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Saturday 2 January 2016

File under "well said" XVIII

Every gun that is made, every warship launched, every rocket fired, signifies in the final sense a theft from those who hunger and are not fed, those who are cold and are not clothed.

Dwight D. Eisenhower


Denying the oasis on account of the desert?

Two quick questions for Professor Coyne
January 1, 2016 Posted by vjtorley under Intelligent Design  

Over at Why Evolution Is True, Professor Jerry Coyne is gleefully celebrating the impending demise of the Discovery Institute and of Intelligent Design. But before he pops the champagne, I wonder if he would care to answer two questions I’d like to ask him, in relation to some remarks he made on Casey Luskin’s recent announcement that he would be leaving Discovery Institute to further his studies.

1. Professor Coyne, you wrote that “the early claim that ENCODE showed that 80% of our genome had a function was incorrect, and there remains a huge portion of the human genome that’s nonfunctional,” and you added: “And even if 80% of the human genome were functional, how does that prove the existence of an intelligent designer? What about the other 20%? Did the Great Designer screw up there?”

Before I pose my question, I’m going to make a concession right up-front that will raise a few eyebrows: after reviewing the arguments, I’m inclined to believe that the critics of ENCODE’s bold claim were mostly right, and that the proportion of our genome which is functional is probably between 10 and 20%. (And as you correctly point out, Professor, even ENCODE has now backtracked from its claim.)


I’d now like to draw your attention to a WEIT post titled, DNA: optimised source code?, written by Professor Matthew Cobb, who is a regular contributor to your Website. (I commented on the post here.) The post discussed the following cartoon from xkcd.



Professor Cobb argued that since at least 85% our genome is junk, our DNA should be viewed as the mindless product of a series of historical accidents. But then he made a startling admission (the first bold emphasis is mine – VJT):

On a final note, in some cases, within this amazing noise, there are also astonishing examples of complexity which do indeed appear to be the result of optimisation – and they would boggle the mind of anyone, not just a cocky computer scientist in a hat. In Drosophila there is a gene called Dscam, which is involved in neuronal development and has four clusters of exons (bits of the gene that are expressed – hence exon – in contrast to the apparently inert introns).

Each of these exons can be read by the cell in twelve, forty-eight, thirty-three or two alternative ways. As a result, the single stretch of DNA that we call Dscam can encode 38,016 different proteins. (For the moment, this is the record number of alternative proteins produced by a single gene. I suspect there are many even more extreme examples.)

Evidently Professor Cobb agrees with agnostic Bill Gates, who wrote twenty years ago: “Human DNA is like a computer program but far, far more advanced than any software ever created.” (The Road Ahead, Penguin: London, Revised Edition, 1996, p. 228.)

So my first question is: if (i) Nature contains systems which accomplish a feat (namely, coding for complex structures) in a manner which is far better than what our best computer scientists can do, and (ii) despite diligent searching, scientists have failed to observe any cases in Nature of unguided processes generating a new code from scratch, then why isn’t it reasonable to infer (at least provisionally) that these systems were designed by a super-human Intelligence? You tell me, Professor.

Regarding your remarks on junk DNA, I’d also like to draw your attention to something I wrote on my post in response to Professor Cobb:

Even if Professor Cobb is right about junk DNA – and I’m inclined to think he is (for reasons I’ll discuss in another post) – that’s beside the point. At most, it shows is that DNA which doesn’t code for anything wasn’t designed. But my question is: what about the DNA which does code for proteins, and which does so in a manner that boggles the ingenuity of our brightest minds? Professor Cobb, it seems, is missing the wood for the trees here.

Junk DNA might be described as degenerate code – but there has to be a code in the first place, before it can degenerate. The existence of junk DNA cannot be used as an argument against design: all it establishes is that the designer of our DNA – whether out of benign neglect, laziness, illness, or ignorance that something has gone amiss – doesn’t always fix the code he created, when it becomes corrupted. Accordingly, junk DNA cannot be used as a legitimate argument against the proposition that the DNA in our cells which codes for genes was designed.

My second question, Professor Coyne, relates to your remarks on epigenetics, which Casey Luskin cited in his latest post as his “Exhibit B” of a prediction made by Intelligent Design that had been fulfilled:

Exhibit B: The burgeoning field of epigenetics has also validated ID’s prediction of new layers of information, code, and complex regulatory mechanisms in life. We’ve seen discoveries of new DNA codes (e.g., multiple meanings for synonymous codons), as well as the histone code, the RNA splicing code, the sugar code, and others. It’s a great time to be an ID proponent!

In response, you wrote:

Umm. . . the “new layer of information” that ID predicted was DIVINE information, not epigenetics. And the part of epigenetics that does add “information” — the epigenetic modifications of DNA already encoded in the genome — have been known for a long time. As for those “Lamarckian” modifications induced by the environment, well, that “information” is erased after a couple of generations, and so has no evolutionary import.

May I point out for the record that epigenetics can be defined as “the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself,” and that the use of the term “epigenetic” to describe processes that are not heritable is highly controversial. But let that pass.

I’d now like to draw your attention to a passage from Dr. Stephen Meyer’s book, Darwin’s Doubt (HarperOne, New York, 2013), concerning the role of epigenetic information in embryonic body-plan formation:

These different sources of epigenetic information in embryonic cells pose an enormous challenge to the sufficiency of the neo-Darwinian mechanism. According to neo-Darwinism, new information, form, and structure arise from natural selection acting on random mutations arising at a very low level within the biological hierarchy — within the genetic text. Yet both body-plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn’t wholly responsible for the way an embryo develops — for body-plan morphogenesis — then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand.

Even in a best-case scenario — one that ignores the immense improbability of generating new genes by mutation and selection — mutations in DNA sequence would merely produce new genetic information. But building a new body plan requires more than just genetic information. It requires both genetic and epigenetic information — information by definition that is not stored in DNA and thus cannot be generated by mutations to the DNA. It follows that the mechanism of natural selection acting on random mutations in DNA cannot by itself generate novel body plans, such as those that first arose in the Cambrian explosion. (pp. 281-282.)

So my second question for you is: will you concede that neo-Darwinism is unable to account for the origin of the epigenetic information needed to create novel body-plans (which must have occurred before the Cambrian explosion took place), and that natural selection therefore doesn’t explain all cases of apparent design in nature, falsifying your previous claim that it’s the “only game in town” for producing adaptations?

Incidentally, are you aware of any good evidence that epigenetic information is not divine in origin? If so, please elaborate.

The Watchtower Society's commentary on "Love"

LOVE:

A feeling of warm personal attachment or deep affection, as for a friend, for a parent or child, and so forth; warm fondness or liking for another; also, the benevolent affection of God for his creatures or the reverent affection due from them to God; also, the kindly affection properly expressed by God’s creatures toward one another; that strong or passionate affection for a person of the opposite sex that constitutes the emotional incentive to conjugal union. One of the synonyms for love is “devotion.”

Aside from those meanings, the Scriptures speak also of love guided by principle, as love of righteousness or even love for one’s enemies, for whom a person may not have affection. This facet or expression of love is an unselfish devotion to righteousness and a sincere concern for the lasting welfare of others, along with an active expression of this for their good.

The verb ʼa·hevʹ or ʼa·havʹ (“love”) and the noun ʼa·havahʹ (“love”) are the words primarily used in Hebrew to denote love in the foregoing senses, the context determining the sense and degree meant.

The Christian Greek Scriptures mainly employ forms of the words a·gaʹpe, phi·liʹa, and two words drawn from stor·geʹ (eʹros, love between the sexes, not being used). A·gaʹpe appears more frequently than the other terms.

Of the noun a·gaʹpe and the verb a·ga·paʹo, Vine’s Expository Dictionary of Old and New Testament Words says: “Love can be known only from the actions it prompts. God’s love is seen in the gift of His Son, I John 4:9, 10. But obviously this is not the love of complacency, or affection, that is, it was not drawn out by any excellency in its objects, Rom. 5:8. It was an exercise of the Divine will in deliberate choice, made without assignable cause save that which lies in the nature of God Himself, cp. Deut. 7:7, 8.”—1981, Vol. 3, p. 21.

