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Dynamic
genomes,
morphological stasis,
and the origin of irreducible complexity
Wolf-Ekkehard Lönnig
Max-Planck-Institut for Plant Breeding Research, Carl-von-Linné-weg 10
50829
Abstract
In spite of an
enormous amount of genetic flux in plants and animals, the basic genetic
processes and major molecular traits are believed to have persisted essentially
unchanged for more than three-and-a-half billion years, and the
molecular mechanisms of animal ontogenesis for more than one billion years. Moreover, 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 hypothesesmight point to a non-gradualistic solution of
the problem.
Correspondence/Reprint request: Dr. Wolf-Ekkehard Lönnig, Max-Planck-Institut
for Plant Breeding Research,
Carl-von-Linné-weg 10, 50829 Cologne, Germany. E-mail: loennig@mpiz-koeln.mpg.de
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. Moreover, by relatively infrequent mutations the genes could produce
alleles thus providing the basis for evolution in Mendelian populations.
Additional variation for evolution was guaranteed by equally rare gross and
small chromosome mutations, which would rearrange the genes by duplications,
inversions, and translocations (including varying position effects of gene
functions) as well as by multiplications of single chromosomes (trisomy) or
entire chromosome sets (polyploidy).
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 further details, see [3, 4, 46, 69]).
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
A reversal of the previous
ideas of the constancy of the genome only occurred in the 1960s when gene
structure and gene regulation were more profoundly elucidated (Jacob-Monod
model, bacterial insertion sequences and transposon-encoded antibiotic
resistance). 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’. Also, this constituted a fresh impetus for many
research groups around the world to concentrate or expand their work not only
on transposable elements but also on a range of further dynamical aspects of
the genomes in the plant and animal kingdoms, most of
which are briefly mentioned below.
As for the question whether
this transformation of ideas from an overall rather constant genome to a
strongly dynamic one was of any consequences for the
theories regarding the origin of species, we will come back to this cardinal
point under the subtitle of “new research topics (f)”.
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:
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 billions
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 (to mention just
a
few of the many further spectacular examples) [3, 4, 9, 40, 46, 50,
61-64,
79, 87]. 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 106 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) [30,
45,
71].
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]. But even within
the same non-polyploid plant species the C-value can vary
notably
even though some original examples for this phenomenon
proved to be
due to technical problems [8].
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. In
addition to some morphological features, many
closely
related plant and animal species can also be distinguished by
more
or less small chromosome rearrangements [64].
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 [25, 26].
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].
For further examples for dynamic aspects of the genome, see the present volume
(V(D)J recombination, VNTR alleles, horizontal
DNA-transmission and others).
Genetic conservation
Becoming fully aware of the
features specifying dynamic genomes
as mentioned above, the overall impression most students of genetics inevitably
have gained, could perhaps best be stated with the Greek philosopher Thales von
Milet (about 625 BC to ca. 546/545 BC), describing the essence of nature by his
famous verdict: panta rei, ouden menei (“all things flow, nothing abides”). For
almost ‘everything’ in the plant and animal genomes
seems to be in a permanent process of flux so that in the long run one should
hardly expect any constant genomic (and corresponding morphological)
characters at all.
Thus, being cognizant of this
background information presented on the overall genetic flux in most genetic
papers, reviews and textbooks [e.g. 30, 40, 85], the
following description of some further basic genetic facts appears to be
absolutely astounding.
Lazcano and Miller report [48]:
“After the explosive metabolic that took place soon
after the beginning
Of life, the basic genetic processes and major molecular
traits have
persisted essentially
unchanged for more than three-and-a-half billion
years, perhaps owing
to the linkages of the genes involved and the
complex interactions between
different metabolic routes. At a
macroevolutionary level,
this represents a case of conservation that
is even more striking
than the maintenance of the major body plans
that appeared at the
base of the Cambrian, and which have remained
basically unchanged
for 600 million years.”
Moreover, at the beginning of the
1990s, a series of discoveries of utterly unforeseen constant or almost
constant gene functions in developmental biology had led to a chain of comments
describing the extraordinary amazement elicited by these findings. The
following few examples may convey the extent of astonishment, which had seized
most minds of the biological community at that time:
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 a similar vein De Robertis commented [20]:
“[I]t is safe to say that no one would have predicted
the degree of
conservation in the
molecular mechanisms that control development....
the molecular mechanisms
that determine the antero-posterior (A-P)
axis has been conserved in
evolution to a degree beyond anyone's
wildest expectations...”
