Are endogenous virus genes evidence for common descent?

Investigation in progress
Investigation in progress

This is a guest post by JoeCoder.

It’s often argued that when two or more organisms share viral genes in the same place, it is evidence those organisms evolved from a common ancestor.  Wikipedia’s Evidence for Common Descent page frames it as follows:

Endogenous retroviruses (or ERVs) are remnant sequences in the genome left from ancient viral infections in an organism. The retroviruses (or virogenes) are always passed on to the next generation of that organism that received the infection. This leaves the virogene left in the genome. Because this event is rare and random, finding identical chromosomal positions of a virogene in two different species suggests common ancestry.

This argument presupposes that the viruses inserted themselves into genomes randomly and stick around as junk DNA baggage, rather than genomes originally being designed with viral-like genes that perform useful functions.  However this argument has unraveled as we’ve discovered useful functions for many viral-like genes, including functions that specifically require a viral-like sequence.  Some examples among many:

  1. ERV sequences protect against viral infection through interference–a matching-but-opposite strand of RNA is created to bind to and disable RNA from a virus.
  2. Likewise, ERV’s seem to function “during embryo implantation to help prevent immune recognition by the mother’s immune system”
  3. In worms, an ERV has been observed to create actual viruses that transfer DNA from somatic cells (skin/brain/heart/etc.) to germline (sperm/egg) cells whenever the worm is exposed to too much heat, allowing them to rewrite their own DNA for future generations.
  4. Viral envelopes from ERV transcripts attach to cell membranes in the placenta and causes them to fuse as a normal part of development: “The HERV-W [a human ERV] envelope glycoprotein named syncytin 1 is expressed in all trophoblastic [part of the placenta] cells and directly involved in human trophoblast fusion and differentiation [cells taking on specialized roles]”

These aren’t isolated cases of function.   Phys.org interviewed one researcher:  “When we investigated public data from embryonic cells, we found that many RNAs originated from regions in the human genome that are ERVs.  We did not only observe isolated events, but systematic activation of these ERVs. Every cell type showed transcription of specific classes, something that is very unlikely to occur by chance”.

Those cases all involve RNA viruses and that’s old news.  But two weeks ago, a single-celled eukaryote called Cafeteria roenbergensis was found to harbor maviruses within its own DNA that remain dormant until it is attacked by a large virus known as CroV.  When this happens the maviruses activate to form an attack fleet, as NewScientist reports:

A voracious marine predator plagued by a giant virus has a defence system we’ve never seen before – it fights back by making its very own virus… Rather than waiting for maviruses to arrive by chance when CroVs attack, it actually carries the genes that code for mavirus inside its own genome.  These genes are usually dormant, but they get turned on when Cafeteria is invaded by CroV. “It acts as an inducible antiviral defence system,” write Fischer and his colleague Thomas Hackl in a new preprint paper.

This process kills the Cafeteria roenbergensis cell, but is useful in defending other members of its own species.  In this experiment maviruses were deliberately inserted into the Cafeteria roenbergensis genome (see the original paper), but more interestingly, sequences similar to the Cafeteria roenbergensis viral genes have been found in a wide range of animals:

A wide range of animals, from sea anemones to crocodiles, harbour genetic elements called Maverick transposons that closely resemble the mavirus genes. It’s possible that some of these organisms can also unleash viruses that attack giant viruses.

In spite of this, New Scientist still argues “our genomes are littered with the mutant remains of viruses and genetic parasites.”  But these discoveries reveal this as a rapidly-shrinking argument of the gaps. 

Save this for the next time someone insists that viral genes are useless junk DNA and therefore evidence of common descent.

LeadPages shuts down #anywhereButTarget web site to promote “diversity”

One sexual assault lawsuit should finish off Target for good
One sexual assault lawsuit should finish off Target for good

This story is from the The Stream.

Excerpt:

A conservative corporate watchdog group’s effort to galvanize conservatives against Target’s restroom and changing-room policies was shut down on Thanksgiving Day by the server company hosting its website, because the campaign allegedly violated the company’s effort to “create an inclusive workplace” respectful of “diversity.”

