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Saturday 6 May 2017

On Spirit:The Watchtower Society's commentary.




SPIRIT
The Greek pneu′ma (spirit) comes from pne′o, meaning “breathe or blow,” and the Hebrew ru′ach (spirit) is believed to come from a root having the same meaning. Ru′ach and pneu′ma, then, basically mean “breath” but have extended meanings beyond that basic sense. (Compare Hab 2:19; Re 13:15.) They can also mean wind; the vital force in living creatures; one’s spirit; spirit persons, including God and his angelic creatures; and God’s active force, or holy spirit. (Compare Koehler and Baumgartner’s Lexicon in Veteris Testamenti Libros, Leiden, 1958, pp. 877-879; Brown, Driver, and Briggs’ Hebrew and English Lexicon of the Old Testament, 1980, pp. 924-926; Theological Dictionary of the New Testament, edited by G. Friedrich, translated by G. Bromiley, 1971, Vol. VI, pp. 332-451.) All these meanings have something in common: They all refer to that which is invisible to human sight and which gives evidence of force in motion. Such invisible force is capable of producing visible effects.
Another Hebrew word, nesha·mah′ (Ge 2:7), also means “breath,” but it is more limited in range of meaning than ru′ach. The Greek pno·e′ seems to have a similar limited sense (Ac 17:25) and was used by the Septuagint translators to render nesha·mah′.
Wind. Consider first the sense that is perhaps easiest to grasp. The context in many cases shows ru′ach to mean “wind,” as the “east wind” (Ex 10:13), “the four winds.” (Zec 2:6) The mention of such things as clouds, storm, the blowing of chaff or things of similar nature appearing in the context often makes evident this sense. (Nu 11:31; 1Ki 18:45; 19:11; Job 21:18) Because the four winds are used to mean the four directions—east, west, north, and south—ru′ach at times may be rendered as ‘direction’ or ‘side.’—1Ch 9:24; Jer 49:36; 52:23; Eze 42:16-20.
Job 41:15, 16 says of Leviathan’s closely fitting scales that “not even air [weru′ach] can come in between them.” Here again ru′ach represents air in motion, not merely air in a quiescent or motionless state. Thus the thought of an invisible force is present, the basic characteristic of the Hebrew ru′ach.
Evidently the only case in the Christian Greek Scriptures in which pneu′ma is used in the sense of “wind” is at John 3:8.
Man cannot exercise control over the wind; he cannot guide, direct, restrain, or possess it. Because of this, “wind [ru′ach]” frequently stands for that which is uncontrollable or unattainable by man—elusive, transitory, in vain, of no genuine benefit. (Compare Job 6:26; 7:7; 8:2; 16:3; Pr 11:29; 27:15, 16; 30:4; Ec 1:14, 17; 2:11; Isa 26:18; 41:29.) For a full discussion of this aspect, see WIND.
Spirit Persons. God is invisible to human eyes (Ex 33:20; Joh 1:18; 1Ti 1:17), and he is alive and exercises unsurpassed force throughout the universe. (2Co 3:3; Isa 40:25-31) Christ Jesus states: “God is a Spirit [Pneu′ma].” The apostle writes: “Now Jehovah is the Spirit.” (Joh 4:24; 2Co 3:17, 18) The temple built on Christ as foundation cornerstone is “a place for God to inhabit by spirit.”—Eph 2:22.
This does not mean that God is an impersonal, bodiless force like the wind. The Scriptures unmistakably testify to his personality; he also has location so that Christ could speak of ‘going to his Father,’ this in order that he might “appear before the person of God [literally, “face of God”] for us.”—Joh 16:28; Heb 9:24; compare 1Ki 8:43; Ps 11:4; 113:5, 6; see JEHOVAH (The Person Identified by the Name).
The expression “my spirit” (ru·chi′) used by God at Genesis 6:3 may mean “I the Spirit,” even as his use of “my soul” (naph·shi′) has the sense of “I the person,” or “my person.” (Isa 1:14; see SOUL [God as Having Soul].) He thereby contrasts his heavenly spiritual position with that of earthly, fleshly man.
God’s Son. God’s “only-begotten son,” the Word, was a spirit person like his Father, hence “existing in God’s form” (Php 2:5-8), but later “became flesh,” residing among mankind as the man Jesus. (Joh 1:1, 14) Completing his earthly course, he was “put to death in the flesh, but [was] made alive in the spirit.” (1Pe 3:18) His Father resurrected him, granted his Son’s request to be glorified alongside the Father with the glory he had had in his prehuman state (Joh 17:4, 5), and God made him “a life-giving spirit.” (1Co 15:45) The Son thus became again invisible to human sight, dwelling “in unapproachable light, whom not one of men has seen or can see.”—1Ti 6:14-16.
Other spirit creatures. Angels are designated by the terms ru′ach and pneu′ma in a number of texts. (1Ki 22:21, 22; Eze 3:12, 14; 8:3; 11:1, 24; 43:5; Ac 23:8, 9; 1Pe 3:19, 20) In the Christian Greek Scriptures, the majority of such references are to wicked spirit creatures, demons.—Mt 8:16; 10:1; 12:43-45; Mr 1:23-27; 3:11, 12, 30.
Psalm 104:4 states that God makes “his angels spirits, his ministers a devouring fire.” Some translations would render this: “Who makest the winds thy messengers, fire and flame thy ministers,” or similarly. (RS, JP, AT, JB) Such translation of the Hebrew text is not inadmissible (compare Ps 148:8); however, the apostle Paul’s quotation of the text (Heb 1:7) coincides with that of the Greek Septuagint and harmonizes with the rendering first given. (In the Greek text of Hebrews 1:7, the definite article [tous] is used before “angels,” not before “spirits [pneu′ma·ta],” making the angels the proper subject of the clause.) Barnes’ Notes on the New Testament (1974) says: “It is to be presumed that [Paul], who had been trained in the knowledge of the Hebrew language, would have had a better opportunity of knowing its [referring to Psalm 104:4] fair construction than we can; and it is morally certain, that he would employ the passage in an argument as it was commonly understood by those to whom he wrote—that is, to those who were familiar with the Hebrew language and literature.”—Compare Heb 1:14.
God’s angels, though capable of materializing human form and appearing to men, are not by nature material or fleshly, hence are invisible. They are actively alive and able to exert great force, and the terms ru′ach and pneu′ma therefore aptly describe them.
Ephesians 6:12 speaks of Christians wrestling, “not against blood and flesh, but against the governments, against the authorities, against the world rulers of this darkness, against the wicked spirit forces in the heavenly places.” The latter part of the text in Greek literally reads: “Toward the spiritual (things) [Gr., pneu·ma·ti·ka′] of the wickedness in the heavenly [places].” Most modern translations recognize that the reference here is not simply to something abstract, “spiritual wickedness” (KJ), but refers to wickedness carried out by spirit persons. Thus, we have such renderings as: “the spirit-forces of evil on high” (AT), “the spiritual hosts of wickedness in the heavenly places” (RS), “the spiritual army of evil in the heavens” (JB), “the superhuman forces of evil in the heavens” (NE).
God’s Active Force; Holy Spirit. By far the majority of occurrences of ru′ach and pneu′ma relate to God’s spirit, his active force, his holy spirit.
Not a person. Not until the fourth century C.E. did the teaching that the holy spirit was a person and part of the “Godhead” become official church dogma. Early church “fathers” did not so teach; Justin Martyr of the second century C.E. taught that the holy spirit was an ‘influence or mode of operation of the Deity’; Hippolytus likewise ascribed no personality to the holy spirit. The Scriptures themselves unite to show that God’s holy spirit is not a person but is God’s active force by which he accomplishes his purpose and executes his will.
It may first be noted that the words “in heaven, the Father, the Word, and the Holy Ghost: and these three are one” (KJ) found in older translations at 1 John 5:7 are actually spurious additions to the original text. A footnote in The Jerusalem Bible, a Catholic translation, says that these words are “not in any of the early Greek MSS [manuscripts], or any of the early translations, or in the best MSS of the Vulg[ate] itself.” A Textual Commentary on the Greek New Testament, by Bruce Metzger (1975, pp. 716-718), traces in detail the history of the spurious passage. It states that the passage is first found in a treatise entitled Liber Apologeticus, of the fourth century, and that it appears in Old Latin and Vulgate manuscripts of the Scriptures, beginning in the sixth century. Modern translations as a whole, both Catholic and Protestant, do not include them in the main body of the text, because of recognizing their spurious nature.—RS, NE, NAB.
Personification does not prove personality. It is true that Jesus spoke of the holy spirit as a “helper” and spoke of such helper as ‘teaching,’ ‘bearing witness,’ ‘giving evidence,’ ‘guiding,’ ‘speaking,’ ‘hearing,’ and ‘receiving.’ In so doing, the original Greek shows Jesus at times applying the personal pronoun “he” to that “helper” (paraclete). (Compare Joh 14:16, 17, 26; 15:26; 16:7-15.) However, it is not unusual in the Scriptures for something that is not actually a person to be personalized or personified. Wisdom is personified in the book of Proverbs (1:20-33; 8:1-36); and feminine pronominal forms are used of it in the original Hebrew, as also in many English translations. (KJ, RS, JP, AT) Wisdom is also personified at Matthew 11:19 and Luke 7:35, where it is depicted as having both “works” and “children.” The apostle Paul personalized sin and death and also undeserved kindness as “kings.” (Ro 5:14, 17, 21; 6:12) He speaks of sin as “receiving an inducement,” ‘working out covetousness,’ ‘seducing,’ and ‘killing.’ (Ro 7:8-11) Yet it is obvious that Paul did not mean that sin was actually a person.
So, likewise with John’s account of Jesus’ words regarding the holy spirit, his remarks must be taken in context. Jesus personalized the holy spirit when speaking of that spirit as a “helper” (which in Greek is the masculine substantive pa·ra′kle·tos). Properly, therefore, John presents Jesus’ words as referring to that “helper” aspect of the spirit with masculine personal pronouns. On the other hand, in the same context, when the Greek pneu′ma is used, John employs a neuter pronoun to refer to the holy spirit, pneu′ma itself being neuter. Hence, we have in John’s use of the masculine personal pronoun in association with pa·ra′kle·tos an example of conformity to grammatical rules, not an expression of doctrine.—Joh 14:16, 17; 16:7, 8.
Lacks personal identification. Since God himself is a Spirit and is holy and since all his faithful angelic sons are spirits and are holy, it is evident that if the “holy spirit” were a person, there should reasonably be given some means in the Scriptures to distinguish and identify such spirit person from all these other ‘holy spirits.’ It would be expected that, at the very least, the definite article would be used with it in all cases where it is not called “God’s holy spirit” or is not modified by some similar expression. This would at least distinguish it as THE Holy Spirit. But, on the contrary, in a large number of cases the expression “holy spirit” appears in the original Greek without the article, thus indicating its lack of personality.—Compare Ac 6:3, 5; 7:55; 8:15, 17, 19; 9:17; 11:24; 13:9, 52; 19:2; Ro 9:1; 14:17; 15:13, 16, 19; 1Co 12:3; Heb 2:4; 6:4; 2Pe 1:21; Jude 20Int and other interlinear translations.
How baptized in its “name.” At Matthew 28:19 reference is made to “the name of the Father and of the Son and of the holy spirit.” A “name” can mean something other than a personal name. When, in English, we say, “in the name of the law,” or “in the name of common sense,” we have no reference to a person as such. By “name” in these expressions we mean ‘what the law stands for or its authority’ and ‘what common sense represents or calls for.’ The Greek term for “name” (o′no·ma) also can have this sense. Thus, while some translations (KJ, AS) follow the Greek text at Matthew 10:41 literally and say that the one that “receiveth a prophet in the name of a prophet, shall receive a prophet’s reward; and he that receiveth a righteous man in the name of a righteous man, shall receive a righteous man’s reward,” more modern translations say, “receives a prophet because he is a prophet” and “receives a righteous man because he is a righteous man,” or similar. (RS, AT, JB, NW) Thus, Robertson’s Word Pictures in the New Testament (1930, Vol. I, p. 245) says on Matthew 28:19: “The use of name (onoma) here is a common one in the Septuagint and the papyri for power or authority.” Hence baptism ‘in the name of the holy spirit’ implies recognition of that spirit as having its source in God and as exercising its function according to the divine will.
