein.

"Our results uncovered a new 'code' within the genetic code. We feel this is quite important, as the finding uncovers an important regulatory process that impacts all biology," said Dr. Yi Liu, Professor of Physiology.

It was long known that almost every amino acid can be encoded by multiple synonymous codons and that every organism, from humans to fungi, has a preference for certain codons. The researchers found that more frequently used codons ? the "preferred codons" ? speed up the process of producing an amino acid chain, while less frequently produced codons slow the process. The use of either preferred or non-preferred codons is like having speed signs on the protein production highway: some segments need to be made fast and others slow.

 "The genetic code of nucleic acids is central to life, as it specifies the amino acid sequences of proteins," said Dr. Liu, the Louise W. Kahn Scholar in Biomedical Research. "By influencing the speed with which a protein is assembled from amino acid building blocks, the use of "fast" and "slow" codons can affect protein folding, which is the process that allows a protein to form the right shape to perform a specific function. This speed control mechanism makes sure that proteins are assembled and folded properly in different cells. Therefore, the genetic code not only specifies the sequence of amino acids but also the shape of the protein."

The researchers found that proteins with identical amino acid sequences can have different functions if they are assembled at different speeds. This can have important implications for identifying human disease-causing mutations because this study indicates that a mutation does not have to change amino acid identity to cause a disease. In fact, most mutations in human DNA do not result in amino acid change.

"Therefore, our study indicates that the new "code" ? the speed limit of assembly ? within the genetic code can dictate the ultimate function of a given protein," said Dr. Liu.

The findings appear as the cover story of the journal Molecular Cell, one of the top molecular biology, biophysics, and biochemistry journals.

The latest findings extend prior research published by Dr. Liu and colleagues in Nature in 2013 that broke new ground by demonstrating that synonymous codons of a circadian clock protein are not the same in making functional proteins, despite the fact that they encode the same amino acids.  Genes can adapt to different environmental changes by choosing the most optimal codon, which is counterintuitive to natural selection.

Dr. Liu and his team are able to study these systems using a type of bread mold fungus called Neurospora crassa. The use of the mold allows for easy manipulation of its genes and codons in the laboratory that are more difficult to do in animals. Dr. Liu's lab is also trying to unravel the secrets of chronobiology and the molecular mechanisms that underlie an organism's daily biological clock, called the circadian clock. Biological clocks have been described in almost all organisms ranging in complexity from single cell organisms to mammals, and to function in the control of daily rhythms such as sleep-wake and activity cycles, body temperature cycles, endocrine functions, and gene expression.

###

Other UT Southwestern researchers involved include postdoctoral researchers Chien-Hung Yu, Yunkun Dang, Zhipeng Zhou, first co-authors, and graduate student researcher Fangzhou Zhao. They collaborated with the lab of Dr. Matthew Sachs, Professor of Biology at Texas A&M University.

The work is supported by grants from the National Institutes of Health and the Welch Foundation.

About UT Southwestern Medical Center


UT Southwestern, one of the premier academic medical centers in the nation, integrates pioneering biomedical research with exceptional clinical care and education. The institution's faculty includes many distinguished members, including six who have been awarded Nobel Prizes since 1985. The faculty of more than 2,700 is responsible for groundbreaking medical advances and is committed to translating science-driven research quickly to new clinical treatments. UT Southwestern physicians provide medical care in 40 specialties to about 92,000 hospitalized patients and oversee approximately 2.1 million outpatient visits a year.

On the Hubris of Scientism?

Human Cloning Advance: Ban Now or Cry Later
Wesley J. Smith November 1, 2015 4:45 AM 


Human cloning used to make big headlines. But "the scientists" got smart, and just started using the scientific term for cloning -- somatic cell nuclear transfer -- as a way of hiding in plain sight.

Thus, when the first human embryos were successfully manufactured via SCNT, the were few headlines and most people yawned -- if they heard about it at all. Of course, I reacted strongly.

Now, the South Koreans have improved the efficiency of cloning, and again, the scientists are keeping mostly mum in the popular media so as to not alert us rubes that Brave New World is approaching. From the KBS World News Radio story:

A group of medical experts has succeeded at improving the efficiency of human somatic cell nuclear transfer (SCNT) by three times.

A research team at Cha Medical Group said Friday that it found ways to enhance the efficiency of SCNT by discovering a correlation between the quality of female eggs and the success rate of SCNT embryo development.,,

The team said it has made five pilot medicine products using the new findings and plans to seek the government's approval for a large-sized clinical test by the end of this year.


Now, add in the jet-speed advance in genetic engineering known as CRSPR. We are coming closer to the day of manufacturing human beings via cloning, genetically engineered for desired traits.

On non-verbal communication

On those still in chains

On pitching a design inference to a hostile audience.

