Changing Views

By Michael Hawkins

What would change my view on evolution?

It depends what is meant by “change”. My view on evolution changes quite frequently, actually. Sometimes it’s a qualitative change: the relationships between our known ancestral cousins are always shifting ever so slightly. Often, there is little consensus about where to place certain members of the genus Homo on the evolutionary tree. As new evidence is found, as more research is done, as further facts come to light, my views are always changing on that aspect of evolution.

And then there are quantitative changes. One excellent example comes from the discovery of tetrapod footprints in 2009. That discovery pushed the evolution of tetrapods back about 18 million years. All the relationships between species of that general time period stayed the same, but our view of when tetrapods began to populate the land changed.

And then there are all sorts of other changes, like recently when it was shown that natural selection works differently on allele fixation in sexually reproducing populations versus more simple asexual populations. (That was also a qualitative change, but on the genetic, not taxonomic, level.)

So if that is what is meant by “change”, then there are all sorts of examples that show how my views on evolution are, well, evolving. The same can be said of biologists around the world. But what if by “change”, the real question being asked is, What would make me dismiss evolution? Then the answer is very different.

A basic fact of how science works is that it does not tend to operate on individual studies. It requires a body of evidence to change views. For example, I reject a connection between cell phone use and cancer. Studies have shown possible links, but they have been far from conclusive, weak even. And more importantly, there is a body of evidence showing no significant link. I’m going with the evidence in bulk, not the individual packaging. This relates directly to the question of what it would take to get me to dismiss evolution because there is a famous quote by J.B.S. Haldane I had in mind when starting this article. When asked what it would take to change his mind, he retorted, “Fossil rabbits in the Precambrian.”

But that wouldn’t change my mind. My very first suspicion would be fraud; I suspect little more from creationists (and we know how much they would be promoting such a discovery). But let’s say it came from a reputable research team, then what? I would admittedly be perplexed. There is no reason a fossil rabbit ought to be found in that era, but that doesn’t mean we get to throw out such a well established theory as evolution. We know evolution is true insomuch as we know gravity is true. It would necessarily take more than a few rabbit fossils to alter the unifying theory of biology, just as it would take more than an apple falling up for us to alter the theory of gravity. Even if we could never explain the fossils satisfactorily, I would have no doubts that evolution still formed the basis of everything in biology.

What would change my view would be the discovery of a number of fossils in all the wrong places. We would need to start finding mammals and birds dating back 800 million years; we would need to see dinosaur fossils embedded in the rocks of 20 million years ago; we would, yes, need to see rabbit fossils in the Precambrian. No, I wouldn’t need these specific examples, but I would need these sorts of examples. I don’t want just individual anomalies that fly in the face of modern theories. I need more than that: it takes a body of evidence to start changing my view.

Because that’s how science works.

A basic of science

By Michael Hawkins

I often find myself reminded of a post I made on just the third day in the life of my blog. It was about a media report on a recent study that said a certain pesticide found in anti-bacterial soaps may actually contribute to the development of antibiotic resistance by bacteria. It was a fine study, but it was far from conclusive. (The news article wasn’t so cautious in its assertions.) Perhaps it would be best if people only used regular old soap, what with that not really qualifying as a real sacrifice, but as for the science, I was far from ready to say that that pesticide was a contributor to antibiotic resistance among bacteria in any significant way in the given environment.

And the reason is quite simple: science does not rely upon individual studies. Of course, we may be able to point back to the results from one lab or one group of researchers as published in a single study as the linchpin that opened up a whole new branch of study. But that doesn’t mean we believe that paper as being conclusive on its own. It only works when we have a body of evidence. In most cases that means a number of studies looking at the same or a similar problem and coming to the same or very similar conclusions. For a single paper that proves itself a linchpin, that means we need a number of other studies which use its findings as their basis. For instance, green fluorescent protein, or GFP, was shown to work as a marker of gene expression in a pretty definitive study. It has about a bajillion (rough estimate) other studies on it, but no one needed to reproduce the study which won one research team the Nobel Prize in chemistry. But people did use that study as a basis for about a gagillion (rough estimate again) studies. If the original study was wrong or faked or otherwise limited, we would be well aware of that by now because of all those subsequent studies. That is one way to compose a body of evidence.

To put this another way, take the studies on intercessory prayer and its efficacy. We have some that show positive results. “Look, God is here to help!” But then we have others that show negative results. “Oh, no! God must be angry!” And then we have a whole bunch which shows a null result. “Uh…God must be indifferent.” So how do we interpret these results?

