Microbes Vs.Darwin

How Microbes Make Earth Habitable:
Evolution News &Views February 10, 2016 3:36 AM

Several recent discoveries point to amazing connections between global forces and Earth's tiniest creatures that maintain the habitability of our planet. Consider some examples and think about the implications.

Atmospheric Requirements

First, let's talk about the atmosphere. As David Klinghoffer reported here last month at Evolution News, it appears we can dispense with the notion that a rise in oxygen caused the Cambrian explosion. That paper in PNAS suggests that "O2 levels capable of supporting animal physiology were present more than 500 million years before the appearance of animals." We know that oxygen is necessary for complex life. This paper says it was already here long before complex multicellular animals appeared.

Less recognized is nitrogen. Elizabeth Howell wrote in NASA's Astrobiology Magazine back in 2014 that oxygen could fool the search for life, but this year she wrote in the same Astrobiology Magazine that nitrogen "may be a sign of habitability."

We might commonly think of Earth as having an oxygen-dominated atmosphere, but in reality the molecule makes up only a fifth of our air. Most of what surrounds us is nitrogen, at 78 percent. Astrobiologists are beginning to see nitrogen -- and not just oxygen -- as a key indicator of a planet's habitability. Nitrogen is essential for life on Earth and could signal an atmosphere thick enough to stabilize liquid water on a planet's surface, fundamental to creating habitable conditions. [Emphasis added.]

Nitrogen and oxygen may not be sufficient for life (Saturn's moon Titan, for instance, has plentiful nitrogen), but they are both necessary. A leading source of free oxygen is photosynthesis in autotrophic microbes; and only microbes have the know-how to "fix" nitrogen by dismantling the triple bonds of atmospheric nitrogen into ammonia and other useful compounds. As we will see, microbes play a major role in maintaining the balance other essential atmospheric elements, too. Without that balance, complex life could not exist.

Nitrogen-Fixing Bacterium Does Solo Performance

Since we reported about the anammox process last fall, a major discovery has been made about nitrogen-fixing bacteria. Nature reported the discovery of a bacterium that can do complete nitrification.

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.

We'll have to add a new term to our vocabulary now: comammox or "complete ammonia oxidizer"; see the summary from the University of Vienna. An article from from the same source describes the "incredibly exciting moment" when they found the "long-sought comammox organism" 1,200 meters deep in a Russian oil exploration well. A bigger surprise came when they realized "comammox was everywhere but was overlooked."

Electric Sediment Buffers Ocean

Life began in the oceans, but without bacteria, it might not survive. According to surprising findings announced in Current Biology:

Animals at the bottom of the sea survive oxygen depletion surprisingly often, and a new study identifies cable bacteria in the sediment as the saviors. The bacterial electrical activity creates an iron 'carpet', trapping toxic hydrogen sulfide.

The paper's title is, "Electrical cable bacteria save marine life." These "key organisms" link up into electrical "wires" in the top layers of ocean sediment, carrying electrons from sulfide oxidation up into the ocean water, where further reactions form an "iron firewall" that protects the ocean from a buildup of toxic hydrogen sulfide. This buffering of the ocean against harmful conditions even undergoes a seasonal cycle:

Essentially, the cable bacteria manage a sulfide storage facility made of reactive iron, where sulfide is stowed away during oxygen-poor periods and regained for efficient energy metabolism when oxygen returns. Seitaj et al. propose that the control of sulfide mediated by cable bacteria, which they observed at Grevelingen, could be widespread and may explain many cases where oxygen depletions are not followed by release of hydrogen sulfide and mass mortality of marine life.

Plankton Maintain Carbon Cycle

Carbon dioxide levels in the atmosphere are an important concern to climate scientists. It's been known for a long time that plankton in the surface ocean waters play a big role in the carbon and oxygen cycles. Researchers at MIT took a closer look at certain members of the plankton community called "mixotrophs" -- those that can feed by photosynthesis and by consuming prey. They realized that "these microscopic, mixotrophic organisms may have a large impact on the ocean's food web and the global carbon cycle."

