Tag Archives: Origins

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.

Stephen C. Meyer and Marcus Ross lecture on the Cambrian explosion

Cambrian Explosion
Cambrian Explosion

Access Research Network is a group that produces recordings  of lectures and debates related to intelligent design. I noticed that on their Youtube channel they are releasing some of their older lectures and debates for FREE. So I decided to write a summary of one that I really like on the Cambrian explosion. This lecture features Dr. Stephen C. Meyer and Dr. Marcus Ross.

The lecture is about two hours. There are really nice slides with lots of illustrations to help you understand what the speakers are saying, even if you are not a scientist.

Here is a summary of the lecture from ARN:

The Cambrian explosion is a term often heard in origins debates, but seldom completely understood by the non-specialist. This lecture by Meyer and Ross is one of the best overviews available on the topic and clearly presents in verbal and pictorial summary the latest fossil data (including the recent finds from Chengjiang China). This lecture is based on a paper recently published by Meyer, Ross, Nelson and Chien “The Cambrian Explosion: Biology’s Big Bang” in Darwinism, Design and Public Education(2003, Michigan State University Press). This 80-page article includes 127 references and the book includes two additional appendices with 63 references documenting the current state of knowledge on the Cambrian explosion data.

The term Cambrian explosion describes the geologically sudden appearance of animals in the fossil record during the Cambrian period of geologic time. During this event, at least nineteen, and perhaps as many as thirty-five (of forty total) phyla made their first appearance on earth. Phyla constitute the highest biological categories in the animal kingdom, with each phylum exhibiting a unique architecture, blueprint, or structural body plan. The word explosion is used to communicate that fact that these life forms appear in an exceedingly narrow window of geologic time (no more than 5 million years). If the standard earth’s history is represented as a 100 yard football field, the Cambrian explosion would represent a four inch section of that field.

For a majority of earth’s life forms to appear so abruptly is completely contrary to the predictions of Neo-Darwinian and Punctuated Equilibrium evolutionary theory, including:

  • the gradual emergence of biological complexity and the existence of numerous transitional forms leading to new phylum-level body plans;
  • small-scale morphological diversity preceding the emergence of large-scale morphological disparity; and
  • a steady increase in the morphological distance between organic forms over time and, consequently, an overall steady increase in the number of phyla over time (taking into account factors such as extinction).

After reviewing how the evidence is completely contrary to evolutionary predictions, Meyer and Ross address three common objections: 1) the artifact hypothesis: Is the Cambrian explosion real?; 2) The Vendian Radiation (a late pre-Cambrian multicellular organism); and 3) the deep divergence hypothesis.

Finally Meyer and Ross argue why design is a better scientific explanation for the Cambrian explosion. They argue that this is not an argument from ignorance, but rather the best explanation of the evidence from our knowledge base of the world. We find in the fossil record distinctive features or hallmarks of designed systems, including:

  • a quantum or discontinuous increase in specified complexity or information
  • a top-down pattern of scale diversity
  • the persistence of structural (or “morphological”) disparities between separate organizational systems; and
  • the discrete or novel organizational body plans

When we encounter objects that manifest any of these several features and we know how they arose, we invariably find that a purposeful agent or intelligent designer played a causal role in their origin.

Recorded April 24, 2004. Approximately 2 hours including audience Q&A.

You can get a DVD of the lecture and other great lectures from Access Research Network. I recommend their origin of life lectures – I have watched the ones with Dean Kenyon and Charles Thaxton probably a dozen times each. Speaking as an engineer, you never get tired of seeing engineering principles applied to questions like the origin of life.

The Cambrian explosion lecture above is a great intermediate-level lecture and will prepare you to be able to understand Dr. Meyer’s new book “Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design“. The Michigan State University book that Dr. Meyer mentions is called “Darwin, Design and Public Education“. That book is one of the two good collections on intelligent design published by academic university presses, the other one being from Cambridge University Press, and titled “Debating Design: From Darwin to DNA“. If you think this lecture is above your level of understanding, then be sure and check out the shorter and more up-to-date DVD “Darwin’s Dilemma“.

