I.D,the limits of science and the nature of design opponents' propaganda.

The Darwinist Misinformation Train:
Casey Luskin September 7, 2005 12:55 PM:

A good friend of mine getting his teaching credential to teach public high school called me this weekend to converse about his professor’s response to a paper he wrote supporting the teaching of ID. Apparently his professor disapproved of teaching ID because he felt that ID was untestable science. The professor’s criticism went something like this:

“My main problem with ID is that it purports to not identify the designer when everyone knows it's really just God. Intelligent design thus shouldn’t be taught because it is essentially creation science repackaged. Thus, it’s just an untestable appeal to the supernatural. However, if I had to choose, I would actually prefer creation science to ID because at least creation scientists are up-front about who they think the designer is.”
This view was also echoed recently in the Seattle Weekly, where a commentator threw in a not-so-subtle, below-the-belt criticism about ID:
“[ID is] the notion … that an unspecified creator (who sounds an awful lot like the Christian notion of God) is responsible for the creation and development of everything, including human beings.”
Without nitpicking over the many inaccurate details of this description, here again we see the same implicit criticism of ID: "ID proponents say it doesn’t identify the designer, but everybody knows the designer is “God” [at this point, Eugenie Scott adds in her famous “wink wink, nudge nudge” line], therefore it isn’t science."
I found this criticism interesting, because a different article on the same day made the exact opposite criticism against intelligent design: ID isn’t science because it supposedly DOES identify the designer as a supernatural deity. This very point was argued recently by University of Utah bioengineering professor Gregory Clark before the Utah State Board of Education:
“Intelligent design fails as science because it does exactly that - it posits that life is too complex to have arisen from natural causes, and instead requires the intervention of an intelligent designer who is beyond natural explanation. Invoking the supernatural can explain anything, and hence explains nothing.”

These misconstruals are not mere trivialities. In fact, they form the basis for the ACLU's lawsuit against teaching intelligent design in Dover, Pennsylvania (Kitzmiller et al. v. Dover Area School District). As read in their complaint:

"Intelligent design is a non-scientific argument or assertion, made in opposition to the scientific theory of evolution, that an intelligent, supernatural actor has intervened in the history of life..."

So on the one hand, intelligent design fails as science because it does identify the designer as supernatural. On the other hand, intelligent design fails because it doesn’t identify the designer. Both positions can’t be right. But what does intelligent design really say, and can it overcome these criticisms?
The truth about ID:
Had my friend’s professor, or Dr. Clark, bothered to actually read (and / or choose to accurately represent) the writings of ID proponents, they would have found this matter of the designer’s identity to be crystal clear:

"Intelligent design is modest in what it attributes to the designing intelligence responsible for the specified complexity in nature. For instance, design theorists recognize that the nature, moral character and purposes of this intelligence lie beyond the competence of science and must be left to religion and philosophy." (William Dembski, The Design Revolution, pg. 42)
"Although intelligent design fits comfortably with a belief in God, it doesn't require it, because the scientific theory doesn't tell you who the designer is. While most people - including myself - will think the designer is God, some people might think that the designer was a space alien or something odd like that." (Michael Behe, Pittsburgh Post-Gazette, 02/08/01).

"[T]the place of intelligent design in science has been troubling for more than a century. That is because on the whole, scientists from within Western culture failed to distinguish between intelligence, which can be recognized by uniform sensory experience, and the supernatural, which cannot. Today we recognize that appeals to intelligent design may be considered in science, as illustrated by current NASA search for extraterrestrial intelligence (SETI). Archaeology has pioneered the development of methods for distinguishing the effects of natural and intelligent causes. We should recognize, however, that if we go further, and conclude that the intelligence responsible for biological origins is outside the universe (supernatural) or within it, we do so without the help of science." (Of Pandas and People, a pro-ID textbook, pg. 126-127, emphasis added)

Reading these quotes from leading ID theorists makes it completely clear that ID theory does not identify the designer, and cannot even really get very far into elaborating upon the nature of the designer. The reason for this is also clear: there are natural empirical limitations to what science can study. If we can’t study the identity of the designer, that’s not ID’s fault, that’s just the nature of the limits of science.
Why then do so many Darwinists publicly criticize ID as if it has the very weakness (i.e. advocating for an explicitly supernatural creator) which it goes out of its way to clearly avoid? The answer is simple: mischaracterizing ID as an appeal to the supernatural places it both outside the scope of science, and also outside legal rules laid down in Edwards v. Aguillard for legitimate origins ideas. But the whole notion that ID does identify the designer as supernatural is false.

The Darwinist Misinformation Train:
I have a 3 step theory for how it comes to pass that many people come to believe that intelligent design is an appeal to the supernatural:

Type I Darwinists critics: It starts with these Darwinist critics who correctly understand ID and realize that it respects the limits of science and doesn’t try to identify the designer. Yet, Type I Critics then purposefully misrepresent ID to the public (and particularly to scientists) as an untestable and unscientific appeal to the supernatural. This is despite the fact that ID proponents understand the nature of scientific inquiry and have formulated their theory to respect its boundaries. The dubious tactics of Type I critics are effective because it results in many people thinking that ID cannot be science because it makes claims about the supernatural -- beyond the scope of what can be studied using the scientific method.
Type II Darwinist critics: These are the people created by the activities of Type I critics. Type II critics misunderstand ID because they have been told by Type I critics that ID is an untestable appeal to the supernatural. This causes them to think it is makes exclusively religious claims, is not scientific, not empirically based, and not appropriate for the laboratory or the classroom. Type II Critics aren’t necessarily to blame for their misapprehensions because they have been misled. Nonetheless, it would behoove them to pick up some of the scholarship of ID proponents they are criticizing before they speak about it publicly. If they did so, they would realize their misunderstandings.
The Public: The Public consists of the people out there who are trying to figure out ID. Some of them may have read books or other literature by ID proponents and know the truth. But, for the most part, the public has been misled by Type I and Type II critics who are telling them that ID is an unscientific appeal to the supernatural, and shouldn’t be studied in labs or taught in science classes.


Though Type II critics are more honest and genuine than Type I critics, both have a common goal: make sure that ID gets construed such that the designer turns out to be a supernatural deity, because then it’s very easy to argue that it isn’t science (and isn’t constitutional to teach). This results in momentum for the Darwinist misinformation train:Some Darwinists critics want to get the ID train from Point A (reality) to Point B (fiction).

Point A represents the actual nature of intelligent design theory, where ID respects the limits of scientific inquiry and cannot identify the designer. At point A, ID relies upon the scientific method and makes no faith-based appeals to God. Here, it is pure science.

