On darwinism's alleged 'tree of life'

Editor's note: This is Part 6 of a 10-part series based upon Casey Luskin's chapter,, "The Top Ten Scientific Problems with Biological and Chemical Evolution," in the volume More than Myth, edited by Paul Brown and Robert Stackpole (Chartwell Press, 2014). Previous installments can be found here:Problem 1, Problem 2, Problem 3, Problem 4, Problem 5. When the series is complete, the full chapter will be posted online.

When fossils failed to demonstrate that animals evolved from a common ancestor, evolutionary scientists turned to another type of evidence -- DNA sequence data -- to demonstrate a tree of life. In the 1960s, around the time the genetic code was first understood, biochemists Émile Zuckerkandl and Linus Pauling hypothesized that if DNA sequences could be used to produce evolutionary trees -- trees that matched those based upon morphological or anatomical characteristics -- this would furnish "the best available single proof of the reality of macro-evolution."⁹⁹ Thus began a decades-long effort to sequence the genes of many organisms and construct "molecular" based evolutionary ("phylogenetic") trees. The ultimate goal has been to construct a grand "tree of life," showing how all living organisms are related through universal common ancestry.

The Main Assumption

The basic logic behind building molecular trees is relatively simple. First, investigators choose a gene, or a suite of genes, found across multiple organisms. Next, those genes are analyzed to determine their nucleotide sequences, so the gene sequences of various organisms can then be compared. Finally, an evolutionary tree is constructed based upon the principle that the more similar the nucleotide sequence, the more closely related the species. A paper in the journalBiological Theory puts it this way:

[M]olecular systematics is (largely) based on the assumption, first clearly articulated

by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness.¹⁰⁰

This assumption is essentially an articulation of a major feature of the theory - the idea of universal common ancestry. Nonetheless, it's important to realize that it is a mere assumption to claim that genetic similarities between different species necessarily result common ancestry.

Operating strictly within a Darwinian paradigm, these assumptions flow naturally. As the aforementioned Biological Theory paper explains, the main assumption underlying molecular trees "derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change."¹⁰¹ So the theory is assumed to be true to construct a tree. But also, if Darwinian evolution is true, construction of trees using different sequences should reveal a reasonably consistent pattern across different genes or sequences.

This makes it all the more significant that efforts to build a grand "tree of life" using DNA or othebiological sequence data have not conformed to expectations. The basic problem is that one gene gives one version of the tree of life, while another gene gives a highly different, and conflicting, version of the tree. For example, as we'll discuss further below, the standard mammalian tree places humans more closely related to rodents than to elephants. But studies of a certain type of DNA called microRNA genes have suggested the opposite -- that humans were closer to elephants than rodents. Such conflicts between gene-based trees are extremely common.

The genetic data is thus not painting a consistent picture of common ancestry, showing the assumptions behind tree-building commonly fail. This leads to justifiable questions about whether universal common ancestry is correct.

Conflicts in the Base of the Tree of Life

Problems first arose when molecular biologists sequenced genes from the three basic domains of life -- bacteria, archaea, and eukarya -- but those genes did not allow these basic groups of life to be resolved into a treelike pattern. In 2009, the journal New Scientist published a cover story titled, "Why Darwin was wrong about the tree of life" which explained these quandaries

The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.¹⁰²

This sort of data led biochemist W. Ford Doolittle to explain that "Molecular phylogenists will have failed to find the 'true tree,' not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree."¹⁰³ New Scientist put it this way: "For a long time the holy grail was to build a tree of life ... But today the project lies in tatters, torn to pieces by an onslaught of negative evidence."¹⁰⁴

Many evolutionists sometimes reply that these problems arise only when studying microorganisms like bacteria -- organisms which can swap genes through a process called "horizontal gene transfer," thereby muddying the signal of evolutionary relationships. But this objection isn't quite true, since the tree of life is challenged even among higher organisms where such gene-swapping is not prevalent. Carl Woese, a pioneer of evolutionary molecular systematics, explains

Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.¹⁰⁵

Likewise, the New Scientist article notes that "research suggests that the evolution of animals and plants isn't exactly tree-like either."¹⁰⁶ The article explains what happened when microbiologist Michael Syvanen tried to create a tree showing evolutionary relationships using 2000 genes from a diverse group of animals:

He failed. The problem was that different genes told contradictory evolutionary stories. ... the genes were sending mixed signals. ... Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another.¹⁰⁷

The data were so difficult to resolve into a tree that Syvanen lamented, "We've just annihilated the tree of life."¹⁰⁸ Many other papers in the technical literature recognize similar problems.

Conflicts Between Higher Branches

A 2009 paper in Trends in Ecology and Evolution notes that, "A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome."¹⁰⁹ Similarly, a paper in Genome Researchstudied the DNA sequences in various animal groups and found that "different proteins generate different phylogenetic tree[s]."¹¹⁰ A June, 2012 article in Nature reported that short strands of RNA called microRNAs "are tearing apart traditional ideas about the animal family tree." Dartmouth biologist Kevin Peterson who studies microRNAs lamented, "I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree." According to the article, microRNAs yielded "a radically different diagram for mammals: one that aligns humans more closely with elephants than with rodents." Peterson put it bluntly: "The microRNAs are totally unambiguous ... they give a totally different tree from what everyone else wants."¹¹¹

