"Nothing in biology makes sense except in the light of evolution"
        T. Dobzhansky, American Biology Teacher 35, (1973), pg 125.
 
 
 

"The same facts of comparative anatomy which proclaim unity also proclaim division; while resemblence suggests evolution, division, especially where it appears profound, is counter evidence against the whole notion of transmutation."
        M. Denton, Evolution:  A Theory in Crisis, 1986, pg 155.
 
 
 

"Every molecular comparison of various life forms is a "repeat observation" of evolution".
        D. Thomas, Albq. Trib., Aug 31, 1996.
 
 

"Perhaps it would be easier, and in the long run more productive, to abandon the attempt to force the data that Zuckerkandl and Pauling stimulated biologists to collect into the mold provided by Darwin."
    W. Ford Doolittle, "Phylogenetic Classification and the Universal Tree", Science 284 (1999),  p2124-2128.
 
 
 

"Circumstantial evidence is a very stricky thing," answered Holmes thoughtfully; "it may seem to point very straight to one thing, but if you shift your own point a little, you may find it pointing in an equally uncompromising manner to something entirely different" ....
        A. Conan Doyle, "The Boscombe Valley Mystery" in The Complete Sherlock Holmes,pg 79.
 
 
 
 
 
 
 
 
 

Goals:

Examine a few circumstantial evidences that are used as support for common ancestry

Demonstrate that circumstantial evidences are often presented selectively, and that evidence that contradicts the hypothesis of common ancestry is often omitted.

Understand the failure of homology

Survey the current status of molecular phylogenies

 
 
 
 
 

Outline:

I.  Homology

II.  Molecular phylogenies

III.  Embryology

IV.  The genetic code
 
 

 
 
 
 

I.  Homology

 
1).  Definitions and examples
2).  How can one tell the difference between homologous and analogous structures?
3).  Berra's Blunder
4).  Molecular sequence comparisons - strong verification or further muddling the picture?

 
 
 
 
 

        1).  Definitions and examples:
 

homologous  - morphological similarities believed to be due to common descent

analogous  -  morphological similarities believed to have evolved independently

        Examples:

                a.  pentadactyl pattern in vertebrate forelimbs
 
 

 Circumstantial-1

 

This resemblence is often cited as evidence of common ancestry

 
 
 
 
 
 
 

b.  pentadactyl pattern in vertebrate hindlimbs

"But the hindlimbs of all vertebrates also conform to the pentadactyl pattern and are stikingly similar to the forelimbs in bone structure and in their detailed embryological development.  Yet no evolutionist claims that the hindlimb evolved from the forelimb, or that hindlimbs and forelimbs evolved from a common source."
        M. Denton, Evolution:  A Theory in Crisis, 1986, pg 151.
 

"There is no doubt that in terms of evolution the fore- and hindlimbs must have arisen independently, the former supposedly evolving from the pectoral fins of a fish, the latter from the pelvic fins.  Here is a case of profound resemblence which cannot be explained in terms of a theory of descent.
       M. Denton, Evolution:  A Theory in Crisis, 1986, pg 151.
 

"Whatever the ultimate explanation for this remarkable pattern turns out to be, there seems little intellectual satisfaction in attributing one case of correpondence to evolution while refusing it in the other."
       M. Denton, Evolution:  A Theory in Crisis, 1986, pg 153.
 
 
 

c.  Certain marsupial and placental mammals

 Circumstantial-2

 
The placentals on the left and the marsupials on the right are said to have evolved independently.  In this view, all of the placentals are more closely related to each other than they are to any of the marsupials, and vice versa.  So the house mouse is believed to be more closely related to the gray wolf than to the marsupial mouse.
 
 

d.  Evolution of visual systems
 

Visual systems are present in six phyla.  These visual systems are very different and are believed to have evolved independently.  From phylogenies based on morphological characteristics, taxonomists think that eyes have evolved more than 40 times.

 How could and eye evolve?

But the Pax6 regulatory gene (called Ey in flies) that controls development of visual systems is very similar in five of the six phyla that have visual systems.

 

Explanation 1.  Convergence - the five different phyla evolved nearly the same gene independently by chance.  This is impossibly improbable, as attested to by the statements below:
 

"Because Pax-6 is involved in the genetic control of eye morphogenesis in both mammals and insects, the traditional view that the vertebrate eye and the compound eye of insects evolved independently has to be reconsidered."
        R. Quiring, U. Walldorf, U. Kloter, W. J. Gehring Science 265, 1994, 785.
 

