Yet More on clarity in the design debate.

In Arguments for Intelligent Design, Definitions and Assumptions Are Important
Ann Gauger

How can random non-coding DNA be, at the same time, both functional (as in the genome) and non-functional (as in extremely unlikely to code for functional proteins)?

   This question was posed recently at Peaceful Science, a discussion site that seeks to promote dialog between atheists, theistic evolutionists, and proponents of intelligent design. (Their success is mixed. ID proponents often feel like Aragorn in the last battle.) It’s a good question. It came out of a conversation about orphan genes, where I was arguing that non-coding DNA was extremely unlikely to give rise to a new coding sequence with any function. Yet ID people claim all the time that the majority of the genome is functional.. How can sequence be both functional and non-functional at the same time? The answer turns on two things. The meaning of “function” and clarity about what’s being tested.

I had been trying to explain Doug Axe’s results to the group of debaters, most of whom did not agree. According to Axe, sequences that can produce a functional protein, namely a protein capable of carrying out an enzymatic reaction, are extremely rare. (They could be rare in number and/or rare in how far apart they are spread in sequence space.) 

Picture a Bank Vault

Think of a situation where you have to crack the code on a bank vault, with many dials in the code, say 150, each specifying 1 out of 10 digits. If there is only one code that will work, the number of possible sequences to try is 10^150, Now say that 100 sequences out of 10^150 would work. That reduces the number you would have to try. It would now be 10^148.

What’s the solution? Well, suppose there was another bank next door, that had a similar code, in fact with 125 of the dials identical! And you happened to know that code. Now the information required is greatly reduced. You have only 10^25 to get. Likely success? And if you are very lucky and know the code nearly completely, all but 3 dials (maybe you know the teller or the person who built the vault), it is definitely easier to break the code. 10^3 =10 x 10 x 10. You have a pretty good chance of success.

The problem is worse for proteins. They have twenty possible amino acids for each position in a protein, so the total possible sequences for a protein 150 amino acids long is 20^150.

To do a random search through that whole space of 20^150 is not possible, just like it would be impossible to search through the 150 dials to find the bank code. But if proteins are not far apart in sequence space, like the bank code where almost all of the code was identical to another bank’s code, then the chances of finding a sequence that will work are greatly improved.

A Crime Spree

Now consider one more thing. Suppose suddenly there were bank robberies everywhere, and it wasn’t by force. The dials had been turned to the correct combinations. What would be your inference? I would say that someone knew the codes.

So unless functional sequences are easy to find (very common), and/or are clustered together (easily reachable from one functional island to another), explaining current protein diversity without design is impossible.

I’ll break that down.

“Unless functional sequences are easy to find (very common), and/or are clustered together (easily reachable from one functional island to another)”: I am laying out the conditions where it might be possible to find function.

“Explaining current protein diversity without design is impossible”: Unless the above conditions are met, namely that functional sequences are easy to find or clustered together, we won’t be able to find functional sequences, unless design has been involved.

Now turn the sentence around.

Explaining current protein diversity without design is impossible, unless functional sequences are easy to find (very common), and/or are clustered together (easily reachable from one functional island to another).

As a consequence, if we find that apparently random non-coding sequences have given rise to new genes and proteins in many genomes, in fact representing 10-30 percent of the genomes analyzed, that result should surprise us, given what I said above. But we need additional evidence still. See below.

Now for the other half of the problem or confusion here. In ENCODE, scientists claimed that the majority of our DNA was functional, meaning it had some sign of biochemical activity. Transcription, methylation, a site for DNA binding, etc., any of these would qualify as functional in some sense. But even ENCODE workers admit they don’t know how much of that “function” will be meaningful.

In the ENCODE sense, most genomic sequence is functional, thus functional sequence is common (20-80 percent was the original range offered). Just remember what function means here — biochemical function, not sequence coding for functional proteins.

So Which Is It? 

If the genome is functional in the sense of ENCODE, that agrees with one part of ID. Some of us argued that the genome would not be junk. We would expect some kind of function for most of it.

But being functional in the biochemical sense (à la ENCODE) does not mean it is easy to give rise to new genes and proteins. When we say functional sequence is rare in sequence space, we mean a different sort of function and sequence than in ENCODE. We mean a sequence that can have the ability to carry out an enzymatic reaction. It is our claim that proteins made from random sequence will rarely if ever have any sort of enzymatic activity. 

That is why experimental tests are to be desired. Can random DNA sequence produce functional proteins with enzymatic activity or not? If experiments say no, that implies something extra is going on, because we do see lots of de novo genes.

