The OOL continues to troll design deniers.

More on Alien Octopi: New Paper Admits Failure of Evolution to Explain Life
Cornelius Hunter

There are many fundamental problems with evolutionary theory. Origin-of-life studies have dramatically failed. Incredibly complex biological designs, both morphological and molecular, arose abruptly with far too little time to have evolved. The concept of punctuated equilibrium is descriptive, not explanatory. The Cambrian explosion is not explained by evolution and, in general, evolutionary mechanisms are inadequate to explain the emergence of new traits, body plans, and new physiologies. Even a single gene is beyond the reach of evolutionary mechanisms.

In fact, the complexity and sophistication of life cannot originate from non-biological matter under any scenario, over any expanse of space and time, however vast. On the other hand, the archenemy of evolutionary theory, Lamarckian inheritance, in its variety of forms, is well established.

As noted here already  (“With New Theory of the Cambrian Explosion, Scientists Reach (Literally) for the Stars”), these scientific observations are laid out in a new peer-reviewed, scientific paper arguing for panspermia.

Origin of Life

Regarding origin-of-life studies, which try to explain how living cells could somehow have arisen in an ancient, inorganic, Earth, the paper explains that this idea should have long since been rejected, but instead it has fueled “sophisticated conjectures with little or no evidential support.”

…the dominant biological paradigm — abiogenesis in a primordial soup. The latter idea was developed at a time when the earliest living cells were considered to be exceedingly simple structures that could subsequently evolve in a Darwinian way. These ideas should of course have been critically examined and rejected after the discovery of the exceedingly complex molecular structures involved in proteins and in DNA. But this did not happen. Modern ideas of abiogenesis in hydrothermal vents or elsewhere on the primitive Earth have developed into sophisticated conjectures with little or no evidential support. 

In fact, abiogenesis has “no empirical support.”

…independent abiogenesis on the cosmologically diminutive scale of oceans, lakes or hydrothermal vents remains a hypothesis with no empirical support…

One problem, of many, is that the early Earth would not have supported such monumental evolution:

The conditions that would most likely to have prevailed near the impact-riddled Earth’s surface 4.1–4.23 billion years ago were too hot even for simple organic molecules to survive let alone evolve into living complexity

In fact, the whole idea strains credibility “beyond the limit.”

The requirement now, on the basis of orthodox abiogenic thinking, is that an essentially instantaneous transformation of non-living organic matter to bacterial life occurs, an assumption we consider strains credibility of Earth-bound abiogenesis beyond the limit.

All laboratory experiments have ended in “dismal failure.” The information hurdle is of “superastronomical proportions” and simply could not have been overcome without a miracle.

The transformation of an ensemble of appropriately chosen biological monomers (e.g. amino acids, nucleotides) into a primitive living cell capable of further evolution appears to require overcoming an information hurdle of superastronomical proportions, an event that could not have happened within the time frame of the Earth except, we believe, as a miracle. All laboratory experiments attempting to simulate such an event have so far led to dismal failure.

Diversity of Life

But the origin of life is just the beginning of evolution’s problems. For science now suggests evolution is incapable of creating the diversity of life and all of its designs:

Before the extensive sequencing of DNA became available it would have been reasonable to speculate that random copying errors in a gene sequence could, over time, lead to the emergence of new traits, body plans and new physiologies that could explain the whole of evolution. However the data we have reviewed here challenge this point of view. It suggests that the Cambrian Explosion of multicellular life that occurred 0.54 billion years ago led to a sudden emergence of essentially all the genes that subsequently came to be rearranged into an exceedingly wide range of multi-celled life forms — Tardigrades, the Squid, Octopus, fruit flies, humans — to name but a few.

As one of the authors writes, “the complexity and sophistication of life cannot originate (from non-biological) matter under any scenario, over any expanse of space and time, however vast.” As an example, consider the octopus.

Octopus

First, the octopus is an example of novel, complex features, rapidly appearing and a vast array of genes without an apparent ancestry:

Its large brain and sophisticated nervous system, camera-like eyes, flexible bodies, instantaneous camouflage via the ability to switch colour and shape are just a few of the striking features that appear suddenly on the evolutionary scene. The transformative genes leading from the consensus ancestral Nautilus (e.g., Nautilus pompilius) to the common Cuttlefish (Sepia officinalis) to Squid (Loligo vulgaris) to the common Octopus (Octopus vulgaris) are not easily to be found in any pre-existing life form.

But it gets worse. As I have explained, the cephalopods demonstrate a unique level of adenosine to inosine mRNA editing. It is yet another striking example of lineage-specific design that utterly contradicts macroevolution:

These data demonstrate extensive evolutionary conserved adenosine to inosine (A-to-I) mRNA editing sites in almost every single protein-coding gene in the behaviorally complex coleoid Cephalopods (Octopus in particular), but not in nautilus. This enormous qualitative difference in Cephalopod protein recoding A-to-I mRNA editing compared to nautilus and other invertebrate and vertebrate animals is striking. Thus in transcriptome-wide screens only 1–3% of Drosophila and human protein coding mRNAs harbour an A-to-I recoding site; and there only about 25 human mRNA messages which contain a conserved A-to-I recoding site across mammals. In Drosophila lineages there are about 65 conserved A-sites in protein coding genes and only a few identified in C. elegans which support the hypothesis that A-to-I RNA editing recoding is mostly either neutral, detrimental, or rarely adaptive. Yet in Squid and particularly Octopus it is the norm, with almost every protein coding gene having an evolutionary conserved A-to-I mRNA editing site isoform, resulting in a nonsynonymous amino acid change. This is a virtual qualitative jump in molecular genetic strategy in a supposed smooth and incremental evolutionary lineage — a type of sudden “great leap forward”. Unless all the new genes expressed in the squid/octopus lineages arose from simple mutations of existing genes in either the squid or in other organisms sharing the same habitat, there is surely no way by which this large qualitative transition in A-to-I mRNA editing can be explained by conventional neo-Darwinian processes, even if horizontal gene transfer is allowed.

Lamarck

In the 20th century, Lamarckian inheritance was anathema for evolutionists. Careers were ruined and every evolutionist knew the inheritance of acquired characteristics sat right alongside the flat earth and geocentrism in the history of ideas. The damning of Lamarck, however, was driven by dogma rather than data, and today the evidence has finally overcome evolutionary theory.

Indeed there is much contemporary discussion, observations and critical analysis consistent with this position led by Corrado Spadafora, Yongsheng Liu, Denis Noble, John Mattick and others, that developments such as Lamarckian Inheritance processes (both direct DNA modifications and indirect, viz. epigenetic, transmissions) in evolutionary biology and adjacent fields now necessitate a complete revision of the standard neo-Darwinian theory of evolution or “New Synthesis ” that emerged from the 1930s and 1940s.

Indeed, we now know of a “plethora of adaptive Lamarckian-like inheritance mechanisms.”

There is, of course, nothing new in this paper. We have discussed these, and many, many other refutations of evolutionary theory. Yet the paper is significant because it appears in a peer-reviewed journal. Science is, if anything, conservative. It doesn’t exactly “follow the data,” at least until it becomes OK to do so. There are careers and reputations at stake.