"the hypothesis that the eye of cephalopods has evolved by convergence with the vertebrate eye is challenged by our recent finding of Pax-6-related sequences in the squid Loligo vulgaris.
        R. Quiring, U. Walldorf, U. Kloter, W. J. Gehring Science 265, 1994, 788.
 

Explanation 2.  Common ancestor - the Pax6 gene that regulates eye development existed in a common ancestor before eyes had evolved, presumably serving another function.  Somehow five phyla independently developed visual systems using this gene as a regulator.

 

 

2).  How can one tell the difference between homologous and analogous structures?
 

Answer:  To attribute simlarities to common ancestry one must show a "continuity of information."  The concept of homology breaks down because such a continuity of information does not hold.
 

The validity of the evolutionary interpretation of homology would have been greatly strengthened if embryological and genetic research could have shown that homologous structures were specified by homologous genes and followed homologous patterns of embryological development.  Such homology would indeed be strongly suggestive of "true relationship"; of inheritance from a common ancestor."  But it has become clear that the principle cannot be extended in this way.
        M. Denton, Evolution:  A Theory in Crisis, 1986, pg 145.
 

"Homologous structures are often specified by non-homologous genetic systems and the concept of homology can seldom be extended back into embryology."
        M. Denton, Evolution:  A Theory in Crisis, 1986, pg 145.
 
 
 

a.  developmental pathways

 
-similar developmental pathways may produce very dissimilar features

-similar features are often produced by very different developmental pathways

"it is the rule rather than the exception that homologous structures form from distinctly dissimilar initial states."
    P. Alberch Systematic Zoology, 34(1), 1985, 46-58.
 

The fact is that correspondence between homologous structures cannot be pressed back to similarity of position of the cells in the embryo, or of the parts of the egg out of which the structures are ultimately composed, or of developmental mechanisms by which they are formed.
        G. de Beer, Embryos and Ancestors, 1958, p 152.
 

"In some ways the egg cell, blastula and gastrula stages in the different vertebrate classes are so dissimilar that, were it not for the close resemblence in the basic body plan of all adult vertebrates, it seems unlikely that they would have been classed as belonging to the same phylum.

There is no question that, because of the great dissimilarity of the early stages of embryogenesis in the different vertebrate classes, organs and structures considered homologous in adult vertebrates cannot be traced back to homologous cells or regions in the earliest stages of embryogenesis.  In other words, homologous structures are arrived at by different routes."
        M. Denton, Evolution:  A Theory in Crisis, 1986, pg 145.
 

 Examples
 

It appears then that Darwin's usage of the term "homology", which he defines in the Originas that "relationship between parts which results from their development from  corresonding embryonic parts" is, as de Beer emphasizes, just what homology is not.
        M. Denton, Evolution:  A Theory in Crisis, 1986, pg 149.
 
 
 

        b. genes

- homologous structures need not be controlled by identical genes
 

"The evolutionary basis of homology is perhaps even more severely damaged by the discovery that apparently homologous structures are specified by quite different genes in different species."
        M. Denton, Evolution:  A Theory in Crisis, 1986, pg 149.
 

"Homologous structures need not be controlled by identical genes and homology of phenotypes does not imply similarity of genotype."
        G. De Beer, Homology:  An Unsolved Problem, 1971, pg 15.
 

"What mechanism can it be that results in the production of homologous organs, the same 'patterns', in spite of their not being controlled by the same genes?  I asked this question in 1938, and it has not been answered."
        G. de Beer, Homology:  An Unsolved Problem, 1971, pg 16

 
"Here then is a gene that is involved in the development of some structures unique to birds - air sacs and downy feathers - and of other structures such as lungs and kidneys, which occur in many other vertebrate classes.  This can only mean that non-homologous genes are involved to some extent in the specification of homologous structures."
        M. Denton, Evolution:  A Theory in Crisis, 1986, pg 149.

- non-homologous structures can arise from very similar genes
 

Pax6 gene (called Ey in flies) that controls development of very different, non-homologous visual systems
 

"Although mice have a gene very similar to the one that can transform a fly's antenna (Antennapedia) into a leg, mice do not have antennae and their corresponding gene affects the hindbrain."
        J. Wells and P. Nelson, Homology: A Concept in Crisis, Origins and Design 18(2), 1997 pg 15.
 

