Reviewing peer review.

Fleming's discovery of penicillin couldn't get published today. That's a huge problem

Updated by Julia Belluz on December 14, 2015, 7:00 a.m. ET


After toiling away for months on revisions for a single academic paper, Columbia University economist Chris Blattman started wondering about the direction of his work.

He had submitted the paper in question to one of the top economics journals earlier this year. In return, he had gotten back nearly 30 pages of single-space comments from peer reviewers (experts in the field who provide feedback on a scientific manuscript). It had taken two or three days a week over three months to address them all.

So Blattman asked himself some simple but profound questions: Was all this work on a single study really worth it? Was it best to spend months revising one study — or could that time have been better spent on publishing multiple smaller studies? He wrote about the conundrum on his blog:

Some days my field feels like an arms race to make each experiment more thorough and technically impressive, with more and more attention to formal theories, structural models, pre-analysis plans, and (most recently) multiple hypothesis testing. The list goes on. In part we push because want to do better work. Plus, how else to get published in the best places and earn the respect of your peers?

It seems to me that all of this is pushing social scientists to produce better quality experiments and more accurate answers. But it’s also raising the size and cost and time of any one experiment.

Over the phone, Blattman explained to me that in the age of "big data," high-quality scientific journals are increasingly pushing for large-scale, comprehensive studies, usually involving hundreds or thousands of participants. And he's now questioning whether a course correction is needed.

Though he can't prove it yet, he suspects social science has made a trade-off: Big, time-consuming studies are coming at the cost of smaller and cheaper studies that, taken together, may be just as valuable and perhaps more applicable (or what researchers call "generalizable") to more people and places.

Do we need more "small" science?

Over in Switzerland, Alzheimer's researcher Lawrence Rajendran has been asking himself a similar question: Should science be smaller again? Rajendran, who heads a laboratory at the University of Zurich, recently founded a journal called Matters. Set to launch in early 2016, the journal aims to publish "the true unit of science" — the observation.

Rajendran notes that Alexander Fleming’s simple observation that penicillin mold seemed to kill off bacteria in his petri dish could never be published today, even though it led to the discovery of lifesaving antibiotics. That's because today's journals want lots of data and positive results that fit into an overarching narrative (what Rajendran calls "storytelling") before they'll publish a given study.

"You would have to solve the structure of penicillin or find the mechanism of action," he added.

But research is complex, and scientific findings may not fit into a neat story — at least not right away. So Rajendran and the staff at Matters hope scientists will be able to share insights in this journal that they may not been able to publish otherwise. He also thinks that if researchers have a place to explore preliminary observations, they may not feel as much pressure to exaggerate their findings in order to add all-important publications to their CVs.

Smaller isn't always better

Science has many structural problems to grapple with right now: The peer review system doesn't function all that well, many studies are poorly designed so their answers are unreliable, and replications of experiments are difficult to execute and very often fail. Researchers have estimated that about $200 billion — or about 85 percent of global spending on research — is routinely wasted on poorly designed and redundant studies.

A big part of the reason science funders started emphasizing large-scale studies is because they were trying to avoid common problems with smaller studies: The results aren't statistically significant, and the sample sizes may be too tiny and therefore unrepresentative.

It's not clear that emphasizing smaller-scale studies and observations will solve these problems. In fact, publishing more observations may just add to the noise. But as Rajendran says, it's very possible that important insights are being lost in the push toward large-scale science. "Science can be small, big, cure diseases," he said. "It can just be curiosity-driven. Academic journals shouldn't block the communication of small scientific observations."

They may lose on every sale but they know how to close.

Darwin’s Finches: An Icon Gets Retouched
Evolution News | @DiscoveryCSC

Some scientists at Georgia Tech collected bacteria from a lake near their campus and “helped” them evolve in a test tube. From their results, they made major pronouncements about the tempo and mode of evolution on the faraway Galápagos Islands. For this, they got funding from the National Science Foundation.

That pretty much sums up John Toon’s write-up for the Georgia Tech News Center, “‘First Arrival’ Hypothesis in Darwin’s Finches Gets Some Caveats.”

What exactly do lake bacteria have to do with Darwin’s finches, you ask? Well, the evolutionary scientists wanted to follow up on the famous study by David Lack in 1947. He had proposed a theory about “first arrivals” in a new ecosystem, but his study lacked some important details.

Among his hypotheses was that the birds were successful in their adaptive radiation — the evolutionary diversification of morphological, physiological and behavior traits — because they were early colonizers of the islands. The finches filled the available ecological niches, taking advantage of the resources in ways that limited the ability of later-arriving birds to similarly establish themselves and diversify, he suggested. [Emphasis added.]
If the early bird gets the evolutionary advantage, what happens if the late bird is a better competitor? It changes the iconic story somewhat. “Being first in a new ecosystem provides major advantages for pioneering species, but the benefits may depend on just how competitive later-arriving species are.” The late bird might just peck the lights out of the early bird.

To find out what happens, the Darwin team under Jiaqi Tan put their lake bacteria into test tubes to watch the games play out.

Tan and other researchers in the laboratory of Georgia Tech Professor Lin Jiang tested that hypothesis using P. fluorescens, which rapidly evolves into two general phenotypes differentiated by the ecological niches they adopt in static test tube microcosms.  Within the two major phenotypes — known as “fuzzy spreaders” and “wrinkly spreaders” — there are additional minor variations.

The researchers allowed the bacterium to colonize newly-established microcosms and diversify before introducing competing bacterial species. The six competitors, which varied in their niche and competitive fitness compared to P. fluorescens, were introduced individually and allowed to grow through multiple generations. Their success and level of diversification were measured by placing microcosm samples onto agar plates and counting the number of colonies from each species and sub-species.
Not surprisingly, the results were complicated. The bacteria reproduce much faster than finches, but they reproduce asexually. Their mutation rates are also probably much different. “Still, Jiang and Tan believe their study offers insights into how different species interact in new environments based on historical advantages.”

