Wednesday, July 5, 2017

Shifting paradigms

In biology, as in all sciences, sometimes an idea gets so big, and so ingrained/entrenched in the culture, the original work does not need to be cited anymore. (Unfortunately, sometimes this means we often forget where the idea originally came from.) This idea becomes so pervasive, we believe it without even thinking about it. It becomes a fall-back idea, a foundation or bedrock, so to speak. Every new discovery is measured against it. Such an idea is called a paradigm.

However, sometimes, upon further review years later, we find that the original research that started the paradigm was flawed. Or the paradigm rests on a particular interpretation of the data from the original research, and not on the data themselves. In that case, the paradigm may shift. But because paradigms are so pervasive, it might take a lot of work and a long time for the shift to occur.

Now, to be clear, I am not claiming that any of the work I have been a part of constitutes a paradigm shift. Not at all. Usually, we reserve that moniker for truly momentous changes in an entire field of science, such as quantum mechanics or relativity. But some of our observations have shown that common illustrations of fly embryos, which have been in people's minds for decades, do have some inaccuracies.

For example, consider the following illustration of a cross section of a fly embryo that is about 2.5 hrs old (left side of jpg below). The green represents the presence of the Dorsal protein (see here for more information about Dorsal). The common thought is that, as Dorsal enters the nuclei on the ventral side (bottom half of illustration), it depletes the surrounding cytoplasm of Dorsal. Hence, the cytoplasm around the ventral nuclei are dark. In contrast, Dorsal protein does not enter the nuclei on the dorsal side of the embryo (top half of illustration), so the nuclei are dark, but the surrounding cytoplasm is bright.

Illustrations like the one on the left have been around for decades. However, about eight years ago, we found out that this illustration is inaccurate. Yet, scientists are still drawing their embryos incorrectly today.

In theory, this "default view" of what happens with Dorsal should last only as long as it takes for someone to just look and see. In 2009, when I was a postdoc in Angela Stathopoulos's lab at Caltech, we published the first quantifiable (i.e., fluorescent) images of Dorsal-stained, cross-sectioned embryos (for example, see jpg above, right side). In several publications thereafter, we always saw the same thing: the cytoplasm is not bright on the dorsal side. In fact, there is no doubt there is just more total Dorsal protein on the ventral side. Yet, these illustrations of Dorsal in the embryo still persist today. I guess it just takes some time and effort for the "default view" to get out of our collective head.

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