Conflicts Between Molecules and Morphology

Not all phylogenetic trees are constructed by comparing molecules like DNA from different species. Many trees are based upon comparing the form, structure, and body plan of different organisms -- also called "morphology." But conflicts between molecule-based trees and morphology-based trees are also common. A 2012 paper studying bat relationships made this clear, stating: "Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species."¹¹² This is hardly the only study to encounter conflicts between DNA-based trees and trees based upon anatomical or characteristics. Textbooks often claim common descent is supported using the example of a tree of animals based upon the enzyme cytochrome c which matches the traditional evolutionary tree based upon morphology.¹¹³ However, textbooks rarely mention that the tree based upon a different enzyme, cytochrome b, sharply conflicts with the standard evolutionary tree. As one article in Trends in Ecology and Evolution observed:

[T]he mitochondrial cytochrome b gene implied . . . an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.¹¹⁴

Strikingly, a different article in Trends in Ecology and Evolution concluded, "the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent [evolutionary relationship] probably being the grouping of elephants and sea cows."¹¹⁵ Because of such conflicts, a major review article in Nature reported, "disparities between molecular and morphological trees" lead to "evolution wars" because "[e]volutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology."¹¹⁶

Finally, a study published in Science in 2005 tried to use genes to reconstruct the relationships of the animal phyla, but concluded that "[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved." The following year, the same authors published a scientific paper titled, "Bushes in the Tree of Life," which offered striking conclusions. The authors acknowledge that "a large fraction of single genes produce phylogenies of poor quality," observing that one study "omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom." The paper suggests that "certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available." The paper even contends that "[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics."¹¹⁷

Unfortunately, one assumption that these evolutionary biologists aren't willing to re-evaluate is the assumption that universal common ancestry is correct. They appeal to a myriad of ad hocarguments -- horizontal gene transfer, long branch attraction, rapid evolution, different rates of evolution, coalescent theory, incomplete sampling, flawed methodology, and convergent evolution -- to explain away inconvenient data which doesn't fit the coveted treelike pattern. As a 2012 paper stated, "phylogenetic conflict is common, and frequently the norm rather than the exception."¹¹⁸ At the end of the day, the dream that DNA sequence data would fit into a nice-neat tree of life has failed, and with it a key prediction of neo-Darwinian theory.

References:

[99.] Zuckerkandl and Pauling, "Evolutionary Divergence and Convergence in Proteins," 101.

[100.] Jeffrey H. Schwartz, Bruno Maresca, "Do Molecular Clocks Run at All? A Critique of Molecular Systematics," Biological Theory, 1(4):357-371, (2006).

[101.] Ibid.

[102.] Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009).

[103.] W. Ford Doolittle, "Phylogenetic Classification and the Universal Tree," Science, 284:2124-2128 (June 25, 1999).

[104.] Partly quoting Eric Bapteste, in Lawton, "Why Darwin was wrong about the tree of life" (internal quotations omitted).

[105.] Carl Woese "The Universal Ancestor," Proceedings of the National Academy of Sciences USA, 95:6854-9859 (June, 1998) (emphasis added).

[106.] Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009).

[107.] Partly quoting Michael Syvanen, in Lawton, "Why Darwin was wrong about the tree of life" (internal quotations omitted).

[108.] Michael Syvanen, quoted in Lawton, "Why Darwin was wrong about the tree of life."

[109.] James H. Degnan and Noah A. Rosenberg, "Gene tree discordance, phylogenetic inference and the multispecies coalescent," Trends in Ecology and Evolution, 24 (2009): 332-340.

[110.] Arcady R. Mushegian, James R. Garey, Jason Martin and Leo X. Liu, "Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes," Genome Research, 8 (1998): 590-598.

[111.] Elie Dolgin, "Rewriting Evolution," Nature, 486: 460-462 (June 28, 2012).

[112.] Liliana M. Dávalos, Andrea L. Cirranello, Jonathan H. Geisler, and Nancy B. Simmons, "Understanding phylogenetic incongruence: lessons from phyllostomid bats," Biological Reviews of the Cambridge Philosophical Society, 87:991-1024 (2012).

[113.] For example, see BSCS Biology: A Molecular Approach (Glencoe/McGraw Hill, 2006), 227; Sylvia S. Mader, Jeffrey A. Isaacson, Kimberly G. Lyle-Ippolito, Andrew T. Storfer, Inquiry Into Life, 13th ed. (McGraw Hill, 2011), 550.

[114.] See Michael S. Y. Lee, "Molecular Phylogenies Become Functional," Trends in Ecology and Evolution, 14: 177 (1999).

[115.]W. W. De Jong, "Molecules remodel the mammalian tree," Trends in Ecology and Evolution, 13(7), pp. 270-274 (July 7, 1998).

[116.] Trisha Gura, "Bones, Molecules or Both?," Nature, 406 (July 20, 2000): 230-233.

[117.] Antonis Rokas & Sean B. Carroll, "Bushes in the Tree of Life," PLoS Biology, 4(11): 1899-1904 (Nov., 2006) (internal citations and figures omitted).

[118.] Liliana M. Dávalos, Andrea L. Cirranello, Jonathan H. Geisler, and Nancy B. Simmons, "Understanding phylogenetic incongruence: lessons from phyllostomid bats," Biological Reviews of the Cambridge Philosophical Society, 87:991-1024 (2012).

Darwinism's quest for junk rolls on.

Why the "Onion Test" Fails as an Argument for "Junk DNA"

Jonathan M. November 2, 2011 6:00 AM

Briefly stated, the often cited "onion test" observes that onion cells have many times more DNA than human cells do. And since the onion is considered to be relatively simple as compared to us, this discrepancy -- it is argued -- can only be accounted for if the preponderance of its DNA is, in fact, junk or non-functional. Let's see whether the concept really holds any water.