However, such experiments may be impossible, because of the inability to test enough sequence to get a handle on a likely small signal. Proving a negative is always difficult. None of the protocols I know can screen enough sequences to test Doug’s hypothesis. 

However, if it is easy to get a functional enzyme from random DNA, if there should be a positive result,  that would definitely argue that de novo genes may be the product of natural processes, and not necessarily design.

As I said earlier, there are labs examining this question of the difficulty of getting enzymatic function from random sequence. I look forward to their results.

There is more that could be said here but I’ll save it for another time.

Reproduction v. Darwin.

Why Evolution and Reproduction Are Unnatural
Granville Sewell

In a recent American Spectator article, “Evolution — More Certain than Gravity?”,Sarah Chaffee and I made the point that to not believe in intelligent design, you have to believe that the four fundamental, unintelligent forces of physics alone (the gravitational, electromagnetic, and strong and weak nuclear forces) could have rearranged the fundamental particles of physics on our once-barren planet into encyclopedias and science texts and computers and airplanes and Apple iPhones.

In a 2017 Physics Essays article, “On ‘Compensating’ Entropy Decreases,” I argued that this spectacular increase in order seems to violate the more general statements of the second law of thermodynamics; at least that you cannot dismiss this claim, as is always done, simply by saying that the Earth is an open system and order can increase in an open system. You have to argue that the increase in order is not really extremely improbable given what has entered our open system from outside.

Darwinists Are Not Impressed

Whether or not you believe that what has happened on Earth violates the second law, I can’t imagine anything in all of science that is more clear and more obvious than that unintelligent forces alone cannot produce such things as Apple iPhones. But Darwinists are not impressed. They believe that natural selection, alone among all natural causes, can create spectacular order out of disorder, and even produce beings that can write science texts and design computers.

That it seems even superficially plausible (until we think about the details) that selection could create such order out of disorder relies completely on the fact that living things are able to reproduce, that they are able to preserve their complex structures and pass them on to their descendants without significant degradation, generation after generation. Without reproduction, there are no variants to select from. Reproduction is the most fundamental characteristic of life. We see it happen everywhere, so we may feel there is nothing “unnatural” about reproduction. 

Imagine Self-Reproducing Cars

But to appreciate how unnatural the astonishing reproductive abilities of living things really are, imagine trying to design cars that are able to give birth to other cars. Although it is far beyond our current technology, imagine that it were possible to construct a fleet of cars that contained completely automated car-building factories inside, with the ability to construct new cars — and not just normal new cars, but new cars containing automated car-building factories inside them. If we left these cars alone and let them reproduce themselves for many generations, is there any chance we would eventually see major advances arise through natural selection of the resulting duplication errors? 

Of course not. Without intelligent humans there to fix the mechanical problems that would inevitably arise, the whole process would grind to a halt after a few generations. We are so accustomed to seeing animals make copies of themselves without significant degradation that we dismiss this as just another “natural” process. But if we actually saw cars with fully automated car factories inside, making new cars with car factories inside them, maybe we would realize what an astonishing process reproduction really is. “How do these instruction sets not make mistakes as they build what is us?” asks mathematician Alexander Tsiaras in the wonderful TED Talk:

How indeed? If you — understandably — cannot accept that something we see happen every day should be called “unnatural,” please watch the video.

The Limits of Natural, Unintelligent Forces

It is not only unnatural that species should evolve from simple to complex, it is unnatural even that they should not degrade over time. Individuals of each species do in fact decay into simpler components, as soon as they die — that is what “natural” looks like. Thus even if the transitions between major groups of animals could be made without encountering irreducible complexity (they certainly cannot), there would still be something very unnatural about evolution, and it still could not be explained without intelligent design. The argument for intelligent design could not be simpler or clearer: natural, unintelligent forces of physics alone cannot rearrange atoms into computers and airplanes and Apple iPhones. Any attempt to explain how they can must run up against reality somewhere, because they obviously can’t.

A Postscript on the Second Law

I hesitate to bring the second law back into this debate because of the controversy it always generates. But people sometimes say that the second law only requires that order should not increase (entropy should not decrease), it does not require that order must actually decrease, so there is nothing unnatural about species simply maintaining their complex structures and passing them on generation after generation without significant degradation. Yet common sense tells us that, when only natural forces are at work, complex things must degrade, and slowly only if everything is almost “frozen in time” (nothing is changing), or else they are already degraded to nearly simplest form. 

