One more reason to doubt.

Fossil Discovery Adds Another Phylum to the Cambrian Explosion

Casey Luskin December 15, 2015 2:04 PM 

The Cambrian explosion just got a bit more explosive with the discovery of a likely member of phylum Kinorhyncha from rocks in South China that are about 530 million years old. If you've never heard of kinorhynch worms, also called "mud dragons," that's probably because they are very tiny, seldom discussed, and found living only in certain marine environments around the world. As the Encyclopedia of Life explains:

Around 150 species of kinorhynchs have been described since this group was first discovered on the northern coast of France in 1841, nearly all of them less than 1 mm long. They have been collected as far north as Greenland and as far south as Antarctica, as well as in the Black Sea. Most live in marine sand or mud from the intertidal zone to a depth of 5000 to 8,000 meters, but some are known from algal mats or holdfasts, sandy beaches, and brackish estuaries and others have been found living on hydrozoans, bryozoans, or sponges.

Science Daily reports on the fossil, noting that "[a]n historic find --- made in South China -- fills a huge gap in the known fossil record of kinorhynchs," since the new fossil species, Eokinorhynchus rarus, is very similar to living kinorhynchs:

Similarities between the fossils of E. rarus and living, modern kinorhynchs include their hollow spines arranged in a five-fold symmetry and their body segments each consisting of articulated plates. However, E. rarus differs from modern species with more numerous segments. Hence the belief of an ancestorship.

The technical paper, "Armored kinorhynch-like scalidophoran animals from the early Cambrian," puts it this way:

Here we describe several early Cambrian (~535 million years old) kinorhynch-like fossils, including the new speciesEokinorhynchus rarus and two unnamed but related forms. E. rarus has characteristic scalidophoran features, including an introvert with pentaradially arranged hollow scalids. Its trunk bears at least 20 annuli each consisting of numerous small rectangular plates, and is armored with five pairs of large and bilaterally placed sclerites. Its trunk annuli are reminiscent of the epidermis segments of kinorhynchs.... Eokinorhynchus rarus also shows intriguing similarities with extant kinorhynchs, suggesting a close phylogenetic relationship.

In Figure 2.5 of Darwin's Doubt, Steve Meyer reports that about 20 of 27 animal phyla with known fossil records appear in the Cambrian period. Prior to this find, phylum Kinorhyncha was not known to have a fossil record. Now we can update Meyer's tabulation to report that 21 of the 28 phyla with known fossil records apparently first appear -- abruptly no less -- in the Cambrian explosion of animal body plans.

Despite this non-Darwinian pattern of origin, the papers' authors speculate that these ancient (and extant) kinorhynchs might shed light on the origin of arthropods, but that's largely only because they are segmented -- as various other living phyla are as well. Given that kinorhynchs entirely lack limbs and also lack arthropod-like eyes, it seems that they aren't going to help us much towards understanding the unique defining characteristics of arthropods.

The paper also explains that these fossils come from about 535 million years ago in a section of strata bearing the "small shelly fossils," in the early Cambrian period. As Meyer and I have discussed, some mistakenly cite the "small shelly fossils" (SSFs) as possible evidence of a gradual evolution of the Cambrian animals. But in this case, studies of the SSFs are showing the Cambrian explosion to be more explosive.

The paper even suggests that studying these enigmatic SSFs may reveal that known phyla are represented in species not previously assigned to living groups:

Nonetheless, the paleontological data and phylogenetic interpretation presented here invite further exploration of the phosphatization taphonomic window and careful re-examination of small shelly fossils (e.g., Paracarinachites spinus and Kaiyangites novoli) in search of Cambrian kinorhynchs.

If they're right, then correctly classifying SSFs might be key to understanding the abrupt appearance, not gradual evolution, of the Cambrian phyla. This reminds me of a comment by Douglas Erwin and James Valentine in The Cambrian Explosion where they predicted that even some small and soft-bodied phyla without fossil records likely first appeared in the early Cambrian:

[A] great variety and abundance of animal fossils appear in deposits dating from a geologically brief interval between about 530 to 520 Ma, early in the Cambrian period. During this time, nearly all the major living animal groups (phyla) that have skeletons first appeared as fossils (at least one appeared earlier). Surprisingly, a number of those localities have yielded fossils that preserve details of complex organs at the tissue level, such as eyes, guts, and appendages. In addition, several groups that were entirely soft-bodied and thus could be preserved only under unusual circumstances also first appear in those faunas. Because many of those fossils represent complex groups such as vertebrates (the subgroup of the phylum Chordata to which humans belong) and arthropods, it seems likely that all or nearly all the major phylum-level groups of living animals, including many small soft-bodied groups that we do not actually find as fossils, had appeared by the end of the early Cambrian. This geologically abrupt and spectacular record of early animal life is called the Cambrian explosion. (The Cambrian Explosion, p. 5, emphases added)

It would seem that this new small, soft-bodied fossil find confirms that Erwin and Valentine are probably correct.

