{"id":1578,"date":"2013-11-20T17:32:42","date_gmt":"2013-11-20T23:32:42","guid":{"rendered":"https:\/\/skepticink.com\/smilodonsretreat\/?p=1578"},"modified":"2013-11-20T17:32:42","modified_gmt":"2013-11-20T23:32:42","slug":"darwins-doubt-another-quote-another-mine","status":"publish","type":"post","link":"https:\/\/skepticink.com\/smilodonsretreat\/2013\/11\/20\/darwins-doubt-another-quote-another-mine\/","title":{"rendered":"Darwin’s Doubt – Another Quote, Another Mine"},"content":{"rendered":"

I’ve been doing some research on the origin of body plans. \u00a0Mainly to address those chapters in\u00a0Darwin’s Doubt<\/em> that deal with them. \u00a0Nick Matzke put me on the trail of some recent work in the area. \u00a0While reading the article (published in 2009), I saw some compelling evidence that the body plans of the various phyla developed prior to the Cambrian explosion. \u00a0If this were true, then the entire point of Meyer’s book is refuted.<\/p>\n

If animals had the genes for the body plans and only something like the regulation of those genes changed, then Meyer’s various claims about body plans suddenly appearing in the Cambrian and no evidence for prior forms are destroyed. \u00a0I’ll get to that evidence in a minute.<\/p>\n

As I was reading this article, I wondered if Meyer had read it. \u00a0Turns out, he does actually quote from the article, but it is only included in a footnote, not in the references. This omission is interesting when we see just what Meyer says… and doesn’t say about the article.<\/p>\n

The article in question is by Charles Marshall and James Valentine, both victims of massive quotemining by Meyer in this book. \u00a0The article is titled “The Importance of Preadapted Genomes in the Origin of the Animal Bodyplans and the Cambrian Explosion<\/a>“. \u00a0Wow, not only is it a mouthful, but something like this should be a primary work cited in a book that concerns itself with the origin of body plans, the genetics of them, and the Cambrian Explosion. \u00a0But it’s just a little, unimportant footnote. \u00a0I wonder why Meyer is hiding this… let’s find out.<\/p>\n

When trying to unravel the origins of the animal phyla… the hardest to examine is the phase between the actual cladogenic origin of a phylum and the time that it acquired its first phylum-specific characteristic(s). Even if we have fossils from this phase in a phylum’s history, we will not be able to prove their kinships at the level of phyla.54 [ed note:\u00a0Darwin’s Doubt <\/em>pg.95]<\/p><\/blockquote>\n

This is what Meyer wrote. \u00a0The “54” is the footnote. \u00a0And there, are those damn ellipses again. \u00a0Let’s see what’s missing, by looking at what the actual article says.<\/p>\n

When trying to unravel the origins of the animal phyla, three\u00a0distinct phases in their evolution must be considered (Fig. 1).\u00a0First, and<\/strong> the hardest to examine,<\/strong> is the phase between the actual\u00a0cladogenic origin of a phylum, and the time that it acquired its\u00a0first phylum-specific characteristic(s). Even if we have fossils\u00a0from this phase in a phylum\u2019s history, we will not be able to\u00a0prove their kinships at the level of phyla, although they may be\u00a0referable to a more inclusive clade within which the phylum has\u00a0branched.<\/strong> \u00a0[ed note: I bolded the differences.]<\/p><\/blockquote>\n

Wow, that’s a pretty blatant quotemine there. \u00a0Notice how Meyer (through the use of those magical ellipses) removed the entire idea that there are three distinct phases AND the idea that phylums can be associated with a clade at all.<\/p>\n

In other words, Meyer took one part of the ideas presented by Marshall and Valentine and created from it the idea of an insurmountable problem, when in reality it’s not insurmountable and it’s not really a major issue at all.<\/p>\n

What do the authors say about the other two pieces that Meyer ignored?<\/p>\n

In contrast, phase 2 consists of the stem lineages that descended from the first species that can be diagnosed morphologically as belonging to the phylum. However, some of the morphological features that define a phylum may have low preservation\u00a0potentials, so that even if we have early fossils from this phase\u00a0of a phylum\u2019s evolution, we may not see the key features that\u00a0would permit accurate assignment. Thus, as a practical paleontological matter, even if we are lucky enough to find early fossils\u00a0that just postdate the origin of the first morphologically diagnostic feature of the phylum, they may not be identified as such.<\/p><\/blockquote>\n

This is really the problem of fossilization that I’ve talked about earlier. \u00a0We’re talking about fossils that have survived over half a billion (with a “B”) years of Earth’s changes. \u00a0The changes are major changes to entire continents and oceans.<\/p>\n