Point B represents where Darwinists would like to take ID theory: where it is an explicit appeal to the supernatural, and thus does not respect the inherent limitations of the scientific method. At point B, ID would have a clearly religious component as it identifies the designer as God. This would make it both unscientific and unconstitutional. Point B is fiction, because, of course, ID respects science and is ultra clear that the theory cannot identify the designer and avoids such religious claims.

Type I critics provide momentum for the train by misinforming the other scientists about intelligent design theory. Having spawned many genuinely believing (but ultimately wrong) Type II critics, both Type I and Type II critics go out to the public to press the case that ID shouldn’t be taught because it is an unscientific appeal to the supernatural.This is another way of representing the misinformation about intelligent design theory: The Misinformation Pyramid Scheme which makes use of the “Trickle Down Theory” of misinformation. Under their model, Type I Critics at the top purposefully misinform scientists and others about the nature of ID theory. Type I critics and their followers (Type II critics) then, relying upon a false understanding of intelligent design (some realizing that falsity, some not), go out and tell the public that ID is supposedly not science and should not be taught in schools, because they wrongly state is an unscientific appeal to the supernatural. In the end, the public is the real loser because they miss out on an accurate understanding of a new and potent scientific theory: ID.

Being Honest
But there are many honest Darwinists out there, like my friend’s professor, who acknowledges that ID does not identify the designer. However, my friend's professor still misunderstands ID because he then turned this strength of ID into a criticism by saying that it doesn’t matter what ID theory says, because we know the designer must be God, therefore ID isn't science. This argument makes no sense: if ID doesn't identify the designer, then how can one claim that ID theory says designer is God? It requires a misconstrual of ID theory which probably stems from critics mistaking some religious beliefs of ID proponents for the conclusions of ID theory.

For example, William Dembski, who in the above quote makes it ultra-clear that ID theory can’t identify the designer, is also clear elsewhere that he believes the designer is indeed God. In fact, when Dembski talks about the identity of the designer, he is often misquoted (the “Logos quote” comes to mind) by reporters and Darwinists who try to twist Dembski’s words into saying that it is ID theory which says the designer is God. This is unfortunate because Dembski makes it clear that he does not derive his beliefs about the identity of the designer from ID theory. Rather, when he identifies the designer, he does so not from ID theory, but from out of his own Christian religious faith.

Darwinists who think that they can misconstrue ID as if it identifies the designer as God simply because they can point to the beliefs of some ID proponents, are using a specious argument. To be accurate and truthful, one has to accept the way ID has been formulated by its proponents. And given the above quotes, there is little doubt as to how ID theory actually works: it can’t identify the designer.

(Besides, if the critics are right and ID theory mandates that the designer is God, then what about those ID sympathizers who aren’t religious—like the agnostic philosopher Antony Flew?)

The moral of this story is that you can’t go from Point A to Point B by going in opposite directions. Darwinists can’t criticize ID on the one-hand because it does identify the designer as supernatural, and then on the other-hand because it doesn’t, and then both claim that ID isn’t science. For those interested, the truth is that ID theory does not identify the designer, doesn’t even focus on studying the designer. While ID proponents may have beliefs about the designer, those beliefs are not derived from ID theory.

Of course, in the end, for all the Type I Critics out there, it doesn’t really matter what I write or whether or not I show clear documentation about how ID theory cannot identify the designer. But for those who are interested in taking ID seriously, I hope they will echo my desire that this Misinformation Train gets stuck at the reality station.

Thanks for reading.

Another failed Darwinian prediction IV

Mutations are not adaptive:

In the twentieth century, the theory of evolution predicted that mutations are not adaptive or directed. In other words, mutations were believed to be random with respect to the needs of the individual. As Julian Huxley put it, “Mutation merely provides the raw material of evolution; it is a random affair, and takes place in all directions. … in all cases they are random in relation to evolution. Their effects are not related to the needs of the organisms.” (Huxley, 36) Or as Jacques Monod explained:

chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact. And nothing warrants the supposition—or the hope—that on this score our position is likely ever to be revised. (Monod, 112)

Ronald Fisher wrote that mutations are “random with respect to the organism’s need” (Orr). This fundamental prediction persisted for decades as a recent paper explained: “mutation is assumed to create heritable variation that is random and undirected.” (Chen, Lowenfeld and Cullis)

But that assumption is now known to be false. The first problem is that the mutation rate is adaptive. For instance, when a population of bacteria is subjected to harsh conditions it tends to increase its mutation rate. It is as though a signal has been sent saying, “It is time to adapt.” Also, a small fraction of the population increases its mutation rates even higher yet. These hypermutators ensure that an even greater variety of adaptive change is explored. (Foster) Experiments have also discovered that duplicated DNA segments may be subject to higher mutation rates. Since the segment is a duplicate it is less important to preserve and, like a test bed, appears to be used to experiment with new designs. (Wright)

The second problem is that organisms use strategies to direct the mutations according to the threat. Adaptive mutations have been extensively studied in bacteria. Experiments typically alter the bacteria food supply or apply some other environmental stress causing mutations that target the specific environmental stress. (Burkala, et. al.; Moxon, et. al; Wright) Adaptive mutations have also been observed in yeast (Fidalgo, et. al.; David, et. al.) and flax plants. (Johnson, Moss and Cullis) One experiment found repeatable mutations in flax in response to fertilizer levels. (Chen, Schneeberger and Cullis) Another exposed the flax to four different growth conditions and found that environmental stress can induce mutations that result in “sizeable, rapid, adaptive evolutionary responses.” (Chen, Lowenfeld and Cullis) In response to this failed prediction some evolutionists now are saying that evolution somehow created the mechanisms that cause mutations to be adaptive.

References

Burkala, E., et. al. 2007. “Secondary structures as predictors of mutation potential in the lacZ gene of Escherichia coli.” Microbiology 153:2180-2189.

Chen, Y., R. Lowenfeld, C. Cullis. 2009. “An environmentally induced adaptive (?) insertion event in flax.” International Journal of Genetics and Molecular Biology 1:38-47.

Chen, Y., R. Schneeberger, C. Cullis. 2005. “A site-specific insertion sequence in flax genotrophs induced by environment.” New Phytologist 167:171-180.

David, L., et. al. 2010. “Inherited adaptation of genome-rewired cells in response to a challenging environment.” HFSP Journal 4:131–141.

Fidalgo, M., et. al. 2006. “Adaptive evolution by mutations in the FLO11 gene.” Proceedings of the National Academy of Sciences 103:11228-11233.

Foster, P. 2005. “Stress responses and genetic variation in bacteria.” Mutation Research / Fundamental and Molecular Mechanisms of Mutagenesis 569:3-11.

Huxley, Julian. 1953. Evolution in Action. New York: Signet Science Library Book.

