Carnival of Evolution No. 33 out now at Genome Engineering

The Carnival of Evolution for March is up at Genome Engineering! No posts by me (because I’m lazy/I forgot/I secretly hate evolutionary biology, but make sure you check out some great posts on breaking Dollo’s Law, the evolution of lizard colouration, an animal phylum’s possible loss of their anuses and disgusting worm sex. Then again, just check them all out! Do it!

The next Carnival of Evolution (for April) will be at… actually, there isn’t a host announced yet! Put your name down if you’d like to host, and submit your evolution-themed posts as soon as you’ve finished writing them!

You’re never too young – a high school student fighting to repeal creationism

Wow. Zack Kopplin is my hero: he is a high school student (!) rallying the troops to help repeal the Louisiana Science Education Act, which was passed in 2008. The act allows for creationist or anti-evolution teachers to bring “supplementary materials” into class that could undermine the proper teaching of evolutionary biology, effectively allowing creationism to enter the classrooms of Louisiana.

Zack and his cause recently received coverage from Michael Zimmerman at the Huffington Post:

Zack doesn’t consider himself to be brave. Rather he says he’s simply out to correct a grievous wrong that was foisted on the people of Louisiana. “When LSEA was originally passed, Louisiana Family Forum told legislators that the bill was not about creationism. The legislators trusted them, but actions in Livingston Parish have shown how the legislators were tricked.” This past summer, after the curriculum director for Livingston’s public schools claimed that LSEA allowed the district to present “critical thinking and creationism” in science classes, board members responded enthusiastically, with one asking, “Why can’t we get someone with religious beliefs to teach creationism?” and another adding, “Teachers should have the freedom to look at creationism and find a way to get it into the classroom.”

Brave or not, Zack Kopplin deserves our praise. Not many among us would be willing to take on the formidable forces in Louisiana promoting creationism. In the face of such opposition, Zack is a realist. “I believe we can pass repeal this year, but if not, I know that overturning this law will become inevitable as more and more people learn what it’s about.”

Christopher Reeve would be proud of this young man.

I’m proud of him too.

For updates on the fight you can follow Zack on his blog or the “Repealing Louisiana’s Creationism Law” Facebook page.

Evolution educators should fear teacher apathy more than creationist activism

A new study in Science has revealed some shocking statistics around the teaching of evolution in US high schools. Michael B. Berkman and Eric Plutzer analysed data from the National Survey of High School Biology and found that only 28% of US high school biology teachers present evolutionary theory properly in the classroom, along the lines of the recommendations of the National Research Council, while 13% explicitly endorse creationism or intelligent design, leaving a whopping 60% of teachers in the middle, endorsing neither evolution nor creationism.

This 60% shouldn’t be underestimated. While they don’t choose the side of creationism and actively pass on false information, they do water down the evidence for evolution and leave their students with a highly inadequate understanding of the science behind the underpinning of the field of biology. Berkman and Plutzer elaborate in the paper on the methods of these apathetic teachers:

Some teach evolutionary biology as though it only applies to molecular biology—completely ignoring macro-evolution of species. … Others defend the teaching of evolution as a necessary evil, using state examination requirements as a convenient means to disassociate themselves from the very material they are expected to teach. … [M]any teachers told us that they tell students that it does not matter if they really “believe” in evolution, so long as they know it for the test. … Finally, a sizable number of teachers expose their students to all positions—scientific or not. Students should make up their own minds, explained a Pennsylvania teacher, “based on their own beliefs and research. Not on what a textbook or on what a teacher says.” … This approach tells students that well-established concepts like common ancestry can be debated in the same way we debate personal opinions.

(Citations removed)

Basically, a majority of teachers aren’t doing their job properly and are failing to lay down a solid, accurate foundation of knowledge in evolutionary biology. Berkman and Plutzer go on to lay out the real damage these teacher are doing:

The cautious 60% may play a far more important role in hindering scientific literacy in the United States than the smaller number of explicit creationists. The strategies of emphasizing microevolution, justifying the curriculum on the basis of state-wide tests, or “teaching the controversy” all undermine the legitimacy of findings that are well established by the combination of peer review and replication. These teachers fail to explain the nature of scientific inquiry, undermine the authority of established experts, and legitimize creationist arguments, even if unintentionally.

(Citations removed, emphasis added)

I agree. What is happening is that students are leaving school without the tools they need to appreciate science and to distinguish what is accepted by the vast majority of expert biologists and what is not. Without these tools they are easy targets for creationist and intelligent design activism outside of the classroom, in later life – anti-evolution activists must be rubbing their hands with glee, to be given an audience this ignorant of basic evolutionary biology!

This study is all the more reason to support the work of organisations such as the National Center for Science Education (NCSE) who are constantly combatting evolution apathy in the 60% and fighting the creationist activism in the 13%.

I wonder what the statistics would look like from a survey of Australian high schools? I suspect it might be better (a lower creationist percentage), but still fairly sobering.

