The genome of the small octopus, Octopus bimaculoides has recently been sequenced. The results are reported in Nature (Albertin et al., 2015).
The octopus is a cephalopod along with squid and cuttlefish. These groups diverged about 270 million years ago making them more distantly related than humans and platypus. As expected, the octopus genome is similar to other mollusc genomes but also shows some special derived features. Some gene families have been expanded—a feature often found in other genomes.
I want to talk about two recent press releases on the origin of life.
The first one is from the BBC and it talks about the work of Haruna Sugahara and Koicha Mimura who presented their results at a recent conference [Comet impacts cook up 'soup of life']. They noted that the impact of a comet carrying organic molecules can produce more complex organic molecules.
The second report is from ScienceDaily. It reports a similar study by Furukawa et al. (2015) who examined the idea that the impact of meteorites in the primitive ocean could create more complex organic molecules than those already found in meteors [Meteorite impacts can create DNA building blocks].
Here's what I'm doing this summer (right) when I'm not fighting creationists, writing a book, giving talks, playing with the grandchildren, and visiting exotic cities in Canada and the United States.
I built the main part of the patio twenty years ago. I recall working on it for 6-8 hours at a stretch but today I'm pooped after three hours.
I think the stones have gotten heavier.
Some of the people who comment here have pointed out that this is the second anniversary of a post by Jonathan McLatchie on Evolution News & Views (sic): A Simple Proposed Model For Function of the Human Vitamin C GULO Pseudogene.
That post is significant for several reasons. Let's review a bit of background.
Intelligent Design Creationists have a problem with pseudogenes. Recall that pseudogenes are stretches of DNA that resemble a gene but they appear to be non-functional because they have acquired disruptive mutations, or because they were never functional to begin with (e.g. processed pseudogenes). All genomes contain pseudogenes. The human genome has more than 15,000 recognizable pseudogenes.1 This is not what you would expect from an intelligent designer so the ID crowd tries to rationalize the existence of pseudogenes by proposing that they have an unknown function.
There are 13 casts of the famous sculpture by Rodin [The Burghers of Calais]. I've seen four of them (Paris, Washington, Los Angeles, New York). I took this photo today at the Metropolitan Museum of Art in New York.
The burghers thought they were sacrificing their lives to save the inhabitants of Calais, which was being starved into submission by Edward III of England in 1347. Their lives were spared after Queen Philippa convinced her husband to be lenient.
One of my ancestors is Paon de Roet. He was a knight in Queen Phillippa's retinue and was one of two knights assigned to protect the burghers of Calais. I descend from Paon de Roet's daughter, Katherine. Her sister, Philippa (named after the Queen), married a poet named Geoffrey Chaucer [My Connection to Geoffrey Chaucer and Medieval Science].
A recent post by some anonymous blogger named "Darwin Quixote" made the following claim [see comment in: Be Careful, Evolution is Behind You]. The discussion was about teaching evolution in Ontario (Canada) schools ....
Of course I agree that these topics should be required, but I would suggest that it’s even more important that human evolution be a required topic because only 51% of Ontarians believe that humans evolved. It is likely that a significant number of teachers fall into the 49% category, and therefore leaving this topic to the discretion of the teacher becomes problematic.
This didn't seem right to me so I checked the latest polls that I could find on the internet.
Here's one by Angus Reid in 2012: Believe In Evolution: Canadians More Likely Than Americans To Endorse Evolution. The results show that 60% of Ontarians believe the following statement: "Human beings evolved from less advanced life forms over millions of years."
24% of Ontarians thought that: "God created human beings in their present form within the last 10,000 years."
16% were not sure.
The results were somewhat different in other provinces. In Quebec, for example, the number of people who accepted evolution was 71% and only 13% believed in Young Earth Creationism. In Alberta only 48% of the population accepted evolution and 35% were Young Earth Creationists.
So Darwin Quixote was off by a bit (51% vs 60%) but not by much. However, I think he makes an error by assuming that a significant number of biology teachers (in high school) would be opposed to evolution and might not teach human evolution.
These are the books I've read, or finished reading, this summer beginning in June.
This is the book that I'm re-reading very carefully.