The MIT scientists note that mixotrophs have been overlooked in climate models. As these heavier plankton die, they take their carbon down into the seafloor sediments with them. Consequently, "mixotrophic organisms may make the ocean more efficient in storing carbon, which in turn enhances the efficiency with which the oceans sequester carbon dioxide." Without mixotrophs, there would likely be more carbon dioxide in the atmosphere -- and we all know what that means. One wonders if the earth would become less habitable over time if it were not for the planet-wide function performed by these tiny organisms.

Diatoms Promote Diatomic Oxygen

One fifth of the oxygen in our atmosphere comes from one-celled algae called diatoms. These incredible organisms, known for the variety of their beautiful silica houses (called tests) inhabit the oceans and fresh waters of the planet in vast numbers. Although Michael Denton doesn't discuss them in his new book Evolution: Still a Theory in Crisis, he well could have pointed to their beautiful shells as non-adaptive forms inexplicable by natural selection. Why would an organism need to create triangles, rods, and five-pointed stars with intricate etched patterns on transparent glass? Every time a diatom divides, the daughter cells recreate the elegant shells of their particular species.

To do their important work for the global atmosphere, they need to find silicon. An exciting new discovery was announced by Friedrich Schiller University Jena. Diatoms can apparently "smell" silicate minerals, and migrate to where they are plentiful. In a petri dish, scientists watched biofilms of diatoms move two micrometers a second toward silicate sources, but away from toxic minerals. How they do this is unknown, but it was clear to them that "The algae have to search their environment for the building material" (italics in original). The results of their study are published in Nature Communications.

If diatoms lacked the ability to seek out and find what they need, the planet might have reduced oxygen, decreasing its ability to support complex life. Thus our pun on "diatoms" (Greek "cut in two") and "diatomic oxygen" ("two atoms," O2) -- two unrelated words about pairs of things that interact in a surprising way.

Microbes make earth a nice place to live. There's more to say on that theme, and we'll do so in an additional post coming up.

From the multiverse did it to little green men from apha centauri did it?

Peace Through ETs? John Zmirak’s Puckish Proposal
David Klinghoffer | @d_klinghoffer

Interested in a resolution of the dispute between scientific atheists and intelligent design? In the context of a thoughtful review of Stephen Meyer’s book  Darwin’s Doubt, John Zmirak at The Stream  has an enjoyably mischievous suggestion.

In “At Last, Common Ground for Atheists and Intelligent Design Advocates,”he proposes a plan for peace: Let both sides admit the evidence of design, the evidence that life did not spring up by unguided, purposeless processes alone. But grant the possibility — or even for the sake of argument, stipulate the certainty — that the evidence is of natural alien origin. 

This, he says, would defuse the personal reasons many people have for preferring to see life as un-designed. There are many such motivations. Darwin himself sought an “alternate explanation…after his daughter’s death drowned his Christian faith in grief.” Zmirak writes:

So I have a suggestion. It might help find common ground between the advocates of Intelligent Design, and committed scientific materialists. Here goes:

How about we stipulate this? All the evidence piling up that random mutations couldn’t possibly have planted and grown the Tree of Life does not point to the God of the Christians and the Jews.

Instead, it points to the design of some higher, alien species. Say, a race of brilliant beings who live in Alpha Centauri, who have learned how to travel by wormholes. No, there’s no evidence for that, but there’s equally little evidence for the “Multiverse.” That’s a favorite fiction of atheists eager to escape the religious implications of the Big Bang. But that didn’t stop Stephen Hawking from touting it.

Okay? It’s not the “Divine Foot” [in Richard Lewontin’s famous formulation] we’re letting in the door. It’s a mysterious alien green foot of a purely natural being. One who doesn’t impose morality on us. Or care if we sleep with our much younger lab assistants.