The term "onion test" was first coined in April 2007 by the Canadian evolutionary biologist and genome biologist T. Ryan Gregory. In a post on his blog, Gregory wrote,

I am not sure how official this is, but here is a term I would like to coin right here on my blog: "The onion test." The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

The onion, Allium cepa, is a diploid (2n = 16) plant with a haploid genome size of about 17 pg. Human, Homo sapiens, is a diploid (2n = 46) animal with a haploid genome size of about 3.5 pg. This comparison is chosen more or less arbitrarily (there are far bigger genomes than onion, and far smaller ones than human), but it makes the problem of universal function for non-coding DNA clear.

Further, if you think perhaps onions are somehow special, consider that members of the genus Allium range in genome size from 7 pg to 31.5 pg. So why can A. altyncolicum make do with one fifth as much regulation, structural maintenance, protection against mutagens, or [insert preferred universal function] as A. ursinum?

There you have it. The onion test. To be applied to any ambitious claims that a universal function has been found for non-coding DNA.

This phenomenon is but one example of a larger issue typically known as the "C-value enigma." The C-value enigma describes the lack of correlation (among eukaryotes) between genome size and organismal complexity; a phenomenon which, curiously, does not extend to prokaryotic domains. The human genome comprises about 3 billion base pairs of DNA: Compare this to the genome size ofAmoeba dubia (670,000,000,000 bp). Indeed, the human genome is only marginally bigger than that of C. elegans and D. melanogaster. Among amphibians, the smallest genomes are just shy of 10 billion base pairs, while the largest are nearly 10^11 base pairs.

When I wrote on this subject at Uncommon Descent, Larry Moran protested that "[t]he Onion test is not about proving the existence of junk DNA and its not about explaining the C-Value Paradox,"but, rather, it's "a test for those people -- like Jonathan Wells -- who think that most of our genome has a function." He further wrote,

I hate to break it to you Jonathan M, you being such a great scientist and all, but the Onion Test is not an argument for junk DNA. It's a test of possible functional explanations. (Didn't I mention that already?) Jonathan M has completely misunderstood the Onion Test. Would it surprise you, dear readers, to learn that Jonathan Wells also flunks the test...This isn't rocket science."

This is a curious claim, not least because T. Ryan Gregory clearly wrote his original blog post with the intent of arguing that much of our DNA is junk. Indeed, he writes,

I do not endorse the use of the term "junk DNA," which I think has deviated far too much from its original meaning and is now little more than a loaded buzzword; the descriptive term "non-coding DNA" is what I use to refer to the majority of eukaryotic sequences (of various types) that do not encode protein products...Some non-coding DNA certainly has a function at the organismal level, but this does not justify a huge leap from "this bit of non-coding DNA [usually less than 5% of the genome] is functional" to "ergo, all non-coding DNA is functional."

While this may be true, as Jonathan Wells has noted, "it is the trend, more than the current total, that should worry any defender of junk DNA." Moran also claims that the "onion test" is not synonymous with the C-value enigma, but he doesn't make the difference very clear.

As I noted previously, the argument is only valid if one can justify the presumption that genome size has no bearing on organismal physiology. The problem is that this assumption can be demonstrated not to be the case.

Transcription Delays and Developmental Timing Mechanisms

Presumably a reflection of the selective-pressure on transcriptional economy with respect to highly expressed genes, genes that are highly expressed tend to have short introns (Castillo-Davis et al., 2002). Other genes are rich in introns: such as the 2400 kb human dystrophin gene, 99% of which is comprised of introns. The time taken to transcribe this gene into mRNA adds up to about 16 hours (Tennyson et al., 1995). To take another example, consider the Y chromosomal loci of Drosophila, which are very long (spanning millions of bases and consisting largely of introns): For instance, a locus such as DhDhc7(Y) is transcribed over the course of two to three days to give rise to a ~5,100,000 nucleotide pre-mRNA (see Reugels et al., 2000; Piergentili et al., 2007; and Redhouse et al., 2011). The time taken to transcribe respective stretches of DNA is not inconsequential to physiological fitness: Indeed, Swinburne and Silver (2010) report that "transcriptional delays have been shown to contribute to developmental timing."

On this, Larry Moran was curiously silent. Responding to the same article, Nick Matzke remarked that "if most of the genome has merely 'sequence independent' function, then Stephen Meyer's statement that the genome is 'chock-full of information' is unsupportable." While there is no doubt that SOME of the genome has a "sequence independent function," it is doubtful that most of the genome falls into such a category. Matzke is mistaken because, if the genetic elements possess a function, the design inference is not negated, even if that function is independent of exact sequence. Even in the case of repetitive DNA, the sequence can be highly relevant (see this paperby Richard Sternberg and James Shapiro on "Why Repetitive DNA is Essential to Genome Function"). Moreover, even if the function is sequence independent, there still might be specified complexity, triggering an explicit design inference.

Alternative Splicing and Genome Size

A second point I made was that the phenomena of alternative splicing and alternative polyadenylation may have some explanatory power when it comes to accounting for the C-value enigma. Alternative splicing allows the exons of pre-mRNA transcript to be spliced into a number of different isoforms to produce multiple proteins from the same transcript. I stated that the level of alternative splicing exhibited in humans (more than 90%, with an average of 2 or 3 transcripts per gene) is much higher than that for C. elegans (about 22%, with less than 2 transcripts per gene), and argued that this may, in part, explain why humans have only marginally more genes than C. elegans, which is otherwise seemingly paradoxical given the complexity of humans as compared to the roundworm. On this point, Moran wrote,

I don't agree with the facts. I don't think it's true that most human genes produce multiple functional copies of mRNA by alternative splicing.

