The stowaways

Aficionados of the Star Trek universe undoubtedly recall the iconic character Jadzia Dax.  Dax was a Trill -- a fusion of a humanoid host and a strange-looking brain symbiont.  The union of the two blended their personalities, resulting in what was truly a new, composite life form.

Star Trek is amazing in a lot of ways, not least because of their attention to current science and an uncanny prescience about where science is heading.  It turns out that we're all composite life forms.  We carry around something like 39 trillion bacterial cells in and on our own bodies -- the vast majority of which are either commensals (neither helpful nor harmful) or are actually beneficial -- a number that is higher than the number of human cells we have.  Each of our cells also contains mitochondria, which are the descendants of endosymbiotic bacteria that have inhabited the cells of eukaryotes for billions of years, and without which we couldn't release energy from our food molecules.  Plants have not only mitochondria but chloroplasts, yet another species of bacteria that like mitochondria, have their own DNA, took up residence in their hosts billions of years ago, and have been there ever since.

But the rabbit hole goes a hell of a lot deeper than that.  By some estimates, between five and eight percent of our genomes are endogenous retroviruses -- genetic fragments left behind by viruses that spliced their DNA into ours.  Like our bacterial hitchhikers, a good many of these are either neutral or beneficial; for example, the production of bile, estrogen, and several proteins essential for the formation of the placenta are all directly affected by endogenous retroviral genes.  A few do seem to be deleterious, and have roles in certain cancers, autoimmune diseases, and neurological disorders like ALS and schizophrenia.

What brings this topic up is an astonishing study led by Tyler Coale, of the University of California - Santa Cruz, that came out in the journal Science this week.  Coale's study found there's yet another example of endosymbiosis -- this one a lot more recently evolved -- which turned a formerly free-living nitrogen-fixing bacterium into a true cellular organelle.

Nitrogen is critical for the production of both proteins and DNA.  Although 78% of the air we breathe is nitrogen, it's completely useless to us; we breathe it right back out.  All the nitrogen in our bodies' proteins and nucleic acids had to pass through a food chain that started with nitrogen-fixing bacteria, the only known organisms that can absorb nitrogen from the air and convert it to an organic compound.  Leguminous plants like beans, peas, alfalfa, and clover have a nifty symbiotic arrangement with nitrogen-fixing bacteria; they create nodules in their roots where the bacteria live, and the bacteria provide the plants with a ready source of nitrogen.

But in legumes, the two remain independent organisms.  What Coale and his colleague discovered is a species of algae (Braarudosphaera bigelowii) in which the bacteria (UCYN-A) have evolved to become inseparable from the host cells.  In other words, they became an organelle, just like mitochondria and chloroplasts.

Although there's no canonical definition of organelle, most biologists include two must-haves: (1) coordinated division of the organelle within the cell; and (2) the evolution of a transport system that allows for specific tagging and importation of proteins into the organelle.  By those standards, UCYN-A is definitely an organelle.  

"Both boxes are checked by Coale," said Jeff Elhai, microbiologist at Virginia Commonwealth University.  "Even to the semantic purists, UCYN-A must be counted as an organelle, joining mitochondria, chloroplasts and chromatophores."

All these stowaways, in the cells of just about every living thing on Earth, call into question what exactly we mean not only by the word organelle but by the word organism.  The high-school-biology-class definition of an organism is "an individual life form of a species."  But is there any such thing?  The ostensibly individual life form called Gordon who is currently writing this post is made of (at least) equal numbers of human cells and cells from different species of bacteria, without many of which I'd be sick as hell, or possibly even dead.  Remove the symbiotic mitochondria from within my cells, and I'd definitely be dead -- within minutes.  Deeper still, at a minimum, one in twenty of the genes in my "human DNA" comes from viruses and bacteria.

Looked at closely, I'm as put together of spare parts as the Junk Man in Lost in Space.  Fortunately, I appear to run a bit more smoothly most days than he did.

