Last year in July a prominent critic of intelligent design theory, Dr. Adam Shapiro, took the Discovery Institute to task for not debunking the lab origin theory. He says,

Behe seems to miss an opportunity to demonstrate that intelligent design theory shows how those pathways are not irreducible complex.

Adam Shapiro, “Did Intelligent Design Just Miss Its Corona Moment?” at American Scientist

and,

How better to demonstrate its own apolitical nature than to apply its scientific process to debunk the Chinese lab myth?

Adam Shapiro, “Did Intelligent Design Just Miss Its Corona Moment?” at American Scientist

First of all, this is a fundamental misunderstanding of ID. ID theory is only resilient against false positives, not false negatives, as Dr. Ewert explains in his well-written article. ID can help debunk design inferences that do not properly apply the explanatory filter, but it cannot demonstrate true negatives, i.e. the virus did not come from a lab. So, ID can be used to debunk a particular theory regarding the coronavirus coming from a lab, but cannot be used to debunk the general proposition “the coronavirus was engineered in a lab.”

Going back to Dr. Shapiro’s request: If Dr. Behe were to show the pathways are not irreducibly complex, this would do nothing to debunk the “virus from the lab” theory. It would be like saying since small rocks naturally break off of big rocks, the pet rock industry cannot exist. Yet, Gary Dahl made a cool $15 million sticking beady eyes on beach stones! Likewise, scientists in a lab can use natural processes to generate bioweapon viruses. Dr. Shapiro’s article is an excellent example of the misuse of the explanatory filter.

Now hold your horses. From all the misuse, you might think the explanatory filter is useless. Maybe it cannot tell us anything about the lab theory. Would you be surprised to know that scientists close to Dr. Anthony Fauci used the explanatory filter to textbook perfection right at the beginning of the pandemic?

According to emails obtained from Dr. Fauci, a scientist named Dr. Kristian Andersen followed the explanatory filter correctly to initially arrive at a design inference regarding the virus’ origin. Quoting from the article:

In an email to Dr. Fauci sent on January 31 last year, Kristian G. Andersen of the Scripps Research Institute told the National Institute of Allergy and Infectious Diseases director that some of SARS-CoV-2’s features “(potentially) look engineered.”

…”I should mention that after discussions earlier today, Eddie, Bob, Mike, and myself all find the genome inconsistent with expectations from evolutionary theory,” the expert added. “But we have to look at this much more closely and there are still further analyses to be done, so those opinions could still change.”

James Walker, “Fauci Emails Show Experts Had Concern COVID Virus Could ‘Look Engineered’” at Newsweek

In a New York Times interview Dr. Andersen expands on what he meant by “inconsistent” with evolutionary theory.

“Those features included a structure known as the Furin cleavage site that allows the SARS-CoV-2 spike protein to be cleaved by Furin, an enzyme found in human cells, and another structure, known as the receptor binding domain, that allowed the virus to anchor to the outside of human cells via a cell-surface protein known as ACE2.”

Interview with Kristian Andersen, “Scientist Opens Up About His Early Email to Fauci on Virus Origins” at The New York Times

Dr. Andersen states that subsequently his research group did find the potentially engineered segments in other viruses, and thus eventually dismissed the lab origin theory.

Ignoring the merits of this later conclusion for now, I’d like to focus on Dr. Andersen’s initial design inference and examine how it maps to the explanatory filter. From there, we can determine what it would take to dislodge the inference, and whether Dr. Andersen’s later conclusion meets those requirements.

First, let’s re-establish the three key steps of the explanatory filter.