But let's assume that it's true. Let's assume that a large fraction of putative junk DNA is there because it promotes alternative splicing. Why do onion cells need so much more alternative splicing and why do related species of onion differ so much in their need for alternative splicing? That's what the Onion Test asks.

On this point, Moran is not just in disagreement with me, he is also out-of-date with the literature by about ten years! As this 2008 article from Science Daily reports,

Nearly all human genes, about 94 percent, generate more than one form of their protein products, the team reports in the Nov. 2 online edition of Nature. Scientists' previous estimates ranged from a few percent 10 years ago to 50-plus percent more recently.

"A decade ago, alternative splicing of a gene was considered unusual, exotic ... but it turns out that's not true at all -- it's a nearly universal feature of human genes," said Christopher Burge, senior author of the paper and the Whitehead Career Development Associate Professor of Biology and Biological Engineering at MIT.

Wang et al. (2008), moreover, report in Nature,

Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analyses in which sequence reads are mapped to exon-exon junctions indicated that 92-94% of human genes undergo alternative splicing, ~86% with a minor isoform frequency of 15% or more.

Moran also misunderstands the point of the argument, since it is not onion cells which would exhibit more alternative splicing but human ones (hence explaining why their genome size need not be as big as it might otherwise be). At any rate, this phenomenon on its own is not sufficient to account for the C-value enigma. Indeed, it is only one of a plethora of factors that make the issue far more complex than it is often portrayed.

Transcription Factors

I also noted that approximately 10% of human genes code for transcription factors (a special class of protein that binds to specific sequences of DNA, namely, enhancers or promoters which are adjacent to genes they regulate the expression of). In contrast, only about 5% of yeast genes code for transcription factors. When coupled with a much larger network of transcriptional enhancers and promoters, such a difference could result in a much larger set of gene expression patterns. This could lead to a non-linear increase in organismal complexity (see Levine and Tjian, 2003). Larry Moran conceded that "[he doesn't] even understand this point." Clearly, he didn't even bother to look up the cited paper. For if he had, he would have read the following:

The yeast genome encodes a total of 300 transcription factors; this includes both sequence-specific DNA-binding proteins and subunits of general transcription complexes such as TFIID9. In contrast, the genome sequences of C. elegans andDrosophila reveal at least 1,000 transcription factors in each organism. There may be as many as 3,000 transcription factors in humans. It would appear that organismal complexity correlates with an increase in both the ratio and absolute number of transcription factors per genome. Yeast contains an average of one transcription factor per 20 genes, while humans appear to contain one factor for every ten genes.Given the combinatorial nature of transcription regulation, even this twofold increase in the number of factors could produce a dramatic expansion in regulatory complexity. [emphasis added]

Limiting Factors

Another point missed by Moran and Matzke is that there are limiting factors on an organism's genome size. For example, in 2002, Andrew George published a paper in Trends in Immunologytitled, "Is the number of genes we possess limited by the presence of an adaptive immune system?" In the paper, he argued that gene count is limited by the presence of an adaptive immune system because of the potential for of self-recognition. As the paper explains,

The factors that are important in limiting the number of functional genes contained within the genome of an organism are presently unknown. Here, it is suggested that in organisms that contain an adaptive immune response, the number of genes in the genome might be limited by the need to delete autoreactive T cells, thus preventing autoimmunity. The more genes an organism has, the more autoantigens are generated, necessitating an increase in the proportion of T cells that are deleted. Is human complexity limited by the presence of an immune system? Although immunity is vital for health, the need to be tolerant to all "self" molecules could restrict the number of genes in our genome.

In a further correlation that has been established, organisms with rapid development typically have lower C-values, presumably because they don't have time to replicate lots of DNA between cell divisions.

In The Myth of Junk DNA, Jonathan Wells observes,

There is a strong positive correlation, however, between the amount of DNA and the volume of a cell and its nucleus -- which affects the rate of cell growth and division. Furthermore, in mammals there is a negative correlation between genome size and the rate of metabolism. Bats have very high metabolic rates and relatively small genomes. In birds, there is a negative correlation between C-value and resting metabolic rate. In salamanders, there is also a negative correlation between genome size and the rate of limb regeneration

In the case of bacteria, which have single replicons per chromosome, they face selective pressure to limit the accumulation of non-genic DNA which might make the replication times longer and thus slow rates of reproduction. This means that their genome size is correlated with gene number, and thus increases in proportion to structural and metabolic complexity.

On this point, the detractors have also remained oddly silent.

Genome Size and Cell Volume

A final point: For creatures as diverse as vertebrates, plants and protozoa (unicellular eukaryotes), there is a positive correlation between genome size and cell volume. Cavalier-Smith and others have suggested that DNA possesses a "structural role" in controlling nuclear volume, cell size and cell-cycle length.

Moran and Matzke want to know whether this phenomenon is a cause or an effect. Cavalier-Smith's view of "skeletal DNA," advocated in the cited paper, would suggest that "larger cells need more DNA," and that "smaller ones need less." Indeed, he explains that "If cell size declines, the nucleus will be too large compared with the cytoplasm for optimal efficiency and the drain on the cell's resources for replicating all that extra DNA and making all the histones it needs will be uneconomic." So, deletions are selectively favored over duplications. In the case of larger cells, the reverse is the case. When the cell size increases, Cavalier-Smith explains, "there is positive selection for a corresponding increase in nuclear volume; it is generally easier to achieve this by increasing the amount of DNA rather than by altering its folding parameters." Cavalier-Smith argues that the abundance of transposons (arising by duplication) is an effect (and not a cause) of the larger genomes. The larger amount of DNA thus provides a selective advantage by contributing to the skeleton and volume of the nucleus.