“If the diversifying species and the competing species are very similar, you can have a strong priority effect in which the first-arriving species can strongly impact the ability of the later species to diversify,” said Jiang, a professor in Georgia Tech’s School of Biological Sciences. “If the species are different enough, then the priority effect is weaker, so there would be less support for the first arrival hypothesis.”
David Lack’s famous book lacked this crucial realization: the first arrival hypothesis works, except when it doesn’t. Evolutionists will now “need to think about the surrounding ecological context of the evolutionary process.”

The paper in Evolution shows that the trajectory of evolution is contingent upon the historical context, which seems to say that anything can happen when the first bird lands on an island:

In the first-arrival hypothesis, David Lack emphasized the importance of species colonization history for adaptive radiation, suggesting that the earlier arrival of a diversifying species would allow it to radiate to a greater extent. Here, we report on the first rigorous experimental test of this hypothesis, using the rapidly evolving bacterium Pseudomonas fluorescens SBW25 and six different bacterial competitors. We show that the earlier arrival of P. fluorescens facilitated its diversification. Nevertheless, significant effects of colonization history, which led to alternative diversification trajectories, were observed only when the competitors shared similar niche and competitive fitness with P. fluorescens. These results highlight the important role of species colonization history, modified by their ecological differences, for adaptive radiation.
Interesting phrase: “alternative diversification trajectories” are possible. The possibility for storytelling just grew exponentially.

It seems unbelievable that nobody performed a rigorous test of David Lack’s hypothesis for seventy years. But it doesn’t matter, because neither study — David Lack’s or Georgia Tech’s –provides any help for Darwinian evolution. The birds hybridize. No origin of species has occurred. The varieties of finches are “trapped in an unpredictable cycle of Sisyphean evolution,” according to McKay and Zink, quoted by Jonathan Wells in his new book  Zombie Science (pp. 69-70).

This means that, like the old king Sisyphus of Greek mythology, condemned by the gods to roll a stone up a hill that always escapes and rolls back down, requiring him to repeat the cycle forever, Darwin’s finches are going nowhere.

So here’s what we know in 2017 about Darwin’s finches, one of Jonathan Wells’ original ten  Icons of Evolution.

Some finches wound up on the Galápagos Islands sometime.
Darwin captured some on his visit, but never used them to promote his theory.
The finches can freely hybridize.
The only major difference between them is the size and shape of the beak.
When the weather is dry, bigger-beaked birds do better.
When the rain returns, smaller-beaked birds return to previous levels.
No speciation has occurred. (This is called “adaptive radiation.”)
There exists a nebulous idea called “fitness,” measured by number of offspring.
Fitness changes from year to year, as circumstances change.
Varieties of finches exchange places as “fittest” from year to year.
The first arriver gets priority, unless a fitter bird arrives later.
Nobody can know in advance what bird will stay the fittest for how long.
The NSF will let you use bacteria as a proxy for birds.
Yes, “Adaptive radiation is an important evolutionary process,” just like the paper begins. Thanks for the money, NSF!

In Zombie Science, Wells points out that in a 1999 pro-evolution booklet for schools, the U.S. National Academy of Sciences called Darwin’s finches “a particularly compelling example of speciation.” He also points out that after 17 years since he exposed the flaws in this evolutionary icon, the “zombie” keeps coming back from the dead, reviving and stalking in biology textbooks. Here, the zombie makes another appearance: research that goes nowhere, proves nothing, and yet pretends that Darwin’s finches, despite “some important caveats,” provide insight into the origin of species.


It’s hard to kill a zombie when the federal government funds its handlers.

The Trinity-Is It Taught in the Bible?:The Watchtower Society's commentary.

"The Catholic Faith is this, that we worship one God in Trinity and Trinity in Unity. . . . So the Father is God, the Son is God, and the Holy Ghost is God. And yet they are not Three Gods, but One God."

IN THESE words the Athanasian Creed describes the central doctrine of Christendom—the Trinity. If you are a church member, Catholic or Protestant, you might be told that this is the most important teaching that you are to believe in. But can you explain the doctrine? Some of the best minds in Christendom have confessed their inability to understand the Trinity.

Why, then, do they believe it? Is it because the Bible teaches the doctrine? The late Anglican bishop John Robinson gave a thought-provoking answer to this question in his best-selling book Honest to God. He wrote: "In practice popular preaching and teaching presents a supranaturalistic view of Christ which cannot be substantiated from the New Testament. It says simply that Jesus was God, in such a way that the terms ‘Christ’ and ‘God’ are interchangeable. But nowhere in Biblical usage is this so. The New Testament says that Jesus was the Word of God, it says that God was in Christ, it says that Jesus is the Son of God; but it does not say that Jesus was God, simply like that."

John Robinson was a controversial figure in the Anglican Church. Nevertheless, was he correct in saying that the "New Testament" nowhere says that "Jesus was God, simply like that"?

What the Bible Does Say

Some may answer that question by quoting the verse that commences John’s Gospel: "In the beginning was the Word, and the Word was with God, and the Word was God." (John 1:1, King James Version) Does that not contradict what the Anglican bishop said? Not really. As John Robinson doubtless knew, some modem translators disagree with the King James Version’s rendering of that text. Why? Because in the expression "the Word was God" in the original Greek, the word for "God" does not have the definite article "the." In the earlier expression "the Word was with God," the word for "God" is definite, that is, it does have the definite article. This makes it unlikely that the two words have the same significance.

Hence, some translations bring out the qualitative aspect in their translations. For example, some render the expression "the Word was divine." (An American Translation, Schonfield) Moffatt renders it "the Logos was divine." However, indicating that "divine" would not be the most appropriate rendering here, John Robinson and the British textual critic Sir Frederick Kenyon both pointed out that if that was what John wanted to emphasize, he could have used the Greek word for "divine," the i’os. The New World Translation, correctly viewing the word "God" as indefinite, as well as bringing out the qualitative aspect indicated by the Greek structure, uses the indefinite article in English: "The Word was a god."