Alexander Vilenkin: “All the evidence we have says that the universe had a beginning”

I’ve decided to explain why physicists believe that there was a creation event in this post. That is to say, I’ve decided to let famous cosmologist Alexander Vilenkin do it.

From Uncommon Descent.


Did the cosmos have a beginning? The Big Bang theory seems to suggest it did, but in recent decades, cosmologists have concocted elaborate theories – for example, an eternally inflating universe or a cyclic universe – which claim to avoid the need for a beginning of the cosmos. Now it appears that the universe really had a beginning after all, even if it wasn’t necessarily the Big Bang.

At a meeting of scientists – titled “State of the Universe” – convened last week at Cambridge University to honor Stephen Hawking’s 70th birthday, cosmologist Alexander Vilenkin of Tufts University in Boston presented evidence that the universe is not eternal after all, leaving scientists at a loss to explain how the cosmos got started without a supernatural creator. The meeting was reported in New Scientist magazine (Why physicists can’t avoid a creation event, 11 January 2012).

[…]In his presentation, Professor Vilenkin discussed three theories which claim to avoid the need for a beginning of the cosmos.

The three theories are chaotic inflationary model, the oscillating model and quantum gravity model. Regular readers will know that those have all been addressed in William Lane Craig’s peer-reviewed paper that evaluates alternatives to the standard Big Bang cosmology.

But let’s see what Vilenkin said.


One popular theory is eternal inflation. Most readers will be familiar with the theory of inflation, which says that the universe increased in volume by a factor of at least 10^78 in its very early stages (from 10^−36 seconds after the Big Bang to sometime between 10^−33 and 10^−32 seconds), before settling into the slower rate of expansion that we see today. The theory of eternal inflation goes further, and holds that the universe is constantly giving birth to smaller “bubble” universes within an ever-expanding multiverse. Each bubble universe undergoes its own initial period of inflation. In some versions of the theory, the bubbles go both backwards and forwards in time, allowing the possibility of an infinite past. Trouble is, the value of one particular cosmic parameter rules out that possibility:

But in 2003, a team including Vilenkin and Guth considered what eternal inflation would mean for the Hubble constant, which describes mathematically the expansion of the universe. They found that the equations didn’t work (Physical Review Letters, DOI: 10.1103/physrevlett.90.151301). “You can’t construct a space-time with this property,” says Vilenkin. It turns out that the constant has a lower limit that prevents inflation in both time directions. “It can’t possibly be eternal in the past,” says Vilenkin. “There must be some kind of boundary.”

A second option explored by Vilenkin was that of a cyclic universe, where the universe goes through an infinite series of big bangs and crunches, with no specific beginning. It was even claimed that a cyclic universe could explain the low observed value of the cosmological constant. But as Vilenkin found, there’s a problem if you look at the disorder in the universe:

Disorder increases with time. So following each cycle, the universe must get more and more disordered. But if there has already been an infinite number of cycles, the universe we inhabit now should be in a state of maximum disorder. Such a universe would be uniformly lukewarm and featureless, and definitely lacking such complicated beings as stars, planets and physicists – nothing like the one we see around us.

One way around that is to propose that the universe just gets bigger with every cycle. Then the amount of disorder per volume doesn’t increase, so needn’t reach the maximum. But Vilenkin found that this scenario falls prey to the same mathematical argument as eternal inflation: if your universe keeps getting bigger, it must have started somewhere.

However, Vilenkin’s options were not exhausted yet. There was another possibility: that the universe had sprung from an eternal cosmic egg:

Vilenkin’s final strike is an attack on a third, lesser-known proposal that the cosmos existed eternally in a static state called the cosmic egg. This finally “cracked” to create the big bang, leading to the expanding universe we see today. Late last year Vilenkin and graduate student Audrey Mithani showed that the egg could not have existed forever after all, as quantum instabilities would force it to collapse after a finite amount of time (arxiv.org/abs/1110.4096). If it cracked instead, leading to the big bang, then this must have happened before it collapsed – and therefore also after a finite amount of time.

