How universal is language of life?

Reply To Kenneth Miller On The Genetic Code
Discovery Institute's Center for Science & Culture
Discovery Institute


On Tuesday, September 25, 2001, Professor Kenneth Miller of Brown University issued a press release entitled "A 'Dying Theory' Fails Again," available here: 

http://www.ncseweb.org/resources/articles/3071_km-3.pdf

In this document, Miller claims that the Discovery Institute (DI) tried to "smear" PBS's Evolution series when the DI charged that program with making a false statement about the universality of the genetic code. Miller also claims that the DI failed to tell the public that "the very discoveries they cite provide elegant and unexpected support for Darwin's theories."

These claims are false. Miller's press release, however, provides an excellent teaching opportunity for the DI, not only to show why Miller's claims are false, but also to amplify our original objection. We shall explain why statements such as "the genetic code is universal" not only harm science -- by creating what Charles Darwin called "false facts" -- but also cheat the public, by concealing the real puzzles facing evolutionary theory. We conclude by touching on some of the deeper issues raised by patterns of evidence such as the genetic code.

We begin with the errors and misrepresentations in Miller's press release.

Miller completely misrepresents the significance of a diagram reproduced in his press release from another source (Knight et al. 2001, Figure 2). This is a serious mistake, as Miller rests his case against the DI on his misunderstanding of this diagram.

Miller equates genetic code variants to minor differences in dialects of the same spoken language (e.g., English). This comparison is erroneous and misleading.

Miller claims that the successes of biotechnology prove the universality of the code. This is untrue, and ignores the literature on experiments employing organisms with variant codes.

Let's consider each problem in more detail:

1. Miller completely misrepresents Knight et al.'s composite phylogeny of genetic codes.

In his press release, Miller writes:

"Look closely at the figure from this paper, and you;ll see something remarkable. The variations from the standard code occur in regular patterns that can be traced directly back to the standard code, which sits at the center of the diagram."

This is false. The variant codes do not "occur in regular patterns," but appear independently in unrelated lineages. Knight et al. explain this pattern of convergent (i.e., non-homologous) appearance in the article itself:

"The genetic code varies in a wide range of organisms (FIG. 2 [reproduced in Miller's press release], some of which share no obvious similarities. Sometimes the same change recurs in different lineages: for instance, the UAA and UAG codons have been reassigned from Stop to Gln in some diplomonads, in several species of ciliates and in the green alga Acetabularia acetabulum (reviewed in Ref. 5). Similarly, animal and yeast mitochondria have independently reassigned AUA from Ile to Met." [1] 

In their caption to Figure 2, Knight et al. note explicitly that variant codes have arisen "repeatedly and independently in different taxa." This pattern of convergent variation has generated much discussion in the primary literature. [2] If these are indeed convergent changes, they do not provide evidence of common descent at all, but rather would be misleading similarities that, taken by themselves, generate a false history of the organisms in question.

In short, Miller completely misrepresents the Knight et al. composite phylogeny. There is no "regular pattern" to the variant codes that maps congruently onto phylogenetic trees from other data. Thus, far from providing what Miller calls "unexpected confirmation of the evolution of the code from a single common ancestor," the pattern of variant codes represents a puzzle for a single tree of life. 

2. Variant genetic codes are not analogous to the differences between dialects of the same language.

In his press release, Miller writes:

"As evolutionary biologists were quick to realize, slight differences in the genetic code are similar to differences between the dialects of a single spoken language. The differences in spelling and word meanings between the American, Canadian, and British dialects of English reflect a common origin. Exactly the same is true for the universal language of DNA."

This is--at best--a wildly inaccurate analogy. From context and other clues, English speakers can discern that the words "center" and "centre," or "color" and "colour," refer to the same object. Meaning is preserved by context, and the reader moves along without a hitch.

But a gene sequence from a ciliated protozoan such as Tetrahymena (for instance), with the codons UAA and UAG in its open reading frame (ORF), cannot be interpreted correctly by the translation machinery of other eukaryotes having the so-called "universal" code. In Tetrahymena, UAA and UAG code for glutamine. In the universal code, these are stop codons. Thus the translation machinery of most other eukaryotes, when reading the Tetrahymena gene, would stop at UAA or UAG. Instead of inserting glutamine into the growing polypeptide chain, and continuing to translate the mRNA, release factors would bind to the codons, and the ribosomes would halt protein synthesis. The resulting protein would be truncated in length and very possibly non-functional. Unlike variant spellings of "center," therefore, context cannot preserve meaning. With the codons UAA and UAG (comparing Tetraphymena thermophila and other eukaryotes) no shared context exists.

Knight et al. present a much better analogy for code changes:

"Any change in the genetic code alters the meaning of a codon, which, analogous to reassigning a key on a keyboard, would introduce errors into every translated message." [3]

Indeed, for two decades (see below), it was exactly this deeply-embedded feature of the genetic code that led to strong predictions about its necessary universality across all organisms. It was widely thought that any change to the genetic code of an organism would affect all the proteins produced by that organism, leading to deleterious consequences (e.g., truncated or misfolded proteins) or lethality. Once the code evolved in the progenitor of all life, it "froze," and all subsequent organisms would carry that code.

In any case, the differences between genetic codes are not properly analogous to minor differences among dialects of a single language. 

3. Miller's references to biotechnology do not accurately represent the experimental literature on variant genetic codes.

In his press release, Miller writes:

"...the entire biotechnology industry is built upon the universality of the genetic code. Genetically-modified organisms are routinely created in the lab by swapping genes between bacteria, plants, animals, and viruses. If the coded instructions in those genes were truly as different as the critics of evolution would have you believe, none of these manipulations would work."