This is still my favorite book 
In Ontario (Canada) there is a province-wide curriculum that all public schools must follow. This includes the Roman Catholic separate schools that receive money from the province. This post is prompted by something written last month by an anonymous blogger who runs Darwnquixote. He claims that human evolution is not taught in Ontario schools [Be Careful, Evolution is Behind You]. Jerry Coyne picks up on this and launches into a tirade about the Ontario curriculum [Ontario schools require teaching evolution—except human evolution]. Coyne urges everyone to write letters of complaint to the Ontario Minister of Education. (Her name is Liz Sandals and she is an excellent (not perfect) Minister of Education.) Is it true that the Ontario curriculum does not teach that humans have evolved?
I've been quite impressed with the science and technology curriculum as revised in 2008 and I'm hearing good things about the next revision. The teaching of evolution, like all aspects of the curriculum, focuses on understanding the basic concepts and on encouraging students to think for themselves. Students learn about evolution and diversity in the primary grades where the emphasis is on the relationship of humans and other species [The Ontario Curriculum: Elementary: Science and Technology]. In grade 1 they learn that "Plants and animals, including people, are living things" (page 44) and in Grade 2 one of the "big ideas" is that humans are animals (page 58).
I came across an interesting article about "PeerWise."
Hardy, J., Bates, S.P., Casey, M.M., Galloway, K.D., Galloway, R.K., Kay, A.E., Kirsop, P., and McQueen, H.A. (2015) Student-Generated Content: Enhancing learning through sharing multiple-choice questions. International Journal of Science Education 36: 2180-2194. [doi: 10.1080/09500693.2014.916831]
Abstract
The relationship between students' use of PeerWise, an online tool that facilitates peer learning through student-generated content in the form of multiple-choice questions (MCQs), and achievement, as measured by their performance in the end-of-module examinations, was investigated in 5 large early-years science modules (in physics, chemistry and biology) across 3 research-intensive UK universities. A complex pattern was observed in terms of which type of activity (writing, answering or commenting on questions) was most beneficial for students; however, there was some evidence that students of lower intermediate ability may have gained particular benefit. In all modules, a modest but statistically significant positive correlation was found between students' PeerWise activity and their examination performance, after taking prior ability into account. This suggests that engaging with the production and discussion of student-generated content in the form of MCQs can support student learning in a way that is not critically dependent on course, institution, instructor or student.
This sounds like a good way to encourage some student-centered learning in large classes. We have several biochemistry classes in our department that could benefit.
Does anyone have any experience with PeerWise?
One of the most difficult concepts to get across to science educators (e.g. professors in a biochemistry department ) is the idea that students need to be exposed to ideas that you think are incorrect and they need to be given the opportunity to make a choice. It's part of critical thinking and it's part of a good science education. Part of the problem is that there's a general reluctance to even teach "ideas" as opposed to facts and techniques.
There's an extensive pedagogical literature on this but university professors are reluctant to admit that there might be better ways to teach. While browsing this literature, I came across a recent article by Henderson et al. (2015) that makes a good case.
David Raup died last month. He was 82 years old. Raup was a paleontologist at the University of Chicago, where he studied the big picture of the history of life, concentrating on mass extinctions. Here's an excerpt from the University of Chicago website [David Raup, paleontologist who transformed his discipline, 1933-2015].
Raup’s former students and colleagues uniformly praised his unique creativity along with his astute capabilities as an academic adviser, senior colleague and paleontological statesman. They remember him for the sweeping scope of the questions he asked, his analytical and quantitative rigor, and his skepticism and humility.
“David Raup ushered in a renaissance in paleontology,” said Raup’s former student and colleague Charles Marshall, SM’86, PhD’89, director of the University of California’s Museum of Paleontology and professor of integrative biology at UC Berkeley. “Before Dave, much of the discipline was centered on describing what was. Dave taught the discipline to think about the processes that might have generated the past record.”
Raup introduced statistical concepts to paleontology that treated the fossil record as an outcome of yet-to-be-discovered processes. Raup was widely known for the new approaches he brought repeatedly to paleontology, such as extensive computation, modern evolutionary biology, theoretical ecology and mathematical modeling.