Other evidence of its impersonal nature. Further evidence against the idea of personality as regards the holy spirit is the way it is used in association with other impersonal things, such as water and fire (Mt 3:11; Mr 1:8); and Christians are spoken of as being baptized “in holy spirit.” (Ac 1:5; 11:16) Persons are urged to become “filled with spirit” instead of with wine. (Eph 5:18) So, too, persons are spoken of as being ‘filled’ with it along with such qualities as wisdom and faith (Ac 6:3, 5; 11:24) or joy (Ac 13:52); and holy spirit is inserted, or sandwiched in, with a number of such qualities at 2 Corinthians 6:6. It is most unlikely that such expressions would be made if the holy spirit were a divine person. As to the spirit’s ‘bearing witness’ (Ac 5:32; 20:23), it may be noted that the same thing is said of the water and the blood at 1 John 5:6-8. While some texts refer to the spirit as ‘witnessing,’ ‘speaking,’ or ‘saying’ things, other texts make clear that it spoke through persons, having no personal voice of its own. (Compare Heb 3:7; 10:15-17; Ps 95:7; Jer 31:33, 34; Ac 19:2-6; 21:4; 28:25.) It may thus be compared to radio waves that can transmit a message from a person speaking into a microphone and cause his voice to be heard by persons a distance away, in effect, ‘speaking’ the message by a radio loudspeaker. God, by his spirit, transmits his messages and communicates his will to the minds and hearts of his servants on earth, who, in turn, may convey that message to yet others.
Distinguished from “power.” Ru′ach and pneu′ma, therefore, when used with reference to God’s holy spirit, refer to God’s invisible active force by which he accomplishes his divine purpose and will. It is “holy” because it is from Him, not of an earthly source, and is free from all corruption as “the spirit of holiness.” (Ro 1:4) It is not Jehovah’s “power,” for this English word more correctly translates other terms in the original languages (Heb., ko′ach; Gr., dy′na·mis). Ru′ach and pneu′ma are used in close association or even in parallel with these terms signifying “power,” which shows that there is an inherent connection between them and yet a definite distinction. (Mic 3:8; Zec 4:6; Lu 1:17, 35; Ac 10:38) “Power” is basically the ability or capacity to act or do things and it can be latent, dormant, or inactively resident in someone or something. “Force,” on the other hand, more specifically describes energy projected and exerted on persons or things, and may be defined as “an influence that produces or tends to produce motion, or change of motion.” “Power” might be likened to the energy stored in a battery, while “force” could be compared to the electric current flowing from such battery. “Force,” then, more accurately represents the sense of the Hebrew and Greek terms as relating to God’s spirit, and this is borne out by a consideration of the Scriptures.
Its Use in Creation. Jehovah God accomplished the creation of the material universe by means of his spirit, or active force. Regarding the planet Earth in its early formative stages, the record states that “God’s active force [or “spirit” (ru′ach)] was moving to and fro over the surface of the waters.” (Ge 1:2Psalm 33:6 says: “By the word of Jehovah the heavens themselves were made, and by the spirit of his mouth all their army.” Like a powerful breath, God’s spirit can be sent forth to exert power even though there is no bodily contact with that which is acted upon. (Compare Ex 15:8, 10.) Where a human craftsman would use the force of his hands and fingers to produce things, God uses his spirit. Hence that spirit is also spoken of as God’s “hand” or “fingers.”—Compare Ps 8:3; 19:1; Mt 12:28 with Lu 11:20.
Modern science speaks of matter as organized energy, like bundles of energy, and recognizes that “matter can be changed into energy and energy into matter.” (The World Book Encyclopedia, 1987, Vol. 13, p. 246) The immensity of the universe that man has thus far been able to discern with his telescopes gives some slight concept of the inexhaustible source of energy to be found in Jehovah God. As the prophet wrote: “Who has taken the proportions of the spirit of Jehovah?”—Isa 40:12, 13, 25, 26.
Source of animate life, reproductive powers. Not only inanimate creation but also all animate creation owes its existence and life to the operation of Jehovah’s spirit that produced the original living creatures through whom all living creatures today have come to exist. (Compare Job 33:4; see section of this article under “Breath; Breath of Life; Life-Force.”) Jehovah used his holy spirit to revive the reproductive powers of Abraham and Sarah, and therefore Isaac could be spoken of as “born in the manner of spirit.” (Ga 4:28, 29) By his spirit God also transferred his Son’s life from heaven to earth, causing conception in the womb of the virgin Jewess Mary.—Mt 1:18, 20; Lu 1:35.
Spirit Used on Behalf of God’s Servants. A principal operation of God’s spirit involves its ability to inform, to illuminate, to reveal things. Therefore David could pray: “Teach me to do your will, for you are my God. Your spirit is good; may it lead me in the land of uprightness.” (Ps 143:10) Much earlier, Joseph had given the interpretation of Pharaoh’s prophetic dreams, being enabled to do so by God’s help. The Egyptian ruler recognized the operation of God’s spirit in him. (Ge 41:16, 25-39) This illuminating power of the spirit is particularly notable in prophecy. Prophecy, as the apostle shows, did not spring from human interpretation of circumstances and events; it was not the result of some innate ability of the prophets to explain the meaning and significance of these or to forecast the shape of coming events. Rather, such men were “borne along by holy spirit”—conveyed, moved, and guided by God’s active force. (2Pe 1:20, 21; 2Sa 23:2; Zec 7:12; Lu 1:67; 2:25-35; Ac 1:16; 28:25; see PROPHECYPROPHET.) So, too, all the inspired Scriptures were “inspired of God,” which translates the Greek the·o′pneu·stos, meaning, literally, “God-breathed.” (2Ti 3:16) The spirit operated in various manners in communicating with such men and guiding them, in some cases causing them to see visions or dreams (Eze 37:1; Joe 2:28, 29; Re 4:1, 2; 17:3; 21:10), but in all cases operating on their minds and hearts to motivate and guide them according to God’s purpose.—Da 7:1; Ac 16:9, 10; Re 1:10, 11; see INSPIRATION.
God’s spirit, then, not only brings revelation and understanding of God’s will but also energizes his servants to accomplish things in accord with that will. That spirit acts as a driving force that moves and impels them, even as Mark says the spirit “impelled” Jesus to go into the wilderness after his baptism. (Mr 1:12; compare Lu 4:1.) It can be like a “fire” within them, causing them to be “aglow” with that force (1Th 5:19; Ac 18:25; Ro 12:11), in a sense ‘building up steam’ or pressure in them to do certain work. (Compare Job 32:8, 18-20; 2Ti 1:6, 7.) They receive the “power of the spirit,” or “power through his spirit.” (Lu 2:27; Eph 3:16; compare Mic 3:8.) Yet it is not merely some unconscious, blind impulse, for their minds and hearts are affected as well so that they can intelligently cooperate with the active force given them. Thus the apostle could say of those who had received the gift of prophecy in the Christian congregation that the “gifts of the spirit of the prophets are to be controlled by the prophets,” so that good order might be maintained.—1Co 14:31-33.
Variety of operations. Even as an electric current can be used to accomplish a tremendous variety of things, so God’s spirit is used to commission and enable persons to do a wide variety of things. (Isa 48:16; 61:1-3) As Paul wrote of the miraculous gifts of the spirit in his day: “Now there are varieties of gifts, but there is the same spirit; and there are varieties of ministries, and yet there is the same Lord; and there are varieties of operations, and yet it is the same God who performs all the operations in all persons. But the manifestation of the spirit is given to each one for a beneficial purpose.”—1Co 12:4-7.
The spirit has qualifying force or capacity; it can qualify persons for a work or for an office. Though Bezalel and Oholiab may have had knowledge of crafts before their appointment in connection with the making of the tabernacle equipment and priestly garments, God’s spirit ‘filled them with wisdom, understanding, and knowledge’ so that the work could be done in the way purposed. It heightened whatever natural abilities and acquired knowledge they already had, and it enabled them to teach others. (Ex 31:1-11; 35:30-35) The architectural plans for the later temple were given to David by inspiration, that is, through the operation of God’s spirit, thus enabling David to undertake extensive preparatory work for the project.—1Ch 28:12.
God’s spirit acted on and through Moses in prophesying and performing miraculous acts, as well as in leading the nation and acting as judge for it, thereby foreshadowing the future role of Christ Jesus. (Isa 63:11-13; Ac 3:20-23) However, Moses as an imperfect human found the load of responsibility heavy, and God ‘took away some of the spirit that was on Moses and placed it upon 70 older men’ so that they might help in carrying the load. (Nu 11:11-17, 24-30) The spirit also became operative on David from the time of his anointing by Samuel onward, guiding and preparing him for his future kingship.—1Sa 16:13.
Joshua became “full of the spirit of wisdom” as Moses’ successor. But the spirit did not produce in him the ability to prophesy and perform miraculous works to the extent that it had in Moses. (De 34:9-12) However, it enabled Joshua to lead Israel in the military campaign that brought about the conquest of Canaan. Similarly, Jehovah’s spirit “enveloped” other men, ‘impelling’ them as fighters on behalf of God’s people, fighters such as Othniel, Gideon, Jephthah, and Samson.—Jg 3:9, 10; 6:34; 11:29; 13:24, 25; 14:5, 6, 19; 15:14.
The spirit of God energized men to speak his message of truth boldly and courageously before opposers and at the risk of their lives.—Mic 3:8.
Its being ‘poured out’ on his people is evidence of his favor, and it results in blessings and makes them prosper.—Eze 39:29; Isa 44:3, 4.
Judging and executing judgment. By his spirit God exercises judgment on men and nations; he also carries out his judgment decrees—punishing or destroying. (Isa 30:27, 28; 59:18, 19) In such cases, ru′ach may be fittingly rendered “blast,” as when Jehovah speaks of causing “a blast [ru′ach] of windstorms to burst forth” in his rage. (Eze 13:11, 13; compare Isa 25:4; 27:8.) God’s spirit can reach everywhere, acting for or against those who receive his attention.—Ps 139:7-12.
At Revelation 1:4 “the seven spirits” of God are mentioned as before his throne, and thereafter seven messages are given, each concluding with an admonition to “hear what the spirit says to the congregations.” (Re 2:7, 11, 17, 29; 3:6, 13, 22) These messages contain heart-searching pronouncements of judgment and promises of reward for faithfulness. God’s Son is shown as having these “seven spirits of God” (Re 3:1); and they are spoken of as being “seven lamps of fire” (Re 4:5), and also as seven eyes of the lamb that is slaughtered, “which eyes mean the seven spirits of God that have been sent forth into the whole earth.” (Re 5:6) Seven being used as representative of completeness in other prophetic texts (see NUMBER, NUMERAL), it appears that these seven spirits symbolize the full active capacity of observation, discernment, or detection of the glorified Jesus Christ, the Lamb of God, enabling him to inspect all the earth.
