Group
Here is an article which throws doubt on one of the foundation stones
of evolution, namely homology, ie. similarity due to characteristics
derived from a common ancestor. Note the last paragraph:
"Homology, then, is an idealized principle that works under idealized
conditions, but such conditions almost never apply." This seems to be
saying that in the non-ideal, real world, determination of homologous
structures almost never apply?
If that is the case, then how do evolutionists know from the fossil
which fossils descended from which? They may look outwardly very similar
but if their genes were available and their developmental pathways known,
it might be discovered that in fact they were not closely related by
descent and their similarities were mere analogies.
When a staunch Darwinist like John Maynard Smith remarks that
homology has become "a word ripe for burning" then there is *big*
problems in the Darwinist camp.
Steve
=========================================================================
Evolutionary biology
Debatable homologies
Diethard Tautz
"Homology: Similarity in structure of an organ or a molecule, reflecting a
common evolutionary origin...." This is the definition of homology in a
contemporary textbook 1. But although the concept lies at the heart of
much of biology, it has become increasingly elusive. Has it therefore
become a word ripe for burning, as J. Maynard Smith (Univ. Sussex)
remarked at a meeting* on the topic? Or is it simply enough to know that
homology exists -- even though we cannot define it -- as D. Wake (Univ.
California, Berkeley) suggested in 1994 in a review 2 of a book 3
commemorating the 150th anniversary of Richard Owen's introduction of
the term?
Owen's original concept of homology did not have a phylogenetic
(evolutionary) perspective. It was based on the philosophy of identifying
and grouping similarities in nature, the 'scala naturae'. Such thinking was
exemplified by Charles Bonnet, who, in 1764, derived the following
similarity series: fish -- flying fish -- aquatic birds -- birds -- bats -- flying
squirrels -- tetrapods -- monkey -man (A. Panchen, Univ. Newcastle upon
Tyne). It is one of the great achievements of applying the principle of
homology that we can now confidently reject the idea that this series
reflects phylogenetic succession. On the other hand, however, we still do
not know the true answer on the phylogenetic descent of tetrapods, as
homology concepts tend to fail when it comes to tracing evolutionary
novelties.
Further challenges arise from molecular comparisons of developmental
genes. The finding that highly conserved 'master regulator' genes such as
Pax6/eyeless are involved in eye development in diverse phyla 4 brings into
question the idea of the independent evolution of eyes. Similarly, the
expression of distal-less homologues in insect and vertebrate legs, as well
as other body outgrowths 5, raises the issue of how often appendages can
arise independently. The problem goes even further -- with biotechnology
companies proposing to use such organisms as Drosophila or zebrafish as
models for understanding human diseases, it will eventually be investors
and shareholders who have to be convinced that invoking homology is
valid.
Taking phylogenetic continuity alone as the prime criterion for homology
causes the problem of circularity, because phylogenies are themselves
deduced from homologous characters. This of course can be avoided by
using a different set of characters for the phylogeny, such as those derived
from DNA sequences. But even in well-established phylogenies, it often
emerges that independent evolution of similar characters (convergence)
must have often occurred. There could, therefore, be dormant genes or
'latent homologies' that are not expressed in a particular 'stem' species, but
that have been regained after further speciation and give the erroneous
impression of convergence (A. Meyer, Univ. Konstanz).
Strict correspondence with phylogeny might also be less important if
homologues are viewed as coherent units of phenotypic evolution with
constraints on the developmental and variational properties (G. Wagner,
Yale Univ.). Applying such criteria, Wagner proposed a beautiful solution
to the old question of the way in which the digits on the limbs of the
urodeles, the newts and salamanders, are homologous to those of the other
tetrapods. In tetrapods, digits 3 and 4 are the first to develop and are also
the ones that are most stable against perturbations. In the urodeles, the
same seems to be the case for digits 1 and 2. So if 3 and 4 are homologous
to 1 and 2, digit 3 would be equivalent to digit 5 in tetrapods and digits 4
and 5 in the urodeles would be novel structures, albeit serially homologous
to the other digits. Closer study of developmental characteristics and
comparative analysis of Hox gene expression seem to confirm this view.
