A Free Man

I’m quite pleased to host this month’s Mendel’s Garden - a blog carnival featuring the best genetics writing on the internets for the last month. Since it’s my party, I’ve picked out a few of my favorite topics to feature. But in the way of introduction for the neophytes in the crowd, let’s define our terms. The first question I ask my students on their first exam is “What is a gene and how is it regulated?”. I’m looking for them to talk about Mendel’s description of units of inheritance and the modern DNA based definition. Well, RPM of Evolgen thinks that it’s time to expand our definition or throw the word out entirely. He makes a solid argument, based on the fact that a lot of things that are transcribed in the genome wouldn’t be considered ‘genes’ by most of us. But if we trash the word, what would geneticists call themselves?

For a perfect example of the beautiful complexity of genetics illustrated, check out this father-son photo from Not Afraid To Use It. About says it all. Without further ado, a few of my favorite things genetical:

I found a couple of great posts about the genetics of autism. Now, to clarify, I’m not a big fan of autism per se, but I got embroiled (in a minor way) in the controversy with this post on the autism-MMR vaccine sham. Since then, I’ve followed the new research on autism with some interest. A post over at Highlight Health describes two genome-wide genetic analyses that identified five genetic loci that contribute to autism susceptibility, lending more support to the argument that autism is largely a heritable disorder. Kristina Chew, of AutismVox, thinks that geneticists sometimes go a bit far, however. Her response to a “sweeping” new theory that an evolutionary tug-of-war between parental genetic contributions is astutely skeptical. And of course, As is the case with any genetic disorder, there is an environmental component to consider. Reviewing an odd study out of Cornell, the Great Beyond details an assertion that autism rates are higher in rainy parts of the world. Take of it what you will, folks.

I’ve become increasingly fascinated with human evolution and in the genomic era research into our roots is just burgeoning. This month, Daniel McArthur at Genetic Future writes about one of the new tools available to evolutionary geneticists and gives an example of its use to look at positive selection at certain human genetic loci. One of the more interesting stories from this field is of the pair of skeletons found in a mass grave in Germany locked in an intimate embrace. The Great Beyond describes the DNA analysis that revealed that the 4600 year old remains were of a parent and child  and appear, with fractured skulls and an arrowhead in the spine, to have been unfortunate victims of humanity’s penchant for genocide. Of course, none of this may matter according to UCL’s Steve Jones (as reported on Dick Dawkins dot net) who says that human evolution is done due to a dearth of older fathers. Jones argues that genetic variation comes, in part, from mutations that men accumulateas they get older. Don’t worry, Steve, I think there are plenty of toxins about to keep us mutating.

Speaking of junk science,  there was some new junk on junk DNA released as a press release from the Genome Institute of Singapore. As Bayblab points out, this is a new and disturbing way of publishing your results - skip all the hassle of peer review and editing and just throw it out there to the mainstream press. Shame really, because this is my third topic of choice - epigenetics. Yann Klimentidis, on his blog, recounts some recent research looking at epigenetic changes in utero brought on by environmental stress. Zamp Bionews has more about epigenetic control of offspring fertility, which in this case is regulated by small RNAs apparently passed on maternally. Alex at The Daily Transcript has RNA, if not epigenetic, regulation in his post describing how each RNA binding protein in yeast tends to associate with mRNAs of a particular type. He hypothesizes that the expression of entire classes of genes may be subject to coordinated regulation at the level of mRNA metabolism.

And finally this month, a technical brief for those of you doing the hard work of science rather than just writing about it.  Sandra, who blogs at Discovering Biology in a Digital World, tells us about a new BLAST feature that allows users to create a custom database. Sandra goes through a step-by-step tut and generates a viral phylogeny. For those Ph.D. students out there in the “Nothing Works Doldrums”, Nick at Bite Size Bio has some reassuring words for you - sometimes things just don’t work. That’s biology.

Next month’s Mendel’s Garden will be hosted by Another Blasted Weblog. If you’re interested in submitting, you can do so here.

 

 R.E.M. - "Gardening At Night (Alternative Radio Sampler Version) [4:48m]: Play Now | Play in Popup | Download

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About midway through Yann Martell’s Man Booker Prize winning novel “The Life of Pi”, the protagonist finds himself washed up on an island populated solely by meerkats. After a time on the island he begins to suspect that all is not as it seems - the meerkats take to the trees every night and one day Pi takes a bite of a fruit growing from one of the island’s trees and finds human teeth inside. It begins to dawn on him that the island is carnivorous, each night digesting anything that has the misfortune to remain on the ground.

For some reason, Pi’s carnivorous island was the first thing that popped into my head when I heard a news story on the NewsHours with Jim Lehrer podcast recently about what was described as our rapidly growing eight continent. There are no meerkats and it is not strictly carnivorous and it’s not really an island, but the Great Pacific Garbage Dump is as disturbing and potentially dangerous as Martell’s fantasy island.

My initial reaction to the NewsHour report is that it was a typical case of what tends to be a melodramatic and lacking in understanding response of the mainstream news media to a juicy science story. Surely there isn’t a continent of garbage out in the Pacific Ocean. The good news is that the media has overreacted, “continent” is not the right word. The Great Pacific Garbage Dump is not visible from the air (because most of it lies slightly below the surface of the water) nor does it have a particular nautical position (due to the shifting wind directions and currents). The bad news is that there are two massive accumulations of plastic waste swirling around in the doldrums of the northern Pacific Ocean. Charles Moore, the founder of the Algalita Marine Research Foundation and the man who had the misfortune of discovering the dump, estimates that the plastic garbage in the Pacific covers approximately five million square miles (about 1.5 times the land mass of the United States) and contains over 3.5 million tons of largely consumer waste.