Regarding the verb phi·leʹo, Vine comments: “[It] is to be distinguished from agapao in this, that phileo more nearly represents tender affection. . . . Again, to love (phileo) life, from an undue desire to preserve it, forgetful of the real object of living, meets with the Lord’s reproof, John 12:25. On the contrary, to love life (agapao) as used in I Pet. 3:10, is to consult the true interests of living. Here the word phileo would be quite inappropriate.”—Vol. 3, pp. 21, 22.

James Strong’s Exhaustive Concordance of the Bible, in its Greek dictionary (1890, pp. 75, 76), remarks under phi·leʹo: “To be a friend to (fond of [an individual or an object]), i.e. have affection for (denoting personal attachment, as a matter of sentiment or feeling; while [a·ga·paʹo] is wider, embracing espec. the judgment and the deliberate assent of the will as a matter of principle, duty and propriety . . . ).”—See AFFECTION.

A·gaʹpe, therefore, carries the meaning of love guided, or governed, by principle. It may or may not include affection and fondness. That a·gaʹpe may include affection and warmth is evident in many passages. At John 3:35, Jesus said: “The Father loves [a·ga·paiʹ] the Son.” At John 5:20, he said: “The Father has affection for [phi·leiʹ] the Son.” Certainly God’s love for Jesus Christ is coupled with much affection. Also Jesus explained: “He that loves [a·ga·ponʹ] me will be loved [a·ga·pe·theʹse·tai] by my Father, and I will love [a·ga·peʹso] him.” (Joh 14:21) This love of the Father and of the Son is accompanied by tender affection for such loving persons. Jehovah’s worshipers must love him and his Son, as well as one another, in the same way.—Joh 21:15-17.

So, although distinguished by respect for principle, a·gaʹpe is not unfeeling; otherwise it would not differ from cold justice. But it is not ruled by feeling or sentiment; it never ignores principle. Christians rightly show a·gaʹpe toward others for whom they may feel no affection or fondness, doing so for the welfare of those persons. (Ga 6:10) Yet, though not feeling affection, they do feel compassion and sincere concern for such fellow humans, to the limits and in the way that righteous principles allow and direct.

However, while a·gaʹpe refers to love governed by principle, there are good and bad principles. A wrong kind of a·gaʹpe could be expressed, guided by bad principles. For example, Jesus said: “If you love [a·ga·paʹte] those loving you, of what credit is it to you? For even the sinners love those loving them. And if you do good to those doing good to you, really of what credit is it to you? Even the sinners do the same. Also, if you lend without interest to those from whom you hope to receive, of what credit is it to you? Even sinners lend without interest to sinners that they may get back as much.” (Lu 6:32-34) The principle upon which such ones operate is: ‘Do good to me and I will do good to you.’

The apostle Paul said of one who had worked alongside him: “Demas has forsaken me because he loved [a·ga·peʹsas] the present system of things.” (2Ti 4:10) Demas apparently loved the world on the principle that love of it will bring material benefits. Jesus says: “Men have loved [e·gaʹpe·san] the darkness rather than the light, for their works were wicked. For he that practices vile things hates the light and does not come to the light, in order that his works may not be reproved.” (Joh 3:19, 20) Because it is a truth or principle that darkness helps cover their wicked deeds, they love it.

Jesus commanded: “Love [a·ga·paʹte] your enemies.” (Mt 5:44) God himself established the principle, as the apostle Paul states: “God recommends his own love [a·gaʹpen] to us in that, while we were yet sinners, Christ died for us. . . . For if, when we were enemies, we became reconciled to God through the death of his Son, much more, now that we have become reconciled, we shall be saved by his life.” (Ro 5:8-10) An outstanding instance of such love is God’s dealing with Saul of Tarsus, who became the apostle Paul. (Ac 9:1-16; 1Ti 1:15) Loving our enemies, therefore, should be governed by the principle established by God and should be exercised in obedience to his commandments, whether or not such love is accompanied by any warmth or affection.

God. The apostle John writes: “God is love.” (1Jo 4:8) He is the very personification of love, which is his dominant quality. The converse is not true, however, that ‘love (the abstract quality) is God.’ He reveals himself in the Bible as a Person and figuratively speaks of his “eyes,” “hands,” “heart,” “soul,” and so forth. He also has other attributes, among them justice, power, and wisdom. (De 32:4; Job 36:22; Re 7:12) Moreover, he has the capacity to hate, a quality the very opposite of love. His love of righteousness requires his hatred of wickedness. (De 12:31; Pr 6:16) Love includes the feeling and expression of warm personal affection, which only a person can have, or which can be extended toward a person. Certainly God’s Son Jesus Christ is not an abstract quality; he spoke of being with his Father, working with him, pleasing him, and hearing him, as well as of angels beholding the face of his Father, things impossible with a mere abstract quality.—Mt 10:32; 18:10; Joh 5:17; 6:46; 8:28, 29, 40; 17:5.

Evidence of his love. The evidence that Jehovah the Creator and God of the universe is love is abundant. This can be seen in the physical creation itself. With what remarkable care it has been made for the health, pleasure, and welfare of man! Man is made not just to exist but to enjoy eating, to delight in viewing the color and beauty of creation, to enjoy animals as well as the company of his fellowmen, and to find pleasure in the countless other delights of living. (Ps 139:14, 17, 18) But Jehovah has displayed his love even more by making man in his image and likeness (Ge 1:26, 27), with the capacity for love and for spirituality, and by revealing himself to man through his Word and his holy spirit.—1Co 2:12, 13.

Jehovah’s love toward mankind is that of a Father toward his children. (Mt 5:45) He spares nothing that is for their good, no matter what it costs him; his love transcends anything that we can feel or express. (Eph 2:4-7; Isa 55:8; Ro 11:33) His greatest manifestation of love, the most loving thing that a parent can do, he did for mankind. That was the giving of the life of his own faithful, only-begotten Son. (Joh 3:16) As the apostle John writes: “As for us, we love, because he first loved us.” (1Jo 4:19) He is, accordingly, the Source of love. John’s fellow apostle, Paul, writes: “For hardly will anyone die for a righteous man; indeed, for the good man, perhaps, someone even dares to die. But God recommends his own love to us in that, while we were yet sinners, Christ died for us.”—Ro 5:7, 8; 1Jo 4:10.

God’s everlasting love. Jehovah’s love for his faithful servants is everlasting; it does not fail or diminish, no matter in what circumstances, high or low, his servants may be, or what things, great or small, may come against them. The apostle Paul exclaimed: “For I am convinced that neither death nor life nor angels nor governments nor things now here nor things to come nor powers nor height nor depth nor any other creation will be able to separate us from God’s love that is in Christ Jesus our Lord.”—Ro 8:38, 39.

God’s sovereignty based on love. Jehovah glories in the fact that his sovereignty and the support of it by his creatures is based primarily on love. He desires only those who love his sovereignty because of his fine qualities and because it is righteous, who prefer his sovereignty to any other. (1Co 2:9) They choose to serve under his sovereignty rather than try to be independent—this because of their knowledge of him and of his love, justice, and wisdom, which they realize far surpasses their own. (Ps 84:10, 11) The Devil failed in this respect, egotistically seeking independence for himself, as did Adam and Eve. In fact, the Devil challenged God’s way of ruling, saying, in effect, that it was unloving, unrighteous (Ge 3:1-5), and that God’s creatures served Him not because of love, but through selfishness.—Job 1:8-12; 2:3-5.

Jehovah God allowed the Devil to live and to put his servants, even his only-begotten Son, to the test, to the point of death. God foretold the faithfulness of Jesus Christ. (Isa 53) How could he do this, staking his word on his Son? Because of love. Jehovah knew his Son and knew the love his Son had for Him and for righteousness. (Heb 1:9) He knew his Son most intimately and thoroughly. (Mt 11:27) He had full trust and confidence in the Son’s faithfulness. More than that, “love . . . is a perfect bond of union.” (Col 3:14) It is the most powerful bond in the universe, perfect love bonding the Son and the Father together unbreakably. For like reasons, God could trust his organization of servants, knowing that love would hold most of them immovably to him under test and that his organization of creatures would never secede in toto.—Ps 110:3.

