The stones crying out again?

Did Archaeologists Discover The Biblical City Of Sodom?
Here's one potential site.
Carol Kuruvilla





The fiery fate of the doomed cities of Sodom and Gomorrah has captured the imaginations of artists, theologians and archaeologists for years. The book of Genesis describes how God "rained down burning sulfur" to punish those cities for their wickedness, destroying all living things inside of them.

But is there any proof that these cities really existed and that they were destroyed by a sudden The answer, for Dr. Steven Collins, a professor of Biblical studies and apologetics at Trinity Southwest University, is yes. He claims he may have located Sodom.

Since 2005, Collins and his team have been studying an archaeological site in the southern Jordan Valley known as Tall el-Hammam. After wrapping up the tenth season of excavations, he believes they've found a "goldmine of ancient monumental structures and artifacts" that suggests the site was a powerful city-state during the Early and Middle Bronze Ages (between 3,500 and 1540 B.C.)

Over the years, his research team has found evidence of a massive defensive wall, a palatial structure and a gateway complex that dates back to the Middle Bronze Age. During the 2015 season, the archaeologists found a few more towers and gates.

For Collins, all of this points to the fact that Tall el-Hammam was likely one of the largest cities east of the "Kikkar," a Hebrew word that describes the plains near the Jordan River. He also claims that Tall el-Hamman is strategically located near ancient water resources and trade routes.  calamity?The answer, for Dr. Steven Collins, a professor of Biblical studies and apologetics at Trinity Southwest University, is yes. He claims he may have located Sodom.

Since 2005, Collins and his team have been studying an archaeological site in the southern Jordan Valley known as Tall el-Hammam. After wrapping up the tenth season of excavations, he believes they've found a "goldmine of ancient monumental structures and artifacts" that suggests the site was a powerful city-state during the Early and Middle Bronze Ages (between 3,500 and 1540 B.C.)

Over the years, his research team has found evidence of a massive defensive wall, a palatial structure and a gateway complex that dates back to the Middle Bronze Age. During the 2015 season, the archaeologists found a few more towers and gates.

For Collins, all of this points to the fact that Tall el-Hammam was likely one of the largest cities east of the "Kikkar," a Hebrew word that describes the plains near the Jordan River. He also claims that Tall el-Hamman is The professor says there's a good chance that the Biblical text is referring to Tall el-Hammam when it describes Sodom.

"Tall el-Hammam seemed to match every Sodom criterion demanded by the [Bible]," he told Popular Archaeology. "When we explored the area, the choice of Tall el-Hammam as the site of Sodom was virtually a no-brainer since it was at least five to ten times larger than all the other Bronze Age sites in the entire region, even beyond the Kikkar of the Jordan."

His team also unearthed evidence that suggests the booming city came to a sudden end near the end of the Middle Bronze Age, which is close to the time that Collins believes the Biblical leaders Abraham and Lot walked the earth. It's unclear what caused the city's change in fortune, but one possibility is that it was destroyed by fire. The site reportedly remained a wasteland for about 700 years after this event.strategically located near ancient water resources and trade routes.  Collins isn't alone in his quest to find Sodom. Other scholars have suggested that Sodom and Gomorrah rose to prominence in the early Bronze Age and that they were located in different regions near the Dead Sea. 

Hershel Shanks, the editor of the Biblical Archaeology Review magazine, agreed that Tall el-Hammam seemed like it could be the site of ancient Sodom -- but he cautioned that locating an ancient city destroyed by God is at its core a theological question.

"Theological questions are not subject to scientific proof—or disproof.  But whoever wrote down this text did have some site in mind when he said that God destroyed Sodom," Shanks told The Huffington Post in an email. "Tall el-Hammam is an excellent candidate for the site the author of the Biblical text had in mind when he said that God destroyed Sodom."

The stones crying out again? II

The stones crying out again? III

The Stones crying out again? IV

The defense of fortress Darwin about to get even tougher?

Design in the 4th Dimension: The 4D Nucleome Project
Evolution News | @DiscoveryCSC

The Human Genome Project completed in 2003 was only the start of something far grander: understanding the entire “nucleome” of genetic activity. First there was the genome: the sequence of nucleotide bases. Then there was the transcriptome, the library of transcribed elements, studied by the ENCODE consortium. Then there was GENCODE and modENCODE, which elaborated the regulatory elements that modify transcription. Now, Nature has introduced the 4D Nucleome Project: an investigation of how all these factors interact in space and time.

