iSoul In the beginning is reality

Evidence of Absence

Evidence of Absence: Completeness of Evidential Datasets

Elliott Sober presents a likelihood argument about the motto “Absence of evidence is not evidence of absence” (Sober 2009).  He states the Law of Likelihood this way:

The Law of Likelihood. Evidence E favors hypothesis H1 over hypothesis H2 precisely when Pr(E│H1) > Pr(E│H2). And the degree to which E favors H1 over H2 is measured by the likelihood ratio Pr(E│H1)/Pr(E│H2).

He argues that the likelihood ratio is more useful than the difference but it has two other problems:  it is not defined if Pr(E│H2) = 0 and has a wider range if the denominator is larger than the numerator than vice versa.  While these are more practical than theoretical objections, they may be eliminated by the following, which we shall call the likelihood ratio index:

Likelihood Ratio Index = log((1+Pr(E│H1))/(1+Pr(E│H2))).

This index ranges from -1 to +1 and equals zero when the two probabilities are equal.

Sober uses the following scenario about the fossil record to illustrate his analysis:

Suppose you are wondering whether two species that you now observe, X and Y, have a common ancestor. … Suppose you observe that there is a fossil whose trait values are intermediate between those exhibited by X and Y. How does the discovery of this fossil intermediate affect the question of whether X and Y have a common ancestor?

His analysis is summed up in two tables, CA is where Common Ancestry and SA is Separate Ancestry.

Figure 5. Either X and Y have a common ancestor (CA) or they do not (SA). Cells represent probabilities of the form Pr(± intermediate│±CA). Gradualism is assumed.
There existed an intermediate. 1 q
There did not. 0 1-q

Concerning this figure, he notes:

If there is an intermediate form, this favors CA over SA, and the strength of this favoring is represented by the ratio 1/q. This ratio has a value greater than unity if q<1. On the other hand, if there is no intermediate, this infinitely favors SA over CA, since (1-q)/0 = ∞ (again assuming that q<1).6 The non-existence of an intermediate form would have a far more profound evidential impact than the existence of an intermediate.

Then he makes an assumption:

(SO)    a = Pr(we have observed an intermediate │CA & there exists an intermediate) =

Pr(we have observed an intermediate │SA & there exists an intermediate).

This leads to the next figure:

Figure 6. Either X and Y have a common ancestor (CA) or they do not (SA). Cells represent probabilities of the form Pr(± we have observed an intermediate│±CA). Gradualism is assumed.
We have observed an intermediate. a qa
We have not. 1-a 1-qa

He concludes:

As long as there is some chance that we’ll observe an intermediate if one exists, and there is some chance that intermediates will not exist if the separate ancestry hypothesis is true, the failure to observe a fossil intermediate favors SA over CA. In this broad circumstance, absence of evidence (for a common ancestor) is evidence that there was no such thing. The motto – that absence of evidence isn’t evidence of absence — is wrong.

And also:

Suppose you look for intermediates and fail to find them. This outcome isn’t equally probable under the two hypotheses if a>0 and q< 1. Entries in each column must sum to unity in Figure 6 just as they must in Figure 5. When the two parameters fall in this rather inclusive value range, failing to observe an intermediate is evidence against the CA hypothesis, contrary to the motto. What is true, without exaggeration, is that for many values of the parameters, not observing an intermediate provides negligible evidence favoring SA, compared with the much stronger evidence that observing an intermediate provides in favor of CA.

The point to be argued for here shows that the last sentence should change in some cases, including the case of intermediate fossils.

First of all, the main question about fossils is not the existence of intermediates but the existence of long sequences of fossils.  The view of “evolutionary stasis” (species fixity) was dying out in the nineteenth century and is extinct today.  There is no controversy about the idea that fossils can be put into short sequences that span varieties, species, or genera.  The controversy is about long sequences of fossils that span families, orders, classes, phyla, kingdoms, and domains, reaching to common (universal) ancestry.  Evolutionists are committed to the existence of long sequences and creationists are committed to their non-existence.

However, this does not affect the form of the analysis.  We could revise the scenario this way:

Suppose you are wondering whether two short fossil sequences that you now observe, X and Y, have a connecting sequence of fossils. To bring evidence to bear on this question, you might look at the similarities and differences (both phenotypic and genetic) that characterize the two short fossil sequences. But the traits of a third object might be relevant as well. Suppose you observe that there is a fossil (or short fossil sequence) whose trait values are intermediate between those exhibited by X and Y. How does the discovery of this intermediate fossil (or short fossil sequence) affect the question of whether X and Y have a connecting sequence of fossils?