Jesus Christ. Because for untold ages Jesus associated most closely with his Father, the Source of love, and knew Him most intimately and thoroughly, he could say: “He that has seen me has seen the Father also.” (Joh 14:9; Mt 11:27) Therefore Jesus’ love is complete, perfect. (Eph 3:19) He told his disciples: “No one has love greater than this, that someone should surrender his soul in behalf of his friends.” (Joh 15:13) He had told them: “I am giving you a new commandment, that you love one another; just as I have loved you, that you also love one another.” (Joh 13:34) This commandment was new, in that the Law, under which Jesus and his disciples were at that time, commanded a person: “You must love your fellow [or neighbor] as yourself.” (Le 19:18; Mt 22:39) It called for love of others as of oneself but not for a self-sacrificing love that went even to the point of giving one’s own life in behalf of another. Jesus’ life and death exemplified the love this new commandment called for. In addition to doing good when the occasion arises, the follower of Christ is to take the initiative, under Christ’s direction, to help others spiritually and otherwise. He is to work actively for their good. The preaching and teaching of the good news to others, some of whom may be enemies, is one of the greatest expressions of love, for it can result in everlasting life to them. The Christian must ‘impart not only the good news of God but also his own soul’ in helping and working with those who accept the good news. (1Th 2:8) And he should be ready to surrender his soul (life) in behalf of them.—1Jo 3:16.

How One Acquires Love. Through holy spirit, the first man and woman were created with a measure of this dominant attribute of God, namely love, and with the capacity to extend, enlarge, and enrich that love. Love is a fruit of God’s spirit. (Ga 5:22) Godly love is not a quality that one has without knowing why, as may be the case with certain physical or mental abilities, such as physical beauty, talent in music, or similar inherited qualities. Godly love cannot exist in the person apart from knowledge and service of God or apart from meditation and appreciation. Only by cultivating love can one become an imitator of God, the Source of love. (Ps 77:11; Eph 5:1, 2; Ro 12:2) Adam failed to cultivate love of God; he did not progress toward perfection of love. This is shown by his not being in union with God, bound to God by that perfect bond of union. Adam, nevertheless, even though imperfect and sinful, passed on to his offspring, “in his image,” the ability and capacity to love. (Ge 5:3) Humankind in general expresses love, but it is often a misguided, deteriorated, twisted love.

Love can be misguided. For these reasons, it is evident that a person can have real, properly directed love only by seeking and following God’s spirit and the knowledge that comes from His Word. For example, a parent may have affection for his child. But he may let that love deteriorate or he may be misguided because of sentimentality, giving the child everything and denying him nothing. He may not exercise his parental authority in giving discipline and at times actual chastisement. (Pr 22:15) Such supposed love may actually be family pride, which is selfishness. The Bible says such a person is exercising, not love, but hate, because he is not taking the course that will save his child’s life.—Pr 13:24; 23:13, 14.

This is not the love that comes from God. Godly love causes one to do what is good and beneficial for the other person. “Love builds up.” (1Co 8:1) Love is not sentimentality. It is firm, strong, directed by godly wisdom, adhering first of all to that which is chaste, right. (Jas 3:17) God demonstrated this with Israel, whom he punished severely for disobedience, for their own everlasting welfare. (De 8:5; Pr 3:12; Heb 12:6) The apostle Paul says to Christians: “It is for discipline you are enduring. God is dealing with you as with sons. For what son is he that a father does not discipline? . . . Furthermore, we used to have fathers who were of our flesh to discipline us, and we used to give them respect. Shall we not much more subject ourselves to the Father of our spiritual life and live? For they for a few days used to discipline us according to what seemed good to them, but he does so for our profit that we may partake of his holiness. True, no discipline seems for the present to be joyous, but grievous; yet afterward to those who have been trained by it it yields peaceable fruit, namely, righteousness.”—Heb 12:7-11.

Knowledge gives love right direction. Love must be directed first to God, above all others. Otherwise it will become misdirected and even lead into the worship of a creature or thing. Knowing God’s purposes is essential, because a person knows then what is best for his own welfare and that of others and will know how to express love in the proper way. Our love for God is to be with our ‘whole heart, mind, soul, and strength.’ (Mt 22:36-38; Mr 12:29, 30) It is to be, not merely an outward expression, but a love that reflects the total inner person. Love involves the emotions. (1Pe 1:22) But if the mind is not equipped with knowledge of what true love is and how it acts, love can be expressed in the wrong direction. (Jer 10:23; 17:9; compare Php 1:9.) The mind must know God and his qualities, his purposes, and how he expresses love. (1Jo 4:7) In harmony with this, and since love is the most important quality, dedication to God is to the person of Jehovah himself (in whom love is the dominant quality) and is not to a work or a cause. Then, love must be carried out with the soul, every fiber of one’s organism; and all one’s strength must be put behind that effort.

Love is expansive. The true love that is a fruit of God’s spirit is expansive. (2Co 6:11-13) It is not stingy, confined, or circumscribed. It must be shared to be complete. A person must first love God (De 6:5), his Son (Eph 6:24), and then the whole association of his Christian brothers throughout the world (1Pe 2:17; 1Jo 2:10; 4:20, 21). He must love his wife; and she, her husband. (Pr 5:18, 19; Ec 9:9; Eph 5:25, 28, 33) Love is to be extended to one’s children. (Tit 2:4) All mankind, even a person’s own enemies, are to be loved, and Christian works are to be exercised toward them. (Mt 5:44; Lu 6:32-36) The Bible, commenting on the fruits of the spirit, of which love is first, says: “Against such things there is no law.” (Ga 5:22, 23) This love has no law that can limit it. It may be practiced at any time or place, to any extent, toward those to whom it is due. In fact, the only debt Christians should be owing one another is love. (Ro 13:8) This love for one another is an identifying mark of true Christians.—Joh 13:35.

How Godly Love Acts. Love, such as God is, is so wonderful that it is hard to define. It is easier to tell how it acts. In the following discussion of this fine quality, its application to Christians will be considered. The apostle Paul, in writing on the subject, first emphasizes how essential it is for a Christian believer and then details how it acts unselfishly: “Love is long-suffering and kind. Love is not jealous, it does not brag, does not get puffed up, does not behave indecently, does not look for its own interests, does not become provoked. It does not keep account of the injury. It does not rejoice over unrighteousness, but rejoices with the truth. It bears all things, believes all things, hopes all things, endures all things.”—1Co 13:4-7.

“Love is long-suffering and kind.” It puts up with unfavorable conditions and wrong actions of others, doing so with a purpose, namely, to work out the eventual salvation of those doing wrong or of others involved in the circumstances, as well as to vindicate, finally, Jehovah’s sovereignty. (2Pe 3:15) Love is kind, no matter what the provocation may be. Roughness or harshness on the part of a Christian toward others would not accomplish any good. Nonetheless, love can be firm and act in justice in behalf of righteousness. Those having authority may discipline wrongdoers, but even then, they are to employ kindness. Unkindness would bring benefit neither to the unkind counselor nor to the one doing unrighteousness, but it could separate that one even farther from repentance and right works.—Ro 2:4; Eph 4:32; Tit 3:4, 5.

“Love is not jealous.” It is not envious of good things coming to others. It rejoices in seeing a fellowman receive a position of greater responsibility. It does not begrudge even one’s enemies receiving good things. It is generous. God makes his rain fall on the righteous and the unrighteous. (Mt 5:45) God’s servants who have love are content with their lot (1Ti 6:6-8) and their place, not getting out of place or selfishly seeking the position occupied by another. Satan the Devil selfishly and enviously did get out of place, even desiring worship to be given to him by Jesus Christ.—Lu 4:5-8.

Love “does not brag, does not get puffed up.” It does not seek the applause and admiration of creatures. (Ps 75:4-7; Jude 16) The person having love will not push another person down to make himself appear greater. Rather, he will exalt God and will sincerely encourage and build up other persons. (Ro 1:8; Col 1:3-5; 1Th 1:2, 3) He will be happy to see another Christian make advancement. And he will not boast of what he is going to do. (Pr 27:1; Lu 12:19, 20; Jas 4:13-16) He will realize that all he does is due to the strength coming from Jehovah. (Ps 34:2; 44:8) Jehovah told Israel: “Let the one bragging about himself brag about himself because of this very thing, the having of insight and the having of knowledge of me, that I am Jehovah, the One exercising loving-kindness, justice and righteousness in the earth; for in these things I do take delight.”—Jer 9:24; 1Co 1:31.