Obviously, neither of these conditions holds for the case of animal reproduction. Common sense is actually confirmed by the equations of entropy change when we consider the application of the second law to diffusion of a substance X. Notice that since usually J = -D*gradient(C), equation A7 of my Physics Essays article (equation A4 for the case where X-entropy is just thermal entropy) says that if “X-order” is not imported from outside (the boundary integral term is zero), the only way X-order cannot decrease rapidly is when either things are almost frozen in time (the diffusion coefficient D is small), or the X-order is already close to the minimum possible (gradient(C) is small).

Darwinism:Where success is an orphan?

About Orphan Genes — What’s the Big Problem for Evolution?
Ann Gauger

Orphan genes — genes that are present in only one species, or a group of closely related species — are of particular interest to advocates of intelligent design. The reason for this has to do with the assumptions of evolutionary biology.

The main evolutionary assumption is common descent, that all life is descended from one or a few ancestors. Following from this, and taken as evidence for this, is the assumption that all life shares DNA in common. Prior to the advent of widespread genome sequencing, it was assumed that living things shared genes, that there was a set of shared housekeeping genes, and a set of genes specific to a taxonomic group, though these would be few in number. It was assumed that the vast majority of genes would be found multiple places in the genomes of living things. The reason? It was assumed that getting new genes was hard, and once a workable solution was found it would be preserved in the descendants that followed. The bulk of genes would have been invented early in evolution, and thus would be broadly shared.

When It All Changed

But all that changed when many genomes were sequenced and their transcripts analyzed. Each genome, or each taxonomic group, such as bivalves or insects, was found to contain unique genes, found only in that group or species. This was a surprise. At first it was attributed to incomplete sampling. As more genomes were sequenced, it was thought, the uniqueness would turn out to be illusory. Other organisms would carry those genes. As a related explanation, the sparsity of their distribution might be due to horizontal gene transfer, or to gene loss. The hypothesis was that what appeared to be unique was so because it was the result of some rare transfer between species, and we hadn’t identified the source. Or what once was widespread had been lost over evolutionary time.

These explanations are not proving true. First, the more genomes that are sequenced, the more the proportion of orphans should shrink, as more and more “orphans” should be shown to be present in other genomes. But that has not proven to be the case. The mountain of orphan genes is growing, not shrinking. Similarly, horizontal gene transfer was not born out. The sister genes of orphans should have been found as sample size increased, reducing the proportion of orphan genes. As for gene loss as an explanation, it would have to be too massive to be realistic to account for the patterns seen.

One last possibility. The orphans could be related to other genes, but their sequences could have diverged so much as to be unrecognizable. Only their protein structures might reveal relatedness. This also has not been born out by studies that have determined structures of orphan proteins.

A Sea Change in Evolutionary Thinking

So what’s the solution? If you are an evolutionary biologist, it’s simple. You decide it must be easy to get new genes directly from random (non-coding) DNA, or by frameshift or overlapping genes (which amounts to random sequence). This represents a sea change in evolutionary thinking.

Now hold it. Saying that it’s easy to get new genes from DNA by those methods overturns a major Darwinian expectation. In 1977, in his famous article “Evolution and Tinkering,” which has been cited many thousands of times, the Nobel laureate François Jacob explained the accepted view of how evolution constructed new genes:

…once life had started in the form of some primitive self-reproducing organism, further evolution had to proceed through alterations of already existing compounds. New functions developed as new proteins appeared. But these were merely variations on previous themes. A sequence of a thousand nucleotides codes for a medium-sized protein. The probability that a functional protein would appear de novo by random association of amino acids is practically zero. In organisms as complex and integrated as those that were already living a long time ago, creation of entirely new nucleotide sequences could not be of any importance in the production of new information. 

New genes must arise from pre-existing genes, leaving the signal of ancestry in their closely related (i.e., homologous) sequences, because the probability of the alternative is “practically zero.” That’s why the discovery of orphan genes, which show no homology to other sequences, came as a great surprise.

No Problem, You Say?

“No problem. Isn’t that what science supposed to be about?” said one evolutionist to me. “Adapting your theory to fit the facts?”

Well, theories have to be amenable to falsification too. They can only bend so far.

So how can we tell whether genes are easy to get or hard? By testing these alternatives in the lab.

At present the preferred theory for the birth of new genes is to take a stretch of DNA that is currently not being transcribed into RNA, then let it acquire the signals necessary for transcription, then have that new transcript have a function, either as an RNA or after being translated into protein. 

This is in fact how many orphan genes are found. An RNA transcript is made in one species from a stretch of DNA that in a sister species does not make RNA. Further work then determines if the RNA is translated into protein, and ultimately, if the protein has a function.

