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Signature of Controversy 29

5. Responding to Stephen

Fletcher in the TimesLiterary Supplement

Stephen C. MeyerS ture the Cellstirred up debate and attracted attention as philosopher

Tomas Nagels selection of SITC as one of the Books of the Yearbrought onan interesting series of letters. Nagel was attacked(heresponded, and he wasattacked again) by a Darwinist who told people to forgo readingSITC andinstead just read Wikipedia.8 Below, Stephen Meyer himself responds in aletter, of which a shortened version was publishedin the TLS. Nagel himself responded with a letter that was published on the same page. Editor

o the Editor

e T mes L ter ry Suppleme tSir

I have been honored by the recent attention my bookS ture the Cell has received in your letters section following Tomas Nagels selection of itas one of your books of the year for 2009.

Unfortunately, the letters from Stephen Fletcher criticizing ProfessorNagel for his choice give no evidence of Dr. Fletcher having read the book orany evidence of his comprehending the severity of the central problem facingchemical evolutionary theories of lifes origin.

In S ture the Cell, I show that, in the era of modern molecular ge-netics, explaining the origin of the rst life requires rst and foremostexplaining the origin of the information or digital code present in DNAand RNA. I also show that various theories of undirected chemical evolu-

tionincluding theories of pre-biological natural selectionfail to explain

8. Fletchers letters may be accessed herehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6940536.ece; and herehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/tls_letters/article6959089.ece.
http://www.signatureinthecell.com/http://www.evolutionnews.org/2009/11/signature_in_the_cell_named_on.htmlhttp://www.evolutionnews.org/2009/11/signature_in_the_cell_named_on.htmlhttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6940536.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6940536.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6950227.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/tls_letters/article6959089.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/tls_letters/article6986702.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/tls_letters/article6986702.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6940536.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6940536.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/tls_letters/article6959089.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/tls_letters/article6959089.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/tls_letters/article6959089.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/tls_letters/article6959089.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6940536.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6940536.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/tls_letters/article6986702.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/tls_letters/article6959089.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6950227.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6940536.ecehttp://www.evolutionnews.org/2009/11/signature_in_the_cell_named_on.htmlhttp://www.signatureinthecell.com/


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the origin of the information necessary to produce the rst self-replicatingorganism.

Yet in his letters to theTLS (2 and 16 December), Stephen Fletcher

rebukes Nagel (and by implication my book) for failing to acknowledge thatnatural selection is a chemical as well as a biological process. Fletcher fur-ther asserts that this process accounts for the origin of DNA and (presum-ably) the genetic information it contains.

Not only does my book address this very proposal at length, but it alsodemonstrates why theories of pre-biotic natural selection involving self-repli-cating RNA catalyststhe version of the idea that Fletcher a rmsfail toaccount for the origin of genetic information.

Indeed, either Dr. Fletcher is blu ng or he is himself ignorant of themany problems that this proposal faces.

First, ribozyme engineering experiments have failed to produce RNAreplicators capable of copying more than about 10 percent of their nucleotidebase sequences (Wendy K. Johnston, et al., RNA-Catalyzed RNA Polym-

erization,Sc e ce292 (2001): 1319-25). Yet, for natural selection to operatein an RNA World (in the strictly chemical rather than biological environ-ment that Fletcher envisions) RNA molecules capable of fully replicatingthemselves must exist.

Second, everything we know about RNA catalysts, including those withpartial self-copying capacity, shows that the function of these molecules de-pends upon the prec searrangement of their information-carrying constitu-ents (i.e., their nucleotide bases). Functional RNA catalysts arise only onceRNA bases are speci cally arranged into information-rich sequencesthatis, function arises after, not before, the information problem has been solved.

F , -

RNA World does not solve the problem of the origin of genetic in-formation; it merely presupposesa solution to the problem in the form

of a hypothetical but necessarily form t o -r ch RNA molecule capable of copying itself. As Nobel laureate Christian de Duve has noted, postulationsof pre-biotic natural selection typically fail because they need information
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which implies they have to presuppose what is to be explained in the rstplace.

Tird, the capacity for even partial replication of genetic information

in RNA molecules results from the activity of chemists, that is, from thetell e ceof the ribozymee eers who design and select the features of

these (partial) RNA replicators. Tese experiments not only demonstratethat even highly limited forms of RNA self-replication depend upon infor-mation-rich RNA molecules, they inadvertently lend additional support tothe hypothesis that intelligent design is the only known cause by which func-tional information arises.

Stephen C. Meyer, PhDC t bSenior Research FellowDiscovery InstituteSeattle, Washington, USA


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6. Responding Again to

Stephen Fletcher in theTimes Literary Supplement

Stephen C. Meyer

After philosopher Tomas Nagel selected S ture the Cellas one of 2009s best books, theT mes L ter ry Suppleme tpublished a vigorous backand forth in its letters section. Te nal salvo9 was by Loughborough Univer-sity chemistry professor Stephen Fletcher. Te response below was submittedby Stephen Meyer toTLS, but the editors chose not to publish it. E

o the Editor

e T mes L ter ry Suppleme tSir

I see that Professor Stephen Fletcher has written yet another letter (Feb-ruary 3, 2010) attempting to refute the thesis of my bookS ture theCell. Tis time he cites two recent experiments in an attempt to show theplausibility of the RNA world hypothesis as an explanation for the origin of the rst life. He claims these experiments have rendered the case I make forthe theory of intelligent design obsolete. If anything, they have done just thereverse.

o support his claim that scienti c developments have overtaken Mey-ers book, Fletcher cites, rst, a scienti c study by chemists Matthew Pown-er, Batrice Gerland and John Sutherland of the University of Manchester(N ture459, pp. 23942). Tis study does partially address one, though only

one, of the many outstanding di culties associated with the RNA worldscenario, the most popular current theory of the undirected chemical evolu-

9. Fletchers letter may be accessed here:http://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article7013742.ece.
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tion of life. Starting with several simple chemical compounds, Powner andcolleagues successfully synthesized a pyrimidine ribonucleotide, one of thebuilding blocks of the RNA molecule.

Nevertheless, this work does nothing to address the much more acuteproblem of explaining how the nucleotide bases in DNA or RNA acquiredtheir speci c information-rich arrangements, which is the central topic of mybook. In e ect, the Powner study helps explain the origin of the letters inthe genetic text, but not their speci c arrangement into functional wordsor sentences. Moreover, Powner and colleagues only partially addressedthe problem of generating the constituent building blocks of RNA underplausible pre-biotic conditions. Te problem, ironically, is their own skillfulintervention. o ensure a biologically relevant outcome, they had to inter-venerepeatedly and intelligentlyin their experiment: rst, by selectingonly the right-handed isomers of sugar that life requires; second, by purifyingtheir reaction products at each step to prevent interfering cross-reactions;and third, by following a very precise procedure in which they carefully se-lected the reagents and choreographed the order in which they were intro-duced into the reaction series. Tus, not only does this study not address theproblem of getting nucleotide bases to arrange themselves into functionallyspeci ed sequences, but the extent to which it does succeed in producingbiologically relevant chemical constituents of RNA actually illustrates theindispensable role of intelligence in generating such chemistry. Te secondstudy that Fletcher cites illustrates this problem even more acutely.

, by racey Lincoln and Gerald Joyce (Sc e ce 323, pp. 22932), ostensibly establishes the capacity of RNA to self-

replicate, thereby rendering plausible one of the key steps in the RNA worldscenario. Nevertheless, the self-replicating RNA molecules that Lincolnand Joyce construct are not capable of copying a template of genetic informa-tion from free-standing nucleotides as the protein (polymerase) machinerydoes in actual cells. Instead, in Lincoln and Joyces experiment, a pre-syn-thesized speci cally sequenced RNA molecule merely catalyzes the forma-tion of a single chemical bond, thus fusing two other pre-synthesized partial


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RNA chains. Teir version of self-replication amounts to nothing morethan joining two sequence-speci c pre-made halves together.

More signi cantly, Lincoln and Joyce themselves intelligently arranged

the base sequences in these RNA chains. Tey generated the functionallyspeci c information that made even this limited form of replication possible.Tus, as I argue in S ture the Cell, Lincoln and Joyces experiment notonly demonstrates that even limited capacity for RNA self-replication de-pends upon information-rich RNA molecules, it also lends additional sup-port to the hypothesis that intelligent design is the only known means bywhich functional information arises.

