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Monday 7 December 2015

A clash of titans.

I.D continues to run up the score.

Less Junk, More ID Predictions Confirmed
December 7, 2015 Posted by PaV under Intelligent Design

It is simply a matter of time before the Darwinists (I know they prefer “evolutionary biologists,” but evolution is not evolution without “Origin of Species”) will have to give up.

Every day in labs around the world, more and more function is being found for “junk” DNA. This is a two-fold problem for the Darwinists.

The first problem is that this is NOT what they predicted, even though, quite cavalierly, they say then never said any such thing. But, of course, we know better.

Second, there’s the problem of “de novo” genes, and the solution for this is to look to so-called “junk” DNA as a potential template for these ‘new’ genes. If “junk” DNA is ‘neutral,’ then no problem; but if it has a function, then the nursery from which they can harvest “de novo” genes from within the genome lessens. As I say, it’s a matter of time.

From Phys.Org we have a snippet from a news summary:

In the first study to run a genome-wide analysis of Short Tandem Repeats (STRs) in gene expression, a large team of computational geneticists led by investigators from Columbia Engineering and the New York Genome Center have shown that STRs, thought to be just neutral, or “junk,” actually play an important role in regulating gene expression. The work, which uncovers a new class of genetic variants that modulate gene expression, is published on Nature Genetics’s Advance Online Publication website on December 7.

Erlich’s study looked at Short Tandem Repeats (STRs), variants that create what look like typos: stutter vs. stututututututter. Most researchers, assuming that STRs were neutral, dismissed them as not important. In addition, these variants are extremely hard to study. “They look so different to analysis algorithms,” Erlich notes, “that they just usually classify them as noise and skip these positions.”

And, revealing a mechanism I have long suspected could be the true purpose, or function, of these repeated elements, they say:


Erlich used a multitude of statistical genetic and integrative genomics analyses to reveal that STRs have a function: they act like springs or knobs that can expand and contract, and fine-tune the nearby gene expression. Different lengths correspond to different tensions of the spring and can control gene expression and disease traits.

File under 'well said' XVI

Whatever is begun in anger ends in shame.
Benjamin Franklin

Psalm46 New World Translation(2013 Edition)

46)1.God is our refuge and strength,+
A help that is readily found in times of distress.+
 2 That is why we will not fear, though the earth undergoes change,
Though the mountains topple into the depths of the sea,+
 3 Though its waters roar and foam over,+
Though the mountains rock on account of its turbulence. (Selah)
 4 There is a river the streams of which make the city of God rejoice,+
The holy grand tabernacle of the Most High.
 5 God is in the city;+ it cannot be overthrown.
God will come to its aid at the break of dawn.+
 6 The nations were in an uproar, the kingdoms were overthrown;
He raised his voice, and the earth melted.+
 7 Jehovah of armies is with us;+
The God of Jacob is our secure refuge.* (Selah)
 8 Come and witness the activities of Jehovah,
How he has done astonishing things on the earth.
 9 He is bringing an end to wars throughout the earth.+
He breaks the bow and shatters the spear;
He burns the military wagons* with fire.
10 “Give in and know that I am God.
I will be exalted among the nations;+
I will be exalted in the earth.”+
11 Jehovah of armies is with us;+
The God of Jacob is a secure refuge for us.+ (Selah)

On global peace:The Watchtower Society's commentary.

Peace on Earth—How Will It Come?:

The Bible’s answer:
Peace on earth will come, not by human efforts, but by means of God’s Kingdom, a heavenly government ruled by Christ Jesus. Notice how the Bible teaches us about this wonderful hope.

