Dynamic Genomes, Morphological Stasis and the Origin of Irreducible Complexity

For purely educational purposes, let's review the next excerpts from the excellent article:

Lönnig, Wolf-Ekkehard. Dynamic genomes, morphological stasis and the origin of irreducible complexity, Dynamical Genetics, Pp. 101-119.

From the Abstract:

"…systematics is based on virtually constant characters in space and time – otherwise this important branch of biology would not be possible. Additionally, the fossil record displays a regular pattern of abrupt appearances of new life forms (instead of their arrival by innumerable small steps in a Darwinian manner), followed by the constancy of higher systematic characters often from the genus level upwards, in many cases succeeded by an equally abrupt disappearance of the major life forms, which have died out after different periods of time. As the doyen of the synthetic theory, Ernst Mayr of Harvard, has just recently admitted, this constancy (stasis) of life forms in the face of tremendously dynamic genomes is one of the greatest problems of contemporary evolutionary biology and demands an explanation. In agreement with several researchers, I refer to arguments and facts supporting the view that irreducible complexity (Behe) in combination with specified complexity (Dembski) characterize basic biological systems and that these hypotheses might point to a non-gradualistic solution of the problem."

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From the Introduction:

"Up to the 1950s the genome was imagined to consist of rather autonomous genes positioned on chromosomes like beads on a string specifying organismic development from their fixed locations."

"In spite of the variation deemed to be necessary for evolution, the comprehensive message was that of rather constant genes in an overall fairly constant genome so much so that when Barbara McClintock proposed her first papers on the discovery of transposable elements (TEs) as parts of evidently much more dynamic genomes to a larger audience at the beginning of the 1950s, her work was either ignored, or met with “puzzlement”, or, in some cases, even “hostility” "

"For the question of the origin of species and higher systematic categories including humans, the dominant genetic view of the 1950s meant a pervasively slow, continuous and gradualistic mode of evolution in the sense defined by Darwin some 100 years earlier."

"...When molecular biology further advanced to clone and sequence eukaryotic genes, the disinterest, puzzlement, and hostility of the 1950s rapidly transformed into approval and recognition of McClintock's merits, culminating in the Nobel Prize for Physiology/Medicine in 1983 – a Nobel Prize, as it were, for the discovery of ‘dynamic genomes’."

Dynamic genomes:

"The ensuing paragraphs present a brief reminder enumerating most of the different aspects of genomic changes so far known, followed by some simple illustrative explanations:

1) Gene mutations; average rate 10^-5 per gene per generation. For the present generation of humans, this means that each gene has recurrently mutated more than 100,000 times (more than 6,2 billion individuals, some 30,000 to 40,000 genes).

2) Transposons – active and dormant (transpostion rate into functional genes up to 10^-2 per generation); nearly 80% of the overall DNA mass of the maize genome appears to consist of transposon-derived sequences, 90% in Vicia faba, 45% in Homo sapiens... At present there is a lively discussion among biologists whether most of these sequences really constitute “junk” DNA and how much may be of functional value [34, 84].

3) Repetitive elements; detected in eukaryotes, their length varies from tens to thousands of bases. The highly repetitive fraction (5-100 bp) is repeated up to 10^6 times and consists of simple sequence DNA (constitutive heterochromatin, especially clustered close to chromosome ends and the centromere). The middle repetitive fraction consists of 100-500 bp, which occur ca. 100 to about 10,000 times in a genome (e.g. genes for coding for ribosomal RNA, transfer RNA, histones)...

4) Pseudogenes; a derivative of a functional eukaryotic gene thought to be produced by reverse transcription of messenger RNA and generally assumed to be non-functional due to rearrangements, disadvantageous point mutations (producing, for instance, stop codons), and absence of promoter-, intron-, and enhancer sequences. However, some functional exceptions have recently been detected [2, 34, 39, 43].

5) Gene duplication and amplification; thought to be up to 20 times more frequent than gene mutations [56]; up to 10% of the cells in animal and human tissue cultures can have gene amplifications [49, 50].

6) C-value-paradox; due to transposon-induced and further changes in DNA mass, the DNA amounts in the haploid genomes of closely related species, can differ enormously from each other (species of the genus Vicia, for example, vary between 1.8-13.3 pg [72, 73]...

