Homology: A Concept in Crisis

Homology: A Concept in Crisis

https://reasonandscience.catsboard.com/t1454-homology-a-concept-in-crisis

Similarly, once we reckon with claims about "convergent evolution" of eyes, flight, whale/bat echolocation "sonar" systems, etc. etc., we begin to see that "everything branches, save when it doesn't." Indeed, we have to reckon with a case where on examining the genome of a kangaroo (the tammar wallaby), it was discovered that "In fact there are great chunks of the [[human] genome sitting right there in the kangaroo genome." The kangaroos are marsupials, not placental mammals, and the fork between the two is held to be 150 million years old. So, Carl Wieland of Creation Ministries incorporated, was fully in his rights to say: "unlike chimps, kangaroos are not supposed to be our ‘close relatives’ . . . . Evolutionists have long proclaimed that apes and people share a high percentage of DNA. Hence their surprise  at these findings that ‘Skippy’ has a genetic makeup similar to ours."  Next, so soon as one looks at molecular similarities -- technically, homologies (and yes, this is an argument from similarity, i.e analogy in the end) -- instead of those of gross anatomy, we run into many, mutually conflicting "trees." Being allegedly 95 - 98+% Chimp in genetics is one thing, being what, ~ 80% kangaroo or ~ 50% banana or the like, is quite another.

Genetic Phylogeny
http://www.detectingdesign.com/geneticphylogeny.html

mollusks (scallops) are more closely related to deuterostomes (sea urchins) than arthropods (brine shrimp).  Of course, this is not too surprising.  Intuitively, a scallop seems more like a sea urchin than a shrimp.  So, the 82% correlation between the scallop and sea urchin is not surprising.  However, in this light it is surprising is that a tarantula (also an arthropod) has a 92% correlation with the scallop.  Here we have two different arthropods, a shrimp and an tarantula.  How can a scallop be much more related to one type of arthropod and much less related to the other type of arthropod? This troubling thought led the authors of the Science article to remark:

Different representative species, in this case brine shrimp or tarantula for the arthropods, yield wildly different inferred relationships among phyla. Both trees have strong bootstrap support (percentage at node). . .  The critical question is whether current models of 18S rRNA evolution are sufficiently accurate to successfully compensate for long branch attraction between the animal phyla. Without knowing the correct tree ahead of time, this question will be hard to answer. However, current models of DNA substitution usually fit the data poorly .

http://www.idscience.ca/tree_of_life_genome.html
http://www.arn.org/docs/odesign/od182/hobi182.htm
http://www.evolutionnews.org/2009/05/a_primer_on_the_tree_of_life_p020141.html
http://iose-gen.blogspot.com.br/2010/06/introduction-and-summary.html#methnat

http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1

The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway

Homology does nothing to demonstrate that the necessary transitions are evolutionarily feasible

Does homology provide evidence of evolutionary naturalism?

Summary

Homology involves the theory that macroevolutionary relationships can be proven by the similarity in the anatomy and physiology of different animals. Since Darwin, homology has been cited in textbooks as a major proof for evolution. A review of the literature on homology indicates that the theory does not provide evidence for evolutionary naturalism, and that the common examples of homology can be better explained by Creation. Furthermore, increased knowledge about the genetic and molecular basis of life has revealed many major exceptions and contradictions to the theory which, as a result, have largely negated homology as a proof of evolution.


