It's still design all the way down II

Seeing the Nucleus in 4-D
Evolution News | @DiscoveryCSC

We know about genes and genomes, and how over six feet of DNA is crammed into a tiny nucleus within a cell. Decades of detailed research have given us the static, 3-D view of the nucleus. What’s new is the frenetic activity going on inside the nucleus as chromosomes move into position and genes switch on and off. The addition of the time dimension is turning our snapshots of the genome into a movie, and it’s a blockbuster.

Two groundbreaking papers in Cell explain how Caltech scientists have peered into the moment-by-moment transcription of genes, watching portions of the genome light up as they become active. What they are finding reveals new levels of design. Who could think of chance after seeing what these scientists witnessed? 

Nuclear Organization

The first paper by Quinodoz et al., “Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus,” reports on work done in the lab of Mitchell Guttman. The results are summarized in the news from Caltech,“The Cartography of the Nucleus.” Notice the design implications in the opening sentences:

Nestled deep in each of your cells is what seems like a magic trick: Six feet of DNA is packaged into a tiny space 50 times smaller than the width of a human hair. Like a long, thin string of genetic spaghetti, this DNA blueprint for your whole body is folded, twisted, and compacted to fit into the nucleus of each cell.

Now, Caltech researchers have shown how cells organize the seemingly immense genome in a clever manner so that they can conveniently find and access important genes.

Nuclear bodies are regions where genes associate with the protein machines that will transcribe and edit them. Next to a rotating 3-D image of chromosomes associating with the nucleolus and other nuclear bodies, the news item describes how the team developed a new imaging tool called SPRITE to watch how genes switch on differently in different types of cells.

Though the vast majority of cells in every human body contain identical genomes, different types of cells are able to have diverse functions because genes can be expressed at varying levels — in other words, they can be turned on or off. For example, when a stem cell is developing into a neuron, a flurry of activity happens in the nucleus to dial up and down levels of gene expression. These levels would be different, for example, if the stem cell was turning into a muscle cell or if the cell were making the decision to self-destruct.

Next we learn about nuclear bodies. Notice the machine language and the efficiency: this is rapid, precision work!

In addition to the genome, the nucleus also contains structures called nuclear bodies, which are like miniature factories in the nucleus that contain a high concentration of cellular machinery all working to accomplish similar tasks, such as turning on specific sets of genes or modifying RNA molecules to produce proteins in the cell. This cellular machinery needs to be able to efficiently search through six feet of DNA — approximately 20,000 total genes, in mammals — in order to precisely find and control its targets. This is made possible because DNA is organized into three-dimensional structures that make certain genes more or less accessible

Figures in the paper show a high degree of organization, indeed. SPRITE places barcode tags on genes that allow scientists to follow chromosome strands as they organize around nuclear bodies. Some nuclear bodies, called nuclear speckles, are where genomic DNA is organized, and where RNA Polymerase II, spliceosomes and lncRNAs transcribe and edit them. Inactive parts of the chromosome associate with the nucleolus, which contains repressive proteins on DNA that keep genes turned off. “Moreover,” they say, “our results suggest that multiple actively transcribed DNA regions can arrange simultaneously around nuclear speckles to form higher-order inter-chromosomal interactions.” 

Together, these results suggest an integrated and global picture of genome organization where individual genomic regions across chromosomes organize around nuclear bodies to shape the overall packaging of genomic DNA in a highly regulated and dynamic manner (Figure 7).

Quinodoz explains what is significant about this advancement:

“With SPRITE, we were able to see thousands of molecules — DNAs and RNAs — coming together at various ‘hubs’ around the nucleus in single cells,” says Quinodoz, the study’s first author. “Previously, researchers theorized that each chromosome is kind of on its own, occupying its own ‘territory’ in the nucleus. But now we see that multiple genes on different chromosomes are clustering together around these bodies of cellular machinery. We think these ‘hubs’ may help the cell keep DNA that are all turned on or turned off neatly organized in different parts of the nucleus to allow cellular machinery to easily access specific genes within the nucleus.”

Nuclear Dynamics

The second paper, by Shah et al., is summarized in this from Caltech, “Ten Thousand Bursting Genes.” This team improved on an existing imaging tool called seqFISH that allowed them to watch not just four or five genes, as before, but 10,421 genes at once within individual cells by tagging them with fluorescent barcodes. The news item shows thousands of colored dots in a map of the nucleus where nascent transcription was seen to be occurring. 

Previous methods followed the messenger RNAs, which have a longer lifetime. By following short-lived introns in the genes with their tags, this team found a purpose behind those mysterious non-coding regions:

In order for genetic instructions to be turned into an actual functioning protein, a process called transcription must first occur. This process often occurs in pulses, or “bursts.” First, a gene will be read and copied into a precursor messenger RNA, or pre-mRNA, like jotting a quick, rough draft. This molecule then matures into a messenger RNA, or mRNA, akin to editing the rough draft. During the “editing” process, certain regions called introns are cut out of the pre-mRNA.

The team chose to focus on labeling introns because they are produced so early in the transcription process, giving a picture of what a cell is doing at the precise moment of gene expression.

Following the introns led to a discovery that

the transcription of genes oscillates globally across many genes on what Cai calls a “surprisingly short” timescale — only about two hours — compared to the time it takes for a cell to divide and replicate itself, which takes from 12 to 24 hours. This means that over the course of a two-hour period, many genes within a cell will burst on and off.

It was like watching a miniature fireworks show in color. The tags reveal what the “nascent transcriptome” is doing, providing more dynamical resolution of nuclear activity. With this improved seqFISH tagging technique, scientists will be able to watch how transcription activity differs between different types of cells. 

The team also learned things about nuclear organization. They were “surprised to discover that most active, protein-encoding genes are located on the surface of the chromosome, not buried inside of it.” Additionally, “Transcriptionally active loci are positioned at the surface of chromosome territories.” This is not “spaghetti code” inside a basketball! (“Spaghetti code” was a term of derision for computer programs tangled up with “go-to” signals all over the place, making it hard to follow. Today’s modular programming is better organized. The cell had it first!)