7) Gene- and genome amplification in ontogenetic development; rDNA amplification in Xenopus is one of the prime examples: in its oogenesis the 500 rDNA genes are replicated 4,000 times resulting in 2,000,000 copies; gene amplication is also found in some insects and protozoa [45]. On the other hand, genome amplification occurs regularly in special tissues of many organisms (e.g. in liver cells of mammals, in tapetum tissue of angiosperms).

8) Chromosome rearrangements: include any structural change of a chromosome resulting in deletions, duplications, inversions, and translocations...

9) Molecular clocks: nucleotide and amino acid substitutions were once believed to occur so regularly that a molecular clock measuring divergence time between different groups of plants and animals could be established. Although the clock seems to run often very irregularly, there is no question that many substitutions due to point mutations have occurred within and between species. In man the substitution rate was found to be faster in mitochondria than in the nucleus [32, 33].

10) Molecular drive: according to Gabriel Dover, a cohesive mode of ‘species’ evolution relevant for many gene families and noncoding sequences perhaps as a consequence of molecular mechanisms of turnover within the genome...

11) Flax genotrophs: different forms of flax (Linum usitatissimum) generated by a process of environmentally induced changes in flax genomes, which “does not appear to be the generation of random variation”. Cullis et al. assume that the heritable changes in this species are due to specific rearrangements at distinct positions of the genome. Highly repetitive, middle-repetitive, and low-copy-number sequences have all been shown to be involved in the polymorphisms detected, and sequence alterations of specific subsets of 5SrDNA have been identified [13, 14].

12) Methylation: methyl transferases can transfer a methyl group from a methyl donor to an acceptor molecule (DNA, RNA, protein). Could be important for the regulation of gene functions in natural populations [12].

13) Genomic shocks: extreme stress situations for genomes (artificially produced, for instance, by protoplast generation and tissue cultures in plant cells) are thought by B. McClintock to bring about accelerated species formation [69].

14) Exon shuffling: intron-mediated recombination of exons is assumed to produce new functional genes.

15) Gene expression: due to alternative splicing and alternative promoters thousands of protein isoforms can be generated from a few genes [70]."

From Genetic conservation:

"Shapiro concurs as follows [78]:

"I think it was a big surprise when a human cDNA clone was found to correct a cdc mutation in yeast. One has only to read News and Views in Nature to find many similar examples. This was really a surprise to people. The degree of conservation in function between proteins from different organisms is something that was totally unexpected.”

He also mentioned the reason why this conservation was so totally unexpected:

"The prevailing idea was that each particular gene is going to accumulate many changes over long periods of time and that this was how one organism turned into another.” "

[in article, other expressions of unexpected amazement by Lazcano and Miller, De Robertis, Nüsslein-Volhard, Hultmark, Cohn and Tickle, and Lewin.]

"[Lewin] discussed several possibilities to answer the question, but thinks that no convincing solution could be given at present."

"No theorist in evolutionary biology will ever derive chicken and insects from a winged common ancestor, and yet, clearly related sequences are specifically expressed in wing buds and imaginal disks."

"…revealed, in fact, a constancy of gene functions ‘to a degree beyond anyone's wildest expectations’ (De Robertis)."

From Morphological stasis

The general constancy of systematically relevant features

"Two of the great pioneers of general and systematic botany, Augustin Pyrame De Candolle, and Christian Konrad Sprengel emphasized a point nearly forgotten in our evolutionary world of today when they made the following comments on the cardinal characters distinguishing species and genera from each other [19]"

"When, for instance, we have remarked for centuries, that Centifolia has always unarmed leaf-stalks, we say correctly, that this property of the Centifolia is invariable...What we know is, that from as early a time as the human race has left memorials of its existence upon the earth, the separate species of plants have maintained the same properties invariably...All properties of plants which are subject to change, form either a Subspecies (subspecies), or a variety (varietas)..."

"…one may conclude that the essentials have hardly changed in morphological systematics: The invariable characters delineating species and genera according to Linné, Cuvier, De Candolle, Sprengel and many other pioneers of systematics have become the conservative characters delineating higher taxa of modern systematics including the morphologically defined genera, tribus and families of today."

