Yet more storytelling masquerading as science?

At Last, the Details of How Proteins Evolve?
Cornelius Hunter

How did proteins evolve? It is a difficult question because, setting aside many other problems, the very starting point — the protein-coding gene — is highly complex. A large number of random mutations would seem to be required before you have a functional protein that helps the organism. Too often such problems are solved with vague accounts of “adaptations” and “selection pressure” doing the job. 

   But this week researchers at the University of Illinois announced ground-breaking research that provides a step-by-step, detailed, description of the evolution of a new protein-coding gene and associated regulatory DNA sequences. The protein in question is a so-called “antifreeze” protein that keeps the blood of Arctic codfish from freezing, and the new research provides the specific sequence of mutations, leading to the new gene. 

     It would be difficult to underestimate the importance of this research. It finally provides scientific details answering the age-old question of how nature’s massive complexity could have arisen. As the paper triumphantly declares, “Here, we report clear evidence and a detailed molecular mechanism for the de novo formation of the northern gadid (codfish) antifreeze glycoprotein (AFGP) gene from a minimal noncoding sequence.” Or as lead researcher, professor Christina Cheng,  explained, “This paper explains how the antifreeze protein in the northern codfish evolved.” 

       

   Just One Problem

This is a monumental finding. Having the scientific details, down to the level of specific mutations, of how a new protein-coding gene evolved — not from a related gene but from non-coding DNA — is something evolutionists could only dream of only a few short years ago. There’s only one problem: it is all junk science.

    The first difficulty is that this new “research” is, in actuality, a just-so story. As Wikipedia defines it:

    In science and philosophy, a just-so story is an unverifiable narrative explanation for a cultural practice, a biological trait, or behavior of humans or other animals. The pejorative nature of the expression is an implicit criticism that reminds the hearer of the essentially fictional and unprovable nature of such an explanation. Such tales are common in folklore and mythology.

     For example, the antifreeze protein is of relatively low complexity chiefly consisting of a repeating sequence of three amino acids (threonine-alanine-alanine), and the evolutionists claim that these repeating sequences “strongly suggest” that the protein-coding gene “evolved from repeated duplications of an ancestral 9-nucleotide threonine-alanine-alanine-coding element.”

Why is that true? Why does a repeating genetic sequence “strongly suggest” that it “evolved from repeated duplications?” What experiment revealed this truth? What evidence gives us this profound principle? The answer, of course, is that there is none. Nowhere do the evolutionists justify this claim because there is no empirical justification.

There is no scientific evidence for it. Zero.

More Non-Empirical Claims 

The paper continues with yet more non-empirical claims. Those nine nucleotides “likely originated within a pair of conserved 27-nucleotide” segments that flank each side of the repetitive region. And these four 27-nucleotide segments are similar to each other, “indicating they resulted from the duplication of an initial copy.” As the paper concludes, “chance duplications” of an ancestral 27-nucleotide segment “produced four tandem copies.”

But why are those claims true? Why do such similarities imply an origin via evolutionary mechanisms? The problem is, they don’t. There is no empirical evidence for any of this. This is completely evidence-free.

The evolutionists next explain that the 9-nucleotide segment duplicated a large number of times because it worked well:

We hypothesize that, upon the onset of selective pressure from cold polar marine conditions, duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred.

The above quote is an example of the non-empirical teleology that pervades evolutionary thought. It was upon the onset of cold conditions that the needed genetic duplications occurred. This is not empirical; this is story-telling.

The paper continues with a series of one-time, contingent events crucial to their story and non-empirical claims. The genetic sequence “was appropriately delimited by an existing in-frame termination codon.” Appropriately delimited?

The presence of a region in two of the species “indicates that it existed in the gadid ancestor before the emergence of the AFGP.” The absence of a thymine nucleotide at a location in some of the species “very likely resulted from a deletion event,” causing a fortuitous frameshift which supplied the crucial signal peptide segment, telling cellular machinery that the protein should be secreted to the bloodstream. As the paper concludes, “the emerging AFGP gene was thus endowed with the necessary secretory signal.”

Endowed with the necessary signal? There is no empirical evidence for any of this.

Substantial Serendipity 

Another problem with this just-so account is the substantial level of serendipity required. The new antifreeze protein did not arise from some random DNA sequence, but rather from crucial, preexisting segments of DNA that just happened to be lying around. In other words, the fish were facing a colder environment, they needed some antifreeze in their blood, and the pieces needed for such an antifreeze gene were fortuitously available.

The authors hint at this serendipity when they conclude that their story of how this protein evolved is an example of “evolutionary ingenuity.” Evolutionary ingenuity?

The press release is even more revealing. Cheng admits that the evolution of this gene “occurred as a result of a series of seemingly improbable, serendipitous events.” For “not just any random DNA sequence can produce a viable protein.” Furthermore, in addition to the gene itself, “several other serendipitous events occurred.”

The DNA was “edited in just the right way,” and “somehow, the gene also obtained the proper control sequence that would allow the new gene to be transcribed into RNA.”

Even the evolutionists admit to the rampant serendipity. Nonetheless they are triumphant, for “the findings offer fresh insights into how a cell can invent ‘a new, functional gene from scratch.’”

In actuality the findings arose from a series of non-empirical claims. Fresh insights? Not so much.

The apostle Paul's epistle to the Hebrews:The Watchtower society's commentary.