By most accounts the trash finds its way to its home in the North Pacific through a long and circuitous route. Trash is dumped into rivers, in both North and South America and Asia, that empty into the Pacific. Ocean currents carry the trash, picking up more debris as it travels, around the Pacific before depositing it in the doldrums of the North Pacific Gyre. 80% of the trash in the ocean originates on land and a majority of that is from consumer products. Thus, it is a hard truth that we - you and I - are the problem. Here is how it works: say that you inadvertantly drop some innocuous bit of plastic - a clear plastic wrapper from a box of candy. The next time it rains, that wrapper gets washed into a storm drain which will flow into your nearest watershed and ultimately into the ocean. That little wrapper floats its way around the Pacific currents until it comes to rest in the Gyre where it will join the rest of the trash. This plastic waste will be around longer than you and I, longer than our children, longer than our grandchildren, longer than our great-grandchildren. Nobody really knows how long it takes for plastic to biodegrade because it basically doesn’t. Conservative estimates are around 450 - 500 years. We are creating a problem that will outlive us by centuries.

It isn’t just an aesthetic problem. In short, it’s devastating to marine ecosystems. Forty percent of albatross chicks are killed each year by consuming plastic accidentally fed to them by their parents. More than a million birds and marine animals die each year from consuming or becoming caught in plastic and other debris. But there is a less obvious and more frightening consequence to our trashing of the oceans. Moore’s group does a lot of research into the ecological effects of plastic debris on marine ecosystems. Recently they have been looking at plastic particulate levels in and around the Garbage Patch. The small bits of plastic that are a byproduct of the slow degradation of the plastic debris have been found to accumulate a lot of nasty chemicals - polycyclic aromatic hydrocarbons, chlorinated and legacy pesticides and hormonally active additives. This latter class are particularly nasty beasties, some of which have been implicated in an increased risk of breast cancer. Moore and his colleagues found that the ratio of plastic particles to plankton in the Gyre was between 1.4:1 and 6.9:1. In other words, there is more plastic particulate matter in this part of the ocean than there is plankton. You don’t have to be a biologist or have an in depth knowledge of food chains to recognize what this means: small fish eat plankton (or plastic particles), big fish eat small fish, humans eat big fish. We are eating our own toxic garbage.

I don’t wish to sound melodramatic or preachy but this is a problem that is getting worse on a daily basis and one that we cannot repair. We can, however, do something to slow the accumulation of rubbish in the oceans. 80% of the trash out there comes from us directly, so it is up to us to do something to make it better.

Here are ten things we can do about it:

1. Don’t use so much plastic. Make a concerted effort to reduce the amount of plastic that you purchase. It’s not easy. I’ve been making a concerted effort since I heard this story and it’s absolutely stunning how much excess plastic you get when you purchase anything. Note how much plastic crap you come home with on your next trip to the supermarket. Preferentially purchase items packaged in glass or paper. Virtually any material is better than plastic.
2. I’m a beach bum. Roughly 10% of the crap out in the Pacific comes from trash left on beaches. So, don’t leave trash on beaches and maybe pick some of it up when you’re out there. Boy Z, Timmins and I are headed out to the beach shortly and I’m bringing a bag with me to pick up.
3. Recycle. Plastic recycling is very low efficiency - only about 3.5% of plastic is recycled in any way. This is due in part to contamination of plastics with non-plastics, food waste and non-recyclable plastics. Clean up your plastic before recycling and make sure that you only include recyclable plastics. If your community does not recycle plastic then demand that they do.
4. Along the same lines, buy recycled products or products containing recycled materials.
5. This is kind of a no-brainer. But do not litter. Most of the Great Pacific Garbage Patch is thought to be a result of litter working its way into the river system.
6. Consider volunteering or donating to the Algalita Marine Research Foundation or other environmental organizations.
7. Think about the watershed when cleaning up around your hose. Sweep your sidewalks rather than hosing them. Wash your car on the grass so that the water sinks into the ground rather than storm drains.
8. When you go shopping do not take a plastic bag. Use a cloth or other reusable bag.
9. Buy in bulk. Most of the plastic that you bring home with you from the shop is packaging, the higher the product to packaging ratio, the less trash generated.
10. For god’s sake, don’t use so much plastic.

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Image credits:

Plastic trash

North Pacific Gyre Map

Food chain

I was leaning towards Radiohead’s “Fake Plastic Trees” for this post, as it seemed appropriately gloomy. But, The Kinks have been in my head lately, possibly because they are apparently reuniting.

 

 The Kinks - "Plastic Man" [3:06m]: Play Now | Play in Popup | Download

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• The latest edition of Tangled Bank, another science blogging carnival, is up at Submitted to a Candid World. Science with a political
• Nichole alerted me to a contest at Grosgrain in which you can win a water color portrait of your progeny. Bad luck for Nichole as I am totally going to win.

Popularity: 50% [?]

I’ve literally got students coming out the wazoo today, so I’ll keep things short and simple…

After ranting about premature Christmas decorations and my general disdain for the holiday, I’ve been tasked with coming up with a personalized message for my company’s Christmas cards. This is, by far, the most difficult three or four sentences I’ve ever had to churn out. Any suggestions?