Love “does not behave indecently.” It is not ill-mannered. It does not engage in indecent behavior, such as sexual abuses or shocking conduct. It is not rude, vulgar, discourteous, insolent, coarse, or disrespectful to anyone. A person who has love will avoid doing things that, in appearance or actions, disturb his Christian brothers. Paul instructed the congregation at Corinth: “Let all things take place decently and by arrangement.” (1Co 14:40) Love will also prompt one to walk honorably in the view of others who are not Christian believers.—Ro 13:13; 1Th 4:12; 1Ti 3:7.

Love “does not look for its own interests.” It follows the principle: “Let each one keep seeking, not his own advantage, but that of the other person.” (1Co 10:24) Here is where concern for the everlasting welfare of others shows itself. This sincere concern for others is one of the strongest motivating forces in love as well as one of the most effective and beneficial in its results. The possessor of love does not demand that everything be done his way. Paul said: “To the weak I became weak, that I might gain the weak. I have become all things to people of all sorts, that I might by all means save some. But I do all things for the sake of the good news, that I may become a sharer of it with others.” (1Co 9:22, 23) Neither does love demand its “rights”; it is more concerned with the spiritual welfare of the other person.—Ro 14:13, 15.

Love “does not become provoked.” It does not look for an occasion or an excuse for provocation. It is not moved to outbursts of anger, which is a work of the flesh. (Ga 5:19, 20) One having love is not easily offended by what others say or do. He is not afraid that his personal “dignity” may be injured.

Love “does not keep account of the injury.” (Literally, it is not “reckoning the bad thing”; Int.) It does not consider itself to be injured and so lay up that injury as something ‘on the books of account,’ to be settled, or paid off, in due time, in the meantime permitting no relations between the injured and the injurer. That would be a vengeful spirit, condemned in the Bible. (Le 19:18; Ro 12:19) Love will not impute evil motives to another but will be inclined to make allowances and give others the benefit of the doubt.—Ro 14:1, 5.

Love “does not rejoice over unrighteousness, but rejoices with the truth.” Love rejoices with the truth even though it upsets previous beliefs held or statements made. It sticks with God’s Word of truth. It always sides with the right, finding no pleasure in wrong, in lies, or in any form of injustice, no matter who the victim is, even if he is an enemy. However, if a thing is wrong or misleading, love does not fear to speak out in the interests of truth and of others. (Ga 2:11-14) Also, it prefers to suffer wrong rather than commit another wrong in an attempt to straighten out the matter. (Ro 12:17, 20) But if another person is properly corrected by one having authority, the loving person will not sentimentally side with the chastised one and find fault with the correction or the authorized one who did the correcting. Such an action would not be an expression of love for the individual. It might gain the favor of the corrected one, but it would harm rather than help him.

Love “bears all things.” It is willing to endure, to suffer for righteousness’ sake. A literal rendering is, “all things it is covering.” (Int) A person having love will be slow to expose to others the one who wrongs him. If the offense is not too serious, he will overlook it. Otherwise, when the course recommended by Jesus at Matthew 18:15-17 is applicable, he will follow it. In such cases, if the other person asks forgiveness after the wrong is privately pointed out to him, and repairs the damage, the one having love will show that his forgiveness is real, that it has completely covered the matter, as God has.—Pr 10:12; 17:9; 1Pe 4:7, 8.

Love “believes all things.” Love has faith in the things God has said in his Word of truth, even if outward appearances are against it and the unbelieving world scoffs. This love, especially toward God, is a recognition of his truthfulness, based on his record of faithfulness and reliability, just as we know and love a true, faithful friend and do not doubt when he tells us something for which we may not have proof. (Jos 23:14) Love believes all God says, though it may not be able to grasp it thoroughly, and it is willing to wait patiently until the matter is more fully explained or until getting a clear understanding. (1Co 13:9-12; 1Pe 1:10-13) Love also trusts in God’s direction of the Christian congregation and his appointed servants and backs up their decisions based on God’s Word. (1Ti 5:17; Heb 13:17) However, love is not gullible, for it follows the counsel of God’s Word to “test the inspired expressions to see whether they originate with God,” and it tests everything by the measuring rule of the Bible. (1Jo 4:1; Ac 17:11, 12) Love produces confidence in one’s faithful Christian brothers; a Christian would not suspect them or disbelieve them unless there was absolute proof that they were wrong.—2Co 2:3; Ga 5:10; Phm 21.

Love “hopes all things.” It has hope in all the things Jehovah has promised. (Ro 12:12; Heb 3:6) It continues to work, waiting patiently for Jehovah to bring fruitage, to make things grow. (1Co 3:7) A person having love will hope the best for his Christian brothers through any circumstances in which they might be, even though some may be weak in faith. He will realize that if Jehovah is patient with such weak ones, he should certainly adopt the same attitude. (2Pe 3:15) And he continues to assist those he is helping to learn the truth, hoping and waiting for them to be moved by God’s spirit to serve him.

Love “endures all things.” Love is required for the Christian to keep his integrity toward Jehovah God. Despite whatever the Devil may do to test the soundness of the Christian’s devotion and faithfulness to God, love will endure in a way that holds the Christian true to God.—Ro 5:3-5; Mt 10:22.

“Love never fails.” It will never come to an end or cease to exist. New knowledge and understanding may correct things we once believed; hope changes as the hoped-for things are realized and new things are hoped for, but love always remains in its fullness and continues to be built up stronger and stronger.—1Co 13:8-13.

“A Time to Love.” Love is held back only from those whom Jehovah shows are unworthy of it, or from those set in a course of badness. Love is extended to all persons until they show they are haters of God. Then the time comes for love’s expression toward them to end. Both Jehovah God and Jesus Christ love righteousness and hate lawlessness. (Ps 45:7; Heb 1:9) Those who intensely hate the true God are not persons toward whom love is to be expressed. Indeed, it would accomplish no good to continue exercising love toward such ones, for those who hate God will not respond to God’s love. (Ps 139:21, 22; Isa 26:10) Therefore God properly hates them and has a time to act against them.—Ps 21:8, 9; Ec 3:1, 8.

Things Not to Be Loved. The apostle John writes: “Do not be loving either the world or the things in the world. If anyone loves the world, the love of the Father is not in him; because everything in the world—the desire of the flesh and the desire of the eyes and the showy display of one’s means of life—does not originate with the Father, but originates with the world.” (1Jo 2:15, 16) He says, later on, “the whole world is lying in the power of the wicked one.” (1Jo 5:19) Accordingly, those who love God hate every wicked way.—Ps 101:3; 119:104, 128; Pr 8:13; 13:5.

While the Bible shows that a husband and wife should love each other and that this love includes the conjugal relationship (Pr 5:18, 19; 1Co 7:3-5), it points out the wrongness of the fleshly, worldly practice of sexual love toward another not one’s spouse. (Pr 7:18, 19, 21-23) Another worldly thing is materialism, “love of money” (phi·lar·gy·riʹa, literally, “fondness of silver”; Int), which is a root of all sorts of injurious things.—1Ti 6:10; Heb 13:5.

Jesus Christ warned against seeking glory from men. He scathingly denounced the hypocritical religious leaders of the Jews who liked to pray standing in the synagogues and on the corners of the broad ways to be visible to men and who loved the prominent places at evening meals and the front seats in the synagogues. He pointed out that they had already received in full their reward, that which they loved and desired, namely, honor and glory from men; therefore no reward at all was due them from God. (Mt 6:5; 23:2, 5-7; Lu 11:43) The record reads: “Many even of the rulers actually put faith in [Jesus], but because of the Pharisees they would not confess him, in order not to be expelled from the synagogue; for they loved the glory of men more than even the glory of God.”—Joh 12:42, 43; 5:44.

In speaking to his disciples, Jesus said: “He that is fond of [phi·lonʹ] his soul destroys it, but he that hates his soul in this world will safeguard it for everlasting life.” (Joh 12:23-25) A person who prefers to protect his life now rather than to be willing to lay down his life as a follower of Christ will lose out on everlasting life, but one who considers life in this world as secondary, and who loves Jehovah and Christ and their righteousness above everything else, will receive everlasting life.