Stasis of systematic categories in time: Some examples

"…Lang continues: …

"in spite of all these environmental variations there was hardly any evolution at all. The actualistic inferences and conclusions drawn from present ecological indicator values to quaternary paleontology are based on “this obviously far-reaching constancy of life forms down to the species”.

"…many well-known present plant families and genera have even been identified in cretaceous formations…"

"…Agashe reports [1]:

"…a detailed comparative study with modern bryophytes indicated that the group has remained almost unchanged since the Paleozoic time. Hence the fossil bryophytes do not help us much in understanding evolution except for the fact that they formed a prominent part of the vegetation from the Paleozoic onwards.”

"Ernst Mayr [declared] "…Why did the horseshoe crabs not change? That's the kind of question that completely stumps us at the present time." "

"In fact, we are literally surrounded by “living fossils” in the present world of organisms when applying the term more inclusively as “an existing species whose similarity to ancient ancestral species indicates that very few morphological changes have occurred over a long period of geological time" [85]."

"Furthermore, Darwin’s argument of the imperfection of the geological record has systematically been refuted for many animal and plant groups during the last 150 years: some 200 million macrofossils have been accumulated and catalogued in museums worldwide and there are, indeed, billions of microfossils..."

"Nor is the phenomenon of this quite unexpected yet generally detected abrupt appearance and stasis of forms a discovery of recent research. Darwin himself commented such facts already in 1852 as follows: "When I see that species even in a state of nature do vary little and seeing how much they vary when domesticated, I look with astonishment at a species which has existed since one of the earlier Tertiary periods. This fixity of character is marvellous". "

"Including the observations and papers of Cuvier (1769-1832), who is generally known to be the founder of comparative anatomy as well as modern paleontology, this unsolved problem is at least 200 years old and hardly anybody denies that it demands a rational explanation."

"Now, since all these “old features”, morphologically as well as molecularly, are still with us, the basic genetical questions should be addressed in the face of all the dynamic features of ever reshuffling and rearranging, shifting genomes, (a) why are these characters stable at all and (b) how is it possible to derive stable features from any given plant or animal species by mutations in their genomes?"

The significance and origin of irreducibly complex systems in biology

"A first hint for answering the questions raised in last paragraph is perhaps also provided by Charles Darwin himself when he suggested the following sufficiency test for his theory [16]: “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” Darwin, however, stated that he could “not find out such a case” – which would, in fact, have invalidated his theory."

"Biochemist Michael J. Behe [5] has refined Darwin's statement by introducing and defining his concept of "irreducibly complex systems", specifying:

“By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.”

"Among the examples discussed by Behe are the origins of (1) the cilium, (2) the bacterial flagellum with filament, hook and motor embedded in the membranes and cell wall and (3) the biochemistry of blood clotting in humans. Moreover, the traps of Utricularia (and some other carnivorous plant genera) [59] as well as several further apparatus in the animal and plant world appear to pose similar problems for the modern synthesis (joints, echo location, deceptive flowers, etc.)."

"One point is clear: granted that there are indeed many systems and/or correlated subsystems in biology, which have to be classified as irreducibly complex and that such systems are essentially involved in the formation of morphological characters of organisms, this would explain both, the regular abrupt appearance of new forms in the fossil record as well as their constancy over enormous periods of time."

"…if “several well-matched, interacting parts that contribute to the basic function” are necessary for biochemical and/or anatomical systems to exist as functioning systems at all (because “the removal of any one of the parts causes the system to effectively cease functioning”) such systems have to (1) originate in a non-gradual manner and (2) must remain constant as long as they are reproduced and exist."

"...Moreover, an additional phenomenon would also be explained: (3) the equally abrupt disappearance of so many life forms in earth history. In a strict gradualistic scenario of the origin and evolution of life forms one would expect that – except in catastrophic events (also long denied in uniformitarian geology) like the Permian or Tertiary impacts – most species would continually adapt to varying environmental conditions. So most forms would not simply die out but continue to evolve gradually. However, this is not what has been found in paleontolgy."

