Please…Discard the Dogma!

Evolutionists have dogmatically insisted that pseudogenes are genes that were broken by mutation and are now useless. Some are now pleading with their colleagues to actually look at the data.

It always troubles me when I read other scientists who ignore the data in order to cling to their cherished dogmas. As a scientist, I know that this holds back the progress of science. As a result, I was heartened to read three scientist calling on their colleagues to abandon evolutionary dogma when it comes to pseudogenes. If others heed their call, we will most certainly learn more about DNA.

What am I talking about? Let’s start with what a pseudogene is. It is a region of DNA that looks like a known gene, but is different enough that it can’t do what the known gene does. As a result, it has become evolutionary dogma that pseudogenes are “broken” genes – genes that became non-functional due to duplication and mutation. Here, for example, is how the Encyclopedia of Genetics definitively describes a pseudogene:

A pseudogene is a nonfunctional genomic region that originated by duplication of, and is still homologous to, an ancestral gene.

In other words, a pseudogene is the result of a gene being copied and then broken. Creationists have long argued that pseudogenes are functional; they just don’t function the way evolutionists expect them to. The three authors of the paper I mentioned above have arrived at that same conclusion (at least for many pseudogenes), and they are asking their colleagues to pay attention to the data and do the same.

To emphasize the point that this evolution-inspired dogma is wrong, they list many pseudogenes that have been demonstrated to have an important function. They then make this important statement:

The examples of pseudogene function elaborated on here should not imply that pseudogene functionality is likely to be confined to isolated instances.

In other words, you can’t say that the known functional pseudogenes are exceptions to the rule. There are enough functional pseudogenes to call into question the assumption that they are mostly non-functional.

At the same time, however, these authors are cautious:

The purpose of this article is not to discard the pseudogene concept or to suggest that all pseudogenes are functional. The majority of currently annotated pseudogenes are neither robustly transcribed nor translated. Such regions fit well the original descriptions of pseudogenes as ‘similar, but defective’. Rather, we argue that their labelling as pseudogenes is not constructive for advancement of understanding of genome function and misdirects experimental design.

In other words, the authors are simply telling their colleagues to follow the data. Do not assume that a pseudogene is non-functional just because it has been identified as a pseudogene. Instead, investigate it to find out whether or not it actually is. The progress of science is hindered when you assume non-functionality because of the way the sequence has been identified.

I not only completely agree with that sentiment, I would also add this: following any dogma (evolutionist, creationist, or other) hinders the progress of science. Scientists should be willing to follow the data wherever they lead. Unfortunately, such scientists tend to be the exception, not the rule.

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15 Responses to Please…Discard the Dogma!

  1. David H says:

    Question to better help me understand what is going on: Are these “pseudogenes” the same thing that evolutionists called “junk DNA”, or is that something different?

  2. Jake says:

    That is not how science works, and I think you know that. Science can’t function without dogma—a paradigm, or a research program if you want to step back from Kuhn and go with Lakatos instead. Without dogma we don’t know what direction to go, or what to do when the data don’t look right. To quote conservative intellectual Richard Weaver, “When we affirm that philosophy begins with wonder, we are affirming in effect that sentiment is anterior to reason.” Even at the most basic level we tend to sweep disagreements between theory and data under the rug; if I’m testing some lab equipment I’ve set up, and it doesn’t do what I expect it to do, the first thing I think is not that the entirety of my theory is wrong, but that I messed up setting up the equipment. And when I have pages and pages of a calculation I’m doing, and one of the steps produces something unexpected, the first thing I do is go through the previous bits of the calculation and perform some theoretical checks to make sure everything is consistent. I don’t assume that I’ve discovered something new, or that my theories are wrong, because I put quite a bit of trust in everything my theories have gotten right already. I.e., dogma. (And who knows where that trust comes from; we tend to make it inductive in science—the theory has gotten all this other stuff right, so it’ll get this next thing right, too—but induction is a logical fallacy, of course, and we have all sorts of personal reasons for liking this or that theory.)

    And more, the notion of “follow[ing] the data wherever they lead” is naive, because raw information is useless without interpretation. Where does the truth that 997 is prime lead? When was the last time anyone even thought that the truth that 997 is prime leads somewhere? It certainly does mathematically, because it means we can expect to have fields with characteristic 997, but that doesn’t seem to lead us very far. So the notion of “leading” somewhere is also invested with the idea of progress, which is politically fraught if not scientifically so.