You can relax. Life is still meaningless. Our ethics are still completely arbitrary. The Green Men in Alpha Centauri don’t care what we do. They haven’t built us a heaven or dug for us a hell. We’re still free to dig that ourselves, right here on earth. Will that do, Professor Lewontin?

Perhaps if intelligent design advocates stipulated such alien designers, they’d hit much less resistance. Biologists wouldn’t work so desperately hard to avoid the evidence of their eyes.

“Famously Slow”

It’s an interesting suggestion. But as Michael Behe noted the other day, Darwinists “are famously slow to recognize problems for their theory.” Why so slow? You have to understand how many careers, and how much of personal image and other factors, are wrapped up with the theory that nature on Earth created itself, only giving the illusory appearance of design.

Stipulating actual design by Little Green Men would still be an affront, requiring Darwinists to admit they were wrong, and not about a small matter. This may not be the way forward after all, John.

Why our homeworld remains previleged.

Exoplanets and the Fermi Paradox
Guillermo Gonzalez

We are living during a golden age of discovery in astronomy. Arguably, it began with the dawning of the space age in 1957. By 1989 our probes had visited every planet in the Solar System (in 2015 New Horizons visited the former planet Pluto). Then, in 1995 we discovered the first planet around another star (an exoplanet). The Extrasolar Planets Encyclopedia listed 3,986 exoplanets as of February 15, 2019! The Keplerspacecraft has discovered the most, but it was retired last fall after running out of the fuel needed to do science observations. Its timely replacement, the Transiting Exoplanet Survey Satellite (TESS), began its science observations last summer. It is expected to discover over 20,000 planets. The ongoing Gaiamission is expected to yield about 20,000 giant planet discoveries by the time its nominal 5-year mission is completed later this year.

    Believers in extraterrestrial intelligence (ETI) have been encouraged by these discoveries (see here and here). But the number of stars with planets is only one of the seven factors in the Drake Equation, which is an attempt to estimate the number of communicating civilizations in the galaxy. One also needs to consider the many Rare Earth factors needed to make a planet habitable to complex life  (see here and here).  It could be that these factors more than compensate for the large numbers of planets, resulting in a very small chance of ETI. We just don’t know yet.

The Great Silence

Do these discoveries help resolve the Fermi Paradox, which asks, Why the Great Silence? Not really, but they do show that mere rarity of planets by itself is not the solution.There is one important, albeit indirect, way that exoplanet discoveries do influence the Fermi Paradox. To understand it, we need to think “backwards.” Consider not our detection of exoplanets but, rather, the detection of our Solar System from afar. Now that we know how to find exoplanets, we can turn the problem around and ask how easy would it be for an ETI to detect the planets in our Solar System.

Right away we can offer some obvious answers. For example, you don’t actually have to send a probe to another star to check if it has planets. The technology required for long-range detection has been available for decades. There are multiple ways to detect exoplanets, but the two most productive primary ones are the spectroscopic Doppler and photometric transit methods.In 1995 the first exoplanet around an ordinary star was discovered, using the Doppler method. Planets could have been discovered using this method one or two decades prior. In principle, exoplanets could have been discovered a century ago using the simpler transit method. 

Notable Properties of the Sun

The Sun possesses a couple of properties that make it an excellent target for planet searches from afar. First, it is an old star and, as such, exhibits slow rotation and small fluctuations in brightness. These qualities are beneficial for both primary planet detection methods. Jupiter would be the easiest Solar System planet to detect using the Doppler method, while Venus would be the easiest one to detect with the transit method, given its relatively short orbital period. One qualification regarding the transit method is that the observer would have to be looking  looking near the ecliptic plane of the Solar System. We have already found several Jupiter and Venus analogs, proving that we could detect at least a few planets around a nearby Solar System twin.Second, the Sun is a relatively rare early-G spectral type main sequence star, making it brighter than about 90 percent of all main sequence stars. ETI conducting a magnitude-limited survey could see the Sun from farther away than they could an intrinsically fainter but more common red dwarf. Or, for a given distance, better quality data could be gathered on the Sun, making it more likely that its planets would be detected.

