Intelligent Design

Do viruses help explain the origin of life?

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Work by a husband-and-wife team of virologists is shedding new light on an old scientific dispute: did viruses emerge before or after the development of cellular life? Until recently, many scientists believed that viruses only appeared after the first cells emerged on the primordial Earth. However, the recent discovery of strange genes in giant viruses is leading some scientists to suggest that the ancestors of viruses evolved before cells.

Are they alive or aren’t they?

Giant viruses, which were first described in 2003, straddle the gap between viruses and bacteria. Despite the fact that viruses undergo natural selection and reproduce by creating multiple copies of themselves through self-assembly – an ability which University of Cape Town virologist Ed Rybicki considers sufficient to qualify them as living things – it has long been argued that viruses are not truly alive, since they lack the machinery required to replicate their genes: instead, they have to make use of the genes belonging to the cells they infect. Consequently, most scientists have argued that viruses could only have emerged after the appearance of the first cells on Earth. Nobel Laureate and Harvard biochemist Jack Szostak espouses this view of viruses, in an interview with science journalist Carrie Arnold in Quanta magazine: “They rely on cellular machinery to help with their replication, so they need to have some sort of primitive cell to make use of that machinery” (Hints of Life’s Start Found in a Giant Virus, July 10, 2014). However, giant viruses possess some genes which are involved in replication, which suggests that they may have once been free-living organisms that devolved into viruses.

In 2013, husband-and-wife team Chantal Abergel and Jean-Michel Claverie discovered the pithovirus, a remarkable virus with some 500 genes – some viruses have as few as four – which are used for complex tasks, such as making proteins and repairing and replicating DNA. Because they possess some of their own replication machinery, pithoviruses are quite different from most viruses, which copy themselves by hijacking their host’s molecular machinery.

As far back as 2003, Abergel and Claverie helped identify the mimivirus (illustrated above, courtesy of Wikipedia and InvaderXan), which was originally thought to be a parasitic bacterium, on account of its large size (>0.7 micrometers) and genomic complexity (>1000 genes). When the husband-and-wife team looked at the organism through a microscope, they instantly recognized the distinctive shape of a virus. More recently, they discovered an even bigger virus growing in amoebae, which they christened the pandoravirus on account of its surprising lack of similarity with previously described viruses. Abergel and Claverie reported on their discovery last year, in Science magazine (Vol. 341 no. 6143, 19 July 2013, pp. 281-286, DOI: 10.1126/science.1239181). As Abergel put it: “More than 90 percent of its genes did not resemble anything else found on Earth.” And how many genes did it have? A staggering 2,500 (by comparison, the bacterium E. coli has 4,300).

A fourth domain of life?

Some researchers contend that the genetic uniqueness of giant viruses indicates that they merit their own branch on the tree of life, as a fourth domain alongside bacteria, archaea and eukaryotes (organisms such as plants, animals, fungi and protists, whose cells contain a nucleus). And it would be a very old branch, too. In a 2012 study in the journal BMC Evolutionary Biology (12:156, doi:10.1186/1471-2148-12-156), Gustavo Caetano-Anolles, a bioinformatics specialist at the University of Illinois, Urbana-Champaign, traced the evolutionary history of proteins occurring in several giant viruses and concluded that these viruses “represent a form of life that either predated or coexisted with the last universal common ancestor,” an organism which is estimated to have lived some 3.5 to 3.8 billion years ago.

Koonin’s Virus World theory

Evolutionary biologist Eugene Koonin has even suggested that modern cells evolved from viruses. In her report for Quanta magazine (July 10, 2014), science journalist Carrie Arnold handily summarizes Koonin’s proposal:

According to his theory, dubbed the Virus World, the ancestors of modern viruses emerged when all life was still a floating stew of genetic information, amino acids and lipids. The earliest pieces of genetic material were likely short pieces of RNA with relatively few genes that often parasitized other floating bits of genetic material to make copies of themselves. These naked pieces of genetic information swapped genes at a primeval genetic flea market, appropriating hand-me-downs from other elements and discarding genes that were no longer needed.

