Homology - evidence for or against evolution?
Most evolutionary biologists and textbooks cite homology as clear evidence in support of common descent and evolution. However, contrary to such popular belief, many supposedly homologous structures in fact are not. This is compelling evidence against both common descent and macroevolution. Unfortunately this evidence that clearly challenges evolution is usually ignored, which is why it is not widely known.
What is homology?
Homology refers to similarities of bodily structures or organs between different groups of organisms. It is illustrated by the vertebrate skeleton: across diverse groups of vertebrates - fish, amphibians, reptiles, mammals and birds - there are striking similarities in their overall skeleton, notably they all have a spine with ribs, and a skull.
A frequently used example is the forelimb of tetrapods (vertebrate with limbs, mostly land animals): despite the substantial differences in overall appearance of e.g. a human arm, dog foreleg, bird wing and whale flipper – the underlying bone arrangements are remarkably similar (Fig. 1).
Figure 1. Forelimbs of human, dog, bird and whale, highlighting homologous bones.
The theory of evolution seems to provide a cogent explanation for these similarities. It proposes that the tetrapod leg, from its first appearance with the early amphibians, as their descendants diversified, was itself progressively modified to adapt to differing uses. In the same way, the similarities of skeleton of all vertebrates are seen as arising by evolution from their common fish ancestors.
This evolutionary explanation for homology has become so widely accepted that it now defines homology as referring to those organs which (are believed to) have been derived from the same structure in a common ancestor.
Homology and embryology
Structures and organs in a mature organism arise and develop of course through the operation of formative processes as the embryo grows and develops. These embryological developmental processes operate consistently, such that it is possible to identify which cells in a very early embryo will develop into specific structures of the mature organism.
With this in mind (and adopting an evolutionary perspective) it is proposed that from a common ancestor (such as an early amphibian with limbs), over the course of evolution, modifications of the embryological developmental processes (leading to formation of the limbs) have resulted in divergence from the common embryological source and immature limb to give the range of modern day adult organs (such as the specialised forelimbs mentioned above). And with this evolutionary account of homology, embryology acquired an important role in identifying and interpreting homologies. The point being that, even if adult structures look rather different (arm, wing, flipper), if they are homologous then they will be derived from equivalent embryological sources.
Conversely, even if structures from different species look similar, if they have developed from different embryological tissues then they would not be regarded as homologous, but due to convergent evolution. A good example of this are the 'camera' eyes of vertebrates and that of the cuttlefish (an invertebrate mollusc related to squid). In overall structure they clearly resemble each other, notably in having a lens and iris, are equally specialised, and have comparable performance.
Figure 2. Comparison of vertebrate and octopus eyes, showing (1) retina, (2) nerve fibres, (3) optic nerve, and (4) blind spot where the nerves pass through the retina.
However, despite the similarities, they are not considered to be homologous, as there is no doubt they have arisen independently. They are in radically different animal groups (called phyla: chordates and molluscs respectively) which have completely different body plans, so there is no possibility of the eyes being derived from comparable or equivalent embryological tissues.
It is also recognised that for homologous organs or tissues the developmental processes should be comparable. It has long been accepted, including by evolutionists, that the early stages of embryological development will not be susceptible to change: because so much later development depends on it, changes to early development will lead to detrimental deformities rather than something useful. And this view is reinforced the more we learn about the complex and coordinated genetic and biochemical mechanisms involved in embryological processes — it is evident that random changes to these mechanisms will merely produce deformities. To produce useful changes would require so many coordinated changes that the chances of these occurring is realistically nil.
Consequently, for example, referring to the tetrapod limb, it’s considered easy (evolutionarily speaking, though in the light of what we now know about embryological development I would challenge this) to see how relatively minor changes to bone size and shape might be achieved, but the key processes leading to arrangement and formation of the skeleton should be essentially the same.
So we have these criteria for homologous organs:
they must be derived from equivalent embryological tissues; and
they should be formed by similar embryological processes, especially in the early stages.
Homology — the inconvenient truth
Although most evolutionary texts convey a consistent and hence persuasive picture of homology, there are in fact many substantial anomalies. In particular, as we discover more of how tissues are formed embryologically, increasing doubt is cast on much of the homology that has been perceived for so long at the morphological level. There are many exceptions: where organs generally considered to be homologous are not formed by equivalent developmental processes, or even arise from different embryological tissues.