For SETI Researchers, Here Is a Guide for Handling Fallacious Objections
Casey Luskin October 30, 2015 11:08 AM


A recent story making the rounds, "Space anomaly gets extraterrestrial intelligence experts' attention," claims that the Search for Extra Terrestrial Intelligence (SETI) project has found "a strange star" that "could mean alien life." As David Klinghoffer noted in an earlier post, the raw data entails odd fluctuations in the intensity of light coming from a star. CNN reports:

The Search for Extraterrestrial Intelligence Institute has its eyes -- and soon possibly one of the United States' premier telescopes -- focused on an anomaly that some astronomers can't quite explain.
[...]

"What was unusual about that was the depth of the light dips, up to 20% decrease in light, and the timescales (of light variation) -- a week to a couple of months."

So what's the explanation? Could it be from a swarm of comets? Some sort of intergalactic phenomenon that Earthbound scientists haven't discovered? Or an effect of planet-sized structures built by some sort of alien civilization?

Comparisons between SETI's methodology and the theory of intelligent design (ID) have been made since ID's earliest days. Both SETI and ID seek to detect the signs of intelligence in the world around us. SETI focuses on looking for evidence of extraterrestrial civilizations far away in the universe. ID looks for signs of intelligent agency in the origin of living organisms and the universe itself.
SETI and ID share something else: they both try to be very conservative and cautious, invoking intelligent causation only when it is clearly warranted by the evidence. Here's how one SETI scientist handles this:

Jason Wright, a Penn State astronomy professor, saw Boyajian's data and can't quite explain it. But in a post Thursday to his website, he cautioned against jumping to conclusions -- as some apparently have -- that intelligent beings far away are behind this oddity.
"My philosophy of SETI," Wright wrote, referring to the search for extraterrestrial intelligence, "is that you should reserve your alien hypothesis as a last resort." He also cited "Cochran's Commandment to planet hunters ... Thou shalt not embarrass thyself and they colleagues by claiming false planets.

That's a good philosophy, and ID takes a similar approach. ID proponents only conclude in favor of design when it's clear that known material causes cannot explain the observed phenomena and when the data is best explained by intelligence.
So far, SETI hasn't found a case that is clearly explained by some extraterrestrial civilization. This recent find of a star with flickering light is nowhere near enough evidence to conclude that aliens are the best explanation -- in fact Tech Insider reports that the data could be explained by a "lopsided star" wherein its irregular shape "creates patches of darker and lighter regions within these kinds of stars, so the light curves that make it back to Earth won't look completely uniform."

But suppose SETI were to one day discover strong evidence of some extraterrestrial civilization -- enough to warrant a design inference. They might expect to face some of the same fallacious objections that ID faces. They might like some friendly tips on handling them. Here's a little guide for SETI folks if that day ever comes:

Who Made the Aliens?

As soon as you claim you've detected aliens, skeptics will say "How can you claim there are aliens when you haven't explained who made the aliens?"

The answer to this is very simple: We don't need to be able to explain the origin of the aliens to recognize evidence of them. For example, let's say that Chewbacca, Spock, and ET were standing right in front of you. Would you say to them, "Look, I'm not going to believe any of you actually exist until you tell me where you came from"?

(I should add that it could be very fair to ask where the aliens came from because in an ultimate sense they require an explanation -- but it's not a fair question to ask if your only purpose is to question whether those aliens exist.)

Where's Your "Alien-O'Meter"?

Some critics might reply "You need some kind of an 'alien-o-meter' to show that these aliens really exist before you can claim that you've detected evidence of an extraterrestrial civilization. After all, how do we know that aliens were behind the evidence you've discovered if we don't know the aliens exist?"

The answer to this one is a bit more complicated. But a little explanation shows this objection to be nonsensical and based upon a complete misunderstanding of how we make scientific inferences.

Some ID critics mistakenly think you have to directly witness the designer in action with your own eyes in order to detect design. Sometimes misguided creationists make an analogous critique of evolution, saying that you can never infer evolution if no one was around to see it. Both groups misunderstand the nature of historical sciences.

Historical sciences operate under the principle of uniformitarianism, which assumes that the way the natural world works today is similar to how it worked in the past. In other words, "the present is the key to the past." If we see certain causes at work in the world as we know it and we learn to recognize their known effects, then when we find those same effects in the historical record, we can infer that the same causes were at work. As I have explained before:

Recently an atheist student emailed me to ask how it's reasonable to claim that an "unobserved designer" is responsible for complex features of nature, like high CSI (complex specified information) and irreducibly complex structures. In reply, I explained that first we must ask the question "What does it mean to 'observe' or 'detect' something?" Here's a start:
Our eyes can help us observe objects in nature by seeing light reflected from those objects.
Our ears can help us detect objects in nature by receiving sound emitted from them.
Our nose can help us detect objects in nature by receiving emitted chemicals which we register as a "smell."
Our skin can help us detect objects in nature by receiving signals that tell us about shape, texture, and even temperature.
So when we see a campfire, how do we "observe" it? Our sense organs receive patterns of light, sound, smell, and heat, which our brains recognize and match to fires we've seen in the past. Our brain thinks, in effect, "Okay, as in the past, when the eyes receive a particular pattern of yellow and red light, the ears hear a crackling sound, the nose receives the smell of smoke, and the skin feels heat, that's a campfire." So we recognize and observe something by receiving a pattern of information through our sense organs and then matching it to a pattern we've seen in the past.
Our senses also make another set of observations about a campfire: the morning after a campfire, we observe that there's a bunch of blackened and charred wood, ash and soot, and smoke rising from within a circle of blackened stones. We smell the smoke and ash, and it might be slightly warm from remaining embers from the night before.

