Monday, August 31, 2015

The origin of eukaryotes and the ring of life

The latest issue of Philosophical Transactions of the Royal Society B (Sept. 26, 2015) is devoted to Eukaryotic origins: progress and challenges. There are 16 articles and anyone interested in this subject has to read all of them.

Many (most) of you aren't going to do that so let me try and summarize the problem and the best current ideas on how to solve it. We begin with the introduction to the issue by the editors, Tom Williams, Martin Embley (Williams and Embly, 2015). Here's the abstract ...

A little learning of biochemistry ...

A little learning is a     dangerous thing;
drink deep, or taste not the     Pierian spring:
there shallow draughts     intoxicate the brain,
and drinking largely     sobers us again.
                  Alexander Pope
I've been following Angelo Grasso on Facebook because he posts a lot of biochemistry stuff. His schtick is to post some complicated pathway or structure then marvel at how complex it is and how it had to be designed. For a while I was commenting on his posts in order to show him why his interpretation was wrong or misleading but he just kept posting more examples gleaned from biochemistry textbooks.

This is a classic examples of someone who knows just enough to be dangerous. His latest post is about glycolysis and membrane-associated electron transport in animals. You can see it on the reasonandscience.heavenforum website: Glycolysis. Here's the bottom line ...

Sunday, August 30, 2015

Ten discoveries that would change the way we think about ourselves

New Scientist has published a list of ten ideas that, if true, would change the way we perceive ourselves and our place in the universe [World Turned Upside Down]. I think some of them are pretty good—many of them really would have a profound effect. Of course, some of them are never going to happen and some of them are silly. One of them is already true.

Here they are ...
  1. What if most of reality is hidden?
  2. What if we discover we can see the future?
  3. What if we learn to talk to animals?
  4. What if we are not alone?
  5. What if we don't need bodies?
  6. What if we have no free will?
  7. What if we came from space?
  8. What if intelligence is a dead end?
  9. What if the universe is an illusion?
  10. What if we find god?

IDiots promote twenty-two falsified predictions of Darwin's theory of evolution

Cornelius Hunter is a fellow at the Center for Science and Culture (Discovery Institute). That makes him a card-carrying Intelligent Design Creationist.

He has a website called .DarwinsPredictions.
Charles Darwin presented his theory of evolution in 1859. In the century and half since then our knowledge of the life sciences has increased dramatically. We now know orders of magnitude more than Darwin and his peers knew about biology. And we can compare what science has discovered with what Darwin’s theory expects.

It is not controversial that a great many predictions made by Darwin’s theory of evolution have been found to be false. There is less consensus, however, on how to interpret these falsifications. In logic, when a hypothesis predicts or entails an observation that is discovered to be false, then the hypothesis is concluded to be false. Not so in science.
I was reminded of these "predictions" a few days ago when Casey Luskin interviewed Cornelius Hunter in ID the Future: Casey Luskin and Cornelius Hunter Discuss Darwin's Predictions. I assume that most Sandwalk readers aren't familiar with all these false predictions of Darwinism so here they are with my own brief description.

Friday, August 28, 2015

Jerry Coyne doubles down on his criticism of how evolution is taught in Ontario schools

A few weeks ago, Jerry Coyne got his knickers in a knot because the Ontario school curriculum didn't specifically prescribe the teaching of evolution in the way that he would like [Ontario schools require teaching evolution—except human evolution].

I replied to that post, quoting the Ontario curriculum and pointing out that it was pretty damn good when it comes to evolution [Teaching evolution in Ontario Schools]. The curriculum concentrates on fundamental principles of evolution as they apply to all species. It does not cover any details of the history of life per se. It doesn't specifically mention the evolution of whales, or birds, or any other lineage. It doesn't say which examples have to be included in the classroom instruction. It refers frequently to the fact that humans are not different than any other animals when it comes to biology.

Jerry take this to mean that detailed descriptions of human evolution are specifically excluded and he now claims that this is due to government policy [Ontario school officials respond—or rather, fail to respond—to queries about why they don’t require teaching human evolution].

Human Evolution: Genes, Genealogies and Phylogenies by Graeme Finlay

Human Evolution: Genes, Genealogies and Phylogenies was published in 2013 by Cambridge University Press. The author is Graeme Finlay, a cancer researcher at the University of Auckland, Auckland, New Zealand.

I first learned about this book from a book review published in the journal Evolution (Johnson, 2014). It sounded interesting so I bought a copy and read it.

There are four main chapters and each one covers a specific topic related to genomes and function. The topics are: Retroviruses, Transposons, Pseudogenes, and New Genes. There's lots and lots of interesting information in these chapters including an up-to-date summary of co-opted DNA that probably serves a biologically relevant function in our genome. This is the book to buy if you want a good review of the scientific literature on those topics.