Conclusion

The so-called onion test, or indeed the "C-value enigma," is predicated on unsupportable assumptions about the physiological effects of -- and/or requirements for -- larger genomes, many of which are contradicted by the scientific evidence. As we learn ever more about the nature and functional inter-dependency of the genome, as the extent of genomic "dark matter" continues to shrink, those who continue to advocate the view that the preponderance of our genome is non-functional should find these facts disconcerting.

The ancient roots of Darwinism

1. Ancient Greek Views

Evolution is not so much a modern discovery as some of its advocates would have us believe. It made its appearance early in Greek philosophy, and maintained its position more or less, with the most diverse modifications, and frequently confused with the idea of emanation, until the close of ancient thought. The Greeks had, it is true, no term exactly equivalent to " evolution"; but when Thales asserts that all things originated from water; when Anaximenes calls air the principle of all things, regarding the subsequent process as a thinning or thickening, they must have considered individual beings and the phenomenal world as, a result of evolution, even if they did not carry the process out in detail. Anaximander is often regarded as a precursor of the modem theory of development. He deduces living beings, in a gradual development, from moisture under the influence of warmth, and suggests the view that men originated from animals of another sort, since if they had come into existence as human beings, needing fostering care for a long time, they would not have been able to maintain their existence. In Empedocles, as in Epicurus and Lucretius, who follow in Hs footsteps, there are rudimentary suggestions of the Darwinian theory in its broader sense; and here too, as with Darwin, the mechanical principle comes in; the process is adapted to a certain end by a sort of natural selection, without regarding nature as deliberately forming its results for these ends.

If the mechanical view is to be found in these philosophers, the teleological occurs in Heraclitus, who conceives the process as a rational development, in accordance with the Logos and names steps of the process, as from igneous air to water, and thence to earth. The Stoics followed Heraclitus in the main lines of their physics. The primal principle is, as with him, igneous air. only that this is named God by them with much greater definiteness. The Godhead has life in itself, and develops into the universe, differentiating primarily into two kinds of elements the finer or active, and the coarser or passive. Formation or development goes on continuously, under the impulse of the formative principle, by whatever name it is known, until all is once more dissolved by theekpyrosis into the fundamental principle, and the whole process begins over again. Their conception of the process as analogous to the development of the seed finds special expression in their term of logos spermatikos. In one point the Stoics differ essentially from Heraclitus. With them the whole process is accomplished according to certain ends indwelling in the Godhead, which is a provident, careful intelligence, while no providence is assumed in Heraclitus.

Empedocles asserts definitely that the sphairos, as the full reconciliation of opposites, is opposed, as the superior, to the individual beings brought into existence by hatred, which are then once more united by love to the primal essence, the interchange of world-periods thus continuing indefinitely. Development is to be found also in the atomistic philosopher Democritus; in a purely mechanical manner without any purpose, bodies come into existence out of atoms, and ultimately entire worlds appear and disappear from and to eternity. Like his predecessors, Deinocritus, deduces organic beings from what is inorganic-moist earth or slime.

Development, as well as the process of becoming, in general, was denied by the Eleatic philosophers. Their doctrine, diametrically opposed to the older thoroughgoing evolutionism, had its influence in determining the acceptance of unchangeable ideas, or forms, by Plato and Aristotle. Though Plato reproduces the doctrine of Heraclitus as to the flux of all things in the phenomenal world, he denies any continuous change in the world of ideas. Change is permanent only in so far as the eternal forms stamp themselves upon individual objects. Though this, as a rule, takes place but imperfectly, the stubborn mass is so far affected that all works out as far as possible for the best. The demiurge willed that all should become as far as possible like himself; and so the world finally becomes beautiful and perfect. Here we have a development, though the principle which has the most real existence does not change; the forms, or archetypal ideas, remain eternally what they are.

In Aristotle also the forms are the real existences, working in matter but eternally remaining the same, at once the motive cause and the effectual end of all things. Here the idea of evolution is clearer than in Plato, especially for the physical world, which is wholly dominated by purpose. The transition from lifeless to living matter is a gradual one, so that the dividing-line between them is scarcely perceptible. Next to lifeless matter comes the vegetable kingdom, which seems, compared with the inorganic, to have life, but appears lifeless compared with the organic. The transition from plants to animals is again a gradual one. The lowest organisms originate from the primeval slime, or from animal differentiation; there is a continual progression from simple, undeveloped types to the higher and more perfect. As the highest stage, the end and aim of the whole process, man appears; all lower forms are merely unsuccessful attempts to produce him. The ape is a transitional stage between man and other viviparous animals. If development has so important a work in Aristotle's physics, it is not less important in his metaphysics. The whole transition from potentiality to actuality (from dynamis toentelecheia) is nothing but a transition from the lower to the higher, everything striving to assimilate itself to the absolutely perfect, to the Divine. Thus Aristotle, like Plato, regards the entire order of the universe as a sort of deification. But the part played in the development by the Godhead, the absolutely immaterial form, is less than that of the forms which operate in matter, since, being already everything,, it is incapable of becoming anything else. Thus Aristotle, despite his evolutionistic notions, does not take the view of a thoroughgoing evolutionist as regards the universe; nor do the Neoplatonists, whose highest principle remains wholly unchanged, though all things emanate from it.