Professor C. H. Dodd, director of the New English Bible project, comments on this approach: "A possible translation. . . would be, ‘The Word was a god’. As a word-for-word translation it cannot be faulted." However, The New English Bible does not render the verse that way. Rather, John 1:1 in that version reads: "When all things began, the Word already was. The Word dwelt with God, and what God was, the Word was." Why did the translation committee not choose the simpler rendering? Professor Dodd answers: "The reason why it is unacceptable is that it runs counter to the current of Johannine thought, and indeed of Christian thought as a whole."— Technical Papers for the Bible Translator, Volume 28, January 1977.

The Plain Sense of Scripture

Would we say that the idea that Jesus was a god and not the same as God the Creator is contrary to Johannine (that is, the apostle John’s) thought, as well as Christian thought as a whole? Let us examine some Bible texts that refer to Jesus and to God, and we will see what some commentators who lived before the Athanasian Creed was formulated thought about those texts.

"I and the Father are one."—JOHN 10:30.

Novatian (c. 200-258 C.E.) commented: "Since He said ‘one’ thing,[] let the heretics understand that He did not say ‘one’ person. For one placed in the neuter, intimates the social concord, not the personal unity.. .. Moreover, that He says one, has reference to the agreement, and to the identity of judgment, and to the loving association itself, as reasonably the Father and Son are one in agreement, in love, and in affection. "— Treatise Concerning the Trinity, chapter 27.

"The Father is greater than I am."—JOHN 14:28.

Irenaeus (c. 130-200 C.E.): "We may learn through Him [Christ] that the Father is above all things. For ‘the Father,’ says He, ‘is greater than I.’ The Father, therefore, has been declared by our Lord to excel with respect to knowledge. "—Against Heresies, Book II, chapter 28.8.

"This means everlasting life, their taking in knowledge of you, the only true God, and of the one whom you sent forth, Jesus Christ." —JOHN 17:3.

Clement of Alexandria (c. 150-215 C.E.): "To know the eternal God, the giver of what is eternal, and by knowledge and comprehension to possess God, who is first, and highest, and one, and good. . . . He then who would live the true life is enjoined first to know Him ‘whom no one knows, except the Son reveal (Him).’ (Matt. 11:27) Next is to be learned the greatness of the Saviour after Him."— Who Is the Rich Man That Shall Be Saved? VII, VIII

"One God and Father of all persons, who is over all and through all and in all."—EPHESIANS 4:6.

Irenaeus: "And thus one God the Father is declared, who is above all, and through all, and in all. The Father is indeed above all, and He is the Head of Christ."— Against Heresies, Book V, chapter 18.2.

These early writers clearly understood these verses to describe the Father as supreme, over everything and everyone including Jesus Christ. Their comments give no hint that they believed in a Trinity.

The Holy Spirit Reveals All Truth

Jesus promised his disciples that after his death and resurrection, the holy spirit would be given to them as a helper. He promised: "When that one arrives, the spirit of the truth, he will guide you into all the truth,.., and he will declare to you the things coming."—John 14:16, 17; 15:26; 16:13.

After Jesus’ death, that promise was fulfilled. The Bible records how new doctrines were revealed or clarified to the Christian congregation through the help of the holy spirit. These new teachings were written down in the books that later became the second part of the Bible, the Christian Greek Scriptures, or "New Testament." In this flood of new light, is there ever any revelation of the existence of a Trinity? No. The holy spirit reveals something very different about God and Jesus.

For example, at Pentecost 33 C.E., after holy spirit came upon the disciples gathered in Jerusalem, the apostle Peter witnessed to the crowd outside about Jesus. Did he speak about a Trinity? Consider some of his statements, and judge for yourself: "Jesus... , a man publicly shown by God to you through powerful works and portents and signs that God did through him in your midst." "This Jesus God resurrected, of which fact we are all witnesses." "God made him both Lord and Christ, this Jesus whom you impaled." (Acts 2:22, 32, 36) Far from teaching a Trinity, these expressions by the spirit-filled Peter highlight Jesus’ subordination to his Father, that he is an instrument for the fulfillment of God’s will.

Soon after, another faithful Christian spoke about Jesus. Stephen was brought before the Sanhedrin to answer accusations. Instead, Stephen turned the situation around, charging that his accusers were like their rebellious ancestors. Finally, the record says: "He, being full of holy spirit, gazed into heaven and caught sight of God’s glory and of Jesus standing at God’s right hand, and he said: ‘Look! I behold the heavens opened up and the Son of man standing at God’s right hand."’ (Acts 7:55, 56) Why did the holy spirit reveal Jesus to be simply the "Son of man" standing at God’s right hand and not part of a godhead equal with his Father? Clearly, Stephen had no concept of a Trinity.

When Peter carried the good news about Jesus to Cornelius, there was a further opportunity to reveal the Trinity doctrine. What happened? Peter explained that Jesus is "Lord of all." But he went on to explain that this lordship came from a higher source. Jesus was "the One decreed by God to be judge of the living and the dead." After Jesus’ resurrection, his Father "granted him [gave him permission] to become manifest" to his followers. And the holy spirit? It does appear in this conversation but not as the third person of a Trinity.

Rather, "God anointed [Jesus] with holy spirit and power." Thus, the holy spirit, far from being a person, is shown to be something impersonal, like the "power" also mentioned in that verse. (Acts 10:36, 38, 40, 42) Check the Bible carefully, and you will find further evidence that the holy spirit is not a personality but an active force that can fill people, impel them, cause them to be aglow, and be poured out upon them.

Finally, the apostle Paul had a fine opportunity to explain the Trinity—if it had been true doctrine—when he was preaching to the Athenians. In his talk, he referred to their altar "To an Unknown God" and said: "What you are unknowingly giving godly devotion to, this I am publishing to you." Did he publish a Trinity? No. He described the "God that made the world and all the things in it, being, as this One is, Lord of heaven and earth." But what of Jesus? "[God] has set a day in which he purposes to judge the inhabited earth in righteousness by a man whom he has appointed." (Acts 17:23, 24, 31) No hint of a Trinity there!