As Marshall put it, Raup created new intellectual space for paleontology. “That was, in my opinion, his greatest contribution. It is not that Dave just transformed the discipline, but his students, and their students, continue to fill and expand that space,” Marshall said.
Another former student and colleague, Michael Foote, expressed similar sentiments.
“By any conception of what it means to be influential, Dave was one of the most influential paleontologists active during the second half of the 20th century,” said Foote, SM’88, PhD’89, a professor in geophysical sciences at UChicago. “In the areas he chose to touch, nobody, in my view, surpassed him.”
I have taken the title of this book from a research article I published in Spain some years ago. I was concerned then with the failure of trilobites in the Paleozoic era. Starting about 570 million years ago, these complex, crab-like organisms dominated life on ocean bottoms—at least they dominated the fossil assemblages of that age. But through the 325 million years of the Paleozoic era, trilobites dwindled in numbers and variety, finally disappearing completely in the mass extinction that ended the era, about 245 million years ago.
My question in Spain is the one I still ask: Why? Did the trilobites do something wrong? Were they fundamentally inferior organisms? Were they stupid? Or did they just have the bad luck to be in the wrong place at the wrong time? The first alternative, bad genes, could be manifested by things like susceptibility to disease, lack of good sensory perception, or poor reproductive capacity. The second, bad luck, could be a freak catastrophe that eliminated all life in areas where tilobites happened to be living. The question is basically one of nature versus nurture. Is proneness to extinction an inherent property of a species—a weakness—or does it depend on vagaries of chance in a risk-ridden world?
Of course, the problem is more complex than I have presented it, just as the nature-nurture question in human behavior is complex. But in both situations, nature (Genetics) and nurture (environment) operate to some degree, and the challenge is to find out which process dominates and whether the imbalance varies in time and space. (pp. 5-6)
If you don't already own a copy of that book, you should buy one right now and read it. They may not be easy to get in the future and your life will be poorer if you don't learn about the difference between bad genes and bad luck.
Raup is famous for the Field of Bullets analogy to explain why extinction is as much bad luck as bad genes. He made a strong case for his belief that chance plays an important role in the history of life. He was not alone in making this claim but it doesn't seem to be popular these days for reasons that confound me. It's part of what I call Evolution by Accident. It means that if you replay the tape of life, things will come out very differently and there's no guarantee that sentient beings like ourselves will evolve [see Café Scientifique: Replaying the tape of life]. You don't have to agree with Raup, Gould, and other experts but if you want to participate in discussions of evolution you have to be familiar with this important concept.
Once again, a group of scientists want to extend and revise the Modern Synthesis version of evolutionary theory in order to bring their pet projects into the mainstream. Once again, these scientists seem to have missed the real revolution that took place 45 years ago so they are attacking a strawman. And, once again, they seem to think that the core principles of evolutionary theory can be defined by how complex animals evolve, ignoring bacteria and single-cell eukaryotes that have been at the heart of the history of life for 3.5 billion years.
But the fact that some geniuses were laughed at does not imply that all who are laughed at are geniuses. They laughed at Columbus, they laughed at Fulton, they laughed at the Wright Brothers. But they also laughed at Bozo the Clown.
                     Carl SaganThe paper by Laland et al. (2015) was published in Proceedings of the Royal Society (UK) Series B just this month (August, 2015). The usual suspects are included in the author list including three of the Altenberg 16: Eva Jablonka, Gerd B. Müller, and John Odling-Smee. This is the same group that defended the "yes" side when Nature posed the question, "Does evolutionary theory need a rethink?" back in October, 2014 [see Rethinking evolutionary theory ].
Here's what he said ....
We discovered some pretty surprising things in reading out the human genome sequence. Here are four highlights.