But some manipulations--namely, those involving organisms with variant codes--do not work, unless the researchers themselves intervene to ensure function. 

Consider, for instance, the release factor from the ciliate Tetrahymena thermophila. Release factors (in eukaryotes, these proteins are abbreviated as "eRF" to distinguish them from prokaryotic release factors) catalyze the separation of completed polypeptide chains (nascent proteins) from the ribosomal machinery. Unlike other eukaryotic release factors, however, that recognize all three stop codons (UAA, UGA, and UAG), the Tetrahymena thermophila release factor recognizes only the UGA codon as "stop."

In 1999, Andrew Karamyshev and colleagues at the University of Tokyo isolated the release factor (Tt-eRF1) from Tetrahymena thermophila. But in order to express and purify the protein, Karamyshev et al. had to manipulate it genetically first. Why? The Tetrahymena thermophila gene for Tt-eRF1 contains 10 codons in its open reading frame that would be interpreted as "stop" by other organisms--whereas Tetrahymena thermophila reads these codons as glutamine:

"To express and purify the recombinant Tt-eRF1 protein under heterologous expression conditions [i.e., in a cell other than Tetrahymena--Karamyshev et al. used yeast cells], 10 UAA/UAG triplets within the coding sequence were changed to the glutamine codon CAA or CAG by site-directed mutagenesis." [4]

Furthermore, Tt-eRF1 would not function when employed in combination with ribosomes (translation machinery) from other species:

"In spite of the overall conservative protein structure of Tt-eRF1 compared with mammalian and yeast eRF1s, the soluble recombinant Tt-eRF1 did not show any polypeptide release activity in vitro using rat or Artemia ribosomes." [5] Thus, when using an organism with a variant code (Tetrahymena thermophila), researchers found that

They needed to modify (i.e., intelligently manipulate) the gene sequences so that they could be expressed by other organisms, and

They discovered that a key component of the genetic code (namely, the release factor that terminates translation) would not function properly with the translation machinery of other organisms.

Experiments to change the identity of transfer RNA (tRNA)--another possible mechanism by which genetic codes might reassign codon "meanings"--have shown that the intermediate steps must be bridged by intelligent (directed) manipulation. In one such experiment, for instance, Margaret Saks, John Abelson, and colleagues at Caltech changed an E. coli arginine tRNA to specify a different amino acid, threonine. They accomplished this, however, only by supplying the bacterial cells (via a plasmid) with another copy of the wild-type threonine tRNA gene. This intelligently-directed intervention bridged the critical transition stage during which the arginine tRNA was being modified by mutations to specify threonine. [6] Indeed, in reporting on an earlier experiment to modify tRNA, Abelson and colleagues noted that "if multiple changes are required to alter the specificity of a tRNA, they cannot be selected but they can be constructed" [7]--constructed, that is, by intelligent design. We stress here that, in contrast to Miller's blithe dismissal of the difficulties raised for biotechnology by variant genetic codes, experts in the field caution that assuming a "universal" code may lead to serious problems. In a recent article on the topic entitled "Codon reassignment and the evolving genetic code: problems and pitfalls in post-genome analysis," Justin O'Sullivan and colleagues at the University of Kent observe:

"The emerging non-universal nature of the genetic code, coupled with the fact that few genetic codes have been experimentally confirmed, has several serious implications for the post-genome era. The production of biologically active recombinant molecules requires that careful consideration be given to both the expression system and the original host genome. The substitution of amino acids within a protein encoded by a nonstandard genetic code could alter the structure, function or antibody recognition of the final product." [8]

Thus, Miller's statements on biotechnology are highly misleading. Variant codes are not a minor matter easily overcome in experiments using different organisms.

We conclude by considering some of the deeper issues raised by Miller's press release. 

A little history and some basic logic

Not so very long ago, the universality of the genetic code was widely regarded as an important prediction (or confirmation) of the theory of common descent. Consider, for instance, an evolutionary biology textbook by the zoologist Mark Ridley, entitled The Problems of Evolution (Oxford University Press, 1985). In his first chapter, "Is Evolution True?" Ridley argues that common descent predicts a universal genetic code. His formulation of this argument mirrors dozens of similar arguments present in the biological literature from the mid-1960s to the mid-1980s:

"The outstanding example of a universal homology is the genetic code...The universality of the code is easy to understand if every species is descended from a common ancestor. Whatever code was used by the common ancestor would, through evolution, be retained. It would be retained because any change in it would be disastrous. A single change would cause all the proteins of the body, perfected over millions of years, to be built wrongly; no such body could live. It would be like trying to communicate, but having swapped letters around in words; if you change every 'a' for an 'x', for example, and tried talking to people, they would not make much sense of it. Thus we expect the genetic code to be universal if all species have descended from a common ancestor." [9]

Shortly after Ridley's argument was published in The Problems of Evolution, the evolutionary biologist Brian Charlesworth reviewed the book. He cautioned that Ridley was "less sound on the more modern aspects" of evolution, including the genetic code. Ridley's genetic code argument, Charlesworth worried,

"provides an opening for the creationists by asserting that the genetic code is universal, whereas it is now known that slight deviations from the standard code occur in mitochondria and in Mycoplasma." [10]

But how did Ridley create "an opening for the creationists," if the genetic code variants are as insignificant as Kenneth Miller suggests?

Here we should consider a basic feature of the logic of scientific prediction. If a theory, T, strongly predicts a particular outcome, O, but O is not observed, then one has grounds for doubting T. Of course, this logical schema greatly oversimplifies how scientists may actually behave when met with a failed prediction. One can shift or broaden the prediction--"T didn't really predict O, but actually O plus something else"--or one can throw doubt onto some theory other than T, and blame it, rather than T, for the failed prediction.