Extensive comparisons of skeletons, muscles, nerves, body organs, cell ultrastructure and biochemistry of different animal kinds have confirmed that a great deal of similarity exists in both their structure and function. By arranging or classifying large sets of anatomical structures according to the similarity of selected traits, evolutionary naturalists have attempted to demonstrate evidence for a long, gradual line of progressive animal changes terminating in the highest organism yet, humans. Proponents of evolution then argue that these comparisons prove the concept that all life evolved from a hypothetical ‘common ancestor’ protocell that they believe lived about 3.5 billion years ago.
Called homology or the homology theory, since Darwin this view has been presented as a major evidence of macroevolution theory. An example of this reasoning is as follows:

'If you look at a 1953 Corvette and compare it to the latest model, only the most general resemblances are evident, but 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 

Homology is not merely a minor proof of evolution, but instead has been widely cited by proponents of evolution as one of the most compelling lines of evidence for their theory. Darwin concluded that homology was critically important evidence for common descent:

'According to Darwin's theory of common descent, the structures that we call homologies represent characteristics inherited with some modification from a corresponding feature in a common ancestor. Darwin devoted an entire book, The Descent of Man and Selection in Relation to Sex, largely to the idea that humans share common descent with apes and other animals … . Darwin built his case mostly on anatomical comparisons revealing homology between humans and apes. To Darwin, the close resemblances between apes and humans could be explained only by common descent.'

Darwin reasoned that the members of the same class of animals resemble each other in the general plan of their design and, in his words, this resemblance is critical because of the fact that 'the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise and the wing of the bat' are all 'constructed on the same pattern' and 'include similar bones in the same relative positions' is specifically what the theory of common descent would expect. An early example of how homology was used to argue for macroevolution is a 1928 biology text which, in answer to the question 'Why do the individuals in a species have all of their parts homologous?', said:

'The obvious answer is, that they all descended from the same ancestors … . Biologists carry this answer a step further and say that since homology within the species is the result of common ancestry therefore all homology is due to common ancestry and the closeness of relationship determines the number of homologous parts.'

The author concludes the answer is evolution. Barr lists homology as the first argument on his list of evidence for evolution. As the above quotes show, the same line of reasoning has been used to 'prove' evolution for more than a century. However, Dobzhansky admitted that 'homology does not prove evolution, in the sense that nobody has actually witnessed the gradual changes in the millions of consecutive generations which led from a common ancestor to a bird on the one hand and to man on the other'. But, he adds, homology strongly suggests evolution; 'the facts of homology make sense if they are supposed to be due to evolution of now-different organisms from a common stock. They do not make sense otherwise.'

The question is: 'Does the similarity that exists prove that one structure evolved into another and, ultimately, that the complex evolved from the simple?' The simplest and most obvious explanation for the fact that morphological similarities between bones, sensory organs, lungs, or gills exist among most higher animals is that the requirements of life are similar for similar living things, and some designs are preferred in constructing animals because these designs are superior to competing designs.

All automobile, bicycle and pushcart tyres are round because this design is superior for the function of most tyres. A tyre homology does not prove common descent, but common design by engineers throughout history because of the superiority of the round structure for rolling. Likewise, most vertebrate kidneys are similar structurally because they have a similar physiological role in the body and consequently must be similar in both structure and function.

Homology also does not prove that a set of animals is related by descent because both similarities and differences exist for any two animal types, and traits often are chosen by evolutionists only because they seem to provide evidence that two animals are related. The only criterion that was used by proponents of evolution to select examples of homology was: 'Does the example support what is assumed to be an evolutionary relationship?' Other examples are ignored or explained away. This fact is so well recognized, and so many examples exist that contradict the explanation of common descent, that proponents of evolution have attempted to separate most putative examples of homology into two types: analogy and homology. The division is based on a distinction between similarity due to common ancestry, or homology, and resemblance which is due solely to similarity of function, called analogy. An example is the forelimbs of humans, horses, whales and birds which are judged homologous because

In other words, if a design similarity supports evolutionary assumptions, it is listed as an homology and is accepted as evidence for evolution. Conversely, if a design similarity does not support evolution, it is called analogy, and the conclusion is drawn that the similarity exists because a certain design is highly functional for a specific body part, and not because of a common ancestor. Many analogous structures are assumed to exist due to convergent evolution, which is defined as the separate evolution of similar structures because of similar environmental demands. Convergent evolution also is used to explain similar structures that have formed from different embryo structures or precursors.
Many examples of homology are actually better explained by analogy, and the resemblance that exists is often due to similarity of function and/or design constraints. The forelimbs of humans, whales and birds are similar because they serve similar functions and have similar design constraints. The conclusion that two homologous bones are similar because they are putatively 'derived from the same ancestral bones'  is not based on direct evidence but instead on a priori conclusions demanded by macroevolution. Jones concluded that

