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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

Americans Not Very Confident in Science

Americans don’t know a lot about the universe but they’re sure it is so complex it had to be created by a god. That’s one possible reading of the latest AP poll where people were asked about their confidence in various scientific statements. 72% agreed at least “somewhat” that, “The universe is so complex, there must be a supreme being guiding its creation.” By contrast, “The Earth is 4.5 billion years old,” only received 60% support, and “The universe began 13.8 billion years ago with a big bang,” got only 46%.

As an article in The Atlantic points out, it is possible some people knew about the big bang but just weren’t confident about the 13.8 billion year figure. Polls in the past suggest that isn’t the case however. Some excerpts from the Atlantic article follow.

Source: A Majority of Americans Still Aren't Sure About the Big Bang
Up until 2010, they asked the following question: True or false, the universe began with a huge explosion. Since 1990, the number of people answering true to that question has bounced between 32 and 38 percent. (The number was anomalously higher in 1988, a discrepancy that they do not explain.)

In 2012, the National Science Board tried to parse out why Americans were different by adding ‘according to astronomers’ into the Big Bang question for half the survey respondents. Like this:

According to astronomers, the universe began with a big explosion.
60 percent of Americans said this statement was true, versus 39 percent who said so when the “according to astronomers” was not present. This would suggest that 40 percent of people know the science, 40 percent of people don’t, and 20 percent have heard the science, but believe otherwise.

Before you lament the fall of the republic, consider that very little has changed in the public awareness of scientific knowledge over the past 20 years. The 2014 report put it bluntly: “The public’s level of factual knowledge about science has not changed much over the past two decades.”

Is Making Weaker Trees a Good Idea?

Source: Cheaper Fuel From Self-Destructing Trees
Wood is great for building and heating homes, but it’s the bane of biofuels. When converting plants to fuels, engineers must remove a key component of wood, known as lignin, to get to the sugary cellulose that’s fermented into alcohols and other energy-rich compounds. That’s costly because it normally requires high temperatures and caustic chemicals. Now, researchers in the United States and Canada have modified the lignin in poplar trees to self-destruct under mild processing conditions—a trick that could slash the cost of turning plant biomass into biofuels.

I’m not an alarmist about genetic modification. Over the years I’ve gone from unsure and cautious to fine with it and even pro-modification for the right applications. This proposal however at the least raises some questions in my mind.

I wonder what the risks are of this new gene getting into the wild population. There are already documented cases of genes inserted in food crops crossing with existing, non-modified, strains of the crop. Now, maybe it would be the case that non-modified trees would just out compete any strains with this modification but nature can be complex and unpredictable. It seems like more fragile trees that are easier targets for pests and disease could be one nightmare result of this idea.

Fire Tornadoes and Barely Constrained Randomness

A couple nifty little science videos.

Fire Tornadoes
Take a dust devil, add fire, and you get this awesome looking spectacle.

“Pillar of fire” Australia- in real-time from chris tangey on Vimeo.
Via The Atlantic

Inside the Cell
Animations showing the inner workings of a living cell often look mechanistic, almost like a little assembly line. The reality is quite different. Cells are just packed full of proteins and near random activity. Science writer Carl Zimmer described it as “barely constrained randomness.” The BioVisions group at Harvard have put together this update to their previous Inside the Cell video to let you see what it is really like.

Inner Life of a Cell | Protein Packing
Via Carl Zimmer

Scientia Salon is Off to a Good Start

Not much progress on the blogging front here. I have a handful of half-written posts that I’ll return to eventually. In the meantime Massimo Pigliucci’s new blog Scientia Salon is churning out some pretty great content. Massimo is a former evolutionary biologist turned philosopher. I’ve been a moderate fan ever since he started doing the podcast circuit several years ago, usually to debate creationists. His last blog Rationally Speaking was decent as well. So far though, the new blog surpasses anything he’s done in the past. He’s got together several great writers in the rationalism/naturalism/science/skepticism community to produce some pretty “heavy” material. I’m just going to link to what has gone up so far.