So let's say now that we're taking a morning stroll and come upon a circle of blackened stones, charred wood, ash, and soot. There's a little smoke rising from the center, and it's slightly warm. We didn't see a fire directly with our eyes. But our senses tell us that there is evidence that a fire was there. In this case, the most reasonable inference to make is that there was a campfire, even though we can't directly observe it.

Thus, just because something is "unobservable" by our eyes at this exact moment, doesn't mean we can't find compelling evidence that it exists, or that it was present. We must not toss out the word "unobservable" as if it somehow blocks the design inference. We regularly make inferences to unobserved objects and events (like a campfire) by using our senses to detect evidence that reliably indicates that a particular object or event was present (like finding a circle of blackened stones, charred wood, soot, and smoke).

We can use exactly the same method of reasoning to detect design at the heart of biology. In all of our experience, high CSI and irreducible complexity ONLY come from intelligent agents. Thus, based upon our experience of the cause-and-effect structure of the world we observe around us, we are justified in inferring that a mind was at work. ...[W]hen we find high CSI entities like language-based digital codes or irreducibly complex molecular machines, we are justified in inferring that an intelligent agent was at work. Why? Because, in our experience, these things always trace back to a mind. We might not directly see that mind, but we can infer that a mind was present to create the known observed effects.

This is the positive argument for intelligent design, and it is just like inferring that a campfire was present based on remaining physical evidence. One need not directly see the fire, or know who tended it, or why he or she or they did so, to draw a reasonable inference that a fire was present.

So to the critic who asks "Where's the alien-o-meter," SETI's response might go like this: We have an alien-o-meter, but it's not what you think it is. We don't need to Skype with ET to potentially know he's there. If we find in space the kind of evidence that, in our experience, only comes from intelligent beings, then we can infer that ETs exist.
Aliens of the Gaps

A last objection the SETI researcher will face goes like this: You're never allowed to conclude that aliens are responsible for anything because someday we might find a fully material, physical explanation other than ETs for the evidence you claim demonstrates an extraterrestrial civilization. As materialist explanations advance, your "alien" theory will just retreat into the gaps of our knowledge.

Now this objection might have a little more traction than the others. Nobody wants to invoke intelligent aliens only to have them later explained away by some unintelligent material cause. As SETI proponent Jason Wright said, it should be a "last resort." And indeed, in this case that's a good philosophy since the "lopsided star" theory seems to explain the observed data quite well.

But does the fact that some cases aren't best explained by intelligence that mean you can never invoke intelligent causes? Of course not! It just means one needs to be careful and cautious about invoking intelligent design.

What the gaps fallacy really says is, "While your explanation may seem correct today, new evidence may be revealed tomorrow to provide a material explanation and show that intelligent causes aren't the best explanation." That's a fair point, but the reality is that every type of explanation -- material or intelligent -- is subject to the same problem.

Indeed, any explanation could be subject to the "gaps" charge. This is a problem that every kind of explanation in science potentially faces. That's why scientific explanations are always held tentatively and never asserted with complete finality or absolute certainty. Scientific explanations are always subject to revision if newly uncovered data shows they are wrong. This is true whether we're dealing with Darwinian evolution or intelligent design, aliens or standard stellar dynamics.

So at the end of the day, what the "gaps" objection really ought to say is "Today X is the best explanation, but let's hold it tentatively." Nothing wrong with that -- that's how all science ought to work.

What the gaps charge often indicates is that some kind of explanation is assumed to be the default, privileged answer, and that we can only deviate from that default answer under extraordinary circumstances. In the case of intelligent design or SETI, it's material causes that are being privileged. Many who make the "gaps" charge want material causes to have an absolute privilege that precludes making a design inference in all circumstances. But given that we can detect intelligent causation, why should material causes enjoy such an absolute privilege?

Unless we are to privilege material causes on principle and deny our ability to ever infer intelligent causes, the gaps objection fails. But since we know what intelligent causes can do, and because we can reliably detect the prior action of intelligent agents, we can't say that in all cases it's wrong to detect design. We can detect design, and so long as we hold the conclusion of design tentatively, the gaps objection isn't fatal.

Don't Miss the Irony

Now I personally don't object to SETI researchers doing their thing, but I'm highly skeptical that they're ever going to find an extraterrestrial civilization. But my reason for writing this isn't to rant against SETI. It's just to point out the irony. People make a lot of fallacious objections against intelligent causation. We in the ID movement get this all the time. It sounds like, "Who designed the designer?" or "Where's your theo-meter?" or "This is just God of the gaps." If SETI claimed to find some extraterrestrial intelligent civilization, most likely the analagous objections would never come up, at least not with much force.

