evolutionnewsandviews--2020-11-30--“Darwin’s Finches”: Galápagos Islands as an Evolutionary Model

Author ’ s note : Are Darwin ’ s finches “ a particularly compelling example of speciation ” as well as “ evolution in action ” ?
In a series of posts , I have offered some notes on the question of whether macroevolution is happening on the Galápagos Islands .
Please find the full series here .
Taking the facts and arguments presented together , it appears to be clear that no macroevolution is happening in “ Darwin ’ s finches ” on the Galápagos Islands .
The following is the English translation of some especially relevant and up-to-date @ @ @ @ @ @ @ Reinhard W. Kaplan 1991 .
He was the director of the Institute of Microbiology ( Lehrstuhl für Mikrobiologie ) at the Johann Wolfgang von Goethe Universität , Frankfurt am Main2 .
He did not continue the discussion .
“ Evolution on an isolated island like the Galápagos , … ” The “ evolution ” on the Galápagos Islands is one of the best examples against the model favored by Prof. K. Because starting from the “ isolated island , ” the new founder populations should grow rapidly , continuously add beneficial hereditary changes @ @ @ @ @ @ @ thereby become large populations themselves .
It is now just one of the more recent significant biological discoveries that island populations do not meet the criteria ( which are decisive for the question of the correctness of neo-Darwinism ) for displacement of the original populations and expansion into large populations .
In this context I refer to the excellent monograph by J .
A. Drake et al .
( 1989 ) , Biological Invasions ( Wiley , Chichester , New York ) .
Would it really occur to anyone that the Galápagos finches @ @ @ @ @ @ @ populations there , and , if transferred to southern Europe and Africa , spread in the same way as , e.g.
, the European house sparrows in North America ?
It is exactly the other way around : the island populations must be protected from invasion by widespread continental species !
Braun reports ( 1989 , p. 86 ) empirically derived rules for this question , for example : “ Isolated environments with a low diversity of native species tend to be differentially susceptible to invasion.
” “ …species that are successful invaders @ @ @ @ @ @ @ to extensive , non-isolated habitats within continents ” ( p. 92 ) .
“ The fact that there are almost no good examples of successful invaders of continents that have come from small islands and other depauperate faunas … suggests that biotic resistance from diverse native species can be effective in repelling invaders ” ( p. 96 ) ( emphasis added , here as in quotations throughout this post ) .
Macdonald et al .
1989 , p. 234 : “ Although only a small percentage of the world ’ s land and @ @ @ @ @ @ @ 93 % of the 93 species and 83 subspecies of birds that have become extinct since 1600 AD have been island forms ’ ( King , 1985 ) .
” Honegger ( 1981 , p. 235 ) lists two amphibians and 28 reptile taxa known to have become extinct since 1600 AD .
The reptiles were all island forms and introduced species are implicated in the extinction of at least eight of them and one of the two amphibians .
Loope et al .
1989 , p. 272 : “ The rigor of @ @ @ @ @ @ @ system may be relaxed by a large number of bottle necks ( founder events ) many groups have undergone in island hopping .
… in many instances ( the island forms ) may not be so well adapted as the ‘ general purpose genotypes ’ of invasive introduced species.
” Pimm 1989 , p. 355 : “ Species with larger ranges were more likely to be successful than species with smaller ranges .
… Many introductions will succeed only if their numbers can increase quickly , beyond the small population size where extinction @ @ @ @ @ @ @ p. 352 : “ The chance of extinction rapidly increases as population sizes decrease .
Even in a perfectly constant environment , small populations face risk of extinction from demographic accidents — the chance fluctuations of deaths and births , and consequent changes of numbers and sex ratios….Another risk of becoming extinct is a low rate of population growth.
” The latter observations are particularly informative for the question of the evolution of species in small populations in 100,000 to 10,000,000 years ( see Prof. K. above ) .
The postulated macroevolution is @ @ @ @ @ @ @ can therefore not be accepted as a general rule for the origin of species .
Other authors have come to similar conclusions .
Wills ( 1990 , p. 398 ) discusses the problem in connection with “ mitochondrial Eva ” and an average population size of 5,000 women : “ Such small sizes would have to be maintained for thousands of years with an attendant risk of extinction.
” And he makes the following comparison : “ The risk posed to the survival of the population in [ this ] … case is @ @ @ @ @ @ @ Niagara Falls on a tightrope.
” Rabb and Lacy 1990 , p. 612 , on the topic of endangered-species biology : Small populations over large numbers of generations with many recessive mutations are therefore an extremely unfavorable starting point for explaining the sudden appearance of Cambrian and other life forms and the fact that the temporal maxima of the construction plans and higher systematic categories occur before the lower ones !
With populations of approximately 10,000 individuals ( see above : 5,000 women ) and 1 million generations , 10 billion individuals would @ @ @ @ @ @ @ there really no chance of fossilization ?
The geologists Bennison and Wright , following the work of Shaw , calculate an average of 1 fossil per 1 million individuals !
Even Galápagos finches have been found in fossil form !
( See Grant 1984 ) .
And what about foraminifera , corals , brachiopods , cephalopods , etc.
, which are so well documented ?
“ … Galápagos , where Darwin received inspiration for his theory.
” According to several historians of science , this is a myth .
Darwin was only made @ @ @ @ @ @ @ , Mimus species by ornithologist John Gould after his return to England .
“ In retrospect , he [ Darwin ] was astonished at what he saw there ” ( Berry 1984 , p. 1 ) .
The following from Sull0way ’ s paper ( 1982 , pp .
57-58 ) on “ The Beagle Collections of Darwin ’ s Finches ( Geospizinae ) ” 3 and my subsequent comment are an addition made September 23 , 2020 ( the footnotes are Sulliway ’ s ) : The celebrated ornithologist John Gould , @ @ @ @ @ @ @ Society , lost no time in examining and naming the unusual finches that Darwin had brought back from the Galápagos Islands .
At the very next meeting of the society ( 10 January ) , Gould described these birds as twelve new species , which he placed in one genus and two closely allied subgenera ( Geospiza , Cactornis , and Camarhynchus ) .
Moreover , he astutely realized the basic peculiarity of these finches , namely , that ‘ the bill appears to form only a secondary character.
’ Soon afterwards Gould @ @ @ @ @ @ @ , as a thirteenth species of the group , belonging to yet another genus16 .
Darwin , who was at this time residing in Cambridge , did not learn of the details of Gould ’ s analysis until he moved to London in early March of 1837 in order to have closer contact with the specialists working on his collections .
Gould ’ s findings , communicated to Darwin during a meeting with the eminent ornithologist , provided Darwin with a number of surprises17 .
While in the Galápagos , Darwin had been @ @ @ @ @ @ @ the various finchlike species he had encountered there .
In particular , he had misidentified several finch species as the forms that they , through extensive evolutionary radiation , now appear to mimic .
For example , he had considered the Cactus Finch , Cactornis scandens , to be a member of the Icteridae ( the family of the orioles and blackbirds ) ; and he had classified the Warbler Finch , Certhidea olivacea , as a ‘ wren ’ , or warbler .
It appears , moreover , that Darwin initially distinguished @ @ @ @ @ @ @ of the eventual 13 forms that Gould named in early 1837 .
Hence Darwin ’ s finches only really became Darwin ’ s after Gould rectified many of Darwin ’ s earlier field misclassifications , and thereby clarified the unity and complexity of the group18 .
More important still for Darwin ’ s evolutionary thinking , Gould ( 1837d ) declared that 3 of the 4 island forms of Galápagos mockingbird brought to England by Darwin were distinct species , a possibility that Darwin had already asserted ‘ would undermine the stability of @ @ @ @ @ @ @ a whole , Gould pronounced 25 of the 26 land birds as new and distinct forms found nowhere else in the world .
Darwin was frankly stunned , not only by the realization that three separate species of mockingbirds indeed inhabited the different islands of the Galápagos , but also by the fact that most of these Galápagos species , even though new , were closely related to those found on the American continent19 .
His conversion to the theory of evolution , which took place shortly after his meeting with Gould in @ @ @ @ @ @ @ consequence of these two conclusions .
This “ conversion ” constitutes , in fact , an astonishing confusion and misunderstanding of the morphological species concept ( cf .
here ) by Darwin as well as Sulloway .
“ This branching out ( typogenesis ) usually happens relatively quickly , as the pace of evolution is usually high during adjustment to new niches ( ways of life ) .
” Typogenesis did not take place in the Galápagos !
Even the formation of species in the finches is still doubtful : “ Intersterility is @ @ @ @ @ @ @ .
Intrageneric hybrids among ground finches are certainly both viable and fertile … and probably the same is true for intergeneric hybrids between tree finches and warbler finches ” ( Grant 1986 , p. 353 ) .
“ … [ S ] ix species of Geospizina ( finches ) in the Galápagos Islands show a genetic distance from 0.004 to 0.065 ” ( Nei 1987 , p. 245 ) .
In humans , the differences are between 0.01 and 0.03 .
The small genetic distances of islanders are in clear contrast to the @ @ @ @ @ @ @ domestic animals .
( These are further proofs that morphological and genetic distances need not be coupled with each other . )
In their study , Loop et al .
( 1989 , pp .
271-272 ) pointed to the general trend of little genetic distance between morphologically and ecologically strongly diverging ( but closely related ) island “ species.
” In the Hawaiian Tetramolopium ( Asteraceae ) , for example , Lowry and Crawford examined 19 populations of 7 “ species ” : “ The ‘ mean genetic identity for pairwise comparison…is @ @ @ @ @ @ @ obtained for conspecific plant populations . '
” The flightless Galápagos cormorants clearly illustrate the degeneration of structures , a process that seems to occur rather quickly in small populations through inbreeding involving homozygous occurrence of numerous recessive alleles ( already accumulated in previous larger populations ) .
What we detect here is not typogenesis , but typolysis !
This also explains the low resistance of island populations to invaders and the high rate of extinction .
The comparison with domestic animals illustrates the situation in several aspects .
In both groups we @ @ @ @ @ @ @ but great morphological variability within the species ( with dogs , e.g.
, one could set up a new family with several genera and over 400 “ species , ” something similar with the many races of pigeons , or of chickens , or horses , etc . )
.4 • Small populations and inbreeding as the starting point for “ speciation.
” • Genetic drift .
Originally stricter selection conditions ( for differential survival ) are no longer applicable , but later there is also selection for certain phenotypes and ecotypes .
@ @ @ @ @ @ @ .
Conclusion : No explanation of the paleontological findings ( among others ) !
“ If a niche has been occupied for a long time by a species that fully utilizes it , rich in individuals , progressive hereditary variants are rare for a long time , and evolution seems to stagnate ( typostasis ) .
If adverse environmental changes are not absorbed ( buffered ) by hereditary variants resistant to them , the population will die out.
” Since the species with a large number of individuals , due to the recurrent @ @ @ @ @ @ @ a significantly greater allelic potential than a small population , it is questionable why the former may have unfavorable environmental conditions to which they can not not adapt , while the individual poor population with low genetic potential ( see above ) should be capable of rapid evolution !
As a rule , the widespread species with its much greater genetic potential should be able to adapt to the new conditions in many places at the same time through allele substitution and thus should have better chances of survival than the small population @ @ @ @ @ @ @ situation — which , as we have seen — is , in fact , the case .
“ According to the theory , the pace of evolution can vary from ( geologically ) fast to slow , depending on the circumstances.
” Since the term “ evolution ” implies the origin of all forms of life , it should be noted here that Prof. K. ’ s theory can not explain the origin of the primary species or the higher systematic categories and Baupläne .
According to the available findings , it is @ @ @ @ @ @ @ rapidly to slowly , depending on the circumstances geologically .
For a full presentation of this series including supplements , please see my Internet Library here .