Yet another own goal?

Alleged Refutation of the Cambrian Explosion Confirms Abruptness, Vindicates Meyer
Günter Bechly

The top-down pattern of appearance of animal phyla during the Cambrian explosion represents major conflicting evidence for Darwinian evolution. Since this is so, there have been numerous attempts in the past to explain away the inconvenient truth and fudge the facts to fit the theory, rather than try to find the best explanation for the pattern of evidence in nature.

Such futile attempts include the claim that the Cambrian explosion was a much longer event, that the sudden appearance is just an artifact of Linnaean classification while cladistic classification makes the problem disappear, that Ediacaran organisms such as Kimberella and Spriggina or Ediacaran trace fossils and small shelly fossils represent putative ancestors of the Cambrian phyla. And of course there is the usual appeal to the incompleteness of the fossil record (aka the artifact hypothesis). All these dubious claims, including those made by staunch ID-critics like Nick Matzke, P.Z. Myers, and Donald Prothero, rather than by actual specialists on Cambrian fossils, have all been addressed and refuted before (e.g., see Meyer 2013, Klinghoffer 2015, and Bechly 2018 ).

New Paper from Allison C. Daley

Now, a new paper by Daley et al. (2018), with an accompanying press release from the University of Oxford (2018), is said to challenge the abruptness of the Cambrian explosion. The paper allegedly settles the case in favor of a more gradual pattern of appearance as predicted by Darwin’s theory. That would be big news indeed, if it were true. Darwinists bloggers are thrilled 

To judge from the hype, you might expect that the authors of the new paper have discovered a well-dated temporal transitional series of fossils, documenting a gradual evolution stretched out over a long period of time, rather than an explosive event. Well, far from that. Actually, the article presents no new fossil evidence, no new phylogenetic studies, nor any new scientific results at all. Instead, it is just a review of other recent work. This is why it was published in the “Perspectives” section of the journal PNAS.

The press release announces, “[N]ew research from the University of Oxford in collaboration with the University of Lausanne suggests that for most animals this ‘explosion’ was in fact a more gradual process.” This is already a highly misleading statement, as the paper only deals with euarthropods and not any other group of animals. At most it could prove a more gradual origin of euarthropods, thus of a single lineage within a single one of the 28 animal phyla. But does it even achieve this limited goal? They continue with the claim, “A team based at Oxford University Museum of Natural History and the University of Lausanne carried out the most comprehensive analysis ever made of early fossil euarthropods from every different possible type of fossil preservation.” This is factually incorrect. What the new study achieves is nothing new at all: based on other cladistic studies, they ordered the fossils according to their inferred sequence of branching from the euarthropod stem line, irrespective of their temporal ordering, and thereby identify a supposed order of character acquisition. 

This has been done before multiple times by other studies on early arthropod phylogeny by eminent paleontologists like Graham Budd, Gregory Edgecombe, and David Legg. The alleged new result is not evidence at all, but rather high level interpretation of evidence based on several unquestioned background assumptions such as universal common ancestry and the principle of parsimony. It is by no means the “most comprehensive analysis” of its kind (e.g., compared to  Legg et al. 2013, who studied 309 panarthropod taxa and 753 morphological characters). The authors also fail to discuss any incongruent evidence, such as the strange fact that lobopodians like Hallucigenia, which are believed to be more basal stem arthropods, do have legs, while radiodonts like Anomalocaris, which are believed to be more advanced stem arthropods, lack any postcephalic legs.

A Welcome Confirmation

Claims from the Darwinist peanut gallery notwithstanding, nothing genuinely new is to be found in the paper. Nevertheless, this publication is still very interesting for other reasons.

Instead of refuting the abruptness of the Cambrian explosion, Daley et al. (2018) confirm that the fossil record of euarthropods is even more abrupt than often believed. How so? Because the oldest body fossils from crown group arthropods like trilobites indeed predate (!) their alleged ancestors by about three million years. The authors recognize that this is a problem. They admit, “It may seem counter-intuitive that crown group euarthropods appear at 521 Ma, while the first appearance of stem lineage euarthropods is not until 518 Ma.” To solve this temporal paradox the authors have to postulate a ghost lineage of stem euarthropods that predate the oldest fossil trilobites but left no record of body fossils. Such hypothetical ghost lineages are required by the unquestioned assumption of universal common descent. Surprisingly, they also appeal to the artifact hypothesis (“… stem lineage euarthropods lack biomineralized exoskeletons and require preservation of soft tissues …”) even though they themselves show in their work that the Burgess-Shale-type (BST) conditions for soft tissue preservation existed all the way down to the Ediacaran period. 

Trying to evaluate the length of the ghost lineage, the authors write: “However, stem lineage euarthropods would have evolved before trilobites, even if they are not preserved, so the real question is how much earlier than 521 Ma did they appear? The answer comes from the trace fossil record.” The problem is that according to the writers, the oldest unequivocal arthropod trace fossils are again made by euarthropod trilobites (537-million-year-old Rusophycus traces) and thus not by stem euarthropods. They admit, “In contrast, Rusophycus … provides definitive evidence of crown group Euarthropoda … This makes Rusophycus the oldest euarthropod trace globally … During the Ediacaran period, euarthropod trace fossils are ‘strikingly absent.’” Consequently, the trace fossil record documents an even earlier presence of euarthropods, long before the morphologically more primitive lobopodian and radiodont fossils, implying even longer ghost lineages for stem euarthropods that conflict with the actual fossil record.

Triple Vindication for Meyer

There is more. Even though Daley et al. (2018) do not bother to mention Darwin’s Doubt,they vindicate three main theses of Stephen Meyer’s book.

First, the authors confirm Stephen Meyer’s refutation of the artifact hypothesis and my own argument from the absence of animals in recently discovered Burgess-Shale-type fossil localities from the Ediacaran period (Bechly 2018). As they clearly affirm in the Abstract

A deep Precambrian root to the euarthropod evolutionary lineage is disproven by a comparison of Ediacaran and Cambrian lagerstätten. BSTs from the latest Ediacaran Period (e.g., Miaohe biota, 550 Ma) are abundantly fossiliferous with algae but completely lack animals, which are also missing from other Ediacaran windows, such as phosphate deposits (e.g., Doushantuo, 560 Ma).

In the article they elaborate: 

Modes of Fossil Preservation Are Comparable in the Cambrian and Precambrian … Hypotheses that regard Precambrian preservation as insufficient to preserve euarthropods can no longer be sustained, given the abundant lagerstätten from the Ediacaran Period. Similarly, claims that euarthropods evolved as a tiny and soft-bodied meiofauna that escaped preservation cannot be substantiated because of how commonly the phosphate window is found in the Ediacaran and lower Cambrian, with microscopic euarthropods not appearing until 514 Ma.

The news item from the University of Oxford makes the point even more clearly: 

“The idea that arthropods are missing from the Precambrian fossil record because of biases in how fossils are preserved can now be rejected,” says Dr. Greg Edgecombe FRS from the Natural History Museum, London, who was not involved in the study. “The authors make a very compelling case that the late Precambrian and Cambrian are in fact very similar in terms of how fossils preserve. There is really just one plausible explanation — arthropods hadn’t yet evolved.”

