Tuesday, 15 July 2014

Christmas Tree Tease for Creationists

The Norway spruce genome sequence and conifer genome evolution : Nature : Nature Publishing Group

Here's a fascinating piece of research from Sweden which is enough to give any self-respecting creationist pseudo-scientists a split personality. It shows how and why a Norwegian spruce (Picea abies a Christmas tree) has a much more extensive and complex genome than humans. I'll get to why it's a problem for creationists in a moment. Incidentally, thanks to Helmer von Helvete, a friend from Google+, for bringing this to my attention.

Abstract
Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

Björn Nystedt, Nathaniel R. Street, et.al.
The Norway spruce genome sequence and conifer genome evolution
Nature 497
, 579–584 (30 May 2013) doi:10.1038/nature12211

Copyright © 2013 Nature Publishing Group.
Reproduced for non-commercial/educational use under Creative Commons Attribution Noncommercial 2.5 license.

This research was carried out by a team from Umeå Plant Science Centre (UPSC) in Umeå and the Science for Life Laboratory (SciLifeLab) in Stockholm, Sweden, led by Björn Nystedt. Apart from its economic importance in that it opens up avenues for plant breeding of this important commercial and ecological species, it is interesting from a evolutionary biology perspective too.

The genome is seven times larger than that of humans and has about 29,000 functional (protein-coding) genes compared to the 17,000 human functional genes, about which I blogged only recently. This of course begs the question, why does it need a genome seven times larger than ours for a functional genome of less than double the size of ours. And why does it take 29,000 functional genes to make a Christmas tree but only 17,000 to make a human being?

One way, common in plants, by which a genome can be increased in size is by gene doubling where a mistake in the production of the reproductive cells produces pollen or ovules with the full complement of chromosomes instead of the normal half set. If this is fertilised with a similar diploid gamete it can result in a tetraploid version. The Cox's Orange apple is a tetraploid apple, for example. Another way is a simple doubling of a length of DNA during its replication so the same length is replicated twice and becomes incorporated in the normal genome.

A third way is by using a crude, near enough is good enough approach to replication. Imagine you are a computer programmer who needs to write a routine for copying a table of data but you don't know how big the table is. So, you write a routine to copy a chunk at a time until you are well past the end of the table and just leave it at that. Much easier than including a routine to work out the exact end of the table and so the exact length of the last chunk to be copied.

You copy all the table and a lot of following junk as well. Next time the routine runs it copies everything you copied earlier and a whole lot of new junk as well. So far as the user is concerned, the table is there and all seems okay, until eventually the memory footprint of the application gets massive because your sloppy, near enough is good enough routine has filled up the hard drive. Not good programming, but evolution isn't bothered about the future because it can't plan. Near enough is good enough works for evolution because evolution is unplanned and utilitarian. As a piece if intelligent design however, it's stupid. The programmer should have been thrown off the programming course.

It is remarkable that the spruce is doing so well despite this unnecessary genetic load. Of course, some of this DNA has a function but it seems strange that it would be beneficial to have so very much. This appears to be something special for conifers.

Professor Pär Ingvarsson, UPSC
The pines are gymnosperms but the scientists who carried out this analysis point out that there is no such evidence of gene doubling in the gymnosperm lineage. The only feasible explanation is a gradual accumulation of mostly redundant DNA due to a faulty replication and a defective correction mechanism which, in other plants, helps correct this faulty mechanism. It's a normal feature of DNA replication in both animals and plants that the ends of DNA sequences are often replicated several times. These are replicated again in the next generation and, over time would lead to a huge amount of redundant coding. In most species this tendency is corrected and it is this which seems to have failed in the Norwegian spruce leading to this accumulation of DNA over about 200 million years.

Now, the obvious problem for creationist pseudo-scientists is how to handle this, apart from it needing 200 million years to accumulate.

Creationist Parodies
Creationism relies on perpetuating several myths about the science of evolution because these myths or parodies are what creationist pseudo-scientists earn their living attacking.

One of the myths is that biologists think that evolution is about how human beings came about and that the entire point of evolution has been to evolve human beings. This means that human beings have to be presented as the most highly evolved and most complex of species, at least in the pseudo-scientific view of evolution.

This is, of course, nonsense since evolution is all about how diversity arose and it has no aim or objective. No single species can be said to be more highly evolved than another since all living species have been diversifying for the same length of time. Never-the-less, if you go to a creationist website you'll see that parody of evolution attacked time and again.

Another myth is that evolution always involves increased complexity and new information. This makes it easier to attack evolution with a scientific-looking claim that it somehow contradicts basic laws of physics such as the Laws of Thermodynamics and some half-understood dogma that no new information can ever arise because that contradicts some fundamental law related somehow to thermodynamics too.

This too is nonsensical and based on a deliberate misrepresentation of the Laws of Thermodynamics, which neither preclude a local decrease in entropy nor prevent new meaning to existing information arising if the environmental context changes, or new information arising for that matter. If it did there could be no life because chemical processes could not occur, nor could automobiles work or any wealth ever be created by doing work.

Thirdly, creation pseudo-scientists present increased complexity in structure as reflecting increased complexity in the genome, so the more complex an organism is, the more complex its DNA must be. This plays to the myth that somehow DNA is like a computer program so more complex output must come from more complex input. This is also nonsense because DNA is more like a recipe than a construction manual. Complexity can come simply from switching controlling genes on or off at different times, hence the human genome has almost the same number of functional genes as chimpanzees and gorillas and only differs from that of a mouse by about ten functional genes. Same ingredients; slightly different recipe.

So, creation pseudo-scientist are faced with several dilemma here:
  1. How do they explain a manifestly less complex organism like a Norwegian spruce having such a vastly more complex genome and almost twice as many functional genes as humans? If their parody of evolution was correct, humans would have the most complex genomes.
  2. If additional DNA means additional information, what new information is there in all the redundant DNA in Picea abies and why does a spruce need seven times the information that humans need?
  3. How do they explain a species which diversified from the last common ancestor shared with humans about 500 million years ago having a more complex genome than humans? If their parody of evolution was correct the human genome should be the largest because humans are the most highly evolved of all creatures.
  4. How do they explain such a huge genome with so much redundant DNA? Why would any intelligent designer create so much redundant DNA?
  5. How do they explain a faulty DNA replication mechanism which needs an error-correction method to prevent it running out of control in the first place, and why would an intelligent designer then break the correcting mechanism it designed to compensate for its earlier mistake?
So what's it to be creationists?

Are you going to claim that the Christmas tree is more complex and more highly evolved than Humans; that genome complexity does not mean new information and increased phenotypic complexity or that the Intelligent Designer just messed up with the Christmas tree? Answers below, please.

I'll leave the problem of the salamanders with their huge genomes for another day.

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