Photo: Medium tree finch, by Jody O'Connor, Public domain, via Wikimedia Commons.
Author’s note: Are Darwin’s finches “a particularly compelling example of speciation” as well as “evolution in action”? In a series of posts, I have offered some notes on the question of whether macroevolution is happening on the Galápagos Islands. Please find the full series here.
Taking the facts and arguments presented together, it appears to be clear that no macroevolution is happening in “Darwin’s finches” on the Galápagos Islands.
The following is the English translation of some especially relevant and up-to-date points from a discussion1 with Professor Dr. Reinhard W. Kaplan 1991. He was the director of the Institute of Microbiology (Lehrstuhl für Mikrobiologie) at the Johann Wolfgang von Goethe Universität, Frankfurt am Main2. He did not continue the discussion.
Professor Kaplan
“Evolution on an isolated island like the Galápagos, …”
Wolf-Ekkehard Lönnig
The “evolution” on the Galápagos Islands is one of the best examples against the model favored by Prof. K. Because starting from the “isolated island,” the new founder populations should grow rapidly, continuously add beneficial hereditary changes, quickly displace their original populations and thereby become large populations themselves. It is now just one of the more recent significant biological discoveries that island populations do not meet the criteria (which are decisive for the question of the correctness of neo-Darwinism) for displacement of the original populations and expansion into large populations. In this context I refer to the excellent monograph by J. A. Drake et al. (1989), Biological Invasions (Wiley, Chichester, New York).
Would it really occur to anyone that the Galápagos finches might conquer mainland South America, displace populations there, and, if transferred to southern Europe and Africa, spread in the same way as, e.g., the European house sparrows in North America?
It is exactly the other way around: the island populations must be protected from invasion by widespread continental species! Braun reports (1989, p. 86) empirically derived rules for this question, for example: “Isolated environments with a low diversity of native species tend to be differentially susceptible to invasion.” “…species that are successful invaders tend to be native to continents and to extensive, non-isolated habitats within continents” (p. 92). “The fact that there are almost no good examples of successful invaders of continents that have come from small islands and other depauperate faunas … suggests that biotic resistance from diverse native species can be effective in repelling invaders” (p. 96) (emphasis added, here as in quotations throughout this post).
Macdonald et al. 1989, p. 234: “Although only a small percentage of the world’s land and freshwater avifauna occurs on oceanic islands ‘93% of the 93 species and 83 subspecies of birds that have become extinct since 1600 AD have been island forms’ (King, 1985).”
Honegger (1981, p. 235) lists two amphibians and 28 reptile taxa known to have become extinct since 1600 AD. The reptiles were all island forms and introduced species are implicated in the extinction of at least eight of them and one of the two amphibians.
Loope et al. 1989, p. 272: “The rigor of natural selection in such an evolving insular system may be relaxed by a large number of bottle necks (founder events) many groups have undergone in island hopping. … in many instances (the island forms) may not be so well adapted as the ‘general purpose genotypes’ of invasive introduced species.”
Pimm 1989, p. 355: “Species with larger ranges were more likely to be successful than species with smaller ranges. … Many introductions will succeed only if their numbers can increase quickly, beyond the small population size where extinction is likely.” The same author on p. 352: “The chance of extinction rapidly increases as population sizes decrease. Even in a perfectly constant environment, small populations face risk of extinction from demographic accidents — the chance fluctuations of deaths and births, and consequent changes of numbers and sex ratios….Another risk of becoming extinct is a low rate of population growth.”
The latter observations are particularly informative for the question of the evolution of species in small populations in 100,000 to 10,000,000 years (see Prof. K. above). The postulated macroevolution is unlikely for demographic and genetic reasons and can therefore not be accepted as a general rule for the origin of species.
Other authors have come to similar conclusions. Wills (1990, p. 398) discusses the problem in connection with “mitochondrial Eva” and an average population size of 5,000 women: “Such small sizes would have to be maintained for thousands of years with an attendant risk of extinction.” And he makes the following comparison: “The risk posed to the survival of the population in [this] … case is equivalent to the risk of crossing the Niagara Falls on a tightrope.”
Rabb and Lacy 1990, p. 612, on the topic of endangered-species biology:
Genetic homogeneity can imperil a species, but such inbreeding occurs as a consequence of population decline and fragmentation. It is just one of several interacting factors that come into play when a population becomes so small that its fate is determined more by randomness than by fitness. … Once populations are reduced and isolated, deleterious genetic and demographic factors ensue that serve to weaken further the survival of the species. The smaller populations also become progressively more vulnerable to environmental catastrophes. Even with amelioration of environmental circumstances, for example, provision of security in protected areas or zoological parks a species may go too far down the so-called “extinction vortex” of multiple causes to be recoverable.
Small populations over large numbers of generations with many recessive mutations are therefore an extremely unfavorable starting point for explaining the sudden appearance of Cambrian and other life forms and the fact that the temporal maxima of the construction plans and higher systematic categories occur before the lower ones!
With populations of approximately 10,000 individuals (see above: 5,000 women) and 1 million generations, 10 billion individuals would have been necessary for speciation. Was there really no chance of fossilization? The geologists Bennison and Wright, following the work of Shaw, calculate an average of 1 fossil per 1 million individuals! Even Galápagos finches have been found in fossil form! (See Grant 1984). And what about foraminifera, corals, brachiopods, cephalopods, etc., which are so well documented?
Prof. K.
“… Galápagos, where Darwin received inspiration for his theory.”
W.-E. L.
According to several historians of science, this is a myth. Darwin was only made aware of the differences in, e.g., Mimus species by ornithologist John Gould after his return to England. “In retrospect, he [Darwin] was astonished at what he saw there” (Berry 1984, p. 1).
The following from Sull0way’s paper (1982, pp. 57-58) on “The Beagle Collections of Darwin’s Finches (Geospizinae)”3 and my subsequent comment are an addition made September 23, 2020 (the footnotes are Sulliway’s):
The celebrated ornithologist John Gould, who was closely associated with the Zoological Society, lost no time in examining and naming the unusual finches that Darwin had brought back from the Galápagos Islands. At the very next meeting of the society (10 January), Gould described these birds as twelve new species, which he placed in one genus and two closely allied subgenera (Geospiza, Cactornis, and Camarhynchus). Moreover, he astutely realized the basic peculiarity of these finches, namely, that ‘the bill appears to form only a secondary character.’ Soon afterwards Gould recognized Certhidea olivacea, the Warbler Finch, as a thirteenth species of the group, belonging to yet another genus16. Darwin, who was at this time residing in Cambridge, did not learn of the details of Gould’s analysis until he moved to London in early March of 1837 in order to have closer contact with the specialists working on his collections. Gould’s findings, communicated to Darwin during a meeting with the eminent ornithologist, provided Darwin with a number of surprises17. While in the Galápagos, Darwin had been rather unclear about the precise relationship among the various finchlike species he had encountered there. In particular, he had misidentified several finch species as the forms that they, through extensive evolutionary radiation, now appear to mimic. For example, he had considered the Cactus Finch, Cactornis scandens, to be a member of the Icteridae (the family of the orioles and blackbirds); and he had classified the Warbler Finch, Certhidea olivacea, as a ‘wren’, or warbler. It appears, moreover, that Darwin initially distinguished as separate species of finches only 6 of the eventual 13 forms that Gould named in early 1837. Hence Darwin’s finches only really became Darwin’s finches after Gould rectified many of Darwin’s earlier field misclassifications, and thereby clarified the unity and complexity of the group18. More important still for Darwin’s evolutionary thinking, Gould (1837d) declared that 3 of the 4 island forms of Galápagos mockingbird brought to England by Darwin were distinct species, a possibility that Darwin had already asserted ‘would undermine the stability of Species’. For the Galápagos as a whole, Gould pronounced 25 of the 26 land birds as new and distinct forms found nowhere else in the world. Darwin was frankly stunned, not only by the realization that three separate species of mockingbirds indeed inhabited the different islands of the Galápagos, but also by the fact that most of these Galápagos species, even though new, were closely related to those found on the American continent19. His conversion to the theory of evolution, which took place shortly after his meeting with Gould in March of 1837, was a direct consequence of these two conclusions.
This “conversion” constitutes, in fact, an astonishing confusion and misunderstanding of the morphological species concept (cf. here) by Darwin as well as Sulloway.
Prof. K.
“This branching out (typogenesis) usually happens relatively quickly, as the pace of evolution is usually high during adjustment to new niches (ways of life).”
W.-E. L.
Typogenesis did not take place in the Galápagos! Even the formation of species in the finches is still doubtful: “Intersterility is not known in Darwin’s finches. Intrageneric hybrids among ground finches are certainly both viable and fertile … and probably the same is true for intergeneric hybrids between tree finches and warbler finches” (Grant 1986, p. 353). “… [S]ix species of Geospizina (finches) in the Galápagos Islands show a genetic distance from 0.004 to 0.065” (Nei 1987, p. 245). In humans, the differences are between 0.01 and 0.03. The small genetic distances of islanders are in clear contrast to the morphological differences that we also find in domestic animals. (These are further proofs that morphological and genetic distances need not be coupled with each other.)
Nei continues:
With domestic animals one normally refrains from establishing new systematic species and genera, — in nature, however, one creates numerous morphospecies and morphogenera, regardless of the genetic situation, which are often used uncritically as evidence of evolution.
In their study, Loop et al. (1989, pp. 271-272) pointed to the general trend of little genetic distance between morphologically and ecologically strongly diverging (but closely related) island “species.” In the Hawaiian Tetramolopium (Asteraceae), for example, Lowry and Crawford examined 19 populations of 7 “species”: “The ‘mean genetic identity for pairwise comparison…is 0.95, a very high value normally obtained for conspecific plant populations.'”
The flightless Galápagos cormorants clearly illustrate the degeneration of structures, a process that seems to occur rather quickly in small populations through inbreeding involving homozygous occurrence of numerous recessive alleles (already accumulated in previous larger populations).
What we detect here is not typogenesis, but typolysis! This also explains the low resistance of island populations to invaders and the high rate of extinction.
The comparison with domestic animals illustrates the situation in several aspects. In both groups we find:
Little genetic distance, but great morphological variability within the species (with dogs, e.g., one could set up a new family with several genera and over 400 “species,” something similar with the many races of pigeons, or of chickens, or horses, etc.).4 Formation of numerous ecotypes. Small populations and inbreeding as the starting point for “speciation.” Numerous recessive genes compared to the wild type. Genetic drift. Originally stricter selection conditions (for differential survival) are no longer applicable, but later there is also selection for certain phenotypes and ecotypes. Low resistance compared to widespread wild populations. Frequent degeneration and breakdown of structures; physiological compensation options. No formation of new primary species.
Conclusion: No explanation of the paleontological findings (among others)!
Prof. K.
“If a niche has been occupied for a long time by a species that fully utilizes it, rich in individuals, progressive hereditary variants are rare for a long time, and evolution seems to stagnate (typostasis). If adverse environmental changes are not absorbed (buffered) by hereditary variants resistant to them, the population will die out.”
W.-E. L.
Since the species with a large number of individuals, due to the recurrent mutations that occur regularly, must have a significantly greater allelic potential than a small population, it is questionable why the former may have unfavorable environmental conditions to which they cannot not adapt, while the individual poor population with low genetic potential (see above) should be capable of rapid evolution! As a rule, the widespread species with its much greater genetic potential should be able to adapt to the new conditions in many places at the same time through allele substitution and thus should have better chances of survival than the small population with its few possibilities in the same situation — which, as we have seen — is, in fact, the case.
Prof. K.
“According to the theory, the pace of evolution can vary from (geologically) fast to slow, depending on the circumstances.”
W.-E. L.
Since the term “evolution” implies the origin of all forms of life, it should be noted here that Prof. K.’s theory cannot explain the origin of the primary species or the higher systematic categories and Baupläne. According to the available findings, it is the pace of degeneration that can vary rapidly to slowly, depending on the circumstances geologically.
For a full presentation of this series including supplements, please see my Internet Library here.
Notes