The problem is that both of these solutions weaken one's case for the theory T. Any theory that predicts an observational outcome and its negation is a theory without much empirical power. "It will rain today and it won't rain today" tells one everything and therefore nothing. If common descent predicts that the genetic code will be universal, except when it is not universal, then common descent does not actually specify any observations about the code.

One might also say that some other theory, linked conceptually to common descent, is responsible for the failed prediction of universality. In this move, the truth of common descent is preserved while another part of our biological knowledge pays the cost. Most biologists working on the evolution of the code have taken this route; Niles Lehman of SUNY-Albany, for instance, writes:

"Once thought universal, the specific relationships between amino acids and codons that are collectively known as the genetic code are now proving to be variable in many taxa. While this realization has been disappointing to some--the genetic code was often hailed as the ultimate evolutionary anchor in that is universality was perhaps the indisputable piece of evidence that all life shared a common ancestor at some point--it has also opened up a rich field of evolutionary analysis by forcing us to consider what sequence of molecular events in a cell could possibly allow for codon reassignment." [11] 

Again, however, this move weakens the case for common descent. One preserves the truth of common descent only by cashing in one of the theory's predictions, namely, the universality of the code. "It seems we were wrong, after all, about the genetic code not being able to vary. So let's figure out how variant codes arise."

Well, how do variant code arise? Kenneth Miller doesn't say, but that is not surprising. No one really knows, although that is not for a lack of theories. Here we refer the curious reader to the superb review article by Knight, Freeland, and Landweber (2001), who list several different theories explaining codon change, none of which (they note) is unequivocally supported by the evidence.

Is it possible that the variant codes derived from a single common ancestor? Yes. 

It is also possible, of course, that they did not. Miller assumes that a single origin is the case, but there is a world of difference between assumptions and real knowledge.

These are matters for legitimate debate. What is not a matter for debate are the following facts:

The genetic code is not universal.

If the theory of common descent predicts a universal genetic code, then the theory predicts something that isn't so.

References

1. Robin D. Knight, Stephen J. Freeland, and Laura F. Landweber, "Rewiring the Keyboard: Evolvability of the Genetic Code," Nature Reviews Genetics, Vol. 2:49-58; p. 49 (2001).

2. Catherine A. Lozupone, Robin D. Knight and Laura F. Landweber, "The molecular basis of nuclear genetic code change in ciliates," Current Biology 11 (2001):65-74; Patrick J. Keeling and W. Ford Doolittle, "Widespread and Ancient Distribution of a Noncanonical Genetic Code in Diplomonads," Molecular Biology and Evolution 14 (1997):895-901; A. Baroin-Tourancheau, N. Tsao, L.A. Klobutcher, R.E. Pearlman, and A. Adoutte, "Genetic code deviations in the ciliates: evidence for multiple and independent events," EMBO Journal 14 (995):3262-3267. 

3. Robin D. Knight, Stephen J. Freeland, and Laura F. Landweber, "Rewiring the Keyboard: Evolvability of the Genetic Code," Nature Reviews Genetics 2 (2001):49-58; p. 49. 

4. Andrew L. Karamyshev, Koichi Ito, and Yoshikazu Nakamura, "Polypepetide release factor eRF1 from Tetrahymena themophila: cDNA cloning, purification and complex formation with yeast eRF3," FEBS Letters 457 (1999):483-488; p. 485. 

5. Ibid., p. 487.

6. Margaret E. Saks, Jeffrey R. Sampson, and John Abelson, "Evolution of a Transfer RNA Gene Through a Point Mutation in the Anticodon," Science 279 (13 March 1998):1665-1670.

7. Jennifer Normanly, Richard C. Ogden, Suzanna J. Horvath & John Abelson, "Changing the identity of a transfer RNA," Nature 321 (15 May 986):213-219. 

8. Justin M. O'Sullivan, J. Bernard Davenport and Mick F. Tuite, "Codon reassignment and the evolving genetic code: problems and pitfalls in post-genome analysis," Trends in Genetics 17 (2001):20-22; p. 21. 

9. Mark Ridley, The Problems of Evolution (Oxford: Oxford University Press, 1985), pp. 10-11.

10. Brian Charlesworth, "Darwinism is alive and well," review of The Problems of Evolution, New Scientist 11 July 1985, p. 58. 


11. Niles Lehman, "Please release me, genetic code," Current Biology 11 (2001):R63-R66; p. R63.

Psalms 8-14 American Standard Version.

8)1 O Jehovah, our Lord, How excellent is thy name in all the earth, Who hast set thy glory upon the heavens!

2Out of the mouth of babes and sucklings hast thou established strength, Because of thine adversaries, That thou mightest still the enemy and the avenger.

3When I consider thy heavens, the work of thy fingers, The moon and the stars, which thou hast ordained;

4What is man, that thou art mindful of him? And the son of man, that thou visitest him?

5For thou hast made him but little lower than God, And crownest him with glory and honor.

6Thou makest him to have dominion over the works of thy hands; Thou hast put all things under his feet:

7All sheep and oxen, Yea, and the beasts of the field,

8The birds of the heavens, and the fish of the sea, Whatsoever passeth through the paths of the seas.

9O Jehovah, our Lord, How excellent is thy name in all the earth!
American Standard Version, 1901
9)1I will give thanks unto Jehovah with my whole heart; I will show forth all thy marvellous works.

2I will be glad and exult in thee; I will sing praise to thy name, O thou Most High.

3When mine enemies turn back, They stumble and perish at thy presence.

4For thou hast maintained my right and my cause; Thou sittest in the throne judging righteously.

5Thou hast rebuked the nations, thou hast destroyed the wicked; Thou hast blotted out their name for ever and ever.