When we find the fossils and when they have parts that fossilize well (chitin, for example), then we can (usually) put the organism into a phylum. But if we don’t have hard parts (things like the cell structure, or DNA, or muscles), then we may not even realize that an organism really should belong into a particular phylum. \u00a0For example, it wasn’t until recently that significant evidence turned up that birds really did come from dinosaurs. And that was only about 100 millions years ago, not 500 million years ago.<\/p>\n

Phase 3 begins with the appearance of the last common ancestor of the living representatives of the phylum, that is, of the\u00a0crown group of the phylum. Here the fossil record, as well as comparative analysis of the living taxa, informs our understanding of\u00a0the morphology of this LCA of the crown group.<\/p><\/blockquote>\n

Here, we get the recognizable phyla and can easily determine the existence of the characters that define the phyla.<\/p>\n

The authors state that the purpose of the article is to deal with phase 1. \u00a0Meyer ignores the remainder of the 9 pages of the article, which contains ideas and evidence about where the body plans of the phyla came from. \u00a0Let me just post some quotes from the article. \u00a0Obviously, if Meyer considers the work good enough to put in his book, then he agrees that Marshall and Valentine are experts right… and I think it’s important to let them have their say.<\/p>\n

To examine this part of the animal tree, the fossil record is of\u00a0little use (but see below). Instead we must rely heavily on both\u00a0the morphology and on molecular characters from living taxa to\u00a0determine the topology of the tree, and then, having secured that,\u00a0turn to comparative genomic data to make inferences about the\u00a0developmental and morphological and ecological capacities of\u00a0those now extinct basal taxa (Table 2).<\/p><\/blockquote>\n

Inferences are good enough to the notions of Intelligent Design right<\/a>? But these inferences will have statistical support.<\/p>\n

Here we are\u00a0interested in the relations between those deeper-branching phyla\u00a0for which whole genomes or significant amounts of data on developmental regulatory genes are available. Of all the topologies that\u00a0have been published, we feel that the topology shown in Figure 2\u00a0is the most likely, and each node finds support from both morphological and molecular data. This topology implies an increase\u00a0in the size of the regulatory gene complement from branch to\u00a0branch, indicated by the increasing numbers of regulatory gene\u00a0families found, as reviewed below.<\/p><\/blockquote>\n

I have added figure 2 below.<\/p>\n

\"Marshall_fig2\"<\/a><\/p>\n

Just so you can see what their reconstruction looks like. \u00a0The important bit is the statement about how the number of regulatory genes increase from branch to branch. \u00a0What the authors are saying is that, unlike the high school level biology that most creationists (and non-specialists) have where DNA makes proteins and that’s it. \u00a0There are lots and lots of genes that don’t create proteins. \u00a0These DNA sequences regulate other DNA sequences and some of those DNA sequences produce proteins. \u00a0I wrote about this earlier<\/a>.<\/p>\n

Clearly, the pre [Cambrian] explosion fauna had to have been phylogenetically diverse, as it included the ancestors of the explosion phyla.\u00a0Furthermore, the position of explosion fossils on the phylogenetic\u00a0tree implies that many phyla that do not appear during the explosion were nevertheless present at least as stems (phases 1 and 2).\u00a0Features associated with larger bodyplans (and not required of\u00a0tiny organisms) were presumably elaborated as the larger forms\u00a0evolved, producing the beautiful stem forms of the explosion\u00a0fauna.<\/p><\/blockquote>\n

What they are saying (with a page and half of data and references), is that the preCambrian animals were very diverse. \u00a0The fossils from the Cambrian imply that the phyla that appeared after the Cambrian were present, just in a form we don’t realize belong to that phyla (phases 1 and 2 mentioned above).<\/p>\n

Far from being a sudden appearance of all the phyla, they were either A) already present, we just can’t tell or B) the ancestors that became those phyla were already present. \u00a0The data presented here (which I haven’t found and read all of yet, there are over two pages of references) suggests that Meyer is totally wrong. \u00a0And his failure to at least include this work (and those referenced by this work) in his book is a scholarly failure of the highest order.<\/p>\n

When taken at face value, the message from all these data\u00a0is that many of the genes that regulate eumetazoan and bilaterian\u00a0development originated in relatively simple animals before and\u00a0during the origin of eumetazoans, before they acquired their well\u00a0known functions in bilaterians, functions commonly conserved\u00a0across many phyla. Certainly the accumulation in early metazoan\u00a0genomes of what are today important regulatory genes does not\u00a0seem to correlate with morphological complexity; that is, the early metazoans are much simpler than one might suspect give those\u00a0gene functions in more derived metazoans. But perhaps any such\u00a0expectation is simply over-interpreting early functions of those\u00a0genes; it seems likely that although they serve in the development
\nof morphologically complex organisms now, their presence does\u00a0not mean that the organisms that possessed them were necessarily\u00a0complex.<\/p><\/blockquote>\n