Thursday, August 27, 2015

Inside the mind of an Intelligent Design Creationist

The blog Evolution News & Views (sic) is part of the public outreach of The Center for Science and Culture, a subsidiary of the The Discovery Institute.

Ann Gauger is a researcher at The Biologic Institute, which is funded by The Discovery Institute. She wrote an article for Evolution News & Views entitled What If People Stopped Believing in Darwin? I think it's safe to assume that this is a common view of a leading Intelligent Design Creationist and close to the position of other members of that cult.

Wednesday, August 26, 2015

Eukaryotic genes come from alphaproteobacteria, cynaobacteria, and two groups of Archaea

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]

Jesus and Mo

Jesus and Mo, August 26, 2015

Tuesday, August 25, 2015

The apophenia of ENCODE or Pangloss looks at the human genome

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]

Monday, August 24, 2015

The genealogy of Jesus

I saw this at The Cloisters when I was in New York last week. It's very hard to read1 so I'm not sure if it's accurate.

Here's what the Metropolitan Museum of Art has to say about The Compendium of History through the Genealogy of Christ by Peter of Poitiers.
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 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.

IDiots, suckers, and the octopus genome

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.

Sunday, August 23, 2015

Comets and meteorites CAN NOT create a primordial soup in the ocean

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].

What am I doing on my summer vacation?

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.

How do Intelligent Design Creationists deal with pseudogenes and false claims?

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.

Wednesday, August 19, 2015

The Burghers of Calais at the Metropolitan Museum of Art in New York

The 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].

Monday, August 17, 2015

Do Canadians "believe" in evolution?

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.

Summer Reading

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

Friday, August 14, 2015

Teaching evolution in Ontario Schools

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).

Wednesday, August 12, 2015

What is "PeerWise"?

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]


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?

The value of critique in science education

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 M. Raup (1933-2015)

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.

Tuesday, August 11, 2015

More calls to extend the defunct Modern Synthesis

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.
 &nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp &nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbspCarl Sagan
The 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 ].

Four things that Francis Collins learned from sequencing the human genome

I've been doing a bit of research on the human genome in preparation for a book. This led me to an article published in 2003 by Francis Collins, former head of the Human Genome Consortium (Collins, 2003). It's mostly about how he deals with science and religion but there was an interesting description of what he learned from completing the human genome sequence.

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.

Monday, August 10, 2015

Insulators, junk DNA, and more hype and misconceptions

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.


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.

Friday, August 07, 2015

Here's why you can ignore Günther Witzany

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.

How to write about RNA

I find it very frustrating to read reports about RNA these days because the writers almost always misrepresent the history of the field and exaggerate the significance of recent discoveries. An article in the July 23, 2015 issue of Nature illustrates the problem. The article is written by Elie Dolgin (@ElieDolgin), a freelance science journalist based in Massachusetts (USA). He graduated from McGill University (Montreal, Quebec, Canada) with a degree in biology and obtained a Ph.D. in genetics and evolution from the University of Edinburgh (Edinburgh, Scotland, UK).

Thursday, August 06, 2015

On this day in 1945

At 8:15 AM on August 6, 1945 an atomic bomb was detonated over Hiroshima, Japan. Approximately 78,000 civilians were killed on that day. Six months later the death toll had risen to about 140,000 people.

There are many arguments in favor of dropping the bomb, just as there are many arguments against it. What's clear is that in the context of 2015 we are not in a good position to judge the actions of countries that had been at war for many years.

The most important lesson of Hiroshima is that war is hell and many innocent people die. It's all very well to enter into a war with the best of intentions—as the Japanese did on December 7, 1941—but it's foolish to pretend that when you start a war there won't be any suffering. When you do that, you can really say that the victims of Hiroshima will have died in vain.

The killing and maiming of civilians is an inevitable outcome of war, no matter how hard you might try to restrict your targets to military objectives. Before going to war you need to take the consequences into account and decide whether the cost is worth it.

Hiroshima was not a glorious victory. It was ugly, heartbreaking, and avoidable. War is not an end in itself, it is the failure of peace. War is not an instrument of foreign policy—it is an admission that you don't have a foreign policy.

[The top photograph shows the mushroom cloud over Hiroshima on the morning of August 6, 1945 (Photo from Encyclopedia Britanica: Hiroshima: mushroom cloud over Hiroshima, 1945. [Photograph]. Retrieved August 7, 2007, from Encyclopædia Britannica Online.

The bottom image is taken from a Japanese postcard (Horoshima and Nagassaki 1945). It shows victims of the attack on Hiroshima.]