A clash of titans II

On countering criminal recidivism:The Norwegian experience.

another failed Darwinian prediction.

Competition is greatest between neighbors:

Darwin’s basic theory of evolution, by itself, did not account for the tree-like, hierarchical pattern the species were thought to form. Darwin was keenly aware of this shortcoming and wrestled with it for years. He finally conceived of a solution for why modified offspring would continue to evolve away and diverge from their parents. The principle of divergence, the last major theoretical addition before Darwin published his book, held that competition tends to be strongest between the more closely related organisms. This would cause a splitting and divergence, resulting in the traditional evolutionary tree pattern. (Desmond and Moore 1991, 419-420; Ridley, 378-379)

But no such trend has been observed. In a major study of competition between freshwater green algae species, the level of competition between pairs of species was found to be uncorrelated with the evolutionary distance between the pair of species. As the researchers explained, Darwin “argued that closely related species should compete more strongly and be less likely to coexist. For much of the last century, Darwin’s hypothesis has been taken at face value […] Our results add to a growing body of literature that fails to support Darwin’s original competition-relatedness hypothesis.” (Venail, et. al., 2, 9) The team spent months trying to resolve the problem, but to no avail. As one of the researchers explained:

It was completely unexpected. When we saw the results, we said “this can’t be.” We sat there banging our heads against the wall. Darwin’s hypothesis has been with us for so long, how can it not be right? … When we started coming up with numbers that showed he [Darwin] wasn’t right, we were completely baffled. … We should be able to look at the Tree of Life, and evolution should make it clear who will win in competition and who will lose. But the traits that regulate competition can’t be predicted from the Tree of Life. (Cimons)

Why this long-standing prediction was not confirmed remains unknown. Apparently there are more complicating factors that influence competition in addition to evolutionary relatedness.

References

Cimons, Marlene. 2014. “Old Idea About Ecology Questioned by New Findings.” National Science Foundation.

Desmond, Adrian, James Moore. 1991. Darwin: The Life of a Tormented Evolutionist. New York: W. W. Norton.

Ridley, Mark. 1993. Evolution. Boston: Blackwell Scientific.

Venail , P.A., A. Narwani , K. Fritschie, M. A. Alexandrou, T. H. Oakley, B. J. Cardinale. 2014. “The influence of phylogenetic relatedness on competition and facilitation among freshwater algae in a mesocosm experiment.” Journal of Ecology, DOI: 10.1111/1365-2745.12271.

A line in the sand XXVII

A line in the sand. XXVI

Yet more Darwinian Hagiography

Darwin's Origin Is Voted Most "Influential," but Here's the Rest of the Story
Sarah Chaffee December 9, 2015 11:13 AM 


Recently to mark Academic Book Week, Charles Darwin's On the Origin of Species was named history's most influential academic book. Out of twenty titles (including works by Plato, Shakespeare, and Marx) assembled by librarians, publishers, and booksellers in the UK, the public voted Darwin's as the most significant.

But in terms of actual scientific value and influence, the Origin may not be number one. Writing in The Guardian, Rebekah Higgitt recommends a different title -- Newton's Principia. She notes:

Along with Opticks it was widely and internationally revered for centuries, setting the model for what successful scientific results and programmes of research should look like. It was not just central to mathematical physics and astronomy, for the aim of developing predictive mathematical theories became the ultimate goal across nearly all sciences and beyond...

...Principia's mathematics may have been improved and developed, but it set the agenda and the theory remained triumphant until the early 20th century and, even after Einstein, has not been overthrown -- after all, it was what was required to land a rocket on the moon.