    Anyway, we don’t have the manual to the universe that tells us exactly what each bit of data tells us, because the data only exists because we relied on some interpretive structure to both gather and interpret it. Switch structures and the data means something else. Does the data that I see the sun move across the sky tell me that the earth revolves around the sun, or that the sun revolves around the earth? We now have a pretty good interpretive structure that says it tells us the earth revolves around the sun, but we used to have another one—and it was a good one for quite a while!—that would say it means the sun revolves around the earth. And what’s more, on Kuhn’s account, sticking to the dogma is what generates the attention to detail—the buy-in, as it were—that leads to people actually worrying that the dogma might be wrong. If you’re interested in rationalizing anomalies away, you’ll invest in doing so—and thus spend the time to realize your rationalization might not be working.

    The more appropriate formulation is that our dogma doesn’t always work for the problems we encounter, as Kuhn explicated. And it can have things wrong about the world, because we don’t work from God’s perspective. I agree with you that the regnant scientific dogma is wrong and bad, but dogma in itself is necessary for science to function.

    • Jay Wile says:

      I disagree, Jake. That is how science works. Science should definitely NOT have a dogma. Sure, it needs an interpretive framework, but a framework is not dogma. It a guide for your thinking. When the data do not fit in the framework, you change the framework. When the data don’t fit in a dogma, you ignore the data. That’s the problem. Right now, many interpretive frameworksa are treated like dogma, and that harms science.

      I absolutely agree with your statements about doing experiments. If you get unexpected results, the first thing you do is check your setup. Most likely, the unexpected results are from some mistake you made. However, suppose you keep getting the same results no matter what you do. Then you ask a colleague to check your results and perhaps replicate your experiment. If he or she gets the same result and you still say that the problem is with the experiment and not the framework, then you are treating the framework as dogma, and you are no longer doing science.

      I really, really hope you were engaging in hyperbole when you said, “Even at the most basic level we tend to sweep disagreements between theory and data under the rug…” If you do that, then you definitely are not doing science. Now…if I have a theory that is successful on many levels but is inconsistent with the data on another, I might not throw the theory away. However, I had better recognize that I can’t sweep that disagreement under the rug. The disagreement should tell me that there is something wrong with the theory, and I need to hold onto that theory less tightly than I hold on to a theory that has no known contradictions with the data. For example, I use quantum mechanics and relativity all the time, and I recognize how well-founded they both are. However, they are incompatible with one another, so I automatically realize that one or both of them has some inherent flaws. I don’t sweep that under the rug. I use the theories, understanding full well that their applications might be severely limited (and some of my conclusions might be wrong) due to their flaws.

      Following the data where they lead is anything but naive. In fact, it is the basis of science. I don’t like the idea that radioactive half-lives are not constant. As a nuclear chemist, I WANT them to be constant. But there are some very convincing lines of evidence that they have changed in the past. If I don’t follow that evidence where it leads, I am no longer doing science. I am clinging to dogma.

      Dogma is not necessary for science to function. Interpretive frameworks are, and there is a huge gulf between a dogma and an interpretive framework!

      • Jake says:

        I challenged the notion that raw information can “lead” anywhere—I think it incoherent, and that the “leading” comes from the interpretation via which that data was curated and is thus subjective—and you didn’t address that.

        I really, really hope you were engaging in hyperbole when you said, “Even at the most basic level we tend to sweep disagreements between theory and data under the rug…” If you do that, then you definitely are not doing science.

        We are talking about scientific instincts here, which are not obvious. At what level does one decide to believe the results of one’s process, and at what point is one skeptical of them? This is a complicated question, one you cannot simply reject by accusing me of not doing science because you don’t make the exact same subjective choice I do. Say I check the first four assumptions, or first ten pages, of my calculation. Why not check 11? I used the term “sweeping under the rug,” which you should realize relies on a subjective assessment of what’s worth spending time on. Was framing quantum mechanics primarily phenomenologically, and not worrying about the philosophical problems it created, sweeping those problems under the rug? I kind of think so, but I also think that continuing to do the phenomenology was still science. Choosing to ignore, or not ignore, anomalies does not automatically make a thing not science, because science is tentative and temporal. We have more than enough historical experience of trying to figure out the world to realize things aren’t so easy.