6The enemy are come to an end, they are desolate for ever; And the cities which thou hast overthrown, The very remembrance of them is perished.

7But Jehovah sitteth as king for ever: He hath prepared his throne for judgment;

8And he will judge the world in righteousness, He will minister judgment to the peoples in uprightness.

9Jehovah also will be a high tower for the oppressed, A high tower in times of trouble;

10And they that know thy name will put their trust in thee; For thou, Jehovah, hast not forsaken them that seek thee.

11Sing praises to Jehovah, who dwelleth in Zion: Declare among the people his doings.

12For he that maketh inquisition for blood remembereth them; He forgetteth not the cry of the poor.

13Have mercy upon me, O Jehovah; Behold my affliction which I suffer of them that hate me, Thou that liftest me up from the gates of death;

14That I may show forth all thy praise. In the gates of the daughter of Zion I will rejoice in thy salvation.

15The nations are sunk down in the pit that they made: In the net which they hid is their own foot taken.

16Jehovah hath made himself known, he hath executed judgment: The wicked is snared in the work of his own hands. Higgaion. Selah

17The wicked shall be turned back unto Sheol, Even all the nations that forget God.

18For the needy shall not alway be forgotten, Nor the expectation of the poor perish for ever.

19Arise, O Jehovah; let not man prevail: Let the nations be judged in thy sight.

20Put them in fear, O Jehovah: Let the nations know themselves to be but men. Selah

American Standard Version, 1901

10)1Why standest thou afar off, O Jehovah? Why hidest thou thyself in times of trouble?

2In the pride of the wicked the poor is hotly pursued; Let them be taken in the devices that they have conceived.

3For the wicked boasteth of his heart's desire, And the covetous renounceth, yea , contemneth Jehovah.

4The wicked, in the pride of his countenance,'saith , He will not require it . All his thoughts are, There is no God.

5His ways are firm at all times; Thy judgments are far above out of his sight: As for all his adversaries, he puffeth at them.

6He saith in his heart, I shall not be moved; To all generations I shall not be in adversity.

7His mouth is full of cursing and deceit and oppression: Under his tongue is mischief and iniquity.

8He sitteth in the lurking-places of the villages; In the secret places doth he murder the innocent; His eyes are privily set against the helpless.

9He lurketh in secret as a lion in his covert; He lieth in wait to catch the poor: He doth catch the poor, when he draweth him in his net.

10He croucheth, he boweth down, And the helpless fall by his strong ones.

11He saith in his heart, God hath forgotten; He hideth his face; he will never see it.

12Arise, O Jehovah; O God, lift up thy hand: Forget not the poor.

13Wherefore doth the wicked contemn God, And say in his heart, Thou wilt not require it ?

14Thou hast seen it ; for thou beholdest mischief and spite, to requite it with thy hand: The helpless committeth himself unto thee; Thou hast been the helper of the fatherless.

15Break thou the arm of the wicked; And as for the evil man, seek out his wickedness till thou find none.

16Jehovah is King for ever and ever: The nations are perished out of his land.

17Jehovah, thou hast heard the desire of the meek: Thou wilt prepare their heart, thou wilt cause thine ear to hear;

18To judge the fatherless and the oppressed, That man who is of the earth may be terrible no more.

American Standard Version, 1901
11)1In Jehovah do I take refuge: How say ye to my soul, Flee as a bird to your mountain;

2For, lo, the wicked bend the bow, They make ready their arrow upon the string, That they may shoot in darkness at the upright in heart;

3If the foundations be destroyed, What can the righteous do?

4Jehovah is in his holy temple; Jehovah, his throne is in heaven; His eyes behold, his eyelids try, the children of men.

5Jehovah trieth the righteous; But the wicked and him that loveth violence his soul hateth.

6Upon the wicked he will rain snares; Fire and brimstone and burning wind shall be the portion of their cup.

7For Jehovah is righteous; he loveth righteousness: The upright shall behold his face.

American Standard Version, 1901
12)1Help, Jehovah; for the godly man ceaseth; For the faithful fail from among the children of men.

2They speak falsehood every one with his neighbor: With flattering lip, and with a double heart, do they speak.

3Jehovah will cut off all flattering lips, The tongue that speaketh great things;

4Who have said, With our tongue will we prevail; Our lips are our own: who is lord over us?

5Because of the oppression of the poor, because of the sighing of the needy, Now will I arise, saith Jehovah; I will set him in the safety he panteth for.

6The words of Jehovah are pure words; As silver tried in a furnace on the earth, Purified seven times.

7Thou wilt keep them, O Jehovah, Thou wilt preserve them from this generation for ever.

8The wicked walk on every side, When vileness is exalted among the sons of men.

American Standard Version, 1901
12)1How long, O Jehovah? wilt thou forget me for ever? How long wilt thou hide thy face from me?

2How long shall I take counsel in my soul, Having sorrow in my heart all the day? How long shall mine enemy be exalted over me?

3Consider and answer me, O Jehovah my God: Lighten mine eyes, lest I sleep the'sleep of death;

4Lest mine enemy say, I have prevailed against him; Lest mine adversaries rejoice when I am moved.

5But I have trusted in thy lovingkindness; My heart shall rejoice in thy salvation.

6I will sing unto Jehovah, Because he hath dealt bountifully with me.

American Standard Version, 1901
14)1The fool hath said in his heart, There is no God. They are corrupt, they have done abominable works; There is none that doeth good.

2Jehovah looked down from heaven upon the children of men, To see if there were any that did understand, That did seek after God.

3They are all gone aside; they are together become filthy; There is none that doeth good, no, not one.

4Have all the workers of iniquity no knowledge, Who eat up my people as they eat bread, And call not upon Jehovah?