Stephen C. Meyer, PhDC t bSenior Research FellowDiscovery InstituteSeattle, Washington, USA


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7. Responding to Stephen

Fletcher in the TimesLiterary Supplement

on the RNA World

David Berlinskio the Editore T mes L ter ry Suppleme t

SirHaving with indignation rejected the assumption that the creation of life

required an intelligent design, Mr. Fletcher has persuaded himself that it hasproceeded instead by means of various chemical scenarios.10

Tese scenarios all require intelligent intervention. In his animadver-sions, Mr. Fletcher suggests nothing so much as a man disposed to denouncealcohol while sipping sherry.

Te RNA world to which Mr. Fletcher has pledged his allegiance wasintroduced by Carl Woese, Leslie Orgel and Francis Crick in 1967. Mysti ed

by the appearance in the contemporary cell of a chicken in the form of thenucleic acids, and an egg in the form of the proteins, Woese, Orgel and Crickargued that at some time in the past, the chicken was the egg.

Tis triumph of poultry management received support in 1981, whenboth Tomas Cech and Sidney Altman discovered the rst of the ribonucleicenzymes. In 1986, their discoveries moved Walter Gilbert to declare the for-mer existence of an RNA world. When Harry Noeller discovered that pro-tein synthesis within the contemporary ribosome is catalyzed by ribosomal

10. Fletchers letters may be accessed herehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6940536.ece; and herehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/tls_letters/article6959089.ece.
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RNA, the existence of an ancient RNA world appeared almost certain toLeslie Orgel.

And to Mr. Fletcher, I imagine.

If experiments conducted in the here and now are to shed light on thethere and then, they must meet two conditions: Tey must demonstrate inthe rst place the existence of a detailed chemical pathway between RNAprecursors and a form of self-replicating RNA; and they must provide in thesecond place a demonstration that the spontaneous appearance of this path-way is plausible under pre-biotic conditions.

Te constituents of RNA are its nitrogenous bases, sugar, and phos-phate. Until quite recently, no completely satisfactory synthesis of the py-rimidine nucleotides has been available.

Te existence of a synthetic pathway has now been established (Mat-thew W. Powner et al., Te synthesis of activated pyrimidine ribonucleo-tides in prebiotically plausible conditions,N ture459, pp. 239242).

Questions of pre-biotic plausibility remain. Can the results of Powner et

al. be reproduced without Powner et al.?It is a question that Powner raises himself: My ultimate goal, he has

remarked, is to get a living system (RNA) emerging from a one-pot experi-ment.

Let us by all means have that pot, and then we shall see further.If the steps leading to the appearance of the pyridimines in a pre-biotic

environment are not yet plausible, then neither is the appearance of a self-replicating form of RNA. Experiments conducted by racey Lincoln andGerald Joyce at the Scripps Institute have demonstrated the existence of self-replicating RNA by a process of in vitro evolution. Tey began with whatthey needed and puri ed what they got until they got what they wanted.

Although an invigorating piece of chemistry, what is missing from theirdemonstration is what is missing from Powners and that is any clear indica-

tion of pre-biotic plausibility.I should not wish to leave this discussion without extending the hand of

friendship to every party.


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Mr. Nagel is correct in remarking that Mr. Fletcher is insu erable. Mr.Walton is correct in observing that the RNA world is imaginary. And Mr.Fletcher is correct in nding the hypothesis of intelligent design unaccept-

able.He should give it up himself and see what happens.

David BerlinskiParis


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8. Why Are Darwinists

Scared to ReadSignature in the Cell?

David Klinghofer

I -nothingism of Darwinian atheists in the U.S. is matched by those in

England, so too not only in our country but in theirs the screechy ig-norance receives its appropriate reply from people with good sense and anopen mind. Some of the latter include atheists who, however, arrived at theirunbelief through honest re ection rather than through the mind-numbingroute of fealty to Darwinist orthodoxy. Such a person is Tomas Nagel, the

distinguished NYU philosopher. He praised Stephen MeyersS ture the Cell: DNA d the Ev de ce for I tell e t Desin the T mes L ter rySuppleme tas a book of the year,concluding with this enviable endorse-ment:

[A] detailed account of the problem of how life came into existencefrom lifeless mattersomething that had to happen before the pro-cess of biological evolution could begin. Meyer is a Christian, but

atheists, and theists who believe God never intervenes in the naturalworld, will be instructed by his careful presentation of this endishlydi cult problem.

Nagels review elicited howls from Darwinists who made no e ort topretend they had even weighed the 611-page volume in their hand, muchless read a page of it. On his blog,Why Evolution Is rue,11 University of Chicago biologist Jerry Coyne complained that they hadnt ought to let such

an opinion even appear in the august columns of theTLS:

11. Coynes comments may be accessed here:http://whyevolutionistrue.wordpress.com/2009/12/01/distinguished-philosopher-blurbs-intelligent-design-book/; and here: http://whyevolutionistrue.wordpress.com/2009/12/02/more-on-nagel-and-meyer/.
http://www.amazon.com/Signature-Cell-Evidence-Intelligent-Design/dp/0061472786/ref=cm_cr_pr_product_tophttp://www.amazon.com/Signature-Cell-Evidence-Intelligent-Design/dp/0061472786/ref=cm_cr_pr_product_tophttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6931364.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6931364.ecehttp://whyevolutionistrue.wordpress.com/2009/12/01/distinguished-philosopher-blurbs-intelligent-design-book/http://whyevolutionistrue.wordpress.com/2009/12/01/distinguished-philosopher-blurbs-intelligent-design-book/http://whyevolutionistrue.wordpress.com/2009/12/01/distinguished-philosopher-blurbs-intelligent-design-book/http://whyevolutionistrue.wordpress.com/2009/12/02/more-on-nagel-and-meyer/http://whyevolutionistrue.wordpress.com/2009/12/02/more-on-nagel-and-meyer/http://whyevolutionistrue.wordpress.com/2009/12/02/more-on-nagel-and-meyer/http://whyevolutionistrue.wordpress.com/2009/12/02/more-on-nagel-and-meyer/http://whyevolutionistrue.wordpress.com/2009/12/02/more-on-nagel-and-meyer/http://whyevolutionistrue.wordpress.com/2009/12/01/distinguished-philosopher-blurbs-intelligent-design-book/http://whyevolutionistrue.wordpress.com/2009/12/01/distinguished-philosopher-blurbs-intelligent-design-book/http://whyevolutionistrue.wordpress.com/2009/12/01/distinguished-philosopher-blurbs-intelligent-design-book/http://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6931364.ecehttp://entertainment.timesonline.co.uk/tol/arts_and_entertainment/the_tls/article6931364.ecehttp://www.amazon.com/Signature-Cell-Evidence-Intelligent-Design/dp/0061472786/ref=cm_cr_pr_product_tophttp://www.amazon.com/Signature-Cell-Evidence-Intelligent-Design/dp/0061472786/ref=cm_cr_pr_product_top


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Detailed account?? How about religious speculation?

Nagel is a respected philosopher whos made big contributions toseveral areas of philosophy, and this is inexplicable, at least to me. I

have already called this to the attention of theTLS, just so they know.No doubt the editors appreciated his letting them know they had erred

by printing a view not in line with the o cial catechism. Coyne then ap-pealed for help. Not having read the book himself, while nevertheless feelingcomfortable dismissing it as religious speculation, he pleaded:

Do any of you know of critiques of Meyers book written by sci-entists? I havent been able to nd any on the Internet, and would

appreciate links.Coyne was later relievedwhen a British chemist, Stephen Fletcher, pub-

lished a critical letter to the editor in theTLS associating Meyers argumentwith a belief in gods, devils, pixies, fairies and recommending that readerslearn about chemical evolution by, instead, reading up on it elsewhere froman unimpeachable source of scienti c knowledge:

Readers who wish to know more about this topic are stronglyadvised to keep their hard-earned cash in their pockets, forgo Meyersbook, and simply read RNA world on Wikipedia.

Responding in turn with his ownletter to the editor, Nagel seemed toexpress doubt whether the chemist had actually readS ture the Cell before writing to object to Nagels praise:

Fletchers statement that It is hard to imagine a worse book sug-

gests that he has read it. If he has, he knows that it includes a chapteron Te RNA World which describes that hypothesis for the originof DNA at least as fully as the Wikipedia article that Fletcher recom-mends. Meyer discusses this and other proposals about the chemicalprecursors of DNA, and argues that they all pose similar problemsabout how the process could have got started.