In any case, calling me "a single organism" is so far from accurate it's almost laughable.

Honestly, it's kind of cool how interconnected everything is.  Back in the days of the first serious taxonomist, Swedish biologist Carl Linnaeus, scientists had the idea that all living things were categorizable into neat little cubbyholes.  Not only is that incorrect on the species level (something I wrote about in detail a couple of years ago), it's not even true on the individual level or on the level of genomes.  Life on Earth is a huge, tangled skein of threads.  The whole thing puts me in mind of a quote from John Muir: "Tug at a single thing in nature, and you find that it is hitched to everything else in the universe."

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The evolution of clumps

If humans operated by logic, rationality, and evidence, there would be arguments we would no longer be having.  A sampler:

• Climate change is real and the vast majority of the change we're seeing is caused by humans.
• Vaccines are safe, effective, and the risk of serious side effects is low.
• Trump lost.
• The Earth is an oblate spheroid.
• The biodiversity we see around us came about from evolution by natural selection.

The last one is the reason this topic comes up, even though -- as I've pointed out umpteen times -- there is zero doubt amongst biologists (and the majority of educated laypeople) that evolution occurred, and is still occurring.  As Richard Dawkins put it, you could instantaneously destroy every fossil in the world, and the remaining evidence for evolution would still be overwhelming.

But the subject resurfaces because of an elegant experiment I found out about because of a buddy of mine, that (should you still be on the fence, belief-in-evolution-wise) is the 3,948,105th nail in the coffin of the various anti-evolutionary models.  The study looks at multicellularity -- a step in the process of the evolution of complex life that has been a bit of a mystery.  We know it happened; there is a clear progression in Precambrian fossils from single-celled life forms to undifferentiated clumps of more-or-less identical cells to multicellular organisms with differentiated cell types, but exactly how it happened was unclear.

The study was led by Lutz Becks, biologist at the Limnological Institute of the University of Konstanz, and used a simple green algae (Chlamydomonas reinhardtii) to show that in short order, with the appropriate natural selection, multicellularity can evolve from a single-celled ancestor species.

C. reinhardtii does sometimes form clumps of cells, but they are usually small and transitory.  (Nota bene: remember that evolution doesn't create traits; it acts on variations that were already present in the population due to mutations.)  Becks and his team introduced a selective predator, the rotifer Brachionus calyciflorus, which is small enough to have a preference for individual algae cells and smaller cell groups.  The researchers then kept track of the proportion of single to multiple cells in the algae population, as well as the size of any multi-cell groups.

You've probably already guessed what happened.  The population of algae containing predators tilted toward becoming composed almost entirely of larger multicellular groups -- in only five hundred generations (which seems like a lot, but for algae that's only about six months).  Algae raised without the predator didn't change, remaining largely single-celled with a few smaller clumps scattered around.

What is coolest about this is that Becks and his team didn't stop there.  They took samples of the algae from both cultures and analyzed them genetically.  They found 76 different genes that showed significant differential expression between the two samples -- so not only were the traits of the population changing, the gene frequencies and activity were, as well.

Just as the evolutionary model predicts.

"We had actually expected that the formation of colonies can be achieved by different mechanisms in the algal cells and we would therefore find different mutations," Becks said, in an interview with Phys.org.  "In fact, we have seen a very high level of repeatability.  This suggests that the selection pressure has had a very targeted effect."

Keep in mind, too, that C. reinhardtii is an asexually-reproducing species -- so the cells are clones, and the only differences genetically are caused by mutations.  This should put to rest the nonsense that mutations can't create "new information" but only corrupt the "old information" that was already there.

In any case, here's yet another experiment supporting the fact that if a population has genetic variations and those variations are subject to a selecting agent, it will evolve.  Here, it's evolved fast enough to see it happening in real time.

Which would be convincing to the anti-evolutionists if they had any respect for evidence.  Which they don't.  So I'm not particularly hopeful that this will change the minds of the creationists and the intelligent-design cadre.  As Thomas Paine put it, "To argue with a man who has renounced the use and authority of reason is like administering medicine to the dead."