5There were they in great fear; For God is in the generation of the righteous.

6Ye put to shame the counsel of the poor, Because Jehovah is his refuge.

7Oh that the salvation of Israel were come out of Zion! When Jehovah bringeth back the captivity of his people, Then shall Jacob rejoice, and Israel shall be glad.
American Standard Version, 1901

Where's Occam's razor when you need it?

As if the Multiverse Wasn't Bizarre Enough ... Meet Many Worlds
Denyse O'Leary December 16, 2013 5:28 AM


In 1957 physicist Hugh Everett suggested the "Many Worlds" hypothesis as a proposed interpretation of quantum mechanics. He suggested that the universe constantly splits into different futures each time a subatomic particle goes one way as opposed to the other. Everett thus promptly exited theoretical physics.

However now, some hope that combining Everett's "many worlds" theory with the multiverse will strengthen current cosmology. New Scientist's Justin Mullins explains:
Two of the strangest ideas in modern physics -- that the cosmos constantly splits into parallel universes in which every conceivable outcome of every event happens, and the notion that our universe is part of a larger multiverse -- have been unified into a single theory.
In other words, not only is there an infinite number of universes, but they come into existence every time you turn right instead of left.
Today, such ideas come thicker, faster. We are told, "Our cosmos was 'bruised' in collisions with other, never-observed universes. Or we are living in a giant hologram.* Alternatively, a University of Washington team enterprisingly suggests that maybe the universe is fine-tuned because we are living in a computer simulation, one constructed by super-intelligent descendants who have gone back in time. Science writer Ray Villard offers:

Before you dismiss this idea as completely loony, the reality of such a Sim Universe might solve a lot of eerie mysteries about the cosmos. About two-dozen of the universe's fundamental constants happen to fall within the narrow range thought to be compatible with life. At first glance it seems as unlikely as balancing a pencil on its tip. Jiggle these parameters and life as we know it would have never appeared. Not even stars and galaxies. This is called the Anthropic principle ... We are also living at a very special time in the universe's history where it switched gears from decelerating to accelerating under the push of dark energy. This begs the question "why me why now?"
Before anyone attempts to offer an alternative to the Sim, he advises:
Biblical creationists can no doubt embrace these seeming cosmic coincidences as unequivocal evidence for their "theory" of Intelligent Design (ID). But is our "God" really a computer programmer rather than a bearded old man living in the sky?
Science-Fictions-square.gifVillard implies that only Biblical creationists think that fine-tuning points to a First Cause. That's a fiction he needs; his proposed alternative is even more bizarre than his caricatured mash-up of creationists and advocates of intelligent design.
Never mind, Lee Smolin and colleagues aim to take relativity to a whole new level, with space-time in their sights: "They say we need to forget about the home Einstein invented for us: we live instead in a place called phase space." Which, we are told, is a "curious eight-dimensional world that merges our familiar four dimensions of space and time and a four-dimensional world called momentum space. Smolin, incidentally, does not think that there is a scientific method, just scientific ethics and that laws of nature can evolve over time, in Darwinian fashion. Physics now bows to Darwinian theory, where once it was the reverse.

The eternal cyclic universe is also back. Perimeter Institute cosmologist Neil Turok informs us:

I'm exploring the idea that the singularity was not the beginning of time. In this new view, time didn't have a beginning, and the Big Bang resulted from a collision of branes, sheetlike spaces that exist within a higher-dimensional reality. These collisions might happen repeatedly, creating an eternal, cyclic universe.
Indeed, we are told, time flows backward. Thinking it travels exclusively forward "may be not just an illusion but a lie ... " Discover's Zeeya Merali says. Max Tegmark suggests, "Perhaps we will gradually get used to the weird ways of our cosmos and find its strangeness to be part of its charm."
"Time need not end in the multiverse," burbles science writer Amanda Gefter, as if time or anything else would mean anything in a multiverse. Others suggest, maybe the universes are a wave function. And our own universe may exist inside a black hole. Not to worry, our "original" universe will eventually be populated by "a near-infinite number of advanced, virtual civilizations" featuring "autonomous, conscious beings."

And there is the usual, indeed endless, moralizing: Tegmark proclaims, "We humans have a well-documented tendency toward hubris, arrogantly imagining ourselves at center stage, with everything revolving around us." And cosmologist Raphael Bousso at the University of California, Berkeley, accuses the science community of the sin of "lying to ourselves," by refusing to assume that the "many worlds" theory may be true. Lack of clear evidence has, apparently, nothing to do with it.

By the way, there is life after death: Some clever beings might survive our universe's predicted demise, provided they develop suitable technologies. Apocalypses are also on offer: Stephen Hawking doubts humans will survive another thousand years without escaping Earth.

And God is back too, but not like you remember him. Agnostic physicist Paul Davies explains:

Far from doing away with a transcendent Creator, the multiverse theory actually injects that very concept at almost every level of its logical structure. Gods and worlds, creators and creatures, lie embedded in each other, forming an infinite regress in unbounded space.
So God turns out to be just one more note of cacophony in the transcendent goofiness.
Remember, all this got started just to explain away fine-tuning.

We are told that we are "on the brink of understanding everything," when our cosmology guarantees that we can understand nothing and there is nothing to understand anyway. Everything, you see, is true -- for fifteen seconds.

* Some say the hologram universe originated in an argument Stephen Hawking had with other physicists.

Loved to death?

National Science Standards Reflect a Growing Anxiety on the Part of Evolution Advocates

Sarah Chaffee November 2, 2015 3:46 PM

Teach science critically -- except when it comes to evolution. In discussions of how to improve public school education in the U.S., that's the message that advocates of national science standards typically convey. Yet that wasn't always the case.