WIlliam Provine doesn't like random genetic drift

William ("Will") Provine is an emeritus professor of history and of evolution at Cornell University (Ithaca, New YOrk, USA). He is no friend of creationism. Here's what Wikipedia has to say about him ...
Provine is an atheist, philosopher, and critic of intelligent design. He has engaged in prominent debates with theist philosophers and scientists about the existence of God and the viability of intelligent design. He has debated the founder of the intelligent design movement Phillip E. Johnson and the two have a friendly relationship. Provine has stated that he starts his course on evolutionary biology by having his students read Johnson's book "Darwin on Trial."

Provine is a determinist in biology, but not a determinist in physics or chemistry, thus rejecting the idea of free will in humans. Provine believes that there is no evidence for God, there is no life after death, there is no absolute foundation for right and wrong, there is no ultimate meaning for life, and that humans don't have free will.
When someone likes that publishes a book with the title, The 'Random Genetic Drift' Fallacy, I pay attention.

Tuesday, August 04, 2015

Orac responds to my post on teaching the controvery

Orac didn't like part of my post On teaching alternative medicine at the University of Toronto. Here's what I said a few days ago ...
From an academic pedagogical perspective, there’s nothing wrong with a course that has a reading list emphasizing quack medicine. This is the view that people outside of the university don’t understand. They appear to want to prevent students from ever learning about, or discussing, the anti-vax movement and how to deal with it.

They are wrong.
Orac took this personally and responded in a post of his own [On teaching pseudoscientific controversies in universities…].
Those of you who read the articles and have seen talks by supporters of science-based medicine like Steve Novella and myself will recognize this for the straw man that it is. We never say anything like this, that we want to prevent students from learning about or discussing the antivaccine movement. That is an assertion that is unsupported and, quite frankly, downright risible. So you should understand that I was more than a little pissed off when I read this part of Moran’s post. We never say that we don’t want alternative medicine to be taught or antivaccine views taught. (Indeed, I really wish that pediatrics residency programs, for instance, would do a better job of teaching antivaccine views, so that they don’t catch pediatricians by surprise when parents start expressing them.) What we complain about is the uncritical teaching of these topics, the teaching, for example, of alternative medicine modalities as though they had scientific merit. This is a massive problem in medical academia. I’ve lost track of how many times I’ve reiterated this very point going back at least a decade.
We agree. I wasn't referring to people like Orac who understand how universities should work. I was referring to those people outside of the university community who really do want to ban any mention of alternative medicine at universities. I guess I didn't make that clear.

I'm pretty sure that Orac knows about this crowd. They are totally opposed to the idea of teaching the controversy. They have some very strong views on what's right and what's wrong and they firmly believe that the only views that should ever be expressed in university classes are the ones they agree with.
In the end, my little fit of pique over Prof. Moran’s condescending and dismissive attitude towards those of us who were so outraged by this course being offered by U. of T. aside, we actually (mostly agree). Moran supports “teaching the controversy” with respect to evolution and with respect to alternative medicine. So do I. Where we disagree is over what “teaching the controversy” actually entails. Can Prof. Moran can honestly say that he wouldn’t be the least bit upset if his own department were to offer an entire course on “controversies in evolution” taught by Ken Ham, Casey Luskin, and a Discovery Institute fellow to be named later? That he would approve of such a class as a great way to “teach the controversy”? If he can, I’d say there’s a problem. If he can’t say that, I congratulate him. That’s the correct reaction. In that case, I also point out that he has no business being so contemptuous of our anger over a homeopath teaching a course in alternative medicine as a way of “teaching the controversy.”
As I said in my earlier post, the problem wasn't that an anti-vaccine point of view was being discussed in a university course. The problem was that the course was being taught by someone who wasn't qualified to offer a university course that encouraged critical thinking. That situation has been rectified.

I would love to invite Casey Luskin to come and give a few lectures on Intelligent Design Creationism to my students. It would be far better for them to hear the other side directly from the horse's mouth than filtered through me.

Sunday, August 02, 2015

On teaching alternative medicine at the University of Toronto

There's been a recent kerfluffle about a course called "Alternative Health: Practive and Theory" taught as part of a program in Health Studies at the University of Toronto's Scarborough campus (Toronto, Ontario, Canada).

Most of the readings in the course emphasized non-evidence-based medicine and health. The instructor was Beth Landau-Halpern, a homeopath who warns her patients about the dangers of vaccines [see Beth Landau-Halpern]. She's also the wife of Rick Halpern, the Dean and Vice-Principle of University of Toronto, Scarborough (UTSC). Ms. Landau-Halpern will no longer be teaching and the Dean has resigned [Rick Halpern Resigns].