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I've loved Neil de Grasse Tyson's brilliant podcast StarTalk for some time.  Tyson's ability to take complex and abstruse theories from astrophysics and make them accessible to the layperson is legendary, as is his animation and sense of humor.

If you've enjoyed it as well, this week's Skeptophilia book-of-the-week is a must-read.  In Cosmic Queries: StarTalk's Guide to Who We Are, How We Got Here, and Where We're Going, Tyson teams up with science writer James Trefil to consider some of the deepest questions there are -- how life on Earth originated, whether it's likely there's life on other planets, whether any life that's out there might be expected to be intelligent, and what the study of physics tells us about the nature of matter, time, and energy.

Just released three months ago, Cosmic Queries will give you the absolute cutting edge of science -- where the questions stand right now.  In a fast-moving scientific world, where books that are five years old are often out-of-date, this fascinating analysis will catch you up to where the scientists stand today, and give you a vision into where we might be headed.  If you're a science aficionado, you need to read this book.

[Note: if you purchase this book using the image/link below, part of the proceeds goes to support Skeptophilia!]

Algae aura

Can I just say that I am sick unto death of people misrepresenting science?

Some scientist somewhere makes a discovery, and it seems to take only milliseconds before every woo-woo with a favorite loony idea about how the world works is using it to support their claims.  These people have taken confirmation bias and raised it to the level of performance art.

A long-time loyal reader of Skeptophilia sent me a particularly good (or bad, as the case may be) example of this yesterday, in the form of an article by Michael Forrester called "People Can Draw Energy From Other People The Same Way Plants Do," that is apparently getting passed all over social media.  So let me illustrate my point by telling you what some of Forrester's conclusions from this scientific research are, and afterwards I'll tell you about the actual research itself.

See if you can connect the two.

Forrester says that we absorb "energies" from our surroundings.  He never defines what he means by "energy," but I'm pretty sure it's not the standard physics definition, because he includes stuff about being around "negative people."  He cites "psychologist and energy healer" Olivia Bader-Lee, who says:

This is exactly why there are certain people who feel uncomfortable in specific group settings where there is a mix of energy and emotions...  The human organism is very much like a plant, it draws needed energy to feed emotional states and this can essentially energize cells or cause increases in cortisol and catabolize cells depending on the emotional trigger...  Humans can absorb and heal through other humans, animals, and any part of nature.  That's why being around nature is often uplifting and energizing for so many people.

We're then given specific recommendations for how to "absorb and heal" efficiently.  These include:

• Stay centered and grounded
• Be in a state of non-resistance
• Own your personal aura space
• Give yourself an energy cleanse
• Call back your energy

I was especially interested in the "energy cleanse" thing, and fortunately, Forrester tells us exactly how to accomplish this:

The color gold has a high vibration which is useful for clearing away foreign energy.  Imagine a gold shower nozzle at the top of your aura (a few feet above your head) and turn it on, allowing clear gold energy to flow through your aura and body space and release down your grounding.  You will immediately feel cleansed and refreshed.

So all I have to do is imagine it, eh?  Given that I spent 32 years working with teenagers, I wish I'd known that "owning your personal aura space" was something that would happen if I imagined it.  Teaching a room full of tenth graders is like trying to herd hyperactive puppies.  Since I found that yelling "BACK OFF" was seldom effective, it would have been nice if all I'd had to do was to picture my "aura space" (gold-colored, of course) and the teenagers would have been repelled backwards in a comical fashion, sort of like Yoda did to Count Dooku at the end of Star Wars: Attack of the Clones.

But I digress.

Okay. So you're probably wondering what scientific research led Forrester and Bader-Lee to come to this conclusion.

Ready?

The discovery by a team of scientists in the Biotechnology Department of Bielefeld University (Germany) that a species of algae can digest cellulose.