In Spelling out Scientism, A to Z John Shook lists off 26 possible meanings of the word Scientism. Scientism is a word that often gets thrown around when some group feels threatened by the knowledge produced by the sciences. It’s can be a statement that the person feels that the science supporter has overstepped their bounds in some way. They’ve trusted too much in science or trusted it in a domain where it doesn’t apply. As you might imagine it gets used quite a lot by people defending some pseudo-scientific belief or another. However, it also gets thrown around within the rationalism community as well. It has reached the point where it seems to be more of a vague pejorative than anything. Shook’s piece is both a call for more clarity for those charging the crime of scientism, and for those defending to say more clearly what they are defending.

David Kyle Johnson has a three-part piece defending the notion that there is a conflict between science and religion, and just what that conflict is. No “non-overlapping magisteria” for Johnson , where religion and science occupy different realms of “knowledge” and therefore can’t conflict with one another. Unfortunately for me, this totally overlaps one of the pieces in my queue, and is much better than anything I’ll probably produce. Oh well, mine is much more narrowly focused on a particular claim made by some Christians so I’ll get it published here eventually. Here are the pieces: Identifying the Conflict between Religion and Science — Part I  and Part II and Part III.

Finally we have another three parter by the famous, in some circles, Alan Sokal. In 1996 he sent a hoax paper to a postmodernist journal to see if they would accept it, as long as it conformed to their ideological stance that science was just another socially constructed truth. The paper itself was filled with wonderful gibberish such as (quoting the linked Wikipedia article):

“it is becoming increasingly apparent that physical ‘reality'” is fundamentally “a social and linguistic construct”. It went on to state that because scientific research is “inherently theory-laden and self-referential”, it “cannot assert a privileged epistemological status with respect to counterhegemonic narratives emanating from dissident or marginalized communities” and that therefore a “liberatory science” and an “emancipatory mathematics”, spurning “the elite caste canon of ‘high science'”, needed to be established for a “postmodern science [that] provide[s] powerful intellectual support for the progressive political project”.

Anyway, his current piece up at Scientia Salon is about three opponents of scientific progress. In What is science and why should we care? — Part I he tackles those same post-modernists and social constructivists, while at the same time advocating a leftism that takes science seriously. Part II turns to pseudo-science, like alternative medicine and religion and Part III finishes up with propagandists and spin doctors.


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.

First Americans May Have Lived on Land Bridge for 10,000 Years

Source: First Americans May Have Been Stuck in Beringia for Millennia

The “Beringian Standstill” hypothesis was first proposed by Latin American geneticists in 1997, as a way to explain the genetic evidence indicating that Native Americans started diverging from Siberians 25,000 years ago. In contrast, the archaeological evidence for the first Americans goes back only 15,000 years, to the end of the ice age known as the Last Glacial Maximum.

In this week’s issue of the journal Science, three researchers report new clues that support the claims for Beringia’s lost world. They say fossilized insects, plants and pollen extracted from Bering Sea sediment cores show that central Beringia was once covered by shrub tundra. That would have made it one of the few regions in the Arctic where wood was available for fuel.

Thousands of Siberian migrants might have found refuge in central Beringia until the climate warmed up enough for glaciers to recede, letting them continue their movement into the Americas, the researchers say.

The Oldest Piece of Earth’s Crust Dates to 4.4 Billion Years Old

The best resource in book form I have found that discusses how the age of the Earth is known is The Age of the Earth by Brent Dalrymple. It is a bit of a dry read but packed with info. There are also good summaries at Talk Origins the first being by Dalrymple himself.

It sounds like they used the Uranium-Lead concordia method (also described here), which takes advantage of the fact that there are two different ways Uranium decays into lead. One from U-238 to Pb-206 and another from U-235 to Pb-207. It is a particularly useful test because zircon doesn’t incorporate lead into its crystal at the time it forms.

Source: Oldest Rock Speck Zeros In On Earth’s Cooling Date

The oldest remaining grain of early Earth’s original solid rock crust has now been confirmed to be a 4.374-billion-year-old old zircon crystal from Jack Hills, Australia.

That age should settle a scientific debate over the accuracy of that mineral’s internal clock, and cuts the time from when Earth was hit by a Mars-sized body (which led to the formation of the Moon) and the cooling and creation of Earth’s first solid crust from 600 million years to 100 million years.

The age of a grain is figured by measuring the amounts of the parent uranium isotopes compared to the daughter lead isotopes.

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.