Asking whether a book has enabled further scientific discoveries seems like a reasonable criterion. Measured that way, contrary to what some have asserted, On the Origin of Species falls short. Judged for its heuristic value, evolutionary theory has had little impact on biology research or medical advancement. Even Jerry Coyne admits as much, writing in Nature:

[I]f truth be told, evolution hasn't yielded many practical or commercial benefits. Yes, bacteria evolve drug resistance, and yes, we must take countermeasures, but beyond that there is not much to say. Evolution cannot help us predict what new vaccines to manufacture because microbes evolve unpredictably. But hasn't evolution helped guide animal and plant breeding? Not very much. Most improvement in crop plants and animals occurred long before we knew anything about evolution, and came about by people following the genetic principle of "like begets like."

But while Darwin's work hasn't done a lot for science or medicine, it has had a great influence on culture.

University of Glasgow's Professor Andrew Prescott told The Guardian:

Darwin used meticulous observation of the world around us, combined with protracted and profound reflection, to create a book which has changed the way we think about everything -- not only the natural world, but religion, history and society. Every researcher, no matter whether they are writing books, creating digital products or producing artworks, aspires to produce something as significant in the history of thought as Origin of Species.

While Prescott praises Darwin's book, the work's influence over the past 150 years, its popularity and acclaim, could rightly be called tragic. Discovery Institute's John G. West summarizes in the Preface to Darwin Day in America: How Our Politics and Culture Have Been Dehumanized in the Name of Science:

At the dawn of the last century, leading scientists and politicians giddily predicted that modern science -- especially Darwinian biology -- would supply solutions to all the intractable problems of American society, from crime to poverty to sexual maladjustment.

Instead, politics and culture were dehumanized as a new generation of "scientific" experts began treating human beings as little more than animals or machines:

In criminal justice, these experts denied the existence of free will and proposed replacing punishment with invasive "cures" such as the lobotomy.

In welfare, they proposed eliminating the poor by sterilizing those deemed biologically unfit.

In business, they urged the selection of workers based on racist theories of human evolution and the development of advertising methods to more effectively manipulate consumer behavior.

In sex education, they advocated creating a new sexual morality based on "normal mammalian behavior," without regard to longstanding ethical or religious imperatives.

See the trailer for Dr. West's book here.

Since the Origin won its latest accolade in the context of Academic Book Week, it's fair to ask what defines an academic book. A fairly coherent standard would be to evaluate a book's contribution to its specific field - be that mathematics, politics, English, philosophy, or natural sciences. Experts could evaluate the scope of its contribution or its importance to further developments in the field. Otherwise, the quest for "most influential academic book" devolves into a popularity contest. In that case, why limit it to academic books at all?

So is On the Origin of Species the most influential academic book? Probably not. Unfortunately, as we know too well, it has been and remains one of the most influential and popular works in the world for reasons that are not necessarily academic at all.

But there is something very positive about the book, a quality that I wish were more influential. Darwin was a great writer, and a candid one. In the Origin, he was very open about possible challenges to his theory. He understood that it had significant potential weaknesses. As Darwin famously noted, "A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question..." He knew that his work must be treated as open to scrutiny.


Yet today, schools present evolution to students as scientific fact. What we need in education is more candor and objectivity -- to look at "the facts and arguments on both sides" of the debate, just as Darwin urged. Students could learn from his humility. So could we all.

The enigma that fuels the doubt

Is the real planet of the apes coming soon?

Stand by for apes entering the Stone Age
December 11, 2015 Posted by News under Animal minds, Intelligent Design




As we saw with tool use, many claims [about ape behaviour] are phrased essentially as predictions that the primates are in the process of developing a culture like that of humans, rather than behaving as they have, largely unnoticed, for tens of millennia. For example, we were told earlier this year that “Apes may be closer to speaking than many scientists think. Koko, the gorilla who has lived with humans for forty years can “control her larynx enough to produce a controlled grunting sound.” While Koko is a very accomplished gorilla, she doesn’t seem to be progressing toward human speech, and it is unclear why she would need to.

Similarly, we are told that bonobo infant noise points to the origin of human language and can challenge “how we think about the evolution of communication and potentially move the dividing line between humans and other apes.” Really? Despite having done nothing similar for bonobos in all this time? We also hear that monkeys recognize the basic structure of language, but they do not go on to but develop a language either.