In molecular studies, the question of phylogenetic continuity becomes even
more blurred. As genes can duplicate in the genome, it has long been clear
that orthologous genes (which are related by phylogenetic common
descent) have to be distinguished from paralogous genes that result from
duplications within a genome. But if gene loss and re-duplications have to
be taken into account, things become even more complex and new
terminology may be required (P. Holland, Univ. Reading). Thus, sequence
similarities alone are not sufficient to infer homology of structures and
developmental processes. Instead, one should look for the conservation of
whole regulatory networks (E. Abouheif, State Univ. New York), a
concept that comes close to that of viewing homologues as coherent units.
But can we be sure that homologous morphological structures are made by
homologous gene networks? For example, closely related species of sea
urchin can develop directly into adults, or go through a feeding larva first,
yet end up with the same adult body plan. These species show different
embryonic cell lineages and differences in patterns of gene expression
during early development (R. Raff, Indiana Univ.)(Fig. 1). Intriguingly,
however, the embryos of hybrids between such species develop partly in a
composite and partly in radically new ways. Further study of these hybrids
should help in understanding evolutionary dissociations of genotype and
phenotype.
It has often been hypothesized that changes in regulatory interactions are
involved in dissociations of this sort, but practical work on the evolution of
regulatory modules (enhancers) has been scarce. Again, research on sea
urchins might pave the way forward. Their enhancers seem to consist of
sub-elements, which can be combined and integrated in different ways 6,
possibly making them perfect targets of evolutionary change (G. Wray,
State Univ. New York). But could this mean that we eventually have to
identify homologues in the individual parts of complex enhancers to
understand the homology of morphological structures? This would indeed
make the word ripe for burning.
Homology, then, is an idealized principle that works under idealized
conditions, but such conditions almost never apply. This is reminiscent of
the concept of the Hardy-Weinberg equilibrium in population genetics. It
exists only under idealized conditions, but it is the tracing of the reasons for
deviation from these conditions that is central to understanding the
evolution of populations. Could one apply a similar thinking to homology?
*Homology, Novartis Foundation, London, 21-23 July 1998. Proceedings
to be published by Wiley.
Diethard Tautz is in the Zoologisches Institut der Universit t Munchen,
Luisenstrasse 14, 80333 Munchen, Germany. e-mail: tautz@zi.biologie.uni-
muenchen.de
References
1. Alberts, B. et al. Molecular Biology of the Cell, 3rd edn (Garland, New
York, 1994). Links
2. Wake, D. B. Science 265, 268-269 (1994). Links
3. Hall, B. K. (ed.) Homology -- The Hierarchical Basis of Comparative
Biology (Academic, San Diego, California, 1994). Links
4. Quiring, R., Walldorf, U., Kloter, U. & Gehring, W. J. Science 265,
785-789 (1994). Links
5. Panganiban, G. et al. Proc. Natl Acad. Sci. USA 94, 5162-5166 (1997).
Links
6. Yuh, C. H., Bolouri, H. & Davidson, E. H. Science 279, 1896-1902
(1998). Links
7. Kissinger, J. C. & Raff, R. A. Dev. Genes Evol. 208, 82-93 (1998).
(Tautz D., "Debatable homologies," Nature, Vol. 395, 3 September 1998, p17)
--------------------------------------------------------------------
Stephen E (Steve) Jones ,--_|\ sejones@ibm.net
3 Hawker Avenue / Oz \ senojes@hotmail.com
Warwick 6024 ->*_,--\_/ Phone +61 8 9448 7439
Perth, West Australia v "Test everything." (1Thess 5:21)
--------------------------------------------------------------------
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Content-Type: text/html; charset="us-ascii"
Content-Transfer-Encoding: 7bit
Group
Here is an article which throws doubt on one of the foundation stones
of evolution, namely homology, ie. similarity due to characteristics
derived from a common ancestor. Note the last paragraph:
"Homology, then, is an idealized principle that works under idealized
conditions, but such conditions almost never apply." This seems to be
saying that in the non-ideal, real world, determination of homologous
structures almost never apply?