Johnson, C., T. Moss, C. Cullis. 2011. “Environmentally induced heritable changes in flax.” J Visualized Experiments 47:2332.

Monod, Jacques. 1971. Chance & Necessity. New York: Vintage Books.

Moxon, E., et. al. 1994. “Adaptive evolution of highly mutable loci in pathogenic bacteria.” Current Biology 4:24-33.

Orr, H. 2005. “The genetic theory of adaptation: a brief history.” Nature Review Genetics 6:119-127.

Wright, B. 2000. “A biochemical mechanism for nonrandom mutations and evolution.” J Bacteriology 182:2993-3001.

The Watchtower Society's commentary on Mildness

MILDNESS:
A New Testament Wordbook, by William Barclay, says of the adjective pra·ysʹ: “In classical Greek this is a lovely word. Of things it means ‘gentle’. It is used, for instance, of a gentle breeze or a gentle voice. Of persons it means ‘mild’ or ‘gracious’. . . . There is gentleness in praus but behind the gentleness there is the strength of steel . . . It is not a spineless gentleness, a sentimental fondness, a passive quietism.” (London, 1956, pp. 103, 104) Vine’s Expository Dictionary of Old and New Testament Words states that the noun form pra·yʹtes “consists not in a person’s ‘outward behaviour only; nor yet in his relations to his fellow-men; as little in his mere natural disposition. Rather it is an inwrought grace of the soul; and the exercises of it are first and chiefly towards God. It is that temper of spirit in which we accept His dealings with us as good, and therefore without disputing or resisting; it is closely linked with the word tapeinophrosunē [humility], and follows directly upon it.’”—1981, Vol. 3, pp. 55, 56.

The word pra·ysʹ is variously translated in Bible versions “meek,” “mild,” “mild-tempered,” and “gentle.” (KJ, AS, NW, NE) However, as expressed in Barclay’s work quoted in the foregoing, pra·ysʹ goes somewhat deeper than gentleness and, when used of persons, means mild, gracious.

Although Jehovah is one who will not tolerate sin and badness, he has lovingly provided the way of approach to himself through the ransom sacrifice and priestly services of Jesus Christ. Jehovah’s worshipers and servants can therefore seek his face without any feeling of morbid fear and dread. (Heb 4:16; 10:19-22; 1Jo 4:17, 18) Jesus represented Jehovah God so perfectly that he could say: “He that has seen me has seen the Father also.” He also said: “Come to me, all you who are toiling and loaded down, and I will refresh you. Take my yoke upon you and learn from me, for I am mild-tempered [Gr., pra·ysʹ] and lowly in heart, and you will find refreshment for your souls. For my yoke is kindly and my load is light.” (Joh 14:9; Mt 11:28-30) Accordingly, Jehovah God is fully approachable by those who love him, and he generates mildness, great confidence, and strength in those appealing to him.

A Trait of Strength. Mildness of temper or of spirit is not an attribute of one weak in character. Jesus Christ said: “I am mild-tempered and lowly in heart.” (Mt 11:29; 2Co 10:1) Yet Jesus had the full power of his Father backing him, and he was firm for what is right; he used great freeness of speech and action when such was called for.—Mt 23:13-39; compare 21:5.

The mild-tempered person is such because he has faith and a source of strength. He is not easily unbalanced or caused to lose his good sense. Lack of mildness of temper is the result of insecurity, frustration, lack of faith and hope, and even desperation. A person who is not mild-tempered is described by the proverb: “As a city broken through, without a wall, is the man that has no restraint for his spirit.” (Pr 25:28) He is open and vulnerable to the invasion of any and all improper thoughts, which may motivate him to improper actions.

A Fruit of the Spirit. Mildness is a fruit of God’s holy spirit, his active force. (Ga 5:22, 23) God is therefore the Source of mildness, and one must apply to him for his spirit and must cultivate this fruit of the spirit to have genuine mildness of temper. Hence, it is not acquired by the exercise of sheer willpower, but results from drawing close to God.

Lack of mildness results in undue excitability, harshness, lack of self-control, and fights. On the other hand, the Christian is counseled to preserve unity and peace by “lowliness of mind and mildness.”—Eph 4:1-3.

Jealousy and contention, if allowed to take root and grow, will lead to disorders of every sort. Mildness, on the other hand, will prevent such conditions from developing among the followers of Christ. Hence, the Bible writer James urges those who are wise and understanding in the congregation to display “fine conduct” in the form of “mildness that belongs to wisdom,” “the wisdom from above.”—Jas 3:13, 17.

“Mildness,” in the Bible, is frequently coupled with “spirit,” for example, “mildness of spirit,” or “mild spirit.” Genuine mildness is, accordingly, something that is more than an outward, transitory or occasional quality; rather, it is a part of one’s makeup, or temperament. The apostle Peter points out this fact when he says: “And do not let your adornment be that of the external braiding of the hair and of the putting on of gold ornaments or the wearing of outer garments, but let it be the secret person of the heart in the incorruptible apparel of the quiet and mild spirit, which is of great value in the eyes of God.”—1Pe 3:3, 4.

The apostle Paul writes: “Clothe yourselves with . . . mildness,” which, superficially read, might seem to indicate that it is somewhat of a veneer for mere outward appearance; but in the same context he admonishes: “Clothe yourselves with the new personality, which through accurate knowledge is being made new according to the image of the One who created it.” (Col 3:10, 12; Eph 4:22-24) This shows that mildness is indeed a personality trait, primarily gained as a fruit of God’s spirit through accurate knowledge and application thereof, rather than just naturally inherited.

Essential for Those Having Oversight. In his letter of instructions to young Timothy on proper care of the congregation, Paul commanded him as to handling difficult matters, saying: “A slave of the Lord does not need to fight, but needs to be gentle toward all, qualified to teach, keeping himself restrained under evil, instructing with mildness those not favorably disposed; as perhaps God may give them repentance.” (2Ti 2:24, 25) Here we see a similarity between mildness and long-suffering. The individual realizes why he has to deal with the difficulty: God has permitted it, and as an overseer he must handle it in the best interests of the individual(s) involved. He must put up with the difficulty until it is settled, without getting overwrought.

Titus, another overseer, residing in Crete, was likewise counseled to remind his Christian brothers “to be reasonable, exhibiting all mildness toward all men.” To impress upon Titus the need for mildness, Paul calls attention to the unsurpassed love and mercy of God as manifested through his Son, calling for a forsaking of the old ways of maliciousness and hatred and following the new way leading to everlasting life.—Tit 3:1-7.

Again, Paul addresses those who are spiritually mature ones in the congregation, outlining the responsibility upon them: “Even though a man takes some false step before he is aware of it, you who have spiritual qualifications try to readjust such a man in a spirit of mildness, as you each keep an eye on yourself, for fear you also may be tempted.” (Ga 6:1) They should keep in mind how God has dealt with them. Doing so, they should not give the erring man a harsh reprimand but should try to readjust him in a spirit of mildness. This will prove to be far more effective and beneficial to all concerned.