evolutionnewsandviews--2020-12-01--Determinism: “An Irrational Rejection of Evidence”

On a new episode of ID the Future , Cornelius Hunter discusses the controversy over determinism and free will .
@ @ @ @ @ historian Michael Keas , Dr. Hunter , a specialist in biophysics and computational biology , @ @ @ @ @ back to Aristotle , then to Newton , then to Pierre-Simon Laplace , who theorized @ @ @ @ @ determine the future based on just the universe ’ s initial conditions and the laws @ @ @ @ @ podcast or listen to it here .
Laplace was a physical determinist : in other @ @ @ @ @ that the laws of nature determine everything .
That includes human choices , which determinists @ @ @ @ @ theoretical physicist Sabine Hossenfelder , take to be merely an illusory experience .
But it @ @ @ @ @ rejection of evidence ” on their part , Hunter argues , evidenced by how blithely @ @ @ @ @

Photo credit: Shane Devlin via Unsplash.
On a new episode of ID the Future, Cornelius Hunter discusses the controversy over determinism and free will. Joined by host and science historian Michael Keas, Dr. Hunter, a specialist in biophysics and computational biology, takes listeners all the way back to Aristotle, then to Newton, then to Pierre-Simon Laplace, who theorized that a sufficient computation could determine the future based on just the universe’s initial conditions and the laws of nature. Download the podcast or listen to it here.
Laplace was a physical determinist: in other words, one who holds that the laws of nature determine everything. That includes human choices, which determinists today, such as German theoretical physicist Sabine Hossenfelder, take to be merely an illusory experience. But it’s “an irrational rejection of evidence” on their part, Hunter argues, evidenced by how blithely they sweep it aside.


evolutionnewsandviews--2020-12-01--Intelligent Design Mugs? We’ve Got Them

Intelligent Design Mugs? We’ve Got Them

If you ’ re looking for affordable Christmas gifts , consider the mugs at our Discovery Institute-CSC Zazzle store .
@ @ @ @ @ and lovely products in their own right .
Some feature quotations by scientists ; some @ @ @ @ @ natural world ; and some feature the CSC logo .
For our biochemistry geeks , @ @ @ @ @ periodic table of elements and a DNA-amino acids codon wheel .
If astronomy is your @ @ @ @ @ “ Ghost of Cassiopeia ” mug .
Appreciate the wonder of water ?
We ’ @ @ @ @ @ ’ ve got water in all three of its forms .
And there are more @ @ @ @ @ cells , nebulae , and fields of poppies .
See them all here .

If you’re looking for affordable Christmas gifts, consider the mugs at our Discovery Institute-CSC Zazzle store. These are great conversation starters and lovely products in their own right. Some feature quotations by scientists; some feature beautiful images from the natural world; and some feature the CSC logo.
For our biochemistry geeks, one mug contains both the periodic table of elements and a DNA-amino acids codon wheel. If astronomy is your thing, check out the “Ghost of Cassiopeia” mug. Appreciate the wonder of water? We’ve got water and we’ve got water in all three of its forms. And there are more designs, including sunsets, cells, nebulae, and fields of poppies. See them all here.


evolutionnewsandviews--2020-12-01--Ixnay on the Ambriancay Plosionexhay

Ixnay on the Ambriancay Plosionexhay

Shhh — don ’ t say it .
Don ’ t say , you know , that .
The geological event , well , not “ event , ” as in something that happened about 541 million years ago…we don ’ t talk that way anymore .
Because people may get the wrong idea .
And we don ’ t want them to have those bad thoughts and wrong ideas .
Changing the names of things helps people to think correctly .
Right ?
A dozen authors at Michigan State University have proposed that the paleontological term “ Cambrian Explosion @ @ @ @ @ @ @ any use other than historical reference.
” The problem , as they see it , is the tendency of “ anti-science ” readers to misappropriate “ Cambrian Explosion , ” to suggest that evolution somehow fails to explain the appearance of nearly all the animal phyla without fossil antecedents of equal complexity .
As they argue : Certainly , biodiversification at the beginning of the Cambrian was unique ( Erwin et al.
, 1987 ) — all those new body plans — but no evolutionary rules were broken , nor is there mystery @ @ @ @ @ @ @ by anti-science concerns who seize on the term “ explosion.
” Their alternative ?
“ Great Cambrian Biodiversification , ” or GCB for short .
GCB , alas , may have a short life of its own , because the geological data haven ’ t changed .
It isn ’ t the name of the paleontological pattern of sudden appearance , at the base of the Cambrian , that matters at the end of the day .
Call that pattern “ Wayne Q. Jones ” or “ cured sausage ” or “ Fossils-a-plenty @ @ @ @ @ @ @ is what it is .
When students find out about the fossil evidence , “ GCB ” will be just as bothersome to certain evolutionary sensibilities as “ Cambrian Explosion ” appears to be today .
GCB = Cambrian Explosion = a pattern that puzzled Charles Darwin over 160 years ago .
Change the name , and the puzzle lives on .