        And I don’t think you’ve made a significant distinction between dogma and what you call an interpretive framework. It’s quite easy to rationalize about why this or that result that seems to counter one’s theory actually fits within it; Kuhn related this to the “puzzle-solving” aspect of every scientific paradigm: How do we solve the problem of reconciling theory and data? And rejecting a single replication doesn’t make one unscientific; it’s already obvious from the argument that more replications are better (as you state), thus there has to be some kind of weighing mechanism. Which is how science actually works: it’s a complicated negotiation among all sorts of data, directions, and ideas.

        • Jay Wile says:

          I thought I addressed that issue. As I said, science needs an interpretive framework. The raw data allow us to evaluate the interpretive framework. The more raw data that support the framework, the more confidence we have in the framework. The more data that contradict the framework, the less confidence we have in the framework.

          I wasn’t accusing you of not doing science because you are making different subjective decisions than me. I was saying that if data contradict the framework and you don’t question the framework, then you are not doing science. That’s not subjective. In fact, it’s quite objective. If the data do not agree with the framework, then either the data are wrong, the framework is wrong, or both. If you don’t question BOTH the framework AND the data, then you aren’t doing science. I am not saying to DISCARD the framework when the data disagree with it. I am saying to QUESTION the framework. If you don’t, you are treating the framework as dogma, and you are not doing science.

          I am using the word “dogma” the way the authors of the paper in the OP use it, and according to the standard defintion:

          a principle or set of principles laid down by an authority as incontrovertibly true.

          So, in the context of this paper, the dogma is that pseudogenes are functionless. This has been laid down by authorities in encylopedias, textbooks, scientific papers, lectures, etc., etc. The data contradict the dogma. As the authors say (and as I quote from the paper), that doesn’t mean all pseudogenes are functional. However, the data clearly show that many pseudogenes are functional. Thus, the dogma of pseudogenes being functionless must be discarded. This is precisely how science is supposed to work.

        • Jake says:

          I think the problem is that you’re insisting on rigid definitions of words when those definitions don’t at all obtain. For example, when I appealed to the notion of “sweeping under the rug,” in no way did I declare that to be identical to not questioning the issue at all. (Indeed, at first you said that “sweeping under the rug” was incompatible with science, and then you backtracked.) And whether or not someone is judged to be sweeping something under the rug (or thinks he’s doing so himself) likely depends on who’s doing the judging.

          So, say you were to ask someone you considered to be dogmatic about the lack of functionality of pseudogenes. Do you think he’d admit he believed without question pseudogenes aren’t functional? No, he’d point to whatever formulation of his scientific dogma explains—i.e., demonstrates with whatever he considers evidence—why pseudogenes aren’t functional. Now, you might not find that a sufficient level of suspicion; you might not even agree his evidence exists. But your “without question” stipulation would have been nullified—he filtered his questioning through his dogma—and you’d still be right to say the person was being dogmatic.

          Why? Because you’re wrong about what dogma means. When you’re among scientists, and someone starts talking about how people in some field believe this or that “dogmatically,” what you really mean is that they stubbornly cling to something just like various stubborn and dogmatic authorities—particularly the church—have in the past. You’re appealing to the social and cultural story surrounding dogmatic approaches to the natural world. This is also what the authors of that paper were doing in using the word dogma—they know the word is charged, and that it will provoke a response. You might ask the authors if they meant specifically that people believe pseudogenes aren’t functional strictly without question, and I guarantee you they’ll give caveats. Just as the church would have when it adhered to geocentrism against the various heliocentric theories. I can also guarantee you that the average scientist in our current scientific community would tell you the church was being dogmatic about geocentrism, but you know that there were many immediately obvious questions they could pose to heliocentrism—like why we don’t fly off the earth if it’s moving in a circle.

          Strict dictionary definitions—constantive utterances—are not at all the whole of communication via language. There is also the performative utterance (which does not mean putting on an act or show), which is the effect of the social weight of the uses of the words comprising the utterance. The primary meaning of the word dogma in the scientific community is performative, referring to historical instances (true or not) of evil authorities suppressing the truth.

        • Jay Wile says:

          Well, Jake, I will have to disagree with you. Especially in science, definitions are very important. If you have alternate definitions for words, then you need to explicitly state them. The phrase “sweeping under the rug” most certainly means to hide something. If you are hiding descrepancies between the data and the framework, you are not doing science, and I would never backtrack on that position. What you seem to be doing is backtracking on what “sweeping under the rug” actually means.

