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Life’s Degenerate Code, Shared Function, and Evidence for Evolution

During the second episode of Cosmos, Tyson took a trip to the realm of the very small to show us the genetic machinery. He talked about how a small mutation can have big long-term consequences and how the differences in the genetic code leads to the differences between the species. After establishing the differences he went on to talk about the similarities between all living things. Proteins involved in metabolizing sugars, for example, are the same across all species. The reason, he explained, is that metabolizing energy sources happened too early, and is too important, to leave room for change later.

At this point there was a graphic on the screen depicting the DNA of various creatures and how it is the same in some locations. I thought for sure he was leading in to an interesting piece of evidence for evolution. I also knew, if any creationists address the point at all, they are likely to say something like, “That’s not evidence for evolution. They are the same because they were made by the same God.” There’s a problem with that response though and as we’ll see these shared functions actually provide a nice illustration of the fact of evolution.

Proteins, Amino Acids, and a Degenerate Code
Before we can see why we’ll need some background information (which I’ll try to keep as short and to the point as possible).

Within living cells genes are ultimately turned into proteins. Genes are sequences of nucleotides (guanine, adenine, thymine, and cytosine) and when taken in threes the nucleotides code for a particular amino acid. Proteins are simply chains of these amino acids.

But the code is degenerate which simply means that different three nucleotide sequences code for the same amino acid. For example the amino acid leucine can be coded for by any of the triplets TTA, TTG, CTT, CTC, CTA, or CTG. What this means is that mutations can happen to these sequences and the overall function of the gene, as expressed in the protein, is not changed at all! They are called neutral mutations because they don’t change anything, and they happen all the time, at a steady rate.

Another Way to Grow an Evolutionary Tree
So here we have a nice way to test for evolutionary relationships. Species that shared a common ancestor more recently should have fewer of these types of neutral mutations separating their DNA sequences in the shared genes. Since the genes do the same thing this can’t be explained as serving some different function in each.

So what do you think we find when we compare sequences? Exactly what we would expect to find if species are related by evolution from common ancestors! Evolutionary trees derived from such comparisons very nicely match the evolutionary trees we had already independently deduced from anatomy and the fossil record. Those species that diverged from each other recently have fewer substitutions (human and chimp genes for cytochrome c differ by only 4 substitutions for example) and those that diverged long ago have many.

Things didn’t have to come out this way. We could have found that there was very little difference between sequences or that they diverged in ways that couldn’t be explained by evolution. Ultimately the creationist dodge I noted at the beginning fails. The genes in question differ in ways that allows us to see how they got that way and, unless their god purposely set out to deceive everyone, they didn’t get there by any special creation of each species.

This piece of genetic evidence is just one of many that can be found in our genome. Genetics today provides some of the most powerful evidence we have today for evolution. Our evolutionary history history is literally written in our genes.

Further Info
I do want to point out a couple simplifications I’ve made. First, the type of mutations I mentioned aren’t the only kind of neutral mutation that is found. More drastic changes can happen while still preserving function. This is because all that matters in the end is how the protein folds up to do its job.

The second is that there are exceptions to the rule. Some species, and comparisons between species, differ from the mutation rate we might expect. This is because mutation is a random process. With so many species it is to be expected that unusual things happen from time to time. The important thing is the big (average) picture which can’t be explained except with evolution. For more information and discussion of these technical details see Douglas Theobald’s excellent article and his rebuttal of a misguided creationist response to it. (Unfortunately I can’t link directly to the relevant section of the second link but look for the heading ‘Insufficient Knowledge of Basic Molecular Biology and Genetics’ and continue until you get to ‘Prediction 4’).

The Pros and Cons of Bruno

There are arguments that could be made both for and against inclusion of a segment on Giordano Bruno in the première episode of the rebooted Cosmos series. There are also some bad arguments I’ve seen today that don’t have anything to do with what was actually in the show.

Giordano Bruno was a friar who was burned at the stake in 1600 for his radical theological and astronomical ideas. The latter consisted of the notion that the Earth wasn’t the only world and that the universe was infinite.

