Over the years I've examined how ignorance in science can be seen as a positive thing and how it can be used to define the discipline, a key contrast to most religions. We're still a long way from understanding many fundamental aspects of the universe, but the religious fundamentalist (see what I did there?) mindset is seemingly unable to come to terms with this position and so incorporates lack of knowledge into arguments disparaging science. After all, the hackneyed train of thought goes, scientific theories are really only that, an idea, not something proven beyond all possible doubt. Of course this isn't the case, but thanks to the dire state of most school science education, with the emphasis on exams and fact-stuffing rather than analysis of what science really is (a group of methods, not a collection of facts) - let alone anything that tries to teach critical thinking - you can see why some people fall prey to such disinformation, i.e. that most science isn't proven to any degree of certainty.
With this in mind, you have to wonder what percentage of general audience science communication describes theories with much more certainty than is warranted, when instead there is really a dearth of data that creates a partial reliance on inferred reasoning. Interestingly, the complete opposite used to be a common statement; for example, in the nineteenth century the composition of stars was thought to be forever unknowable, but thanks to spectroscopy that particular wonder came to fruition from the 1860s onwards. It is presumably the speed of technological change today that has reduced that negativity, yet it can play into the anti-rationalist hands of religious hardliners if scientists claim absolute certainty for any particular theory (the Second Law of Thermodynamics excepted).
As it is, many theories are based on a limited amount of knowledge (both evidential and mathematical) that rely on an expert filling in of the gaps. As an aside, the central tenet of evolution by natural selection really isn't one of these: the various sources of evidence, from fossils to DNA, provide comprehensive support to the theory. However, there are numerous other areas which rely on a fairly small smattering of physical evidence and a lot of inference. This isn't to say the latter is wrong - Nobel-winning physicist Richard Feynman once said that a scientific idea starts with a guess - but to a non-specialist this approach can appear somewhat slapdash.
Geophysics appears to rely on what a layman might consider vague correlations rather than exact matches. For example, non-direct observation techniques such as measuring seismic waves have allowed the mapping of the interior composition of the Earth; unless you are an expert in the field, the connection between the experimental results and clear-cut zones seem more like guesswork. Similarly, geologists have been able to create maps of the continental plates dating back around 600 million years, before which the position of land masses hasn't been so much vague as completely unknown.
The time back to the Cambrian is less than fifteen percent of the age our 4.5 billion year old planet. This (hopefully) doesn't keep the experts up at night, as well-understood geophysical forces mean that rock is constantly being subducted underground, to be transformed and so no longer available for recording. In addition, for its first 1.3 billion years the planet's surface would have been too hot to allow plates to form. Even so, the position of the continental crust from the Cambrian period until today is mapped to a high level of detail at frequent time intervals; this is because enough is known of the mechanisms involved that if a region at the start of a period is in position A and is later found at position Z, it must have passed through intermediate positions B through Y en route.
One key geological puzzle related to the building and movement of continental rock strata is known as the Great Unconformity, essentially a 100 million year gap in the record that occurs in numerous locations worldwide for the period when complex multicellular life arose. In some locales the period expands both forwards and backwards to as much as a billion years of missing rock; that's a lot of vanished material! Most of the popular science I've read tends to downplay the absent strata, presumably because in the 150 years since the Great Unconformity was first noticed there hasn't been a comprehensive resolution to its cause. The sheer scale of the issue suggests a profound level of ignorance within geology. Yes, it is a challenge, but it doesn't negate the science in its entirety; on the other hand, it's exactly the sort of problem that fundamentalists can use as ammunition to promote their own versions of history, such as young Earth creationism.
In recent decades, the usually conservative science of geology has been examining the evidence for an almost global glaciation nicknamed 'Snowball Earth' (or 'Slushball Earth', depending on how widespread you interpret the evidence for glaciation). It appears to have occurred several times in the planet's history, with the strongest evidence for it occurring between 720 and 635 million years ago. What is so important about this era is that it is precisely the time (at least in geological terms) when after several billion years of microbial life, large and sophisticated, multicellular organisms rapidly evolved during the inaccurately-titled Cambrian explosion.
All in all then, the epoch under question is extremely important. But just how are the Great Unconformity, global glaciation and the evolution of complex biota connected? Since 2017 research, including from three Australian universities, has led to the publication of the first tectonic plate map centred on this critical period. Using various techniques, including measuring the oxygen isotopes within zircon crystals, the movements of the continents has been reconstructed further back in time than ever before. The resulting hypothesis is a neat one (perhaps overly so, although it appears to be tenable): the top 3km to 5km of surface rock was first eroded by glacial activity, then washed into the oceans - where the minerals kick-started the Ediacaran and early Cambrian biota - before being subducted by tectonic activity.
The conclusion doesn't please some skeptics but the combined evidence, including the erosion of impact craters and a huge increase in sedimentation during the period, gives further support, with the additional inference that an immense increase in shallow marine environments (thanks to the eroded material raising the seafloor) had become available for new ecological niches. In addition, the glacial scouring of the primary biominerals calcium carbonate, calcium phosphate and silicon dioxide into the oceans altered the water chemistry and could have paved the way for the first exoskeletons and hard shells, both by providing their source material and also generating a need for them in the first place, in order to gain protection from the changes in water chemistry.
Deep-time thermochronology isn't a term most of us are familiar with, but the use of new dating techniques is beginning to suggest solutions to some big questions. Not that there aren't plenty of other fundamental questions (the nature of non-baryonic matter and dark energy, anyone?) still to be answered. The scale of the unknown should not be used to denigrate science; not knowing something doesn't mean science isn't the tool for the job. One of its more comforting (at least to its practitioners) aspects is that good science always generates more questions than it answers. To expect simple, easy, straightforward solutions should be left to other human endeavours that relish just-so stories. While working theories are often elegant and simpler than alternatives, we should expect filling in the gaps as a necessity, not a weapon used to invalidate the scientific method or its discoveries.