In an e-mail, Leadpages Director of Operations Doug Storbeck ordered 2nd Vote to take down its #AnywhereButTARGET website. According to Storbeck, “at Leadpages, we strive to create an inclusive workplace that upholds the dignity of all people. We value, respect, and celebrate everyone’s individualities and honor their unique strengths from all different walks of life.”

2nd Vote’s campaign encouraged conservatives to shop #AnywhereButTARGET because of the company’s policy that allows males who identify as females to use the restroom and changing room of their choice. Conservatives have boycotted the retail giant, though Target executives said in August that a stock drop and an investment in single-sex restrooms was unrelated to the backlash.

Storbeck continued:

We believe that embracing diversity of thought and perspective encourages collaboration that leads to product innovation, diverse products and a successful business. Staying true to our core values is something we take very seriously and we feel this is reinforced in our Terms of Service. Specifically, and according to our Acceptable Use and Conduct policy (to which you have agreed), we prohibit any content which: “(g) is hateful or discriminatory based on race, color, sex, religion, nationality, ethnic or national origin, marital status, disability, sexual orientation or age or is otherwise objectionable, as reasonably determined by Ave. 81;”

For the reasons stated above, I am respectfully requesting that you to take down your #AnywhereButTarget landing page upon receipt of this notice, but no later than 8:00am CST on Thursday November 24, 2016.

Storbeck’s LinkedIn page says that he lives in the Minneapolis area, which is also where Target’s headquarters are located. The Stream was unable to determine whether this played a role in Leadpages’ decision.

The actual-email is linked in the Stream article, so you can see for yourself how someone can invoke diversity and inclusion to shut down a viewpoint that they disagree with. You need a college education in the liberal arts to call acts of censorship “diversity and inclusion”.

Fox 10 News reports on some of the diversity and inclusion that the Target CEO and Doug Storbeck celebrate:

An O’Fallon, Missouri man was arrested on April 23, 2015 after allegedly secretly filming women in a Target dressing room.

Matthew Foerstel, 26, faces felony charges for invasion of privacy in the second degree and unlawful possession of a firearm.

Foerstel has a plea hearing on Monday, May 2, 2016.

The Brentwood Police Department arrested Foerstel on April 23 after he allegedly held a camera phone under a dressing room door while a female shopper tried on swim suits at the Target store in Brentwood.

An officer went to Ranken Technical College to place Foerstel under arrest and reportedly found him in possession of a loaded handgun.

In 2013, Foerstel was convicted of invasion of privacy in St. Charles County for “knowingly and intentionally” filming an 11-year-old girl while she was partially nude inside a department store dressing room.

In case you are wondering, the CEO of Target, Brian Cornell, still thinks that men dressed as women should be allowed to use women’s bathrooms.

NewsMax explains:

Target CEO Brian Cornell defended the company’s transgender bathroom policy decision to shareholders while also denying that the $10 billion in losses suffered since had anything to do with the controversial decision, Breitbart reported.

The new policy, instituted seven weeks ago, allows transgender men and women to use the bathrooms and changing rooms of the gender they identify with at all Target stores.

That decision has been the impetus behind a boycott of Target by about 1 million Americans.

“We’re a company that believes strongly in diversity and inclusion,” LifeSiteNews quoted Cornell at Wednesday’s shareholder meeting in Costa Mesa, Calif. “We’re a company that is very guest-centered.”

All these people on the corporate left like to throw around words like “diversity”, “tolerance” and “inclusion”. But they don’t know what those words even mean.

The true story of Thanksgiving: Squanto’s miraculous path to Plymouth

"The First Thanksgiving at Plymouth" by Jennie Augusta Brownscombe (1914)
“The First Thanksgiving at Plymouth” by Jennie Augusta Brownscombe (1914)

God’s providence in action, as reported by Eric Metaxas in the Wall Street Journal.

