Casually Refuting Creationism With Codfish Genes

Polar cod, Boreogadus saida

Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids | PNAS

The amazing thing is that creationists never seem to notice how frequently scientific research, quite incidentally and without conscious intent, casually refutes creationism and the claims of creationists. It's as though there is a complete detachment from reality in creationism.

This paper, for example, about the evolution of 'antifreeze' genes in an arctic fish related to cod, utterly refutes four creationist claims whilst giving a completely consistent evolutionary explanation supported by evidence.

The refuted creationist claims are:

• No new information can arise by mutation.
• There is no such thing as non-coding DNA.
• 'Irreducible complexity' can't arise by a gradual process.
• The Theory of Evolution is a theory in crisis about to be overthrown and replaced by the notion of 'Intelligent Design'.

A team of researchers from the School of Integrative Biology, University of Illinois at Urbana–Champaign, Urbana, IL, USA has shown that the antifreeze glycoprotein gene of the northern codfish originated from a noncoding region and describe the detailed mechanism of its "evolutionary transformation into a full-fledged crucial life-saving gene". The gene in question is the Antifreeze Glycoprotein (AFGP) gene.

Significance
The diverse antifreeze proteins enabling the survival of different polar fishes in freezing seas offer unparalleled vistas into the breadth of genetic sources and mechanisms that produce crucial new functions. Although most new genes evolved from preexisting genic ancestors, some are deemed to have arisen from noncoding DNA. However, the pertinent mechanisms, functions, and selective forces remain uncertain. Our paper presents clear evidence that the antifreeze glycoprotein gene of the northern codfish originated from a noncoding region. We further describe the detailed mechanism of its evolutionary transformation into a full-fledged crucial life-saving gene. This paper is a concrete dissection of the process of a de novo gene birth that has conferred a vital adaptive function directly linked to natural selection.

Abstract
A fundamental question in evolutionary biology is how genetic novelty arises. De novo gene birth is a recently recognized mechanism, but the evolutionary process and function of putative de novo genes remain largely obscure. With a clear life-saving function, the diverse antifreeze proteins of polar fishes are exemplary adaptive innovations and models for investigating new gene evolution. Here, we report clear evidence and a detailed molecular mechanism for the de novo formation of the northern gadid (codfish) antifreeze glycoprotein (AFGP) gene from a minimal noncoding sequence. We constructed genomic DNA libraries for AFGP-bearing and AFGP-lacking species across the gadid phylogeny and performed fine-scale comparative analyses of the AFGP genomic loci and homologs. We identified the noncoding founder region and a nine-nucleotide (9-nt) element therein that supplied the codons for one Thr-Ala-Ala unit from which the extant repetitive AFGP-coding sequence (cds) arose through tandem duplications. The latent signal peptide (SP)-coding exons were fortuitous noncoding DNA sequence immediately upstream of the 9-nt element, which, when spliced, supplied a typical secretory signal. Through a 1-nt frameshift mutation, these two parts formed a single read-through open reading frame (ORF). It became functionalized when a putative translocation event conferred the essential cis promoter for transcriptional initiation. We experimentally proved that all genic components of the extant gadid AFGP originated from entirely nongenic DNA. The gadid AFGP evolutionary process also represents a rare example of the proto-ORF model of de novo gene birth where a fully formed ORF existed before the regulatory element to activate transcription was acquired.

Xuan Zhuang, Chun Yang, Katherine R. Murphy, and C.-H. Christina Cheng
Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids
PNAS March 5, 2019 116 (10) 4400-4405. DOI: 10.1073/pnas.1817138116

Copyright: © 2019 the Author(s). Published by PNAS.
Open Access
Reprinted under the terms of a Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).

By comparing the genome of the AFGP-bearing fish, the Polar cod, Boreogadus saida, the Atlantic cod, Gadus morhua and the Atlantic tomcod, Microgadus tomcod with those of other related, non-AFGP-bearing related species, whiting, Merlangius merlangus, Norway pout, Trisopterus esmarkii, cusk, Brosme brosme and the freshwater burbot, Lota lota, they were able to show a clear evolutionary progress for the three component parts of the antifreeze system.

