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Theory of Intelligent Design, the best explanation of Origins » Photosynthesis, Protozoans,Plants and Bacterias » The amazing diversity, beauty, and enigmatic genome of Diatoms

The amazing diversity, beauty, and enigmatic genome of Diatoms

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The amazing diversity,  beauty, and enigmatic genome of Diatoms

http://reasonandscience.heavenforum.org/t2466-the-amazing-diversity-beauty-and-enigmatic-genome-of-diatoms

Diatoms are one of the most important lifeforms on the planet. Plankton are responsible for 50% of earth’s oxygen. They have a very efficient way to dissipate excess solar energy, known as non-photochemical quenching. The real distinguishing feature of the diatoms is their shells. The valves are heavily embedded with silica (up to 71%). This glass-like wall reflects light creating intricate patterns that are striking and beautiful.

Chris Bowler from the Ecole Normale Supérieure at Paris thinks this clash of concepts just represents our anthropocentric and simplistic world view. “While we might want to call diatoms ‘plantimals,’ these things are much more complex than we think,” he says.

Diatoms have a sophisticated calcium and nitric oxide-based surveillance system for monitoring environmental stresses that can detect the release of aldehydes by its wounded neighbours. 18 Diatoms appear to have a highly mosaic genome, with genes originating from many different sources. Most notably, a large fraction of the genes may have been acquired by horizontal gene transfer (HGT) from bacteria. Although genomic data have shown that HGT — the swapping of genes between species that don't reproduce with one another — is much more common in eukaryotes than once thought, gene transfer between such distant relatives (diatoms and bacteria last shared a common ancestor a few billion years ago) is rare. 

Unless there was no common ancestor of the two.

Researchers at University of Gothenburg have found diatom spores buried in seafloor sediments that were able to revive after more than 100 years in a state of suspended animation. 

Diatoms detect and respond to physicochemical changes in their environment using sophisticated perception systems. 

At the end of a diatom bloom, massive cell loss usually occurs. In addition to sedimentation and grazing by herbivores, programmed cell death (PCD) of stressed cells is also considered one of the major causes for the decline of algal blooms. 8 The process of PCD executed by a superfamily of cysteine aspartate-specific proteinases (caspases) is a conserved mechanism of cell suicide.

Caspases are the principal proteases that are activated during animal apoptosis and mediate cleavage of a variety of proteins ultimately leading to cell disintegration 6 Caspases have undergone remarkable proliferation and specialization in vertebrates, in which they function in a cascade including several cleavage events. Structural comparisons showed that caspases belong to a distinct class of cysteine proteases, which also includes hemoglobinases, gingipains and clostripains (hereinafter CHF-class, after Caspase-Hemoglobinase Fold). Recent studies that involved a combination of in-depth sequence analysis, structural analysis and direct experiments revealed a substantially greater diversity of caspase-related proteases than previously suspected. In particular, two families of predicted CHF-proteases that are more closely related to the classic caspases than to other proteases of this class, designated paracaspases and metacaspases, were identified

If Darwins survival of the fittest is the goal of evolution, cell suicide is counter-intuitive, and it would make no sense for cells to emerge with proteins specifically with the function to trigger suicide.
If caspases are evolutionarily conserved, it means there was no evolution, but stasis.  Conservation is not evolution. its actually the oposit of evolution.  Its common parlance that evoution is inserted even where it does not belong.  Caspases have to emerge fully setup and functional. (Undoubtedly, similar mechanisms go back even further; scientists just happened to study this mechanism in a favorite lab worm, C. elegans.)  There are at least seven genes involved in apoptosis. Failure of apoptotis  has serious consequences for inflammation and autoimmunity.