“This is also not a good candidate for a beginningless universe,” Vilenkin concludes.

So at the end of the day, what is Vilenkin’s verdict?

“All the evidence we have says that the universe had a beginning.”

This is consistent with the Borde-Guth-Vilenkin Theorem, which I blogged about before, and which William Lane Craig leveraged to his advantage in his debate with Peter Millican.

The Borde-Guth-Vilenkin (BGV) proof shows that every universe that expands must have a space-time boundary in the past. That means that no expanding universe, no matter what the model, can be eternal into the past. No one denies the expansion of space in our universe, and so we are left with a cosmic beginning. Even speculative alternative cosmologies do not escape the need for a beginning.


If the universe came into being out of nothing, which seems to be the case from science, then the universe has a cause. Things do not pop into being, uncaused, out of nothing. The cause of the universe must be transcendent and supernatural. It must be uncaused, because there cannot be an infinite regress of causes. It must be eternal, because it created time. It must be non-physical, because it created space. There are only two possibilities for such a cause. It could be an abstract object or an agent. Abstract objects cannot cause effects. Therefore, the cause is an agent.

Now, let’s have a discussion about this science in our churches, and see if we can’t train Christians to engage with non-Christians about the evidence so that everyone accepts what science tells us about the origin of the universe.

Stephen C. Meyer debates intelligent design with two scientists on NPR

British Spitfire and German Messerschmitt Me 109 locked in a dogfight
British Spitfire and German Messerschmitt Me 109 locked in a dogfight

Evolution News reported on a 27-minute debate featuring Dr. Stephen C. Meyer – probably the best proponent of intelligent design there is.


We often say that Darwinists are reluctant to debate advocates of intelligent design, but here are two who deserve a tip of the hat. Keith Pannell is a chemist at the University of Texas at El Paso who hosts a program, Science Studio, on the NPR station there. He invited Stephen Meyer on to talk about the science of ID, pegged to the Dover anniversary.

Clearly Pannell is an ID critic so he gets kudos for being willing to have a civil and informative conversation. Perhaps feeling insecure about facing the author of Darwin’s Doubt by himself, Dr. Pannell invited a biologist colleague, Ricardo Bernal, to serve as “co-host.”

So it was two against one, but no worries. Meyer is, as always, superb, and the discussion sounds like it was an education for the two Texas scientists. Listen and enjoy.

I took a back-up of the MP3 file here.


