“[Mr. X] told the assembled groups that science itself is subjective, and that he could have three different groups bring him three different supposedly scientific opinions.”

Any guesses on the identity of Mr. X? Could he be a creationist arguing for the inclusion of intelligent design alongside science in the classroom? A new-age radical arguing that alternative medicines are just as scientifically effective was … well medicine? Maybe the most likely bet would be a sceptic of global warming, they’ve been in the press a lot lately, what with temperatures falling across the northern hemisphere (it’s apparently winter you see).

Unfortunately the person in question is (according to an article posted in the wall street journal), US Secretary of Agriculture Tom Vilsack.

According to the Wall Street Journal, Secretary Vilsack made these comments during a meeting lead by himself and Deputy Secretary Kathleen Merrigan to address the re-deregulation of alfalfa engineered to be resistant to the herbicide glyphosate, after a lawsuit which required that the USDA conduct a more thorough study of the environmental impacts of the alfalfa’s release. Another source reported:

not once mentioning the health or safety aspects of Roundup Ready alfalfa during the more-than-three-hour meeting

So this is what it comes down to. There are no demonstrated health and safety concerns for this particular crop, even after the further court mandated evaluations, but it appears the US Secretary of Agriculture has lost faith in the idea that science is something more than a system of compromising between everyone’s equally valid opinion.

But it’s not true. Scientists aren’t always right, and yes you can often find scientists who disagree. But the wonderful thing about science is that when reasonable people disagree, we don’t compromise and say the answer is probably somewhere in the middle but we’ll never know for sure. We design new experiments, go out and collect new data, and, in the end, discover which ideas are probably correct, and which are provably false and wrong.

It’s important to note my concerns are based on a paraphrased quote in a single news article. There is a distinct possibility the reporter misunderstood the point Secretary Vilsack was trying to make (I’ve certainly seen similar things happen in print before), but if so I hope he will publicly and vocally denounce the mischaracterization of his postion on scientific inquiry as it has the potential to do serious harm to the already embattled position of science holds public discourse of our nation.

This goes for everything I write, but let me reinterate that the post above represents solely my own opinion and does not reflect views of my employer, supervisor, co-workers, fellow bloggers, family members, friends (both old and new), nor the opinion of my parent’s pet cat.

Today’s plant is the woodland strawberry (Fragaria vesca). Now these aren’t the strawberries you probably see at your local grocery store, those are garden strawberries (Fragaria x ananassa). Woodland strawberries were the predominant strawberries grown throughout europe until around 250 years ago when they were displaced by the new garden strawberries — created when a strawberry species brought from north america crossed with another species from chile when they were grown next to each other in france. The new hybrid species bore larger fruit than the woodland strawberry.

Wild strawberry (left) and domesticated strawberry (right). I'm not sure which species these are, downside of having to hunt down public domain photos.

Sequencing the genome of the garden strawberry directly would be a real mess, as the genome of that species is made up of four closely related genome-copies*. With modern DNA-sequencing technology, generating the raw sequence data that makes up a genome is — relatively — cheap and easy, but afterwards you are left with a lot of small pieces of DNA sequence, and putting those pieces together (like putting together a puzzle with millions of pieces) remains challenging. Mix together pieces from four closely related puzzles together with no way to tell them apart and the project becomes even more challenging.

Fortunately the woodland strawberry side-steps that problem, being a normal diploid plant without any of the whole genome duplications that would make sequencing garden strawberries such a terrible mess. It also has a pleasingly small genome, with a genome of 206 million base pairs spread over seven chromosomes, making it only slightly larger than the genome of the first plant to be sequenced (Arabidopsis 157 million base pairs and five chromosomes). Small genomes are easier to put together, with less total pieces to go around.

The research consortium that sequenced and assembled the strawberry genome, first assembled overlapping pieces of sequenced DNA into larger pieces called contigs and then using genetic map data to line those contigs up into seven pseudomolecules, each of which represents a whole strawberry chromosome. The strawberry genome itself wasn’t released prior to the publication of the paper, so I haven’t had a chance to look at it myself, but both the fact that they’ve been able to assemble all the way to the chromosome level, and that they developed and used genetic map data argue for a well done assembly.

Speaking of assembly, here are all the vital genome stats that I normally would have to hunt around for after reading a “new genome sequenced!” story in the popular press (some of these I’ve already mentioned above):

• Strawberries have a haploid number of 7, and a genome size of 206 MB
• The average base pair in the strawberry genome was sequenced 39 times using second generation technology (a label that includes Illumina, 454, and SOLiD sequencers, in this case a mixture of all three technologies were employed)
• 34,809 predicted genes were identified across the strawberry genome.
• The authors found no evidence of the whole genome duplications found in other rosids (I’m assuming this means the most recent whole genome duplication in the ancestors of strawberries was the pre-rosid hexaploidy.)
• The paper describing the genome will shortly be available from Nature Genetics. The title is “The genome of the woodland strawberry (Fragaria vesca)” and the last name of the first author is Shulaev. UPDATE: Here’s the link to the genome paper.

Strawberry genome browser.

