On seeing the Father.

Seen Me: Seen Father-John 14:7-9

"Seen Me: Seen Father" - Jn 14:7-9

John 14:1 - "believe in God, believe also in me." 14:7 - "If ye had known me, ye would have known my Father also: from henceforth ye know him, and haveseen him. (:8) Philip saith unto him, Lord, show us the Father, and it sufficeth us. (:9) Jesus saith unto him, Have I been so long time with you, and dost thou not know me, Philip? He that hath seen me hath seen the Father; how sayest thou, Show us the Father? (:10) Believest thou not that I am in the Father, and the Father in me? the words that I say unto you I speak not from myself: but the  Father abiding in me doeth his works." - ASV.

We can understand what Jesus actually intended when he said "I am in the Father and the Father is in me" and "the Father is abiding in me." And it is not very difficult to understand his saying, "If you had known me, you would have known my Father" since Jesus is in perfect harmony with the Father's will and purpose (i.e. "one," "in," etc.). But what about "he that has seen me has seen the Father"?

First, let's examine the relationship between "abiding in," "knowing," and "seeing" (horao in NT Greek) as commonly used figuratively in the Bible. 1 John 2:3, 5, 6 - "by this we know that we have come to know Him, if we keep His commandments .... By this we know that we are in Him: the one who says he abides in Him ought himself to walk in the same manner He walked [your purpose, actions words, and life must reflect his example]." - NASB. And 1 John 3:29, "he that keeps His [God's] commandments abides in Him, and He in him." - NASB. These scriptures show, again, the intended meaning for the figurative use of "abides."

Now notice the relationship between "know" and "see": 3 John 11 - "the one who does good is of God; the one who does evil has not seen [horao] God." And 1 John 3:6 - "No one who abides in Him sins; no one who sins has seen [horao] Him or knows Him." - NASB.

We can see, then, that horao ("see") can mean the same thing as "abiding in" or  "knowing," and all three may have the figurative meaning of agreement in purpose and will with someone else.

The International Standard Bible Encyclopedia, vol. 4, p. 380, tells us:

"What is seen in a vision is a revelation from God. Statements that human beings have seen or will see God Himself do not refer to a perception of a physical aspect of God by human physical senses but a process of coming to some amount of understanding of God, often just a simple realization of His greatness or some other aspect of His nature, either by a revelatory vision (Isa. 6:15; Ezk. 1:26-28), … or by their acquaintance with Jesus Christ (Jn 14:9, cf. 1:18)." – Eerdmans, 1991.

The New International Dictionary of New Testament Theology, Vol. 3, 1986 printing, Zondervan, pp. 513, 515, 518, explains the meanings of horao.

"Horao" means "... become aware (Gen. 37:1). (b) figuratively it comes to be used of intellectual or spiritual perception .... It also means ... attend to, know or have experienced (Deut. 11:2), or be concerned about something (Gen. 37:14; Is. 5:12)." - p. 513. - - "Besides the general meaning of to know, horao and its derivatives can mean to obtain knowledge". - p. 515.

This trinitarian reference also states:

"For the NT God is utterly invisible (Jn 6:46; 1 Tim. 1:17; 6:16; Col. 1:15) ... yet the resurrection narratives especially stress that the risen Christ is visible." - p. 518.

Professor Joseph H. Thayer (who was "the dean of New Testament scholars in America" - Dictionary of American Biography, Vol. IX) in his Greek-English Lexicon of the New Testament ("a standard in the field") also defines horao with similar meanings and specifically tells us that John 14:7, 9 is in the category of "2. to see with the mind, to perceive, to KNOW."

In discussing this meaning of "horao," Thayer writes:

"to know God's will, 3 John 11; from the intercourse and influence of Christ to have come to see (know) God's majesty, saving purposes, and WILL, Jn. xiv. 7, 9". - p. 451, Baker Book House, 1984 printing.

We can understand, then, why the very trinitarian The NIV Study Bible, 1985, Zondervan, explains John 14:7 this way:

"Once more Jesus stresses the intimate connection between the Father and himself. Jesus brought a full revelation of the Father (cf. 1:18), so that the apostles had real knowledge of him." - footnote for John 14:7.

Trinitarian minister and acclaimed New Testament scholar, Dr. William Barclay, also comments on John 14:7-9:

"The Jews [including Jesus, of course, and those to whom he spoke] would count it as an article of faith that no man had seen God at any time .... To see Jesus is to see what God is like." - p. 159. "`He who has seen me has seen the Father,' Jesus is the revelation of God." - p. 161.

And,

"The danger of the Christian faith is that we may set up Jesus as a kind of secondary God. But Jesus himself insists that the things he said and the things he did did not come from his own initiative or his own power or his own knowledge but from God. His words were God's voice speaking to men; His deeds were God's power flowing through him to men. He was the channel by which God came to men." - The Daily Study Bible Series: The Gospel of John, pp. 159, 161, 162, Vol. 2, The Westminster Press, 1975.

So there is no real reason to insist that John 14:7, 9 shows Jesus as being equally God with his Father. The probability is that, in harmony with the usage of the time, Jesus was merely saying that what he spoke came from God, and what he did is what God directed. He meant that understanding what he did and said was like knowing ("seeing") God* (as, in a similar sense, those who literally saw angels sent by God and speaking God's words were said to have "seen God"). Jesus is totally in harmony with ("one" with) the Father in purpose (see the ONE study paper) so that we can "see" the Father's will in Jesus.

As in all other "Jesus is equally God" evidence, we find that the trinitarian "proof" is a scripture that can honestly be translated or interpreted in at least one other way which would prove no such thing!

We never find a statement clearly stating that "Jesus is equally and fully God" in the entire Bible. And yet other such essential knowledge that leads to eternal life is clearly and repeatedly emphasized: "Jesus is the Christ [Messiah]," "our savior and king" - the one who appears before God in heaven in our behalf, the one through whom we must approach God. Surely this most important information in the Bible of exactly who God is and exactly who Jesus is would not be hidden from us in the slightest degree

A clash of Titans. LIII

Should we all be gamers?:Pros and cons.

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.