A Rare Jewel Sure to Enthrall!

All this is interesting from the perspective of a space-faring ETI searching for other habitable or inhabited worlds. An advanced ETI just starting to go boldly out into interstellar space would very likely have mapped out all the planetary systems within the nearest few hundred light years of their home system. It seems likely that our Solar System would be included in their catalog of planetary systems (assuming they start out in our sector of the Milky Way galaxy). 

If all planetary systems were created equal, then the Solar System would not stand out. ETIs might eventually visit it, but it wouldn’t be a high priority. But all planetary systems are not created equal. The many Rare Earth factors show that the Solar System is anything but typical and that only a small subset of planetary systems are likely to be habitable (and far fewer actually inhabited). 

Just knowing that our Sun is a rare early-G spectral type main sequence single star orbiting far from the dangerous galactic center would substantially increase the Solar System’s ranking in the ETI’s travel itinerary. Knowing further that the orbits of the planets in the Solar System are nearly circular would boost its rank more. Of course, a space-faring ETI would probably know more about exoplanets than we do, given their more advanced technology.

Still, the technology we use to study exoplanets is advancing rapidly. For example, the James Webb Space Telescope, due to be launched in 2021, should be able to detect whether nearby exoplanets have oceans and ozone. Knowing that the Earth has oceans of water, an oxygen-rich, carbon dioxide-poor atmosphere, and a large moon should boost the Solar System’s rank to the top of the ETI’s list. Their travel brochure might describe it as a rare jewel that is sure to enthrall!

Not Likely to Be “Passed Over”

All this strongly implies that the Earth would not have been “passed over” during a “colonization wave” through the galaxy. Yet, there is no convincing evidence of ETI visitation or communication. Yes, I know there are speculative responses to the Great Silence in attempts to rescue ETIs from the obvious implications of the Fermi Paradox. There are good responses to these. I would recommend If the Universe is Teeming with Aliens … Where is Everybody? (2nd edition). Contrary to first impressions, then, exoplanet discoveries actually strengthen the impact of the Fermi Paradox.

Stalinism redux? V

Jehovah’s Witnesses Tortured in Surgut, Russia

Just nine days after Dennis Christensen was unjustly convicted in a Russian court, at least seven of Jehovah’s Witnesses were subjected to physical abuse—electric shocks, suffocation, and beatings—by Russian investigators in the western Siberian city of Surgut. While torturing our brothers, the officers demanded to know the locations of their meetings and the identity of other Witnesses.

The incident began when authorities in Surgut carried out raids in the early morning hours of February 15, 2019. After arresting some Witnesses and taking them to the Investigative Committee offices, the authorities began interrogating our brothers, who refused to disclose details about their fellow worshippers. After the only legal representative present left, the victims report that the following occurred: agents put a bag over their head and sealed it with tape, tied their hands behind their back, and beat them. After stripping the Witnesses naked and dousing them with water, the agents shocked them with stun guns. This sadistic torture lasted for about two hours.

At least three Witnesses are still imprisoned. Those who have been released sought medical attention for their injuries and filed complaints with supervisory agencies.

Additionally, after the mass searches were completed, the Russian authorities initiated criminal cases against a total of 19 Witnesses for so-called “participating in extremist activity” and “organizing an extremist organization.”

Such an egregious abuse of authority is punishable under the Russian Criminal Code. Additionally, the Russian Federation is subject to several international bodies that protect individuals from torture. Therefore, we will pursue all available legal remedies, both domestic and international, for this crime.

Ultimately, we know that Jehovah has seen the persecution of our brothers in Russia and will act as their ‘helper and rescuer.’—Psalm 70:5.