HEBREWS, LETTER TO THE

An inspired letter of the Christian Greek Scriptures. Evidence indicates that it was written by the apostle Paul to the Hebrew Christians in Judea about 61 C.E. To those Hebrew Christians the letter was most timely. It had then been about 28 years since Jesus Christ’s death and resurrection. In the earlier part of that period severe persecution had been brought upon these Jewish Christians in Jerusalem and Judea by the Jewish religious leaders, resulting in the death of some Christians and the scattering of most of the others from Jerusalem. (Ac 8:1) The scattered ones remained active in spreading the good news everywhere they went. (Ac 8:4) The apostles had stayed in Jerusalem and had held the remaining congregation together there, and it had grown, even under stiff opposition. (Ac 8:14) Then, for a time, the congregation entered into a period of peace. (Ac 9:31) Later, Herod Agrippa I caused the death of the apostle James, John’s brother, and mistreated others of the congregation. (Ac 12:1-5) Sometime after this, there developed a material need among the Christians in Judea, giving opportunity for those in Achaia and Macedonia (in about 55 C.E.) to demonstrate their love and unity by sending aid. (1Co 16:1-3; 2Co 9:1-5) So the Jerusalem congregation had suffered many hardships.

Purpose of the Letter. The congregation in Jerusalem was comprised almost entirely of Jews and those who had been proselytes to the Jews’ religion. Many of these had come to a knowledge of the truth after the time of the most bitter persecution. At the time the letter to the Hebrews was written, the congregation was enjoying comparative peace, for Paul told them: “You have never yet resisted as far as blood.” (Heb 12:4) Nevertheless, the lessening of outright physical persecution to death did not mean that strong opposition from the Jewish religious leaders had ceased. The newer members of the congregation had to face the opposition just as the rest did. And some others were immature, not having made the progress toward maturity that they should have made in view of the time. (5:12) The opposition they faced daily from the Jews put their faith to a test. They needed to build up the quality of endurance.​—12:1, 2.

Time was running out for Jerusalem. Neither the apostle Paul nor those in the congregation at Jerusalem knew when the foretold desolation would occur, but God did know. (Lu 21:20-24; Da 9:24, 27) The situation would call for the Christians there to be alert and to exercise faith so that they would flee from the city when they saw Jerusalem surrounded by encamped armies. All in the congregation needed to strengthen themselves for these momentous events. According to tradition, it was just about five years after the writing of this letter that Cestius Gallus’ troops attacked the city and then withdrew. Four years after that, Jerusalem and its temple were leveled by the Romans under General Titus. But before either of these events took place, Jehovah had provided the inspired counsel that his servants needed.

Jewish opposition. The Jewish religious leaders, by lying propaganda, had done everything they could to stir up hatred against Christ’s followers. Their determination to fight Christianity with every possible weapon is demonstrated by their actions, as recorded in Acts 22:22; 23:12-15, 23, 24; 24:1-4; 25:1-3. They and their supporters constantly harassed the Christians, evidently using arguments in an effort to break their loyalty to Christ. They attacked Christianity with what might seem to a Jew to be powerful reasoning, hard to answer.

At that time Judaism had much to offer in the way of tangible, material things and outward appearance. The Jews might say that these things proved Judaism superior and Christianity foolish. Why, they had told Jesus that the nation had as their father Abraham, to whom the promises were given. (Joh 8:33, 39) Moses, to whom God spoke “mouth to mouth,” was God’s great servant and prophet. (Nu 12:7, 8) The Jews had the Law and the words of the prophets from the beginning. ‘Did not this very antiquity establish Judaism as the true religion?’ they might ask. At the inaugurating of the Law covenant, God had spoken by means of angels; in fact, the Law was transmitted through angels by the hand of the mediator Moses. (Ac 7:53; Ga 3:19) On this occasion God had given a fear-inspiring demonstration of power in shaking Mount Sinai; the loud sound of a horn, smoke, thunder, and lightning accompanied the glorious display.​—Ex 19:16-19; 20:18; Heb 12:18-21.

Besides all these things of antiquity, there stood the magnificent temple with its priesthood instituted by Jehovah. Priests officiated at the temple, daily handling many sacrifices. Accompanying these things were the costly priestly garments and the splendor of the services conducted at the temple. ‘Had not Jehovah commanded that sacrifices for sin be brought to the sanctuary, and did not the high priest, the descendant of Moses’ own brother Aaron, enter the Most Holy on the Day of Atonement with a sacrifice for the sins of the whole nation? On this occasion, did he not approach representatively into the very presence of God?,’ the Jews might argue. (Le 16) ‘Furthermore, was not the kingdom the possession of the Jews, with one (the Messiah, who would later come, as they said) to sit on the throne at Jerusalem to rule?’

If the letter to the Hebrews was being written to equip the Christians to answer objections that were actually being raised by the Jews, then those enemies of Christianity had contended in this way: ‘What did this new “heresy” have to point to as evidence of its genuineness and of God’s favor? Where was their temple, and where their priesthood? In fact, where was their leader? Was he of any importance among the leaders of the nation during his lifetime​—this Jesus, a Galilean, a carpenter’s son, with no rabbinic education? And did he not die an ignominious death? Where was his kingdom? And who were his apostles and followers? Mere fishermen and tax collectors. Furthermore, whom did Christianity draw, for the most part? The poor and lowly persons of the earth and, even worse, uncircumcised Gentiles, not of the seed of Abraham, were accepted. Why should anyone put his trust in this Jesus, who had been put to death as a blasphemer and a seditionist? Why listen to his disciples, men unlettered and ordinary?’​—Ac 4:13.

Superiority of Christian system. Some of the immature Christians may have become neglectful of their salvation through Christ. (Heb 2:1-4) Or they may have been swayed by the unbelieving Jews who surrounded them. Coming to their aid with masterful argument, using the Hebrew Scriptures, on which the Jews claimed to rely, the apostle shows irrefutably the superiority of the Christian system of things and of the priesthood and kingship of Jesus Christ. He Scripturally demonstrates that Jesus Christ is the Son of God, greater than angels (1:4-6), than Abraham (7:1-7), than Moses (3:1-6), and than the prophets (1:1, 2). In fact, Christ is the appointed heir of all things, crowned with glory and honor and appointed over the works of Jehovah’s hands.​—1:2; 2:7-9.

