Important Clarification: Science of "TOE" vs. Metaphysics of the Eucharist?

Faith & Science Conversation
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It would be impossible for me to be comprehensive here. Let’s start with:

  1. The most important is genomes and all the precise patterns we see within them
  2. De novo mutation rates and distributions in genomes
  3. The variation in populations of genomes
  4. The fossil record and geology
  5. A very very large list of mechanisms for modifying genomes (crossing over, point-mutation, transposons and transposases, horizontal gene transfer, introngenesis, DNA repair and repair defects, noisy replication, mutagens, etc. etc. etc.).
  6. The genetics and neofunctionalization of cancer (quite underappreciated for unfortunate reasons).
  7. The mammalian immune system.
  8. Evolution of novel function in proteins by mutation and selection in the laboratory (e.g. phage display).
  9. Comparative physiology.

All these things are directly observable. Most (but not all, e.g. the fossil record) can be replicated and studied in laboratory settings. To be clear, for evolution to work, biological systems today need to behave in specific and precise ways. We have gobs of evidence that they do in fact work in just the way we expect.

To be clear, I’m speaking as a computational biologist with nearly two decades experience in science. There are certainly bad ways to apply and think about evolution and what implies about how biological systems work today. However, there is an immense body of work showing that, when applied the right way, evolution is the only thing that makes sense of the current day function of biological systems.

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One might add the changes in surface proteins on flu viruses, and the epidemological studies leading to development of which strains to include in an effective flu vaccine, as well as changes affecting the infectivity and allowing crossover of infections between species.

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Don’t we use the fossil record and geology to make strong inferences about evolution?

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About alleles. Without genetic variation there is no evolution possible. And by definition, genetic variation depends on having different alleles. If there is only one allele, then there will be no evolution at that genetic locus. Alleles result from mutations.

In your example, (if I understand it correctly,) a mutation in a regulatory gene produces a new allele of that gene, which could affect the expression of other genes off (or on) in contrast to the original (or wild type allele, which does not show a mutation. In other words, when there is a mutation, a new allele is produced, but the original allele doesnt disappear in the population. Remember that evolution is defined as a change in allele frequency in a population

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@Sy_Garte

Thank you for your help in this matter. Your description of my scenario is not quite what I had in mind. Let me re-state:

  1. Instead of discussing a change in an operational gene,

  2. I propose a change in a non-operational part of the chromosome.

  3. And rather than having this activated area become one of several possible expressions,

  4. the newly activated part of the chromosome SUPPRESSES the expression of a set of alleles vs.
    the form of the chromosome where it doesn’t have any affect on any other part of the chromosome.

And so I’m wondering if INSISTING on the term “allele” is overly restrictive instead of just using the term “gene”.

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It goes both ways. We use the fossil record to make inferences about evolution. We also do the same to make inferences about what we might find in the fossil record. In fact the whole effort to find hominid fossils is, essentially, a prospective experimental test of evolution. The existence of the fossils was inferred even before they were found. More amazingly, we can now sequence the more recent remains (probably not properly called “fossils”), and we can make inferences about what we expect to see there too.

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George

Im still not sure what you mean, but my point is that whether we are talking about two forms of a section of DNA that are active structural genes with two different functions, or we are talking about in active part of the chromosome than undergoes a change (a mutation of some kind) to become active (which means it is now expressed) it is still a different allele. So you can have an expressed allele and a non expressed allele, regardless of what the functions are.

I dont think we need to insist on the word allele, and I dont have any objection to the use of the word gene instead of allele, since everyone knows what that means. But the problem with using that in the definition of evolution is that its meaningless to say there is a difference in gene frequency in populations over time. You could say there is a difference in gene copy number, (due to amplification) but that is a different thing.

If I am still not following you, it could be helpful if you could cite an actual example of what you mean.

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No. There are many different adjectives that we use to further describe alleles, such as “null” and “hylomorphic,” you know.

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Hello Swamidass,

There seems to be a misunderstanding.

Of course there is very strong direct experimental SUPPORT, but that still involves inferences. The only truly empirical FACT of evolution is changes in allele frequency in populations over time. Common descent requires inference from a massive amount of consilient data.

I am using FACT in the sense of something we can observe directly without any interpretation. Does that make my point clear?

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That is an interesting definition of FACT. Never quite heard that before?. Doesn’t everything require interpretation? Including allele changes in populations? I cannot think of even one piece of scientific information that does not require interpretation. Isn’t science entirely about inferences?

Hmm, maybe you could explain more? In what matter do allele frequency changes different then, say, human and chimpanzee genomes.

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Yes. Like I said, an inference.

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Very good. I’m not sure if this is the best example, but it is a good start at least:

The discussion focuses on the MMP20 gene, which seems to have had an ON and OFF effect on TEETH in whales. Is the MMP20 gene that has been broken in half in the toothless whales an ALLELE? Or is it a BROKEN gene?

"Such an uneven distribution of mutations can mean a couple of things. One explanation could be that all the baleen whales lost their enamel independently from each other, due to different mutations in each lineage. Another possibility is that an hitherto unknown mutation that can be found in all baleen whales is responsible for the loss of enamel. Enamel-covered teeth would have been only lost once by the common ancestor of baleen whales. The fossil evidence supports this scenario: the distribution of toothed baleen whales is not nearly as patchy as the distribution of tooth gene mutations.