But in order for this scenario for orphan gene creation to work, functional protein sequences have to be easy to acquire, within reach of an evolutionary search starting from an existing non-functional stretch of DNA. Evolutionists tend to think that such a thing happens easily. Evolutionary processes can produce a new gene or structure or chemical activity easily. This must be true if evolutionary processes are the explanation for orphan genes.

The Rarity of Functional Protein Folds

In contrast, ID proponents think that it’s very difficult to get function from random sequence. There’s a definite reason for this. Experiments by Dr. Douglas Axe measured the rarity of functional protein folds in sequence space (only 1 in 10^77 proteins form a fold with a target function, a very, very, very small number). If functional proteins are very rare in sequence space, that makes it very difficult to get new genes or structures or chemical activities. Others have found similar answers, when asking for the requirements to produce an enzymatic activity. Others, when asking for simple kinds of activity, like sticking to a column loaded with a substrate like ATP, get numbers that are conceivably within range of evolutionary processes. Just sticking to a column is not nearly as demanding as carrying out an enzymatic reaction. 

There are strong points of view as to the reliability of the various methods. How the various experiments are judged tends to be influenced by one’s particular view on the question of evolution. So the best thing is to do more experiments, which is precisely what the scientific community is doing. 

Work is in progress now in many labs to test the question of how hard it is to get an orphan gene from non-coding sequence. Some are asking how hard it is to get a promoter (necessary to promote active transcription). Some are asking how likely it is for random sequence to have function. The sticking point, literally, seems to be that random sequences don’t fold properly and are insoluble in water. They aggregate. That makes most kinds of function difficult, to say the least. Lastly, how likely is it that the function will actually be helpful? We’ll see.

The answer is not in. If Doug Axe is right (and remember, he is not the only researcher to have found that functional proteins are very rare in sequence space), then getting an orphan gene by an evolutionary process is extremely unlikely. But orphan genes are possible, maybe even to be expected, when a designing intelligence acts.

Someday we'll look back and laugh.

Our Hairlessness: Another Evolutionary Enigma Suggestive of Intelligent Design

David Klinghoffer March 18, 2013 2:53 PM

Nina Jablonski, Penn State anthropologist and author of Skin: A Natural History, gives an interesting interview to CNN on how our presumed pre-human ancestors lost their fur. It's a bit of a puzzle because (per the conventional set of evolutionary assumptions and deductions) our ancestors were furry like chimps, and Jablonski reasons that they lost their fur so as to allow for improved sweating required by the innovation of our becoming excellent long-distance runners.

CNN: When did we first lose our fur and gain this pigmentation?

Jablonski: The human lineage evolved in Africa. If we start at a starting point of 6 to 7 million years ago, when humans first parted ways from the ancestors of chimpanzees, we have a lot of fossils that indicate that humans were walking on two legs, but they were not modern-looking. They were fairly short, and they still had quite ape-like body proportions: fairly long arms, relatively short legs. These were Australopithecus species of various kinds. They were good bipeds, but they were also capable tree-climbers. But when we look at their skeletons in detail, it's pretty clear that they were not active runners. They could walk on two legs but they weren't running or striding purposefully across the savanna most of the time, they were sort of living lives that are much like those of chimpanzees: fairly close to the edge of the forest, sometimes going into trees for protection, and then walking for short distances in the open to forage.

We hypothesize that, at that stage in our lineage's evolution, we still would have had quite a bit of body hair, because the reason we started to lose body hair is related to the need for controlling body heat.

It turns out that primates lose most of their heat through radiation from the surface of the body into the environment, and by evaporation of sweat. The hotter it is outside, the more important sweat becomes, especially if the animal is exercising vigorously and generating a lot of internal body heat. Internal body heat is good to a point, but you have to be able to liberate excess heat, otherwise your brain, organs and muscles get too hot.

Primates as a lineage almost exclusively use sweating for this purpose (versus other mechanisms such as panting). There have been a lot of hypotheses made about why we lost most of our body hair. And I definitely, and many colleagues of mine definitely are of the opinion -- based on the environmental, anatomical and genetic evidence at hand -- that we lost most of our body hair because of the needs of heat regulation.

But as Jablonski also points out, chimps beneath their fur have light-colored skin. Take away the fur and you've a light-colored animal that, in the hot African sun, would be extremely vulnerable to the damaging rays of the sun. So you need dark skin. But what would the evolutionary advantage of that be before the transition to going furless? None that's apparent. So which came first?