' … the evolutionist argument from homology lacks scientific content. This particular lack has very serious implications; it strikes at the root of all attempts by  to give proponents of evolution homology an objective basis and distinguish homology (similarities due to descent) from analogy (similarities not due to descent). The only way they can recognize analogous variation, especially when due to convergent evolution is by criteria (e.g. genetic or embryological) which we now know do not hold for organs of "unquestionable" homology. The proponents of evolution concept of homology is now shown to be entirely subjective.'

Stephen J. Gould suggested that 'the central task of evolutionary biology is … the separation of homologous from analogous likeness', and then emphasized that 'homology is similarity due to descent from a common ancestor, period'. The problem with this definition is that without direct knowledge we cannot know ancestry. In answer to the question 'Can we identify fossil ancestors of species alive today?', University of Michigan Professor Mark Siddall contends that this is impossible and that the use of stratigraphic data when assembling phylogenies must be based on speculation.

Huxley understood as far back as 1870 that when dealing with fossils, which are the only evidence we have of past life, one cannot distinguish uncles and nephews from fathers and sons. Among the many reasons ancestors cannot be distinguished from sister taxa,  is that there can be no positive evidence of ancestry, only inferences. Lack of evidence can only allow it as a possibility or an ad hoc postulate.
Although many similarities exist in almost all animal structures, structural variations are the norm. Often the variations found in the animal world seem to exist solely to produce variety, and not for the purpose of conferring a survival advantage.
To argue for macroevolution via comparisons according to 'complexity' judgments also is problematic because an enormous number of exceptions exist.
The comparative anatomy argument fails completely when an attempt is made to trace all living forms of life (and even fossils) back to their postulated universal common ancestor(s). Few skeleton, muscle and brain counterparts exist in single-celled animals (or in many developmental stages afterward).


The many similarities that exist among members of the animal kingdom is the result of the fact that a single designer created the basic kinds of living 'systems', then specially modified each type of life to enable it to survive in its unique environmental niche.


Structural similarities among automobiles, however, even similarities between older and newer models  are due to construction according to pre-existing patterns, i.e., to design. Ironically, even striking similarities are not sufficient to exclude design-based explanations. In order to demonstrate naturalistic evolution, it is necessary to show that the mechanism by which organisms are constructed (unlike the mechanism by which automobiles are constructed) does not involve design.

Convergent evolution

A major problem with homology theory is that many structures appear similar superficially yet differ significantly in such areas as anatomy, physiology, etc. Since such examples are not explained easily by homology, proponents of evolution  have hypothesized an explanation for this problem called convergent evolution, which attempts to explain the analogy found.
One of the most common examples of convergent evolution is wing evolution. Wings are believed to have evolved a minimum of four times; in birds, bats (in the order chiroptera), insects and reptiles (such as the pterodactyl). Scientists have also concluded that bird wings did not evolve from fly wings for several reasons. The main one is that no evidence of insects evolving into birds (or any other animal) exists in the many insect impressions in stone, or the many examples of insects in amber, that have been discovered.
Consequently, although the evolutionary progenitors of birds are highly debated among evolutionists, insects are not considered likely candidates. The most common theory of bird evolution suggests that they evolved from dinosaurs or other reptiles. Thus, the wings of birds and insects are labeled not as homologous, but analogous, because powerful evidence refutes the idea that birds evolved directly from insects. This is one of many examples that proponents of evolution claim does not falsify homology theory because it was caused by convergent evolution. However, no evidence exists to support the convergent evolution theory.

