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Saturday 9 June 2018

Information v. Darwin.

Groundbreaking Paper Shows Thousands of New Genes Needed for the Origin of Animals

Someday we may get tired of being vindicated. But not yet! Günter Bechly recently  discussed a new paper that confirmed Stephen Meyer’s claims in Darwin’s Doubt that arthropods appeared abruptly in the Cambrian explosion, without evolutionary precursors in the Precambrian. Another recent groundbreaking paper in Nature Communications has also provided massive confirmation of Meyer’s arguments in the book that new genes were required at the origin of animals.

An Uncontroversial Idea?

Whether you’re an evolutionary biologist or a proponent of intelligent design, the notion that the origin of animals required new genes — even numerous new genes — might strike you as uncontroversial. But this claim was strongly challenged by UC Berkeley evolutionary paleontologist Charles Marshall who reviewed Darwin’s Doubt in the journal Science. It actually became a centerpiece of the debate between Marshall and Meyer about the Cambrian explosion. (For replies to Marshall, hereherehereherehere, and here.) Here’s the substance of Marshall’s counter-argument, as it was published in Science:

His [Meyer’s] case against current scientific explanations of the relatively rapid appearance of the animal phyla rests on the claim that the origin of new animal body plans requires vast amounts of novel genetic information coupled with the unsubstantiated assertion that this new genetic information must include many new protein folds. In fact, our present understanding of morphogenesis indicates that new phyla were not made by new genes but largely emerged through the rewiring of the gene regulatory networks (GRNs) of already existing genes (1).

Marshall didn’t stop there. He went further, saying that Meyer has an “idiosyncratic fixation with new protein folds” and “an outdated understanding of morphogenesis” — all due to Meyer’s supposedly inaccurate claims that the Cambrian explosion would have required the origin of many new genes. Now this new paper, Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty,” provides a direct refutation of Marshall’s insistence that the origin of animals didn’t require lots of new genes.


From the paper:

Recent studies show that many genes typically associated with metazoan functions actually pre-date animals themselves, supporting functional co-option of ‘unicellular genes’ during the genesis of metazoans. 


However, the role of genome novelty in animal origins has not been fully evaluated. We hypothesize that genomic novelty had a major impact in this transition, particularly involving biological functions which are hallmarks of animal multicellularity (gene regulation, signalling, cell adhesion, and cell cycle). Here we apply a comparative genomics approach using sophisticated methods, newly developed programs, and a comprehensive taxon sampling. The reconstruction of the ancestral genome of the last common ancestor of animals shows a set of biological functions similar to other eukaryote ancestors, while revealing an unexpected expansion of gene diversity. These analyses also highlight 25 groups of genes only found in animals that are highly retained in all their genomes, with essential functions linked to animal multicellularity.

They conclude that “many new” genes were necessary during the origin of animals: 

Thus, the first animal genome was not only showing a higher proportion of Novel HG [homology groups], but these also perform major multicellular functions in the modern fruit fly genome. The implication is that the transition was accompanied by an increase of genomic innovation, including many new, divergent, and subsequently ubiquitous genes encoding regulatory functions associated with animal multicellularity.

These “homology groups” (HGs) are exactly what they sound like — groups of genes that are similar. A “novel HG” is a group of genes that is found in animals, or particular groups of animals, that do not exist elsewhere. This indicates that these groups of genes were necessary for these animals to exist.

An Open-Access Paper; Check It Out 

Just how many novel HGs (and genes) are we talking about? The paper is open access, and readers can easily see that  Figure 1 shows that while 1189 HGs are necessary for the origin of Metazoa (multicellular organisms with differentiated tissues), as one moves farther up the animal tree, hundreds if not thousands of additional novel HGs are required:

For the origin of Eumetazoa (sponges + Planulozoa + Bilateria), 494 novel HGs are required.
For the origin of Planulozoa (ctenophores, placozoans, cnidarians + bilaterians), 1201 novel HGs are needed.
For the origin of Bilateria (animals with two-sided symmetry — a left and a right side), an additional 1580 HGs are required! According to Figure 2, about 16 percent of the bilaterian genome entails novel HGs!

No wonder  a commentary by the paper’s lead author at The Conversation cites “a burst of new genes” associated with the origin of animals:

We discovered the first animal had an exceptional number of novel genes, four times more than other ancestors. This means the evolution of animals was driven by a burst of new genes not seen in the evolution of their unicellular ancestors.

Straightforward Methodology

The methodology used by the paper is relatively straightforward. It compared the genomes of modern-day animals to determine what genes they share in common. This was then used to determine which genes were present in the genomes of the putative common ancestors of various animal groups. By comparing the common genes shared at different levels of the animal taxonomic hierarchy, they were able to determine how many new genes would have to appear at various stages of animal evolution. 