Full text:

The story of how the Pilgrims arrived at our shores on the Mayflower—and how a friendly Patuxet native named Squanto showed them how to plant corn, using fish as fertilizer—is well-known. But Squanto’s full story is not, as National Geographic’s new Thanksgiving miniseries, “Saints & Strangers,” shows. That might be because some details of Squanto’s life are in dispute. The important ones are not, however. His story is astonishing, even raising profound questions about God’s role in American history.

Every Thanksgiving we remember that, to escape religious persecution, the Pilgrims sailed to the New World, landing at Plymouth Rock in 1620. But numerous trading ships had visited the area earlier. Around 1608 an English ship dropped anchor off the coast of what is today Plymouth, Mass., ostensibly to trade metal goods for the natives’ beads and pelts. The friendly Patuxets received the crew but soon discovered their dark intentions. A number of the braves were brutally captured, taken to Spain and sold into slavery.

One of them, a young man named Tisquantum, or Squanto, was bought by a group of Catholic friars, who evidently treated him well and freed him, even allowing him to dream of somehow returning to the New World, an almost unimaginable thought at the time. Around 1612, Squanto made his way to London, where he stayed with a man namedJohn Slany and learned his ways and language. In 1618, a ship was found, and in return for serving as an interpreter, Squanto would be given one-way passage back to the New World.

After spending a winter in Newfoundland, the ship made its way down the coast of Maine and Cape Cod, where Squanto at last reached his own shore. After 10 years, Squanto returned to the village where he had been born. But when he arrived, to his unfathomable disappointment, there was no one to greet him. What had happened?

It seems that since he had been away, nearly every member of the Patuxets had perished from disease, perhaps smallpox, brought by European ships. Had Squanto not been kidnapped, he would almost surely have died. But perhaps he didn’t feel lucky to have been spared. Surely, he must have wondered how his extraordinary efforts could amount to this. At first he wandered to another Wampanoag tribe, but they weren’t his people. He was a man without a family or tribe, and eventually lived alone in the woods.

But his story didn’t end there. In the bleak November of 1620, the Mayflower passengers, unable to navigate south to the warmer land of Virginia, decided to settle at Plymouth, the very spot where Squanto had grown up. They had come in search of religious freedom, hoping to found a colony based on Christian principles.

Their journey was very difficult, and their celebrated landing on the frigid shores of Plymouth proved even more so. Forced to sleep in miserably wet and cold conditions, many of them fell gravely ill. Half of them died during that terrible winter. One can imagine how they must have wept and wondered how the God they trusted and followed could lead them to this agonizing pass. They seriously considered returning to Europe.

But one day during that spring of 1621, a Wampanoag walked out of the woods to greet them. Somehow he spoke perfect English. In fact, he had lived in London more recently than they had. And if that weren’t strange enough, he had grown up on the exact land where they had settled.

Because of this, he knew everything about how to survive there; not only how to plant corn and squash, but how to find fish and lobsters and eels and much else. The lone Patuxet survivor had nowhere to go, so the Pilgrims adopted him as one of their own and he lived with them on the land of his childhood.

No one disputes that Squanto’s advent among the Pilgrims changed everything, making it possible for them to stay and thrive. Squanto even helped broker a peace with the local tribes, one that lasted 50 years, a staggering accomplishment considering the troubles settlers would face later.

So the question is: Can all of this have been sheer happenstance, as most versions of the story would have us believe? The Pilgrims hardly thought so. To them, Squanto was a living answer to their tearful prayers, an outrageous miracle of God. Plymouth Colony Governor William Bradford declared in his journal that Squanto “became a special instrument sent of God” who didn’t leave them “till he died.”

Indeed, when Squanto died from a mysterious disease in 1622, Bradford wrote that he wanted “the Governor to pray for him, that he might go to the Englishmen’s God in heaven.” And Squanto bequeathed his possessions to the Pilgrims “as remembrances of his love.”

These are historical facts. May we be forgiven for interpreting them as the answered prayers of a suffering people, and a warm touch at the cold dawn of our history of an Almighty Hand?

America is truly a blessed nation. Why this story is not taught in all the schools of the nation is beyond me.