The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental technologies will be combined with biophysical approaches to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells. [Emphasis added.]

We have reason to expect more problems for Darwinism with this bold initiative. For one thing, there is no mention of evolution in the lengthy paper, or of natural selection or any other Darwinian term: fitness, beneficial mutation, selective pressure — nothing. There are, in contrast, plenty of design-friendly words, particularly function and regulation and their derivatives.

The human genome contains over 20,000 genes and a larger number of regulatory elements. Large-scale studies over the last decade have catalogued these components of our genome and the cell types in which they are active. The ENCODE, Roadmap Epigenome, International Human Epigenome Consortium, EpiGeneSys (http://www.epigenesys.eu/en/) and FANTOM projects have annotated thousands of genes and millions of candidate regulatory elements. However, our understanding of the mechanisms by which these elements exert regulatory effects on specific target genes across distances of kilobases, and in some cases megabases, remains incomplete.

Another reason for expecting good material for ID advocates is that the consortium is focused on looking for reasons for things. We can expect the junk DNA myth to continue to vanish.

In the section “Relating Structure to Function,” the authors describe how researchers in the 4D Nucleome Network will use tried-and-true methods of tweaking genes to see what breaks:

An important and overarching goal is to determine how genome structure and chromatin conformation modulate genome function in health and disease. To this end, the 4DN Network will explore experimental approaches to manipulate and perturb different features of the 4D nucleome. First, using CRISPR–Cas9 technologies, DNA elements involved in specific chromatin structures, for example, domain boundaries or chromatin loops, can be altered, re-located or deleted. Second, defined chromatin structures, such as chromatin loops will be engineered de novo by targeting proteins that can (be induced to) dimerize with their partner looping proteins (for example, ref. 7). Third, other CRISPR–Cas9 approaches will be used to target enzymes (for example, histone-modifying enzymes, structural proteins) or ncRNAs to specific sites in the genome. Fourth, several groups will perturb nuclear compartmentalization by developing methods for ‘rewiring’ chromosome regions to different nuclear compartments, either by integrating specific DNA sequences that are capable of autonomous targeting of the locus to different nuclear compartments or by tethering certain proteins to these loci to accomplish similar re-positioning. Fifth, cell lines will be generated for conditional or temporal ablation of nuclear bodies or candidate chromosome architectural proteins (such as CTCF and cohesin) or RNAs. Sixth, additional methods will be developed to nucleate nuclear bodies at specific chromosomal loci. Finally, biophysical approaches will be developed to micro-mechanically perturb cell nuclei and chromosomes followed by direct imaging of specific loci. Although it remains challenging to establish direct cause-and-effect relationships, analysis of the effects of any of these perturbations on processes, such as gene expression and DNA replication, can provide deeper mechanistic insights into the roles of chromosome structure and nuclear organization in regulating the genome.

“If it ain’t broke, don’t fix it,” the proverb goes, but sometimes breaking things is the best way to learn how something works. What happens if we change the shape of a chromosome? What happens if we remove a non-coding RNA (ncRNA), or send it to a different site? What happens if we “rewire” chromosome regions to different nuclear compartments? Experiments will allow teams to build up pictures of what elements regulate what processes.

Just as ENCODE teams at multiple institutions determined that most of the genome is transcribed, the 4D Nucleome Network is likely to find that most of the genome is functional.

After determining the complete DNA sequence of the human genome and subsequent mapping of most genes and potential regulatory elements, we are now in a position that can be considered the third phase of the human genome project. In this phase, which builds upon and extends other epigenome mapping efforts mentioned above, the spatial organization of the genome is elucidated and its functional implications revealed. This requires a wide array of technologies from the fields of imaging, genomics, genetic engineering, biophysics, computational biology and mathematical modelling. The 4DN Network, as presented here, provides a mechanism to address this uniquely interdisciplinary challenge. Furthermore, the policy of openness and transparency both within the Network and with the broader scientific community, and the public sharing of all methods, data and models will ensure rapid dissemination of new knowledge, further enhancing the potential impact of the work. This will also require fostering collaborations and establishing connections to other related efforts around the world, for example, the initiative to start a European 4DN project (https://www.4dnucleome.eu), that are currently under development. Together these integrated studies promise to allow moving from a one-dimensional representation of the genome as a long DNA sequence to a spatially and dynamically organized three-dimensional structure of the living and functional genome inside cells.