Nüsslein-Volhard speaks of such facts thus [74]:
“[O]ne great surprise of the past five years has been
the discovery
that very similar basic
mechanisms, involving similar genes and
transcription factors,
operate in early development throughout the
animal kingdom.”
Lewin illustrated the problem by the example of the Hox loci [49]:
“The most striking feature of organization of the Hox
loci still
defies explanation: why has
the organization of the cluster,
in which genomic position
correlates with embryonic expression,
been maintained in
evolution?”
Subsequently he discussed several possibilities to answer the question,
but thinks that no convincing solution could be given at present.
Hultmark compared vertebrates with insects and commented on some
molecular similarities as follows [42]:
“Insects look nothing like vertebrates,
and their organ systems
seem to be built on entirely
different principles. Nevertheless, as
we get a better
understanding of how these systems operate at
the molecular level,
unexpected similarities are emerging. Among
them must must now be
counted similarities in the respective
immune defences, as reported
in two recent papers.”
Even more staggering were the discoveries of molecular similarities
involved in the development of supposedly fully convergent anatomical features.
After an account onnumerous molecular similarities
within the vertebrates, Cohn and Tickle continue [11]:
“Even more remarkable is the conservation of
molecules involved
in patterning insect wings
and vertebrate limbs. Signalling
molecules common to
vertebrates and Drosophila limbs include Shh
(hh), Wn 7a (wg) and Bmp
(dpp). The recent finding that chick
LMX1 and the related apterous gene in Drosophila are
expressed
dorsally in wing buds and
imaginal discs is striking.”
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.
Thus, the “basic genetic processes
and major molecular traits” are thought to have “persisted essentially
unchanged for more than three-and-a-half billion years”, and the molecular
mechanisms of animal ontogenesis for more than a billion years. On the
background of the prevailing idea of the synthetic theory from the 1940s well
into the 1990s, 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’ (Shapiro), as well as that of the many features of dynamical genetics
as briefly summed up above (beginning in the 1960s and reaching its climax in
the early 1990s), the discovery of the molecular conservation just documented
was, indeed, ‘totally unexpected’ (Shapiro) and revealed, in fact, a constancy
of gene functions ‘to a degree beyond anyone's wildest expectations’ (De
Robertis).
Similar phenomenon have been described in
plants, too [90].
Now, the fact that so many
“old features” are molecularly still with us, nearly inevitably leads us to the
basic biological question whether there are correspondingly constant morphological features in the plant and animal kingdoms –
which point will be the topic of the next paragraphs.
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] - and we would like to invite
our readers to especially focus their attention on the use of the terms
“invariable” (invariably), “invariableness” and “constant” in the ensuing
paragraph:
“By
Species (species), we understand a number of plants, which agree with one
another in invariable marks. In this matter every thing depends upon the idea
of invariableness. When an organ, or property of
it is changed neither by difference of soil, of climate, or of treatment, nor by continued
breeding, this organ or property is said to be invariable. 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)... By
a Genus we understand the sum of the species which
agree in certain constant
properties of the essential parts... The generic
character (character genericus) is the expression of the peculiar and
invariable marks by which a genus of plants is distinguished from all
others... every generic character must state shortly and distinctly
the common marks which belong invariably to all species of the same genus…
The generic character of the higher plants is borrowed solely from the
organs of fructification.”
Since these expositions
on “invariableness” in systematics are almost 200 years old and were, indeed,
first published 40 years before Darwin’s Origin of Species in 1859, let us
directly turn to some comments of modern systematics on the same questions. One
hundred and thirty years later Stace comments in agreement with almost all
contemporary authors [80]:
“Although
flowers are no longer regarded as ‘essential’ and therefore taxonomically
particularly important, they still provide the bulk of information contained in
the diagnosis of angiosperm taxa. This is because in general the flowers appear
to be more conservative than do most other organs.”