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I’m pleased to be the host for Mendel’s Garden #26. Mendel’s Garden, the genetics blog carnival, is looking for the best genetics posts in the blogosphere. I’m hosting the December edition and am actively looking for submissions. Everything from transcription to evolution to genetic counseling and social implications of genetics research are welcome. I’m particularly interested in non-specialists, so if you’ve got something that you could tag with “genetics” send it my way. If you’d be interested in having a post featured, please e-mail me your latest and greatest to chris (at) afreeman (dot) org.

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Finally, when things have gotten harried this week, I’ve turned to this video for a dose of serenity. The internets are awash with cute kid videos, but I have the cutest kid (and possibly the most patient dog) around.

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Image Credit

I’d never heard of The Bouncing Souls until this track came my way, but I can’t stop listening to it. They’ve been around for ages and I’m thinking of checking out more of the New Jersey quartet’s music. Buy the self-titled record that featured “Serenity” and other records here.

 

 Podcast Video: Play Now | Play in Popup | Download

 

 The Bouncing Souls - "Serenity" [2:28m]: Play Now | Play in Popup | Download

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Getting in the middle of a scientific controversy is more dangerous than you might think. I have fond memories of a conference at which, under the influence of the product of yeast anaerobic sugar metabolim, I watched two well known professors very nearly come to blows over a question regarding the role of chromatin in gene expression. When you throw in a group of pseudo-scientific know nothings, that debate becomes both fiercer and more absurd. Such is the “controversy” around macroevolution - evolution at the species level - it regrettably melds science, religion and politics in a sort of perfect storm of dispute.

Catherine Boisvert knows a little bit about this particular scientific controversy. The Canadian graduate student (studying at Uppsala in Sweden) found herself in the midst of an ridiculous debate when some creationists took, completely out of context, a couple of quotes that she gave in an interview with The Scientist and loudly and ignorantly claimed that they supported their position.

In reality, Boisvert’s recent Nature paper offers irrefutable evidence supporting macroevolution. Boisvert and her colleagues at Uppsala used fossilized remains of Panderichthys, a prehistoric fish, to shed light on an age old evolutionary question: whether digits (fingers and toes) are an evolutionary novelty to tetrapods (four limbed critters like us) or were present in some form in the last common ancestor of tetrapods and our fishy kin.

Recently, Boisvert was kind enough to take a seat on A Free Man’s virtual couch for a chat about evolution, fish and creationism. In a nod to my audience’s diversity, I’ve tried to start the interview out with more general topics and to move into the hard science as we move on.

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AFM: My readers run the gamut from working scientists to lay persons. Can you clearly and concisely explain to the latter class why they should pay attention to your research?

CB: Anybody interested in their origins and how they evolved would be interested in knowing where their fingers come from. The origin of finger precursors in fish is fascinating given the fact that it allowed fish to transform into land animals and later exploit all ecological niches, from land, trees, air and even returning to the seas! The success of land vertebrates is closely tied to the evolution of limbs and fingers and I certainly would not be able to type this, or play violin for that matter, without them!

AFM: I’m interested in Panderichthys as a species. Where would it have fit in the food chain of the late middle Devonian? What kind of species roamed the sea with Panderichthys? What did it eat? What ate it? Paint a picture of Panderichthys’ neighbourhood.

CB: Panderichthys was a medium to large predator (1 - 1.5 m in length) living in shallow waters in deltaic systems (so probably a mix of salt and fresh water). It ate other fish, so you could say it was at the top of the food chain and I doubt that it had many, if any predators. At the time, the seas (in terms of vertebrate life) were dominated by lobe-finned fish such as Eusthenopteron and Panderichthys, placoderms (armoured jawed fish) as well as acanthodians. Sharks were beginning their radiation and so were ray-finned fish, which were still relatively rare and very small in the Devonian. There were of course an abundance of invertebrates at the time and insects were beginning their foray onto land, only preceded by plants.

AFM: It’s been proposed that the driving pressure to diversify limbs came from demands of feeding and locomotion in the Ordovician and Silurian seas (Shubin, et al. 1997). Do you agree with this assessment? What were the challenges faced by paleozoic fish?

CB: It is obvious that feeding and locomotion are main drivers of evolution since they are so closely related to survival. What Shubin and co-authors refer to in their 1997 article pertains to the diversity of fin forms observed in vertebrates in the Ordovician and Silurian seas and how much “experimentation” there was. As agnathans (jawless vertebrates) are being outcompeted by gnathostomes (jawed vertebrates) in the Silurian, the body plan of vertebrates stabilizes at two sets of paired fins (pectoral and pelvic) (the body plans of gnathostomes). The challenges of moving to feed and of moving to avoid predators are no different in gnathostomes than they were in agnathans and are therefore some of the challenges faced by Paleozoic fish.

AFM: Your paper has pretty much put the nail in the coffin of the hypothesis that gained some credence in the 1990’s that fingers and toes are an evolutionary novelty. What was that hypothesis based on? And for those who haven’t read your paper, can you briefly outline how your finding rejects that hypothesis.

CB: The hypothesis was based on the comparison of developmental data from Zebrafish and mice. Zebrafish lack the second phase of expression of the gene Hoxd13 which is responsible for the formation of digits in mice. This led Denis Duboule’s team to hypothesize that digits were novelty in tetrapods (four footed vertebrates like amphibians, reptiles, birds and mammals). This was supported at the time by the fact that the pectoral fins of the fossil fish Panderichthys, then the closest fish to tetrapods, had been described as being composed of large plates at the end of the fin. This pointed to the fact that this fossil did not have any elements that could be identified as precursors of fingers. Our new analysis of Panderichthys performed by CT-scan showed that this was an artefact of preparation. Panderichthys has small elements at the end of its pectoral fins that we interpret as fingers precursors.