As to priesthood, Christ’s is far superior to the Aaronic priesthood of the tribe of Levi. It is dependent, not on inheritance from sinful flesh, but on an oath of God. (Heb 6:13-20; 7:5-17, 20-28) Why, though, did he endure such hardships and die a death of suffering? This was foretold as essential to mankind’s salvation and to qualify him as High Priest and the one to whom God will subject all things. (2:8-10; 9:27, 28; compare Isa 53:12.) He had to become blood and flesh and die in order to emancipate all those who through fear of death were in slavery. Through his death he is able to bring to nothing the Devil, a thing no human priest could do. (Heb 2:14-16) He, having so suffered, is a High Priest who can sympathize with our weaknesses and can come to our help, having been tested in all respects.​—2:17, 18; 4:15.

Moreover, argues the apostle, this High Priest “passed through the heavens” and appeared in the very presence of God, not in a mere earthly tent or building that was only pictorial of heavenly things. (Heb 4:14; 8:1; 9:9, 10, 24) He needed to appear only once with his perfect, sinless sacrifice, not over and over again. (7:26-28; 9:25-28) He has no successors, as did the Aaronic priests, but lives forever to save completely those to whom he ministers. (7:15-17, 23-25) Christ is Mediator of the better covenant foretold through Jeremiah, under which sins can really be forgiven and consciences can be made clean, things that the Law could never accomplish. The Ten Words, the basic laws of the Law covenant, were written on stone; the law of the new covenant, on hearts. This prophetic word of Jehovah by Jeremiah made the Law covenant obsolete, to vanish away in time.​—8:6-13; Jer 31:31-34; De 4:13; 10:4.

It is true, the writer of Hebrews continues, that an awesome display of power was manifested at Sinai, demonstrating God’s approval of the Law covenant. But even more forcefully God bore witness at the inauguration of the new covenant with signs, portents, and powerful works, along with distributions of holy spirit to all the members of the congregation assembled. (Heb 2:2-4; compare Ac 2:1-4.) And as to Christ’s Kingship, his throne is in the heavens itself, far higher than that of the kings of the line of David who sat on the throne in earthly Jerusalem. (Heb 1:9) God is the foundation of Christ’s throne, and his Kingdom cannot be shaken, as was the kingdom in Jerusalem in 607 B.C.E. (1:8; 12:28) Furthermore, God has gathered his people before something far more awe inspiring than the miraculous display at Mount Sinai. He has caused anointed Christians to approach the heavenly Mount Zion, and he will yet shake not only the earth but also the heaven.​—12:18-27.

The letter to the Hebrews is of inestimable value to Christians. Without it, many of the realities concerning Christ as foreshadowed by the Law would be unclear. For example, the Jews had known all along from the Hebrew Scriptures that when their high priest went into the Most Holy compartment of the sanctuary in their behalf he was representing them before Jehovah. But they never appreciated this reality: Someday the real High Priest would actually appear in the heavens in Jehovah’s very presence! And as we read the Hebrew Scriptures, how could we realize the tremendous significance of the account of Abraham’s meeting with Melchizedek, or understand so clearly what this king-priest typified? This, of course, is to cite only two examples out of the many realities that we come to visualize in reading the letter.

The faith that the letter builds helps Christians to hold on to their hope by means of “the evident demonstration of realities though not beheld.” (Heb 11:1) At a time when many persons rely on antiquity, on the material wealth and power of organizations, on the splendor of rites and ceremonies, and look to the wisdom of this world instead of to God, the divinely inspired letter to the Hebrews admirably helps to make the man of God “fully competent, completely equipped for every good work.”​—2Ti 3:16, 17.

Writership and Time, Place Written. Writership of the letter to the Hebrews has been widely ascribed to the apostle Paul. It was accepted as an epistle of Paul by early writers. The Chester Beatty Papyrus No. 2 (P⁠46) (of about 200 C.E.) contains Hebrews among nine of Paul’s letters, and Hebrews is listed among “fourteen letters of Paul the apostle” in “The Canon of Athanasius,” of the fourth century C.E.

The writer of Hebrews does not identify himself by name. Even though all his other letters do bear his name, this lack of identification of the writer would obviously not rule out Paul. Internal evidence in the letter strongly points to Paul as its writer and to Italy, probably Rome, as the place of writing. (Heb 13:24) It was in Rome, evidently during the years 59 to 61 C.E., that Paul was first imprisoned. Timothy was with Paul in Rome, being mentioned in the apostle’s letters to the Philippians, the Colossians, and Philemon, written from Rome during that imprisonment. (Php 1:1; 2:19; Col 1:1, 2; Phm 1) This circumstance fits the remark at Hebrews 13:23 about Timothy’s release from prison and the writer’s desire to visit Jerusalem soon.

The time of writing was before the destruction of Jerusalem in 70 C.E., for the temple at Jerusalem still stood, with services being performed there, as is evident from the argument in the letter. And Paul’s remark about Timothy’s being released reasonably fixes the time of writing about nine years earlier, namely, 61 C.E., when it is thought that Paul himself was released from his first imprisonment.​—Heb 13:23.

[Box on page 1078]

HIGHLIGHTS OF HEBREWS

A powerful treatise that fortified Hebrew Christians and enabled them to help sincere fellow countrymen during the final years of the Jewish system

Evidently written by the apostle Paul less than a decade before Jerusalem was destroyed in 70 C.E.