Mildness will accomplish good when dealing with a difficult situation or an angry person, breaking down difficulty, whereas harshness would magnify the bad situation. The proverb says: “An answer, when mild, turns away rage, but a word causing pain makes anger to come up.” (Pr 15:1) Mildness can have great force. “By patience a commander is induced, and a mild tongue itself can break a bone.”—Pr 25:15.

Essential When Under Discipline. Another fine principle involving mildness or calmness is set forth by Solomon. It concerns the tendency we may have to show a rebellious spirit when corrected or chastised by one in authority. We may get so indignant as to leave our place of proper submission, hastily giving up our assigned position. But Solomon warns: “If the spirit of a ruler should mount up against you, do not leave your own place, for calmness itself allays great sins.” (Ec 10:4; compare Tit 3:2.) The proper attitude of calmness and mildness under discipline not only avoids further anger from the authority but also enables us to improve our personality through keeping our temper and our assigned place, or position, and applying the discipline.


This is especially true when the ruler is Jehovah God and when discipline comes through those set in authority by him. (Heb 12:7-11; 13:17) It also applies in our relationship to those permitted by God to wield worldly governing authority. (Ro 13:1-7) Even when such a ruler may make a harsh demand of the Christian as to the reason for the hope he has, the Christian, while firmly putting obedience to God first, should answer “with a mild temper and deep respect.”—1Pe 3:15.

On the British Monarchy

A whale of a challenge for Darwinism.

In search of earth 2.0

Common design vs. common descent

Modular Paint-Box Explains Butterfly Color Patterns:
Evolution News & Views January 21, 2016 12:32 AM

Butterflies of the Amazon exhibit astonishing beauty and diversity. The Heliconius genus, in particular, is striking for its examples of mimicry, where members of different species have converged on the same color patterns on their wings. Collections of these butterflies can be arranged into series where yellow and red spots grow and shrink, grading into one another. How did this diversity come about?

The usual answer is Darwinian evolution -- a mutation of a gene leading to a novelty, then common ancestry and natural selection. A new model, published in PLOS Biology, does not dispute that kind of evolution, but offers different mechanisms that fit with intelligent design. As the authors discuss in news from the University of Cambridge, it's a story of shared technology.

Research finds independent genetic switches control different splotches of colour and pattern on Heliconius butterfly wings, and that these switches have been shared between species over millions of years, becoming "jumbled up" to create new and diverse wing displays. [Emphasis added.]

Everything else about the butterflies appears normal; the body anatomy; the antennae; even the basic wing shape. It's primarily the color splotches that vary. Each one has a so-called dennis patch at the base of the wing, and red "ray" streaks that fan out across the hindwing. Within any individual, though, the patterns remain symmetrical: the left wing is a mirror image of the right wing.

The Cambridge researchers looked at the genomes of dozens of specimens.

New research on butterfly genomes has revealed that the genetic components that produce different splotches of colour on wings can be mixed up between species by interbreeding to create new patterns, like a "genetic paint box."

This is not the usual mutation-selection mechanism of Darwinian evolution, in other words. The researchers believe that existing genetic switches can be "shared" between species by interbreeding, hybridization and introgression, a process of gene flow from one species into another population that results from repeated backcrossing of an interspecific hybrid with one of its parent species.

Novelty is not originating by mutation, in short, but rather by new combinations of genetic switches that were already present. Interbreeding and hybridization shuffles these genetic switches that turn particular colors on and off in different parts of the wings. Is this type of sharing common in the world?

It has been known for some time that exchange of genes between species can be important for evolution: humans have exchanged genes with our now extinct relatives which may help survival at high altitudes, and Darwin's Finches have exchanged a gene that influences beak shape. In butterflies, the swapping of wing pattern elements allows different species to share common warning signs that ward off predators -- a phenomenon known as mimicry.

However, the new study, published today in the journal PLOS Biology, is the first to show such mixing of genetic material can produce entirely new wing patterns, by generating new combinations of genes.

One wonders if these researchers realize they have undermined Neo-Darwinism in these famous examples. Swapping of genetic elements does not require mutation and selection. Moreover, early humans, finches and butterflies had to be able to interbreed or at least hybridize to benefit from the shared information.

The authors state that these switches evolved just once, then are used in different parts of the wings. In different individuals, they can see little regions of color "jumping about all over the place." And because of pleiotropy -- the linkage of the color function to other functions on the gene -- the gene itself cannot evolve:

The key to this evolutionary butterfly painting is the independence of each genetic switch. "The gene that these switches are controlling is identical in all these butterflies, it is coding for the same protein each time. That can't change as the gene is doing other important things," said lead author Dr Richard Wallbank, also from Cambridge's Department of Zoology.

"It is the switches that are independent, which is much more subtle and powerful, allowing evolutionary tinkering with the wing pattern without affecting parts of the genetic software that control the brain or eyes.

"This modularity means switching on a tiny piece of the gene's DNA produces one piece of pattern or another on the wings -- like a genetic paint box," Wallbank said.

We must not get confused about the meaning of "evolution" in these papers. The wing patterns may vary, but all the species are members of one genus. We're looking at a mechanism for robustness and flexibility that is consistent with intelligent design. In the tropics where these butterflies live, the ability to try out new color patterns can be advantageous to attract mates and avoid predators. These are tiny changes to combinations of existing switches, not matters of great transformations, such as gaining a new organ. It's mere shuffling of what already exists.

The paper is even more emphatic about nature preventing novelty by mutation:

One of the major impediments to evolutionary innovation is the constraint on genetic change imposed by existing function. Mutations that confer advantageous phenotypic effects in a novel trait will often result in negative pleiotropic effects in other traits influenced by the same gene. Several mechanisms have been proposed by which evolution can circumvent such constraints, resulting in phenotypic diversification. In particular, the modularity of cis-regulatory elements means that novel modules can encode new expression domains and functions without disrupting existing expression patterns. This modularity underlying gene regulation has led to the assertion that much of morphological diversity has arisen through regulatory evolution.

What does this do to old-fashioned Darwinian gradualism?

This might seem to imply that the evolution of novel regulatory alleles is relatively gradual, requiring the evolution of many small effect substitutions, but recent adaptive radiations can show extremely rapid rates of morphological change. The role of regulatory modularity therefore remains to be tested in adaptive radiations in which morphological variation evolves very rapidly.

Although this paper is full of the word "evolution," it's really a different concept they are proposing.