Why is that? Most materialists would see extraterrestrial life as proof that a naturalistic origin of life is possible, and that perhaps life is therefore common in our universe. After all, what drives many materialists to look for evidence of extraterrestrial life is a misguided assumption that if aliens exist, it would somehow validates their worldview.


But they are mistaken about what SETI means. If we found evidence of an alien civilization, that wouldn't be evidence that life evolves naturally. It would just be evidence for an extraterrestrial civilization. That's it. How it arose would be an entirely different question. And all indications we have so far show that life could not arise naturally, whether on earth or anywhere else. For all we know, finding evidence of extraterrestrial life could end up being yet another piece of evidence pointing to intelligent design.

Yet more realism about the Cambrian explosion from Darwinists

The Economist Admits Cambrian Explosion Is a "Mystery"

Casey Luskin October 29, 2015 11:12 AM 

A recent video from The Economist takes on the evolution of animals in the Cambrian explosion, conceding something that many Darwin advocates refuse to fully acknowledge: that "biology's big bang" is a "mystery." Find it here. Among other important admissions, it says:

• Narrator: "The cause of this sudden burst of life, which geologists call the Cambrian explosion, remains a mystery."


• Andrew Parker, Professor of Life Sciences at the Natural History Museum of London: "The Cambrian explosion was really biology's big bang. Things went from moving really slowly on the sea floor without any predation to suddenly all the different type of ecologies that we see today. Life literally exploded."


• Simon Conway Morris, Professor of Evolutionary Paleobiology at the University of Cambridge: "What triggered the Cambrian explosion? We don't really know. There are many different possibilities, different hypotheses. And we've got to remember that cause and effect are often difficult to disentangle."

The video then discusses the period prior to the Cambrian called the Ediacaran. But Conway Morris admits that the organisms that lived in this period are not clearly related to the Cambrian animals: "Before the Cambrian we go into what's called the Ediacaran times. And this is an extraordinary interval where we have the sea floor populated by basically weird creatures. And quite frankly we're not quite sure if they're animals or something else entirely." He explains that these strange organisms "seem to more or less disappear as the Cambrian explosion kicks off."

This is a nice statement of the problem. The video offers some of the standard weak and inadequate explanations we've seen in the past for how the Cambrian explosion occurred. For example, it cites rising oxygen levels as a possible trigger for building larger animals. We have discussed the problems with that theory here, here, here, and here. The video admits, "Evidence to support this theory of higher oxygen levels is scarce" since the ice ages that might have led to larger algae populations which raised oxygen levels "ended 90 million years before the Cambrian." Indeed, Simon Conway Morris casts doubt on this theory by acknowledging that "oxygen was increasing already, much, much before" the Cambrian period.

The video also notes the hypothesis "that minerals became increasingly available in the oceans due to post-glacial erosion." These minerals might have spurred the evolution of shells, but the video notes a problem with this hypothesis:

But Cambrian shells were made from a range of materials. This suggests they [were] the result of parallel evolution in different animals lines, not a single innovation. That means something encouraged them to develop on more than one occasion. And shells are costly to make. It's unlikely mere abundance of minerals would have been enough.

We've discussed problems with this hypothesis here and here.

So how did the Cambrian animals evolve so rapidly? The key to understanding the typical evolutionary position on this question is to appreciate that most evolutionists really aren't trying to answer that question -- at least not in any meaningful way.

ID proponents look at the question and think, "Well, to build all these animals you're going to need an extraordinary amount of new genetic and epigenetic information, and it's got to arise very quickly. We must identify some mechanism -- evolutionary or otherwise -- that can accomplish this feat."

Evolutionary scientists look at the same question and usually assume that all the information could arise whenever it's needed. They're just looking for some kind of trigger to create a selectable need for complex biological systems, and voila, everything happens. They assume that the information needed to build the Cambrian animals already existed prior to the Cambrian explosion. For example, consider what Shuhai Xiao, a professor of geobiology at Virginia Tech university, says in the video:

The Cambrian explosion happens after a series of events, in my opinion. First you have genetic building blocks to build an animal. You also need oxygen to support metabolism. But that alone is not sufficient. You also need a mechanism to drive the system into a runaway situation. You need to make the system work very fast. And one of the mechanisms to drive the system to a runaway situation is ecological feedback.

Notice that Xiao simply assumes the existence of a full-fledged animal with all of the requisite "genetic building blocks" from the start. Then, all you need is oxygen and the right ecological conditions and all major animal diversity arises. It seems so easy! But they never even attempt to tackle the origin of new biological information.

Simon Conway Morris takes the same approach:

We're inventing nervous systems. We're inventing eyes and other sensor systems. We're learning how to move fast, how to swim effectively. So you have a whole cascade of feedbacks. And it's really trying to pinpoint "the trigger" versus all the other consequences that flowed from that point.

In other words, explaining the Cambrian explosion entails assuming that a cascade of feedbacks can produce all animal body plans. You just have to look for that one "trigger" that set off the cascade and the rest takes care of itself. But where is the explanation for the origin of all the biological information needed to build these animals? They never touch that question.