God’s Word is the spirit’s “sword” (Eph 6:17), revealing what a person really is, exposing hidden qualities or heart attitudes and causing him either to soften his heart and conform to God’s will expressed by that Word or to harden his heart in rebellion. (Compare Heb 4:11-13; Isa 6:9, 10; 66:2, 5.) God’s Word therefore plays a forceful part in predicting adverse judgment, and since God’s word or message must be carried out, the fulfillment of that word produces an action like that of fire on straw and like that of a forge hammer in smashing the crag. (Jer 23:28, 29) Christ Jesus, as God’s principal Spokesman, as “The Word of God,” declares the divine judgment messages and is authorized to order the execution of such judgments upon those judged. This is doubtless what is meant by references to his doing away with God’s enemies “by the spirit [activating force] of his mouth.”—Compare 2Th 2:8; Isa 11:3, 4; Re 19:13-16, 21.
God’s spirit acts as “helper” for congregation. As he promised, Jesus upon ascending to heaven requested of his Father the holy spirit, or active force of God, and was granted the authority to employ this spirit. He ‘poured it out’ on his faithful disciples on the day of Pentecost, continuing to do so thereafter for those turning to God through his Son. (Joh 14:16, 17, 26; 15:26; 16:7; Ac 1:4, 5; 2:1-4, 14-18, 32, 33, 38) As they had been baptized in water, now they were all “baptized into one body” by that one spirit, immersed in it, as it were, somewhat like a piece of iron can be immersed in a magnetic field and thereby be imbued with magnetic force. (1Co 12:12, 13; compare Mr 1:8; Ac 1:5.) Though God’s spirit had operated on the disciples before, as evidenced by their being able to cast out demons (compare Mt 12:28; Mr 3:14, 15), it now operated on them in a heightened and more extensive manner and in new ways not previously experienced.—Compare Joh 7:39.
As the Messianic King, Christ Jesus has the “spirit of wisdom and of understanding, the spirit of counsel and of mightiness, the spirit of knowledge and of the fear of Jehovah.” (Isa 11:1, 2; 42:1-4; Mt 12:18-21) This force for righteousness is manifest in his use of God’s active force, or spirit, in directing the Christian congregation on earth, Jesus being, by God’s appointment, its Head, Owner, and Lord. (Col 1:18; Jude 4) As a “helper,” that spirit now gave them increased understanding of God’s will and purpose and opened up God’s prophetic Word to them. (1Co 2:10-16; Col 1:9, 10; Heb 9:8-10) They were energized to serve as witnesses in all the earth (Lu 24:49; Ac 1:8; Eph 3:5, 6); they were granted miraculous ‘gifts of the spirit,’ enabling them to speak in foreign languages, prophesy, heal, and perform other activities that would both facilitate their proclamation of the good news and serve as evidence of their divine commission and backing.—Ro 15:18, 19; 1Co 12:4-11; 14:1, 2, 12-16; compare Isa 59:21; see GIFTS FROM GOD (Gifts of the Spirit).
As the congregation’s Overseer, Jesus used the spirit in a governmental way—guiding in the selection of men for special missions and for serving in the oversight, teaching, and “readjustment” of the congregation. (Ac 13:2-4; 20:28; Eph 4:11, 12) He moved them, as well as restricted them, indicating where to concentrate their ministerial efforts (Ac 16:6-10; 20:22), and made them effective as writers of ‘letters of Christ, inscribed with the spirit of God on fleshly tablets, human hearts.’ (2Co 3:2, 3; 1Th 1:5) As promised, the spirit refreshed their memories, stimulated their mental powers, and emboldened them in bearing witness even before rulers.—Compare Mt 10:18-20; Joh 14:26; Ac 4:5-8, 13, 31; 6:8-10.
As “living stones,” they were being formed into a spiritual temple based on Christ, one through which “spiritual sacrifices” would be made (1Pe 2:4-6; Ro 15:15, 16) and spiritual songs sung (Eph 5:18, 19) and in which God would reside by spirit. (1Co 3:16; 6:19, 20; Eph 2:20-22; compare Hag 2:5.) God’s spirit is a unifying force of enormous strength, and as long as such Christians allowed it free course among them, it joined them peacefully together in bonds of love and devotion to God, his Son, and one another. (Eph 4:3-6; 1Jo 3:23, 24; 4:12, 13; compare 1Ch 12:18.) The gift of the spirit did not equip them for mechanical types of activity, as it had Bezalel and others who manufactured and produced material structures and equipment, but it fitted them for spiritual works of teaching, guiding, shepherding, and counseling. The spiritual temple they formed was to be adorned with the beautiful fruits of God’s spirit, and that fruitage of “love, joy, peace, long-suffering, kindness, goodness, faith,” and similar qualities was proof positive that God’s spirit was operating in and among them. (Ga 5:22, 23; compare Lu 10:21; Ro 14:17.) This was the basic and primary factor producing good order and effective guidance among them. (Ga 5:24-26; 6:1; Ac 6:1-7; compare Eze 36:26, 27.) They submitted themselves to the ‘law of the spirit,’ an effective force for righteousness working to keep out the practices of the innately sinful flesh. (Ro 8:2; Ga 5:16-21; Jude 19-21) Their confidence was in God’s spirit operating on them, not in fleshly abilities or background.—1Co 2:1-5; Eph 3:14-17; Php 3:1-8.
When questions arose, the holy spirit was a helper in arriving at a decision, as in the question of circumcision, decided by the body, or council, of apostles and older men at Jerusalem. Peter told of the spirit’s being granted to uncircumcised people of the nations; Paul and Barnabas related the spirit’s operations in their ministry among such persons; and James, his memory of the Scriptures doubtless aided by holy spirit, called attention to the inspired prophecy of Amos foretelling that God’s name would be called on people of the nations. Thus all the thrust or drive of God’s holy spirit pointed in one direction, and hence, in recognition of this, when writing the letter conveying their decision, this body or council said: “For the holy spirit and we ourselves have favored adding no further burden to you, except these necessary things.”—Ac 15:1-29.
Anoints, begets, gives ‘spiritual life.’ As God had anointed Jesus with his holy spirit at the time of Jesus’ baptism (Mr 1:10; Lu 3:22; 4:18; Ac 10:38), so he now anointed Jesus’ disciples. This anointing with the spirit was a “token” to them of the heavenly inheritance to which they were now called (2Co 1:21, 22; 5:1, 5; Eph 1:13, 14), and it bore witness to them that they had been ‘begotten,’ or brought forth, by God to be his sons with the promise of spirit life in the heavens. (Joh 3:5-8; Ro 8:14-17, 23; Tit 3:5; Heb 6:4, 5) They were made clean, sanctified, and declared righteous “in the name of our Lord Jesus Christ and with the spirit of our God,” by which spirit Jesus had been qualified to provide the ransom sacrifice and become God’s high priest.—1Co 6:11; 2Th 2:13; Heb 9:14; 1Pe 1:1, 2.
Because of this heavenly calling and inheritance, Jesus’ spirit-anointed followers had a spiritual life, though yet living as imperfect, fleshly creatures. This is evidently what the apostle refers to when contrasting earthly fathers with Jehovah God, “the Father of our spiritual life [literally, “Father of the spirits”].” (Heb 12:9; compare Heb 12 verse 23.) As joint heirs with Christ, who are due to be raised up from death in a spiritual body bearing his heavenly image, they should live on earth as “one spirit” in union with him as their Head, not letting the desires or immoral tendencies of their flesh be the force controlling them, such a thing even resulting perhaps in their becoming “one flesh” with a harlot.—1Co 6:15-18; 15:44-49; Ro 8:5-17.
Gaining and retaining God’s spirit. The holy spirit is God’s “free gift,” which he gladly grants to those who sincerely seek and request it. (Ac 2:38; Lu 11:9-13) A right heart is the key factor (Ac 15:8), but knowledge and conformity to God’s requirements are also essential factors. (Compare Ac 5:32; 19:2-6.) Once received, the Christian should not ‘grieve’ God’s spirit by disregarding it (Eph 4:30; compare Isa 63:10), taking a course contrary to its leading, fixing the heart on goals other than that to which it points and impels, rejecting the inspired Word of God and its counsel and application to oneself. (Ac 7:51-53; 1Th 4:8; compare Isa 30:1, 2.) By hypocrisy one can “play false” to that holy spirit by which Christ directs the congregation, and those who “make a test” of its power in this way follow a disastrous course. (Ac 5:1-11; contrast Ro 9:1.) Deliberate opposition to and rebellion against the evident manifestation of God’s spirit can mean blasphemy against that spirit, a sin that is unforgivable.—Mt 12:31, 32; Mr 3:29, 30; compare Heb 10:26-31.
Breath; Breath of Life; Life-Force. The account of the creation of man states that God formed man from the dust of the ground and proceeded to “blow [form of na·phach′] into his nostrils the breath [form of nesha·mah′] of life, and the man came to be a living soul [ne′phesh].” (Ge 2:7; see SOUL.) Ne′phesh may be translated literally as “a breather,” that is, “a breathing creature,” either human or animal. Nesha·mah′ is, in fact, used to mean “breathing thing [or creature]” and as such is used as a virtual synonym of ne′phesh, “soul.” (Compare De 20:16; Jos 10:39, 40; 11:11; 1Ki 15:29.) The record at Genesis 2:7 uses nesha·mah′ in describing God’s causing Adam’s body to have life so that the man became “a living soul.” Other texts, however, show that more was involved than simple breathing of air, that is, more than the mere introduction of air into the lungs and its expulsion therefrom. Thus, at Genesis 7:22, in describing the destruction of human and animal life outside the ark at the time of the Flood, we read: “Everything in which the breath [form of nesha·mah′] of the force [or, “spirit” (ru′ach)] of life was active in its nostrils, namely, all that were on the dry ground, died.” Nesha·mah′, “breath,” is thus directly associated or linked with ru′ach, which here describes the spirit, or life-force, that is active in all living creatures—human and animal souls.
As the Theological Dictionary of the New Testament (Vol. VI, p. 336) states: “Breath may be discerned only in movement [as in the movement of the chest or the expanding of the nostrils], and it is also a sign, condition and agent of life, which seems to be esp[ecially] tied up with breathing.” Hence, the nesha·mah′, or “breath,” is both the product of the ru′ach, or life-force, and also a principal means of sustaining that life-force in living creatures. It is known from scientific studies, for example, that life is present in every single cell of the body’s one hundred trillion cells and that, while thousands of millions of cells die each minute, constant reproduction of new living cells goes on. The life-force active in all the living cells is dependent upon the oxygen that breathing brings into the body, which oxygen is transported to all the cells by the bloodstream. Without oxygen some cells begin to die after several minutes, others after a longer period. While a person can go without breathing for a few minutes and still survive, without the life-force in his cells he is dead beyond all human ability to revive him. The Hebrew Scriptures, inspired by man’s Designer and Creator, evidently use ru′ach to denote this vital force that is the very principle of life, and nesha·mah′ to represent the breathing that sustains it.
Because breathing is so inseparably connected with life, nesha·mah′ and ru′ach are used in clear parallel in various texts. Job voiced his determination to avoid unrighteousness “while my breath [form of nesha·mah′] is yet whole within me, and the spirit [weru′ach] of God is in my nostrils.” (Job 27:3-5) Elihu said: “If that one’s spirit [form of ru′ach] and breath [form of nesha·mah′] he [God] gathers to himself, all flesh will expire [that is, “breathe out”] together, and earthling man himself will return to the very dust.” (Job 34:14, 15) Similarly, Psalm 104:29 says of earth’s creatures, human and animal: “If you [God] take away their spirit, they expire, and back to their dust they go.” At Isaiah 42:5 Jehovah is spoken of as “the One laying out the earth and its produce, the One giving breath to the people on it, and spirit to those walking in it.” The breath (nesha·mah′) sustains their existence; the spirit (ru′ach) energizes and is the life-force that enables man to be an animated creature, to move, walk, be actively alive. (Compare Ac 17:28.) He is not like the lifeless, breathless, inanimate idols of human fabrication.—Ps 135:15, 17; Jer 10:14; 51:17; Hab 2:19.