We show that two patterning switches -- one that produces red rays on the hindwing and the other a red patch on the base of the forewing -- are located adjacent to one another in the genome. These switches have each evolved just once among a group of 16 species but have then been repeatedly shared between species by hybridisation and introgression. Despite the fact that they are now part of a common pattern in the Amazon basin, these two pattern components actually arose in completely different species before being brought together through hybridisation. In addition, recombination among these switches has produced new combinations of patterns within species. Such sharing of genetic variation is one way in which mimicry can evolve, whereby patterns are shared between species to send a common signal to predators. Our work suggests a new mechanism for generating evolutionary novelty, by shuffling these genetic switches among lineages and within species.

In addition, they appeal to "convergent evolution" to explain some spectacular cases of mimicry. But if this were all due to chance, why are the patterns symmetrical? What about Darwinian mechanisms would require the left and right wings match?

None of what they describe requires neo-Darwinism or supports macroevolution. The switches were already there. They only control how much color goes into each spot. They can be shared within and across species by shuffling mechanisms, allowing rapid changes in wing patterns. It sounds like a great way for butterflies to quickly send different signals in different situations, so that they remain viable. Think of a flagman, using the same flags but in different combinations to send different messages. The flags were already there, and the man (or a programmable robot) knows how to use them.

Evolutionists have focused long and hard on the patterns on butterfly wings, which indeed are interesting, but they need to explain the weightier matters: how an egg becomes a crawling caterpillar, enters a chrysalis, and emerges a flying butterfly. As illustrated in Metamorphosis: The Beauty and Design of Butterflies, that's like turning a Model T into a helicopter.


The very traits they have focused on (wing patterns) turn out to be non-Darwinian and restrained by pleiotropy, reliant on "switches" that look designed. How much more must the critical organs for digestion, reproduction, and flight require specific information targeted for those functions? Only intelligence creates that kind of information.

A clash of titans V

Civil War IV

PZ Myers on Royal Society “rethink evolution” meet:
January 19, 2016 Posted by News under Evolution, Darwinism

But that’s not how science works.”

From his blog Pharyngula,
Larry Moran is attending — not as a representative of the crackpot contingent, but, I suspect, to cast a cynical eye on the shenanigans. The Third Way of Evolution gang seems to be excited about the meeting, which is not a good sign — these are people who have taken some useful ideas in evolutionary theory, like epigenetics and niche construction, and turned the dial up to 11 to argue that these concepts are so revolutionary that they demand a complete upheaval of neo-Darwinian thinking.
Many evidence-based concepts do demand it, actually.

What’s changed is this: Darwinism (natural selection acting on random mutation) was once a default explanation of change in life forms over time. Now it competes with a variety of evidence-based explanations. The question is, which one or combination best explains the pattern we see in a given case?

From a lay perspective, it is somewhat like this: We grew up with Big Phone, Inc.’s monopoly on communications (cross them, and your best bet is smoke signals on a windless hill).

Then we moved, and found ourselves in a region where five different phone companies’ signals are carried through the wires and towers. So which one is best for a given situation? We must think about that.

Meanwhile, Big Phone is shrieking from the sidelines that all this chaos is a disaster. Mainly, it appears, for Big Phone. Most communicators have never been more connected than now, for better or worse. But back to Myers:

… And, unfortunately, I’ve just learned that the Queen of Hyperbolic Revolutionary Evolution, Susan Mazur, Journalistic Flibbertigibbent, is all wound up about it, which is also not a good sign. She’s raving about Paradigm-Shifters who will come up with a replacement for the modern synthesis.


The correct term and pronunciation is “flibbertigibbet,” Dr. Myers.Flibbertigibbets like Mazur are what happens to people who are tone deaf.

As we mentioned in connection with University of Toronto’s Larry Moran a couple months back,
Moran also misses the point about interviewer Suzan Mazur, of whom he says dismissive things. When journalists who publish in key venues become interested in an otherwise obscure train wreck, we can reasonably suspect that a shift is taking place. That’s why we call it “news” and not “olds.”
Myers also shares this insight:
Mazur clearly has no idea at all how science works. Twenty people attending a meeting don’t get to suddenly declare that a theory is replaced, and I don’t care who they are. More.
Yes, maybe twenty is too many. Even one person can replace a big theory, even some guy standing at an obscure lectern in a patent office in Switzerland in the early 1900s…

But we will assume that the organizers are correct in thinking that twenty is a reasonable number in this case.

See also: So who’s in and who’s out at Royal Society 2016 “rethink evolution” meet?

and

Progressive Review hopes for post-Darwinian science “But Darwin clearly didn’t have all the answers, and science has moved many miles since his time.”

On formalising design detection III

Back to Basics: Understanding the Design Inference:
January 18, 2016 Posted by Eric Anderson under Intelligent Design, Design inference, Darwinist rhetorical tactics, Darwinian Debating Devices, Back to Basics of ID




This is prompted primarily by a recent post and by the unfortunate realization that some people still do not understand the design inference, despite years of involvement in the debate. Specifically, there was discussion at Barry’s prior post about whether Elizabeth Liddle admits that “biological design inferences” may be valid in principle. Over 200 comments appeared on the prior thread, including a fair amount of back and forth between Barry, Elizabeth and me, all of which may be worth reviewing for those who are interested.

However, the primary takeaway from that thread is that we need another back-to-basics primer on intelligent design – specifically, what the design inference is and how it works. Yes, I know regular readers have a great deal of exposure to this topic. And I know that many of you have an excellent grasp of the design inference. But please stay with me to the end and I trust this post will shed some additional light and provide perhaps some additional nuances on the issues. Perhaps less in terms of providing you with additional insight and more in terms of understanding the rhetorical tools and mindset of intelligent design opponents (or proponents who may have misunderstood some basic issues).

With that need clearly established from the prior thread and a more recent thread, I have finally taken a deep breath, gathered my courage, and set aside many hours to put this together. (Yes, that is the amount of time it takes to carefully analyze, lay out, and properly articulate an issue like this. Unfortunately, the quick one-liner complaints and dismissals are much more facile to post.) I apologize in advance for the length, as I dislike lengthy head posts in general, but there are some key issues here that need to be fleshed out in detail.

Background

We hear from time to time, as in the two threads I cite above, claims essentially equivalent to the following:

“The design inference is a valid mode of inquiry in principle, but it cannot be applied to biological systems.”

or

“The design inference only works with human artifacts and cannot be applied to life because we have never seen a designer of life.”

or

“It is possible to detect design in theory, but it cannot be applied without knowing characteristics of the designer.”

or, this zinger:

“Design detection works with some phenomena, but life is ‘too complex to have been designed.’”