AFM: Macroevolution isn’t my strong suit and as a geneticist I’m often swayed by developmental genetic data. Is there any molecular work that has been done that supports your hypothesis?

CB: Indeed, there is. It is in combination with new fossil data (from Tiktaalik and Gogonasus for example) as well as developmental genetic data from skarks, the basal actinopterygian (ray finned fish such as zebrafish and salmon), Polyodon (paddlefish, a close relative of the sturgeon) and the sarcopterygian (lobe finned fish who gave rise to all amphibians, reptiles, birds and mammals) Neoceratodus (the Australian lungfish) that we are able to confidently homologize the distal radials to fingers. Several studies have been conducted in the past few years about the expression of Hoxd13 in those species and, in all of them, a second, late phase of expression is present. Zebrafish, being a derived ray finned fish, has a very reduced fin. It lacks the metapterygium, from which the entire fin of lobe finned fish is derived. It is therefore understandable that by loosing this part of the fin, genetic expression associated with it would be lost as well. Sharks and paddlefish have a more primitive fin retaining all parts and therefore show Hoxd13 expression in their fins where the metapterygium develops. In the Australian lungfish as well as all tetrapods, only the metapterygium is retained and the late phase of Hoxd13 is expressed where distal radials, or in the case of tetrapods, fingers, develop.

AFM: As you’re no doubt aware, creationism in the mantle of “Intelligent Design” is creeping back into schools in the U.S., Britain and many other parts of the world. What could a secondary school teacher take from your research into their classroom to serve as a counterpoint to the pseudo-science of ID?

CB: Our work shows how similar the fins of Panderichthys are to that of Tiktaalik, Eusthenopteron and the arms of Acanthostega while being slightly different. These similarities and how they differ can only be explained by shared ancestry and evolution. Paleontologists have hypothesised a long time ago that Panderichthys was more closely related to tetrapods than Eusthenopteron was and by examining the fossil and finding that its fins are intermediate in morphology between Eusthenopteron and Acanthostega for example, it proves the predictive nature of evolution.

AFM: The creationist Discovery Institute has pounced on some of the statements in your paper regarding sample quality as evidence that scientists are trying to backpedal on previous hypotheses regarding digit development and evolution. Can you clarify your statements regarding sample quality of Tiktaalik and Panderichthys?

CB: As you know, the “Discovery” Institute tactic is not to go to the primary literature in order to understand it but rather to use quotations from secondary, even tertiary sources, reorganise or use them out of context opportunistically to their own convenience. In this case, they used an article where the journalists unfortunately misunderstood me. Tiktaalik’s material is in fact exquisite, it is very well preserved, basically uncrushed and can be prepared out to be examined in three dimensions. I never said the quality was poor. I have simply explained that the morphology of the fin of Panderichthys is more tetrapod-like than that of Tiktaalik, which has nothing to do with the quality of the material.

AFM: Specifically regarding the sample quality of Panderichthys, how does CT scanning permit the type of analysis that you presented in the Nature paper?

CB: The material of Panderichthys is of high quality but it is material that is extremely difficult to prepare and manipulate because it is so fragile and preserved in clay. Previous analyses of the fin was based on prepared material but when I visited the institution in Moscow where the specimens were housed, I noticed that it was incompletely prepared, producing the results published in the 1990’s. It is almost impossible to prepare this material without destroying the underlying fin endoskeleton and I do not think many palaeontologists would have dared preparing this precious specimen. Our analysis was based on the CT-scanning of another specimen, housed in Estonia. This technique permitted us to visualise the endoskeleton, the scale covering as well as the shoulder girdle without destroying anything. We then produced three-dimensional models that can be rotated and manipulated to understand the morphology.

AFM: What’s next for you? I see that you’ve joined us Down Under. What have you got going on in Australia?

CB: I was indeed in Australia when you joined me. I was continuing developmental studies on the Australian lungfish, provided by Jean Joss’ laboratory at Macquarie University. I am interested in understanding how the pelvic girdle transformed during the fish tetrapod transition and, in addition to my fossil work, I am studying the development of that structure in the Australian lungfish and salamanders. I will be finishing my PhD soon, here in Sweden and will return to Australia for a post-doc in developmental genetics.

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Man, they don’t mess around in Uppsala. Catherine has two first author Nature papers to her name and is still working toward her Ph.D.! Thanks to Catherine for taking a time out from a clearly strenuous Ph.D. project to talk about her work today.

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Image Credits:

One Small Step

Devonian sea

Fins to fingers

Catherine Boisvert

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Radiohead helped to break the Big 4’s iron grip on musical sales last year by making their new album, “In Rainbows” on the net as a “pay what you will” release. It was a risky experiment, but one that worked out well, netting the band about $9 million (USD). This figures dwarfs the sales of their previous studio records and hopefully will encourage more artists to cut out the middle man. “In Rainbows” is the band’s best record since “Kid A” and if you like this track, support blogger-friendly artists by buying the whole record.

 

 Radiohead - "Weird Fishes - Arpeggi": Play Now | Play in Popup | Download

Popularity: 71% [?]

