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Monthly Archives: March 2014

Link Roundup 3/26/2014

A feature I like at some of the blogs that I read is an occasional post with links to articles they’ve read but have nothing much to say about. It seems a waste to put each on in its own post. I’d like to automate it too, so that I could just bookmark something on Delicious with a specific tag and have it auto-posted here. There are WordPress plugins that do that but they want to create a separate post for each link, which is exactly what I’m trying to avoid.

Oh well, for now, here is a manual link roundup from the last few days.

Astronomers Surprised to Find Asteroid With Rings

When Nature Looks Unnatural

Biblical epic ‘Noah’ tests director Aronofsky’s blockbuster chops I have to admit I’m already enjoying the reactions from the religious to the fact giant six-armed angels called the watchers are included in the movie. Yes, shocking, there is obviously mythological stuff in the Bible. Did you know Joshua defeated the last of the giants? (Rephaim)

[GMO Golden Rice] A senseless fight

[Hobby Lobby] Right-wing judges face huge moral dilemma: How Hobby Lobby could expose SCOTUS’ hypocrisy In the past Scalia has said that the first amendment doesn’t mean a religion gets to have its own set of laws. That was then, this is now. Now that the issue is something that touches on his personal beliefs he will be changing his tune.

Corporations Have Consciences and Contraceptives Are Cheap: Hobby Lobby at the Supreme Court “It was hard not to sense that somehow, if the coverage had been for something other than contraceptives — say, as Sotomayor pressed several times, vaccinations or blood transfusions — the question of the impact on employees might have been treated differently.”

Seeing Famous Places From Above Is Surreal.

No Comments?

Someone asked me through another channel why there was nowhere to leave comments. The answer is, time. I just don’t have a lot of it. I’m taking care of a 5 year old and a 5 month old all day. My wife is awesome about me spending time on the blog (writing or messing with code) once she gets home, but I like to see her too, so I average about an hour or two per night tops.

Moderating comments and interacting with a blog community is very time consuming. I feel that if I leave the comments open I would owe it to the readers (few as they might be) to make sure the comments are worth reading and don’t misinform the reader. Unfortunately, with the topics I’ve covered, I have already received a couple crazed comments when I had them turned on. I also have to know myself a little. I know when I get comments that are silly or wrong, I feel compelled to respond. I just don’t have time to do so.

So, do I just let the site get over-run by junk? Delete everything I don’t have time to respond to? Neither of those are particularly appealing to me. The downside is that I might miss out on accurate corrections, good discussion, and words of encouragement. It isn’t an easy decision for me, but for now I’m keeping comments turned off.

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.

Teach the Controversy T-shirts

Creationists want schools to “teach the controversy” even though there is no controversy to teach. This t-shirt company has some funny ideas about what other “controversies” we could teach kids.


A Future Series on the Historicity of Jesus

One of the projects that I hope to actually knuckle down and use this blog for is to blog my way through Richard Carrier’s book On the Historicity of Jesus when it comes out. We’ll see if the demands of family life actually let me accomplish that. I definitely have some time occasionally but will I want to spend it doing that? We’ll see. I actually have been following the question of whether or not Jesus existed for quite some time so perhaps I can provide some context to those who haven’t.

Richard Carrier Reviewed Maurice Casey’s New Book

As is his wont, Richard Carrier has written a very thorough review of Maurice Casey’s new book Jesus: Evidence and Argument or Mythicist Myths? I can’t say I’m surprised that Casey wrote what sounds like a terrible book. The few times I have read him, at Jospeh Hoffmann’s blog for example, I found him to be rambling and incapable of making clear arguments. In other words, he fit right in at Hoffmann’s blog. Apparently Casey’s main argument rests on his ridiculous (and thoroughly rejected by his entire field) notion that the gospels were written very early and are based on original Aramaic versions.

Source: Critical Review of Maurice Casey’s Defense of the Historicity of Jesus

Casey’s Jesus has no structure or organization capable of being analyzed. It is basically just a random jump from digression to digression, very loosely grouped into eight topical chapters, as he randomly picks some item or other from mythicist literature in that general topic (why that one and not others, no idea), rants about it for a bit, then suddenly starts ranting about another random topic, with only the barest thread of connected thought process between them. It is an extraordinarily frustrating book to read for that reason. He also repeats himself frequently, digresses at odd times on topics not significantly related to the book’s thesis, and never actually gets around to explaining what his argument for the historicity of Jesus actually is. You can sort of reconstruct it on your own, if you have patience and endurance, but it’s weird that you have to do this.

There is also an extraordinary amount of dishonesty and misrepresentation (although I suspect in many cases this is actually a cognitive defect: Casey literally doesn’t understand what his opponents are saying quite a lot of the time–I will have more to say on this point below), as well as a fairly consistent reliance on straw man argumentation (he often ignores–in fact, completely fails even to mention–all the strong points made by an opponent on some subject and only mentions and critiques the weak ones, or only chooses to address an argument as made by a lousy mythicist, ignoring the much better versions of the same argument made by more reliable mythicists).

This book is also characterized by an awe-inspiringly near-total reliance on a single argument for historicity that is monumentally illogical (the Criterion of Aramaicism). I say near-total, because he has one other argument to stand on, borrowed from Christian apologetics, which is his mildly contradictory insistence that in his letters Paul is talking about the historical Jesus all the time, and simultaneously didn’t talk about the historical Jesus because he never had to. (Yes, those are his only two arguments in defense of historicity. He wisely dodges relying on any extrabiblical evidence, although he briefly flirts with the James passage in Josephus, and he mentions the other passage in Josephus and the one in Tacitus, but doesn’t make any clear argument from them.)