The superior position occupied by God’s Son (1:1–3:6)

He is the unique Son, appointed heir, exact representation of his Father’s very being, through whom all that was made is also sustained

Compared with the Son, angels are but servants. The Father calls him alone “my son,” the Firstborn to whom even angels would do obeisance; of him and not of angels can it be said that his royal rule rests upon God as his throne, his permanence surpasses that of heavens and earth made through him, and his position is at the Father’s right hand

If the Law conveyed through angels could not be disregarded without punishment, what was spoken by God through the Son, who is higher than angels, must be given extraordinary attention

Though lower than angels as a man, Jesus Christ was afterward exalted above them and granted dominion over the inhabited earth to come

Moses was an attendant in the house of God, but Jesus Christ is over the entire house

Entering God’s rest still possible (3:7–4:13)

Because of disobedience and lack of faith, the Israelites who left Egypt failed to enter God’s rest

Christians can enter God’s rest, provided they avoid Israel’s disobedience and exert themselves in a course of faithfulness

The living word promising entrance into God’s rest is sharper than a sword, dividing (by a person’s response to it) between what he may appear to be as a soul and what he really is as to his spirit

Superiority of Christ’s priesthood and the new covenant (4:14–10:31)

Because of having been tested in all respects yet remaining sinless, Jesus Christ as high priest can sympathize with sinful humans and deal compassionately with them

He is priest by God’s appointment according to the manner of Melchizedek, whose priesthood was greater than the Levitical priesthood

Unlike Levite priests in Aaron’s family, Jesus Christ possesses an indestructible life and thus requires no successors to continue his saving work; he is sinless and so does not need to present sacrifices for himself; he offered up his own body, not animals, and entered, not an earthly sanctuary, but heaven itself with the value of his outpoured blood, thereby validating the new covenant

The new covenant, with Jesus as Mediator, is superior to the Law covenant in that those in it have God’s laws in their hearts and enjoy true forgiveness of sins

Appreciation for these benefits will move Christians to make public declaration of hope and to assemble regularly

Faith essential to please God (10:32–12:29)

Jehovah is displeased with those faithlessly shrinking back from him instead of enduring so as to receive what he has promised

The exemplary faith of integrity-keepers from Abel onward serves as encouragement to endurance in the Christian race, while considering closely Jesus Christ and his flawless course under suffering

The suffering that God permits to befall faithful Christians may be viewed as a form of discipline from him, designed to produce the peaceful fruit of righteousness

Exhortations to pursue a faithful course (13:1-25)

Manifest brotherly love, be hospitable, remember believers who are suffering, maintain marriage in honor, and be content with present things, confident of Jehovah’s help

Imitate the faith of those taking the lead, and avoid succumbing to strange teachings

Be willing to bear reproach as Christ did; always offer to God sacrifice of praise through him

Be obedient to those taking the lead

File under only in academia.

‘Sokal Squared’: Is Huge Publishing Hoax ‘Hilarious and Delightful’ or an Ugly Example of Dishonesty and Bad Faith?

By Alexander C. Kafka 

Reactions to an elaborate academic-journal hoax, dubbed "Sokal Squared" by one observer, came fast and furious on Wednesday. Some scholars applauded the hoax for unmasking what they called academe’s leftist, victim-obsessed ideological slant and low publishing standards. Others said it had proved nothing beyond the bad faith and dishonesty of its authors.

Three scholars — Helen Pluckrose, a self-described "exile from the humanities" who studies medieval religious writings about women; James A. Lindsay, an author and mathematician; and Peter Boghossian, an assistant professor of philosophy at Portland State University — spent 10 months writing 20 hoax papers that illustrate and parody what they call "grievance studies," and submitted them to "the best journals in the relevant fields." Of the 20, seven papers were accepted, four were published online, and three were in process when the authors "had to take the project public prematurely and thus stop the study, before it could be properly concluded." A skeptical Wall Street Journal editorial writer, Jillian Kay Melchior, began raising questions about some of the papers over the summer.

Beyond the acceptances, the authors said, they also received four requests to peer-review other papers "as a result of our own exemplary scholarship." And one paper — about canine rape culture in dog parks in Portland, Ore. — "gained special recognition for excellence from its journal, Gender, Place, and Culture … as one of 12 leading pieces in feminist geography as a part of the journal’s 25th anniversary celebration."

RELATED CONTENT

Anatomy of a Hoax  PREMIUM

Hoax Article in Social-Science Journal Gets a Rise Out of Some Scholars

Not all readers accepted the work as laudable scholarship. National Review took "Helen Wilson," the fictional author of the dog-park study, to task in June for her approach. "The whole reasoning behind Wilson’s study," wrote a staff writer, Katherine Timpf, "is the belief that researching rape culture and sexuality among dogs in parks is a brilliant way to understand more about rape culture and sexuality among humans. This is, of course, idiotic. Why? Because humans are not dogs."

Another published paper, "Going In Through the Back Door: Challenging Straight Male Homohysteria, Transhysteria, and Transphobia Through Receptive Penetrative Sex Toy Use," appeared in Sexuality and Culture. It recommends that men anally self-penetrate "to become less transphobic, more feminist, and more concerned about the horrors of rape culture."

The trolling trio wondered, they write, if a journal might even "publish a feminist rewrite of a chapter from Adolf Hitler’s Mein Kampf." Yup. "Our Struggle Is My Struggle: Solidarity Feminism as an Intersectional Reply to Neoliberal and Choice Feminism" was accepted by the feminist social-work journal Affilia.

Darts and Laurels

Some scholars applauded the hoax.

"Is there any idea so outlandish that it won’t be published in a Critical/PoMo/Identity/‘Theory’ journal?" tweeted the Harvard psychologist Steven Pinker.