“Where does a lot of that earmark money end up anyway? […] You’ve heard about some of these pet projects they really don’t make a whole lot of sense and sometimes these dollars go to projects that have little or nothing to do with the public good. Things like fruit fly research in Paris, France. I kid you not“

-Sarah Palin, October 24

Damn it. I had placed a voluntary moratorium  on political posts here at A Free Man. My vote is in. My guy is well ahead. I was happy to get on with my life here on the other side of the world and ignore the nonsense of the last few weeks of this campaign. But this is just ridiculous. Sarah Palin is probably not going to be the Vice President. But she is a dangerous idiot. And in the Republican party, dangerous idiots are a little like bad pennies.

Here’s the background on what’s inspired this particular rant. Basically, Palin was talking about funding for autism research and in her inimitable sarcastic/moronic style dismissed both basic and collaborative research in a single breath of hot air.

Governor Palin, basic research drives innovation in the life sciences. Most of the advances in medicine over the last century have been initiated in labs that were working on what seems, to an outsider (or a dangerous idiot), as pointless research. Because of the ethics that scientists live by, most genetic research has to be undertaken in model organisms. These are critters like yeast, roundworms, mice and fruit flies. These are organisms that are amenable to genetic manipulation. Because we understand their evolutionary relationship (I know, evolution, scary and evil) to man we can make assumptions, for example, about what’s happening in your brain based on things that happen in a mouse’s brain. Probably not much of a leap there.

As for the France bit, scientists - unlike politicians - work best in a collaborative manner. Most major advances are done by groups of scientists from different universities who work toward the common goal of gaining knowledge about a particular topic. Sometimes, those collaborations cross national borders. Now, I know you were trying to drum up the hatred of France that worked so well for the Republicans back in the ‘02 midterms, but come on. If I can speak personally, it would have taken me another couple of years to finish my Ph.D. without a collaboration with a group that was working on a similar problem in Germany. I’m not particularly fond of Germans, but I put that personal prejudice aside and just got on with it - for mutual benefit.  This is how science works. Maybe, Governor Palin, you could try a similar approach to governing.

Governor Palin, just because you don’t understand it doesn’t mean it is not for the “public good”. Don’t you have some Russians to look out for up in Alaska?

With apologies to Dr. Seuss and Art Buchwald:

Sarah L. Palin will you please go now!
The time has come.
The time has come.
The time is now.
Just go.
Go.
Go!
I don’t care how.
You can go by foot.
You can go by cow.
Sarah L. Palin will you please go now!
You can go on skates.
You can go on skis.
You can go in a hat.
But
Please go. Now.

UPDATE

Check out NATUI’s “My fruit flies are smarter than Palin” shirts. The t-shirt every Drosophila geneticist needs.

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I’m all about the Treepeople covers this week, but this Carly Simon cover just seemed perfect. Treepeople were an Idaho band that used to tear up the Seattle clubs back during my time there. They were led by Doug Martsch, who subsequently went on to form the outstanding Built To Spill. If you like what you hear you can buy Treepeople’s records from C/Z Records.

 

 Treepeople - "Flies In My Coffee" [3:05m]: Play Now | Play in Popup | Download

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I’m running out of energy for political posts this election cycle and am on the verge of putting a moratorium on politics on A Free Man. But, I’ve had this one in the queue for some time and wanted to throw it out there before the ban. Today, I want to talk about science and politics. That’s right, boys and girls, a two-fer. Chris from Formerly Fun* sent me a link to the Scientists and Engineers for America’s comparison of the two major presidential candidates statements on issues of science, health care and technology. Inspired, I went through a number of interviews focusing on science and engineering that have been published with both candidates and picked out a few issues on which the candidates differ.

One of the things I found most remarkable was the similarities in the two candidates’ platforms when it comes to science and engineering. When it comes to important issues like embryonic stem cell research, climate change, scientific integrity and even alternative energy, there are little or no differences between the two candidates’ statements. There are little differences in numbers and approaches on things like offshore drilling, reduction of emissions and nuclear power, but these have been well covered by the media.

It’s important to keep in mind that what follows is what the candidates say in interviews to science publications. Now, it should be noted for those of you who were born yesterday that what a politician says and what a politician does are often entirely different things. It’s worth looking back in the past to see how each candidate has actually voted.

But let’s look at a few important differences on issues that aren’t being covered by the media. I’ve found three major science issues in which McCain and Obama have expressed notable disagreements. I’ve tried to be objective, but in the interest of full disclosure,  I am an Obama supporter.

Basic Research

This is the type of science that often gets picked up on by politicians as wasteful of the government’s money. You’ve seen the headlines, millions of dollars spent to study grizzly bear DNA in Montana. The thing is, basic research drives most innovation in science and engineering. In general, drug companies don’t come up with the major breakthroughs in drug discovery, researchers in universities and publically funded institutes looking at things that seem trivial to the public at large make these discoveries. Drug companies fine tune them. The scientists that you’ve heard of - Einstein, Darwin, Mendel, Pasteur, Curie, Watson, and so on - we’re doing research that would have seemed as laughable to the layperson as studying the reproductive habits of blue crabs . Take home message, basic research is absolutely essential to scientific progress.

Obama has stated that federally funded basic research is one of his highest priorities in the science and engineering arena. He has pledged to double the basic research budget for engineering, mathematics and physical and life sciences over the next 10 years. McCain also has promised to fight for increases in funding for some scientific agencies. Crucially, however, he has promised a freeze in discretionary spending (which includes federal money for research) for one year.