While nesha·mah′ (breath) and ru′ach (spirit; active force; life-force) are sometimes used in a parallel sense, they are not identical. True, the “spirit,” or ru′ach, is at times spoken of as though it were the respiration (nesha·mah′) itself, but this seems to be simply because breathing is the prime visible evidence of the life-force in one’s body.—Job 9:18; 19:17; 27:3.
Thus at Ezekiel 37:1-10 the symbolic vision of the valley of dry bones is presented, the bones coming together, becoming covered with sinews, flesh, and skin, but “as regards breath [weru′ach], there was none in them.” Ezekiel was told to prophesy to “the wind [ha·ru′ach],” saying, “From the four winds [form of ru′ach] come in, O wind, and blow upon these killed people, that they may come to life.” The reference to the four winds shows that wind is the appropriate rendering for ru′ach in this case. However, when such “wind,” which is simply air in motion, entered the nostrils of the dead persons of the vision, it became “breath,” which is also air in motion. Thus, the rendering of ru′ach as “breath” at this point of the account (Eze 37 vs 10) is also more appropriate than “spirit” or “life-force.” Ezekiel also would be able to see the bodies begin to breathe, even though he could not see the life-force, or spirit, energizing their bodies. As Eze 37 verses 11-14 show, this vision was symbolic of a spiritual (not physical) revivification of the people of Israel who were for a time in a spiritually dead state due to their Babylonian exile. Since they were already physically alive and breathing, it is logical to render ru′ach as “spirit” in Eze 37 verse 14, where God states that he will put ‘his spirit’ in his people so that they would become alive, spiritually speaking.
A similar symbolic vision is given at Revelation chapter 11. The picture is presented of “two witnesses” who are killed and whose corpses are allowed to lie on the street for three and a half days. Then “spirit [or breath, pneu′ma] of life from God entered into them, and they stood upon their feet.” (Re 11:1-11) This vision again draws on a physical reality to illustrate a spiritual revivification. It also shows that the Greek pneu′ma, like the Hebrew ru′ach, may represent the life-giving force from God that animates the human soul or person. As James 2:26 states: “The body without spirit [pneu′ma·tos] is dead.”—Int.
Therefore, when God created man in Eden and blew into his nostrils “the breath [form of nesha·mah′] of life,” it is evident that, in addition to filling the man’s lungs with air, God caused the life-force, or spirit (ru′ach), to vitalize all the cells in Adam’s body.—Ge 2:7; compare Ps 104:30; Ac 17:25.
This life-force is passed on from parents to offspring through conception. Since Jehovah was the original Source of this life-force for man, and the Author of the procreation process, one’s life can properly be attributed to Him, though received not directly but indirectly through one’s parents.—Compare Job 10:9-12; Ps 139:13-16; Ec 11:5.
Life-force, or spirit, is impersonal. As noted, the Scriptures refer to the ru′ach, or life-force, as being not only in humans but also in animals. (Ge 6:17; 7:15, 22Ecclesiastes 3:18-22 shows that man dies in the same manner as the beasts, for “they all have but one spirit [weru′ach], so that there is no superiority of the man over the beast,” that is, as to the life-force common to both. This being so, it is clear that the “spirit,” or life-force (ru′ach), as used in this sense is impersonal. As an illustration, one might compare it to another invisible force, electricity, which may be used to make various types of machines operate—causing stoves to produce heat, fans to produce wind, computers to solve problems, television sets to produce figures, voices and other sounds—yet which electric current never takes on any of the characteristics of the machines in which it functions or is active.
Thus, Psalm 146:3, 4 says that when man’s “spirit [form of ru′ach] goes out, he goes back to his ground; in that day his thoughts do perish.” The spirit, or life-force, that was active in man’s body cells does not retain any of the characteristics of those cells, such as the brain cells and their part in the thinking process. If the spirit, or life-force (ru′ach; pneu′ma), were not impersonal, then it would mean that the children of certain Israelite women who were resurrected by the prophets Elijah and Elisha were actually in conscious existence somewhere in the period during which they were dead. So, too, with Lazarus, who was resurrected some four days after his death. (1Ki 17:17-23; 2Ki 4:32-37; Joh 11:38-44) If such had been the case, it is reasonable that they would have remembered such conscious existence during that period and upon being resurrected would have described it, told about it. There is nothing to indicate that any of them did so. Hence, the personality of the dead individual is not perpetuated in the life-force, or spirit, that stops functioning in the deceased person’s body cells.
Ecclesiastes 12:7 states that at death the person’s body returns to the dust, “and the spirit itself returns to the true God who gave it.” The person himself was never in heaven with God; what “returns” to God is therefore the vital force that enabled the person to live.
In view of the impersonal nature of the life-force, or spirit, found in man (as also in the animal creation), it is evident that David’s statement at Psalm 31:5, quoted by Jesus at the time of his death (Lu 23:46), “Into your hand I entrust my spirit,” meant that God was being called upon to guard, or care for, that one’s life-force. (Compare Ac 7:59.) That there be an actual and literal transmission of some force from this planet to the heavenly presence of God is not necessarily required. Even as the fragrant scent of animal sacrifices was spoken of as being ‘smelled’ by God (Ge 8:20, 21), whereas such scent undoubtedly remained within earth’s atmosphere, so, too, God could ‘gather in,’ or could accept as entrusted to him, the spirit or life-force in a figurative sense, that is, without any literal transmission of vital force from earth. (Job 34:14; Lu 23:46) A person’s entrusting his spirit evidently means, then, that he places his hope in God for a future restoration of such life-force to himself through a resurrection.—Compare Nu 16:22; 27:16; Job 12:10; Ps 104:29, 30.
Impelling Mental Inclination. Ru′ach and pneu′ma are both used to designate the force that causes a person to display a certain attitude, disposition, or emotion or to take a certain action or course. While that force within the person is itself invisible, it produces visible effects. This use of the Hebrew and Greek terms rendered “spirit” and basically related to breath or to air in motion is paralleled to a considerable degree by English expressions. Thus, we speak of a person as ‘putting on airs,’ or of manifesting an ‘air of calmness’ or of ‘having a bad spirit.’ We speak of ‘breaking a person’s spirit,’ in the sense of discouraging and disheartening him. As applying to a group of persons and the dominant force activating them, we may talk of ‘getting into the spirit of an occasion,’ or we may refer to the ‘mob spirit’ that infects them. Metaphorically we may refer to an ‘atmosphere of discontent’ or to ‘winds of change and revolution blowing through a nation.’ By all of these we refer to this invisible activating force working in persons, moving them to speak and act as they do.
Similarly, we read of Isaac and Rebekah’s “bitterness of spirit” resulting from Esau’s marriage to Hittite women (Ge 26:34, 35) and of the sadness of spirit that overwhelmed Ahab, robbing him of his appetite. (1Ki 21:5) A “spirit of jealousy” could move a man to view his wife with suspicion, even to bring charges against her of adultery.—Nu 5:14, 30.
The basic sense of a force that moves and gives “drive” or “thrust” to one’s actions and speech is also seen in the reference to Joshua as “a man in whom there is spirit” (Nu 27:18), and to Caleb as demonstrating “a different spirit” from that of the majority of the Israelites who had become demoralized by the bad report of ten spies. (Nu 14:24) Elijah was a man of much drive and force in his zealous service to God, and Elisha sought a two-part share in Elijah’s spirit as his successor. (2Ki 2:9, 15) John the Baptizer demonstrated the same vigorous drive and energetic zeal that Elijah had shown, and this resulted in John’s having a powerful effect on his listeners; hence he could be said to have gone forth “with Elijah’s spirit and power.” (Lu 1:17) By contrast, Solomon’s wealth and wisdom had such an overwhelming and breathtaking effect on the queen of Sheba that “there proved to be no more spirit in her.” (1Ki 10:4, 5) In this same fundamental sense one’s spirit may be “stirred up” or “roused” (1Ch 5:26; Ezr 1:1, 5; Hag 1:14; compare Ec 10:4), become “agitated” or “irritated” (Ge 41:8; Da 2:1, 3; Ac 17:16), be “calmed down” (Jg 8:3), be ‘distressed,’ be made to ‘faint’ (Job 7:11; Ps 142:2, 3; compare Joh 11:33; 13:21), be ‘revived’ or “refreshed” (Ge 45:27, 28; Isa 57:15, 16; 1Co 16:17, 18; 2Co 7:13; compare 2Co 2:13).
Heart and spirit. The heart is frequently tied in with the spirit, indicating a definite relationship. Since the figurative heart is shown to have the capacity for thinking and motivation, and to be intimately related with emotions and affection (see HEART), it undoubtedly has a major share in the development of the spirit (the dominant mental inclination) that one shows. Exodus 35:21 places heart and spirit in parallel in saying that “everyone whose heart impelled him, . . . everyone whose spirit incited him,” brought contributions for the tabernacle construction. Conversely, on learning of Jehovah’s powerful works on behalf of Israel, the Canaanites’ ‘hearts began to melt and no spirit arose among them,’ that is, there was no urge to initiate action against the Israelite forces. (Jos 2:11; 5:1; compare Eze 21:7.) References are also made to ‘pain of heart and breakdown of spirit’ (Isa 65:14) or similar expressions. (Compare Ps 34:18; 143:4, 7; Pr 15:13.) Evidently because of the powerful effect of the activating force on the mind, Paul admonishes: “You should be made new in the force actuating [form of pneu′ma] your mind, and should put on the new personality which was created according to God’s will in true righteousness and loyalty.”—Eph 4:23, 24.
The vital necessity to control one’s spirit is strongly emphasized. “As a city broken through, without a wall, is the man that has no restraint for his spirit.” (Pr 25:28) Under provocation a person may act as the stupid one who impatiently ‘lets all his spirit out,’ whereas the wise one “keeps it calm to the last.” (Pr 29:11; compare 14:29, 30.) Moses allowed himself to become unduly provoked when the Israelites “embittered his spirit” on one occasion, and he “began to speak rashly with his lips,” to his own loss. (Ps 106:32, 33) Thus, “he that is slow to anger is better than a mighty man, and he that is controlling his spirit than the one capturing a city.” (Pr 16:32) Humility is essential for this (Pr 16:18, 19; Ec 7:8, 9), and the one “humble in spirit will take hold of glory.” (Pr 29:23) Knowledge and discernment keep a man “cool of spirit,” in control of his tongue. (Pr 17:27; 15:4) Jehovah makes “an estimate of spirits” and judges those who fail to ‘guard themselves respecting their spirit.’—Pr 16:2; Mal 2:14-16.
Spirit shown by a body of persons. As an individual may show a certain spirit, so too a group or body of people may manifest a certain spirit, a dominant mental inclination. (Ga 6:18; 1Th 5:23) The Christian congregation was to be united in spirit, reflecting the spirit of their Head, Christ Jesus.—2Co 11:4; Php 1:27; compare 2Co 12:18; Php 2:19-21.
Paul refers to “the spirit of the world” in contrast with God’s spirit. (1Co 2:12) Under the control of God’s Adversary (1Jo 5:19), the world shows a spirit of catering to the desires of the fallen flesh, of selfishness, bringing enmity toward God. (Eph 2:1-3; Jas 4:5) Like unfaithful Israel, the world’s unclean motivation promotes fornication, either physical or spiritual, with idolatry.—Ho 4:12, 13; 5:4; Zec 13:2; compare 2Co 7:1.