Image: Opabinia regalis, a creature from the Cambrian seas, by Nobu Tamura (http://spinops.blogspot.ca/), CC BY-SA 4.0 , via Wikimedia Commons.
Shhh — don’t say it. Don’t say, you know, that. The geological event, well, not “event,” as in something that happened about 541 million years ago…we don’t talk that way anymore.
Because people may get the wrong idea. And we don’t want them to have those bad thoughts and wrong ideas. Changing the names of things helps people to think correctly. Right?
A dozen authors at Michigan State University have proposed that the paleontological term “Cambrian Explosion” be laid “to rest for any use other than historical reference.” The problem, as they see it, is the tendency of “anti-science” readers to misappropriate “Cambrian Explosion,” to suggest that evolution somehow fails to explain the appearance of nearly all the animal phyla without fossil antecedents of equal complexity. As they argue:
Certainly, biodiversification at the beginning of the Cambrian was unique (Erwin et al., 1987) — all those new body plans — but no evolutionary rules were broken, nor is there mystery or discipline-dividing controversy, as is claimed by anti-science concerns who seize on the term “explosion.”
Their alternative? “Great Cambrian Biodiversification,” or GCB for short.
GCB, alas, may have a short life of its own, because the geological data haven’t changed. It isn’t the name of the paleontological pattern of sudden appearance, at the base of the Cambrian, that matters at the end of the day. Call that pattern “Wayne Q. Jones” or “cured sausage” or “Fossils-a-plenty,” the evidence in the rocks is what it is. When students find out about the fossil evidence, “GCB” will be just as bothersome to certain evolutionary sensibilities as “Cambrian Explosion” appears to be today.
GCB = Cambrian Explosion = a pattern that puzzled Charles Darwin over 160 years ago. Change the name, and the puzzle lives on.


evolutionnewsandviews--2020-12-01--“Resolution Revolution”: Intelligent Design, Now at the Atomic Level

Never say never , because humans are clever .
Physics teachers used to say that humans will never be able to see atoms through any microscope due to a fundamental barrier to resolution called the diffraction limit .
But like the four-minute mile and the sound barrier , this record was made to be broken .
Today , optical engineers are doing it .
Individual atoms are coming into focus !
A review published in 2015 in Methods in Molecular Biology explained how the diffraction limit was breached : Super-resolution microscopy has exploded since the diffraction limit was surpassed .
@ @ @ @ @ @ @ objects at 10nm and smaller .
Each new paper pushes the limit : down to 5nm , 4nm , 3nm , where individual domains of molecular machines can be seen .
These successes are largely due to the introduction of cryo-electron microscopy ( see paper in Protein Science ) , which shock-freezes the specimen to stabilize it before imaging it in an electron microscope .
The technique earned three biophysicists the Nobel Prize in Chemistry in 2017 .
Conceived of in the late 1990s , cryo-EM went mainstream about 2013 and is now @ @ @ @ @ @ @ , cryo-EM had its own resolution barrier .
In October , the Max Planck Institute announced a new world record for cryo-EM by Holger Stark that broke through the barrier .
“ For the first time , his group succeeded in observing individual atoms in a protein structure and taking the sharpest images ever with this method.
” Now , scientists will no longer be measuring in nanometers but in Angstrom units — an order of magnitude smaller .
Nature News and Views comments that “ This unprecedented feat would not have been @ @ @ @ @ @ @ The technique used by Stark ’ s team ( published in the same issue of Nature by Yip et al . )
is called “ single particle cryo-EM.
” It ’ s part of a “ resolution revolution ” that began in 2013 .
Stark ’ s team imaged a ferritin molecule , a benchmark for cryo-EM because of its stability and symmetry , but a companion paper in Nature by Nakane et al .
describes their success at imaging a portion of a more motile protein complex at 1.7 angstrom resolution .
@ @ @ @ @ @ @ bond ( 1.5 angstroms , according to Phys.org ) .
Adaptive Optics has long been used by astronomers to sharpen images of stars by reducing the smearing caused by turbulence in the atmosphere .
The technique uses a laser beam as a guide , and rapidly shifts the telescope ’ s mirror to keep the reference beam steady .
Can that technique be used at the other end of the tube — i.e.
, in a microscope ?
Yes !
A team led by Daniel Hammer of the Food and Drug Administration ( @ @ @ @ @ @ @ microglia in the inner limiting membrane of the human retina using adaptive optics ( AO ) .
Combining this with optical coherence tomography ( OCT ) , which allows optical depth sectioning of images for a 3-D view , they were able to follow these microglia , the “ first responders to neural injury , ” in real time in live human subjects .
That is only one of many possible applications of this method , they say ; “ the ability to visualize macrophage cells without fluorescent labeling in the live human @ @ @ @ @ @ @ ophthalmology and neuroscience , which may lead to novel disease biomarkers and new avenues of exploration in disease progression.
” The results were published last month in PNAS .
More about super resolution imaging can be found in the Journal of the American Chemical Society : “ Super-resolution Microscopy with Single Molecules in Biology and Beyond — Essentials , Current Trends , and Future Challenges.
” Authors Leonhard Möckl and W. E. Moerner of Stanford say , “ Despite the tremendous progress , the full potential of single-molecule super-resolution microscopy is yet to @ @ @ @ @ @ @ by the research ahead of us.
” Multifocus 3-D Imaging took a leap with a new technique that Phys.org calls a “ simple way to capture high quality 3-D images of live cells and organisms.
” A team led by Sheng Xiao of Boston University used a z-splitter prism to split light beams from the specimen into “ several images , each focused to a different depth in the sample , in a single camera frame.
” Instead of a flat image at one focal plane , this technique yields 3-D images from @ @ @ @ @ @ @ a z-splitter prism that can be assembled entirely from off-the-shelf components and is easily applied to a variety of imaging modalities such as fluorescence , phase-contrast or darkfield imaging , ” said Xiao .
It can be “ simply added to most existing systems and is easy to replicate , making it accessible to other researchers.
” Their technique is described in the journal Optica .
Needless to say , these advances in imaging will be a boon for design science .
Instead of being restricted to the hazy image of the bacterial @ @ @ @ @ @ @ , scientists can now look in detail at individual molecules making up the machine .
Many journal papers are already describing several iconic molecular machines in unprecedented detail .
Here are some recent examples : Mitochondria .
Austrian scientists resolved the coupling mechanism in the mammalian respiratory Complex I ( the first machine in the mitochondrion ’ s electron transport chain ) at 2.3 angstroms ( Kampjut and Sazanov , Science ) .
“ The resolution of some structures was sufficient to see water molecules and to trace putative paths for proton transfer @ @ @ @ @ @ @ a summary paragraph says .
“ The structures add valuable details that provide a basis for generating mechanistic hypotheses for this crucial complex.
” Visual proof of cryo-EM ’ s value can be seen in two movies they made , available in the Supplementary Materials .
Ribosome .
How molecular machines are assembled is of great interest to design science .
The ribosome , which translates mRNA into protein , consists of a small 40S subunit and a large 60S subunit .
These come together into a working machine with the aid of @ @ @ @ @ @ @ manner , ” say Michael Ameismeyer et al .
in Nature .
Using cryo-EM , the team was able to figure out the “ structural basis for the final steps of human 40S ribosome maturation.
” ATP synthase .
Another favorite ID icon has been imaged with cryo-EM in enough detail to see how the peripheral stalk is assembled .
The team of Jiulia He included Nobel laureate John E. Walker and has been published in PNAS .
Assembly of human ATP synthase requires 27 nucleus-encoded proteins and two others encoded in the @ @ @ @ @ @ @ scientists to see “ how components of the peripheral stalk and three associated membrane subunits are assembled and introduced into the enzyme complex.
” Another paper in Nature Structural & Molecular Biology reveals “ Cryo-EM structure of the entire mammalian F-type ATP synthase.
” Bacterial flagellum .
How could we not mention the molecular machine that opened the eyes of many to intelligent design ?
New results using cryo-EM technology reveal details about the flagellum that Chang et al.
, in Nature Structural & Molecular Biology , used cryo-EM to propose a “ @ @ @ @ @ @ @ bacterial flagellar motor.
” In the team ’ s surprising model , the rotor is set in motion by other rotors !
A ring of MotA subunits turns the rotor like a set of gears , and can rapidly switch to turn the other way .
Commenting on this model in Nature Structural & Molecular Biology , Keiichi Namba described it as a “ two-cogwheel ” arrangement .
This might explain how the rotor can switch directions in a quarter turn , as Jed Macosco has said .
Namba says , These new @ @ @ @ @ @ @ Behe and all other ID proponents .
Imagine peering under the hood of this machine and observing the rotor and stator of this motor at high resolution .
Namba was clearly impressed , saying that the flagellum operates at “ almost 100 % efficiency ” and has been measured with a maximum speed of “ 1,700 revolutions per second ” ( 102.000 rpm ) , “ which is much faster than that of a Formula One racing car engine.
” The Closer You Look Super resolution microscopy will certainly be a boon for @ @ @ @ @ @ @ pointed out that the closer one looks at biological systems , the more engineered they look .
For now , the state of the art requires piecing static images into models of motion .
Will scientists ever succeed at watching machines like the ribosome , ATP synthase , and the bacterial flagellum in real time , like movies , at super resolution ?
Remember , never say never , because humans are clever .
We can already take great interest and delight in what the “ resolution revolution ” has brought us .