God hates liars, for they have no love of the truth. He declared to the apostle John in vision: “Outside [the holy city, New Jerusalem] are the dogs and those who practice spiritism and the fornicators and the murderers and the idolaters and everyone liking [phi·lonʹ] and carrying on a lie.”—Re 22:15; 2Th 2:10-12.


One’s Love Can Cool Off. Jesus Christ, in telling his disciples of the things ahead, indicated that the love (a·gaʹpe) of many who professed belief in God would cool off. (Mt 24:3, 12) The apostle Paul said that, as a feature of the critical times to come, men would become “lovers of money.” (2Ti 3:1, 2) It is evident, therefore, that a person can lose sight of right principles and that the proper love he once had can fade away. This emphasizes the importance of constant exercise and development of love by meditation on God’s Word and by molding one’s life according to His principles.—Eph 4:15, 22-24.

At the feet of the original artist/technologist.

A Designer Encourages Scientists to Think Like Designers:

Evolution News & Views January 2, 2016 3:54 AM

Recently Live Science had a reflective piece by Ayse Birsel, an award-winning designer, co-founder of Birsel + Seck, and author of the book, Design the Life You Love. The title of the article is eye-catching: "The Art of Science: Why Researchers Should Think Like Designers." That's an unusual headline for a science site that generally takes the anti-ID position whenever it can.

Birsel's article is not about intelligent design theory or the intelligent design movement. It is, however, very much about "design" -- exploring how designers think. (It's hard to fathom any good designer not being intelligent; "evolutionary design" is an oxymoron, like "unguided purpose" or "aimless goal.")

Ayse Birsel describes her own design process in four stages: (1) Deconstruction, (2) Point of View, (3) Reconstruction, and (4) Expression. Let's see what these mean and what they have to teach about intelligent design in science.

"Deconstruction is breaking the whole apart to see what it's made of," she says. We see this aspect in the upwardly trending science of biomimetics. The "bioneers" movement is focused on deconstructing living designs to understand their design principles, with the goal of designing applications based on those principles. Birsel adds, "You can even deconstruct something very familiar, like science, to see what goes into it." She did that herself, defining science in a quadrant of (a) emotion of science, (b) physical of science, (c) intellect of science, and (d) spirit of science. Her holistic approach exalts science above intellectual drudgery and puts the A (art) back in STEM, producing STEAM (science, technology, engineering, art, and math). The "A," by the way, refers to "Art and Design," she points out.

"Point of View" refers to shifting your point of view intentionally. "In design," she says, "you want to shift from what you know to what you can imagine." Who would ever think, for instance, of creating a carnival dunk tank that engulfs the victim in flames instead of water? Someone actually designed a "Dunk Tank Flambé" at a carnival to teach people about science. "Luckily for John, he is wearing a super-flame-retardant suit," she hastens to add for gasping viewers of a photo of her friend John on fire in the contraption. It's an effective way to shock people out of the rut of the familiar. Certainly in the ID movement, we see the importance of helping people break out of the often-unchallenged Darwinian point of view.

"Reconstruction," Birsel continues, is the other side of Deconstruction. "It is about putting the subject back together again, knowing that you cannot have everything." This means understanding your constraints as a designer, and making choices that to optimize your effort. ID proponents have seen optimization as an example of design-based science. They have used it to answer ID critics who toss up supposed examples of bad design, showing that optimization provides the best compromise between competing trade-offs. What can Reconstruction do for science? It will undoubtedly give biomimetics engineers a new appreciation for biological designs when they try to reconstruct the design principles they encountered in the "Deconstruction" stage. Any scientist taking apart a cell and trying to reassemble it will likely find Darwinian thinking quite unhelpful.

"Expression," finally, is "giving your idea form." Scientists as well as product designers need to do this. "You build on the foundation of your new idea, and you express it as a unique prototype, a product, a strategy, a mathematical formula or a hypothesis." Clearly all five of those things require intelligent design. A scientist thinking like a designer, furthermore, can involve lay people's creativity and optimism to solve problems together. We're seeing progress in this direction, as social media breaks down the walls of stodgy scientific institutions, inviting scientists out into the sunshine of the Internet. More and more, scientists can pre-publish their hypotheses and have them tested by large communities of scientists out in the open, rather than by faceless reviewers behind journal paywalls.

Whether or not one agrees with Birsel's particular analysis, it is encouraging to see Live Science give good press to "design thinking" as a serious proposal for helping scientists improve their work:

Since I often work closely with engineers, I've come to realize that the design process has uncanny similarity to the scientific and engineering processes, yet it differs in key ways. By understanding the design process I use, everyone, including scientists, can gain insight into solving complex problems that they might want to think differently about ... including how to live a complete life. [Emphasis added.]

Birsel's "spirit of science" quadrant includes the words "Honest, Truth, Humanist, Persevering, Universal, Illuminating" -- each of which presupposes a creative and moral human mind with free will. Can science even operate without these? Notice, too, the subtext of human exceptionalism.


It's time to bring the designing mind back into the spotlight. Darwinian thinking has diminished the spirit of science, relegating the human mind to the end product of impersonal, unguided natural processes. "Thinking like a designer" will put STEAM back into the engine of scientific progress.

Wednesday 30 December 2015

A thousand words 43 years thence.

Russia needs to allow JWs to speak for themselves.

Experts Object to Russia’s Banning of JW.ORG:

ST. PETERSBURG, Russia—On July 21, 2015, the Russian Federation banned jw.org, the official website of Jehovah’s Witnesses, making it a criminal offense to promote it from within the federation. Russia is the only country in the world to ban jw.org.

Religious studies specialist and professor at the Academy of Labor and Social Relations in Moscow, Yekaterina Elbakyan, comments on jw.org: “I think the website is necessary because it contains objective information directly from Jehovah’s Witnesses about their organization rather than third-party opinions. . . . Not only are its members interested in the website, but also those who are simply interested in various religions. And I’m not only speaking about professional religious scholars like myself but also journalists and publicists who write about religion.”

“I think the website is necessary because it contains objective information directly from Jehovah’s Witnesses”—Yekaterina Elbakyan, Professor, Academy of Labor and Social Relations, Moscow
A legal expert at the Human Rights Institute in Moscow, Lev Levinson, puts this action by the government in historical context: “Twenty-first century Russia has a constitution that guarantees freedom of religion and equality of religious associations before the law. However, as in the 19th century, Russia is again restricting the freedom of sharing one’s religious views by confiscating literature and banning websites. And this is all being done by judges and experts who apply unlawful regulations under the guise of counteracting extremism.”

The ban is the latest development in a legal battle stretching back to 2013. On August 7 of that year, a Russian district court declared the website “extremist” during a secret trial, but that decision was reversed by a regional court on January 22, 2014. However, a Deputy of the Prosecutor General of the Russian Federation appealed to the Supreme Court of the Russian Federation to reinstate the trial decision. On December 2, 2014, the Supreme Court heard the prosecution’s appeal without the Witnesses present to defend themselves, as they were not properly notified of the hearing. The Supreme Court reinstated the trial decision, declaring the entire website “extremist” although the court conceded that the website no longer contained any religious material prohibited by the Russian authorities. The Witnesses contested the decision and appealed to the chairman of the Supreme Court, but without success. As a result of that decision, on July 21, 2015, the Ministry of Justice of the Russian Federation added the website to the Federal List of Extremist Materials, banning the website throughout Russia.

Yaroslav Sivulskiy, a spokesman for Jehovah’s Witnesses in Russia, comments on the impact of the ban: “We are disappointed that the Russian authorities have taken this unwarranted action. This ban curtails the worship of over 170,000 in this country who are Jehovah’s Witnesses. But when you consider that some 285,000 people in Russia accessed the website every day, it is clear that even those who are not members of our faith have been deprived of an excellent resource for Bible study.”

Speaking from the Witnesses’ world headquarters in Brooklyn, New York, J. R. Brown, an international spokesman for Jehovah’s Witnesses, states: “Our official website, jw.org, hosts award-winning videos, publications for Bible study in hundreds of languages, and the two most widely distributed magazines in the world, The Watchtower and Awake! It has been featured in some of the largest international book fairs and has even been used extensively in schools. It has benefited many communities around the world and was widely used in Russia. Really, this is a website that should be promoted.”