In fact, Paul explained something about God’s purposes that makes it impossible that Jesus and his Father are equal parts of a Trinity. I-fe wrote: "God ‘subjected all things under his [Jesus’] feet.’ But when he says that ‘all things have been subjected,’ it is evident that it is with the exception of the one who subjected all things to him. But when all things will have been subjected to him, then the Son himself will also subject himself to the One who subjected all things to him, that God may be all things to everyone." (1 Corinthians 15:27, 28) Thus, God will still be over all, including Jesus.

Is the Trinity taught in the Bible, then? No. John Robinson was right. It is not in the Bible, nor is it a part of "Christian thought." Do you view this as important to your worship? You should. Jesus said: "This means everlasting life, their taking in knowledge of you, the only true God, and of the one whom you sent forth, Jesus Christ." (John 17:3) If we take our worship of God seriously, it is vital that we know him as he really is, as he has revealed himself to us. Only then can we truly say that we are among the "true worshipers" who "worship the Father with spirit and truth." —John 4:23.

Yet more iconoclasm.

Toppling Another Evolutionary Icon, ENCODE Suggests Endogenous Retroviruses are Functional

Casey Luskin 

Recently a reader emailed us to ask about how to respond to the argument that some endogenous retroviruses (ERVs) seem to match the standard phylogeny of higher primates, supporting common descent. Endogenous retroviruses are thought to be parasitic junk sequences in our genome that were derived from viral DNA. Evolutionists often cite them as supposed evidence of common ancestry. The reader asked how many ERVs are shared between humans and apes.

These are good questions. ERVs are a favorite with Darwin defenders -- so much so that one particularly uncivil activist, Abbie Smith, even named her popular science blog after them, "ERV."

In response, I suggested that, when analyzing common descent, the number of ERVs shared by humans and chimps is beginning to look like it's not a very important question. An assumption in the question (and in the arguments from supporters of common ancestry) is that ERVs are a type of functionless "junk" DNA. Thus if apes and humans share ERVs in the same position in our genomes, that would seemingly count as evidence for common descent. But what if ERVs aren't junk? What if they are a type of functional DNA? If that's the case, then shared ERVs could easily be explained by common design rather than common descent, and they would certainly no longer be some kind of special argument for common ancestry.

In fact there is good evidence that ERVs as a class of DNA are functional. A 2013 paper in PLOS Genetics using ENCODE data reported that very high percentages of endogenous retroviruses in the human genome are associated with open chromatin -- strong evidence of transcription -- and that they are transcribed non-randomly, suggesting some functional role:

Although emerging evidence suggests that transposable elements (TEs) have contributed novel regulatory elements to the human genome, their global impact on transcriptional networks remains largely uncharacterized. Here we show that TEs have contributed to the human genome nearly half of its active elements. Using DNase I hypersensitivity data sets from ENCODE in normal, embryonic, and cancer cells, we found that 44% of open chromatin regions were in TEs and that this proportion reached 63% for primate-specific regions.We also showed that distinct subfamilies of endogenous retroviruses (ERVs) contributed significantly more accessible regions than expected by chance, with up to 80% of their instances in open chromatin. Based on these results, we further characterized 2,150 TE subfamily-transcription factor pairs that were bound in vivo or enriched for specific binding motifs, and observed that TEs contributing to open chromatin had higher levels of sequence conservation. We also showed that thousands of ERV-derived sequences were activated in a cell type-specific manner, especially in embryonic and cancer cells, and we demonstrated that this activity was associated with cell type-specific expression of neighboring genes. Taken together, these results demonstrate that TEs, and in particular ERVs, have contributed hundreds of thousands of novel regulatory elements to the primate lineage and reshaped the human transcriptional landscape.

(Pierre-Étienne Jacques, Justin Jeyakani, Guillaume Bourque, "The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements," PLOS Genetics (May 9, 2013) (emphases added).)

Again, we see from this that a great number of ERVs are found within open chromatin, strongly suggesting they are transcribed into RNA. Junk-DNA advocates respond that this isn't enough to show function because the transcribed DNA might just be producing "junk RNA." That's a weak rebuttal. As the paper states, ERV-based RNA was produced "in a cell type-specific manner" and was "associated with cell type-specific expression of neighboring genes." In other words, ERVs are being transcribed in a highly non-random manner that correlates with embryological patterns in association with other functional genetic elements. That is strongly suggestive of function.

Junk-DNA defenders rarely address such evidence showing that transcription is not random. For example, we see this in a recent paper in Genome Biology and Evolution by Brunet and Doolittle which critiques the PLOS Genetics paper. They write: "Jacques et al. (2013) for instance used ENCODE DNase I hypersensitivity data to place 80% of ERVs within open chromatin, and TEs in 63% of primate-specific regions." However, because specific functions for each ERV haven't yet been discovered they argue "It seems premature to imagine that a function for TEs as a class has been found!"

Their guilty-until-proven-innocent argument assumes that ERVs are by default non-functional. This reminds me of ENCODE critic Dan Graur who has stated, "If you don't know a function assume as a null hypothesis that it doesn't have function."

Worse, their approach ignores the specific empirical evidence raised in the PLOS Genetics paper, which shows ERVs aren't merely transcribed -- they are transcribed in a non-random, cell type-specific manner that correlates with the transcription of other functional genetic elements and strongly suggests function.

