Monday, 8 June 2015

Night-Flowering Bloomer For The Unintelligent Designer

Night-flowering catchfly (Silene noctiflora)
Maintaining a massive mitochondrial genome

This pretty little plant, known as the night-flowering catchfly (Silene noctiflora), is a native to Eurasia and is an introduced species in North America where it is a weed in cereal crops. It's also a major embarrassment for the Intelligent Design industry - or would be if they weren't carefully ignoring it.

Like so much else in biology, when you look at the detail, the notion of Intelligent Design is reduced to an absurdly ignorant superstition.

But first a little background (skip the next three paragraphs if you know about mitochondria):

Like all eukaryotic organisms, S. noctiflora has organelles called mitochondria within its cells. These are the powerhouse of the cell whose role is to convert glucose and oxygen into carbon dioxide and water and to use the released energy to turn ADP into ATP by adding an additional phosphate and so binding up some of the energy in a chemical bond. This energy store is then used to power the cells metabolic processes by breaking ATP back down to ADP and phosphate.

Mitochondria are known to be descendants of early cyanobacteria which have formed a symbiotic relationship with more primitive prokaryotic cells, probably along with a few other prokaryotes. All the other organelles have contributed their genome to the cell nucleus but, for reasons which are not entirely understood yet, mitochondria have retained some or most of theirs.

Like other prokaryotes such as archaea and other bacteria, mitochondria have circular chromosomes on which the few genes they still use as arranged. The normal arrangement for mitochondria is a single chromosome but there are variations and some rare forms have linear chromosomes - and this is where our little night-flowering catchfly excels itself.

The mitochondria in the night-flowering catchfly has more than 50 chromosomes totalling more than 7 Mb of information and, even more worryingly for 'Intelligent Design' advocates, this can vary by 19 entire chromosomes between populations, yet however many chromosomes an individual has, it only uses 54 genes comprising only a tiny fraction of this massive and variable genome. Many of the chromosomes have no genes at all.

Across eukaryotes, mitochondria exhibit staggering diversity in genomic architecture, including the repeated evolution of multichromosomal structures. Unlike in the nucleus, where mitosis and meiosis ensure faithful transmission of chromosomes, the mechanisms of inheritance in fragmented mitochondrial genomes remain mysterious. Multichromosomal mitochondrial genomes have recently been found in multiple species of flowering plants, including Silene noctiflora, which harbors an unusually large and complex mitochondrial genome with more than 50 circular-mapping chromosomes totaling ∼7 Mb in size. To determine the extent to which such genomes are stably maintained, we analyzed intraspecific variation in the mitochondrial genome of S. noctiflora. Complete genomes from two populations revealed a high degree of similarity in the sequence, structure, and relative abundance of mitochondrial chromosomes. For example, there are no inversions between the genomes, and there are only nine SNPs in 25 kb of protein-coding sequence. Remarkably, however, these genomes differ in the presence or absence of 19 entire chromosomes, all of which lack any identifiable genes or contain only duplicate gene copies. Thus, these mitochondrial genomes retain a full gene complement but carry a highly variable set of chromosomes that are filled with presumably dispensable sequence. In S. noctiflora, conventional mechanisms of mitochondrial sequence divergence are being outstripped by an apparently nonadaptive process of whole-chromosome gain/loss, highlighting the inherent challenge in maintaining a fragmented genome. We discuss the implications of these findings in relation to the question of why mitochondria, more so than plastids and bacterial endosymbionts, are prone to the repeated evolution of multichromosomal genomes.

Copyright © 2015, American Association for the Advancement of Science. Published under licence #3644351501154

In the words of the authors, "...these mitochondrial genomes retain a full gene complement but carry a highly variable set of chromosomes that are filled with presumably dispensable sequence.".

Now, creationists confidently tell us that no new information can arise and mutations always result in loss of information, and claim that genomes are intelligently designed by a perfect magic designer.

So, how does that fit in with the observable fact that not only is almost all the genome of the mitochondria in S. noctiflora dispensable, in other words, a complete waste of space, resource and time making it, but that the genome appears to have been replicated needlessly multiple times simply to pass on a tiny functional fraction of it, ending up with about 7 Mb of information?

Did the Intelligent Designer just go berserk or lose control of the process, creating masses of redundant information for the sake of it? If so, if this is an example of intelligent design, what should we expect an example of inept, stupid and incompetent design to look like?

If you think this example of ineptitude is bad enough, a relative of S. noctiflora, S. conica is even bigger at over 11 Mb arranged in 59 chromosomes. In terms of evolutionary biology, where DNA replication is known to be prone to errors, none of this is a mystery. If anything, the mystery is why this isn't more common. In the case of S. conica and S. noctiflora, the fact that they both display this multichromosomal structure is almost certainly due to that fact that a common ancestor also had it.

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