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Coursera: Emergence of Life

I’ve signed up for a few online course through Coursera but, to be honest, I never end up having time to do everything required. I’m going to do my best to make time for this one though.

Source: Emergence of Life
How did life emerge on Earth? How have life and Earth co-evolved through geological time? Is life elsewhere in the universe? Take a look through the 4-billion-year history of life on Earth through the lens of the modern Tree of Life.

Course Syllabus
Week 1. Course Welcome, Geological Time, and the Nature of Science
Week 2. The Tree of Life and Early Earth Environments
Week 3. Fossilization and Precambrian Life-Earth Interaction
Week 4. Paleozoic Life After the Advent of Skeletons
Week 5. Paleozoic Plants, Reptiles, and the Transition to Land
Week 6. Mesozoic Reign of Dinosaurs and the Development of Flight
Week 7. Cenozoic Mammals and Global Environmental Change
Week 8. Astrobiology and the Search for Life in the Cosmos

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’).

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.


Egregious Misrepresentation of Lenski’s E. Coli Experiment

What do you do when a scientist runs a long-term experiment where E. coli bacteria evolve a new metabolic pathway in the lab thus completely refuting the creationist claim that evolution can’t add new information? You lie of course. Well, you get a friend of yours to make a video for you where he lies for you. That’s just what Ken Ham did during his recent debate with Bill Nye.

Richard Lenski’s lab has been running a long term evolution experiment with E. coli for the last 25 years. During the course of the experiment the bacteria evolved the ability to metabolize citrate. This is a direct and deadly blow to creationist claims that evolution can’t create “new information,” like new metabolic pathways.

The thing to realize is the researchers still have the strains frozen and available to work with, in addition to having “snapshot” samples taken every so often during the experiment. Because of this they are able to sequence the genomes of the relevant strains. From doing so they know this is definitely not a case of an existing ability that was suddenly “turned on.”

The link below includes commentary by one of the experimenters involved.

Source: Zachary Blount on “Ham on Nye” Debate, Follow-up #3 | Telliamed Revisited

Of course, this attention has also been a bit troubling because it has led to repeated disparagement, dismissal, distortion, and misrepresentation of my work by both professional and amateur creationists. These creationists often get entirely wrong the work my colleagues and I toiled long and hard to do, likely because they haven’t bothered to read our papers, learn the details and methods, or think much about the results. (I suspect some duplicity is in there, too.) Reflexive, unthinking dismissal bothers me – maybe because my parents and devoutly Southern Baptist Granny told me when I was a child that this is something that civilized folk simply should not do.

The second argument was more direct. Both Ham and Fabich asserted that the Cit+ function did not evolve because using citrate did not involve “any kind of new information … it’s just a switch that gets turned on and off.” (Fabich went on to state that this “switch” is what we reported. That is emphatically not true. It beggars belief that anyone, much less a trained microbiologist, could actually read our 2012 paper, where we reported the genetic basis of Cit+, and come away thinking this.) Variations on that wording are often used by creationists who discuss the citrate work because it implies that Cit+ arose because of a pre-existing regulatory switch and involved no evolution at all. But that simply is not the case – that wording, dare I say it, is a lie.

Regular E. coli cells have no existing genetic regulatory circuitry that “flips a switch” to allow them to start growing on citrate in the presence of oxygen.

Silly Claims by Ken Ham About Evidence for a Young Earth

This article tackles a few of the claims made by Ken Ham in his debate with Bill Nye. As is the norm with creationist arguments the claims are fact-challenged, full of shoddy (or dare I say deceitful) logic, and have been debunked for decades. I found this excerpt particularly amusing for its analogy.

Ken Ham uses young earth arguments debunked over 20 years ago in Bill Nye debate

The “amount of helium,” “amount of sediment in the sea” and other “amount” arguments have also been debunked because the young earth creationists only take into account the factors that add certain substances and then ignore the processes that remove these substances and the point of which equilibrium is met.

Through measuring the amount of trash in your house, we can conclude that your home is no more than a week old. We can reach that conclusion by factoring the trash that comes into your residence every day and by completely ignoring the weekly trash pickup or any other consideration. Using half of equations in conjunction with “we don’t know something therefore god did it” is how young earth creationist arguments work.