Here I shall outline just one example. For more detailed information see the companion article ‘Anomalous homology refutes evolution’.
Of particular note, in view of the importance attached to the apparent homology of the vertebrate skeleton, it is especially relevant that vertebrae – the hallmark of vertebrates – form embryologically in significantly different ways in different groups of vertebrate, even from different embryonic sources. That is, despite the similar roles of vertebrae in all vertebrates, the vertebrae are not actually homologous.
In the very early embryo of all vertebrates a rod of tissue (called the notochord) forms along the back of the embryo where the spinal column will form (in fact the notochord is a defining feature of vertebrates). But there are substantial differences in how the vertebrae form:
Tetrapods (e.g. reptiles, birds, mammals)
In most land vertebrates, following formation of the notochord, sets of embryonic tissue (called somites) form in pairs either side of, and along the length of, the notochord. Cells from the somites move towards the notochord, surround it, and transform into the vertebrae.
An interesting (and unexpected) feature is that the vertebrae do not form one-for-one from each pair of somites, but from adjacent halves of neighbouring pairs. This is called resegmentation.
The notochord all but disappears: some residual tissue contributes to the discs between the vertebrae, but none of the notochord is incorporated into the actual vertebrae.
Cartilaginous fish (e.g. shark)
Formation of vertebrae is quite different in cartilaginous fish such as sharks and many so-called ‘primitive’ bony fish such as sturgeons. In these, cells from the somites migrate towards the notochord, but rather than surrounding it they form into blocks of cartilaginous tissue called arcualia on either side of the notochord. The arcualia then transform into a vertebra, with each of the arcualia becoming a specific part of it. There is no resegmentation.
So, even though in tetrapods and cartilaginous fish the vertebrae are formed from somites, the developmental route and final vertebrae are very different, and are not homologous.
Teleosts (most fish)
A completely different development route is used in teleosts. In these the innermost part of the vertebrae arises directly from the notochord (i.e. unlike tetrapods where the notochord does not contribute to vertebrae at all) and not from the somites, although these contribute to outer parts of the vertebrae. And again there is no resegmentation.
So it is clear that the vertebrae of most fish are not homologous to most land animals.
More generally, the vertebrae of different types of vertebrate are not homologous, which is clear evidence that they do not share a common ancestor.
Why the evidence about homology is important – and hence ignored!
Superficially it had seemed that evolution provided a cogent explanation for homology, but it is clear that there are substantial examples of apparently homologues structures in fact not being homologous. This is extremely significant: it doesn’t just remove evidence in support of evolution – it constitutes clear counter-evidence against the organisms concerned having evolved from e.g. a common vertebrate ancestor.
But what it is the evolutionary responses? - Largely it is to ignore these examples that do not fit in with the evolutionary paradigm. It is typified by Darwin. He saw embryology as one of the lines of evidence supporting common descent; but even he knew there were anomalies. And what was his response?
community of embryonic structures reveals community of descent; but dissimilarity in embryonic development does not prove discommunity of descent’ 
In other words he tried to embrace the evidence that supported his theory, but ignore the evidence that didn’t. Darwin can be excused for thinking that radical changes in early embryonic development could occur; because in his time almost nothing was known of the genetic and biochemical implications of doing so.
But today’s biologists have no such excuse. Yet take almost any textbook on evolution and it will present homology as one of the lines of evidence in support of evolution; and almost none make any mention at all of any of the exceptions. 
 Image by (Own work) [CC BY-SA 4.0 (http://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons. Used in Wikipedia article ‘Homology (Biology)’.
 Image by Caerbannog [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/)], via Wikimedia Commons - Own Work, based on Image: Evolution_eye.png created by Jerry Crimson Mann 07:07, 2 August 2005 UTC (itself under GFDL). Used in Wikipedia article ‘Evolution of the eye’
 Darwin Origin 4th edn Chapter 13.
 This may make some readers doubt the truth of the examples I’ve given. So here is a mainstream textbook that describes some of the embryological differences: Kardong, Vertebrates: comparative anatomy, function, evolution, McGraw-Hill (2009), Chapter 8: Skeletal system: The axial skeleton.
Thumbnail - as for Note 1 above.