The unfounded complaint I’ve seen from both religious and secular commentators is that the show incorrectly portrays Bruno as a martyr for science, and therefore basically gets the history wrong. I think this is just a case of people stuffing the narrative of the actual show into preconceived boxes and not noticing it doesn’t really fit.

For some religious commentators the problem is that Bruno wasn’t tried because of his support of the Copernican heliocentric universe but more for his theology. I’m not sure how anyone could watch the segment and not notice the religious source of Bruno’s speculations. When the inquisitor is grilling him he leads off quite clearly with several theological charges. There is also repeated mention that Bruno’s ideas were grounded in his beliefs about the nature of his god. Similarly, from the secular side there are complaints that Bruno’s speculations were religious in nature and therefore he doesn’t make a very good martyr for science (or a very good club to whack the religious over the head with). This, however, assumes that a martyr for science is what they were going for.

Instead, I think the show was trying to promote the values that make scientific inquiry possible. Specifically, a society needs to value curiosity, open inquiry, and have a commitment to go where the evidence leads. While Bruno may not be a good example of the latter he is an excellent example of the first two. He dared to be curious about what the cosmos was like and to step outside the bounds of established dogma.

The show was pretty clear about the nature of Bruno’s speculations when Tyson said, “Bruno was no scientist. His vision of the cosmos was a lucky guess because he had no evidence to support it. Like most guesses it could well have turned out wrong. But, once the idea was in the air it gave others a target to aim at, even if just to disprove it.” The last sentence there is also important because, scientist or not, Bruno did play a real role in inspiring others who came after him. After all, a history of thinking about the cosmos seems to be fair game in a show about the cosmos.

I think that perhaps a more mild complaint along the same lines might be valid. What I quoted above did come at the end of the segment and almost felt like a throw-away disclaimer at the end. Maybe it could have had a little more emphasis up front. There are also other options if one is looking for an example of the restrictive range of allowable thinking at the time. There is always Galileo. He hits on all three of the scientific values and might have been a better choice. Did they go with Bruno because his being burnt at the stake has more emotional impact than Galileo’s house arrest? Perhaps.

There may have been another reason for the choice as well. The new show incorporated Carl Sagan’s cosmic calendar as a way to grasp our place in the immense history of the universe. Near the end Tyson mentions that at 5 seconds before midnight was when Jesus walked the Earth, and that at 3 seconds Muhammad did. I just got the impression they were making a conscious effort to not lose segments of the religious audience. Bruno seems like a particularly apt choice if that was a goal. Though not explicitly mentioned he presents an example of how one can be religious and still make peace with the how the universe really is, by adjusting one’s conception of god. And also possibly showing that ideas can come from anywhere as long as one is willing to test them against the facts.

Maybe I’m reaching a bit on the last part but in the end I think including Bruno was a reasonable decision. Galileo might have been a better choice in some respects but I’m OK with their choice. Now, Fox accepting an ad for the new Noah movie in the middle of a science documentary is a whole other thing.

Cosmos: A Space-Time Odyssey to be Available in Half a Billion Homes

I’m psyched. No pressure Mr. Tyson.

Source: Cosmos: A Space-Time Odyssey

Fox Networks Group (FNG) announced today that COSMOS: A SPACETIME ODYSSEY will debut simultaneously across multiple U.S. Fox networks, including Fox Broadcasting Company (FOX), National Geographic Channel, FX, FXX, FXM, FOX Sports 1, FOX Sports 2, Nat Geo Wild, Nat Geo Mundo and FOX Life on Sunday, March 9 (9:00-10:00 PM ET/PT). This first multi-network launch event for Fox Networks Group, along with the series debut on Fox International Channels and National Geographic Channels International, will make COSMOS: A SPACETIME ODYSSEY available on 220 channels in 181 countries, with an overall footprint of more than half a billion homes.

After the cross-network premiere event, COSMOS: A SPACETIME ODYSSEY will continue its epic 13-episode run, airing Sundays (9:00-10:00 PM ET/PT) on FOX, and Mondays – with all-new bonus footage and behind-the-scenes content – on the National Geographic Channel (NGC) (10:00-11:00 PM ET/PT).