Exciting days are ahead. If the sequence alone was sufficient for a design inference, how much more will a 3-D spatial organization operating in the 4th dimension of time be likely to proclaim design?

The focus of this project on function is driving innovation. To accomplish their goals, researchers will have to come up with new instruments, techniques, and models. Instead of dismissing what they don’t understand as junk, they want to know what the nucleome is doing. This is healthy for science. It’s bound to engender profound discoveries, deepening our understanding of genetics and epigenetics. It’s bound to provide practical applications for health and medicine.

Let’s make some ID predictions: (1) The spatial arrangement of nuclear elements (such as chromosomes) will prove to be functional. (2) The time interactions of elements will prove to be functional. (3)  Dan Graur will get angrier.

The turtle v. Darwin

Turtles All the Way Down?
Evolution News | @DiscoveryCSC

We ordered and have now just received our copy of  Turtles as Hopeful Monsters: Origins and Evolution (University of Indiana Press), by paleontologist Olivier Rieppel at the Field Museum of Natural History in Chicago. Thus far, the book appears to be worth every dime. From the Amazon description:

Where do turtles hail from? Why and how did they acquire shells? These questions have spurred heated debate and intense research for more than two hundred years. Brilliantly weaving evidence from the latest paleontological discoveries with an accessible, incisive look at different theories of biological evolution and their proponents, Turtles as Hopeful Monsters tells the fascinating evolutionary story of the shelled reptiles. Paleontologist Olivier Rieppel traces the evolution of turtles from over 220 million years ago, examining closely the relationship of turtles to other reptiles and charting the development of the shell. Turtle issues fuel a debate between proponents of gradual evolutionary change and authors favoring change through bursts and leaps of macromutation.

We opened the book and started browsing. Here’s a great passage, picked more or less at random:

The problem of the transformational paradigm results — to use the terminology of Adolf Remane — from the nonexistence of a zero-value ancestor, one that would show no special adaptations of any kind to any particular environment, and for this reason would not have been viable (Nullwertahne). To derive a transformed, newly adapted structure from an ancestral one requires the ancestral structure to be primitive, or generalized, in all aspects relative to the derived structure. Such a totally generalized ancestral structure would, however, not be adapted to any specific mode of life. But every living organism must somehow be adapted to some sort of mode of life. This renders such a generalized, zero-value ancestor that is not adapted to any specific mode of life a biological impossibility.  (p. 122)

Reminds one, doesn’t it, of Stephen Meyer’s discussion in Darwin’s Doubt of the implausibility of the “shmoo” common ancestor for the Metazoa (pp. 111-113).  You’ve gotta love Rieppel’s term for this: “zero-value ancestor.”

A revelation uncorrupted.

But let us be clear believing that the  revelation of the God of Abraham to the Hebrews(including the Hebrew Messianists of the 1st century) remains uncorrupted does not mean that one must now subscribe to nonsensical notions such as that there are three who are almighty God or that that humble and loyal servant of God Jesus son of Mary ever claimed to be almighty God or one third of almighty God or that it is lawful to address his Mother Mary in prayer,or to have idols in ones holy place even if these are claimed to be in the likeness of he or his mother.

 Rest assured that if such nonsense has been a barrier to your examining these scriptures your concerns are utterly unfounded.No,rather a Careful consideration of these scriptures will leave you better equipped to re-adjust those who have been misled by Christendom's clergy in these matters.

 For instance in the gospel of the apostle John Companion of Jesus.Jesus Christ is recorded to have stated the Following:John7:16-18NKJV"Jesus answered them and said,"My doctrine is not mine,His who sent me.If anyone wills to do his will,he shall know concerning the doctrine,whether it is from God or whether I speak of my own authority.He who speaks from himself seeks his own glory;but he who seeks the glory of the one who sent him is true,and know unrighteousness is in him."

  Thus we have the word the messiah himself that if he were seeking his own glory(and certainly if he were claiming to be the almighty God of Abraham,Isaac and Israel he would have been seeking his own Glory) that his message should not be trusted.But repeatedly he urged the worship of the creator of the heavens and the earth alone as God almighty.