Remember, we need to be looking at the evidence as a body. As one of those intolerant, bigoted, hate-filled evilutionist atheists, I would find it humorous, at least on one level, if prayer gave negative health results. But I don’t get to have that laugh. Instead, I have to conclude that prayer has no detectable effect on health. None of the studies are conclusive; they suffer from bias, or are statistically insignificant in either direction, or just show a blatant null result. The most likely conclusion is that prayer does nothing. No study has convinced me otherwise, and most of the studies have shown prayer to be inconsequential to the well being of people anyway.

What I hope this post enables readers to do is recognize a fundamental aspect of how science works so that next time they see a study which concludes a link between this or that, they know what to think. That doesn’t mean it is okay to just dismiss a non-bias confirming study (i.e., a study that doesn’t give a result one likes). It just means that it is always necessary to look at the entire body of evidence before drawing a conclusion.

Mitochondria and Microsatellites

By Michael Hawkins

Mitochondrial DNA (mtDNA) is useful for determining the phylogeny, or relationships, between closely related species. It is inherited, generally, only from mother to offspring, so it doesn’t face problems such as recombination since it isn’t recombining with other DNA before being passed on (except through horizontal transfer, or “genetic swapping” between bacteria).

One recent discovery using mtDNA has found that a sort of “pre-human” was walking around while humans and Neanderthals were still rocking out. Johannes Krause of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany and his colleagues wrote in the journal Nature that they had sequenced mtDNA from a fossil discovered in a Siberian cave. Results showed that the former owner of those long dead bones had diverged from humans and Neanderthals a million years ago. (Human and Neanderthals then diverged 500,000 years later.)

The authors go on to state that more research is needed to determine just where the species qualitatively sits on the evolutionary tree. The point, however, is that mtDNA has proved useful in this analysis, giving a tentative quantitative determination and a tentative qualitative indication.

This is all in stark contrast to microsatellites. These are short tandem repeats, or units of repeating DNA sequences. For example, CACACACACACACACACACA is commonly seen throughout eukaryotes and the chloroplastic genomes of plants (usually every few thousand base pairs). They are generally neutral.

Microsatellites have relatively high mutational rates for a variety of reasons. Whereas in mitochondria the mutational rate can partially be chalked up to the fact that mitochondria is bacterial in origin, microsatellites have polymerase slippage to thank, or bad DNA replication, let’s say. Other studies suggest unequal crossing-over. At any rate, this mutation rate lends itself to population studies using microsatellites.

By using microsatellites as genetic markers, it is possible to determine genetic variation within a population. This works for investigating both temporal and spatial population structure, two important factors in management and conservation of species. For instance, Lage et al. 2004 looked at Atlantic cod populations ranging across Browns Bank, Georges Bank, and Nantucket Shoals.

At the time of the research, the Gulf of Maine cod were treated as a separate stock from the Nantucket Shoals and Georges Bank Atlantic cod. Browns Bank cod were even more separate as a stock since they are in Canadian waters. Using microsatellites, the researchers found Nantucket Shoals cod to have a distinct population structure from those on Georges Bank and Browns Bank, which were genetically similar. One likely reason is due to currents which keep Georges Bank cod on Georges Bank as well as somewhat rare currents which likely transport larvae from Browns Bank over the Fundian Channel (which adult cod are unlikely to traverse since they are ground-huggers and the channel is deep and cold). The conclusion is that the health of Atlantic cod populations might be better served by treating them as separate stocks based upon the discovered genetic variation, instead of the current method of utilizing particular geographical lines which may not reflect all population ‘barriers’.

The shortcoming, however, with microsatellites is that they are not useful for deep phylogenetic analysis. Their high mutation rate makes them virtually useless after a few thousand generations; they are good for pedigrees and population structure analysis, but they do not offer insights into distant relationships. Occasionally they may remain the same or nearly the same over long periods of time, but the rhyme and reason probably has nothing to do with the microsatellites themselves. Instead, they likely are located near a site of selection on a locus, thus conserving them for longer than just those few thousand generations.

Lage CR, Kuhn K, Kornfield I. (2004) Genetic differentiation among Atlantic cod (Gadus morhua) from Browns Bank, Georges Bank, and Nantucket Shoals. Fishery Bulletin, 102:289-297.