In an earlier chapter Stace
had already remarked that “This reliance on the flower is remarkable when one
considers that most of the time the majority of angiosperms lack any flowers at
all”. This appears to be also true for seed- and fruit-structures. Concerning
the conservative key systematic characters he further points out that
“endomorphic vegetative characters are more conservative than exomorphic ones”
and continues on p. 183 of his book [80]:
“Conservative
characters are...most useful in delineating the higher taxa, where the emphasis
is on the recognition of similarity between the members of a taxon.”
Yet, for species and systematic categories below the species, he insists
that the non-conservative characters seem to dominate.
Considering the general shift in systematics during the last 250 years, Stace
is most probably correct in his analysis (Haeckel’s verdict for zoology that
“related species which had been united within a genus by Linné and within a
family by Cuvier, now constitute an inclusive order with several families and
many genera” [41] – implying that many of Linné’s species have been elevated to
the position of genera during the last centuries – is also valid for botany;
for further details, see [53]). Hence, 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
Taking the descriptions and
definitions of the plant species produced by Linné some 250 years ago in his
Species Plantarum (1753) or of the animal species in his Regnum Animale a few
years later (Systema Naturae 1758), we have no difficulty in identifying the
different species today on the basis of his descriptions [51, 52]. The same is
true for the drawings and descriptions of plant species by Leonhard Fuchs (1542)
[31], and Tabernaemontanus (1588/1590) [88] on maize and many other plants.
Moreover, Cuvier had absolutely no difficulty in identifying the mummified
animals of old
If some 250 to 500 or even several
thousand years is simply nothing on an evolutionary time scale, what about the
last 2.3 million years of European life history? This is characterized by
“comparatively slow rates of evolution” [47], and Lang continues: “At the end
of the tertiary the organisms consisted of species, almost all of which can be
assigned to present genera, a large section even to living species. This
applies not only for the European flora but also for its fauna” and appears to
be true for other parts of the world, too. Moreover the environmental
conditions for this time period have been characterized as excessively varying,
temperatures rising and falling producing among other effects a series of ice
ages – and 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”.
Additionally,
about half of the genera of flowering plants found in geological formations
dated to be 37 million years old have been assigned to present genera [81], and
many well-known present plant families and genera have even been identified in
cretaceous formations (taxa sometimes dated to be older than 100 million years
before present).
Or, to take a glimpse at another well-known plant group, the bryophytes.
Agashe reports [1]:
“Members
of both the major groups of bryophytes, i.e. Hepaticopsida (liverworts) and
Bryopsida (mosses), are well represented in the known fossils. However, 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.”
Thus, bryophytes are assumed to have existed "almost
unchanged" for some 400 million years on earth.
A comprehensive survey about
the phenomenon of constancy in the fossil record is beyond the scope of the
present paper (for further details, see [10, 27-29, 35-38, 53, 58, 64, 68,
86]). The theory of punctuated equilibrium [27-29, 35-38], was developed to
come to grips with the general phenomenon of abrupt appearance and stasis (constancy of the gestalt of organisms usually
documented for millions of years) in the fossil record. The well-known “living
fossils” in the restricted definition of the term (“They must today exhibit
primitive morphological characters, having undergone
little evolutionary change since dwindling to low diversity at some time in the
past” [82]) are referring only to a very small minority of life forms also
revealing that general phenomenon of abrupt appearance and constancy described
by the theory of punctuated equilibrium as deduced from the paleontological documents
[58].
Ernst Mayr, the doyen of the modern synthesis, has just recently called
the phenomenon of morphological stasis
(constancy) one of the basic unresolved problems of evolutionary theory
specifying the problem in a recent interview as follows [67]:
“In
evolutionary biology we have species like horseshoe crabs. The horseshoe crab
goes back in the fossil record over two hundred million years without any major
changes. So obviously they have a very invariant genome type, right? Wrong,
they don't. Study the genotype of a series of horseshoe crabs and you'll find
there's a great deal of genetic variation. How come, in spite of all this
genetic variation, they haven't changed at all in over two hundred million
years while other members of
their ecosystem in which they were living two
hundred million years ago are either extinct or have developed into something
totally different? Why did the horseshoe crabs not change? That's the kind of
question that completely stumps us at the present time.”
All the living fossils investigated so far also reveal most or all of
the dynamics of genome reshuffling as pointed out to above – from transposable
elements to multiple promoters and enhancers.