The work by Shah et al. could lead to other exciting discoveries. In conclusion, they look ahead:

Using pulsatile and oscillatory dynamics, cells can achieve states not accessible with amplitude-based regulation schemes (Letsou and Cai, 2016). For example, cells can use fluctuations in global transcriptional activity to coordinate the stoichiometry of many transcripts in a mechanisms [sic] akin to the frequency-modulated signaling observed in yeast and mammalian pathways (Cai et al., 2008; Yissachar et al., 2013). 

Finally, an exciting recent work showed that intron-to-exon ratios across the transcriptome can be used to determine the direction of of [sic] cells on the developmental trajectory (La Manno et al., 2017). As we showed, the nascent transcriptome profiles can not only distinguish cell types and cell states, but also detect fast dynamics in single cells. Applications of intron seqFISH with signal amplification (Shah et al., 2016a), along with mRNA seq- FISH (Shah et al., 2016b, Lignell et al., 2017), can enable simultaneous profiling of nascent and mature RNAs in tissues, with spatial information preserved. It will be fascinating to explore the nascent transcriptome in single cells in many tissue settings and developmental contexts.

In short, cells could take advantage of the observed two-hour oscillation for additional levels of coordination and regulation. They can use it like signals superimposed on an FM radio carrier wave!

Conclusion

The really exciting work in genetics is being done with an eye to design. These researchers did not need to explicitly endorse intelligent design to show why this is the case. The message of design comes through loud and clear in the questions they ask, and in the findings that result. The absence of evolutionary speculation improves the signal-to-noise ratio.

Is the rise of the machines a thing?:Pros and cons.

Better a cooling planet than a warming economy?:Pros and cons.

The Ransom:The Watchtower society's commentary.

RANSOM

A price paid to buy back or to bring about release from some obligation or undesirable circumstance. The basic idea of “ransom” is a price that covers (as in payment for damages or to satisfy justice), while “redemption” emphasizes the releasing accomplished as a result of the ransom paid. The most significant ransom price is the shed blood of Jesus Christ, which made deliverance from sin and death possible for the offspring of Adam.

In the various Hebrew and Greek terms translated “ransom” and “redeem,” the inherent similarity lies in the idea of a price, or thing of value, given to effect the ransom, or redemption. The thought of exchange, as well as that of correspondency, equivalence, or substitution, is common in all. That is, one thing is given for another, satisfying the demands of justice and resulting in a balancing of matters.​—See RECONCILIATION.

A Price That Covers. The Hebrew noun koʹpher comes from the verb ka·pharʹ, meaning, basically, “cover,” as in Noah’s covering the ark with tar. (Ge 6:14) Ka·pharʹ, however, is used almost entirely to describe the satisfying of justice through the covering of or atoning for sins. The noun koʹpher refers to the thing given to accomplish this, the ransom price. (Ps 65:3; 78:38; 79:8, 9) A covering corresponds to the thing it covers, either in its form (as in a material lid, such as the “cover [kap·poʹreth]” of the ark of the covenant; Ex 25:17-22), or in its value (as in a payment to cover the damages caused by an injury).

As a means for balancing justice and setting matters straight with his people Israel, Jehovah, in the Law covenant, designated various sacrifices and offerings to atone for, or cover, sins, including those of the priests and the Levites (Ex 29:33-37; Le 16:6, 11), of other individuals, or of the nation as a whole (Le 1:4; 4:20, 26, 31, 35), as well as to purify the altar and tabernacle, making atonement because of the sins of the people surrounding these. (Le 16:16-20) In effect, the life of the animal sacrificed went in place of the life of the sinner, its blood making atonement on God’s altar, that is, to the extent that it could. (Le 17:11; compare Heb 9:13, 14; 10:1-4.) The “day of atonement [yohm hak·kip·pu·rimʹ]” could just as properly be referred to as the “day of the ransoms.” (Le 23:26-28) These sacrifices were required if the nation and its worship were to have and maintain the acceptance and approval of the righteous God.

Well illustrating the sense of a redeeming exchange is the law regarding a bull known to gore. If the owner allowed the bull to go loose so that it killed someone, the owner was to be put to death, paying for the life of the slain person with his own life. However, since he did not deliberately or directly kill another, if the judges viewed it proper to impose upon him a “ransom [koʹpher]” instead, then he must pay that redemption price. The sum assessed and paid was viewed as taking the place of his own life and compensating for the life lost. (Ex 21:28-32; compare De 19:21.) On the other hand, no ransom could be accepted for the deliberate murderer; only his own life could cover the death of the victim. (Nu 35:31-33) Evidently because a census involved lives, at the time such was taken each male over 20 had to have a ransom (koʹpher) of half a shekel ($1.10) given for his soul to Jehovah, the same price applying whether the individual was rich or poor.​—Ex 30:11-16.

Since any imbalance of justice is displeasing to God, as well as among humans, the ransom, or covering, could have the additional effect of averting or quelling anger. (Compare Jer 18:23; also Ge 32:20, where “appease” translates ka·pharʹ.) The husband enraged at the man committing adultery with his wife, however, refuses any “ransom [koʹpher].” (Pr 6:35) The term may also be used with regard to those who should execute justice but who instead accept a bribe or gift as “hush money [koʹpher]” to cover over the wrongdoing in their sight.​—1Sa 12:3; Am 5:12.