"…most life forms appear abruptly, remain constant, and disappear equally abrupty from the world’s scene…"

"The reason why irreducibly complex systems would also behave in accord with point (3) is also nearly self-evident: if environmental conditions deteriorate so much for certain life forms (defined and specified by systems and/or subsystems of irreducible complexity), so that their very existence be in question, they could only adapt by integrating further correspondingly specified and useful parts into their overall organization, which prima facie could be an improbable process – or perish."

"Thus, it appears to be entirely clear that irreducible complexity of biological systems and/or correlated subsystems could explain the typical features of the fossil record and the foundations of systematics (morphological stasis – the basic constancy of characters distinguishing higher systematic categories) and the “basic genetic processes and major molecular traits” "

"According to Behe and several other authors... the only adequate hypothesis so far known for the origin of irreducibly complex systems is intelligent design (ID)..."

Dembski’s definition of specified complexity as a scientific tool explaining the origin of irreducible complexity

"...about the scientific criteria to testably distinguish between necessity, chance, and intelligent design (ID), Dembski [21-23] has proposed and elaborated the term “specified complexity” by incorporating five main factors to guarantee its applicability not only to diverse human branches of research (e.g. forensic science, cryptography, intellectual property law, random number generation, insurance claim investigation, archaeology, SETI), but also to the origin of species and higher systematic categories [22, 23]."

"To identify design, an event has to display the following five features:

(a) high probabilistic complexity (e.g. a combination lock with ten billion possible combinations has less probability to be opened by just a few chance trials than one with only 64,000).

(b) conditionally independent patterns (e.g. in coin tossing all the billions of the possible sequences of a series of say flipping a fair coin 100 times are equally unlikely (about 1 in 10^30)..."

(c) the probabilistic resources have to be low compared to the probabilistic complexity (refers to the number of opportunies for an event to occur, e.g. with ten billion possibilities one will open a combination lock with 64,000 possible combinations about 156,250 times; vice versa, however, with 64,000 accidental combinations, the probablity to open the combination lock with 10 billion possible combinations is only 1 in 156,250 serial trials).

(d) low specificational complexity (not to be confused with specified complexity): although pure chaos has a high probabilistic complexity, it displays no meaningful patterns and thus is uninteresting. “Rather, it’s at the edge of chaos, neatly ensconsed between order and chaos, that interesting things happen. That’s where specified complexity sits” [23].

(e) universal probability bound of 1 in 10^150 – the most conservative of several others (Borel: 1 in 10^50, National Research Councel: 1 in 10^94; Loyd: 1 in 10^120..."

“For something to exhibit specified complexity therefore means that it matches a conditionally independent pattern (i.e., specification) of low specificational complexity, but where the event corresponding to that pattern has a probability less than the universal probability bound and therefore high probabilistic complexity”

"For instance, regarding the origin of the bacterial flagellum, Dembski calculated a probability of 10^-234[22]"

"…Presently we count only about 18,750 extant plant genera and altogether some 7,000 animal families (for the details on this differentiation for plants and animals as well as the numbers given, see [53]). Thus, as to the origin and constancy (stasis) so regularly found in systematics and paleontology, it is essentially the constancy of the defining features of higher systematic categories that have to be explained genetically (not to mention the contribution to stasis by cell organelles, membranes, and cell walls)."

From New research topics:

"On the strictly scientific level the combination of stasis and ID does not mean the end of inquiry (as is sometimes objected), but the very beginning of entirely new research programmes…"

"(a) The hypothetical irreducible complexity of biological systems and/or correlated subsystems has first to be fully established on the different functional levels, i.e. genetically, anatomically, and physiologically..."

"(b) Granted that such systems can be established, the correlation between the organism/species and its different environmental conditions have to be carefully studied pertaining the question, to what extent a species can relinquish certain subsystems without selective disadvantages under special circumstances. Although a subsystem could be irreducibly complex as such, some organisms might florish without it (the topic of regressive evolution holds a large series of instructive examples for this question)... find the boundaries of functional phenotypic and physiological variation under different realistic environmental conditions"

"(c) Specified complexity is not necessarily irreducible. So, what could be the molecular connection/relation between specified complexity ‘only’ and the phenotypic constancy found in most of the higher systematic categories of living organisms? … some parts appear to be reducible in the sense given in paragraphs (b) and (e), and yet might display marks of specified complexity."