If that is the case, then how do evolutionists know from the fossil
which fossils descended from which? They may look outwardly very similar
but if their genes were available and their developmental pathways known,
it might be discovered that in fact they were not closely related by
descent and their similarities were mere analogies.
When a staunch Darwinist like John Maynard Smith remarks that
homology has become "a word ripe for burning" then there is *big*
problems in the Darwinist camp.
Steve
=========================================================================
Evolutionary biology
Debatable homologies
Diethard Tautz
"Homology: Similarity in structure of an organ or a molecule, reflecting a
common evolutionary origin...." This is the definition of homology in a
contemporary textbook 1. But although the concept lies at the heart of
much of biology, it has become increasingly elusive. Has it therefore
become a word ripe for burning, as J. Maynard Smith (Univ. Sussex)
remarked at a meeting* on the topic? Or is it simply enough to know that
homology exists -- even though we cannot define it -- as D. Wake (Univ.
California, Berkeley) suggested in 1994 in a review 2 of a book 3
commemorating the 150th anniversary of Richard Owen's introduction of
the term?
Owen's original concept of homology did not have a phylogenetic
(evolutionary) perspective. It was based on the philosophy of identifying
and grouping similarities in nature, the 'scala naturae'. Such thinking was
exemplified by Charles Bonnet, who, in 1764, derived the following
similarity series: fish -- flying fish -- aquatic birds -- birds -- bats -- flying
squirrels -- tetrapods -- monkey -man (A. Panchen, Univ. Newcastle upon
Tyne). It is one of the great achievements of applying the principle of
homology that we can now confidently reject the idea that this series
reflects phylogenetic succession. On the other hand, however, we still do
not know the true answer on the phylogenetic descent of tetrapods, as
homology concepts tend to fail when it comes to tracing evolutionary
novelties.
Further challenges arise from molecular comparisons of developmental
genes. The finding that highly conserved 'master regulator' genes such as
Pax6/eyeless are involved in eye development in diverse phyla 4 brings into
question the idea of the independent evolution of eyes. Similarly, the
expression of distal-less homologues in insect and vertebrate legs, as well
as other body outgrowths 5, raises the issue of how often appendages can
arise independently. The problem goes even further -- with biotechnology
companies proposing to use such organisms as Drosophila or zebrafish as
models for understanding human diseases, it will eventually be investors
and shareholders who have to be convinced that invoking homology is
valid.
Taking phylogenetic continuity alone as the prime criterion for homology
causes the problem of circularity, because phylogenies are themselves
deduced from homologous characters. This of course can be avoided by
using a different set of characters for the phylogeny, such as those derived
from DNA sequences. But even in well-established phylogenies, it often
emerges that independent evolution of similar characters (convergence)
must have often occurred. There could, therefore, be dormant genes or
'latent homologies' that are not expressed in a particular 'stem' species, but
that have been regained after further speciation and give the erroneous
impression of convergence (A. Meyer, Univ. Konstanz).
Strict correspondence with phylogeny might also be less important if
homologues are viewed as coherent units of phenotypic evolution with
constraints on the developmental and variational properties (G. Wagner,
Yale Univ.). Applying such criteria, Wagner proposed a beautiful solution
to the old question of the way in which the digits on the limbs of the
urodeles, the newts and salamanders, are homologous to those of the other
tetrapods. In tetrapods, digits 3 and 4 are the first to develop and are also
the ones that are most stable against perturbations. In the urodeles, the
same seems to be the case for digits 1 and 2. So if 3 and 4 are homologous
to 1 and 2, digit 3 would be equivalent to digit 5 in tetrapods and digits 4
and 5 in the urodeles would be novel structures, albeit serially homologous
to the other digits. Closer study of developmental characteristics and
comparative analysis of Hox gene expression seem to confirm this view.