Photo: Atomium, Belgium, by Raphaël Biscaldi, via Unsplash.
Never say never, because humans are clever. Physics teachers used to say that humans will never be able to see atoms through any microscope due to a fundamental barrier to resolution called the diffraction limit. But like the four-minute mile and the sound barrier, this record was made to be broken. Today, optical engineers are doing it. Individual atoms are coming into focus!
A review published in 2015 in Methods in Molecular Biology explained how the diffraction limit was breached:
Conventional microscopy techniques, namely the confocal microscope or deconvolution processes, are resolution limited, ~250 nm, by the diffraction properties of light as developed by Ernst Abbe in 1873. This diffraction limit is appreciably above the size of most multi-protein complexes, which are typically 20–50 nm in diameter. In the mid 2000s, biophysicists moved beyond the diffraction barrier by structuring the illumination pattern and then applying mathematical principles and algorithms to allow a resolution of approximately 100 nm, sufficient to address protein subcellular colocalization questions. This “breaking” of the diffraction barrier, affording resolution beyond 200 nm is termed super resolution microscopy. More recent approaches include single molecule localization (such as PhotoActivated Localization Microscopy (PALM)/STochastic Optical Reconstruction Microscopy (STORM)) and point spread function engineering (such as STimulated Emission Depletion (STED) microscopy). [Emphasis added.]
Super-resolution microscopy has exploded since the diffraction limit was surpassed. Instead of 100nm, scientists are imaging objects at 10nm and smaller. Each new paper pushes the limit: down to 5nm, 4nm, 3nm, where individual domains of molecular machines can be seen.
Cryo-Electron Microscopy
These successes are largely due to the introduction of cryo-electron microscopy (see paper in Protein Science), which shock-freezes the specimen to stabilize it before imaging it in an electron microscope. The technique earned three biophysicists the Nobel Prize in Chemistry in 2017. Conceived of in the late 1990s, cryo-EM went mainstream about 2013 and is now state of the art. Even so, cryo-EM had its own resolution barrier.
In October, the Max Planck Institute announced a new world record for cryo-EM by Holger Stark that broke through the barrier. “For the first time, his group succeeded in observing individual atoms in a protein structure and taking the sharpest images ever with this method.” Now, scientists will no longer be measuring in nanometers but in Angstrom units — an order of magnitude smaller.
Using the new microscope, the scientists have taken more than one million images of the protein apoferritin to map the molecular structure with a resolution of 1.25 angstroms. One angstrom is equivalent to a ten millionth of a millimeter. “We now visualize single atoms in the protein — a milestone in our field,” explains structural biologist Stark. “For us, it was like putting super glasses on the microscope. The new structure reveals details never seen before: We can even see the density for hydrogen atoms and single atom chemical modifications.”
Nature News and Views comments that “This unprecedented feat would not have been thought feasible merely a decade ago.” The technique used by Stark’s team (published in the same issue of Nature by Yip et al.) is called “single particle cryo-EM.” It’s part of a “resolution revolution” that began in 2013. Stark’s team imaged a ferritin molecule, a benchmark for cryo-EM because of its stability and symmetry, but a companion paper in Nature by Nakane et al. describes their success at imaging a portion of a more motile protein complex at 1.7 angstrom resolution. This approaches the length of a carbon-carbon bond (1.5 angstroms, according to Phys.org).
The developments in cryo-EM hardware described by Yip, Nakane and their respective colleagues have driven a major advance in the resolution of single-particle cryo-EM. Each team used hardware that tackled distinct aspects of cryo-EM imaging that had previously limited the resolution attainable. With these technologies, the increased signal-to-noise ratio of cryo-EM images will expand the technique’s applicability. For example, this might include using the technique to determine high-resolution structures of heterogeneous samples such as those formed of membrane proteins, or macromolecular complexes that vary in conformation or composition. Perhaps the melding of these technologies will enable the determination of cryo-EM structures at a resolution beyond even 1 Å. This once might have seemed a near impossible quest to embark upon.
More Imaging Advances
Adaptive Optics has long been used by astronomers to sharpen images of stars by reducing the smearing caused by turbulence in the atmosphere. The technique uses a laser beam as a guide, and rapidly shifts the telescope’s mirror to keep the reference beam steady. Can that technique be used at the other end of the tube — i.e., in a microscope? Yes! A team led by Daniel Hammer of the Food and Drug Administration (FDA) was able to image tiny microglia in the inner limiting membrane of the human retina using adaptive optics (AO). Combining this with optical coherence tomography (OCT), which allows optical depth sectioning of images for a 3-D view, they were able to follow these microglia, the “first responders to neural injury,” in real time in live human subjects. That is only one of many possible applications of this method, they say; “the ability to visualize macrophage cells without fluorescent labeling in the live human eye represents an important advance for both ophthalmology and neuroscience, which may lead to novel disease biomarkers and new avenues of exploration in disease progression.” The results were published last month in PNAS.
More about super resolution imaging can be found in the Journal of the American Chemical Society: “Super-resolution Microscopy with Single Molecules in Biology and Beyond — Essentials, Current Trends, and Future Challenges.” Authors Leonhard Möckl and W. E. Moerner of Stanford say, “Despite the tremendous progress, the full potential of single-molecule super-resolution microscopy is yet to be realized, which will be enabled by the research ahead of us.”
Multifocus 3-D Imaging took a leap with a new technique that Phys.org calls a “simple way to capture high quality 3-D images of live cells and organisms.” A team led by Sheng Xiao of Boston University used a z-splitter prism to split light beams from the specimen into “several images, each focused to a different depth in the sample, in a single camera frame.” Instead of a flat image at one focal plane, this technique yields 3-D images from standard optical microscopes. “We used a z-splitter prism that can be assembled entirely from off-the-shelf components and is easily applied to a variety of imaging modalities such as fluorescence, phase-contrast or darkfield imaging,” said Xiao. It can be “simply added to most existing systems and is easy to replicate, making it accessible to other researchers.” Their technique is described in the journal Optica.
Great Tools for ID
Needless to say, these advances in imaging will be a boon for design science. Instead of being restricted to the hazy image of the bacterial flagellum available to Michael Behe in 1996, scientists can now look in detail at individual molecules making up the machine. Many journal papers are already describing several iconic molecular machines in unprecedented detail. Here are some recent examples:
Mitochondria. Austrian scientists resolved the coupling mechanism in the mammalian respiratory Complex I (the first machine in the mitochondrion’s electron transport chain) at 2.3 angstroms (Kampjut and Sazanov, Science). “The resolution of some structures was sufficient to see water molecules and to trace putative paths for proton transfer within the proton-pumping membrane domain,” a summary paragraph says. “The structures add valuable details that provide a basis for generating mechanistic hypotheses for this crucial complex.” Visual proof of cryo-EM’s value can be seen in two movies they made, available in the Supplementary Materials.
Ribosome. How molecular machines are assembled is of great interest to design science. The ribosome, which translates mRNA into protein, consists of a small 40S subunit and a large 60S subunit. These come together into a working machine with the aid of 200 factors in “a highly coordinated manner,” say Michael Ameismeyer et al. in Nature. Using cryo-EM, the team was able to figure out the “structural basis for the final steps of human 40S ribosome maturation.”
ATP synthase. Another favorite ID icon has been imaged with cryo-EM in enough detail to see how the peripheral stalk is assembled. The team of Jiulia He included Nobel laureate John E. Walker and has been published in PNAS. Assembly of human ATP synthase requires 27 nucleus-encoded proteins and two others encoded in the mitochondria. Super resolution microscopy now allows scientists to see “how components of the peripheral stalk and three associated membrane subunits are assembled and introduced into the enzyme complex.” Another paper in Nature Structural & Molecular Biology reveals “Cryo-EM structure of the entire mammalian F-type ATP synthase.”
Bacterial flagellum. How could we not mention the molecular machine that opened the eyes of many to intelligent design? New results using cryo-EM technology reveal details about the flagellum that Chang et al., in Nature Structural & Molecular Biology, used cryo-EM to propose a “Molecular mechanism for rotational switching of the bacterial flagellar motor.” In the team’s surprising model, the rotor is set in motion by other rotors! A ring of MotA subunits turns the rotor like a set of gears, and can rapidly switch to turn the other way.
Commenting on this model in Nature Structural & Molecular Biology, Keiichi Namba described it as a “two-cogwheel” arrangement. This might explain how the rotor can switch directions in a quarter turn, as Jed Macosco has said. Namba says,
The CW rotation of MotA CD could generate the torque for C ring rotation in either CCW or CW directionsthrough different interaction modes with FliG at the top of the C ring, that is, either with the inner side of the tube (closer to the motor axis) or with the opposite outer side… This is just like a two-cogwheel gear system, composed of small and large cogwheels, with cogs at the cylinder edges that can switch their relative positions; the small cogwheel (MotA) always generates torque in one direction, but it can mesh with the large cogwheel(FliG in the C ring) via either its internal or external edges, hence driving rotation of the large cogwheel in either direction.
These new high-res images should be eye candy to Behe and all other ID proponents. Imagine peering under the hood of this machine and observing the rotor and stator of this motor at high resolution. Namba was clearly impressed, saying that the flagellum operates at “almost 100% efficiency” and has been measured with a maximum speed of “1,700 revolutions per second” (102.000 rpm), “which is much faster than that of a Formula One racing car engine.”
The Closer You Look
Super resolution microscopy will certainly be a boon for design science. ID advocates have often pointed out that the closer one looks at biological systems, the more engineered they look. For now, the state of the art requires piecing static images into models of motion. Will scientists ever succeed at watching machines like the ribosome, ATP synthase, and the bacterial flagellum in real time, like movies, at super resolution? Remember, never say never, because humans are clever. We can already take great interest and delight in what the “resolution revolution” has brought us.


evolutionnewsandviews--2020-12-03--Preview: James Tour, Brian Miller on the Origin of “Data Risk Management” in DNA

I observed earlier today , noting a new recognition for the recent book The Mystery of Life ’ s Origin , that 2020 is not going to go down in history as the Year of the Expert .
Of course , I didn ’ t mean to run down experts or expertise in general .
But sometimes you get a situation where experts with crucial insights simply haven ’ t been invited to the conversation about a particular question .
When it comes to the origin of biological wonders , a couple of examples might be doctors and engineers , @ @ @ @ @ @ @ , members of these professions succeed or fail based on their ability to keep things working , or in the case of engineers , their ability to design functional things from the ground up .
They know exactly what goes into operation , in a way that evolutionary biologists don ’ t .
The complexity of devising and maintaining function is a consideration that bears , obviously , on the origin of life itself .
Two contributors to the Mystery book are synthetic organic chemist James Tour at Rice University and physicist Brian @ @ @ @ @ @ @ re in for a treat this Friday , December 4 at 5:30 pm Pacific time/8:30 Eastern , when Dr. Tour and Dr. Miller discuss “ Thermodynamics and Origin of Life ” for Professor Tour ’ s Science & Faith podcast .
Look for it here : In a sneak preview , Miller and Tour discuss a fascinating engineering perspective : parallels between how biological information is handled in living cells and how — oh my , what a timely topic !
— how it is safeguarded from loss , or perhaps hacking or @ @ @ @ @ @ @ information technology .
Tour wants to know , “ What is the origin of the data risk management characteristics of DNA ?
” He ’ s referring to “ redundant systems ” that are “ not necessary for operation but to protect against data loss.
” “ That ’ s a wonderful question , ” says Miller .
And who can disagree ?
“ [ Computer ] engineers looked at this and said , ‘ That ’ s exactly what we do !
’ ” If intelligent computer scientists build systems like that @ @ @ @ @ @ @ also incorporates them , for the very same reasons , that ’ s rather suggestive .
Join James Tour and Brian Miller for their conversation about this and related subjects on Friday !