How does this affect the motto?  Consider the example Sober relates in a footnote:

The administration of George W. Bush justified its 2003 invasion of Iraq by saying that there was evidence that Iraq possessed “weapons of mass destruction.” After the invasion, when none turned up, Donald Rumsfeld, who then was Bush’s Secretary of Defense, addressed the doubters by invoking the motto; see

The Washington Post reported on January 12, 2005 (

The hunt for biological, chemical and nuclear weapons in Iraq has come to an end nearly two years after President Bush ordered U.S. troops to disarm Saddam Hussein. The top CIA weapons hunter is home, and analysts are back at Langley.

The Post article quoted an unnamed intelligence official who said:

“We’ve talked to so many people that someone would have said something. We received nothing that contradicts the picture we’ve put forward. It’s possible there is a supply someplace, but what is much more likely is that [as time goes by] we will find a greater substantiation of the picture that we’ve already put forward.”

This is how a search ends in failure: (1) there is an absence of evidence of what was sought, and (2) there is a reasonable expectation that what would be found in the future would merely substantiate what has already been discovered.

Knowledge management consists of various efforts to gather and mine information of value.  A database of knowledge on a certain subject, called a knowledge base, is complete if closed-world reasoning applies to it, which means whatever it does not know to be true must be false.  In other words, all relevant knowledge about that subject is in the knowledge base.  This might be true for example of a company’s employee information database; if someone’s name is not in the database, they are not an employee of the company.

Let us call a knowledge base “effectively complete” precisely when all knowledge about the subject is either in the knowledge base or similar to what is in the knowledge base.  The quotation from the intelligence official above presents an instance of an effectively complete knowledge base because the expectation is that as time goes by “we will find a greater substantiation of the picture that we’ve already put forward.”

Because of the common assumption of the uniformity of nature, it is common in science to consider a knowledge base what we are calling effectively complete.  Essentially this means that the knowledge at hand is as all the knowledge required.  So, for example, one can examine a database about the properties of copper and make conclusions about all the copper in the universe.

Something similar may be said about the fossil record.  After more than two hundred years of fossil hunting, large databases of fossils are available for research [footnote].  Many interesting fossils have been discovered but there is still a complete absence of long fossil sequences.  At this point, there is no substantial reason to expect that long fossil sequences will ever be found.  In this sense at least, the knowledge base called the fossil record is effectively complete.

If a database is effectively complete, then the closed-world premise may be invoked: what is not currently known to be true is false, or what is not currently known to exist does not exist.  In this sense, the absence of evidence is evidence of absence.  What’s not in the database of evidence, must not exist; what’s not known in the database of facts, must be false.


Elliott Sober, Absence of evidence and evidence of absence: Evidential transitivity in connection with fossils, fishing, fine-tuning, and firing squads. Philosophical Studies 143 (1):63 – 90 (2009)

November 2013

The Bible vs. secular historical sciences

The Bible is diachronic but secular historical sciences are synchronic.  Let me explain.

The term “diachronic” arose in the study of the development of languages over a long time, which was the focus of linguistics in the 19th century.  But to make linguistics more scientific in the 20th century this changed to study languages as systems during particular time periods. The former approach was called diachronic, the latter synchronic.  These terms have come into use in history as the study of a people or place over a long stretch of time (diachronic) vs. the study of a time period over a large area (synchronic).

The Bible follows the Hebrew people over a long stretch of time, from their beginning on, which is diachronic.  The historical sciences are strongly synchronic: they study a wide area over a distinct period (or series of distinct periods) of time.

Synchronic linguistics is unified by the premise that languages have a common origin, a genetic relationship.  So the question becomes how to explain the differences between languages.  When this synchronic premise was applied to biological species, the question became how to explain the differences between species.

The Bible presents the opposite:  that biological kinds/baramin are distinct, though they have the same Creator.  So the question for a biblical biology is how to explain the similarities between distinct kinds/baramin.  A particular study might study a baramin over a long time.  Several of such studies might lead to the discovery of parallel changes in baramin that are explained by environmental changes and similar ways of adapting.  These are diachronic studies.

So the Bible and secular historical sciences diverge, not only because they have different premises but because they have different approaches to historical science.  The Bible is diachronic and secular science is synchronic.

November 2013

Appearance and reality

There’s a common idea that science shows appearances are often wrong.  It is said science shows that earth is not flat, the sun doesn’t go around the earth, and that life is not designed, all despite appearances to the contrary.  I think this is a mistaken view of what science has done.

Surveyors work with a flat earth model that works just fine for most purposes, and the sun’s motion relative to the earth can be described geocentrically.  Newton’s laws work fine for many purposes despite their being superseded by general relativity.