Diatoms are one of the most important lifeforms on the planet. These single celled organisms have shells of silica and make almost half of all the organic compounds produced in the ocean. These are just a few of the reasons why plankton deserve the title “Earth’s most important creatures”. Plankton are responsible for 50% of earth’s oxygen. They are an essential part of the food chain. And billions of billions of ancient plankton have given their bodies to form the crude oil that powers modern society. Yet we rarely recognise their contribution to life on this planet, including our own. No one really knows how many different diatoms are out there, but conservative estimates suggest around 100,000 to 200,000 species, making them among the most species-rich lineages of eukaryotes. 19

The mysteries of the diatoms 14
Diatoms — single-celled algae typically enshrined in a cell wall made of intricately laced silica — have fascinated researchers with a whole range of mysteries, from their evolutionary origins through to their morphogenesis and reproduction.   They have spread around the globe and diversified into hundreds of genera and around 100,000 species in a short fraction of  timescale. Today, they are present wherever there is liquid water, in the oceans, in freshwater, and even in soil. They play a significant role in the global cycles of carbon and nitrogen, and are responsible for large sediments of silica including diatomaceous earth. Why have diatoms been so successful? Is it to do with their silica wall, as research from Paul Falkowski at Rutgers University has suggested? Silica cell walls are energy efficient to produce and unlike the carbonate biominerals of other species are not sensitive to ocean pH.  Alternatively, results from Christian Wilhelm at Leipzig show that they have a very efficient way to dissipate excess solar energy, known as non-photochemical quenching. Some experts believe that may be a crucial factor explaining their success. 

The Anatomy of The Diatom 5
The actual protoplast of a diatom is quite similar to that of other algae. Organelles such as the nucleus, mitochondria, and prominent plastids (chromatophores) are typical of most diatoms. The real distinguishing feature of the diatoms is their shells. The valves are heavily embedded with silica (up to 71%). This glass-like wall reflects light creating intricate patterns that are striking and beautiful. The nucleus in diatoms is usually centrally located, migrating to specific sites in the cell as the diatom prepares for cell division. DNA in diatoms is often organized as a large number of very small chromosomes. Upon cell division these often appear as a band of chromasomes surrounding the mitotic spindle. In contrast to many animal mitotic spindles, the spindle fibers in diatoms are often organised as a tight cylender of parallel microtubules.

The shell of the diatom is actually two overlapping halves called valves. One half (epitheca) is a remnant from the previous cell division, while the younger half (hypotheca) is the newly formed side. The hypotheca overlaps the epitheca like two halves of a petri dish. The valve itself of the epitheca is called the epivalve and the girdle elements (cincture or pleura) are named the epicingulum. The prefixes are the same for the hypotheca. The silica shells of diatoms are formed by exocytosis from the protoplast. Since the valves and the girdle elements are rigid, the growth is a unidirectional single plane of growth. There are also slits in the shell that are used for movement called the raphe. Diatoms usually have only one or two raphes per cell. The slits are aided by minuscule pores for material exchange

Genomes growing apart
In recent years, complete genome sequences of four diatom species have become available. In 2004, the group of Virginia Armbrust at the University of Washington in Seattle reported the genome of the diatom Thalassiosira pseudonana, which was followed by Phaeodactylum tricornutum, Fragilariopsis cylindrus and Pseudo-nitzschia multiseries (Nature (2009) 459, 185–192). Of these, Thalassiosira belongs to the group of centric (radially symmetric) diatoms, while the other three are raphid pennates, where the defining ‘raphe’ is a slit along the bottom that enables motility on surfaces.

The first two genome sequences showed that, in their relatively short evolutionary history, diatom species have grown apart much more than comparable groups. T. pseudonana and P. tricornutum, for instance, only parted company around 90 million years ago, but their genomes are as different as human and fish, which evolved separately for 550 million years.

The genomes also shed light on the unusual endosymbiotic origin and gene mixing of diatoms. Primary endosymbiosis, the process that gave us green algae and higher plants, happened around 1.5 billion years ago when an ancestral eukaryote acquired a cyanobacterium, which became the ancestor of today's chloroplasts.

In secondary endosymbiosis, by contrast, a eukaryote engulfed another eukaryote, namely a red alga, complete with its chloroplasts, mitochondria, and its nuclear genome. The alga in question may also have been infected by intracellular bacteria. The descendants of this more complicated merger, which happened only around one billion years ago, include diatoms, brown macroalgae, and oomycetes, important plant pathogens.