An article at Ars Technica recounts the development of the most recent set of proposed standards: the Next Generation Science Standards (NGSS), finalized in 2013. Ironically, teaching students to engage in scientific inquiry, rather than simply expecting them all to absorb the same "facts," was the main impetus.

NGSS began as separate projects of the American Association for the Advancement of Science (AAAS) and National Academies of Sciences (NAS). Their efforts were eventually merged and became the NGSS. John Timmer at Ars Technica writes:

Inspired by the visit of Halley's comet in the 1980s, the AAAS started Project 2061, an attempt to envision where the organization would like to see science literacy in the year the comet would return. Jo Ellen Roseman, Project 2061's Director, told Ars that the goal was to "characterize what the knowledge, skills, and habits of mind would constitute adult science literacy."

Instead of insisting on a "just the facts" approach, the AAAS focused on training young people to think like scientists. After all, the body of knowledge would change over the decades, but the process of scientific inquiry would not.

"While we had no idea what the world would be like, we could guarantee that it would be shaped by science, mathematics, and technology," Roseman said. "And therefore every citizen of the US, every high school graduate had to be literate in those fields."

... Driven by this concept, AAAS gathered scientists and educators to produce a document called Science for All Americans. This publication, while not a set of education standards, laid out the ideas they should contain. Written in prose, it describes basic facts about the Universe that people should know.But over half the document is focused on the nature of science, technology and math, the historic development of these fields, and the "habits of mind" essential for scientific literacy.

The NAS's National Research Council (NRC), meanwhile, produced itsNational Science Education Standards, with a similar emphasis:

"The NRC document took a very strong position about scientific inquiry," Roseman said. "It went beyond what kids should know and be able to do and really articulated what should be going on in classrooms. Students should be engaged in inquiry."

Exactly! At Discovery Institute, we advocate teaching the controversy about evolution. That is for several reasons. Students should learn the full range of evidence on evolution. Teaching the controversy aids in developing critical thinking. And it trains students to think like scientists. Jo Ellen Roseman's comments highlight a further advantage to this pedagogic strategy: that while the content of science may change, the process of scientific inquiry remains vital and valid.

The documents produced by the AAAS and NAS, Science for All Americans and the National Science Education Standards, are persuasive in explaining the importance of critical thinking. Science for All Americansnotes:

In science classrooms, it should be the normal practice for teachers to raise such questions as: How do we know? What is the evidence? What is the argument that interprets the evidence? Are there alternative explanations or other ways of solving the problem that could be better? The aim should be to get students into the habit of posing such questions and framing answers.

Avoid Dogmatism

Students should experience science as a process for extending understanding, not as unalterable truth. This means that teachers take care not to convey the impression that they themselves or the textbooks are absolute authorities whose conclusions are always correct. By dealing with the credibility of scientific claims, the overturn of accepted scientific beliefs, and what to make out of disagreement among scientists, science teachers can help students to balance the necessity for accepting a great deal of science on faith against the importance of keeping an open mind.

The NAS document, National Science Education Standards, recommends:

Students at all grade levels and in every domain of science should have the opportunity to use scientific inquiry and develop the ability to think and act in ways associated with inquiry, including...thinking critically and logically about relationships between evidence and explanations, constructing and analyzing alternative explanations, and communicating scientific arguments.

Building on this foundation, the set of current national science standards, the NGSS, agrees that critical analysis is important. The NGSS were developed in two phases. First, the National Academy of Sciences laid out the basic scientific information students should learn. Second, states worked together to develop specific grade-level standards. The document produced in the first phase, A Framework for K-12 Science Education, takes a very positive view of critical analysis:

Chief among these features [of science] is a commitment to data and evidence as the foundation for developing claims. The argumentation and analysis that relate evidence and theory are also essential features of science; scientists need to be able to examine, review, and evaluate their own knowledge and ideas and critique those of others. Argumentation and analysis include appraisal of data quality, modeling of theories, development of new testable questions from those models, and modification of theories and models as evidence indicates they are needed.

Major science journals also hold that inquiry is central to quality science education. Yet when it comes to evolution, the NGSS abruptly switch gears, rejecting inquiry-based learning and opting for dogmatism.

In middle school, we read, "students can analyze data from the fossil record to describe evidence of the history of life on Earth and can construct explanations for similarities in organisms. They have a beginning understanding of the role of variation in natural selection and how this leads to speciation."

In high school, students are to "demonstrate understanding of how multiple lines of evidence contribute to the strength of scientific theories of natural selection and evolution." This seems to be nearly the opposite of what Science for All Americans says:

Students should experience science as a process for extending understanding, not as unalterable truth. This means that teachers take care not to convey the impression that they themselves or the textbooks are absolute authorities whose conclusions are always correct.

It is inconsistent to oppose the freedom to critically analyze evolutionary thinking, while proclaiming that inquiry is the cornerstone of quality science education. The inconsistency, though, is not all that surprising. It's plainly defensive, a circling of wagons around a theory under increasing pressure from scientific criticisms. The NGSS reflect the anxious mood on the part of evolution defenders in the larger debate about origins.

Students deserve better. If we really want nationwide scientific literacy by the time Halley's comet returns in 2061, we should teach young people to question and analyze across the board, whether the context is biological origins or any other scientific field.

Examining a challenge to Life's no free lunch law

The GUC Bug
Winston Ewert December 4, 2015 10:55 AM

In a series of posts, of which this is the third, I am examining criticisms from Joe Felsenstein (University of Washington geneticist) and Tom English (Oklahoma City computer scientist) in response to two arguments for intelligent design: specified complexity and conservation of information. See here for Parts 1 and 2 in the series.