"(d) There appear to be many ornamental and even luxurious structures in the plant and animal kingdoms, structures that – from a purely functional point of view – do not seem to be absolutely necessary, to say the least... to what extend can specified and irreducible complexity be detected on the genetic, anatomical, and physiological levels of such more or less selectionally ‘neutral’ or even hypertrophic organismic structures, too, and can this research programme provide scientifically more realistic answers than those given so far?" [see original text for the examples of the peacock’s tail and the orchid family.]

"(e) Also, there exist many constant features delineating morphological species and genera from each other that are probably due to further factors than specified and irreducible complexity. For example, features due to losses of more or less redundant gene functions [63] affecting morphological features, but with a very low probability to revert or being counteracted by compensating mutations in other genes (modifiers), can be constant for all the time a species survives..." [see in original text the example of loss of flower pigment]

"(f) There are some indications that at least a part of biodiversity is, so to speak, predestined by the constitution of the genome and its mechanisms, possibilities, and limits to generate functional DNA-variations, including preferential insertions of transposons of an initial line or species [64]… A research project testing the possibilities and limits of species formation by TEs could also include the issue of the evidence for specified and irreducible complexity on the DNA- and morphological levels…"

"(g) Another question that should be investigated is, to what extent the correlations between the genome and its cellular surroundings (cell organelles, membranes, cell walls, physiological cascades and their interrelationships) can be lighted up and explained by a research programme addressing particularly specified and irreducible complexities in this area. For the first steps into such a research programme, see Behe [5] and Lönnig [53]."

Some basic objections

"…as to the candidates of irreducibly complex systems mentioned above (the cilium, bacterial flagellum, blood clotting, traps of Utricularia and some other carnivorous plant genera, joints, echo location, deceptive flowers as displayed by Coryanthes and Catasetum, etc.), it can be confidently stated that up to now, none of these synorganized systems has been satisfactorily explained by the modern synthesis or any other evolutionary theory."

"Nor has a testable naturalistic theory been advanced for the basic features of the fossil record (abrupt appearance of most life forms, stasis, and later often also abrupt disappearance)."

"…Additionally, natural selection itself may not have the stringency and power usually ascribed to it..."

"Last not least, it should perhaps be pointed out that research on irreducible and/or specified complexities in biology definitely do not constitute metaphysical research programmes, but is at least as scientifically valid as the SETI (search for extraterrestrial intelligence), which is presently supported by thousands of scientists worldwide, not to mention the affiliated network of more than 4 million computers in over 200 countries around the globe."

"(for an exhaustive discussion of further basic questions, see the contributions of Behe, Dembski, Lönnig, Meyer, and others [5-7, 21-23, 53-58, 68, 86])."

"Irreducible and specified complexity are inspiring tools that can and should be empirically investigated. Also, the concepts are potentially falsifiable in actual research (Popper) and thus clearly belong to the realm of science."

"It should be stated that the hypotheses of Behe and Dembski and my applications of them to the further biological phenomena as decribed above have been formulated in an intellectual climate of enormous tensions between different world views, often so much so that it seems to be necessary to point out that an author supporting ID is speaking not in the name of an institution, but gives his personal opinion. However, I am fully convinced that there is a range of cogent scientific arguments (of which some have been discussed above) encouraging open-minded researchers to carefully consider and investigate the topic within their different biological disciplines."

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To see some interesting comments on this paper, go to The Intelligent Design Weblog of William A. Dembski.

Example,

On June 23, 2005 PaV wrote,

"Let’s note that at the end of Lonnig’s article, he basically sets out an experimental program for ID.

I think it’s signifcant (and about time) that scientists take ID as a serious, and highly significant, “fact” of biological reality that looms on the horizon as a powerful heuristic approach to understanding life. He seems to be suggesting that ID is a kind of a mind-set–just as evolutionary theory might be–that the scientist might find useful as he explores, intellectually, and tries to explain, known biological evidence from field and lab studies alike. I think Lonnig has sounded the clarion call for a program of fruitful ID investigation. I hope lots of scientists hear this call."