Second, the authors mention that “Spriggina, for example, does not possess bilateral symmetry, but instead has a marked offset along the midline, and this alone is sufficient to reject a euarthropod affinity … No euarthropod claim from the Ediacaran biota can therefore be substantiated.” Thus, Daley et al. clearly reject any arthropod affinity of Ediacaran organisms such as Spriggina, also because of their non-bilaterian glide symmetry. Guess who made exactly this point before? Yes, it was Stephen Meyer (2013) in Darwin’s Doubt.

A Very Acute Waiting Time Problem

Finally, the paper by Daley et al. confirms that the Cambrian explosion implies a very acute waiting time problem, again as elaborated by Meyer (2013). Based on their postulated ghost lineages and on molecular clock data, the authors suggest that euarthropods originated about 541 million years ago. They conclude, “Rather than being a sudden event, this diversification unfolded gradually over the ∼40 million years of the lower to middle Cambrian, with no evidence of a deep Precambrian history.” However, this conclusion is totally speculative and an artifact of their methodological assumptions. It is not based on actual fossil evidence (see above). The latter indeed suggests that the euarthropod body plan appeared with trilobites in the Lower Cambrian, as if out of thin air without any known precursors and without any fossil evidence for a gradual step-wise generation of this body plan. 

Far from being a refutation of the abruptness of the Cambrian explosion, this study actually confirms it and makes the abruptness of the event even more acute. Here is why: since the authors refute the existence of stem group arthropods in the Ediacaran period before 550 million years, and euarthropods are documented already for the Lower Cambrian at 537 million years, there remains a window of time of only 13 million years to evolve the stem arthropod body plan from unknown ecdysozoan worm-like ancestors and to make the transition from lobododian pro-arthropods to the fully developed euarthropod body plan, with exoskeleton, articulated legs, compound eyes, etc. Since the average longevity of a single marine invertebrate species is about 5-10 million years (Levinton 2001: 384, table 7.2), this available window of time equals only about two successive species. Considering the implied enormous re-engineering involved, this time is much too short to accommodate the waiting times for the necessary genetic changes to occur and spread according to the laws of population genetics.

Literature:

• Bechly G 2018. “A Paleontologist on Why the ‘Cambrian Explosion’ Label Persists.” ID the Future April 23, 2018.
• Daley AC, Antcliffe JB, Drage HB, Pates S 2018. “Early fossil record of Euarthropoda and the Cambrian Explosion.” PNAS, 9 pp.
• Klinghoffer D 2015. Debating Darwin’s Doubt: A Scientific Controversy That Can No Longer Be Denied. Discovery Institute Press, 350 pp.
• Legg DA, Sutton MD, Edgecombe GD 2013. “Arthropod fossil data increase congruence of morphological and molecular phylogenies.” Nature Communications 4, 2485.
• Levinton JS 2001. Genetics, Paleontology, and Macroevolution. Cambridge University Press, 617 pp. (Google Books).
• Meyer SC 2013. Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design. HarperOne, 512 pp.
• University of Oxford 2018. “Major fossil study sheds new light on emergence of early animal life 540 million years ago.” EurekAlert! 21-May-2018; Phys.org May 21, 2018.

On the apostle(s):The Watchtower society's commentary.

APOSTLE

The Greek word a·poʹsto·los is derived from the common verb a·po·stelʹlo, meaning simply “send forth (or off).” (Mt 10:5; Mr 11:3) Its basic sense is clearly illustrated in Jesus’ statement: “A slave is not greater than his master, nor is one that is sent forth [a·poʹsto·los] greater than the one that sent him.” (Joh 13:16) In this sense the word also applies to Christ Jesus as “the apostle and high priest whom we confess.” (Heb 3:1; compare Mt 10:40; 15:24; Lu 4:18, 43; 9:48; 10:16; Joh 3:17; 5:36, 38; 6:29, 57; 7:29; 8:42; 10:36; 11:42; 17:3, 8, 18, 21-25; 20:21.) Jesus was sent forth by God as his appointed and commissioned representative.

The term is principally applied, however, to those disciples whom Jesus personally selected as a body of 12 appointed representatives. The names of the original 12 selected are given at Matthew 10:2-4; Mark 3:16-19, and Luke 6:13-16. One of the original 12, Judas Iscariot, proved to be a traitor, thereby fulfilling earlier prophecies. (Ps 41:9; 109:8) The remaining 11 faithful apostles are again listed at Acts 1:13.

Some of the apostles had been disciples of John the Baptizer before becoming Jesus’ disciples. (Joh 1:35-42) Eleven of them were evidently Galileans (Ac 2:7), Judas Iscariot being considered the sole Judean. They were from the working class; four were definitely fishermen by trade; one had been a tax collector. (Mt 4:18-21; 9:9-13) At least two of them appear to have been cousins of Jesus (James and John, the sons of Zebedee). They were men who were viewed by the religious leaders as “unlettered and ordinary,” indicating that their education was elementary and not from the schools of higher learning. A number of them, including Peter (Cephas), were married men.​—Ac 4:13; 1Co 9:5.

Of the 12, Peter, James, and John seem to have enjoyed the closest relationship with Jesus. They alone witnessed the resurrection of Jairus’ daughter (Mr 5:35-43) and the transfiguration of Jesus (Mt 17:1, 2), and they accompanied him farther into the garden of Gethsemane than the other apostles on the night of his arrest. (Mr 14:32, 33) A special affinity appears to have existed between Jesus and John, and John is accepted as being the one referred to as “the disciple whom Jesus used to love.”​—Joh 21:20-24; 13:23.

Selection and Early Ministry. The 12 were selected out of a larger group of disciples and were designated “apostles” by Jesus, “that they might continue with him and that he might send them out [a·po·stelʹlei] to preach and to have authority to expel the demons.” (Mr 3:13-15) Thereafter they did “continue with him” in very close association during the remainder of his earthly ministry, receiving extensive personal instruction and ministerial training. (Mt 10:1-42; Lu 8:1) Since they continued to be Jesus’ pupils, they were still called “disciples,” particularly in accounts of events prior to Pentecost. (Mt 11:1; 14:26; 20:17; Joh 20:2) Thereafter they are consistently called “apostles.” At the time of their appointment, Jesus gave them miraculous powers to heal, as well as to expel demons, and they used these powers to some extent during Jesus’ ministry. (Mr 3:14, 15; 6:13; Mt 10:1-8; Lu 9:6; compare Mt 17:16.) This activity, however, is shown to be always subordinate to their principal work of preaching. Though forming an inner circle of followers, their instruction and training included no mysterious rituals or ceremonies.