God will make “wars to cease to the extremity of the earth,” fulfilling his promise to bring “peace on earth to those with whom he is pleased!”—Psalm 46:9; Luke 2:14, Good News Translation.
God’s Kingdom will rule from heaven over the entire earth. (Daniel 7:14) As a world government, it will eliminate nationalism, which is at the root of many conflicts.
Jesus, the Ruler of God’s Kingdom, is called the “Prince of Peace,” and he will ensure that “to peace there will be no end.”—Isaiah 9:6, 7.
People determined to keep fighting will not be allowed to live under the Kingdom, since “anyone loving violence [God’s] soul certainly hates.”—Psalm 11:5; Proverbs 2:22.
God teaches his subjects how to live in peace. Describing the results of this instruction, the Bible says: “They will have to beat their swords into plowshares and their spears into pruning shears. Nation will not lift up sword against nation, neither will they learn war anymore.”—Isaiah 2:3, 4.
Already, millions of Jehovah’s Witnesses around the world are learning from God how to be peaceable. (Matthew 5:9) Although we belong to many different ethnic groups and live in over 230 different lands, we refuse to take up arms against our fellow man.


Jehovah’s Witnesses are learning the ways of peace today

Was God the original Rube Goldberg?

In Shadow of Oz, Biologist Wayne Rossiter Critiques Theistic Evolution
Casey Luskin December 6, 2015 12:26 PM 


A new book, Shadow of Oz: Theistic Evolution and the Absent God, by Wayne Rossiter, offers a keen scientific, philosophical, and theological critique of theistic evolution. Rossiter, who holds a PhD in biology from Rutgers where he studied ecology and evolution, is an assistant biology professor at Waynesburg University. Because he has interests in both the scientific and the philosophical/theological dimensions of the debate over Darwinian evolution, Shadow of Oz is one of the most comprehensive books critiquing theistic evolution to date.The title is a reference to The Wizard of Oz, in which Dorothy is told that you can never see the "Wizard" and so she reasonably asks, "Well, then -- how do you know there is one?" By analogy, Rossiter argues that theistic evolution gives no reasons to believe there is a God guiding nature. In his view, intelligent design offers a much more satisfying approach.

Rossiter tells some of his own personal story. He entered grad school as a "staunch and cantankerous atheist," studying under "an equally atheistic advisor who was of Dawkins's ilk." But soon he started having doubts about atheism, sparked in part by his increasing doubts about Darwin. As he puts it:

I started to read and listen to scientists and intellectuals who had found faith in God compelling. Just as I was converting, so too was the famed atheist Antony Flew (though never to Christianity). I started to realize that there were good reasons to doubt the metanarrative of naturalism (the centerpiece of which is Darwinian evolution), and that many secular thinkers in fields related to the topic had also come to doubt the entire enterprise (and Darwin in specific). (p. 5)
After going through a deconversion process, leaving behind atheism and Darwinism, and now with a doctorate in hand, he landed a job teaching biology at a Christian university. There, however, he saw that many Christian students were moving in the opposite direction. Under the influence of the Darwinian evolution they had been dogmatically taught they must believe, they were losing their religious faith:
As a Christian professor at a Christian university, I can attest to the countless students who find the central tenets of their Christian faith difficult to retain in light of the neo-Darwinian theory of evolution, or more precisely, its implications. (p. 5)
Rossiter appreciates the confusing and conflicting messages, and the misinformation about Darwinism, that students face:
Proponents [of theistic evolution] argue that the idea of God is perfectly compatible with evolutionary theory, that there are no doubts regarding the full efficacy of Darwin's theory, and that acceptance of the full form of this theory should have no real bearing on our capacity to believe in the Judeo-Christian God. This is a startling juxtaposition. On the one hand, numerous secular evolutionists have told us that Darwin greatly compromises faith in a God that is (or ever was) active in his creation, and that there is no need for theology in our descriptions of the workings of the natural world. On the other hand, theistic evolutionists are pushing Darwin in every aspect of our faith discussion. Moreover, they present it as if there is no conflict between the two ideas (Darwin and God). The Christian student sitting in a high school or college classroom is told not to be uncomfortable with what Darwin has to say. Our educators point to names like Francis Collins or the late Theodosius Dobzhansky, and say, "See. These scientists are Christians, and yet they accept Darwin." So the theist is being asked to fully ascribe to Darwinian evolution. But none of these educators, lecturers, or writers are making an equally forceful case to atheistic evolutionists that, "These evolutionists also believe in God." (p. 6)
He makes an apt point. In the "conversation" that theistic evolutionists say they want to have about science and faith, theistic evolutionists capitulate to nearly all of the ideas and beliefs of atheists, thinking this will somehow attract atheists into the religious camp. It won't work, because theistic evolutionists almost never challenge anything at the core of atheist beliefs. This leaves Christians -- and anyone else for that matter -- facing some confusing and conflicting messages:
"New Atheists" proclaim that neo-Darwinian evolution is unassailable and refutes Christianity, and that we have no scientific evidence that God exists. As one New Atheist author puts it, "There is no God, no Intelligent Designer, and no higher purpose to our lives."
The increasingly vocal theistic evolutionist camp claims neo-Darwinian evolution is correct, perfectly compatible with Christianity, and we have no scientific evidence that God exists. If you disagree, you'll be labeled ignorant, "anti-science," and an embarrassment to the church.
Shadow of Oz cuts through this confusion. Quoting numerous leading writers, Rossiter first explains the illogic of theistic evolutionist attempts to reconcile God with Darwin. His logic is devastatingly clear and simple: "[T]he Darwinian paradigm stands opposed to the classical understanding of a Christian God. The reason is plain and obvious; something cannot be intended and unintended at the same time." (p. 28)