An analogy that comes to mind is one we've used before -- the famous Monty Python skit "How to Do It":n the skit, they explain how to cure the diseases of the world, but only in the vaguest and most superficial terms. They never actually give enough information to explain how to "do it" in the real world. The absurdity, of course, is what makes it funny.

The video from The Economist bears a resemblance that's not as funny. Andrew Parker, for example, says that perhaps "vision was actually the only thing that was required to trigger the Cambrian explosion." The Monty Python version might go like this:Question: What's the evolutionary explanation for the origin of all the complex animals that appeared suddenly in the Cambrian explosion?Answer: Well, you see, you start with a full-fledged animal and then it evolved eyes and became very good at catching prey. And then all kinds of other animals had to evolve complicated ways of avoiding being eaten, and then everything evolved!Aside from the fact that this never even touches the origin of information, their explanation assumes that there is some evolutionary mechanism capable of generating eyes, and then that there are evolutionary mechanisms capable of generating all animal body plans once eyes evolved. But there's another major problem: Simon Conway Morris thinks that the eyes of the animals in the Cambrian period couldn't see things well enough to find them easily, and so eyes couldn't have been the driver of Cambrian complexity.

There's one final explanation the video tries out -- that the Cambrian explosion was a long, slow process and the early animals were just too small to be recorded in the fossil record: "Perhaps the bilateral ancestors of today's animals were simply hiding in the shadows of the Ediacaran world until opportunity knocked."

As Stephen Meyer points out in Darwin's Doubt, there are small fossils preserved from the Ediacaran period and earlier. So size fails to explain why we don't see these Precambrian animal ancestors. In any case, the video then says: "Whatever did happen, they took that opportunity, with momentous consequences for the future."

"Whatever did happen" is right. If you want to understand the origin of information, you're going to need something capable of generating that information. Returning to the admission at the beginning of the video, from an evolutionary viewpoint that mechanism really is a "mystery." Allowing for the possibility of intelligent design, however, the answer is evident.

The design inference defined and refined

Are Hexagons Natural?

Evolution News & Views October 27, 2015 3:38 AM 

Hexagons (at least macroscopic ones) are relatively rare in nature. The most common place we see them is in beehives. It could be argued that if bees are intelligently designed, for which there is ample independent evidence, then the structures they create are also intelligently designed. We might argue that hexagons are the most efficient packing spaces for the least amount of material. We might point out that the design also provides more robust protection against stress than square-shaped cells. We can see that the structural design performs a function.

Our propensity to infer design, though, has to face up to other examples of hexagons in the non-living world. Some have been difficult to explain by natural law.

Columnar Basalt

When lava cools, it often forms polygonal-shaped columns, and hexagons are the most common shape. Many physicists have tried to understand how this occurs. There have been partial solutions, but nothing fully satisfying. Now, a paper in Physical Review Lettersreproduces the hexagonal columns with a mathematical model. The basic idea is summarized in a news release at APS Physics, along with a stunning photo of a pyramid of hexagonal basalt columns at the Giant's Causeway in Ireland. It sure looks designed. How do we make a proper inference?

The surface of cooling lava contracts more quickly than the still-warm liquid underneath, creating a stress that is relievedby the formation of cracks. Martin Hofmann from the Dresden University of Technology, Germany, and colleagues considered a uniform lava layer and calculated the energy released from different crack patterns. They found that, in the initial stages of cooling, when the cracks start to appear atrandom places on the surface, the energy release is greatest if the cracks intersect at 90-degree angles. But as the lava continues to cool and shrink, and the cracks collectively start to penetrate into the bulk, more energy is released per crack if they intersect at 120-degree angles. This transition fromindividual to collective growth of the cracks drives the pattern from rectangular to hexagonal. The hexagonal pattern is then maintained as the lava cools further, eventually leading to an array of hexagonal columns, similar to those seen in nature.

One can find columnar basalt in many locations: in the Grand Canyon, in Yellowstone Canyon, in Utah's Zion National Park, in the Rocky Mountains, at Devil's Postpile in the Sierra Nevada, and of course at the Giant's Causeway, along with other places around the world. The uniformity of the columns can be impressive, but they are rarely perfect. Many times other polygons are mixed in with the hexagons.

Saturn's North Pole Hexagon

A giant hexagon made up of clouds has persisted for decades on Saturn's north pole. This formation has baffled scientists since it was first discovered by the Voyager spacecraft in 1981. It appears to be unique in the Solar System, and it's huge: 20,000 miles across and 60 miles deep. Saturn's south pole also has a giant vortex, but not this polygonal shape. Space.com describes attempts to explain the feature:

Scientists have bandied about a number of explanations for the hexagon's origin. For instance, water swirling inside a bucket can generate whirlpools possessing holes with geometric shapes. However, there is of course no giant bucket on Saturn holding this gargantuan hexagon.

Voyager and Cassini did identify many features of this strange hexagon that could help explain how it formed. For example, the points of the hexagon rotate around its center atalmost exactly the same rate Saturn rotates on its axis. Moreover, a jet stream air current, much like the ones seen on Earth, flows eastward at up to about 220 mph (360 km/h) on Saturn, on a path that appears to follow the hexagon's outline.