The Redemption, or Releasing. The Hebrew verb pa·dhahʹ means “redeem,” and the related noun pidh·yohnʹ means “redemption price.” (Ex 21:30) These terms evidently emphasize the releasing accomplished by the redemption price, while ka·pharʹ places stress on the quality or content of the price and its efficacy in balancing the scales of justice. The releasing, or redeeming (pa·dhahʹ), may be from slavery (Le 19:20; De 7:8), from other distressing or oppressive conditions (2Sa 4:9; Job 6:23; Ps 55:18), or from death and the grave. (Job 33:28; Ps 49:15) Frequent reference is made to Jehovah’s redeeming the nation of Israel from Egypt to be his “private property” (De 9:26; Ps 78:42) and to his redeeming them from Assyrian and Babylonian exile many centuries later. (Isa 35:10; 51:11; Jer 31:11, 12; Zec 10:8-10) Here, too, the redemption involved a price, an exchange. In redeeming Israel from Egypt, Jehovah evidently caused the price to be paid by Egypt. Israel was, in effect, God’s “firstborn,” and Jehovah warned Pharaoh that his stubborn refusal to release Israel would cause the life of Pharaoh’s firstborn and the firstborn of all Egypt, human and animals, to be exacted. (Ex 4:21-23; 11:4-8) Similarly, in return for Cyrus’ overthrow of Babylon and his liberation of the Jews from their exiled state, Jehovah gave “Egypt as a ransom [form of koʹpher] for [his people], Ethiopia and Seba” in their place. The Persian Empire thus later conquered those regions, and so ‘national groups were given in place of the Israelites’ souls.’ (Isa 43:1-4) These exchanges are in harmony with the inspired declaration that the “wicked is [or serves as] a ransom [koʹpher] for the righteous one; and the one dealing treacherously takes the place of the upright ones.”​—Pr 21:18.

Another Hebrew term associated with redemption is ga·ʼalʹ, and this conveys primarily the thought of reclaiming, recovering, or repurchasing. (Jer 32:7, 8) Its similarity to pa·dhahʹ is seen by its parallel use with that term at Hosea 13:14: “From the hand of Sheol I shall redeem [form of pa·dhahʹ] them; from death I shall recover [form of ga·ʼalʹ] them.” (Compare Ps 69:18.) Ga·ʼalʹ gives emphasis to the right of reclaiming or repurchasing, either by a near kinsman of a person whose property or whose very person needed to be repurchased or reclaimed, or by the original owner or seller himself. A near kinsman, called a go·ʼelʹ, was thus “a repurchaser” (Ru 2:20; 3:9, 13) or, in cases where a murder was involved, a “blood avenger.”​—Nu 35:12.

The Law provided that in the case of a poor Israelite whose circumstances forced him to sell his hereditary lands, his city house, or even to sell himself into servitude, “a repurchaser closely related to him,” or go·ʼelʹ, had the right to “buy back [ga·ʼalʹ] what his brother sold,” or the seller could do so himself if funds became available to him. (Le 25:23-27, 29-34, 47-49; compare Ru 4:1-15.) If a man should make a vow offering to God of a house or a field and then desire to buy it back, he had to pay the valuation placed on the property plus a fifth in addition to that estimated value. (Le 27:14-19) However, no exchange could be made for anything “devoted to destruction.”​—Le 27:28, 29.

In the case of murder, the murderer was not allowed sanctuary in the appointed cities of refuge but, after the judicial hearing, was turned over by the judges to the “avenger [go·ʼelʹ] of blood,” a near kinsman of the victim, who then put the murderer to death. Since no “ransom [koʹpher]” was allowed for the murderer and since the near kinsman with right of repurchase could not reclaim or recover the life of his dead relative, he rightfully claimed the life of the one who had taken his relative’s life by murder.​—Nu 35:9-32; De 19:1-13.

Not Always a Tangible Price. As has been shown, Jehovah “redeemed” (pa·dhahʹ) or ‘reclaimed’ (ga·ʼalʹ) Israel from Egypt. (Ex 6:6; Isa 51:10, 11) Later, because the Israelites kept “selling themselves to do what was bad” (2Ki 17:16, 17), Jehovah on several occasions ‘sold them into the hands of their enemies.’ (De 32:30; Jg 2:14; 3:8; 10:7; 1Sa 12:9) Their repentance caused him to buy them back, or reclaim them, out of distress or exile (Ps 107:2, 3; Isa 35:9, 10; Mic 4:10), thereby performing the work of a Go·ʼelʹ, a Repurchaser related to them inasmuch as he had espoused the nation to himself. (Isa 43:1, 14; 48:20; 49:26; 50:1, 2; 54:5-7) In ‘selling’ them, Jehovah was not paid some material compensation by the pagan nations. His payment was the satisfaction of his justice and the fulfillment of his purpose to have them corrected and disciplined for their rebellion and disrespect.​—Compare Isa 48:17, 18.

God’s ‘repurchasing’ likewise need not involve the payment of something tangible. When Jehovah repurchased the Israelites exiled in Babylon, Cyrus willingly liberated them, without tangible compensation in his lifetime. However, when redeeming his people from oppressor nations that had acted with malice against Israel, Jehovah exacted the price from the oppressors themselves, making them pay with their own lives. (Compare Ps 106:10, 11; Isa 41:11-14; 49:26.) When the people of the kingdom of Judah were “sold,” or delivered over, to the Babylonians, Jehovah received no personal compensation. And the deported Jews did not pay money either to the Babylonians or to Jehovah to buy back their freedom. It was “for nothing” that they were sold and “without money” that they were repurchased. Jehovah therefore needed to make no payment to their captors to balance matters out. Instead, he effected the repurchase through the power of “his holy arm.”​—Isa 52:3-10; Ps 77:14, 15.

Jehovah’s role of Go·ʼelʹ thus embraced the avenging of wrongs done to his servants and resulted in the clearing of his own name of the charges raised by those who used Israel’s distress as an excuse to reproach him. (Ps 78:35; Isa 59:15-20; 63:3-6, 9) As the Great Kinsman and Redeemer of both the nation and its individuals, he conducted their “legal case” to effect justice.​—Ps 119:153, 154; Jer 50:33, 34; La 3:58-60; compare Pr 23:10, 11.

Though living before and outside the nation of Israel, the disease-stricken Job said: “I myself well know that my redeemer is alive, and that, coming after me, he will rise up over the dust.” (Job 19:25; compare Ps 69:18; 103:4.) Following God’s own example, Israel’s king was to act as a redeemer in behalf of the lowly and poor ones of the nation.​—Ps 72:1, 2, 14.

