Friday, February 12, 2016

Tiny Eyeballs and Purple Socks

Some cyanobacteria — pond scum — swim toward brighter areas. Scientists didn't know how the microorganisms could tell where the light is, until now.

Other scientists discovered four new species of an odd-looking sort of critter: including one that looks like a purple sock.

I'm fascinated by this sort of thing, your experience may vary:
  1. Learning How Bacteria "See"
  2. Solving the Purple Sock Mystery

Psalms, Wisdom, and Accepting Reality

We've known that the universe is big and old for millennia. We've also known that humanity is "little less than a god."
"The heavens declare the glory of God; the sky proclaims its builder's craft."
(Psalms 19:2)

"When I see your heavens, the work of your fingers, the moon and stars that you set in place -

"4 What are humans that you are mindful of them, mere mortals that you care for them?

"5 Yet you have made them little less than a god, crowned them with glory and honor. "
(Psalms 8:4-6)

"4 Indeed, before you the whole universe is as a grain from a balance, or a drop of morning dew come down upon the earth.

"But you have mercy on all, because you can do all things; and you overlook the sins of men that they may repent.

"For you love all things that are and loathe nothing that you have made; for what you hated, you would not have fashioned.

"And how could a thing remain, unless you willed it; or be preserved, had it not been called forth by you? "
(Wisdom 11:22-25)
I don't have a problem with that, which is just as well. Taking Sacred Scripture seriously is 'in the rules.' (Catechism of the Catholic Church, 101-133)

So is accepting reality, and I've been over that before. Often. (November 20, 2015; June 19, 2015; March 29, 2015)

Also distinctions between "little less than a god" and God. (March 29, 2015; December 12, 2014)


We've been learning that this universe is almost unimaginably huge and ancient:
  • 13,798,000,000 - universe starts
  • 4,540,000,000 - Earth forms
  • 3,500,000,000 - life starts
  • 2,600,000 - Oldowan stone tools
  • 151 - Maxwell's radio equations
  • 119 - Marconi's wireless telegraphy
That list's from a discussion of talking drums, the Inmarsat network, and space aliens: and that's another topic. (June 19, 2015)

I still run into folks who insist that Ussher was right, that Creation happened at nightfall on October 22, 4004 BC.

That was plausible back in 1654, but my faith doesn't involve clinging to a long-dead Calvinist's timetable.

If it did, Christianity would have started crumbling shortly after 1778, when Georges-Louis Leclerc, Comte de Buffon, published "Les époques de la nature." I've said that before, too. (September 18, 2015)

Somewhere around the mid-19th century, some folks started saying that since the universe operates according to rational laws, a rational Creator cannot exist.

Around the same time Darwin published "On the Origin of Species," which gave tightly-wound folks conniptions — and still does. (July 15, 2014)

I keep saying this: seeking truth and seeking God are compatible — and turning my brain off isn't required. (Catechism, 154, 274, 1706)

As a Catholic, I believe that truth is very important. (Catechism, Prologue, 27, 74, more under Truth in the index)

That applies to truths that we've known about since before Genesis was written — and facets of reality we didn't know about until earlier this year.

I see humanity's expanding knowledge as opportunities for greater admiration of God's greatness. (Catechism, 283)

I also keep saying that things of faith come from God. Things of the world come from God. Honest, ethical, study of this astounding universe cannot hurt our faith in God. (Catechism, 159)

If a newly-found facet of reality doesn't match our preconceived notions of what's true: that's our problem, not God's.

If we keep studying the facts, use our brains, and don't assume our preconceived notions are the only possible explanation, sooner or later we'll understand:
"...God, the Creator and Ruler of all things, is also the Author of the Scriptures - and that therefore nothing can be proved either by physical science or archaeology which can really contradict the Scriptures. ... Even if the difficulty is after all not cleared up and the discrepancy seems to remain, the contest must not be abandoned; truth cannot contradict truth...."
("Providentissimus Deus,"1 Pope Leo XIII (November 18, 1893) [emphasis mine])

1. Learning How Bacteria "See"

(From Conrad Mullineaux, via BBC News, used w/o permission.)
("The idea first dawned when researchers looked down a microscope at bacteria lit from the side"
(BBC News))
"Bacteria 'see' like tiny eyeballs"
Jonathan Webb, BBC News (February 9, 2016)

"Biologists say they have solved the riddle of how a tiny bacterium senses light and moves towards it: the entire organism acts like an eyeball.