'Some similarities between distant species may be caused by adaptation to similar environments, which is known as convergent evolution. Development of streamlined fins in fish (teleosts) and flippers in dolphins (mammals) are analogous: they function alike, but are very different in underlying structure. … Linnaeus's original classification of animals does not distinguish between analogous and homologous structures. Creatures were often put in the same groups by resemblances to an imagined "divine plan" or "design". Since Darwin … species are classified to reflect the relative closeness or distance of their common ancestry.'

One problem with the convergent evolution hypothesis is that it requires 'reinvention of the wheel' scores or even hundreds of times. The eye is hypothesized to have evolved independently as many as 60 different times.²⁶ Given the small probability of the evolution of a single eye or organism, the likelihood of it occurring numerous times is indefensible. Gould noted that even if evolution were repeated a thousand times, it probably would not produce the human mind again.²⁷

Vestigial organs and homology

Another branch of comparative anatomy studies structures in humans (and other so called 'higher' forms of life) that were believed by evolutionists to be the remains of structures that were required or useful in 'lower', less evolved and less complex ancestral forms, but that now no longer are necessary. In this case, the homologous organ in the more advanced animal is less developed, or even deemed useless. Such homologous structures or organs are referred to as vestigial, with most examples being assumed remnants that resulted from the loss of an earlier, better developed structure. Evolutionists used to proudly point to over a hundred such structures in humans, but the number has decreased consistently as anatomical knowledge has increased.
Today, only a couple of examples at most are usually mentioned (and there is no doubt that even the few examples usually mentioned are useful and not vestigial). As Howitt²⁸ noted, the celebrated German anatomist, Wiedersheim, listed 180 vestigial organs in the human body, but with the increase of knowledge it has been found that every one of them has an important function, although the functions of some organs is presently viewed as minor, or as serving a back-up capacity.^29,30
Moreover, if some vestigial organs can be proven to exist, they provide support not for evolution, but for de-evolution|--|i.e. evolution-in-reverse. What the evolutionists must demonstrate is that the development of new and useful organs is occurring today. They also must prove that a process exists that can form new structures called nascent organs, instead of trying to document that once-useful organs now are useless. Evidence for the development of new organs, or those in the process of evolving, would be evidence of evolution. As of now, no evidence of any nascent organ exists.

Embryology and homology

One major problem is that in many cases organs and structures which appear identical (or very similar) in different animals do not develop from the same structure or group of embryo cells. It is not uncommon to find fundamental structures (e.g. the alimentary canal) that form from different embryological tissues in different animals. For example, in sharks the alimentary canal is formed from the roof of the embryonic gut cavity; in frogs it is formed from the gut roof and floor; and in birds and reptiles it is formed from the lower layer of the embryonic disc or blastoderm.³¹
Even the classic example of vertebrate forelimbs referred to by Darwin (and cited in hundreds of textbooks as proof for evolution) has now turned out to be flawed as an example of homology. The reason is that the forelimbs often develop from different body segments in different species in a pattern that cannot be explained by evolution. The forelimbs in the newt develop from trunk segments 2 through 5; in the lizard they develop from trunk segments 6 to 9; in humans they develop from trunk segments 13 through 18.³² Denton concluded that this evidence shows the forelimbs usually are not developmentally homologous at all. As an example, he cited the development of the vertebrate kidney which provides a challenge to the assumption that homologous organs are produced from homologous embryonic tissues.

'In fish and amphibia the kidney is derived directly from an embryonic organ known as the mesonephros, while in reptiles and mammals the mesonephros degenerates towards the end of embryonic life and plays no role in the formation of the adult kidney, which is formed instead from a discrete spherical mass of mesodermal tissue, the metanephros, which develops quite independently from the mesonephros.'