"Three intrepid academics," wrote Yascha Mounk, an author and lecturer on government at Harvard, "just perpetrated a giant version of the Sokal Hoax, placing … fake papers in major academic journals. Call it Sokal Squared. The result is hilarious and delightful. It also showcases a serious problem with big parts of academia."In the original Sokal Hoax, in 1996, a New York University physicist named Alan Sokal published a bogus paper that took aim at some of the same targets as his latter-day successors.

Others were less receptive than Mounk. "This is a genre," tweeted Kieran Healy, a sociologist at Duke, "and they’re in it for the lulz" — the laughs. "Best not to lose sight of that."

"Good work is hard to do," he wrote, "incentives to publish are perverse; there’s a lot of crap out there; if you hate an area enough, you can gin up a fake paper and get it published somewhere if you try. The question is, what do you hate? And why is that?"

Reviews of several of the papers "were partly conditional on claims to have done some sort of actual (very bad) fieldwork," Healy noted.

And that’s where the question of bad faith comes in.

"I am so utterly unimpressed," wrote Jacob T. Levy, a political theorist at McGill University, "by the fact that an enterprise that relies on a widespread presumption of not-fraud can be fooled some of the time by three people with Ph.D.s who spend 10 months deliberately trying to defraud it."

“The chain of thought and action that encourages you to spend 10 months 'pulling a fast one' on academic journals disqualifies you from a community of scholarship.”

Karen Gregory, a lecturer in sociology at the University of Edinburgh, wrote that "the chain of thought and action that encourages you to spend 10 months ‘pulling a fast one’ on academic journals disqualifies you from a community of scholarship. It only proves you are a bad-faith actor."

Karl Steel, an associate professor of English at Brooklyn College and the Graduate Center of the City University of New York, called the trio’s work "simply not rigorous research" and described three objections to it. It is too narrow in disciplinary scope, he said. It focuses on exposing weaknesses in gender and ethnic studies, conspicuously ideological fields, when that effort would be better spent looking at more-substantive problems like the replication crisis in psychology, or unfounded scholarly claims in cold fusion or laissez-faire economics.

The trio could have reached out to colleagues in physics and other fields, but instead opted for "poor experimental design." And they targeted groups that are "likely to be laughed at anyway," showing not intellectual bravery but cowardice. "These three researchers have demonstrated that they’re not to be trusted," he said.

‘Deep Doubt’

Other online commenters said the hoax papers lack a control group of papers for comparative purposes.

Pluckrose, Lindsay, and Boghossian, reached by phone in Portland, said the papers that were rejected serve as a control of sorts. Better yet, they said, consider this meta-control thought experiment: Look at your journals and the articles they published, and see if you can distinguish them from the hoax articles. If the answer is often no, then there is your control.

Mounk, by phone, also said the control-group criticism is misguided. He called it a "confused attempt to import statistics into a question where it doesn’t apply." If the authors were claiming that their work proves that some publications are, say, 50 percent more susceptible to hoaxes than the average, or that 100 percent of articles published are nonsense because these seven articles were accepted, then you would obviously need controls. But the authors "do nothing of the sort. They demonstrate that it’s possible, with relatively little effort, to get bullshit published." It "sows deep doubt" about the nature of the academic enterprise in these disciplines.

Time will tell, the trio said, but they think the mega-hoax will effectively snuff out their academic futures. Pluckrose thinks she’ll have a hard time getting into a doctoral program, Lindsay predicted that he would become "an academic pariah," and Boghossian, who doesn’t have tenure, thinks he will be punished, and possibly fired. Still, this isn’t the first time that Lindsay and Boghossian have teamed up to mock trendy scholarship. Last year their spurious paper "The Conceptual Penis as a Social Construct" was published in the journal Cogent Social Sciences.

Meanwhile, Pluckrose and Boghossian are working on a book together, and Pluckrose is writing one on the 50-year development of grievance studies and the leftist academic culture of victimization.

If the three are exiled from academe, said Mounk, that will be unjust and a shame. Through "courage and quite a lot of work," they have shown that "clearly there’s a big corner of academia where the emperors wear no clothes." He called the hoax "a more serious contribution to our understanding of the world than many Ph.D. theses." The three of them, Mounk said, "should absolutely be celebrated."

1Corinthians 3:19 NASB  "For the wisdom of this world is foolishness...

Daring to doubt (aloud).

Listen: Dissent from Darwin List Tops 1,000 — Now the Scientists Weigh In

 Evolution News | @DiscoveryCSC

 

 

Did you know that a growing number of scientists doubt the Darwinian theory of evolution? This in spite of the fact that over the past two decades the scientific establishment has ramped up its support of modern Darwinism with increasing agitation. And ramped up the persecution of scientists who dissent from Darwinian evolution.

On a new episode of ID the Future, host Robert Crowther explores why some scientists are willing to risk their research and careers to voice their skepticism of the theory. Download the podcast or listen to it here. Be sure to visit the Scientific Dissent from Darwinism website to learn more and meet some of the scientists on the list.

Were neanderthals just as 'sapien'

Did Neanderthals Teach Modern Humans How to Make Tools? 
By Charles Q. Choi, Live Science Contributor

Neanderthals apparently created the oldest known examples of a kind of bone tool used in Europe, thus raising the possibility that modern humans may have learned how to make these tools from Neanderthals, researchers say.

Neanderthals were once the closest living relatives of modern humans, dwelling across a vast area ranging from Europe to the Middle East to western Asia. This ancient lineage of humans went extinct about 40,000 years ago, about the same time modern humans expanded across the world.

Neanderthals created artifacts similar to ones made at about the same time by modern humans arriving in Europe, such as body ornaments and small blades. Scientists hotly debated whether such behavior developed before or after contact with modern humans. "There is a huge debate about how different Neanderthals were from modern humans," said Shannon McPherron, an archaeologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Now, McPherron and his colleagues have discovered that Neanderthals created a specialized kind of bone tool previously only seen in modern humans. These tools are about 51,000 years old, making them the oldest known examples of such tools in Europe and predating the known arrival of modern humans.