On Peace :The Watchtower Society's Commentary.

PEACE:

Sha·lohmʹ, the Hebrew word rendered “peace,” refers to the state of being free from war or disturbance (Jg 4:17; 1Sa 7:14; 1Ki 4:24; 2Ch 15:5; Job 21:9; Ec 3:8); it can convey the idea of health, safety, soundness (Ge 37:14, ftn), welfare (Ge 41:16), friendship (Ps 41:9), and entirety or completeness (Jer 13:19). The Greek word for peace (ei·reʹne) has taken on the same broad connotations as the Hebrew word sha·lohmʹ and may express the ideas of well-being, salvation, and concord, in addition to the absence of conflict. It occurs in the farewell exclamation “go in peace,” which somewhat corresponds to the expression ‘may it go well with you.’—Mr 5:34; Lu 7:50; 8:48; Jas 2:16; compare 1Sa 1:17; 20:42; 25:35; 29:7; 2Sa 15:9; 2Ki 5:19.

Since “peace” is not always the exact equivalent for the original-language words, the context must be taken into consideration to determine what is meant. For example, to be ‘sent away in peace’ could signify being sent away amicably, with no fear of interference from the one granting permission to leave. (Ge 26:29; 44:17; Ex 4:18) To ‘return in peace,’ as from battle, meant returning unharmed or victoriously. (Ge 28:21; Jos 10:21; Jg 8:9; 11:31; 2Ch 18:26, 27; 19:1) ‘Asking concerning the peace’ of a person meant inquiring as to how he was getting along. (Ge 29:6, ftn; 43:27, ftn) ‘Working for the peace’ of someone denoted working for that one’s welfare. (De 23:6) For a person to die in peace could mean his dying a tranquil death after having enjoyed a full life or the realization of a cherished hope. (Compare Ge 15:15; Lu 2:29; 1Ki 2:6.) The prophecy concerning Josiah’s ‘being gathered to his own graveyard in peace’ indicated that he would die before the foretold calamity upon Jerusalem. (2Ki 22:20; 2Ch 34:28; compare 2Ki 20:19.) At Isaiah 57:1, 2 the righteous one is depicted as entering into peace at death, thereby escaping calamity.

Acquiring Peace. Jehovah is the God of peace (1Co 14:33; 2Co 13:11; 1Th 5:23; Heb 13:20) and the Source of peace (Nu 6:26; 1Ch 22:9; Ps 4:8; 29:11; 147:14; Isa 45:7; Ro 15:33; 16:20), it being a fruit of his spirit. (Ga 5:22) For this reason true peace can be had only by those who are at peace with God. Serious transgressions put a strain on a person’s relationship with God and cause the individual to be disturbed. The psalmist said: “There is no peace in my bones on account of my sin.” (Ps 38:3) Those who desire to seek and pursue peace must therefore “turn away from what is bad, and do what is good.” (Ps 34:14) Without righteousness, there can be no peace. (Ps 72:3; 85:10; Isa 32:17) That is why the wicked cannot have peace. (Isa 48:22; 57:21; compare Isa 59:2-8.) On the other hand, peace is the possession of those who are fully devoted to Jehovah, love his law (Ps 119:165), and heed his commandments.—Isa 48:18.

When Christ Jesus was on earth, neither the natural Jews nor the non-Jews were at peace with Jehovah God. Having transgressed God’s law, the Jews had come under the curse of the Law. (Ga 3:12, 13) As for the non-Jews outside God’s covenant, they “had no hope and were without God in the world.” (Eph 2:12) However, by means of Christ Jesus both peoples were given the opportunity to come into a peaceful relationship with God. Pointing forward to this was the angelic announcement made to shepherds at Jesus’ birth: “Upon earth peace among men of goodwill.”—Lu 2:14.

The peaceful message proclaimed by Jesus and his followers appealed to ‘friends of peace,’ that is, to persons desiring to be reconciled to God. (Mt 10:13; Lu 10:5, 6; Ac 10:36) At the same time this message caused divisions in households, as some accepted it while others rejected it. (Mt 10:34; Lu 12:51) The majority of the Jews rejected the message and thus failed to discern “the things having to do with peace,” evidently including repentance and acceptance of Jesus as the Messiah. (Compare Lu 1:79; 3:3-6; Joh 1:29-34.) Their failure resulted in the destruction of Jerusalem by the Roman armies in 70 C.E.—Lu 19:42-44.

However, even the Jews who did accept “the good news of peace” were sinners and needed to have their transgressions atoned for so as to enjoy peace with Jehovah God. Jesus’ death as a ransom sacrifice cared for this need. As had been foretold: “The chastisement meant for our peace was upon him, and because of his wounds there has been a healing for us.” (Isa 53:5) Jesus’ sacrificial death on the torture stake also provided the basis for canceling the Mosaic Law, which divided the Jews from the non-Jews. Therefore, upon becoming Christians, both peoples could be at peace with God and with one another. The apostle Paul wrote: “[Jesus] is our peace, he who made the two parties one and destroyed the wall in between that fenced them off. By means of his flesh he abolished the enmity, the Law of commandments consisting in decrees, that he might create the two peoples in union with himself into one new man and make peace; and that he might fully reconcile both peoples in one body to God through the torture stake, because he had killed off the enmity by means of himself. And he came and declared the good news of peace to you, the ones far off, and peace to those near, because through him we, both peoples, have the approach to the Father by one spirit.”—Eph 2:14-18; compare Ro 2:10, 11; Col 1:20-23.

“The peace of God,” that is the calmness and tranquillity that result from a Christian’s precious relationship with Jehovah God, guards his heart and mental powers from becoming anxious about his needs. He has the assurance that Jehovah God provides for his servants and answers their prayers. This puts his heart and mind at rest. (Php 4:6, 7) Similarly, the peace that Jesus Christ gave to his disciples, based on their faith in him as God’s Son, served to calm their hearts and minds. Although Jesus told them that the time was coming when he would no longer be with them personally, they had no reason to be concerned or to give way to fear. He was not leaving them without help but promised to send them the holy spirit.—Joh 14:26, 27; 16:33; compare Col 3:15.

The peace that Christians enjoyed was not to be taken for granted. They were to be “peaceable”; that is, they were to be peacemakers, going out of their way to establish and to maintain peace. (1Th 5:13) To preserve peace among themselves, they had to exercise care so as not to stumble fellow believers. (Ro 14:13-23) In the Sermon on the Mount, Jesus stated: “Happy are the peaceable [literally, peacemakers], since they will be called ‘sons of God.’” (Mt 5:9, ftn; compare Jas 3:18.) Christians were counseled to pursue peace and to do their utmost to be found at peace with God. (2Ti 2:22; Heb 12:14; 1Pe 3:11; 2Pe 3:14) Therefore, they had to fight against the desires of the flesh, as these would cause them to be at enmity with God. (Ro 8:6-8) The fact that remaining in a peaceful relationship with God was necessary for divine approval lends much weight to the oft-repeated prayerful expression ‘may you have peace.’—Ro 1:7; 1Co 1:3; 2Co 1:2; Ga 1:3; 6:16; Eph 1:2; 6:23; Php 1:2.

Christians also wanted others to enjoy peace. Therefore, “shod with the equipment of the good news of peace,” they carried on their spiritual warfare. (Eph 6:15) Even within the congregation they waged warfare in overturning reasonings that were out of harmony with the knowledge of God, so that these reasonings did not damage their relationship with God. (2Co 10:4, 5) However, it was not a verbal fight or quarrel, not even when correcting those who had deviated from the truth. With reference to handling cases of those who had departed from a right course, the apostle Paul counseled Timothy: “A slave of the Lord does not need to fight, but needs to be gentle toward all, qualified to teach, keeping himself restrained under evil, instructing with mildness those not favorably disposed; as perhaps God may give them repentance leading to an accurate knowledge of truth, and they may come back to their proper senses out from the snare of the Devil, seeing that they have been caught alive by him for the will of that one.”—2Ti 2:24-26.

Peaceful Rule. The Son of God, as the one to have ‘the princely rule upon his shoulder,’ is called the “Prince of Peace.” (Isa 9:6, 7) It is, therefore, noteworthy that Christ Jesus, while on earth, showed that his servants should not arm themselves for physical warfare, when saying to Peter: “Return your sword to its place, for all those who take the sword will perish by the sword.” (Mt 26:52) Figuratively speaking, those who became Christians “beat their swords into plowshares and their spears into pruning shears.” They learned war no more. (Isa 2:4) This and God’s past activities, especially in connection with Israel during Solomon’s reign, point to the peace that will prevail during Jesus’ rule as King. Regarding Solomon’s reign, the Bible reports: “Peace itself became his in every region of his, all around. And Judah and Israel continued to dwell in security, everyone under his own vine and under his own fig tree, from Dan to Beer-sheba, all the days of Solomon.” (1Ki 4:24, 25; 1Ch 22:9) As is evident from other scriptures (compare Ps 72:7, 8; Mic 4:4; Zec 9:9, 10; Mt 21:4, 5), this served as a pattern of what would take place under the rule of Christ Jesus, the One greater than Solomon, which name comes from a root meaning “peace.”—Mt 12:42.