This statement follows another page or so of data and references. \u00a0If you can read through all the odd names, this breaks down to the genes that are important bilateralians (animals with a left and a right side, like humans) are present well before the first bilateralian existed. \u00a0Metaazoans are animals. \u00a0The early metazoans were simple organisms, but they already had the genes that were needed to make more complex organisms.<\/p>\n

It seems reasonable to suggest that the\u00a0Cambrian explosion in bilaterian body plans was underlain chiefly\u00a0by selection for novel patterns of gene expression, including regulatory RNAs as well (see below), mediating the morphological\u00a0radiation as the bilaterian lineages responded to new adaptive\u00a0opportunities.<\/p><\/blockquote>\n

I am reminded of Ghostbusters here. \u00a0I can see this little organism saying “We have the tools, and we have the talent.” \u00a0We need to get away from (again) this high school biology idea of an organism (or population) changing in response to a stimulus. \u00a0Evolution isn’t “It’s getting hotter, we have to adapt.” \u00a0Evolution is, “this is what we have, what can we do with it”. \u00a0Provided we anthropomorphicize evolution, which we shouldn’t do, because it’s wrong.<\/p>\n

We see, through the data that Marshall and Valentine provide that the genes were already in place. \u00a0Maybe they weren’t yet doing what they do in modern organisms, but they were there. \u00a0How do we know that?<\/p>\n

Some genes are present in every single animal on the planet. \u00a0Genes like the\u00a0Hox<\/em> genes. \u00a0It is much more likely that these genes evolved once, in the last common ancestor of all animals, than evolved almost exactly the same, many times, in many different phyla. \u00a0Now, a design advocate would say, “It’ not common ancestry, but common design.”<\/p>\n

That’s fine as far as it goes, but all that claim is doing is pawning off the issue until the designer is found. \u00a0Until ID advocates find the designer, then that argument is essentially useless.<\/p>\n

Given that the genomes of the many invertebrate lineages that\u00a0were ancestral to the disparate stem and crown groups of the explosion fauna harbored rich developmental genomes (as is certain\u00a0regardless of whether they were reduced or cryptic), it is easier\u00a0to understand the relatively abrupt evolution of the bodyplans\u00a0of larger, more complex explosion fossils. The requirements for\u00a0increased developmental complexity and refinement needed to\u00a0generate those morphological novelties did not have to be met\u00a0from scratch; by and large the required pool of regulatory genes\u00a0was already present in the more basal bilaterian lineages and\u00a0the mechanisms of signaling and transcription pattern evolution\u00a0were already well established, even if they were later elaborated\u00a0through gene duplication in some lineages.<\/p><\/blockquote>\n

Again, the authors are just stating what we’ve already talked about. \u00a0The genes for complexity were already present. \u00a0Unlike what Meyer claims, the genes needed to create these body plans didn’t have to ‘suddenly appear’, but just minor regulatory changes and you get massive changes in the appearance of the organisms. \u00a0Just as humans have individuals ranging from 3 foot tall to almost 9 feet tall… and there weren’t massive changes to the entire genetic code to generate those differences.<\/p>\n

This paper is a really amazing piece of work and I’m still digesting it. \u00a0I’ll probably do more writing on it later. \u00a0If I haven’t been clear, please let me know, this was kind of a rush writing job (and I detest editing myself… as you can probably tell).<\/p>\n

In conclusion, Meyer, once again, takes a quote out of context and mangles it in the hopes that no one will call him on it. \u00a0Sorry buddy, but I’m calling you on it. \u00a0There are two pages of references that support the work in this article… when you have refuted the majority of them with data… well, even then your quotemine isn’t justified.<\/p>\n

 <\/p>\n

____________________________<\/p>\n

Marshall, Charles , and James Valentine. \u201cThe importance of preadapted genomes in the origin of the animal bodyplans and the Cambrian explosion.\u201dEvolution; international journal of organic evolution<\/i>, 30 Apr. 2010. Available: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19930449.<\/p>\n","protected":false},"excerpt":{"rendered":"

I’ve been doing some research on the origin of body plans. \u00a0Mainly to address those chapters in\u00a0Darwin’s Doubt that deal…<\/p>\n","protected":false},"author":27,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[81,24,597,28,562,6],"tags":[939,467,117,283,599,937,600],"class_list":["post-1578","post","type-post","status-publish","format-standard","hentry","category-book-review","category-creationism","category-featured","category-genetics","category-paleontology","category-science","tag-creationism","tag-darwins-doubt","tag-genetics-2","tag-intelligent-design","tag-marshall","tag-science","tag-valentine"],"_links":{"self":[{"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/posts\/1578","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/users\/27"}],"replies":[{"embeddable":true,"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/comments?post=1578"}],"version-history":[{"count":0,"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/posts\/1578\/revisions"}],"wp:attachment":[{"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/media?parent=1578"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/categories?post=1578"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/skepticink.com\/smilodonsretreat\/wp-json\/wp\/v2\/tags?post=1578"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}