Then, he puts his biologist hat on and asks (my paraphrase), "Why would anyone try to reconcile God with Darwin when the modern Darwinian viewpoint is so scientifically flawed?" Since I'm more of a science-nerd than a philosopher, this is my favorite part of the book. After all, if Darwinian evolution is wrong, why waste time trying to go through illogical attempts to reconcile it with theism? Again, Rossiter's framing of the issue is spot-on:

The second [premise of theistic evolution] -- that Darwin's theory explains nature -- is the appraisal of the theistic evolutionist, but is frankly no longer a consensus among biologists. I will pause here briefly to illustrate another spurious position. In his book, The Language of God, [Francis] Collins finds "overwhelming" evidence for Darwinian evolution. Among those evidences is junk DNA, shared pseudo-genes, the DNA-based case for universal common descent, and several cases of microevolution. As Jonathan Wells has written, many of Collins's points of evidence have either been entirely reversed, have been called into question, or require additional assumptions. I deal with many of these in Chapter 6 of this book. (p. 47)
Rossiter explains what many college students face from their professors:
Most freshmen in college get a cursory treatment of evolutionary theory, and the assurance that it somehow will not erode or alter their beliefs or sense of being. As Richard T. Wright has written, the trick for theistic evolutionists is, "on the one hand to deny the worldview extensions of evolution, and on the other to claim the evolutionary process as part of God's activity in his world." This is dangerous and intentional intellectual dishonesty. (p. 104)
How do theistic evolutionists affirm that blind, chance-based processes are what created us -- but then deny that blind, chance-based processes are what created us? According to Rossiter, it's because their "loyalties lie with Darwin, but they deeply desire to hang on to their prior religiosity." (p. 105) Yet Rossiter finds that Darwin is scientifically wrong, so the loyalties of theistic evolutionists are entirely misplaced. He knows what the evidence says, and he reviews many scientific problems with Darwinian evolution. He discusses:
Mainstream scientists who now challenge the efficacy of Darwinian theory as evidence mounts against it.
Why homology cannot be used as an argument for common ancestry, and how DNA evidence fails to generate a grand "tree of life." This leads to the following apt riposte from Rossiter: "When Karl Giberson claims that, Biologists today consider the common ancestry of all life a fact on par with the sphericity of the earth or its motion around the sun, he seems to be massively overstating the degree of scientific consensus."
The lack of fossil evidence for common ancestry.
The difficulty with demonstrating the veracity of many adaptive explanations for the origin of complex features.
That last argument is one of my favorites in the book. Ask anyone why cheetahs run fast and they will tell you, "Why of course it's to catch gazelles (or other fast prey)." But there are many tasty, nutritious animals that run much slower than gazelles, so why couldn't cheetahs just catch slower prey that didn't require so much specialized musculature to allow them to run fast? Rossiter elaborates on why adaptive explanations that "everyone knows are true" are often much less obvious than they would seem:

The classic co-evolutionary "arms race" between cheetahs and gazelles is a surprising example. The assumption is that these two species have been tightly bound to one another, such that the strongest selective pressure acting on one is the other, and that this dynamic has been persistent over evolutionary time. An ancestral cheetah eats an ancestral gazelle. The ancestral cheetah is blessed with a faster phenotype that enables it to more efficiently capture gazelles. The ancestral gazelle is then under a strong selective pressure, which can be satisfied by a reciprocal increase in speed. Back-and-forth the two species go, until we end up with two of the fastest species on land, still interacting in space and time. So, what evidence exists for such a story? The answer is surprising: very little. The prominence of this story is a consequence of the rhetorical force that all evolutionary post hoc explanations carry. In present day savannas cheetahs eat gazelles. Cheetahs are very fast. So too are gazelles. Their living relatives are not as fast. Therefore, as the circular logic dictates, selection has acted to preserve changes that increased speed in both species.
So, try it for yourself. Use the search engine (or textbooks) of your choosing and find a paper that demonstrates the specific adaptations ... that led to this current situation. It gets messy immediately. You get tacit admissions like, "The big cat's evolutionary history is poorly understood because few fossils have been found" and great debate over which big cat is related to which other cats, and from whence all big cats come (and when). ... Where Darwin's general theory (as well as the extensions like this scenario) postulates a series of incremental, back-and-forth nudges from one form to the next, implicating selection the entire time, the evidence is not forthcoming, and is never discussed in the public. (pp. 134-135)

Throughout, Rossiter's depth of reference to the literature is very impressive. The book aims to be readable by a non-specialist. It is full of citations to and quotations from the literature of theistic evolutionists, atheistic evolutionists, and mainstream scientific papers. This will satisfy the technical reader and the lay reader.
More importantly, Rossiter is keenly aware of the theological and scientific arguments that theistic evolutionists make, and he's got ready rebuttals to nearly all of them. If you are a college student hearing professors tell you (a) that Darwinian evolution is perfectly compatible with faith, and (b) that Darwinian evolution is unquestionably scientifically correct -- but you sense that your professor isn't telling the whole story -- then you need to put Shadow of Oz on your Christmas wish list. If you know a college student who is going through the typical pro-Darwin indoctrination program that so many undergraduates face, then you need to buy this book for your friend. In fact, Christmas might not be soon enough.

On pitching a design inference to a hostile audience II

How Do We Know These Artifacts Are Designed if We Don't Know the Designer?
Evolution News & Views December 7, 2015 3:50 AM

We don't know who made them. We don't know how they were made. We don't know what purpose they served. But we know they were intentionally made by mindful individuals. At least, Live Science never questions the design inference about strange stone structures in Middle Eastern deserts that are shaped like wheels, triangles, and long lines (see the photo gallery). Why is design the obvious inference?

There are hundreds of these structures. They extend over much of the Middle East: Syria, Jordan, Saudi Arabia, and Yemen.

The "works of the old men" include wheels, which often have spokes radiating out from the center, kites (stone structures used for funnelling and killing animals), pendants (lines of stone cairns) and meandering walls, which are mysterious structures that meander across the landscape for up to several hundred feet.

The works "demonstrate specific geometric patterns and extend from a few tens of meters up to several kilometers, evoking parallels to the well-known system of geometric lines of Nazca, Peru," wrote an archaeological team in a paper published recently in the Journal of Archaeological Science. (Peru's Nazca Lines date to between 200 B.C. and A.D. 500.). [Emphasis added.]

World War I pilots readily inferred they were man-made. Bedouins call them the "works of the old men," but apparently do not know who the "old men" were. It's not clear what they were used for. The wheels might have been for forecasting seasons, since they tend to be aligned northwest to southeast to match sunrise at the winter solstice. But why the triangles? And the hundreds of "gates" with their long parallel lines? Who would make large structures that can't be seen readily from ground level?