In any event, when primate researchers say that bonobo infant noise challenges “how we think about the evolution of communication and potentially move the dividing line between humans and other apes,” who are the “we” who are challenged? They themselves seem quite convinced that there is no significant dividing line, no matter what the state of the evidence.

And their position cannot easily be assailed. They can go on looking for evidence indefinitely, and the developments in ape consciousness that would prove them right would, if they ever occur, be millennia in the future.

Meanwhile, subsequent research did not support one claim that chimps learn other troupes’ “languages.”More.

Lots of people have to want to believe this stuff. Otherwise, it would be challenged more.

Question: Couldn’t we care about apes, humane treatment of apes, and their conservation without all the “just like us” nonsense? Do current stats show that the nonsense is really helping numbers?:

Gorilla and chimpanzee populations in Central Africa continue to decline due to poaching, habitat loss and disease. National parks and reserves in six range countries protect only 21 percent of western lowland gorillas and central chimpanzees, according to a new report.


See also: What can we hope to learn about animal minds?

The lion and the lamb may be able to get along after all.

Converting carnivores to herbivores
December 12, 2015 Posted by News under Evolution, Genetics, News


By knocking out plants’ don’t-eat-my-seeds chemicals

From The Scientist:

Researchers are converting carnivores into herbivores in a bid to make raising animals such as alligators, trout, and salmon more sustainable.

It’s no mean feat turning a meat-hungry predator into a plant eater. The American alligator is an apex predator of southern waterways from Texas to the Carolinas. In the wild, adult alligators eat fish, frogs, turtles, snakes, birds, and just about any small mammal they can catch. On alligator farms, the animals chow down on fishmeal and oil processed from wild stocks of sardines, anchovies, and other forage fish harvested from the open ocean. While populations of these fish species have plummeted over the past two decades due to intense fishing pressure, global demand for fishmeal and fish oil has continued to climb, and prices have quadrupled in recent decades. Now, researchers are searching for alternative feed ingredients for alligators and other carnivores farmed for human consumption.

Talk about the lion lying down with the lamb … the alligators were switched from fishmeal to vegan with only a slight reduction in growth.

Scientists have learned that fishmeal and fish oil contain a balance of about 40 nutrients, including vitamins A and D, amino acids (such as methionine and lysine), minerals (such as iron, zinc, selenium, and iodine), and long-chain fatty acids. More.

The trick is to balance the nutrients so that the ‘gator version of Boost is equivalent to the nutrients from whatever the ‘gator can catch.

Get this:

The most common ingredient today in aquaculture feed is soybeans. Soybean meal is widely available, nutritious, and relatively inexpensive, usually costing about one-quarter of fishmeal’s price. But soybeans, like many other plants, have evolved chemicals called “antinutrients” to discourage predators from consuming their seeds. Soybean’s antinutrients include lectins, oligosaccharides, and trypsin inhibitors. Each anti-nutrient might be harmless alone, but together they can cause an inflammatory condition in some fish called intestinal enteritis, which can reduce growth and produce additional waste that must be cleaned up.

They just happened to have evolved “antinutrients” and a chemical ecology balance was somehow struck.

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.

On the search for earth II

On the darkside of the net.

This time machine runs on elbow grease.

On tool making among subhuman primates.

Bonobos use tools on a “pre-agricultural” level?
December 5, 2015 Posted by News under Animal minds, Intelligent Design, News



From ScienceDaily:


Among other findings, a bonobo was observed for the first time making and using spears in a social setting for the purpose of attack and defense. “I believe that the current study will break down our cultural hang-up as humans concerning the inherent capabilities and potential of bonobos and chimpanzees,” says Itai Roffman of the Institute of Evolution at the University of Haifa, who undertook the study …

Interestingly, the bonobos are considered less sophisticated than their chimpanzee siblings. Chimpanzees have been observed in nature using branches to dig for tubers in the ground and to break into termite nests and beehives. As part of their cultural diversity, they have also been documented breaking nuts with hammer and anvil, and even manipulating branches into spears for use in hunting small prosimians that hide in tree hollows. By contrast, bonobos were known as a social species that engages in extensive sexual behavior and have not been observed in nature using tools. Roffman’s doctorate thesis (under the supervision of Professors Eviatar Nevo and Avraham Ronen of the University of Haifa) examines diverse pre-human/Homo characteristics among chimpanzees and bonobos. Three years ago, Roffman already managed to show that two bonobos were capable of preparing and using a range of early Homo type stone tools in order to reach inaccessible food in natural contexts. These two bonobos — famous siblings Kanzi and Pan-banisha — grew up in a human environment and have even learned to communicate using computerized English Lexigram symbols, allowing them to competently engage in rational discourse with humans.