Human Weaknesses. Though greatly favored as apostles of God’s Son, they manifested normal human failings and weaknesses. Peter was inclined to be rash and impetuous (Mt 16:22, 23; Joh 21:7, 8); Thomas was slow to be convinced (Joh 20:24, 25); James and John manifested youthful impatience (Lu 9:49, 54). They quarreled over the issue of their future greatness in the earthly kingdom that they expected Jesus to establish. (Mt 20:20-28; Mr 10:35-45; compare Ac 1:6; Lu 24:21.) They acknowledged their need for greater faith. (Lu 17:5; compare Mt 17:20.) Despite their years of intimate association with Jesus and though knowing him to be the Messiah, they all abandoned him at the time of his arrest (Mt 26:56); the matter of his burial was handled by others. The apostles were slow at first to accept the testimony of the women who first saw Jesus after his resurrection. (Lu 24:10, 11) Because of fear they met behind locked doors. (Joh 20:19, 26) The resurrected Jesus gave them further enlightenment, and following his ascension to heaven on the 40th day from his resurrection, they manifested great joy and “were continually in the temple blessing God.”​—Lu 24:44-53.

Activity in Christian Congregation. The outpouring of God’s spirit upon them at Pentecost greatly strengthened the apostles. The first five chapters of the Acts of Apostles testify to the great fearlessness of the apostles and their boldness in declaring the good news and the resurrection of Jesus in spite of jailing, beatings, and threats of death from their rulers. During those early days after Pentecost, the dynamic leadership of the apostles, under the power of the holy spirit, resulted in amazing expansion in the Christian congregation. (Ac 2:41; 4:4) Their ministry was at first concentrated in Jerusalem, then extended to Samaria, and in time, throughout the known world.​—Ac 5:42; 6:7; 8:5-17, 25; 1:8.

Their primary function as apostles was to be witnesses as to Jesus’ fulfillment of Jehovah God’s purposes and prophecies, particularly of his resurrection and exaltation, and to do a discipling work among all nations; and this commission was emphasized to them by Jesus just before his ascension to heaven. (Mt 28:19, 20; Ac 1:8, 22; 2:32-36; 3:15-26) Their testimony concerning the resurrection was that of eyewitnesses.​—Ac 13:30-34.

Miraculous powers. Additionally, to fortify their testimony, the apostles continued to exercise the miraculous powers previously granted them by Jesus, and also other gifts of the spirit received from Pentecost forward. (Ac 5:12; 9:36-40; see GIFTS FROM GOD [Gifts of the Spirit].) While others, too, received such miraculous gifts of the spirit, the account shows that such was the case only when one or more of the apostles were present, or by the laying on of the hands of the apostles. Paul, though not one of the 12, also served in this way as an apostle personally appointed by Jesus Christ. (Ac 2:1, 4, 14; 8:14-18; 10:44; 19:6) Thus the power to transmit such gifts was unique with these apostles. Such miraculous gifts would therefore pass away with the passing away of these apostles and of those who had received these gifts through the apostles (1Co 13:2, 8-11), and thus we read that these powers were “missing in the 2nd-century church, the writers of those days speaking of them as a thing in the past​—in the apostolic age, in fact.”​—The Illustrated Bible Dictionary, edited by J. D. Douglas, 1980, Vol. 1, p. 79.

Administrative position. In the formation, organization, and subsequent direction of the Christian congregation, the apostles occupied a primary position. (1Co 12:28; Eph 4:11) Although they were joined by others of the “older men” in such supervision, they formed a principal part of the governing body of the expanding Christian congregation, and this body was recognized by the early Christians everywhere as the channel of communication used by God to render decisions and direct the affairs of the congregation throughout the earth. (Ac 2:42; 8:14-17; 11:22; 15:1, 2, 6-31; 16:4, 5) This was possible for these men only because of the fulfillment of the promises about guidance by God’s holy spirit. (Joh 15:26, 27) Such help enabled them to recall Jesus’ instructions and teachings, to clarify points of doctrine, and to be progressively guided “into all the truth” revealed through them at that apostolic period. (Joh 14:26; 16:13-15; compare Joh 2:22; 12:16.) They made appointments to positions of service within the congregation and also designated areas in which certain ones would engage in missionary activity.​—Ac 6:2, 3; Ga 2:8, 9.

The apostles, therefore, served as a foundation, resting on Christ Jesus himself as the cornerstone, for the building up of the “holy temple for Jehovah.” (Eph 2:20-22; 1Pe 2:4-6) There is no evidence of the primacy of any one apostle in the established Christian congregation. (See PETER.) Peter and John appear to have been especially prominent at Pentecost and immediately thereafter, with Peter acting as the principal spokesman. (Ac 2:14, 37, 38; 3:1, 4, 11; 4:1, 13, 19; 5:3, 8, 15, 29) However, in the decisions made at that time neither of these appears to have had a superiority over the others of the governing body, and when news arrived of the baptisms taking place in Samaria, the apostles in Jerusalem “dispatched [a·peʹstei·lan] Peter and John to them,” so that these two served, in effect, as apostles of the apostles. (Ac 6:2-6; 8:14, 15) Following the death of the apostle James, the disciple of the same name, James the half brother of Jesus, appears to have presided in the governing body. Paul speaks of this James and also Peter (Cephas) and John as “the ones who seemed to be pillars.” (Ac 12:1, 2, 16, 17; Ga 1:18, 19; 2:9, 11-14) It was James who announced the final decision on the important issue of circumcision as involving the Gentile believers, at which meeting Peter and Paul both presented testimony.​—Ac 15:1, 2, 6-21.

Who replaced Judas Iscariot as a twelfth apostle?

Because of the defection of Judas Iscariot, who died unfaithful, there were only 11 apostles remaining, and during the 40 days from Jesus’ resurrection until his ascension to heaven he made no appointment of a replacement. Sometime during the ten days between Jesus’ ascension and the day of Pentecost it was viewed as necessary that another be selected to fill the vacancy left by Judas, not simply on the basis of his death but, rather, on the basis of his wicked defection, as the Scriptures quoted by Peter indicate. (Ac 1:15-22; Ps 69:25; 109:8; compare Re 3:11.) Thus, by contrast, when the faithful apostle James was put to death, there is no record of any concern to appoint anyone to succeed him in his position of apostle.​—Ac 12:2.

It is evident from Peter’s statements that it was then considered that any individual filling the position of an apostle of Jesus Christ must have the qualifications of having been personally conversant with him, having been an eyewitness of his works, his miracles, and particularly his resurrection. In view of this it can be seen that any apostolic succession would in course of time become an impossibility, unless there were divine action to supply these requirements in each individual case. At that particular time before Pentecost, however, there were men meeting these requirements, and two were put forth as suitable for replacing unfaithful Judas. Doubtless having in mind Proverbs 16:33, lots were cast, and Matthias was selected and was thereafter “reckoned along with the eleven apostles.” (Ac 1:23-26) He is thus included among “the twelve” who settled the problem concerning the Greek-speaking disciples (Ac 6:1, 2), and evidently Paul includes him in referring to “the twelve” when speaking of Jesus’ postresurrection appearances at 1 Corinthians 15:4-8. Thus, when Pentecost arrived, there were 12 apostolic foundations on which the spiritual Israel then formed could rest.