2. Medieval Views

The idea of evolution was not particularly dominant in patristic and scholastic theology and philosophy, both on account of the dualism which runs through them as an echo of Plato and Aristotle, and on account of the generally accepted Christian theory of creation. However, evolution is not generally denied; and with Augustine (De civitate dei, xv. 1) it is taken as the basis for a philosophy of history. Erigena and some of his followers seem to teach a sort of evolution. The issue of finite beings from God is called analysis or resolution in contrast to the reverse ordeification the return to God, who once more assimilates all things. God himself, although denominated the beginning, middle, and end, all in all remains unmixed in his own essence, transcendent though immanent in the world. The teaching of. Nicholas of Cusa is similar to Erigena's, though a certain amount of Pythagoreanism comes in here. The world exhibits explicitly what the Godhead implicitly contains; the world is an animated, ordered whole, in which God is everywhere present. Since God embraces all things in himself, he unites all opposites: he is thecomplicatio omnium contradictoriorum. The idea of evolution thus appears in Nicholas in a rather pantheistic form, but it is not developed.

In spite of some obscurities in his conception of the world Giordano Bruno is a little clearer. According to him God is the immanent first cause in the universe; there is no difference between matter and form; matter, which includes in itself forms and ends, is the source of all becoming and of all actuality. The infinite ether which fills infinite space conceals within itself the nucleus of all things, and they proceed from it according to determinate laws, yet in a teleological manner. Thus the worlds originate not by an arbitrary act, but by an inner necessity of the divine nature. They arenatura naturata, as distinguished from the operative nature of God, natitra naturans, which is present in all thin-S as the being- of all that is, the beauty of all that is fair. As in the Stoic teaching, with which Bruno's philosophy has much in common, the conception of evolution comes out clearly both for physics and metaphysics.

The Mystery revealed.

BABYLON THE GREAT

Among John’s visions recorded in the book of Revelation appear pronouncements of judgment against “Babylon the Great,” as well as a description of her and of her downfall.—Re 14:8; 16:19; chaps 17, 18; 19:1-3.

In Revelation 17:3-5, Babylon the Great is described as a woman arrayed in purple and scarlet, richly adorned, and sitting upon a scarlet-colored wild beast having seven heads and ten horns. Upon her forehead a name is written, “a mystery: ‘Babylon the Great, the mother of the harlots and of the disgusting things of the earth.’” She is also depicted as sitting on “many waters” representing “peoples and crowds and nations and tongues.”—Re 17:1-15.

The luxury and the dominion attributed to Babylon the Great do not allow for simply equating her with the literal city of Babylon in Mesopotamia. After ancient Babylon fell to Cyrus the Persian in 539 B.C.E., it lost its position as a dominant world power, its captives, including the Jews, being freed. Although the city continued to exist even beyond the days of the apostles, and hence existed in John’s day, it was no longer a city of world importance, and it eventually fell into decay and utter ruin. Thus, Babylon the Great must be viewed as a symbolic city, one of which the literal city of Babylon was the prototype. Because the ancient city gives the mystic city its name, it is helpful to consider briefly the outstanding features of Babylon on the Euphrates, features that provide clues as to the identity of the symbolic city of John’s vision.

Characteristics of Ancient Babylon. The founding of the city of Babylon on the Plains of Shinar was concurrent with the attempt at building the Tower of Babel. (Ge 11:2-9) The popular cause to be advanced by the tower and city construction was, not the exaltation of God’s name, but that the builders might “make a celebrated name” for themselves. The ziggurat towers uncovered not only in the ruins of ancient Babylon but elsewhere in Mesopotamia would seem to confirm the essentially religious nature of the original tower, whatever its form or style. The decisive action taken by Jehovah God to overthrow the temple construction clearly condemns it as of a false religious origin. Whereas the Hebrew name given the city, Babel, means “Confusion,” the Sumerian name (Ka-dingir-ra) and the Akkadian name (Bab-ilu) both mean “Gate of God.” Thus the remaining inhabitants of the city altered the form of its name to avoid the original condemnatory sense, but the new or substitute form still identified the city with religion.

The Bible lists Babel first when giving the ‘beginning of Nimrod’s kingdom.’ (Ge 10:8-10) Throughout the Hebrew Scriptures the ancient city of Babylon is featured prominently as the longtime enemy of Jehovah God and his people.

Though Babylon became the capital of a political empire in the seventh and sixth centuries B.C.E., it was outstandingly prominent during its entire history as a religious center from which religious influence radiated in many directions.

Professor Morris Jastrow, Jr., in his work The Religion of Babylonia and Assyria (1898, pp. 699-701), says regarding this: “In the ancient world, prior to the rise of Christianity, Egypt, Persia, and Greece felt the influence of the Babylonian religion. . . . In Persia, the Mithra cult reveals the unmistakable influence of Babylonian conceptions; and if it be recalled what a degree of importance the mysteries connected with this cult acquired among the Romans, another link will be added connecting the ramifications of ancient culture with the civilization of the Euphrates Valley.” In conclusion he refers to “the profound impression made upon the ancient world by the remarkable manifestations of religious thought in Babylonia and by the religious activity that prevailed in that region.”

Babylon’s religious influence is traced eastward to India in the book New Light on the Most Ancient East, by archaeologist V. Childe (1957, p. 185). Among other points he states: “The swastika and the cross, common on stamps and plaques, were religious or magical symbols as in Babylonia and Elam in the earliest prehistoric period, but preserve that character also in modern India as elsewhere.” Thus, ancient Babylon’s religious influence spread out to many peoples and nations, much farther and with greater potency and endurance than did her political strength.

