Models should match observations

Ever since Galileo dropped two objects out of the Leaning Tower of Pisa (according to apocryphal accounts), it has been recognized that our scientific theories should be tested by observation. Sure, you could just make something up about how things work, but eventually someone will come along and just look to see if you're right.

Last week I wrote about an example in modern-day science where this hasn't happened. It was a small example...we are not talking about anything as momentous as testing the acceleration of gravity. But the example illustrated a point: sometimes ideas get so stuck in our heads that it may take a while before we realize that the observations are saying something different. 

Here is another example. Because of the action of the Dorsal nuclear concentration gradient (see here for more information about Dorsal), different genes are expressed in different locations around the circumference of the embryo. For example, the gene snail (sna) is expressed on the ventral-most 20% of the embryo (see figure below; by convention, the dorsal side is up and the ventral side is down). But measurements of where other genes are expressed were not so easy to do. Before we performed quantitative experiments in cross-sectioned embryos (where you could see the entire circumference of the embryo), it was thought that sog extended from about 25% to 70% around the embryo (see lavender colored arc on left figure). It was also thought that dpp was only in the cells on the dorsal-most 30% of the embryo.

Patterns of gene expression along the dorsal-ventral axis in the early Drosophila embryo (about 2.5 hours old). Illustration on the left (adapted from Stathopoulos and Levine, 2004) depicts sog as extending from 25% to 70% around the embryo (ventral-to-dorsal). dpp is shown as taking up the dorsal-most 30% of the embryo. More recently, fluorescent imaging in cross sections has become possible. The image in the middle is of a cross-sectioned embryo with several different genes detected by fluorescence. In particular, sog extends from 20% to 50% of the embryo circumference, while dpp takes up almost the entire dorsal-half of the embryo (adapted from Reeves and Stathopoulos, 2009). Both of these observations (plus those regarding other gene expression patterns) can be quantified and plotted as graphs (on right; adapted from Reeves et al., 2012). A border of a gene is defined as when it drops to 50% intensity.

However, after we began to make quantitative observations (using fluorescence) in cross-sectioned embryos, we could easily see that sog extends from 20% to 50% (see green fluorescence in middle figure and green curve in graph on right), while dpp takes up almost the entire dorsal half of the embryo (yellow fluorescence and yellow curve). However, even though this has been known since 2009, scientists are still publishing illustrations like the one on the left.

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.