New Neanderthal behavior

The bone tools in question are known as lissoirs ("polishing stones"), which are used to smooth out hides to make them tougher, impermeable and lustrous. Scientists unearthed fragments of four examples of such tools at two Neanderthal sites in southwestern France. The uniform smoothness and rounded edges of the lissoir tips probably resulted from scraping, thus hinting that they were, indeed, used against soft materials such as hides.
"We have found an entirely new aspect of Neanderthal behavior," McPherron said.

Until now, all known Neanderthal bone tools researchers found "have looked just like their stone tools," McPherron said. "In other words, Neanderthals looked at bone as just another raw material to flake into stone tool types like scrapers, notches and hand axes."

"Modern humans, on the other hand, made lots of different kinds of bone tools that took advantage of the properties of bone, to be ground into specific shapes like points, awls and smoothers," McPherron added. "Here, for the first time, we have evidence of Neanderthals doing exactly the same thing. They were taking ribs and shaping them into a tool that looks identical to the modern human tools found 40,000 years ago and to tools still in use today for preparing hides."

"What this means is that Neanderthals did, in fact, recognize that bone could be worked in special ways to create new kinds of tools, and in this way, Neanderthals are not different from later modern humans," McPherron added. "For many researchers, specialized bone tools were thought to be one of the technologies that separate the two groups of humans. This is no longer the case." [Top 10 Things That Make Humans Special]

McPherron cautioned that the researchers are not suggesting that Neanderthals were the first to make bone tools.

"There are sophisticated bone tools that are even older in Africa, for instance," McPherron said. "Neanderthals were, however, the first in Europe to make specialized bone tools."

And these aren't the first Neanderthal bone tools, but instead the first Neanderthal bone tools that weren't just replicas of their stone tools.
   Neanderthal invention?
It remains unclear whether Neanderthals learned how to make lissoirs from modern humans or invented them entirely on their own, or even whether modern humans learned how to make this particular kind of bone tool from Neanderthals.

"The date we have of approximately 51,000 years old is earlier than the best evidence we have of modern humans in Europe, but it is still close enough that we have to mention the possibility," McPherron said. "What we need to do now is look in even older sites for these same tools, to see if Neanderthals had been making these tools for much longer."

"I think that as others look for this bone-tool type amongst their small bones, we will find many more," McPherron added. "I suspect that this new aspect of Neanderthal behavior was actually rather widespread."

For now, these findings "are the best evidence we have that Neanderthals were capable of inventing on their own one aspect of what has been called modern human culture," McPherron said.

The scientists detailed their findings online Aug. 12 in the journal Proceedings of the National Academy of Sciences.

Yet more on how pre Darwinian design continues to make nonsense of the Darwinian narrative.

Greenland Fossils, Earth's Oldest, Pose an Evolutionary Dilemma
David Klinghoffer

The origin of cellular life, with all that implies by way of mind-bogglingly sophisticated biological information in action, now seems to have occurred as early in earth's history as it could have done -- 3.7 billion years ago. Just right off the bat it happens, "immediately," as one paleontologist puts it in amazement: genetic code, proteins, photosynthesis, the works.

It's reported in Nature ("Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures"). From the New York Times:

Geologists have discovered in Greenland evidence for ancient life in rocks that are 3.7 billion years old. The find, if confirmed, would make these fossils the oldest on Earth and may change scientific understanding of the origins of life.

Experts are likely to debate whether the structures described in the new report were formed biologically or through natural processes. If biological, the great age of the fossils complicates the task of reconstructing the evolution of life from the chemicals naturally present on the early Earth. It leaves comparatively little time for evolution to have occurred and puts the process close to a time when Earth was being bombarded by destructive asteroids. [Emphasis added.]

The microbial mats from the Isua Greenstone Belt involved creatures already "fairly evolved."

Several different species of microbes are involved in stromatolite creation. The Isua structures, if indeed stromatolites, would represent fairly evolved organisms.

Here's the problem:

If life on Earth did not begin until after the Late Heavy Bombardment, then it had a mere 100 million years in which to evolve to the quite advanced stage seen in the new fossils.

If so, Dr. [Abigail] Allwood wrote, then "life is not a fussy, reluctant and unlikely thing." It will emerge whenever there's an opportunity.

But the argument that life seems to have evolved very early and quickly, so therefore is inherently likely, can be turned around, Dr. [Gerald] Joyce said. "You could ask why, if life were such a probable event, we don't have evidence of multiple origins," he said.

In fact, with trivial variations, there is only one genetic code for all known forms of life, pointing to a single origin.

If some unguided chemical and biological evolutionary model must be assumed as explaining the origins of life, then something is wrong. Life springs up easily. It must, "whenever there's an opportunity." If so, it should have happened repeatedly on earth -- why not? -- leaving evidence in the form of multiple genetic codes. But there is no such evidence.

It should also have happened elsewhere in the cosmos, perhaps in our own Solar System, like on Mars. Not just the most simple life, either, but something "fairly evolved." Why not intelligent, too? But there's no evidence of any of that either.

For evolutionists, it's a dilemma without an apparent solution. For advocates of intelligent design, it can be taken in stride. Whether the origin of life, of complex animals, or of homo sapiens with our gift of speech, wonderful things have a funny way of "slipping suddenly into being," in Michael Denton's phrase.


Remember, this is all apart from the devilish difficulties for theories of unguided origins raised by Meyer in Signature in the Cell and Darwin's Doubt. Innovations don't "evolve." They spring into existence, we find again and again, with an alarming abruptness. As if by design.