Congregational Apostleships. Matthias was not a mere apostle of the Jerusalem congregation, any more than the remaining 11 apostles were. His case is different from that of the Levite Joseph Barnabas who became an apostle of the congregation of Antioch, Syria. (Ac 13:1-4; 14:4, 14; 1Co 9:4-6) Other men also are referred to as “apostles of congregations” in the sense that they were sent forth by such congregations to represent them. (2Co 8:23) And, in writing to the Philippians, Paul speaks of Epaphroditus as “your envoy [a·poʹsto·lon] and private servant for my need.” (Php 2:25) The apostleship of these men was clearly not by virtue of any apostolic succession, nor did they form part of “the twelve” as did Matthias.

The correct understanding of the wider application of the term “apostle” can help to clear away any apparent discrepancy between Acts 9:26, 27 and Galatians 1:17-19, when applied to the same occasion. The first account states that Paul, on arriving in Jerusalem, was led “to the apostles” by Barnabas. In the account in Galatians, however, Paul states that he visited with Peter and adds: “But I saw no one else of the apostles, only James the brother of the Lord.” James (not the original apostle James the son of Zebedee nor James the son of Alphaeus, but the half brother of Jesus) was evidently viewed as an “apostle” in the wider sense, namely, as “one sent forth” by the Jerusalem congregation. This would allow for the Acts account to use the title in the plural in saying that Paul was led “to the apostles” (that is, Peter and James).​—Compare 1Co 15:5-7; Ga 2:9.

The Selection of Paul. Probably about the year 34 C.E., Saul of Tarsus was converted and is later referred to as Paul. He did become a true apostle of Jesus Christ and was the direct choice of the resurrected and ascended Jesus Christ. (Ac 9:1-22; 22:6-21; 26:12-23; 13:9) He argued on behalf of his apostleship and presented as his qualification the fact that he had seen the resurrected Lord Jesus Christ, that he had performed miracles, and that he had served as a channel for imparting the holy spirit to baptized believers. (1Co 9:1, 2; 15:9, 10; 2Co 12:12; 2Ti 1:1, 11; Ro 1:1; 11:13; Ac 19:5, 6) Since the apostle James (the brother of John) was not killed until about the year 44 C.E., “the twelve” were yet alive at the time of Paul’s becoming an apostle. He nowhere includes himself among such “twelve,” while at the same time he acknowledges no inferiority in his apostleship compared with that of such ones.​—Ga 2:6-9.

Matthias’ and Paul’s apostleships were both valid for the purpose for which those men were “sent forth,” yet when the apostle John saw the vision of the heavenly New Jerusalem in the Revelation (given about 96 C.E.) he saw only 12 foundation stones and on them inscribed “the twelve names of the twelve apostles of the Lamb.” (Re 21:14) The testimony of the Holy Scriptures is clear that the apostle Paul was never referred to as one of “the twelve.” Therefore, it logically follows that one of “the twelve names of the twelve apostles of the Lamb” inscribed on the foundation stones of the New Jerusalem is that of Matthias and not that of Paul. This means that the vision of the apostle John reflects the situation that existed at the start of the Christian congregation on the day of Pentecost in the year 33 C.E.​—See PAUL.

End of the Apostolic Period. Though the Bible does not relate the death of the 12 apostles, aside from that of James, the evidence available indicates that they maintained their faithfulness until death and therefore needed no replacement. Concerning history in the following centuries, the observation is made that “whenever it [the term “apostle”] is applied to individuals in later Christian literature, the use of the term is metaphorical. The church has never had apostles in the N[ew] T[estament] sense since the first century.”​—The Interpreter’s Dictionary of the Bible, edited by G. A. Buttrick, 1962, Vol. 1, p. 172.

During their lifetime the apostles’ presence served as a restraint upon the influences of apostasy, holding back the forces of false worship within the Christian congregation. It is evidently to this “restraint” that the apostle Paul referred at 2 Thessalonians 2:7: “True, the mystery of this lawlessness is already at work; but only till he who is right now acting as a restraint gets to be out of the way.” (Compare Mt 13:24, 25; Ac 20:29, 30.) This apostolic influence, including the authority and powers unique with them, continued until the death of John about 100 C.E. (1Jo 2:26; 3Jo 9, 10) The rapid influx of apostasy and false doctrine and practices after the death of the apostles shows that any pretended apostolic successors had none of the restraining influence of the apostles.

The reference to Andronicus and Junias at Romans 16:7 as “men of note among the apostles” indicates, not that they were apostles, but, rather, that they were held in high repute by the apostles. That some made false pretenses of being “apostles of Christ” is shown at 2 Corinthians 11:5, 13; 12:11, 12; Revelation 2:2.

Yet More on doubting the trinity.

And still yet more commonsense re:eternal torment

Matthew 25:46 Does Not Prove Eternal Torment – Part 1
by Joseph Dear


Matthew 25:46 is one of the most commonly used texts to prove that hell is a place of eternal torment. The text reads, “These will go away into eternal punishment, but the righteous into eternal life.”1 It is this reference to “eternal punishment” that is seen as a slam dunk, proving beyond a reasonable doubt that hell is a place of eternal conscious suffering.

Of course, it proves no such thing, and this passage has come up numerous times in the Rethinking Hell universe. It came up in a response to Tom Ascol’s “4 Truths About Hell.” It is addressed by Chris Date in Episode 7 of the Rethinking Hell podcast. Chris Date also addressed some specific grammatical elements of the passage in response to the blogger Turretinfan and a follow-up response.

However, there has yet to be a single, (relatively) succinct post (or series of posts) specifically about this text that can be referred to when the question comes up about how evangelical conditionalists might address the fact that the unsaved are condemned to “eternal punishment.” My goal here is to give such a response.


I want to be clear; my ultimate goal is not to make an affirmative case that Matthew 25:46 is evidence for annihilationism (though I will draw attention to an oft-overlooked aspect of the passage that does weigh in our favor some). All that I am ultimately arguing is that this verse does not prove the traditional doctrine, and that annihilation is at least logically consistent with its warning of “eternal punishment.”

“Eternal Punishment” Does Not Necessarily Mean An Ongoing Act of Punishing

I do agree with most traditionalists that, in this passage, “eternal” speaks of something lasting for eternity. It lasts for ever and ever. It is everlasting. So then, please ignore all objections you may have heard or read that attempt to refute annihilationism by saying that we make “eternal” not mean eternal (which is most of them). The meaning of eternal is not the key assumption that I am refuting here.

The assumption is made that “eternal punishment” means that the act of punishing the unsaved is what continues on for eternity. Most traditionalists take that for granted. This would include me when I was a traditionalist. This likely includes most conditionalists who were once traditionalists. This assumption is the underpinning of the whole argument from this verse.

However, this assumption is unwarranted, and despite the fact that we have to talk about grammar, the reason for this is actually quite simple. In a nutshell, when other nouns of action are qualified as eternal, it is often the results of the act, and not the act itself, that lasts for eternity. If this is even a reasonable possibility with Matthew 25:46, then we can no longer say that this proves the wicked always consciously exist; the one-time act of destroying them as punishment would yield the eternal result of them no longer being around.

