Since there appears to be an ongoing confusion about the work by Haeckel, the relevance of his work to Darwinian theory and the work by von Baer, I have researched these issues and despite the somewhat unorganized nature of my thoughts and findings, I have decided to present the results now rather than wait another 1 or 2 months before I have time to revisit this issue in more depth.
In Iconoclasts of Evolution: Haeckel, Behe, Wells & the Ontogeny of a Fraud The American Biology Teacher Volume: 67 Issue: 5 Pages: 275-282, authors, Pickett, Kurt M., Wenzel, John W., and Rissing, Steven W. examine the arguments by Behe and Wells about Haeckel and von Baer.
They conclude that, contrary to the claims (by Wells and Behe):
Darwin did not rely on Haeckel, but rather on von Baer. von Baer’s stance against ‘evolution’ is irrelevant. Behe (1998) and Wells (1999, 2000) are deeply confused or intentionally confusing regarding the history and significance of this well-known field, an area they claim has special meaning in their political movement.
A particular ironic statement is made by Wells:
But Darwin persisted in citing him [von Baer] anyway, making him look like a supporter of the very doctrine of evolutionary parallelism he explicitly rejected
Jonathan Wells, Icons of Evolution 2000, page 86.
I wonder how Wells feels about the DI bibliography, given the above objections.…
A companion presentation (available in both Microsoft PowerPoint and Apple Keynote formats) for use by teachers that parallels the arguments discussed here is available via free anonymous download at this FTP site.
But as Pickett et al argue, that Darwin incorporated other data and cited work by others, is not surprising. Any new theory will have to deal with the existing data. And this is the problem with ID namely that is has no theory to deal with the existing data, let alone with additional data. I apologize to the interested reader and hope that the links and references provide sufficient resources for the reader to explore these issues in further detail.
Pickett et al. explain why they are addressing this topic:
The confusion by Behe and Wells, while obvious to trained scientists, needs some explanation for teachers [and ID proponents PvM].
Their argument is simple: Darwin could not have relied on Haeckel since he published his work 15 years after “Origins”. And while Darwin did rely on von Baer, the argument that he cannot rely on von Baer because he disagreed with Darwin is irrelevant.
In other words, a strawman was created and refuted, and Darwinism survives. But that may not be self evident to the casual observer, especially those who rely on the arguments as presented by ID about Haeckel and Darwinian theory.
Support from embryology has been challenged throughout history in various ways by early critics of evolution including creationists, who now speak under the banner of ‘Intelligent Design.’ Behe (1998) and Wells (1999) claimed that embryological support for Darwinian evolution is based on the drawings of 19th century embryologist Ernst Haeckel (1834-1919). They reiterate Richardson et al.’s (1997) work indicating has been known since at least 1894 Haeckel’s embryological drawings are inaccurate perhaps fraudulent. Accordingly, Behe (1998) claims that because of this, “ … the problem of within evolution remains unsolved.” Later, Wells (2000, Chapter 5) claimed that the embryological Darwinian evolution is based on the work 19th century embryologist, Karl von Baer (1792-1876). Wells says that as von Baer was not a proponent of evolution, so Darwin’s use of his embryological contributions in support of evolutionary theory is in fact misuse. Later in the same chapter, Wells (2000) claims Baer’s laws-which describe continual change and specialization during development-cannot accommodate reality because they do not allow for the Haeckelian notion of a conserved stage midway during development. As we will show, von Baer’s view, and sequent view of a mid-embryological conserved overwhelmingly supported by available data. Notwithstanding this, Behe (1998) and Wells both claim that the alleged existence of stage midway through development shows, also, that Haeckel’s biogenetic law, “ontogeny recapitulates phylogeny,” is false. Wells and Behe claim that Darwin’s thesis, as set forth in On the Origin of Species, relied upon embryological conclusions drawn before and after the publication of Origin. Further, they imply that current support of Darwinism is based on either von Baer or Haeckel, and that if embryological support for evolution comes from von Baer, then it is misuse; if it comes from Haeckel, it is fraudulent. While these simplistic claims are easily dismissed by embryologists and systematists, it can seem quite confusing to other biology teachers. We present the background necessary for teachers and students to evaluate this conflict objectively.
