Fact vs inference in defining evolution

Faith & Science Conversation
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Continuing the discussion from Important Clarification: Science of "TOE" vs. Metaphysics of the Eucharist?:

Hello Swamidass,

Apologies for the delay in my reply.

Genomes are not facts. Genomes are not observable data.

Genome sequences are facts. Allele frequencies are facts.

We infer common descent from the mathematical relationships between genome sequences, which make further mathematical predictions about sequence we do not yet have. Thus, common descent is not the fact of evolution.

Allele frequencies change over time, no interpretation required–unless you want to make the claim that the statement “X is greater than or less than Y” is an interpretation. This is the only way to define evolution as a fact IMO.

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I admit struggling to understand the difference.

Genomes consist of molecular sequences. That’s a fact. They are certainly observable. I don’t understand how a genome sequence can be a fact but a genome is not.

And did Francis Collin err in using the term Human Genome Project instead of Human Genome Sequence Project?

For years I’ve listened to scientists say that evolution is BOTH a fact and a theory. Evolutionary processes are observable and factual. And the Theory of Evolution is a theory so well attested as to meet the general English definition of a fact, even though that’s another instance where a scientific definition and a general lexical definition are different. (Equivocation fallacies concerning the word theory are extremely common.)

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@Socratic.Fanatic

I’m just spit-balling here … I’m not a genetic scientist. But the astute @benkirk sometimes struggles to put together words that would help a layman.

Let’s see what he thinks of my attempt to explain:

  1. A Genome sequence is a FACT. To use the first four letters of the alphabet:

A+C+C+D+B+A+A+C+D+etc+etc

This sequence is measurable and definable, down to the molecular level.

But where does the genome end? Where does it begin? How do we know that a genome is really 50 units long… instead of 2 genomes of 20, with 10 non-functioning units in between?

I’m not saying these are IMPOSSIBLE to discover. But they require interpretation. They require analysis. And some very clever scientist might eventually discover that the middle 10 really does do something.

Hey, @benkirk, did I get close?

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Very. Thanks for your assistance.

Put another way, there are many facts about a genome that are not sequences. Size, number of chromosomes, etc.

I’m just trying to be completely conservative and honest about what is fact and what is inference.

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[quote=“Socratic.Fanatic, post:2, topic:5354”]
Genomes consist of molecular sequences. That’s a fact.[/quote]
They can be sequenced, and those sequences are facts, not the genomes. I’m not sure what “molecular” adds to “sequences.”

For starters, look at the ambiguity in your use of “they.” Sequences are the observations. The genomes aren’t directly observable, only other facts about them that are NOT sequences.

And I’m trying to clarify that.

That’s maddeningly vague. Please be specific about “processes” and you may begin to see what I mean!

[quote]And the Theory of Evolution is a theory so well attested as to meet the general English definition of a fact, even though that’s another instance where a scientific definition and a general lexical definition are different. (Equivocation fallacies concerning the word theory are extremely common.)
[/quote]And the theory starts with common descent, an inference that in turn makes specific mathematical observations about the relationships between sequences. The only truly observable fact is allele frequency changes in populations over time.

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It is interesting that the science of genetics is now used to support evolution. When Mendel’s work on genetics was re-discovered around 1990, it was thought to be the death knell of Darwin’s theory. Until then, offspring were assumed to be a blending of their parents’ characteristics. Mendel’s experiments showed that peas came in yellow and green, or square and round. They did not come in in-between variations. Mendel had actually chosen peas for his research because this either–or characteristic of peas was known, and that simplified his work.

Later work in the ensuing decades showed the wide range of gene expression, from either–or to blends, to the spontaneous appearance of mutations.

The facts that Darwin used to form his theory included the fossil record, which showed that life had changed over time, and the wide variety of changes that artificial selection by farmers had made upon domestic animals and farm crops. He concluded that the struggle for survival in nature had had the same effect on wild plants and animals that selective breeding had had on domestic plants and animals.

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I think you’re about a century off there, Larry.

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I wonder if the age of the Earth would be less controversial (with agreement that it was 5 billion years old) … if Darwin had never lived to inject natural selection into the controversy…

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I meant 1900. Clumsy fingers and declining eyesight are a bad combination. Thanks for the catch.

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Or if there were no fossils at all and we first approached this from the sequence evidence…

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Does it seem to you guys that most people even in evangelical circles seem to have a dualistic belief? They profess to believe in a young earth, literal flood etc., yet marvel at the old universe and geological formations with no problems accepting the deep age of things. I wonder how much is simply agreeing to remain in the tribe, even though intellectually they know it is not true.
I guess personally I have that view, as I find it impossible to reconcile a God of truth and holiness with the fabricated gyrations of young earthers, and can’t see how anyone else could either, if they are truthful with themselves.

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I don’t find a distinction between inferences and facts to be at all helpful. As far as I can tell, virtually all facts about the physical world are the result of inference. Sure, we infer common descent from sequence data, but the sequence data is itself the result of a very long inferential chain.

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I entirely understand why the redundancy seems strange, so I’ll explain.

I deal with a lot of evolution-deniers, especially Young Earth Creationists. And I’ve found it necessary, to where it has become an unconscious habit for me, to regularly us a lot of redundancy and synonyms to help them get their bearings.

Obviously, the sequencing of genomes involves data compiled from the molecular level (in contrast to the morphological/anatomical and other “macro” phenomena providing the data for traditional phylogenetic trees) and that is something an elementary school science student can grasp. Yet, I’ve learned to take absolutely nothing for granted with people who get their science education from creationist websites.