The arguments used by evolutionists have taken on new meaning in view of the past half-century of research. For example Dobzhansky argued that

'To be sure, some diehard anti-evolutionists still insist that homology means only that the Creator gratuitously chose to make homologous organs in quite unrelated organisms. This opinion may be said to be implicitly blasphemous: it actually accuses the Creator of arranging things so that they suggest evolution merely to mislead honest students of His works.'³⁴

This research supports ReMine's biotic message theory, the conclusion that the natural world was specifically designed to look like it did notevolve, but was created.³⁵ ReMine uses a wide variety of examples to support his thesis which has been very favorably reviewed by the creationist community. ReMine notes that homology has been used as evidence against a designer for decades, but as this review shows, it strongly supports the biotic message theory.

Biochemical homology

The homology argument from biochemistry parallels the argument in anatomy. Evolutionists suggest that just as the study of comparative anatomy has found evidence of anatomical homologies, likewise research on

' … the biochemistry of different organisms has revealed biochemical homologies. In fact, the biochemical similarity of living organisms is one of the most remarkable features of life … . Cytochrome enzymes are found in almost every living organism: plant, animal and protist. The enzymes of the citric acid cycle are also almost universally distributed. Chlorophyll a is found in all green plants and almost all photosynthetic protists. DNA and RNA are found in every living organism and, so far as we can determine, contain the same hereditary coding mechanism. The fact that underneath the incredible diversity of living things lies a great uniformity of biochemical function is difficult to interpret in any other way but an evolutionary one. Presumably these molecules were put to their current use very early in the history of life and almost all modern forms have inherited the ability to manufacture and use them.'

The fact that animals are 'so similar in their chemical make-up' has long been used to support Darwinism. But extensive biochemical research has revealed that the simplest reason for biochemical homology is that all life requires similar inorganic elements, compounds and biomolecules; consequently, all life is required to use similar metabolic pathways to process these compounds. Most organisms that use oxygen and rely on the metabolism of carbohydrates, fats and proteins must use a citric acid cycle which is remarkably similar in all organisms. Furthermore, the metabolism of most proteins into energy produces ammonia, which is processed for removal in similar ways in a wide variety of organisms. What evolutionists must explain is why billions of years of evolution have not produced major differences in the biochemistry of life.
Many biochemical structures/systems in yeasts and other so-called 'primitive life' forms are almost identical to the biochemical familiesused in humans. With some minor variations, all life uses the same sugar and lipid family, the same 20 amino acids, about 14 vitamins and the same basic genetic code.

Even the complex proteins used in all life are often identical or very similar. Correspondence even exists between very different forms of life such as prokaryotes and eukaryotes. Ribosomes from bacteria, even though translation signals and other differences exist, have enough similarity that they can be made to 'translate human messenger RNAs into human proteins—and vice versa'.³⁹ The problem for evolutionists is that the biochemistry of all life, even that allegedly separated by hundreds of millions of years of geologic time and evolution, is too similar. Despite the many significant differences between the two basic cell forms (eukaryotes and prokaryotes), they are both

' … remarkably similar on the biochemical level … . Procaryotes and eucaryotes are composed of similar chemical constituents. With a few exceptions, the genetic code is the same in both, as is the way in which the genetic information in DNA is expressed. The principles underlying metabolic processes and most of the more important metabolic pathways are identical. Thus, beneath the profound structural and functional differences between procaryotes and eucaryotes, there is an even more fundamental unity: a molecular unity that is basic to life processes.'

Although many biochemical similarities exist in life, millions of biochemical differences exist that are inexplicable via evolution. Many of these differences do not provide a selective advantage as implied by the claim that Darwinistic mechanisms have fine tuned life for the past 3.6 billion years. Creationists suggest that such differences exist due to the need for ecological balance and because the Creator chose to employ variety. Also, were one compound in an organism to be altered, scores of other compounds with which it interacts would often also need to be changed so that the entire biological system could function as a harmonious unit.