  • How did Dr. Meyer get interested in science?
  • What is intelligent design? (origin of life, fine-tuning)
  • What is creationism? (young Earth, different epistemology)
  • Who does Dr. Meyer think the intelligent designer is?
  • Finding the best explanation from multiple competing hypotheses
  • Critic: aren’t you arguing for a designer from ignorance, then?
  • The importance of naturalists acknowledging what they do and do not know about the origin of life
  • We do have experience with intelligent causation, whenever we sequence symbols to have meaning and purpose, e.g. – writing
  • Critic: information in DNA is not digital information, is it?
  • Information in the cell follows a 4-character alphabet
  • the sequences are composed of many parts / symbols
  • the sequences themselves are specified to have function
  • Critic: the complexity just emerges from change over time
  • the origin of the first life is immune to explanation of change over time, because there is no replication – this is the first replicator
  • Critic: but isn’t it just ignorance about the origin of life?
  • what we do is look at a number of competing hypothesis and what they are capable of, and see whether each cause is capable of generating the effects we observe in nature
  • Critic: where is the experimental verification of your theory?
  • well, in the appendices of Signature of the Cell, we predicted that the non-coding regions of DNA (junk DNA) would be found to have function, and that was later proven out
  • the Darwinists said that non-coding regions of the DNA was junk, but that’s not what has been proven experimentally
  • Critic: where was this prediction written up, who wrote it?
  • intelligent design theorists predicted it: Dembski, Kenyon, Mims, Sternberg
  • Critic: but we used the scientific method to disprove the Darwinian predictions, you don’t like the scientific method
  • intelligent design proponents love science, and the scientific method, and they do work in labs to confirm their hypotheses, (WK:for example, the probability of generating a protein by chance)
  • Critic: what about the Dover court case that you lost?
  • the Discovery Institute objected to actions taken by the Dover school board
  • Critic: what about the molecular machines, how are they related to intelligent design?
  • even in the simplest living organisms, there are tiny machines that are tightly integrated, and cannot be built up in a stepwise fashion
  • Critic: I’ve worked with the ATP-synthase and other molecular machines, but “you can kind of begin to tease how some of these molecular machines have come about” – pieces have multiple functions, and they are co-opted into larger systems
  • the problem with the co-option argument breaks down when you look at the specific details of different machines
  • for example – the type III secretory system cannot be an precursor to the bacterial flagellum, it is younger, not older than the bacterial flagellum
  • Critic: what would it take for your view to be falsified?
  • demonstrable undirected processes that are capable of creating functional information in DNA, or processes that can build up an irreducibly complex molecular machine within the time available with a decent probability

If you like this debate, check out Stephen C. Meyer’s two books: “Signature in the Cell” and “Darwin’s Doubt”.

Is belief in a Creator / Designer compatible with belief in Darwinian evolution?

Sherlock Holmes and John Watson: let's take a look at the facts
Sherlock Holmes and John Watson: let’s take a look at the facts

What should we make of theistic evolutionists telling us that you can believe in God, while still knowing that matter, law and chance fully explain the development of all of biological life?

Consider this quotation from Phillip E. Johnson.


The National Academy’s way of dealing with the religious implications of evolution is akin to the two-platoon system in American football. When the leading figures of evolutionary science feel free to say what they really believe, writers such as Edward O. Wilson, Richard Dawkins, Daniel Dennett, Carl Sagan, Steven Pinker, Stephen Jay Gould, Richard Lewontin and others state the “God is dead” thesis aggressively, invoking the authority of science to silence any theistic protest. That is the offensive platoon, and the National Academy never raises any objection to its promoting this worldview.

At other times, however, the scientific elite has to protect the teaching of the “fact of evolution” from objections by religious conservatives who know what the offensive platoon is saying and who argue that the science educators are insinuating a worldview that goes far beyond the data. When the objectors are too numerous or influential to be ignored, the defensive platoon takes the field. That is when we read those spin-doctored reassurances saying that many scientists are religious (in some sense), that science does not claim to have proved that God does not exist (but merely that he does not affect the natural world), and that science and religion are separate realms which should never be mixed (unless it is the materialists who are doing the mixing). Once the defensive platoon has done its job it leaves the field, and the offensive platoon goes right back to telling the public that science has shown that “God” is permanently out of business.

(Phillip E. Johnson: “The Wedge of Truth”, IVP 2000, pp. 88-89).

So what naturalistic scientists believe is that God didn’t do anything to create the diversity of life – that nature does all of its own creating without God. In fact, it doesn’t matter if the best naturalistic explanation is improbable or implausible – naturalists must bitterly cling to materialistic explanations of natural phenomena. Any doubts about the efficacy of naturalistic mechanisms get met by “theistic evolutionists” – scientists who think that science shows that God didn’t do anything in the history of life.

When it comes to discussing origins, you have to be very careful with theistic evolutionists. The one question they want to avoid is whether science, done in the ordinary naturalistic way, can discover evidence of intelligent agency in the history of the development of life. And that’s why you have to ask them that question first. “Is there any scientific evidence that intelligent causes were active during the history of the development of life on this planet?” Their answer to that is the same as atheists, namely: “there is no scientific evidence that intelligent causes are responsible for the effects we see in the history of life on Earth”. Theistic evolutionists and atheists agree on that: as far as pure scientific evidence is concerned, nature can do its own creating without any intelligence writing genetic code or engineering animal body plans.