Carnival of Evolution No. 31 out now at The Dispersal of Darwin

The Carnival of Evolution for January is up at The Dispersal of Darwin! I’ve got two posts in there this month, but you’ve probably read those already – check out some brilliant pieces on the Denisovan genome, the motivation of Charles Darwin, a critical review of Benjamin Wiker’s anti-Darwin book “The Darwin Myth” and a 5 year-old understanding evolution instead. Then again, just check them all out!

The next Carnival of Evolution will be at Denim and Tweed on the 1st of February, and make sure to submit your own evolution-themed blog posts.

“Evolution and its rivals” – free Synthese papers!

Most people don’t have journal access, so it’s always wonderful when academic papers are made available for free online – it’s even better when the papers are related to ID and evolution! The latest edition of Synthese, a philosophy journal, has a theme, and that theme is “Evolution and its rivals” (in other words: “Intelligent design and why it’s wrong – philosophers of science give their perspective”). The edition’s ten papers are free to download until the 31st of December, but don’t be lazy and miss out!

Highlights?

Hat-tip to John S. Wilkins himself.

Carnival of Evolution No. 30 out at This Scientific Life

Another Carnival of Evolution is out, this time at This Scientific Life, one of the blogs of Bob O’Hara (the CoE author) and Grrlscientist (not the CoE author). I actually got a post into this edition, having remembered to send one as soon as the last one was posted – but don’t worry about my submission, go read the submissions of others, that’s what’s important!

The next CoE is at The Dispersal of Darwin, on the 1st of January. You can submit posts here.

The Prominent People Project, Eugenie Scott and the process of evolution

Martin Pribble, on his blog Martin S Pribble (which used to be called Atheist Climber), has been conducting series of written interviews with “people who are prominent in the worlds of atheism, science, skepticism and rational thought”, collectively entitled the Prominent People Project. His latest interview is with Eugenie Scott, the director of the US’s National Center for Science Education and tireless campaigner for creationism-less science education in public schools.

While Martin was preparing for the interview he asked if anyone wanted to submit questions to Eugenie – and it just so happened I had something I wanted to ask her, related to some recent tangential comments made by a few bloggers at the Discovery Institute over the issue of some biologists questioning the Neo-Darwinian model of evolutionary progress.

Here’s my question and her response, from Martin’s interview:

MSP: [The following question comes from fellow blogger and online friend Jack Scanlan, author of the Homologous Legs blog] Jack says: The Discovery Institute has recently taken to quoting scientists who are critical of the Neo-Darwinian model (also known as the modern synthesis) of evolutionary change out of context, implying that the problems they identify with the model can be extrapolated to the entire theory, while in reality they are simply promoting what has been called the “postmodern synthesis”, a newer model of evolution that has a larger role for neutral and non-adaptive mechanisms, and places less emphasis on natural selection as the dominant evolutionary force.

Some ID proponents at the Discovery Institute have claimed the NCSE supports Neo-Darwinism, using the growing anti-Darwinian/pro-postmodern trend in academic circles to cast you in a dogmatic light, seemingly holding onto a failed theory as it crumbles around you. Does the NCSE support Neo-Darwinism, or is it neutral with respect to the broad model of evolution that is supported at any one time?

ECS: This is why I encourage people to understand evolution as a three-part idea. The big idea is common ancestry, which we study by examining the patterns of evolution (how the tree of life branches) and the processes of evolution (the mechanisms that affect it). Neo-Darwinism and the new-new-synthesis are both in the process category and it is a category mistake to, as do the creationists, confuse that if scientists argue about the process, then the big idea of common ancestry is called into question. Personally, I think it’s obvious that evolutionary biology like any other science is going to modify its explanations over time. We’re not in the 1950s and ‘60s, and we know more about how biology works. The post-modern synthesis folks it seems to me are just expanding the ideas of Mayr, Dobzhansky, et al with new insights, mostly from molecular biology. In academia there tends to be a somewhat unfortunate tendency to present every new interpretation as a big breakthrough, but the “old guys” of the neo-Darwinian synthesis were more pluralistic than they are held to be by some of the neo-neos! And you can probably guess that I don’t have a dog in that fight.

While she didn’t answer my question directly, she made it clear that the NCSE has a far better understanding of the true nature of evolutionary theory than the Discovery Institute, which continues to equate the various processes of evolution with the overall theory itself. The post-modern synthesis is just an expansion of Neo-Darwinism and doesn’t conflict with what we already knew, except that it stops scientists from making claims like “Natural selection is the only important evolutionary force for producing complexity”.

Also, Eugenie shied away from using the term “post-modern synthesis”, and I don’t blame her – it’s an ugly term that I shouldn’t have used, one that draws parallels with various anti-scientific movements in philosophy and popular culture. Her alternatives, “Neo-Neo-Darwinism” and “the new-new-synthesis”, aren’t bad, but they don’t really roll off the tongue very easily. So, I’ve constructed a list of a few of my own hip and trendy candidates:

  • The Ultramodern Synthesis
  • The Trés-Modern Synthesis
  • Chic-Darwinism
  • The Fast and the Furious: Genetic Drift
  • Selection v. Drift, feat: MC Genome and Kid Phylogeny

They’re not going to stick, are they? Damn.