"The Dllgene encodes a homeodomain, a DNA-binding protein.  This protein is expressed during the embyonic development of such diverse (i.e. non-homologous) structures as the mouse limb, the sea urchin's tube feet and spines, and the velvet worm's lobopods and antennae."
        J. Wells and P. Nelson, Homology: A Concept in Crisis, Origins and Design 18(2), 1997 pg 18.

 
 
 

3.  Berra's Blunder

 
"If you compare a 1953 and a 1954 Corvette, side by side, then a 1954 and a 1955 model, and so on, the descent with modification is overwhelmingly obvious.  This is what paleontologists do with fossils, and the evidence is so solid and comprehensive that it cannot be denied by reasonable people."
    T. Berra, Evolution and the myth of creationism,1990, pg 117-119.

In fact, this example actually demonstrates that similarity can be due to an archtype in the mind of a designer!

 

4.  Molecular sequence comparisons - strong verification or further muddling the picture?

identifying homologous sequences is as problematic as identifying homologous organs or structures

"Some proponents of molecular techniques have claimed that molecular biology 'solves the problem of homology'.  ...  [but] the difficulties of assigning homology to molecules parallel many of the difficulties of assigning homology to morphological structures."
        David. M. Hillis, "Homology in Molecular Biology", in "Homology:  The Hierarchical Basis of Comparative Biology", p339-368.
 

"Congruence between molecular phylogenies is as elusive as it is in morphology",
        C. Patterson, D. M. Williams, C. J. Humphries, "Congruence between Molecular and Morphological Phylogenies", Ann. Rev. Ecology and Systematics 24 (1993) p 153-188.
 
 
 
 
 
 
 

II.  Molecular phylogenies
 

Data are obtained only from existing organisms, beyond that all is conjecture
 
 

Different molecules give different answers
 

Early expectation that data from more molecules would lead to a clearer answer "began to crumble a decade ago when scientists started analyzing a variety of genes from different organisms and found that their relationship to each other contradicted the evolutionary tree of life derived from rRNA analysis alone."

J. Lake, R. Jain, M. Rivera, Science283 (1999), p 2027-2028.

"With more and more sequences available, it turned out that most protein phylogenies contradict each other as well as the rRNA trees"

H. Philippe and P. Forterre, Journal of Molecular Evolution 49 (1999), p509-523.

"No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced.  Phylogenetic incongruities can be seen everywhere in the universal tree from its root to the major branchings within and among the various [groups] to the makeup of the primary groupings themselves".

C. Woese, Procedings of the National Academy of Sciences 95 (1998), pg 6854-6859.

"Clarification of the phylogenetic relationships of the major animal phyla has been an elusive problem, with analyses based on different genes and even different analyses based on the same genes yielding a diversity of phylogenetic trees."

M. Lynch, Evolution 53 (1999) p 323.
 

The problem is particularly bad with respect to major domains and kingdoms of life.  Microorganisms are found to be a mosaic of components and genes.    The hypothesis of a "simple" last common ancester has not been validated by the data.
 

"Each new prokaryotic genome that appears contains dozens, if not hundreds, of genes not found in the genomes of its nearest sequenced relatives but found elsewhere among Bacteria or Archaea."

W. Ford Doolittle Science 286, 1999.
 

Phillippe and Forterre performed perhaps the most rigorous and unbiased analysis, limiting their analysis to only the sequences which they believe evolve very slowly.   Their analysis points to a cell with a nucleus as the last common ancestor.

H. Philippe and P. Forterre, Journal of Molecular Evolution 49 (1999), p509-523.
 

Woese believes that the common ancester was "an evolutionarily communal state of living systems in the sense that the aboriginal organismal community evolved as a collective whole, not as individual cellular lineages".

C. Woese, Procedings of the National Academy of Sciences 97 (2000), pg 8396.
 

Hope for a basis for organizing molecular data into a tree of life (ancestor-decendent relationships) is dwindling.  This is attributed by some to lateral gene transfers.
 

the incongruities "are sufficiently frequent and statistically solid that they can neither be overlooked nor trivially dismissed on methodological grounds." ...  "It is time to question underlying assumptions".

C. Woese, Procedings of the National Academy of Sciences 95 (1998), pg 6854-6859.
 

"Perhaps it would be easier, and in the long run more productive, to abandon the attempt to force the data the Zuckerkandl and Pauling stimulated biologists to collect into the mold provided by Darwin."