If you're going, "Um, but wait... but... how... what?" you should realize that I had exactly the same response.  I spent several minutes thinking that I had clicked on the wrong link. But no. In fact, Forrester even mentions the gist of the research himself:

Members of Professor Dr. Olaf Kruse’s biological research team have confirmed for the first time that a plant, the green alga Chlamydomonas reinhardtii, not only engages in photosynthesis, but also has an alternative source of energy: it can draw it from other plants.

And from this he deduces that all you have to do to be happy is to picture yourself underneath a gold shower nozzle.

I've seen some misrepresentations and far-fetched deductions before, but this one has to take the grand prize.

I get that people are always casting about looking for support for their favorite theories.  So as wacky as Forrester's pronouncements are, at least I see why he made them.  But what baffles me is how other people can look at what he wrote, and say, "Yes!  That makes complete sense!  Algae that can digest cellulose!  Therefore aura spaces and energetic quantum vibrations of happiness!

Okay, I admit that I can be a hardass rationalist at times.  But seriously, what are these people thinking?

Not much, is my guess.

So anyhow, watch out for those negative energies.  Those can be a bummer.  But if you're feeling like your vibrations are low, don't despair.  I hear that getting into psychic communication with algae can help.

********************************

If, like me, you love birds, I have a book for you.

It's about a bird I'd never heard of, which makes it even cooler.  Turns out that Charles Darwin, on his epic voyage around the world on the HMS Beagle, came across a species of predatory bird -- the Striated Caracara -- in the remote Falkland Islands, off the coast of Argentina.  They had some fascinating qualities; Darwin said they were "tame and inquisitive... quarrelsome and passionate," and so curious about the odd interlopers who'd showed up in their cold, windswept habitat that they kept stealing things from the ship and generally making fascinating nuisances of themselves.

In A Most Remarkable Creature: The Hidden Life and Epic Journey of the World's Smartest Birds of Prey, by Jonathan Meiberg, we find out not only about Darwin's observations of them, but observations by British naturalist William Henry Hudson, who brought some caracaras back with him to England.  His inquiries into the birds' behavior showed that they were capable of stupendous feats of problem solving, putting them up there with crows and parrots in contention for the title of World's Most Intelligent Bird.

This book is thoroughly entertaining, and in its pages we're brought through remote areas in South America that most of us will never get to visit.  Along the way we learn about some fascinating creatures that will make you reconsider ever using the epithet of "birdbrain" again.

[Note: if you purchase this book using the image/link below, part of the proceeds goes to support Skeptophilia!]

Science news briefs

Okay, after some recent posts that fall into the "I don't want to live on this planet any more" category, time to go to my happy place, namely: some cool recent science news.

First, we have a study of "starquakes" -- turbulence in the outer layers of stars -- giving us information about the conditions in the gas clouds from which those stars formed millions of years ago.

A study of 48 stars in a cluster in the Milky Way, which condensed from the same gas cloud, showed that their rotational axes are all aligned.  According to Dennis Stello, of the University of New South Wales, it had been assumed that chaotic forces in the primordial gas cloud would have scrambled the stars' angular momentum, and made it impossible to determine that they had come from the same origins.  "Just as seismologists use earthquakes to understand the interior of our planet, we use starquakes to understand the interior of stars," Stello said.  "Our new study provides the first evidence that this approach is a powerful way to gain insights into processes that occurred billions of years ago, close to the beginning of the universe."

What has been learned from this study has the potential of extending further back in time what we can infer about the conditions that exist as stars are being formed.  "The benefit of studying ancient star clusters is that the interfering dust and gas has gone, yet the stars still preserve the signature of the initial conditions in the cloud where they were born," Stello said.  "Our finding that the spins of about 70 per cent of the stars in each cluster are strongly aligned, and not randomly orientated as was expected, tells us that the angular momentum of the gas and dust cloud was efficiently transferred to the new stars.  It’s remarkable that the imprint of these initial conditions can still be seen billions of years later, by studying tiny oscillations in stars that are many light years away."