In this context the point should be
emphasized again that examples like the horseshoe crab are by no means rare
exceptions from the rule of gradually evolving life forms in
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" [76].
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.”
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
furtherapparatus 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. For, 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. And this
could mean no less than the enormous time periods mentioned for all the living
fossils hinted at above. 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 inpaleontolgy. Instead, most life forms appear abruptly,
remain constant, and disappear equally abrupty from the world’s scene (for the
details, see [10, 27-29, 35-38, 53, 58, 64, 68, 86]. 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
byintegrating further correspondingly specified and useful parts into their
overall organization, which prima facie could be an improbably process – or
perish.
Thus, it appears to be
entirely clear that irreducible complexity of biological systemsand/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”, which are thought to have “persisted essentially unchanged
for more than three-and-a-half billion years”, and the perseverance of the
molecular mechanisms of animal ontogenesis for more than a billion years
equally well.
According to Behe and
several other authors [5-7, 21-23, 53-60, 68, 86] the only adequate hypothesis
so far known for the origin of irreducibly complex systems is intelligent
design (ID), a hypothesis, whose scientific basis will be further discussed in
the following paragraphs in connection with Dembski’s criterion of specified
complexity.
Dembski’s definition of specified complexity as a scientific
tool explaining the origin of irreducible complexity
In three monographs 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, for whose mathematical formulation and
exemplary composition the interested reader is referred to Dembski’s monographs
(in the ensuing paragraphs again a few unsophisticated but illustrative
examples, mostly following Dembski, may besufficient for our present purposes):
(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 1030).
However, if a certain
series is
specified before (or independently of) the event and the
event is found
to be identical with the series, the inference to ID is
already practiced
in everyday life).
(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 4,000 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 10150 – the most conservative
of several
others (Borel: 1 in 1050, National Research Councel: 1 in
1094;
Loyd: 1 in 10120 – for the details see again [23])
“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” [23]. For instance, regarding the origin of the
bacterial flagellum, Dembski calculated a probability of 10-234 [22]
(for further points, see below).
Yet, if we assume with the Dembski
and Behe that organisms in general display signs of specified and often also
irreducible complexities, this does not mean that the extant 100,000,000 or so morphological species of plants and animals [53] have
directly been originated by ID. On the contrary, usually a combination of
several of the factors specifying the dynamics of the organism’s genomes as enumerated above, appears to be sufficient to
have generated more than 99.99% of such species, albeit not necessarily in a
gradualistic manner [53, 55, 56], nor due to the input of new complex
information [53, 63, 64]. Or, to state one essential aspect of the question in
Ohno’s pointed words on dispensable genes, which appear to be especially
relevant for neutral and regressive evolution: “...the notion that all the
still functioning genes in the genome ought to be indispensable for the well
being of the host should be abandoned once and for all" [75]. However, as
further explicated below, the hypothesis of a link between the genetic
potential of a primary species and ID should also be considered.
The systematic stasis referred to above is generally valid only for higher
systematic categories from (many) genera upwards (i.e. genera, families,
orders, classes, phyla). 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).
New research topics
On the strictly scientific level the
combination of stasis and ID does not mean the end of
enquiry (as is sometimes objected), but the very beginning of entirely new
research programmes. For several questions have to be thoroughly investigated
before valid scientific inferences can be suggested. To name but a few:
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. Since there are hardly any entirely
non-redundant systems in biology, the irreducibly complex core systems have to
be discovered and scientifically be defined and analyzed on the levels just
mentioned. Closely associated with that task is the problem of developing
realistic models for the initial/primary biological boundary conditions for the
origin of new putative irreducibly complex systems, i.e. for thoroughly
delineating the gap between them and hypothetical evolutionary precursors.