Sex Education

OK, it’s becoming clear as I write this that I will not be able to be completely objective. For the last eight years, the Bush Administration has funded only abstinence-only sex education in the public schools. This has not worked. In 2006, the teenage pregnancy rate in the USA (already the highest in the industrialized world) rose for the first time in 14 years. Rates of syphilis and gonorrhea have risen steadily since 2000. McCain supports continuing this failed policy. Obama supports comprehensive sex education. This would include abstinence programs, but also would ensure that all taxpayer-funded federal programs are medically accurate and include information about contraception.

Evolution vs Creationism

Now, this is one of my biggest science and education issues. Both candidates are committed Christians and both candidates believe firmly in evolution. When asked if intelligent design (creationism) should be taught in the schools, McCain said in an interview with the Arizona Star that “all points of view” should be presented and “to say that we can only choose one line of thinking or one belief on how people and the world was created…there is nothing wrong with teaching different schools of thought.” Obama said in an interview with Nature, “I do not believe that it is helpful to our students to cloud discussions of science with non-scientific theories like intelligent design that are not subject to experimental scrutiny.” Read between the lines and I think you’ll discover the differences between the two candidates.  McCain is OK with teaching creationism, Obama is not.

There are also some differences of opinion on things like NASA (Obama may cut funding), net neutrality (McCain proposes letting the market handle it, we know how well that works) and nuclear energy and offshore drilling. I’m trying to keep this post short and to the point. I report, you decide.**

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Ryan Adams’ wonderful “Love Is Hell” is available from .

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Image Credits:

Parties in a flask

Robot wars

A reassuring lie

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* If you aren’t reading Chris’ blog then stop what you’re doing right now and go and read it. Ignore the scary pink theme and see what she’s got to say. Simply one of the best around, particularly when she writes about politics and society. And I’m not just saying that because we’ve arranged a marriage between her daughter and my son.

** Please don’t sue me Rupert.

 

 Ryan Adams - "Political Scientist": Play Now | Play in Popup | Download

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Your underwhelming correspondent is slowly spreading his tentacles around the interweb.

Check out my guest post on America’s game over at esmon dot net. And I’m delighted to have one of my science posts picked up by  Tangled Bank, a biweekly blog carnival featuring the best science and medicine posts in the blogosphere. See which one they chose here at Evolved and Rational.

“Behold, I can make fire from a little box.”

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When I was born, thirty-ahremeah years ago, there were about 3.7 billion people in the world. The most recent estimates place the population of this planet at 6.725 billion, which means that world’s population has nearly doubled in less than four decades. At our current growth rate we face an imminent Malthusian crisis. Maybe not today, maybe not tomorrow but at some point we’re going to reach the tipping point at which there will not be enough agriculture to sustain the world’s population. Food prices are on the rise and This is one of the reasons that I chose to do a Ph.D. in the field and the place that I did. It turns out that, in the long run, I’m neither breeding nor genetically engineering better crops but it is a field which I still follow with some interest.

There has been a renaissance in plant biotechnology in the last quarter century, which has made it possible to increase crop yield, develop new strains with resistance to many diseases or to too much salt, heat, drought or soil toxins. A big part of this golden age has involved transgenic, or genetically modified (GM), crops. A GM plant is one that has had a foreign gene inserted into its genome. This usually results in an added or modified trait. For example, some of the most common GM plants have had a gene from a soil bacterium which produces a protein that is toxic to some herbivorous pests. When these pests feed on Bt crops they are killed without the addition of pesticide.
The use of transgenic or genetically modified (GM) crops has been a contentious issue around the world for the last couple of decades and made the news here in Australia earlier this month. The governing Labor Party in Western Australia banned the growth of GM crops in that state four years ago. However, in recent elections, Labor was ousted and a Liberal and National coalition have promised to rescind that ban. This follows lifting of bans on GM crops in New South Wales and Victoria earlier in the year. With a changing environment and mired in a seemingly endless drought, Australian wheat farmers are poised to reap the benefits of transgenic technology if drought resistant or salt tolerant varieties could be developed. In other news from earlier this month, China announced a $3.5 billion GM crops initiative  to help the world’s most populous nation catch up with the West in the race to patent new plant genes. The Chinese are beginning to place a priority on food security and see GM crops as the best way forward.

I’m in the minority of plant scientists in the sense that I’ve always been a little hesitant about the use of GM crops. I’m not an alarmist, nor would I support a ban of GM crops for human consumption as the European Union has instated. I believe that most GM crops are perfectly safe and that the technology does have potential to revolutionize agriculture. Hell, I’ve made transgenic plants myself, though none that are going to find their way to your dinner plate. (Unless you have a rather unusual palate.) I do, however, have some pretty serious concerns about regulation, environmental issues and intellectual property.

In terms of regulation, my concerns revolve around scrutiny of GM crops that make their way into the human food pool. GM crops have been approved for consumption in the U.S. since 1994 and there have been exactly zero reports of ill health effects. However, there are an increasing number of instances in which unapproved GM crops are finding their way to the supermarket. The inadvertent release of Starlink corn, a GM line approved only for animal feed,  into the human food supply in 2001 raised some fairly serious concerns regarding regulation and ones that have not been fully resolved. There were no reliable reports of health effects of any kind, despite concerns over potential allergic reaction. More recently, in 2006,  a GM variety of rice that had never been approved or marketed appeared in commercially available supplies in both the U.S. and Europe. It is still unclear how the GM line “got loose”. This is the crux of the problem, regulation of transgenic plants is spotty and inconsistent with different universities, research institutes and companies having wildly different regulations. American consumers in particular should be vigilant here as there is a combination of lots of GM acreage and regulatory agencies stripped of many of their powers after 8 years of the Bush Administration.