Nagels letter appeared beside another from a di erent British chemist, John C. Walton at the University of St. Andrews, who presumably did readthe book since he blurbs it on the back cover as a delightful read. In his let-ter, Walton re ects:
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It is an amusing irony that while castigating students of religionfor believing in the supernatural, [Fletcher] o ers in its place an en-tirely imaginary RNA world the only support for which is specula-tion!

A a pattern here at all? All the people who hate Mey-ers book appear not to have read it. So too we have the complaint of Darwinian-atheist agitator P. Z. Myers,12 a popular blogger and biologist.Myers explains that he was unable to read the book, which he slimes as astinker and as drivel, due to his not having received a promised free reviewcopy! But rest assured. Te check is in the mail: I suppose Ill have to readthat 600 page pile of slop sometime maybe in January.

Dr. Myers teaches at the Morris, Minnesota, satellite campus of theUniversity of Minnesota, a college well known as the Harvard of Morris,Minnesota. So you know when he evaluates a book and calls it slop, a bookon which he has not laid on eye, thats a view that carries weight.

In all seriousness, what is this with people having any opinion at all of

a book that, allow me to repeat,they h ve t re dand of which, as with JerryCoyne, they admit they havent so much as read a review? Even a far moremeasured writer like Jonathan Derbybshire,reporting for theNew St tes-m on the Nagel-TLS dustup, concedes, I havent read Myers [s c] book,nor am I competent to assess Fletchers contention that Nagel had simply gotthe science wrong. Honesty counts for something, though Derbyshire (notto be confused withN t o l Rev ews John Derbyshire) might have at least

taken the trouble to spell Steve Meyers name correctly.Alas, carelessness and dishonesty are hallmarks of the Darwinian pro-

pagandists. Hordes of whom, by the way, have been trying to overwhelm S tures Amazon page. Tey post abusive reviews making, again, littlepretense of having turned a single page even as they then try to boost theirown phony evaluations by gathering in mobs generated by email lists andclicking on the Yes button at the question, Was this review helpful to you?Per Amazons easily exploited house rules, this has the e ect of boosting thereview to enhanced prominence. Its a fraudulent tactic, and sadly typical.

12. http://scienceblogs.com/pharyngula/2009/12/you_know_its_a_stinker_when_th.php.
http://scienceblogs.com/pharyngula/2009/12/you_know_its_a_stinker_when_th.phphttp://www.newstatesman.com/blogs/cultural-capital/2009/12/nagel-fletcher-everythinghttp://www.newstatesman.com/blogs/cultural-capital/2009/12/nagel-fletcher-everythinghttp://www.newstatesman.com/blogs/cultural-capital/2009/12/nagel-fletcher-everythinghttp://www.amazon.com/Signature-Cell-Evidence-Intelligent-Design/product-reviews/0061472786/ref=dp_db_cm_cr_acr_txt%3Fie=UTF8%26showViewpoints=1http://www.amazon.com/Signature-Cell-Evidence-Intelligent-Design/product-reviews/0061472786/ref=dp_db_cm_cr_acr_txt%3Fie=UTF8%26showViewpoints=1http://scienceblogs.com/pharyngula/2009/12/you_know_its_a_stinker_when_th.phphttp://scienceblogs.com/pharyngula/2009/12/you_know_its_a_stinker_when_th.phphttp://www.amazon.com/Signature-Cell-Evidence-Intelligent-Design/product-reviews/0061472786/ref=dp_db_cm_cr_acr_txt%3Fie=UTF8%26showViewpoints=1http://www.newstatesman.com/blogs/cultural-capital/2009/12/nagel-fletcher-everythinghttp://www.newstatesman.com/blogs/cultural-capital/2009/12/nagel-fletcher-everythinghttp://scienceblogs.com/pharyngula/2009/12/you_know_its_a_stinker_when_th.php


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9. Every Bit Digital: DNAs

Programming ReallyBugs Some ID Critics

Casey Luskin

G D B E , -nately, not all who work at the search engine behemoth seem to

practice the slogan.Mark Chu-Carroll, a mathematician andGoogle software engineer, called Stephen MeyersS ture the Cella re-hash of the same old st, even though he admitted, I have not read anypart of Meyers book. Chu-Carroll further decried the dishonesty of Mey-er, whom he called a bozo for merely claiming that DNA contains digital

code that functions like a computer.It seems that Meyers book isnt the only relevant literature that Chu-

Carroll hasnt read.In 2003 renowned biologist Leroy Hood and biotech guru David Ga-

las authored a review article in the worlds leading scienti c journal,N ture,titled, Te Digital Code of DNA. Te article explained, A remarkable fea-ture of the structure is that DNA can accommodate almost any sequence of base pairsany combination of the bases adenine (A), cytosine (C), guanine(G) and thymine ( )and, hence any digital message or information. MIProfessor of Mechanical Engineering Seth Lloyd (no friend of ID) likewiseeloquently explains why DNA has a digital nature:

Its been known since the structure of DNA was elucidated thatDNA is very digital. Tere are four possible base pairs per site, twobits per site, three and a half billion sites, seven billion bits of infor-mation in the human DNA. Teres a very recognizable digital codeof the kind that electrical engineers rediscovered in the 1950s thatmaps the codes for sequences of DNA onto expressions of proteins.
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DNAs computer-like attributes have also been noted by leading think-ers. Software mogul Bill Gates said, Human DNA is like a computerprogram but far, far more advanced than any software weve ever created.

Francis Collinswho headed the Human Genome project and is a notedproponent of Darwinism, describes DNA as a digital code, and observesthat DNA is something like the hard drive on your computer that containsprogramming. Even Richard Dawkins has observed that the machine codeof the genes is uncannily computer-like. Apart from di erences in jargon, thepages of a molecular biology journal might be interchanged with those of acomputer engineering journal.

B the computer code doing? It turns out that its program-ming nothing less than nanotechnologymicromolecular machinesinside the cell. In the words of Bruce Alberts, former president of the U.S.National Academy of Sciences, Te entire cell can be viewed as a factorythat contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.

For Chu-Carroll to ignore the many leading evolutionary scientists andthinkers who have compared the cell to computers or machines, and insteadto accuse Meyer of dishonesty is, well, a low form of argument that theGoogle motto probably prevents us from naming. But where in our experi-ence do digital code, computer programming, and factories lled with ma-chines come from? Chu-Carroll knows the answer, which is probably why hedoesnt like Meyers argument.


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II

On Reading Stephen

Meyers Signaturein the Cell


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10. Responding to

Darrel Falks Review ofSignature in the Cell

Stephen C. MeyerDr. Darrel Falk, biology professor at Point Loma Nazarene University, re-

viewedS ture the Cellfor the BioLogos Foundations blog, Sc e ce & theS cred.13 Below is Dr. Meyers response. E

I I problem in origin-of-life biology to my attentionthe problem of ex-plaining how the information necessary to produce the rst living cellarose. At the time, I was working as a geophysicist doing digital signal pro-

cessing, a form of information analysis and technology. A year later, I en-rolled in graduate school at the University of Cambridge, where I eventuallycompleted a PhD in the philosophy of science after doing interdisciplinaryresearch on the scienti c and methodological issues in origin-of-life biology.In the ensuing years, I continued to study the problem of the origin of life andhave authored peer-reviewed and peer-edited scienti c articles on the topic of biological origins, as well as co-authoring a peer-reviewed biology textbook.

Last year, after having researched the subject for more than two decades, Ipublished S ture the Cell , which provides an extensive evaluation of the principal competing theories of the origin of biological information andthe related question of the origin of life. Since its completion, the book hasbeen endorsed by prominent scientists including Philip Skell, a member of the National Academy of Sciences; Scott urner, an evolutionary biologistat the State University of New York; and Professor Norman Nevin, one of Britains leading geneticists.