Dan Graur shares Brunet and Doolittle's dubious, assumption-filled approach. He claims that "transcription is fundamentally a stochastic [random] process," but as I explained previously in response to the ENCODE critics, ENCODE shows transcription isn't random:

ENCODE didn't merely study the genome to determine which DNA elements are biochemically active and making RNA. It also studied patterns of biochemical activity, uncovering highly non-random patterns of RNA production--patterns which indicate that these vast quantities of RNA transcripts aren't junk.... ENCODE's results suggest that a cell's type and functional role in an organism are critically influenced by complex and carefully orchestrated patterns of expression of RNAs inside that cell. As Stamatoyannopoulos observes, ENCODE found that "the majority of regulatory DNA regions are highly cell type-selective," and "the genomic landscape rapidly becomes crowded with regulatory DNA as the number of cell types" studied increases. Thus, as two pro-ENCODE biochemists explain, "Assertions that the observed transcription represents random noise . . . is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell- and tissue-specific transcription in human cells."

ERVs fit exactly the same pattern. If they are functional, then they don't provide any kind of special evidence for common ancestry, even if they do fit into a nested hierarchy. Here's my view of how evidence can count for or against (or neither for nor against) common ancestry:

(1) Shared functional biological similarity that fits a nested hierarchy (i.e., a treelike pattern): Explained equally well by common design or common descent.

(2) Shared non-functional biological similarity that fits a nested hierarchy: Best explained by common descent.

(3) Shared functional similarity that doesn't fit a nested hierarchy: Best explained by common design.

Defenders of common ancestry would have you think that ERVs belong in category (2). But the best genetic evidence now suggests they belong in category (1), thus toppling another evolutionary icon. If ERVs are functional, that means even if they do fit into a nested hierarchy, they are equally well explained by common design as by common descent.

Implicit admissions that Darwin had good reason to doubt.

More Admissions of Cambrian Explosiveness
Evolution News | @DiscoveryCSC

In these days of anti-ID “consensus,” don’t expect to find science journals publishing overt statements like, “Well, what do you know! Stephen Meyer and the intelligent design people were right!” Darwinian natural selection must remain omnipotent. Observational evidence, however, is more powerful than the language used to suppress it. Here are a couple of examples.

Rapid Arthropods

We reported two years about Marble Canyon, a remarkable Cambrian fossil deposit in British Columbia that rivals the famous Burgess Shale in significance. More extensive and detailed than its famous neighbor 26 miles to the northwest, Marble Canyon will likely provide years of discoveries to illuminate the Cambrian explosion. The site is of special interest because it was announced a year after Darwin’s Doubt (2013) was published.

Meet Tokummia, a creature found at Marble Canyon. The Calgary Sun calls it an “ancient arthropod with gnarly claws.” By all appearances, this four-inch animal was highly complex, possessing over 50 pairs of jointed legs, a shell, antennae, pincers, eyes, and mouth parts (implying a gut). Undoubtedly it was capable of sexual reproduction and partial metamorphosis, as are other arthropods. It is assigned a date of 508 million years old.

Jean-Bernard Caron, the discoverer of the Marble Canyon fossil trove (who also found a vertebrate fish there), with colleague Cédric Aria from the University of Toronto, studied 21 specimens of Tokummia. They tried to figure out where it fits in the evolutionary scheme. Writing in Nature, they conclude that it might have represented the start of the taxon Mandibulate (“biting things”). The Editor’s Summary offers hope that a gap has been partially filled:

Fossils from the famous 508-million-year-old Burgess Shale in Canada have been vital for shaping our understanding of the origin and early evolution of arthropods, the group of invertebrate animals recognized by their segmented bodies with jointed limbs and an exoskeleton. In recent years, research has found support for a single group of arthropods known as mandibulates that comprises insects, crustaceans and myriapods (centipedes and millipedes) but excludes chelicerates (spiders, scorpions and their allies). Few fossils have been found to illuminate the earliest mandibulates. Cédric Aria and Jean-Bernard Caron now show that this gap is partially filled by the arrival of the Burgess Shale fossil Tokummia katalepsis, whose anatomy allows the reconstruction of the anatomical and evolutionary history of this important animal group. [Emphasis added.]
It’s hard to find, however, more than mere suggestions that certain protrusions on the face of this animal might suffice to “partially” fill the gap. They present a theory story that modern mandibulates emerged from larval forms:

The presence of crustaceomorph traits in the Cambrian larvae of various clades basal to Mandibulata is reinterpreted as evidence for the existence of distinct ontogenetic niches among stem arthropods. Larvae would therefore have constituted an important source of morphological novelty during the Cambrian period, and, through heterochronic processes, may have contributed to the rapid acquisition of crown-group characters and thus to greater evolutionary rates during the early radiation of euarthropods.
Pause to understand what they are saying. This statement does nothing more than push the lucky mutations into the larva instead of the adult. Instead of the adult constituting “an important source of morphological novelty” (i.e., body luck), the larva becomes the source. Then, through “heterochronic [different-time] processes,” some things evolved more rapidly than others. Presto! You “greater evolutionary rates” in the Cambrian, speeding up the “acquisition” of arthropod traits. A more vacuous suggestion could hardly be concocted: basically, “some things happened, and some of them happened faster.” Now, watch how some things happened over and over:

The integration of larval taxa in the phylogeny (Extended Data Fig. 10 and Supplementary Discussion) suggests that morphological traits typically associated with crustaceans or their larvae (large labrum, segmented cephalic exopods, antennule-like frontalmost appendages) have occurred across multiple euarthropod clades (Cheiromorpha, Artiopoda, Pycnogonida) with non-mandibulate adult morphologies.
From there, they launch into full-bore storytelling mode. Putting the lucky mutations into the larvae open up wondrous possibilities:

This implies that crustacean-like characters appeared early in the evolution of euarthropods, as a result of adaptation to ecological niches specific to ontogenetic stages, and may have persisted across the ancestors of major clades before their paedomorphic appearance in adult mandibulates. Because ontogenetic niches create new characters upon which natural selection can act intraspecifically, the emergence of specialized larval forms may have constituted an important catalyst for the rapid evolution of euarthropods during the Cambrian period, and a notable source of morphological novelty for the first mandibulates.
Imagine that lucky mutations appeared in larvae, which exposed them to new “ecological niches” where natural selection could act. Those that stayed young-looking as adults (paedomorphs) “emerged” as new kinds of arthropods. That “emergence” triggered “rapid evolution.” This explanation is indistinguishable from magic. It should be dismissed as a non-scientific affirmation of presumptive Darwinian belief.