From the world of biology, we have a study from scientists at the University of Basel (Switzerland) and Lund University (Sweden), wherein we find that the most efficient and beneficial predators in the world are... spiders.

Using statistical sampling techniques, a team of zoologists has calculated the mass of the prey consumed by spiders, and found that the 45,000-odd species of spiders worldwide consume between 400 and 800 million tons of prey a year, many of which are insects that have the potential of damaging crops or spreading disease.  

"Our calculations let us quantify for the first time on a global scale that spiders are major natural enemies of insects. In concert with other insectivorous animals such as ants and birds, they help to reduce the population densities of insects significantly," said Martin Nyffeler of the University of Basel, who was lead author of the study.  "Spiders thus make an essential contribution to maintaining the ecological balance of nature."

So think about that next time you see a spider in your house and are torn between squashing it or scooping it up and putting it outside.

Then, from the paleontologists, we have a discovery in India that pushes back the fossil record of the earliest photosynthesizing eukaryotes -- better known as algae -- by 400 million years.

Not only did a team of scientists led by Stefan Bengston of the Swedish Museum of Natural History identify 1.6 billion year old single-celled fossils from dolomite formed in shallow marine environments in what is now the Vindhyan Basin in central India, they were able to use a highly accurate scanning technique -- synchrotron-radiation X-ray tomographic microscopy -- to see the cellular machinery therein.

So yes: they took a look at the organelles in the cells of a 1.6 billion year old fossil.

And inside it were all of the familiar subcellular bits you learned about in high school biology, indicating that these were indeed eukaryotes (organisms with membrane-bound structures such as nuclei) instead of the more primitive prokaryotes (organisms that lack most cellular organelles, and which include bacteria).  The upshot: complex life has been around a lot longer than anyone realized.

Last, from medical research, we have a groundbreaking study of brain/body computer interfaces led by Ujwal Chaudhary of the Institute of Medical Psychology and Behavioral Neurobiology at the University of Tübingen (Germany) which allowed patients with locked-in syndrome to answer questions yes or no -- just by thinking about it.

Locked-in syndrome, which is top of my list of disorders I wouldn't wish on my worst enemy, occurs when because of an injury, stroke, or neurodegenerative disease (like ALS) a person becomes completely unable to move, but without any loss of cognitive function.  In other words, you are aware but trapped inside a totally unresponsive body.  This condition was brought into the public eye by the phenomenal book (later made into a movie) The Diving Bell and the Butterfly, by Jean-Dominique Bauby, who developed LIS after a massive stroke, but who eventually was able to communicate through eye movements well enough to write a memoir of his experience.

The authors write:

Despite scientific and technological advances, communication has remained impossible for persons suffering from complete motor paralysis but intact cognitive and emotional processing, a condition that is called completely locked-in state.  Brain–computer interfaces based on neuroelectrical technology (like an electroencephalogram) have failed at providing patients in a completely locked-in state with means to communicate.  Therefore, here we explored if a brain–computer interface based on functional near infrared spectroscopy (fNIRS)—which measures brain hemodynamic responses associated with neuronal activity—could overcome this barrier.  Four patients suffering from advanced amyotrophic lateral sclerosis (ALS), two of them in permanent completely locked-in state and two entering the completely locked-in state without reliable means of communication, learned to answer personal questions with known answers and open questions requiring a “yes” or “no” by using frontocentral oxygenation changes measured with fNIRS.  These results are, potentially, the first step towards abolition of completely locked-in states, at least for patients with ALS.

Which is only the first step toward a brain/computer interface that might allow them to do much more -- at least allowing them to communicate despite having a condition that otherwise would shut them off completely from the world around them.

So there you are.  Some interesting news from science.  I don't know about you, but I feel much better now.  It's nice to know that despite the lunacy in the world, there are still people who are working toward improving our understanding of the universe.