For example, I recently had a very confusing conversation with a YEC evolution-denier until I realized that she thought “gene” was a nickname for “genome.” Worst yet, she thought sequencing was when an “evolutionist scientists” (her term) claimed that some ancient mammal evolved into an ape which evolved into a “cave man”. She thought that “changing from one species into another” in a series of magical leaps was what the “gene sequencing” was about!

The more I think about it, I probably often fail to consider that I’m posting on Biologos and not Amazon book review comments or Facebook group forums where I resort to this kind of scientific “baby talk” of redundancies and compound synonyms.

That draws to mind a discussion I used to have annually with my Western Civilization students when we dealt with the history of the Scientific Method and the amazingly novel emphasis on empiricism. Drawing lines between observation and inference can get very interesting. Many students start out assuming that “seeing is believing” and that only our eyes constitute “direct observation” of the evidence. Most don’t stop to consider that our eyes give us “indirect” information (of a sort) about surfaces of objects due to (for example) the frequencies of sunlight or artificial light being reflected rather than absorbed by that surface.

I can see why so many people are vulnerable to the “observational science” versus “historical science” nonsense spun by Ken Ham at AIG.

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True, but none of the inferences we use to produce sequence data are challenged by evolution denialists or anyone else, while the inference of common descent is challenged.

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Oh sure, but that doesn’t mean I have to agree with them that sequences are facts, while common descent is in the less certain category of inference.

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A genome consists of all the chromosomes in an organism. Each chromosome is one long DNA molecule. In sexually reproducing organisms – like humans – chromosomes come in pairs.

DNA consists of a sequence of nucleotides. Each nucleotide is a deoxyribose sugar, phosphate, and a base. There are 4 bases used in nucleotides: adenine (A), guanine (G), cytosine (C) and thymine (T).

In the “Human Genome Project” the team headed by Dr. Collins obtained the sequence of nucleotides in each chromosome of the human genome. A sequence of, say, ATTGGCATTCGG would be part of a DNA molecule – a chromosome. What is done is sequence the nucleotides from one end of the chromosome to the other.

What we can do is take a cell, lyse (disrupt the cell), obtain the chromosomes, and stain them so that they can be seen under a microscope. This is called “karyotyping” and lets us know about the whole genome. http://www.nature.com/scitable/topicpage/karyotyping-for-chromosomal-abnormalities-298.

So, it is a “fact” how many chromosomes are in a genome. We can observe them under a very powerful light microscope.

When you ask “where does the genome end”, it appears you are asking “where does a gene end?” Much study has gone into what DNA sequences are “start” sequences for a gene and what are the “stop” sequences. There are specific DNA sequences for both. So, when DNA is sequenced we know the entire gene – find the “start” sequence and then find the “stop” sequence.

The situation is a bit more complicated. The entire gene goes from start sequence to stop sequence. When DNA is transcribed to messenger RNA, the entire length of DNA is transcribed. However, within that entire length, there are areas called “introns” that will not be present in the final messenger RNA: Transcription/translation - Exons and introns :: CSHL DNA Learning Center

These introns are excised, leaving only the “exons” and the ends of the exons are spliced together to form the final version of messenger RNA that is translated to proteins. Transcription/translation - Exons and introns :: CSHL DNA Learning Center Intron - Wikipedia

Within the gene there are DNA sequences that tell the enzymes doing the splicing were the intron starts and ends. We find them by comparing the sequences of the DNA to the sequence of the messenger RNA. http://www.scientistsolutions.com/forum/dna-pcr-real-time-pcr-sequencing/how-look-exonintron-sequence Again, that would be observation.

And yes, scientists have discovered that some introns are used for other tasks: some introns contain non-coding RNAs. These are RNAs that are not translated to proteins but instead have functions (generally regulatory functions) inside the cell.

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“For years I’ve listened to scientists say that evolution is BOTH a fact and a theory.”

This came about as a response to creationist claims that evolution was “only a theory”, with the definition of “theory” being a wild guess devoid of fact. In trying to deny that claim (which is false), Stephen Jay Gould first proposed the “fact vs theory” idea:

“Facts are the world’s data. Theories are structures of ideas that explain and interpret facts. Facts don’t go away when scientists debate rival theories to explain them. Einstein’s theory of gravitation replaced Newton’s in this century, but apples didn’t suspend themselves in midair, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin’s proposed mechanism or by some other yet to be discovered.” Gould defines a scientific fact as “confirmed to such a degree that it would be perverse to withhold provisional assent.”

“Evolutionists have been clear about this distinction of fact and theory from the very beginning, if only because we have always acknowledged how far we are from completely understanding the mechanisms (theory) by which evolution (fact) occurred. Darwin continually emphasized the difference between his two great and separate accomplishments: establishing the fact of evolution, and proposing a theory – natural selection – to explain the mechanism of evolution.” SJ Gould, Science and Creationism, ed. by Ashley Montagu, 1984.

Look at Gould’s definition of “scientific fact”: “confirmed to such a degree that it would be perverse to withhold provisional assent.”

This actually applies to some theories, as well. Take the statement “the earth is round.” Technically, that is a theory. Or take the statement “the planets of the solar system orbit the sun.” Again, a theory! This theory is known as “heliocentrism” Or, since we are talking about DNA, the statement “DNA exists as a double helix with the bases toward the center.” A theory.

Yet each of those theories are supported by so many observations and tests that everyone accepts them as factual. NASA plots the courses of planetary probes based upon the truth and factuality that the planets orbit the sun. The recent arrival of the spacecraft at Jupiter is another test, and confirmation, of the theory.

So, in that sense, evolution is a “fact”. A theory that is so well confirmed that it is “perverse to withhold provisional assent.”

Not all theories have reached that level of confirmation. Modified Newtonian Gravity (MOND) has not, for instance. Some theories have been tested and shown to be wrong. Geocentrism (sun and planets orbit the earth) certainly has. So has creationism.

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