Source: The powerpoint presentation
Recent Attacks on Embryological Support for Darwinism
Support from embryology has been challenged throughout history in various ways by early critics of evolution including creationists, who now speak under the banner of “Intelligent Design.” Behe (1998) claimed that embryological support for Darwinian evolution is based on the drawings of 19th century embryologist Ernst Haeckel by reiterating Richardson et al�s (1997) work indicating what has been known since at least 1894 (Sedgwick): Haeckel’s embryological drawings are inaccurate and perhaps fraudulent. Accordingly, Behe claims that because of this, “ … the problem of development within evolution remains unsolved.” Later, Wells (2000) claimed that the embryological support for Darwinian evolution is based on the work of another 19th century embryologist, Karl von Baer. Wells says that as von Baer was not a proponent of evolution, so Darwin’s use of his embryological contributions in support of evolutionary theory is in fact misuse. Later in the same chapter, Wells (2000) claims that von Baer’s laws cannot accommodate reality because they do not allow for a conserved stage midway during development. Wells (2000) and Behe (1998) both claim that the existence of a conserved stage midway through development shows, also, that Haeckel’s biogenetic law, “ontogeny recapitulates phylogeny,” is false. Essentially, Wells and Behe claim that embryological support of Darwinism is based on either von Baer or Haeckel, and that if embryological support for evolution comes from von Baer, then it is misuse; if it comes from Haeckel, it is fraudulent.
- Behe (1998): Support is based on Ernst Haeckel’s embryo drawings, which are inaccurate. 
- Wells (2000): Support is based on work of Karl von Baer, who was not an evolutionist 
- Wells(2000): Support based on von Baer cannot accommodate the conserved stage. 
The real story
(1) the validity of Haeckel’s drawings or his “biogenetic law” has no impact on Darwinian evolution because Darwin published On the Origin of Species some 15 years before Haeckel’s drawings were published;
(2) Richardson et al.’s (1997) critical claim is there no conserved stage during development, and it is incidental that Haeckel’s drawings are in error; and
(3) von Baer’s rejection of Darwin is immaterial because his primary, empirical data support Darwin.
- The validity of Haeckel’s drawings has no impact on Darwinian biology because Darwin published Origin 15 years before Haeckel’s drawings. 
- Von Baer’s rejection of Darwin is immaterial.
- There is no conserved stage of embryological development.
- Darwin did not rely on Haeckel, but rather on von Baer.
- Von Baer’s stance against evolution is irrelevant.
- Behe (1998) and Wells (1999, 2000) are deeply confused regarding the history and significance of this well-known field, and area they claim has special meaning in their political movement
 Letter by Behe MJ Embryology and evolution SCIENCE 281 (5375): 348-348 JUL 17 1998
 Wells Icons of Evolution
… Wells (2000, Chapter 5) claimed that the embryological support for Darwinian evolution is based on the work of another 19th century embryologist, Karl von Baer (1792-1876). Wells says that as von Baer was not a proponent of evolution, so Darwin’s use of his embryological contributions in support of evolutionary theory is in fact misuse. Later in the same chapter, Wells (2000) claims that von Baer’s laws, which describe continual change and specialization during development, cannot accommodate reality because they do not allow for the Haeckelian notion of a conserved stage midway during development. As we will show, von Baer’s view, and not the subsequent view of a mid-embryological conserved stage, is overwhelmingly supported by available data.
Chapter 5, Icons of Evolution From ICONS OF EVOLUTION? Why much of what Jonathan Wells writes about evolution is wrong by Alan D. Gishlick
Although Darwin did not use Haeckel on embryology, he did use von Baer. Recognizing Darwin’s use of von Baer, Wells then accuses Darwin of “misusing” von Baer’s work, twisting the data to fit his views. But Darwin does not. Wells claims that von Baer’s embryological laws are incompatible with Darwin’s conclusions, but they are not. Von Baer may have disagreed with Darwin about his conclusions, but his laws do not prohibit development elucidating common ancestry. Darwin came to a different conclusion from the same body of evidence – this is not “distorting” the evidence. Darwin was making a general inductive argument and searched for data that could test the general proposition of common descent; he argued that von Baer’s data could be reinterpreted in terms of common ancestry. This was no more a “misuse” of von Baer than was Alfred Wegener’s reinterpretations of the data of geology in light of mobile continents. New scientific theories always use previous data. Is Wells implying that evolutionary biology cannot cite any research that predates 1859? Is Wells implying that developmental sequences such as those illustrated by von Baer and others are not data?