Over time, Koonin argues, the parasitic genetic elements remained unable to replicate on their own and evolved into modern-day viruses that mooch off their cellular hosts. The genes they parasitized began to evolve different types of genetic information and other barriers to protect themselves from the genetic freeloaders, which ultimately evolved into cells.

A curious omission: Koonin himself believes the emergence of life on Earth was overwhelmingly unlikely

What I find most astonishing about this report, however, is that it makes no mention of Koonin’s valuable work in demonstrating that the origin of life was an astronomically improbable event. Indeed, Koonin estimates that the likelihood of life’s evolving anywhere in the observable universe over its 13.8-billion-year lifetime is just 1 in 101,018 – that’s 1 in 1 followed by 1,018 zeroes! And that’s an estimate that Koonin himself describes as generous, in an article he wrote in 2007, titled, The Cosmological Model of Eternal Inflation and the Transition from Chance to Biological Evolution in the History of Life (Biology Direct 2 (2007): 15, doi:10.1186/1745-6150-2-15). In the passage below, the term “O-region” refers to an observable universe, like our own. Koonin considers the emergence of life in our observable universe to be such an unlikely event that he is forced to postulate the existence of a vast and possibly infinite number of universes like our own, in order to make the origin of life somewhere reasonably probable. Even assuming the existence of self-replicating RNA molecules, the difficulty of generating a translation-replication system (which is found in all cellular organisms) by a process of Darwinian selection is truly staggering. As Koonin puts it:

In other words, even in this toy model that assumes a deliberately inflated rate of RNA production, the probability that a coupled translation-replication emerges by chance in a single O-region is P < 10-1018. Obviously, this version of the breakthrough stage can be considered only in the context of a universe with an infinite (or, at the very least, extremely vast) number of O-regions.

The argument presented in Koonin’s peer-reviewed paper has been republished in his recent book, The Logic of Chance: The Nature and Origin of Biological Evolution (Upper Saddle River: FT Press, 2011, ISBN 978-0-13-262317-9), which can be viewed online.

A new chicken-and-egg paradox relating to the origin of life

Valerian Dolja, a virologist at Oregon State University and a professional colleague of Koonin’s, is a strong supporter of his Virus World theory. She argues that if viruses developed from cells, they should be genetically less diverse than cells, as cells would contain the entire range of genes found in viruses – but in fact, scientists have found that the reverse is the case. Patrick Forterre, a virologist at Paris-Sud University, is another advocate of Koonin’s theory. He points out that viruses are also more diverse than cellular organisms in their methods of reproduction: the latter have only two main methods of reproduction, while viruses have many different methods. Forterre believes, however, that viruses evolved after primitive cells, but before modern cells.

Harvard biochemist Jack Szostak offers a more cautious interpretation of the evidence: although he is willing to accept that parasitic genetic elements (bits of genetic material that use other bits in order to make copies of themselves) may have existed on Earth before cells, he nonetheless insists that true viruses only emerged after cellular organisms did. In her report for Quanta magazine, Carrie Arnold highlights the disagreement between the two camps:

“Whenever you mix a bunch of small RNA molecules together, you get a bunch of parasitic sequences that aren’t good at anything except making copies of themselves faster than anything else,” Szostak said. For these sequences to become similar to modern viruses, they need to parasitize a living cell, not just another strand of RNA.

Dolja disagrees, saying that cells could not have evolved without viruses. “In order to move from RNA to DNA, you need an enzyme called reverse transcriptase,” Dolja said. “It’s only found in viruses like HIV, not in cells. So how could cells begin to use DNA without the help of a virus?