"In a single-celled pond slime, they observed how incoming rays are bent by the bug's spherical surface and focused in a spot on the far side of the cell.

"By shuffling along in the opposite direction to that bright spot, the microbe then moves towards the light.

"Other scientists were surprised and impressed by this 'elegant' discovery.

"Despite being just three micrometres (0.003mm) in diameter, the bacteria in the study use the same physical principles as the eye of a camera or a human...."
"Organism??" Describing a single-cell critter with no organs? I checked, and it's correct usage.

The Oxford American English dictionary says that organism means: "An individual animal, plant, or single-celled life form." Since that's how a BBC News article uses the term, looks like it's British usage, too.

Cyanobacteria are bacteria, prokaryotes; not algae, which are eukaryotes: but they're called blue-green algae anyway. Besides, "algae" is what most folks call pond scum — then there's seaweed like brown algae, which includes giant kelp.

Eukaryotes are critters whose cells (usually) have nuclei; prokaryotes don't have a distinct cell nucleus. We're eukaryotes, although our red blood cells don't have any nuclei, scientists have been rearranging the 'tree of life' recently, and that's yet another topic. (June 19, 2015)

Where was I? Pond scum, dictionaries, Linnaean taxonomy. Right.

Cyanobacteria would most likely have been called "plants" when I was in high school, since they get energy from light. On the other hand, they swim toward light; which was puzzling, since they're just tiny cells: no eyes.

Queen Mary University of London's Conrad Mullineaux and his team - - - back to the BBC News article —

"We Noticed it Accidentally"

(From Sinclair Stammers/Science Photo Library, via BBC News, used w/o permission.)
("Cyanobacteria are found in huge numbers in bodies of water and can form a slimy film"
(BBC News))
"...'We noticed it accidentally, because we had cells on a surface and we were shining light from one side, in order to watch the movement towards the light.

" 'We suddenly saw these focused bright spots and we thought, "bloody hell!". Immediately, it was pretty obvious what was going on.'

"After more than three centuries of scientists eyeballing bugs under microscopes, Prof Mullineaux said it was remarkable that nobody had picked up on this before.

" 'It seemed really, really obvious afterwards.'..."
(Jonathan Webb, BBC News)
I figure the 20-20 hindsight principle applies here. Anyway, the scientists studied the bacteria's 'imaging' abilities with different sorts of microscopes; and set up a test involving a laser beam.

They put the cyanobacteria in a dish with a laser beam focused on its center, and a larger light on one side. The little critters swam toward the big light, unless their path took them into the laser beam.

When its 'forward' side touched the beam the bacterium "bounced off it," starting to swim in the opposite direction.

These cyanobacteria almost certainly can't perceive images. For one thing, images formed on their cell walls are pretty fuzzy: with a resolution of about 21 degrees, compared to the 0.02 resolution of our eyes.

Mostly, though, they're single cells — with no brain to collect and process the data. They respond to light because photoreceptor molecules embedded in their cell walls react when illuminated.

Synechocystis, the species of cyanobacteria used in this study, have been around for quite a while, but didn't branch off from other cyanobacteria until after the Great Oxygenation Event, roughly 2,300,000,000 years back.

They're used as model organisms; partly because they photosynthesize and aren't particularly delicate. They're not used much for genetic engineering, though. They don't reproduce particularly fast, for one thing.

I've talked about mutant mosquitoes, CRISPR, and Laban's sheep before. Basically, there's no such thing as "safe" technology. Even basic tech like string or fire can kill if we don't use our brains. On the other hand, using tech is part of being human. (October 16, 2015; January 23, 2015)

Finally, I'd be astonished if scientists finally know everything there is to know about cyanobacteria. My guess is that this year's discovery will answer some questions: and raise a great many others.

2. Solving the Purple Sock Mystery

(From MBARI, via BBC News, used w/o permission.)
("This strange deep-sea beast has baffled scientists for more than 60 years"
(BBC News))
"Mystery of deep-sea 'purple sock' solved"
Rebecca Morelle, BBC News (February 3, 2016)

"The mystery of a deep-sea creature that resembles a discarded purple sock has been solved, scientists report.