Media Contact(s):

International: J. R. Brown, Office of Public Information, tel. +1 718 560 5000


Russia: Yaroslav Sivulskiy, tel. +7 812 702 2691

The Watchtower Society's commentary on Joy.

JOY:

The emotion excited by the acquisition or expectation of good; state of happiness; exultation. The Hebrew and Greek words used in the Bible for joy, exultation, rejoicing, and being glad express various shades of meaning, different stages or degrees of joy. The verbs involved express the inner feeling and the outward manifestation of joy and variously mean “be joyful; exult; shout for joy; leap for joy.”

Jehovah God and Jesus Christ. Jehovah is called “the happy God.” (1Ti 1:11) He creates and works with joy for himself and his creatures. What he brings about makes him joyful. (Ps 104:31) He wants his creatures likewise to enjoy his works and to enjoy their own work. (Ec 5:19) Since he is the Source of all good things (Jas 1:17), all intelligent creatures, both mankind and angels, can find their chief enjoyment in coming to know him. (Jer 9:23, 24) King David said: “Let my musing about him be pleasurable. I, for my part, shall rejoice in Jehovah.” (Ps 104:34) He also sang: “The righteous one will rejoice in Jehovah and will indeed take refuge in him; and all the upright in heart will boast.” (Ps 64:10) The apostle Paul urged Christians to take joy at all times in their knowledge of Jehovah and his dealing with them, writing to them: “Always rejoice in the Lord [“Jehovah,” in several versions]. Once more I will say, Rejoice!”—Php 4:4.

Jesus Christ, who was the intimate one of Jehovah, knows him best (Mt 11:27), and he is able to explain Him to his followers. (Joh 1:18) Jesus is therefore joyful, being called “the happy and only Potentate.” (1Ti 6:14, 15) Out of love for his Father, he is eager to do always the things that please Him. (Joh 8:29) Therefore, when there was set before him the task of coming to earth, suffering, and dying in order that he might clear his Father’s name of reproach, “for the joy that was set before him he endured a torture stake, despising shame.” (Heb 12:2) He also had great love for and joy in mankind. The Scriptures, personifying him in his prehuman existence as wisdom, represent him as saying: “Then I came to be beside [Jehovah] as a master worker, and I came to be the one he was specially fond of day by day, I being glad before him all the time, being glad at the productive land of his earth, and the things I was fond of were with the sons of men.”—Pr 8:30, 31.

Jesus desired his followers to have the same joy, telling them: “These things I have spoken to you, that my joy may be in you and your joy may be made full.” The angels had joy at the creation of the earth. (Joh 15:11; 17:13; Job 38:4-7) They also view the course of God’s people, taking joy in their faithful course and especially exulting when an individual turns from his sinful ways to the pure worship and service of God.—Lu 15:7, 10.

What makes God joyful. Jehovah’s heart can be made glad by his servants because of their faithfulness and loyalty to him. Satan the Devil has constantly challenged the rightfulness of God’s sovereignty and the integrity of all those serving God. (Job 1:9-11; 2:4, 5; Re 12:10) To them apply the words: “Be wise, my son, and make my heart rejoice, that I may make a reply to him that is taunting me.” (Pr 27:11) Jehovah’s people in the earth can cause God to rejoice by faithfulness and loyalty to him.—Isa 65:19; Zep 3:17.

A Fruit of the Spirit. Since Jehovah is the Source of joy and he desires joyfulness for his people, joy is a fruit of his holy spirit. Joy is named immediately after love in the list at Galatians 5:22, 23. The apostle wrote to the Christians at Thessalonica: “You became imitators of us and of the Lord, seeing that you accepted the word under much tribulation with joy of holy spirit.” (1Th 1:6) Accordingly, Paul counseled the Christians at Rome that the Kingdom of God “means righteousness and peace and joy with holy spirit.”—Ro 14:17.

True joy is a quality of the heart and can affect the whole body for good. “A joyful heart has a good effect on the countenance,” and “a heart that is joyful does good as a curer [or, “does good to the body”],” says the wise writer of Proverbs.—Pr 15:13; 17:22, ftn.

Joy in God’s Service. What Jehovah asks of his servants is not burdensome. (1Jo 5:3) He wants them to enjoy his service. His people Israel were to enjoy the seasonal festivals that he arranged for them, and they were to rejoice in other aspects of their life and worship of God. (Le 23:40; De 12:7, 12, 18) They were to speak out about God joyfully. (Ps 20:5; 51:14; 59:16) If they did not serve with joy of heart, there was something wrong with their hearts and their appreciation of his loving-kindness and goodness. Therefore he warned what would take place if they became disobedient and took no joy in serving him: “All these maledictions will certainly come upon you . . . because you did not listen to the voice of Jehovah your God by keeping his commandments and his statutes . . . And they must continue on you and your offspring . . . due to the fact that you did not serve Jehovah your God with rejoicing and joy of heart for the abundance of everything.”—De 28:45-47.

The Christian, no less, should enjoy his service to God. Otherwise, something is lacking in heart appreciation. (Ps 100:2) “The joy of Jehovah is your stronghold,” said one of God’s faithful servants. (Ne 8:10) The good news the Christian proclaims was announced by God’s angel as “good news of a great joy that all the people will have.” (Lu 2:10) Jehovah’s name upon his witnesses and the truth as found in the Bible should themselves be a joy to them. The prophet Jeremiah said: “Your word becomes to me the exultation and the rejoicing of my heart; for your name has been called upon me, O Jehovah God of armies.”—Jer 15:16.

Moreover, Jehovah’s just, right judicial decisions put into effect in the Christian congregation and in the lives of Christians are cause for joy, especially in a time when the world has thrown justice and righteousness to the ground. (Ps 48:11) Then, too, the marvelous hope ahead surely gives strong ground for joyfulness. (“Rejoice in the hope”; Ro 12:12; Pr 10:28.) Their salvation is a basis for joy. (Ps 13:5) Additionally, there is the joy that the servant of God has in those whom he aids in coming to the knowledge and service of Jehovah. (Php 4:1; 1Th 2:19) Meeting together and working together with God’s people is one of the greatest joys.—Ps 106:4, 5; 122:1.

Persecution a cause for joy. For the Christian who guards his heart, even persecution, though not in itself enjoyable, should be viewed with joy, for endurance of it with integrity is a victory. God will help the faithful one. (Col 1:11) Additionally, it is proof that one is approved by God. Jesus said that when reproach and persecution come, the Christian should “leap for joy.”—Mt 5:11, 12; Jas 1:2-4; 1Pe 4:13, 14.

Other Joys Provided by God. Jehovah has provided many other things that mankind may enjoy day by day. Some of these are marriage (De 24:5; Pr 5:18), being father or mother of a righteous and wise child (Pr 23:24, 25), food (Ec 10:19; Ac 14:17), wine (Ps 104:14, 15; Ec 10:19), and the multitudinous things of His creation (Jas 1:17; 1Ti 6:17).

False or Nonlasting Joys. Jesus speaks of some who would hear the truth and receive it with joy but without getting the real sense of it. Such do not cultivate the implanted word in their hearts and, as a consequence, soon lose their joy by being stumbled when tribulation or persecution arises on account of the word. (Mt 13:20, 21) Joy based on materialism is a false joy that is in error and will be short-lived. Also, a person rejoicing over the calamity of another, even of one who hates him, must account to Jehovah for his sin. (Job 31:25-30; Pr 17:5; 24:17, 18) A young man is foolish to think that enjoyment of life requires that he give in to following “the desires incidental to youth.” (2Ti 2:22; Ec 11:9, 10) Similarly, love of merriment will bring one into a bad situation. (Pr 21:17; Ec 7:4) Even the Christian who exults in comparing himself with others is in error. Rather, he should prove what his own work is and have cause for exultation in himself alone.—Ga 6:4.

Everlasting Joy. Jehovah promised to restore his people Israel after their exile in Babylon. He did bring them back to Jerusalem in 537 B.C.E., and they greatly rejoiced when the temple foundation was laid. (Isa 35:10; 51:11; 65:17-19; Ezr 3:10-13) But Isaiah’s prophecy (65:17) has a greater fulfillment in the establishment of “a new heaven and a new earth,” in which arrangement all mankind will have joy forever under the “New Jerusalem.”—Re 21:1-3.