Like mystic Babylon, the ancient city of Babylon, in effect, sat on the waters, located, as it was, astride the Euphrates River and having various canals and water-filled moats. (Jer 51:1, 13; Re 17:1, 15) These waters served as a defense to the city, and they provided the thoroughfares upon which ships brought wealth and luxuries from many sources. Notably, the water of the Euphrates is depicted as drying up prior to Babylon the Great’s experiencing the wrath of divine judgment.—Re 16:12, 19.

Distinguishing Features of Mystic Babylon. The symbolic woman bearing the name Babylon the Great is “the great city that has a kingdom over the kings of the earth,” a kingdom that allows her, in effect, to sit on “peoples and crowds and nations and tongues.” (Re 17:1, 15, 18) A kingdom over other kingdoms and nations is what is defined as an “empire.” Babylon the Great places herself above earthly kings, exercising power and influence over them. She rides the symbolic seven-headed beast, beasts being used elsewhere in the Bible as symbols of political world powers.—See BEASTS, SYMBOLIC.

Some scholars assume that Babylon the Great is a political empire, either Babylon or Rome. We have already seen that Babylon as a political empire had long since ceased to exist when John received his prophetic vision. As to Rome, the nature of its political rule does not harmonize with the description of Babylon the Great’s course and her methods of dominating. She is a harlot, committing fornication with the kings of the earth, making them drunk with the wine of her fornication, misleading the nations by her “spiritistic practice.” (Re 17:1, 2; 18:3, 23) Rome’s dominion, by contrast, was gained and maintained by its ironlike military might and its firm application of Roman law among its provinces and colonies. Recognizing this fact, The Interpreter’s Dictionary of the Bible says: “It is not sufficient to identify Rome and Babylon. Babylon embraces more than one empire or culture. It is defined rather by dominant idolatries than by geographical or temporal boundaries. Babylon is coextensive with the kingdom of that beast which has corrupted and enslaved mankind, and whom the Lamb must conquer (Rev. 17:14) if mankind is to be freed.”—Edited by G. Buttrick, 1962, Vol. 1, p. 338.

The symbol of a harlot or a fornicatrix is used frequently in the Hebrew Scriptures. The nation of Israel was warned against entering into covenant relations with the nations of Canaan because this would lead them to commit “immoral intercourse [“play the harlot,” RS] with their gods.” (Ex 34:12-16) Both Israel and Judah apostatized from the true worship of Jehovah God and were condemned by him as having engaged in harlotry, prostituting themselves to the political nations and their gods. (Isa 1:21; Jer 3:6-10, 13; Eze 16:15-17, 28, 29, 38; Ho 6:10; 7:11; 8:9, 10) It may be noted here that God was not viewing Israel or Judah as mere political entities entering into relations with other political governments. Instead God reprimanded them on the basis of their being in a sacred covenant with him, hence responsible to be a holy people devoted to him and his pure worship.—Jer 2:1-3, 17-21.

A similar usage of this figure is found in the Christian Greek Scriptures. The Christian congregation is likened to a virgin espoused to Christ as her Head and King. (2Co 11:2; Eph 5:22-27) The disciple James warned Christians against committing spiritual adultery through friendship with the world. (Jas 4:4; compare Joh 15:19.) The fornications of Babylon the Great and her “daughters” are of a similar nature and not some unique exception. (The term “daughters” at times is employed in the Bible to refer to the suburbs or surrounding towns of a city or metropolis, as the “dependent towns” [literally, “daughters” in Hebrew] of Samaria and Sodom; see Eze 16:46-48.)

An additional significant factor is that when Babylon the Great goes down under the devastating attack of the ten horns of the symbolic wild beast, her fall is mourned by her companions in fornication, the kings of the earth, and also by the merchants and shippers who dealt with her in supplying luxurious commodities and gorgeous fineries. While these political and commercial representatives survive her desolation, notably no religious representatives are depicted as still on the scene to share in mourning her downfall. (Re 17:16, 17; 18:9-19) The kings of the earth are shown as having judgment executed upon them sometime after mystic Babylon’s annihilation, and their destruction comes, not from the “ten horns,” but from the sword of the King of kings, the Word of God.—Re 19:1, 2, 11-18.

A further distinguishing characteristic of Babylon the Great is her drunkenness, she being pictured as “drunk with the blood of the holy ones and with the blood of the witnesses of Jesus.” (Re 17:4, 6; 18:24; 19:1, 2) She thus is the spiritual counterpart of the ancient city of Babylon, expressing the same enmity toward the true people of God. Significantly, it was to the charge of religious leaders that Jesus laid the responsibility for “all the righteous blood spilled on earth, from the blood of righteous Abel to the blood of Zechariah.” While those words were addressed to religious leaders from among Jesus’ own race, the Jewish nation, and while persecution against Jesus’ followers was particularly intense from that sector for a time, history shows that thereafter the opposition to genuine Christianity came from other sources (the Jews themselves suffering considerable persecution).—Mt 23:29-35.

All the above factors are significant, and they must all be considered in arriving at a true picture of symbolic Babylon the Great and what it represents.

Revelation17NKJV

17 Then one of the seven angels who had the seven bowls came and talked with me, saying to me,[a]“Come, I will show you the judgment of the great harlot who sits on many waters, 2 with whom the kings of the earth committed fornication, and the inhabitants of the earth were made drunk with the wine of her fornication.”