It is claims like these I wish to address. For present purposes and to keep this to some merciful length, I am setting aside issues about whether ID is science, whether ID is falsifiable, whether ID has a positive case, whether ID is directly testable, and so on. Our present purpose is to examine specifically the situation in which an individual asserts that (a) the design inference has some application, but (b) it cannot be applied to biological systems or to non-human designers.

How Can We Determine Design?

There are a couple of approaches to determining whether something is designed.* These can be broken into two broad categories: namely, actual knowledge and inference.

In the first category, we have actual knowledge of the artifact being designed. In this situation we see or experience as directly as possible a creative event – something being designed. All of us have experience with this: we have created or built something with our own hands, or have worked on a schematic, or have written lines of code. In such cases we have direct, actual knowledge that the artifact in question was designed. We can also include in this category creative events that we witness directly.** No-one disputes these examples and there is no need to infer anything when we have actual knowledge. We need not discuss this category further.

In the second category, we don’t have actual knowledge of the artifact being designed. Rather, we infer it was designed by examining indirect evidence after the fact. These pieces of indirect evidence can be legion. Indeed, in some cases they can seem so many and so obvious that we are tempted to think we have “actual knowledge” of the design. However, on closer inspection we realize we are really drawing an inference.Was the iPhone designed? Of course, you say, only a fool would think otherwise. Fair enough, but why are you so sure it was designed? Did you personally design it? Did you actually witness someone else design it? Even if you personally worked on a couple of the parts, how do you know the rest of the iPhone was designed?

Make no mistake, the fact that Apple claims it was designed, or that Apple sells it, or that no-one questions it was designed, or that patents were filed, or that you have actual personal knowledge of some similar system being designed – none of these things shifts the iPhone into the category of “Actual Knowledge.” No, when we say the iPhone was designed we are still drawing an inference. A correct one, undoubtedly, but still an inference.

And what is it that gives us such confidence the iPhone was designed?

There are many possible pieces of indirect evidence that could bolster our claim that the iPhone was designed. A key list might include: (a) perhaps we know an Apple engineer who claims actual knowledge of its design; (b) there were lots of engineers around at the time who could have been available to work on it; (c) perhaps we know of some similar system that was designed; (d) the iPhone contains multiple components that have been brought together into a greater functional whole; and (e) to our knowledge there is no natural event or other non-design process that can produce something like an iPhone.

Excellent. So we are pretty confident the iPhone was designed. Confident enough that we would stake a great deal on it. And we can draw the same conclusion for millions upon millions of other human inventions. But it is still an inference.
Let’s up the ante a bit. What about something like Stonehenge? Let’s go through the same list:

(a) We know an engineer who actually worked on Stonehenge? No. But how cool would that be!

(b) Lots of engineers around at the time? This one is more tricky and deserves some discussion.

We don’t know if there were lots of engineers, but, we might argue, perhaps a small handful, or even one, would suffice. On the other hand, do we have actual knowledge that there was even one engineer capable of designing Stonehenge around at the time? No. We do not.

We have corroborating evidence (bone fragments, burial mounds, and the like) that there were humans around at the time. So we can infer that there was a designer around at the time. But we have no evidence – none at all – outside of Stonehenge itself, that there was a designer around at the time capable of producing Stonehenge. Indeed, it is the very existence of Stonehenge itself, coupled with our conclusion that Stonehenge was designed, which gives us the following piece of information and allows us to draw the following conclusion: there was a designer around at the time capable of designing Stonehenge. This is the way it always works, whether we are talking about some newly-discovered structure, a previously-unknown manuscript, or otherwise.

It is absolutely critical to understand this point: In archaeological and other investigations of the past, we do not infer that an artifact was designed because we have knowledge of a designer capable of producing the artifact. Rather, we infer there was a designer capable of producing the artifact, because we have found the artifact and concluded that it was designed.

Do not get this backwards. Doing so is a failure of logic at the most basic level and a failure to understand the process of investigation.

Let me briefly add one last related point here. Stonehenge is a somewhat simple case (though perhaps a more confusing case to those who aren’t thinking through the chain of logic clearly), because there is much corroborating evidence in the Stonehenge area for the existence of humans. However, there are many other examples in archaeology where independent evidence of whether designers were around is absent. In those cases, the chain of logic works precisely the same way it always does: we eventually infer that there were capable designers around, because we have found an artifact and concluded that it was designed.

(c) Actual knowledge of a similar system being designed? Perhaps.

This turns on how “similar” something needs to be. Stonehenge, by many accounts, is a fantastic, singular monument. And, no, we cannot rely on the fact that lots of other henges have been found in the surrounding area – we don’t have any actual knowledge about their design either and must draw an inference just the same. So we might have actual knowledge of some stones being cut and placed generally, but we really have no actual knowledge of something highly similar to Stonehenge being produced.

Nevertheless, under this particular criterion we might reasonably conclude that we know of designed systems which at least contain analogous characteristics or which have a number of similarities to aspects of Stonehenge.

(Incidentally, there are some interesting documentaries on recent work done at Stonehenge with cutting-edge mapping technologies. The area turns out to contain an entire massive complex of henges and other structures, not just a single henge. Well worth checking out.)

(d) Stonehenge contains multiple components that have been brought together into a greater functional whole? Definitely.

(e) To our knowledge there is no natural process or event that could produce Stonehenge. Correct.

So, to review, why are we so utterly, completely, unabashedly confident that Stonehenge was designed? Is it because we have actual knowledge and were there at the time to witness it? Is it because we know someone who claims to have worked on it? No and no.

Is it because we know there were engineers around at the time who were capable of producing Stonehenge? No. Quite the opposite: it is our conclusion of design that allows us to infer there were engineers at the time capable of producing Stonehenge.

Is it because we have actual knowledge of similar systems being designed? Perhaps, turning a bit on how we define “similar.” Is it because it contains multiple components that have been brought together into a greater functional whole. Yes. Is it, in part, because to our knowledge there is no natural process that could reasonably produce Stonehenge? Yes.

How the Inference Runs

Take another close look at the above. There is a fundamental point here that seems lost on some critics of the design inference and which is absolutely critical: We infer that Stonehenge was designed not, as sometimes claimed by design critics, because we know there were designers around at the time capable of producing the artifact in question, but because of the characteristics of the artifact itself.

Then, having concluded the artifact was designed, we can infer that there were designers around at the time capable of producing the artifact. This is the directional arrow of the logic. This is the way the design inference works. This is the way it always works.

Furthermore, let us note for completeness that the arrow of reasoning can never run in the opposite direction. Even if we know for certain that a designer exists in the right time and place, and even if we know for certain that the designer has the capability of designing, we still cannot conclude, based simply on those facts, that an artifact was designed. After all, there is no requirement that a designer actually produce anything. The designer may have existed; the designer may have been capable. But the only way we know that the designer actually designed the artifact in question is by examining the artifact itself.