For their part, Abergel and Claverie propose that giant viruses evolved from a line of cells that lost its ability to replicate on their own and was forced to rely on other cells to copy its DNA. The husband-and-wife team reject the view that life developed from a single common ancestor, arguing instead that competition between several different kinds of cell-like organisms accounts for the diversity of life on Earth today.

What I find most remarkable about the contemporary debate regarding the role of viruses in the origin of life on Earth is that a new chicken-and-egg paradox has received so little attention in the popular science media. On the one hand, Szostak argues convincingly that in order for parasitic genetic elements to become like modern viruses, they need to parasitize a living cell. On the other hand, Dolja contends that cells could not have evolved without viruses, as they need reverse transcriptase (which is found only in viruses) in order to move from RNA to DNA.

In other words, instead of helping to solve the problem of the origin of life on Earth, recent research has only served to highlight one of its central paradoxes. And yet the science media reports the latest discoveries as if the solution is just around the corner. Don’t you find that just a little strange?

What do readers think? Comments are welcome.

13 Replies to “Do viruses help explain the origin of life?

  1. 1
    mahuna says:

    Of course if cells and viruses were both designed before they were constructed, then there is no paradox and either one could have been “installed” on Earth first.

    Slightly off topic, is there any widely accepted explanation for the chicken-egg problem that cell DNA is assembled from proteins but proteins are made by cells, so how did the first cells get their proteins.

  2. 2
    johnp says:

    You don’t understand evolution. OOL and evolution are two totally separate concepts and one has nothing to do with the other. When will you IDiots get a clue?

  3. 3
    Mapou says:

    johnp:

    You don’t understand evolution.

    We heard that one before.

  4. 4
    Acartia_bogart says:

    Johnp, it is not that they don’t understand that OOL and evolution are mutually independent. It is that they chose to conflate the two because it fits better with their belief system.

    But when rationale people try to argue that ID and creationism are the same thing (which it is) we are accused of not understanding.

  5. 5
    Mapou says:

    If the dirt worshippers cannot explain how life originated, then they don’t have a theory. All they have is superstition.

  6. 6
    Acartia_bogart says:

    “If the dirt worshippers cannot explain how life originated, then they don’t have a theory. All they have is superstition.”

    Really? What has evolutionary theories ever said about origin of life? I can answer that for you. Nothing. Evolution is only about the change of life over time. This does not mean evolutionary biologists do not have their own opinions about OOL, but it is completely separate from their chosen field of study.

  7. 7
    Mapou says:

    Acartia_bogart @6,

    It’s just a matter of extrapolation. The dirt worshippers want us to believe that living organisms evolved all by themselves from the simple to the complex. If you run the evolutionary clock backward, you run into absurdity. Hell, you run into absurdity before you even start to run the clock backward.

  8. 8
    Acartia_bogart says:

    Mapou: “It’s just a matter of extrapolation”

    As is the extrapolation from ID to creationism to religion to faith. I am willing to accept the one extrapolation if you are willing to accept the other.

  9. 9
    Mapou says:

    Acartia_bogart,

    Personally, I don’t deny that that ID requires an intelligent designer/creator. That is the whole point of ID. What bothers me is the hypocrisy and silliness of those who pretend that they don’t have a religion to defend. In the end it’s all about religion. May the best religion win.

  10. 10
    Eric Anderson says:

    mahuna @1:

    Slightly off topic, is there any widely accepted explanation for the chicken-egg problem that cell DNA is assembled from proteins but proteins are made by cells, so how did the first cells get their proteins.

    No, there is no explanation. Serious researchers acknowledge this as a serious issue. Which is partly why there is so much effort to find other options than DNA-first or protein-first scenarios for the origin of life.

    There are many of these chicken-and-egg problems in living systems. OOL is simply the most obvious case (because it prevents Darwinists from invoking the silly but oft-cited magic of natural selection as the driving force behind new innovations).

  11. 11
    Acartia_bogart says:

    Mapou: “In the end it’s all about religion. May the best religion win.”