Peace Between Man and Animals. Jehovah God promised to the Israelites, if obedient: “I will put peace in the land, and you will indeed lie down, with no one making you tremble; and I will make the injurious wild beast cease out of the land.” (Le 26:6) This meant that the wild animals would stay within the confines of their habitat and not bring harm to the Israelites and their domestic animals. On the other hand, if the Israelites proved to be disobedient, Jehovah would allow their land to be invaded and devastated by foreign armies. As this would result in reducing the population, wild animals would multiply, penetrate formerly inhabited areas, and do injury to the survivors and their domestic animals.—Compare Ex 23:29; Le 26:22; 2Ki 17:5, 6, 24-26.

The peace promised to the Israelites in connection with the wild animals differed from that enjoyed by the first man and woman in the garden of Eden, for Adam and Eve enjoyed full dominion over the animal creation. (Ge 1:28) By contrast, in prophecy, like dominion is attributed only to Christ Jesus. (Ps 8:4-8; Heb 2:5-9) Therefore, it is under the government of Jesus Christ, “a twig out of the stump of Jesse,” or God’s “servant David,” that peace will again prevail between men and the animals. (Isa 11:1, 6-9; 65:25; Eze 34:23-25) These last cited texts have a figurative application, for it is obvious that the peace between animals, such as the wolf and the lamb, there described did not find literal fulfillment in ancient Israel. It was thus foretold that persons of harmful, beastlike disposition would cease their vicious ways and live in peace with their more docile neighbors. However, the prophetic use of the animals figuratively to portray the peaceful conditions to prevail among God’s people implies that there will also be peace among literal animals under the rule of Christ Jesus, even as there evidently was in Eden.

Friday 5 May 2017

An Extrapolation revisited II

The Nylonase Story: How Unusual Is That?
Ann Gauger

Editor’s note: Nylon is a modern synthetic product used in the manufacturing, most familiarly, of ladies’ stockings but also a range of other goods, from rope to parachutes to auto tires. Nylonase is a popular evolutionary icon, brandished by theistic evolutionist Dennis Venema among others. In a series of three posts, of which this is the second, Discovery Institute biologist Ann Gauger takes a closer look.

In an article yesterday, The Nylonase Story: When Imagination and Facts Collide,” I described how some biologists claim that the enzyme nylonase demonstrates that it is easy to get new functional proteins. It has been proposed that nylonase is the result of a frameshift mutation that produced an entirely new coding sequence from an alternate reading frame. I showed why such a claim is false. Now I will explain what that means and something about the unusual properties of the nylB gene that caught molecular geneticist and evolutionary biologist Susumu Ohno’s attention.

What are alternate reading frames? To answer that question, I first need to provide some background information. I will begin by defining some terms I used in yesterday’s post. DNA is composed of two anti-parallel strands of nucleotides. The order of the nucleotides in each strand is what specifies the information the DNA carries. The two strands, called the sense and antisense strands, run in opposite directions. Even though their sequences are complementary, with A always paired with T, and C with G, each strand carries different potential information.

ATG GCA TGC ACC GGC ATT AG → sense
TAC CGT ACG TGG CCG TAA TC ← antisense

Before the information in DNA can be used, it must be copied into what we call messenger RNA. The sequence of one strand of DNA, usually the sense strand, is copied using the same base complementarity: G pairs with C, and A with U (U is used in place of T in RNA). We call that copying transcription. The message that has been transcribed from the DNA into that sequence of RNA is now ready to be translated into protein.


Notice the language of information shot throughout these processes. The names for these processes were given by men fully committed to a naturalistic worldview, men such as Francis Crick and Sydney Brenner. Indeed, they were materialists one and all. Yet they saw the parallels between these processes and the human manipulation of text (language) or code (another form of language). The genetic code is the framework that determines the relationship between groups of nucleotides (codons), and the amino acids they specify. The code specifies how to translate the messenger RNA that has been copied or transcribed from the DNA, so that it can be translated into a new language, the language of proteins. Below is an illustration of the standard genetic code (source here, used with permission):




Notice that the information in DNA is read in groups of three nucleotides (each group is called a codon), and each codon specifies a particular amino acid. Sometimes more than one codon can specify the same amino acid. For example in the top left corner, the table shows that UUU and UUC both specify the amino acid phenylalanine.

The nature of the code is such that it matters where the first codon begins — the first codon to be read establishes the codon groupings going forward. In the table above the “start” codon is AUG (it also specifies the amino acid methionine). The sequence of codons is “read” by a cellular machine called the ribosome, which starts reading the RNA message at AUG, and then proceeds three nucleotides at a time to translate the message into amino acids. In the sequence below, for example, the first codon to be read would be AUG and that codon determines the frame in which of all the other codons are read.

AUG GCA UGC ACC GGC AUU AGU

Now here’s where it gets interesting. Potentially, DNA can be grouped into different codons, or frames, depending on where the ribosome starts reading. See below for an illustration. For example, the sequence could potentially be read with the groupings shown in frame one (ATG GCA etc.) or frame two (TGG CAT etc., if a proper ATG exists somewhere upstream), leading ultimately to a different amino acid sequences for each. In fact there are six possible ways to group the DNA into codons — three frames on the sense strand going left to right (labeled 1-3), and three frames on the antisense strand (labeled 4-6), going right to left. Below I have laid out the six possible frames for the sequence we began with, but with the alternate frames staggered, and the alternate codons separated by spaces. Notice the sequence stays the same — the only thing that changes from frame to frame is how the nucleotides are grouped. It’s the same sequence, but it could be read and translated differently in each frame. This is because each codon specifies a particular amino acid. Thus, each frame results in a completely different string of amino acids.

frame 1  ATG GCA TGC ACC GGC ATT AG
frame 2   TGG CAT GCA CCG GCA TTA G
frame 3    GGC ATG CAC CGG CAT TAG

frame 4  TAC CGT ACG TGG CCG TAA TC
frame 5   ACC GTA CGT GGC CGT AAT C
frame 6    CCG TAC GTG GCC GTA ATC

The codons TAA, TAG, and TGA are stop codons — they specify where the gene ends and protein translation stops. (For extra credit, can you find any ATG or stop codons in the above frames? They are there in both the forward and reverse direction. For more extra credit, can you use the code table to translate different frames, and demonstrate that each frame encodes a different protein?)

So when Venema and others say that nylonase arose by a frameshift mutation that produced a novel protein 392 amino acids long, they are claiming that a completely new coding sequence with frame-shifted codons could generate a functional protein. How likely is that? Not very, given the rarity of functional proteins in sequence space (see my first post). And, as I have already shown in my first post, such an unlikely hypothesis is unnecessary. The nylB gene appears to be the product of a simple gene duplication followed by two stepwise mutations to increase nylonase activity.

There is something special about the nylonase gene’s sequence though, something very odd. nylB has multiple large, overlapping (alternate) open frames that lack stop codons.

How hard is it to get a gene with multiple reading frames?

Let me explain. Roughly one in twenty codons are stop codons. A random DNA sequence will have stop codons about every sixty bases, and may or may not have a start codon. Usually the alternate frames of DNA sequences are interrupted by stop codons. Only the frame that actually specifies the correct gene will have no stop codons at all over a significant length. This system is actually very ingenious. The one frame that needs to be read and translated is identified by an ATG. The other frames will usually lack an ATG and/or will have several stop codons that interrupt their translation, thus preventing the cell from wasting energy on nonsense transcripts.

According to the nylonase story, as told by Ohno and Venema and numerous others, a new ATG start codon was formed by the insertion of a T between an A and G, thus creating a new start codon after the original ATG, which shifted the reading frame for that sequence to that specified by the new ATG, and creating a completely different coding sequence and thus a new protein. Let us grant that scenario for the sake of argument. Normally such a shift would produce a new coding sequence that would be interrupted by stop codons, so the newly frameshifted protein would be truncated. Thus the only reason this frameshift hypothesis for nylonase is even remotely possible is because the sequence coding for nylonase is most unusual, and contains not one, not two, but three open frames Although frameshift mutations are ordinarily considered to be quite disruptive, at least in this case the putative brand new protein sequence would not terminate early due to stop codons.

My point? The first step to getting a new functional protein of any length from a frameshift is to avoid stop codons. The odds of a random coding sequence having an open alternate frame, without stops, are poor. As a consequence, if a protein does have an open frame in addition to its coding sequence, it’s worth paying attention to. And it so happens that nylonase does have more than one open frame. The DNA sequence above illustrates the six frames, numbering them frames 1 through 6. Using that convention, frames 1 and 3 are read from the sense strand. Both have no stop codons over the length of the gene in the sense direction. Frame 4 on the antisense direction has no stop codons either. Frame 1 is the coding frame that specifies the nylonase protein, otherwise known as the open reading frame (ORF). It is defined by the presence of both a start and stop codon. The other two frames have no start codons or stop codons, so I’ll call them non-stop frames (NSFs). They are frames 3 and 4.

The probability of a DNA sequence with an ORF on the sense strand and 2 NSFs is very small. Just exactly how small are the chances of avoiding a stop codon in three out of six frames? We set out to determine that by performing a numerical simulation using pseudorandom numbers to generate sequences at various levels of GC content. (By we I mean that my husband, Patrick Achey, who is an actuary, did the programming work, while I determined the parameters.) We chose to vary the GC content because sequences with a higher GC content have fewer stop codons. Remember, a stop codon always has an A and a T (TAA, TAG, and TGA are the stop codons) so having a sequence with a lower percentage of AT content will reduce the frequency of stop codons. Conversely, higher GC content makes the chances of avoiding stop codons and getting longer ORFs much greater, thus also increasing the chances of NSFs. The genomes of bacteria vary in their GC content, from less than 20 percent to as much as 75 percent, though the reason why is not known. One species of Flavobacterium has a genome with about 32 percent GC and 2400 genes — the precise values varies with the strain. The plasmid on which nylB resides is very different. It has 65 percent GC content. The gene encoding nylonase has an even higher 70 percent GC content, which is near the observed bacterial maximum of 75 percent.

We chose to use a target ORF size of 900 nucleotides (or 300 amino acids) because it is an average size for a functional protein. Nylonase is 392 amino acids long; the small domain of beta lactamase, the enzyme my colleague Doug Axe studied, is about 150 amino acids long. The median length for an E. coli protein is 278 amino acids; for humans, the median length is 375.