Now, many will quickly object, reasoning like Alan Gomes of Biola University’s Talbot School of Theology: “One could argue that annihilation might be the result of punishment. But the Scriptures say that it is the punishment itself which is eternal, not merely its result.”2 But this rebuttal is insufficient, and later on, you will see why this reasoning completely fails to account for similar instances in the Bible, none of which say “the results of” but instead read just like “eternal punishment.”

Nouns of Action (Like “Punishment”)

You see, nouns of action, in English and in Greek and just in general, can often be taken in more than one way. This is not complex linguistic gymnastics that Jesus’ listeners would not have understood. This is a basic rule of language that a small child understands, at least in practice. In a previous post, Chris Date used “translation” as an example; “translation” may refer to the act of translating (“the translation of the book took ten years”), or to the result of translating (“the translation has been published recently”).3

The word “punishment” is no different. So before we even get into biblical examples, it must be pointed out that Gomes and others give us a false dilemma. They frame it as punishment vs. the results of punishment. In reality, it is about one meaning of punishment vs. another. The question is, what meaning of “punishment” was intended? Was Jesus referring to the act of punishing (like “the translation of the book took ten years”), or was he referring to the result of the act of punishing (like “the translation has been published recently”)? Either one would be “punishment.”

With this in mind, annihilation is eternal punishment. God punishes the wicked at one time, by destroying them, while they are alive and punishable. The result, the punishment that results from the act of punishing, is that they are destroyed and will never ever come back to life.

If this sounds like I am twisting language, you will see below why I am doing no such thing. The Bible treats language the same way.

Biblical Examples

“Eternal Judgment” – Hebrews 6:2

What does “eternal judgment” mean? It’s pretty simple; God judges, and the result is everlasting. Few traditionalists, if any, argue that this verse teaches that God is continually judging for eternity, banging his gavel and repeatedly declaring saved or unsaved the same finite number of existent people.

But wait a minute; it doesn’t say “the eternal results of judgment.” It says “eternal judgment.” Following the reasoning applied to Matthew 25:46, this verse must teach that God is continually in the act of judging! Following Gomes’ reasoning, “One could argue that [a universe in which God is not longer in the act of judging but the effects remain] might be the result of [judgment]. But the Scriptures say that it is the [judgment] itself which is eternal, not merely its result.” However, we all know that that would be absurd, so no one believes it.

Regarding Hebrews 6:2 and “eternal judgment,” what is eternal is the outcome; God judges, and the judgment is the result. Likewise, it at least could be the case that God punishes the unsaved by destroying them, and the punishment is the results, results that last for eternity.

Some may still be tempted to say “but it doesn’t say the ‘the result of punishment!’” However, unless they are to say that God will forever be continuously in the act of judging, this is really no longer an option.

Hebrews 6:2 would be sufficient to prove my point, but I will point to more examples to show that this is actually not an uncommon occurrence.

“Eternal Sin” – Mark 3:29

The person who commits the “eternal sin” is not doing the act for eternity. How would that even work? If that were the case, they would never actually finish the act! Context clues us in even further. This passage isn’t referring to some vague “unpardonable sin.” The text tells us what is in view: the Pharisees saying that Jesus had an unclean spirit. In other words, after having seen Jesus cast out demons, clearly an act of God, they instead slander him and accuse him of working on behalf of the devil! To do so was to blaspheme the Holy Spirit, by whose power Jesus was working.

It was an act of finite duration that they committed (though probably more than once). They said “he has an unclean spirit,” not “he has an unclean spppppppppppppiiiiiiiiiiiirrrrrrrrrrrrriiiiiiiiiii…” unto eternity! It is a sin with eternal consequences. Once one has done it, they have no hope ever.45

“Eternal Redemption” – Hebrews 9:12

Jesus obtained “eternal redemption” for us. Certainly Jesus isn’t continually in the act of redeeming us. After all, we gained redemption “through His blood” (Ephesians 1:7). That certainly isn’t going to happen again and again throughout eternity! He died once for all (Hebrews 10:10). It does not say “the results of redemption”; nonetheless, redemption as an act, i.e. the act of redeeming, was done once, not continually for ever and ever. The result of the act of redeeming, the “redemption,” is what lasts for ever and ever.

“Eternal Salvation” – Hebrews 5:9

The same is true as above. The act of saving us will not go on for eternity. Why would it need to? Jesus already died an rose again to save us. Most would take this for granted.6 Jesus will not be continually in the act of saving us, but the result, that we are saved (our “salvation”), lasts for ever and ever.

“Eternal Inheritance” – Hebrews 9:15

Our inheritance, the thing which we inherit, the result of our inheriting the kingdom, is what is eternal. We certainly are not going to be in the act of inheriting for eternity. We inherit, and we forever have what we inherit.

So Then…

It may be hasty to say that Matthew 25:46 must be like these passages. Nevertheless, it certainly is a reasonable possibility that it is. With this in mind, Matthew 25:46 certainly does not prove anything in rebuttal to evangelical conditionalism.

Being Killed/Annihilated/Destroyed Is A Form of Punishment

There is another element to this that is worth discussing, and that is the meaning of punishment. In some senses it is moot, given that in the previous section I showed that “eternal punishment” need not mean that the act of punishing is continuing for eternity in the first place. But I want to cover all of the necessary bases.

A major reason why this passage is believed to prove eternal torment is because it says “punishment,” and punishment, it is argued, must mean pain or some sort of conscious suffering, and therefore must mean that the person is alive and conscious to suffer.

This is partially true, but the part that is not true is what makes all the difference. Let us grant that someone has to exist as a sentient being to be punished, at least in any meaningful sense. It would make little sense, for example, to punish someone by beating their corpse since a corpse can’t feel. However, I am not denying that the hypothetical unsaved person is conscious and alive when God punishes them with destruction. They certainly are. But it is not the case that the punishment, the result of being punished, continues only as long as the person is alive/conscious to feel it and be aware.

Consider capital punishment, what is most often the most severe penalty inflicted on earth for crimes. Yes, the person is alive when the punishment is inflicted, but we don’t simply measure the punishment in terms of their conscious suffering. If that were the case, a short stint in prison or maybe even a fine would be more severe. The punishment is the years of life that were lost. The punishment continues on after the infliction of punishment and the consciousness of it ends.7

Under the evangelical conditionalist scenario, the fate of the wicked is similar. They are alive at judgment, and God inflicts punishment unto them. He punishes them by killing them, body and soul. But just as the judgment of Hebrews 6:2 has not ended the moment that God stops the act of judging, so here the punishment does not end the moment that God stops punishing. Just as Christ redeemed us once and for all and yet the redemption lasts for eternity, so here God punishes the wicked once and for all (by destroying them), and yet the punishment lasts for eternity. They are annihilated. They are killed and dead forever, deprived of the eternity of life they would have otherwise had. And this time, it is at God’s hand, done in body and soul, and there is no escaping it or reversing it. It is “eternal punishment.”