Christ Jesus’ Role as Ransomer. The foregoing information lays the basis for understanding the ransom provided for humankind through God’s Son, Christ Jesus. Mankind’s need for a ransom came about through the rebellion in Eden. Adam sold himself to do evil for the selfish pleasure of keeping continued company with his wife, now a sinful transgressor, so he shared the same condemned standing with her before God. He thereby sold himself and his descendants into slavery to sin and to death, the price that God’s justice required. (Ro 5:12-19; compare Ro 7:14-25.) Having possessed human perfection, Adam lost this valuable possession for himself and all his offspring.

The Law, which had “a shadow of the good things to come,” provided for animal sacrifices as a covering for sin. This, however, was only a symbolic or token covering, since such animals were inferior to man; hence, it was “not possible for the blood of bulls and of goats [actually] to take sins away,” as the apostle points out. (Heb 10:1-4) Those pictorial animal sacrifices had to be without blemish, perfect specimens. (Le 22:21) The real ransom sacrifice, a human actually capable of removing sins, must therefore also be perfect, free from blemish. He would have to correspond to the perfect Adam and possess human perfection, if he were to pay the price of redemption that would release Adam’s offspring from the debt, disability, and enslavement into which their first father Adam had sold them. (Compare Ro 7:14; Ps 51:5.) Only thereby could he satisfy God’s perfect justice that requires like for like, a ‘soul for a soul.’​—Ex 21:23-25; De 19:21.

The strictness of God’s justice made it impossible for mankind itself to provide its own redeemer. (Ps 49:6-9) However, this results in the magnifying of God’s own love and mercy in that he met his own requirements at tremendous cost to himself, giving the life of his own Son to provide the redemption price. (Ro 5:6-8) This required his Son’s becoming human to correspond to the perfect Adam. God accomplished this by transferring his Son’s life from heaven to the womb of the Jewish virgin Mary. (Lu 1:26-37; Joh 1:14) Since Jesus did not owe his life to any human father descended from the sinner Adam, and since God’s holy spirit ‘overshadowed’ Mary, evidently from the time she conceived until the time of Jesus’ birth, Jesus was born free from any inheritance of sin or imperfection, being, as it were, “an unblemished and spotless lamb,” whose blood could prove to be an acceptable sacrifice. (Lu 1:35; Joh 1:29; 1Pe 1:18, 19) He maintained that sinless state throughout his life and thus did not disqualify himself. (Heb 4:15; 7:26; 1Pe 2:22) As a ‘sharer of blood and flesh,’ he was a near kinsman of mankind and he had the thing of value, his own perfect life maintained pure through tests of integrity, with which to repurchase mankind, emancipate them.​—Heb 2:14, 15.

The Christian Greek Scriptures make clear that the release from sin and death is indeed by the paying of a price. Christians are said to be “bought with a price” (1Co 6:20; 7:23), having an “owner that bought them” (2Pe 2:1), and Jesus is presented as the Lamb who ‘was slaughtered and with his blood bought persons for God out of every tribe, tongue, and nation.’ (Re 5:9) In these texts the verb a·go·raʹzo is used, meaning simply “buy at the market [a·go·raʹ].” The related e·xa·go·raʹzo (release by purchase) is used by Paul in showing that Christ released “by purchase those under law” through his death on the stake. (Ga 4:5; 3:13) But the thought of redemption or ransoming is more frequently and more fully expressed by the Greek lyʹtron and related terms.

Lyʹtron (from the verb lyʹo, meaning “loose”) was especially used by Greek writers to refer to a price paid to ransom prisoners of war or to release those under bond or in slavery. (Compare Heb 11:35.) In its two Scriptural occurrences it describes Christ’s giving “his soul a ransom in exchange for many.” (Mt 20:28; Mr 10:45) The related word an·tiʹly·tron appears at 1 Timothy 2:6. Parkhurst’s Greek and English Lexicon to the New Testament says it means: “a ransom, price of redemption, or rather a correspondent ransom.” He quotes Hyperius as saying: “It properly signifies a price by which captives are redeemed from the enemy; and that kind of exchange in which the life of one is redeemed by the life of another.” He concludes by saying: “So Aristotle uses the verb [an·ti·ly·troʹo] for redeeming life by life.” (London, 1845, p. 47) Thus Christ “gave himself a corresponding ransom for all.” (1Ti 2:5, 6) Other related words are ly·troʹo·mai, “loose by ransom” (Tit 2:14; 1Pe 1:18, 19), and a·po·lyʹtro·sis, “a releasing by ransom.” (Eph 1:7, 14; Col 1:14) The similarity of the usage of these words with that of the Hebrew terms considered is evident. They describe, not an ordinary purchase or releasing, but a redeeming or ransoming, a deliverance effected by payment of a corresponding price.

Though available to all, Christ’s ransom sacrifice is not accepted by all, and “the wrath of God remains” upon those not accepting it, as it also comes upon those who first accept and then turn away from that provision. (Joh 3:36; Heb 10:26-29; contrast Ro 5:9, 10.) They gain no deliverance from the enslavement to Kings Sin and Death. (Ro 5:21) Under the Law the deliberate murderer could not be ransomed. Adam, by his willful course, brought death on all mankind, hence was a murderer. (Ro 5:12) Thus, the sacrificed life of Jesus is not acceptable to God as a ransom for the sinner Adam.

But God is pleased to approve the application of the ransom to redeem those of Adam’s offspring who avail themselves of such a release. As Paul states, “as through the disobedience of the one man many were constituted sinners, likewise also through the obedience of the one person many will be constituted righteous.” (Ro 5:18, 19) At the time of Adam’s sin and his being sentenced to death, his offspring or race were all unborn in his loins and so all died with him. (Compare Heb 7:4-10.) Jesus as a perfect man, “the last Adam” (1Co 15:45), had a race or offspring unborn in his loins, and when he died innocently as a perfect human sacrifice this potential human race died with him. He had willingly abstained from producing a family of his own by natural procreation. Instead, Jesus uses the authority granted by Jehovah on the basis of his ransom to give life to all those who accept this provision.​—1Co 15:45; compare Ro 5:15-17.