As expected, the simulation showed that the higher the GC content, the greater the likelihood that ORFs that are 900+ nucleotides long exist. At 50 percent GC, the average ORF length we obtained was about 60 nucleotides; most ORFs terminate well before 900 nucleotides. Indeed, in our simulation only two out of a million random sequences made it to 900 nucleotides before encountering a stop codon. As a result, we could not determine the rarity of NSFs at 50 percent GC — we would probably have to run the simulation for more than a billion trials to get any significant number of NSFs at all.

Sequences at 60 percent GC gave 57 ORFs at least 900 nucleotides long out of a million trials, while sequences at 65 percent GC produced 404 out of a million, one of which also had an NSF.

NSFs were much more probable for sequences that were 70 percent GC, like nylB. In our simulation 3,021 out of a million trials were ORFs at least 900 nucleotides long. That’s a frequency of .3 percent. Of those 3,021 ORFs, 86 had 1 NSF, and none had 2 NSFs. We had to run 10 million trials at 70 percent GC to see any ORFs with 2 NSFs. From those 10 million randomly generated sequences, we obtained 28,603 ORFs; 903 had 1 NSF and only 9 had 2 NSFs.

Interestingly, at 80 percent GC we got a few sequences with 4 NSFs; but I don’t know of any bacterium with a GC content that high.

Our simulation shows that multiple NSFs are very rare. The probability that an ORF 900 nucleotides long with 70 percent GC content will have two NSFs is 9 out of 28,603, or 0.0003. If these figures are recast to include the total number of trials required to get an ORF of that length and GC content and with 2 NSFs, the probability would be 9 out of 10,000,000 trials.

A sequence like nylB is very rare. In fact, I suspect that for all cases where overlapping genes exist, in other words where alternate frames from the same sequence have the potential to code for different proteins, unusual sequence will necessarily be found. Likely it will be high in GC content. Could such rare sequences be accidental? I think that if we compare the expected number of alternate or overlapping NSFs per ORF, with the actual number we will find that there are more of these alternate open reading frames than would be predicted by chance.

From another study of overlapping genes:

Thus, bacterial genomes contain a larger number of long shadow ORFs [ORFs on alternate frames] than expected based on statistical analysis. Random mutational drift would have eliminated the signal long ago, if no selection pressures were stabilizing shadow ORFs. Deviations between the statistical model and bacterial genomes directly call for a functional explanation, since selection is the only force known to stabilize the depletion of stop codons. Most shadow genes have escaped discovery, as they are dismissed as false positives in most genome annotation programs. This is in sharp contrast to many embedded overlapping genes that have been discovered in bacteriophages. Since phages reside in a long term evolutionary equilibrium with the bacterial host genome, we suggest that overlooked shadow genes also exist in bacterial genomes.
Indeed, a study of the pOAD2 plasmid from which nylB came indicates that there are potentially many overlapping genes on that plasmid. nylB′, for example, a homologous gene on the same plasmid that differs by 47 amino acids from nylB, also has 2 NSFs. These unusual and unexpected features of DNA have consequences for how we think about the origin of information in DNA sequences, as I shall discuss in the next post.

An extrapolation revisited.

The Nylonase Story: When Imagination and Facts Collide
Ann Gauger

Editor’s note: Nylon is a modern synthetic product used in the manufacturing, most familiarly, of ladies’ stockings but also a range of other goods, from rope to parachutes to auto tires. Nylonase is a popular evolutionary icon, brandished by theistic evolutionist Dennis Venema among others. In a series of three posts, Discovery Institute biologist Ann Gauger takes a closer look.

A significant problem for the neo-Darwinian story is the origin of new biological information. Clearly, information has increased over the course of life’s history — new life forms appeared, requiring new genes, proteins, and other functional information. The question is — how did it happen? This is the central question concerning the origin of living things.

Stephen Meyer and Douglas Axe have made this strong claim:

[T]he neo-Darwinian mechanism — with its reliance on a random mutational search to generate novel gene sequences — is not an adequate mechanism to produce the information necessary for even a single new protein fold, let alone a novel animal form, in available evolutionary deep time.
Their claim is based on the experimental finding  by Doug Axe that functional protein folds are exceedingly rare, on the order on 1 in 10 to the 77th power, meaning that all the creatures of the Earth searching for the age of the Earth by random mutation could not find even one medium-size protein fold.

In contrast, Dennis Venema, professor of biology at Trinity Western University, claims in his book Adam and the Genome and in posts at the BioLogos website that getting new information is not hard. In his book, he presents several examples he thinks demonstrate the appearance of new information — the apparent evolution of new protein binding sites, for example. But the best way to reveal Axe and Meyer’s folly, he thinks, (and says so in his book and  a post at BioLogos) would be to show that a genuinely “new” protein can evolve.

…[E]ven more convincing… would be an actual example of a functional protein coming into existence from scratch — catching a novel protein forming “in the act” as it were. We know of such an example — the formation of an enzyme that breaks down a man-made chemical.

In the 1970s, scientists made a surprising discovery: a bacterium that can digest nylon, a synthetic chemical not found in nature. These bacteria were living in the wastewater ponds of chemical factories, and they were able to use nylon as their only source of food. Nylon, however, was only about 40 years old at the time — how had these bacteria adapted to this novel chemical in their environment so quickly? Intrigued, the scientists investigated. What they discovered was that the bacteria had an enzyme (which they called “nylonase”) that effectively digested the chemical. This enzyme, interestingly, arose from scratch as an insertion mutation into the coding sequence of another gene. This insertion simultaneously formed a “stop” codon early in the original gene (a codon that tells the ribosome to stop adding amino acids to a protein) and formed a brand new “start” codon in a different reading frame. The new reading frame ran for 392 amino acids before the first “stop” codon, producing a large, novel protein. As in our example above, this new protein was based on different codons due to the frameshift. It was truly “de novo” — a new sequence.
Venema is right. If the nylonase enzyme did evolve from a frameshifted protein, it would genuinely be a demonstration that new proteins are easy to evolve. It would be proof positive that intelligent design advocates are wrong, that it’s not hard to get a new protein from random sequence. But the story bears reexamining. Is the new protein really the product of a frameshift, or did it pre-exist the introduction of nylon into the environment? What exactly do we know about this enzyme? Does the evidence substantiate the claims of Venema and others, or does it lead to other conclusions?

First, some history. In the 1970s Japanese scientists discovered that certain bacteria had developed the ability to degrade the synthetic polymer nylon. Okada et al. identified three enzymes responsible for nylon degradation, and named them EI, EII, and EIII. The genes that encoded them were named nylA, nylB, and nylC. They sequenced the plasmid on which the genes were found, and discovered that there was another gene on the same plasmid that was very similar to nylB; they named it nylB′. (We will focus on the story of nylB and nylB′ because they are the ones relevant to Venema’s story.)

So far all I have given you are the facts. Now here’s the interpretation of these facts. Some claimed that the nylonase enzyme, as it was called, had originated some time after people began making nylon (in the 1930s). That seemed plausible because nylonase was unable to degrade naturally occurring amide bonds — it could degrade only the amide bonds in nylon — and so had not existed previously, it was thought. The popular conclusion was that the nylonase activity evolved in response to the presence of nylon in the environment, and thus was only forty years old. And here’s the big interpretive leap: it must not be hard to get new enzymes if a new one can evolve within a period of forty years.

Okada et al. had sequenced the genes encoding nylB and nylB′. They concluded that the nylonase activity was the result of a gene duplication followed by several mutations to the nylB gene. But at this point Susumu Ohno, an eminent molecular geneticist and evolutionary biologist, noticed something unusual about the nylB gene sequence (Ohno, 1984). Ohno had a theory that DNA with repeats of the right kind had the potential to code for protein in multiple frames, with no interrupting stop codons, and might thus be a source for “new” proteins. (If you are unfamiliar with the terms I just used, I invite you to take a look at my post tomorrow, where I will explain the necessary concepts. For those already familiar, I present some relevant data concerning the rarity of sequences that can be frameshifted.)

Ohno noticed that nylB, the gene for nylonase, might originally have encoded something else if a certain T was removed. The nylonase gene as it exists now has 1179 bases, which encode a 392 amino acid protein. Without a particular T embedded in the ATG start codon, though, the sequence would have specified a hypothetical original gene with a longer open reading frame (ORF) of 427 amino acids, in a different frame. Thus, Ohno proposed a “new” protein with a new function acting on a new substrate was born when a T inserted in between a particular A and G in the DNA, making a new ATG start codon and shifting the frame to code for a new protein, the protein we now call nylonase.

Ingenious. According to Ohno, nylonase could be a new enzyme, appearing suddenly with no known precursors via a sudden frameshift. (Note that all of this assumes that new protein folds are easy to get.) Ohno published this hypothesis in the Proceedings of the National Academy of Sciences. It was a hypothesis only, however, as a careful reading of his paper shows. One heading, for example:

R-IIA Coding Sequence [nylB] for 6-AHA LOH [nylonase] Embodies an Alternative, Longer Open Reading Frame That Might Have Been the Original Coding Sequence [Emphasis added.]
and the text says:

I suggest that the RS-IIA base sequence [nylB] was originally a coding sequence for an arginine-rich polypeptide chain 427 or so residues long in its length and that the coding sequence for one of the two isozymic forms of 6-ALA LOH [nylonase] arose from its alternative open reading frame. [Emphasis added.]
Ohno presented arguments for why his suggestion was plausible, but did not provide evidence that the “original” gene ever existed or was used (in fact he says it was unlikely to be useful based on its amino acid composition), or that the insertion ever happened. Nonetheless, the frame-shift hypothesis for the origin of nylonase has been widely proclaimed as fact (though, notably, not by Okada et al. who have done most of the work).

If the nylonase story as told above were true, namely that a frameshift mutation resulted in the de novo generation of a new protein fold with a new function, it would indeed constitute a substantial refutation to Meyer and Axe’s claim. If a frame-shift mutation can produce a random new open reading frame in real, observable time, and give rise to a new functional enzyme, then it must not be that hard to make new functional protein folds. In other words, functional protein folds must not be rare in sequence space. And therefore Stephen Meyer’s arguments about the difficulty of getting enough new biological information to generate a new fold must be wrong as well. Venema flatly asserts:

If de novo protein-coding genes such as nylonase can come into being from scratch, as it were, then it is demonstrably the case that new protein folds can be formed by evolutionary mechanisms without difficulty….[I]f Meyer had understood de novo gene formation — as we have seen, he mistakenly thought it was an unexplained process — he would have known that new protein folds could indeed be easily developed by evolutionary processes.
Slam dunk, right?

A little caution in accepting this story without hard evidence would be wise. In genetics we are taught that frame-shift mutations are extremely disruptive, completely changing the coding sequence and resulting in truncated nonsense. In fact, one term for a frameshift mutation is “nonsense mutation.” A biologist’s basic intuition should be that frameshifts are highly unlikely to produce something useful. The only reasons for the widespread acceptance of Ohno’s hypothesis that I can come up with are the unusual character of the sequence itself, Ohno reputation as a brilliant scientist (which he was), and wish-fulfillment on the part of some evolutionary biologists.