What happens is that theories are extrapolated (or interpolated) too far and they break down. A theory is superseded by one with a larger scope but the old theory may be valid within a restricted domain.  What Niels Bohr called the correspondence principle is the idea that a new theory should reproduce the results of older well-established theories in those domains where the old theories work.

So the problem is over-extrapolation (or over-interpolation).  Too often people make overly broad claims for a theory.  But until the limits of a theory are found, it may not be clear what the scope of the theory really is.

What is the scope of Darwinism?  As far as I can tell its scope is “life” as a single category, without differentiation of kinds organically or temporally.  This is a very narrow perspective, one that does not support the grandiose claims made for it.  And it is not helpful in understanding different kinds of life, particularly human life, or the age of the earth.

The Bible uses the language of appearances.  This is perfectly acceptable.  The Bible also gives God’s perspective, which is not a theory but something that theories can aspire to.  This is essentially what theologies do.

Nature is not out to trick us with deceptive appearances.  Old theories that worked still work.  All theories are limited.

November 2013


What is design?

“Design” is one of those terms many people use but few define.  Two aspects of design are: (1) to plan and (2) to make.  An evolutionist might say that “nature made man” but would never say “nature planned man.”  The theistic evolutionist might say “God planned man” but avoids saying “God made man” except in some secondary, remote way.  Design involves both planning and making.

There seems to be a third aspect: (3) to partially surprise.  Someone who does not plan their days either does the same thing over and over or else has a haphazard kind of life.  Language has an element of surprise in what is communicated and redundancy in the medium of communication.  An artist who makes something totally unique confuses people; an artist who is too conventional bores people — good art is a design between these extremes.

These two extremes have low and high entropy.  So evidence of design in this sense would be an entropy in the middle.  A mid-entropy is evidence of design.

October 2013

Different sciences

It’s easy to forget that “nature” means the essence or form of something.  Over the centuries this morphed into nature as a “natural world” as if only some things have a nature — which is wrong.  Every thing or being has a nature, including God.  A natural science is the study of things/beings with a common nature or essence.

There is a hierarchy of natures/essences.  People have a human nature which includes the properties of an animal nature.  Animals have an animal nature which includes the properties that living beings in general have.  This should mean that the sciences of biology, zoology, and anthropology are related as a hierarchy.

Evolutionism undermines this hierarchy.  Evolutionism makes zoology a mere subset of biology.  But zoology should be more: it should be concerned with how the natural kind called “animal” is different in kind, not merely in degree, from other living beings.  Evolutionism denies that some beings are different in kind from other beings.  In fact extreme evolutionism makes everything from molecule to man to differ only in degree, not in kind.  Hence evolutionists talk about “science” rather than “sciences” because the differences are considered minor.

Different sciences should be distinguished according to the different kinds of things/beings that are studied.  This applies to geology, for example.  If geology is merely physics applied to earth, it is different in degree but not in kind from physics.  Geology should be understood as studying a unique kind of thing, the earth.  We could we even distinguish antediluvian geology as a separate science since the earth then was different in kind, not just in degree.

October 2013


Emil Brunner in Christianity and Civilization (1948) wrote: “the popular belief that the idea of evolution and progress was first worked out within natural science, and thence affected the conception of history, is false. The reverse is true: the idea has been transplanted from an evolutionary conception of history into natural science. Lamarck and Darwin are not the pioneers but the heirs of this modern idea. The real pioneers are men like Rousseau, Lessing, Herder, Hegel. The idea of progress and evolution is a child of the optimistic philosophy of the Enlightenment.”

Darwin cannot be toppled without toppling Rousseau/the Romantics, Hegel/Marx/”the Left”, Adam_Smith/Herbert_Spencer/”the Right”, etc.  The idea that progress is natural, inevitable, unlimited, etc. is thoroughly embedded in contemporary thought. No one wants to be on “the wrong side of history.”  So shooting at Darwin does not get to the foundations of the problem.

The idea of progress is seductive and has enough association with Christianity to make Christians fall for it.  After all, there is progressive revelation, Christianity has led to moral progress, knowledge has increased, etc. But true progress requires spiritual and moral development or intervention by God.  Progress is not naturalistic.

One thing creationists can do to make a difference is supporting alternatives to naturalistic progress.  As an example, the sustainability movement is aware how the myth of progress impedes the ability of Western civilization to continue much longer.  While political interests try to co-opt movements such as this, there is the potential for creationists to provide a biblical and scientific foundation for sustainability.  To do this would require an enlarged vision about the problem and the solution.

October 2013

Scientific history

The discipline of history investigates what actually happened in the past as far as that is known from records or other evidence.  Scientific history is what could have happened in the past without being inconsistent with the data or laws of science.  Note the difference: scientific history is about possibilities; real history is about actualities.