 To further confirm this we read also at:John8:50NKJV" And I do not seek my own glory;There is one who seeks and who judges."

  In other words there is one seeking his own glory and who judges those who do not give him due Honor(i.e almighty God) but this one is not me.This really ought to leave the matter clear in the mind of any sincere truth seeker.Indeed a prayerful study of the Gospels and the writings of the companions of Jesus the messiah will indeed prove to be a blessing from the creator of mankind.

Occam's razor to too dull for Darwinism?

With Two New Fossils, Evolutionists Rewrite Narratives to Accommodate Conflicting Evidence
Günter Bechly 

Two new fossils, described in August and September 2017, have again forced evolutionists to rewrite their fanciful narratives of how major transitions in the history of life occurred. In this case the new fossils disarrayed, respectively, the origin of tetrapod land vertebrates and of bird feathers and flight.

The first fossil, described by Lefèvre et al. (2017), is a feathered dinosaur named Serikornis sungei (nicknamed “Silky”), which lived about 160 million years ago during the Upper Jurassic era. Found in China’s Liaoning province, it is a beautifully preserved complete animal with visible dino-fuzz covering its body. It was about the size of a pheasant and its morphology suggests that it was unable to fly and “spent its life scampering around on the forest floor” (Pickrell 2017). The most striking feature is the fact that even though its arms and legs have long feathers, so that the fossil seems to qualify as a member of the four-winged group of “dino-birds” such as Microraptor, Anchiornis, and Xiaotingia, the arms are much too short for wings. The feathers also lack the second order branchings (barbules) of true pennaceous flight feathers.

There are two interesting issues with this remarkable feathered dinosaur (and no, it does not seem to be a forgery like the “missing link” Archaeoraptor, Rowe et al. 2001):

The distribution and type of feathers on its body are not consistent with the currently preferred scenario about the evolution of bird feathers and flight. That scenario assumes that long pennaceous feathers on arms and legs originated with arboreal four-winged gliders such as Microraptor (Pickrell 2017)

The new phylogenetic tree in the original publication by Lefèvre et al. again reshuffles the feathered dinosaurs and early birds into a new branching pattern, disagreeing with previous trees that, in turn, all disagree with each other. Constructing phylogenetic trees looks more and more like an arbitrary enterprise, evolutionary biology’s equivalent of other pseudoscientific methods such as psychoanalysis or the Rorschach test.

The second fossil discovery, by  Zhu et al. (2017), is a new species of lobe-finned fish named Hongyu chowi from the Late Devonian. Discovered at the Shixiagou quarry in northern China, it was about 1.5 metres long, and lived 370 to 360 million years ago. One of its describers happens to be the famous Swedish paleontologist Per Ahlberg from Uppsala University, who also made worldwide headlines this month (e.g.,“Ancient footprints in Greece trample on the theory of human evolution,” in The Times of London) with the description of 5.7-million-year-old human footprints from Crete (see Bechly 2017).

Barras (2017) announces at New Scientist that this “Weird fish fossil changes the story of how we moved onto land.” From the article:

The evolutionary story we have written to explain our ancestors’ move from sea to land  may need a rethink. …

[W]hen the researchers tried to fit H. chowi into the existing evolutionary tree, it didn’t fit easily.

That’s because in some respects, H. chowi looks like an ancient predatory fish called rhizodonts. These are thought to have branched off from lobe-finned fish long before the group gave rise to four-legged land animals.

But Ahlberg says H. chowi has aspects that look surprisingly like those seen in early four-legged animals and their nearest fishy relatives —an extinct group called the elpistostegids. These include the shoulder girdle and the support region for its gill covers.

This implies one of two things, the researchers say. The first possibility is that H. chowi is some sort of rhizodont that independently evolved the shoulders and gill cover supports of a four-legged animal.

Alternatively, the rhizodonts may be more closely related to the four-legged animals and the elpistostegids than we thought. But this would also imply a certain amount of independent evolution of similar features, because the rhizodonts would then sit between two groups that have many features in common – features the two groups would have had to evolve independently. …

The find confirms an earlier suspicion that there was independent or “parallel” evolution between the rhizodonts, the elpistostegids and the first four-legged animals, says Neil Shubin at the University of Chicago.