More.

Okay. As soon as someone starts talking about “our cultural hang-up as humans concerning the inherent capabilities and potential of bonobos and chimpanzees,” we had better check the wind sock.

Chimpanzees use tools, so do ravens, and a variety of other species. So, while bonobo tool use is an interesting find, it is not a major or unexpected discovery.

It’s not clear what “pre-agricultural” means, but if we could come back fifteen thousand years from now, bonobos will probably still be doing it the same say.

The bonobos are not engaging in “rational discourse” with humans. They are using a sign language taught to them by humans. Alex the parrot also learned that. The trouble is, none of these species invent, develop, or pass on such languages, probably because they do not need them except to communicate with humans.


It’s quite possible that friendly contact with humans plays a role in how easily bonobos adapt to tools. They have hands, after all, so it isn’t difficult for them to see in principle, what could be done. A variety of animals can be taught to manipulate objects; they tend to reach a plateau that meets their needs and then stop learning*. But it is fun while it lasts.

I.D's opponents keep ignoring the scoreboard.

What is Wrong with Sober's Attack on ID? (Part III): Ignoring the Widely Discussed Positive Predictions of Intelligent Design
Casey Luskin March 30, 2007 2:30 AM

Philosopher Elliott Sober recently published an article entitled, "What is Wrong With Intelligent Design?" which claimed that intelligent design is not testable. In Part I, I rebutted Sober's early history of intelligent design. Part II explained how Sober made the curious charge that auxiliary prediction weaken the testability of a scientific theory, something which Darwinists are famous for doing. This third installment will assess Sober's characterization of ID and explain how Sober ignores positive predictions of intelligent design. Sober misses 2 key points about intelligent design, leading him to false conclusions:

(1) It's simple: intelligent design detects the past action of intelligence, nothing more, and nothing less

Sober states: "We have no independent evidence concerning which auxiliary propositions about the putative designer's goals and abilities are true." That's not correct. While the "goals" of the designer may be beyond the reach of the scientific inquiry, ID does make claims about the "abilities" of the designer. Sober then provides quotes from design-proponents, and he fails to recognize that they always refer to detecting intelligence! We understand the abilities of an intelligent agent and we understand what intelligence produces (discussed below). Sober doubly misrepresents ID: He wrongly expects ID to identify the "goals" of the designer, but then fails to recognize that ID identifies the "abilities" of the designer.

(2) Studies of intelligence show that a unique hallmark of intelligence is its ability to produce high levels of complex and specified information.

Intelligence is a feature we understand and comprehend from our studies of human intelligence in the natural world. From these studies, William Dembski explains that "the primarily, empirically verifiable thing that intelligences do is generate specified complexity." (Dembski, The Design Revolution, pg. 194). But does the generation of specified complexity make ID testable in a "comparative" sense (see Part II) with respect to neo-Darwinism? Yes, it does.

Dembski explains that natural processes like the neo-Darwinian mechanism do not generate high levels of specified complexity:

[Intelligent design is] a fully scientific claim and follows directly from the complexity-specification criterion. In particular this is not an argument from ignorance. Just as physicists reject perpetual motion machines because of what they know about the inherent constraints on energy and matter, so too design theorists reject any naturalistic reduction of specified complexity because of what they know about the inherent constraints on natural causes. Natural causes are too stupid to keep pace with intelligent causes. Intelligent design theory provides a rigorous scientific demonstration of this long-standing intuition. Let me stress, the complexity-specification criterion is not a principle that comes to us demanding our unexamined acceptance--it is not an article of faith. Rather it is the outcome of a careful and sustained argument about the precise interrelationships between necessity, chance and design.
(William Dembski, Intelligent Design: The Bridge Between Science and Theology, pg. 223 (InterVarsity Press, 1999).)