3 So he carried me away in the Spirit into the wilderness. And I saw a woman sitting on a scarlet beast which was full of names of blasphemy, having seven heads and ten horns. 4 The woman was arrayed in purple and scarlet, and adorned with gold and precious stones and pearls, having in her hand a golden cup full of abominations and the filthiness of her fornication.[b] 5 And on her forehead a name was written:

MYSTERY, BABYLON THE GREAT,

THE MOTHER OF HARLOTS

AND OF THE ABOMINATIONS

OF THE EARTH.

6 I saw the woman, drunk with the blood of the saints and with the blood of the martyrs of Jesus. And when I saw her, I marveled with great amazement.

The Meaning of the Woman and the Beast

7 But the angel said to me, “Why did you marvel? I will tell you the mystery of the woman and of the beast that carries her, which has the seven heads and the ten horns. 8 The beast that you saw was, and is not, and will ascend out of the bottomless pit and go to perdition. And those who dwell on the earth will marvel, whose names are not written in the Book of Life from the foundation of the world, when they see the beast that was, and is not, and yet is.[c]

9 “Here is the mind which has wisdom: The seven heads are seven mountains on which the woman sits.10 There are also seven kings. Five have fallen, one is, and the other has not yet come. And when he comes, he must continue a short time. 11 The beast that was, and is not, is himself also the eighth, and is of the seven, and is going to perdition.

12 “The ten horns which you saw are ten kings who have received no kingdom as yet, but they receive authority for one hour as kings with the beast. 13 These are of one mind, and they will give their power and authority to the beast. 14 These will make war with the Lamb, and the Lamb will overcome them, for He is Lord of lords and King of kings; and those who are with Him are called, chosen, and faithful.”

15 Then he said to me, “The waters which you saw, where the harlot sits, are peoples, multitudes, nations, and tongues. 16 And the ten horns which you saw on[d] the beast, these will hate the harlot, make her desolate and naked, eat her flesh and burn her with fire. 17 For God has put it into their hearts to fulfill His purpose, to be of one mind, and to give their kingdom to the beast, until the words of God are fulfilled. 18 And the woman whom you saw is that great city which reigns over the kings of the earth.”

The late Charles Townes on evidence of design in the cosmos.

More from Nobel Laureate Charles Townes on Scientific Evidence of Design and Purpose in the Cosmos

Casey Luskin January 28, 2015 7:35 PM | 

Earlier I noted the passing of Dr. Charles Townes, the Nobel Prize-winning physicist. In case you wondered if Townes's comment on intelligent design in cosmology, which I quoted, was just a stray remark not representative of his general thinking, in fact he made a number of comments over the years that are clearly favorable to a design perspective. He told Esquire makgazine:

The laws of physics are very special, and the creation of human life is really quite striking. One has to believe that either it was planned or it was a fantastically improbable accidentCharles Townes, quoted in Scott Carrier, "What I've Learned: Charles H. Townes,"Esquire (November 30, 2001).)

Likewise, in accepting the Templeton Prize in 2005, he stated:

Increasingly, science is showing how special our universe and we are, which has raised questions about whether it was indeed planned or influenced -- one of many examples where science and religion naturally interact. The British physicist, Fred Hoyle, who was skeptical that there was any creation of the universe, nevertheless wrote, after he discovered how remarkable nuclear properties produced important chemical elements, "Would you not say to yourself, 'some super-calculating intellect must have designed the properties of the carbon atom?' Of course you would. A common sense interpretation of the facts suggests that some super intellect has monkeyed with physics -- and there are no blind forces worth speaking about in nature."

(Charles Townes, "Comments at the Templeton Prize Press Conference," New York City (March 9, 2005).

Note how he cites Fred Hoyle. How ironic that recent critics of Eric Metaxas excoriated him for quoting Hoyle -- the very same quote used by a Nobel laureate physicist in support of cosmic design.

Townes was also a man with a deep Christian commitment who believed that faith was vital to practicing good science, and that faith deserves credit for rescuing humanity from superstition:

Faith is necessary for the scientist even to get started, and deep faith is necessary for it is

 necessary for him to carry out his tougher tasks. Why? Because he must have confidence that there is order in the universe and that the human mind -- in fact his own mind -- has a good chance of understanding this order. Without this confidence, there would be little point in intense effort to try to understand a presumably disorderly or incomprehensible world. Such a world would take us back to the days of superstition, when man thought capricious forces manipulated his universe. In fact, it is just this faith in an orderly universe, understandable to man, which allows the basic change from an age of superstition to an age of science, and has made possible our scientific progress.

The necessity of faith in science is reminiscent of the description of religious faith attributed to Constantine: "I believe so that I may know." But such faith is now so deeply rooted in the scientist that most of us never even stop to think that it is there at all.

(Charles Townes, "The Convergence of Science and Religion," IBM's Think Magazine, Volume 32, pp. 2-7 (March-April, 1966).

Townes said something similar when accepting the Templeton Prize:

My own view is that, while science and religion may seem different, they have many similarities, and should interact and enlighten each other. ... If the universe has a purpose or meaning, this must be reflected in its structure and functioning, and hence in science. In addition, to best understand either science or religion, we must use all of our human resources -- logic, evidence (observations or experiment), carefully chosen assumptions, intuition, and faith. ... Many people don't realize that science basically involves assumptions and faith...We must make the best assumptions we can envisage, and have faith. And wonderful things in both science and religion come from our efforts based on observations, thoughtful assumptions, faith, and logic.

It's true that Townes apparently accepted standard scientific views about biological evolution. But when it came to the origin of the cosmos, he argued that the best scientific, not religious, explanation was intelligent design.