Genetics and homology

According to the evolutionary theory, homologous features are programmed by similar genes. Gene sequence similarity would indicate common ancestry since such similarities are unlikely to originate independently through random mutations. If the bones of the human arm evolved from the same precursors as the wing of a bat and the hoof of a horse as evolution teaches, then we should be able to trace these alleged homologies to the DNA that codes for them. Some geneticists thought this knowledge would allow them to find the chemical formula needed to produce an arm, leg, or other structure. But once biologists acquired a greater understanding of genetics, they found that what are labeled as homologous structures in different species often are produced by quite different genes.

Homology predicted that features produced by similar genetic sequences are phylogenetically homologous. There are now so many exceptions to this prediction that the concept of genetic homology cannot now be said to be a rule, but the exception. The classic example is mutations in certain homeotic genes which can cause wholesale changes in morphology such as producing two pairs of wings instead of the normal single pair, or replacing a fly's antenna with a leg (or can even cause eyes to develop on the fly's leg). Genes that produce results similar to the homeotic genes for flies' wings have been found in most other animal kinds, including mammals and humans.
In another example, the gene that controls mouse eye colour also happens to control the mouse's physical size; but the gene that controls the fruit fly's eye colour controls not the fruit fly's size, but female sex organ morphology.⁴³ Although mice and flies share a similar gene (called eyeless) which functions to control their eye development, the fly's multifaceted eye is profoundly different from a mouse's mammal eye. In both the fly Antennapedia and mouse eyeless, similar homeotic genes control development of structures which are not homologous by either the post-Darwinian phylogenetic or the classical morphological definition. 
The finding that similar genes regulate such radically different structures strongly argues against the concept of homology. So many genes used in higher organisms have multiple effects that Ernst Mayr once suggested that genes which control only a single characteristic are rare or nonexistent. The finding that a consistent one-gene/one-characteristic correspondence does not exist has been a major set back to the Darwinian interpretation of homology. Because evolutionary biologists have failed to provide a biological basis for their homology research findings, Roth concluded 'that the title of de Beer's 1971 essay|--|Homology, an unsolved problem|--|remains an accurate description … . The relationships between processes at genetic, developmental, gross phenotypic and evolutionary levels remain a black box'.⁴⁵ Research at the molecular level has failed to demonstrate the expected correspondence between gene product changes and the organismal changes predicted by evolution.²⁴
Evolution by DNA mutations 'is largely uncoupled from morphological evolution'.⁴⁶ An example of this is the large morphological dissimilarity that exists between humans and chimpanzees despite a high similarity in their DNA.⁴⁶ In short we now know:

' … in general the homology of structures such as organs or modules cannot be ascribed to inheritance of homologous genes or sets of genes. Consequently, organ homology cannot be reduced to gene homology. Van Valen recognizes this too and therefore suggests, as an alternative, to reduce homology to a continuity of [developmental] information. Information is not the same as genotypic nucleic acid. But what it is exactly, and how it is continuous, is still an unsolved problem.'⁴⁷

Conclusion

As scientists learnt more about anatomy, physiology and especially genetics, the concept of homology increasingly came under attack. 
One problem however, was that examples which seemed to fit evolutionary assumptions were often cited, while the many examples that do not fit were ignored.
 And, in time, more and more examples were discovered that had to be ignored. Eventually, as one observer noted, homology led Darwinists to assemble very select examples that seemed to prove ancestor-descendant relationships that often were quite convincing. In addition, as Milton has observed,

'It is homology that Darwinists rely on to bridge the gaps in the fossil record. … It is homology that underlies the diagrams drawn up by Darwinists from Haeckel to the present day showing how every living thing is related. Ultimately, however, it is homology that has provided the greatest stumbling block to Darwinian theory, for at the final and most crucial hurdle, homology has fallen.'⁴⁸