In molecular studies, the question of phylogenetic continuity becomes even
more blurred. As genes can duplicate in the genome, it has long been clear
that orthologous genes (which are related by phylogenetic common
descent) have to be distinguished from paralogous genes that result from
duplications within a genome. But if gene loss and re-duplications have to
be taken into account, things become even more complex and new
terminology may be required (P. Holland, Univ. Reading). Thus, sequence
similarities alone are not sufficient to infer homology of structures and
developmental processes. Instead, one should look for the conservation of
whole regulatory networks (E. Abouheif, State Univ. New York), a
concept that comes close to that of viewing homologues as coherent units.
But can we be sure that homologous morphological structures are made by
homologous gene networks? For example, closely related species of sea
urchin can develop directly into adults, or go through a feeding larva first,
yet end up with the same adult body plan. These species show different
embryonic cell lineages and differences in patterns of gene expression
during early development (R. Raff, Indiana Univ.)(Fig. 1). Intriguingly,
however, the embryos of hybrids between such species develop partly in a
composite and partly in radically new ways. Further study of these hybrids
should help in understanding evolutionary dissociations of genotype and
phenotype.
It has often been hypothesized that changes in regulatory interactions are
involved in dissociations of this sort, but practical work on the evolution of
regulatory modules (enhancers) has been scarce. Again, research on sea
urchins might pave the way forward. Their enhancers seem to consist of
sub-elements, which can be combined and integrated in different ways 6,
possibly making them perfect targets of evolutionary change (G. Wray,
State Univ. New York). But could this mean that we eventually have to
identify homologues in the individual parts of complex enhancers to
understand the homology of morphological structures? This would indeed
make the word ripe for burning.
Homology, then, is an idealized principle that works under idealized
conditions, but such conditions almost never apply. This is reminiscent of
the concept of the Hardy-Weinberg equilibrium in population genetics. It
exists only under idealized conditions, but it is the tracing of the reasons for
deviation from these conditions that is central to understanding the
evolution of populations. Could one apply a similar thinking to homology?
*Homology, Novartis Foundation, London, 21-23 July 1998. Proceedings
to be published by Wiley.
Diethard Tautz is in the Zoologisches Institut der Universit t Munchen,
Luisenstrasse 14, 80333 Munchen, Germany. e-mail: tautz@zi.biologie.uni-
muenchen.de
References
1. Alberts, B. et al. Molecular Biology of the Cell, 3rd edn (Garland, New
York, 1994). Links
2. Wake, D. B. Science 265, 268-269 (1994). Links
3. Hall, B. K. (ed.) Homology -- The Hierarchical Basis of Comparative
Biology (Academic, San Diego, California, 1994). Links
4. Quiring, R., Walldorf, U., Kloter, U. & Gehring, W. J. Science 265,
785-789 (1994). Links
5. Panganiban, G. et al. Proc. Natl Acad. Sci. USA 94, 5162-5166 (1997).
Links
6. Yuh, C. H., Bolouri, H. & Davidson, E. H. Science 279, 1896-1902
(1998). Links
7. Kissinger, J. C. & Raff, R. A. Dev. Genes Evol. 208, 82-93 (1998).
(Tautz D., "Debatable homologies," Nature, Vol. 395, 3 September 1998, p17)
--------------------------------------------------------------------
Stephen E (Steve) Jones ,--_|\ sejones@ibm.net
3 Hawker Avenue / Oz \ senojes@hotmail.com
Warwick 6024 ->*_,--\_/ Phone +61 8 9448 7439
Perth, West Australia v "Test everything." (1Thess 5:21)
----------------------------------------------------------------------_=_=_=IMA.BOUNDARY.HTML_4820800=_=_=_--