Photo credit: Markus Spiske via Unsplash.
I observed earlier today, noting a new recognition for the recent book The Mystery of Life’s Origin, that 2020 is not going to go down in history as the Year of the Expert. Of course, I didn’t mean to run down experts or expertise in general. But sometimes you get a situation where experts with crucial insights simply haven’t been invited to the conversation about a particular question.
When it comes to the origin of biological wonders, a couple of examples might be doctors and engineers, including computer engineers. Unlike evolutionary biologists, members of these professions succeed or fail based on their ability to keep things working, or in the case of engineers, their ability to design functional things from the ground up. They know exactly what goes into operation, in a way that evolutionary biologists don’t.
The complexity of devising and maintaining function is a consideration that bears, obviously, on the origin of life itself. Two contributors to the Mystery book are synthetic organic chemist James Tour at Rice University and physicist Brian Miller at Discovery Institute. We’re in for a treat this Friday, December 4 at 5:30 pm Pacific time/8:30 Eastern, when Dr. Tour and Dr. Miller discuss “Thermodynamics and Origin of Life” for Professor Tour’s Science & Faith podcast. Look for it here:
In a sneak preview, Miller and Tour discuss a fascinating engineering perspective: parallels between how biological information is handled in living cells and how — oh my, what a timely topic! — how it is safeguarded from loss, or perhaps hacking or other interference, in the context of information technology.
Tour wants to know, “What is the origin of the data risk management characteristics of DNA?” He’s referring to “redundant systems” that are “not necessary for operation but to protect against data loss.”
“That’s a wonderful question,” says Miller. And who can disagree? “[Computer] engineers looked at this and said, ‘That’s exactly what we do!’” If intelligent computer scientists build systems like that, and life at the DNA level also incorporates them, for the very same reasons, that’s rather suggestive. Join James Tour and Brian Miller for their conversation about this and related subjects on Friday!


evolutionnewsandviews--2020-12-02--Life’s Origin — A “Mystery” Made Accessible

2020 as the Year of the Expert ?
Not exactly .
In fact , for many observers , one of the motifs in this annus horribilis has been the failure of experts to get things right .
To “ follow the science ” or “ listen to the scientists ” was revealed , like never quite before , as a questionable piece of unsolicited advice : What science ?
What scientists ?
And why ?
The hopeful flip-side of this has been that thoughtful people who aren ’ t scientists were empowered — again , like never quite before — @ @ @ @ @ @ @ .
So kudos to World Magazine and its editor-in-chief , Marvin Olasky , for slightly refocusing their Book of the Year awards .
For 2020 they highlight books for being accessible to a general audience , with categories like Accessible History , Accessible Theology , and Accessible Science .
As the winner under the last of these headings , it ’ s great to be able to recognize one of the year ’ s titles from Discovery Institute Press .
It is The Mystery of Life ’ s Origin : The Continuing Controversy @ @ @ @ @ @ @ Accessible Science Book of the Year is actually “ two books in one : a classic that in 1984 provided the base for the intelligent design movement of the 1990s , and a series of newly written , cutting-edge chapters that set the stage for a Roaring 20s decade of scientific advance.
” The original book by Charles Thaxton , Walter Bradley , and Roger Olsen is updated with contributions by scientists and scholars — James Tour , Stephen Meyer , Brian Miller , Guillermo Gonzalez , Jonathan Wells .
I wrote a @ @ @ @ @ @ @ profound impact on the intelligent design movement .
Olasky writes : The classic came into existence because Walter Bradley , then a professor at the Colorado School of Mines , understood that how life originated was one missing link in Darwinism : He asked “ how you get started from scratch , ” how does life come from nonlife ?
Bradley and Roger Olsen wrote a draft that found its way into the hands of chemist Charles Thaxton , whose first reaction was “ Wow , this is kind of interesting .
But @ @ @ @ @ @ @ it ?
” The three scientists met at Texas A & M , where Bradley had taken a teaching job , and Bradley and Olsen almost simultaneously responded to Thaxton ’ s objection : “ You ’ re the chemist .
You write it.
” He did , and the reaction was both historic and hysterical .
The Mystery of Life ’ s Origin received praise from Dean Kenyon , who came to doubt his own conventional theory of chemical evolution , and other scholars .
It powerfully influenced today ’ s most @ @ @ @ @ @ @ , as well as mathematician William Dembski and a whole new generation of pioneers .
But chemist Richard Lemmon snorted about “ religious creationists , ” as did others , and Mystery became tantamount to a banned book among conventional scientists .
Now to the present : Rice chemistry professor James Tour ’ s essay , which starts off the second half of the new volume , has the apt title , “ We ’ re Still Clueless About the Origin of Life.
” Tour appropriately ridicules reporters who fall for media hype @ @ @ @ @ @ @ Is Life ?
by famed science writer Ed Regis , who explains , “ Life began with little bags of garbage , random assortments of molecules doing some crude kind of metabolism .
That is stage one .
The garbage bags grow and occasionally split in two , and the ones that grow and split fastest win.
” Tour : “ Those ‘ little bags of garbage ’ have no more resemblance to living cells than a big bag of garbage resembles a horse.
” Cells , we now know , are hugely @ @ @ @ @ @ @ the 1952 Miller-Urey experiment feature an electrical discharge forming some amino acids , thus showing that life could emerge apart from God ?
That ’ s what I learned in a chemistry class 53 years ago , and many WORLD readers probably did as well .
Jonathan Wells in his Mystery chapter — “ Textbooks Still Misrepresent the Origin of Life ” — blows up the mistaken assumptions essential to the famous experiment and quotes what famed physicist Freeman Dyson said before his death in 2000 : Miller-Urey “ was supposed to be @ @ @ @ @ @ @ the primitive Earth .
But now nobody believes this anymore.
” Read the rest here .
If you “ listen to the experts , ” or anyway some of the experts , cells are “ little bags of garbage ” and Miller-Urey is a “ true simulation of prebiotic chemistry.
” Both notions are utter baloney , yet they persist .
The updated Mystery of Life ’ s Origin empowers all curious readers to examine such claims for themselves .
In a year that almost seems designed to break us down , recognizing @ @ @ @ @ @ @ life can ’ t help but give you hope .
The word “ miracle ” is seldom seen in scientific literature , but looked at objectively , the “ mystery ” here , of life from non-life , seems to demand it .
Speaking of which , World also offers its readers some “ honorable mentions ” in the Accessible Science category , and again it ’ s gratifying to see another DI Press book get its just recognition .
Biologist Michael Denton wrote the short and quite accessible book The Miracle of @ @ @ @ @ @ @ latest in his Privileged Species series .
Olasky notes : For centuries “ fearfully and wonderfully made ” were just words about our bodies from Psalm 139 .
Now we have proof : Biochemist Michael Denton shows how vast is the chasm between some chemical soup and a cell filled with genetic information encoded in the double helix , and much besides .
Despite decades of experimentation and hypotheses , Denton reports that “ no one has produced any convincing explanation of how nature could have overcome this chasm .
… Science , @ @ @ @ @ @ @ ” Logically , those with yard signs saying , “ I believe in science , ” should also have signs saying , “ I believe in intelligent design.
” Denton says this realization and road-mapping regarding cells “ will be of far greater intellectual consequence than any other discovery in science ” during the past 500 years .
Ha , I love the idea of a yard sign like the one Olasky suggests , modeled on the ubiquitous signs in our , and perhaps your , neighborhood .
They begin , “ In @ @ @ @ @ @ @ the virtue-signaling statements that follows is “ Science is real.
” Please , who the heck doesn ’ t believe that ?
It would indeed be cheeky to substitute , “ Intelligent design is real.
” And how long do you think it would take for that sign to be knocked down , stolen , or vandalized ?
Here in Seattle , anyway , not long .
Thanks as always to the folks at World Magazine for their fine independent journalism and support for smart and well-informed skepticism .
Read their full list @ @ @ @ @ @ @ ” here .