Scientific history is open to abuse by historical ideologies which are mere possibilities but are promoted fervently by their adherents.  Such historical ideologies arose in the 19th century with Marxism and evolutionism.  Ideologues use the language of science to claim the high ground which will only be given up if others show the impossibility of their ideologies.

It is analogous to a judicial court in which the defendant is “innocent until proven guilty.”  The prosecution must show that every reasonable construal of the evidence is against the defendant; otherwise the verdict must be “not guilty.”  On their telling the only thing evolutionists need to do to defend themselves is show that evidence presented against them can be construed neutrally or in their favor.  They do not have to present any evidence that supports their case.  Judicial courts give an advantage to the defendant but science should not have an inherent bias.

The problem is one of flawed logic.  Scientific history is flawed unless it is grounded in what actually happened in the past, not merely what could have happened.  Creationists use the Bible as the source of history to ground the practice of scientific history.  Conventional scientists have nothing on which to base their historical science so they adopt ideologies instead: naturalism and scientism.  The advantage of evolution to their mind is that it is possible and consistent with “science” which they define ideologically.

It would be a mistake to accept evolutionists’ terms of the debate and try to show that evolutionism is impossible.  It should be rejected on the basis of logic and the avoidance of ideology.  Evolutionary science is captive to ideology.

The Bible is a trustworthy chronicle of history, not merely a spiritual revelation.  This is important to critics who accuse creationists of being sectarian.  The Bible is in the first place a book, not religious object.  Much of it is a chronicle of a particular people, and the earliest part chronicles universal history.  Even the first chapter of Genesis comes to us as Adam’s chronicle, and although he did not observe it all, he was in the best position to know what happened.

Evolution is not real history; it is imaginary history.  We have real history as our starting point.  That is our best argument.

October 2013

Time and biological diversity

Based on the standard biological taxonomy here is a logarithmic model of the relationship between the time it takes life to reach the diversity that is observed today and possible positions on the lowest rank of the initial taxa of life, which I shall call prototypes.

Prototypes of the species rank would take tens of years to arrive at presently observed diversity.  This represents the position of biologists a few centuries ago in which species were considered fixed and the age of the earth was immaterial.

Prototypes of the genus rank would take hundreds of years to arrive at presently observed diversity.

Prototypes of the family rank would take thousands of years to arrive at presently observed diversity. This is approximately the position of YECs today.

Prototypes of the order rank would take tens of thousands of years to arrive at presently observed diversity.

Prototypes of the class rank would take hundreds of thousands of years to arrive at presently observed diversity.

Prototypes of the phylum rank would take millions of years to arrive at presently observed diversity.

Prototypes of the kingdom rank would take tens of millions of to arrive at presently observed diversity.

Prototypes of the domain rank would take hundreds of millions of years to arrive at presently observed diversity.

A prototype of the life rank would take billions of years to arrive at presently observed diversity.  This is the position of evolutionists, who accept only a single prototype (or LUCA) for all organic life forms.

ID advocates seem to place prototypes somewhere below the kingdom rank.

This model of time and diversity provides a simple way to compare different positions in a common framework.

October 2013

Undetermination and dependence

The underdetermination of scientific theory is well-known in the philosophy of science.  It comes down to the fact that if theory A implies fact B and fact B is observed that does not logically confirm theory A.  Without multiple controlled experiments to isolate causation (which can only be done some cases), there is no logical confirmation of scientific theories: other theories could also work (or seem to work).

Add to this the background assumptions that are required for any scientific explanation and modern science loses its claim to pure objectivity.  This is part of the post-modern impasse that contemporary culture is in.

In practice this has led to other criteria being used for theory selection: parsimony and naturalism in particular.  For creationists, consistency with the Bible is the other criteria.

There is no way within science to overcome underdetermination.  Science must ally itself with a philosophy or a religion.  That does not necessarily make science part of that philosophy or religion.  It means science is dependent on a philosophy or a religion, contrary to the claims for independence that are made for science.  Creationists and materialists accept that.  Others have yet to realize it.

September 2013


In the late 18th and early 19th century several proposals were made such as Lamarck’s that species were transformed into new species.  This culminated in Darwin’s theory that all species were transformed from other species (hence there is common descent).  In the 19th century creationists continued to hold to a non-transformist view that all species were specially created by God and were fixed and unchangeable.  A new creationist position arose in the 20th century that might be called “semi-tranformism” because it allows for speciation and extinction but affirms the creation of a limited number of fixed kinds of organisms.

This simple narrative is not being communicated very well.  Creationists today are still considered non-transformists because they have not clearly articulated the difference between the new creationism and the old creationism.

July 2013