Why people in prehistoric times would build wheel-shaped structures that can't be seen well from the ground remains a mystery. No balloon or glider technologies existed at that time. Additionally, researchers say that climbing to a higher elevation to view them was probably not possible, at least not in most cases.

New research using optically stimulated luminescence on the stones has produced dates of about 8,500 years for a couple of the structures. That makes them older than the Nazca lines. Were they burial structures? Signals to their gods? Animal traps?

Other points of interest aside, the mystery serves to illustrate the logic of the design inference. These structures demonstrate that it's not necessary to know (1) the identity of the designer, (2) the motivation or purpose of the designer, or (3) the function of the design. It's also not necessary to know when they were made, or how.

To make the design inference robust, however, it's important not to jump to conclusions. There are similar shapes in nature that are not considered designed. In fact, there are vast areas of circular shapes in the Namibian desert that have defied explanation for years (see Science Daily).

Desert fairy circles are considered one of nature's greatest mysteries because no one knows how they form. Different from mushroom rings, these fairy circles are large barren patches of earth ringed by short grass dotting the desert like craters on the moon or big freckles. Several groups are racing to figure out this bizarre phenomenon.

Geometric structures made by animals -- like circular shells of diatoms, bird nests, or honeycombs -- we do not attribute to the work of sentient beings. These are built instinctively for reproduction, feeding, or other life necessities. Intelligent agents like humans can organize natural materials for necessities, too, but have the free will to make things for other purposes -- "gratuitous" purposes like art, conceptual communication or ritual. Crows and chimps can make crude tools, but humans can make tools to make other tools. Animals make tools to eat. Humans make tools to explore outer space and email currency across the globe.

Admittedly those are extreme examples. The line can get fuzzy in the middle. So how do we infer design for the geoglyphs in Jordan, but not the fairy circles in Namibia or the intricate circles in diatom shells? Here is where the Design Filter comes in:

Can the geoglyphs be explained by chance? No; stones do not randomly collect into triangles, wheels with spokes, and parallel lines due to unguided causes like storms or earthquakes. Circular craters can emerge by chance, due to meteor impacts or volcanic eruptions, but they do not look like these, and there is no evidence of shocked minerals or lava present.

Can they be explained by natural law? Natural forces can produce spirals like galaxies and hurricanes. They do not typically produce spoked wheels or triangles (see this earlier article at Evolution News). A bent-over blade of grass could trace out a circle as the wind shifts direction, like a compass. Snowflakes can produce a semblance of spoked wheels, but we know about the atomic forces that cause water to crystallize in hexagonal shapes. Nothing like that works on the scale of kilometers to arrange stones that way, especially aligning them with sunrise at winter solstice.

Is there a specification? Yes; we see an independent specification of the solstice that could guide a sentient being to choose to arrange stones with that preferred orientation. We also understand the human mind's attraction for geometry and mathematics.

To be sure, the design inference for these structures is more intuitive than robust. It's conceivable that scientists may find a combination of natural laws and chance that generates these structures in that part of the world; unlikely, but possible. And since we don't know of any clear purpose for the structures, our third test (specification) is weaker than one might like. Despite these caveats, the design inference is pretty sound. Nobody from the Bedouins to the pilots is questioning it. Compare this case to earlier archaeological mysteries that are more dubious.

Evolutionists try to explain the human mind as the product chance and natural law, claiming it is the product of natural selection. The human mind is like animal design, they will say, simply more of the same. What's the answer to that? Just turn it around. Such a position implies that the scientist's propensity to speculate about evolution is also a product of natural selection. So if the evolutionists' position is the result of blind, unguided processes, and if mental activity is an illusion, then reason evaporates; they have no way of knowing anything is true. John West's book The Magician's Twin sheds further light on this "argument from reason."


Meanwhile, design advocates think that animals and their designs pass the design filter, too. Their bodies, behaviors, and instincts are the products of genetic instructions, making them act in a programmed way. We reasonably infer that their origins are the result of an intelligent cause.