Thus, according to Dembski, intelligence produces highly specified complexity, but neo-Darwinian processes do not. Sober never mentions specified complexity once in his article, which is strange since it's such a central component of intelligent design today.
Sober Botches Irreducible Complexity
Similarly, Sober also ignores that irreducible complexity is a unique indicator of intelligent design, but he states that irreducible complexity "does nothing to test ID. For ID to be testable, it must make predictions." Claiming that irreducible complexity is nothing more than a critique of evolution, Sober writes "The fact that a different theory makes a prediction says nothing about whether ID is testable. Behe has merely changed the subject." Here, Sober is repeating the Darwinist plaintiffs' arguments in the Kitzmiller case. But Sober misrepresents ID and ignores the fact that ID theorists have argued extensively that irreducible complexity is not just a negative argument against evolution, but also a positive indicator of design. Behe writes:

[I]rreducibly complex systems such as mousetraps and flagella serve both as negative arguments against gradualistic explanations like Darwin's and as positive arguments for design. The negative argument is that such interactive systems resist explanation by the tiny steps that a Darwinian path would be expected to take. The positive argument is that their parts appear arranged to serve a purpose, which is exactly how we detect design.
(Michael Behe, Darwin's Black Box, Afterward, pgs. 263-264 (Free Press, Reprint, 2006), emphasis added.)

Similarly, Scott Minnich and Steve Meyer see that irreducible complexity is a unique, positive argument for intelligent design:
Molecular machines display a key signature or hallmark of design, namely, irreducible complexity. In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role the origin of the system. Given that neither standard neo-Darwinism, nor co-option has adequately accounted for the origin of these machines, or the appearance of design that they manifest, one might now consider the design hypothesis as the best explanation for the origin of irreducibly complex systems in living organisms. ... Although some may argue this is a merely an argument from ignorance, we regard it as an inference to the best explanation, given what we know about the powers of intelligent as opposed to strictly natural or material causes.
(Scott A. Minnich & Stephen C. Meyer, Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria, in Proceedings of the Second International Conference on Design & Nature.)


Incredibly, Sober makes no mention of the fact that design proponents have formulated irreducible complexity or specified complexity as positive indicators and predictions of design. He completely ignores these in order to make his central point that ID makes no positive predictions.

Machine code Vs. Darwinism.

Time Machine: An Early Argument for Intelligent Design
Granville Sewell December 1, 2015 5:45 PM

As I begin my 12th year of work on TWODEPEP (now PDE/PROTRAN), I am intrigued by the analogy between the 11-year evolution of this computer code and the multi-billion year history of the genetic code of life, which contains a blueprint for a species encoded into billions of bits of information. Like the code of life, TWODEPEP began with primitive features, being capable of solving only a single linear elliptic equation in polygonal regions, with simple boundary conditions. It passed through many useful stages as it adapted to non-linear and time-dependent problems, systems of PDEs, eigenvalue problems, and as it evolved cubic and quartic elements and isoparametric elements for curved boundaries. It grew a preprocessor and a graphical output package, and out-of-core frontal and conjugate gradient methods were added to solve the linear systems.

Each of these changes represented major evolutionary steps -- new orders, classes or phyla, if you will. The conjugate gradient method, in turn, also passed through several less major variations as the basic method was modified to precondition the matrix, to handle nonsymmetric systems, and as stopping criteria were altered, etc. Some of these variations might be considered new families, some new genera, and some only special changes.

I see one flaw in the analogy, however. While I am told that the DNA code was designed by a natural process capable of recognizing improvements but incapable of planning beyond the next random mutation, I find it difficult to believe that TWODEPEP could have been designed by a programmer incapable of thinking ahead more than a few characters at a time.

But perhaps, it might be suggested, a programmer capable of making only random changes, but quite skilled at recognizing improvements could, given 4.5 billion years to work on it, evolve such a program. A few simple calculations would convince him that this programmer would have to rely on very tiny improvements. For example, if he could produce a billion random "mutations" per second (or, for a better analogy, suppose a billion programmers could produce one "mutation" per second each), he could not, statistically, hope to produce any predetermined 20-character improvement during this time period. Could such a programmer, with no programming or mathematical skills other than the ability to recognize and select out very small improvements through testing, design a sophisticated finite element program?

The Darwinist would presumably say, yes, but to anyone who has had minimal programming experience such an idea is preposterous. The major changes to TWODEPEP, such as the addition of a new linear equation solver or new element, required the addition or modification of hundreds of lines of code before the new feature was functional. None of the changes made during this period were of any use whatever until all were in place.