Image credit: Brian Gage.
2020 as the Year of the Expert? Not exactly. In fact, for many observers, one of the motifs in this annus horribilis has been the failure of experts to get things right. To “follow the science” or “listen to the scientists” was revealed, like never quite before, as a questionable piece of unsolicited advice: What science? What scientists? And why? The hopeful flip-side of this has been that thoughtful people who aren’t scientists were empowered — again, like never quite before — to think skeptically and independently for themselves.
So kudos to World Magazine and its editor-in-chief, Marvin Olasky, for slightly refocusing their Book of the Year awards. For 2020 they highlight books for being accessible to a general audience, with categories like Accessible History, Accessible Theology, and Accessible Science.
A Profound Impact on ID
As the winner under the last of these headings, it’s great to be able to recognize one of the year’s titles from Discovery Institute Press. It is The Mystery of Life’s Origin: The Continuing Controversy. As Olasky points out, this Accessible Science Book of the Year is actually “two books in one: a classic that in 1984 provided the base for the intelligent design movement of the 1990s, and a series of newly written, cutting-edge chapters that set the stage for a Roaring 20s decade of scientific advance.”
The original book by Charles Thaxton, Walter Bradley, and Roger Olsen is updated with contributions by scientists and scholars — James Tour, Stephen Meyer, Brian Miller, Guillermo Gonzalez, Jonathan Wells. I wrote a historical introduction to the book detailing its profound impact on the intelligent design movement. Olasky writes:
The classic came into existence because Walter Bradley, then a professor at the Colorado School of Mines, understood that how life originated was one missing link in Darwinism: He asked “how you get started from scratch,” how does life come from nonlife? Bradley and Roger Olsen wrote a draft that found its way into the hands of chemist Charles Thaxton, whose first reaction was “Wow, this is kind of interesting. But why is there not more chemistry in it?” The three scientists met at Texas A&M, where Bradley had taken a teaching job, and Bradley and Olsen almost simultaneously responded to Thaxton’s objection: “You’re the chemist. You write it.” He did, and the reaction was both historic and hysterical. The Mystery of Life’s Origin received praise from Dean Kenyon, who came to doubt his own conventional theory of chemical evolution, and other scholars. It powerfully influenced today’s most influential intelligent design advocate, Stephen Meyer, as well as mathematician William Dembski and a whole new generation of pioneers. But chemist Richard Lemmon snorted about “religious creationists,” as did others, and Mystery became tantamount to a banned book among conventional scientists. Now to the present: Rice chemistry professor James Tour’s essay, which starts off the second half of the new volume, has the apt title, “We’re Still Clueless About the Origin of Life.” Tour appropriately ridicules reporters who fall for media hype about purported progress. He quotes What Is Life? by famed science writer Ed Regis, who explains, “Life began with little bags of garbage, random assortments of molecules doing some crude kind of metabolism. That is stage one. The garbage bags grow and occasionally split in two, and the ones that grow and split fastest win.” Tour: “Those ‘little bags of garbage’ have no more resemblance to living cells than a big bag of garbage resembles a horse.” Cells, we now know, are hugely complicated factories. But didn’t the 1952 Miller-Urey experiment feature an electrical discharge forming some amino acids, thus showing that life could emerge apart from God? That’s what I learned in a chemistry class 53 years ago, and many WORLD readers probably did as well. Jonathan Wells in his Mystery chapter — “Textbooks Still Misrepresent the Origin of Life” — blows up the mistaken assumptions essential to the famous experiment and quotes what famed physicist Freeman Dyson said before his death in 2000: Miller-Urey “was supposed to be a true simulation of prebiotic chemistry on the primitive Earth. But now nobody believes this anymore.”
Mystery and Miracle
Read the rest here. If you “listen to the experts,” or anyway some of the experts, cells are “little bags of garbage” and Miller-Urey is a “true simulation of prebiotic chemistry.” Both notions are utter baloney, yet they persist. The updated Mystery of Life’s Origin empowers all curious readers to examine such claims for themselves. In a year that almost seems designed to break us down, recognizing the true design at the start of life can’t help but give you hope. The word “miracle” is seldom seen in scientific literature, but looked at objectively, the “mystery” here, of life from non-life, seems to demand it.
Speaking of which, World also offers its readers some “honorable mentions” in the Accessible Science category, and again it’s gratifying to see another DI Press book get its just recognition. Biologist Michael Denton wrote the short and quite accessible book The Miracle of the Cell. It’s the latest in his Privileged Species series. Olasky notes:
For centuries “fearfully and wonderfully made” were just words about our bodies from Psalm 139. Now we have proof: Biochemist Michael Denton shows how vast is the chasm between some chemical soup and a cell filled with genetic information encoded in the double helix, and much besides. Despite decades of experimentation and hypotheses, Denton reports that “no one has produced any convincing explanation of how nature could have overcome this chasm. … Science, it seems, has reached an impasse.” Logically, those with yard signs saying, “I believe in science,” should also have signs saying, “I believe in intelligent design.” Denton says this realization and road-mapping regarding cells “will be of far greater intellectual consequence than any other discovery in science” during the past 500 years.
“Science Is Real”
Ha, I love the idea of a yard sign like the one Olasky suggests, modeled on the ubiquitous signs in our, and perhaps your, neighborhood. They begin, “In this house we believe…” One of the virtue-signaling statements that follows is “Science is real.” Please, who the heck doesn’t believe that? It would indeed be cheeky to substitute, “Intelligent design is real.” And how long do you think it would take for that sign to be knocked down, stolen, or vandalized? Here in Seattle, anyway, not long.
Thanks as always to the folks at World Magazine for their fine independent journalism and support for smart and well-informed skepticism. Read their full list of “2020 Books of the Year” here.
Update from the Center for Science & Culture: For a limited time, we’re offering a FREE download of two chapters from The Mystery of Life’s Origin: The Continuing Controversy. In “We’re Still Clueless about the Origin of Life,” Rice University chemist James Tour documents current failures to explain the origin of life. In “Evidence of Intelligent Design in the Origin of Life,” New York Times-bestselling author Stephen Meyer explains why intelligent design is the best explanation for the origin of life. Download the chapters here.


evolutionnewsandviews--2020-12-02--Missing the Point: Codes Are Not Products of Physics

Elaborate schemes to explain the origin of the genetic code from the laws of physics and chemistry miss the whole point about codes : the origin of information .
ID books make this abundantly clear , such as in Signature in the Cell by Stephen Meyer , and The Mystery of Life ’ s Origin : The Continuing Controversy ( expanded reprint ) by Thaxton , Bradley , and Olsen and contributing authors .
Whether intentionally or not , origin-of-life researchers continue to ignore the main point about codes : a code is a message , and a message presupposes @ @ @ @ @ @ @ material process can explain the arrangement of building blocks in a sequence , it is not a code .
Codes may make use of material building blocks , such as letters on a printed page or radio pulses through space , but the essence of a code is the information it conveys .
The essence of a message is the intended meaning from the messenger .
The meaning may be live or programmed .
In either case , a code conveys the foresight of a mind with the intention to communicate .
With @ @ @ @ @ @ @ of codes by ID scientists for the past 36 years ( and more ) , it is sad to see other scientists continuing to belabor the fallacy that codes can emerge from mindless processes .
If that were true , it would be the equivalent of a miracle .
If other want to dismiss the “ miracles ” they think that intelligent design requires , what should design advocates say about the evolutionists ’ miracles of chance ?
If others wish to limit their explanatory toolkit to “ natural laws , ” what @ @ @ @ @ @ @ the Quarterly Reviews of Biophysics , Klump , Völker , and Breslauer attempt to argue that the existing DNA code was naturally selected as the most optimal for energy stability .
That natural selection is the intended meaning is clear from their title : “ Energy mapping of the genetic code and genomic domains : implications for code evolution and molecular Darwinism.
” In other words , they propose that natural selection extended down into prebiotic life , despite the common understanding that accurate replication is a prerequisite for natural selection .
In @ @ @ @ @ @ @ do the selecting .
This is made clear in the title of a news piece from Rutgers University , “ Genetic Code Evolution and Darwin ’ s Evolution Theory Should Consider DNA an ‘ Energy Code ’ — ‘ Survival of the fittest ’ phenomenon is only part of the evolution equation.
” But how does meaning ( semantics ) emerge in an “ energy code ” created by “ molecular Darwinism ” ?
Their hypothesis ignores this requirement entirely .
“ The origins of the evolution of the DNA genetic code and @ @ @ @ @ @ @ embedded in the different energy profiles of their molecular DNA blueprints .
Under the influence of the laws of thermodynamics , this energy code evolved , out of an astronomical number of alternative possibilities , into a nearly singular code across all living species.
” Scientists investigated this so-called “ universal enigma , ” probing the origins of the astounding observation that the genetic code evolved into a nearly uniform blueprint that arose from trillions of possibilities .
The scientists expanded the underpinnings of the landmark “ survival of the fittest ” Darwinian @ @ @ @ @ @ @ ” Darwin ’ s revolutionary theory is based on the generational persistence of a species ’ physical features that allow it to survive in a given environment through “ natural selection.
” Molecular Darwinism refers to physical characteristics that persist through generations because the regions of the molecular DNA that code for those traits are unusually stable .
[ Emphasis added . ]
Their argument is akin to the multiverse hypothesis : out of “ trillions of possibilities ” a universe was naturally selected with conditions permitting complex life — and here we @ @ @ @ @ @ @ ” story , the laws of thermodynamics “ selected ” arrangements of DNA building blocks that were stable , and presto !
Functional information !
That ’ s why all life forms use it !
( Notice the non-sequitur . )
The folks at Rutgers don ’ t mention information , and they only mention function in an after-the-fact way , intimating that “ molecular Darwinism ” might enable or favor biological functions .
The following quote from the paper has to be read to be appreciated as a classic example of academic @ @ @ @ @ @ @ the genetic code from the second law of thermodynamics , the very law that degrades information !
When the iconic DNA genetic code is expressed in terms of energy differentials , one observes that informationembedded in chemical sequences , including some biological outcomes , correlate with distinctive free energy profiles .
Specifically , we find correlations between codon usage and codon free energy , suggestive of a thermodynamic selection for codon usage .
We also find correlations between what are considered ancient amino acids and high codon free energy values .
Such correlations @ @ @ @ @ @ @ code fundamentally mapping as an energy code .
In such a perspective , one can envision the genetic code as composed of interlocking thermodynamic cycles that allow codons to ‘ evolve ’ from each other through a series of sequential transitions and transversions , which are influenced by an energy landscape modulated by both thermodynamic and kinetic factors .
As such , early evolution of the genetic code may have been driven , in part , by differential energetics , as opposed exclusively by the functionality of any gene product .
In such @ @ @ @ @ @ @ in part , derive from the optimization of biophysical properties ( e.g .
relative stabilities and relative rates ) , in addition to the classic perspective of being driven by a phenotypical adaptive advantage ( natural selection ) .
Such differential energy mapping of the genetic code , as well as larger genomic domains , may reflect an energetically resolved and evolved genomic landscape , consistent with a type of differential , energy-driven ‘ molecular Darwinism ’ .
It should not be surprising that evolution of the code was influenced by differential energetics @ @ @ @ @ @ @ and universal branch of science that operates over all time and length scales .
The stability of a DNA double helix has no correlation with its information content .
Presumably , a repetitive sequence of A-G-T-C-A-G-T-C throughout the whole strand might be the most stable of all , but it would convey no message and have no function .
An “ energy code ” that settled out of entropy would never translate into a molecular machine with a sophisticated function .
The authors assume that because the existing code is stable and has @ @ @ @ @ @ @ will be naturally selected to be rich with information .
This is nonsense .
Will the emergence of shopping carts that are more stable with four wheels instead of three wheels guarantee that they will be filled with groceries ?
No amount of rhetoric can defend such an idea .
The authors realize their hypothesis has a long way to go : Good luck with that .
No amount of research can justify a flawed premise .
Another paper tries to get codes by material processes .
It is found in PNAS by @ @ @ @ @ @ @ the genetic code ; Evidence from serine codon use disparity in Escherichia coli.
” This team bounces off the concept of synonymous codons , where one amino acid can be represented by two to six codons .
The code for serine , for instance , can be represented by AGU/C ( one “ box ” ) or UCU/C/A/G ( a second box ) .
This is the only case where it takes two base substitutions to move from one box to the other .
“ Deciphering how this came to be will provide @ @ @ @ @ @ @ and the genetic code , ” they promise .
The authors attempt to arrange amino acids into phylogenetic trees .
At the origin of life , only seven amino acids were in use , they propose ; then alanine branched into the second box for serine , and so forth .
They assume that the ones with the most synonymous codons evolved first , and later , the ones with single codons .
They count how many amino acid species exist in bacteria , and off they go , working out a scenario @ @ @ @ @ @ @ Strangely absent is the word information in the scheme .
How do these codons translate into a function ?
Why , they “ acquire ” it !
The Enlightenment has dawned !
There ’ s no sense in continuing this notion .
It ’ s all mixed up .
Don ’ t read this paper as the scientific method at work .
Read it as a bedtime story .
Emerged .
Yes children , thanks to Darwin , we know that codes and other wondrous things can emerge from matter — all by @ @ @ @ @ @ @ Darwin ’ s mechanism continue striving for natural ways to get codes .
They look at energy .
They look at building blocks .
They connect building blocks to energy .
But like plugging an extension cord into itself , there is no power that “ emerges ” in the system — except via speculative stories in the imaginations of materialists .
Meyer , Thaxton , and the others remain vindicated : the power in a code only flows when plugged into information .