Parallel Between Eternal Life and Eternal Punishment

The parallelism that Jesus makes between “eternal life” and “eternal punishment” is the biggest aspect appealed to. Since at least the time of Augustine,8 it has been argued that since the phrase “eternal” is used twice in this verse, and the other time it describe the life of the saved (which certainly lasts for eternity), it means that the punishment also lasts for ever and ever. However, in light of the above, this is of little relevance. I agree that in both cases, “eternal” means the same thing. So if you should see a polemical writing against annihilationism where the author argues that, in light of “eternal life,” punishment must also last for eternity, you can ignore it, as it does not even address my argument here.

Far less common arguments that “eternal punishment” must entail an ongoing process since “eternal life” entails people consciously living forever will be addressed in Part 2.

Taking the Passage at “Face Value”

As I have written about previously, some may appeal to the fact that the Bible, when taken at face value, supports their view. After all, God’s word should be accessible to everyone, shouldn’t it? But this argument is problematic because no one side can take the Bible at face value all the time. Admittedly, some may be able to do so more than others (compare the many references to death and destruction for the unsaved compared to the very few references to torment). However, every view will have trouble passages.

With that in mind, consider that to many, this passage sounds more like eternal torment, when taken at face value, and so that is seen as evidence for that view.  But aside from the fact that face value can be misleading, this sword cuts both ways.

This is because this passage doesn’t just reference “eternal punishment.” The passage directly contrasts “eternal punishment” with “eternal life.” Now, some will argue that “eternal life” has nothing to do with having conscious existence and is only about the quality of existence (although in light of the Bible’s descriptions of “life,” as discussed here, that claim is rather tenuous). Be that as it may, we are talking about face value. At face value, “eternal life” sounds like living forever (i.e. being a consciously existent sentient being). At face value, it sounds like life and living in the way that we normally mean it, in the way that even a number of notable traditionalists mean it when speaking of the unsaved living forever in hell (until, of course, a conditionalist points out that the Bible says that the unsaved don’t have life).

Think about it. At face value, the saved get eternal life. They get to live for ever and ever. Since the alternative is eternal punishment, the punishment must be not having life (for eternity, no less). The punishment is not getting eternal life, so it means being eternally like a corpse or a pile of ashes. It is like if someone, on earth, had the option of life or capital punishment. It sounds like the punishment is being put to death.

In a nutshell, this passage says that the unsaved don’t get eternal life, so how can they be alive to be tormented forever? At face value, this flies in the face of the traditional doctrine.

Like I said, this sword cuts both ways. When “eternal life” comes up, suddenly the face value meaning of phrases isn’t so important, and examining the scripture more in-depth is not seen as unnecessarily complicating the matter.

Conclusion

Given how deeply ingrained the doctrine of eternal torment is in Christendom, it is understandable that to the average person, the meaning of “eternal punishment” is eternal torment. But when we compare scripture with scripture, and look into the matter further, we see that it is hardly that simple.

It should be apparent already how evangelical conditionalism is consistent with this passage, though it will be useful to address further issues, lest we leave important stones unturned. In Part 2, we will look at some rebuttals made to what I have put forth here. We will also look at an alternative conditionalist interpretation of Matthew 25:46.

Unless otherwise noted, all scripture quotations I give are from the New American Standard Bible (NASB). Scripture taken from the NEW AMERICAN STANDARD BIBLE®, Copyright © 1960,1962,1963,1968,1971,1972,1973,1975,1977,1995 by The Lockman Foundation. Used by permission. [↩]
Alan Gomes. “Evangelicals and the Annihilation of Hell: Part One,” Christian Research Journal (Spring, 1991), 14-19, n.d., http://www.bible-researcher.com/hell4.html (accessed on December 16, 2013). [↩]
Chris Date. “‘Punishment’ and the Polysemy of Deverbal Nouns.” Rethinking Hell [blog], posted June 19, 2012, http://www.rethinkinghell.com/2012/06/eternal-punishment-and-the-polysemy-of-deverbal-nouns (accessed January 2, 2014). [↩]
Fortunately, to be in the position as these Pharisees would be rare. Even those who blaspheme God can be forgiven if the person acts in ignorance, as Paul did (1 Timothy 1:13). You have to really know what you are doing (like one who would have just seen Jesus cast out demons). If you think you may have committed the sin of Mark 3:29, and you give a darn about it, then I think it is safe to say that you haven’t committed the eternal sin. [↩]
Some manuscripts vary and do not refer to an “eternal sin,” but even if the alternative rendering is correct and it does not say “eternal sin,” it is still the case that the idea of something like “eternal sin” made perfect sense to the 1st or 2nd-century scribe who copied it wrong. [↩]
For one instance of a traditionalist arguing that Jesus will be eternally in the act of saving us, see Part 2. [↩]
Of course, this is complicated somewhat if there is a conscious intermediate state, especially in the case of someone who is punished with death but has found Christ and therefore enters into his presence upon death. For them, death would actually lead to glory. But this complicates all sides, since surely that is not the intention of those who inflict the punishment. They aren’t going into it with the plan of sending the person to heaven as punishment! Rather, this would be demonstrative of the imperfections of earthly action, since humans can only kill the body. But God can destroy body and soul (Matthew 10:28). [↩]

Augustine of Hippo. City of God ed. Phillip Schaff (Veritatis Splendor, 2012), 21:23, 629. [↩]

A clash of Titans. LXXI

Just enough religion to make them hate?

Exjunk: From brass to gold.

The Un-Junk Industry

Evolution News & Views 

Junk DNA" is so 1972. Why is it hard to shed worn-out phrases? One bad stain can wear out dozens of wipes. Fortunately, we don't have to do all the wiping. Science reporters are getting better at helping clean up this genomic blemish.

A recent example is a paper in PNAS summarized on EurekAlert. The paper doesn't refer to junk DNA, but the news item does. "Punctuating messages encoded in human genome with transposable elements" is the title:

The vast majority of the human genome (~98% of the total genetic information) is not dedicated to encoding proteins, andthis non-coding sequence was initially designated as "junk DNA" to underscore its lack of apparent function. Much of the so-called junk DNA in our genomes has accumulated over evolutionary time due to the activity of retrotransposable elements (RTEs), which are capable of moving (transposing) from one location to another in the genome and make copies of themselves when they do so. These elements have been considered as genomic parasites that exist by virtue of their ability to replicate themselves to high numbers within genomeswithout providing any beneficial function for the hosts in which they reside. However, recent studies on RTEs have shown that they can in fact encode important functions, and much of their functional activity turns out to be related to how genomes areregulated. RTEs have been linked to stem cell function, tissue differentiation, cancer progression and ultimately to aging and age-related pathologies. [Emphasis added.]

Although this statement credits evolution with the accumulation of RTEs, the original paper is loaded with the word "function" and says nothing of significance about evolution. It also never claims that "cancer progression" or "aging" constitute functions for RTEs.