Dembski’s improbability calculation of of 10-234 for the origin of
the bacterial flagellum quoted above constitutes nothing but a first
potentially falsifiable hypothesis in that research programme [7, 64].
b) Granted that such systems
can be established, the correlation between the organism/species and its
different environmental conditions have to 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) [46, 53, 63]. Problem (b) is intimately
connected with the question for the boundaries of morphological
variation of functional phenotypes [53, 55, 56]. In
simple terms, a part of the ID research programme could thus be put: 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? Although it seems that many gene functions specifying constant
generic and higher systematic characters are somehow (and this ‘somehow’ is a
research programme of its own) integrated in a correlated web of interdependent
cascades in Behe`s sense, nevertheless 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. For instance, in terms of population
density, reproductive success, and geographical distribution, the house sparrow
(Passer domesticus) is much more successful than the peacock (Pavo cristatus),
whose males display the ingenious beauty of its fanned tail to perform
courtship display and mate with a female – yet often also inviting a tiger for
an easy prey and meal. In the plant kingdom the orchid family is one of several
groups providing a range of further intricate ornamental as well as functional
structures (e.g. the extreme examples of the reproductive organs of Coryanthes
and Catasetum, which have posed enormous problems for gradualism [57]), whilst
most plant species survive – again often much more successfully in the terms
just mentioned above – by much simpler devices. Even independently of the fact
that the often quoted answer of sexual selection for the origin of the
peacock’s tail (and similar examples) in itself poses a series of further
unsolved problems [53] and, what is more, can hardly be applied to plants, the
ensuing questions have to be investigated: 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?
e) Also, there exist many
constant features delineating morphological
speciesand 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. Let’s have a look at an event, which has repeatetly
occurred in wild as well as in cultivated species: originally red flowering
plant species have irreversibly lost their ability to generate anthocyanin –
and these species might produce white flowers almost forever. Other
possibilities to generate rather stable features by mutations include buffering
gene functions by gene duplications and polyploidy. On the other hand,
mutations in essential gene functions involved in the formation of species- or
genera-specific structures, – functions, which were originally buffered by
accessory redundant genes – could become regularly lethal after mutational loss
of that redundancy.
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]. Assuming an original vast
genetic potential for functional morphologic deviations – to what extend is
specified and irreducible complexity relevant for that originally purely
potential part of genetic variation realized in time and space of the history
of a genus? [53] Moreover, several transposon specialists have, in fact,
postulated rapid species formations by transposable elements (thus we are
coming back to the question posed at the end of the introduction): concurring
with McClintock [69], Syvanen [87] stated: "I believe that transposons
have the potential to induce highly complex changes in a single event".
Also, Shapiro [79] is convinced that "there must exist
mechanisms for large-scale, rapid reorganisations of diverse sequence elements
into new configurations" for the integrated mosaic genome to make
evolutionary sense. However, to date hardly any positive experimental evidence
can be cited for this view [46, 53, 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, e.g. can TEs be
key factors in releasing a dormant genetical potential possibly displaying the
marks of ID – say a master regulator with a set of corresponding target genes –
for abrupt morpho-species formations?
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
Nevertheless, in the face of all
the different dynamic genetic mechanisms generating
enormous masses of quantitatively and qualitatively different DNA sequence
variations as shown above – the question may be raised whether is it really necessary to postulate ID for the origin of
basic structures and processes of living organisms.
In the following paragraphs, we
will discuss a few of the points that could be relevant for this question:
A fait accompli is that during the
last few hundred years at least 680 animal species have died out (and presently
at least 5,438 are critically endangered/endangered or
vulnerable) and at least 449 plant species have become extinct
(37,969 plant species are threatened) [44, 89]. As far as these species are
concerned, all the impressive possibilities and quantities of DNA sequence
variations known so far have indisputably not been sufficient to avoid the
extinction of these species.
However, it could be objected
that most of these extinctions are due to environmental shifts in the wake of
human activities, which happened too fast for nature to follow, and that there
is, in fact, evidence for the hypothesis that there has existed an enormous
genetic potential for a wide range of environmental adaptations in many plant
and animal genera and/or families, yet within certain physiological, anatomical
and morphological boundaries, producing altogether
the some 100,000,000 morpho-species mentioned above (for a detailed discussion,
see again [53]).
On the other hand, 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
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). Whether the totality of factors
contributing to the genomic dynamism with all the above named mutagenic
consequences can solve the questions posed remains doubtful – in several cases
the systems to be explained have been well-known for more than a hundred years:
Utricularia, Coryanthes, Catasetum and others have already been investigated by
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
emperically investigated. Also, the concepts are potentially falsifiable in actual
research (Popper) and thus clearly belong to the realm of science.
--------------------------------------------------------------------------
Note: 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 are 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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