Scientists from the University of California suspected a gene called MMP20 might contain the mutation that had been overlooked so far. This gene seemed to be a good candidate, because the MMP20 protein is involved in processing tooth proteins such as enamelin and ameloblastin. A mutation in MMP20 could affect multiple enamel proteins downstream. Moreover, humans and mice that have a defective MMP20 gene develop bad and brittle enamel (amelogenesis imperfecta).

[Text for image of whale tree in article.]
The family tree of whales, including extinct relatives. Baleen whales (top) and some pygmy sperm whales (bottom) have mutations in their tooth genes. Every orange symbol denotes a mutation; different letters represent different genes.

The team initially screened four different species of baleen whales for mutations in MMP20. They hit the jackpot right away. In all four whales, a stretch of DNA (a SINE) had inserted itself right inside MMP20, splitting the gene in two. When they extended their search to other species, they found that whale after whale had the same DNA insertion inside MMP20. This ubiquity gives a clear message: it is this insertion that rung the death knell for the whale’s teeth.

But the researchers discovered that some pygmy sperm whales (Kogia), that belong to the branch of toothed whales, also carry mutations in their MMP20 genes. These pygmy sperm whales are also known to have enamel-less teeth. But whereas baleen whales first lost MMP20 before the other tooth genes mutated, these sperm whales seem to have lost the tooth protein enamelin first, with MMP20 now having mutated secondarily in some individuals.

So here are two lineages of whales, caught in the act of evolving on different, but similar paths. Evolution is sometimes criticized for not being amenable to experimental scrutiny in the lab, but the pygmy sperm whales prove these critics wrong. As the authors note, “mammalian diversity presents a unique laboratory, complete with replicated experiments.” Life herself presents us with a multitude of ingenious experiments. It is up to us to interpret them. Personally, I couldn’t imagine a more exciting science."

http://www.lucasbrouwers.nl/blog/2011/03/how-baleen-whales-lost-a-gene-and-their-teeth/

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OK, George, that is indeed a good example.

What happened is that the SINE element inserted itself into the MMP20 gene in an ancestral whale at some point in time, creating a new allele (just as a mutation would have and in fact did do in the sperm whales). This was a null allele, meaning the gene was rendered useless, not able to function. (There are also null alleles where the entire gene is actually gone). Whales with inactive MMP20 did not make enamelin. We cant understand if that allele was selected for, or the selection step only came later after other mutations occurred, but at some point, there was a selective advantage for whales without teeth. So the frequency of the null MMP20 gene began to increase in the whale population, until the functional MMP20 was completely lost. We say that the null MMP20 allele has become fixed.

So that;s the story for the MMP20 gene and its alleles. If you are wondering about the SINE (short interspersed nuclear element) that caused the mutation, that is a form of retrotransposon or “jumping gene”, which is originally derived from an RNA virus that inserted into the mammalian genome and which are known to move around and cause changes to gene function. SINES are not really genes, in the sense that most of them no longer code for anything or they arent expressed. They are DNA fragments that are found throughout all genomes. They do not have alleles in the sense of active genes, just as pseudogenes, (long dead genes) may have multiple forms (there is no selection to weed them out) but we dont think of those as alleles either.

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@Sy_Garte

It’s complexity like this that makes me prefer to say that evolution is “any change in the gene pool”. The average YEC is not going to follow the nuances about non-functioning alleles.

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You could be right George. Biology, despite the opinions of lots of people, (including certain other scientists) is actually pretty hard stuff. And like in all sciences, precision of language is useful, perhaps even more so in biology, since we dont use a lot of math (which is precise by itself). But, since many YECs know very little about biology, I think your point is well taken.

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@Sy_Garte, you are being very generous. It is appreciated.

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I too thought you made an excellent point. It may initially seem like a minor point to make but I think it is very important to keep ourselves realistic about what most people manage to retain from a high school biology class of long ago!

I browse and skim on these threads more than I post but I’ve found this a stimulating and educational place.

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Me:
I am using FACT in the sense of something we can observe directly without any interpretation. Does that make my point clear?

[quote=“Swamidass, post:89, topic:5252”]

That is an interesting definition of FACT. Never quite heard that before?. Doesn’t everything require interpretation? Including allele changes in populations?[/quote]
How did you get from my writing “something we can observe directly without any interpretation” to attributing to me the claim that interpretation is not required in science?

[quote]
I cannot think of even one piece of scientific information that does not require interpretation.[/quote]
Repetition doesn’t make your characterization of my position correct.

What do we infer from? Data. Facts.

[quote]Hmm, maybe you could explain more? In what matter do allele frequency changes different then, say, human and chimpanzee genomes.
[/quote]Sorry, but I have no idea what the construction “In what matter do Xs different then” means.

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I’m not sure if this is clear in writing, but I am not being sarcastic. Just trying to understand you.You said…

So in what sense is the human and chimpanzee genomes not a FACT, but just SUPPORT? Both allele frequency changes and genomes are observable data. Both require interpretation. Both support evolution. What is the difference between these two classes of data?

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