13.http://biologos.org/blog/signature-in-the-cell/ .
http://biologos.org/blog/signature-in-the-cell/http://biologos.org/blog/signature-in-the-cell/http://www.signatureinthecell.com/http://biologos.org/blog/signature-in-the-cell/http://biologos.org/blog/signature-in-the-cell/http://www.signatureinthecell.com/http://biologos.org/blog/signature-in-the-cell/http://biologos.org/blog/signature-in-the-cell/


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Nevertheless, in his recent review on the BioLogos website, ProfessorDarrel Falk characterizes me as merely a well-meaning, but ultimately un-quali ed, philosopher and religious believer who lacks the scienti c exper-

tise to evaluate origin-of-life research and who, in any case, has overlookedthe promise of recent pre-biotic simulation experiments. On the basis of twosuch experiments, Falk suggests I have jumped prematurely to the conclu-sion that pre-biotic chemistry cannot account for the origin of life. Yet nei-ther of the scienti c experiments he cites provides evidence that refutes theargument of my book or solves the central mystery that it addresses. Indeed,both experiments actually reinforceif inadvertentlythe main argumentof S ture the Cell.

Te central argument of my book is that intelligent designthe activityof a conscious and rational deliberative agentbest explains the origin of theinformation necessary to produce the rst living cell. I argue this because of two things that we know from our uniform and repeated experience, whichfollowing Charles Darwin I take to be the basis of all scienti c reasoningabout the past. First, intelligent agents have demonstrated the capacity toproduce large amounts of functionally speci ed information (especially ina digital form). Second, no undirected chemical process has demonstratedthis power. Hence, intelligent design provides the bestmost causally ad-equateexplanation for the origin of the information necessary to producethe rst life from simpler non-living chemicals. In other words, intelligentdesign is the only explanation that cites a cause known to have the capacity

to produce the key e ect in question.Nowhere in his review does Falk refute this claim or provide another

explanation for the origin of biological information. In order to do so, Falkwould need to show that some undirected material cause has demonstratedthe power to produce functional biological information apart from the guid-ance or activity of a designing mind. Neither Falk, nor anyone working inorigin-of-life biology, has succeeded in doing this. Tus, Falk opts insteadto make a mainly personal and procedural argument against my book bydismissing me as unquali ed and insisting that it is premature to draw anynegative conclusions about the adequacy of undirected chemical processes.


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claim that I rushed to judgment, Falk rst cites a sci-enti c study published last spring after my book was in press. Tepa-

per, authored by University of Manchester chemist John Sutherland and two

colleagues, does partially address one of the many outstanding di cultiesassociated with the RNA world, the most popular current theory about theorigin of the rst life.

Starting with a 3-carbon sugar (D-gylceraldehyde), and another mol-ecule called 2-aminooxazole, Sutherland successfully synthesized a 5-car-bon sugar in association with a base and a phosphate group. In other words,he produced a ribonucleotide. Te scienti c press justi ably heralded thisas a breakthrough in pre-biotic chemistry because previously chemists hadthought (as I noted in my book) that the conditions under which ribose andbases could be synthesized were starkly incompatible with each other.

Nevertheless, Sutherlands work does not refute the central argument of my book, nor does it support the claim that it is premature to conclude thatonly intelligent agents have demonstrated the power to produce functionally

speci ed information. If anything, it illustrates the reverse.In Chapter 14 of my book I describe and critique the RNA world sce-

nario. Tere I describe ve major problems associated with the theory.Sutherlands work only partially addresses the rst and least severe of thesedi culties: the problem of generating the constituent building blocks ormonomers in plausible pre-biotic conditions. It does not address the moresevere problem of explaining how the bases in nucleic acids (either DNA

or RNA) acquired their speci c information-rich arrangements. In otherwords, Sutherlands experiment helps explain the origin of the letters inthe genetic text, but not their speci c arrangement into functional wordsor sentences.

Even so, Sutherlands work lacks pre-biotic plausibility and does so inthree ways that actually underscore my argument.

First, Sutherland chose to begin his reaction with only the right-handedisomer of the 3-carbon sugars he needed to initiate his reaction sequence.Why? Because he knew that otherwise the likely result would have had littlebiological signi cance. Had Sutherland chosen to use a far more plausible
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racemic mixture of both right- and left-handed sugar isomers, his reactionwould have generated undesirable mixtures of stereoisomersmixtures thatwould seriously complicate any subsequent biologically relevant polymeriza-

tion. Tus, he himself solved the so-called chirality problem in origin-of-lifechemistry by intelligently selecting a single enantiomer, i.e., only the right-handed sugars that life itself requires. Yet there is no demonstrated sourcefor such non-racemic mixture of sugars in any plausible pre-biotic environ-ment.

Second, the reaction that Sutherland used to produce ribonucleotidesinvolved numerous separate chemical steps. At each intermediate stage inhis multi-step reaction sequence, Sutherland himself intervened to purifythe chemical by-products of the previous step by removing undesirable sideproducts. In so doing, he preventedby his own will, intellect and experi-mental techniquethe occurrence of interfering cross-reactions, the scourgeof the pre-biotic chemist.

Tird, in order to produce the desired chemical productribonucleo-

tidesSutherland followed a very precise recipe or procedure in which hecarefully selected the reagents and choreographed the order in which theywere introduced into the reaction series, just as he also selected which sideproducts to be removed and when. Such recipes, and the actions of chemistswho follow them, represent what the late Hungarian physical chemist Mi-chael Polanyi called profoundly informative intervention[s]. Information isbeing added to the chemical system as the result of the deliberative actions

the intelligent designof the chemist himself.

I , only did Sutherlands experimentotaddress the more fun-damental problem of getting the nucleotide bases to arrange themselvesinto functionally speci ed sequences; the extent to which it did succeed inproducing more life-friendly chemical constituents actually illustrates theindispensable role of intelligence in generating such chemistry.

Te second experiment that Falk cites to refute my book illustrates thisproblem even more acutely. Tis experiment is reported in ascienti c paper by racey Lincoln and Gerald Joyce ostensibly establishing the capacity of RNA to self-replicate, thereby rendering plausible one of the key steps in the
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RNA world hypothesis. Falk incorrectly intimates that I did not discuss thisexperiment in my book. In fact, I do on page 537.

In any case, it is Falk who draws exactly the wrong conclusion from this

paper. Te central problem facing origin-of-life researchers is neither thesynthesis of pre-biotic building blocks (which Sutherlands work addresses)or even the synthesis of a self-replicating RNA molecule (the plausibility of which Joyce and raceys work seeks to establish,albeit unsuccessfully: seebelow). Instead, the fundamental problem is getting the chemical buildingblocks to arrange themselves into the large information-bearing molecules(whether DNA or RNA). As I show inS ture the Cell, even the ex-tremely limited capacity for RNA self-replication that has been demon-strated depends critically on the speci city of the arrangement of nucleotidebasesthat is, upon pre-existing sequence-speci c information.

Te Lincoln and Joyce experiment that Falk describes approvingly doesnot solve this problem, at least not apart from the intelligence of Lincolnand Joyce. In the rst place, the self-replicating RNA molecules that they

construct are not capable of copying a template of genetic information fromfree-standing chemical subunits as the polymerase machinery does in actualcells. Instead, in Lincoln and Joyces experiment, a pre-synthesizedspec c llyseque cedRNA molecule merely catalyzes the formation of a single chemicalbond, thus fusing two other pre-synthesized partial RNA chains. In otherwords, their version of self-replication amounts to nothing more than join-ing two sequence speci c pre-made halves together. More signi cantly, Lin-

coln and Joyce themselves tell e tly rr edthe matching base sequencesin these RNA chains. Tey did the work of replication. Tey generated thefunctionally speci c information that made even this limited form of replica-tion possible.

Te Lincoln and Joyce experiment actually con rms three related claimsthat I make inS ture the Cell. First, it demonstrates that even the capac-ity for modest partial self-replication in RNA itself depends upon sequencespeci c (i.e., information-rich) base sequences in these molecules. Second,it shows that even the capacity for partial replication of genetic informationin RNA molecules results from the activity of chemists, that is, from the
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intelligence of the ribozyme engineers who design and select the featuresof these (partial) RNA replicators. Tird, pre-biotic simulation experimentsthemselves con rm what we know from ordinary experience, namely, that

intelligent design is the only known means by which functionally speci edinformation arises.

