Evolution in the News - November 2014
by Do-While Jones

Holes in Evolution

The evolution of sponges is riddled with holes.

The theory of evolution proposes that simple one-celled creatures evolved into simple multi-celled creatures, which evolved into more complex multi-celled creatures, which inherited the genes of those simpler creatures and added some more genes to them which gave them additional functionality. Evolutionists believe that sponges and jellyfish are some of the simplest animals, which should make them the easiest to study. The more scientists study sponges, the more holes they find.

Last June, we told you about two problems evolutionists had discovered while studying jellyfish. 1 One had to do with bilateral symmetry, and the second had to do with their nervous system. This month we want to write about the problem that studies of sponges have presented to evolutionists.

There are certain genes, called Hox genes, which are so basic to life that all animals have them. Therefore, evolutionists are especially interested in the origin and evolution of Hox genes. Studies of these genes have failed to match evolutionary expectations.

Transcription-factor-encoding genes belonging to one class — Antennapedia (ANTP) — are present throughout the animal kingdom and usually have a key role in development. The ANTP group includes the Hox, ParaHox and NK genes, all of which are paralogues, meaning that they have arisen in different animals from a shared ancestor as a result of gene-duplication events. However, the origins, evolution and, in particular, the timing of these duplication events have been unclear. 2

They “know” that these genes came from an ancient shared ancestor through gene duplication, but, darn it, what they “know” just isn’t consistent with genetic analysis! It is so “unclear!”

The sequences of two sponge genomes provide evidence that the ParaHox developmental genes are older than previously thought. This has implications for animal taxonomy and for developmental and evolutionary biology. 3

Animals that are most similar are presumed to have evolved from a close common ancestor. Just as you are more closely related to your father than your grandfather, your birth year is closer to your father’s birth year than your grandfather’s birth year. So, there are two aspects to genetic relationships (similarity and timing) which need to be consistent for evolution to be true. But when evolutionists try to construct an evolutionary tree, they often run into timing problems. Sponges are an example of this.

The authors first constructed a phylogenetic tree [evolutionary relationships] of a large family of ANTP genes. Given the great phylogenetic breadth that is spanned by the tree, it is unsurprising that high statistical support for relationships is not achieved. 4

It certainly is unsurprising for creationists because the evolutionary premise is false; but it should be surprising for evolutionists. The more data one has about so many different creatures (that is, the greater the phylogenetic breadth), the better the statistics should be, resulting in a clearer picture of what is going on. (An opinion survey of three people is not nearly as conclusive or informative as an opinion survey of three thousand people.) The data does not confirm their evolutionary expectations about relationships, but they just brush the data aside, saying it is “unsurprising” without justification.

In order to explain away the difference between their theory and their data, the “ghost locus hypothesis” was invented. Like “dark matter” in astronomy (which was made up to explain why the amount of matter measured in the universe isn’t anywhere near the amount of matter predicted by the Big Bang theory) the “ghost locus” depends upon imaginary ancestral DNA which must have been there, but can’t be found.

A substantial puzzle has arisen concerning the repertoire of ParaHox and Hox genes in animals. The first sponge genome to be sequenced was that of the demosponge (class Demospongiae) Amphimedon queenslandica. Although there seem to be no Hox or ParaHox genes in this genome, the evolutionary conservation of clusters of genes known to be neighbours of Hox and ParaHox genes in other organisms led to the proposal that Hox and ParaHox genes were present in the common ancestor of all animals but had been lost in sponges. The researchers called their idea the 'ghost locus' hypothesis. However, this evidence, although intriguing, was indirect, because it was based on an inference of ancestral gene content. 5

If one infers that there actually were ancestral genes, for which no actual evidence exists, then one comes to this conclusion:

This idea leads to the intriguing question of whether the common ancestor of all animals was in fact more developmentally complex than present-day sponges, cnidarians and placozoans, and that these groups have lost complexity, rather than that complexity has been gained in other animal lineages. 6

In other words, evolution must have taken a big step backwards. Some complex sponges evolved millions of years ago, and then devolved into the simpler sponges living today. There’s no real evidence for these ancient complex sponges; but they must have existed for the theory of evolution to be true.

Fossil Frustration

Coincidentally, fossils of “primitve” mammals described in scientific literature last month also frustrate evolutionists.