Figure 1

Gadid phylogeny and AFGP gene/homolog structures. The phylogenetic tree of Gadidae is a congruent cladogram derived from Bayesian and maximum likelihood trees using complete ND2 gene sequences. Light blue branches indicate lineages of the Gadinae subfamily. The two gadine subclades containing AFGP-bearing species (red vertical bars), their most recent common ancestor (blue dot), and the emergence of the AFGP trait are as indicated. The three AFGP-bearing species (AFGP+) and four AFGP-lacking species analyzed in this paper are shaded in blue and yellow, respectively. The structure of their AFGP gene or nongenic homolog is shown to the right. Gray and purple shaded areas indicate homologous regions. Cyan segments are sequence repeats. The dark blue segment is a repetitive AFGP cds or AFGP-like sequence.

The monophyletic Gadidae family [sensu (18)] includes both AFGP-bearing and non-AFGP-bearing species; the former occurs in two subclades within the subfamily Gadinae (Fig. 1). The selected AFGP-bearing Boreogadus saida (polar cod) (19) and Gadus morhua (Atlantic cod) (20) represent one gadine subclade, and Microgadus tomcod (Atlantic tomcod) (21) represents the other. The four AFGP-lacking gadids were chosen for their evolutionary distances from the AFGP bearers. Two of them are gadines; Merlangius merlangus (whiting) nests within the AFGP-bearing subclade containing B. saida and G. morhua and thus shares the last common ancestor with all AFGP-bearing species (Fig. 1, blue dot), whereas Trisopterus esmarkii (Norway pout) is basal to the two AFGP-bearing subclades. The other two, Brosme brosme (cusk) and the freshwater Lota lota (burbot) belong to the subfamily Lotinae and are basal species that serve as ancestral proxies before the AFGP trait emerged (Fig. 1).

For references, see the original paper.

Figure 4

Evolutionary mechanism of the gadid AFGP gene from noncoding DNA. The color codes of the sequence components follow Fig. 1. (A) The ancestral noncoding DNA contained latent signal peptide-coding exons with a 5′ Kozak motif, adjacent to a duplication-prone 27-nt GCA-rich sequence. (B) The 27-nt GCA(Ala)-rich sequence duplicated forming four tandem copies. (C) A 9-nt in the midst of the four 27-nt duplicates became the three codons for one AFGP Thr-Ala-Ala unit and underwent microsatellitelike duplication forming a proto-ORF. (D) A proximal upstream regulatory region acquired through a putative translocation event. (E) A 1-nt frameshift led to a contiguous SP, a propeptide, and a Thr-Ala-Ala-like cds in a read-through ORF. (F) Intragenic (Thr-Ala-Ala)n cds amplification, fulfilling the antifreeze function under natural selection.

The antifreeze system consists of the antifreeze (a relatively simple peptide chain consisting of a repeated sequence of three amino acids, threonine-alanine-alanine (Thr-Ala-Ala)), a 'signal' protein that triggers the release of the antifreeze into the blood, and a DNA promoter region that enables transcription of the DNA into RNA to produce the antifreeze molecules.

The team showed that all three of these component parts were derived from duplicated and translocated existing DNA, with the complete system unable to function until the promoter region translocated to the right position. By examining the DNA of relatives, the entire series of steps was reconstructed so we can see a clear evolutionary order, resulting in a systems that is functionally irreducibly complex and yet which arose a step at a time by a clear evolutionary pathway consisting of random mutations, gene duplication and translocation, the result was new information and a de novo gene.

Spot the lie. Creationist misrepresentation of evolution.

Not surprisingly, the creation disinformation industry has enlisted a creationist biochemist, Dr Ross Anderson, to try to do a hatchet job on the paper. He does this by impugning the professional integrity of the authors, accusing them of 'just storytelling', but offers no alternative explanation for the evidence they present and is reduced to invoking the known creationist falsehood in his final sentence, that mutations always results in loss of function.

Quite how he would expect mutation in non-coding (ie, functionless) DNA to lead to a loss of function is not immediately obvious and Anderson does nothing to clarify it, presumably not expecting creationists to notice this absurdity.

With his final flourish he appeals to the conspiracy theorists who are an essential part of the creationist cult, implying that the paper would not have been published if the authors had been honest. For good measure, in case any of his dupes have still not go it, he illustrates his article with a childish fantasy cartoon which misrepresents the evolutionary process by presupposing a required outcome and ignoring the role of natural selection and presents scientists as mindless idiots so his dupes can feel superior.

It really is about time that creationists started to ask themselves why science keeps on refuting their basic claims and why the creation industry needs to blatantly misrepresent science and indulge in ad hominem attacks on scientists when they can't refute their findings nor offer a better explanation for the evidence.

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