1. Humans have fewer genes than expected. My definition of a gene here—because different people use different terminology—is a stretch of DNA that codes for a particular protein. There are probably stretches of DNA that code for RNAs that do not go on to make proteins. That understanding is only now beginning to emerge and may be fairly complicated. But the standard definition of “a segment of DNA that codes for a protein” gives one a surprisingly small number of about 30,000 for the number of human genes. Considering that we’ve been talking about 100,000 genes for the last fifteen years (that’s what most of the textbooks still say), this was a bit of a shock. In fact, some people took it quite personally. I think they were particularly distressed because the gene count for some other simpler organisms had been previously determined. After all, a roundworm has 19,000 genes, and mustard weed has 25,000 genes, and we only have 30,000? Does that seem fair? Even worse, when they decoded the genome of the rice, it looks as if rice has about 55,000 genes. So you need to have more respect for dinner tonight! What does that mean? Surely, an alien coming from outer space looking at a human being and looking at a rice plant would say the human being is biologically more complex. I don’t think there’s much doubt about that. So gene count must not be the whole story. So what is going on?
2. Human genes make more proteins than those of other critters. One of the things going on is that we begin to realize that one gene does not just make one protein in humans and other mammals. On the average, it makes about three, using the phenomenon of alternative splicing to create proteins with different architectures. One is beginning to recover some sense of pride here in our genome, which was briefly under attack, because now we can say, “Well, we don’t have very many genes but boy are they clever genes. Look what they can do!”
3. The male mutation rate is twice that of females. We also discovered that simply by looking at the Y chromosome and comparing it to the rest of the genome—of course, the Y chromosome only passes from fathers to sons, so it only travels through males—you can get a fix on the mutation rate in males compared to females. This was not particularly good news for the boys in this project because it seems that we make mistakes about twice as often as the women do in passing our DNA to the next generation. That means, guys, we have to take responsibility for the majority of genetic disease. It has to start somewhere; the majority of the time, it starts in us. If you are feeling depressed about that, let me also point out we can take credit for the majority of evolutionary progress, which after all is the same phenomenon.
4. “Junk” DNA may not be junk after all. I have been troubled for a long time about the way in which we dismissed about 95% of the genome as being junk because we didn’t know what its function was. We did not think it had one because we had not discovered one yet. I found it quite gratifying to discover that when you have the whole genome in front of you, it is pretty clear that a lot of the stuff we call “junk” has the fingerprints of being a DNA sequence that is actually doing something, at least, judging by the way evolution has treated it. So I think we should probably remove the term “junk” from the genome. At least most of it looks like it may very well have some kind of function.
The folks at Evolution News & Views (sic) can serve a very useful purpose. They are constantly scanning the scientific literature for any hint of evidence to support their claim about junk DNA. Recall that Intelligent Design Creationists have declared that if most of our genome is junk then intelligent design is falsified since one of the main predictions of intelligent design is that most of our genome will be functional.
THEME
Genomes & Junk DNA
They must be getting worried because their most recent posts sounds quite desperate. The last one is: The Un-Junk Industry. It quotes a popular press report on a paper published recently in Procedings of the National Academy of Sciences (USA). The creationists concede that the paper itself doesn't even mention junk DNA but the article in EurekAlert does.
Günther Witzany is one of those people who think the Modern Synthesis needs to be overthrown but he missed the real revolution that took place in the late 1960s. He's part of The Third Way crowd that includes Denis Noble and Jim Shapiro [see Physiologists fall for the Third Way and The Third Fourth Way].
Susan Mazur interviews him for the Huffington Post [Günther Witzany: Modern Synthesis "Must Be Replaced," Communication Key to Evolution]. Recall that Susan Mazur is fixated on the Altenburg 16 and their attempts to radically revise evolutionary theory without understanding anything about Neutral Theory and random genetic drift. Günther Witzany is a philosopher. He was not one of the Altenberg 16 but he clearly wants to be part of the outer circle. It's not clear why anyone should consider him an expert on evolutionary biology.
Susan Mazur did us a great favor when she asked him if he would like to make a final point. His answer shows us why we can ignore him.
The older concepts we have now for a half century cannot sufficiently explain the complex tendency of the genetic code. They can't explain the functions of mobile genetic elements and the endogenous retroviruses and non-coding RNAs. Also, the central dogma of molecular biology has been falsified -- that is, the way is always from DNA to RNA to proteins to anything else, or the other "dogmas," e.g., replication errors drive evolutionary genetic variation, that one gene codes for one protein and that non-coding DNA is junk. All these concepts that dominated science for half a century are falsified now. ...
Thank-you Susan. Keep up the good work. Fools need to be exposed.