In my previous post, I reviewed the arguments by William Dembski and Robert Marks in their paper "Life's Conservation Law." I showed that the paper is not based on any simplistic claim that all active information must derive from an intelligent source. However, it does argue that all known computer and mathematical models of Darwinian evolution are teleological. Dembski and Marks argued:

In these models, careful tailoring of fitness functions that assist in locating targets is always present and clearly teleological.

If one could demonstrate such a model that lacked teleology, then their claims would be falsified.

In a post at Panda's Thumb, "Fitness surfaces and searches: Dembski, Ewert, and Marks's search for design," Felsenstein and English spend some time discussing a simple greedy search algorithm, which they name the GUC (Greedy Uphill Climber) Bug. English, in his post "The Law of Conservation of Information is defunct," brings it up again. It is a fairly standard hill-climbing algorithm. It begins with a sequence of DNA one thousand bases long. In each "generation," it evaluates the three thousand DNA sequences that are one nucleotide substitution away from that current sequence. The best sequence is adopted as the new current sequence, and the process repeats itself.

English tested the GUC Bug on a random fitness function. It cannot possibly be argued that a random fitness function was carefully tailored to assist in locating a target. Thus, the success of this bug rests clearly on nonteleological grounds. They describe its performance:

Running the bug until it reached a local peak of the fitness surface, where no immediate neighbor is more fit, [Tom English] found that these peaks were typically higher than 99.98% of all points. So even on one of the worst possible fitness surfaces, a GUC Bug does far better than choosing a DNA sequence at random.

However, we have not claimed that a search algorithm like GUC can't do better than choosing a DNA sequence at random. In fact, Dembski and Marks showed that it could and provided a limit on the active information available through such a scheme. In "Conservation of Information in Search: Measuring the Cost of Success," they wrote:

Multiple queries clearly contain more information than a single query. Active information is therefore introduced from repeated queries.

Demonstrating an algorithm using multiple random queries that outperforms a single random query is not at all surprising. It is precisely what Dembski and Marks indicated would happen. The idea that doing better than choosing a DNA sequence at random would prove our case incorrect derives from the mistaken claim that we think all active information must derive from an intelligent source.

However, does this GUC Bug constitute a nonteleological model of Darwinian evolution, which Dembski and Marks claimed (in "Life's Conservation Law") does not exist? No. It is not a model of Darwinian evolution because it cannot do what is required of Darwinian evolution. Darwinian evolution has to account for finding rare protein folds and complex functional systems. The GUC Bug, operating on a random fitness landscape, does not even come close.

The GUC Bug finds a sequence better than 99.98% of all other sequences, which may sound impressive. But consider, as do English and Felsenstein, this algorithm running for fifty generations. That corresponds to 150,000 different sequences. If we simply took 150,000 random genotypes, we'd expect to find one better than about 99.999% of all the other genotypes. The GUC Bug does worse than random queries, due to getting stuck in a local optimum rather quickly. I hardly need to rehearse the insufficiency of even large numbers of random queries to solve biological problems. This model will have an even harder time solving problems.

However, Felsenstein and English note that a more realistic model of evolution wouldn't have a random fitness landscape. Felsenstein, in particular, argues that "the ordinary laws of physics, with their weakness of long-range interactions, lead to fitness surfaces much smoother than white-noise fitness surfaces." I agree that weak long-range interactions should produce a fitness landscape somewhat smoother than random chance and this fitness landscape would thus be a source of some active information.

We disagree in that I do not think that is going to be a sufficient source of active information to account for biology. I do not have a proof of this. But neither does Felsenstein have a demonstration that it will produce sufficient active information. What I do have is the observation of existing models of evolution. The smoothness present in those models does not derive from some notion of weak long-range physics, but rather from telelogy as explored in my various papers on them.

The GUC Bug falls within the expectations of active information. It extracts active information through repeated queries. Running on a random fitness landscape, it fails to be a model of evolution, because it performs even worse than random search would have. If run on a smooth landscape, it may be a model of Darwinian evolution. However, in order for it to be a non-teleological model of evolution, that fitness landscape would have to be derived in a non-teleological fashion. It remains to be demonstrated that it is possible to construct such a fitness landscape. Thus far, models of evolution have consistently devised the fitness landscape in a teleological fashion.

The Watchtower Society's commentary on Ecclesiastes

ECCLESIASTES:

The Hebrew name Qo·heʹleth (meaning “Congregator; Assembler; Convener; Convoker”) fittingly describes the role of the king in the theocratic government that Israel enjoyed. (Ec 1:1, 12) It was the responsibility of the ruler to hold the dedicated people of God together in faithfulness to their true King and God. (1Ki 8:1-5, 41-43, 66) For that reason, whether a king was good or bad for the nation was determined by whether he led the nation in the worship of Jehovah or not. (2Ki 16:1-4; 18:1-6) The congregator, who was Solomon, had already done much congregating of Israel and their companions, the temporary residents, to the temple. In this book he sought to congregate God’s people away from the vain and fruitless works of this world to the works worthy of the God to whom they as a nation were dedicated. The name used in our English Bibles is taken from the translation of Qo·heʹleth in the Greek Septuagint, namely, Ek·kle·si·a·stesʹ (Ecclesiastes), meaning “a member of an ecclesia (congregation; assembly).”