And I, for one, find that very heartening.

Algae aura

Can I just say that I am sick unto death of people misrepresenting science?

Some scientist somewhere makes a discovery, and it seems to take only milliseconds before every woo-woo with a favorite loony idea about how the world works is using it to support their claims.  These people have taken confirmation bias and raised it to an art form.

I saw a particularly good (or bad, as the case may be) example of this yesterday in an article by Michael Forrester called "People Can Draw Energy From Other People The Same Way Plants Do," that is getting passed all over social media.  So let me illustrate my point by telling you what some of Forrester's conclusions from this scientific research are, and afterwards I'll tell you about the actual research itself.

See if you can connect the two.

Forrester says that we absorb "energies" from our surroundings.  He never defines what he means by "energy," but I'm pretty sure it's not the standard physics definition, because he includes stuff about being around "negative people."  He cites "psychologist and energy healer" Olivia Bader-Lee, who says:

This is exactly why there are certain people who feel uncomfortable in specific group settings where there is a mix of energy and emotions...  The human organism is very much like a plant, it draws needed energy to feed emotional states and this can essentially energize cells or cause increases in cortisol and catabolize cells depending on the emotional trigger...  Humans can absorb and heal through other humans, animals, and any part of nature.  That's why being around nature is often uplifting and energizing for so many people.

We're then given specific recommendations for how to "absorb and heal" efficiently.  These include:

• Stay centered and grounded
• Be in a state of non-resistance
• Own your personal aura space
• Give yourself an energy cleanse
• Call back your energy

I was especially interested in the "energy cleanse" thing, and fortunately, Forrester tells us exactly how to accomplish this:

The color gold has a high vibration which is useful for clearing away foreign energy.  Imagine a gold shower nozzle at the top of your aura (a few feet above your head) and turn it on, allowing clear gold energy to flow through your aura and body space and release down your grounding.  You will immediately feel cleansed and refreshed.

So all I have to do is imagine it, eh?  Given that I work with teenagers, I wish the "owning your personal aura space" was something that would happen if I imagined it.  Teaching a room full of tenth graders is like trying to herd puppies.  Since yelling "BACK OFF" is seldom effective, it'd be nice if all I had to do was to picture my "aura space" (gold-colored, of course) and the teenagers would be repelled backwards in a comical fashion, sort of like Yoda did to Count Dooku at the end of Star Wars: Attack of the Clones.

But I digress.

[image courtesy of the Wikimedia Commons]

Okay.  So you're probably wondering what scientific research led Forrester and Bader-Lee to come to this conclusion.

Ready?

The discovery by a team of scientists in the Biotechnology Department of Bielefeld University (Germany) that a species of algae can digest cellulose.

If you're going, "Um, but wait... but... how... what?" you should realize that I had exactly the same response.  I spent several minutes thinking that I had clicked on the wrong link.  But no.  In fact, Forrester even mentions the gist of the research himself:

Members of Professor Dr. Olaf Kruse’s biological research team have confirmed for the first time that a plant, the green alga Chlamydomonas reinhardtii, not only engages in photosynthesis, but also has an alternative source of energy: it can draw it from other plants.

And from this he deduces that all you have to do to be happy is to picture yourself underneath a gold shower nozzle.

I've seen some misrepresentations and far-fetched deductions before, but this one has to take the prize.

I get that people are always casting about looking for support for their favorite theories.  So as wacky as Forrester's pronouncements are, at least I see why he made them.  But what baffles me is how other people can look at what he wrote, and say, "Yes!  That makes complete sense!  Algae that can digest cellulose!  Therefore aura spaces and energetic vibrations of happiness!

Okay, I admit that I can be a hardass rationalist at times.  But seriously, what are these people thinking?

Not much, is my guess.

So anyhow, watch out for those negative energies.  Those can be a bummer.  But if you're feeling like your vibrations are low, don't despair.  I hear that getting into psychic communication with algae can help.