Aside from the enjoyment I always feel when a new genome goes live, I’m particularly happy to see the strawberry genome come out for two reasons.

The first is that there was no “strawberry genome” grant. Funding for sequencing the genome came from a number of sources. I take this as a sign that in addition to the rapidly declining cost of sequencing itself, the cost and difficulty of assembling and annotating the genome a new plant species are also continuing to decline at a rapid pace.

The second reason is that I once before announced the sequencing of the strawberry genome on this site. It was almost a year ago, after a reporter misunderstood a presentation at PAG and posted a “new genome sequenced” story online that was rapidly picked up by  a number of websites including my own. It was a bad break for the folks working hard to sequence, assemble, and annotate the real strawberry genome, and I’m very glad to see them get the moment in the spotlight they so richly deserve. The people who sequence genomes make the work of so many other researchers, including myself, possible.

Links to other coverage (updated as I find them):

• Scientific American
• EurakAlert (focusing on the genome assembly at Oregon State)
• Nature Blog (focuses more on the chocolate genome that was published at the same time in Nature Genetics, also I’m not sure two genomes qualifies as a “Smorgasbord”)
• MyGenomix (in Italian)
• The story behind how the strawberry genome came to be published (written by one of the authors)

*Either the result of duplicated copies of a single genome that have since evolved independently (autotetraploidy), or hybrids that merged the genomes of closely related strawberry species together in a single plant (allotetraploidy).

To understand how superweeds survive, we first have to understand why normal weeds (the Jimmy Olsens and Lois Lanes of the plant world) die. <– last superhero reference of this post I promise.

Plants are not like people. The list of differences goes on and on, but today the difference we’re concerned about is where amino acids come from. Amino acids are the building blocks of proteins, the same way Adenine (A), Thymine (T), Guanine (G) and Cytosine (C) are the building blocks of DNA. Both our bodies and plants (and almost every other living thing) use the same twenty amino acids to build proteins. Our bodies can make ~12 of the twenty animo acids for themselves, but there are at least eight amino acids that the human body cannot produce (called essential amino acids). Our only source of these amino acids is from protein in our food.

It’s all well and good for us to get amino acids from our food, but plants don’t eat. They’re made of pretty much nothing more than water, sunlight and air. And trust me, none of those things are a good source of protein.

Unlike us, plants have to be able to make all twenty amino acids from scratch. That means they need whole biochemical pathways* that aren’t found in animals. But a biochemical pathway is like an assembly line. Break one of the steps in the middle and the whole thing falls apart. That’s what glyphosate/round-up does.

This part of the story starts with an enzyme called 5-enolpyruvylshikimate-3-phosphate synthase (or EPSPS for short). Do you don’t have to understand what EPSPS does specifically**, what is important is that its job is an important step in making the three amino acids Tryptophan, Phenylalanine, and Tyrosine***. When EPSPS can’t do its job, the next protein in the biochemical pathway won’t get the parts it needs to do its job, and in short order the whole pipeline shuts down, none of those three amino acids get produced, and the plant dies.

How does glyphosate keep EPSPS from doing it’s job? It imitates one of the the chemical building blocks EPSPS normally works with, so EPSPS proteins will bind to it like they would to the actual chemical compound. But since glyphosate isn’t the compound EPSPS actually work with, it sticks in the protein. If it helps you can think of this as feeding the wrong sort of paper into a printer, causing a paper jam. Lots of individual molecules of glyphosate get into each plant cell. They stick in EPSPS proteins floating within the cell, which keeps EPSPS from doing its job, and once EPSPS stops working, the plant cell can’t make the amino acids it needs to survive, and dies.

Glyphosate is very good at doing what it does: killing plants. And as weed-killers go, it’s a lot less nasty for animals since it works by breaking a protein animals don’t need or even have. But there is one problem. Some weeds are becoming less effected by the herbicide, able to survive larger and large doses. There are a number of ways plants can evolve to survive large doses of glyphosate. Let’s talk about three:

1. The first, and probably most obvious, is to change the shape of the EPSPS protein so glyphosate can no longer jam the mechanism. As it turns out mutations that change which amino acid is used at one specific point can produce a version of the EPSPS gene that is less likely to be broken by glyphosate. Think of it as changing the design of a print so paper that would jam the mechanism either won’t fit in the printer at all or passes through harmlessly. This method of getting “superweed” powers has been used by malaysian goose-grass and and australian ryegrass.
2. A second way for plants to become superweeds is to stop transporting glyphosate around the plant. I don’t have a good printer metaphor for this one. Cells in the leaves of plants are mostly completely grown and don’t need to make as many new proteins as the rapidly dividing cells in meristems and newly developing leaves. When a farmer sprays glyphosate it will mostly land on the mature leaves of the plant. If plants can keep the herbicide in those leaves and keep it from traveling throughout the rest of the plants, they stand a better chance of survival, and that’s exactly what has been found in resistant stiffstalk rye and pigweed.
3. The first two methods are all well and good, but I probably wouldn’t have bother to write this post if it wasn’t for the method of resistance discovered in Amaranthus palmeri (one of the many species that share the common name pigweed). Palmer amaranth’s approach to resisting glyphosate is charming in its brute force. Resistant plants have duplicated the gene for EPSPS many times (up to 160 copies in some plants!). All those extra genes mean the plants produce a lot more EPSPS protein, so no matter how many individual EPSPSs get jammed by glyphosate molecules, there are still plenty more working EPSPSs to keep doing the job, and the biochemical pathway never stops. Sure a problem with paper jams can be fixed by more advanced printers, or more strict controls on what kind of paper is allowed into the building… but Palmer amaranth’s solution was simply to build a lot more printers.