Fortunately, science marches on, and evidence continues to accumulate. The same group of Japanese scientists continued their study of the nylonase genes. nylB appeared to be the result of a gene duplication of nylB′ that occurred some time ago. EII′ (the enzyme encoded by nylB′) had very little nylonase activity, while EII (the enzyme encoded by nylB) was about 1000 fold higher in activity. The two enzymes differed in amino acid sequence at 47 positions out of 392. With some painstaking work, the Japanese determined that just two mutations were sufficient to convert EII′ to the EII level of activity.

They then obtained the three-dimensional structure of an EII-EII′ hybrid protein. And with those results everything changed — or should have.

Here’s what Venema takes from the paper and interprets the evidence:

…the three-dimensional structure of the protein has been solved using X-ray crystallography, a method that gives us the precise shape of the protein at high resolution. Nylonase is chock full of protein folds— exactly the sort of folds Meyer claims must be the result of design because evolution could not have produced them even with all the time since the origin of life. [Emphasis added.]
Unfortunately, Venema doesn’t have the story straight. Nylonase has a particular fold, a particular three-dimensional, stable shape. Most proteins have a distinct fold — there are several thousand kinds of folds known so far, each with a distinct topology and structure. Folds are typically made up of small secondary structures called alpha helices and beta strands, which help to assemble the tertiary structure — the fold as a whole. Venema seems unclear about what a protein fold is, and the distinction between secondary and tertiary structures. Nylonase is not “chock full of folds.” No structural biologist would describe nylonase as “chock full of protein folds.” Indeed, no protein is “chock full of folds.” Perhaps Venema was referring to the smaller units of secondary structure I mentioned above, the alpha helices or beta strands. But it would appear he doesn’t know what a protein fold is.

Maybe that explains why Venema missed the essential point of the paper describing nylonase’s structure. The crystal structure of EII-EII’ (a nylonase hybrid necessary to be able to crystalize the protein) revealed that it is not a new kind of fold, but a member of the beta-lactamase fold family. More specifically, it resembles carboxylesterases, a subgrouping of that family. In addition, when the scientists checked EII′ and EII, they found that both enzymes had previously undetected carboxylesterase activity. In other words, the EII’ and EII enzymes were carboxylesterases. If it looks like a duck and quacks like a duck, it is a duck.

Thus, EII′ and EII did not have frameshifted new folds. They had pre-existing folds with activity characteristic of their fold type. There was no brand-new protein. No novel protein fold had emerged. And no frameshift mutation was required to produce nylonase.

Where did the nylon-eating ability come from? Carboxylesterases are enzymes with broad substrate specificities; they can carry out a variety of reactions. Their binding pocket is large and can accommodate a lot of different substrates. They are “promiscuous” enzymes, in other words. Furthermore, the carboxylesterase reaction hydrolyzes a chemical bond similar to the one hydrolyzed by nylonase. Tests revealed that both the EII and EII′ enzymes have carboxylesterase and nylonase activity. They can hydrolyze both substrates. In fact it is possible both had carboxylesterase activity and a low level of nylonase activity from the beginning, even before the appearance of nylon.

nylB′ may be the original gene from which nylB came. Apparently there was a gene duplication at some point in the past. The two genes appear to have acquired mutations since then — they differ by 47 amino acids out of 392. The time of that duplication is unknown, but not recent, because it takes time to accumulate that many mutations. However, at least some of those mutations must confer a high level of nylonase activity on EII, the enzyme made by nylB. The enzyme EII’ made by nylB’ has only a low ability to degrade nylon, while EII degrades nylon 1000 fold better. So one or more of those 47 amino acid differences must be the cause of the high level of nylonase activity in EII. Through careful work, the Japanese workers Kato et al. identified which amino acid changes were responsible for the increased nylonase activity. Just two step-wise mutations present in EII, when introduced into EII’, could convert the weak enzyme EII’ to full nylonase activity.

From Kato et al. (1991):

Our studies demonstrated that among the 47 amino acids altered between the EII and EII’ proteins, a single amino acid substitution at position 181 was essential for the activity of 6-aminohexanoate-dimer hydrolase [nylonase] and substitution at position 266 enhanced the effect.
So. This is not the story of a highly improbable frame-shift producing a new functional enzyme. This is the story of a pre-existing enzyme with a low level of promiscuous nylonase activity, which improved its activity toward nylon by first one, then another selectable mutation. In other words this is a completely plausible case of gene duplication, mutation, and selection operating on a pre-existing enzyme to improve a pre-existing low-level activity, exactly the kind of event that Meyer and Axe specifically acknowledge as a possibility, given the time and probabilistic resources available. Indeed, the origin of nylonase actually provides a nice example of the optimization of a pre-existing fold’s function, not the innovation or creation of a novel fold.

As the scientists who carried out the structural determination for nylonase themselves note:

Here, we propose that amino acid replacements in the catalytic cleft of a preexisting esterase with the beta-lactamase fold resulted in the evolution of the nylon oligomer hydrolase. [Emphasis added.]
Let’s put to bed the fable that the nylon oligomer hydrolase EII, colloquially known as nylonase, arose by a frame-shift mutation, leading to the creation of a new functional protein fold. There is absolutely no need to postulate such a highly improbable event, and no justification for making this extravagant claim. Instead, there is a much more parsimonious explanation — that nylonase arose by a gene duplication event some time in the past, followed by a series of two mutations occurring after the introduction of nylon into the environment, which increased the nylon oligomer hydrolase activity of the nylB gene product to current levels. Could this series of events happen in forty years? Most certainly. Probably in much less time. In fact, it has been reported to happen in the lab under the right selective conditions. And most definitely, the evolution of nylonase does not call for the creation of a novel protein fold, nor did one arise. EII’s fold is part of the carboxylesterase fold family. Carboxylesterases serve many functions and have been around much longer than forty years.


Douglas Axe and Stephen Meyer readily admit that this kind of evolutionary adaptation happens easily. A protein that already has a low level of activity for a particular substrate can be mutated to favor that side reaction over its original one, often in just a few steps. There are many cases of this in the literature. What Axe and Meyer do claim is that generating an entirely new protein fold via mutation and selection is implausible in the extreme. Nothing in the nylonase story that Dennis Venema tells shows otherwise.

Why attempting to design the undesignable remains a fools errand.

Why Evolution Simulations Fail: Author of Evolutionary Informatics Book Explains
Evolution News @DiscoveryCSC

f you search for the phrase “evolution simulation” in Google, you’ll get many hits. Come to think of it, computer evolution simulations are an evolutionary icon. What of them? Do they falsify the claims of intelligent design theory?On a new episode of ID the Future, Ray Bohlin takes up the issue with Dr. Winston Ewert, co-author with William Dembski and Robert Marks II of a new book,  An Introduction to Evolutionary Informatics.

Ewert argues that Richard Dawkins’s “Methinks It Is Like a Weasel” simulation doesn’t prove biological evolution and isn’t even very interesting. Ewert says there are some interesting computer evolution simulations, but he explains that they fail to model anything biologically realistic.

Instead they set up a straw man version of intelligent design, and simultaneously sneak teleology in, which kind of defeats the purpose.  Download the podcast here, or listen to it here .

Dr. Ewert’s book is getting raves from some impressive scientists, including star mathematician Gregory Chaitin, author of Proving Darwin: Making Biology Mathematical. He calls the book, “An honest attempt to discuss what few people seem to realize is an important problem.”

Speaking of Chaitin, says Dr. Bijan Nemati of the Jet Propulsion Laboratory and Caltech:

With penetrating brilliance, and with a masterful exercise of pedagogy and wit, the authors take on Chaitin’s challenge, that Darwin’s theory should be subjectable to a mathematical assessment and either pass or fail. Surveying over seven decades of development in algorithmics and information theory, they make a compelling case that it fails.
Congratulations, Dr. Ewert, Dr. Marks, and Dr. Dembski! Get your copy now.

Wednesday 3 May 2017

Wanted:a theory of devolution.

Crime and Punishment, and Darwin's Theory


Species passed into history seven years ago. In the years that followed 1859, the impact of evolutionary thinking seeped across the culture of Europe and America. For years to come, we'll be tracing a series of century-and-a-half anniversaries of the effects of that seepage, and reflections on it as it was happening. This year, among other things, it's the publication of Dostoyevsky's Crime and Punishment (1866). 
In The New Criterion, Gary Saul Morson writes on "The disease of theory: 'Crime & Punishment' at 150." By "disease of theory" he means something recognizable from our contemporary culture:
The decade after [Tsar Alexander II] ascended the throne witnessed the birth of the "intelligentsia," a word we get from Russian, where it meant not well-educated people but a group sharing a set of radical beliefs, including atheism, materialism, revolutionism, and some form of socialismIntelligents (members of the intelligentsia) were expected to identify not as members of a profession or social class but with each other. They expressed disdain for everyday virtues and placed their faith entirely in one or another theory. Lenin, Trotsky, and Stalin were typical intelligents....
The intelligentsia prided itself on ideas discrediting all traditional morality. Utilitarianism suggested that people do, and should do, nothing but maximize pleasure. Darwin's Origin of Species, which took Russia by storm, seemed to reduce people to biological specimens. In 1862 the Russian neurologist Ivan Sechenov published his Reflexes of the Brain, which argued that all so-called free choice is merely "reflex movements in the strict sense of the word." And it was common to quote the physiologist Jacob Moleschott's remark that the mind secretes thought the way the liver secretes bile. These ideas all seemed to converge on revolutionary violence.
The hero of Crime and Punishment, Rodion Raskolnikov, discusses disturbances then in progress, including the radicals' revolutionary proclamations and a series of fires they may have set. But by nature he is no bloodthirsty killer. Quite the contrary, he has an immensely soft heart and is tortured by the sight of human suffering, which he cannot and refuses to get used to. "Man gets used to everything, the scoundrel!" he mutters, but then immediately embraces the opposite position: "And what if I'm wrong . . . what if man is not really a scoundrel . . . then all the rest is prejudice, simply artificial terrors and there are no barriers and it's all as it should be."...He means that man cannot be a "scoundrel" because that is a moral category, and morality is simply "artificial terrors" imposed by religion and sheer "prejudice." There is only nature, and nature has causes, not moral purposes. It follows that all is as it should be because if moral concepts are illusions then things just are what they are. [Emphasis added.]
More:
The questions this masterpiece poses still haunt us, perhaps even more than when it first appeared. Revolution still attracts. "New atheists" and stale materialists advance arguments that were crude a hundred fifty years ago. Social scientists describe human decisions in absurdly simplistic terms. Our intelligentsia entertains theory after theory elevating them above the ordinary people they would control. Morality is explained away neurologically, sociobiologically, or as mere social convention.
My goodness, since Dostoyevsky documented the toxin of "theories," how little has changed. 
Except that 150 years ago there were still abundant great men in defense of the view opposite to materialism, while our own contemporaries, even the ones with their heart in the right place, seem increasingly diminutive in stature. The difference made in just a couple of decades -- a mere generation, the passage from father to son -- is remarkable. Unthinking surrender to the most prestigious theories, or evading serious confrontation with them, is now the order of the day. What we need is a theory not of evolution but of devolution.