          If you want to define dogma differently than the standard definition, which happens to be the way the authors of the article being discussed are using it, then you need to make that clear. This is important, because I have actually spoken to biologists who unquestionably accept that pseudogenes are functionless. They even dismiss studies that indicate the functionality of specific pseudogenes simply because they accept without question the dogma that pseudogenes are functionless. In my experience, this is not rare. Many scientific dogmas get treated exactly as the dictionary definition describes. I have no idea what the authors of the study paper say if confronted on the issue, but if you read the paper, you will see that they are clearly using the word dogma in the strict dictionary-defined way.

          I would agree with those who would say that the church was being dogmatic about geocentrism. Yes, there were questions that could be posed in support of geocentrism, but there was also strong observational evidence against it, some of which could be traced to centuries before the scientific revolution. Thus, there were clear reasons to question it. Nevertheless, the church held tightly to geocentrism, despite the large amount of evidence against it. That’s exactly what geocentrism is, and it’s exactly how many biologists treat pseudogenes.

          I agree that strict dictionary definitions are not the whole of communicative language, but serious discussions of scientific issues demands strict definitions. If you want to redefine words in a scientific discussion, you need to do that up front.

        • Jake says:

          Is “hiding something” always the same as “sweeping under the rug,” and are either the same as strictly not questioning one’s beliefs? No. That alone demonstrates you’re trying to load more into definitions than they’ll hold.

          I would posit that neither you, nor the authors of this paper, were being particularly careful. And that, while it doesn’t matter for the authors of the paper, because casting aspersions of dogmatism was their goal, it does matter for you, who are attempting to define science. People who are more serious about their study of the philosophy of science would not agree with you, like Kuhn, Feyerabend, Lakatos, or even Popper. Popper understood that data is cheap, and that there are tons of possible theories that comport to the data, many of which we’d probably never think of.

        • Jay Wile says:

          No, hiding something is not ALWAYS the same as sweeping it under the rug. Sweeping it under the rug is ONE WAY of hiding things. That doesn’t avoid the fact that sweeping something under the rug means hiding things, and one should NEVER hide the data when it comes to science. I am not loading more into the definitions. I am, in fact, adhering to the definitions. You are not.

          I would posit that you are not being careful at all. Instead of trying to understand what is being written, you immediately decide what someone means without even referring to the standard definitions. If you are interested in being serious about the study of the philosophy of science, you need to be serious about the definitions of terms.

        • Jake says:

          At this point you’re just proliferating words, and pretending what matters is strict adherence to your supposedly clear definitions, to avoid the truth that you, and the people who you claim are being dogmatic about pseudogenes, would disagree about whether or not they’re being dogmatic, and that being dogmatic isn’t so easily resolvable hiding or not hiding data, or sweeping something under the rug or not doing so, or of asking certain questions or not asking them. Science isn’t that rigid, and you aren’t its arbiter.

          I think I am done discussing philosophy with you, Dr. Wile. I don’t think you take it seriously.

        • Jay Wile says:

          I never claimed that science was rigid, and I never claimed to be its arbiter. I am simply communicating what other scientists have said and indicating whether I agree or disagree with it. I am sorry that you are reading things into my piece that clearly are not there.

          I am sorry, Jake, but you seem to be the one who is not taking philosophy seriously. If you don’t bother to learn the definitions of words used in a philosophical discussion, there is no way you can take it seriously.

  3. John D says:

    Evolutionists are so fond of referring to Intelligent Design as a “God of the Gaps” theory. As data like this continues to close the gaps in our knowledge of the genome it seems as if that monikor has come back to haunt them.

  4. Bruce Burns says:

    Jay,

    This “framework” to which you refer sounds to me a bit like an hypothesis. Because, we must start our interpretive process somewhere, we select (or invent) an hypothesis which explains our findings and successfully predicts other findings.

    In my case, of the hypotheses available for the origins of life, I find. “in the beginning, God created the heaven and the earth,” as the most compelling on both counts, but I stand ready to discard that hypothesis for a better one, should I find one which fits the evidence more accurately.

    Edgar Andrews was the first to suggest this approach in his book, “Who Made God?”

    Thanks for bringing this up.

    • Jay Wile says:

      You are essentially correct. A framework is more of a set of hypotheses or theories into which we try to understand the data that we collect. I certainly agree that the framework of God creating everything is the most productive scientific framework available!

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