Of course the paper’s authors assume that these organisms share common ancestors and evolved by Darwinian natural selection — ideas that are challenged by the abrupt appearance of animals in the Cambrian period and by experimental work showing the difficulty of evolving new genes by standard Darwinian mechanisms of random mutation and blind natural selection. However, regarding the paper’s claims that many new genes were required during the origin of animals, the reasoning is sound, and it demonstrates conclusively that thousands of new genes would have been necessary for the origin of animals. Marshall was wrong. 
It wasn’t only in the journal Science that Marshall attacked Meyer on this subject. He said much the same in a radio debate against Meyer. In our “Listener’s Guide to the Meyer-Marshall Radio Debate” we explained what happened:
During the debate, Marshall amplified this argument by claiming that Meyer’s argument presupposed an outdated “1980s model of the way genes operate” and that his book “confronted a different set of problems that hark back to an older age.” According to Marshall, biologists no longer believe that building the diverse forms of Cambrian animals would require evolving new genes (or, at least, many new genes). Instead, Marshall argued, again, that new body plans could be generated by rewiring networks of already-existing genes, especially those which are part of the developmental gene regulatory networks (dGRNs) that control the timing and expression of pre-existing genes during animal development. Marshall pointed out that animals have far fewer genes than we once expected, and that today it is thought that “animals use essentially the same genes, just deployed slightly differently.” By changing the deployment of those genes — by rewiring their dGRNs — Marshall thinks new body plans can arise. 
It’s worth noting that throughout the debate, Meyer didn’t concede on Marshall’s claims that new genes aren’t necessary. Instead, he argued that even if we assume for the sake of the argument that Marshall is right that new genes aren’t necessary to build animals, that doesn’t solve the problem because rewiring the dGRNs still requires a huge input of information.
Dual Information Problems
In that regard, the new Nature Communications paper shows that Marshall’s evolutionary viewpoint faces information problems on two fronts. Figure 2c indicates that by far the largest classes of novel genes in the metazoa are related to generating nucleic acid binding proteins, and transcription factors. This suggests that not only were many new genes needed in the origin of Metazoa, but those new genes had profound influences on gene regulation — i.e., they were involved with rewiring of GRNs. 

Thus both Meyer and Marshall were right that dGRNs needed to be wired to build animals — but they were right in the most devastating manner for Darwinism, namely that the rewiring of the dGRNS was mediated by entirely new genes. The paper’s demonstration that thousands of new genes would have been required during the origin of animals is nothing short of a spectacular vindication of Meyer’s perspective on this question, and a strong falsification of Marshall’s viewpoint.

On Christian neutrality:The Watchtower Society's commentary.