Instead, the paper offers a design prediction and found it largely true. Wanget al. predicted that RTEs act as "insulators" to keep related that help to organize eukaryotic chromatin via enhancer-blocking and chromatin barrier activity." Of the 1,178 mammalian-wide interspersed repeats (MIRs, a form of RTE) they predicted would be functional, they found that 58 percent of them do, indeed, function as insulators (the rest may have so-far-unknown functions). The news item calls them a form of "punctuation":

"We randomly picked a hand full of the MIR sequences predicted to serve as boundary elements by the Jordan lab andexperimentally validated their activity in mouse cell lines and, with help of our Spanish collaborators, in Zebra fish upon embryonic development," Dr. Lunyak said. "This testing revealed that MIR sequences can serve as punctuation marks within our genome that enable cells to correctly read and comprehend the message transmitted by the genomic sequences."

"One thing that is particularly striking is the fact that these punctuation marks, as Victoria calls them, play a role that is deeply evolutionary conserved," said Dr. Jordan. "The same exact MIR sequences were able to function as boundaries in humanCD4+ lymphocytes, in mouse cell models and in Zebrafish."

You wouldn't toss out all the punctuation in a book as "junk ABC" now, would you? Punctuation has a function -- an important one. It came late in human written language (try reading ancient Greek). Human intelligent agents recognized that punctuation could help the understanding of texts. If it took intelligence to design punctuation, why would we credit genetic punctuation to blind processes? The fact that it is deeply conserved in unrelated animals argues against its being randomly accumulated for no purpose.

Here's another function for these MIR sequences: tissue-specific regulation of gene expression. This helps explain why cell types can differ dramatically even though they all contain the same genetic library:

Boundary elements are epigenetic regulatory sequences thatseparate transcriptionally active regions of the human genome from transcriptionally silent regions in a cell-type specific manner. In so doing, these critical regulatory elements help to provide distinct identities to different cell types, although they all contain identical sets of information. The regulatory programs that underlie these cell- and tissue-specific functions and identities are based largely on genome packaging. Genes that should not be expressed in a given cell or tissue are located intightly packaged regions of the genome and inaccessible to the transcription factors that would otherwise turn them on. These boundary elements help to establish the geography of genome packaging by delineating the margins between silent regions in which genes are not expressed and active regions in which they are. In this critical role, boundary elements help to control the timing and extent of gene expression across the entire genome. As a result, defects in the organization of the genome by boundary elements are highly relevant for physiological and pathological processes.

Another benefit of looking for design instead of junk lies in gaining knowledge that has positive applications. Dr. Lunyak comments, "This is an important discovery because the understanding of how RTEs punctuate messages encoded in the human genome can help researchers to develop treatments for a wide variety of human diseases, including aging." You have to understand punctuation in order to fix it. Would the "junk DNA" concept have led to this productive line of inquiry? Incidentally, we can thank the ENCODE Project for motivating Dr. Jordan's project.

Functional Transfer-RNA "Litter"

Another example is this research from UC Santa Cruz. The annoucement doesn't mention junk DNA, but it shows the benefit of looking for function. All geneticists know the well-characterized functions of transfer RNA (tRNA), but the research team wondered why the nucleus is "littered" with pieces of tRNA. Notice the focus on function:

Transfer RNA was characterized decades ago and plays a well-defined role, together with messenger RNA and ribosomal RNA, in translating the genetic instructions encoded in DNA into proteins. The discovery of RNA interference and genetic regulation by microRNA, however, revolutionized scientists'understanding of RNA's role in gene regulation and other cellularfunctions. Since then, a bewildering abundance and variety of small RNA molecules has been found in cells, and scientists are still struggling to sort out what they all do.

One doesn't struggle to find out what junk does. The search for function is a good motivation for research. It inquires: these pieces must be there for a reason. As for the "Transfer RNA fragments," the search for function is only in the early stages, but an important one was found:

"In the past five years, we're starting to see that transfer RNAs are not just translating genes into proteins, they are being chopped up into fragments that do other things in the cell," Lowe said. "Just recently, a subset of these fragments was found to suppress breast cancer progression."

Many women can be relieved these UCSC researchers didn't give up on "litter" they didn't understand.

Endogenous Retroviruses

As Casey Luskin has explained, endogenous retroviruses (ERVs) also have functions and are not junk. Current Biology published a "Quick Guide" to ERVs this month. The authors seem ambivalent about these former poster children for useless, selfish invaders in our genome. On one hand, they point to examples that appear invasive and parasitic. On the other, they show examples of function, where ERVs are expressed purposefully by the "host":

At each end of the ERV genome are long terminal repeats (LTRs), which contain regulatory sequences that can alter the expression, splicing, and polyadenylation of those host genes located near the ERV insertion site. LTRs regulate the cell typethat the virus replicates in by controlling its expression, and so can be co-opted by their hosts as alternative promoters, resulting in tissue-specific expression of host genes. Often, solitary LTRs have been generated by homologous recombination between the two LTRs present in a single ERV, resulting in loss of the internal sequence. Consequently, host genomes are peppered with solo LTRs of potential regulatory significance.

The best evolutionary story the authors come up with is that the host learns to "co-opt" its ERVs and turn them into benefits. However, a search for design of ERVs would be more productive. Why must we always view viruses as destructive invaders? Many are neutral or beneficial. Why not look at ERVs as functional at the ecological level, instead of portraying them in the Dawkins selfish-gene way? The latter would motivate scientists to want to eliminate them, overlooking their potential benefits. It certainly is not helpful to ascribe mental planning to evolution, as the authors say in conclusion:

Taken together, the evidence suggests that sequences sequestered from ERVs have had a considerable influence on the evolution of their vertebrate hosts. So, not only is evolution a tinkerer, but it is also a conscientious recycler.

That word "recycler" represents a tacit admission that there was function there in the first place.

The Future of Genomics

PLOS Biology published a collection of short essays under the title, "Where Next for Genetics and Genomics?" Gil McVean looked back at the revolution in understanding when geneticists turned their attention from junk to gems:

The study of genetic variation has, over the last decade, been turned from a polite discipline focused on the finer points of evolutionary modelling to a fast, exhilarating, and sometimes messy hunt for gems hiding within the mines of genome-wide, population-scale datasets, most of which have been from humans. The coming years will only see the data rush grow: bigger samples, new species, extinct species, data linked to phenotype, temporal data, and so on. What, in this great whirlwind, am I most excited by?

Data are at their most fun when they bring to light things you would never have imagined.

Although he thinks the future will revisit "some of those big questions in evolution that never went away," like "How does adaptation actually work?" (You mean that after 156 years they don't know?), one thing is clear: focusing on "the finer points of evolutionary modelling" is passé. What's "exhilarating" now is "the hunt for gems." Things evolutionists "would never have imagined" -- like finding functions in assumed junk -- have been the "most fun."

Conclusions

The demise of the "junk DNA" meme is a powerful reminder of the positive benefit of design thinking. "Junk DNA" was a science stopper, relegating non-coding sequences in the genome to the trash basket. Many years of fruitful research were lost because of it. Had scientists been focused ondesign and function back in the 1970s, who knows how much further along we would be?

Here is a challenge to all researchers to look at nature with a different focus. When something in a cell or organism appears useless, learn to think: It must be there for a reason. History has shown that approach often leads to fundamental new insights into the design of life, yielding practical applications for health and understanding.

In the battle for conservation hunters are the good guys?:Pros and cons.