F years origin-of-life researchers have attempted to usepre-biotic simulation experiments to nd a plausible pathway by whichlife might have arisen from simpler non-living chemicals, thereby providingsupport for chemical evolutionary theory. While these experiments have

occasionally yielded interesting insights about the conditions under whichcertain reactions will or wont produce the various small molecule constitu-ents of larger bio-macromolecules, they have shed no light on how the in-formation in these larger macromolecules (particularly in DNA and RNA)could have arisen. Nor should this be surprising in light of what we have longknown about the chemical structures of DNA and RNA. As I show inS -

ture the Cell, the chemical structures of DNA and RNA allow them to

store information precisely because chemical a nities between their smallermolecular subunits do not determine the speci c arrangements of the basesin the DNA and RNA molecules. Instead, the same type of chemical bond(an N-glycosidic bond) forms between the backbone and each one of the fourbases, allowing any one of the bases to attach at any site along the backbone,in turn allowing an innumerable variety of di erent sequences. Tis chemi-cal indeterminacy is precisely what permits DNA and RNA to function as

information carriers. It also dooms attempts to account for the origin of theinformationthe precise sequencing of the basesin these molecules as theresult of deterministic chemical interactions.

Nevertheless, for Professor Falk, drawing any negative conclusions aboutthe adequacy of purely undirected chemical processes or worsemakingan inference to intelligent design, is inherently premature. Indeed, for himsuch thinking constitutes giving up on science or making an argument fromignorance. But this betrays a misunderstanding of both science and the basisof the design argument that I am making.


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Scienti c investigations not only tell us what nature does, they also fre-quently tell us what nature doesnt do. Te conservation laws in thermody-namics, for example, proscribe certain outcomes. Te rst law tells us that

energy is never created or destroyed. Te second tells us that the entropy of aclosed system will everdecrease over time. Moreover, because these laws arebased upon our uniform and repeated experience, we have great con dencein them. Tat is why physicists dont, for example, still consider research onperpetual motion machines to be worth investigating or funding.

In the same way, we now have a wealth of experience showing that whatI callspec edor fu ct o linformation (especially if encoded in digital form)does not arise from purely physical or chemical antecedents. Indeed, the ri-bozyme engineering and pre-biotic simulation experiments that ProfessorFalk commends to my attention actually lend additional inductive supportto this generalization. On the other hand, we do know of a causea type of causethat has demonstrated the power to produce functionally speci edinformation. Tat cause is intelligence or conscious rational deliberation. Asthe pioneering information theorist Henry Quastler once observed, Tecreation of information is habitually associated with conscious activity. And,of course, he was right. Whenever we nd informationwhether embeddedin a radio signal, carved in a stone monument, written in a book or etchedon a magnetic discand we trace it back to its source, invariably we cometo mind, not merely a material process. Tus, the discovery of functionallyspeci ed, digitally encoded information along the spine of DNA provides

compelling positive evidence of the activity of a prior designing intelligence.Tis conclusion is not based upon what wedo tknow. It is based upon whatwedo k owfrom our uniform experience about the cause and e ect structureof the worldspeci cally, what we know about what does, and does not,have the power to produce large amounts of speci ed information.

P F rejects this knowledges k owled e, and thecase for design based on it, re ects his own commitment to nding

a solution to the origin of life problem within a strictly materialistic frame-work. Indeed, he and his colleagues atB oLo oshave made clear that theyaccept the principle of methodological naturalism, the idea that scientists,


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to be scientists, must limit themselves to positing only materialistic explana-tions for all phenomena. Of course, it is their right to accept this intellectuallimitation on theorizing if they wish. But it needs to be noted that the prin-

ciple of methodological naturalism is an arbitrary philosophical assumption,not a principle that can be established or justi ed by scienti c observationitself. Others of us, having long ago seen the pattern in pre-biotic simulationexperiments, to say nothing of the clear testimony of thousands of years of human experience, have decided to move on. We see in the information-richstructure of life a clear indicator of intelligent activity and have begun to in-vestigate living systems accordingly. If, by Professor Falks de nition, thatmakes us philosophers rather than scientists, then so be it. But I suspect thatthe shoe is now, instead, rmly on the other foot.


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11. Asking Darrel Falk to

Pick a Number, Any NumberRichard Sternberg

I

DNA sequences are nonsensical or junk. And given the data thathave emerged over the past seven or so years, a functionalist view of the

genome has robust empirical support. It is for this reason that I think manyof the arguments presented by the BioLogos Foundation are wrong on manycounts, to borrow a phrase from Darrel Falk.

Here is an example. While reading the critique of Steve Meyersbook, S ture the Cell, by Francisco Ayala,14 a number struck me that Iknow to be incorrect. Te integer that I am referring to is 25,000 and it is

claimed to be the known tally of genes in our chromosomes:

Te human genome includes about 25,000 genes and lots of oth-er (mostly short) switch sequences

Now, the problem with such a statement is this: While there are ~25,000 prote -cod e esin our DNA, the number of RNA-cod e esis pre-dicted to be much higher, >450,000.15 Some of the latter range in lengthfrom being quite shortonly 20 or so genetic lettersto being millionsof letters long. Since 2004 we have learned that over 90 percent of ourDNA is transcribed into RNA sequences at some developmental stage, indi erent cell and tissue types. (Our brain cells are unusually rich in thesenon-translated RNAs.) Tese RNAs are then processed into regulatoryand structural sequences of all sizes.16 14.http://biologos.org/blog/on-reading-the-cells-signature/.15. Rederstor , M., S. H. Bernhart, A. anzer, M. Zywicki, K. Per er, M. Lukasser, I. L.

Hofacker and A. Httenhofer (in press), RNPomics: De ning the ncRNA transcriptome bycDNA library generation from ribonucleo-protein particles,Nucle c Ac ds Rese rch(2010).16. Amaral, P. P., M.E. Dinger, . R. Mercer and J. S. Mattick, Te eukaryotic genome as anRNA machine,Sc e ce319:5871 (2008), pp. 1787-1789; Dinger, M. E., P. P. Amaral, . R.Mercer and J. S. Mattick, Pervasive transcription of the eukaryotic genome: functional indicesand conceptual implications,Br e s Fu ct o l Ge om cs d Proteom cs8:6 (2009), pp.
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It could of course be argued, as it has been, that most of these RNAtranscripts are themselves junk. But a host of them are packaged into com-plexes with di erent proteins.

So the true number of genes in our DNA is probably >450,000 +25,000 = >475,000. What is more, these >450,000 genes cover more than88.5 percent of our 3 billion genetic letters. Tats rightmost, if not closeto all, of our chromosomal DNA consists of di erent types of genes thathave only recently been discovered.

How do these facts square with this commentmade by Falk?17

but this still doesnt negate the fact that almost certainly much, if notmost, of the DNA plays no role, and in many cases can be harmful.

W , depends on how he is using the words much andmost. I really dont know. So I have a question for him:Ex ctly what fraction of the transcribed 88.5 percent of our DNA are you willing tosay plays no role or can be harmful? All I am asking for is a prediction, suchas 90 percent of these DNA letters is super uous (or 79.5 percent of the

RNAs are nonsensical). Since he also said almost certainly in the abovestatement, he must have a gure in mind. So I say pick a number, any num-ber. But to be a good sport, Ill show my prediction: All of the expressed88.5 percent of our DNA has diverse roles in our development.

407-423; Mercer, . R., I. A. Qureshi, S. Gokhan, M. E. Dinger, G. Li, J. S. Mattick and M.F. Mehler, Long noncoding RNAs in neuronal-glial fate speci cation and oligodendrocytelineage maturation,BMC Neurosc e ce11:1 (2010), p. 14.17. http://biologos.org/blog/on-reading-the-signature-a-response-to-stephen-meyer/.
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12. Ayala and Falk Miss

the Signs in the GenomeRichard Sternberg

I S M Signa in

Cell, Francisco Ayalaclaimed that repetitive portions of our DNAcalled Alu sequences are nonsensical. Ayala wrote: Would a func-

tion ever be found for these one million nearly identicalAlu sequences? Itseems most unlikely. In his response to Ayala, Meyer showed that Ayala isfactually wrong about this. According to recent technical papers in genom-ics,Alusequences perform multiple functions.

In a rejoinder to Meyer, Darrel Falkdefended Ayala and claimedal-though a number of functional regions have been discovered withinAlu

sequences, there is no question that manyAlu sequences really have nofunction.18

In my previous chapter, I showed that the vast majority of the genomeis transcribed, either into protein-coding genes or into regulatory RNAs.Te technical literaturesome of which I cited in that blogreports thatthe genome is an RNA-coding machine. Clearly, most DNA reallydoeshavefunction.

In this and subsequent posts, I will provide other sorts of evidence thatso-called junk DNA is not junk at all, but functional.