Thus, this fossil raises two important problems for evolutionary biology:

The character distribution is incongruent and implies independent parallel origins of the same tetrapod-like or rhizodont-like characters (convergence). The alternative explanations of independent origin (homoplasy) versus common origin (homology) of a character trait is not alone decided based on anatomic (dis)similarities but mainly based on the (in)congruence with other data. The same data that are considered evidence of convergence can become evidence for common ancestry when you switch positions in the tree, and vice versa. What most evolutionary biologists have exorcised from their mind is that such incongruences (homoplasies) per se are not evidence for evolution as some evolutionists boldly proclaim (Wells 2017) but, instead, prima facie conflicting evidence against it (Hunter 2017). Convergence, which Lee Spetner has called “even more implausible than evolution itself” (Klinghoffer 2017), and other incongruent similarities have to be explained away with ad hoc hypotheses. In past decades, convergence morphed from an inconvenient exception to the rule — to a ubiquitous phenomenon, found virtually everywhere in living nature. In his book Life’s Solution, paleontologist Conway Morris (2003) felt compelled to declare it a kind of necessary natural law. It thus cannot really be considered a success story for the Darwinian paradigm.

Rhizodontids,the group to which this fossil fish belongs, are believed to have branched off early from the lobefin-tetrapod lineage, more than 415 million years ago. However, the oldest fossils are dated to only 377 million years ago, implying a so-called “ghost lineage” of 38 million years when the group should have existed but left no fossil record at all. Such “ghost lineages” are one of the many instances of discontinuity in the fossil record and require ad hoc assumptions in order to be accommodated by evolutionary storytelling.

These two new fossils represent further evidence conflicting with previously accepted evolutionary narratives. But thank God evolutionary theory can easily adapt to such inconvenient evidence, simply by rewriting the story. That way, the new evidence fits perfectly.

Dubious procedures like these would be unthinkable in other natural sciences, such as physics. They call into question whether evolutionary biology really qualifies as a hard science at all. Arguably it is not a testable theory, or even a well-defined one, but merely a loose collection of narratives that are forged to fit the evidence — any evidence whatsoever.

Literature:

Barras C 2017. Weird fish fossil changes the story of how we moved onto land.  New Scientist 4 September 2017.

Bechly G 2017. Fossil Footprints from Crete Deepen Controversy on Human Origins. Evolution News September 6, 2017.

Carassava A 2017. Ancient footprints in Greece trample on the theory of human evolution.  The TimesSeptember 4 2017.

Hunter C 2017. The Real Problem With Convergence. Evolution News May 25, 2017.

Klinghoffer D 2017. “Convergent Evolution Is Even More Improbable than Evolution Itself.”  Evolution News September 5, 2017.

Lefèvre U, Cau A, Cincotta A, Hu D, Chinsamy A, Escuillié F, Godefroit P 2017. A new Jurassic theropod from China documents a transitional step in the macrostructure of feathers.  The Science of Nature 104:74.

Conway Morris S 2003. Life’s Solution: Inevitable Humans in a Lonely Universe. Cambridge University Press.

Pickrell J 2017. New Feathered Dinosaur Had Four Wings but Couldn’t Fly.  National Geographic August 28, 2017.

Rowe T et al. 2001. Forensic palaeontology: The Archaeoraptor forgery. Nature 410: 539-540.

Wells J 2017. Zombie Science: Jonathan Wells on Convergence Versus Common Ancestry.  Evolution News June 28, 2017.

Zhu M, Ahlberg PE, Zhao W-J, Jia L-T 2017. A Devonian tetrapod-like fish reveals substantial parallelism in stem tetrapod evolution. Nature Ecology & Evolution.

Talk about fighting for your life!

Wesley Smith Visits Jahi McMath
David Klinghoffer | @d_klinghoffer  

Jahi McMath is a neurologically disabled young woman who, like Schrödinger’s cat, is, or has been, both dead and alive. Our colleague Wesley Smith visited the patient and offers a powerful account for First Things.

In California, Jahi McMath is legally dead. In New Jersey, she is legally alive. Now, the deceased — or profoundly disabled — teenager is the subject of litigation that could make history.

Wesley witnessed what appeared to be a response on Jahi’s part to a request that she move her thumb and index finger — “I nearly jumped out of my shoes,” he reports. I think I would, too.