Neutrality
Definition: The position of those who do not take sides with or give support to either of two or more contending parties. It is a fact of ancient and modern-day history that in every nation and under all circumstances true Christians have endeavored to maintain complete neutrality as to conflicts between factions of the world. They do not interfere with what others do about sharing in patriotic ceremonies, serving in the armed forces, joining a political party, running for a political office, or voting. But they themselves worship only Jehovah, the God of the Bible; they have dedicated their lives unreservedly to him and give their full support to his Kingdom.
What scriptures have had a bearing on the attitude of Christians toward the authority of secular governments?
Rom. 13:1, 5-7: “Let every soul be in subjection to the superior authorities [governmental rulers], for there is no authority except by God . . . There is therefore compelling reason for you people to be in subjection, not only on account of that wrath but also on account of your conscience. . . . Render to all their dues, to him who calls for the tax, the tax; to him who calls for the tribute, the tribute; to him who calls for fear, such fear; to him who calls for honor, such honor.” (No government could exist without God’s permission. Regardless of the conduct of individual officials, true Christians have shown them respect because of the office they occupied. For example, regardless of the use that governments have made of tax money, worshipers of Jehovah have made honest payment of their taxes in return for those services from which everyone could benefit.)
Mark 12:17: “Jesus then said: ‘Pay back Caesar’s things to Caesar, but God’s things to God.’” (So Christians have always recognized that they must not only “pay back” money in the form of taxes to the secular government but also fulfill the superior obligations they have toward God.)
Acts 5:28, 29: “[A spokesman for the Jewish high court] said: ‘We positively ordered you [the apostles] not to keep teaching upon the basis of this name [of Jesus Christ], and yet, look! you have filled Jerusalem with your teaching, and you are determined to bring the blood of this man upon us.’ In answer Peter and the other apostles said: ‘We must obey God as ruler rather than men.’” (When there has been a direct conflict between the commands of human rulers and the requirements of God, true Christians have imitated the example of the apostles by putting obedience to God first.)
What scriptures have always had a bearing on the attitude of true Christians toward participation in carnal warfare?
Matt. 26:52: “Jesus said to him: ‘Return your sword to its place, for all those who take the sword will perish by the sword.’” (Could there have been any higher cause for which to fight than to safeguard the Son of God? Yet, Jesus here indicated that those disciples were not to resort to weapons of physical warfare.)
Isa. 2:2-4: “It must occur in the final part of the days that the mountain of the house of Jehovah will become firmly established above the top of the mountains . . . And he will certainly render judgment among the nations and set matters straight respecting many peoples. And they will have to beat their swords into plowshares and their spears into pruning shears. Nation will not lift up sword against nation, neither will they learn war anymore.” (Individuals out of all nations must personally decide what course they will pursue. Those who have heeded Jehovah’s judgment give evidence that he is their God.)
2 Cor. 10:3, 4: “Though we walk in the flesh, we do not wage warfare according to what we are in the flesh. For the weapons of our warfare are not fleshly, but powerful by God for overturning strongly entrenched things.” (Paul here states that he never resorted to fleshly weapons, such as trickery, high-sounding language, or carnal weapons, to protect the congregation against false teachings.)
Luke 6:27, 28: “I [Jesus Christ] say to you who are listening, Continue to love your enemies, to do good to those hating you, to bless those cursing you, to pray for those who are insulting you.”
Is it not true that Jehovah allowed ancient Israel to engage in warfare?
Jehovah directed ancient Israel to use warfare to take possession of the land that he himself designated as their inheritance and to execute people whose depraved practices and defiance of the true God caused Jehovah to view them as being no longer fit to live. (Deut. 7:1, 2, 5; 9:5; Lev. 18:24, 25Nevertheless, mercy was shown to Rahab and to the Gibeonites because they demonstrated faith in Jehovah. (Josh. 2:9-13; 9:24-27) In the Law covenant God laid down rules for warfare that he would approve, stipulating exemptions and the manner in which this warfare was to be carried out. Such were truly holy wars of Jehovah. That is not true of the carnal warfare of any nation today.
With the establishing of the Christian congregation, a new situation came into existence. Christians are not under the Mosaic Law. Christ’s followers were to make disciples of people of all nations; so worshipers of the true God would in time be found in all those nations. However, what is the motive of those nations when they go to war? Is it to carry out the will of the Creator of all the earth or is it to further some nationalistic interest? If true Christians in one nation were to go to war against another nation, they would be fighting against fellow believers, against people who prayed for help to the same God that they did. Appropriately, Christ directed his followers to lay down the sword. (Matt. 26:52) He himself, glorified in the heavens, would henceforth carry out the execution of those who showed defiance of the true God and His will.—2 Thess. 1:6-8; Rev. 19:11-21.
As to serving in the armed forces, what does secular history disclose about the attitude of early Christians?
“A careful review of all the information available goes to show that, until the time of Marcus Aurelius [Roman emperor from 161 to 180 C.E.], no Christian became a soldier; and no soldier, after becoming a Christian, remained in military service.”—The Rise of Christianity (London, 1947), E. W. Barnes, p. 333.
“We who were filled with war, and mutual slaughter, and every wickedness, have each through the whole earth changed our warlike weapons,—our swords into ploughshares, and our spears into implements of tillage,—and we cultivate piety, righteousness, philanthropy, faith, and hope, which we have from the Father Himself through Him who was crucified.”—Justin Martyr in “Dialogue With Trypho, a Jew” (2nd century C.E.), The Ante-Nicene Fathers (Grand Rapids, Mich.; reprint of 1885 Edinburgh edition), edited by A. Roberts and J. Donaldson, Vol. I, p. 254.