We have all seen a variant of the plot in a movie. A strange signal ap-pearsin one lm it is a recurrent wireless telegraph code that is transmittedfrom San Diego after a global nuclear holocaust (O the Be ch); in anotherit is radio transmissions from deep space (Co t ct); in still another it is crop

circles (S s). In the rst movie, the signal turns out to be due to a Coca-Colabottle: Wind blowing on a window shade next to the bottle results in the

18. Ayala and Falks comments may be accessed here:http://biologos.org/blog/on-reading-the-cells-signature/; and here:http://biologos.org/blog/a-rejoinder-to-meyer-2.
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latter being occasionally nudged, which sometimes leads to a telegraph keybeing tapped by the very same. But in the second movie, the signals receivedturn out to contain a complex set of encrypted data with an intricate math-

ematical patternthey are the speci cations for building a device that cantravel through space-time wormholes, sent from a friendly alien civilization.So also are the crop circles in the third lm messages from an extraterrestrialrace, except that the designs portend an attack on humanity.

Now, the reason we are drawn in by such stories is obvious: Te signalshave serious implications for the characters. It could mean the survival of mankind after a thermonuclear war; it could mean that there are other sen-tient beings in the universe. Tat is why we would quickly lose interest inthe plot if, say, in every scene where a scientist appeared before an importantgovernmental group and said, Te outer space signal contains over sixtythousand, multidimensional pages of complex architectural plans, she werecountered with, Tis is exactly the predicted outcome of billions of years of cosmic evolutionyou see, random interstellar events lead to just this kindof complex speci ed informationwe are not impressed. We would wantour money back.

M bringing up this subject is that I have a mysteriousgenomic signal for you to seewhich I will show you in the nextchapter. We detected it some time ago and it has aroused the interest of somegenomicists, but you will nd no mention of it in books such as Francis Col-linss e L u e of Godwhich is peculiar. But I have another aim inmind, too, in broaching this possible chromosomal code: A key rst indica-tor of functionality is a distinctly non-random pattern. Te persistence of adistinct signal in di erent contexts often suggests functional constraints areoperativethat is why genomicists look for them. And since I want to focuson the lob lfunctions of suchShort I terspersed Nucle r Eleme ts(SINEs)as humanAlusand their mouse and rat counterparts, their far-from-randomplacement cannot be elided. In fact, I will argue that it is a critical part of thegenome story that the folks at BioLogos arent telling you.

o prepare for the mysterious genomic signal, though, I want to drawyour attention to this gure:


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Reprinted by permission from Macmillan Publishers Ltd:Nature gure 9d, Genome sequence of theBrown Norway rat yields insights into mammalian evolution. Nature 428: 493-521), copyright 2004.

What you are seeing are the relative densities of Lo I terspersed Nu-cle r Eleme t(LINE) L1s and SINEs along 110,000,000 DNA letters of rat chromosome 10.19 (From Fig. 9d of reference 1.) Te x-axis representsthe sequence of letters in DNA and the blue line indicates where SINEsoccurwhat Ayala calls obnoxious sequences that aresupposedlydue todegenerative biological processes that are not the result of ID. Te red lineindicates where LINE sequences occur.

By the way, Francis Collins is a principal author of theN turepaper

where these results are published.Both LINEs and SINEs are types of mobile DNA, namely,retrotr spo-

so s, and together they can comprise around half of the mammalian genome.As should be clear from the gure, LINEs tend to peak in abundance whereSINEs taper o andv ce vers(see the blue boxes). We have known aboutthis pattern since the late 1980s, so it is no surprise to someone who hasbeen following the subject. What should be surprising to anyone, however,

is that the same machinery is responsible for the movement of both types of retrotransposon. A complete L1 element encodes the proteins necessary toreverse transcribe an RNA copy of itself back into DNA, and to insert thegenerated duplicate into some chromosomal site. SINEs, by way of contrast,rely on the L1-speci ed proteins for all their copying and pasting routines.

19. Rat Genome Sequencing Project Consortium, Genome sequence of the Brown Norwayrat yields insights into mammalian evolution,N ture428 (2004), pp. 493-521.
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Tis compartmentalization of LINEs and SINEs along the mammalianchromosome can also be detected by using molecular probes for L1 orAlu(-like) sequences:20

F - that can make up 50 percent of a mam-mals mostly junkety-junk genome, the rule seems to be: Location, loca-tion, location.

Interestingly, this higher-order pattern cannot be detected when smallsections of DNA are examined. It only becomes evident when stretchesthat are millions of nucleotides long are studied.

Tis banding pattern has been known for decadesbut for some rea-son it is rarely (if ever) discussed by junk DNA advocates. Te bands onthe chromosome arms fall into two general categories:

R b ds: DNA compartments that are enriched with the genetic let-ters G and C, have a high concentration of protein-coding genes,a preponderance of Alu or Alu-like repetitive elements (e.g., mouse

B1s), and replicate early in the DNA synthesis phase of the cell cycle. G b ds: DNA compartments that are enriched with the genetic

letters A and , have a low concentration of protein-coding genes,a high density of theL1 retrotransposon, and replicate late in theDNA synthesis phase of the cell cycle.

20. Chen, . L. and L. Manuelidis, SINEs and LINEs cluster in distinct DNA fragmentsof Giemsa band size,Chromosom98 (1989), pp. 309-316; Korenberg, J. R. and M. C.Rykowski, Human genome organization:Alu, lines, and the molecular structure of metaphasechromosome bands,Cell53:3 (1988), pp. 391-400; Costantini, M., O. Clay, C. Federico, S.Saccone, F. Auletta and G. Bernardi, Human chromosomal bands: nested structure, high-de nition map and molecular basis,Chromosom116 (2007), pp. 29-40.


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Tere are other strong functional correlations, too, such as the distribu-tion of types of chromatin and how the genome is packaged in the nucleus.But Im getting way ahead of myself.

N . Which DNA regions of the mammalian ge-nome are enriched in the codes for the most essential functions?Pre-c sely where you dAlus dAlu-l ke seque ces(the dark blue bands on thechromosome). Which sections of the mammalian genome have the highestrates of transcription?Prec sely where you dAlus dAlu-l ke seque ces.Where do you nd the strongest organizational correlations between any

two mammalian genomes?Prec sely where you dAlus dAlu-l ke seque c-es.Arent these correlations a bit strange for genomes that supposedly

consist mostly of junk and are constantly being corrupted by degenerativeprocesses? Why do such obnoxious sequences have any kind of co servedhigher-order bar code pattern? Tese facts of mammalian chromosomebiology have been known for years, if not decades. But, alas, no mention of

them is to be found in the literature that wants to emphasize the unintel-ligent design of our genome. o make up for this lack, then, I am going todiscuss such facts in more detailfterI show you the mystery signal in thenext chapter.


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13. Discovering Signs in

the Genome by ThinkingOutside the BioLogos Box

Richard Sternberg

H I -nomic signal, I shall now ful ll that promise. Teprevious chap-

ter was devoted to describing the linear distribution of LINEsand SINEs along mammalian chromosomal DNA. We saw thatL1 ret-rotransposons tend to be densest in the regions whereAlus and Alu-like ele-ments are the least common andv ce vers. I included the following gurefrom an article co-authored by Francis Collins that showed this compart-

mentalization of LINEs and SINEs along over a hundred million geneticletters of rat chromosome 10:


Te blue line indicates the distribution of SINEs along a 110-millionbase pair interval of rat chromosome 10.

Intriguing as this non-random distribution of repetitive elements maybe, it gets even more interesting when one realizes that SINEs are speci cto taxonomic groups. Each primate genome has distinct subfamilies of theAlusequence. Te mouse genome, on the other hand, has noAlus but it doeshave three unique SINE families called B1, B2, and B4. While mouse B1
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shares some sequence similarity withAlu, it has no relationship to the B2or B4 elements; the latter two are also unrelated to each other. What thenabout the rat SINEs along chromosome 10, which were depicted as a blue

line? Well, the genome of the rat has one main SINE family called ID, forthe Identi er sequence. Te ID elements have nothing in common at theDNA sequence level with the mouse B1s, B2s, or B4s, and they are whollydissimilar toAlus.

So we have three di erent mammal genomes (primate, mouse, and rat)and three di erent sets of SINEs. But since I showed you rat chromosome10 yesterday, lets just focus on the two rodent genomes.