Under present conditions, wickedness, sickness, and death prevent full and undiminished joy. But in harmony with the Bible rule, “A wise king is scattering wicked people,” Jesus Christ as King will bring an end to all enemies of God and of righteousness. (Pr 20:26; 1Co 15:25, 26) Thus all obstacles to complete joy will be removed, for even “death will be no more, neither will mourning nor outcry nor pain be anymore.” (Re 21:4) Sorrow for those who have died will be completely gone, removed by the resurrection of the dead. This knowledge comforts Christians even today, who, on this account, do not “sorrow just as the rest also do who have no hope.”—1Th 4:13, 14; Joh 5:28, 29.

On Formalising design detection II

Peer-Reviewed Scientific Paper Develops New Ways of Measuring Complex and Specified Information in Life
Casey Luskin December 28, 2015 11:28 AM

Winston Ewert, Bill Dembski, and Bob Marks have recently published a new peer-reviewed paper in the journal IEEE Transactions on Systems, Man, and Cybernetic: Systems, titled "Algorithmic Specified Complexity in the Game of Life." The purpose of the paper is to develop the concept of algorithmic specified complexity as a new and improved method of measuring biological (and other forms of) information.

They start by observing that "Neither fundamental Shannon nor Kolmogorov information models are equipped" to measure "meaningful" information. As I recently explained, "the purpose of Shannon information is to help measure fidelity of transmission of information. What the transmission says doesn't matter" and:

Kolmogorov information is not necessarily tied to likelihood. In fact, higher Kolmogorov bits could mean more randomness. In that regard, it's not useful for distinguishing functional information from non-functional.
Complex and specified information (CSI) has long been cited as an improved method of measuring the functional meaning of information. But recently the team at the Evolutionary Informatics Lab has developed a new variation on CSI, algorithmic specified complexity (ASC), to measure the degree to which information is meaningful. As they put it:
We propose an information theoretic method to measure meaning. Fundamentally, we model meaning to be in the context of the observer. A page filled with Kanji symbols will have little meaning to someone who neither speaks nor reads Japanese. Likewise, a machine is an arrangement of parts that exhibit some meaningful function whose appreciation requires context. The distinguishing characteristic of machines is that the parts themselves are not responsible for the machine's functionality, but rather they are only functional due to the particular arrangement of the parts. Almost any other arrangement of the same parts would not produce anything interesting. A functioning computational machine is more meaningful than a large drawer full of computer parts.
They explain why Shannon Information and Kolmogorov-Chaitin-Solomonoff (KCS) measures of information don't help measure functionality:
The arranging of a large collection of parts into a working machine is highly improbable. However, any arrangement would be improbable regardless of whether the configuration had any functionality whatsoever. For this reason, neither Shannon nor KCS information models are capable of directly measuring meaning. Functional machines are specified -- they follow some independent pattern. When something is both improbable and specified, we say that it exhibits specified complexity. An elaborate functional machine exemplifies high specified complexity. We propose a model, algorithmic specified complexity (ASC), whereby specified complexity can be measured in bits.
ASC is similar to KCS in that it assumes a computer environment where we can describe some event, object, or scenario in terms of computer programming commands. This can allow, as they put it, a "quantitative measurement of specified complexity." To show how it works, they use Conway's famous "Game of Life."
The "Game of Life" is a computer simulation that's meant to mimic living systems by creating a grid in which some cells on the grid are "alive" and some are dead. A series of rules based upon the number of alive or dead neighboring cells determine whether a given cell will remain alive, remain dead, or come to life, or die, after each successive generation. They describe the rules as follows

1) Under-Population: A living cell with fewer than two live neighbors dies.
2) Family: A living cell with two or three live neighbors lives on to the next generation.
3) Overcrowding: A living cell with more than three living neighbors dies.
4) Reproduction: A dead cell with exactly three living neighbors becomes a living cell.
If you deliberately create certain patterns in the Game of Life, they can do unexpected things, like "gliders" which can move across the screen, or a really complicated pattern called "Gemini" that can make copies of itself every 33.6 million generations. Ewert, Dembski, and Marks use these features of "Game of Life" to apply ASC:
Our goal is to formulate and apply specified complexity measures to these patterns. We would like to be able to quantify what separates a simple glider, readily produced from almost any randomly configured soup, from Gemini -- a large, complex design whose formation by chance is probabilistically minuscule. Likewise, we would like to be able to differentiate the functionality of Gemini from a soup of randomly chosen pixels over a similarly sized field of grid squares.
A highly probable object can be explained by randomness, but it will lack complexity and thus not have specified complexity. Conversely, any sample of random noise will be improbable, but will lack specification and thus also lack specified complexity. In order to have specified complexity, both components must be present. The object must exhibit a describable functioning pattern while being improbable.

They find that some of these patterns in the Game of Life are "simple enough that they arise from random configurations of cell space," but "[o]thers required careful construction." They measured the ASC in these patterns, and then asked whether the patterns are known to appear randomly, or whether they require intelligent design. Their model predicts that high ASC patterns would arise only by design, and that patterns that are known to appear randomly would always have low ASC. They found that their method is generally a good predictor of whether low ASC patterns can appear at random or require design:
We have merely calculated the probability of generating the pattern through some simply random process not through the actual Game of Life process. We hypothesized that it was close enough to differentiate randomly achievable patterns from one that were deliberately created. This appears to work, with the exception of the unix pattern. However, even that pattern was less than an order of magnitude more probable than the bound suggested. This suggests the approximation was reasonable, but there is room for improvement.
We conclude that many of the machines built in the Game of Life do exhibit significant ASC. ASC was able to largely distinguish constructed patterns from those which were produced by random configurations. They do not appear to have been generated by a stochastic process approximated by the probability model we presented.

In other words, many of the high ASC patterns that appear in Game of Life don't appear at random. But is that surprising? After all, the Game of Life is a computer program created by intelligent agents that's designed to mimic living systems -- systems that also have high ASC. As they conclude, "Our work here demonstrates the applicability of ASC to the measure of functional meaning."

Image credit: aussiegall (Laceflower abstract) [CC BY 2.0], via Wikimedia 

On formalising design detection.

Peer-Reviewed Paper Successfully Measures Specified Complexity in Computer Images:
Casey Luskin December 29, 2015 11:31 AM 

A new peer-reviewed article in the journal IET Computer Vision, "Measuring meaningful information in images: algorithmic specified complexity," by Winston Ewert, William A. Dembski, and Robert J. Marks II, again attempts to apply the concept of algorithmic specified complexity (ASC) as a measure of meaning vs. randomness in a dataset. In a previous article I noted that the team at the Evolutionary Informatics Lab tried to apply algorithmic specified complexity (ASC) to successfully predict random patterns in Conway's Game of Life versus those that were constructed by a programmer. In this paper the authors try to distinguish between "images which contain content from those which are simply redundancies, meaningless or random noise." They begin by asking:

Is information being created when we snap a picture of Niagara Falls? Would a generic picture of Niagara Falls on a post card contain less information than the first published image of a bona fide extraterrestrial being?
They attempt to answer these questions by stating:
For an image to be meaningfully distinguishable, it must relate to some external independent pattern or specification. The image of the sunset is meaningful because the viewer experientially relates it to other sunsets in their experience. Any image containing content rather than random noise fits some contextual pattern. Naturally, any image looks like itself, but the requirement is that the pattern must be independent of the observation and therefore the image cannot be self-referential in establishing meaning. External context is required. If an object is both improbable and specified, we say that it exhibits "specified complexity."
So how can we detect whether there is such a complex and specified pattern?
The more the image can be described in terms of a pattern, the more compressible it is, and the more specified. For example, a black square is entirely described by a simple pattern, and a very short computer programme suffices to recreate it. As a result, we conclude that it is highly specified. In contrast, an image of randomly selected pixels cannot be compressed much if at all, and thus we conclude that the image is not specified at all. Images with content such as sunsets take more space to describe than the black square, but are more specified than random noise. Redundancy in some images is evidenced by the ability to approximately restore groups of missing pixels from those remaining.
The black square might be compressible and specified, but that does not mean it is complex. As they note, "The random image is significantly more complex, whereas the solid square is much less complex."
But these are relatively simple cases. They then try to tackle more complex cases, such as a photograph of Louis Pasteur with increasing amounts of random noise added. As ASC predicts, they find that the more noise is added to the image, the lower the ASC. Similarly, as you resize an image of Einstein so that it loses some of its clarity, it also loses ASC. This is all as their model predicts.