Writer. There was only one “son of David,” namely, Solomon, who was “king over Israel in Jerusalem” (Ec 1:1, 12), for kings after Solomon did not reign over all Israel. Solomon was the king so well known for his surpassing wisdom. (Ec 1:16; 1Ki 4:29-34) He was a builder. (Ec 2:4-6; 1Ki 6:1; 7:1-8) He was a composer of proverbs. (Ec 12:9; 1Ki 4:32) Solomon was renowned for his wealth. (Ec 2:4-9; 1Ki 9:17-19; 10:4-10, 14-29) Since the book mentions the building program of Solomon, it must have been written after that time but before he “began to do what was bad in the eyes of Jehovah.” (1Ki 11:6) The book was therefore written before 1000 B.C.E., in Jerusalem. That Solomon would be one of the best qualified men to write the book is supported by the fact that he was not only the richest but probably one of the best informed kings of his day; his sailors and tradesmen as well as visiting dignitaries would bring news and knowledge of people of other lands.—1Ki 9:26-28; 10:23-25, 28, 29.

Authenticity. Qo·heʹleth, or Ecclesiastes, is accepted as canonical by both the Jewish and the Christian churches. It is in agreement with other portions of the Bible that treat the same subjects. For example, it agrees with Genesis on man’s being made up of a body composed of the dust of the ground and having the spirit or life-force from God and the breath that sustains it. (Ec 3:20, 21; 12:7; Ge 2:7; 7:22; Isa 42:5) It affirms the Bible teaching that man was created upright but willfully chose to disobey God. (Ec 7:29; Ge 1:31; 3:17; De 32:4, 5) It acknowledges God as the Creator. (Ec 12:1; Ge 1:1) It concurs with the rest of the Bible as to the state of the dead. (Ec 9:5, 10; Ge 3:19; Ps 6:5; 115:17; Joh 11:11-14; Ro 6:23) It strongly advocates the worship and the fear of God. It uses the expression ha·ʼElo·himʹ, “the true God,” 32 times. The equivalent for the name Jehovah is found in the Syriac Peshitta and Jewish Targum of the book at Ecclesiastes 2:24. While some claim that the book contradicts itself, this is only because they do not see that the book many times sets forth the common view as opposed to the view that reflects divine wisdom. (Compare Ec 1:18; 7:11, 12.) So one must read with a view to getting the sense and must keep in mind the theme of the book.

[Box on page 675]

HIGHLIGHTS OF ECCLESIASTES

A vivid description of works that are vain and those that are worth while

Written by Solomon in the latter part of his kingship, after he had engaged in the numerous pursuits that he describes

A life devoted to vain pursuits is empty

To a natural man all is vanity; one generation is replaced by another, and even natural cycles are repetitious and wearisome (1:1-11)

Increased human wisdom can result in increased pain; what is crooked in this system cannot be made straight (1:12-18)

Devoting oneself to pleasure-seeking through materialism is like striving after the wind (2:1-11, 26)

Wisdom is better than folly, but both the wise and the stupid ones die and are forgotten (2:12-16)

Working hard all one’s life only to leave everything to a man who may not appreciate it—this is calamitous (2:17-23)

Events in earthly life often occur in cycles, many of which are beyond human control (3:1-9)

In the present system, all (both man and beast) eventually die (3:18-22)

Many acts of oppression take place, with no hope from a human standpoint (4:1-3)

Hard work and proficiency because of rivalry or simply to accumulate wealth is vanity, and the lazy person is stupid (4:4-8)

The life of a ruler can also be vain (4:13-16)

Accumulating riches will not bring contentment, but it may rob the owner of his sleep; and when he dies he will leave them all behind (5:9-17)

Though a person has many possessions, circumstances—perhaps illness or an unfulfilled longing—may prevent him from finding contentment (6:1-12)

In the present system, the same eventuality awaits both righteous and wicked—all die; so, some give free rein to badness (9:2, 3)

Wisdom is not always appreciated when it comes from a needy man (9:13-18)

Indulging in foolishness gives one a bad reputation; when such incompetent ones are in positions of authority, it is hazardous for them and hard on others (10:1-19)

Youth and the prime of life are vanity; the duration of youthful vigor is so uncertain (11:10)

If a person has not been guided in life by constant remembrance of the Creator, everything is vanity! (12:8)

Things that are worth while and that give meaning to one’s life

Enjoy the fruits of your work, recognizing these as a gift from God (2:24, 25; 5:18-20)

The works of God are all pretty; before mankind he has set the prospect of life to time indefinite (3:10-13)

The general pattern of human life that exists according to God’s permission or purpose cannot be changed by man; so wait on God to act as Judge in his appointed time (3:14-17; 5:8)

A person who works with a partner is better off than a loner (4:9-12)

Proper fear of God should move us to listen carefully to what he requires of us and to fulfill any vow we make to him (5:1-7)

Appreciate the importance of a good name and the brevity of our present life in which to acquire it, the benefit of patience, the superior value of wisdom, and the need to submit humbly to what God permits (7:1-15)

Avoid going to extremes but be guided by fear of God; do not get overly concerned about what other people say; shun the snare of a prostitute (7:16-29)

Be law abiding; even though men dominate others to their injury and human justice is lax, do not let it spoil your enjoyment of life; remember, it will turn out well with those who fear the true God; do not expect to fathom all the reasons for what God does and permits to occur (8:1-17; 10:20)

The righteous ones and the wise ones are in the hand of the true God—they will not lose their reward; but in death a person knows nothing and can do nothing, so use your life now in a manner that God will approve; enjoy it in wholesome ways while you have it (9:1, 4-12)

Seize appropriate opportunities to be generous, to accomplish good; do not let uncertainties of life stifle your activity (11:1-8)

Young man, enjoy your youth, but do not forget that you are accountable to God for your actions; remember your Grand Creator while you are young, before the weakness and decrepitude of old age come, before life ends (11:9; 12:1-7)

The most beneficial writings are those that reflect the wisdom of the “one shepherd,” Jehovah God (12:9-12)

Fear the true God and keep his commandments; he sees everything that we do, and he will bring our works into judgment (12:13, 14)