One of the benefits cited for the use of GM crops is the reduction of pesticides and fertilizers required for cultivation. For example, growing Bt crops can vastly reduce the amount of pesticide required. Some researchers are concerned, however, that there are also environmental costs of the use of transgenic crops. The most serious of these is potential transgene escape. Recent studies of transgenic sugar beet and canola have shown that cross-pollination of non-transgenic relatives of transgenic crops can occur and that the presence of the transgene can persist for at least six years. This becomes especially problematic when GM and non-GM crops are grown in close proximity and is the most likely explanation for the GM rice escape in 2006. Beyond transgene transfer, there is an issue of harmful effects of transgene products. One of the toxins expressed in Bt crops has been detected in the guts of predators of plant pests. For example, aphids that feed on Bt corn are themselves fed on by ladybugs. Researchers at the University of Kentucky have been able to detect low levels of Bt toxin in the latter. In a controversial study published in PNAS by researchers from the University of Wisconsin, it was claimed that corn byproducts enter streams and are subject to storage, consumption, and transport to downstream water bodies and result in reduced growth and increased mortality of nontarget stream insects. It is worth noting that the large-scale mono-crop agriculture that predominates in the West is environmentally disastrous anyway. Most researchers think that GM crops offer, if anything, a slight improvement on environmental effects.

The final issue that I have with GM crops is that I’m not sure that, as things stand now, they will solve world food supply issues. The vast majority of GM crops are owned by one of a handful of large biotech companies. Monsanto produces more than 90% of crops worldwide with Syngenta, Bayer Cropscience, Dow and Du Pont producing the remainder. It is of some concern that these companies will have too much control over world food productionor will force traditional farmers out of the market.  The biggest fears around world hunger are in developing countries where farmers generally can not afford to buy new seed stocks each season and rely on ‘recycling seed’. Most corporations aren’t in the business of giving their products away for free and thus legally obliagte farmers to buy new GM seed each year. There are instances of biotech companies aggressively protecting their intellectual property. Call me a cynic, I just doubt that the biotech companies that hold the patents for most of the useful GM crops are that interested in solving world poverty.

I know I’ve spent most of this post discussing some of the concerns surrounding transgenic crops, but at the bottom of everything I do think that GM crops could, in the words of Nina Fedoroff, be the source of a new Green Revolution. The Golden Rice story is a wonderful example of academic scientists working with biotech companies for humanitarian purposes. I just think that regulation, on a global scale, is absolutely key. Because we now live in a global economy and agricultural products are shipped around the world, there needs to be a global consensus on how to regulate GM crops. The biggest unresolved issue, and potential for trouble, surrounds inadvertant spreading of GM pollen to neighboring fields or wild relatives. Regulations need to be established to minimize this risk. Importantly, you can not force people to accept a technology with which they are uncomfortable. Just as now we have organic produce alternatives, as GM crops become more prevalent, there should be non-GM alternatives. This requires either labelling of GM products or non-GM products to allow consumers an opportunity to make an informed decision.

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Some of you probably know that one of my jobs right now is teaching Biotechnology at one of Adelaide’s universities. I’m currently working on my next lecture, which is supposed to cover Comparative Genomics and Human Origins - evolution. By working on my lecture, of course, I mean working on a blog post about working on my lecture. This is not meant to be a controversial post. It is not a post about evolution vs. creationism, I’ve been there and done that and have the scars to prove it. Nor is this a post  about Sarah Palin and her fundamentalist beliefs, that all got a bit controversial. Nope, this post was inspired by my predilection to procrastination and stumbling on this post from Genomicron about evolution and creationism in the classroom. My interest piqued and justified by the vaguely topical nature of the post led me to this special issue of Integrative & Comparative Biology which in turn sucked up the bulk of my afternoon.

Before we get too far into this, let’s get some things straight. Science and religion, as Linda Kondrick points out in her ICB paper, are ways of knowing, ways of interpreting human experience, ways of defining ‘truth’. However, the two disciplines rely on entirely different logical approaches. Religion is deductive, beginning with a “known” - a sacred text or divine revelation - to explain what we see around us. Science is inductive, beginning with observations of the human experience and building a model to explain those observations. I’m not making a judgment on which approach is better, but I’m guessing most of you know where my allegiances lie.

Evolution at its most basic is descent with modification, the theory that the common ancestor of life on Earth gave rise to the fantastic diversity that we see documented in the fossil record and around us today. Evolution is not “just a theory” but a critical principle of biology. As Lovely and Kondrick eloquently put it in their ICB paper, it “is the backbone, the beautiful and efficient explanation for why organisms today are different from organisms in the past and why there is such an amazing diversity of fascinating biological organisms with awe inspiring lifestyles and body plans.” Evolution is basically the same kind of theory as gravity.

Creationism and intelligent design are effectively and legally identical. According to the creationist Discovery Institute, ID is the assertion that “certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.” The courts have recently ruled that ID is essentially the offspring of “creation science”, which was outlawed from American public schools by the U.S. Supreme Court in 1987. Effectively, they are the same theory - that an Intelligent Designer (a Christian God) is responsible for the variation that we see in life. As Barbara Forrest reports in her ICB paper, despite claims by proponents that “ID is not based on religion”  they freely admit that their ”natural constituency” is Christians. Despite couching ID in pseudo-scientific language and making a cursory attempt to include some scientific data (generally taken out of context), ID is at its heart dependent on a literal interpretation of Genesis.