Thus, Jesus was indeed “a corresponding ransom,” not for the redemption of the one sinner, Adam, but for the redemption of all mankind descended from Adam. He repurchased them so that they could become his family, doing this by presenting the full value of his ransom sacrifice to the God of absolute justice in heaven. (Heb 9:24) He thereby gains a Bride, a heavenly congregation formed of his followers. (Compare Eph 5:23-27; Re 1:5, 6; 5:9, 10; 14:3, 4.) Messianic prophecies also show he will have “offspring” as an “Eternal Father.” (Isa 53:10-12; 9:6, 7) To be such, his ransom must embrace more than those of his “Bride.” In addition to those “bought from among mankind as firstfruits” to form that heavenly congregation, therefore, others are to benefit from his ransom sacrifice and gain everlasting life through the removal of their sins and accompanying imperfection. (Re 14:4; 1Jo 2:1, 2) Since those of the heavenly congregation serve with Christ as priests and “kings over the earth,” such other recipients of the ransom benefits must be earthly subjects of Christ’s Kingdom, and as children of an “Eternal Father” they attain everlasting life. (Re 5:10; 20:6; 21:2-4, 9, 10; 22:17; compare Ps 103:2-5.) The entire arrangement manifests Jehovah’s wisdom and his righteousness in perfectly balancing the scales of justice while showing undeserved kindness and forgiving sins.​—Ro 3:21-26.

The hermit's handbook?

No mere machine?

Design in Living Things Goes Far Beyond Machines
Jonathan Wells

Seventeenth-century French philosopher René Descartes conceived of living things as complex machines, a concept now known as the “machine metaphor.” In 1998, Bruce Alberts (who was then president of the U.S. National Academy of Sciences) wrote that “the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.”1

In Salvo 20, Casey Luskin wrote about how such machines pose a problem for unguided evolution and provide evidence for intelligent design (ID).2 Luskin focused on three molecular machines in particular: 

ATP synthase, which operates like a rotary engine, recharges molecules of adenosine triphosphate (ATP), which in turn provide energy for just about every function in a living cell. 

Kinesin, which runs along microscopic fibers called microtubules, transports cargoes throughout the cell.

The ribosome, which is a combination of proteins and RNAs, translates messenger RNA (which is transcribed from DNA) into proteins. 

These are only a few of the many hundreds of molecular machines that have been identified in living cells.

Luskin argued that complex molecular machines, which function only after all of their parts are in place, could not have been produced by unguided evolution but only by a goal-directed intelligence. In other words, molecular machines provide evidence for intelligent design. 

Sometimes the Metaphor Backfires

Charles Darwin called his theory of evolution “descent with modification,” and he insisted that the process was undirected. Some people have tried to use the machine metaphor to illustrate evolution, but their efforts have backfired. In 1990, biologist Tim Berra published a book titled Evolution and the Myth of Creationism that included photographs of some automobiles. Berra wrote, “if you compare a 1953 and a 1954 Corvette, side by side, then a 1954 and a 1955 model, and so on, the descent with modification is overwhelmingly obvious.”3 Since automobiles are engineered, however, the series of Corvettes actually illustrated design rather than undirected evolution. In 1997 Phillip E. Johnson, a critic of Darwinism and advocate of intelligent design, called this “Berra’s blunder.”4

In 2014, three engineers published an article in the Journal of Applied Physics comparing the evolution of airplanes to the evolution of animals. According to the authors, “Evolution means a flow organization (design) that changes over time,” and they argued that animals and “the human-and-machine species” (airplanes) “evolved in the same way.”5 But once again, the comparison of machines and living things implied design rather than undirected evolution.

According to pro-evolution philosophers Massimo Pigliucci and Maarten Boudry, the machine metaphor should be abandoned altogether. In 2010 they wrote: “Creationists and their modern heirs of the Intelligent Design movement have been eager to exploit mechanical metaphors for their own purposes.” So “if we want to keep Intelligent Design out of the classroom, not only do we have to exclude the ‘theory’ from the biology curriculum, but we also have to be weary [sic] of using scientific metaphors that bolster design-like misconceptions about living systems.” Pigliucci and Boudry concluded that since machine metaphors “have been grist to the mill of ID creationism, fostering design intuitions and other misconceptions about living systems, we think it is time to dispense with them altogether.”6

Organized from the Inside Out

But there are better reasons for us to be wary of the machine metaphor than wanting to keep intelligent design out of classroom. Eighteenth-century German philosopher Immanuel Kant pointed out that a machine is organized by an external agent from the outside in, while a living thing organizes itself from the inside out. Kant wrote that a living thing “is then not a mere machine, for that has merely moving power, but it possesses in itself formative power of a self-propagating kind which it communicates to its materials though they have it not of themselves; it organizes them.”7

According to philosopher of biology Daniel Nicholson, “despite some interesting similarities, organisms and machines are fundamentally different kinds of systems . . . the former are intrinsically purposive whereas the latter are extrinsically purposive.” Thus, the machine metaphor “fails to provide an appropriate theoretical understanding of what living systems are.”8

Biologist (and intelligent design advocate) Ann Gauger has written that “the machine metaphor fails,” in part, because living organisms are “causally circular beings.”9 Not only do new cells require existing cells, but also many biosynthetic pathways require the very molecule that is being synthesized. For example, the biosynthesis of the amino acid cysteine requires an enzyme that contains cysteine.10 Without cysteine, a cell cannot make cysteine. Similarly, ATP synthase consists of more than a half-dozen protein subunits, each of which requires ATP for its biosynthesis.11 In other words, ATP is needed to make the molecular motor that makes ATP.

So the machine metaphor is inadequate as a description of living organisms. Then what about the inference to design from molecular machines? The inference is still justified, because the machine metaphor is appropriate for isolated structures such as ATP synthase, kinesin, and the ribosome. Each of these consists of several parts that are precisely arranged by a cell to utilize energy to perform a specific function (which is how “machine” is usually defined). None of them can perform their functions if parts are missing or arranged incorrectly. They point to intelligent design just as much as machines made by humans.

Awe-Inspiring Design

An organism, however, in contrast to an isolated structure, rearranges its parts over time. An organism imposes organization on the materials it comprises, and its organization changes throughout its life cycle. 