Wells does mention that Darwin quoted Haeckel in “On the origin of Species”, 1859. In Chapter XIV. Mutual Affinities of Organic Beings: Morphology – Embryology – Rudimentary Organs On the nature of the affinities connecting organic beings Darwin wrote:
Professor Haeckel in his “Generelle Morphologie” and in another works, has recently brought his great knowledge and abilities to bear on what he calls phylogeny, or the lines of descent of all organic beings. In drawing up the several series he trusts chiefly to embryological characters, but receives aid from homologous and rudimentary organs, as well as from the successive periods at which the various forms of life are believed to have first appeared in our geological formations. He has thus boldly made a great beginning, and shows us how classification will in the future be treated.
But it was not until 1874, 15 years after Darwin published his Origins, that Haeckel published the infamous drawings.
Darwin is quoted by Wells as “[Darwin conluded that early embryos] show us, more or less completely, the condition of the progenitor of the whole group in its adult state” but the quote is from a chapter which does not mention Haeckel but does mention von Baer.
More links on Haeckel and von Baer
- Richardson MK, Keuck G. (2001) A question of intent: when is a �schematic� illustration a fraud? Nature. 2001 Mar 8;410(6825):144.
- Richardson MK Keuck G (2002). Haeckel�s ABC of evolution and development. Biol. Revs. 77 495-528.
One of the central, unresolved controversies in biology concerns the distribution of primitive versus advanced characters at different stages of vertebrate development. This controversy has major implications for evolutionary developmental biology and phylogenetics. Ernst Haeckel addressed the issue with his Biogenetic Law, and his embryo drawings functioned as supporting data. We re-examine Haeckel’s work and its significance for modern efforts to develop a rigorous comparative framework for developmental studies. Haeckel’s comparative embryology was evolutionary but non-quantitative. It was based on developmental sequences, and treated heterochrony as a sequence change. It is not always clear whether he believed in recapitulation of single characters or entire stages. The Biogenetic Law is supported by several recent studies - if applied to single characters only. Haeckel’s important but overlooked alphabetical analogy of evolution and development is an advance on von Baer. Haeckel recognized the evolutionary diversity in early embryonic stages, in line with modern thinking. He did not necessarily advocate the strict form of recapitulation and terminal addition commonly attributed to him. Haeckel’s much-criticized embryo drawings are important as phylogenetic hypotheses, teaching aids, and evidence for evolution. While some criticisms of the drawings are legitimate, others are more tendentious. In opposition to Haeckel and his embryo drawings, Wilhelm His made major advances towards developing a quantitative comparative embryology based on morphometrics. Unfortunately His’s work in this area is largely forgotten. Despite his obvious flaws, Haeckel can be seen as the father of a sequence-based phylogenetic embryology.
- Scott F. Gilbert The Reception of Karl Ernst von Baer’s Law
In September 10, 1860, Charles Darwin wrote to his friend, the Harvard biologist Asa Gray, “Embryology is to me by far the strongest class of facts in favor of change of forms.” This statement is remarkable in that it had been assumed that embryology provided evidence against evolution, and another Harvard biologist, Louis Agassiz, indeed was using embryology against Darwin’s hypothesis. How could Darwin say that embryological evidence supported evolution? The key was the embryological law of Karl Ernst von Baer, a law that was supposed to be against the transformation of species.
Von Baer’s law of development provided Darwin with three essential pieces of his evolutionary theory. First, it offered Darwin a natural mechanism for a branched tree-like pattern of evolutionary divergence. Darwin’s evolutionary theory would not have to be confined to the linear view of the transformationists before him. Second, von Baer’s observations of vertebrate embryos offered Darwin the notion that homologous structures could be explained by common descent. Third, and conversely, it gave him the insight that embryonic structures could provide the basis for biological classification. Thus, he would conclude in the Origin of Species, (1859, p. 449) “Community of embryonic structure reveals community of descent.”
- John Wilkins Darwin’s Precursors and Influences
- PZ Myers Wells and Haeckel’s Embryos: A Review of Chapter 5 of Icons of Evolution