“They refused to take any active part in the civil administration or the military defence of the empire. . . . it was impossible that the Christians, without renouncing a more sacred duty, could assume the character of soldiers, of magistrates, or of princes.”—History of Christianity (New York, 1891), Edward Gibbon, pp. 162, 163.
What scriptures have always had a bearing on the attitude of true Christians toward involvement in political issues and activities?
John 17:16: “They are no part of the world, just as I [Jesus] am no part of the world.”
John 6:15: “Jesus, knowing they [the Jews] were about to come and seize him to make him king, withdrew again into the mountain all alone.” Later, he told the Roman governor: “My kingdom is no part of this world. If my kingdom were part of this world, my attendants would have fought that I should not be delivered up to the Jews. But, as it is, my kingdom is not from this source.”—John 18:36.
Jas. 4:4: “Adulteresses, do you not know that the friendship with the world is enmity with God? Whoever, therefore, wants to be a friend of the world is constituting himself an enemy of God.” (Why is the matter so serious? Because, as 1 John 5:19 says, “the whole world is lying in the power of the wicked one.” At John 14:30, Jesus referred to Satan as being “the ruler of the world.” So, no matter what worldly faction a person might support, under whose control would he really come?)
Regarding political involvement, what do secular historians report as being the attitude of those known as early Christians?
“Early Christianity was little understood and was regarded with little favor by those who ruled the pagan world. . . . Christians refused to share certain duties of Roman citizens. . . . They would not hold political office.”—On the Road to Civilization, A World History (Philadelphia, 1937), A. Heckel and J. Sigman, pp. 237, 238.
“The Christians stood aloof and distinct from the state, as a priestly and spiritual race, and Christianity seemed able to influence civil life only in that manner which, it must be confessed, is the purest, by practically endeavouring to instil more and more of holy feeling into the citizens of the state.”—The History of the Christian Religion and Church, During the Three First Centuries (New York, 1848), Augustus Neander, translated from German by H. J. Rose, p. 168.
What scriptures have always had a bearing on the attitude of true Christians toward ceremonies involving flags and national anthems?
1 Cor. 10:14: “Flee from idolatry.” (Also Exodus 20:4, 5)
1 John 5:21: “Little children, guard yourselves from idols.”
Luke 4:8: “In reply Jesus said to him: ‘It is written, “It is Jehovah your God you must worship, and it is to him alone you must render sacred service.”’”
See also Daniel 3:1-28.
Do such patriotic symbols and ceremonies really have religious significance?
“[Historian] Carlton Hayes pointed out long ago that the ritual of flag-worship and oath-taking in an American school is a religious observance. . . . And that these daily rituals are religious has been at last affirmed by the Supreme Court in a series of cases.”—The American Character (New York, 1956), D. W. Brogan, pp. 163, 164.
“Early flags were almost purely of a religious character. . . . The national banner of England for centuries—the red cross of St. George—was a religious one; in fact the aid of religion seems ever to have been sought to give sanctity to national flags, and the origin of many can be traced to a sacred banner.”—Encyclopædia Britannica (1946), Vol. 9, p. 343.
“In a public ceremony presided over by the vice president of the [Military Supreme] Court, on the 19th of November, honors were shown to the Brazilian flag. . . . After the flag was hoisted, Minister General of the Army Tristao de Alencar Araripe expressed himself concerning the commemoration in this manner: ‘ . . . flags have become a divinity of patriotic religion which imposes worship . . . The flag is venerated and worshiped . . . The flag is worshiped, just as the Fatherland is worshiped.’”—Diario da Justiça (Federal Capital, Brazil), February 16, 1956, p. 1906.
With reference to patriotic ceremonies, what does secular history say about the attitude of those known as early Christians?
“Christians refused to . . . sacrifice to the emperor’s genius—roughly equivalent today to refusing to salute the flag or repeat the oath of allegiance. . . . Very few of the Christians recanted, although an altar with a fire burning on it was generally kept in the arena for their convenience. All a prisoner had to do was scatter a pinch of incense on the flame and he was given a Certificate of Sacrifice and turned free. It was also carefully explained to him that he was not worshiping the emperor; merely acknowledging the divine character of the emperor as head of the Roman state. Still, almost no Christians availed themselves of the chance to escape.”—Those About to Die (New York, 1958), D. P. Mannix, pp. 135, 137.
“The act of emperor worship consisted in sprinkling a few grains of incense or a few drops of wine on an altar which stood before an image of the emperor. Perhaps at our long remove from the situation we see in the act nothing different from . . . lifting the hand in salute to the flag or to some distinguished ruler of state, an expression of courtesy, respect, and patriotism. Possibly a good many people in the first century felt just that way about it but not so the Christians. They viewed the whole matter as one of religious worship, acknowledging the emperor as a deity and therefore being disloyal to God and Christ, and they refused to do it.”—The Beginnings of the Christian Religion (New Haven, Conn.; 1958), M. F. Eller, pp. 208, 209.
Has the neutrality of Christians meant that they are not interested in the welfare of their neighbors?
Certainly not. They know well and conscientiously endeavor to apply the command repeated by Jesus: “You must love your neighbor as yourself.” (Matt. 22:39) Also the counsel recorded by the apostle Paul: “Let us work what is good toward all, but especially toward those related to us in the faith.” (Gal. 6:10) They have been convinced that the greatest good that they can do for their neighbors is to share with them the good news of God’s Kingdom, which will lastingly solve the problems facing mankind and which opens up to those who embrace it the marvelous prospect of eternal life.