Genome of Diatom Reveals Unanticipated Complexity

“Let’s play 20 questions.”:
“OK, I’m game.  Animal, vegetable or mineral?”
“Yes.”
“I give up.”
The answer is: a diatom.  Some of the most abundant one-celled organisms in the sea, and essential for regulating the global carbon cycle, diatoms seem to be part animal, vegetable and mineral.  Scientists aren’t sure how to classify them.  They do photosynthesis like plants, but have some animal-like genes, and they build crystal houses of exquisite beauty out of silica (see 07/21/2004 headline).  Now, for the first time, the genome of one species of diatom was sequenced.  It was reported Oct. 1 in the journal Science.¹  The glass house of this organism, Thalassiosira pseudonana, looks like a pill box with a lid (for picture, see the news story on EurekAlert).
    The evolutionary story of the origin of diatoms is that once upon a time, a heterotrophic (other-feeding) microbe engulfed a red alga.  The two became one, and lived happily ever after in an arrangement called endosymbiosis.  The researchers did indeed find homologous genes to red algae and protozoa, but were not prepared for the complexity of the gene library of something so small.  This diatom has 24 pairs of chromosomes and 11,242 protein-coding genes in its 34 million base-pair genome.  The team was surprised to find genes for the urea cycle, a nitrogen-processing system commonly found in animals that eat meat, in a plant-like photosynthetic organism: “Identification of enzymes necessary for a complete urea cycle was unanticipated, because this pathway has not previously been described in a eukaryotic photoautotroph”.  This nitrogen cycle was not just an idle subroutine, either: “The urea cycle appears to be fully integrated into diatom metabolism in ways not previously suspected,” they said.  Also, who would have thought a little transparent sea creature would be an expert in fat metabolism?

We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.

Apparently even diatoms can store fat for the winter in a manner “unusual among eukaryotes.”  Another unique feature of many diatoms is their ability to manufacture little hairs of chitin that protrude from their glass shells, so that they don’t sink so easily.  This enables them to stay near the sunlit surface on which they depend.
    Although the research team believes their discovery of alga-like genes supports the notion of a primordial endosymbiosis for the origin of diatoms, their paper exhibited two unsolved problems with the idea.  First, in a Venn diagram of homologous genes, the report showed 1853 genes not found in animals, green or red algae (3738 common to all three), and 2550 genes not found among cyanobacteria, green or red algae (922 common to all three).  “About half the genes in the diatom cannot be assigned functions on the basis of similarity to genes in other organisms, in part because diatoms have distinctive features that cannot be understood by appeal to model systems.”  That’s a lot of functionality for an organism to develop de novo, even if some of the knowledge was gained through a merger.
    Second, the team is baffled over how the alga genes made it past the barriers into the genome.  “Establishment of a stable secondary endosymbiosis required evolution of a protein import system to allow cytoplasmically synthesized proteins to traverse the two additional membranes that surround the plastid,” they note.  They can understand the first crossing of the endoplasmic reticulum, “but the mechanism of transit across the next three membranes remains unclear.”
    Scientists are eagerly striving to understand the exquisite glass-blowing capability of these creatures.  Their shells are beautifully designed, yet so small that 70 could fit across the width of a human hair.  “Diatoms can manipulate silica in ways that nanotechnologists can only dream about,” said one researcher.  For information on the importance of diatoms to the global ecology and climate, see the summary on EurekAlert, where oceanographer Virginia Armbrust (U of Washington) said, “These organisms are incredibly important in the global carbon cycle.”  The report elaborates, “Together, the single-celled organisms generate as much as 40 percent of the 50 billion to 55 billion tons of organic carbon produced each year in the sea and in the process use carbon dioxide and produce oxygen.  And they are an important food source for many other marine organisms.”

¹Armbrust et al., “The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism,” Science, Vol 306, Issue 5693, 79-86, 1 October 2004, [DOI: 10.1126/science.1101156].

Thank God for little things.  If it is phenomenally, inconceivably improbable for a cell to develop one usable protein by chance (see online book), how are we supposed to believe that after the hypothetical merger in some dim chapter of the evolutionary past, the new diatom evolved a “protein import system” to get the new genes past three more membranes?  Organisms don’t normally tolerate foreign proteins; they destroy them.  This explanation has all the flaws of the typical Darwinian just-so story.  It is a mere tentative suggestion, generalizing the broad-brush picture but ignoring the nasty details.  Who could possibly believe that diatoms just invented, in salty water, glass-sculpturing expertise that “nanotechnologists can only dream about,” to say nothing of evolving half its genes that are unique?  Such wishful thinking should be laughed out of court.
    Their endosymbiont tall tale doesn’t help Darwinism anyway, because it pushes even farther back in time the “evolutionarily ancient divergence of Plantae (red algae, green algae, and plants), Opisthokonta (animals/fungi), and the unknown secondary host that gave rise to the heterokont (diatom) lineage.”  Imagine their surprise at this admission: “ Interestingly, 806 diatom proteins align with mouse proteins but not with green plant or red alga proteins.”  So how to save the Darwin story now?  It gets even more convoluted: “The most straightforward interpretation is that these ‘animal-like’ genes were derived from the heterotrophic secondary host, although scenarios involving gene loss in the plant/red algal lineage cannot be ruled out.”  But the former would mean that these genes underwent no evolution from near the beginning of life all the way to the origin of mammals like mice, and the latter explanation would be devolution, not evolution.  Any story that violates Occam’s razor this badly should be rejected.  Both cases mean high levels of complexity already existed from the beginning.  The only explanation that fits the evidence is that diatoms are marvels of intelligent design, doing their part to maintain the biosphere of a privileged planet.