1. Eliminate high probability (necessity). This step eliminates events that occur with near certainty. For example, if I flip a coin, I know with almost 100% confidence the result will be heads or tails.
2. Eliminate small probability (chance). There are many events that occur with small probability, like getting a straight flush in poker. They do not happen often, but when they do happen, we do not automatically infer design (unless a couple aces fall out of the player’s sleeve). To do this, we set a probability bound, such as Dembski’s universal probability bound of 2 to the power negative 500, and only events that have a lower probability pass the second stage.
3. Event conforms to an independent pattern (specification). Even after eliminating events of small probability, events that surpass the universal probability bound happen all the time. In fact, we can easily generate such an event ourselves by flipping a coin 501 times. The specific sequence of coins has a probability of 2 to the negative 501 of occurring, so small probability is eliminated. To complete the final step, the sequence must also correspond to an independently provided pattern. For example, if we wrote out 501 heads and tails, and then proceeded to flip that exact sequence, one would justifiably reject the possibility this happened by chance.

So, how does Dr. Andersen’s analysis stack up against these steps?

Step 1 is eliminated off the bat, since all genetic sequences are improbable.

Step 2 is where things get interesting. Dr. Andersen states a few specific sequences are “inconsistent” with evolutionary theory. This means the probability of the sites evolving naturally within the given timeframe is very small. So, the coronavirus’ emergence is not an event of small probability.

Step 3 is where Dr. Andersen initially makes his design inference. This is not stated explicitly, but we can see he has an independent pattern in mind in his words to The New York Times. The specific sections he notes are the sites that make the virus especially good at connecting to specifically human cells, i.e. it is not a binding site that’s widespread across all species. Something must be making the virus target human cells. This sounds a lot like an independently provided pattern, thus passing the third and final hurdle of the design inference, and that is Dr. Andersen’s initial conclusion. But is the pattern really independent?

The final question of whether the pattern is independent can dislodge the design inference, and show the inference is invalid. What does it mean for the pattern to be independent? It must be a genetic sequence that is not derived from the event under question. For example, if after observing 501 coin flips, I made the specification pattern that exact sequence, the pattern would not be independent. A 501 coin flip sequence only counts as an independent pattern if it is given before the coin is flipped.

Dr. Andersen later found the sites to also occur in other viruses, which led him to conclude the pattern is not independent.

“Furin cleavage sites are found all across the coronavirus family, including in the betacoronavirus genus that SARS-CoV-2 belongs to.”

So, we can see that Dr. Andersen followed the explanatory filter to a T with his initial inference to design, and then subsequent rejection of the inference. Thus, contrary to Dr. Shapiro’s charge, and though it was not carried out by the Discovery Institute, the explanatory filter was used correctly by scientists when dealing with the lab origin theory.

Now, what is the upshot of all this analysis? Is it merely bragging rights, claiming important real world application of Intelligent Design, albeit after the fact? In itself, this is nothing to sniff at. People were falling off cliffs way before Newton formalized the theory of gravity. An after-the-fact identification of scientists using the explanatory filter is a great validation of intelligent design theory.

Like Newton’s theory of gravity, formalizing and identifying the explanatory filter allows us to break down the design inference and get clarity on how to proceed. People fell down cliffs before Newton, but we only launched people into space after Newton. Because of Dembski’s work, we know that Dr. Andersen’s rejection of the design inference revolves around the question of whether the specification is independent, and we can analyze his rejection on the grounds of whether his evidence shows the specification pattern is not independent.

Dr. Andersen decided the furin cleavage site pattern is not independent because it occurs in other viruses in the same genus as the coronavirus. Is this adequate grounds to conclude the pattern is not independent? Maybe not. Remember that Dr. Andersen’s team initially concluded the furin site was not compatible with evolutionary theory. So, even if the site shows up in other closely related viruses, the site is still an independent pattern because it is not a likely pattern given evolutionary theory. This means insofar the team’s original conclusion that the sites are highly unlikely to evolve, Dr. Andersen rejected the design inference without an adequate reason to show the pattern is not independent. To dislodge the design inference, Dr. Andersen and his team need to go back to step 2 and show the sites are likely to evolve.

Consequently, Dr. Andersen’s initial design inference stands on sturdier ground than his later retraction.