In the diatom genomes, researchers found a very eclectic mixture of genes, some resembling plants, others animals or bacteria. “One might say diatoms are animals with chloroplasts,” says Nicole Poulsen from the B CUBE Centre at the Technical University Dresden. Chris Bowler from the Ecole Normale Supérieure at Paris thinks this clash of concepts just represents our anthropocentric and simplistic world view. “While we might want to call diatoms ‘plantimals,’ these things are much more complex than we think,” he says.

Diatoms have a sophisticated calcium and nitric oxide-based surveillance system for monitoring environmental stresses that can detect the release of aldehydes by its wounded neighbours. 18 Diatoms appear to have a highly mosaic genome, with genes originating from many different sources. Most notably, a large fraction of the genes may have been acquired by horizontal gene transfer (HGT) from bacteria. Although genomic data have shown that HGT — the swapping of genes between species that don't reproduce with one another — is much more common in eukaryotes than once thought, gene transfer between such distant relatives (diatoms and bacteria last shared a common ancestor a few billion years ago) is rare. Unless there was no common ancestor of the two.

Cell signaling in marine diatoms 9
Diatoms detect and respond to physicochemical changes in their environment using sophisticated perception systems based on changes in [Ca21]cyt. Such processes are likely to improve algal adaptation to ubiquitous ocean processes such as mixing and to changes in chemical (for example, nutrient) gradients in time and space. Based on the knowledge of calcium signaling in other organisms, the physiological responses of diatoms to environmental changes are likely to be regulated by sense-process-respond chains involving specific receptors and feedback mechanisms, whose activity is determined by the previous history of the cell.

At the end of a diatom bloom, massive cell loss usually occurs. In addition to sedimentation and grazing by herbivores, programmed cell death (PCD) of stressed cells is also considered one of the major causes for the decline of algal blooms. 8 The process of PCD executed by a superfamily of cysteine aspartate-specific proteinases (caspases) is a conserved mechanism of cell suicide.

Caspases are the principal proteases that are activated during animal apoptosis and mediate cleavage of a variety of proteins ultimately leading to cell disintegration 6 Caspases have undergone remarkable proliferation and specialization in vertebrates, in which they function in a cascade including several cleavage events. Structural comparisons showed that caspases belong to a distinct class of cysteine proteases, which also includes hemoglobinases, gingipains and clostripains (hereinafter CHF-class, after Caspase-Hemoglobinase Fold). Recent studies that involved a combination of in-depth sequence analysis, structural analysis and direct experiments revealed a substantially greater diversity of caspase-related proteases than previously suspected. In particular, two families of predicted CHF-proteases that are more closely related to the classic caspases than to other proteases of this class, designated paracaspases and metacaspases, were identified

If Darwins survival of the fittest is the goal of evolution, cell suicide is counter-intuitive, and it would make no sense for cells to emerge with proteins specifically with the function to trigger suicide.
If caspases are evolutionarily conserved, it means there was no evolution, but stasis.  Conservation is not evolution. its actually the oposit of evolution.  Its common parlance that evoution is inserted even where it does not belong.  Caspases have to emerge fully setup and functional. (Undoubtedly, similar mechanisms go back even further; scientists just happened to study this mechanism in a favorite lab worm, C. elegans.)  There are at least seven genes involved in apoptosis. Failure of apoptotis  has serious consequences for inflammation and autoimmunity.

Apoptosis is "programmed cell death." When a cell becomes unstable or diseased, genetic algorithms kill it in an orderly way, to prevent further harm to the organism.  Specialized enzymes (especially the TNF superfamilies) switch on the program, setting locked-up destroyers called caspases loose in the cell. 7

Ancient Diatoms Lead To New Technology For Solar Energy 20
Engineers have discovered a way to use an ancient life form to create one of the newest technologies for solar energy, in systems that may be surprisingly simple to build compared to existing silicon-based solar cells. The secret: diatoms. Let’s start with the operative quote before the subject matter: “Nature is the engineer, not high tech tools.  This is providing a more efficient, less costly way to produce some of the most advanced materials in the world.”  OK, now the subject: how to build better solar cells, by imitating diatoms.  See the story on Science Daily.