He has changed his mind about her status.

If Jahi is not — or, perhaps better, no longer — brain dead, this may be an unprecedented event, as there are no known cases of a properly diagnosed brain-dead patient experiencing restored neurological function. And I am stunned that the medical and bioethics communities generally show such a pronounced lack of curiosity about Jahi’s situation. True, there have been rare cases of the bodies of brain-dead people not deteriorating over time. But surely the other factors described by [Dr. Alan] Shewmon and the videos should pique their interest.

Perhaps it is just a case of “experts” not wanting to know — because if Jahi isn’t dead, it would have epochal legal, social, medical, and scientific ramifications. But so what? Jahi deserves justice. If alive, she is a full and equal member of the moral community.

I hope that several prominent neurologists without a stake in the situation will step forward and volunteer to examine Jahi — and not just for a day or two but over an extended period of time, to test her brain and body functions thoroughly and determine whether she does indeed respond to requests. Then, if she lacks even one criterion for brain death, Jahi’s California death certificate should be revoked — let the chips fall where they may.

No longer brain dead? This is quite remarkable and testifies among other things to the tenacious commitment of Jahi’s mother, Nailah, whom Wesley also interviewed, to “choose life” on behalf of her daughter. Read the rest here.

Yet more on the undeniability of the case for design.

The Unmistakable Imprint of Purpose — Response to a Theistic Evolutionist
Douglas Axe | @DougAxe 

I’ve been discussing my book  Undeniable with Hans Vodder, who favors the evolutionary explanation of life. In our fifth exchange,Hans referred to what has been called a “natural nuclear reactor.” Whatever it was, it seems to have existed eons ago in the rock formations of what is now the Oklo region of Gabon. Hans thinks this so-called reactor may have exhibited the kind of functional coherence I point to as a hallmark of invention, making it a noteworthy counterexample to my argument.

I responded by suggesting that reactor is an overblown term for what was really nothing more than a reaction. Back in its day, that Oklo reaction required only: 1) a moderately large uranium deposit, and 2) a source of water to percolate through it. This, I said, doesn’t qualify as high-level functional coherence.

I brought up the comparison to an adjustable wrench — a very modest example of functional coherence. How is it, I asked, that people expected natural nuclear reactions to be found but no one expects a natural adjustable wrench to be found?

Here is Hans’s reply:

Your two-condition assessment of the requirements for the reactor seems a little minimalistic. The Kuroda study (cited in the  Scientific American article) mentions four general conditions, and Maynard Smith and Szathmary describe further particulars in  The Major Transitions in Evolution. The latter authors mention things like the 45 degree tilt of the sandstone and underlying granite layers which allowed the reactions to occur in a self-sustaining manner; the increased solubility of oxidized uranium, which helped it accumulate in the delta in the first place; and so on. So whether something is considered functionally coherent might depend largely on how relevant conditions are assessed.

But suppose we go with the two-condition assessment. There still doesn’t seem to be anything in the bare definition of functional coherence — “the hierarchical arrangement of parts needed for anything to produce a high-level function — each part contributing in a coordinated way to the whole” (144) — that would exclude Oklo. Consider this adaptation of figure 9.3 from your book:

A critic might reasonably argue that Oklo qualifies as functionally coherent. To make the case more “extensive,” all said critic would have to do is add a few more components or break down the current ones into further detail.

Now, I  suspect this doesn’t really capture the property of “functional coherence” that Undeniable is after. But here’s the rub: It does seem, so far as I can tell, to satisfy the definitional criteria laid out in the book. If that’s right, then one of two conclusions seems to follow. Either:

a) Oklo is a genuine case of functional coherence, with the result that nature can produce at least some functional coherence (pace the “Summary of the Argument” on p. 160 of Undeniable), or

b) Oklo is only a superficial case of functional coherence, with the result that further criteria are needed to distinguish Oklo-type cases from genuine ones.

Sure. Going strictly from my bare definition, one could easily call things functionally coherent that, as you say, don’t really capture the sense of the term as used in Undeniable.

So, I agree with your b option, except I would say context is needed instead of criteria, and I think the book supplies that context. In other words, my definition of functional coherence should make sense to readers who have followed the discussion up to the point where that term is introduced (more on that in a moment).