Carnival of Evolution No. 28 is out – Genomic viruses to eusociality

The Carnival of Evolution is a monthly blog carnival about, well, evolutionary biology, and its 28th incarnation is out at the Carnival of Evolution blog (blog carnivals are usually hosted on a different blog every week, but for some reason the CoE’s home blog was chosen this time around – not that it really matters anyway, it’s all about the content).

It has a feature on Sandwalk, which you should probably follow if you like blogs about evolution and religion written by biochemistry professors, but the real meat of the post is, of course, from the 19 blogs that contributed content. Topics discussed range from fossil viruses in songbird genomes to the evolution of eusociality, so make sure you check out all of them. It’s evolution overload! But that’s never a bad thing!

What do you mean it’s not a valid statistical test!?

Yesterday I briefly mentioned (in the “Rapid fire ID news” segment) a post by “niwrad” on Uncommon Descent about the apparent dissimilarities between the human and chimpanzee genomes. I was wary about commenting on it, since I have little statistical training and didn’t want to make a fool of myself more than I usually do, but a post by Joe Fenselstein over on The Panda’s Thumb about the analysis “niwrad” conducted has given me the confidence (read: basic understanding) to address its very fundamental flaw.

There’s no point going into detail about the various different types of statistical tests you can perform on genomes to determine sequence similarity – I don’t know enough about them and a majority of you probably don’t want to read about advanced statistics. But the problem with what “niwrad” did is very straightforward and can illustrated simply with an example.

In the well-known paper Initial sequence of the chimpanzee genome and comparison with the human genome, by The Chimpanzee Sequencing and Analysis Consortium (Vol. 437/1 September 2005/doi:10.1038/nature04072), the researchers found that

Single-nucleotide substitutions occur at a mean rate of 1.23% between copies of the human and chimpanzee genome

meaning that for the parts of the chimpanzee and human genomes that are directly comparable, the differences between them are, on average, 1.23% (adding in insertions and deletions raises the differences to about 4%). The chimpanzee genome and the human genome are approximately 99% identical for large-scale conserved sequences.

The analysis performed by “niwrad”, however, finds something different:

On average the overall 30BPM similarity, when all chromosomes are taken into consideration, is approximately 62%.

Whaaaat? 62% similarity? 38% difference? How can this be? Something must be wrong here.

Indeed, something is wrong, and it’s all to do with the “30BPM” technique that “niwrad” uses. Instead of randomly picking single nucleotides from one genome and seeing how often they don’t match the nucleotide in the same position on the other genome, “niwrad” used 1000 30-nucleotide-long sequences to compare between both genomes. Why is this a problem?

Consider two sequences of 100 playing cards each, Deck A and Deck B. They are almost identical, except that B has 10 single card differences from what is found on A. Now, if you did a test and chose a number of single cards to compare between the two decks, on average you would find the difference between A and B to be 10%, the true difference (A and B share 90 cards out of 100), because 10% of the single card samples would not match their cousin sample on the other deck.

However, if you increased the size of the samples used from single cards to 10 cards, then the reported difference between the decks A and B would increase to higher than 10%. This is because you’re now measuring whether or not larger sequences match, and if a single mismatched cards happens to be in that sequence then it is deemed different even though only one of the cards was different – the other 9 cards were identical between the decks.

This effect becomes even more pronounced as the sample sequences increase in size – in fact, if you chose a sample sequence length of 100 cards then the test would conclude that the decks A and B are 100% different! Using sample lengths larger than one clearly produces artificially high results on the differences between two sequences.

This was the problem with “niwrad”‘s analysis. Instead of single nucleotide sample sequences, 30-nucleotide-long sequences were used, which produced a higher calculated difference between the human and chimpanzee genomes than the real difference – 38% as opposed to the real value of 1.23%.

Intelligent design proponents and creationists can’t get enough of attempts to discredit the idea of common descent, even thought none of them have ever been successful. While I don’t know if “niwrad” botched the test on purpose, it’s still shoddy statistics backing up the rejection of a well-established fact in mammalian genomics.

Eugenie Scott’s tips for writing about evolutionary biology

The NCSE‘s Eugenie Scott is one of my personal scientific heroes: she’s been fighting in all the tough battles over evolution education in high schools in the US in recent years. It’s a bit of an understatement then to say that she’s knows what she’s talking about when it comes to science communication, so any advice from Eugenie in that area should be listened to and implemented as soon as possible.

This video of a talk by Eugenie Scott was recently posted by the NCSE, and it’s a valuable resource for anyone wanting to start writing about evolutionary biology in any popular context: blogging, newspapers, etc. Give it a listen, it’ll be worth your time if you’re unsure about how to go about communicating this popularly misunderstood scientific field.

(h/t to A Natural Evolution)