The running? But that requires the furless feature (not to mention a massive investment in tightly coordinated anatomical reengineering under the skin, as Ann Gauger discusses in Science and Human Origins). The furless feature then? But that requires the dark skin. OK so the dark skin came first? But that seems to somehow look forward to future usefulness before any evolutionary advantage comes into play, which in turn sounds dangerously teleological.

Darwinian evolution can't just put things like that in the bank, with a view toward their being helpful in some future stage of the evolving lineage. Such anticipation, on the other hand, is a hallmark of intelligent design as we're all familiar with it from daily life. Otherwise, blind Darwinian churning seems to have got very lucky in pulling off these three simultaneous innovations just at the right time, together. That sounds more like an illustration of design innovation, doesn't it?

Another day another missing link or business as usual in Darwinville

The Evolution of "Ida": Darwinius masillae Fossil Downgraded From Ancestor to Pet
Casey Luskin

A few months ago, "Ida" was sitting on top of the world. She'd been lauded as the "eighth wonder of the world" whose "impact on the world of palaeontology" would be like "an asteroid falling down to Earth." Falling, indeed. On October 21, Nature published an article announcing that "[a] 37-million-year-old fossil primate from Egypt, described today in Nature, moves a controversial German fossil known as Ida out of the human lineage." Wired also published a story, noting that, "[f]ar from spawning the ancestors of humans, the 47 million-year-old Darwinius seems merely to have gone extinct, leaving no descendants," further quoting a paleontologist calling Ida "a third cousin twice removed ... only very distantly related to living and fossil anthropoids."

But Ida was given quite a ride by the mainstream media, while it lasted. Originally:

Famed BBC broadcaster Sir David Attenborough got involved, making a documentary titled Uncovering Our Earliest Ancestor: The Link, to explain why Ida is "the link that connects us directly with the rest of the animal kingdom." Co-sponsored by both the BBC and the History Channel, the program attracted a massive audience. ...
Good Morning America and Nightline covered the fossil.
National Geographic called her the "critical 'missing link' species."
ScienceDaily and a Discover magazine commentator praised Ida as our "47-million-year-old human ancestor."
Skynews told the public that "proof of this transitional species finally confirms Charles Darwin's theory of evolution."
With Google's eager assistance, Ida went viral: One of the leading search terms that day was "missing link found." Even the Drudge Report was reeled in by the media frenzy, briefly featuring Ida as the headline story.
(Casey Luskin, "The Big Ida: The Rise & Fall of Another Missing Link & Other Media Hype," Salvo 10 (Autumn, 2009).)

scientificideas_sm.jpgIt only took a few months for Ida to go from celebrity-status "missing link" to just another extinct lower primate. As Nature is now reporting:
Teeth and ankle bones of the new Egyptian specimen show that the 47-million-year-old Ida, formally called Darwinius masillae, is not in the lineage of early apes and monkeys (haplorhines), but instead belongs to ancestors (adapiforms) of today's lemurs and lorises.
"Ida is as far away from the human lineage as you can get and still be considered a primate," says Christopher Beard, a palaeoanthropologist at the Carnegie Museum of Natural History in Pittsburgh, Pennsylvania, who was not involved in either research team.

(Rex Dalton, "Fossil primate challenges Ida's place," Nature, Vol. 461:1040 (October 21, 2009).)

The good news is that it seems that cooler heads are now prevailing regarding Ida. Wired notes that the current reporting about disagreements over Ida are an improvement, "the sort of dialogue that was missing from Darwinius' overhyped debut."
Where else have we seen an "overhyped debut" of a fossil, without "dialogue"? Exhibit A: "Ardi" (Ardipithecus ramidus).

In fact, with its article titled "Humanity Has New 4.4 Million-Year-Old Baby Mama," Wired was one of the numerous major media outlets assisting in the overhyped debut of Ardi. But most of those abettors didn't say anything about the ambiguity and dissent over Ardi's reconstructed skeleton. It seems that other missing links also debut with a lot of hype and without much dialogue.

Calm, collected, and careful scientific analysis is going on somewhere in the background here, but little scientific dissent from the media's storyline is being disclosed to the public. Instead, we see that the media, working with certain evangelistic tribes within the academy (see illustration at left), are unashamedly using these fossils as opportunities to push Darwin.

How long "Ardi" will retain favored link status is anyone's guess.

On the origins debate and Jehovah's transcendent technology.