The recent information explosion in embryology, microbiology, genetics and especially molecular biology has revealed in minute detail how plants and animals are constructed at the molecular level. If the Darwinian interpretation of homology were correct, then we would expect that the same homologies found at the macroscopic level also exist at the microscopic, biochemical and genetic levels. What researchers in each of these fields often find, has greatly undermined the homology concept. So many exceptions now exist that molecular biologist Michael Denton concluded that the homology theory should be rejected. His main argument is that genetic research has not shown that homologous structures are produced by homologous genes and follow homologous patterns of embryological development. Instead, genetics has found that homologous structures are 'often specified by non-homologous genetic systems' and furthermore, the homology 'can seldom be extended back into embryology'.⁴⁹
Why do most scientists accept macroevolution theory? A major reason is that it is now the accepted world view of scientists—an idea to which they are exposed from the earliest days of training, and by which they are surrounded daily. Most scientists are influenced by social pressure, and many believers fear recriminations from their fellow scientists if they do not conform to what currently is viewed as correct. To prove their orthodoxy, many scientists have become unscientific and have embraced the religion of 20^th century-naturalism.⁵⁰ Belief in evolutionism requires a credulity induced partly by pressure to conform to a world of science that is saturated with naturalism.

http://creation.com/does-homology-provide-evidence-of-evolutionary-naturalism

http://www.mythofhomology.com/myth_of_homology_02.htm

The discovery which really overthrew homology is that organs accepted as "homologous" are almost all controlled by very different genetic codes. As we know, the theory of evolution proposes that living things developed through small, chance changes in their genes, in other words, mutations. For this reason, the genetic structures of living things which are seen as close evolutionary relatives should resemble each other. And, in particular, similar organs should be controlled by similar genetic structures. However, in point of fact, genetic researchers have made discoveries which conflict totally with this evolutionary thesis.

Similar organs are usually governed by very different genetic (DNA) codes. Furthermore, similar genetic codes in the DNA of different creatures are often associated with completely different organs. The chapter titled "The Failure of Homology" in Michael Denton's book, Evolution: A Theory in Crisis, gives several examples of this, and sums the subject up in this way:

Homologous structures are often specified by non-homologous genetic systems and the concept of homology can seldom be extended back into embryology.285

This genetic question has also been raised by the well-known evolutionary biologist Gavin de Beer. In his book Homology: An Unsolved Problem, published in 1971, de Beer put forward a very wide-ranging analysis of this subject. He sums up why homology is a problem for the theory of evolution as follows:

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.286

Although some 30 years have passed since de Beer wrote those words, they have still received no answer.

A third proof which undermines the homology claim is the question of embryological development, which we mentioned at the start. In order for the evolutionary thesis regarding homology to be taken seriously, the periods of similar structures' embryological development-in other words, the stages of development in the egg or the mother's womb-would need to be parallel, whereas, in reality, these embryological periods for similar structures are quite different from each other in every living creature. Pere Alberch, an eminent developmental biologist, noted, it is "the rule rather than the exception" that "homologous structures form from distinctly dissimilar initial states."287

The emergence of similar structures as the result of totally dissimilar processes is frequently seen in the latter stages of the development phase. As we know, many species of animal go through a stage known as "indirect development" (in other words the larva stage), on their way to adulthood. For instance, most frogs begin life as swimming tadpoles and turn into four-legged animals at the last stage of metamorphosis. But alongside this there are several species of frog which skip the larva stage and develop directly. But the adults of most of these species that develop directly are practically indistinguishable from those species which pass through the tadpole stage. The same phenomenon is to be seen in water chestnuts and some other similar species.288

To conclude, we can say that genetic and embryological research has proven that the concept of homology defined by Darwin as "evidence of the evolution of living things from a common ancestor" can by no means be regarded as any evidence at all. The inconsistency of homology, which looks quite convincing on the surface, is clearly revealed when examined more closely.

http://cavern.uark.edu/~cdm/creation/shame2.htm

"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).

"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).

"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.
"Homologous structures are often specified by non-homologous genetic systems and the concept of homology can seldom be extended back into embryology.
"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 resemblance 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).

"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).

"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).