With respect to Oklo, keep in mind that Maynard Smith and Szathmary, being evolutionary biologists, wanted to “see some parallels with the origin of life” (p. 20 of their book). This raises the possibility that they saw what wasn’t really there.

Here’s a more objective account of the requirements for a uranium-235 fission chain reaction from the Department of Physics and Astronomy at Georgia State University:

If at least one neutron from U-235 fission strikes another nucleus and causes it to fission, then the chain reaction will continue. If the reaction sustains itself, it is said to be “critical,” and the mass of U-235 required to produce the critical condition is said to be a “critical mass.” A critical chain reaction can be achieved at low concentrations of U-235 if the neutrons from fission are moderated to lower their speed, since the probability for fission with slow neutrons is greater.

Strictly speaking, then, all that’s needed for a sustained nuclear chain reaction is a critical mass of uranium-235. Uranium is number 92 on the periodic table of elements, so it literally belongs on the bottom layer of the hierarchy in that figure (you can’t get more elementary than an element). Despite all the fuss over Oklo, then, it really didn’t rise above the behavior of that one element.

Interestingly, Maynard Smith and Szathmary acknowledged the obvious fact that “the Oklo reactor does not look like a man-made reactor.” My question is — what makes this so obvious?

The answer is hinted at by the way these authors inadvertently portray the Oklo reaction as though it had been intended. For example, they say “some moderator material was needed to slow down neutrons.”

Needed?

The raw fact is merely that water happened to be present as a moderator, causing the neutrons to be slowed. To say that water was needed is to imply not just that something important was at stake but that this was somehow recognized at the time — as though the Oklo reaction had been arranged for a purpose.

Neither Maynard Smith nor Szathmary believed that for a moment, but somehow they couldn’t keep themselves from implying it. Their next sentence reads: “Perhaps most surprising of all, the reaction had to be self-regulating.” Really? Who says it had to be self-regulating? And what definition of “regulate” are we using here? All the usual definitions invoke purpose.

Returning to raw facts, the evidence suggests that the rate of fission at Oklo may have oscillated, peaking when water was present and dropping when it was absent. But again, so what? Fission chain reactions are always limited. They end when critical mass is exhausted. So the suggestion that Oklo was “regulated” is just plain odd. Regulated to what end?

By the time I introduce readers of Undeniable to functional coherence, they know the book is all about purpose. In that context, they know purpose is at the heart of this term. Our design intuition tells us that “tasks that we would need knowledge to accomplish can be accomplished only by someone who has that knowledge.” Despite their exaggeration, Maynard Smith and Szathmary knew full well that the Oklo reaction wasn’t an accomplishment. Indeed, we can’t see Oklo as a task that required things to be cleverly arranged because it shows absolutely no sign of having been that.

With sufficient cleverness and determination, the elements from the periodic table can be arranged to accomplish tasks that aren’t even hinted at by the properties of the elements themselves — challenges whose solutions have to be dreamed up by fertile imaginations. We instantly spot the fruits of those imaginations by spotting their characteristic functional coherence. Dragonflies. Smartphones. Nuclear power plants. Even adjustable wrenches.

I’m sure this reasoning can be formalized, Hans, but do keep in mind that Undeniable isn’t meant to be that. Undeniable shows in a commonsensical way how it is that no one confuses things like radioactive rocks for inventions and, conversely, how no one confuses things like adjustable wrenches for accidents.

Nothing you’ve said so far challenges that main thesis, Hans. So if we’re in agreement there, I’m wondering why you think life should be exempt from reasoning that works everywhere else.

Intelligence is not magical.

Intelligent Design and Methodological Naturalism — No Necessary Contradiction
Evolution News | @DiscoveryCSC

Another  corespondent draws our attention to a comment from atheist and “poetic naturalist” Sean Carroll, in his recent book  The Big Picture: On the Origins of Life, Meaning, and the Universe Itself

Science should be interested in determining the truth, whatever that truth may be – natural, supernatural, or otherwise. The stance known as methodological naturalism, while deployed with the best of intentions by supporters of science, amounts to assuming part of the answer ahead of time. If finding truth is our goal, that is just about the biggest mistake we can make.

Such a statement may or may not be surprising to you, considering the source. Well, what about it? Methodological naturalism (MN) in relationship to intelligent design has been a source of some discussion and confusion over the years.