Pearcey: “Stephen Hawking’s Final Salvo”

David Klinghoffer | @d_klinghoffer

Before his death back in March, I found that every new prophetic statement from Stephen Hawking, invariably heralded by the media, was bound to make me sad. It seemed clear he was being exploited for his famous name to promote lugubrious causes having nothing to do with the genuine source of his scientific renown. And this still goes on, with Dr. Hawking having already passed on to the next world.

A new book is out under his name, Brief Answers to the Big Questions,  “published posthumously with material pulled from interviews, essays, speeches, and questions often asked of the famous physicist,” as Center for Science & Culture fellow  Nancy Pearcey writes at CNS News. She responds to the book’s most touted claim. The first chapter asks, “Is there a God?” Answer: No.

 “I think the universe was spontaneously created out of nothing, according to the laws of science.” After all, [Hawking] argues, “If you accept, as I do, that the laws of nature are fixed, then it doesn’t take long to ask: What role is there for God?”

An Open Cosmos

Pearcey replies:

Is Hawking right that scientific laws rule out any role for God? Despite being a brilliant physicist, he seemed unaware that his objection has already been answered — most famously by the popular literature professor C.S. Lewis, himself a former atheist, who taught at both Oxford and Cambridge University.

In his book “Miracles,” Lewis concedes that, at first glance, the regularity of nature does seem to rule out the possibility that God is able to act into the world.

But not so fast. Natural laws tell us only what happens if nothing interferes. People playing a game of pool are applying the laws of physics, which decree that when a billiard ball hits another one, the second ball will start moving. But the laws do not tell what will happen if a mischievous child grabs the ball.

The laws are still true, of course, but the child has interfered with the physics.

Humans interfere with natural processes all the time, yet we do not break any laws of nature. We cut down trees to make houses, we weave plant fiber into cloth, we smelt metals to build bridges, we turn sand into silicon chips for computers. Through technology, we are constantly accomplishing things that nature on its own could not produce.

But do we break a single law of nature? No.

“All interferences leave the law perfectly true,” Lewis points out. And it’s the same when God acts in the world: He does not need to break any scientific laws. The cosmos is open to the actions of creative humans and a creator God.A better way to understand miracles, Lewis writes, is that they feed new events into the existing structure of nature: “The divine art of miracle is not an art of suspending the pattern to which events conform but of feeding new events into that pattern.”

Pearcey offers the helpful image of the universe not as an inviolable clockwork but as a musical instrument, implying the need for an artist’s hand in designing and creating the instrument and in playing it.

Dembski Expands on a Helpful Image

William Dembski has written about this in some detail. A musical instrument without someone to play it is incomplete:

Granted, if the universe is like a clockwork (cf. the design arguments of the British natural theologians), then it would be inappropriate for God, who presumably is a consummate designer, to intervene periodically to adjust the clock. Instead of periodically giving the universe the gift of “clock-winding and clock-setting,” God should simply have created a universe that never needed winding or setting. But what if instead the universe is like a musical instrument (cf. the design arguments of the Church Fathers, like Gregory of Nazianzus, who compared the universe to a lute — in this respect I much prefer the design arguments of the early Church to the design arguments of the British natural theologians)? Then it is entirely appropriate for God to interact with the universe by introducing design (or in this analogy, by skillfully playing a musical instrument). Change the metaphor from a clockwork to a musical instrument, and the charge of “withholding gifts” dissolves. So long as there are consummate pianists and composers, player-pianos will always remain inferior to real pianos. The incompleteness of the real piano taken by itself is therefore irrelevant here. Musical instruments require a musician to complete them. Thus, if the universe is more like a musical instrument than a clock, it is appropriate for a designer to interact with it in ways that affect its physical state.

The “clockwork” notion is one that ID critics adore because it makes design appear naïve and clumsy. If you look up intelligent design on Wikipedia, you’ll see that the editors have used the insides of a pocket watch to brand all their series of (highly misleading) articles on ID. If it were actually possible to edit Wikipedia, I’d substitute a different image; among musical instruments, a lute seems as good a choice as any.

How our Star sheds light on the origins debate

Denton Turns Sagan’s “Humdrum Star” on Its Head

David Klinghoffer | @d_klinghoffer

On a new ID the Future episode, biologist Michael Denton talks with host Sarah Chaffee about the remarkable fitness of a range of properties seen in water and in light. Download the podcast or listen to it here.t’s particularly satisfying to hear Denton turn a frequently heard dismissal of our Sun on its head.