The phylogeny of Allotheria, including Multituberculata and Haramiyida, remains unsolved and has generated contentious views on the origin and earliest evolution of mammals. 7

Allotheria are some mysterious mammals, allegedly from the age of the dinosaurs, making them some of the first mammals. Evolutionists think they know things about these animals, and their evolutionary history, based on their teeth and ear bones, and a few other bones.

With the discoveries of the new euharamiyidans, it becomes increasingly evident that the cranial and postcranial features of euharamiyidans and multituberculates are similar to each other and to other mammals. However, the fundamental obstacle in interpreting their mammalian affinity remains the fact that the tooth pattern consists of two main rows of multiple cusps that are capable of longitudinal (palinal) chewing function in allotherians. If allotherians were placed outside mammals, it is equally difficult to derive the allotherian tooth pattern from other mammaliaformes, such as tritylodontids. Our phylogenetic analyses (Fig. 4) suggest that the primitive allotherian tooth pattern, as represented by Haramiyavia, was probably derived by developing an extra cusp row, or rows, from a triconodont-like tooth pattern or even from a tooth pattern with an initially reversed triangular cusp arrangement. 8

Let’s try to translate that paragraph into plain English. They have found some new fossils. Bones in their skulls (their craniums) and their bodies (postcranial) are a lot like other mammal bones—but their teeth are not. Are they mammals, or not?

But, as they admit, you can’t really tell much from a single tooth that isn’t in a jaw.

Nonetheless, the orientation of an isolated tooth in early mammals is not always certain, as demonstrated in the case of eleutherodontids (this study). … Better material with teeth in situ [in place] from each taxon of interest, such as Woutersia, is needed to test this hypothesis. 9

That’s their “out.” If they are wrong it is because they don’t really have enough fossils to go on.

The other distinguishing characteristic of mammals is the arrangement of ear bones, which supposedly evolved from jaw bones. As we pointed out several years ago, it is truly amazing that jaw bones could accidentally become excellent impedance matchers for auditory systems. 10 But apparently this same miraculous improvement to hearing happened twice, independently through convirgent evolution.

Our findings also favour a Late Triassic origin of mammals in Laurasia and two independent detachment events of the middle ear bones during mammalian evolution.

Finally, by reinterpretating Hadrocodium as having postdentary bones (see Supplementary Information, section G), our phylogeny suggests that detachment of the postdentary bones evolved twice independently during the early evolution of mammals, once in the clade leading to monotremes and once towards the clade containing Eutricondonta, Allotheria and Trechnotheria. 11

Just as in sponges, and underground trees, the same features supposedly accidentally evolved in mammals independently. But, before the criticism comes, they offer an excuse for why they might be wrong!

However, our phylogeny (Fig. 4 and Extended Data Figs 9 and 10) indicates that Euharamiyida and Multituberculata were probably derived from a Haramiyavia-like common ancestor at a minimum oldest age (according to current fossil records; future finds may reveal an earlier ancestor) in the Late Triassic and diversified thereafter during the Jurassic epoch, with known euharamiyidans adapting to a scansorial and/or arboreal lifestyle which may explain their rare fossil record. 12

They have hardly any fossils to base their opinions upon, and new fossil discoveries may prove them wrong, but at least they got their research published, so their funding will probably continue!

They need to get “better material with teeth in situ from each taxon of interest,” so send more money to finance more digging to prove evolution is true!

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1 Disclosure, June 2014, “Jellyfish, Kiwis, and Moa”
2 James O. McInerney & Mary J. O'Connell, Nature, 30 October 2014, “Evolutionary developmental biology: Ghost locus appears”, pp 570-571, http://www.nature.com/nature/journal/v514/n7524/full/514570a.html
3 ibid.
4 ibid.
5 ibid.
6 ibid.
7 Shundong Bi, et al., Nature, 30 October 2014, “Three new Jurassic euharamiyidan species reinforce early divergence of mammals”, pp 579-584, http://www.nature.com/nature/journal/v514/n7524/full/nature13718.html
8 ibid.
9 ibid.
10 Disclosure, April 2012, “I Heard it Through My Jaw Bones”
11 Shundong Bi, et al., Nature, 30 October 2014, “Three new Jurassic euharamiyidan species reinforce early divergence of mammals”, pp 579-584, http://www.nature.com/nature/journal/v514/n7524/full/nature13718.html
12 ibid.