What’s more interesting for design advocates is their admission of “rapid evolution of euarthropods during the Cambrian period,” and “rapid acquisition of crown-group characters,” viz., the Cambrian explosion. You can’t hide an explosion in post-hoc distractions like “emergence” and “acquisition” and “arrival”. Like all the other Marble Canyon fossils, Tokummia appears in the rock record fully formed as a complex, successful animal.

Elsewhere in their paper, they admit to serious problems in the evolutionary story of arthropods, the most diverse and successful animals in all of nature:

Retracing the evolutionary history of arthropods has been one of the greatest challenges in biology.
Protocaridids are retrieved with Canadaspis and Odaraia (in Hymenocarina, emended) as part of an expanded mandibulate clade, refuting the idea that these problematic bivalved taxa, as well as other related forms, are representatives of the basalmost
The origin of the mandibulate body plan, …which encompasses myriapods, crustaceans and hexapods, has remained poorly documented.
These results, which had been influenced by an interpretation of the heads of large bivalved Cambrian arthropods as two-segmented, have fuelled a number of macroevolutionary hypotheses about the emergence of arthropod body plans and the evolution of frontal appendages, most notably with the objective to resolve the arthropod head problem.
The only fossil taxa put forward as the earliest crown mandibulates have been euthycarcinoids, historically problematic Palaeozoic centipede-like arthropods with multisegmented legs.
How the morphological characters and anatomies of the most successful animal body plan came into place has thus remained largely unknown.
(Regarding the “arthropod head problem,” see here.)

It’s clear that putting lucky mutations into larvae is not going to solve any of these problems. Meyer’s book stands unanswered.

Unrelated Ediacarans

What about earlier Ediacaran organisms? Can they be considered ancestral? Meyer dealt with one called Parvancorina on page 89, refuting suggestions that it had superficial resemblances to an ancestral trilobite-like body plan.

A new paper in Nature Scientific Reports focuses on another topic, a suggestion that Parvancorina displayed an early instance of rheotaxis (active alignment with a fluid current). The evidence, however, is circumstantial and admittedly open to interpretation. The authors do not present any evidence of organs, genes, or tissues capable of controlling movement.

Of more interest to us is their affirmation of Meyer’s view, that the Ediacaran animals bear no ancestral relationship with the Cambrian animals. Here, in regard to one of the leading candidates of such a relationship, these authors say, “Apart from possessing a bilaterally symmetrical body, there are no unequivocal morphological characters to support placement of Parvancorina within the Euarthropoda or even the Bilateria.”


These papers show that four years after Meyer’s book, and 13 years after his paper in the Smithsonian journal, evolutionists are still failing to come up with plausible evolutionary hypotheses for the sudden appearance of the Cambrian animals. As paleontologists hold these stunning fossils in their hands, they need to stop the storytelling about magic appearances, the desperate attempts to force-fit the fossils into mythical evolutionary trees, and take seriously Meyer’s proposal that intelligent design provides the best explanation.

Pro the consensus II

War by other means?

Scientism v. science yet again.

How Naturalism Rots Science from the Head Down
Denyse O'Leary

“Post-truth” was the Oxford Dictionaries’ word of the year for 2016. The term “post-fact” is also heard more often   now. Oxford  tells us  that “post-fact” relates to or denotes “circumstances in which objective facts are less influential in shaping public opinion than appeals to emotion and personal belief.”

Post-fact has certainly hit science. Pundits blame everyone but themselves   for its growing presence. But a post-fact and post-truth world are implicit and inevitable in the metaphysical naturalist view (nature is all there is) that is now equated with science  and often stands in for it.

Let’s start at the top, with cosmology. Some say there is a crisis  in cosmology; others say there are merely  challenges. Decades of accumulated evidence have not produced the universe that metaphysical naturalism expects and needs. The Big Bang has not given way to a theory with fewer theistic implications. There is a great deal of evidence for fine-tuning of this universe; worse, the evidence for alternatives is fanciful or merely ridiculous. Put charitably, it would not even be considered evidence outside of current science.

One response has simply been to develop ever more fanciful theories. Peter Woit, a Columbia University mathematician, is an atheist critic of fashionable but unsupported ideas like string theory (Not Even Wrong, 2007) and the multiverse that it supports. Recently, Woit dubbed 2016 the worst year ever for  “fake physics”  (as in “fake news“ ). As he  told Dennis Horgan recently at Scientific American, he is referring to “misleading, overhyped stories about fundamental physics promoting empty or unsuccessful theoretical ideas, with a clickbait headline.”

Fake physics (he links to a number of examples at  at his blog) presents cosmology essentially as an art form. It uses the trappings of science as mere decor (the universe is a computer simulation, the multiverse means that physics cannot predict anything…). Conflicts with reality call for a revolution in our understanding of physics rather than emptying the waste basket.

Woit blames the Templeton Foundation for funding   this stuff. But Templeton caters, as it must, to an audience. Perhaps a more pressing issue is this: The need to defend the multiverse without evidence has led to a growing discomfort with traditional decision-making tools of science, for example,  falsifiability  and Occam’s razor.   And metaphysical naturalism, not traditional religion, is sponsoring this war on reality.

Can science survive the idea that nature is all there is? The initial results are troubling.  Where evidence can be ignored, theory needs only a tangential relationship to the methods and tools of science. Physicist Chad Orzel expressed disappointment with the 2014 Cosmos remake,  saying  “I find the choice to prioritize wildly speculative but vaguely inspirational material like panspermia and the whole ‘future cosmic calendar’ stuff kind of disappointing. There’s so much that they haven’t talked about yet that’s based on good, solid evidence, but we’re getting soaring vagueness.” But what if a disquieting amount of the available evidence is unwanted?