The inference simply cannot operate any other way.

What is so often happening in the design critic’s mind, the essentially philosophical stance being taken, is that design can only be considered in certain circumstances. Not that the artifact doesn’t need to be examined on its own merits. It does. Not that we need to have independent evidence of the designers and their characteristics beforehand. We don’t. The design inference works across the spectrum. In can be applied just fine. It is just that the critic is unwilling to apply the design inference in certain unpalatable circumstances.

Is Life is Too Complex to Be Designed?

Let us now turn to a particularly remarkable stance taken by Elizabeth Liddle on the prior thread. I refer to Elizabeth only because it is a convenient example and because it also highlights some of the mistakes made by critics of intelligent design generally. Specifically, although she claimed willingness to consider design in the case of human ingenuity, when it comes to biology she says, “I think [life] is too complex to have been designed.”

Let that sink in for a moment.

How could someone say that and what could it possibly mean? In the context of the design inference, we are looking for indicia of design as we examine an artifact: complex specified information, irreducibly complex functional structures, and so on. What does it mean to claim that we can infer some simpler things are designed, but that life is “too complex” to have been designed? (Please don’t get hung up on the fact that Elizabeth misuses the term “complex.” She is essentially talking about indicia of design, otherwise her whole statement is meaningless.)

Essentially, she is arguing that there are certain indicia of design we can look to, but when there are too many, then we cannot infer design because it is too much. Here is how it looks graphically:

The first column is easy and makes sense; the second is fine as well.

It scarcely bears mentioning that the conclusion in the last column is nonsensical. Blatantly inconsistent. Utterly irrational and illogical. Indeed, it is difficult to understand how anyone could be so completely off track as to even countenance such a viewpoint. We might be tempted to conclude that such an individual can only be either (1) incapable of rational thought, or (2) purposely deceptive.

At least in the context of the design inference.

A Third Way

But is there another way to think about a conclusion of design? Is there a third possibility that might explain how someone could take the view that some indicia of design = design while even more indicia of design = non-design? There is indeed another way of looking at it, and this is precisely what is happening with Elizabeth.

Elizabeth, as she has made clear, does not believe it is possible to infer design without knowing about the designer’s existence and something about the designer’s capabilities. For those intrepid souls who have stayed with me to this point, you know this is wrong, and demonstrably so, as has already been shown above. Nevertheless, let’s run with it for a moment to see if we can at least identify the chain of thought that leads to this remarkable “too complex to be designed” idea.

If one mistakenly thinks that we have to know that (a) a designer exists and (b) the designer is capable of producing the artifact in question, then it follows that we cannot infer life was designed. After all, the argument goes, we do not have direct independent evidence that a designer existed at the time nor that the designer was capable of producing the artifact in question. Thus, even though life is teeming with indicia of design, even though life is “too complex” compared with other things Elizabeth believes are designed, she is unwilling to infer design because she doesn’t have independent evidence about the designer and the designer’s capabilities.

She unfortunately fails, as do so many others, to realize that the exact same situation applies to almost every other inference of design – certainly to artifacts from the remote past, whether Stonehenge or otherwise. So her attempt to identify design is, at best, poorly thought through and inconsistently applied.

The Demand for Evidence Beyond the Artifact

Elizabeth says, regarding her conclusion that life was not designed:

But were evidence to arise, say, of optimised solutions from one lineage being transferred to another (as we install cameras in phones), or of evidence of artefactual fabrication, or of the presence of designers on early earth, or possibly something I haven’t thought of that indicated that living things were designed, I might have to think again.

Note the part I have highlighted in bold. This is the crux of the matter. She is looking for actual evidence of design – or at least a version of actual evidence she is willing to accept.  In other words, if we find independent evidence to our liking that something was designed then we will acknowledge it was designed.

This is not to say that Elizabeth never infers design. She clearly does. But she reserves her willingness to infer design to those cases in which there is some other reason, something other than the characteristics of the artifact in question, to conclude the artifact may have been designed. Let’s say she concludes artifact x, such as Stonehenge, is designed. We might do well to ask how she could come to that conclusion in the case of artifact x, but not in the case of living systems.

The answer is rather simple.  Perhaps she feels artifact x is closer in time to other things that are known to be designed; perhaps she feels that artifact x is more “similar” to things known to be designed; perhaps she just has a difficult time accepting the idea that a designer could be capable of designing living systems (remember, she thinks they are “too complex”); perhaps it is the pedestrian (but rapidly weakening) observation that no designer she knows of has yet designed a complex living system. Fine. As with the iPhone, we can infer design based on a number of criteria, apart from the characteristics of the artifact itself.

But that is not what the design inference is about. The design inference is precisely about identifying design from the artifact itself in the absence of additional evidence, in particular evidence about the existence or capabilities of the designer. Furthermore, as pointed out above, absent actual knowledge of design we must always fall back to an analysis of the artifact in question. Thus, any inference that relies only on other evidence will never be as solid or as robust as an inference based on the characteristics of the artifact itself.

Whatever the case, Elizabeth is clearly not willing to accept the design inference,*** despite any statements that could be understood as such. The most that can be said for Elizabeth’s approach is that in certain cases she is willing to make a design inference. Just not the design inference relevant for purposes of intelligent design. Her approach is not based on an examination of the artifact to find complex specified information, for example. Rather, it is a vague, ill-defined, “I need to see some additional corroborating evidence beyond the artifact that looks good to me” type of approach.

To be sure, one might indeed infer design with reference to other pieces of evidence beyond the artifact itself, or with reference to some poorly-defined “similar” system or some independent corroboration that designers were around at the time or some other piece of evidence that is palatable or seems subjectively good enough. But such an approach (i) does not constitute the design inference for purposes of intelligent design, and (ii) is embarrassingly poorly-defined and terribly inconsistent in application and practice.

Here we come face to face with the irony of the situation. The oft-repeated allegations that the design inference is poorly defined or difficult to apply are multiplied by orders of magnitude when the magnifying lens of critical thinking is turned on the inconsistent, poorly-defined approach of those individuals wont to claim that design can only be discerned in this field of study but not that, or in this time and place but not that, or with this type of designer but not that.

Conclusion

Despite continued criticisms of the design inference, upon closer examination the arguments of critics fail to meet the tests of objectivity, logic, and practical application. The design inference, properly understood, continues as an extremely reliable and robust, and in some cases our only, avenue to determine design.

Absent actual knowledge, which rarely, and in the case of historical events and artifacts almost never, exists, an inference to design always turns on an examination of the artifact in question. This is true with Stonehenge and other ancient artifacts just as much as with living systems. Assertions that we must have independent knowledge about the existence or characteristics of a designer before design can be inferred are misguided and demonstrate a basic lack of understanding of both how the design inference works and the direction of reasoning in investigation.