To see how remarkable this is, imagine a machine familiar to most of us: a laptop computer. If a laptop computer were a plant or animal, it would start out as a protocomputer consisting of perhaps a few transistors, a little memory with some software, and a battery on a small circuit board. Then it would obtain materials from its surroundings to fabricate other components, and it would make its circuit board larger and more complex. Along the way, it would find ways to recharge its own battery. It would also write more programs. After reaching maturity, the laptop would run its programs by itself — imagine keys on the keyboard going up and down as though pressed by some unseen finger. If components were damaged, the computer could repair or replace them while continuing to operate. Eventually, the computer would fabricate one or more protocomputers, each capable of developing into other laptops just like it.

A lot of design goes into laptop computers. How much more design would have to go into making a laptop computer that could do all the things listed above? No one knows. But such a computer would certainly require more design, not less. And the design would be radically different from human design, because after the origin of the protocomputer the design it would be intrinsic rather than extrinsic. 

So the inference to design from molecular machines is robust, but it’s only the beginning. There is design in living things that far transcends the machine metaphor — and it should inspire awe.

Notes:

1. Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell 92:291 (1998).
2. Casey Luskin, “Biomechanics: Isn’t the Intricacy of Ubiquitous Molecular Machines Evidence for Design?” Salvo 20 (2012), 52–54.
3. Tim Berra, Evolution and the Myth of Creationism (Stanford University Press, 1990), 117–119.
4. Phillip E. Johnson, Defeating Darwinism by Opening Minds (Intervarsity Press, 1997), 62–63.
5. Adrian Bejan et al., “The evolution of airplanes,” Journal of Applied Physics 116:044901  (2014).
6. Massimo Pigliucci and Maarten Boudry, “Why Machine-Information Metaphors are Bad for Science and Science Education,” Science & Education (June 11, 2010).
7. Immanuel Kant, The Critique of Judgement (Kritik der Urteilskraft), trans. J. H. Bernard (Macmillan, 1914), §65.
8. Daniel Nicholson, “The Machine Conception of the Organism in Development and Evolution: A Critical Analysis,” Studies in History and Philosophy of Biological and Biomedical Sciences 48B (2014), 162–174.
9. Ann Gauger, “Life, Purpose, Mind: Where the Machine Metaphor Fails,” Evolution News & Views (June 1, 2011).
10. Ruma Banerjee et al., “Reaction mechanism and regulation of cystathionine beta-synthase,” Biochimica et Biophysica Acta 1647 (2003), 30–35. Alexander Schiffer et al., “Structure of the dissimilatory sulfite reductase from the hyperthermophilic archaeon Archaeoglobus fulgidus,” Journal of Molecular Biology 379 (2008), 1063–1074.
11. Robert K. Nakamoto et al., “The Rotary Mechanism of the ATP Synthase,” Archives of Biochemistry and Biophysics 476 (2008), 43–50.

Yet more on education over indoctrination.

Yale President Calls for Objectivity in Science Education

Sarah Chaffee

A new article in Scientific American argues that “We Should Teach All Students, in Every Discipline, to Think Like Scientists.”The author, Peter Salovey, is notable. He is President of Yale University where he also teaches psychology. He might not welcome my saying so, but his emphasis on thinking critically and examining evidence is spot-on. 

Salovey wants Superhero Science. The picture with the article is a graphic of a female scientist standing on top of a building with her coat flowing behind her like a cape. His hope comes through in his first sentence: “If knowledge is power, scientists should easily be able to influence the behavior of others and world events.” 

The emphasis on “power” and “influencing behavior” sounds like an invitation to scientism, or worse. This innovation, for one, could easily be abused in the service of political and other agendas:

Students at Yale, the California Institute of Technology and the University of Waterloo, for instance, developed an Internet browser plug-in that helps users distinguish bias in their news feeds.

Yet the article also calls for better science education and education in general. The language is excellent. Salovey notes: 

Educating global citizens is one of the most important charges to universities, and the best way we can transcend ideology is to teach our students, regardless of their majors, to think like scientists. From American history to urban studies, we have an obligation to challenge them to be inquisitive about the world, to weigh the quality and objectivity of data presented to them, and to change their minds when confronted with contrary evidence.

Likewise, STEM majors’ college experience must be integrated into a broader model of liberal education to prepare them to think critically and imaginatively about the world and to understand different viewpoints.

He concludes:

Knowledge is power but only if individuals are able to analyze and compare information against their personal beliefs, are willing to champion data-driven decision making over ideology, and have access to a wealth of research findings to inform policy discussions and decisions.

Yes! Students learning to “weigh the quality and objectivity of data presented to them, and to change their minds when confronted with contrary evidence” as well as to “think critically and imaginatively about the world and to understand different viewpoints” — what a wonderful vision! Sounds familiar, too.

If applied objectively, this approach would enhance evolution education along with all parts of the curriculum! What do you say, Dr. Salovey? 

Question all(less one?)

Inquiry-Based Science Education -- on Everything but Evolution:
Sarah Chaffee 

Unfortunately, it's typical for advocates of inquiry-based science teaching to apply their good ideas to everything but evolution. Case in point: here is physician Danielle Teller writing over at Quartz to suggest that teaching science as a collection of facts, rather than a process, has contributed to a lack of "science savvy." Yet in the same article she denounces the public's doubts on evolution -- as if Darwinian theory were one "fact" that they ought to have simply swallowed whole.

Dr. Teller laments that "[a]bout a third of Americans think there is no sound evidence for the existence of evolution." She wrongly lumps doubt over the scientific accuracy of evolution with vaccine and climate skepticism, and she is certainly mistaken in dismissing questions about Darwinian theory as a sign of scientific illiteracy. However, Teller is correct in describing science as a process of inquiry rather than the mere gathering of data.

She notes:

Most importantly, if we want future generations to be truly scientifically literate, we should teach our children that science is not a collection of immutable facts but a method for temporarily setting aside some of our ubiquitous human frailties, our biases and irrationality, our longing to confirm our most comforting beliefs, our mental laziness.