But what about the case of a picture of "stick men on a sea of noise"? They found that ASC was still able to detect the presence of a complex and specified feature even when it was surrounded by noise. They conclude that ASC is an effective methodology for distinguishing random image data from meaningful images:

We have estimated the probability of various images by using the number of bits required for the PNG encoding. This allows us to approximate the ASC of the various images. We have shown hundreds of thousands of bits of ASC in various circumstances. Given the bound established on producing high levels of ASC, we conclude that the images containing meaningful information are not simply noise. Additionally, the simplicity of an image such as the solid square also does not exhibit ASC. Thus, we have demonstrated the theoretical applicability of ASC to the problem of distinguishing information from noise and have outlined a methodology where sizes of compressed files can be used to estimate the meaningful information content of images.

The applicability in the context of intelligent design is clear: If ASC is a useful tool for distinguishing designed images from random ones, then perhaps it can be applied to biological systems or other natural structures to detect design there as well.

Tuesday 29 December 2015

The Twilight zone is closer than you think.

Another failed Darwinian prediction II

The cell’s fundamental molecules are universal:

In addition to the DNA code, there are other fundamental molecular processes that appear to be common to all life. One intriguing example is DNA replication which copies both strands of the DNA molecule, but in different directions. Evolution predicts these fundamental processes to be common to all life. Indeed this was commonly said to be an important successful prediction for the theory. As Niles Eldredge explained, the “underlying chemical uniformity of life” was a severe test that evolution passed with flying colors. (Eldredge, 41) Likewise Christian de Duve declared that evolution is in part confirmed by the fact that all extant living organisms function according to the same principles. (de Duve, 1) And Michael Ruse concluded that the essential macromolecules of life help to make evolution beyond reasonable doubt. (Ruse, 4)

But this conclusion that the fundamental molecular processes within the cell are common to all species was superficial. In later years, as the details were investigated, important differences between species emerged. For example, key DNA replication proteins surprisingly “show very little or no sequence similarity between bacteria and archaea/eukaryotes.” (Leipe) Also different DNA replication processes have been discovered. These results were not what were expected:

In particular, and counter-intuitively, given the central role of DNA in all cells and the mechanistic uniformity of replication, the core enzymes of the replication systems of bacteria and archaea (as well as eukaryotes) are unrelated or extremely distantly related. Viruses and plasmids, in addition, possess at least two unique DNA replication systems, namely, the protein-primed and rolling circle modalities of replication. This unexpected diversity makes the origin and evolution of DNA replication systems a particularly challenging and intriguing problem in evolutionary biology. (Koonin)

Some evolutionists are reconsidering the assumption that all life on Earth shares the same basic molecular architecture and biochemistry, and instead examining the possibility of independent evolution, and multiple origins of fundamentally different life forms. (Cleland, Leipe)

References

Cleland, Carol. 2007. “Epistemological issues in the study of microbial life: alternative terran biospheres?.” Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 38:847-861.

de Duve, Christian. 1995. Vital Dust. New York: BasicBooks.

Eldredge, Niles. 1982. The Monkey Business. New York: Washington Square Press.

Koonin, E. 2006. “Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases.” Biology Direct 18:1-39.

Leipe, D., L. Aravind, E. Koonin. 1999. “Did DNA replication evolve twice independently?.” Nucleic Acids Research 27:3389-3401.

Ruse, Michael. 1986. Taking Darwin Seriously. New York: Basil Blackwell.

Monday 28 December 2015

A clash of Titans III

Evolution or Revolution?

In a few short centuries, the Yakutian horse has gained a large body and long, mammoth-like shaggy hair, allowing it to survive truly harsh conditions


  • By Jane Palmer
28 December 2015 Local legend has it that when the god of creation flew around the world to distribute riches, he dropped all of his treasures when he arrived in the Yakutian region of Siberia. His hands were simply numb with cold.
The myth is an attempt to explain why Yakutia has such an abundance of precious diamonds, but it is easy to see why the story developed. This republic of Russia gets very cold indeed. Temperatures can dip to -70 °C (-94 °F) and its capitol, Yakutsk, is the coldest city in the northern hemisphere.
There is life in the freezer though, including a population of stocky, shaggy steeds known as Yakutian horses. The Yakuts would undoubtedly have perished if not for these beasts. Locals relied on the horses for transportation, food in the form of horsemeat, and clothing made from horse hides. Horses have played a central role in the region's economy for hundreds of years.
It turns out that these horses adapted to the extreme Siberian climates with astonishing speed.
Averaging about 150cm, the Yakutian stands a little smaller than most horses. Its winter hair can reach about 10cm in length and it has a thick bushy tail and long mane that, like a shawl, covers both its neck and shoulders.
We could really track the whole temporal line
In short, its appearance is a little like the woolly mammoth version of a horse. It is clearly well suited to the brutal and enduring Siberian winters.
But how long has it taken the Yakutian horses to adapt to this extreme environment? Are they ancient natives to the region, like the now-extinct mammoths? Or did the Yakuts bring them to the area when they fled Mongolia in the 13th or 14th Century to escape Genghis Khan?
To answer such questions, scientists recently turned to genome sampling.
"We wanted to take horses from today, horses from after the 13th century, and from prior to the 13th century," says Ludovic Orlando of the University of Copenhagen in Denmark, the lead author of the study. "Because that way, we could really track the whole temporal line and see whether or not those population of horses are actually the same through time."
The team sampled the genomes of nine modern day Yakutian horses, one genome from an early 19th Century horse, and another from a horse that lived in the region 5,200 years ago. The scientists then compared the genomes to one another and to existing sequences for dozens of domestic horses, wild Przewalski's horses that are native to the steppes of central Asia, and ancient horses.
They have adapted to their new environment in just 800 years
The findings of the study were unequivocal. In the genomes of the modern Yakutian horses the researchers found a strong signal of a "founder effect": a reduction in genetic variation that results when a small population is used to establish a new colony. The precise level of genetic variation indicates that the small founding population of horses arrived in the Yakutian region about 800 years ago, in the 13th Century.
"We can exclude the possibility that the Yakutian horses descended from the horses that existed in Yakutia in ancient times," Orlando says.
The team's analyses placed the nine modern-day Yakutian horses and the Yakutian horse from the 19th century within the "evolutionary tree" of domesticated horses. They fall closest to the Mongolian, Fjord and Icelandic horses, with the Mongolian horses their most likely ancestors.
But the Yakutian horses differ significantly in appearance to these Mongol horses. They have adapted to their new environment in just 800 years.
"This is blink-of-an-eye evolution," says Doug Antczak, a veterinarian and equine scientist at Cornell University in Ithaca, New York. "What really captures peoples' imaginations from this research is the evidence for rapid adaption to the environment – in this case a cold, harsh, dry environment."
It shows that there are only so many ways a mammal can get adapted to such environments
Focusing on the variation in the Yakutian horse genome, the team identified the key biological functions involved in the adaptive process: those that modified the morphology, hormones and metabolism of the horses. They found variations in the gene pathways involved in hair development, limb length and body size, explaining the Yakutian horses' unique appearance.
Icelandic and Fjord horses are also squat and fat with thick hair coats, whereas horses that live in the desert, such as Arabian horses, have shorter and finer hair coats. "There's an infinite gradation between the horses that have fine hair coats and the Yakutian horses," Antczak says.
The geneticists also found genes associated with the metabolism of sugars including glucose, which can have anti-freezing properties in the blood.
In July 2015, a team of scientists compared the genomes of ancient woolly mammoths to those of elephants to determine the features that contributed to the mammoth's appearance and ability to withstand extreme cold. The researchers found similar variations in hair growth, metabolism and stature.
"It shows that there are only so many ways a mammal can get adapted to such environments," Orlando says.
But typically, a mammal would take millennia to reach the level of hardiness that Yakutian horses exhibit today.
"It is amazing that in just 800 years, which is only about a hundred generations for horses, you can get from a regular horse, a type of Mongolian horse, to the Yakutian horses we have today," Orlando says. "It tells you how fast evolution can go."