How Silly the Old People Were

Carl Sagan in Cosmos gave the idea perhaps its most iconic expression. In Episode 7, he lectures to a classroom of Brooklyn schoolchildren about how it was once thought that Earth occupied an “important” place in the cosmos. Tut-tut, how silly the old people were, before we realized that our solar system is not at the center of things but way out on the edge of the galaxy, thereby guaranteeing (this leap doesn’t quite follow) our cosmic insignificance. He goes on to ponder:

For as long as there have been humans we have searched for our place in the cosmos. Where are we? Who are we? We find that we live on an insignificant planet of a humdrum star lost in a galaxy tucked away in some forgotten corner of a universe in which there are far more galaxies than people.

Yet the fact that the Sun is “humdrum” or “ordinary” may be the most extraordinary thing about it. Dr. Denton discusses the fortunate circumstances characterizing visual light, needed for vision and photosynthesis. He concludes:

The big deal is that being an ordinary star means that the vast majority of stars in the cosmos put out their energy in the visual and infrared area, bands of the electromagnetic spectrum. So being “ordinary,” what this means is that the universe — it’s somewhat ironic and it seems a bit counterintuitive — it means the universe is profoundly fit for biological systems like ourselves. The Sun is an ordinary star, and that’s a very big deal. The universe, as I describe it Children of Light, is flooded with the light of life.

A Double Dilemma

“Flooded with the light of life”: What a beautiful way of putting it. You could add that it creates a double dilemma for materialists. The universe is “flooded with the light of life,” in Denton’s apt phrase. Yet so far as we know, life on Earth is a singularity. This is certainly counter to Carl Sagan’s expectations. Yet it’s possible that Sagan, and  Stephen Hawking and others, may prove right about the cosmos being home to many forms of extraterrestrial life, including intelligent forms. Only time can tell. If Sagan was correct, then Denton’s “ironic” observation about light’s insanely special fitness for life, life like ours, really comes to the fore.Light was finely tuned for life, whether in a multitude of homes in the cosmos or in just one. Either way, we’re prompted to ask the same question: Finely tuned by whom? And why?

Denton’s new book is Children of the Light: The Astonishing Properties of Sunlight that Make Us Possible. It is the latest entry in the Privileged Species series.

Mssrs. Denton and Berlinski v. Darwinism II

Listen: Why Does Darwinism Hang On?
Evolution News | @DiscoveryCSC

On an episode of ID The Future, philosopher and author David Berlinski joins geneticist and researcher Michael Denton for continued discussion on the debate over Darwinian evolution. Evolution News editor David Klinghoffer asks: Why has the theory persisted? What weaknesses threaten its existence in the 21st century?

Download the podcast or listen to it here.

Listen in as Berlinski and Denton explain why the Darwinian mechanism is being widely questioned as a viable theory of the origin and development of life. As Berlinski puts it: “Applying Darwinian principles to problems of this level of complexity is like putting a Band-Aid on a wound caused by an atomic weapon. It’s just not going to work.”

And still even yet more on the real world's anti-Darwinian bias.

The Blink of an Eye — And More Wonders of Human Body Design
Evolution News | @DiscoveryCSC

Darwinists insist on your body’s “poor design.” By contrast, a prediction of intelligent design for biology is that phenomena should appear more functionally complex and elegantly coordinated the closer one looks. Evolutionist cavils aside, this is certainly true for the human body.

Vision

We blink all day long, once about every 5 seconds. Why doesn’t the world go dark in those moments? How do we perceive a continuous image? “The brain seems to remember the percepts that have just happened,” an article in Science Dailysays. “Scientists have now identified a brain area that plays a crucial role in perceptual memory.” At the German Primate Center, they found the spot where visual information is stored briefly during each eye blink. “Our research shows that the medial prefrontal cortex calibrates current visual information with previously obtained information and thus enables us to perceive the world with more stability, even when we briefly close our eyes to blink,” says the lead author of a paper in Current Biology. This implies a process of calibration, interpolation, and calculation happening literally in the blink of an eye.

“Ghost images” can be detected by the human vision system, an article inLive Science says. These are not direct images that we are familiar with, but rather computed images arrived at by multiplying the light in each pixel from a projected scene onto a background scene. The product produces the ghost image, but it can only be perceived under the right circumstances.

Experiments with participants viewing a superimposed checkerboard on a background photo showed that the ability to see the ghost image is a function of the eye’s refresh rate. The photo only became visible when a single-pixel detector collected the light from each pixel and then fed it into a projector at the right speed. Reporter Stephanie Pappas says this is akin to the optical illusion of seeing a movie when the frame rate matches the eye’s refresh rate. 

The reason this works, [Daniele] Faccio said, is that the human eye has a slow refresh rate. It’s not unlike the reason that movies work: When images are flickered on the screen faster than this refresh rate, it creates the illusion of smooth movement.