Now, the mouse and rat are estimated to have diverged 22 million yearsago. During that interval, individual SINEs have been coming and going andgoing and coming, in and out of chromosomes. Tis ongoing insertion/de-letion of these retrotransposons is precisely the degenerative process thatFrancisco Ayala referred to when mentioningAlus.

For the 22 million years that have occurred since the mouse and rat lin-

eages went their separate ways, both genomes have been subjected to hun-dreds of thousandsif not millionsof separate SINE insertion events.Putting on our junk DNA thinking caps, lets try to predict what the out-comes of such long-term mutational bombardments would bev s--v sthelinear distributions of SINEs along a chromosome. o do this, lets connectthese two statements:

1) almost certainly much, if not most, of the DNA plays no role2) Perhaps one could attribute the obnoxious presence of theAlu se-

quences to degenerative biological processesOr to restate, we have much, if not most rodent DNA that is not func-

tional having being subjected to extensive degenerative events over the courseof twenty-two million years. Te only di erence that we must keep in mindis that the obnoxious elements that were involved in this example of decay

in the mouse genome are B1s, B2s, and B4s; whereas the destructive force inthe rat genome in this case was primarily the ID elements.

O . W we expect in general from degenerating processesthat have no functional consequences? Lets do a thought experiment.
http://biologos.org/blog/a-rejoinder-to-meyer-2http://biologos.org/blog/on-reading-the-cells-signature/http://biologos.org/blog/on-reading-the-cells-signature/http://biologos.org/blog/on-reading-the-cells-signature/http://biologos.org/blog/on-reading-the-cells-signature/http://biologos.org/blog/on-reading-the-cells-signature/http://biologos.org/blog/on-reading-the-cells-signature/http://biologos.org/blog/a-rejoinder-to-meyer-2


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Consider the surfaces of two moons that were once part of the same plan-etary body 22 million years ago. Since their separation, both have been subjected to independent collisions with asteroids, meteorites, and other pieces

of space debris. Question: Would you expect the scar patterns on both to bedi erent or identical? (It may seem like a silly question, but bear with me.)

Replace now the word moons with the mouse and rat genomes andasteroids and meteorites and other pieces of space debris with SINEs, andyou will see what I am asking. So Ill rephrase my question. What should weexpect regarding the linear distribution of independent SINE impacts alongmouse and rat chromosomes?

A. Completely independent patternslike meteorite impact sites onmoons;

B. A few overlapping patterns, due to chance; orC. Nearly identical patterns.

And the mystery signal is

Reprinted by permission from Macmillan Publishers Ltd:Nature ( gure 9c, Genome sequence of theBrown Norway rat yields insights into mammalian evolution. Nature 428: 493-521), copyright 2004.

Tis is a second gure from the article co-authored by Francis Collins(from Fig. 9c of Ref. 1). Te scale on the x-axis is the same as that of the pre-

vious graphit is the same 110,000,000 genetic letters of rat chromosome10. Te scale on the y-axis is di erent, with the red line in this gure corre-sponding to the distribution of rat-speci c SINEs in the rat genome (i.e., IDsequences). Te ree line in this gure, however, corresponds to the patternof B1s, B2s, and B4s in themousegenome.

Was it what you expected from a degenerative process? Why?At this point the theistic evolutionist might saySilly Rick: Common

descent explains this pattern!Wrong, wrong, wrong.
http://www.nature.com/nature/index.html)http://www.nature.com/nature/index.html)


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Let me repeate ch r ph de otes o ly l e e-spec c mut t o l set o s.

e mut t o l s l from mouse B1s, B2s, d B4s s equ v le t to the

mut t o l s l of r t IDs.It almost looks as if, say, the rat graph was copied, slightly redrawn, la-

beled mouse, and then pasted above the previous line. (Of course, it wasnt.)How strange that two independently acting degenerative processesa ect-ing mostly junk DNA would lead to the same higher-order pattern.

I pattern. And this correlation occurs throughout both ge-

nomes.Te Rat Genome Consortiumand thus Francis Collinsapparently

thought it worthy to devote a whole section to the phenomenon. itled Co-Localization of SINEs in Rat and Mouse, the section states:

Despite the di erent fates of SINE families, the number of SINEs inserted after speciation in each lineage is remarkably similar:~300,000 copies Figure 9c displays the lineage-speci c SINE den-

sities on rat chromosome 10 and in the mouse orthologous blocks,show stro er correl t o th y other fe ture. Te cause of the u usu l d str but o p tter s of SINEs, ccumul t e e-r ch re o s where other interspersed repeats are scarce,s pp re tly co served fe ture, depe de t of the pr m ry seque ce of the SINEand e ectiveover regions smaller than isochors [emphasis added].

Te potential signal in these two genomes, then, should be obvious. If

not, I will belabor the point: Te strongest correlation between mouse and rat genomes is SINE

linear patterning. Tough these SINE families have no sequence similarities, their

placements areco served. And they are concentrated in protein-coding genes.Am I suggesting that extraterrestrials were ddling with rodent DNA?

No. Am I implying that we are seeing the language of God in rodent-script?I havent the foggiest notion. WhatI m s y is that we know a lot aboutthe genome that is being glossed over in the popular works that the theistic


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evolutionists write. I am also saying that instead of nding nothing but dis-order along our chromosomes, we are nding instead a high degree of order.

Is this an anomaly? No. As Ill discuss in the next chapter, we see a sim-

ilar pattern when we compare the linear positioning of humanAlus withmouse SINEs. Is there an explanation? Yes. But to discover it, you have tothink outside the BioLogos box.


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14. Beginning to Decipher

the SINE SignalRichard Sternberg

R I

discuss the distribution of SINEs in the mouse and rat genomes?Well, I am going to use it again today, but only for a moment.

Suppose you are keenly interested in the topography of one of themoons, named Y6-9. Suppose also that the books you rst select to read onthe topic are popular works, written by experts who are living legends. Asyou read through the works, you nd paragraphs here and there about howutterly decrepit Y6-9 is, and how this space body exempli es eons of randomevents. Te authors argue that we already knew all there was to know about

that moon back in 1859, and that the evidence demonstrates either that Goddoesnt exist or that the deity left the cosmos to itself after the Big Bang.

You nd, however, that these books almost totally ignore the ndingsof the billion-dollar missions sent to the surface of Y6-9 since the 1960s.Indeed, there is next to nothing in them about Y6-9s actual geology.

So you contact the LunarLogos Foundation, a Christian group that pro-motes such books. You tell them that you have a few speci c questions aboutthe Y6-9 mission ndings. Te response you get is that because you are a lay-man, you would not be able to comprehend the details. Besides, the Lunar-Logos folks say, the mainstream experts have spoken authoritatively aboutthe subject and that should be enough for you. As a consolation, though,they send you a CD that has songs that are sung by one of their foundingmembers.

Somewhat disgruntled, you decide to spend a day at a university library.You ask a librarian for maps of Y6-9 and technical journals that discussits features. An hour or so later, with stacks of data before you, somethingcatches your eyesomething never mentioned in any of the books youve
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read. Sitting in a Y6-9 crater is a large monolith. High resolution photosreveal it to be rectangular in shape, with a polished surface, and composedof some dense black material. Tis must be a mistake, you think. So you

look at other craters on Y6-9 and many of them also contain the same kindof monolith. You discern their overall distribution to be non-randomandthe monoliths themselves are highly non-random. Ten, after consulting theliterature, you learn: Te existence of such objects has been known for overtwo decades. In fact, one of the experts at LunarLogos wrote about them inthe technical reports of the Y6-9 probe missions.

Now, more than disgruntled, you decide to write about what you havelearned, citing the relevant literature in case someone might want to readabout this topic himself. After posting what you write on the Internet, Lu-narLogos posts their reply. Teir response reads something like this:

Okay. Sure. Tere are obnoxious monoliths littering Y6-9 ev-erybody knows this. In fact, there are about a million of them. Butthey got there because of degenerative cosmic processes. While manyof the structures Mr. X mentioned are suggestive of some possiblyunknown cause that we have never denied, it is almost certain thatmuch, if not most, of the Y6-9 surface is without any remarkablefeatures. Besides, why would God put them there? Tey are simplynonsensical.

We have one more thing to say. We dont appreciate how disre-spectful Mr. X has been to our team of experts. Although Mr. X is aPhD planetary scientist, he is not as quali ed to write on this subject

as scientists approved by LunarLogos. So we ask him, for the sake of having meaningful dialogue: Please stop writing about this subject.