Photo credit: xaviercanserra, via Pixabay.
Elaborate schemes to explain the origin of the genetic code from the laws of physics and chemistry miss the whole point about codes: the origin of information. ID books make this abundantly clear, such as in Signature in the Cell by Stephen Meyer, and The Mystery of Life’s Origin: The Continuing Controversy (expanded reprint) by Thaxton, Bradley, and Olsen and contributing authors. Whether intentionally or not, origin-of-life researchers continue to ignore the main point about codes: a code is a set of abstract symbols that represent information which can be used to convey a message, and both a code and a message presuppose a mind. Conversely, if a material process can explain the arrangement of building blocks in a sequence, it is neither a code nor a message.
Codes may make use of material building blocks, such as letters on a printed page or radio pulses through space, but the essence of a code is the information it is able to convey. The essence of a message is the intended meaning from the messenger. The meaning may be live or programmed. In either case, codes and messages convey the foresight of a mind with the intention to communicate.
With all the insistence about this fundamental aspect of codes by ID scientists for the past 36 years (and more), it is sad to see other scientists continuing to belabor the fallacy that codes can emerge from mindless processes. If that were true, it would be the equivalent of a miracle. If other want to dismiss the “miracles” they think that intelligent design requires, what should design advocates say about the evolutionists’ miracles of chance? If others wish to limit their explanatory toolkit to “natural laws,” what about the laws of probability?
Case 1: Codes from Thermodynamics
In the Quarterly Reviews of Biophysics, Klump, Völker, and Breslauer attempt to argue that the existing DNA code was naturally selected as the most optimal for energy stability. That natural selection is the intended meaning is clear from their title: “Energy mapping of the genetic code and genomic domains: implications for code evolution and molecular Darwinism.” In other words, they propose that natural selection extended down into prebiotic life, despite the common understanding that accurate replication is a prerequisite for natural selection. In this case, the laws of thermodynamics do the selecting. This is made clear in the title of a news piece from Rutgers University, “Genetic Code Evolution and Darwin’s Evolution Theory Should Consider DNA an ‘Energy Code’ — ‘Survival of the fittest’ phenomenon is only part of the evolution equation.” But how does meaning (semantics) emerge in an “energy code” created by “molecular Darwinism”? Their hypothesis ignores this requirement entirely.
“The origins of the evolution of the DNA genetic code and the evolution of all living species are embedded in the different energy profiles of their molecular DNA blueprints. Under the influence of the laws of thermodynamics, this energy code evolved, out of an astronomical number of alternative possibilities, into a nearly singular code across all living species.”
Scientists investigated this so-called “universal enigma,” probing the origins of the astounding observation that the genetic code evolved into a nearly uniform blueprint that arose from trillions of possibilities.
The scientists expanded the underpinnings of the landmark “survival of the fittest” Darwinian evolutionary theory to include “molecular Darwinism.” Darwin’s revolutionary theory is based on the generational persistence of a species’ physical features that allow it to survive in a given environment through “natural selection.” Molecular Darwinism refers to physical characteristics that persist through generations because the regions of the molecular DNA that code for those traits are unusually stable. [Emphasis added.]
Their argument is akin to the multiverse hypothesis: out of “trillions of possibilities” a universe was naturally selected with conditions permitting complex life — and here we are! In the “molecular Darwinism” story, the laws of thermodynamics “selected” arrangements of DNA building blocks that were stable, and presto! Functional information! That’s why all life forms use it! (Notice the non-sequitur.)
The folks at Rutgers don’t mention information, and they only mention function in an after-the-fact way, intimating that “molecular Darwinism” might enable or favor biological functions.
Different DNA regions can exhibit differential energy signatures that may favor physical structures in organisms that enable specific biological functions, Breslauer said.
The following quote from the paper has to be read to be appreciated as a classic example of academic gobbledygook. In short, they derive the genetic code from the second law of thermodynamics, the very law that degrades information!
When the iconic DNA genetic code is expressed in terms of energy differentials, one observes that information embedded in chemical sequences, including some biological outcomes, correlate with distinctive free energy profiles. Specifically, we find correlations between codon usage and codon free energy, suggestive of a thermodynamic selection for codon usage. We also find correlations between what are considered ancient amino acids and high codon free energy values. Such correlations may be reflective of the sequence-based genetic code fundamentally mapping as an energy code. In such a perspective, one can envision the genetic code as composed of interlocking thermodynamic cycles that allow codons to ‘evolve’ from each other through a series of sequential transitions and transversions, which are influenced by an energy landscape modulated by both thermodynamic and kinetic factors. As such, early evolution of the genetic code may have been driven, in part, by differential energetics, as opposed exclusively by the functionality of any gene product. In such a scenario, evolutionary pressures can, in part, derive from the optimization of biophysical properties (e.g. relative stabilities and relative rates), in addition to the classic perspective of being driven by a phenotypical adaptive advantage (natural selection). Such differential energy mapping of the genetic code, as well as larger genomic domains, may reflect an energetically resolved and evolved genomic landscape, consistent with a type of differential, energy-driven ‘molecular Darwinism’. It should not be surprising that evolution of the code was influenced by differential energetics, as thermodynamics is the most general and universal branch of science that operates over all time and length scales.
The stability of a DNA double helix has no correlation with its information content. Presumably, a repetitive sequence of A-G-T-C-A-G-T-C throughout the whole strand might be the most stable of all, but it would convey no message and have no function. An “energy code” that settled out of entropy would never translate into a molecular machine with a sophisticated function. The authors assume that because the existing code is stable and has the potential to be information-rich, it will be naturally selected to be rich with information. This is nonsense. Will the emergence of shopping carts that are more stable with four wheels instead of three wheels guarantee that they will be filled with groceries? No amount of rhetoric can defend such an idea.
The authors realize their hypothesis has a long way to go:
Next steps include recasting and mapping the human genome chemical sequence into an “energy genome,” so DNA regions with different energy stabilities can be correlated with physical structures and biological functions.
Good luck with that. No amount of research can justify a flawed premise.
Case 2: Natural Sequences
Another paper tries to get codes by material processes. It is found in PNAS by Inouye et al., “Evolution of the genetic code; Evidence from serine codon use disparity in Escherichia coli.” This team bounces off the concept of synonymous codons, where one amino acid can be represented by two to six codons. The code for serine, for instance, can be represented by AGU/C (one “box”) or UCU/C/A/G (a second box). This is the only case where it takes two base substitutions to move from one box to the other. “Deciphering how this came to be will provide important insight into the origin of life and the genetic code,” they promise.
The authors attempt to arrange amino acids into phylogenetic trees. At the origin of life, only seven amino acids were in use, they propose; then alanine branched into the second box for serine, and so forth. They assume that the ones with the most synonymous codons evolved first, and later, the ones with single codons. They count how many amino acid species exist in bacteria, and off they go, working out a scenario for how the genetic code evolved. Strangely absent is the word information in the scheme. How do these codons translate into a function? Why, they “acquire” it! The Enlightenment has dawned!
Substitution of Ala residues with Ser not only makes a protein more hydrophilic but also, in some cases, may cause a protein to acquire an enzymatic function or provide a site for protein modification, such as phosphorylation and acetylation.
There’s no sense in continuing this notion. It’s all mixed up.
Therefore, it is further speculated that Ser residues encoded by AGU or AGC in proteins had originally different functions from Ser residues encoded by UCX. Since then, the two different sets of Ser codons have been thoroughly mixed up during evolution.
Don’t read this paper as the scientific method at work. Read it as a bedtime story.
Looking at the codon table (Table 1), we seem to be able to decipher hidden stories about how genetic codons evolved. Based on the hypothesis that the simplest and thus the most primitive amino acid among the 20 amino acids is GGX or Gly, the codons for other amino acids are proposed to have evolved from GGX. In the second step of codon evolution, new sets of the codons for seven amino acids emerged….
Emerged. Yes children, thanks to Darwin, we know that codes, messages, and other wondrous things can emerge from matter — all by themselves.
The Power in a Code
Materialists who limit themselves to Darwin’s mechanism continue striving for natural ways to get codes. They look at energy. They look at building blocks. They connect building blocks to energy. But like plugging an extension cord into itself, there is no power that “emerges” in the system — except via speculative stories in the imaginations of materialists. Meyer, Thaxton, and the others remain vindicated: the power in a code only flows when plugged into information.