Bill Martin and a group of collaborators from several countries have analyzed gene trees from a wide variety of species (Ku et al., 2015). They looked at the phylogenies of 2500 different genes with representatives in both prokaryotes and eukaryotes.
The goal of this massive project was to find out if you could construct reliable consensus trees of prokaryotes and eukaryotes given that lateral gene transfer (LGT)1 is so common.
The results show that LGT is very common in prokaryotes making it quite difficult to identify the evolutionary history of prokaryotic groups based on just a small number of gene trees.
In contrast, eukaryotes appear to be a monophyletic group where all living eukaryotes are descendants of a single ancestral species. There's very little LGT in eukaryotic lineages apart from one major event in algae and plants (see below).
The genes currently found in eukaryotic genomes show that eukaryotes arose from an endosymbiotic event where a primitive alphabacterium fused with a primitive archaebacterium. The remnant of the alphaproteobacterium genome are still present in mitochondria but the majority of the bacterial genes have merged with archaebacterial genes in the nuclear chromosomes. Thus, eukaryotes are hybrids formed from two distantly related prokaryotic species.
A second round of new genes was acquired in eukaryotes when a primitve single-cell species merged with a species of cyanobacterium. The remnant of the cyanobactrial genome is found in chloroplasts but, like the case with alphaproteobacteria, the majority of the cyanobacterial genes merged with other genes in the nuclear genome.
The exact number of trees was 2,585. Among those trees, 49% of eukaryotic genes cluster with proteobacteria, 38% derive from cynaobacterial ancestors, and only 13% come from the archaebacterial ancestor. Thus, it's fair to say that the dominant ancestor of eukaryotes, in terms of genetic contribution, is bacterial, not archaeal.
One of the authors on the paper is James O. McInerney of the National University of Ireland, in Maynooth, County Kildare, Ireland. He made a short video that explains the result.2
1. Also known as horizontal gene transfer (HGT).
2. I hate to contaminate a scientific post by referring to creationists but I can't help but wonder how they explain this data. I'd love it if some Intelligent Design Creationist could describe how this fits in with their understanding of the history of life.
Ku, C., Nelson-Sathi, S., Roettger, M., Sousa, F.L., Lockhart, P.J., Bryant, D., Hazkani-Covo, E., McInerney, J.O., Landan, G., Martin, W.F. (2015) Endosymbiotic origin and differential loss of eukaryotic genes. Nature Published online Aug. 19, 2015 [doi: 10.1038/nature14963]
This is a paper in French by Casane et al. (2015). Most of you won't be able to read it but the English abstract gives you the gist of the argument. I had to look up "apophenia": "Apophenia has come to imply a universal human tendency to seek patterns in random information, such as gambling."
In September 2012, a batch of more than 30 articles presenting the results of the ENCODE (Encyclopaedia of DNA Elements) project was released. Many of these articles appeared in Nature and Science, the two most prestigious interdisciplinary scientific journals. Since that time, hundreds of other articles dedicated to the further analyses of the Encode data have been published. The time of hundreds of scientists and hundreds of millions of dollars were not invested in vain since this project had led to an apparent paradigm shift: contrary to the classical view, 80% of the human genome is not junk DNA, but is functional. This hypothesis has been criticized by evolutionary biologists, sometimes eagerly, and detailed refutations have been published in specialized journals with impact factors far below those that published the main contribution of the Encode project to our understanding of genome architecture. In 2014, the Encode consortium released a new batch of articles that neither suggested that 80% of the genome is functional nor commented on the disappearance of their 2012 scientific breakthrough. Unfortunately, by that time many biologists had accepted the idea that 80% of the genome is functional, or at least, that this idea is a valid alternative to the long held evolutionary genetic view that it is not. In order to understand the dynamics of the genome, it is necessary to re-examine the basics of evolutionary genetics because, not only are they well established, they also will allow us to avoid the pitfall of a panglossian interpretation of Encode. Actually, the architecture of the genome and its dynamics are the product of trade-offs between various evolutionary forces, and many structural features are not related to functional properties. In other words, evolution does not produce the best of all worlds, not even the best of all possible worlds, but only one possible world.
Casane, D., Fumey, J., et Laurenti, P. (2015) L’apophénie d’ENCODE ou Pangloss examine le génome humain. Med. Sci. (Paris) 31: 680-686. [doi: 10.1051/medsci/20153106023]
Admirable for its concision and graphic boldness, this imposing scroll presents a history of the known world from the creation of Adam until the birth of Jesus. It is a teaching tool—a graphic summary of a classroom text. The ancestry of Jesus, traced back to the first man, is shown through a stemma (a system of lines and framed circles that runs down the center of the scroll’s length). Noteworthy ancestors, including King David with his harp, are pictured at regular intervals along the stemma. Successions of biblical rulers, as well as the lineage of ancient rulers of the Near East, Greece, and Rome appear on less elaborate stemmata that diverge from, converge with, and run parallel to that central history.
Sounds authentic to me. I wonder who is listed as the father of Jesus and if the genealogy covers the ancestors of Mary all the way back to Eve?
Peter of Poiters lived in England and the scroll was created in the 1200s. I bet he had lots of fun searching ancestry.com and all the census records from Ur and Egypt.
Here's photo that I took at The Cloisters.
1. It was in a dark corner and my Latin is a bit rusty.
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].
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.
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.
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.
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.”
Raup hung out with the likes of John Sepkoski, Steven Stanley, and Stephen Jay Gould and they shared many of the same views on evolution. He was very good at describing those views in books for the general public and that's why I rate him as one of the best scientists who are also science writers [Good Science Writers: David Raup]. His book, Extinction: Bad Genes or Bad Luck? (1991), is one of my top five books on evolution [Top Five Books on Evolution]. Here's a quotation from the introduction to that book ...
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.