The increasingly popular idea that consciousness is an  illusion flows together naturally with the new cosmology. Contradictory theories do not seriously conflict because any resolution would just be another user illusion. Readers notice how strange the new science literature sounds but, to the extent that they accept metaphysical naturalism, they can base their objections only on personal discomfort.

What if a theory, such as intelligent design, challenges metaphysical naturalism? It will certainly stand out. And it will stand out because it is a threat to all other theories in the entire system. Merely contradictory or incoherent theories clashing against each other are not a threat in any similar way; there are just so many more of them waiting up the spout.

Could intelligent design theory offer insights? Yes, but they come at a cost. We must first acknowledge that metaphysical naturalism is death for science. Metaphysical naturalists are currently putting the science claims that are failing them beyond the reach of disconfirmation by evidence and casting doubt on our ability to understand evidence anyway.

ID is first and foremost a demand that evidence matter, underwritten by a conviction that reason-based thinking is not an illusion. That means, of course, accepting fine-tuning as a fact like any other, not to be explained away by equating vivid speculations about alternative universes with observable facts. Second, ID theorists insist that the information content of our universe and life forms is the missing factor in our attempt to understand our world. Understanding the relationship between information on the one hand and matter and energy on the other is an essential next discovery. That’s work, not elegant essays.


We will get there eventually. But perhaps not in this culture; perhaps in a later one.  Science can throw so many resources into protecting metaphysical naturalism that it begins to decline. Periods of great discovery are often followed by centuries of doldrums. These declines are usually based on philosophical declines. The prevalence of, for example, fake physics, shows that we are in the midst of just such a philosophical decline. It’s a stark choice for our day.

On the tyranny of the consensus.

Stephen Meyer: Appeals to Evolution “Consensus” Undercut Scientific Methodology
David Klinghoffer | @d_klinghoffer

“Darwin’s public defenders,” as Stephen Meyers calls them – Nye, Dawkins, Krauss, & Co. – loudly contend that evolutionary theory has “no weaknesses,” is “undeniable,” enjoys the support of a scientific “consensus,” and therefore is questioned only by science “deniers.” In a presentation at the Heritage Foundation in Washington, D.C., ahead of last month’s March for Science, Dr. Meyer debunked these claims.

You can hear him now on a new ID the Future   podcast episode. Download it here.


A significant point Meyer makes is that to invoke the idea of a “consensus” on evolution itself undercuts the scientific methodology. The latter entails spirited debate among scientists about competing hypotheses regarding how to interpret data. To shut the door on debate, as the Science Marchers would like to do, means shutting the door on science.

On name calling in the name of 'Science'

Abusing the “Anti-Science” Label — Editors of Nature Agree with Wesley Smith!
David Klinghoffer | @d_klinghoffer

On a new episode of ID the Future, Wesley Smith discusses the “anti-science” label and identifies some trends in the academy and the media that truly are inimical to science. He notes the tendency to confuse science with ethics, and to use the idea of science itself as a weapon to silence debate.

Download the episode here, or listen to it here. Wesley spoke at the Heritage Foundation in Washington, DC, along with other Discovery Institute colleagues ahead of last month’s March for Science.

Meanwhile, this is sure refreshing. Nature, the world’s foremost science journal, urges readers to cool it with the “anti-science” slur. They do so in an editorial,  “Beware the anti-science label,”  that is uncompromising in its common sense:

Antimatter annihilates matter. Anti-science, it is said, destroys what matters. And fears are increasing that anti-science forces are on the march. Indeed, on last month’s March for Science, a ‘war on science’ was frequently invoked as a reason for researchers to mobilize. Signs held aloft warned of a conflict.

True anti-science policies — the early Soviet Union’s suppression of genetics research, for example, and its imprisonment of biologists while trying to revamp agriculture — can wreck lives and threaten progress. But it’s important not to cheapen the term by overusing it. And it’s wrong for researchers and others to smear all political decisions they disagree with as being anti-science.
Well, what do you know? Sure, they throw in the expected criticisms directed at “climate denial” (strange expression — who denies that there’s a climate? — but you know what they mean). Otherwise, they are singing our tune. Just as Wesley says, disagreements about policy or ethics should not be translated into “science” versus “anti-science.”

Science is only one of many factors and interests that a thoughtful politician needs to weigh when choosing a position on a complex topic. If science sometimes loses out to concerns about employment or economics, scientists should not immediately take it as a personal slight. Rather, it is a reason to look for common ground on which to discuss the concerns and work out how science can help: creating jobs in green energy, for instance, or revamping wasteful grant programmes.

Of course, corruption and conflicts of interest can frequently motivate political decisions as well, and researchers and others should not hesitate to highlight them. But name-calling and portraying the current political climate as a war between facts and ignorance simply sows division.
Yes! As a bonus, they note the obvious that is nevertheless habitually denied, that scientists don’t agree on everything, and that’s OK:

Science does not speak with a single voice. Sit at a hotel bar during any conference and you will hear impassioned debate over what the data have to say about a certain question. Equally credentialled researchers fall out on whether carbon dioxide levels in the atmosphere have passed a tipping point, or on the health risks of sugar.

Good for you, Nature editors. When establishment pillars like yourselves finally get fed up and speak out against the weaponizing of science rhetoric to political and ideological ends, that’s a welcome and very healthy sign.

Dancing on the razor's edge?

Recognizing Life Is Different from Natural Processes, Science Balances on the Edge of ID
Evolution News | @DiscoveryCSC

Scientific materialists must live in a state of cognitive dissonance. They believe everything is “natural” (within nature), but they don’t hesitate to look for decidedly “un”-natural things about life. Consider this from New Scientist  about how to detect alien life:

Now Lee Cronin, a chemist at the University of Glasgow, UK, argues that complexity could be a biosignature that doesn’t depend on any assumptions about the life forms that produce it. “Biology has one signature: the ability to produce complex things that could not arise in the natural environment,” Cronin says. [Emphasis added.]
We saw Lee Cronin last June arguing for a “radical rethink” of origin-of-life scenarios. Here, he’s thinking about generic life that could be found in space. Alien life might not be made of “amino acids, unequal proportions of mirror-image molecules, and unusual ratios of carbon isotopes, all of which are signatures of life here on Earth.” It could be totally different. Consequently, it could be missed by Earth-centric detection strategies.