Now, take a look at this article by Jay Richards. He cites some theistic evolutionists.


Biologist Ken Miller:

For his part, [Ken] Miller, a biologist, has no qualms about telling us what God would do: “And in Catholicism, he said, God wouldn’t micromanage that way. ‘Surely he can set things up without having to violate his own laws.'”

I am unaware of any tenet of Catholic theology that requires God not to micromanage. It is, however, a tenet of deism.

Got that? What really happened is that God didn’t do anything. How does he know that? From the science? No. Because he assumes naturalism. Oh, it’s true that he says that God is lurking somewhere behind the material processes that created life. But God’s agency is undetectable by the methods of science. And he is hoping that you will accept his subjective pious God-talk as proof that a fundamentally atheistic reality is somehow reconcilable with a robust conception of theism.

More from Richards:

Then we get Stephen Barr offering his private definition of “chance.”

It is possible to believe simultaneously in a world that is shaped by chance and one following a divine plan. “God is in charge and there’s a lot of accident,” said Barr, also a Catholic. “It’s all part of a plan. . . . God may have known where every molecule was going to move.”

What does Barr really believe? He believes that what science shows is that nature created life without any interference by an intelligent agent. Barr then offers believers his subjective pious God-talk to reassure them that evolution is compatible with religion. He has a personal belief – NOT BASED ON SCIENCE – that the material processes that created all of life are “all part of a plan”. He cannot demonstrate that from science – it’s his faith commitment. And more speculations: “God may have known…”. He can’t demonstrate that God did know anything from science. He is just offering a personal opinion about what God “could have” done. The purpose of these subjective opinions is to appease those who ask questions about what natural mechanisms can really create. Can natural causes really account for the development of functional proteins? Never mind that – look at my shiny spiritual-sounding testimony!

That’s theistic evolution. What really happened is that no intelligent causes are needed to explain life. What they say is “God could” and “God might” and “I pray” and “I attend this church” and “I received a Christian award” and “I sing praise hymns in church”. None of these religious opinions and speculations are relevant to the science – they are just opinions, speculations and biographical trivia. Atheists and theistic evolutionists agree on what science shows about the diversity of life – intelligent causes didn’t do anything.


One of the ways that theistic evolutionists try to affirm design is by insisting that the design is “front-loaded”. The design for all the information and body plans is somehow embedded in matter.

Here is Stephen C. Meyer to assess that:

It’s very important to understand that there is no scientific evidence for design (information) being front-loaded. So although the theistic evolutionists are talking about design, it’s still in the realm of faith – not detectable to scientific investigation. And as Dr. Meyer explained, it doesn’t work to explain design anyway.

I attended a Wheaton College philosophy conference where Dr. Michael Murray read a paper advocating for this front-loaded view of design. I raised my hand to ask him a question, “hey, philosophy guy, did God front-load the information in that paper you’re reading, or did you write it yourself?” But the philosophy moderators must have known that I was an engineer, and would talk sense into him, because they never called on me. However, I did e-mail him later and asked him if he had any evidence for this front-loading theory, and couldn’t God write sequence information in time the same way he had sequenced information in his essay. He replied and said that front-loading was more emotionally satisfying for him. That’s philosophy, I guess. Thank goodness an engineer wrote his e-mail program so that he could at least come clean about his silly view.

The quickest way to disarm a theistic evolutionist is to ask them for a naturalistic explanation of the origin of life. And for a naturalistic explanation of the Cambrian explosion. And so on. Focus on the science – don’t let them turn the conversation to their personal beliefs, or to the Bible, or to religion. No one cares about the psychology of the theistic evolutionist. We only care what science can show.