Science educators are increasingly finding it difficult to effectively teach evolution. The challenge that is presented to scientists and to science educators is that we are not effectively teaching and communication the principle of evolution to students and the lay public. As I wrote in my previous post, a shocking percentage of the American public doubt that evolution has occurred at all. Lest you think its an American problem, a 2006 Ipsos MORI survey in the UK found that only 48% of Britons thought that evolution best explained their origin and the variation of life that they see around them. High school and university educators increasingly report problems when it comes to covering evolution in their courses. Lovely & Kondrick write of a “wedge effect” among college students who come into a semester long Biology course undecided about evolution. At the end of the course, about half of the students shifted to a scientific viewpoint but the other half shifted towards a creationist viewpoint. So, despite being presented with overwhelming evidence supporting the principle of evolution, students are as likely to choose the invalid creationist viewpoint, even moreso when dealing with questions of human ancestry.

Clearly we are failing as educators when it comes to teaching evolution and we’re failing as scientists in communicating about evolution to the lay community. We can not assume that because we know that something is true and not a matter for debate that everyone believes that something is true and not a matter for debate. Forrest correctly points out that as scientists, parents and citizens it is our duty to counteract ID whenever and wherever possible. Our expertise is valuable whether it be in working with teachers, testifying to school board or local councils or wherever the opportunity arises. Scientists who are also educators bear a bigger obligation. The consensus of the ICB papers was that our current teaching methods, particularly in terms of evolution are dated and ineffective. Craig Nelson proposed the most sweeping changes, stating his belief that “traditional ways of teaching are inferior” and proposes the alternative approach of combining extensive use of interactive engagement and a focus on critical thinking in science to help students compare their initial misconceptions with scientific conceptions. Nelson supports a peer driven approach, with lots of student interaction and replacing “recipe” practicals with “inquiry labs”. This all sounds a bit chaotic to me, particularly if you’re unfortunate enough to be a high school teacher, but his point is well made and Nelson offers extensive resources to make changes toward “interactive learning”.

Kevin Padian proposes similar sweeping curriculum changes in his ICB paper. Padian feels that the biggest problem we face is with the textbooks available. For general biology in both high school and college, the most popular texts do not dedicate much space to evolution as a whole and even less to macroevolution. These texts often use non-controversial language such as “many paleontologists think that birds are close relatives of dinosaurs.” The fact is that virtually every biologist has known for at least a decade that birds evolved from carnivorous dinosaurs in the Late Jurassic period. The use of “many paleontologists” and “think” introduces artificial uncertainty. Padian also proposes a change in the way that evolution is graphically presented and suggests a move to “evograms” (see below and click to enlarge) that show fossil, morphological and molecular evidence in a single illustration.

I’m not likely to make a major shift in teaching style between now and my next lecture nor find a perfect new textbook, but one suggestion that Nelson and others make can be incorporated immediately. Many of us take the approach of ignoring creationism and the controversy and conflict between science and religion when teaching evolution. Fair enough, astronomers don’t have to address astrology, chemists don’t have to address alchemy. But a couple of the ICB authors have proposed addressing science, religion and the controversy head on. Now, this is ground that needs to be trodden upon lightly. If we’re derisive or supercilious about religion then we do more harm than good. We reinforce religious students preconceptions of arrogant, godless scientists. Equally important, however, is not giving any credence to creationism as a valid alternative to evolution. It is not and should not be treated as one. Michael Reiss, writing in Studies in Science Education errs too much in the direction of giving creationism undue credibility.

So when teaching evolution, there is much to be said for allowing students to raise any doubts they have (hardly a revolutionary idea in science teaching) and doing one’s best to have a genuine discussion. The word ‘genuine’ doesn’t mean that creationism or intelligent design deserve equal time. However, in certain classes, depending on the comfort of the teacher in dealing with such issues and the make up of the student body, it can be appropriate to deal with the issue.

I think that Reiss’ proposals go too far, as too much discussion on the merits (or lack thereof) of creationism would just help to drive that metaphorical wedge. Nelson proposes teaching that rather than the false dichotomy of atheistic evolution versus religious creationism that there is a broad interfaith consensus that acceptance of evolution is compatible with faith. Kondrick proposes taking this discussion even further by exploring the historical philosophical divide between religion and science going back to a compromise brokered by Thomas Aquinas in 1252. Aquinas devised a system for resolving the disparities between the two by showing them to be philosophically complementary.

Now, Thomism may be a bit of a stretch for your average hormone riddled teenager. But the most positive feedback that I’ve gotten from my students this term is when we came of the rails a bit in a lecture about medical genomics. We started talking, in a bit more casual way, about the ethics surrounding the topic. That deviation from the standard lecture and foray into philosophizing got the students really interested, really engaged. I haven’t tested that material yet, but I’d be willing to bet that they do better on it than on anything else. Maybe breaking up a dry lecture on molecular evolution and the origin of the human species with a discussion about science and religion and the nature of truth would wake up those laggards in the back row.

Or maybe the best way to teach evolution is for me to stop fannying about and write the lecture.

Web Resources:

Understanding Evolution

Panda’s Thumb

The Butler Letter

PBS Evolution

ICB: Evolutionism vs Creationism in the Classroom

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