"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).

http://darwins-god.blogspot.com.br/2012/05/when-i-pointed-out-evolutionary-tree.html


The Evolutionary Tree Failed But Evolutionists Still Insist Evolution is a Fact


http://darwins-god.blogspot.com.br/2012/05/evolutionary-tree-failed-but.html


The fundamental thesis of evolution is that the species evolved according to the evolutionary tree. Students learn about the evolutionary tree in biology class and biologists use the evolutionary tree in their research. But in fact the evolutionary tree is based on a limited, and carefully selected, set of observations. Ever since Darwin, science has continued to document exceptions and anomalies—species that don’t fit neatly into the evolutionary pattern. These biological contradictions come in various forms and are found throughout the tree. For instance, species that in many regards appear to be quite similar, which evolutionists have placed on neighboring twigs of the evolutionary tree, are routinely found to have profound differences. On the other hand, species that are obviously quite different, which evolutionists have placed on distant limbs of the evolutionary tree, are often found to have profound similarities. And these various differences and similarities are found in every imaginable aspect of the species designs, ranging from the visible features of the adult form to the developing embryonic form to the underlying cellular and molecular structures. At this point, such cases are no longer exceptions and anomalies. For years evolutionists attempted to explain this growing list of contradictions using their evolutionary tree model. But it is obvious that this was an exercise in forcing the evidence to fit the theory rather than the other way around. The inexorable march of science has taken its toll and in recent years evolutionists have finally begun to deemphasize their iconic evolutionary tree model. What this does not change, however, is their insistence that evolution is a fact.

While the failure of the evolutionary tree model can be seen in data even as far back as the nineteenth century, such contradictions were generally discussed only in the highly technical scientific journals. Textbooks held to evolutionary orthodoxy and journalists dutifully reported that evolution was a scientific fact. Even today students are taught that the species fall into the expected tree pattern. But some venturesome writers are beginning to mention this unmentionable. A few years ago, for instance, the Telegraph reported that “Charles Darwin's tree of life is ‘wrong and misleading’, claim scientists.” The article reported:

They believe the concept misleads us because his [Darwin’s] theory limits and even obscures the study of organisms and their ancestries. …

Researchers say although for much of the past 150 years biology has largely concerned itself with filling in the details of the tree it is now obsolete and needs to be discarded. …

“For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality.” …

More fundamentally recent research suggests the evolution of animals and plants isn't exactly tree-like either. …

Dr Rose said: "The tree of life is being politely buried – we all know that. What's less accepted is our whole fundamental view of biology needs to change." He says biology is vastly more complex than we thought and facing up to this complexity will be as scary as the conceptual upheavals physicists had to take on board in the early 20th century.

All of this was important not because it was reporting on any new scientific findings, but rather that a fundamental failure of evolutionary theory was being reported, period. Contrary evidence was being openly discussed.

But of course none of this was allowed to cast any doubt on evolutionary theory itself. As the article reported:

"If you don't have a tree of life what does it mean for evolutionary biology. At first it's very scary – but in the past couple of years people have begun to free their minds." Both he and co-researcher Dr Ford Doolittle stressed that downgrading the tree of life doesn't mean the theory of evolution is wrong just that evolution is not as tidy as we would like to believe.

It is yet another example of how well protected evolution is from the scientific evidence. The tree of life is just one of many failures of evolutionary theory. Over and over the theory fails to elucidate the science, but rather must be repeatedly modified and augmented to try to fit the data. At some point the theory becomes little more than a tautology. Whatever we discover in biology, evolution must have created it, no matter how contradictory and unlikely. The real story here is not that another prediction of evolution has failed, the real story is that evolution is protected from such failures.

Refuting phylogenetic relationships
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1574289/

Molecular Phylogeny Proves Evolution is False.
https://blueprintsforliving.com/molecular-phylogeny-prove-evolution-false/
2000 gene sequences common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes were compared.(1) Theoretically, the results should have constructed a tree that revealed evolutionary relationships. However, different genes aligned in different sequence among the 6 types of life forms. No tree is possible in such an analysis. Ultimately, there appears to be no consistent relationship among these animals. Evolution is undone.