We know that standing waves can maintain nodes that are stationary with respect to their reference frame. Something like that appears to be at work in Saturn's polar winds. The article says that the "bizarre giant hexagon on Saturn may finally be explained." A new model by a planetary scientist from New Mexico reproduces many of the observed properties of the hexagon.

The scientists ran computer simulations of an eastward jet flowing in a curving path near Saturn's north pole. Small perturbations in the jet -- the kind one might expect from jostling with other air currents -- made it meander into a hexagonal shape. Moreover, this simulated hexagon spun around its center at speeds close to that of the real one.

The scenario that best fits Saturn's hexagon involves shallow jets at the cloud level, study team members said. Winds below the cloud level apparently help keep the shape of the hexagon sharp and control the rate at which the hexagon drifts.

This hexagon may not be permanent, since it is subject to perturbations by processes that have no particular reason to maintain it. A simpler case is seen in Jupiter's Great Red Spot that appears to be shrinkingafter three hundred years since it was first observed.

Tiny Non-Living Hexagons

Snowflakes are classic examples of orderly structures with a hexagonal shape. Other non-living hexagons include the ring structures of many organic molecules (at least the way they are diagrammed by chemists). Some minerals also display hexagonal packing. Most of us have seen soap bubbles form hexagonal interfaces when they are packed together. An occasional hexagon can be found in mud cracks on a dry creek bed.

Life-Produced Hexagons

Bees are not the only hexagon-makers in the living world. We find hexagons on tortoise shells and in the ommatidia of insects' compound eyes. Some diatom species form free-standing hexagons in addition to the more common circles, triangles, squares, and pentagons. We humans, of course, are great hexagon-makers. Understanding their ideal packing geometry, we make them in telescope mirrors, geodesic domes, and soccer ball covers. Sometimes we create them just for their artistic value.

Proper Inferences

If humans create hexagons by intelligent design, is that true for other living things that make them? And how should we distinguish the design inference in life from the natural hexagons on Saturn or in columnar basalt? These questions provide an opportunity to understand William Dembski's Design Filter.

It's not enough that something be orderly. Casey Luskin discussed columnar basalt in 2010, answering ID critics' accusations that the Design Filter would generate a false positive. We also explained last year why snowflakes do not pass the design filter, despite their elegance and beauty. It's not enough, further, that something be rare or unique, like the Saturn hexagon. The Design Filter prefers a natural-law explanation if one can be found, or if the probability of the phenomenon's occurrence by chance is sufficiently high.

But do we wait forever for a natural explanation? Planetary scientists struggled for 35 years to explain Saturn's hexagon. Shouldn't we wait to explain beehives and compound eyes without reference to intelligent design? Isn't natural selection a natural law? (Actually, it's more like magic than a law of nature, but we'll entertain the question for the sake of argument.)

Intelligent design is not a gaps argument. It's a positive argument based on uniform experience. We have experience watching melting lava or drying mud forming geometric patterns. We have no other experience with hexagons forming on gas giants like Saturn, though. What do we do?

The Information Enigma

The short answer involves information. The hexagon on Saturn performs no function. Columnar basalt doesn't say anything. Snowflakes don't carry a message. They are mere emergent phenomena that are not that improbable, given laws of nature with which we are familiar. The Design Filter works properly by rejecting a design inference for these on the basis of probability and natural law.

All the living examples of hexagons, by contrast, are produced by codes. Beeswax will not form into hexagon cells on its own, nor will silica arrange itself into the geometric shells of diatoms. A digital code made of DNA dictates the placement of ommatidia in the insect eye and patterns in the turtle shell. Each of these structures performs a function and is the outcome of processes directed by a code.

The coded information makes use of natural laws, to be sure, but it arranges the parts into hexagons for a functional purpose. In our uniform experience, we know of one cause that can generate codes or instructions that lead to functional geometries -- intelligence.

There is one sense, though, in which we could make a design inference for the nonliving hexagons like snowflakes, basalt columns, and planetary atmospheres. Certain features of the universe are so finely tuned that without them, water, atoms, stars, and planets would not exist. It takes a higher-order design to have a universe at all.

You might even say that the elegant mathematics that allows us to describe hexagons is conceptual, not material, as are the aesthetic values that allow us to appreciate them. So even if the Design Filter rejects a design inference for some of the hexagons at one level, the mere existence of atoms, natural laws, and beauty warrants a design inference in a broader context for all of them. Without minds, we wouldn't even be debating these questions.

Darwinism Vs. Arithmetic yet again.

Proteins by Accident? Replying to a Critic of The Information Enigma

Douglas Axe October 27, 2015 9:51 AM 

Stephen Meyer and I appear in a new video from Discovery Institute, The Information Enigma, that shows how the information in DNA and proteins provides strong evidence for intelligent design. At the YouTube channel for the Center for Science & Culture, the video has generated somespirited discussion, which is good.