The tiny pores in the silica tests (cases) of diatoms are very efficient at scattering light.  “These tiny, single-celled marine life forms have existed for at least 100 million years and are the basis for much of the life in the oceans,” the article said, assuming the evolutionary timeline, “but they also have rigid shells that can be used to create order in a natural way at the extraordinarily small level of nanotechnology.”
Researchers at Oregon State (OSU) have found a way to not just imitate the diatoms, but actually incorporate them.  “The new system is based on living diatoms, which are extremely small, single-celled algae, which already have shells with the nanostructure that is needed,” the press release says.  “They are allowed to settle on a transparent conductive glass surface, and then the living organic material is removed, leaving behind the tiny skeletons of the diatoms to form a template.”  Presto: a solar cell with better efficiency than those hard-to-manufacture ones.  It’s cheaper, easier, and better: “Steps that had been difficult to accomplish with conventional methods have been made easy through the use of these natural biological systems, using simple and inexpensive materials” that are already available in abundance. The researchers don’t even understand the physics.  They just know it works: “the tiny holes in diatom shells appear to increase the interaction between photons and the dye to promote the conversion of light to electricity, and improve energy production in the process.” That’s good news to a world looking for green ways to extract energy from renewable resources.

Researchers at University of Gothenburg have found diatom spores buried in seafloor sediments that were able to revive after more than 100 years in a state of suspended animation.  “We revived hundreds of genetic individuals of diatoms and induced them to start dividing again and to form cloned cultures,” a team member said.  “The oldest are more than 100 years old, the youngest quite fresh.”
How does this translate to our experience?  “As diatoms normally divide once a day, this means that for a diatom a period of 100 years is equivalent to 40,000 generations,” the article explained.  “In human terms, this means genetic material equivalent to around 800,000 years.” There’s a reason for this capability.  “What makes diatoms special is that if the environment they live in becomes too inhospitable they form resting spores, which gather in sediment at the bottom of the sea.  When conditions improve, the spores can be revived.”

The life of diatoms in the world’s oceans 16


5.  http://condor.depaul.edu/diatom/anat2.html
6.  http://www.nature.com/cdd/journal/v9/n4/full/4400991a.html#tbl1
7.  https://www.evolutionnews.org/2014/06/apoptosis_is_un/
8.  http://aem.asm.org/content/74/21/6521.full
9.  https://www.researchgate.net/publication/12442896_Perception_of_Environmental_Signals_by_a_Marine_Diatom
10. A privildedged plantet, Gonzalez, page 55
11. http://www.nationalgeographic.org/media/plankton-revealed/
12. http://www.mintpressnews.com/the-fabulous-history-of-plankton-and-why-our-survival-depends-on-it/44732/
13. https://www.guam.net/pub/sshs/depart/science/mancuso/apbiolecture/03_carbon/carbon.htm
14. http://www.cell.com/current-biology/fulltext/S0960-9822(12)00866-4
15. Environmental microbiology, page 38
16. http://www.nature.com/nature/journal/v459/n7244/full/nature08057.html
17. http://creation.com/gods-micro-world
18. http://www2.cnrs.fr/en/519.htm
19. http://www.livescience.com/46250-teasing-apart-the-diatom-genome.html
20. https://www.sciencedaily.com/releases/2009/04/090408145556.htm

More on How Microbes Make Earth Habitable
These Kaleidoscopic Masterpieces Are Invisible to the Naked Eye
[url=Microgeometric Design of Diatoms: Jewels of the Sea]http://www.icr.org/article/microgeometric-design-diatoms-jewels-sea/[/url]



Last edited by Admin on Fri Mar 24, 2017 1:39 pm; edited 11 times in total

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God’s micro world 17
Diatoms are marvels of complex architectural engineering. They have the unique ability to fashion intricate glass-houses for themselves by using the silica found naturally in sea-water. Not only are they intricately built, but they are found in all known geometrical shapes and are symmetrical in three dimensions, having perfectly matched tops and bottoms that are held together until the plant dies and the two halves come apart. Very rarely in biological systems do you find the use of straight lines for structural support. But diatoms are masters, not only at straight lines, but also at circles, triangles, squares, and ovals.
































































































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