A Reasonable Definition

A reasonable definition of MN is: “The belief that, whether or not the supernatural exists, we must pretend that it doesn’t when practicing science.” This idea was neatly expressed in a letter to the editor published in Nature:

Even if all the data point to an intelligent designer, such an hypothesis is excluded from science because it is not naturalistic.

(Scott C. Todd, “A view from Kansas on that evolution debate,” Nature, Vol. 401:423 (Sept. 30, 1999))

For a list of other sources similarly claiming MN is a requirement of science, please see, "Primer: Naturalism in Science.”

Now obviously, many critics of the theory of intelligent design (ID) maintain that ID isn’t science because they claim that MN is a “rule” that all science must conform to and obey. For a moment, leave aside whether MN makes a good “rule” for doing science. Let’s approach the question of whether ID is science pragmatically, and, for the sake of argument, let us assume MN. Even if we accept the rationale behind MN, ID is not excluded from being scientific.

ID Doesn’t Violate the Letter of MN

MN states that science cannot appeal to the supernatural. But ID does not appeal to the supernatural, and thus does not require non-natural causes.

ID begins with observations of the types of information and complexity produced by intelligent agents. Intelligent agents are natural causes that we can understand by studying the world around us. This makes intelligent agency a proper subject of scientific study. When ID finds high levels of complex and specified information, or CSI, in nature, the most it can infer is that intelligence was at work. Because ID respects the limits of scientific inquiry, it does not make claims beyond the data by trying to identify the designer.

Stephen Meyer explains:

Though the designing agent responsible for life may well have been an omnipotent deity, the theory of intelligent design does not claim to be able to determine that. Because the inference to design depends upon our uniform experience of cause and effect in this world, the theory cannot determine whether or not the designing intelligence putatively responsible for life has powers beyond those on display in our experience. Nor can the theory of intelligent design determine whether the intelligent agent responsible for information life acted from the natural or the “supernatural” realm. Instead, the theory of intelligent design merely claims to detect the action of some intelligent cause (with power, at least, equivalent to those we know from experience) and affirms this because we know from experience that only conscious, intelligent agents produce large amounts of specified information.

(Stephen C. Meyer, Signature in the Cell, pp. 428-429 (HarperOne, 2009))

Many other ID proponents have pointed out that ID only appeals to intelligent causes, not supernatural ones. Michael Behe writes:

[A]s regards the identity of the designer, modern ID theory happily echoes Isaac Newton’s phrase hypothesis non fingo [“I frame no hypothesis”].

(Michael Behe, “The Modern Intelligent Design Hypothesis,” Philosophia Christi, 2 (3): 165 (2001))

William Dembski and Jonathan Wells explain:

Supernatural explanations invoke miracles and therefore are not properly part of science. Explanations that call on intelligent causes require no miracles but cannot be reduced to materialistic explanations.

(William Dembski and Jonathan Wells, The Design of Life: Discovering Signs of Intelligence in Biological Systems, pp. 13-14 (FTE, 2008))

Likewise, an early ID textbook affirms MN, stating:

[I]ntelligence…can be recognized by uniform sensory experience, and the supernatural…cannot.

(Percival Davis and Dean H. Kenyon, Of Pandas and People, p. 126 (FTE, 1993))

Now some might argue that ID violates MN by leaving open the possibility of a supernatural designer. It true that ID leaves open such a possibility. But ID does not claim to scientifically detect a supernatural creator. Again, the most ID claims to detect is intelligent causation. Many (though not all) ID proponents may believe the designer is God, but they do not claim this is a scientific conclusion of ID. In this respect, ID is no different from Darwinian evolution, which claims that if there is a supernatural creator, that would be beyond science’s power to detect.

ID Doesn’t Offend the Spirit of MN

Proponents of MN often justify this “rule” by arguing that it ensures that science uses only testable, predictable, and reliable explanations. However, ID generates testable hypotheses based upon our knowledge of how the world works, and can be reliably inferred through the scientific method. In this way, intelligent design does not violate any mandates of predictability, testability, or reliability laid down for science by MN.

For details on how ID makes testable predictions, please see the following:

• “FAQ: Does intelligent design make predictions? Is it testable?”

• “A Positive, Testable Case for Intelligent Design”

We’ve remarked on this before, but clarification is always in order.