Toward a testable design filter? II

Unifying Specified Complexity: Rediscovering Ancient Technology
Evolution News | @DiscoveryCSC

Editor’s note: We have been reviewing and explaining a new article in the journal BIO-Complexity, “A Unified Model of Complex Specified Information,” by George D. Montañez. For earlier posts, see:

• “BIO-Complexity Article Offers an Objective Method for Weighing Darwinian Explanations”
• “Measuring Surprise — A Frontier of Design Theory”

Specified complexity, the property of being both unlikely and functionally specified, was introduced into the origins debate two decades ago by William Dembski by way of his book, The Design Inference. In it, he developed a theory of design detection based on observing objects that were both unlikely and matched an independently given pattern, called a specification. Dembski continued to refine his vision of specified complexity, introducing variations of his model in subsequent publications (Dembski 2001, 2002, 2005). Dembski’s independent work in specified complexity culminated with a semiotic specified complexity model (Dembski 2005), where functional specificity was measured by how succinctly a symbol-using agent could describe an object in the context of the linguistic patterns available to the agent. Objects that were complex yet could be simply described resulted in high specified complexity values.

Although Dembski’s work on specified complexity became the most widely known, bioinformatics specialist Aleksandar Milosavljević appears to have developed the first fully mathematical specified complexity model with his algorithmic significance method (Milosavljević 1993, 1995). Milosavljević presented his work in the early 1990s, which by tech standards, is ancient times. His specified complexity model used algorithmic information theory to test independence between DNA sequences based on the improbability of encountering a sequence under some probability distribution and the length of the sequence’s compressed encoding relative to a second sequence. A similar method of measuring specified complexity was later independently rediscovered (as great ideas often are) by Ewert, Marks, and Dembski with their algorithmic specified complexity model (Ewert, Dembski, and Marks II 2012, 2015).

Given Milosavljević’s early work with algorithmic significance, mathematical specified complexity models have successfully been used in fields outside of intelligent design for a quarter of a century. A new paper, published in the open-access journal BIO-Complexity, aims to push forward the development of specified complexity methods by developing a detailed mathematical theory of complex specified information.

Unified Models of Specified Complexity

In “A Unified Model of Complex Specified Information,” George D. Montañez introduces a new framework that brings together various specified complexity models by uncovering a shared mathematical identity between them. This shared identity, called the common form, consists of three main components, combined into what is called a kardis function. The components are:

a probability term, p(x),

a specification term, ν(x), and

a scaling constant, r.

For an object x, the first of these gives a sense of how likely the object is to be generated by some probabilistic process modeled by p. When this value is low, the object is not one that is often generated by the process. The specification term, ν(x), captures to what degree x conforms to an independently given specification, modeled as a nonnegative function over the (typically restricted) space of possible objects. When this value is large, the object is considered highly specified. Lastly, the scaling constant r (also called the “replicational resources”) can be interpreted as a normalization factor for the specification values (rescaling the values to some predefined range) or as the number of “attempts” the probabilistic process is given to generate the object in question. (The paper discusses in detail both interpretations of the scaling constant.) Given these components, the kardis function κ(x) is defined as

κ(x) = r [p(x) / ν(x)].

Taking the negative log, base-2, of κ(x) defines the common form for specified complexity models.

Common Form Models

The paper presents Dembski’s semiotic specified complexity and Ewert et. al’s algorithmic specified complexity as common form models, mapping the parts of each model to kardis components. This mapping is done for additional specified complexity models, as well.

Dembski’s semiotic model contains three core components (a probability term P(T|H), specification term φS(T), and scaling constant 10120), which can be mapped to kardis components as p(x) = P(T|H), ν(x) = φS(T)-1, and r = 10120. Dembski defines his specified complexity as

χ = -log2[10120φS(T)P(T|H)] = -log2κ(x),

which we see is a common form model with x = T.

Similarly, Ewert et al.’s algorithmic specified complexity contains a probability term p(x), a specification term ν(x) = 2–K(x|c), and an implicit scaling term r = 1, making it a common form model.

Lastly, Milosavljević’s algorithmic significance model is also of common form, with a kardis containing probability term p0(x), specification term 2-IA(x|s), and implicit scaling constant r = 1. Through this mapping, the connection to algorithmic specified complexity becomes clear, and the model’s status as a form of specified complexity becomes indisputable.

Canonical Specified Complexity

For any common form model, adding a constraint that r is at least as large as the sum (or integral) of specification values over the entire domain of ν, we obtain a canonical specified complexity model. The paper primarily works with canonical models, proving theorems related to them, although some results are also given for simple common form models. Tweaks to some common form models (such as Demsbki’s semiotic model and Hazen et al.’s functional information model) allow them to become canonical model variants, to which the theorems derived in the paper apply. Canonical models represent a subset of common form models, and have several interesting properties. These properties include the scarcity of large values, such that under any fixed random or semi-random process the probability of observing large values is strictly bounded (and exponentially small, when large value observations are desired). The paper gives further detail, for those interested.

The Power of a Good Abstraction

What does it mean for existing specified complexity models to all share a single underlying form? First, it allows us to reason about many specified complexity models simultaneously and prove theorems for them collectively. It allows us to better understand each model, since we can relate it to other specified complexity models. Second, it hints strongly that any attempt to solve the problem of measuring anomalous events will converge on a similar solution, increasing our confidence that the common form represents the solution to the problem. Third, we can build from a simplified framework, clearing away incidental details to focus on the behavior of specified complexity models at their core essence.