The eye “is very fast in acquiring the information,” Faccio said. “It’s just very slow in getting rid of it.”

The researchers figured out that the flickering patterns remained in the eye’s “memory” for about 20 milliseconds, slowly fading out over that time. If the 20-millisecond patterns overlap, the eye sums them up like a movie, allowing the ghost image to emerge.

Although ghost images are unlikely to appear in natural settings, the experiments provide a new way for neuroscientists to understand vision. For design advocates, they open windows into the moment-by-moment calculations that our eyes and brain have to perform to give us a smooth picture.

Olfaction

What we perceive as odors are collections of molecules. Why similar molecules produce very different perceptions of smell has long been a puzzle to physiologists, making odor classification difficult. Is there a way to classify odors, the way audible tones can be classified by frequency?The Salk Institute looked into this “unsolved problem,” hoping to find a pattern that might allow scientists to predict how a molecule (or combination of molecules) would smell. They found that mapping molecules in 2D was too simplistic. Patterns emerged only when they mapped the molecules onto a hyperboloid, a shape similar to a Pringles potato chip.

When the team looked at how the molecules clustered on this surface, they found there were pleasant and unpleasant directions, as well as directions that correlated with acidity or how easily odors evaporate from surfaces. These observations now make it easier to construct pleasant odor mixtures to use, for example, in artificial environments (such as a space station).

The paper in Science Advances explains why this pattern makes sense in nature:

In the natural environment, the sense of smell, or olfaction, serves to detect toxins and judge nutritional content by taking advantage of the associations between compounds as they are created in biochemical reactions. This suggests that the nervous system can classify odors based on statistics of their co-occurrence within natural mixtures rather than from the chemical structures of the ligands themselves.

Meanwhile, at the Monell Center in Philadelphia, scientists learned something new about “mysterious sensory cella” in the nose adjacent to the olfactory sensory neurons, called microvillous cells. “The findings suggest that the so-called microvillous cells (MVCs) may protect the vulnerable olfactory epithelium by detecting and initiating defenses against viruses, bacteria, and other potentially harmful invaders.” MVCs may also helped regenerate damaged cells in the olfactory epithelium. This suggests “multiple levels of protection in the airways,” says a co-author of the paper in  PLOS ONE that, fortunately, appears more interested in the function of these cells than their evolution. 

Mother’s Milk

Two news items show the benefits of human milk for newborns. Scientists at the University of Edinburgh find that “Breast milk may help babies’ brain development.” Pre-term babies showed better brain development when fed breast milk instead of formula. Brain scans were performed on 47 pre-term babies at 40 weeks that had been delivered at 33 weeks

The team also collected information about how the infants had been fed while in intensive care — either formula milk or breast milk from either the mother or a donor.

Babies who exclusively received breast milk for at least three-quarters of the days they spent in hospital showed improved brain connectivity compared with others.

The effects were greatest in babies who were fed breast milk for a greater proportion of their time spent in intensive care.

HealthDay  reports on a paper in the journal Pediatrics where scientists compared the “healthy weight trajectory” of babies who were fed directly from the breast, or by pumping, or by formula. Healthy weight gain was best for those babies with direct breast feeding, scientists found. “Researchers stressed that breast milk, in any form, is better than formula,” they said. “But they said the findings support the notion that the method of feeding matters, too.” Often this is difficult for mothers having to work. A healthy society should promote this natural function of mother and baby.

Liver

The liver is appropriately named; it wants to live. It has an uncanny ability to regenerate itself, and can regrow 70 percent of its mass in a few weeks if damaged, and function like new. Researchers at the University of Illinois wondered how it does that at the molecular level. The secret involves signaling and alternative splicing that puts the liver back into a neonatal state:

“We found that the liver cells after birth use a specific RNA-binding protein called ESRP2 to generate the right assortment of alternatively spliced RNAs that can produce the protein products necessary for meeting the functional demands of the adult liver,” said graduate student Sushant Bangru, the lead author of the study. “When damaged, the liver cells lower the quantity of ESRP2 protein. This reactivates fetal RNA splicing in what is called the ‘Hippo signaling pathway,’ giving it instructions about how to restore and repopulate the liver with new and healthy cells.”

Conclusions

Many non-living objects, such as crystals and metals, look the same practically all the way down. Living things, by contrast, become more wondrous as you zoom in from organism to organ to tissue to cell to nucleus. New imaging techniques are bringing wonders into focus that were unimaginable for most of human history. If ever there was a heyday for intelligent design.