A LunarLogos sympathizer writes on another blog:We think youre a nice guy, but your arguments are insane.

What would you think?

with LunarLogos brings something to

your attention. He shows you a map of the sister moon of Y6-9, calledQ7-10. You are aware that Y6-9 and Q7-10 went their separate ways after acosmic collision 22 million years ago. But something strange catches youreye. Q7-10 has polished black monoliths, too, except that they are pyramids


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instead of rectangles. Tats not the weirdest thing, though. Te weirdestthing is that the eo r ph c l d str but o of the mo ol ths o Y6-9 very e rm tches the eo r ph c l d str but o of the mo ol ths o Q7-10.

Now what would you think?Te almost one-to-one correspondence of mouse-speci c and rat-speci c

SINE insertion events along homologous regions of the two genomes is al-most as remarkable as the matching geographical distributions of the mono-liths in the analogy of the two moons. Remember the graph (from Figure 9cof Ref. 1):

Reprinted by permission from Macmillan Publishers Ltd:Nature ( gure 9c, Genome sequence of theBrown Norway rat yields insights into mammalian evolution. Nature 428: 493-521), copyright 2004.

We have two genomes that went their separate ways 22 million yearsago. We have two lineages that have been subjected to di erent historicalevents. Yet, when we compare the chromosome locations of mouse B1s/B2s/B4s with those of rat IDs, they look almost the same. Where the ID SINEsrise in density, so do the B1s/B2s/B4s SINEs; where the ID SINE levelsdecrease, so also do the B1s/B2s/B4s SINE levels. Independent mutationalevents have generated equivalent genomic patterns. How can we causally ac-count for this striking pattern?

In the paper written by Francis Collins and his colleagues, under theheading Co-Localization of Sines in Rat and Mouse, we read:Te cause of the unusual distribution patterns of SINEs is ap-

parently a conserved feature, independent of the primary sequence of the SINE... [emphasis added].

Lets unpack this part of the sentence. We have:

1. A cause of some sort.2. A cause that is conserved between the mouse and rat.3. A cause that is independent of SINE primary DNA sequences.


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Tats all very well and good, but the speci c cause is never mentioned.Where, then, can we nd it?

Experts such as John Avise, Francisco Ayala, Francis Collins, and Darrel

Falk tell us that we must think like Darwinians before we can begin to makesense of the data, since nothing else is scienti c, or indeed even reasonable.So lets play along and think like Darwinians, limiting ourselves to what Col-lins and his colleagues have authoritatively provided. Recall that they are:

Chance mutations continually degrade genomes that are largely junk SINEs are for the most part nonsensical junk

Natural selection is the sole creative force in evolution Except when genetic drift (neutral evolution) is also a factor.We can call this conceptual scheme the BioLogos box.Well start, then, with chance mutations. We know that the enzymes

encoded by the L1 retrotransposon copy and paste SINEs into mammali-an genomes. So perhaps this is the causative agent that acts independentlyof primary DNA sequence? And since L1 is present in all mammalian ge-nomes, we may just be on the trail of the conserved cause.

But wait. L1 also mobilizes itself. Tis is a problem, for when we com-pare LINE and SINE distributions along chromosomes, it is clear that inthe regions where the former is abundant the latter is not, andv ce vers.Remember the graph (from Figure 9d of Ref. 1):


But we have no plausible mechanistic explanation for why the mouseL1 machinery would have pasted B1s/B2s/B4sover 22 million years, nolessinto the same general locations and at much the same densities, as therat L1 machinery pasted ID elements over the same period of time.


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N . We still have to consider that worker of miracles, naturalselection. Tis mechanism eliminates harmful features while preserv-ing those that enhance survival. So lets construct a hypothesis: Mouse and

rat SINE distributions re ect the di erential removal of these DNA repeatsfrom regions where their presence would be harmful. In other words, we pre-dict that sequences where mouse B1s/B2s/B4s and rat IDs peak in densityare segments of the genome that are largely junk; conversely, in the sectionswhere these SINEs taper o , functional coding regions are to be found.

Does this hypothesis point in the right causal direction? I dont thinkso. Here is why. Remember the statement made byFalk in defense of Ayala co tr Meyer:21

He [Ayala] doessay that on average there are about 40 copies of Alusequences between every two genes, but this is simply a fact.

Well, both Falk and Ayala are correctandth tis the problem with theselection hypothesis. Protein-coding genes make up only ~1.5 percent of themammalian genome. Where do the peaks of B1s/B2s/B4s and IDs occur

along the mouse and rat chromosomes, respectively? In and around the ~1.5percent of the genome that is protein-coding. Remember the following state-ment in the sentence of theN turepaper quoted above:

Te cause of the unusual distribution patterns of SINEs, c-cumul t e e-r ch re o swhere other interspersed repeats arescarce, is apparently a conserved feature, independent of the primarysequence of the SINE... [emphasis added].

Whatever the mystery cause is, it plucked out the species-speci c SINEsfrom the junkety-junk LINE regions, and piled them high around the25,000 genes of the mouse and rat. Or it directed the SINEs to rain downon the gene-rich regions and in much lesser amounts elsewhere. Tis contra-dicts our selection hypothesis,u less the SINEs re do someth mport t

d rou d those prote -cod re o s. But since so much ink has beenspilled arguing that nothing of the sort is the casethese are junk elements,

even harmfulwe must turn to some other factor.

21.http://biologos.org/blog/a-rejoinder-to-meyer-2.
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R BioLogos box, we now pull out genetic drift.Neutral evolution means that a mutationregardless of whether it isbene cial, neutral, or negativecan become xed or lost in a lineage solely by

chance. With respect to a SINE insertion, its persistence in a lineage wouldhave to be a genetic coin toss: If heads, the SINE stays in a site; if tails, it islost. So for a pure neutralist model to account for the graphs we have seen,~300,000 random mutation events in the mouse have to match, somehow,the ~300,000 random mutation events in the rat.

What are the odds of that?Like the imaginary scientist trying to make sense of the far-from-ran-

dom lunar evidence that LunarLogos glossed over, I think we have to lookelsewhere for the mystery cause of equivalent SINE patterns in the mouseand rat genomes. But where? A technical term was used in the sentence thatI quoted above that you may have missed. I will highlight it for you:

Te cause of the unusual distribution patterns of SINEs, accu-mulating in gene-rich regions where other interspersed repeats arescarce, is apparently a conserved feature, independent of the primarysequence of the SINE and e ective over regions smaller than iso-chores.

Ever heard of isochores? Well, they are to DNA sequence organizationalong a chromosome what mountains and valleys are to a continent. Imaginebuying a book about the geographical features of Africa and not nding asingle word about Mount Kilimanjaro or the Great Rift Valley.

Imagine nding instead a lot of musings about what God couldnt orwouldnt have done with Africa. What would you think about such a book?

Well, turn to the index of Francis Collinsse L u e of God, or JohnAvisesI s de the Hum Ge ome: A C se for No -I tell e t Des, and lookfor isochore. You wont nd it.

Isochores might provide a clue to cause of the mystery signal, but thecausewhatever it may beis outside the BioLogos box.


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15. Intelligent Design,

Frontloading andTheistic Evolution

Jay Richards

A S M K B , -entist has started a review thread22 on Steve Meyers book.S -

ture the Cell. While the blogger (RJS) says she ultimatelydisagrees with Meyers argument, its clear that she takes Meyers argumentseriously and is trying to do her best to present the argument accurately.Tis is much more than can be said for the many hysterical and misinformedcritiques of Meyers argument that are now oating around the Internet.

Anyone whos actually read the book will know that most of these critiquesare cliches that Meyer addresses in detail in the book, suggesting that thecritics dont even know the argument they are criticizing.

A civil review like this is welcomed, and I look forward to reading theinstallments.

In her rst installment, RJS suggests that theres a promising third waythat Meyer doesnt address in the book:

It seems to me that there is a middle ground between the insis-tence that chance, happenstance, and law (the laws of physics) suf-

ce to explain all and the suggestion that biologylifecan onlybe explained with reference to a creative mind. Alister McGrath (AF e-Tu ed U verse) and Simon Conway Morris (L fes Solut o) pro-vide some insight into this middle ground. Te fabric of the universemakes life possible and inevitablenot a highly contingent accident.

Tinking scienti cally we look for the causally connected series of events that resulted in the present realityas part of Gods methodin creation.

22. http://blog.beliefnet.com/jesuscreed/2010/0

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