Finally, having discovered the common form parameterization, we can establish that Milosavljević’s algorithmic significance model is not just like a specified complexity model, but is a specified complexity model, definitively refuting claims that specified complexity methods have no practical value, are unworkable, or have not been used in applied fields like machine learning or bioinformatics. We have now come to discover that they’ve been in use for at least 25 years. Milosavljević couldn’t access the vocabulary of common forms and canonical models, so what he saw as the difference between a surprisal term and its compressed relative encoding, we now more clearly see as a compression-based canonical specified complexity model.

Symbols in Steel and Stone

Returning to your winter retreat, mentioned in the last post, the symbols you discovered remain on your mind. A portion of the symbols, those on the metal pieces, you’ve been able to map to numbers coded in a base-7 number system. Your conviction is strengthened once you realize the numbers include a sequence of prime digits, spanning from 2 to 31. You imagine that some ancient mathematician etched the symbols into the metal, someone that either had knowledge of the primes or did not. If they did not, there would be some probability p(x) that they produced the sequence xwithout intention.

Given that the sequence also matches an independent pattern (primes), you ask yourself, how many sequences using the first thirty-one positive integers would match any recognizable numeric pattern, of which the primes are just one example? The on-line encyclopedia of integer sequences has an estimated 300,000 sequences which could serve as a pattern (to someone more knowledgeable than yourself). You imagine that perhaps this number underestimates the number of interesting patterns, so you double it to be safe, and assume 600,000 possible matchable patterns, of which the prime sequence is just one instance.

You’ve spent time studying the manuscript on specified complexity you brought along with you, and are eager to understand your discovery in light of the framework it presents, that of canonical specified complexity. You let the space of possible sequences be all the 3111 sequences of length 11 using the first 31 positive integers. You let ν(x) equal to one whenever sequence x exists in the OEIS repository (representing an “interesting” number pattern), and upper bound r by 600,000, the number of interesting patterns that possible sequences could match. You know these are rough estimates which will undoubtedly need to be revised in the future, but you’d like to get a notion for just how anomalous the sequence you’ve discovered actually is. Your instinct tells you “very,” but mapping your quantities to a canonical model kardis gives you the first step along a more objective path, and you turn to the paper to see what you can infer about the origin of your sequence based on your model. You have much work ahead, but after many more hours of study and reflection, the darkening night compels you to set aside your workbook and get some rest.

Bibliography

Dembski, William A. 2001. “Detecting Design by Eliminating Chance: A Response to Robin Collins.” Christian Scholar’s Review 30 (3): 343–58.

———. 2002. No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence. Lanham: Rowman & Littlefield.

———. 2005. “Specification: The Pattern That Signifies Intelligence.” Philosophia Christi 7 (2): 299–343. https://doi.org/10.5840/pc20057230.

Ewert, Winston, William A Dembski, and Robert J Marks II. 2012. “Algorithmic Specified Complexity.” Engineering and Metaphysics. https://doi.org/10.33014/isbn.0975283863.7.

———. 2015. “Algorithmic Specified Complexity in the Game of Life.” IEEE Transactions on Systems, Man, and Cybernetics: Systems 45 (4): 584–94. https://doi.org/10.1109/TSMC.2014.2331917.

Milosavljević, Aleksandar. 1993. “Discovering Sequence Similarity by the Algorithmic Significance Method.” Proc Int Conf Intell Syst Mol Biol 1: 284–91.

———. 1995. “Discovering Dependencies via Algorithmic Mutual Information: A Case Study in DNA Sequence Comparisons.” Machine Learning 21 (1-2): 35–50. https://doi.org/10.1007/BF00993378.

Finally,something we can all agree on:The war on science is real.

Fetal Pain – Another Case Where the “Science Denial” Insult Has Been Misapplied
David Klinghoffer | @d_klinghoffer

In a New York Times op-ed, law professor Mary Ziegler lashes pro-life advocates for claiming to have “science on their side” and “praising legal restrictions based on what science supposedly says about fetal pain.”

“Supposedly”? It’s a blatant untruth that “fetuses cannot feel pain,” as  neuroscientist Michael Egnor explains at Mind Matters. Quite the contrary, fetuses are more sensitive to pain than mature humans like you and me. This makes sense if you think about it for a moment, especially if you’re a parent: sensations that we would shrug off, babies find excruciating and intolerable. Did you think this sensitivity pops into being out of nowhere at birth?

A Timely Reminder

From “The Junk Science of the Abortion Lobby,” a particularly timely reminder as New York State celebrates its barbaric new abortion law:

The science of fetal pain is also well established. The core of the abortionists’ argument against the fact that young fetuses in the womb feel pain is the immaturity of the thalamocortical connections in the fetal nervous system. Because of this neurological immaturity, pro-abortionists claim, fetuses cannot feel pain. This claim is, however, a profound misrepresentation of neuroscience and embryology. Thalamocortical projections continue to mature throughout childhood and into early adult life — they are not fully mature until about 25 years of age. Yet children obviously feel pain, so the immaturity of thalamocortical projections does not in any way preclude the experience of pain.

In fact, pain is unlike any other sensory modality in that pain appears to enter consciousness awareness at subcortical (probably thalamic) levels. The cerebral cortex is not necessary to experience pain — it appears to modulate the experience of pain. Furthermore, cortical modulation of pain serves to diminish the severity of the pain. Decorticate animals (animals whose cerebral cortex has been removed) appear to experience pain more intensely than corticate animals do.

Babies obviously experience pain, and indeed appear to experience it more intensely than do adults. A bit of intestinal gas or a needle prick to draw blood can cause an infant to scream in agony. This extreme sensitivity to pain in young fetuses and babies is well-recognized in medical science1-3 and forms the basis for the anesthetic management of fetuses and young infants.

Read the rest at Mind Matters. The “anti-science” aka “science denial” label is slung around a lot, mostly at those who fail to line up with the expected progressive viewpoint on any given issue. As Dr. Egnor notes, this is another case where the insult has been misapplied.