In addition, willingness to apply the design inference to only a particular field, or only a particular timeframe, or only a particular kind of designer bespeaks a fundamental confusion of the issues and, too often, an unspoken philosophical bias.

—–



* To nip a common red herring in the bud, we are talking about actual design, as commonly understood, by an intelligent being. Please, for the sake of rational discourse and for clarity of discussion in this thread, do not twist words and make claims about “nature designing” or something being “designed by a natural process” or similar nonsense. That is not what design means in the context of intelligent design and it is not what this thread is about.

** To nip the next red herring in the bud, we do not need to get into an angels-on-the-head-of-a-pin discussion about what reality is, whether we can trust our senses, whether what we see is actually real. Such philosophical musings, interesting as they may be, are completely irrelevant to the present discussion and are not what this thread is about.

*** There is another important reason for Elizabeth’s unwillingness to accept the design inference, but that will have to wait for a subsequent post.



Bear with me for a moment while we dive into some examples that I think will be very helpful in elucidating the issues. Two specific examples will suffice.

Yet more on reality's antidarwinian bias III

An "Exquisitely Designed" Enzyme that Maintains DNA Building Blocks
Evolution News & Views January 16, 2016 4:49 AM

It's molecular machine time, and today we'll be looking at a particularly amazing one. It's essential, it's "evolutionarily ancient," and it's unique. This machine, named ribonucleotide reductase, or RNR for short, is a beauty. News from MIT explains why your life depends on this machine:

Cell survival depends on having a plentiful and balanced pool of the four chemical building blocks that make up DNA -- the deoxyribonucleosides deoxyadenosine, deoxyguanosine, deoxycytidine, and thymidine, often abbreviated as A, G, C, and T. However, if too many of these components pile up, or if their usual ratio is disrupted, that can be deadly for the cell.

A new study from MIT chemists sheds light on a longstanding puzzle: how a single enzyme known as ribonucleotide reductase (RNR) generates all four of these building blocks and maintains the correct balance among them. [Emphasis added.]

The image shows the complex machine with active sites that precisely fit the four different building blocks. Its job is to take the ribonucleotides that make up RNA and turn them into the deoxyribonucleotides that make up DNA.

"There's no other enzyme that really can do that chemistry," she says. "It's the only one, and it's very different than most enzymes and has a lot of really unusual features."

In order for the machine's moving parts to work, one of several "effector molecules" has to fit into its special spot, like a key that opens a latch. This causes the enzyme to open up a "distant" active site and let the appropriate RNA building block in. Then, the enzyme latches it into place for its operation.

Depending on which of these effectors is bound to the distant regulatory site, the active site can accommodate one of the four ribounucleotide substrates. Effector binding promotes closing of part of the protein over the active site like a latch to lock in the substrate. If the wrong base is in the active site, the latch can't close and the substrate will diffuse out.

"It's exquisitely designed so that if you have the wrong substrate in there, you can't close up the active site," Drennan says. "It's a really elegant set of movements that allows for this kind of molecular screening process."

This four-in-one machine takes on four different shapes depending on whether the RNA nucleotide is A, G, C, or U. It sends out DNA's four, A, G, C, and T with the appropriate sugar deoxyribose instead of ribose (replacing an OH radical with a hydrogen atom, a "reduction" reaction). But that's not all this amazing machine does:

The effectors can also shut off production completely, by binding to a completely different site on the enzyme, if the pool of building blocks is getting too big.

RNR is a multi-tool if there ever was one. The effectors, the substrates and the active sites are all closely matched to the operation at hand, whether generating more DNA building blocks or regulating their supply in the cell. A paper from the Annual Review of Biochemistry (2007) puts it this way:

An intricate interplay between gene activation, enzyme inhibition, and protein degradation regulates, together with the allosteric effects, enzyme activity and provides the appropriate amount of deoxynucleotides for DNA replication and repair.

A lot of new building blocks are needed for repair and replication. You can see why this enzyme is essential for a cell when it divides or suffers stress.

The news item mentioned a latch, but another paper from 2015 in the Journal of Biological Chemistry speaks of a switch mechanism:

Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to the corresponding deoxyribonucleotides, which are used as building blocks for DNA replication and repair. This process is tightly regulated via two allosteric sites, the specificity site (s-site) and the overall activity site (a-site). The a-site resides in an N-terminal ATP cone domain that binds dATP or ATP and functions as an on/off switch, whereas the composite s-site binds ATP, dATP, dTTP, or dGTP and determines which substrate to reduce.

It's like a surgical robot that has a clamp with an on-off switch. The switch (the effector) turns the machine on, opening up the distant active site and letting the appropriate substrate in. The enzyme then clamps down on the substrate and "reduces" it by replacing the oxygen radical with a hydrogen. When released, the DNA building block is ready for use, the effector switches the machine off, and the enzyme is ready for the next operation.

Somehow, when there are too many building blocks floating around in the cell, an effector binds to a different active site, disabling the machine. It's uncanny how each part seems to know what's needed and how to provide it. This involves feedback from the nucleus, where genes respond to the supply by either locking the RNR enzymes or making more of them.

Catherine Drennan on the MIT team calls this enzyme "evolutionarily ancient" and speculates about its origin.

Deoxyribonucleotides are generated from ribonucleotides, which are the building blocks for RNAs -- molecules that perform many important roles in gene expression. RNR, which catalyzes the conversion of ribonucleotides to deoxyribonucleotides, is an evolutionarily ancient enzyme that may have been responsible for the conversion of the earliest life forms, which were based on RNA, into DNA-based organisms, Drennan says.

She buys into the "RNA World" scenario for the origin of life, a view that is loaded with problems. RNR is an enzyme made of protein. Did a world of floating RNA fragments somehow build this complex, multi-part protein machine before DNA-based organisms existed? That makes no sense. A ribozyme with enough "code" for RNR would itself be impossibly complex to imagine forming by chance. It would have no way to translate that code into a polypeptide without a ribosome, also made of RNA and protein. Finally, even if by multiple miracles a primitive RNR appeared with its effectors and started cranking out product, the "RNA world" would have no idea what to do with a bunch of DNA building blocks floating around. Notably, Drennan's paper in eLife says nothing about any of this. Instead, it praises the "elegant set of protein rearrangements" performed by RNR.


RNR is one of a multitude of complex, highly-specific, multi-component machines with moving parts. Found in the simplest bacteria and archaea all the way up to human beings, it deserves better than to be treated like hopeful junk that arose by chance and found a job by accident. It deserves to be honored as an "exquisitely designed" molecular machine that performs an "intricate interplay" of functions vital to life, just like an intelligent designer would envision, plan, and create.