Even the smallest modifications to that new feature, once it was functional, required adding several lines, no one of which made any sense, or provided any "selective advantage," when added by itself.

Consider, by way of analogy, the airtight trap of the carnivorous bladderwort plant, which has a double sealed, valve-like door which is opened when a trigger hair is activated, causing the victim to be sucked into the vacuum of the trap (described by R.F. Daubenmire in Plants and Environment, John Wiley and Sons, N.Y. 1947). It is difficult to see what selective advantage this trap provided until it was almost perfect.

This, then, is the fallacy of Darwin's explanation for the causes of evolution -- the idea that major (complex) improvements can be broken down into many minor improvements. French biologist Jean Rostand, in A Biologist's View (William Heinemann Ltd., London, 1956) recognized this:

It does not seem strictly impossible that mutations should have introduced into the animal kingdom the differences which exist between one species and the next...hence it is very tempting to lay also at their door the differences between classes, families and orders, and, in short, the whole of evolution. But it is obvious that such an extrapolation involves the gratuitous attribution to the mutations of the past of a magnitude and power of innovation much greater than is shown by those of today.

The famous "problem of novelties" is another formulation of the objection raised here. How can natural selection cause new organs to arise and guide their development through the initial stages during which they present no selective advantage, the argument goes. The Darwinist is forced to argue that there are no useless stages. He believes that new organs and new systems of organs arose gradually, through many small improvements. But this is like saying that TWODEPEP could have made the transition from a single PDE to systems of PDEs through many five or six character improvements, each of which made it work slightly better on systems.

It is interesting to note that this belief is not supported even by the fossil evidence. Harvard paleontologist George Gaylord Simpson, for example, in The History of Life, Volume II of Evolution after Darwin, (University of Chicago Press, 1960) points out:

It is a feature of the known fossil record that most taxa appear abruptly. They are not, as a rule, led up to by a sequence of almost imperceptibly changing forerunners such as Darwin believed should be usual in evolution...This phenomenon becomes more universal and more intense as the hierarchy of categories is ascended. Gaps among known species are sporadic and often small. Gaps among known orders, classes and phyla are systematic and almost always large. These peculiarities of the record pose one of the most important theoretical problems in the whole history of life: Is the sudden appearance of higher categories a phenomenon of evolution or of the record only, due to sampling bias and other inadequacies?

Another way of describing this same structure is expressed in a recent Life magazine article (Francis Hitching, "Was Darwin Wrong on Evolution?", April 1982, which concludes that "natural selection has been tested and found wanting") which focuses on the "curious consistency" of the fossil gaps:

These are not negligible gaps. They are periods, in all the major evolutionary transitions, when immense physiological changes had to take place.

Unless we are willing to believe that useless, "developing" organs (and insect traps which could almost catch insects) abounded in the past, we should have expected the fossil structure outlined above, with large gaps between the higher categories, where new organs and new systems of organs appeared.

Nevertheless, despite the fact that the structure of the fossil record is the only argument against Darwin which has received much attention lately, this is not the real issue. The "problem of novelties" correctly states the real argument, but too weakly. Consider, for example, the human eye, with an aperture whose size varies automatically according to the light intensity, controlled by reflex signals from the brain; with a lens whose curvature varies automatically according to the distance to the object in view; and with a retina which receives the picture on color sensitive cells and transmits it, complete with coded intensity and frequency information, through the optic nerve to the brain. The brain superimposes the pictures from the two eyes and stores this 3D picture somehow in memory, and it will be able to search for and recall this image later and use it to recognize an older but familiar face in a different picture. Like TWODEPEP, the eye has passed through various useful stages in its development, but it contains a large number of features which could not reach usefulness in a single random mutation and which provided no selective advantage until useful (e.g. the nerves and arteries which service it), and many groups of features which are useless individually. The Darwinist may bridge the gaps between taxa with a long chain of tiny improvements in his imagination, but the analogy with software puts his ideas into perspective. The idea that all the magnificent species in the living world, or the human brain with its human consciousness, could have arisen from simple organic molecules guided by a natural process unable to plan beyond the next tiny mutation, is entirely comparable to the idea that a programmer incapable of thinking ahead more than a few characters at a time could, given a lot of time, design any sophisticated computer program.


I suggest that, with Jean Rostand, "we must have the courage to recognize that we know nothing of the mechanism" of evolution.