    Science and atheism are not religions. Religion, by its nature, accepts the gospel regardless of evidence. As a scientist, I have modified my view of how the universe operates over time as new evidence arises. And as an atheist, I will be more than happy to be demonstrated wrong

  12. 12
    DavidD says:

    A.B. – “Science and atheism are not religions.”

    Absolutely untrue. Any human being is capable of making a religion out of anything and given the massive amounts of faith affirmations spewed by evolutionists, it definitely qualifies as a religion in the definition sense. Often times the definition for atheism is given as simply “non-belief”, which is retarded because everyone believes in something. The biblical definition and explanation of who or what a god is or religion does not according to the Bible (which is always the main target in any debate) is that an intelligent agency is not required, which fits the evolutionary belief system and atheism.

    Philippians 3:19 – Common English Bible (CEB)

    19 “Their lives end with destruction. Their god is their stomach, and they take pride in their disgrace because their thoughts focus on earthly things.”

    So the concept and belief in any kind of a god according to biblical definition given above is actually defined as Any “THING” any human holds in reverential awe and/or ANY “THING” devoutly pursued. Example, a god to an Alcoholic is liquor, to a Smoker it’s Cigarettes, to a Drug Addict is drugs and so forth. None of those things like the Bible’s use of the word “Stomach” are an intelligent entity. Even the pursuit of materialism or as the text defined “earthly things” can be considered religious.

    A.B. – “Religion, by its nature, accepts the gospel regardless of evidence.”

    This is hilarious. Darwin’s holy book is taken as religious gospel, although most of his predictions have been proven false. Here recently Scientists were still trying to prove Darwin’s religious faith affirmations using an algae experiment written about in Live Science back on April 2014. Without actually ever experimenting previously to prove this Darwinian Doctrine on feeding competition, the article stated this about Biologists: “Most biologists long have accepted this to be true.” That’s called Faith! When they did finally experiment and the Holy Guru’s dogma proved false, this is what the article had to say about the response of biologists: “Thus, three researchers were more than a little shaken to find that their experiments on fresh water green algae failed to support Darwin’s theory”

    Again, their faith was shaken, because the scriptural texts of Darwin didn’t match the evidence they previous failed to look for, but rather opted for taking it on faith that this Guru had it correct. Over at Cornelius Hunter’s blog there are a number of combative Darwin defenders who often reveal the uncanny ability of a Wiccan to channel Darwin and tell everyone what he actually meant or what he actually believed , which is far different than what he actually wrote in his scriptural text. They find themselves forced to make up these statements on the fly in defending the man’s religious concepts because his limited 19th century understanding and knowledge could not have possibly known nor understood what we all now know today in modern times. So Darwin worshipers will dogmatically defend every faith affirmation the man ever put down in print.

    A.B. – “And as an atheist, I will be more than happy to be demonstrated wrong”

    Thanks, but you’ve already proven everyone’s point on this time and again. Yet you’ll always deny you have faith despite the fact that you waste so much time here proselytizing this faith and defending the gross flaws of your Guru to others

  13. 13
    Paul White says:

    “… which is retarded…”

    The only attitude/behaviour here that I find retarded is basing your whole philosophy and belief system on a book written 2000 years ago and never updated since.

    (Oh, sorry, that deals with only one in the multiverse of One True Religions)

    Scientists quite understandably get wedded to their beliefs but, taken as a whole, the Book of Science continues to be evolved (cautiously and conservatively) in accordance with the consensus of many highly educated and well-trained and well-published men and women.

    Sadly, a bunch of uneducated, scientifically untrained “retards” with big trumpets do make rather a nuisance of themselves.

    For all I care, followers of these OTRs can piddle around with all their petty rules and ceremonies until Heat Death. Just as long as they don’t eat my grandchildren or chop my hands off.

    It’s just rather a shame I can’t find the switch to shut out their prattle.

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