One commenter, who goes by the name ExtantFrodo2, has risen to the defense of Darwinism by enlisting several familiar Darwinian arguments, all of which make the evolutionary invention of new functional proteins sound much easier than it really is. The heavy use of arguments along these lines makes a response worthwhile, I think.

This excerpt from one of ExtantFrodo2's comments expresses the evolutionary thinking well:

The proteins are simply shapes. Mutation makes the shapes different. Different shapes are new tools. Some are bad & cause death to the organism. Others have no affect. Very rarely one shape turns out to be useful somewhere in the cell. It's only a metaphor to call it 'information'. DNA is a mutable template (or jig) that is cast into protein. Change the template & you change the protein. The protein may be more effective, less effective, or even completely changed (frame-shift and/or critical linkage points like di-sulfide bonds). Furthermore mutations often occur on copies or duplicates of a gene, so no former functionality (protein production) need be lost at all. As the jig or mold is transformed by mutation it produces different proteins that interact with the environment (and the cell) in new & different ways.

The first misconception here has to do with protein shapes. Since proteins are long flexible chains of linked amino acids, it's somewhat surprising that they can have fixed three-dimensional shapes at all. A strand of beads, for example, has no fixed shape. Why would a strand of amino acids be different?

In fact, the vast majority of possible protein chains are like strands of beads -- lacking any fixed shape. Life, however, makes critical use of a very special subset of the possibilities. These special proteins are coaxed into forming precise shapes by the sequence of amino acids along their chains. The process triggered by this coaxing, where a floppy protein chain rapidly acquires a well-formed structure, is known asfolding.

To give you an idea of how special these folding sequences are, theJournal of Molecular Biology paper referred to in the video estimates the proportion of chains that fold to be in the range of one in 10⁵⁰ to one in 10⁷⁴, depending on the complexity of the fold.

Even for simple folds, this means fewer than one in a trillion trillion trillion trillion amino acid sequences forms any well-defined shape at all. So the idea that every protein sequence has a shape is not at all accurate.

Secondly, the related idea that mutations merely change the shapes of proteins is equally inaccurate. The highly cooperative nature of protein folding means that it tends to be all-or-nothing. A particular protein sequence either forms structure A or it doesn't, and likewise for structure B. So for a series of mutations to convert a protein from forming structure A to forming structure B, they would first have to undothe A structure (producing a chain with no well-defined structure) and then stabilize the B structure.

In other words, changing the structure of a protein isn't nearly as easy as changing the shape of a lump of clay. The clay always has a shape, and with a little imagination we can even say the shape always represents something (which is all we ask of a lump of clay).

Proteins are different. Only highly exceptional proteins even have a shape, and these shapes are therefore fragile. Mutations are tolerated to a modest extent, after which all shape is lost.

Finally, the idea that it isn't hard to stumble upon things that are good for something, while very popular in evolutionary circles, doesn't explain the origin of exquisite things. Sure, the blobs of solder and scraps of metal or plastic you find on the floor of a workshop can be used for something -- this one a straight edge (in a pinch), that one a makeshift coaster, maybe a paperweight over there. But this make-do approach clearly doesn't work for impressive things -- not for the things we humans set out to make, and still less for the far more exquisite things we see in life.

Such things never happen by accident.

Grabbing some more of that suboptimal design I see.

To convergent evolution be the glory?

Squaring the circle?

Is Evolution Random? Answering a Common Challenge
Ann Gauger October 26, 2015 12:45 PM 

Evolutionists often challenge us for referring to Darwinian evolution as "random." They point to the fact that natural selection, the force that supposedly drives the train, always selects more "fit" organisms, and so is not random. That is only part of the story, though, and to understand why evolution can indeed be called random, the rest needs to be told.

Evolution can be considered to be composed of four parts. The first part, the grist for the mill, is the process by which mutations are generated. Generally this is thought to be a random process, with some qualifications. Single base changes occur more or less randomly, but there is some skewing as to which bases are substituted for which. Other kinds of mutations, like deletions or rearrangements or recombinations (where DNA is exchanged between chromosomes), often occur in hotspots, but not always. The net effect is that mutations occur without regard for what the organism requires, but higgledy-piggledy. In that sense mutation is random

The next part, random drift, is like a roll of the dice that decides which changes are preserved and which are lost. As the name implies, this process is also random, the result of accidental events, and without regard for the benefit of the organism. Most mutations get lost in the mix, especially when newly emerging, just because their host organisms fail to reproduce, or die from causes unrelated to genetics. It can also happen that new mutations are combined with other mutations that are harmful, and so get eliminated.

The random effects of drift are large enough to overwhelm natural selection in organisms with small breeding populations, less than a million, say. New mutations are not born fast enough to escape loss due to drift. There is a fractional threshold in the population that must be crossed before a new mutation can become "fixed," that is, universally present in every individual. A new mutation generally is lost to drift before that population threshold is crossed.

The third part, natural selection, is not random. It acts to preserve beneficial change and eliminate harmful ones. It can be said to be directional. But there are several caveats. Beneficial mutations are rare, and usually only weakly beneficial, so the effects of natural selection are not usually all that strong. Most changes provide only a slight advantage.