One reason science should be taught as a process, Teller says, is because facts change. Or rather, the body of facts we know expands. This is well recognized. Indeed, one of the precursors to modern national science standards, Project 2061, focused on scientific inquiry rather than facts. Developed in the 1980s, it aimed to prepare a scientifically knowledgeable population in time for the return of Halley's comet in 2061. The project's director, Jo Ellen Roseman, told Ars Technica: "While we had no idea what the world would be like, we could guarantee that it would be shaped by science, mathematics, and technology."

But macroevolutionary theory has run into trouble precisely because it is a 19th-century idea in a world where the body of known facts has broadened dramatically. Consider Darwin's explanation of the evolution of the eye. He thought that one could go from a light-sensitive spot to our complex human eyes. But that was understandable. In his era, no one recognized the eye's intricacies as we do now. Or take the case of so-called vestigial organs. To cite two examples, much of what we thought we knew about the appendix and tonsils as "vestigial" by-products of evolution has been falsified as scientists find important immune and other functions.

Yet neo-Darwinism's defenders hang on because humans have a tendency to reject ideas that challenge preconceived notions. As Thomas Kuhn wrote in The Structure of Scientific Revolutions, when faced with an anomaly, a theory's defenders "will devise numerous articulations and ad hoc modifications of their theory in order to eliminate any apparent conflict."

The result in the context of origins science is a sort of "fundamentalist" evolutionary thinking that rejects counterevidence and dismisses any suggestion that evolution might have weaknesses. Teller writes of her own experience in learning to follow the evidence instead of what she had been taught, noting, "my own personal coda is that I never rejected out-of-hand a theory that challenged my preconceived notions again." Why the exception, then, for neo-Darwinism?

Science, finally, should be taught as a process because the interpretation of data requires critical thinking. Science education theorists agree. In a joint issue on the theme of reform in STEM (Science, Technology, Engineering, Math) education, Nature and Scientific American noted, "[S]tudents gain a much deeper understanding of science when they actively grapple with questions than when they passively listen to answers."

Nevertheless, in public school science classrooms, evolution is often presented in a one-sided, dogmatic manner. At Discovery Institute, we support education that promotes critical thinking by teaching the evolution controversy. What would that look like in the classroom? Teachers could engage their biology students on such questions as: Do Galápagos finches provide evidence for macro-, or only micro-evolution? Are vertebrate embryos really similar in their earliest stages? How likely is it that the Miller-Urey experiment represents conditions present on early earth? Such analysis makes students confront the data before them and look at it from multiple angles, considering a variety of possible interpretations. That, after all, is what the scientific method is all about.

In fact, you don't have to be a student, a teacher, or a scientist to engage in scientific inquiry. Thinking critically is for adults, all adults, too. Teller notes:

It's not possible for everyone -- or anyone -- to be sufficiently well trained in science to analyze data from multiple fields and come up with sound, independent interpretations. I spent decades in medical research, but I will never understand particle physics, and I've forgotten almost everything I ever learned about inorganic chemistry. It is possible, however, to learn enough about the powers and limitations of the scientific method to intelligently determine which claims made by scientists are likely to be true and which deserve skepticism. [Emphasis added.]

Yes, exactly! It is possible. Although Teller goes on to echo the media's normal neo-Darwinian rhetoric -- extol inquiry, but affirm the validity of dogmatic belief in evolution -- what she says there could not be more right.

From the ark?

New Paper in Evolution Journal: Humans and Animals Are (Mostly) the Same Age?
Andrew Jones

Could it be that animals were designed together with humans and instantiated at the same time too? Or did they get off the same spaceship? Or off the same boat?
An exciting new paper in the journal Human Evolution has been published which you can read here. Popular science reports such as this have incautiously claimed, “They found out that 9 out of 10 animal species on the planet came to being at the same time as humans did some 100,000 to 200,000 years ago.”

But to be more precise, what they actually found is that the most recent common ancestor of those species seems to have lived during that time period. 

This could indicate intelligent design, an event where species came into existence for the first time. But it could also indicate something else, such as a population crash (or crashes) that affected almost all life on Earth. Either way, if the paper is right, it would be a shock to established scientific expectations.

“This conclusion is very surprising,” co-author David Thaler of the University of Basel is quoted as saying, “and I fought against it as hard as I could.” His co-author is fellow geneticist Mark Stoeckle of Rockefeller University in New York.


Here is how the scientific reasoning works:

Nucleotide diversity π is the average number of differences per site between two aligned nucleotide sequences. The differences are assumed to be due to mutations accumulated on both sequences since they diverged. Therefore the nucleotide diversity π should be twice the mutation rate multiplied by the time to common ancestor of those sequences:  π = 2 μ T, where μ is the mutation rate per generation and T is the time since the common ancestor in generations.

If ordinary steady neutral evolution has been happening, then the time to common ancestor is expected to be about N, the effective population size. Therefore the nucleotide diversity is expected to be about 2 μ N. 

The mutation rate μ shows some variation, but N is believed to vary widely across the animal kingdom. Therefore the nucleotide diversity that we observe should vary widely too. 


But, according to these authors using data from the BOLD database, the nucleotide diversity does not vary greatly. Instead, these authors find that for 90% of all species, the observed levels of π suggest that T falls within the last 100-200kYr.

I am intrigued, but to be honest, I don’t quite know what to make of it just yet, and don’t want to jump to any conclusions. This kind of inference is complicated; the paper does not explain where they sourced estimates of mutation rate and effective population size. 


Moreover, studies of different kinds of sequences can seem to tell widely different stories. In an earlier paper from 2014,the authors point out that the idea of a single global population crash is, “almost a Noah’s Ark hypothesis,” though “This appears unlikely.” They speculate instead that “perhaps long-term climate cycles might cause widespread periodic bottlenecks.” 

In any case, one thing is clear: reconstructing the past is a complicated business and it is still full of surprises. There may be even bigger surprises in store.

Scientism's attempted shotgun wedding?

In Defense of Theistic Evolution, Denis Lamoureux Rewrites History
Jonathan Witt | @JonathanRWitt

Writing in the Journal of the American Scientific Affiliation, Denis O. Lamoureux has published a dismissive review of Theistic Evolution: A Scientific, Philosophical, and Theological Critique.