Potentially there’s potentially a fourth way to develop glyphosate resistance, which would be for the resistant version of the EPSPS protein engineered into glyphosate resistant crops**** to be introgressed into wild relatives allowing those wild crop relatives to become herbicide resistant “super weeds”. This gets talked about a lot and clearly the risk is going to depend on a lot of factors*****. In researching this post I couldn’t find any papers describing herbicide resistant weeds that owe their resistance to a gene from an herbicide resistant crop. And given how much ink has been spilled on the subject, I would expect any such papers to makes a big splash.

*Biochemical pathways are just a bunch of steps needed to get from some molecule an organism already has, to some other molecule the organism wants. Usually each individual chemical change is performed by some specific protein, like workers on an assembly line. (Sometimes its even arranged like an assembly line with intermediate molecules being passed directly from one protein to another, although it isn’t always that way)

**Although if you’re interested you can read more about the details of the EPSPS protein here.

***The first two are certainly essential amino acids. Our bodies can produce our own tyrosine, but all we do is modify phenylalanine. We can’t make it from scratch.

****Weeds that resist glyphosate are “super weeds”, but I can’t imagine ever hearing the crops that resist the exact same herbicide called “super crops” .

*****How the crop reproduces, whether its being grown near any wild ancestors, how weedy those wild ancestors are to begin with, which crop alleles are in close linkage with the resistance gene (crop-like traits tend to make weeds much less successful).

Gaines, T., Zhang, W., Wang, D., Bukun, B., Chisholm, S., Shaner, D., Nissen, S., Patzoldt, W., Tranel, P., Culpepper, A., Grey, T., Webster, T., Vencill, W., Sammons, R., Jiang, J., Preston, C., Leach, J., & Westra, P. (2009). Gene amplification confers glyphosate resistance in Amaranthus palmeri Proceedings of the National Academy of Sciences, 107 (3), 1029-1034 DOI: 10.1073/pnas.0906649107

POWLES, S., & PRESTON, C. (2006). Evolved Glyphosate Resistance in Plants: Biochemical and Genetic Basis of Resistance Weed Technology, 20 (2), 282-289 DOI: 10.1614/WT-04-142R.1

This story was originally posted at James and the Giant Corn.

Popped corn Photo: D3 San Francisco, flickr (click to see photo in original context

Popping corn, or anything else, all comes down to pressure. Pop-corn has a particularly impermeable pericarp (the corn kernel’s shell), so as it is heated, the water inside the kernel vaporizes into steam and the starch turns into something close to a liquid. Eventually the heat creates enough pressure to split the pericarp and the starch of the corn kernel bursts out, resolidifying into the distinctive shape of popcorn. If there is even the smallest hole in the pericarp, the steam can escape from the kernel as it’s generated so the pressure never builds up enough to explode the pericarp — the reason some kernels will fail to pop in every batch. The explosive build up of steam is also the reason tea kettles need to be able to release steam while they’re used to boil water. The alternative would be exploding tea kettles which are a lot more dangerous (and a lot less tasty) than exploding corn kernels.

Un-popped popcorn photo: MissTessmacher, flickr (click to see photo in its original context)

It was this reason (along with my discovery of the website on April 1st) that I was so suspicious of the idea of popped sorghum a few days ago. Thanks to Party Cactus and Jeremy, I now know that sorghum does indeed pop like corn (there’s even a variety called “Tarahumara Popping”) and, in fact, thanks to the link Jeremy provided, I’ve discovered that most grains and even some other things (including cowpeas!) can be popped using the proper equipment.

By using a machine that is in some ways similar a pressure cooker, even grains without hard impermeable pericarps can be popped. The popping machine lets pressure rise equally inside and outside of whatever grain is being popped. When the outside pressure is released, the grains/kernels/seeds instantly pop.

It doesn’t sound as visually satisfying at the pop-corn popper I remember from my childhood, where half the fun was watching in anticipation for the first kernels to leap into the air, but a very cool invention never the less.

I’ll certainly be keeping an eye open for popped sorghum to show up out here in the bay area.

A. Normal popcorn kernel. Applying heat makes the pressure build up inside the kernel until the kernel pops open. B. A popcorn seed with a hole in the pericarp. Heat creates pressure, but it escapes through the hole so it never builds up enough to pop open the kernel. C. Even in grains with permiable pericarps, the pressure can build up inside, if the pressure outside is also high. Dropping the outside pressure suddenly still caused the grain to pop.