In addition, it can happen, and often does, that a "beneficial" mutation involves breaking something, meaning a loss of information, and a loss of potential improvement. This breaking can be irreversible for all intents and purposes. The premiere example in human evolution is that of sickle cell disease. Sickle cell disease is caused by a mutation to the hemoglobin gene that makes red blood cells resistant to the malarial parasite. In one copy the broken gene is beneficial (it increases resistance to malaria), but when two copies are present (both chromosomes carry the mutation), the red blood cells are deformed and cause painful debilitation. The broken gene is actually functionally worse than its normal version, except where malaria is present.

This brings out an important point. Natural selection does not always select the same mutations. The environment determines which mutations are favored. For example, natural selection acts to favor individuals carrying one copy of the sickle cell trait where malaria is present, but acts against the sickle cell gene where malaria is absent. So in this context, selection meanders over a fluctuating landscape of varying criteria for what is beneficial and what is not. Now it is beneficial to carry the sickle cell trait, now it is not. Different populations get favored at different times. In this sense one might say selection has a random component too, because only rarely is selection strong and unidirectional, always favoring the same mutation.

We see this variation in selection with another example, the evolution of finch beaks on the Galápagos Islands. In drought, large beaks are favored, in wet years, small beaks. The weather fluctuates, and so do the beak sizes.

Subpopulations may acquire traits, but because of environmental variation the traits do not become universal. For example, lactose intolerance -- we do not all carry the version of the gene that allows us to digest lactose as adults. Unless suddenly everyone in the world has to eat cheese as a major part of their diet, lactose intolerance won't disappear from our population.

There is a special way evolution can occur -- a sudden bottleneck in the population will tend to fix the traits that predominate in that population. Suppose a nuclear holocaust wiped out everyone except Swedes. The lactose-digesting gene would almost certainly become fixed, as would blond hair, blue eyes, and other Scandinavian traits, provided they ate cheese and lived at high latitudes. Until new mutations in new environments occurred, that would remain the case.

Now you know more about the population genetics of evolution than you imagined could be true. The sum of all these factors is what is responsible for evolution, or change over time. Mutation, drift, selection, and environmental change all play a role. Three out of these four forces are random, without regard for the needs of the organism. Even selection can be random in its direction, depending on the environment.


So tell me. Is evolution random? Most of the processes at work definitely are. Certainly evolution won't make steady progress in one direction without some other factor at work. What that factor might be remains to be seen. I personally do not think a material explanation will be found, because any process to guide evolution in a purposeful way will require a purposeful designer to create it.

Why some just say no to Halloween.:The Watchtower Society's commentary

The Origins of Halloween—What Does the Bible Say About Them?:

The Bible’s answer:

The Bible does not mention Halloween. However, both the ancient origins of Halloween and its modern customs show it to be a celebration based on false beliefs about the dead and invisible spirits, or demons.—See  “Halloween history and customs.”


The Bible warns: “There must never be anyone among you who . . . consults ghosts or spirits, or calls up the dead.” (Deuteronomy 18:10-12, The Jerusalem Bible) While some view Halloween as harmless fun, the Bible indicates that the practices associated with it are not. At 1 Corinthians 10:20, 21, the Bible says: “I do not want you to be participants with demons. You cannot drink the cup of the Lord and the cup of demons too.”—New International Version.

Halloween history and customs:

Samhain: The origin of Halloween can be traced to this “ancient pagan festival celebrated by Celtic people over 2,000 years ago,” states The World Book Encyclopedia. “The Celts believed that the dead could walk among the living at this time. During Samhain, the living could visit with the dead.” However, the Bible clearly teaches that the dead “are conscious of nothing at all.” (Ecclesiastes 9:5) Thus, they cannot contact the living.
Halloween costumes, candy, and trick or treat: According to the book Halloween—An American Holiday, An American History, some of the Celts wore ghoulish costumes so that wandering spirits would mistake them for one of their own and leave them alone. Others offered sweets to the spirits to appease them. In medieval Europe, the Catholic clergy adopted local pagan customs and had their adherents go from house to house wearing costumes and requesting small gifts. The Bible, on the other hand, does not permit merging false religious practices with the worship of God.—2 Corinthians 6:17.
Ghosts, vampires, werewolves, witches, and zombies: These have long been associated with the evil spirit world. (Halloween Trivia) The Bible clearly states that we should oppose wicked spirit forces, not celebrate with them.—Ephesians 6:12.

Halloween pumpkins, or jack-o’-lanterns: In medieval Britain, “supplicants moved from door to door asking for food in return for a prayer for the dead,” and they would carry “hollowed-out turnip lanterns, whose candle connoted a soul trapped in purgatory.” (Halloween—From Pagan Ritual to Party Night) Others say that the lanterns were used to ward off evil spirits. During the 1800’s in North America, pumpkins replaced turnips because they were plentiful as well as easy to hollow out and carve. The beliefs behind this custom—the immortality of the soul, purgatory, and prayers for the dead—are not based on the Bible.—Ezekiel 18:4.