"The animal, called Xenoturbella, is so bizarre that for 60 years researchers could not work out what it was - or where it fitted into the family tree.

"But the discovery of four new species in the Pacific has enabled scientists to conclude that this animal belongs to one of the earliest branches of life.

"The study is published in the journal Nature.

"Lead researcher Prof Greg Rouse, from the Scripps Institution of Oceanography in the US, said: 'Our nickname for them was purple socks.

" 'So if you think of a sock that you have taken off and thrown on the floor - they literally look like that.

" 'Or a deflated balloon.'..."
The Wikipedia page says Sixten Bock noticed these odd critters in 1915, but it wasn't until 1949 that Einar Westblad published a description of them.

Four species of these critters were discovered this year: Xenoturbella monstrosa, the "purple sock;" Xenoturbella hollandorum; Xenoturbella profunda; and Xenoturbella churro. More about that:
The smaller ones live near(er) the surface, in water up to 650 metres (2,130 ft) deep. They grow up to 4 centimeters, 1.6 inches, long. Big ones, 10 centimeters, 3.9 inches or more long, live deeper: 1,700 to 3,700 meters 5,600 to 12,100 feet, down.

X. monstrosa is the biggest, up to 20 centimeters, 7.9 inches. Don't bother trying to remember those names, like I keep saying, there won't be a test on this.

Scientists analyzing DNA from these critters discovered mollusk genes — and suggested that they were mollusks that had 'devolved,' once-sophisticated creatures that lost their complex features as they evolved.

Turns out that they'd analyzed DNA from the critter, and what the critter had eaten. I'll get back to that.

Case Closed for Xenoturbella?

(From MBARI, via BBC News, used w/o permission.)
("Genetic tests now reveal that the organism is primitive and is positioned at the base of the evolutionary family tree"
(BBC News))
"...But the discovery of four new species from the depths of Pacific Ocean has allowed scientists to study this animal more closely.

"With Remotely Operated Vehicles (ROVs), they have been able to film these creatures for the first time....

"... 'We corroborate the fact that they should be thought of as a fairly primitive group,' said Prof Rouse.

"They sit near the base of the family tree, he added.

" 'A major branch on the evolutionary tree of life has now got another four new species instead of just one.'

"But if you think it is cased [!] closed for Xenoturbella, think again.

" 'We've never seen it feeding," said Prof Rouse.

" 'We find it where these molluscs are, and when we sequence it, we find these molluscs, their DNA, is inside. But when we open them up, we find their gut is empty.

" 'And they just have a tiny little mouth opening. They don't have teeth, they don't have any sucking proboscis structure that could tear off a piece of some bivalve.

" 'It is a great unsolved mystery as to how Xenoturbella eats.'..."
(Rebecca Morelle, BBC News)
If Xenoturbella eat mollusks, it's quite a trick: since they don't have teeth, eyes, or brains. Their nervous system is diffuse: a nerve net.. The only organ they've got is a statocyst, a tiny sack holding a pellet that works a bit like our semicircular canals.

Animals like hydras have nerve nets, respond the same way a stimulus no matter what part gets touched: so it looks like critters with nerve nets can tell where a stimulus comes from. Sea stars have nerve nets in their arms, connected by a nerve ring, which apparently acts a bit like a brain.

Most critters with nerve nets have radial symmetry, like sea anemones and jellyfish. Bilateral critters, with left and right sides, generally have something like a brain near the 'front' end. Then there's the typical mollusk, a nominally-bilateral critter with a lumpy nerve ring around its esophagus.

Looks like we have a great deal left to learn. And that's yet again another topic. (July 17, 2015; May 29, 2015; April 10, 2015)

More, including why God's design decisions don't offend me:


Brigid said...

Stutter: "shortly after 1778, when when Georges-Louis Leclerc, Comte de Buffon, published"

Extra word: "Basically, I there's no such thing as "safe" technology."

Missing word: "respond the same way a stimulus no matter"

The Friendly Neighborhood Proofreader

Brian Gill said...

I do double words quite a bit. Curious. About the extra word - that started as a qualifier ("I think") - - - but what the hey, I'll assume that readers will realize that I'm expressing an opinion: one I am quite sure is correct.

And thanks!

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