The review article’s title, “Intelligent Design Theory: The God of the Gaps Rooted in Concordism,” deftly signals Lamoureux’s two-pronged strategy: First, paint intelligent design as a fallacious God-of-the-gaps argument (when in fact it’s an argument to the best explanation  based on what we know).

And second: Motive monger — in this case, by attributing the anthology’s conclusions to a religious motivation while giving short shrift to the book’s hundreds of pages of scientific evidence and argument.

Those criticisms of ID are low-hanging fruit for the writers at Evolution News, but here I want to focus on another problem with the review.

Scientism’s Grand Progress Narrative

At one point early on, Lamoureux confidently asserts the following:

First, according to a God-of-the-gaps approach to divine action, there are “gaps” in the continuum of natural processes, and these “discontinuities” in nature indicate places where God has miraculously intervened  in the world. …

If there are gaps in the continuum of natural processes, then science will identify them, and over time these gaps will “widen” with further research. That is, as scientists explore a true gap in nature where God has intervened, evidence will increase and demonstrate that there are no natural mechanisms to account for the origin or operation of a physical feature.

There is an indisputable pattern in the history of science. The God-of-the-gaps understanding of divine action has repeatedly failed. Instead of the gaps in nature getting wider with the advance of science, they have always been closed or filled by the ever-growing body of scientific information. In other words, history reveals that these purported gaps have always been gaps in knowledge  and not actual gaps in nature  indicative of the intervening hand of the Lord.

The lesser problem here is his tendentious use of the word “gaps.” The language suggests that it’s somehow a failure of God for the universe to be something less than a deist’s fantasy — a grand pool shot from the Big Bang without any need for subsequent creative involvement. That’s an aesthetic presupposition, and a manifestly suspect aesthetic presupposition.

That’s the lesser problem with the quote above, a problem  to delve into more fully at another time. Here I want to highlight the more glaring problem: Lamoureux’s assertion of “an indisputable pattern in the history of science.” The alleged historical pattern is manifestly untrue.

It was given formal structure by the 19th-century French philosopher August Comte, but in common parlance the claim runs something like this:

Humans used to attribute practically every mysterious force in nature to the doings of the gods. They stuffed a god into any and every gap in their knowledge of the natural world, shrugged, and moved on. Since then, the number of gaps has been shrinking without pause, filled with purely material explanations for everything from lightning bolts to romantic attraction. The moral of this grand story: always hold out for the purely material explanation, even when the evidence seems to point in the other direction. Materialism, in other words, is our manifest destiny; get used to it colonizing every cause in the cosmos.

This grand progress narrative is regularly employed with great confidence, but it’s contradicted by key developments in the physical and life sciences.

For example, through much of the 19th century, the scientific consensus was that microscopic life was relatively simple, little more than microscopic sacks of Jell-O. The scientific community also accepted the idea of spontaneous generation — that creatures sprang to life spontaneously out of things like dew and rotting meat. Taken together, these pieces of conventional scientific wisdom suggested that the origin of the first living cell deep in the past was hardly worthy of the term “mystery” — a material explanation seemed obvious.

But in 1861 Louis Pasteur conducted a series of experiments that discredited the notion of spontaneous generation. And in the next century, scientists began amassing evidence of just how complex even the simplest cell is. Today we know that cells are micro-miniaturized factories of astonishing sophistication and that, even more to the point, such sophistication is essential for them to be able to survive and reproduce.Origin-of-life researchers concede  that no adequate material explanation has been found for the origin of the cell.

So, we have come to learn that spontaneous generation was a fantasy. We have discovered that even the simplest cells are highly sophisticated and information-rich organisms. And the only cause we have ever witnessed actually producing novel information is intelligent design. Thus, modern scientific observations have collapsed a long-standing material explanation for the origin of life and simultaneously strengthened the competing design explanation. This development runs directly counter to scientism’s grand narrative.

A common rebuttal is that inferring design in such cases amounts to “giving up on science,” and that science should always hold out for a purely material explanation. But this is mere question begging. What if the first living cell really was the work of intelligent design? Being open to that possibility and following the evidence isn’t giving up on science but on scientism, a dogma resting on a progress narrative flatly contradicted by the historical record.

Evidence from Cosmology

Cosmology and physics provide another counter-example to the grand narrative Lamoureux asserts. In Darwin’s time, conventional scientific wisdom held that the universe was eternal. Given this, it was broadly assumed that there could hardly be any mystery about its origin: it simply had always existed. But developments in physics and astronomy have overturned the easy embrace of an eternal cosmos, and scientists are now in broad agreement that our universe had a beginning. What many thought had never happened and so required no explanation — the origin of the universe — suddenly cried out for an explanation.

Near the same time that scientists were realizing this, there was a growing awareness of what is now widely known in cosmology as the fine-tuning problem. This is the curious fact that the various laws and constants of nature appear finely calibrated to allow for life in the universe — calibrated to such a precise degree that even committed materialists have abandoned blunt appeals to chance.

To explain away this problem, the disciples of scientism have now resorted to saying there must be countless other universes, with our universe simply being one of the lucky ones with the right configuration to allow intelligent life to evolve.

Not every physicist has played along. Several, including some Nobel laureates, have assessed the growing body of evidence for fine-tuning and pointed to intelligent design as the most reasonable explanation. Physicist and Nobel laureate Charles Townes put it this way:

Intelligent design, as one sees it from a scientific point of view, seems to be quite real. This is a very special universe: it’s remarkable that it came out just this way. If the laws of physics weren’t just the way they are, we couldn’t be here at all. The sun couldn’t be there, the laws of gravity and nuclear laws and magnetic theory, quantum mechanics, and so on have to be just the way they are for us to be here.

Scientism’s grand progress narrative holds that as we learn more and more about the world, purely natural or material explanations inevitably will arise and grow stronger, while design arguments will inevitably collapse under the weight of new discoveries. But the opposite has happened in cosmology and origin-of-life studies.

Despite this, Lamoureux and other critics of intelligent design go right on recycling their grand narrative as if it were the whole truth and nothing but the truth. It is not. It ignores truths both historical and scientific.