Astrobiology

There is one thing that would distinguish life from non-life, Cronin reasons: its complex organization. Here, the article by Bob Holmes engages in a delicate balancing act, coming dangerously close to intelligent design:

Obviously, an aircraft or a mobile phone could not assemble spontaneously, so their existence points to a living — and even intelligent — being that built them. But simpler things like proteins, DNA molecules or steroid hormones are also highly unlikely to occur without being assembled by a living organism, Cronin says.
Now that is dancing on the edge! We presume Cronin and Holmes are being careful not to topple over into the ID camp, but their ideas are closer than the usual materialist/reductionist talk of spontaneous emergence that makes life out to be a natural byproduct of matter. There’s even a faint echo of Thomas Nagel’s appeal to common sense in Mind and Cosmos where he intuits a limit to what can credibly be called natural:

And the coming into existence of the genetic code — an arbitrary mapping of nucleotide sequences into amino acids, together with mechanisms that can read the code and carry out its instructions — seems particularly resistant to being revealed as probable given physical law alone.
Cronin proposes a method for measuring complexity that doesn’t depend on life as we know it. He counts the number of unique steps required to get a molecule. Some molecules require so few steps that they can be explained by natural causes. But for a molecule of sufficient complexity, at some point in the sequence of events in its formation, probability would demand a “life inference” if not an inference to intelligence:

Any structure requiring more than about 15 steps is so complex it must be biological in origin, he said this week at the Astrobiology Science Conference in Mesa, Arizona.
Let’s pause to consider what this means. For something to be “biological in origin,” it cannot have emerged by natural law alone. It would be “un”-natural enough to warrant the inference that life or intelligence caused it to come into being.

One might argue that purely physical things can have unique signatures as well. For instance, planetary scientists find signatures of volcanism on the surfaces of Mercury, Io, and even Pluto and Ceres (ice volcanism). What’s the difference, then, between looking for a biosignature in one scientific context and a heat signature in another context? Clearly, it must be the degree of complexity. Heat is common everywhere just by normal thermodynamics. But some complex phenomena are never observed to emerge through natural law alone.

With volcanoes, laws of heat and buoyancy are sufficient to figure out how material makes its way up through a crust. If a volcano had to take a sequence of 15 unique steps, however, then we might be justified in looking into non-natural causes at work. That’s not likely, since well-known laws of physics can account for eruptions, and we witness volcanoes all the time. We never witness unguided chemical reactions going through 15 or more unique independent steps to arrive at a complex molecule, much less to produce a coding system with transcription, translation, and reproduction. That’s why the “complexity” Cronin tries to measure must equate to specified complexity.

SETI

The distinction between natural and intelligent causes becomes especially clear in SETI. In another piece in New Scientist, Geraint Lewis from the University of Sydney discusses not just bio-signatures but mind-signatures. Frustrated by the silence of traditional SETI, and realizing that the Fermi paradox (the “Where is everybody?” question posed by Enrico Fermi) has never been answered, he suggests a different search strategy closer to home: finding the remains of extinct civilizations in our own celestial backyard.

This apparent absence of evidence is known as the Fermi paradox. It has led to considerable head-scratching for more than half a century. Now, U.S. astronomer Jason Wright has a new twist on it, rephrasing Fermi’s question to: “Where was everybody?” In particular, one answer could be our own solar system. He wonders if “prior indigenous technological species” arose here, and what trace might they have left behind?
David Klinghoffer commented on Wright’s idea here last week. ID advocates should feel right at home with this strategy. It’s like archaeology. We know it’s possible in many cases to separate natural causes from intelligent causes when examining artifacts (see “Intelligent Design in Action: Archaeology”). It’s not even necessary to know anything about the builders to infer that an intelligent cause probably brought a structure into existence (see here for an example). Extending the same reasoning, we can expand the search space to other nearby worlds.

If they existed here, or on the other planets and moons, what signs should we look for and where? In the crushing environment of Venus, and the churning plate tectonics of Earth, buildings and monuments would be eroded and destroyed on such long timescales. But on slow-changing Mars, our moon, and possibly the frozen satellites of outer solar system planets, the tunnels and cities of ancient lost civilisations could survive buried under the soil and ice.
Lewis implies that the inference to intelligence is not only intuitive but robust. Tunnels, cities, and habitable structures are decidedly “un”-natural because, applying the same reasoning used by Cronin, too many unique steps would be required for their origin. Lewis is even willing to lower the bar for design detection:

Other signatures would be more durable still, with the slow decay of nuclear power sources apparent for billions of years, with distinct mixtures of elements and radioactivity.
We saw a similar type of reasoning used by experts in “nuclear forensics” a while back. Scientists can determine, through intuition supported by probability calculations, that certain things don’t “just happen” naturally.

Lewis admits that his thoughts about extinct civilizations are “pure speculation” at this point. But he implies that in principle one can distinguish natural causes from intelligent causes. That’s all intelligent design tries to do. He says, “When we finally start digging into the dirt of other worlds, we might uncover definitive signs that someone else has been there before.” This, too, dances right up to the perilous edge of ID.

Conclusion

ID is the science of determining “definitive signs” that “someone” (a mind) has been at work; a mind with the intelligence, intention, and ability to take natural materials and organize them into complex structures unreachable by unguided natural processes. For SETI, the inference to intelligent causation is intuitive and direct. For astrobiology, the inference is indirect, but logically similar: a biosignature points to a non-natural chain of events that had a goal and a purpose (life).


These scientists may not call it intelligent design, but ID is alive and well in their work. The challenge is to help them recognize it.