W. Ford Doolittle, "Phylogenetic Classification and the Universal Tree", Science 284 (1999), p 2124-2128.
 

"Now new hypotheses, having final forms we cannot yet guess, are called for."

W. Ford Doolittle, "Uprooting the Tree of Life", Scientific American 282 (Feb. 2000), p 90-95.
 

"One of the key assumptions about the origin of life is under fire.  The widely held belief that all life on Earth today originated from a single ancestor cell is being challenged by a theory that several different lineages evolved independently.
    In his "doctrine of common descent" Darwin was the first to argue that all life on the planet began with single "primordial form", generally interpreted nowadays as the first living cell.  Not so, says Carl Woese of the University of Illinois at Urbana-Champaign.  In a controversial new theory published this week, he argues that the three fundamental types of cells that form the building blocks of present-day life actually evolved independently, not in an orderly succession from a common ancestor.

Andy Coghlan, New Scientist, 22 June 2002, pg 10.
 
 

Moreover, a recent analysis indicates that, even away from the active site, certain enzymes can tolerate very little variability before loss of function.  This seems to challenge the idea of continuous variability within sequence space, even for nominally closely related sequences.
 

"Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular.  Homologues sharing less than about two-thirds sequence identity should probably be viewed as distinct designs with their own sets of optimizing features."

D. D. Axe, J. of Molecular Biology, 2000, 301, 585.

The results of this analysis are presented in the "seascape representation" below:
 
 

 functional islands

 

Many patterns are consistent with morphology-based phylogenies, but patterns that conflict with morphology-based phylogenies also are found:

 
1996 study using 88 protein sequences grouped rabits with primates instead of rodents

1998 analysis of 13 genes in 19 animal species placed sea urchins among the chordates

1998 study based on 12 proteins put cows closer to whales than to horses

cited by J. Wells in Icons of Evolution, 2000, pg 51.
 
 

Tree of life (simple to complex, ancestor-descendent) versus independent clusters (major taxa separate, easily distinguishable)

 
Key prediction of common ancestry - increasing divergence on the molecular level with increasing taxonomonic distance (time from last branching point)

 

  Circumstantial-3

 

"...the most striking thing about the matrix is that each identifiable subclass of sequences is isolated and distinct.  Every sequence can be un ambiguously assigned to a particular subclass.  No sequence or group of sequences can be designated as intermediate with respect to other groups.  All the sequences of each subclass are equally isolated from the members of another group.  Transitional or intermediate classes are completely absent from the matrix."
        M. Denton, Evolution:  A Theory in Crisis, 1986, pg 280.
 
 

Drawing from the more complete data base, Denton gives the following examples:
 

"..no eukaryotic cytochrome is intermediate between the bacterial cytochrome and other eukaryotic cytochromes.

Examination of the sequential divergence among eukaryotic cytochromes reveals three basic subgroups:  the yeasts, the plants, and the animals. Each type is quite isolated.  Just as there are no intermediates to bridge the gap between prokaryotes and eukaryotes so there are no intermediate types among the three basic eukaryotic groups.

The same ordered isolation is seen when the plants are compared with other eukaryontes.  Similarly no animal cytochrome is intermediate between the animals and the other two eukaryotic groups.

At a still lower taxonomic level the same phenomenon is observed. ... it is clear that the insects and vertyebrates are closely related, but when comparisons are made between insect species and a variety of vertebrate groups, no vertebrate group is primitive or in any sense a link between phylum Arthropoda and phylum Vertebrata.  All the many diverse vertebrate types, including cyclosomes and mammals, are uniformly distant from the insects.

Each class is isolated and unique.  No classes are intermediate or partially inclusive of other classes.  The isolation of each class becomes greater as the taxonomic hierachy is ascended, but even relatively closely related classes such as insects and vertebrates are still clearly distinguished.

There is not a trace at a molecular level of the traditional evolutionary series: cyclosomes to fish to amphibian to reptile to mammal.  Incredibly, man is as close to lamprey as are fish!  None of the higher jawed vertebrate groups is in any sense intermediate between the jawless vertebrates and other jawed vertebrate groups.

When the various terrestrial vertebrate groups, amphibia, reptile, or mammal, are compared with fishes all are equally isolated. ...  At a molecular level there is no trace of the evolutionary transition from fish to amphibian to reptile to mammal.

etc. etc.

        quotes from M. Denton, Evolution:  A Theory in Crisis, 1986, pg 278-286

 
 

III.  Embryology

(under construction)
 
 

IV.  The genetic code

(under construction)